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Sample records for 3-d weight function

  1. 3D Cell Entrapment as a Function of the Weight Percent of Peptide-Amphiphile Hydrogels

    PubMed Central

    Scott, Carolyn M.; Forster, Colleen L.; Kokkoli, Efrosini

    2015-01-01

    The design of scaffolds which mimic the stiffness, nanofiber structure, and biochemistry of the native extra-cellular matrix (ECM) has been a major objective for the tissue engineering field. Furthermore, mimicking the innate three dimensional (3D) environment of the ECM has been shown to significantly alter cellular response compared to traditional two dimensional (2D) culture. We report the development of a self-assembling, fibronectin-mimetic, peptide-amphiphile nanofiber scaffold for 3D cell culture. To form such a scaffold, 5 mol% of a bioactive PR_g fibronectin-mimetic peptide-amphiphile was mixed with 95 mol% of a diluent peptide-amphiphile (E2) whose purpose was to neutralize electrostatic interactions, increase the gelation kinetics and promote cell survival. Atomic force microscopy verified the fibrilar structure of the gels and the mechanical properties were characterized for various weight percent (wt%) formulations of the 5 mol% PR_g - 95 mol% E2 peptide-amphiphile mixture. The 0.5 wt% formulations had an elastic modulus of 429.0 ± 21.3 Pa while the 1.0 wt% peptide-amphiphile hydrogels had an elastic modulus of 808.6 ± 38.1 Pa. The presence of entrapped cells in the gels decreased the elastic modulus and the decrease was a function of the cell loading. While both formulations supported cell proliferation, the 0.5 wt% gels supported significantly greater NIH3T3/GFP fibroblast cell proliferation throughout the gels than the 1.0 wt% gels. However, compared to the 0.5 wt% formulations, the 1.0 wt% hydrogels promoted greater increase in mRNA expression and production of fibronectin and type IV collagen ECM proteins. This study suggests that this fibronectin-mimetic scaffold holds great promise in the advance of 3D culture applications and cell therapies. PMID:25970351

  2. Analysis of corner cracks at hole by a 3-D weight function method with stresses from finite element method

    NASA Technical Reports Server (NTRS)

    Zhao, W.; Newman, J. C., Jr.; Sutton, M. A.; Wu, X. R.; Shivakumar, K. N.

    1995-01-01

    Stress intensity factors for quarter-elliptical corner cracks emanating from a circular hole are determined using a 3-D weight function method combined with a 3-D finite element method. The 3-D finite element method is used to analyze uncracked configuration and provide stress distribution in the region where crack is to occur. Using this stress distribution as input, the 3-D weight function method is used to determine stress intensity factors. Three different loading conditions, i.e. remote tension, remote bending and wedge loading, are considered for a wide range in geometrical parameters. The significance in using 3-D uncracked stress distribution and the difference between single and double corner cracks are studied. Typical crack opening displacements are also provided. Comparisons are made with solutions available in the literature.

  3. Analysis of surface cracks at hole by a 3-D weight function method with stresses from finite element method

    NASA Technical Reports Server (NTRS)

    Zhao, W.; Newman, J. C., Jr.; Sutton, M. A.; Shivakumar, K. N.; Wu, X. R.

    1995-01-01

    Parallel with the work in Part-1, stress intensity factors for semi-elliptical surface cracks emanating from a circular hole are determined. The 3-D weight function method with the 3D finite element solutions for the uncracked stress distribution as in Part-1 is used for the analysis. Two different loading conditions, i.e. remote tension and wedge loading, are considered for a wide range in geometrical parameters. Both single and double surface cracks are studied and compared with other solutions available in the literature. Typical crack opening displacements are also provided.

  4. Orientation-weighted local Minkowski functionals in 3D for quantitative assessment of trabecular bone structure in the hip

    NASA Astrophysics Data System (ADS)

    Boehm, H. F.; Bitterling, H.; Weber, C.; Kuhn, V.; Eckstein, F.; Reiser, M.

    2007-03-01

    Fragility fractures or pathologic fractures of the hip, i.e. fractures with no apparent trauma, represent the worst complication in osteoporosis with a mortality close to 25% during the first post-traumatic year. Over 90% of hip fractures result from falls from standing height. A substantial number of femoral fractures are initiated in the femoral neck or the trochanteric regions which contain an internal architecture of trabeculae that are functionally highly specialized to withstand the complex pattern of external and internal forces associated with human gait. Prediction of the mechanical strength of bone tissue can be achieved by dedicated texture analysis of data obtained by high resolution imaging modalities, e.g. computed tomography (CT) or magnetic resonance tomography (MRI). Since in the case of the proximal femur, the connectivity, regional distribution and - most of all - the preferred orientation of individual trabeculae change considerably within narrow spatial limits, it seems most reasonable to evaluate the femoral bone structure on an orientation-weighted, local scale. In past studies, we could demonstrate the advantages of topological analysis of bone structure using the Minkowski Functionals in 3D on a global and on a local scale. The current study was designed to test the hypothesis that the prediction of the mechanical competence of the proximal femur by a new algorithm considering orientational changes of topological properties in the trabecular architecture is feasible and better suited than conventional methods based on the measurement of the mineral density of bone tissue (BMD).

  5. 3D Weight Matrices in Modeling Real Estate Prices

    NASA Astrophysics Data System (ADS)

    Mimis, A.

    2016-10-01

    Central role in spatial econometric models of real estate data has the definition of the weight matrix by which we capture the spatial dependence between the observations. The weight matrices presented in literature so far, treats space in a two dimensional manner leaving out the effect of the third dimension or in our case the difference in height where the property resides. To overcome this, we propose a new definition of the weight matrix including the third dimensional effect by using the Hadamard product. The results illustrated that the level effect can be absorbed into the new weight matrix.

  6. Robust Locally Weighted Regression For Ground Surface Extraction In Mobile Laser Scanning 3D Data

    NASA Astrophysics Data System (ADS)

    Nurunnabi, A.; West, G.; Belton, D.

    2013-10-01

    A new robust way for ground surface extraction from mobile laser scanning 3D point cloud data is proposed in this paper. Fitting polynomials along 2D/3D points is one of the well-known methods for filtering ground points, but it is evident that unorganized point clouds consist of multiple complex structures by nature so it is not suitable for fitting a parametric global model. The aim of this research is to develop and implement an algorithm to classify ground and non-ground points based on statistically robust locally weighted regression which fits a regression surface (line in 2D) by fitting without any predefined global functional relation among the variables of interest. Afterwards, the z (elevation)-values are robustly down weighted based on the residuals for the fitted points. The new set of down weighted z-values along with x (or y) values are used to get a new fit of the (lower) surface (line). The process of fitting and down-weighting continues until the difference between two consecutive fits is insignificant. Then the final fit represents the ground level of the given point cloud and the ground surface points can be extracted. The performance of the new method has been demonstrated through vehicle based mobile laser scanning 3D point cloud data from urban areas which include different problematic objects such as short walls, large buildings, electric poles, sign posts and cars. The method has potential in areas like building/construction footprint determination, 3D city modelling, corridor mapping and asset management.

  7. 3D printing of functional biomaterials for tissue engineering.

    PubMed

    Zhu, Wei; Ma, Xuanyi; Gou, Maling; Mei, Deqing; Zhang, Kang; Chen, Shaochen

    2016-08-01

    3D printing is emerging as a powerful tool for tissue engineering by enabling 3D cell culture within complex 3D biomimetic architectures. This review discusses the prevailing 3D printing techniques and their most recent applications in building tissue constructs. The work associated with relatively well-known inkjet and extrusion-based bioprinting is presented with the latest advances in the fields. Emphasis is put on introducing two relatively new light-assisted bioprinting techniques, including digital light processing (DLP)-based bioprinting and laser based two photon polymerization (TPP) bioprinting. 3D bioprinting of vasculature network is particularly discussed for its foremost significance in maintaining tissue viability and promoting functional maturation. Limitations to current bioprinting approaches, as well as future directions of bioprinting functional tissues are also discussed.

  8. 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/.

  9. Towards functional assembly of 3D and 2D nanomaterials

    NASA Astrophysics Data System (ADS)

    Jacobs, Christopher B.; Wang, Kai; Ievlev, Anton V.; Muckley, Eric S.; Ivanov, Ilia N.

    2016-09-01

    Functional assemblies of materials can be realized by tuning the work function and band gap of nanomaterials by rational material selection and design. Here we demonstrate the structural assembly of 2D and 3D nanomaterials and show that layering a 2D material monolayer on a 3D metal oxide leads to substantial alteration of both the surface potential and optical properties of the 3D material. A 40 nm thick film of polycrystalline NiO was produced by room temperature rf-sputtering, resulting in a 3D nanoparticle assembly. Chemical vapor deposition (CVD) grown 10-30 μm WS2 flakes (2D material) were placed on the NiO surface using a PDMS stamp transfer technique. The 2D/3D WS2/NiO assembly was characterized using confocal micro Raman spectroscopy to evaluate the vibrational properties and using Kelvin probe force microscopy (KPFM) to evaluate the surface potential. Raman maps of the 2D/3D assembly show spatial non-uniformity of the A1g mode ( 418 cm-1) and the disorder-enhanced longitudinal acoustic mode, 2LA(M) ( 350 cm-1), suggesting that the WS2 exists in a strained condition on when transferred onto 3D polycrystalline NiO. KPFM measurements show that single layer WS2 on SiO2 has a surface potential 75 mV lower than that of SiO2, whereas the surface potential of WS2 on NiO is 15 mV higher than NiO, indicating that WS2 could act as electron donor or acceptor depending on the 3D material it is interfaced with. Thus 2D and 3D materials can be organized into functional assemblies with electron flow controlled by the WS2 either as the electron donor or acceptor.

  10. Embedding objects during 3D printing to add new functionalities.

    PubMed

    Yuen, Po Ki

    2016-07-01

    A novel method for integrating and embedding objects to add new functionalities during 3D printing based on fused deposition modeling (FDM) (also known as fused filament fabrication or molten polymer deposition) is presented. Unlike typical 3D printing, FDM-based 3D printing could allow objects to be integrated and embedded during 3D printing and the FDM-based 3D printed devices do not typically require any post-processing and finishing. Thus, various fluidic devices with integrated glass cover slips or polystyrene films with and without an embedded porous membrane, and optical devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber were 3D printed to demonstrate the versatility of the FDM-based 3D printing and embedding method. Fluid perfusion flow experiments with a blue colored food dye solution were used to visually confirm fluid flow and/or fluid perfusion through the embedded porous membrane in the 3D printed fluidic devices. Similar to typical 3D printed devices, FDM-based 3D printed devices are translucent at best unless post-polishing is performed and optical transparency is highly desirable in any fluidic devices; integrated glass cover slips or polystyrene films would provide a perfect optical transparent window for observation and visualization. In addition, they also provide a compatible flat smooth surface for biological or biomolecular applications. The 3D printed fluidic devices with an embedded porous membrane are applicable to biological or chemical applications such as continuous perfusion cell culture or biocatalytic synthesis but without the need for any post-device assembly and finishing. The 3D printed devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber would have applications in display, illumination, or optical applications. Furthermore, the FDM-based 3D printing and embedding method could also be utilized to print casting molds with an integrated glass bottom for polydimethylsiloxane (PDMS) device replication

  11. Generation of flat viewing zone in DFVZ autostereoscopic multiview 3D display by weighting factor

    NASA Astrophysics Data System (ADS)

    Kim, Sung-Kyu; Yoon, Seon-Kyu; Yoon, Ky-Hyuk

    2013-05-01

    A new method is introduced to reduce three crosstalk problems and the brightness variation in 3D image by means of the dynamic fusion of viewing zones (DFVZ) using weighting factor. The new method effectively generates the flat viewing zone at the center of viewing zone. The new type autostereoscopic 3D display can give less brightness variation of 3D image when observer moves.

  12. Realistic microwave breast models through T1-weighted 3-D MRI data.

    PubMed

    Tunçay, Ahmet Hakan; Akduman, Ibrahim

    2015-02-01

    In this paper we present an effective method for developing realistic numerical three-dimensional (3-D) microwave breast models of different shape, size, and tissue density. These models are especially convenient for microwave breast cancer imaging applications and numerical analysis of human breast-microwave interactions. As in the recent studies on this area, anatomical information of the breast tissue is collected from T1-weighted 3-D MRI data of different patients' in prone position. The method presented in this paper offers significant improvements including efficient noise reduction and tissue segmentation, nonlinear mapping of electromagnetic properties, realistically asymmetric phantom shape, and a realistic classification of breast phantoms. Our method contains a five-step approach where each MRI voxel is classified and mapped to the appropriate dielectric properties. In the first step, the MRI data are denoised by estimating and removing the bias field from each slice, after which the voxels are segmented into two main tissues as fibro-glandular and adipose. Using the distribution of the voxel intensities in MRI histogram, two nonlinear mapping functions are generated for dielectric permittivity and conductivity profiles, which allow each MRI voxel to map to its proper dielectric properties. Obtained dielectric profiles are then converted into 3-D numerical breast phantoms using several image processing techniques, including morphologic operations, filtering. Resultant phantoms are classified according to their adipose content, which is a critical parameter that affects penetration depth during microwave breast imaging.

  13. Protein function prediction using local 3D templates.

    PubMed

    Laskowski, Roman A; Watson, James D; Thornton, Janet M

    2005-08-19

    The prediction of a protein's function from its 3D structure is becoming more and more important as the worldwide structural genomics initiatives gather pace and continue to solve 3D structures, many of which are of proteins of unknown function. Here, we present a methodology for predicting function from structure that shows great promise. It is based on 3D templates that are defined as specific 3D conformations of small numbers of residues. We use four types of template, covering enzyme active sites, ligand-binding residues, DNA-binding residues and reverse templates. The latter are templates generated from the target structure itself and scanned against a representative subset of all known protein structures. Together, the templates provide a fairly thorough coverage of the known structures and ensure that if there is a match to a known structure it is unlikely to be missed. A new scoring scheme provides a highly sensitive means of discriminating between true positive and false positive template matches. In all, the methodology provides a powerful new tool for function prediction to complement those already in use.

  14. Robust bioengineered 3D functional human intestinal epithelium

    PubMed Central

    Chen, Ying; Lin, Yinan; Davis, Kimberly M.; Wang, Qianrui; Rnjak-Kovacina, Jelena; Li, Chunmei; Isberg, Ralph R.; Kumamoto, Carol A.; Mecsas, Joan; Kaplan, David L.

    2015-01-01

    Intestinal functions are central to human physiology, health and disease. Options to study these functions with direct relevance to the human condition remain severely limited when using conventional cell cultures, microfluidic systems, organoids, animal surrogates or human studies. To replicate in vitro the tissue architecture and microenvironments of native intestine, we developed a 3D porous protein scaffolding system, containing a geometrically-engineered hollow lumen, with adaptability to both large and small intestines. These intestinal tissues demonstrated representative human responses by permitting continuous accumulation of mucous secretions on the epithelial surface, establishing low oxygen tension in the lumen, and interacting with gut-colonizing bacteria. The newly developed 3D intestine model enabled months-long sustained access to these intestinal functions in vitro, readily integrable with a multitude of different organ mimics and will therefore ensure a reliable ex vivo tissue system for studies in a broad context of human intestinal diseases and treatments. PMID:26374193

  15. Robust bioengineered 3D functional human intestinal epithelium.

    PubMed

    Chen, Ying; Lin, Yinan; Davis, Kimberly M; Wang, Qianrui; Rnjak-Kovacina, Jelena; Li, Chunmei; Isberg, Ralph R; Kumamoto, Carol A; Mecsas, Joan; Kaplan, David L

    2015-09-16

    Intestinal functions are central to human physiology, health and disease. Options to study these functions with direct relevance to the human condition remain severely limited when using conventional cell cultures, microfluidic systems, organoids, animal surrogates or human studies. To replicate in vitro the tissue architecture and microenvironments of native intestine, we developed a 3D porous protein scaffolding system, containing a geometrically-engineered hollow lumen, with adaptability to both large and small intestines. These intestinal tissues demonstrated representative human responses by permitting continuous accumulation of mucous secretions on the epithelial surface, establishing low oxygen tension in the lumen, and interacting with gut-colonizing bacteria. The newly developed 3D intestine model enabled months-long sustained access to these intestinal functions in vitro, readily integrable with a multitude of different organ mimics and will therefore ensure a reliable ex vivo tissue system for studies in a broad context of human intestinal diseases and treatments.

  16. 3-D residual eddy current field characterisation: applied to diffusion weighted magnetic resonance imaging.

    PubMed

    O'Brien, Kieran; Daducci, Alessandro; Kickler, Nils; Lazeyras, Francois; Gruetter, Rolf; Feiweier, Thorsten; Krueger, Gunnar

    2013-08-01

    Clinical use of the Stejskal-Tanner diffusion weighted images is hampered by the geometric distortions that result from the large residual 3-D eddy current field induced. In this work, we aimed to predict, using linear response theory, the residual 3-D eddy current field required for geometric distortion correction based on phantom eddy current field measurements. The predicted 3-D eddy current field induced by the diffusion-weighting gradients was able to reduce the root mean square error of the residual eddy current field to ~1 Hz. The model's performance was tested on diffusion weighted images of four normal volunteers, following distortion correction, the quality of the Stejskal-Tanner diffusion-weighted images was found to have comparable quality to image registration based corrections (FSL) at low b-values. Unlike registration techniques the correction was not hindered by low SNR at high b-values, and results in improved image quality relative to FSL. Characterization of the 3-D eddy current field with linear response theory enables the prediction of the 3-D eddy current field required to correct eddy current induced geometric distortions for a wide range of clinical and high b-value protocols.

  17. Added Value of 3D Proton-Density Weighted Images in Diagnosis of Intracranial Arterial Dissection

    PubMed Central

    Kim, Jin Woo; Kim, Young Dae; Lee, Seung-Koo; Lim, Soo Mee; Oh, Se Won

    2016-01-01

    Background An early and reliable diagnosis of intracranial arterial dissection is important to reduce the risk of neurological complication. The purpose of this study was to assess the clinical usefulness of three-dimensional high-resolution MRI (3D-HR-MRI) including pre- and post-contrast T1-weighted volumetric isotropic turbo spin echo acquisition with improved motion-sensitized driven equilibrium preparation (3D-iMSDE-T1) and proton-density weighted image (3D-PD) in detecting dissection and to evaluate the added value of 3D-PD in diagnosing intracranial arterial dissection. Methods We retrospectively recruited patients who underwent 3D-HR-MRI with clinical suspicion of arterial dissection. Among them, we selected patients who were diagnosed with definite dissection according to the Spontaneous Cervicocephalic Arterial Dissections Study criteria. For each patient, the presence of intimal flap, intramural hematoma, and vessel dilatation were evaluated independently by two neuroradiologists on each sequence. Interobserver agreement was assessed. Results Seventeen patients (mean age: 41 ± 10 [SD] years; 13 men) were diagnosed with definite dissection. The intimal flaps were more frequently detected on 3D-PD (88.2%, 15/17) than on 3D-iMSDE-T1 (29.4%, 5/17), and post-contrast 3D-iMSDE-T1 (35.3%, 6/17; P = 0.006 and P = 0.004, respectively). No significant difference was found in the detection rate of intramural hematomas (59–71%) and vascular dilatations (47%) on each sequence. Interobserver agreement for detection of dissection findings showed almost perfect agreement (k = 0.84–1.00), except for detection of intimal flaps on pre-contrast 3D-iMSDE-T1 (k = 0.62). After addition of 3D-PD to pre- and post-contrast 3D-iMSDE-T1, more patients were diagnosed with definite dissection with the initial MRI (88.2% vs. 47.1%; P = 0.039). Conclusions The intimal flap might be better visualized on the 3D-PD sequence than the 3D-iMSDE-T1 sequences, allowing diagnosis of

  18. Multiprocess 3D printing for increasing component functionality.

    PubMed

    MacDonald, Eric; Wicker, Ryan

    2016-09-30

    Layer-by-layer deposition of materials to manufacture parts-better known as three-dimensional (3D) printing or additive manufacturing-has been flourishing as a fabrication process in the past several years and now can create complex geometries for use as models, assembly fixtures, and production molds. Increasing interest has focused on the use of this technology for direct manufacturing of production parts; however, it remains generally limited to single-material fabrication, which can limit the end-use functionality of the fabricated structures. The next generation of 3D printing will entail not only the integration of dissimilar materials but the embedding of active components in order to deliver functionality that was not possible previously. Examples could include arbitrarily shaped electronics with integrated microfluidic thermal management and intelligent prostheses custom-fit to the anatomy of a specific patient. We review the state of the art in multiprocess (or hybrid) 3D printing, in which complementary processes, both novel and traditional, are combined to advance the future of manufacturing.

  19. Noise reduction for low-dose helical CT by 3D penalized weighted least-squares sinogram smoothing

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Li, Tianfang; Lu, Hongbing; Liang, Zhengrong

    2006-03-01

    Helical computed tomography (HCT) has several advantages over conventional step-and-shoot CT for imaging a relatively large object, especially for dynamic studies. However, HCT may increase X-ray exposure significantly to the patient. This work aims to reduce the radiation by lowering the X-ray tube current (mA) and filtering the low-mA (or dose) sinogram noise. Based on the noise properties of HCT sinogram, a three-dimensional (3D) penalized weighted least-squares (PWLS) objective function was constructed and an optimal sinogram was estimated by minimizing the objective function. To consider the difference of signal correlation among different direction of the HCT sinogram, an anisotropic Markov random filed (MRF) Gibbs function was designed as the penalty. The minimization of the objection function was performed by iterative Gauss-Seidel updating strategy. The effectiveness of the 3D-PWLS sinogram smoothing for low-dose HCT was demonstrated by a 3D Shepp-Logan head phantom study. Comparison studies with our previously developed KL domain PWLS sinogram smoothing algorithm indicate that the KL+2D-PWLS algorithm shows better performance on in-plane noise-resolution trade-off while the 3D-PLWS shows better performance on z-axis noise-resolution trade-off. Receiver operating characteristic (ROC) studies by using channelized Hotelling observer (CHO) shows that 3D-PWLS and KL+2DPWLS algorithms have similar performance on detectability in low-contrast environment.

  20. 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.

  1. Probability Density Function at the 3D Anderson Transition

    NASA Astrophysics Data System (ADS)

    Rodriguez, Alberto; Vasquez, Louella J.; Roemer, Rudolf

    2009-03-01

    The probability density function (PDF) for the wavefunction amplitudes is studied at the metal-insulator transition of the 3D Anderson model, for very large systems up to L^3=240^3. The implications of the multifractal nature of the state upon the PDF are presented in detail. A formal expression between the PDF and the singularity spectrum f(α) is given. The PDF can be easily used to carry out a numerical multifractal analysis and it appears as a valid alternative to the more usual approach based on the scaling law of the general inverse participation rations.

  2. Weighted f-values, A-values, and line strengths for the E1 transitions among 3d 6, 3d 54s, and 3d 54p levels of Fe III

    NASA Astrophysics Data System (ADS)

    Deb, Narayan C.; Hibbert, Alan

    2009-03-01

    Weighted oscillator strengths, weighted radiative rates, and line strengths for all the E1 transitions between 285 fine-structure levels belonging to the 3d 6, 3d 54s, and 3d 54p configurations of Fe III are presented, in ascending order of wavelength. Calculations have been undertaken using the general configuration interaction (CI) code CIV3. The large configuration set is constructed by allowing single and double replacements from any of 3d 6, 3d 54s, 3d 54p, and 3d 54d configurations to nl orbitals with n⩽5,l⩽3 as well as 6p. Additional selective promotions from 3s and 3p subshells are also included in the CI expansions to incorporate the important correlation effects in the n=3 shell. Results of some strong transitions between levels of 3d 6, 3d 54s, and 3d 54p configurations are also presented and compared with other available calculations. It is found that large disagreements occur in many transitions among the existing calculations.

  3. [Depiction of the cranial nerves around the cavernous sinus by 3D reversed FISP with diffusion weighted imaging (3D PSIF-DWI)].

    PubMed

    Ishida, Go; Oishi, Makoto; Jinguji, Shinya; Yoneoka, Yuichiro; Sato, Mitsuya; Fujii, Yukihiko

    2011-10-01

    To evaluate the anatomy of cranial nerves running in and around the cavernous sinus, we employed three-dimensional reversed fast imaging with steady-state precession (FISP) with diffusion weighted imaging (3D PSIF-DWI) on 3-T magnetic resonance (MR) system. After determining the proper parameters to obtain sufficient resolution of 3D PSIF-DWI, we collected imaging data of 20-side cavernous regions in 10 normal subjects. 3D PSIF-DWI provided high contrast between the cranial nerves and other soft tissues, fluid, and blood in all subjects. We also created volume-rendered images of 3D PSIF-DWI and anatomically evaluated the reliability of visualizing optic, oculomotor, trochlear, trigeminal, and abducens nerves on 3D PSIF-DWI. All 20 sets of cranial nerves were visualized and 12 trochlear nerves and 6 abducens nerves were partially identified. We also presented preliminary clinical experiences in two cases with pituitary adenomas. The anatomical relationship between the tumor and cranial nerves running in and around the cavernous sinus could be three-dimensionally comprehended by 3D PSIF-DWI and the volume-rendered images. In conclusion, 3D PSIF-DWI has great potential to provide high resolution "cranial nerve imaging", which visualizes the whole length of the cranial nerves including the parts in the blood flow as in the cavernous sinus region.

  4. High-resolution DTI of a localized volume using 3D single-shot diffusion-weighted STimulated echo-planar imaging (3D ss-DWSTEPI).

    PubMed

    Jeong, Eun-Kee; Kim, Seong-Eun; Kholmovski, Eugene G; Parker, Dennis L

    2006-12-01

    Diffusion tensor MRI (DTI) using conventional single-shot (SS) 2D diffusion-weighted (DW)-EPI is subject to severe susceptibility artifacts. Multishot DW imaging (DWI) techniques can reduce these distortions, but they generally suffer from artifacts caused by motion-induced phase errors. Parallel imaging can also reduce the distortions if the sensitivity profiles of the receiver coils allow a sufficiently high reduction factor for the desired field of view (FOV). A novel 3D DTI technique, termed 3D single-shot STimulated EPI (3D ss-STEPI), was developed to acquire high-resolution DW images of a localized region. The new technique completes k-space acquisition of a limited 3D volume after a single diffusion preparation. Because the DW magnetization is stored in the longitudinal direction until readout, it undergoes T(1) rather than T(2) decay. Inner volume imaging (IVI) is used to limit the imaging volume. This reduces the time required for EPI readout of each complete k(x)-k(y) plane, and hence reduces T(2)(*) decay during the readout and T(1) decay between the readout of each k(z). 3D ss-STEPI images appear to be free of severe susceptibility and motion artifacts. 3D ss-STEPI allows high-resolution DTI of limited volumes of interest, such as localized brain regions, cervical spinal cord, optic nerve, and other extracranial organs.

  5. 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.

  6. Density functional theory optimized basis sets for gradient corrected functionals: 3d transition metal systems.

    PubMed

    Calaminici, Patrizia; Janetzko, Florian; Köster, Andreas M; Mejia-Olvera, Roberto; Zuniga-Gutierrez, Bernardo

    2007-01-28

    Density functional theory optimized basis sets for gradient corrected functionals for 3d transition metal atoms are presented. Double zeta valence polarization and triple zeta valence polarization basis sets are optimized with the PW86 functional. The performance of the newly optimized basis sets is tested in atomic and molecular calculations. Excitation energies of 3d transition metal atoms, as well as electronic configurations, structural parameters, dissociation energies, and harmonic vibrational frequencies of a large number of molecules containing 3d transition metal elements, are presented. The obtained results are compared with available experimental data as well as with other theoretical data from the literature.

  7. Episcopic 3D Imaging Methods: Tools for Researching Gene Function

    PubMed Central

    Weninger, Wolfgang J; Geyer, Stefan H

    2008-01-01

    This work aims at describing episcopic 3D imaging methods and at discussing how these methods can contribute to researching the genetic mechanisms driving embryogenesis and tissue remodelling, and the genesis of pathologies. Several episcopic 3D imaging methods exist. The most advanced are capable of generating high-resolution volume data (voxel sizes from 0.5x0.5x1 µm upwards) of small to large embryos of model organisms and tissue samples. Beside anatomy and tissue architecture, gene expression and gene product patterns can be three dimensionally analyzed in their precise anatomical and histological context with the aid of whole mount in situ hybridization or whole mount immunohistochemical staining techniques. Episcopic 3D imaging techniques were and are employed for analyzing the precise morphological phenotype of experimentally malformed, randomly produced, or genetically engineered embryos of biomedical model organisms. It has been shown that episcopic 3D imaging also fits for describing the spatial distribution of genes and gene products during embryogenesis, and that it can be used for analyzing tissue samples of adult model animals and humans. The latter offers the possibility to use episcopic 3D imaging techniques for researching the causality and treatment of pathologies or for staging cancer. Such applications, however, are not yet routine and currently only preliminary results are available. We conclude that, although episcopic 3D imaging is in its very beginnings, it represents an upcoming methodology, which in short terms will become an indispensable tool for researching the genetic regulation of embryo development as well as the genesis of malformations and diseases. PMID:19452045

  8. Creating perfused functional vascular channels using 3D bio-printing technology.

    PubMed

    Lee, Vivian K; Kim, Diana Y; Ngo, Haygan; Lee, Young; Seo, Lan; Yoo, Seung-Schik; Vincent, Peter A; Dai, Guohao

    2014-09-01

    We developed a methodology using 3D bio-printing technology to create a functional in vitro vascular channel with perfused open lumen using only cells and biological matrices. The fabricated vasculature has a tight, confluent endothelium lining, presenting barrier function for both plasma protein and high-molecular weight dextran molecule. The fluidic vascular channel is capable of supporting the viability of tissue up to 5 mm in distance at 5 million cells/mL density under the physiological flow condition. In static-cultured vascular channels, active angiogenic sprouting from the vessel surface was observed whereas physiological flow strongly suppressed this process. Gene expression analysis was reported in this study to show the potential of this vessel model in vascular biology research. The methods have great potential in vascularized tissue fabrication using 3D bio-printing technology as the vascular channel is simultaneously created while cells and matrix are printed around the channel in desired 3D patterns. It can also serve as a unique experimental tool for investigating fundamental mechanisms of vascular remodeling with extracellular matrix and maturation process under 3D flow condition.

  9. 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.

  10. Molecular weight specific impact of soluble and immobilized hyaluronan on CD44 expressing melanoma cells in 3D collagen matrices.

    PubMed

    Sapudom, Jiranuwat; Ullm, Franziska; Martin, Steve; Kalbitzer, Liv; Naab, Johanna; Möller, Stephanie; Schnabelrauch, Matthias; Anderegg, Ulf; Schmidt, Stephan; Pompe, Tilo

    2017-03-01

    Hyaluronan (HA) and its principal receptor CD44 are known to be involved in regulating tumor cell dissemination and metastasis. The direct correlation of CD44-HA interaction on proliferation and invasion of tumor cells in dependence on the molecular weight and the presentation form of HA is not fully understood because of lack of appropriate matrix models. To address this issue, we reconstituted 3D collagen (Coll I) matrices and functionalized them with HA of molecular weight of 30-50kDa (low molecular weight; LMW-HA) and 500-750kDa (high molecular weight; HMW-HA). A post-modification strategy was applied to covalently immobilize HA to reconstituted fibrillar Coll I matrices, resulting in a non-altered Coll I network microstructure and stable immobilization over days. Functionalized Coll I matrices were characterized regarding topological and mechanical characteristics as well as HA amount using confocal laser scanning microscopy, colloidal probe force spectroscopy and quantitative Alcian blue assay, respectively. To elucidate HA dependent tumor cell behavior, BRO melanoma cell lines with and without CD44 receptor expression were used for in vitro cell experiments. We demonstrated that only soluble LMW-HA promoted cell proliferation in a CD44 dependent manner, while HMW-HA and immobilized LMW-HA did not. Furthermore, an enhanced cell invasion was found only for immobilized LMW-HA. Both findings correlated with a very strong and specific adhesive interaction of LMW-HA and CD44+ cells quantified in single cell adhesion measurements using soft colloidal force spectroscopy. Overall, our results introduce an in vitro biomaterials model allowing to test presentation mode and molecular weight specificity of HA in a 3D fibrillar matrix thus mimicking important in vivo features of tumor microenvironments.

  11. Automatic hip cartilage segmentation from 3D MR images using arc-weighted graph searching.

    PubMed

    Xia, Ying; Chandra, Shekhar S; Engstrom, Craig; Strudwick, Mark W; Crozier, Stuart; Fripp, Jurgen

    2014-12-07

    Accurate segmentation of hip joint cartilage from magnetic resonance (MR) images offers opportunities for quantitative investigations of pathoanatomical conditions such as osteoarthritis. In this paper, we present a fully automatic scheme for the segmentation of the individual femoral and acetabular cartilage plates in the human hip joint from high-resolution 3D MR images. The developed scheme uses an improved optimal multi-object multi-surface graph search framework with an arc-weighted graph representation that incorporates prior morphological knowledge as a basis for segmentation of the individual femoral and acetabular cartilage plates despite weak or incomplete boundary interfaces. This automated scheme was validated against manual segmentations from 3D true fast imaging with steady-state precession (TrueFISP) MR examinations of the right hip joints in 52 asymptomatic volunteers. Compared with expert manual segmentations of the combined, femoral and acetabular cartilage volumes, the automatic scheme obtained mean (± standard deviation) Dice's similarity coefficients of 0.81 (± 0.03), 0.79 (± 0.03) and 0.72 (± 0.05). The corresponding mean absolute volume difference errors were 8.44% (± 6.36), 9.44% (± 7.19) and 9.05% (± 8.02). The mean absolute differences between manual and automated measures of cartilage thickness for femoral and acetabular cartilage plates were 0.13 mm (± 0.12) and 0.11 mm (± 0.11), respectively.

  12. An endoscope designed with 3D measurement functions

    NASA Astrophysics Data System (ADS)

    Zhu, Qi-hai; Li, Zheng-lin; Wang, Li-qiang; Zhao, Chang-Ming; Xu, Peng

    2016-10-01

    The endoscopic system is widely used in medical and industrial areas, but how to realize the high-precision three-dimensional measurement in the limited space scale still faces many challenges. A method based on the four-step phase-shifting structured light illumination is proposed in this paper for endoscopic 3D measurements. Structured light of which the adjacent phase shift is 90 degrees is generated by the different parts of the time-sharing lighting stripe grating of the optical fiber bundle; CMOS camera is used to collect four structured light images with the phase shift. Finally, the method of four-step phase-shifting is used to demodulate 3D information from the images, and a relative measurement accuracy of 95% within the range of 15-200mm can be obtained. The endoscope with a field of view of 90 degrees, a image resolution of 1280 * 800 and 3D depth calculation time of 0.2 seconds has advantages of simple structure, large field of view, high accuracy and good real-time measurement.

  13. Pancreas segmentation from 3D abdominal CT images using patient-specific weighted subspatial probabilistic atlases

    NASA Astrophysics Data System (ADS)

    Karasawa, Kenichi; Oda, Masahiro; Hayashi, Yuichiro; Nimura, Yukitaka; Kitasaka, Takayuki; Misawa, Kazunari; Fujiwara, Michitaka; Rueckert, Daniel; Mori, Kensaku

    2015-03-01

    Abdominal organ segmentations from CT volumes are now widely used in the computer-aided diagnosis and surgery assistance systems. Among abdominal organs, the pancreas is especially difficult to segment because of its large individual differences of the shape and position. In this paper, we propose a new pancreas segmentation method from 3D abdominal CT volumes using patient-specific weighted-subspatial probabilistic atlases. First of all, we perform normalization of organ shapes in training volumes and an input volume. We extract the Volume Of Interest (VOI) of the pancreas from the training volumes and an input volume. We divide each training VOI and input VOI into some cubic regions. We use a nonrigid registration method to register these cubic regions of the training VOI to corresponding regions of the input VOI. Based on the registration results, we calculate similarities between each cubic region of the training VOI and corresponding region of the input VOI. We select cubic regions of training volumes having the top N similarities in each cubic region. We subspatially construct probabilistic atlases weighted by the similarities in each cubic region. After integrating these probabilistic atlases in cubic regions into one, we perform a rough-to-precise segmentation of the pancreas using the atlas. The results of the experiments showed that utilization of the training volumes having the top N similarities in each cubic region led good results of the pancreas segmentation. The Jaccard Index and the average surface distance of the result were 58.9% and 2.04mm on average, respectively.

  14. Comparison of 3D Orientation Distribution Functions Measured with Confocal Microscopy and Diffusion MRI

    PubMed Central

    Schilling, Kurt; Janve, Vaibhav; Gao, Yurui; Stepniewska, Iwona; Landman, Bennett A; Anderson, Adam W

    2016-01-01

    The ability of diffusion MRI (dMRI) fiber tractography to non-invasively map three-dimensional (3D) anatomical networks in the human brain has made it a valuable tool in both clinical and research settings. However, there are many assumptions inherent to any tractography algorithm that can limit the accuracy of the reconstructed fiber tracts. Among them is the assumption that the diffusion-weighted images accurately reflect the underlying fiber orientation distribution (FOD) in the MRI voxel. Consequently, validating dMRI’s ability to assess the underlying fiber orientation in each voxel is critical for its use as a biomedical tool. Here, using post-mortem histology and confocal microscopy, we present a method to perform histological validation of orientation functions in 3D, which has previously been limited to two-dimensional analysis of tissue sections. We demonstrate the ability to extract the 3D FOD from confocal z-stacks, and quantify the agreement between the MRI estimates of orientation information obtained using constrained spherical deconvolution (CSD) and the true geometry of the fibers. We find an orientation error of approximately 6° in voxels containing nearly parallel fibers, and 10-11° in crossing fiber regions, and note that CSD was unable to resolve fibers crossing at angles below 60° in our dataset. This is the first time the 3D white matter orientation distribution is calculated from histology and compared to dMRI. Thus, this technique serves as a gold standard for dMRI validation studies - providing the ability to determine the extent to which the dMRI signal is consistent with the histological FOD, and to establish how well different dMRI models can predict the ground truth FOD. PMID:26804781

  15. 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.

  16. Error Analysis of Multi-Source Data for 3D Geological Modeling Using Entropy-based Weighting

    NASA Astrophysics Data System (ADS)

    Hou, W.; Yang, L.; Clarke, K.

    2013-12-01

    In each step of geological modeling, errors always have an impact on workflow processes and so have consequences that challenge 3D geological modeling. Methods such as geostatistics, fuzzy set theory and spatial error theory have been used to analyze errors that exist in the raw data behind geological models and these methods assume that a single error distribution exist in all kinds of data. However, different kinds of raw data, such as borehole, user-defined section and geological maps, even within a single kind of data, they may exist different types of positional error distributions. Consequently, analyzing errors of multi-source data for geological modeling remains a vital problem in geological modeling. In this study, we developed a novel approach to quantitatively analyze the distributions of errors in multi-source raw data used for constructing 3D geological structural models. Errors among raw data are usually discussed directly based on the error distributions of points, supposing that the positional error of geological boundaries is caused by spatial measurement rather than uncertainties in the geological attributes. In reality, geological boundaries are given by the distribution of geological attributes of related strata, which are themselves vaguely defined. Therefore, the spatial error in geological boundaries is mainly caused by the uncertainties of geological attributes. Here, we supposed that spatial position is fixed and geological attributes of each point in space vary. According to the spatial relationship between geological attributes and geological boundaries, the spatial error of geological boundaries is transferred into a specific probability of each geological attribute for each point, termed the ';Geological attribute probability'. The key problem in this research is to construct a function for transforming the 3D spatial problem into a 1-D probability distribution problem. We transferred several kinds of spatial error distributions into

  17. Engineering EMT using 3D micro-scaffold to promote hepatic functions for drug hepatotoxicity evaluation.

    PubMed

    Wang, Jingyu; Chen, Fengling; Liu, Longwei; Qi, Chunxiao; Wang, Bingjie; Yan, Xiaojun; Huang, Chenyu; Hou, Wei; Zhang, Michael Q; Chen, Yang; Du, Yanan

    2016-06-01

    Accompanied by decreased hepatic functions, epithelial-mesenchymal transition (EMT) was observed in two dimensional (2D) cultured hepatocytes with elongated morphology, loss of polarity and weakened cell-cell interaction, while upgrading to 3D culture has been considered as significant improvement of its 2D counterpart for hepatocyte maintenance. Here we hypothesize that 3D culture enhances hepatic functions through regulating the EMT status. Biomaterial-engineered EMT was achieved by culturing HepaRG as 3D spheroids (SP-3D) or 3D stretched cells (ST-3D) in non-adherent and adherent micro-scaffold respectively. In SP-3D, constrained EMT of HepaRG, a hepatic stem cell line, as represented by increased epithelial markers and decreased mesenchymal markers, was echoed by improved hepatic functions. To investigate the relationship between EMT status and hepatic functions, time-series RNA-Seq and gene network analysis were used for comparing different cell culture models, which identified histone deacetylases (HDACs) as key mediating factors. Protein analysis confirmed that high HDAC activity was correlated with high expression of Cadherin-1 (CDH1) and hepatic function genes, which were decreased upon HDAC inhibitor treatment in SP-3D, suggesting HDACs may play positive role in regulating EMT and hepatic functions. To illustrate the application of 3D micro-scaffold culture in drug safety evaluation, hepatotoxicity and metabolism assays of two hepatotoxins (i.e. N-acetyl-p-aminophenol and Doxorubicin) were performed and SP-3D showed more biomimetic toxicity response, indicating regulation of EMT as a vital consideration in designing 3D hepatocyte culture configuration.

  18. Sub-millimeter T2 weighted fMRI at 7 T: comparison of 3D-GRASE and 2D SE-EPI.

    PubMed

    Kemper, Valentin G; De Martino, Federico; Vu, An T; Poser, Benedikt A; Feinberg, David A; Goebel, Rainer; Yacoub, Essa

    2015-01-01

    Functional magnetic resonance imaging (fMRI) allows studying human brain function non-invasively up to the spatial resolution of cortical columns and layers. Most fMRI acquisitions rely on the blood oxygenation level dependent (BOLD) contrast employing T(*) 2 weighted 2D multi-slice echo-planar imaging (EPI). At ultra-high magnetic field (i.e., 7 T and above), it has been shown experimentally and by simulation, that T2 weighted acquisitions yield a signal that is spatially more specific to the site of neuronal activity at the cost of functional sensitivity. This study compared two T2 weighted imaging sequences, inner-volume 3D Gradient-and-Spin-Echo (3D-GRASE) and 2D Spin-Echo EPI (SE-EPI), with evaluation of their imaging point-spread function (PSF), functional specificity, and functional sensitivity at sub-millimeter resolution. Simulations and measurements of the imaging PSF revealed that the strongest anisotropic blurring in 3D-GRASE (along the second phase-encoding direction) was about 60% higher than the strongest anisotropic blurring in 2D SE-EPI (along the phase-encoding direction). In a visual paradigm, the BOLD sensitivity of 3D-GRASE was found to be superior due to its higher temporal signal-to-noise ratio (tSNR). High resolution cortical depth profiles suggested that the contrast mechanisms are similar between the two sequences, however, 2D SE-EPI had a higher surface bias owing to the higher T(*) 2 contribution of the longer in-plane EPI echo-train for full field of view compared to the reduced field of view of zoomed 3D-GRASE.

  19. Guiding Cell Attachment in 3D Microscaffolds Selectively Functionalized with Two Distinct Adhesion Proteins.

    PubMed

    Richter, Benjamin; Hahn, Vincent; Bertels, Sarah; Claus, Tanja K; Wegener, Martin; Delaittre, Guillaume; Barner-Kowollik, Christopher; Bastmeyer, Martin

    2017-02-01

    The combination of three different photoresists into a single direct laser written 3D microscaffold permits functionalization with two bioactive full-length proteins. The cell-instructive microscaffolds consist of a passivating framework equipped with light activatable constituents featuring distinct protein-binding properties. This allows directed cell attachment of epithelial or fibroblast cells in 3D.

  20. 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

  1. 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.

  2. Optimal-tradeoff circular harmonic function filters for 3D target recognition

    NASA Astrophysics Data System (ADS)

    Vijaya Kumar, Bhagavatula V. K.; Xie, Chunyan; Mahalanobis, Abhijit

    2003-09-01

    3D target recognition is of significant interest because representing the object in 3D space couuld essentially provide a solution to pose variation and self-occlusion problems that are big challenges in 2D pattern recognition. Correlation filers have been used in a variety of 2D pattern matching applications and many correlation filter designs have been developed to handle problems such as rotations. Correlation filters also offer other benefits such as shift-invariance, graceful degradation and closed-form solutions. The 3D extension of correlation filter is a natural extension to handle 3D pattern recognition problem. In this paper, we propose a 3D correlation filter design method based on cylindrical circular harmonic function (CCHF) and use LADAR imagery to illustrate the good performance of CCHF filters.

  3. Three-dimensional potential flows from functions of a 3D complex variable

    NASA Technical Reports Server (NTRS)

    Kelly, Patrick; Panton, Ronald L.; Martin, E. D.

    1990-01-01

    Potential, or ideal, flow velocities can be found from the gradient of an harmonic function. An ordinary complex valued analytic function can be written as the sum of two real valued functions, both of which are harmonic. Thus, 2D complex valued functions serve as a source of functions that describe two-dimensional potential flows. However, this use of complex variables has been limited to two-dimensions. Recently, a new system of three-dimensional complex variables has been developed at the NASA Ames Research Center. As a step toward application of this theory to the analysis of 3D potential flow, several functions of a three-dimensional complex variable have been investigated. The results for two such functions, the 3D exponential and 3D logarithm, are presented in this paper. Potential flows found from these functions are investigated. Important characteristics of these flows fields are noted.

  4. Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions

    PubMed Central

    Capurso, Daniel; Bengtsson, Henrik; Segal, Mark R.

    2016-01-01

    The spatial organization of the genome influences cellular function, notably gene regulation. Recent studies have assessed the three-dimensional (3D) co-localization of functional annotations (e.g. centromeres, long terminal repeats) using 3D genome reconstructions from Hi-C (genome-wide chromosome conformation capture) data; however, corresponding assessments for continuous functional genomic data (e.g. chromatin immunoprecipitation-sequencing (ChIP-seq) peak height) are lacking. Here, we demonstrate that applying bump hunting via the patient rule induction method (PRIM) to ChIP-seq data superposed on a Saccharomyces cerevisiae 3D genome reconstruction can discover ‘functional 3D hotspots’, regions in 3-space for which the mean ChIP-seq peak height is significantly elevated. For the transcription factor Swi6, the top hotspot by P-value contains MSB2 and ERG11 – known Swi6 target genes on different chromosomes. We verify this finding in a number of ways. First, this top hotspot is relatively stable under PRIM across parameter settings. Second, this hotspot is among the top hotspots by mean outcome identified by an alternative algorithm, k-Nearest Neighbor (k-NN) regression. Third, the distance between MSB2 and ERG11 is smaller than expected (by resampling) in two other 3D reconstructions generated via different normalization and reconstruction algorithms. This analytic approach can discover functional 3D hotspots and potentially reveal novel regulatory interactions. PMID:26869583

  5. 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

  6. Pt nanoparticles functionalized 3D SnO2 nanoflowers for gas sensor application

    NASA Astrophysics Data System (ADS)

    Liu, Yinglin; Huang, Jing; Yang, Jiedi; Wang, Shurong

    2017-04-01

    3D SnO2 nanoflowers (NFs) assembled by rod-like nanostructures were synthesized by a facile hydrothermal method only using simple and inexpensive SnCl4·5H2O and NaOH as the starting materials, without using any surfactants or templates. The as-synthesized 3D SnO2 NFs were further functionalized by Pt nanoparticles (NPs) by a simple ammonia precipitate method, and the derived Pt NP-functionalized 3D SnO2 NFs were further investigated for gas sensor application using ethanol as a probe gas. Obtained results showed that the Pt NP-functionalized 3D SnO2 NF sensor exhibited much higher response in comparison with pure SnO2 sensor, altogether with short response/recovery times and good reproducibility. The enhanced gas sensing performances could be attributed to spill-over effect of Pt NPs for promoting gas sensing reactions, the synergic electronic interaction between Pt NPs and SnO2 support, the high surface-to-volume ratio and good electron mobility of the 1D SnO2 nanorod units, and unique 3D hierarchical flower-like nanostructures. It is also expected that the as-prepared 3D SnO2 NFs and Pt NP-functionalized product can be used in other fields such as optoelectronic devices, Li-ion battery and dye sensitized solar cells.

  7. Fabrication of 3D-culture platform with sandwich architecture for preserving liver-specific functions of hepatocytes using 3D bioprinter.

    PubMed

    Arai, Kenichi; Yoshida, Toshiko; Okabe, Motonori; Goto, Mitsuaki; Mir, Tanveer Ahmad; Soko, Chika; Tsukamoto, Yoshinari; Akaike, Toshihiro; Nikaido, Toshio; Zhou, Kaixuan; Nakamura, Makoto

    2016-09-19

    The development of new three-dimensional (3D) cell culture system that maintains the physiologically relevant signals of hepatocytes is essential in drug discovery and tissue engineering research. Conventional two-dimensional (2D) culture yields cell growth, proliferation, and differentiation. However, gene expression and signaling profiles can be different from in vivo environment. Here, we report the fabrication of a 3D culture system using an artificial scaffold and our custom-made inkjet 3D bioprinter as a new strategy for studying liver-specific functions of hepatocytes. We built a 3D culture platform for hepatocytes-attachment and formation of cell monolayer by interacting the galactose chain of galactosylated alginate gel (GA-gel) with asialoglycoprotein receptor (ASGPR) of hepatocytes. The 3D geometrical arrangement of cells was controlled by using 3D bioprinter, and cell polarity was controlled with the galactosylated hydrogels. The fabricated GA-gel was able to successfully promote adhesion of hepatocytes. To observe liver-specific functions and to mimic hepatic cord, an additional parallel layer of hepatocytes was generated using two gel sheets. These results indicated that GA-gel biomimetic matrices can be used as a 3D culture system that could be effective for the engineering of liver tissues. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2016.

  8. Wearable 3-D Photoacoustic Tomography for Functional Brain Imaging in Behaving Rats

    PubMed Central

    Tang, Jianbo; Coleman, Jason E.; Dai, Xianjin; Jiang, Huabei

    2016-01-01

    Understanding the relationship between brain function and behavior remains a major challenge in neuroscience. Photoacoustic tomography (PAT) is an emerging technique that allows for noninvasive in vivo brain imaging at micrometer-millisecond spatiotemporal resolution. In this article, a novel, miniaturized 3D wearable PAT (3D-wPAT) technique is described for brain imaging in behaving rats. 3D-wPAT has three layers of fully functional acoustic transducer arrays. Phantom imaging experiments revealed that the in-plane X-Y spatial resolutions were ~200 μm for each acoustic detection layer. The functional imaging capacity of 3D-wPAT was demonstrated by mapping the cerebral oxygen saturation via multi-wavelength irradiation in behaving hyperoxic rats. In addition, we demonstrated that 3D-wPAT could be used for monitoring sensory stimulus-evoked responses in behaving rats by measuring hemodynamic responses in the primary visual cortex during visual stimulation. Together, these results show the potential of 3D-wPAT for brain study in behaving rodents. PMID:27146026

  9. 3-D, bluff body drag estimation using a Green's function/Gram-Charlier series approach.

    SciTech Connect

    Barone, Matthew Franklin; De Chant, Lawrence Justin

    2004-05-01

    In this study, we describe the extension of the 2-d preliminary design bluff body drag estimation tool developed by De Chant to apply for 3-d flows. As with the 2-d method, the 3-d extension uses a combined approximate Green's function/Gram-Charlier series approach to retain the body geometry information. Whereas, the 2-d methodology relied solely upon the use of small disturbance theory for the inviscid flow field associated with the body of interest to estimate the near-field initial conditions, e.g. velocity defect, the 3-d methodology uses both analytical (where available) and numerical inviscid solutions. The defect solution is then used as an initial condition in an approximate 3-d Green's function solution. Finally, the Green's function solution is matched to the 3-d analog of the classical 2-d Gram-Charlier series and then integrated to yield the net form drag on the bluff body. Preliminary results indicate that drag estimates computed are of accuracy equivalent to the 2-d method for flows with large separation, i.e. less than 20% relative error. As was the lower dimensional method, the 3-d concept is intended to be a supplement to turbulent Navier-Stokes and experimental solution for estimating drag coefficients over blunt bodies.

  10. 3-D, bluff body drag estimation using a Green's function/Gram-Charlier series approach.

    SciTech Connect

    Barone, Matthew Franklin; De Chant, Lawrence Justin

    2005-01-01

    In this study, we describe the extension of the 2-d preliminary design bluff body drag estimation tool developed by De Chant1 to apply for 3-d flows. As with the 2-d method, the 3-d extension uses a combined approximate Green's function/Gram-Charlier series approach to retain the body geometry information. Whereas, the 2-d methodology relied solely upon the use of small disturbance theory for the inviscid flow field associated with the body of interest to estimate the near-field initial conditions, e.g. velocity defect, the 3-d methodology uses both analytical (where available) and numerical inviscid solutions. The defect solution is then used as an initial condition in an approximate 3-d Green's function solution. Finally, the Green's function solution is matched to the 3-d analog of the classical 2-d Gram-Charlier series and then integrated to yield the net form drag on the bluff body. Preliminary results indicate that drag estimates computed are of accuracy equivalent to the 2-d method for flows with large separation, i.e. less than 20% relative error. As was the lower dimensional method, the 3-d concept is intended to be a supplement to turbulent Navier-Stokes and experimental solution for estimating drag coefficients over blunt bodies.

  11. Generalized recovery algorithm for 3D super-resolution microscopy using rotating point spread functions

    PubMed Central

    Shuang, Bo; Wang, Wenxiao; Shen, Hao; Tauzin, Lawrence J.; Flatebo, Charlotte; Chen, Jianbo; Moringo, Nicholas A.; Bishop, Logan D. C.; Kelly, Kevin F.; Landes, Christy F.

    2016-01-01

    Super-resolution microscopy with phase masks is a promising technique for 3D imaging and tracking. Due to the complexity of the resultant point spread functions, generalized recovery algorithms are still missing. We introduce a 3D super-resolution recovery algorithm that works for a variety of phase masks generating 3D point spread functions. A fast deconvolution process generates initial guesses, which are further refined by least squares fitting. Overfitting is suppressed using a machine learning determined threshold. Preliminary results on experimental data show that our algorithm can be used to super-localize 3D adsorption events within a porous polymer film and is useful for evaluating potential phase masks. Finally, we demonstrate that parallel computation on graphics processing units can reduce the processing time required for 3D recovery. Simulations reveal that, through desktop parallelization, the ultimate limit of real-time processing is possible. Our program is the first open source recovery program for generalized 3D recovery using rotating point spread functions. PMID:27488312

  12. Wearable 3-D Photoacoustic Tomography for Functional Brain Imaging in Behaving Rats.

    PubMed

    Tang, Jianbo; Coleman, Jason E; Dai, Xianjin; Jiang, Huabei

    2016-05-05

    Understanding the relationship between brain function and behavior remains a major challenge in neuroscience. Photoacoustic tomography (PAT) is an emerging technique that allows for noninvasive in vivo brain imaging at micrometer-millisecond spatiotemporal resolution. In this article, a novel, miniaturized 3D wearable PAT (3D-wPAT) technique is described for brain imaging in behaving rats. 3D-wPAT has three layers of fully functional acoustic transducer arrays. Phantom imaging experiments revealed that the in-plane X-Y spatial resolutions were ~200 μm for each acoustic detection layer. The functional imaging capacity of 3D-wPAT was demonstrated by mapping the cerebral oxygen saturation via multi-wavelength irradiation in behaving hyperoxic rats. In addition, we demonstrated that 3D-wPAT could be used for monitoring sensory stimulus-evoked responses in behaving rats by measuring hemodynamic responses in the primary visual cortex during visual stimulation. Together, these results show the potential of 3D-wPAT for brain study in behaving rodents.

  13. Modulating mechanical behaviour of 3D-printed cartilage-mimetic PCL scaffolds: influence of molecular weight and pore geometry.

    PubMed

    Olubamiji, Adeola D; Izadifar, Zohreh; Si, Jennifer L; Cooper, David M L; Eames, B Frank; Chen, Daniel X B

    2016-06-22

    Three-dimensional (3D)-printed poly(ε)-caprolactone (PCL)-based scaffolds are increasingly being explored for cartilage tissue engineering (CTE) applications. However, ensuring that the mechanical properties of these PCL-based constructs are comparable to that of articular cartilage that they are meant to regenerate is an area that has been under-explored. This paper presents the effects of PCL's molecular weight (MW) and scaffold's pore geometric configurations; strand size (SZ), strand spacing (SS), and strand orientation (SO), on mechanical properties of 3D-printed PCL scaffolds. The results illustrate that MW has significant effect on compressive moduli and yield strength of 3D-printed PCL scaffolds. Specifically, PCL with MW of 45 K was a more feasible choice for fabrication of visco-elastic, flexible and load-bearing PCL scaffolds. Furthermore, pore geometric configurations; SZ, SS, and SO, all significantly affect on tensile moduli of scaffolds. However, only SZ and SS have statistically significant effects on compressive moduli and porosity of these scaffolds. That said, inverse linear relationship was observed between porosity and mechanical properties of 3D-printed PCL scaffolds in Pearson's correlation test. Altogether, this study illustrates that modulating MW of PCL and pore geometrical configurations of the scaffolds enabled design and fabrication of PCL scaffolds with mechanical and biomimetic properties that better mimic mechanical behaviour of human articular cartilage. Thus, the modulated PCL scaffold proposed in this study is a framework that offers great potentials for CTE applications.

  14. Functional Equivalence Acceptance Testing of FUN3D for Entry Descent and Landing Applications

    NASA Technical Reports Server (NTRS)

    Gnoffo, Peter A.; Wood, William A.; Kleb, William L.; Alter, Stephen J.; Glass, Christopher E.; Padilla, Jose F.; Hammond, Dana P.; White, Jeffery A.

    2013-01-01

    The functional equivalence of the unstructured grid code FUN3D to the the structured grid code LAURA (Langley Aerothermodynamic Upwind Relaxation Algorithm) is documented for applications of interest to the Entry, Descent, and Landing (EDL) community. Examples from an existing suite of regression tests are used to demonstrate the functional equivalence, encompassing various thermochemical models and vehicle configurations. Algorithm modifications required for the node-based unstructured grid code (FUN3D) to reproduce functionality of the cell-centered structured code (LAURA) are also documented. Challenges associated with computation on tetrahedral grids versus computation on structured-grid derived hexahedral systems are discussed.

  15. 3D Cell Printing of Functional Skeletal Muscle Constructs Using Skeletal Muscle-Derived Bioink.

    PubMed

    Choi, Yeong-Jin; Kim, Taek Gyoung; Jeong, Jonghyeon; Yi, Hee-Gyeong; Park, Ji Won; Hwang, Woonbong; Cho, Dong-Woo

    2016-10-01

    Engineered skeletal muscle tissues that mimic the structure and function of native muscle have been considered as an alternative strategy for the treatment of various muscular diseases and injuries. Here, it is demonstrated that 3D cell-printing of decellularized skeletal muscle extracellular matrix (mdECM)-based bioink facilitates the fabrication of functional skeletal muscle constructs. The cellular alignment and the shape of the tissue constructs are controlled by 3D cell-printing technology. mdECM bioink provides the 3D cell-printed muscle constructs with a myogenic environment that supports high viability and contractility as well as myotube formation, differentiation, and maturation. More interestingly, the preservation of agrin is confirmed in the mdECM, and significant increases in the formation of acetylcholine receptor clusters are exhibited in the 3D cell-printed muscle constructs. In conclusion, mdECM bioink and 3D cell-printing technology facilitate the mimicking of both the structural and functional properties of native muscle and hold great promise for producing clinically relevant engineered muscle for the treatment of muscular injuries.

  16. Does shape co-variation between the skull and the mandible have functional consequences? A 3D approach for a 3D problem.

    PubMed

    Cornette, Raphaël; Baylac, Michel; Souter, Thibaud; Herrel, Anthony

    2013-10-01

    Morpho-functional patterns are important drivers of phenotypic diversity given their importance in a fitness-related context. Although modularity of the mandible and skull has been studied extensively in mammals, few studies have explored shape co-variation between these two structures. Despite being developmentally independent, the skull and mandible form a functionally integrated unit. In the present paper we use 3D surface geometric morphometric methods allowing us to explore the form of both skull and mandible in its 3D complexity using the greater white-toothed shrew as a model. This approach allows an accurate 3D description of zones devoid of anatomical landmarks that are functionally important. Two-block partial least-squares approaches were used to describe the co-variation of form between skull and mandible. Moreover, a 3D biomechanical model was used to explore the functional consequences of the observed patterns of co-variation. Our results show the efficiency of the method in investigations of complex morpho-functional patterns. Indeed, the description of shape co-variation between the skull and the mandible highlighted the location and the intensity of their functional relationships through the jaw adductor muscles linking these two structures. Our results also demonstrated that shape co-variation in form between the skull and mandible has direct functional consequences on the recruitment of muscles during biting.

  17. Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

    PubMed Central

    Kristensen, David M; Ward, R Matthew; Lisewski, Andreas Martin; Erdin, Serkan; Chen, Brian Y; Fofanov, Viacheslav Y; Kimmel, Marek; Kavraki, Lydia E; Lichtarge, Olivier

    2008-01-01

    Background Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions. One approach to recover this information is to use 3D templates – structure-function motifs that consist of a few functionally critical amino acids and may suggest functional similarity when geometrically matched to other structures. Since experimentally determined functional sites are not common enough to define 3D templates on a large scale, this work tests a computational strategy to select relevant residues for 3D templates. Results Based on evolutionary information and heuristics, an Evolutionary Trace Annotation (ETA) pipeline built templates for 98 enzymes, half taken from the PSI, and sought matches in a non-redundant structure database. On average each template matched 2.7 distinct proteins, of which 2.0 share the first three Enzyme Commission digits as the template's enzyme of origin. In many cases (61%) a single most likely function could be predicted as the annotation with the most matches, and in these cases such a plurality vote identified the correct function with 87% accuracy. ETA was also found to be complementary to sequence homology-based annotations. When matches are required to both geometrically match the 3D template and to be sequence homologs found by BLAST or PSI-BLAST, the annotation accuracy is greater than either method alone, especially in the region of lower sequence identity where homology-based annotations are least reliable. Conclusion These data suggest that knowledge of evolutionarily important residues improves functional annotation among distant enzyme homologs. Since, unlike other 3D template approaches, the ETA method bypasses the need for experimental knowledge of the catalytic mechanism, it should prove a useful, large scale, and general adjunct to combine with other methods to decipher protein function in the structural proteome. PMID:18190718

  18. Solving 3D relativistic hydrodynamical problems with weighted essentially nonoscillatory discontinuous Galerkin methods

    NASA Astrophysics Data System (ADS)

    Bugner, Marcus; Dietrich, Tim; Bernuzzi, Sebastiano; Weyhausen, Andreas; Brügmann, Bernd

    2016-10-01

    Discontinuous Galerkin (DG) methods coupled to weighted essentially nonoscillatory (WENO) algorithms allow high order convergence for smooth problems and for the simulation of discontinuities and shocks. In this work, we investigate WENO-DG algorithms in the context of numerical general relativity, in particular for general relativistic hydrodynamics. We implement the standard WENO method at different orders, a compact (simple) WENO scheme, as well as an alternative subcell evolution algorithm. To evaluate the performance of the different numerical schemes, we study nonrelativistic, special relativistic, and general relativistic test beds. We present the first three-dimensional simulations of general relativistic hydrodynamics, albeit for a fixed spacetime background, within the framework of WENO-DG methods. The most important test bed is a single Tolman-Oppenheimer-Volkoff star in three dimensions, showing that long term stable simulations of single isolated neutron stars can be obtained with WENO-DG methods.

  19. 3D segmentation of annulus fibrosus and nucleus pulposus from T2-weighted magnetic resonance images

    NASA Astrophysics Data System (ADS)

    Castro-Mateos, Isaac; Pozo, Jose M.; Eltes, Peter E.; Del Rio, Luis; Lazary, Aron; Frangi, Alejandro F.

    2014-12-01

    Computational medicine aims at employing personalised computational models in diagnosis and treatment planning. The use of such models to help physicians in finding the best treatment for low back pain (LBP) is becoming popular. One of the challenges of creating such models is to derive patient-specific anatomical and tissue models of the lumbar intervertebral discs (IVDs), as a prior step. This article presents a segmentation scheme that obtains accurate results irrespective of the degree of IVD degeneration, including pathological discs with protrusion or herniation. The segmentation algorithm, employing a novel feature selector, iteratively deforms an initial shape, which is projected into a statistical shape model space at first and then, into a B-Spline space to improve accuracy. The method was tested on a MR dataset of 59 patients suffering from LBP. The images follow a standard T2-weighted protocol in coronal and sagittal acquisitions. These two image volumes were fused in order to overcome large inter-slice spacing. The agreement between expert-delineated structures, used here as gold-standard, and our automatic segmentation was evaluated using Dice Similarity Index and surface-to-surface distances, obtaining a mean error of 0.68 mm in the annulus segmentation and 1.88 mm in the nucleus, which are the best results with respect to the image resolution in the current literature.

  20. 3D segmentation of annulus fibrosus and nucleus pulposus from T2-weighted magnetic resonance images.

    PubMed

    Castro-Mateos, Isaac; Pozo, Jose M; Eltes, Peter E; Rio, Luis Del; Lazary, Aron; Frangi, Alejandro F

    2014-12-21

    Computational medicine aims at employing personalised computational models in diagnosis and treatment planning. The use of such models to help physicians in finding the best treatment for low back pain (LBP) is becoming popular. One of the challenges of creating such models is to derive patient-specific anatomical and tissue models of the lumbar intervertebral discs (IVDs), as a prior step. This article presents a segmentation scheme that obtains accurate results irrespective of the degree of IVD degeneration, including pathological discs with protrusion or herniation. The segmentation algorithm, employing a novel feature selector, iteratively deforms an initial shape, which is projected into a statistical shape model space at first and then, into a B-Spline space to improve accuracy.The method was tested on a MR dataset of 59 patients suffering from LBP. The images follow a standard T2-weighted protocol in coronal and sagittal acquisitions. These two image volumes were fused in order to overcome large inter-slice spacing. The agreement between expert-delineated structures, used here as gold-standard, and our automatic segmentation was evaluated using Dice Similarity Index and surface-to-surface distances, obtaining a mean error of 0.68 mm in the annulus segmentation and 1.88 mm in the nucleus, which are the best results with respect to the image resolution in the current literature.

  1. Functionalized 3D Architected Materials via Thiol-Michael Addition and Two-Photon Lithography.

    PubMed

    Yee, Daryl W; Schulz, Michael D; Grubbs, Robert H; Greer, Julia R

    2017-02-20

    Fabrication of functionalized 3D architected materials is achieved by a facile method using functionalized acrylates synthesized via thiol-Michael addition, which are then polymerized using two-photon lithography. A wide variety of functional groups can be attached, from Boc-protected amines to fluoroalkanes. Modification of surface wetting properties and conjugation with fluorescent tags are demonstrated to highlight the potential applications of this technique.

  2. Motion corrected LV quantification based on 3D modelling for improved functional assessment in cardiac MRI

    NASA Astrophysics Data System (ADS)

    Liew, Y. M.; McLaughlin, R. A.; Chan, B. T.; Aziz, Y. F. Abdul; Chee, K. H.; Ung, N. M.; Tan, L. K.; Lai, K. W.; Ng, S.; Lim, E.

    2015-04-01

    Cine MRI is a clinical reference standard for the quantitative assessment of cardiac function, but reproducibility is confounded by motion artefacts. We explore the feasibility of a motion corrected 3D left ventricle (LV) quantification method, incorporating multislice image registration into the 3D model reconstruction, to improve reproducibility of 3D LV functional quantification. Multi-breath-hold short-axis and radial long-axis images were acquired from 10 patients and 10 healthy subjects. The proposed framework reduced misalignment between slices to subpixel accuracy (2.88 to 1.21 mm), and improved interstudy reproducibility for 5 important clinical functional measures, i.e. end-diastolic volume, end-systolic volume, ejection fraction, myocardial mass and 3D-sphericity index, as reflected in a reduction in the sample size required to detect statistically significant cardiac changes: a reduction of 21-66%. Our investigation on the optimum registration parameters, including both cardiac time frames and number of long-axis (LA) slices, suggested that a single time frame is adequate for motion correction whereas integrating more LA slices can improve registration and model reconstruction accuracy for improved functional quantification especially on datasets with severe motion artefacts.

  3. Analysis of a 3-D system function measured for magnetic particle imaging.

    PubMed

    Rahmer, Jürgen; Weizenecker, Jürgen; Gleich, Bernhard; Borgert, Jörn

    2012-06-01

    Magnetic particle imaging (MPI) is a new tomographic imaging approach that can quantitatively map magnetic nanoparticle distributions in vivo. It is capable of volumetric real-time imaging at particle concentrations low enough to enable clinical applications. For image reconstruction in 3-D MPI, a system function (SF) is used, which describes the relation between the acquired MPI signal and the spatial origin of the signal. The SF depends on the instrumental configuration, the applied field sequence, and the magnetic particle characteristics. Its properties reflect the quality of the spatial encoding process. This work presents a detailed analysis of a measured SF to give experimental evidence that 3-D MPI encodes information using a set of 3-D spatial patterns or basis functions that is stored in the SF. This resembles filling 3-D k-space in magnetic resonance imaging, but is faster since all information is gathered simultaneously over a broad acquisition bandwidth. A frequency domain analysis shows that the finest structures that can be encoded with the presented SF are as small as 0.6 mm. SF simulations are performed to demonstrate that larger particle cores extend the set of basis functions towards higher resolution and that the experimentally observed spatial patterns require the existence of particles with core sizes of about 30 nm in the calibration sample. A simple formula is presented that qualitatively describes the basis functions to be expected at a certain frequency.

  4. Realistic 3D coherent transfer function inverse filtering of complex fields

    PubMed Central

    Cotte, Yann; Toy, Fatih M.; Arfire, Cristian; Kou, Shan Shan; Boss, Daniel; Bergoënd, Isabelle; Depeursinge, Christian

    2011-01-01

    We present a novel technique for three-dimensional (3D) image processing of complex fields. It consists in inverting the coherent image formation by filtering the complex spectrum with a realistic 3D coherent transfer function (CTF) of a high-NA digital holographic microscope. By combining scattering theory and signal processing, the method is demonstrated to yield the reconstruction of a scattering object field. Experimental reconstructions in phase and amplitude are presented under non-design imaging conditions. The suggested technique is best suited for an implementation in high-resolution diffraction tomography based on sample or illumination rotation. PMID:21833359

  5. Realistic 3D coherent transfer function inverse filtering of complex fields.

    PubMed

    Cotte, Yann; Toy, Fatih M; Arfire, Cristian; Kou, Shan Shan; Boss, Daniel; Bergoënd, Isabelle; Depeursinge, Christian

    2011-08-01

    We present a novel technique for three-dimensional (3D) image processing of complex fields. It consists in inverting the coherent image formation by filtering the complex spectrum with a realistic 3D coherent transfer function (CTF) of a high-NA digital holographic microscope. By combining scattering theory and signal processing, the method is demonstrated to yield the reconstruction of a scattering object field. Experimental reconstructions in phase and amplitude are presented under non-design imaging conditions. The suggested technique is best suited for an implementation in high-resolution diffraction tomography based on sample or illumination rotation.

  6. A Novel Human Tissue-Engineered 3-D Functional Vascularized Cardiac Muscle Construct

    PubMed Central

    Valarmathi, Mani T.; Fuseler, John W.; Davis, Jeffrey M.; Price, Robert L.

    2017-01-01

    Organ tissue engineering, including cardiovascular tissues, has been an area of intense investigation. The major challenge to these approaches has been the inability to vascularize and perfuse the in vitro engineered tissue constructs. Attempts to provide oxygen and nutrients to the cells contained in the biomaterial constructs have had varying degrees of success. The aim of this current study is to develop a three-dimensional (3-D) model of vascularized cardiac tissue to examine the concurrent temporal and spatial regulation of cardiomyogenesis in the context of postnatal de novo vasculogenesis during stem cell cardiac regeneration. In order to achieve the above aim, we have developed an in vitro 3-D functional vascularized cardiac muscle construct using human induced pluripotent stem cell-derived embryonic cardiac myocytes (hiPSC-ECMs) and human mesenchymal stem cells (hMSCs). First, to generate the prevascularized scaffold, human cardiac microvascular endothelial cells (hCMVECs) and hMSCs were co-cultured onto a 3-D collagen cell carrier (CCC) for 7 days under vasculogenic culture conditions. In this milieu, hCMVECs/hMSCs underwent maturation, differentiation, and morphogenesis characteristic of microvessels, and formed extensive plexuses of vascular networks. Next, the hiPSC-ECMs and hMSCs were co-cultured onto this generated prevascularized CCCs for further 7 or 14 days in myogenic culture conditions. Finally, the vascular and cardiac phenotypic inductions were analyzed at the morphological, immunological, biochemical, molecular, and functional levels. Expression and functional analyses of the differentiated cells revealed neo-angiogenesis and neo-cardiomyogenesis. Thus, our unique 3-D co-culture system provided us the apt in vitro functional vascularized 3-D cardiac patch that can be utilized for cellular cardiomyoplasty. PMID:28194397

  7. A Novel Human Tissue-Engineered 3-D Functional Vascularized Cardiac Muscle Construct.

    PubMed

    Valarmathi, Mani T; Fuseler, John W; Davis, Jeffrey M; Price, Robert L

    2017-01-01

    Organ tissue engineering, including cardiovascular tissues, has been an area of intense investigation. The major challenge to these approaches has been the inability to vascularize and perfuse the in vitro engineered tissue constructs. Attempts to provide oxygen and nutrients to the cells contained in the biomaterial constructs have had varying degrees of success. The aim of this current study is to develop a three-dimensional (3-D) model of vascularized cardiac tissue to examine the concurrent temporal and spatial regulation of cardiomyogenesis in the context of postnatal de novo vasculogenesis during stem cell cardiac regeneration. In order to achieve the above aim, we have developed an in vitro 3-D functional vascularized cardiac muscle construct using human induced pluripotent stem cell-derived embryonic cardiac myocytes (hiPSC-ECMs) and human mesenchymal stem cells (hMSCs). First, to generate the prevascularized scaffold, human cardiac microvascular endothelial cells (hCMVECs) and hMSCs were co-cultured onto a 3-D collagen cell carrier (CCC) for 7 days under vasculogenic culture conditions. In this milieu, hCMVECs/hMSCs underwent maturation, differentiation, and morphogenesis characteristic of microvessels, and formed extensive plexuses of vascular networks. Next, the hiPSC-ECMs and hMSCs were co-cultured onto this generated prevascularized CCCs for further 7 or 14 days in myogenic culture conditions. Finally, the vascular and cardiac phenotypic inductions were analyzed at the morphological, immunological, biochemical, molecular, and functional levels. Expression and functional analyses of the differentiated cells revealed neo-angiogenesis and neo-cardiomyogenesis. Thus, our unique 3-D co-culture system provided us the apt in vitro functional vascularized 3-D cardiac patch that can be utilized for cellular cardiomyoplasty.

  8. 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.

  9. Measuring a hidden coordinate: Rate-exchange kinetics from 3D correlation functions.

    PubMed

    Berg, Mark A; Darvin, Jason R

    2016-08-07

    Nonexponential kinetics imply the existence of at least one slow variable other than the observable, that is, the system has a "hidden" coordinate. We develop a simple, but general, model that allows multidimensional correlation functions to be calculated for these systems. Homogeneous and heterogeneous mechanisms are both included, and slow exchange of the rates is allowed. This model shows that 2D and 3D correlation functions of the observable measure the distribution and kinetics of the hidden coordinate controlling the rate exchange. Both the mean exchange time and the shape of the exchange relaxation are measurable. However, complications arise because higher correlation functions are sums of multiple "pathways," each of which measures different dynamics. Only one 3D pathway involves exchange dynamics. Care must be used to extract exchange dynamics without contamination from other processes.

  10. A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies

    PubMed Central

    2014-01-01

    We show that an Ng bridge function modified version of the three-dimensional reference interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict the hydration free energy (HFE) of a set of 504 organic molecules. To achieve this, a single unique constant parameter was adjusted to the computed HFE of single atom Lennard-Jones solutes. It is shown that 3D-RISM is relatively accurate at predicting the electrostatic component of the HFE without correction but requires a modification of the nonpolar contribution that originates in the formation of the cavity created by the solute in water. We use a free energy functional with the Ng scaling of the direct correlation function [Ng, K. C. J. Chem. Phys.1974, 61, 2680]. This produces a rapid, reliable small molecule HFE calculation for applications in drug design. PMID:24634616

  11. Magnetic resonance imaging of the cervical spine: comparison of 2D T2-weighted turbo spin echo, 2D T2*weighted gradient-recalled echo and 3D T2-weighted variable flip-angle turbo spin echo sequences.

    PubMed

    Meindl, T; Wirth, S; Weckbach, S; Dietrich, O; Reiser, M; Schoenberg, S O

    2009-03-01

    To compare an isotropic three-dimensional (3D) high-resolution T2-weighted (w) MR sequence and its reformations with conventional sequences for imaging of the cervical spine. Fifteen volunteers were examined at 1.5 T using sagittal and axial 3D T2-w, sagittal and axial 2D T2w, and axial 2D T2*w MR sequences. Axial reformations of the sagittal 3D dataset were generated (3D MPR T2w). Signal-to-noise and image homogeneity were evaluated in a phantom and in vivo. Visibility of ten anatomical structures of the cervical spine was evaluated. Artifacts were assessed. For statistical analysis, Cohen's kappa, Wilcoxon matched pairs, and t-testing were utilized. There were no significant differences in homogeneity between the sequences. Sagittal 3D T2w enabled better delineation of nerve roots, neural foramina, and intraforaminal structures compared to sagittal 2D T2w. Axial 3D T2w and axial 3D MPR T2w resulted in superior visibility of most anatomical structures compared to axial 2D T2w and comparable results to 2D T2*w concerning the spinal cord, nerve roots, intraforaminal structures, and fat. Artifacts were most pronounced in axial 2D T2w and axial 3D T2w. Acquisition of a 3D T2w data set is feasible in the cervical spine with superior delineation of anatomical structures compared to 2D sequences.

  12. Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging

    PubMed Central

    Axer, Markus; Strohmer, Sven; Gräßel, David; Bücker, Oliver; Dohmen, Melanie; Reckfort, Julia; Zilles, Karl; Amunts, Katrin

    2016-01-01

    Research of the human brain connectome requires multiscale approaches derived from independent imaging methods ideally applied to the same object. Hence, comprehensible strategies for data integration across modalities and across scales are essential. We have successfully established a concept to bridge the spatial scales from microscopic fiber orientation measurements based on 3D-Polarized Light Imaging (3D-PLI) to meso- or macroscopic dimensions. By creating orientation distribution functions (pliODFs) from high-resolution vector data via series expansion with spherical harmonics utilizing high performance computing and supercomputing technologies, data fusion with Diffusion Magnetic Resonance Imaging has become feasible, even for a large-scale dataset such as the human brain. Validation of our approach was done effectively by means of two types of datasets that were transferred from fiber orientation maps into pliODFs: simulated 3D-PLI data showing artificial, but clearly defined fiber patterns and real 3D-PLI data derived from sections through the human brain and the brain of a hooded seal. PMID:27147981

  13. Shaping functional nano-objects by 3D confined supramolecular assembly.

    PubMed

    Deng, Renhua; Liang, Fuxin; Li, Weikun; Liu, Shanqin; Liang, Ruijing; Cai, Mingle; Yang, Zhenzhong; Zhu, Jintao

    2013-12-20

    Nano-objects are generated through 3D confined supramolecular assembly, followed by a sequential disintegration by rupturing the hydrogen bonding. The shape of the nano-objects is tunable, ranging from nano-disc, nano-cup, to nano-toroid. The nano-objects are pH-responsive. Functional materials for example inorganic or metal nanoparticles are easily complexed onto the external surface, to extend both composition and microstructure of the nano-objects.

  14. Engineering of functional, perfusable 3D microvascular networks on a chip.

    PubMed

    Kim, Sudong; Lee, Hyunjae; Chung, Minhwan; Jeon, Noo Li

    2013-04-21

    Generating perfusable 3D microvessels in vitro is an important goal for tissue engineering, as well as for reliable modelling of blood vessel function. To date, in vitro blood vessel models have not been able to accurately reproduce the dynamics and responses of endothelial cells to grow perfusable and functional 3D vascular networks. Here we describe a microfluidic-based platform whereby we model natural cellular programs found during normal development and angiogenesis to form perfusable networks of intact 3D microvessels as well as tumor vasculatures based on the spatially controlled co-culture of endothelial cells with stromal fibroblasts, pericytes or cancer cells. The microvessels possess the characteristic morphological and biochemical markers of in vivo blood vessels, and exhibit strong barrier function and long-term stability. An open, unobstructed microvasculature allows the delivery of nutrients, chemical compounds, biomolecules and cell suspensions, as well as flow-induced mechanical stimuli into the luminal space of the endothelium, and exhibits faithful responses to physiological shear stress as demonstrated by cytoskeleton rearrangement and increased nitric oxide synthesis. This simple and versatile platform provides a wide range of applications in vascular physiology studies as well as in developing vascularized organ-on-a-chip and human disease models for pharmaceutical screening.

  15. A range/depth modulation transfer function (RMTF) framework for characterizing 3D imaging LADAR performance

    NASA Astrophysics Data System (ADS)

    Staple, Bevan; Earhart, R. P.; Slaymaker, Philip A.; Drouillard, Thomas F., II; Mahony, Thomas

    2005-05-01

    3D imaging LADARs have emerged as the key technology for producing high-resolution imagery of targets in 3-dimensions (X and Y spatial, and Z in the range/depth dimension). Ball Aerospace & Technologies Corp. continues to make significant investments in this technology to enable critical NASA, Department of Defense, and national security missions. As a consequence of rapid technology developments, two issues have emerged that need resolution. First, the terminology used to rate LADAR performance (e.g., range resolution) is inconsistently defined, is improperly used, and thus has become misleading. Second, the terminology does not include a metric of the system"s ability to resolve the 3D depth features of targets. These two issues create confusion when translating customer requirements into hardware. This paper presents a candidate framework for addressing these issues. To address the consistency issue, the framework utilizes only those terminologies proposed and tested by leading LADAR research and standards institutions. We also provide suggestions for strengthening these definitions by linking them to the well-known Rayleigh criterion extended into the range dimension. To address the inadequate 3D image quality metrics, the framework introduces the concept of a Range/Depth Modulation Transfer Function (RMTF). The RMTF measures the impact of the spatial frequencies of a 3D target on its measured modulation in range/depth. It is determined using a new, Range-Based, Slanted Knife-Edge test. We present simulated results for two LADAR pulse detection techniques and compare them to a baseline centroid technique. Consistency in terminology plus a 3D image quality metric enable improved system standardization.

  16. 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.

  17. SERS Active Nanobiosensor Functionalized by Self-Assembled 3D Nickel Nanonetworks for Glutathione Detection.

    PubMed

    Chinnakkannu Vijayakumar, Sivaprasad; Venkatakrishnan, Krishnan; Tan, Bo

    2017-02-15

    We introduce a "non-noble metal" based SERS active nanobiosensor using a self-assembled 3D hybrid nickel nanonetwork. A tunable biomolecule detector fabricated by a bottom-up approach was functionalized using a multiphoton ionization energy mechanism to create a self-assembled 3D hybrid nickel nanonetwork. The nanonetwork was tested for SERS detection of crystal violet (CV) and glutathione (GSH) at two excitation wavelengths, 532 and 785 nm. The results reveal indiscernible peaks with a limit of detection (LOD) of 1 picomolar (pM) concentration. An enhancement factor (EF) of 9.3 × 10(8) was achieved for the chemical molecule CV and 1.8 × 10(9) for the biomolecule GSH, which are the highest reported values so far. The two results, one being the CV molecule proved that nickel nanonetwork is indeed SERS active and the second being the GSH biomolecule detection at both 532 and 785 nm, confirm that the nanonetwork is a biosensor which has potential for both in vivo and in vitro sensing. In addition, the selectivity and versatility of this biosensor is examined with biomolecules such as l-Cysteine, l-Methionine, and sensing GSH in cell culture medium which mimics the complex biological environment. The functionalized self-assembled 3D hybrid nickel nanonetwork exhibits electromagnetic and charge transfer based SERS activation mechanisms.

  18. How spatial abilities and dynamic visualizations interplay when learning functional anatomy with 3D anatomical models.

    PubMed

    Berney, Sandra; Bétrancourt, Mireille; Molinari, Gaëlle; Hoyek, Nady

    2015-01-01

    The emergence of dynamic visualizations of three-dimensional (3D) models in anatomy curricula may be an adequate solution for spatial difficulties encountered with traditional static learning, as they provide direct visualization of change throughout the viewpoints. However, little research has explored the interplay between learning material presentation formats, spatial abilities, and anatomical tasks. First, to understand the cognitive challenges a novice learner would be faced with when first exposed to 3D anatomical content, a six-step cognitive task analysis was developed. Following this, an experimental study was conducted to explore how presentation formats (dynamic vs. static visualizations) support learning of functional anatomy, and affect subsequent anatomical tasks derived from the cognitive task analysis. A second aim was to investigate the interplay between spatial abilities (spatial visualization and spatial relation) and presentation formats when the functional anatomy of a 3D scapula and the associated shoulder flexion movement are learned. Findings showed no main effect of the presentation formats on performances, but revealed the predictive influence of spatial visualization and spatial relation abilities on performance. However, an interesting interaction between presentation formats and spatial relation ability for a specific anatomical task was found. This result highlighted the influence of presentation formats when spatial abilities are involved as well as the differentiated influence of spatial abilities on anatomical tasks.

  19. Bundled-optode implementation for 3D imaging in functional near-infrared spectroscopy

    PubMed Central

    Nguyen, Hoang-Dung; Hong, Keum-Shik

    2016-01-01

    The paper presents a functional near-infrared spectroscopy (fNIRS)-based bundled-optode method for detection of the changes of oxy-hemoglobin (HbO) and deoxy-hemoglobin (HbR) concentrations. fNIRS with 32 optodes is utilized to measure five healthy male subjects’ brain-hemodynamic responses to arithmetic tasks. Specifically, the coordinates of 256 voxels in the three-dimensional (3D) volume are computed according to the known probe geometry. The mean path length factor in the Beer-Lambert equation is estimated as a function of the emitter-detector distance, which is utilized for computation of the absorption coefficient. The mean values of HbO and HbR obtained from the absorption coefficient are then applied for construction of a 3D fNIRS image. Our results show that the proposed method, as compared with the conventional approach, can detect brain activity with higher spatial resolution. This method can be extended for 3D fNIRS imaging in real-time applications. PMID:27699115

  20. Sustainable approach toward synthesis of green functional carbonaceous 3-D micro/nanostructures from biomass

    NASA Astrophysics Data System (ADS)

    Tavangar, Amirhossein; Tan, Bo; Venkatakrishnan, Krishnan

    2013-08-01

    This study proposes a novel technique to synthesize functional carbonaceous three-dimensional (3-D) micro/nanocompounds from agricultural by-products using femtosecond laser irradiation. Biowastes of rice husk and wheat straw are value-engineered to carbonaceous structures in a single-step process under ambient conditions. Our results demonstrate that by controlling the laser fluence, structures with a variety of different morphologies from nanostructures to microstructures can be achieved. Also, the results indicate that altering the laser processing parameters influences the chemical composition of the synthesized structures. This sustainable approach presents an important step towards synthesizing 3-D micro/nanofibrous compounds from biowaste materials. These structures, as-synthesized or as nanocomposite fillers, can have practical uses in electronic, sensing, biological, and environmental applications.

  1. Testing hypotheses of bat baculum function with 3D models derived from microCT

    PubMed Central

    Herdina, Anna Nele; Kelly, Diane A; Jahelková, Helena; Lina, Peter H C; Horáček, Ivan; Metscher, Brian D

    2015-01-01

    The baculum (os penis) has been extensively studied as a taxon-specific character in bats and other mammals but its mechanical function is still unclear. There is a wide consensus in the literature that the baculum is probably a sexually selected character. Using a novel approach combining postmortem manipulation and three-dimensional (3D) imaging, we tested two functional hypotheses in the common noctule bat Nyctalus noctula, the common pipistrelle Pipistrellus pipistrellus, and Nathusius’ pipistrelle Pipistrellus nathusii: (i) whether the baculum can protect the distal urethra and urethral opening from compression during erection and copulation; and (ii) whether the baculum and corpora cavernosa form a functional unit to support both the penile shaft and the more distal glans tip. In freshly dead or frozen and thawed bats, we compared flaccid penises with artificially ‘erect’ penises that were inflated with 10% formalin. Penises were stained with alcoholic iodine and imaged with a lab-based high-resolution x-ray microtomography system. Analysis of the 3D images enabled us to compare the changes in relative positions of the baculum, corpora cavernosa, urethra, and corpus spongiosum with one another between flaccid and ‘erect’ penises. Our results support both functional hypotheses, indicating that the baculum probably performs two different roles during erection. Our approach should prove valuable for comparing and testing the functions of different baculum morphologies in bats and other mammals. Moreover, we have validated an essential component of the groundwork necessary to extend this approach with finite element analysis for quantitative 3D biomechanical modeling of penis function. PMID:25655647

  2. Earthquake source tensor inversion with the gCAP method and 3D Green's functions

    NASA Astrophysics Data System (ADS)

    Zheng, J.; Ben-Zion, Y.; Zhu, L.; Ross, Z.

    2013-12-01

    We develop and apply a method to invert earthquake seismograms for source properties using a general tensor representation and 3D Green's functions. The method employs (i) a general representation of earthquake potency/moment tensors with double couple (DC), compensated linear vector dipole (CLVD), and isotropic (ISO) components, and (ii) a corresponding generalized CAP (gCap) scheme where the continuous wave trains are broken into Pnl and surface waves (Zhu & Ben-Zion, 2013). For comparison, we also use the waveform inversion method of Zheng & Chen (2012) and Ammon et al. (1998). Sets of 3D Green's functions are calculated on a grid of 1 km3 using the 3-D community velocity model CVM-4 (Kohler et al. 2003). A bootstrap technique is adopted to establish robustness of the inversion results using the gCap method (Ross & Ben-Zion, 2013). Synthetic tests with 1-D and 3-D waveform calculations show that the source tensor inversion procedure is reasonably reliable and robust. As initial application, the method is used to investigate source properties of the March 11, 2013, Mw=4.7 earthquake on the San Jacinto fault using recordings of ~45 stations up to ~0.2Hz. Both the best fitting and most probable solutions include ISO component of ~1% and CLVD component of ~0%. The obtained ISO component, while small, is found to be a non-negligible positive value that can have significant implications for the physics of the failure process. Work on using higher frequency data for this and other earthquakes is in progress.

  3. Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates

    PubMed Central

    Matthew Ward, R.; Venner, Eric; Daines, Bryce; Murray, Stephen; Erdin, Serkan; Kristensen, David M.; Lichtarge, Olivier

    2009-01-01

    Summary:The Evolutionary Trace Annotation (ETA) Server predicts enzymatic activity. ETA starts with a structure of unknown function, such as those from structural genomics, and with no prior knowledge of its mechanism uses the phylogenetic Evolutionary Trace (ET) method to extract key functional residues and propose a function-associated 3D motif, called a 3D template. ETA then searches previously annotated structures for geometric template matches that suggest molecular and thus functional mimicry. In order to maximize the predictive value of these matches, ETA next applies distinctive specificity filters—evolutionary similarity, function plurality and match reciprocity. In large scale controls on enzymes, prediction coverage is 43% but the positive predictive value rises to 92%, thus minimizing false annotations. Users may modify any search parameter, including the template. ETA thus expands the ET suite for protein structure annotation, and can contribute to the annotation efforts of metaservers. Availability:The ETA Server is a web application available at http://mammoth.bcm.tmc.edu/eta/. Contact: lichtarge@bcm.edu PMID:19307237

  4. Source Process of the 1923 Kanto Earthquake Using New Fault Geometry and 3-D Green's Functions

    NASA Astrophysics Data System (ADS)

    Kobayashi, R.; Koketsu, K.

    2005-12-01

    The September 1, 1923, Kanto earthquake caused severe damage and more than 100,000 fatalities in the Tokyo metropolitan area. This earthquake is an interplate event along the Sagami trough where the Philippine Sea plate is subducting beneath a continental plate. We have investigated the source process of this earthquake using the geodetic, teleseismic, and strong motion data (Kobayashi and Koketsu, 2005). The resultant slip distributions show that two asperities (areas of large slips) are located around the base of the Izu peninsula and the Uraga channel. In 2002 and 2003, four seismic surveys were carried out to determine crustal structures and fault locations in the Kanto region (Sato et al., 2005). The seismic reflections from the surface of the Philippine Sea slab suggested that the slab surface should be shallower than the previous models (e.g., Ishida, 1992; Matsu'ura et al., 1980). The fault model of Kobayashi and Koketsu (2005) was also based on Matsu'ura et al. (1980). In this study, we adopt new fault geometry consistent with the result of the reflection surveys and perform another source process inversion. The new slip distribution showed that the western asperity moved from the Uraga channel to the tip of the Miura peninsula, while the western asperity did not move considerably. Green's functions that Kobayashi and Koketsu (2005) used were calculated in a halfspace for geodetic data or in a 1-D model for strong motions. However, the real structure in the Kanto region is three-dimensionally complex as suggested by the geographical setting and seismic surveys. In fact, Kobayashi and Koketsu (2005) showed that the long coda of the observed seismogram at Hongo, Tokyo, was not reproduced in the synthetic one. The forward modeling with a 3-D structure (Sato et al., 1999) suggested that surface waves excited along the boundary between the Kanto mountains and Kanto basin can explain the large coda. Thus we calculate 3-D Green's functions for the strong motion

  5. 3D finite element model of the chinchilla ear for characterizing middle ear functions.

    PubMed

    Wang, Xuelin; Gan, Rong Z

    2016-10-01

    Chinchilla is a commonly used animal model for research of sound transmission through the ear. Experimental measurements of the middle ear transfer function in chinchillas have shown that the middle ear cavity greatly affects the tympanic membrane (TM) and stapes footplate (FP) displacements. However, there is no finite element (FE) model of the chinchilla ear available in the literature to characterize the middle ear functions with the anatomical features of the chinchilla ear. This paper reports a recently completed 3D FE model of the chinchilla ear based on X-ray micro-computed tomography images of a chinchilla bulla. The model consisted of the ear canal, TM, middle ear ossicles and suspensory ligaments, and the middle ear cavity. Two boundary conditions of the middle ear cavity wall were simulated in the model as the rigid structure and the partially flexible surface, and the acoustic-mechanical coupled analysis was conducted with these two conditions to characterize the middle ear function. The model results were compared with experimental measurements reported in the literature including the TM and FP displacements and the middle ear input admittance in chinchilla ear. An application of this model was presented to identify the acoustic role of the middle ear septa-a unique feature of chinchilla middle ear cavity. This study provides the first 3D FE model of the chinchilla ear for characterizing the middle ear functions through the acoustic-mechanical coupled FE analysis.

  6. Laminar optical tomography: high-resolution 3D functional imaging of superficial tissues

    NASA Astrophysics Data System (ADS)

    Hillman, Elizabeth M. C.; Devor, Anna; Dunn, Andrew K.; Boas, David A.

    2006-03-01

    Laminar Optical Tomography (LOT) is a new medical imaging modality for high-resolution, depth-resolved, functional imaging of superficial tissue such as rodent cortex, skin and the retina. LOT uses visible laser light to image to depths of >2mm (far deeper than microscopy) and is highly sensitive to absorption and fluorescence contrast, enabling spectroscopic functional information such as hemoglobin oxygenation to be imaged with 100-200 micron resolution. LOT has been used to image the hemodynamic response to stimulus in the somatosensory cortex of rats. The resulting three-dimensional (3D) images through the depth of the cortex can be used to delineate the arterial, capillary and venous responses, revealing new information about the intricacies of the oxygenation and blood flow dynamics related to neuronal activation. Additional applications of LOT are being explored, including the integration of 3D Voltage Sensitive Dye fluorescence imaging. LOT imaging uses a system similar to a confocal microscope, quickly scanning a focused beam of light over the surface of the tissue (~8Hz frame rate). Light is detected from both the focus of the scanning beam, and also at increasing distances from the beam's focus. This scattered light has penetrated more deeply into the tissue, and allows features at different depths to be distinguished. An algorithm that includes photon migration modeling of light scattering converts the raw data into 3D images. The motivation for functional optical imaging will be outlined, the basic principles of LOT imaging will be described, and the latest in-vivo results will be presented.

  7. Spherical cavity-expansion forcing function in PRONTO 3D for application to penetration problems

    SciTech Connect

    Warren, T.L.; Tabbara, M.R.

    1997-05-01

    In certain penetration events the primary mode of deformation of the target can be approximated by known analytical expressions. In the context of an analysis code, this approximation eliminates the need for modeling the target as well as the need for a contact algorithm. This technique substantially reduces execution time. In this spirit, a forcing function which is derived from a spherical-cavity expansion analysis has been implemented in PRONTO 3D. This implementation is capable of computing the structural and component responses of a projectile due to three dimensional penetration events. Sample problems demonstrate good agreement with experimental and analytical results.

  8. Low temperature assembly of functional 3D DNA-PNA-protein complexes.

    PubMed

    Flory, Justin D; Simmons, Chad R; Lin, Su; Johnson, Trey; Andreoni, Alessio; Zook, James; Ghirlanda, Giovanna; Liu, Yan; Yan, Hao; Fromme, Petra

    2014-06-11

    Proteins have evolved to carry out nearly all the work required of living organisms within complex inter- and intracellular environments. However, systematically investigating the range of interactions experienced by a protein that influence its function remains challenging. DNA nanostructures are emerging as a convenient method to arrange a broad range of guest molecules. However, flexible methods are needed for arranging proteins in more biologically relevant 3D geometries under mild conditions that preserve protein function. Here we demonstrate how peptide nucleic acid (PNA) can be used to control the assembly of cytochrome c (12.5 kDa, pI 10.5) and azurin (13.9 kDa, pI 5.7) proteins into separate 3D DNA nanocages, in a process that maintains protein function. Toehold-mediated DNA strand displacement is introduced as a method to purify PNA-protein conjugates. The PNA-proteins were assembled within 2 min at room temperature and within 4 min at 11 °C, and hybridize with even greater efficiency than PNA conjugated to a short peptide. Gel electrophoresis and steady state and time-resolved fluorescence spectroscopy were used to investigate the effect of protein surface charge on its interaction with the negatively charged DNA nanocage. These data were used to generate a model of the DNA-PNA-protein complexes that show the negatively charged azurin protein repelled away from the DNA nanocage while the positively charged cytochrome c protein remains within and closely interacts with the DNA nanocage. When conjugated to PNA and incorporated into the DNA nanocage, the cytochrome c secondary structure and catalytic activity were maintained, and its redox potential was reduced modestly by 20 mV possibly due to neutralization of some positive surface charges. This work demonstrates a flexible new approach for using 3D nucleic acid (PNA-DNA) nanostructures to control the assembly of functional proteins, and facilitates further investigation of protein interactions as well

  9. Relating functional connectivity in V1 neural circuits and 3D natural scenes using Boltzmann machines

    PubMed Central

    Zhang, Yimeng; Li, Xiong; Samonds, Jason M.

    2015-01-01

    Bayesian theory has provided a compelling conceptualization for perceptual inference in the brain. Central to Bayesian inference is the notion of statistical priors. To understand the neural mechanisms of Bayesian inference, we need to understand the neural representation of statistical regularities in the natural environment. In this paper, we investigated empirically how statistical regularities in natural 3D scenes are represented in the functional connectivity of disparity-tuned neurons in the primary visual cortex of primates. We applied a Boltzmann machine model to learn from 3D natural scenes, and found that the units in the model exhibited cooperative and competitive interactions, forming a “disparity association field”, analogous to the contour association field. The cooperative and competitive interactions in the disparity association field are consistent with constraints of computational models for stereo matching. In addition, we simulated neurophysiological experiments on the model, and found the results to be consistent with neurophysiological data in terms of the functional connectivity measurements between disparity-tuned neurons in the macaque primary visual cortex. These findings demonstrate that there is a relationship between the functional connectivity observed in the visual cortex and the statistics of natural scenes. They also suggest that the Boltzmann machine can be a viable model for conceptualizing computations in the visual cortex and, as such, can be used to predict neural circuits in the visual cortex from natural scene statistics. PMID:26712581

  10. Fluorescence fluctuation microscopy to reveal 3D architecture and function in the cell nucleus.

    PubMed

    Lenser, Thorsten; Weisshart, Klaus; Ulbricht, Tobias; Klement, Karolin; Hemmerich, Peter

    2010-01-01

    The three-dimensional (3D) architecture of the cell nucleus is determined not only by the presence of subnuclear domains, such as the nuclear envelope, chromosome territories, and nuclear bodies, but also by smaller domains which form in response to specific functions, such as RNA transcription, DNA replication, and DNA repair. Since both stable and dynamic structures contribute to nuclear morphology, it is important to study the biophysical principles of the formation of macromolecular assemblies within the nucleus. For this purpose, a variety of fluorescence fluctuation microscopy techniques can be applied. Here, we summarize our current knowledge on the 3D architecture of the mammalian cell nucleus and describe in detail how the assembly of functional nuclear protein complexes can be analyzed in living cells using fluorescence bleaching techniques, fluorescence correlation spectroscopy, raster image correlation spectroscopy, and mathematical modeling. In conclusion, the application of all these techniques in combination is a powerful tool to assess the full spectrum of nuclear protein dynamics and to understand the biophysical principles underlying nuclear structure and function.

  11. Relating functional connectivity in V1 neural circuits and 3D natural scenes using Boltzmann machines.

    PubMed

    Zhang, Yimeng; Li, Xiong; Samonds, Jason M; Lee, Tai Sing

    2016-03-01

    Bayesian theory has provided a compelling conceptualization for perceptual inference in the brain. Central to Bayesian inference is the notion of statistical priors. To understand the neural mechanisms of Bayesian inference, we need to understand the neural representation of statistical regularities in the natural environment. In this paper, we investigated empirically how statistical regularities in natural 3D scenes are represented in the functional connectivity of disparity-tuned neurons in the primary visual cortex of primates. We applied a Boltzmann machine model to learn from 3D natural scenes, and found that the units in the model exhibited cooperative and competitive interactions, forming a "disparity association field", analogous to the contour association field. The cooperative and competitive interactions in the disparity association field are consistent with constraints of computational models for stereo matching. In addition, we simulated neurophysiological experiments on the model, and found the results to be consistent with neurophysiological data in terms of the functional connectivity measurements between disparity-tuned neurons in the macaque primary visual cortex. These findings demonstrate that there is a relationship between the functional connectivity observed in the visual cortex and the statistics of natural scenes. They also suggest that the Boltzmann machine can be a viable model for conceptualizing computations in the visual cortex and, as such, can be used to predict neural circuits in the visual cortex from natural scene statistics.

  12. Exploring the surface reactivity of 3d metal endofullerenes: a density-functional theory study.

    PubMed

    Estrada-Salas, Rubén E; Valladares, Ariel A

    2009-09-24

    Changes in the preferential sites of electrophilic, nucleophilic, and radical attacks on the pristine C60 surface with endohedral doping using 3d transition metal atoms were studied via two useful reactivity indices, namely the Fukui functions and the molecular electrostatic potential. Both of these were calculated at the density functional BPW91 level of theory with the DNP basis set. Our results clearly show changes in the preferential reactivity sites on the fullerene surface when it is doped with Mn, Fe, Co, or Ni atoms, whereas there are no significant changes in the preferential reactivity sites on the C60 surface upon endohedral doping with Cu and Zn atoms. Electron affinities (EA), ionization potentials (IP), and HOMO-LUMO gaps (Eg) were also calculated to complete the study of the endofullerene's surface reactivity. These findings provide insight into endofullerene functionalization, an important issue in their application.

  13. Density Functional Theory of Open-Shell Systems. The 3d-Series Transition-Metal Atoms and Their Cations.

    PubMed

    Luo, Sijie; Averkiev, Boris; Yang, Ke R; Xu, Xuefei; Truhlar, Donald G

    2014-01-14

    The 3d-series transition metals (also called the fourth-period transition metals), Sc to Zn, are very important in industry and biology, but they provide unique challenges to computing the electronic structure of their compounds. In order to successfully describe the compounds by theory, one must be able to describe their components, in particular the constituent atoms and cations. In order to understand the ingredients required for successful computations with density functional theory, it is useful to examine the performance of various exchange-correlation functionals; we do this here for 4s(N)3d(N') transition-metal atoms and their cations. We analyze the results using three ways to compute the energy of the open-shell states: the direct variational method, the weighted-averaged broken symmetry (WABS) method, and a new broken-symmetry method called the reinterpreted broken symmetry (RBS) method. We find the RBS method to be comparable in accuracy with the WABS method. By examining the overall accuracy in treating 18 multiplicity-changing excitations and 10 ionization potentials with the RBS method, 10 functionals are found to have a mean-unsigned error of <5 kcal/mol, with ωB97X-D topping the list. For local density functionals, which are more practical for extended systems, the M06-L functional is the most accurate. And by combining the results with our previous studies of p-block and 4d-series elements as well as databases for alkyl bond dissociation, main-group atomization energies, and π-π noncovalent interactions, we find five functionals, namely, PW6B95, MPW1B95, M08-SO, SOGGA11-X, and MPWB1K, to be highly recommended. We also studied the performance of PW86 and C09 exchange functionals, which have drawn wide interest in recent studies due to their claimed ability to reproduce Hartree-Fock exchange at long distance. By combining them with four correlation functionals, we find the performance of the resulting functionals disappointing both for 3d

  14. 3D functional ultrasound imaging of the cerebral visual system in rodents.

    PubMed

    Gesnik, Marc; Blaize, Kevin; Deffieux, Thomas; Gennisson, Jean-Luc; Sahel, José-Alain; Fink, Mathias; Picaud, Serge; Tanter, Mickaël

    2017-02-03

    3D functional imaging of the whole brain activity during visual task is a challenging task in rodents due to the complex tri-dimensional shape of involved brain regions and the fine spatial and temporal resolutions required to reveal the visual tract. By coupling functional ultrasound (fUS) imaging with a translational motorized stage and an episodic visual stimulation device, we managed to accurately map and to recover the activity of the visual cortices, the Superior Colliculus (SC) and the Lateral Geniculate Nuclei (LGN) in 3D. Cerebral Blood Volume (CBV) responses during visual stimuli were found to be highly correlated with the visual stimulus time profile in visual cortices (r=0.6), SC (r=0.7) and LGN (r=0.7). These responses were found dependent on flickering frequency and contrast, and optimal stimulus parameters for largest CBV increases were obtained. In particular, increasing the flickering frequency higher than 7Hz revealed a decrease of visual cortices response while the SC response was preserved. Finally, cross-correlation between CBV signals exhibited significant delays (d=0.35s +/-0.1s) between blood volume response in SC and visual cortices in response to our visual stimulus. These results emphasize the interest of fUS imaging as a whole brain neuroimaging modality for brain vision studies in rodent models.

  15. Bounds for weighted Lebesgue functions for exponential weights

    NASA Astrophysics Data System (ADS)

    Kubayi, D. G.

    2001-08-01

    The weighted Lebesgue functions for even weights W=e-Q on the real line have been intensively studied in recent years. In this paper, we discuss the corresponding results for a class of weights that includes non-even weights.

  16. Mapping 3-D functional capillary geometry in rat skeletal muscle in vivo

    PubMed Central

    Milkovich, Stephanie; Goldman, Daniel; Ellis, Christopher G.

    2012-01-01

    We have developed a novel mapping software package to reconstruct microvascular networks in three dimensions (3-D) from in vivo video images for use in blood flow and O2 transport modeling. An intravital optical imaging system was used to collect video sequences of blood flow in microvessels at different depths in the tissue. Functional images of vessels were produced from the video sequences and were processed using automated edge tracking software to yield location and geometry data for construction of the 3-D network. The same video sequences were analyzed for hemodynamic and O2 saturation data from individual capillaries in the network. Simple user-driven commands allowed the connection of vessel segments at bifurcations, and semiautomated registration enabled the tracking of vessels across multiple focal planes and fields of view. The reconstructed networks can be rotated and manipulated in 3-D to verify vessel connections and continuity. Hemodynamic and O2 saturation measurements made in vivo can be indexed to corresponding vessels and visualized using colorized maps of the vascular geometry. Vessels in each reconstruction are saved as text-based files that can be easily imported into flow or O2 transport models with complete geometry, hemodynamic, and O2 transport conditions. The results of digital morphometric analysis of seven microvascular networks showed mean capillary diameters and overall capillary density consistent with previous findings using histology and corrosion cast techniques. The described mapping software is a valuable tool for the quantification of in vivo microvascular geometry, hemodynamics, and oxygenation, thus providing rich data sets for experiment-based computational models. PMID:22140042

  17. 3-D joint inversion of the magnetotelluric phase tensor and vertical magnetic transfer functions

    NASA Astrophysics Data System (ADS)

    Tietze, Kristina; Ritter, Oliver; Egbert, Gary D.

    2015-11-01

    With advancing computational resources, 3-D inversion techniques have become feasible in recent years and are now a more widely used tool for magnetotelluric (MT) data interpretation. Galvanic distortion caused by small-scale near-surface inhomogeneities remains an obstacle for 3-D MT inversion which so far has experienced little attention. If not considered properly, the effect on 3-D inversion can be immense and result in erroneous subsurface models and interpretations. To tackle the problem we implemented inversion of the distortion-free phase tensor into the ModEM inversion package. The dimensionless phase tensor components describe only variations of the conductivity structure. When inverting these data, particular care has to be taken of the conductivity structure in the a priori model, which provides the reference frame when transferring the information from phase tensors into absolute conductivity values. Our results obtained with synthetic data show that phase tensor inversion can recover the regional conductivity structure in presence of galvanic distortion if the a priori model provides a reasonable assumption for the regional resistivity average. Joint inversion of phase tensor data and vertical magnetic transfer functions improves recovery of the absolute resistivity structure and is less dependent on the prior model. We also used phase tensor inversion for a data set of more than 250 MT sites from the central San Andreas fault, California, where a number of sites showed significant galvanic distortion. We find the regional structure of the phase tensor inversion results compatible with previously obtained models from impedance inversion. In the vicinity of distorted sites, phase tensor inversion models exhibit more homogeneous/smoother conductivity structures.

  18. 3D bioprinting of functional human skin: production and in vivo analysis.

    PubMed

    Cubo, Nieves; Garcia, Marta; Del Cañizo, Juan F; Velasco, Diego; Jorcano, Jose L

    2016-12-05

    Significant progress has been made over the past 25 years in the development of in vitro-engineered substitutes that mimic human skin, either to be used as grafts for the replacement of lost skin, or for the establishment of in vitro human skin models. In this sense, laboratory-grown skin substitutes containing dermal and epidermal components offer a promising approach to skin engineering. In particular, a human plasma-based bilayered skin generated by our group, has been applied successfully to treat burns as well as traumatic and surgical wounds in a large number of patients in Spain. There are some aspects requiring improvements in the production process of this skin; for example, the relatively long time (three weeks) needed to produce the surface required to cover an extensive burn or a large wound, and the necessity to automatize and standardize a process currently performed manually. 3D bioprinting has emerged as a flexible tool in regenerative medicine and it provides a platform to address these challenges. In the present study, we have used this technique to print a human bilayered skin using bioinks containing human plasma as well as primary human fibroblasts and keratinocytes that were obtained from skin biopsies. We were able to generate 100 cm(2), a standard P100 tissue culture plate, of printed skin in less than 35 min (including the 30 min required for fibrin gelation). We have analysed the structure and function of the printed skin using histological and immunohistochemical methods, both in 3D in vitro cultures and after long-term transplantation to immunodeficient mice. In both cases, the generated skin was very similar to human skin and, furthermore, it was indistinguishable from bilayered dermo-epidermal equivalents, handmade in our laboratories. These results demonstrate that 3D bioprinting is a suitable technology to generate bioengineered skin for therapeutical and industrial applications in an automatized manner.

  19. In Vitro Model of the Epidermis: Connecting Protein Function to 3D Structure.

    PubMed

    Arnette, Christopher; Koetsier, Jennifer L; Hoover, Paul; Getsios, Spiro; Green, Kathleen J

    2016-01-01

    Much of our understanding of the biological processes that underlie cellular functions in humans, such as cell-cell communication, intracellular signaling, and transcriptional and posttranscriptional control of gene expression, has been acquired from studying cells in a two-dimensional (2D) tissue culture environment. However, it has become increasingly evident that the 2D environment does not support certain cell functions. The need for more physiologically relevant models prompted the development of three-dimensional (3D) cultures of epithelial, endothelial, and neuronal tissues (Shamir & Ewald, 2014). These models afford investigators with powerful tools to study the contribution of spatial organization, often in the context of relevant extracellular matrix and stromal components, to cellular and tissue homeostasis in normal and disease states.

  20. A novel time dependent gamma evaluation function for dynamic 2D and 3D dose distributions.

    PubMed

    Podesta, Mark; Persoon, Lucas C G G; Verhaegen, Frank

    2014-10-21

    Modern external beam radiotherapy requires detailed verification and quality assurance so that confidence can be placed on both the delivery of a single treatment fraction and on the consistency of delivery throughout the treatment course. To verify dose distributions, a comparison between prediction and measurement must be made. Comparisons between two dose distributions are commonly performed using a Gamma evaluation which is a calculation of two quantities on a pixel by pixel basis; the dose difference, and the distance to agreement. By providing acceptance criteria (e.g. 3%, 3 mm), the function will find the most appropriate match within its two degrees of freedom. For complex dynamic treatments such as IMRT or VMAT it is important to verify the dose delivery in a time dependent manner and so a gamma evaluation that includes a degree of freedom in the time domain via a third parameter, time to agreement, is presented here. A C++ (mex) based gamma function was created that could be run on either CPU and GPU computing platforms that would allow a degree of freedom in the time domain. Simple test cases were created in both 2D and 3D comprising of simple geometrical shapes with well-defined boundaries varying over time. Changes of varying magnitude in either space or time were introduced and repeated gamma analyses were performed varying the criteria. A clinical VMAT case was also included, artificial air bubbles of varying size were introduced to a patient geometry, along with shifts of varying magnitude in treatment time. For all test cases where errors in distance, dose or time were introduced, the time dependent gamma evaluation could accurately highlight the errors.The time dependent gamma function presented here allows time to be included as a degree of freedom in gamma evaluations. The function allows for 2D and 3D data sets which are varying over time to be compared using appropriate criteria without penalising minor offsets of subsequent radiation fields

  1. 3D printed fluidics with embedded analytic functionality for automated reaction optimisation

    PubMed Central

    Capel, Andrew J; Wright, Andrew; Harding, Matthew J; Weaver, George W; Li, Yuqi; Harris, Russell A; Edmondson, Steve; Goodridge, Ruth D

    2017-01-01

    Additive manufacturing or ‘3D printing’ is being developed as a novel manufacturing process for the production of bespoke micro- and milliscale fluidic devices. When coupled with online monitoring and optimisation software, this offers an advanced, customised method for performing automated chemical synthesis. This paper reports the use of two additive manufacturing processes, stereolithography and selective laser melting, to create multifunctional fluidic devices with embedded reaction monitoring capability. The selectively laser melted parts are the first published examples of multifunctional 3D printed metal fluidic devices. These devices allow high temperature and pressure chemistry to be performed in solvent systems destructive to the majority of devices manufactured via stereolithography, polymer jetting and fused deposition modelling processes previously utilised for this application. These devices were integrated with commercially available flow chemistry, chromatographic and spectroscopic analysis equipment, allowing automated online and inline optimisation of the reaction medium. This set-up allowed the optimisation of two reactions, a ketone functional group interconversion and a fused polycyclic heterocycle formation, via spectroscopic and chromatographic analysis. PMID:28228852

  2. Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information

    PubMed Central

    Blouin, Christian; Boucher, Yan; Roger, Andrew J.

    2003-01-01

    Comparative sequence analysis has been used to study specific questions about the structure and function of proteins for many years. Here we propose a knowledge-based framework in which the maximum likelihood rate of evolution is used to quantify the level of constraint on the identity of a site. We demonstrate that site-rate mapping on 3D structures using datasets of rhodopsin-like G-protein receptors and α- and β-tubulins provides an excellent tool for pinpointing the functional features shared between orthologous and paralogous proteins. In addition, functional divergence within protein families can be inferred by examining the differences in the site rates, the differences in the chemical properties of the side chains or amino acid usage between aligned sites. Two novel analytical methods are introduced to characterize rate- independent functional divergence. These are tested using a dataset of two classes of HMG-CoA reductases for which only one class can perform both the forward and reverse reaction. We show that functionally divergent sites occur in a cluster of sites interacting with the catalytic residues and that this information should facilitate the design of experimental strategies to directly test functional properties of residues. PMID:12527789

  3. Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.

    PubMed

    Blouin, Christian; Boucher, Yan; Roger, Andrew J

    2003-01-15

    Comparative sequence analysis has been used to study specific questions about the structure and function of proteins for many years. Here we propose a knowledge-based framework in which the maximum likelihood rate of evolution is used to quantify the level of constraint on the identity of a site. We demonstrate that site-rate mapping on 3D structures using datasets of rhodopsin-like G-protein receptors and alpha- and beta-tubulins provides an excellent tool for pinpointing the functional features shared between orthologous and paralogous proteins. In addition, functional divergence within protein families can be inferred by examining the differences in the site rates, the differences in the chemical properties of the side chains or amino acid usage between aligned sites. Two novel analytical methods are introduced to characterize rate- independent functional divergence. These are tested using a dataset of two classes of HMG-CoA reductases for which only one class can perform both the forward and reverse reaction. We show that functionally divergent sites occur in a cluster of sites interacting with the catalytic residues and that this information should facilitate the design of experimental strategies to directly test functional properties of residues.

  4. ProFunc: a server for predicting protein function from 3D structure.

    PubMed

    Laskowski, Roman A; Watson, James D; Thornton, Janet M

    2005-07-01

    ProFunc (http://www.ebi.ac.uk/thornton-srv/databases/ProFunc) is a web server for predicting the likely function of proteins whose 3D structure is known but whose function is not. Users submit the coordinates of their structure to the server in PDB format. ProFunc makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins. A summary of the analyses provides an at-a-glance view of what each of the different methods has found. More detailed results are available on separate pages. Often where one method has failed to find anything useful another may be more forthcoming. The server is likely to be of most use in structural genomics where a large proportion of the proteins whose structures are solved are of hypothetical proteins of unknown function. However, it may also find use in a comparative analysis of members of large protein families. It provides a convenient compendium of sequence and structural information that often hold vital functional clues to be followed up experimentally.

  5. 3D mapping of somatotopic reorganization with small animal functional MRI

    PubMed Central

    Yu, Xin; Wang, Shumin; Chen, Der-Yow; Dodd, Stephen; Goloshevsky, Artem; Koretsky, Alan P.

    2009-01-01

    There are few in vivo noninvasive methods to study neuroplasticity in animal brains. Functional MRI (fMRI) has been developed for animal brain mapping, but few fMRI studies have analyzed functional alteration due to plasticity in animal models. One major limitation is that fMRI maps are characterized by statistical parametric mapping making the apparent boundary dependent on the statistical threshold used. Here, we developed a method to characterize the location of center-of-mass in fMRI maps that is shown not to be sensitive to statistical threshold. Utilizing centers-of-mass as anchor points to fit the spatial distribution of the BOLD response enabled quantitative group analysis of altered boundaries of functional somatosensory maps. This approach was used to study cortical reorganization in the rat primary somatosensory cortex (S1) after sensory deprivation to the barrel cortex by follicle ablation (F.A.). FMRI demonstrated an enlarged nose S1 representation in the 3D somatotopic functional maps. This result clearly demonstrates that fMRI enables the spatial mapping of functional changes that can characterize multiple regions of S1 cortex and still be sensitive to changes due to plasticity. PMID:19770051

  6. Identifying ultrasensitive HGF dose-response functions in a 3D mammalian system for synthetic morphogenesis

    PubMed Central

    Senthivel, Vivek Raj; Sturrock, Marc; Piedrafita, Gabriel; Isalan, Mark

    2016-01-01

    Nonlinear responses to signals are widespread natural phenomena that affect various cellular processes. Nonlinearity can be a desirable characteristic for engineering living organisms because it can lead to more switch-like responses, similar to those underlying the wiring in electronics. Steeper functions are described as ultrasensitive, and can be applied in synthetic biology by using various techniques including receptor decoys, multiple co-operative binding sites, and sequential positive feedbacks. Here, we explore the inherent non-linearity of a biological signaling system to identify functions that can potentially be exploited using cell genome engineering. For this, we performed genome-wide transcription profiling to identify genes with ultrasensitive response functions to Hepatocyte Growth Factor (HGF). We identified 3,527 genes that react to increasing concentrations of HGF, in Madin-Darby canine kidney (MDCK) cells, grown as cysts in 3D collagen cell culture. By fitting a generic Hill function to the dose-responses of these genes we obtained a measure of the ultrasensitivity of HGF-responsive genes, identifying a subset with higher apparent Hill coefficients (e.g. MMP1, TIMP1, SNORD75, SNORD86 and ERRFI1). The regulatory regions of these genes are potential candidates for future engineering of synthetic mammalian gene circuits requiring nonlinear responses to HGF signalling. PMID:27982133

  7. 3D Functional Elements Deep Inside Silicon with Nonlinear Laser Lithography

    NASA Astrophysics Data System (ADS)

    Tokel, Onur; Turnali, Ahmet; Ergecen, Emre; Pavlov, Ihor; Ilday, Fatih Omer

    Functional optical and electrical elements fabricated on silicon (Si) constitute fundamental building blocks of electronics and Si-photonics. However, since the highly successful established lithography are geared towards surface processing, elements embedded inside Si simply do not exist. Here, we present a novel direct-laser writing method for positioning buried functional elements inside Si wafers. This new phenomenon is distinct from previous work, in that the surface of Si is not modified. By exploiting nonlinear interactions of a focused laser, permanent refractive index changes are induced inside Si. The imprinted index contrast is then used to demonstrate a plethora of functional elements and capabilities embedded inside Si. In particular, we demonstrate the first functional optical element inside Si, the first information-storage capability inside Si, creation of high-resolution subsurface holograms, buried multilevel structures, and complex 3D architectures in Si, none of which is currently possible with other methods. This new approach complements available techniques by taking advantage of the real estate under Si, and therefore can pave the way for creating entirely new multilevel devices through electronic-photonic integration.

  8. 3D crustal velocity structure beneath the broadband seismic array in the Gyeongju area of Korea by receiver function analyses

    NASA Astrophysics Data System (ADS)

    Lee, Dong Hun; Lee, Jung Mo; Cho, Hyun-Moo; Kang, Tae-Seob

    2016-10-01

    A temporary seismic array was in operation between October 2010 and March 2013 in the Gyeongju area of Korea. Teleseismic records of the seismic array appropriate for receiver function analysis were collected, and selected seismograms were split into five groups based on epicenters-the Banda-Molucca, Sumatra, Iran, Aleutian, and Vanuatu groups. 1D velocity structures beneath each seismic station were estimated by inverting the stacked receiver functions for possible groups. The inversion was done by applying a genetic algorithm, whereas surface wave dispersion data were used as constraints to avoid non-uniqueness in the inversion. The composite velocity structure was constructed by averaging the velocity structures weighted by the number of receiver functions used in stacking. The uncertainty analysis for the velocity structures showed that the average of 95% confidence intervals was ± 0.1 km/s. The 3D velocity structure was modeled through interpolation of 1D composite velocity structures. Moho depths were determined in each composite velocity structure based on the AK135-F S-wave velocity model, and the depths were similar to the H-κ analysis results. The deepest Moho depth in the study area was found to be 31.9 km, and the shallowest, was 25.9 km. The Moho discontinuity dips in a southwestward direction beneath the area. A low velocity layer was also detected between 4 and 14 km depth. Adakitic intrusions and/or a high geothermal gradient appear to be the causes of this low velocity layer. The 3D velocity structure can be used to reliably assess seismic hazards in this area.

  9. A comparison study between 3D T2-weighted SPACE and conventional 2D T2-weighted turbo spin echo in assessment of carotid plaque.

    PubMed

    Lv, Peng; Dai, Yuanyuan; Lin, Jiang; Zhang, Weisheng; Liu, Hao; Liu, Hui; Tang, Xiao

    2017-03-01

    The aim of this study was to compare 3D T2-weighted sampling perfection with application optimized contrast using different flip angle evolutions (T2w SPACE) with conventional 2D T2w turbo-spin echo (TSE) in plaque imaging of carotid artery. 45 patients underwent 3.0-T MRI for carotid arteries imaging. MR sequences included T2w SPACE, T2w TSE, Time of flight (TOF) and T1-weighted (T1w) TSE. The signal intensity of intra-plaque hemorrhage (IPH), lipid-rich necrotic core (LRNC), and loose matrix (LM) were measured and their contrast ratios (CRs) against adjacent muscle were calculated. CRs from T2w SPACE and T2w TSE were compared to each other. CRs of LM, LRNC, and IPH measured on T2w SPACE were 1.74-3.04 (2.44), 0.98-1.66 (1.39), and 1.91-2.93 (2.51), respectively. CRs of LM, LRNC, and IPH on T2w TSE were 1.97-3.41 (2.44), 1.18-1.73 (1.43), and 2.26-3.75 (2.26), respectively. There was no significant difference of CR of the carotid plaques between T2w SPACE and T2w TSE (p = 0.455). Markedly significant differences of CRs were found between LM and LRNC (p < 0.001), and between LRNC and IPH (p < 0.001) on T2w SPACE and T2w TSE. T2w SPACE was comparable with conventional T2w TSE in characterization of carotid plaque.

  10. Probability distribution functions for cover used in 3-D model simulating concrete deterioration in port assets.

    NASA Astrophysics Data System (ADS)

    Homer, Rachel M.; Law, David W.; Molyneaux, Thomas C. K.

    2015-07-01

    In previous studies, a 1-D numerical predictive tool to simulate the salt induced corrosion of port assets in Australia has been developed into a 2-D and 3-D model based on current predictive probabilistic models. These studies use a probability distribution function based on the mean and standard deviation of the parameters for a structure incorporating surface chloride concentration, diffusion coefficient and cover. In this paper, this previous work is extended through an investigation of the distribution of actual cover by specified cover, element type and method of construction. Significant differences are found for the measured cover within structures, by method of construction, element type and specified cover. The data are not normally distributed and extreme values, usually low, are found in a number of locations. Elements cast insitu are less likely to meet the specified cover and the measured cover is more dispersed than those in elements which are precast. Individual probability distribution functions are available and are tested against the original function. Methods of combining results so that one distribution is available for a structure are formulated and evaluated. The ability to utilise the model for structures where no measurement have been taken is achieved by transposing results based on the specified cover.

  11. 3D Printing Multi-Functionality: Embedded RF Antennas and Components

    NASA Technical Reports Server (NTRS)

    Shemelya, C. M.; Zemba, M.; Liang, M.; Espalin, D.; Kief, C.; Xin, H.; Wicker, R. B.; MacDonald, E. W.

    2015-01-01

    Significant research and press has recently focused on the fabrication freedom of Additive Manufacturing (AM) to create both conceptual models and final end-use products. This flexibility allows design modifications to be immediately reflected in 3D printed structures, creating new paradigms within the manufacturing process. 3D printed products will inevitably be fabricated locally, with unit-level customization, optimized to unique mission requirements. However, for the technology to be universally adopted, the processes must be enhanced to incorporate additional technologies; such as electronics, actuation, and electromagnetics. Recently, a novel 3D printing platform, Multi3D manufacturing, was funded by the presidential initiative for revitalizing manufacturing in the USA using 3D printing (America Makes - also known as the National Additive Manufacturing Innovation Institute). The Multi3D system specifically targets 3D printed electronics in arbitrary form; and building upon the potential of this system, this paper describes RF antennas and components fabricated through the integration of material extrusion 3D printing with embedded wire, mesh, and RF elements.

  12. Surface functionalization of 3D glass-ceramic porous scaffolds for enhanced mineralization in vitro

    NASA Astrophysics Data System (ADS)

    Ferraris, Sara; Vitale-Brovarone, Chiara; Bretcanu, Oana; Cassinelli, Clara; Vernè, Enrica

    2013-04-01

    Bone reconstruction after tissue loosening due to traumatic, pathological or surgical causes is in increasing demand. 3D scaffolds are a widely studied solution for supporting new bone growth. Bioactive glass-ceramic porous materials can offer a three-dimensional structure that is able to chemically bond to bone. The ability to surface modify these devices by grafting biologically active molecules represents a challenge, with the aim of stimulating physiological bone regeneration with both inorganic and organic signals. In this research work glass ceramic scaffolds with very high mechanical properties and moderate bioactivity have been functionalized with the enzyme alkaline phosphatase (ALP). The material surface was activated in order to expose hydroxyl groups. The activated surface was further grafted with ALP both via silanization and also via direct grafting to the surface active hydroxyl groups. Enzymatic activity of grafted samples were measured by means of UV-vis spectroscopy before and after ultrasonic washing in TRIS-HCl buffer solution. In vitro inorganic bioactivity was investigated by soaking the scaffolds after the different steps of functionalization in a simulated body fluid (SBF). SEM observations allowed the monitoring of the scaffold morphology and surface chemical composition after soaking in SBF. The presence of ALP enhanced the in vitro inorganic bioactivity of the tested material.

  13. 3D printing enables separation of orthogonal functions within a hydrogel particle.

    PubMed

    Raman, Ritu; Clay, Nicholas E; Sen, Sanjeet; Melhem, Molly; Qin, Ellen; Kong, Hyunjoon; Bashir, Rashid

    2016-06-01

    Multifunctional particles with distinct physiochemical phases are required by a variety of applications in biomedical engineering, such as diagnostic imaging and targeted drug delivery. This motivates the development of a repeatable, efficient, and customizable approach to manufacturing particles with spatially segregated bioactive moieties. This study demonstrates a stereolithographic 3D printing approach for designing and fabricating large arrays of biphasic poly (ethylene glycol) diacrylate (PEGDA) gel particles. The fabrication parameters governing the physical and biochemical properties of multi-layered particles are thoroughly investigated, yielding a readily tunable approach to manufacturing customizable arrays of multifunctional particles. The advantage in spatially organizing functional epitopes is examined by loading superparamagnetic iron oxide nanoparticles (SPIONs) and bovine serum albumin (BSA) in separate layers of biphasic PEGDA gel particles and examining SPION-induced magnetic resonance (MR) contrast and BSA-release kinetics. Particles with spatial segregation of functional moieties have demonstrably higher MR contrast and BSA release. Overall, this study will contribute significant knowledge to the preparation of multifunctional particles for use as biomedical tools.

  14. A MATLAB function for 3-D and 4-D topographical visualization in geosciences

    NASA Astrophysics Data System (ADS)

    Zekollari, Harry

    2016-04-01

    Combining topographical information and spatially varying variables in visualizations is often crucial and inherent to geoscientific problems. Despite this, it is often an impossible or a very time-consuming and difficult task to create such figures by using classic software packages. This is also the case in the widely used numerical computing environment MATLAB. Here a MATLAB function is introduced for plotting a variety of natural environments with a pronounced topography, such as for instance glaciers, volcanoes and lakes in mountainous regions. Landscapes can be visualized in 3-D, with a single colour defining a featured surface type (e.g. ice, snow, water, lava), or with a colour scale defining the magnitude of a variable (e.g. ice thickness, snow depth, water depth, surface velocity, gradient, elevation). As an input only the elevation of the subsurface (typically the bedrock) and the surface are needed, which can be complemented by various input parameters in order to adapt the figure to specific needs. The figures are particularly suited to make time-evolving animations of natural processes, such as for instance a glacier retreat or a lake drainage event. Several visualization examples will be provided alongside with animations. The function, which is freely available for download, only requires the basic package of MATLAB and can be run on any standard stationary or portable personal computer.

  15. Prescribed intensity in 3D rotational geometry for extended sources by using a conversion function in 2D design.

    PubMed

    Li, Xiufeng; Ge, Peng; Wang, Hong

    2017-02-20

    To obtain a prescribed intensity in three-dimensional (3D) rotationally symmetric geometry for an extended source, a two-dimensional (2D) intensity design method is often used. The 3D entity of the lens can be gained by rotating the profile of the lens obtained by the 2D design method. However, the intensity we set in 2D design is quite different from the one we obtain through ray-tracing by the Monte Carlo method in the 3D rotational geometry. Noting the differences of intensity patterns between 2D and 3D, a 3D conversion function (3DCF) should be deduced to convert the prescribed 3D intensity into a 2D intensity in the 2D design process. The extended Lambertian source properties are taken into account during the derivation process. Using the 3DCF, we can quickly obtain the prescribed intensity in 3D rotationally symmetric geometry for an LED extended source without the fussy feedback strategy. The error is small enough for most general illumination. Three examples are presented to demonstrate the correction effectiveness of the proposed conversion function.

  16. Function of pretribosphenic and tribosphenic mammalian molars inferred from 3D animation.

    PubMed

    Schultz, Julia A; Martin, Thomas

    2014-10-01

    Appearance of the tribosphenic molar in the Late Jurassic (160 Ma) is a crucial innovation for food processing in mammalian evolution. This molar type is characterized by a protocone, a talonid basin and a two-phased chewing cycle, all of which are apomorphic. In this functional study on the teeth of Late Jurassic Dryolestes leiriensis and the living marsupial Monodelphis domestica, we demonstrate that pretribosphenic and tribosphenic molars show fundamental differences of food reduction strategies, representing a shift in dental function during the transition of tribosphenic mammals. By using the Occlusal Fingerprint Analyser (OFA), we simulated the chewing motions of the pretribosphenic Dryolestes that represents an evolutionary precursor condition to such tribosphenic mammals as Monodelphis. Animation of chewing path and detection of collisional contacts between virtual models of teeth suggests that Dryolestes differs from the classical two-phased chewing movement of tribosphenidans, due to the narrowing of the interdental space in cervical (crown-root transition) direction, the inclination angle of the hypoflexid groove, and the unicuspid talonid. The pretribosphenic chewing cycle is equivalent to phase I of the tribosphenic chewing cycle, but the former lacks phase II of the tribosphenic chewing. The new approach can analyze the chewing cycle of the jaw by using polygonal 3D models of tooth surfaces, in a way that is complementary to the electromyography and strain gauge studies of muscle function of living animals. The technique allows alignment and scaling of isolated fossil teeth and utilizes the wear facet orientation and striation of the teeth to reconstruct the chewing path of extinct mammals.

  17. Function of pretribosphenic and tribosphenic mammalian molars inferred from 3D animation

    NASA Astrophysics Data System (ADS)

    Schultz, Julia A.; Martin, Thomas

    2014-10-01

    Appearance of the tribosphenic molar in the Late Jurassic (160 Ma) is a crucial innovation for food processing in mammalian evolution. This molar type is characterized by a protocone, a talonid basin and a two-phased chewing cycle, all of which are apomorphic. In this functional study on the teeth of Late Jurassic Dryolestes leiriensis and the living marsupial Monodelphis domestica, we demonstrate that pretribosphenic and tribosphenic molars show fundamental differences of food reduction strategies, representing a shift in dental function during the transition of tribosphenic mammals. By using the Occlusal Fingerprint Analyser (OFA), we simulated the chewing motions of the pretribosphenic Dryolestes that represents an evolutionary precursor condition to such tribosphenic mammals as Monodelphis. Animation of chewing path and detection of collisional contacts between virtual models of teeth suggests that Dryolestes differs from the classical two-phased chewing movement of tribosphenidans, due to the narrowing of the interdental space in cervical (crown-root transition) direction, the inclination angle of the hypoflexid groove, and the unicuspid talonid. The pretribosphenic chewing cycle is equivalent to phase I of the tribosphenic chewing cycle, but the former lacks phase II of the tribosphenic chewing. The new approach can analyze the chewing cycle of the jaw by using polygonal 3D models of tooth surfaces, in a way that is complementary to the electromyography and strain gauge studies of muscle function of living animals. The technique allows alignment and scaling of isolated fossil teeth and utilizes the wear facet orientation and striation of the teeth to reconstruct the chewing path of extinct mammals.

  18. Revealing the Functions of Tenascin-C in 3-D Breast Cancer Models Using Cell Biological and in Silico Approaches

    DTIC Science & Technology

    2008-03-01

    renditions of mammary acini, which were then used to assess and quantify acinar topography and volume. Although TN-C increased acinar surface roughness...epithelial 3-D tissue structure and function. In essence, we devised an algorithm to quantify acinar surface topography and volume in 3-D cultures of...deficient mice, Nature 1995, 377:539-544 39 34. Matsuda A, Yoshiki A, Tagawa Y, Matsuda H, Kusakabe M: Corneal wound healing in tenascin knockout mouse

  19. Function and 3D Structure of the N-Glycans on Glycoproteins

    PubMed Central

    Nagae, Masamichi; Yamaguchi, Yoshiki

    2012-01-01

    Glycosylation is one of the most common post-translational modifications in eukaryotic cells and plays important roles in many biological processes, such as the immune response and protein quality control systems. It has been notoriously difficult to study glycoproteins by X-ray crystallography since the glycan moieties usually have a heterogeneous chemical structure and conformation, and are often mobile. Nonetheless, recent technical advances in glycoprotein crystallography have accelerated the accumulation of 3D structural information. Statistical analysis of “snapshots” of glycoproteins can provide clues to understanding their structural and dynamic aspects. In this review, we provide an overview of crystallographic analyses of glycoproteins, in which electron density of the glycan moiety is clearly observed. These well-defined N-glycan structures are in most cases attributed to carbohydrate-protein and/or carbohydrate-carbohydrate interactions and may function as “molecular glue” to help stabilize inter- and intra-molecular interactions. However, the more mobile N-glycans on cell surface receptors, the electron density of which is usually missing on X-ray crystallography, seem to guide the partner ligand to its binding site and prevent irregular protein aggregation by covering oligomerization sites away from the ligand-binding site. PMID:22942711

  20. Mimicking liver sinusoidal structures and functions using a 3D-configured microfluidic chip.

    PubMed

    Du, Yu; Li, Ning; Yang, Hao; Luo, Chunhua; Gong, Yixin; Tong, Chunfang; Gao, Yuxin; Lü, Shouqin; Long, Mian

    2017-02-28

    Physiologically, four major types of hepatic cells - the liver sinusoidal endothelial cells, Kupffer cells, hepatic stellate cells, and hepatocytes - reside inside liver sinusoids and interact with flowing peripheral cells under blood flow. It is hard to mimic an in vivo liver sinusoid due to its complex multiple cell-cell interactions, spatiotemporal construction, and mechanical microenvironment. Here we developed an in vitro liver sinusoid chip by integrating the four types of primary murine hepatic cells into two adjacent fluid channels separated by a porous permeable membrane, replicating liver's key structures and configurations. Each type of cells was identified with its respective markers, and the assembled chip presented the liver-specific unique morphology of fenestration. The flow field in the liver chip was quantitatively analyzed by computational fluid dynamics simulations and particle tracking visualization tests. Intriguingly, co-culture and shear flow enhance albumin secretion independently or cooperatively, while shear flow alone enhances HGF production and CYP450 metabolism. Under lipopolysaccharide (LPS) stimulations, the hepatic cell co-culture facilitated neutrophil recruitment in the liver chip. Thus, this 3D-configured in vitro liver chip integrates the two key factors of shear flow and the four types of primary hepatic cells to replicate key structures, hepatic functions, and primary immune responses and provides a new in vitro model to investigate the short-duration hepatic cellular interactions under a microenvironment mimicking the physiology of a liver.

  1. Active surface model improvement by energy function optimization for 3D segmentation.

    PubMed

    Azimifar, Zohreh; Mohaddesi, Mahsa

    2015-04-01

    This paper proposes an optimized and efficient active surface model by improving the energy functions, searching method, neighborhood definition and resampling criterion. Extracting an accurate surface of the desired object from a number of 3D images using active surface and deformable models plays an important role in computer vision especially medical image processing. Different powerful segmentation algorithms have been suggested to address the limitations associated with the model initialization, poor convergence to surface concavities and slow convergence rate. This paper proposes a method to improve one of the strongest and recent segmentation algorithms, namely the Decoupled Active Surface (DAS) method. We consider a gradient of wavelet edge extracted image and local phase coherence as external energy to extract more information from images and we use curvature integral as internal energy to focus on high curvature region extraction. Similarly, we use resampling of points and a line search for point selection to improve the accuracy of the algorithm. We further employ an estimation of the desired object as an initialization for the active surface model. A number of tests and experiments have been done and the results show the improvements with regards to the extracted surface accuracy and computational time of the presented algorithm compared with the best and recent active surface models.

  2. Development of 3D functionally graded models by laser-assisted coaxial powder injection

    NASA Astrophysics Data System (ADS)

    Yakovlev, Artem; Bertrand, Ph.; Smurov, Igor Y.

    2004-04-01

    Relatively new method of producing 3D objects with Functionally Graded Material (FGM) structure is realized by coaxial powder injection with variable composition into the zone of laser beam action. The desired 3-dimensional material distribution is realized by repetitive deposition process. Theoretical analysis and experimental results show essential role of radiation mode and powder granularity as optimization parameters. Applied laser sources are continuous wave Nd:YAG(HAAS 2006D, 2kW), pulse-periodic Nd:YAG(HAAS HL304P, avg. power 300 W), quazi-cw CO2 (Rofin-Sinar, 300 W). Among applied materials are nanostructured WC/Co, CuSn, Stainless steel 316L, 430L, Co-base alloy, nanostructured FeCu, etc. The originality of obtained results is that different gradient types are produced "in situ" and combined within one sample: smooth, sharp or multilayered gradients. The number of samples is produced and examined with metallographical and SEM analysis. The minimal spatial gradient resolution (transition zone between two different materials) is starting from 10 microns and can be varied in a wide range; the surface roughness depends from powder granularity, best value of Ra is about 5 μm, microhardness of differet zones of samples is varied from 120 to 450 HV. The achieved geometry spatial resolution is 200 μm.

  3. Laser-assisted direct manufacturing of functionally graded 3D objects

    NASA Astrophysics Data System (ADS)

    Iakovlev, A.; Trunova, E.; Grevey, Dominique; Smurov, Igor

    2003-09-01

    Coaxial powder injection into a laser beam was applied for the laser-assisted direct manufacturing of 3D functionally graded (FG) objects. The powders of Stainless Steel 316L and Stellite grade 12 were applied. The following laser sources were used: (1) quasi-cw CO2 Rofin Sinar laser with 120 μm focal spot diameter and (2) pulsed-periodic Nd:YAG (HAAS HL 304P) with 200 μm focal spot diameter. The objects were fabricated layer-by-layer in the form of "walls", having the thickness of about 200 μm for CO2 laser and 300 μm for Nd:YAG laser. SEM analysis was applied for the FG objects fabricated by CO2 laser, yielding wall elements distribution in vertical direction. It was found that microhardness distribution is fully correlated with the components distribution. The compositional gradient can be smooth or sharp. Periodic multi-layered structures can be obtained as well. Minimal thickness of a layer with the fixed composition (for cw CO2 laser) is about 50 μm. Minimal thickness of a graded material zone, i.e. zone with composition variation from pure stainless steel to pure stellite is about 30 μm.

  4. (Bio)Chemical Tailoring of Biogenic 3-D Nanopatterned Templates with Energy-Relevant Functionalities

    SciTech Connect

    Sandhage, Kenneth H; Kroger, Nils

    2014-09-08

    The overall aim of this research has been to obtain fundamental understanding of (bio)chemical methodologies that will enable utilization of the unique 3-D nanopatterned architectures naturally produced by diatoms for the syntheses of advanced functional materials attractive for applications in energy harvesting/conversion and storage. This research has been conducted in three thrusts: Thrust 1 (In vivo immobilization of proteins in diatom biosilica) is directed towards elucidating the fundamental mechanism(s) underlying the cellular processes of in vivo immobilization of proteins in diatom silica. Thrust 2 (Shape-preserving reactive conversion of diatom biosilica into porous, high-surface area inorganic replicas) is aimed at understanding the fundamental mechanisms of shape preservation and nanostructural evolution associated with the reactive conversion and/or coating-based conversion of diatom biosilica templates into porous inorganic replicas. Thrust 3 (Immobilization of energy-relevant enzymes in diatom biosilica and onto diatom biosilica-derived inorganic replicas) involves use of the results from both Thrust 1 and 2 to develop strategies for in vivo and in vitro immobilization of enzymes in/on diatom biosilica and diatom biosilica-derived inorganic replicas, respectively. This Final Report describes progress achieved in all 3 of these thrusts.

  5. Mesoporous bioactive glass nanolayer-functionalized 3D-printed scaffolds for accelerating osteogenesis and angiogenesis

    NASA Astrophysics Data System (ADS)

    Zhang, Yali; Xia, Lunguo; Zhai, Dong; Shi, Mengchao; Luo, Yongxiang; Feng, Chun; Fang, Bing; Yin, Jingbo; Chang, Jiang; Wu, Chengtie

    2015-11-01

    The hierarchical microstructure, surface and interface of biomaterials are important factors influencing their bioactivity. Porous bioceramic scaffolds have been widely used for bone tissue engineering by optimizing their chemical composition and large-pore structure. However, the surface and interface of struts in bioceramic scaffolds are often ignored. The aim of this study is to incorporate hierarchical pores and bioactive components into the bioceramic scaffolds by constructing nanopores and bioactive elements on the struts of scaffolds and further improve their bone-forming activity. Mesoporous bioactive glass (MBG) modified β-tricalcium phosphate (MBG-β-TCP) scaffolds with a hierarchical pore structure and a functional strut surface (~100 nm of MBG nanolayer) were successfully prepared via 3D printing and spin coating. The compressive strength and apatite-mineralization ability of MBG-β-TCP scaffolds were significantly enhanced as compared to β-TCP scaffolds without the MBG nanolayer. The attachment, viability, alkaline phosphatase (ALP) activity, osteogenic gene expression (Runx2, BMP2, OPN and Col I) and protein expression (OPN, Col I, VEGF, HIF-1α) of rabbit bone marrow stromal cells (rBMSCs) as well as the attachment, viability and angiogenic gene expression (VEGF and HIF-1α) of human umbilical vein endothelial cells (HUVECs) in MBG-β-TCP scaffolds were significantly upregulated compared with conventional bioactive glass (BG)-modified β-TCP (BG-β-TCP) and pure β-TCP scaffolds. Furthermore, MBG-β-TCP scaffolds significantly enhanced the formation of new bone in vivo as compared to BG-β-TCP and β-TCP scaffolds. The results suggest that application of the MBG nanolayer to modify 3D-printed bioceramic scaffolds offers a new strategy to construct hierarchically porous scaffolds with significantly improved physicochemical and biological properties, such as mechanical properties, osteogenesis, angiogenesis and protein expression for bone tissue

  6. The performance of semilocal and hybrid density functionals in 3d transition-metal chemistry

    NASA Astrophysics Data System (ADS)

    Furche, Filipp; Perdew, John P.

    2006-01-01

    We investigate the performance of contemporary semilocal and hybrid density functionals for bond energetics, structures, dipole moments, and harmonic frequencies of 3d transition-metal (TM) compounds by comparison with gas-phase experiments. Special attention is given to the nonempirical metageneralized gradient approximation (meta-GGA) of Tao, Perdew, Staroverov, and Scuseria (TPSS) [Phys. Rev. Lett. 91, 146401 (2003)], which has been implemented in TURBOMOLE for the present work. Trends and error patterns for classes of homologous compounds are analyzed, including dimers, monohydrides, mononitrides, monoxides, monofluorides, polyatomic oxides and halogenides, carbonyls, and complexes with organic π ligands such as benzene and cyclopentadienyl. Weakly bound systems such as Ca2, Mn2, and Zn2 are discussed. We propose a reference set of reaction energies for benchmark purposes. Our all-electron results with quadruple zeta valence basis sets validate semilocal density-functional theory as the workhorse of computational TM chemistry. Typical errors in bond energies are substantially larger than in (organic) main group chemistry, however. The Becke-Perdew'86 [Phys. Rev. A 38, 3098 (1988); Phys. Rev. B 33, 8822 (1986)] GGA and the TPSS meta-GGA have the best price/performance ratio, while the TPSS hybrid functional achieves a slightly lower mean absolute error in bond energies. The popular Becke three-parameter hybrid B3LYP underbinds significantly and tends to overestimate bond distances; we give a possible explanation for this. We further show that hybrid mixing does not reduce the width of the error distribution on our reference set. The error of a functional for the s-d transfer energy of a TM atom does not predict its error for TM bond energies and bond lengths. For semilocal functionals, self-interaction error in one- and three-electron bonds appears to be a major source of error in TM reaction energies. Nevertheless, TPSS predicts the correct ground

  7. 3D meshes of carbon nanotubes guide functional reconnection of segregated spinal explants.

    PubMed

    Usmani, Sadaf; Aurand, Emily Rose; Medelin, Manuela; Fabbro, Alessandra; Scaini, Denis; Laishram, Jummi; Rosselli, Federica B; Ansuini, Alessio; Zoccolan, Davide; Scarselli, Manuela; De Crescenzi, Maurizio; Bosi, Susanna; Prato, Maurizio; Ballerini, Laura

    2016-07-01

    In modern neuroscience, significant progress in developing structural scaffolds integrated with the brain is provided by the increasing use of nanomaterials. We show that a multiwalled carbon nanotube self-standing framework, consisting of a three-dimensional (3D) mesh of interconnected, conductive, pure carbon nanotubes, can guide the formation of neural webs in vitro where the spontaneous regrowth of neurite bundles is molded into a dense random net. This morphology of the fiber regrowth shaped by the 3D structure supports the successful reconnection of segregated spinal cord segments. We further observed in vivo the adaptability of these 3D devices in a healthy physiological environment. Our study shows that 3D artificial scaffolds may drive local rewiring in vitro and hold great potential for the development of future in vivo interfaces.

  8. 3D meshes of carbon nanotubes guide functional reconnection of segregated spinal explants

    PubMed Central

    Usmani, Sadaf; Aurand, Emily Rose; Medelin, Manuela; Fabbro, Alessandra; Scaini, Denis; Laishram, Jummi; Rosselli, Federica B.; Ansuini, Alessio; Zoccolan, Davide; Scarselli, Manuela; De Crescenzi, Maurizio; Bosi, Susanna; Prato, Maurizio; Ballerini, Laura

    2016-01-01

    In modern neuroscience, significant progress in developing structural scaffolds integrated with the brain is provided by the increasing use of nanomaterials. We show that a multiwalled carbon nanotube self-standing framework, consisting of a three-dimensional (3D) mesh of interconnected, conductive, pure carbon nanotubes, can guide the formation of neural webs in vitro where the spontaneous regrowth of neurite bundles is molded into a dense random net. This morphology of the fiber regrowth shaped by the 3D structure supports the successful reconnection of segregated spinal cord segments. We further observed in vivo the adaptability of these 3D devices in a healthy physiological environment. Our study shows that 3D artificial scaffolds may drive local rewiring in vitro and hold great potential for the development of future in vivo interfaces. PMID:27453939

  9. 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.

  10. Template-Free Synthesis of Functional 3D BN architecture for removal of dyes from water

    NASA Astrophysics Data System (ADS)

    Liu, Dan; Lei, Weiwei; Qin, Si; Chen, Ying

    2014-03-01

    Three-dimensional (3D) architectures are of interest in applications in electronics, catalysis devices, sensors and adsorption materials. However, it is still a challenge to fabricate 3D BN architectures by a simple method. Here, we report the direct synthesis of 3D BN architectures by a simple thermal treatment process. A 3D BN architecture consists of an interconnected flexible network of nanosheets. The typical nitrogen adsorption/desorption results demonstrate that the specific surface area for the as-prepared samples is up to 1156 m2 g-1, and the total pore volume is about 1.17 cm3 g-1. The 3D BN architecture displays very high adsorption rates and large capacities for organic dyes in water without any other additives due to its low densities, high resistance to oxidation, good chemical inertness and high surface area. Importantly, 88% of the starting adsorption capacity is maintained after 15 cycles. These results indicate that the 3D BN architecture is potential environmental materials for water purification and treatment.

  11. Beating heart on a chip: a novel microfluidic platform to generate functional 3D cardiac microtissues.

    PubMed

    Marsano, Anna; Conficconi, Chiara; Lemme, Marta; Occhetta, Paola; Gaudiello, Emanuele; Votta, Emiliano; Cerino, Giulia; Redaelli, Alberto; Rasponi, Marco

    2016-02-07

    In the past few years, microfluidic-based technology has developed microscale models recapitulating key physical and biological cues typical of the native myocardium. However, the application of controlled physiological uniaxial cyclic strains on a defined three-dimension cellular environment is not yet possible. Two-dimension mechanical stimulation was particularly investigated, neglecting the complex three-dimensional cell-cell and cell-matrix interactions. For this purpose, we developed a heart-on-a-chip platform, which recapitulates the physiologic mechanical environment experienced by cells in the native myocardium. The device includes an array of hanging posts to confine cell-laden gels, and a pneumatic actuation system to induce homogeneous uniaxial cyclic strains to the 3D cell constructs during culture. The device was used to generate mature and highly functional micro-engineered cardiac tissues (μECTs), from both neonatal rat and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM), strongly suggesting the robustness of our engineered cardiac micro-niche. Our results demonstrated that the cyclic strain was effectively highly uniaxial and uniformly transferred to cells in culture. As compared to control, stimulated μECTs showed superior cardiac differentiation, as well as electrical and mechanical coupling, owing to a remarkable increase in junction complexes. Mechanical stimulation also promoted early spontaneous synchronous beating and better contractile capability in response to electric pacing. Pacing analyses of hiPSC-CM constructs upon controlled administration of isoprenaline showed further promising applications of our platform in drug discovery, delivery and toxicology fields. The proposed heart-on-a-chip device represents a relevant step forward in the field, providing a standard functional three-dimensional cardiac model to possibly predict signs of hypertrophic changes in cardiac phenotype by mechanical and biochemical co-stimulation.

  12. Detection of Leptomeningeal Metastasis by Contrast-Enhanced 3D T1-SPACE: Comparison with 2D FLAIR and Contrast-Enhanced 2D T1-Weighted Images

    PubMed Central

    Gil, Bomi; Hwang, Eo-Jin; Lee, Song; Jang, Jinhee; Jung, So-Lyung; Ahn, Kook-Jin; Kim, Bum-soo

    2016-01-01

    Introduction To compare the diagnostic accuracy of contrast-enhanced 3D(dimensional) T1-weighted sampling perfection with application-optimized contrasts by using different flip angle evolutions (T1-SPACE), 2D fluid attenuated inversion recovery (FLAIR) images and 2D contrast-enhanced T1-weighted image in detection of leptomeningeal metastasis except for invasive procedures such as a CSF tapping. Materials and Methods Three groups of patients were included retrospectively for 9 months (from 2013-04-01 to 2013-12-31). Group 1 patients with positive malignant cells in CSF cytology (n = 22); group 2, stroke patients with steno-occlusion in ICA or MCA (n = 16); and group 3, patients with negative results on MRI, whose symptom were dizziness or headache (n = 25). A total of 63 sets of MR images are separately collected and randomly arranged: (1) CE 3D T1-SPACE; (2) 2D FLAIR; and (3) CE T1-GRE using a 3-Tesla MR system. A faculty neuroradiologist with 8-year-experience and another 2nd grade trainee in radiology reviewed each MR image- blinded by the results of CSF cytology and coded their observations as positives or negatives of leptomeningeal metastasis. The CSF cytology result was considered as a gold standard. Sensitivity and specificity of each MR images were calculated. Diagnostic accuracy was compared using a McNemar’s test. A Cohen's kappa analysis was performed to assess inter-observer agreements. Results Diagnostic accuracy was not different between 3D T1-SPACE and CSF cytology by both raters. However, the accuracy test of 2D FLAIR and 2D contrast-enhanced T1-weighted GRE was inconsistent by the two raters. The Kappa statistic results were 0.657 (3D T1-SPACE), 0.420 (2D FLAIR), and 0.160 (2D contrast-enhanced T1-weighted GRE). The 3D T1-SPACE images showed the highest inter-observer agreements between the raters. Conclusions Compared to 2D FLAIR and 2D contrast-enhanced T1-weighted GRE, contrast-enhanced 3D T1 SPACE showed a better detection rate of

  13. Poly(acrylic acid) brushes pattern as a 3D functional biosensor surface for microchips

    NASA Astrophysics Data System (ADS)

    Wang, Yan-Mei; Cui, Yi; Cheng, Zhi-Qiang; Song, Lu-Sheng; Wang, Zhi-You; Han, Bao-Hang; Zhu, Jin-Song

    2013-02-01

    Poly(acrylic acid) (PAA) brushes, a novel three dimensional (3D) precursor layer of biosensor or protein microarrays, possess high protein loading level and low non-specific protein adsorption. In this article, we describe a simple and convenient way to fabricate 3D PAA brushes pattern by microcontact printing (μCP) and characterize it with FT-IR and optical microscopy. The carboxyl groups of PAA brushes can be applied to covalently immobilize protein for immunoassay. Thriving 3D space made by patterning PAA brushes thin film is available to enhance protein immobilization, which is confirmed by measuring model protein interaction between human immunoglobulin G (H-IgG) and goat anti-H-IgG (G-H-IgG) with fluorescence microscopy and surface plasmon resonance imaging (SPRi). As expected, the SPRi signals of H-IgG coating on 3D PAA brushes pattern and further measuring specific binding with G-H-IgG are all larger than that of 3D PAA brushes without pattern and 2D bare gold surface. We further revealed that this surface can be used for high-throughput screening and clinical diagnosis by label-free assaying of Hepatitis-B-Virus surface antibody (HBsAb) with Hepatitis-B-Virus surface antigen (HBsAg) concentration array chip. The linearity range for HBsAb assay is wider than that of conventional ELISA method.

  14. Cloud 3D Effects Evidenced in Landsat Power Spectra and Autocorrelation Functions

    NASA Technical Reports Server (NTRS)

    Oreopoulos, Lazaros; Marshak, Alexander; Cahalan, Robert F.; Wen, Guoyong

    1999-01-01

    the spectral signatures of decorrelation between reflectance and optical depth at large scales becoming stronger as the magnitude of cloud top variations increase. Finally, the usefulness of power spectral analysis in evaluating the skill of novel optical depth retrieval techniques in removing 3D radiative effects is demonstrated. New techniques using inverse Non-local Independent Pixel Approximation (NIPA) and Normalized Difference of Nadir Reflectivity (NDNR) yield optical depth fields which better match the scale-by-scale variability of the true optical depth field.

  15. A 3D profile function suitable for integration of neutron time-of-flight single crystal diffraction peaks

    NASA Astrophysics Data System (ADS)

    Gutmann, Matthias J.

    2017-03-01

    A 3D profile function is presented suitable to integrate reflections arising in time-of-flight (TOF) single crystal neutron diffraction experiments. In order to account for the large asymmetry of the peak shape in the TOF direction, a 3D Gaussian ellipsoid in the pixel (x, z) and time-of-flight coordinates is convoluted with a rising and falling exponential along the time-of-flight direction. An analytic expression is derived, making it suitable for least-squares fitting. The application of this function in detector space or reciprocal space is straightforward.

  16. 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…

  17. Functional metabolic interactions of human neuron-astrocyte 3D in vitro networks

    PubMed Central

    Simão, Daniel; Terrasso, Ana P.; Teixeira, Ana P.; Brito, Catarina; Sonnewald, Ursula; Alves, Paula M.

    2016-01-01

    The generation of human neural tissue-like 3D structures holds great promise for disease modeling, drug discovery and regenerative medicine strategies. Promoting the establishment of complex cell-cell interactions, 3D culture systems enable the development of human cell-based models with increased physiological relevance, over monolayer cultures. Here, we demonstrate the establishment of neuronal and astrocytic metabolic signatures and shuttles in a human 3D neural cell model, namely the glutamine-glutamate-GABA shuttle. This was indicated by labeling of neuronal GABA following incubation with the glia-specific substrate [2-13C]acetate, which decreased by methionine sulfoximine-induced inhibition of the glial enzyme glutamine synthetase. Cell metabolic specialization was further demonstrated by higher pyruvate carboxylase-derived labeling in glutamine than in glutamate, indicating its activity in astrocytes and not in neurons. Exposure to the neurotoxin acrylamide resulted in intracellular accumulation of glutamate and decreased GABA synthesis. These results suggest an acrylamide-induced impairment of neuronal synaptic vesicle trafficking and imbalanced glutamine-glutamate-GABA cycle, due to loss of cell-cell contacts at synaptic sites. This work demonstrates, for the first time to our knowledge, that neural differentiation of human cells in a 3D setting recapitulates neuronal-astrocytic metabolic interactions, highlighting the relevance of these models for toxicology and better understanding the crosstalk between human neural cells. PMID:27619889

  18. How Spatial Abilities and Dynamic Visualizations Interplay When Learning Functional Anatomy with 3D Anatomical Models

    ERIC Educational Resources Information Center

    Berney, Sandra; Bétrancourt, Mireille; Molinari, Gaëlle; Hoyek, Nady

    2015-01-01

    The emergence of dynamic visualizations of three-dimensional (3D) models in anatomy curricula may be an adequate solution for spatial difficulties encountered with traditional static learning, as they provide direct visualization of change throughout the viewpoints. However, little research has explored the interplay between learning material…

  19. 3D Dewetting for Crystal Patterning: Toward Regular Single-Crystalline Belt Arrays and Their Functionality.

    PubMed

    Wu, Yuchen; Feng, Jiangang; Su, Bin; Jiang, Lei

    2016-03-16

    Arrays of unidirectional dewetting behaviors can be generated by using 3D-wettability-difference micropillars, yielding highly ordered organic single-crystalline belt arrays. These patterned organic belts show an improved mobility record and can be used as flexible pressure sensors with high sensitivity.

  20. Functional response of osteoblasts in functionally gradient titanium alloy mesh arrays processed by 3D additive manufacturing.

    PubMed

    Nune, K C; Kumar, A; Misra, R D K; Li, S J; Hao, Y L; Yang, R

    2017-02-01

    We elucidate here the osteoblasts functions and cellular activity in 3D printed interconnected porous architecture of functionally gradient Ti-6Al-4V alloy mesh structures in terms of cell proliferation and growth, distribution of cell nuclei, synthesis of proteins (actin, vinculin, and fibronectin), and calcium deposition. Cell culture studies with pre-osteoblasts indicated that the interconnected porous architecture of functionally gradient mesh arrays was conducive to osteoblast functions. However, there were statistically significant differences in the cellular response depending on the pore size in the functionally gradient structure. The interconnected porous architecture contributed to the distribution of cells from the large pore size (G1) to the small pore size (G3), with consequent synthesis of extracellular matrix and calcium precipitation. The gradient mesh structure significantly impacted cell adhesion and influenced the proliferation stage, such that there was high distribution of cells on struts of the gradient mesh structure. Actin and vinculin showed a significant difference in normalized expression level of protein per cell, which was absent in the case of fibronectin. Osteoblasts present on mesh struts formed a confluent sheet, bridging the pores through numerous cytoplasmic extensions. The gradient mesh structure fabricated by electron beam melting was explored to obtain fundamental insights on cellular activity with respect to osteoblast functions.

  1. Reproducibly creating hierarchical 3D carbon to study the effect of Si surface functionalization on the oxygen reduction reaction

    NASA Astrophysics Data System (ADS)

    Zeng, Yuze; Flores, Jose F.; Shao, Yu-Cheng; Guo, Jinghua; Chuang, Yi-De; Lu, Jennifer Q.

    2016-06-01

    We report a new method to reproducibly fabricate functional 3D carbon structures directly on a current collector, e.g. stainless steel. The 3D carbon platform is formed by direct growth of upright arrays of carbon nanofiber bundles on a roughened surface of stainless steel via the seed-assisted approach. Each bundle consists of about 30 individual carbon nanofibers with a diameter of 18 nm on average. We have found that this new platform offers adequate structural integrity. As a result, no reduction of the surface area during downstream chemical functionalization was observed. With a fixed and reproducible 3D structure, the effect of the chemistry of the grafted species on the oxygen reduction reaction has been systematically investigated. This investigation reveals for the first time that non-conductive Si with an appropriate electronic structure distorts the carbon electronic structure and consequently enhances ORR electrocatalysis. The strong interface provides excellent electron connectivity according to electrochemical analysis. This highly reproducible and stable 3D platform can serve as a stepping-stone for the investigation of the effect of carbon surface functionalization on electrochemical reactions in general.We report a new method to reproducibly fabricate functional 3D carbon structures directly on a current collector, e.g. stainless steel. The 3D carbon platform is formed by direct growth of upright arrays of carbon nanofiber bundles on a roughened surface of stainless steel via the seed-assisted approach. Each bundle consists of about 30 individual carbon nanofibers with a diameter of 18 nm on average. We have found that this new platform offers adequate structural integrity. As a result, no reduction of the surface area during downstream chemical functionalization was observed. With a fixed and reproducible 3D structure, the effect of the chemistry of the grafted species on the oxygen reduction reaction has been systematically investigated. This

  2. The stationary Navier-Stokes equations in 3D exterior domains. An approach in anisotropically weighted L spaces

    NASA Astrophysics Data System (ADS)

    Razafison, Ulrich

    We consider the three-dimensional exterior problem for stationary Navier-Stokes equations. We prove, under assumptions of smallness of the data, existence and uniqueness of solutions. By setting the problem in weighted spaces where the weights reflect the anisotropic decay properties of the fundamental solution of Oseen, we show the better decay of the solutions outside the wake region. Moreover, the solutions we obtained have a finite Dirichlet integral and under additional assumptions on the weights they are also PR-solutions in the sense of Finn [R. Finn, On the exterior stationary problem for the Navier-Stokes equations, and associated perturbation problems, Arch. Ration. Mech. Anal. 19 (1965) 363-406]. The study relies on an L-theory for 1

  3. Application of contrast-enhanced T1-weighted MRI-based 3D reconstruction of the dural tail sign in meningioma resection.

    PubMed

    You, Binsheng; Cheng, Yanhao; Zhang, Jian; Song, Qimin; Dai, Chao; Heng, Xueyuan; Fei, Chang

    2016-07-01

    OBJECT The goal of this study was to investigate the significance of contrast-enhanced T1-weighted (T1W) MRI-based 3D reconstruction of dural tail sign (DTS) in meningioma resection. METHODS Between May 2013 and August 2014, 18 cases of convexity and parasagittal meningiomas showing DTS on contrast-enhanced T1W MRI were selected. Contrast-enhanced T1W MRI-based 3D reconstruction of DTS was conducted before surgical treatment. The vertical and anteroposterior diameters of DTS on the contrast-enhanced T1W MR images and 3D reconstruction images were measured and compared. Surgical incisions were designed by referring to the 3D reconstruction and MR images, and then the efficiency of the 2 methods was evaluated with assistance of neuronavigation. RESULTS Three-dimensional reconstruction of DTS can reveal its overall picture. In most cases, the DTS around the tumor is uneven, whereas the DTS around the dural vessels presents longer extensions. There was no significant difference (p > 0.05) between the vertical and anteroposterior diameters of DTS measured on the contrast-enhanced T1W MR and 3D reconstruction images. The 3D images of DTS were more intuitive, and the overall picture of DTS could be revealed in 1 image, which made it easier to design the incision than by using the MR images. Meanwhile, assessment showed that the incisions designed using 3D images were more accurate than those designed using MR images (ridit analysis by SAS, F = 7.95; p = 0.008). Pathological examination showed that 34 dural specimens (except 2 specimens from 1 tumor) displayed tumor invasion. The distance of tumor cell invasion was 1.0-21.6 mm (5.4 ± 4.41 mm [mean ± SD]). Tumor cell invasion was not observed at the dural resection margin in all 36 specimens. CONCLUSIONS Contrast-enhanced T1W MRI-based 3D reconstruction can intuitively and accurately reveal the size and shape of DTS, and thus provides guidance for designing meningioma incisions.

  4. Assembly of one dimensional inorganic nanostructures into functional 2D and 3D architectures. Synthesis, arrangement and functionality.

    PubMed

    Joshi, Ravi K; Schneider, Jörg J

    2012-08-07

    This review will focus on the synthesis, arrangement, structural assembly, for current and future applications, of 1D nanomaterials (tubes, wires, rods) in 2D and 3D ordered arrangements. The ability to synthesize and arrange one dimensional nanomaterials into ordered 2D or 3D micro or macro sized structures is of utmost importance in developing new devices and applications of these materials. Micro and macro sized architectures based on such 1D nanomaterials (e.g. tubes, wires, rods) provide a platform to integrate nanostructures at a larger and thus manageable scale into high performance electronic devices like field effect transistors, as chemo- and biosensors, catalysts, or in energy material applications. Carbon based, metal oxide and metal based 1D arranged materials as well as hybrid or composite 1D materials of the latter provide a broad materials platform, offering a perspective for new entries into fascinating structures and future applications of such assembled architectures. These architectures allow bridging the gap between 1D nanostructures and the micro and macro world and are the basis for an assembly of 1D materials into higher hierarchy domains. This critical review is intended to provide an interesting starting point to view the current state of the art and show perspectives for future developments in this field. The emphasis is on selected nanomaterials and the possibilities for building three dimensional arrays starting from one dimensional building blocks. Carbon nanotubes, metal oxide nanotubes and nanowires (e.g. ZnO, TiO(2), V(2)O(5), Cu(2)O, NiO, Fe(2)O(3)), silicon and germanium nanowires, and group III-V or II-VI based 1D semiconductor nanostructures like GaS and GaN, pure metals as well as 1D hybrid materials and their higher organized architectures (foremost in 3D) will be focussed. These materials have been the most intensively studied within the last 5-10 years with respect to nano-micro integration aspects and their functional and

  5. Phosphonate-functionalized large pore 3-D cubic mesoporous (KIT-6) hybrid as highly efficient actinide extracting agent.

    PubMed

    Lebed, Pablo J; de Souza, Kellen; Bilodeau, François; Larivière, Dominic; Kleitz, Freddy

    2011-11-07

    A new type of radionuclide extraction material is reported based on phosphonate functionalities covalently anchored on the mesopore surface of 3-D cubic mesoporous silica (KIT-6). The easily prepared nanoporous hybrid shows largely superior performance in selective sorption of uranium and thorium as compared to the U/TEVA commercial resin and 2-D hexagonal SBA-15 equivalent.

  6. Printing Functional 3D Microdevices by Laser-Induced Forward Transfer.

    PubMed

    Luo, Jun; Pohl, Ralph; Qi, Lehua; Römer, Gert-Willem; Sun, Chao; Lohse, Detlef; Visser, Claas Willem

    2017-03-01

    Slender, out-of-plane metal microdevices are made in a new spatial domain, by using laser-induced forward transfer (LIFT) of metals. Here, a thermocouple with a thickness of 10 µm and a height of 250 µm, consisting of platinum and gold pillars is demonstrated. Multimaterial LIFT enables manufacturing in the micrometer to millimeter range, i.e., between lithography and other 3D printing technologies.

  7. A facile one-step process for 3D N-doped noncovalent functionalization PS/rGO composites

    NASA Astrophysics Data System (ADS)

    Huang, Weiqi; Wang, Hua; Su, Zheng; Tian, Konghu; Ye, Xianzhu; Bao, Chao; Guo, Yulan; He, Jing; Tian, Xingyou

    2017-03-01

    This work reports a simple, versatile and facile one-step process to prepare the three-dimensional (3D) N-doped noncovalent functionalization polystyrene/reduced graphene oxide (PS/rGO) composites. In this, N, N-dimethylformamide (DMF) acts as the solvent, reducing agent, and more importantly, the N-doping agent. Various measurements have been carried out to characterize the structure and morphology of PS/rGO composites, in particular for the excellent electrical conductivity of PS/rGO composites compared with virgin PS, which was attributed to the 3D pores structure and the N-doping. With regards to the unique properties of graphene, the 3D framework structure and the N-doping, this composite material has great potential properties such as electro-magnetic interference shielding effectiveness (EMI) to be explored.

  8. 3-D inelastic analysis methods for hot section components. Volume 2: Advanced special functions models

    NASA Technical Reports Server (NTRS)

    Wilson, R. B.; Banerjee, P. K.

    1987-01-01

    This Annual Status Report presents the results of work performed during the third year of the 3-D Inelastic Analysis Methods for Hot Sections Components program (NASA Contract NAS3-23697). The objective of the program is to produce a series of computer codes that permit more accurate and efficient three-dimensional analyses of selected hot section components, i.e., combustor liners, turbine blades, and turbine vanes. The computer codes embody a progression of mathematical models and are streamlined to take advantage of geometrical features, loading conditions, and forms of material response that distinguish each group of selected components.

  9. Validation of a Node-Centered Wall Function Model for the Unstructured Flow Code FUN3D

    NASA Technical Reports Server (NTRS)

    Carlson, Jan-Renee; Vasta, Veer N.; White, Jeffery

    2015-01-01

    In this paper, the implementation of two wall function models in the Reynolds averaged Navier-Stokes (RANS) computational uid dynamics (CFD) code FUN3D is described. FUN3D is a node centered method for solving the three-dimensional Navier-Stokes equations on unstructured computational grids. The first wall function model, based on the work of Knopp et al., is used in conjunction with the one-equation turbulence model of Spalart-Allmaras. The second wall function model, also based on the work of Knopp, is used in conjunction with the two-equation k-! turbulence model of Menter. The wall function models compute the wall momentum and energy flux, which are used to weakly enforce the wall velocity and pressure flux boundary conditions in the mean flow momentum and energy equations. These wall conditions are implemented in an implicit form where the contribution of the wall function model to the Jacobian are also included. The boundary conditions of the turbulence transport equations are enforced explicitly (strongly) on all solid boundaries. The use of the wall function models is demonstrated on four test cases: a at plate boundary layer, a subsonic di user, a 2D airfoil, and a 3D semi-span wing. Where possible, different near-wall viscous spacing tactics are examined. Iterative residual convergence was obtained in most cases. Solution results are compared with theoretical and experimental data for several variations of grid spacing. In general, very good comparisons with data were achieved.

  10. GEM printer: 3D gel printer for free shaping of functional gel engineering materials

    NASA Astrophysics Data System (ADS)

    Furukawa, Hidemitsu; Muroi, Hisato; Yamamoto, Kouki; Serizawa, Ryo; Gong, Jin

    2013-04-01

    In the past decade, several high-strength gels have been developed. These gels are expected to use as a kind of new engineering materials in the fields of industry and medical as substitutes to polyester fibers, which are materials of artificial blood vessels. The gels have both low surface friction and well permeability due to a large amount of water absorbed in the gels, which are superiority of the gels compering to the polyester fibers. It is, however, difficult for gels to be forked structure or cavity structure by using cutting or mold. Consequently, it is necessary to develop the additive manufacturing device to synthesize and mode freely gels at the same time. Here we try to develop an optical 3D gel printer that enables gels to be shaped precisely and freely. For the free forming of high-strength gels, the 1st gels are ground to particles and mixed with 2nd pregel solution, and the mixed solution is gelled by the irradiation of UV laser beam through an optical fiber. The use of the optical fiber makes one-point UV irradiation possible. Since the optical fiber is controlled by 3D-CAD, the precise and free molding in XYZ directions is easily realized. We successfully synthesized tough gels using the gel printer.

  11. Diagnostic Utility of Contrast-enhanced 3D T1-weighted Imaging in Acute Cerebral Infarction Associated with Graves Disease.

    PubMed

    Gon, Yasufumi; Sakaguchi, Manabu; Oyama, Naoki; Mochizuki, Hideki

    2017-02-01

    Graves disease is rarely complicated with cerebrovascular steno-occlusive diseases. Previous studies have suggested several hypotheses for this occurrence, including excess thyroid hormone, which stimulates the sympathetic nervous system, which in turn causes an abnormal hemodynamic response with consequent atherosclerotic changes, and antithyroid antibodies cause local vascular inflammation in patients with Graves disease. However, radiological findings of vasculitis in patients with Graves disease and cerebral infarction remain less known. We report the case of a 30-year-old Japanese woman with acute cerebral infarction due to vasculitis associated with Graves disease. She was admitted to our hospital with a 4-day history of intermittent transient dysarthria and limb shaking of the left leg when standing. Three weeks before admission, she went to a local hospital because of general malaise and was diagnosed with Graves disease. Neurological examination revealed paralytic dysarthria, left central facial nerve palsy, and left hemiparesis (manual muscle testing, 4 of 5). Blood examinations showed hyperthyroidism (thyroid-stimulating hormone ≤.010 µU/mL; free T3 ≥25.0 pg/mL; free T4 ≥8.0 ng/dL) and elevation of antithyroid antibody levels (thyroid peroxidase antibody, 87 IU/mL). The vessel wall of the right internal carotid artery was markedly enhanced on contrast-enhanced three-dimensional T1-weighted magnetic resonance imaging, suggesting vasculitis. Magnetic resonance angiography revealed right internal carotid artery occlusion after the branching ophthalmic artery. Arterial stenosis due to vasculitis was considered the cause of hemodynamic ischemic stroke. Vessel wall imaging such as high-resolution contrast-enhanced T1-weighted imaging seems useful for assessing the underlying mechanism of stroke in patients with Graves disease.

  12. Massively parallel patterning of complex 2D and 3D functional polymer brushes by polymer pen lithography.

    PubMed

    Xie, Zhuang; Chen, Chaojian; Zhou, Xuechang; Gao, Tingting; Liu, Danqing; Miao, Qian; Zheng, Zijian

    2014-08-13

    We report the first demonstration of centimeter-area serial patterning of complex 2D and 3D functional polymer brushes by high-throughput polymer pen lithography. Arbitrary 2D and 3D structures of poly(glycidyl methacrylate) (PGMA) brushes are fabricated over areas as large as 2 cm × 1 cm, with a remarkable throughput being 3 orders of magnitudes higher than the state-of-the-arts. Patterned PGMA brushes are further employed as resist for fabricating Au micro/nanostructures and hard molds for the subsequent replica molding of soft stamps. On the other hand, these 2D and 3D PGMA brushes are also utilized as robust and versatile platforms for the immobilization of bioactive molecules to form 2D and 3D patterned DNA oligonucleotide and protein chips. Therefore, this low-cost, yet high-throughput "bench-top" serial fabrication method can be readily applied to a wide range of fields including micro/nanofabrication, optics and electronics, smart surfaces, and biorelated studies.

  13. Preoperative 3D FSE T1-Weighted MR Plaque Imaging for Severely Stenotic Cervical ICA: Accuracy of Predicting Emboli during Carotid Endarterectomy.

    PubMed

    Ogasawara, Yasushi; Sato, Yuiko; Narumi, Shinsuke; Sasaki, Makoto; Fujiwara, Shunrou; Kobayashi, Masakazu; Yoshida, Kenji; Terayama, Yasuo; Ogasawara, Kuniaki

    2016-10-27

    The aim of the present study was to determine whether preoperative three-dimensional (3D) fast spin-echo (FSE) T1-weighted magnetic resonance (MR) plaque imaging for severely stenotic cervical carotid arteries could accurately predict the development of artery-to-artery emboli during exposure of the carotid arteries in carotid endarterectomy (CEA). Seventy-five patients underwent preoperative MR plaque imaging and CEA under transcranial Doppler ultrasonography of the ipsilateral middle cerebral artery. On reformatted axial MR image slices showing the maximum plaque occupation rate (POR) and maximum plaque intensity for each patient, the contrast ratio (CR) was calculated by dividing the internal carotid artery plaque signal intensity by the sternocleidomastoid muscle signal intensity. For all patients, the area under the receiver operating characteristic curve (AUC)-used to discriminate between the presence and absence of microembolic signals-was significantly greater for the CR on the axial image with maximum plaque intensity (CRmax intensity) (0.941) than for that with the maximum POR (0.885) (p < 0.05). For 32 patients in whom both the maximum POR and the maximum plaque density were identified, the AUCs for the CR were 1.000. Preoperative 3D FSE T1-weighted MR plaque imaging accurately predicts the development of artery-to-artery emboli during exposure of the carotid arteries in CEA.

  14. Preoperative 3D FSE T1-Weighted MR Plaque Imaging for Severely Stenotic Cervical ICA: Accuracy of Predicting Emboli during Carotid Endarterectomy

    PubMed Central

    Ogasawara, Yasushi; Sato, Yuiko; Narumi, Shinsuke; Sasaki, Makoto; Fujiwara, Shunrou; Kobayashi, Masakazu; Yoshida, Kenji; Terayama, Yasuo; Ogasawara, Kuniaki

    2016-01-01

    The aim of the present study was to determine whether preoperative three-dimensional (3D) fast spin-echo (FSE) T1-weighted magnetic resonance (MR) plaque imaging for severely stenotic cervical carotid arteries could accurately predict the development of artery-to-artery emboli during exposure of the carotid arteries in carotid endarterectomy (CEA). Seventy-five patients underwent preoperative MR plaque imaging and CEA under transcranial Doppler ultrasonography of the ipsilateral middle cerebral artery. On reformatted axial MR image slices showing the maximum plaque occupation rate (POR) and maximum plaque intensity for each patient, the contrast ratio (CR) was calculated by dividing the internal carotid artery plaque signal intensity by the sternocleidomastoid muscle signal intensity. For all patients, the area under the receiver operating characteristic curve (AUC)—used to discriminate between the presence and absence of microembolic signals—was significantly greater for the CR on the axial image with maximum plaque intensity (CRmax intensity) (0.941) than for that with the maximum POR (0.885) (p < 0.05). For 32 patients in whom both the maximum POR and the maximum plaque density were identified, the AUCs for the CR were 1.000. Preoperative 3D FSE T1-weighted MR plaque imaging accurately predicts the development of artery-to-artery emboli during exposure of the carotid arteries in CEA. PMID:27801780

  15. Improving compact gravity inversion using new weighting functions

    NASA Astrophysics Data System (ADS)

    Ghalehnoee, Mohammad Hossein; Ansari, Abdolhamid; Ghorbani, Ahmad

    2017-01-01

    We have developed a method to estimate the geometry, location and densities of anomalies coming from 2-D gravity data based on compact gravity inversion technique. Compact gravity inversion is simple, fast and user friendly but severely depends on the number of model parameters, that is, by increasing the model parameters, the anomalies tend to concentrate near the surface. To overcome this ambiguity new weighting functions based on density contrast, depth, and compactness models have been introduced. Variable compactness factors have been defined here to get either a sharp or a smooth model based on the depth of the source or existence of prior information. Depth weighting derived from one station of gravity data whereas the effect of gravity data is 2-D and 3-D. To compensate this limitation an innovating weighting function namely kernel function has been introduced which multiplies with weight and compactness matrixes to yield a general model weighting function. The method is tested using three different sets of synthetic examples: a body at various depths (20, 40, 80 and 140 m), two bodies at the same depth but various distances to estimate lateral resolution and three bodies with negative and positive density contrast in different depths. The method is also applied to three real gravity data of Woodlawn massive sulphide body, sulphides mineralization of British Colombia and iron ore body of Missouri. The method produces solutions consistent with the known geologic attributes of the gravity sources, illustrating its potential practicality.

  16. Differentiation of liver progenitor cell line to functional organotypic cultures in 3D nanofibrillar cellulose and hyaluronan-gelatin hydrogels.

    PubMed

    Malinen, Melina M; Kanninen, Liisa K; Corlu, Anne; Isoniemi, Helena M; Lou, Yan-Ru; Yliperttula, Marjo L; Urtti, Arto O

    2014-06-01

    Physiologically relevant hepatic cell culture models must be based on three-dimensional (3D) culture of human cells. However, liver cells are generally cultured in two-dimensional (2D) format that deviates from the normal in vivo morphology. We generated 3D culture environment for HepaRG liver progenitor cells using wood-derived nanofibrillar cellulose (NFC) and hyaluronan-gelatin (HG) hydrogels. Culture of undifferentiated HepaRG cells in NFC and HG hydrogels induced formation of 3D multicellular spheroids with apicobasal polarity and functional bile canaliculi-like structures, structural hallmarks of the liver tissue. Furthermore, hepatobiliary drug transporters, MRP2 and MDR1, were localized on the canalicular membranes of the spheroids and vectorial transport of fluorescent probes towards the biliary compartment was demonstrated. Cell culture in 3D hydrogel supported the mRNA expression of hepatocyte markers (albumin and CYP3A4), and metabolic activity of CYP3A4 in the HepaRG cell cultures. On the contrary, the 3D hydrogel cultures with pre-differentiated HepaRG cells showed decreasing expression of albumin and CYP3A4 transcripts as well as CYP3A4 activity. It is concluded that NFC and HG hydrogels expedite the hepatic differentiation of HepaRG liver progenitor cells better than the standard 2D culture environment. This was shown as improved cell morphology, expression and localization of hepatic markers, metabolic activity and vectorial transport. The NFC and HG hydrogels are promising materials for hepatic cell culture and tissue engineering.

  17. Hydrogel with chains functionalized with carboxyl groups as universal 3D platform in DNA biosensors.

    PubMed

    Kowalczyk, Agata; Fau, Michal; Karbarz, Marcin; Donten, Mikolaj; Stojek, Zbigniew; Nowicka, Anna M

    2014-04-15

    Application of hydrogel based on N-isopropylacrylamide with carboxyl groups grafted to the chains enabled the immobilization of DNA at an extent exceeding that for flat surfaces by at least one order of magnitude. The probe DNA strands in the 3D platform were fully available for the hybridization process. The examination of the gels containing different amounts of grafted carboxyl groups (1-10%) was done using quartz crystal microbalance, electrochemical impedance spectroscopy, chronoamperometry and ionic coupled plasma with laser ablation. The optimal carboxyl group content was determined to be 5%. A very good agreement of the data obtained with independent techniques on content of DNA in the gel was obtained. In comparison to the other methods of immobilization of DNA the new platform enabled complete removal of DNA after the measurements and analysis and, therefore, could be used many times. After a 10-fold exchange of the DNA-sensing layer the efficiency of hybridization and analytical signal did not change by more than 5%. The sensor response increased linearly with logarithm of concentration of target DNA in the range 1×10(-13)-1×10(-6) M. The obtained detection limit was circa 8×10(-13) M of target DNA in the sample which is a substantial improvement over the planar sensing layers.

  18. 3D printed glass: surface finish and bulk properties as a function of the printing process

    NASA Astrophysics Data System (ADS)

    Klein, Susanne; Avery, Michael P.; Richardson, Robert; Bartlett, Paul; Frei, Regina; Simske, Steven

    2015-03-01

    It is impossible to print glass directly from a melt, layer by layer. Glass is not only very sensitive to temperature gradients between different layers but also to the cooling process. To achieve a glass state the melt, has to be cooled rapidly to avoid crystallization of the material and then annealed to remove cooling induced stress. In 3D-printing of glass the objects are shaped at room temperature and then fired. The material properties of the final objects are crucially dependent on the frit size of the glass powder used during shaping, the chemical formula of the binder and the firing procedure. For frit sizes below 250 μm, we seem to find a constant volume of pores of less than 5%. Decreasing frit size leads to an increase in the number of pores which then leads to an increase of opacity. The two different binders, 2- hydroxyethyl cellulose and carboxymethylcellulose sodium salt, generate very different porosities. The porosity of samples with 2-hydroxyethyl cellulose is similar to frit-only samples, whereas carboxymethylcellulose sodium salt creates a glass foam. The surface finish is determined by the material the glass comes into contact with during firing.

  19. Visualization of Potential Energy Function Using an Isoenergy Approach and 3D Prototyping

    ERIC Educational Resources Information Center

    Teplukhin, Alexander; Babikov, Dmitri

    2015-01-01

    In our three-dimensional world, one can plot, see, and comprehend a function of two variables at most, V(x,y). One cannot plot a function of three or more variables. For this reason, visualization of the potential energy function in its full dimensionality is impossible even for the smallest polyatomic molecules, such as triatomics. This creates…

  20. Synergistic Behavior of Tubes, Junctions, and Sheets Imparts Mechano-Mutable Functionality in 3D Porous Boron Nitride Nanostructures.

    PubMed

    Sakhavand, Navid; Shahsavari, Rouzbeh

    2014-10-02

    One-dimensional (1D) boron nitride nanotube (BNNT) and 2D hexagonal BN (h-BN) are attractive for demonstrating fundamental physics and promising applications in nano-/microscale devices. However, there is a high anisotropy associated with these BN allotropes as their excellent properties are either along the tube axis or in-plane directions, posing an obstacle in their widespread use in technological and industrial applications. Herein, we report a series of 3D BN prototypes, namely, pillared boron nitride (PBN), by fusing single-wall BNNT and monolayer h-BN aimed at filling this gap. We use density functional theory and molecular dynamics simulations to probe the diverse mechano-mutable properties of PBN prototypes. Our results demonstrate that the synergistic effect of the tubes, junctions, and sheets imparts cooperative deformation mechanisms, which overcome the intrinsic limitations of the PBN constituents and provide a number of superior characteristics including 3D balance of strength and toughness, emergence of negative Poisson's ratio, and elimination of strain softening along the armchair orientation. These features, combined with the ultrahigh surface area and lightweight structure, render PBN as a 3D multifunctional template for applications in graphene-based nanoelectronics, optoelectronics, gas storage, and functional composites with fascinating in-plane and out-of-plane tailorable properties.

  1. Synergistic Behavior of Tubes, Junctions, and Sheets Imparts Mechano-Mutable Functionality in 3D Porous Boron Nitride Nanostructures

    PubMed Central

    2015-01-01

    One-dimensional (1D) boron nitride nanotube (BNNT) and 2D hexagonal BN (h-BN) are attractive for demonstrating fundamental physics and promising applications in nano-/microscale devices. However, there is a high anisotropy associated with these BN allotropes as their excellent properties are either along the tube axis or in-plane directions, posing an obstacle in their widespread use in technological and industrial applications. Herein, we report a series of 3D BN prototypes, namely, pillared boron nitride (PBN), by fusing single-wall BNNT and monolayer h-BN aimed at filling this gap. We use density functional theory and molecular dynamics simulations to probe the diverse mechano-mutable properties of PBN prototypes. Our results demonstrate that the synergistic effect of the tubes, junctions, and sheets imparts cooperative deformation mechanisms, which overcome the intrinsic limitations of the PBN constituents and provide a number of superior characteristics including 3D balance of strength and toughness, emergence of negative Poisson’s ratio, and elimination of strain softening along the armchair orientation. These features, combined with the ultrahigh surface area and lightweight structure, render PBN as a 3D multifunctional template for applications in graphene-based nanoelectronics, optoelectronics, gas storage, and functional composites with fascinating in-plane and out-of-plane tailorable properties. PMID:25289114

  2. Corrosion-Mediated Self-Assembly (CMSA): Direct Writing Towards Sculpturing of 3D Tunable Functional Nanostructures.

    PubMed

    Wang, Jing; Ho, Ghim Wei

    2015-12-21

    Inexpensive and readily available metal foils have been extracted and sculptured into nanocomposites without the expense of applied energy. The unwanted corrosion phenomenon has been contrarily utilized to realize desirable 3D nanostructures through a corrosion-mediated self-assembly (CMSA) method, which is unattainable by conventional 2D patterning routes. By virtue of electrochemical dissolution/re-deposition initiated by brass corrosion, ionic derivatives (Zn(2+) and Cu(2+) ) are continuously supplied and seized by etchant ions (PO4 (3-) ) to self-assemble into well-defined nanocomposites. Beyond 3D geometry patterning, CMSA enables arbitrarily tailoring of structures and chemical compositions with in situ multiphase amalgamation of hybrid materials, which improves homogeneity and thus mitigates phase separation issues. Importantly, the CMSA technique is demonstrated on transition metals for functional photocatalytic applications.

  3. 3D imaging of the Corinth rift from a new passive seismic tomography and receiver function analysis

    NASA Astrophysics Data System (ADS)

    Godano, Maxime; Gesret, Alexandrine; Noble, Mark; Lyon-Caen, Hélène; Gautier, Stéphanie; Deschamps, Anne

    2016-04-01

    The Corinth Rift is the most seismically active zone in Europe. The area is characterized by very localized NS extension at a rate of ~ 1.5cm/year, the occurrence of frequent and intensive microseismic crises and occasional moderate to large earthquakes like in 1995 (Mw=6.1). Since the year 2000, the Corinth Rift Laboratory (CRL, http://crlab.eu) consisting in a multidisciplinary natural observatory, aims at understanding the mechanics of faulting and earthquake nucleation in the Rift. Recent studies have improved our view about fault geometry and mechanics within CRL, but there is still a critical need for a better knowledge of the structure at depth both for the accuracy of earthquake locations and for mechanical interpretation of the seismicity. In this project, we aim to analyze the complete seismological database (13 years of recordings) of CRL by using recently developed methodologies of structural imaging, in order to determine at the same time and with high resolution, the local 3D structure and the earthquake locations. We perform an iterative joint determination of 3D velocity model and earthquake coordinates. In a first step, P and S velocity models are determined using first arrival time tomography method proposed by Taillandier et al. (2009). It consists in the minimization of the cost function between observed and theoretical arrival times which is achieved by the steepest descent method (e.g. Tarantola 1987). This latter requires computing the gradient of the cost function by using the adjoint state method (Chavent 1974). In a second step, earthquakes are located in the new velocity model with a non-linear inversion method based on a Bayesian formulation (Gesret et al. 2015). Step 1 and 2 are repeated until the cost function no longer decreases. We present preliminary results consisting in: (1) the adjustement of a 1D velocity model that is used as initial model of the 3D tomography and (2) a first attempt of the joint determination of 3D velocity

  4. 2.5D real waveform and real noise simulation of receiver functions in 3D models

    NASA Astrophysics Data System (ADS)

    Schiffer, Christian; Jacobsen, Bo; Balling, Niels

    2014-05-01

    There are several reasons why a real-data receiver function differs from the theoretical receiver function in a 1D model representing the stratification under the seismometer. Main reasons are ambient noise, spectral deficiencies in the impinging P-waveform, and wavefield propagation in laterally varying velocity variations. We present a rapid "2.5D" modelling approach which takes these aspects into account, so that a given 3D velocity model of the crust and uppermost mantle can be tested more realistically against observed recordings from seismometer arrays. Each recorded event at each seismometer is simulated individually through the following steps: A 2D section is extracted from the 3D model along the direction towards the hypocentre. A properly slanted plane or curved impulsive wavefront is propagated through this 2D section, resulting in noise free and spectrally complete synthetic seismometer data. The real vertical component signal is taken as a proxy of the real impingent wavefield, so by convolution and subsequent addition of real ambient noise recorded just before the P-arrival we get synthetic vertical and horizontal component data which very closely match the spectral signal content and signal to noise ratio of this specific recording. When these realistic synthetic data undergo exactly the same receiver function estimation and subsequent graphical display we get a much more realistic image to compare to the real-data receiver functions. We applied this approach to the Central Fjord area in East Greenland (Schiffer et al., 2013), where a 3D velocity model of crust and uppermost mantle was adjusted to receiver functions from 2 years of seismometer recordings and wide angle crustal profiles (Schlindwein and Jokat, 1999; Voss and Jokat, 2007). Computationally this substitutes tens or hundreds of heavy 3D computations with hundreds or thousands of single-core 2D computations which parallelize very efficiently on common multicore systems. In perspective

  5. 3D-partition functions on the sphere: exact evaluation and mirror symmetry

    NASA Astrophysics Data System (ADS)

    Benvenuti, Sergio; Pasquetti, Sara

    2012-05-01

    We study {N} = {4} quiver theories on the three-sphere. We compute partition functions using the localisation method by Kapustin et al. solving exactly the matrix integrals at finite N, as functions of mass and Fayet-Iliopoulos parameters. We find a simple explicit formula for the partition function of the quiver tail T(SU( N)). This formula opens the way for the analysis of star-shaped quivers and their mirrors (that are the Gaiotto-type theories arising from M5 branes on punctured Riemann surfaces). We provide non-perturbative checks of mirror symmetry for infinite classes of theories and find the partition functions of the T N theory, the building block of generalised quiver theories.

  6. A 3D sphere culture system containing functional polymers for large-scale human pluripotent stem cell production.

    PubMed

    Otsuji, Tomomi G; Bin, Jiang; Yoshimura, Azumi; Tomura, Misayo; Tateyama, Daiki; Minami, Itsunari; Yoshikawa, Yoshihiro; Aiba, Kazuhiro; Heuser, John E; Nishino, Taito; Hasegawa, Kouichi; Nakatsuji, Norio

    2014-05-06

    Utilizing human pluripotent stem cells (hPSCs) in cell-based therapy and drug discovery requires large-scale cell production. However, scaling up conventional adherent cultures presents challenges of maintaining a uniform high quality at low cost. In this regard, suspension cultures are a viable alternative, because they are scalable and do not require adhesion surfaces. 3D culture systems such as bioreactors can be exploited for large-scale production. However, the limitations of current suspension culture methods include spontaneous fusion between cell aggregates and suboptimal passaging methods by dissociation and reaggregation. 3D culture systems that dynamically stir carrier beads or cell aggregates should be refined to reduce shearing forces that damage hPSCs. Here, we report a simple 3D sphere culture system that incorporates mechanical passaging and functional polymers. This setup resolves major problems associated with suspension culture methods and dynamic stirring systems and may be optimal for applications involving large-scale hPSC production.

  7. Rollable Microfluidic Systems with Microscale Bending Radius and Tuning of Device Function with Reconfigurable 3D Channel Geometry.

    PubMed

    Kim, Jihye; You, Jae Bem; Nam, Sung Min; Seo, Sumin; Im, Sung Gap; Lee, Wonhee

    2017-03-29

    Flexible microfluidic system is an essential component of wearable biosensors to handle body fluids. A parylene-based, thin-film microfluidic system is developed to achieve flexible microfluidics with microscale bending radius. A new molding and bonding technique is developed for parylene microchannel fabrication. Bonding with nanoadhesive layers deposited by initiated chemical vapor deposition (iCVD) enables the construction of microfluidic channels with short fabrication time and high bonding strength. The high mechanical strength of parylene allows less channel deformation from the internal pressure for the thin-film parylene channel than bulk PDMS channel. At the same time, negligible channel sagging or collapse is observed during channel bending down to a few hundreds of micrometers due to stress relaxation by prestretch structure. The flexible parylene channels are also developed into a rollable microfluidic system. In a rollable microfluidics format, 2D parylene channels can be rolled around a capillary tubing working as inlets to minimize the device footprint. In addition, we show that creating reconfigurable 3D channel geometry with microscale bending radius can lead to tunable device function: tunable Dean-flow mixer is demonstrated using reconfigurable microscale 3D curved channel. Flexible parylene microfluidics with microscale bending radius is expected to provide an important breakthrough for many fields including wearable biosensors and tunable 3D microfluidics.

  8. A mesh adaptivity scheme on the Landau-de Gennes functional minimization case in 3D, and its driving efficiency

    NASA Astrophysics Data System (ADS)

    Bajc, Iztok; Hecht, Frédéric; Žumer, Slobodan

    2016-09-01

    This paper presents a 3D mesh adaptivity strategy on unstructured tetrahedral meshes by a posteriori error estimates based on metrics derived from the Hessian of a solution. The study is made on the case of a nonlinear finite element minimization scheme for the Landau-de Gennes free energy functional of nematic liquid crystals. Newton's iteration for tensor fields is employed with steepest descent method possibly stepping in. Aspects relating the driving of mesh adaptivity within the nonlinear scheme are considered. The algorithmic performance is found to depend on at least two factors: when to trigger each single mesh adaptation, and the precision of the correlated remeshing. Each factor is represented by a parameter, with its values possibly varying for every new mesh adaptation. We empirically show that the time of the overall algorithm convergence can vary considerably when different sequences of parameters are used, thus posing a question about optimality. The extensive testings and debugging done within this work on the simulation of systems of nematic colloids substantially contributed to the upgrade of an open source finite element-oriented programming language to its 3D meshing possibilities, as also to an outer 3D remeshing module.

  9. Functional activities characteristics of shoulder complex movements: Exploration with a 3-D electromagnetic measurement system.

    PubMed

    Lin, Jiu-Jenq; Hanten, William P; Olson, Sharon L; Roddey, Toni S; Soto-Quijano, David A; Lim, Hyun K; Sherwood, Arthur M

    2005-01-01

    The high prevalence of shoulder-related dysfunction has focused increased attention on functional activity assessment. This study (1) tested the reliability of three-dimensional shoulder complex movements during four functional tasks representing different levels of task difficulty, (2) characterized the four functional tasks, and (3) examined the relationships between age and shoulder movements. Twenty-five asymptomatic subjects, all veterans aged 30-82, performed the four functional tasks. Good within-session reliability was found (movement pattern: similarity index = 0.81 to 0.97, peak values: intraclass correlation coefficients = 0.88 to 0.99). The raising arm to overhead height task (hard task) placed the greatest demand on scapular motions and humeral elevation (p < 0.005). During the functional tasks, significant correlations existed between age and scapular tipping, humeral elevation, and scapular upward rotation (r = -0.62 to 0.50, p < 0.05). Correlation results indicated that elderly subjects have a greater potential for serratus anterior muscle weakness and shoulder capsule tightness.

  10. Strategies for Directing the Structure and Function of 3D Collagen Biomaterials across Length Scales

    PubMed Central

    Walters, Brandan D.; Stegemann, Jan P.

    2013-01-01

    Collagen type I is a widely used natural biomaterial that has found utility in a variety of biological and medical applications. Its well characterized structure and role as an extracellular matrix protein make it a highly relevant material for controlling cell function and mimicking tissue properties. Collagen type I is abundant in a number of tissues, and can be isolated as a purified protein. This review focuses on hydrogel biomaterials made by reconstituting collagen type I from a solubilized form, with an emphasis on in vitro studies in which collagen structure can be controlled. The hierarchical structure of collagen from the nanoscale to the macroscale is described, with an emphasis on how structure is related to function across scales. Methods of reconstituting collagen into hydrogel materials are presented, including molding of macroscopic constructs, creation of microscale modules, and electrospinning of nanoscale fibers. The modification of collagen biomaterials to achieve desired structures and functions is also addressed, with particular emphasis on mechanical control of collagen structure, creation of collagen composite materials, and crosslinking of collagenous matrices. Biomaterials scientists have made remarkable progress in rationally designing collagen-based biomaterials and in applying them to both the study of biology and for therapeutic benefit. This broad review illustrates recent examples of techniques used to control collagen structure, and to thereby direct its biological and mechanical functions. PMID:24012608

  11. High Performance 3D PET Reconstruction Using Spherical Basis Functions on a Polar Grid

    PubMed Central

    Cabello, J.; Gillam, J. E.; Rafecas, M.

    2012-01-01

    Statistical iterative methods are a widely used method of image reconstruction in emission tomography. Traditionally, the image space is modelled as a combination of cubic voxels as a matter of simplicity. After reconstruction, images are routinely filtered to reduce statistical noise at the cost of spatial resolution degradation. An alternative to produce lower noise during reconstruction is to model the image space with spherical basis functions. These basis functions overlap in space producing a significantly large number of non-zero elements in the system response matrix (SRM) to store, which additionally leads to long reconstruction times. These two problems are partly overcome by exploiting spherical symmetries, although computation time is still slower compared to non-overlapping basis functions. In this work, we have implemented the reconstruction algorithm using Graphical Processing Unit (GPU) technology for speed and a precomputed Monte-Carlo-calculated SRM for accuracy. The reconstruction time achieved using spherical basis functions on a GPU was 4.3 times faster than the Central Processing Unit (CPU) and 2.5 times faster than a CPU-multi-core parallel implementation using eight cores. Overwriting hazards are minimized by combining a random line of response ordering and constrained atomic writing. Small differences in image quality were observed between implementations. PMID:22548047

  12. Distinct Functional Roles of Cardiac Mitochondrial Subpopulations Revealed by a 3D Simulation Model

    PubMed Central

    Hatano, Asuka; Okada, Jun-ichi; Washio, Takumi; Hisada, Toshiaki; Sugiura, Seiryo

    2015-01-01

    Experimental characterization of two cardiac mitochondrial subpopulations, namely, subsarcolemmal mitochondria (SSM) and interfibrillar mitochondria (IFM), has been hampered by technical difficulties, and an alternative approach is eagerly awaited. We previously developed a three-dimensional computational cardiomyocyte model that integrates electrophysiology, metabolism, and mechanics with subcellular structure. In this study, we further developed our model to include intracellular oxygen diffusion, and determined whether mitochondrial localization or intrinsic properties cause functional variations. For this purpose, we created two models: one with equal SSM and IFM properties and one with IFM having higher activity levels. Using these two models to compare the SSM and IFM responses of [Ca2+], tricarboxylic acid cycle activity, [NADH], and mitochondrial inner membrane potential to abrupt changes in pacing frequency (0.25–2 Hz), we found that the reported functional differences between these subpopulations appear to be mostly related to local [Ca2+] heterogeneity, and variations in intrinsic properties only serve to augment these differences. We also examined the effect of hypoxia on mitochondrial function. Under normoxic conditions, intracellular oxygen is much higher throughout the cell than the half-saturation concentration for oxidative phosphorylation. However, under limited oxygen supply, oxygen is mostly exhausted in SSM, leaving the core region in an anoxic condition. Reflecting this heterogeneous oxygen environment, the inner membrane potential continues to decrease in IFM, whereas it is maintained to nearly normal levels in SSM, thereby ensuring ATP supply to this region. Our simulation results provide clues to understanding the origin of functional variations in two cardiac mitochondrial subpopulations and their differential roles in maintaining cardiomyocyte function as a whole. PMID:26039174

  13. Large-scale 3D galaxy correlation function and non-Gaussianity

    SciTech Connect

    Raccanelli, Alvise; Doré, Olivier; Bertacca, Daniele; Maartens, Roy E-mail: daniele.bertacca@gmail.com E-mail: roy.maartens@gmail.com

    2014-08-01

    We investigate the properties of the 2-point galaxy correlation function at very large scales, including all geometric and local relativistic effects --- wide-angle effects, redshift space distortions, Doppler terms and Sachs-Wolfe type terms in the gravitational potentials. The general three-dimensional correlation function has a nonzero dipole and octupole, in addition to the even multipoles of the flat-sky limit. We study how corrections due to primordial non-Gaussianity and General Relativity affect the multipolar expansion, and we show that they are of similar magnitude (when f{sub NL} is small), so that a relativistic approach is needed. Furthermore, we look at how large-scale corrections depend on the model for the growth rate in the context of modified gravity, and we discuss how a modified growth can affect the non-Gaussian signal in the multipoles.

  14. Thermal weights for semiclassical vibrational response functions

    SciTech Connect

    Moberg, Daniel R.; Alemi, Mallory; Loring, Roger F.

    2015-08-28

    Semiclassical approximations to response functions can allow the calculation of linear and nonlinear spectroscopic observables from classical dynamics. Evaluating a canonical response function requires the related tasks of determining thermal weights for initial states and computing the dynamics of these states. A class of approximations for vibrational response functions employs classical trajectories at quantized values of action variables and represents the effects of the radiation-matter interaction by discontinuous transitions. Here, we evaluate choices for a thermal weight function which are consistent with this dynamical approximation. Weight functions associated with different semiclassical approximations are compared, and two forms are constructed which yield the correct linear response function for a harmonic potential at any temperature and are also correct for anharmonic potentials in the classical mechanical limit of high temperature. Approximations to the vibrational linear response function with quantized classical trajectories and proposed thermal weight functions are assessed for ensembles of one-dimensional anharmonic oscillators. This approach is shown to perform well for an anharmonic potential that is not locally harmonic over a temperature range encompassing the quantum limit of a two-level system and the limit of classical dynamics.

  15. Feasibility of single breath-hold left ventricular function with 3 Tesla TSENSE acquisition and 3D modeling analysis

    PubMed Central

    Young, Alistair A; Cowan, Brett R; Schoenberg, Stefan O; Wintersperger, Bernd J

    2008-01-01

    Background A single breath-hold evaluation of ventricular function would allow assessment in cases where scan time or patient tolerance is limited. Spatiotemporal acceleration techniques such as TSENSE decrease cardiovascular MR acquisition time, but standard slice summation analysis requires enough short axis slices to cover the left ventricle (LV). By reducing the number of short axis slices, incorporating long axis slices, and applying a 3D model based analysis, it may be possible to obtain accurate LV mass and volumes. We evaluated LV volume, mass and ejection fraction at 3.0T using a 3D modeling analysis in 9 patients with a history of myocardial infarction and one healthy volunteer. Acquisition consisted of a standard short axis SSFP stack and a 15 heart-beat single breath-hold six slice multi-planar (4 short and 2 long axis) TSENSE SSFP protocol with an acceleration factor of R = 4. Results Differences (standard minus accelerated protocol mean ± s.d.) and coefficients of variation (s.d. of differences as a percentage of the average estimate) were 7.5 ± 9.6 mL and 6% for end-diastolic volume (p = 0.035), 0.4 ± 5.1 mL and 7% for end-systolic volume (p = NS), 7.1 ± 8.1 mL and 9% for stroke volume (p = 0.022), 2.2 ± 2.8% and 5% for ejection fraction (p = 0.035), and -7.1 ± 6.2 g and 4% for LV mass (p = 0.005), respectively. Intra- and inter-observer errors were similar for both protocols (p = NS for all measures). Conclusion These results suggest that clinically useful estimates of LV function can be obtained in a TSENSE accelerated single breath-hold reduced slice acquisition at 3T using 3D modeling analysis techniques. PMID:18495040

  16. Collagen esterification enhances the function and survival of pancreatic β cells in 2D and 3D culture systems

    SciTech Connect

    Ko, Jae Hyung; Kim, Yang Hee; Jeong, Seong Hee; Lee, Song; Park, Si-Nae; Shim, In Kyong; Kim, Song Cheol

    2015-08-07

    Collagen, one of the most important components of the extracellular matrix (ECM), may play a role in the survival of pancreatic islet cells. In addition, chemical modifications that change the collagen charge profile to a net positive charge by esterification have been shown to increase the adhesion and proliferation of various cell types. The purpose of this study was to characterize and compare the effects of native collagen (NC) and esterified collagen (EC) on β cell function and survival. After isolation by the collagenase digestion technique, rat islets were cultured with NC and EC in 2 dimensional (2D) and 3 dimensional (3D) environments for a long-term duration in vitro. The cells were assessed for islet adhesion, morphology, viability, glucose-induced insulin secretion, and mRNA expression of glucose metabolism-related genes, and visualized by scanning electron microscopy (SEM). Islet cells attached tightly in the NC group, but islet cell viability was similar in both the NC and EC groups. Glucose-stimulated insulin secretion was higher in the EC group than in the NC group in both 2D and 3D culture. Furthermore, the mRNA expression levels of glucokinase in the EC group were higher than those in the NC group and were associated with glucose metabolism and insulin secretion. Finally, SEM observation confirmed that islets had more intact component cells on EC sponges than on NC sponges. These results indicate that modification of collagen may offer opportunities to improve function and viability of islet cells. - Highlights: • We changed the collagen charge profile to a net positive charge by esterification. • Islets cultured on esterified collagen improved survival in both 2D and 3D culture. • Islets cultured on esterified collagen enhanced glucose-stimulated insulin release. • High levels of glucokinase mRNA may be associated with increased insulin release.

  17. Assessing the performance of density functional theory for the electronic structure of metal-salens: the 3d(0)-metals.

    PubMed

    Sears, John S; Sherrill, C David

    2008-04-17

    A series of metal-salen complexes of the 3d(0) metals Sc(III), Ti(IV), V(V), Cr(VI), and Mn(VII) have been explored using high-level electronic structure methods including coupled-cluster theory with singles, doubles, and perturbative triples as well as complete active-space third-order perturbation theory. The performance of three common density functional theory approaches has been assessed for both the geometries and the relative energies of the low-lying electronic states. The nondynamical correlation effects are demonstrated to be extremely large in all of the systems examined. Although density functional theory provides reasonable results for some of the systems, the overall agreement is quite poor. This said, the density functional theory approaches are shown to outperform the single-reference perturbation theory and coupled-cluster theory approaches for cases of strong nondynamical correlation.

  18. REGULARIZED 3D FUNCTIONAL REGRESSION FOR BRAIN IMAGE DATA VIA HAAR WAVELETS.

    PubMed

    Wang, Xuejing; Nan, Bin; Zhu, Ji; Koeppe, Robert

    2014-06-01

    The primary motivation and application in this article come from brain imaging studies on cognitive impairment in elderly subjects with brain disorders. We propose a regularized Haar wavelet-based approach for the analysis of three-dimensional brain image data in the framework of functional data analysis, which automatically takes into account the spatial information among neighboring voxels. We conduct extensive simulation studies to evaluate the prediction performance of the proposed approach and its ability to identify related regions to the outcome of interest, with the underlying assumption that only few relatively small subregions are truly predictive of the outcome of interest. We then apply the proposed approach to searching for brain subregions that are associated with cognition using PET images of patients with Alzheimer's disease, patients with mild cognitive impairment, and normal controls.

  19. Implications of 3D domain swapping for protein folding, misfolding and function.

    PubMed

    Rousseau, Frederic; Schymkowitz, Joost; Itzhaki, Laura S

    2012-01-01

    Three-dimensional domain swapping is the process by which two identical protein chains exchange a part of their structure to form an intertwined dimer or higher-order oligomer. The phenomenon has been observed in the crystal structures of a range of different proteins. In this chapter we review the experiments that have been performed in order to understand the sequence and structural determinants of domain-swapping and these show how the general principles obtained can be used to engineer proteins to domain swap. We discuss the role of domain swapping in regulating protein function and as one possible mechanism of protein misfolding that can lead to aggregation and disease. We also review a number of interesting pathways of macromolecular assembly involving β-strand insertion or complementation that are related to the domain-swapping phenomenon.

  20. 3D functional and perfusable microvascular networks for organotypic microfluidic models.

    PubMed

    Bersini, Simone; Moretti, Matteo

    2015-05-01

    The metastatic dissemination of cancer cells from primary tumors to secondary loci is a complex and multistep process including local invasion, intravasation, survival in the blood stream and extravasation towards the metastatic site. It is well known cancer metastases follow organ-specific pathways with selected primary tumors mainly metastasizing towards a specific panel of secondary organs (Steven Paget's theory 1889). However, circulatory patterns and microarchitecture of capillary networks play a key role in the metastatic spread as well (James Ewing's theory 1929). Taking into account both these factors would be critical to develop more complex and physiologically relevant in vitro cancer models. This review presents recent advances in the generation of microvascularized systems through microfluidic approaches and discusses promising results achieved by organ-on-a-chip platforms mimicking the pathophysiology of the functional units of specific organs. The combination of physiologically-like microvascular networks and organotypic microenvironments would foster a new generation of in vitro cancer models to more effectively screen new therapeutics, design personalized medicine treatments and investigate molecular pathways involved in cancer metastases.

  1. Studying topological structure of 21-cm line fluctuations with 3D Minkowski functionals before reionization

    NASA Astrophysics Data System (ADS)

    Yoshiura, Shintaro; Shimabukuro, Hayato; Takahashi, Keitaro; Matsubara, Takahiko

    2017-02-01

    The brightness temperature of the redshifted 21-cm line brings rich information about the intergalactic medium (IGM) from the cosmic dawn and epoch of reionization (EoR). While the power spectrum is a useful tool to investigate the 21-cm signal statistically, the 21-cm brightness temperature field is highly non-Gaussian and the power spectrum is inadequate to characterize the non-Gaussianity. Minkowski functionals (MFs) are promising tools to extract non-Gaussian features of the 21-cm signal and give topological information, such as morphology of ionized bubbles. In this work, we study the 21-cm line signal in detail with MFs. To promote understanding of basic features of the 21-cm signal, we calculate the MFs of not only the hydrogen neutral fraction but also the matter density and spin temperature, which contribute to brightness-temperature fluctuations. We find that the structure of the brightness temperature depends mainly on the ionized fraction and the spin temperature at late and early stages of the EoR, respectively. Further, we investigate the redshift evolution of MFs at 7 < z < 20. We find that, after the onset of reionization, MFs mainly reflect the ionized bubble property. In addition, MFs are sensitive to model parameters related to the topology of ionized bubbles and we consider the possibility of constraining the parameters using future 21-cm signal observations.

  2. Structure functions of passive scalar: evolution in fully 3D shock-driven transition to turbulence

    NASA Astrophysics Data System (ADS)

    Vorobieff, Peter; Olmstead, Dell; Simons, Dylan; Wayne, Patrick; Truman, C. Randall; Kumar, Sanjay

    2015-11-01

    Oblique interaction between a planar shock and a cylindrical density interface results in baroclinic vorticity deposition. The character of the evolving flow is thus different from a similar flow produced by planar normal shock acceleration of the same density interface. In the latter case (planar normal shock), vorticity deposited by the shock is predominantly two-dimensional (directed along the axis of the cylinder), while in the case we consider the shock-induced vorticity field is fully three-dimensional. This results in a complex interplay of vortical structures with different orientations. The statistical properties of the flow are analyzed based on images from two orthogonal visualization planes, using second-order structure functions of the intensity maps of fluorescent tracer pre-mixed with the heavy gas. Scalings consistent with fully developed turbulence are observed at late times. The character of the emergence of these scalings is affected by the flow Mach number, Atwood number, and initial geometry. This work is supported by the US National Nuclear Security Agency (NNSA) via grant DE-NA0002913.

  3. Multisensor fusion for 3-D defect characterization using wavelet basis function neural networks

    NASA Astrophysics Data System (ADS)

    Lim, Jaein; Udpa, Satish S.; Udpa, Lalita; Afzal, Muhammad

    2001-04-01

    The primary objective of multi-sensor data fusion, which offers both quantitative and qualitative benefits, has the ability to draw inferences that may not be feasible with data from a single sensor alone. In this paper, data from two sets of sensors are fused to estimate the defect profile from magnetic flux leakage (MFL) inspection data. The two sensors measure the axial and circumferential components of the MFL. Data is fused at the signal level. If the flux is oriented axially, the samples of the axial signal are measured along a direction parallel to the flaw, while the circumferential signal is measured in a direction that is perpendicular to the flaw. The two signals are combined as the real and imaginary components of a complex valued signal. Signals from an array of sensors are arranged in contiguous rows to obtain a complex valued image. A boundary extraction algorithm is used to extract the defect areas in the image. Signals from the defect regions are then processed to minimize noise and the effects of lift-off. Finally, a wavelet basis function (WBF) neural network is employed to map the complex valued image appropriately to obtain the geometrical profile of the defect. The feasibility of the approach was evaluated using the data obtained from the MFL inspection of natural gas transmission pipelines. Results show the effectiveness of the approach.

  4. Synthesis and Functionalization of 3D Nano-graphene Materials: Graphene Aerogels and Graphene Macro Assemblies.

    PubMed

    Campbell, Patrick G; Worsley, Marcus A; Hiszpanski, Anna M; Baumann, Theodore F; Biener, Juergen

    2015-11-05

    Efforts to assemble graphene into three-dimensional monolithic structures have been hampered by the high cost and poor processability of graphene. Additionally, most reported graphene assemblies are held together through physical interactions (e.g., van der Waals forces) rather than chemical bonds, which limit their mechanical strength and conductivity. This video method details recently developed strategies to fabricate mass-producible, graphene-based bulk materials derived from either polymer foams or single layer graphene oxide. These materials consist primarily of individual graphene sheets connected through covalently bound carbon linkers. They maintain the favorable properties of graphene such as high surface area and high electrical and thermal conductivity, combined with tunable pore morphology and exceptional mechanical strength and elasticity. This flexible synthetic method can be extended to the fabrication of polymer/carbon nanotube (CNT) and polymer/graphene oxide (GO) composite materials. Furthermore, additional post-synthetic functionalization with anthraquinone is described, which enables a dramatic increase in charge storage performance in supercapacitor applications.

  5. MR diffusion-weighted imaging-based subcutaneous tumour volumetry in a xenografted nude mouse model using 3D Slicer: an accurate and repeatable method

    PubMed Central

    Ma, Zelan; Chen, Xin; Huang, Yanqi; He, Lan; Liang, Cuishan; Liang, Changhong; Liu, Zaiyi

    2015-01-01

    Accurate and repeatable measurement of the gross tumour volume(GTV) of subcutaneous xenografts is crucial in the evaluation of anti-tumour therapy. Formula and image-based manual segmentation methods are commonly used for GTV measurement but are hindered by low accuracy and reproducibility. 3D Slicer is open-source software that provides semiautomatic segmentation for GTV measurements. In our study, subcutaneous GTVs from nude mouse xenografts were measured by semiautomatic segmentation with 3D Slicer based on morphological magnetic resonance imaging(mMRI) or diffusion-weighted imaging(DWI)(b = 0,20,800 s/mm2) . These GTVs were then compared with those obtained via the formula and image-based manual segmentation methods with ITK software using the true tumour volume as the standard reference. The effects of tumour size and shape on GTVs measurements were also investigated. Our results showed that, when compared with the true tumour volume, segmentation for DWI(P = 0.060–0.671) resulted in better accuracy than that mMRI(P < 0.001) and the formula method(P < 0.001). Furthermore, semiautomatic segmentation for DWI(intraclass correlation coefficient, ICC = 0.9999) resulted in higher reliability than manual segmentation(ICC = 0.9996–0.9998). Tumour size and shape had no effects on GTV measurement across all methods. Therefore, DWI-based semiautomatic segmentation, which is accurate and reproducible and also provides biological information, is the optimal GTV measurement method in the assessment of anti-tumour treatments. PMID:26489359

  6. Corrigendum to "Measuring the 3-D wind vector with a weight-shiftmicrolight aircraft" published in Atmos. Meas. Tech., 4, 1421-1444, 2011

    NASA Astrophysics Data System (ADS)

    Metzger, S.; Junkermann, W.; Butterbach-Bahl, K.; Schmid, H. P.; Foken, T.

    2011-07-01

    This study investigates whether the 3-D wind vector can be measured reliably from a highly transportable and low-cost weight-shift microlight aircraft. We draw up a transferable procedure to accommodate flow distortion originating from the aircraft body and -wing. This procedure consists of the analysis of aircraft dynamics and seven successive calibration steps. For our aircraft the horizontal wind components receive their greatest single amendment (14 %, relative to the initial uncertainty) from the correction of flow distortion magnitude in the dynamic pressure computation. Conversely the vertical wind component is most of all improved (31 %) by subsequent steps considering the 3-D flow distortion distribution in the flow angle computations. Therein the influences of the aircraft's trim (53 %), as well as changes in the aircraft lift (16 %) are considered by using the measured lift coefficient as explanatory variable. Three independent lines of analysis are used to evaluate the quality of the wind measurement: (a) A wind tunnel study in combination with the propagation of sensor uncertainties defines the systems input uncertainty to ≈0.6 m s-1 at the extremes of a 95 % confidence interval. (b) During severe vertical flight manoeuvres the deviation range of the vertical wind component does not exceed 0.3 m s-1. (c) The comparison with ground based wind measurements yields an overall operational uncertainty (root mean square error) of ≈0.4 m s-1 for the horizontal and ≈0.3 m s-1 for the vertical wind components. No conclusive dependence of the uncertainty on the wind magnitude (<8 m s-1) or true airspeed (ranging from 23-30 m s-1) is found. Hence our analysis provides the necessary basis to study the wind measurement precision and spectral quality, which is prerequisite for reliable Eddy-Covariance flux measurements.

  7. A Second Chance at Health: How a 3D Virtual World Can Improve Health Self-Efficacy for Weight Loss Management Among Adults.

    PubMed

    Behm-Morawitz, Elizabeth; Lewallen, Jennifer; Choi, Grace

    2016-02-01

    Health self-efficacy, or the beliefs in one's capabilities to perform health behaviors, is a significant factor in eliciting health behavior change, such as weight loss. Research has demonstrated that virtual embodiment has the potential to alter one's psychology and physicality, particularly in health contexts; however, little is known about the impacts embodiment in a virtual world has on health self-efficacy. The present research is a randomized controlled trial (N = 90) examining the effectiveness of virtual embodiment and play in a social virtual world (Second Life [SL]) for increasing health self-efficacy (exercise and nutrition efficacy) among overweight adults. Participants were randomly assigned to a 3D social virtual world (avatar virtual interaction experimental condition), 2D social networking site (no avatar virtual interaction control condition), or no intervention (no virtual interaction control condition). The findings of this study provide initial evidence for the use of SL to improve exercise efficacy and to support weight loss. Results also suggest that individuals who have higher self-presence with their avatar reap more benefits. Finally, quantitative findings are triangulated with qualitative data to increase confidence in the results and provide richer insight into the perceived effectiveness and limitations of SL for meeting weight loss goals. Themes resulting from the qualitative analysis indicate that participation in SL can improve motivation and efficacy to try new physical activities; however, individuals who have a dislike for video games may not be benefitted by avatar-based virtual interventions. Implications for research on the transformative potential of virtual embodiment and self-presence in general are discussed.

  8. Optoacoustic system for 3D functional and molecular imaging in nude mice

    NASA Astrophysics Data System (ADS)

    Fronheiser, Matthew P.; Stein, Alan; Herzog, Don; Thompson, Scott; Liopo, Anton; Eghtedari, Mohammad; Motamedi, Massoud; Ermilov, Sergey; Conjusteau, Andre; Gharieb, Reda; Lacewell, Ron; Miller, Tom; Mehta, Ketan; Oraevsky, Alexander A.

    2008-02-01

    A three-dimensional laser optoacoustic imaging system was developed, which combines the advantages of optical spectroscopy and high resolution ultrasonic detection, to produce high contrast maps of optical absorbance in tissues. This system was tested in a nude mouse model of breast cancer and produced tissue images of tumors and vasculature. The imaging can utilize either optical properties of hemoglobin and oxyhemoglobin, which are the main endogenous tissue chromophores in the red and near-infrared spectral ranges, or exogenous contrast agent based on gold nanorods. Visualization of tissue molecules targeted by the contrast agent provides molecular information. Visulization of blood at multiple colors of light provides functional information on blood concentration and oxygen saturation. Optoacoustic imaging, using two or more laser illumination wavelengths, permits an assessment of the angiogenesis-related microvasculature, and thereby, an evaluation of the tumor stage and its metastatic potential. The optoacoustic imaging system was also used to generate molecular images of the malignancy-related receptors induced by the xenografts of BT474 mammary adenocarcinoma cells in nude mice. The development of the latter images was facilitated by the use of an optoacoustic contrast agent that utilizes gold nanorods conjugated to monoclonal antibody raised against HER2/neu antigens. These nanorods possess a very strong optical absorption peak that can be tuned in the near-infrared by changing their aspect ratio. The effective conversion of the optical energy into heat by the gold nanorods, followed by the thermal expansion of the surrounding water, makes these nanoparticles an effective optoacoustic contrast agent. Optical scattering methods and x-ray tomography may also benefit from the application of this contrast agent. Administration of the gold nanorod bioconjugates to mice resulted in an enhanced contrast of breast tumors relative the background of normal tissues

  9. Visualization and mapping of neurosurgical functional brain data onto a 3-D MR-based model of the brain surface.

    PubMed

    Modayur, B R; Prothero, J; Rosse, C; Jakobovits, R; Brinkley, J F

    1996-01-01

    The Human Brain Project was initiated with the goal of developing methods for managing and sharing information about the brain. As a prototype Human Brain Project application we are developing a system for organizing, visualizing, integrating and sharing information about human language function. The goal of the brain mapping component of our work, described in this article, is to generate the 3D location and extent of cortical language sites with respect to a uniform, 3D patient coordinate system. The language sites of individual patients can then be combined with or related to other patient data in terms of a Talairach, surface-based, or other deformable coordinate systems. Language site mapping is done by visually comparing an intraoperative photograph with the rendered image (from MRI data). The techniques outlined in this article have been utilized to map cortical language sites of six patients. Preliminary results point to the adequacy of our volume visualizations for language mapping. The strength of the visualization scheme lies in the combination of interactive segmentation with volume and surface visualization. We are now in the process of acquiring more patient data to further validate the usefulness of our method.

  10. 3D photonic crystal-based biosensor functionalized with quantum dot-based aptamer for thrombine detection

    NASA Astrophysics Data System (ADS)

    Lim, Chae Young; Choi, Eunpyo; Park, Youngkyu; Park, Jungyul

    2013-05-01

    In this paper, we propose a new technique for protein detection by using the enhancement of intensity in quantum dots (Qdot) whose emission is guided by 3D photonic crystal (PC) structures. For easy to use, we design the emitted light from the sensor can be recovered, when the chemical antibody (aptamer) conjugated with guard DNA (g-DNA) labeled with a quencher (Black FQ) hybridizes with the target proteins. In detail, we synthesis a Qdot-aptamer complex and then immobilize these complex on the PC surfaces. Next, we perform the hybridization of the Qdot-aptamer complex with g-DNA labeled with the quencher. It induces the quenching effect of fluoresce intensity in the Qdot-aptamer. In presence of target protein (thrombin), the Qdot-aptamer complex prefers to form the thrombin-aptamer complex: this results in the release of Black FQ-g-DNA and the quenched light intensity recovers into the original high intensity with Qdot. The intensity recovery varies quantitatively according to the level of the target protein concentration. This proposed sensor shows much higher detection sensitivity than the general fluorescent detection mechanism, which is functionalized on the flat surfaces because of the light guiding effect from 3D photonic crystal structures.

  11. Performance of density functional theory for 3d transition metal-containing complexes: utilization of the correlation consistent basis sets.

    PubMed

    Tekarli, Sammer M; Drummond, Michael L; Williams, T Gavin; Cundari, Thomas R; Wilson, Angela K

    2009-07-30

    The performance of 44 density functionals used in conjunction with the correlation consistent basis sets (cc-pVnZ where n = T and Q) has been assessed for the gas-phase enthalpies of formation at 298.15 K of 3d transition metal (TM) containing systems. Nineteen molecules were examined: ScS, VO, VO(2), Cr(CO)(6), MnS, MnCl(2), Mn(CO)(5)Cl, FeCl(3), Fe(CO)(5), CoH(CO)(4), NiCl(2), Ni(CO)(4), CuH, CuF, CuCl, ZnH, ZnO, ZnCl, and Zn(CH(3))(2). Of the functionals examined, the functionals that resulted in the smallest mean absolute deviation (MAD, in parentheses, kcal mol(-1)) from experiment were B97-1 (6.9), PBE1KCIS (8.1), TPSS1KCIS (9.6), B97-2 (9.7), and B98 (10.7). All five of these functionals include some degree of Hartree-Fock (HF) exchange. The impact of increasing the basis set from cc-pVTZ to cc-pVQZ was found to be slight for the generalized gradient approximation (GGA) and meta-GGA (MGGA) functionals studied, indicating basis set saturation at the triple-zeta level. By contrast, for most of the generalized gradient exchange (GGE), hybrid GGA (HGGA), and hybrid meta-GGA (HMGGA) functionals considered, improvements in the average MAD of 2-3 kcal mol(-1) were seen upon progressing to a quadruple-zeta level basis set. Overall, it was found that the functionals that include Hartree-Fock exchange performed best overall, but those with greater than 40% HF exchange exhibit significantly poor performance for the prediction of enthalpies of formation for 3d TM complexes. Carbonyl-containing complexes, a mainstay in organometallic TM chemistry, are demonstrated to be exceedingly difficult to describe accurately with all but 2 of the 44 functionals considered. The most accurate functional, for both CO-containing and CO-free compounds, is B97-1/cc-pVQZ, which is shown to be capable of yielding results within 1 kcal mol(-1) of high-level ab initio composite methodologies.

  12. Bootstrapping 3D fermions

    DOE PAGES

    Iliesiu, Luca; Kos, Filip; Poland, David; ...

    2016-03-17

    We study the conformal bootstrap for a 4-point function of fermions <ψψψψ> in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge CT. We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N. Finally, we also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  13. Bootstrapping 3D fermions

    SciTech Connect

    Iliesiu, Luca; Kos, Filip; Poland, David; Pufu, Silviu S.; Simmons-Duffin, David; Yacoby, Ran

    2016-03-17

    We study the conformal bootstrap for a 4-point function of fermions <ψψψψ> in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge CT. We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N. Finally, we also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  14. Kinematic analysis of healthy hips during weight-bearing activities by 3D-to-2D model-to-image registration technique.

    PubMed

    Hara, Daisuke; Nakashima, Yasuharu; Hamai, Satoshi; Higaki, Hidehiko; Ikebe, Satoru; Shimoto, Takeshi; Hirata, Masanobu; Kanazawa, Masayuki; Kohno, Yusuke; Iwamoto, Yukihide

    2014-01-01

    Dynamic hip kinematics during weight-bearing activities were analyzed for six healthy subjects. Continuous X-ray images of gait, chair-rising, squatting, and twisting were taken using a flat panel X-ray detector. Digitally reconstructed radiographic images were used for 3D-to-2D model-to-image registration technique. The root-mean-square errors associated with tracking the pelvis and femur were less than 0.3 mm and 0.3° for translations and rotations. For gait, chair-rising, and squatting, the maximum hip flexion angles averaged 29.6°, 81.3°, and 102.4°, respectively. The pelvis was tilted anteriorly around 4.4° on average during full gait cycle. For chair-rising and squatting, the maximum absolute value of anterior/posterior pelvic tilt averaged 12.4°/11.7° and 10.7°/10.8°, respectively. Hip flexion peaked on the way of movement due to further anterior pelvic tilt during both chair-rising and squatting. For twisting, the maximum absolute value of hip internal/external rotation averaged 29.2°/30.7°. This study revealed activity dependent kinematics of healthy hip joints with coordinated pelvic and femoral dynamic movements. Kinematics' data during activities of daily living may provide important insight as to the evaluating kinematics of pathological and reconstructed hips.

  15. Using Parameters of Dynamic Pulse Function for 3d Modeling in LOD3 Based on Random Textures

    NASA Astrophysics Data System (ADS)

    Alizadehashrafi, B.

    2015-12-01

    The pulse function (PF) is a technique based on procedural preprocessing system to generate a computerized virtual photo of the façade with in a fixed size square(Alizadehashrafi et al., 2009, Musliman et al., 2010). Dynamic Pulse Function (DPF) is an enhanced version of PF which can create the final photo, proportional to real geometry. This can avoid distortion while projecting the computerized photo on the generated 3D model(Alizadehashrafi and Rahman, 2013). The challenging issue that might be handled for having 3D model in LoD3 rather than LOD2, is the final aim that have been achieved in this paper. In the technique based DPF the geometries of the windows and doors are saved in an XML file schema which does not have any connections with the 3D model in LoD2 and CityGML format. In this research the parameters of Dynamic Pulse Functions are utilized via Ruby programming language in SketchUp Trimble to generate (exact position and deepness) the windows and doors automatically in LoD3 based on the same concept of DPF. The advantage of this technique is automatic generation of huge number of similar geometries e.g. windows by utilizing parameters of DPF along with defining entities and window layers. In case of converting the SKP file to CityGML via FME software or CityGML plugins the 3D model contains the semantic database about the entities and window layers which can connect the CityGML to MySQL(Alizadehashrafi and Baig, 2014). The concept behind DPF, is to use logical operations to project the texture on the background image which is dynamically proportional to real geometry. The process of projection is based on two vertical and horizontal dynamic pulses starting from upper-left corner of the background wall in down and right directions respectively based on image coordinate system. The logical one/zero on the intersections of two vertical and horizontal dynamic pulses projects/does not project the texture on the background image. It is possible to define

  16. How well can levator ani muscle morphology on 3D pelvic floor ultrasound predict the levator ani muscle function?

    PubMed Central

    Rostaminia, G.; Peck, J. D.; Quiroz, L. H.; Shobeiri, S. A.

    2016-01-01

    Introduction and hypothesis The aim of our study was to assess the performance of levator ani muscle deficiency (LAD) evaluated by 3D endovaginal ultrasound (EVUS) to detect pelvic floor muscle function as assessed by digital examination. Methods This cross-sectional study was conducted among 77 patients referred to our urogynecology clinic for pelvic floor dysfunction symptoms. Patients underwent physical examinations including digital pelvic muscle strength assessment using the Modified Oxford scale (MOS). EVUS volumes were evaluated and levator ani muscles were scored according to a validated LAD scoring system. MOS scores were categorized as nonfunctional (scores 0–1) and functional (scores 2–5). Results Mean age of participants was 56 (SD± 12.5) and 71% were menopausal. Overall, 32.5% had nonfunctional muscle strength and 44.2% were classified as having significant LAD. LAD identified by ultrasound had a sensitivity of 60% (95% CI 41%–79%) for detecting nonfunctional muscle and a specificity of 63% (95% CI 50%–77%) for detecting functional muscle. Overall, LAD demonstrated fair ability to discriminate between patient with and without poor muscle function (area under the ROC curve = 0.70 (95% CI 0.58–0.83). Among patients with an LAD score of 16–18, representing almost total muscle avulsion, 70% had nonfunctional MOS scores. Whereas, in patients with normal/minimal LAD (scores of 0–4), 89.5% had functional MOS scores Conclusions LAD and MOS scales were moderately negatively correlated Among patients with normal morphology or the most severe muscle deficiency, LAD scores can identify the majority of patients with functional or non-functional MOS scores, respectively. PMID:25246297

  17. 3D Functional Corneal Stromal Tissue Equivalent Based on Corneal Stromal Stem Cells and Multi-Layered Silk Film Architecture

    PubMed Central

    Marelli, Benedetto; Omenetto, Fiorenzo G.; Funderburgh, James L.; Kaplan, David L.

    2017-01-01

    The worldwide need for human cornea equivalents continues to grow. Few clinical options are limited to allogenic and synthetic material replacements. We hypothesized that tissue engineered human cornea systems based on mechanically robust, patterned, porous, thin, optically clear silk protein films, in combination with human corneal stromal stem cells (hCSSCs), would generate 3D functional corneal stroma tissue equivalents, in comparison to previously developed 2D approaches. Silk film contact guidance was used to control the alignment and distribution of hCSSCs on RGD-treated single porous silk films, which were then stacked in an orthogonally, multi-layered architecture and cultured for 9 weeks. These systems were compared similar systems generated with human corneal fibroblasts (hCFs). Both cell types were viable and preferentially aligned along the biomaterial patterns for up to 9 weeks in culture. H&E histological sections showed that the systems seeded with the hCSSCs displayed ECM production throughout the entire thickness of the constructs. In addition, the ECM proteins tested positive for keratocyte-specific tissue markers, including keratan sulfate, lumican, and keratocan. The quantification of hCSSC gene expression of keratocyte-tissue markers, including keratocan, lumican, human aldehyde dehydrogenase 3A1 (ALDH3A1), prostaglandin D2 synthase (PTDGS), and pyruvate dehydrogenase kinase, isozyme 4 (PDK4), within the 3D tissue systems demonstrated upregulation when compared to 2D single silk films and to the systems generated with the hCFs. Furthermore, the production of ECM from the hCSSC seeded systems and subsequent remodeling of the initial matrix significantly improved cohesiveness and mechanical performance of the constructs, while maintaining transparency after 9 weeks. PMID:28099503

  18. Comparison of NSTX FIDA, Charge Exchange, and Neutron Fluxes with Calculated Signals Based on CQL3D-FOW Distribution Functions

    NASA Astrophysics Data System (ADS)

    Harvey, R. W.; Petrov, Yu. V.; Kinsey, J. E.; Liu, D.; Heidbrink, W. W.; Taylor, G.; Bonoli, P. T.

    2014-10-01

    Ion distribution function calculations with CQL3D have been substantially advanced through implementation of guiding-center-orbit-based Fokker-Planck Coefficients. The resulting finite-orbit-width (FOW) calculations are carried out with a fast CQL3D-Hybrid-FOW option, and in a slower but neoclassically complete (except no Er yet) CQL3D-FOW option. Good comparison between time-dependent Fast Ion Diagnostic FIDA, NPA, and neutron signals resulting from neutral beaminjection(NBI) and high harmonic fast wave (HHFW) power injected into the NSTX spherical tokamak have been simulated with the CQL3D-Hybrid-FOW, using only the FOW effects on QL diffusion, and particle losses, direct and CX. Comparisons are also made with recent CQL3D-FOW results, as well as between the original FIDA calculation code and a recent fortran version. Supported by USDOE Grants SC0006614, ER54744, and ER44649.

  19. A Bayesian mixture model relating dose to critical organs and functional complication in 3D conformal radiation therapy.

    PubMed

    Johnson, Timothy D; Taylor, Jeremy M G; Ten Haken, Randall K; Eisbruch, Avraham

    2005-10-01

    A goal of cancer radiation therapy is to deliver maximum dose to the target tumor while minimizing complications due to irradiation of critical organs. Technological advances in 3D conformal radiation therapy has allowed great strides in realizing this goal; however, complications may still arise. Critical organs may be adjacent to tumors or in the path of the radiation beam. Several mathematical models have been proposed that describe the relationship between dose and observed functional complication; however, only a few published studies have successfully fit these models to data using modern statistical methods which make efficient use of the data. One complication following radiation therapy of head and neck cancers is the patient's inability to produce saliva. Xerostomia (dry mouth) leads to high susceptibility to oral infection and dental caries and is, in general, unpleasant and an annoyance. We present a dose-damage-injury model that subsumes any of the various mathematical models relating dose to damage. The model is a nonlinear, longitudinal mixed effects model where the outcome (saliva flow rate) is modeled as a mixture of a Dirac measure at zero and a gamma distribution whose mean is a function of time and dose. Bayesian methods are used to estimate the relationship between dose delivered to the parotid glands and the observational outcome-saliva flow rate. A summary measure of the dose-damage relationship is modeled and assessed by a Bayesian chi(2) test for goodness-of-fit.

  20. 3D Ion and Electron Distribution Function Measurements from the Fast Plasma Investigation on the Magnetospheric Multiscale Mission

    NASA Astrophysics Data System (ADS)

    Giles, B. L.; Pollock, C. J.; Avanov, L. A.; Barrie, A. C.; Burch, J. L.; Chandler, M. O.; Clark, G. B.; Coffey, V. N.; Dickson, C.; Dorelli, J.; Ergun, R. E.; Fuselier, S. A.; Gershman, D. J.; Gliese, U.; Holland, M. P.; Jacques, A. D.; Kreisler, S.; Lavraud, B.; MacDonald, E.; Mauk, B.; Moore, T. E.; Mukai, T.; Nakamura, R.; Paterson, W. R.; Rager, A. C.; Saito, Y.; Salo, C.; Sauvaud, J. A.; Torbert, R. B.; Vinas, A. F.; Yokota, S.

    2015-12-01

    The primary focus of the Magnetospheric Multiscale (MMS) mission, launched in March 2015, is magnetic reconnection and associated processes. Understanding hinges critically on the kinetic physics that allows reconnection to take place. The Fast Plasma Investigation (FPI) provides electron and ion distribution functions at 4.5s cadence and, for select periods of time, at cadences of 30ms for electrons and 150ms for ions. These select time periods are chosen after in situ acquisition based on inspection of the low resolution data. Thus the FPI provides, independent of spacecraft spin rate, the time resolution needed to resolve the small, fast-moving reconnection diffusion regions. The first mission phase focuses on the dayside magnetopause and this presentation is intended to demonstrate the capabilities of FPI to resolve the important spatial scales relevant to the reconnection process. Magnetopause and other boundary crossings will be examined and the phase-space trajectories identified at the tetrahedral satellite locations through analysis of the 3D distribution functions.

  1. Anti-aliasing weighting functions for multislice helical CT

    NASA Astrophysics Data System (ADS)

    La Riviere, Patrick J.; Pan, Xiaochuan

    2002-05-01

    We develop a new projection weighting function for interpolation and reconstruction of multi-slice helical computed tomography data with the hope of reducing longitudinal aliasing in reconstructed volumes. The weighting function is based on the application of the Papoulis generalized sampling theorem to the interlaced longitudinal samples acquired by the multi-slice scanner. We call the approach 180MAA, for multi-slice anti-aliasing. For pitch 3, the 180MAA approach yields high-quality images of the 3D Shepp-Logan phantom as well as a longitudinal MTF superior to that of the 180MLI approach, which is based on the use of linear interpolation. However, it is not as successful at mitigating aliasing as had been doped due to the presence of a significant and unexpected aliasing component that can be attributed to the small cone angle in multi-slice helical CT. The presence of this effect is interesting and significant in its own right, however.

  2. 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.

  3. 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

  4. 3D position of radiation sources using an automated gamma camera and ML algorithm with energy-dependent response functions

    NASA Astrophysics Data System (ADS)

    Lee, Wonho; Wehe, David

    2004-09-01

    Portable γ-ray imaging systems operating from 100keV to 3MeV are used in nuclear medicine, astrophysics and industrial applications. 2D images of γ-rays are common in many fields using radiation-detection systems (Appl. Opt. 17 (3) (1978) 337; IEEE Trans. Nucl. Sci. Ns- 31 (1984) 771; IEEE Trans. Nucl. Sci. NS- 44 (3) (1997) 911). In this work, the 3D position of a radiation source is determined by a portable gamma-ray imaging system. 2D gamma-ray images were obtained from different positions of the gamma camera and the third dimension, the distance between the detector and the radiation source, was calculated using triangulation. The imaging system consists of a 4×4 array of CsI(Tl) detectors coupled to photodiode detectors that are mounted on an automated table which can precisely position the angular axis of the camera. Lead shields the detector array from the background radiation. Additionally, a CCD camera is attached to the top of the gamma camera and provides coincident 2D visual information. The inferred distances from the center of the two measurement points and a radiation source had less than a 3% error within a range of 3m. The radiation image from the gamma camera and the visual image from CCD camera are superimposed into one combined image using a maximum-likelihood (ML) algorithm to make the image more precise. The response functions for the ML algorithm depend on the energy of incident radiation, and are obtained from both experiments and simulations. The energy-dependent response functions are shown to yield better imaging performance compared with the fixed energy response function commonly used previously.

  5. Diacylglycerol kinase α promotes 3D cancer cell growth and limits drug sensitivity through functional interaction with Src

    PubMed Central

    Torres-Ayuso, Pedro; Daza-Martín, Manuel; Martín-Pérez, Jorge; Ávila-Flores, Antonia; Mérida, Isabel

    2014-01-01

    Diacylglycerol kinase (DGK)α converts diacylglycerol to phosphatidic acid. This lipid kinase sustains survival, migration and invasion of tumor cells, with no effect over untransformed cells, suggesting its potential as a cancer-specific target. Nonetheless the mechanisms that underlie DGKα specific contribution to cancer survival have not been elucidated. Using three-dimensional (3D) colon and breast cancer cell cultures, we demonstrate that DGKα upregulation is part of the transcriptional program that results in Src activation in these culture conditions. Pharmacological or genetic DGKα silencing impaired tumor growth in vivo confirming its function in malignant transformation. DGKα-mediated Src regulation contributed to limit the effect of Src inhibitors, and its transcriptional upregulation in response to PI3K/Akt inhibitors resulted in reduced toxicity. Src oncogenic properties and contribution to pharmacological resistance have been linked to its overactivation in cancer. DGKα participation in this central node helps to explain why its pharmacological inhibition or siRNA-mediated targeting specifically alters tumor viability with no effect on untransformed cells. Our results identify DGKα-mediated stabilization of Src activation as an important mechanism in tumor growth, and suggest that targeting this enzyme, alone or in combination with other inhibitors in wide clinical use, could constitute a treatment strategy for aggressive forms of cancer. PMID:25339152

  6. New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.

    PubMed

    Sillitoe, Ian; Cuff, Alison L; Dessailly, Benoit H; Dawson, Natalie L; Furnham, Nicholas; Lee, David; Lees, Jonathan G; Lewis, Tony E; Studer, Romain A; Rentzsch, Robert; Yeats, Corin; Thornton, Janet M; Orengo, Christine A

    2013-01-01

    CATH version 3.5 (Class, Architecture, Topology, Homology, available at http://www.cathdb.info/) contains 173 536 domains, 2626 homologous superfamilies and 1313 fold groups. When focusing on structural genomics (SG) structures, we observe that the number of new folds for CATH v3.5 is slightly less than for previous releases, and this observation suggests that we may now know the majority of folds that are easily accessible to structure determination. We have improved the accuracy of our functional family (FunFams) sub-classification method and the CATH sequence domain search facility has been extended to provide FunFam annotations for each domain. The CATH website has been redesigned. We have improved the display of functional data and of conserved sequence features associated with FunFams within each CATH superfamily.

  7. Evaluation of multimodal segmentation based on 3D T1-, T2- and FLAIR-weighted images - the difficulty of choosing.

    PubMed

    Lindig, Tobias; Kotikalapudi, Raviteja; Schweikardt, Daniel; Martin, Pascal; Bender, Friedemann; Klose, Uwe; Ernemann, Ulrike; Focke, Niels K; Bender, Benjamin

    2017-02-07

    Voxel-based morphometry is still mainly based on T1-weighted MRI scans. Misclassification of vessels and dura mater as gray matter has been previously reported. Goal of the present work was to evaluate the effect of multimodal segmentation methods available in SPM12, and their influence on identification of age related atrophy and lesion detection in epilepsy patients. 3D T1-, T2- and FLAIR-images of 77 healthy adults (mean age 35.8 years, 19-66 years, 45 females), 7 patients with malformation of cortical development (MCD) (mean age 28.1 years,19-40 years, 3 females), and 5 patients with left hippocampal sclerosis (LHS) (mean age 49.0 years, 25-67 years, 3 females) from a 3T scanner were evaluated. Segmentation based on T1-only, T1+T2, T1+FLAIR, T2+FLAIR, and T1+T2+FLAIR were compared in the healthy subjects. Clinical VBM results based on the different segmentation approaches for MCD and for LHS were compared. T1-only segmentation overestimated total intracranial volume by about 80ml compared to the other segmentation methods. This was due to misclassification of dura mater and vessels as GM and CSF. Significant differences were found for several anatomical regions: the occipital lobe, the basal ganglia/thalamus, the pre- and postcentral gyrus, the cerebellum, and the brainstem. None of the segmentation methods yielded completely satisfying results for the basal ganglia/thalamus and the brainstem. The best correlation with age could be found for the multimodal T1+T2+FLAIR segmentation. Highest T-scores for identification of LHS were found for T1+T2 segmentation, while highest T-scores for MCD were dependent on lesion and anatomical location. Multimodal segmentation is superior to T1-only segmentation and reduces the misclassification of dura mater and vessels as GM and CSF. Depending on the anatomical region and the pathology of interest (atrophy, lesion detection, etc.), different combinations of T1, T2 and FLAIR yield optimal results.

  8. The advantages of complementing MT profiles in 3-D environments with geomagnetic transfer function and interstation horizontal magnetic transfer function data: results from a synthetic case study

    NASA Astrophysics Data System (ADS)

    Campanyà, Joan; Ogaya, Xènia; Jones, Alan G.; Rath, Volker; Vozar, Jan; Meqbel, Naser

    2016-12-01

    As a consequence of measuring time variations of the electric and the magnetic field, which are related to current flow and charge distribution, magnetotelluric (MT) data in 2-D and 3-D environments are not only sensitive to the geoelectrical structures below the measuring points but also to any lateral anomalies surrounding the acquisition site. This behaviour complicates the characterization of the electrical resistivity distribution of the subsurface, particularly in complex areas. In this manuscript we assess the main advantages of complementing the standard MT impedance tensor (Z) data with interstation horizontal magnetic tensor (H) and geomagnetic transfer function (T) data in constraining the subsurface in a 3-D environment beneath a MT profile. Our analysis was performed using synthetic responses with added normally distributed and scattered random noise. The sensitivity of each type of data to different resistivity anomalies was evaluated, showing that the degree to which each site and each period is affected by the same anomaly depends on the type of data. A dimensionality analysis, using Z, H and T data, identified the presence of the 3-D anomalies close to the profile, suggesting a 3-D approach for recovering the electrical resistivity values of the subsurface. Finally, the capacity for recovering the geoelectrical structures of the subsurface was evaluated by performing joint inversion using different data combinations, quantifying the differences between the true synthetic model and the models from inversion process. Four main improvements were observed when performing joint inversion of Z, H and T data: (1) superior precision and accuracy at characterizing the electrical resistivity values of the anomalies below and outside the profile; (2) the potential to recover high electrical resistivity anomalies that are poorly recovered using Z data alone; (3) improvement in the characterization of the bottom and lateral boundaries of the anomalies with low

  9. 3D graphene preparation via covalent amide functionalization for efficient metal-free electrocatalysis in oxygen reduction

    PubMed Central

    Ahmed, Mohammad Shamsuddin; Kim, Young-Bae

    2017-01-01

    3D and porous reduced graphene oxide (rGO) catalysts have been prepared with sp3-hybridized 1,4-diaminobutane (sp3-DABu, rGO-sp3-rGO) and sp2-hybridized 1,4-diaminobenzene (sp2-DABe, rGO-sp2-rGO) through a covalent amidation and have employed as a metal-free electrocatalyst for oxygen reduction reaction (ORR) in alkaline media. Both compounds have used as a junction between functionalized rGO layers to improve electrical conductivity and impart electrocatalytic activity to the ORR resulting from the interlayer charge transfer. The successful amidation and the subsequent reduction in the process of catalyst preparation have confirmed by X-ray photoelectron spectroscopy. A hierarchical porous structure is also confirmed by surface morphological analysis. Specific surface area and thermal stability have increased after successful the amidation by sp3-DABu. The investigated ORR mechanism reveals that both functionalized rGO is better ORR active than nonfunctionalized rGO due to pyridinic-like N content and rGO-sp3-rGO is better ORR active than rGO-sp2-rGO due to higher pyridinic-like N content and π-electron interaction-free interlayer charge transfer. Thus, the rGO-sp3-rGO has proven as an efficient metal-free electrocatalyst with better electrocatalytic activity, stability, and tolerance to the crossover effect than the commercially available Pt/C for ORR. PMID:28240302

  10. Validation for 2D/3D registration II: The comparison of intensity- and gradient-based merit functions using a new gold standard data set

    SciTech Connect

    Gendrin, Christelle; Markelj, Primoz; Pawiro, Supriyanto Ardjo; Spoerk, Jakob; Bloch, Christoph; Weber, Christoph; Figl, Michael; Bergmann, Helmar; Birkfellner, Wolfgang; Likar, Bostjan; Pernus, Franjo

    2011-03-15

    Purpose: A new gold standard data set for validation of 2D/3D registration based on a porcine cadaver head with attached fiducial markers was presented in the first part of this article. The advantage of this new phantom is the large amount of soft tissue, which simulates realistic conditions for registration. This article tests the performance of intensity- and gradient-based algorithms for 2D/3D registration using the new phantom data set. Methods: Intensity-based methods with four merit functions, namely, cross correlation, rank correlation, correlation ratio, and mutual information (MI), and two gradient-based algorithms, the backprojection gradient-based (BGB) registration method and the reconstruction gradient-based (RGB) registration method, were compared. Four volumes consisting of CBCT with two fields of view, 64 slice multidetector CT, and magnetic resonance-T1 weighted images were registered to a pair of kV x-ray images and a pair of MV images. A standardized evaluation methodology was employed. Targets were evenly spread over the volumes and 250 starting positions of the 3D volumes with initial displacements of up to 25 mm from the gold standard position were calculated. After the registration, the displacement from the gold standard was retrieved and the root mean square (RMS), mean, and standard deviation mean target registration errors (mTREs) over 250 registrations were derived. Additionally, the following merit properties were computed: Accuracy, capture range, number of minima, risk of nonconvergence, and distinctiveness of optimum for better comparison of the robustness of each merit. Results: Among the merit functions used for the intensity-based method, MI reached the best accuracy with an RMS mTRE down to 1.30 mm. Furthermore, it was the only merit function that could accurately register the CT to the kV x rays with the presence of tissue deformation. As for the gradient-based methods, BGB and RGB methods achieved subvoxel accuracy (RMS m

  11. 3D-printing of pH-responsive and functional polymers on an affordable desktop printer.

    PubMed

    Nadgorny, Milena; Xiao, Zeyun; Chen, Chao; Connal, Luke A

    2016-10-03

    In this work we describe the synthesis, thermal and rheological characterization, hot-melt extrusion and three-dimensional printing (3DP) of poly(2-vinylpyridine) (P2VP). We investigate the effect of thermal processing conditions on physical properties of produced filaments in order to achieve high quality, 3D- printable filaments for fused deposition modeling (FDM). We 3D-print P2VP filaments using an affordable 3D printer. The pyridine moieties are crosslinked and quaternized post-printing to form 3D-printed pH-responsive hydrogels. The printed objects exhibited dynamic and reversible pH-dependent swelling. These hydrogels act as flow regulating valves, controlling the flow rate with pH. Additionally, a macroporous P2VP membrane was 3D-printed and the coordinating ability of the pyridyl groups was harassed to immobilize silver precursors on its surface. After the reduction of silver ions, the structure was used to catalyze the reduction of 4-nitrophenol to 4-aminophenol with a high efficiency. This is a facile technique to print recyclable catalytic objects.

  12. Size-based emphysema cluster analysis on low attenuation area in 3D volumetric CT: comparison with pulmonary functional test

    NASA Astrophysics Data System (ADS)

    Lee, Minho; Kim, Namkug; Lee, Sang Min; Seo, Joon Beom; Oh, Sang Young

    2015-03-01

    To quantify low attenuation area (LAA) of emphysematous regions according to cluster size in 3D volumetric CT data of chronic obstructive pulmonary disease (COPD) patients and to compare these indices with their pulmonary functional test (PFT). Sixty patients with COPD were scanned by a more than 16-multi detector row CT scanner (Siemens Sensation 16 and 64) within 0.75mm collimation. Based on these LAA masks, a length scale analysis to estimate each emphysema LAA's size was performed as follows. At first, Gaussian low pass filter from 30mm to 1mm kernel size with 1mm interval on the mask was performed from large to small size, iteratively. Centroid voxels resistant to the each filter were selected and dilated by the size of the kernel, which was regarded as the specific size emphysema mask. The slopes of area and number of size based LAA (slope of semi-log plot) were analyzed and compared with PFT. PFT parameters including DLco, FEV1, and FEV1/FVC were significantly (all p-value< 0.002) correlated with the slopes (r-values; -0.73, 0.54, 0.69, respectively) and EI (r-values; -0.84, -0.60, -0.68, respectively). In addition, the D independently contributed regression for FEV1 and FEV1/FVC (adjust R sq. of regression study: EI only, 0.70, 0.45; EI and D, 0.71, 0.51, respectively). By the size based LAA segmentation and analysis, we evaluated the Ds of area, number, and distribution of size based LAA, which would be independent factors for predictor of PFT parameters.

  13. Histamine-functionalized copolymer micelles as a drug delivery system in 2D and 3D models of breast cancer

    PubMed Central

    Zhang, Yuning; Lundberg, Pontus; Diether, Maren; Porsch, Christian; Janson, Caroline; Lynd, Nathaniel A.; Ducani, Cosimo; Malkoch, Michael; Malmström, Eva; Hawker, Craig J.; Nyström, Andreas M.

    2015-01-01

    Histamine functionalized block copolymers based on poly(allyl glycidyl ether)-b-poly(ethylene oxide) (PAGE-b-PEO) were prepared with different ratios of histamine and octyl or benzyl groups using UV-initiated thiol-ene click chemistry. At neutral pH, the histamine units are uncharged and hydrophobic, while in acidic environments, such as in the endosome, lysosomes, or extracellular sites of tumours, the histamine groups are positively charged and hydrophilic. pH responsible polymer drug delivery systems is a promising route to site specific delivery of drugs and offers the potential to avoid side effects of systemic treatment. Our detailed in vitro experiments of the efficacy of drug delivery and the intracellular localization characteristics of this library of NPs in 2D and 3D cultures of breast cancer revealed that the 50% histamine-modified polymer loaded with DOX exhibited rapid accumulation in the nucleus of free DOX within 2 h. Confocal studies showed enhanced mitochondrial localization and lysosomal escape when compared to controls. From these combined studies, it was shown that by accurately tuning the structure of the initial block copolymers, the resulting self-assembled NPs can be designed to exploit histamine as an endosomal escape trigger and the octyl/benzyl units give rise to a hydrophobic core resulting in highly efficacious drug delivery systems (DDS) with control over intracellular localization. Optimization and rational control of the intracellular localization of both DDS and the parent drug can give nanomedicines a substantial increase in efficacy and should be explored in future studies. PMID:26257912

  14. 3D and beyond

    NASA Astrophysics Data System (ADS)

    Fung, Y. C.

    1995-05-01

    This conference on physiology and function covers a wide range of subjects, including the vasculature and blood flow, the flow of gas, water, and blood in the lung, the neurological structure and function, the modeling, and the motion and mechanics of organs. Many technologies are discussed. I believe that the list would include a robotic photographer, to hold the optical equipment in a precisely controlled way to obtain the images for the user. Why are 3D images needed? They are to achieve certain objectives through measurements of some objects. For example, in order to improve performance in sports or beauty of a person, we measure the form, dimensions, appearance, and movements.

  15. Water-based polyurethane 3D printed scaffolds with controlled release function for customized cartilage tissue engineering.

    PubMed

    Hung, Kun-Che; Tseng, Ching-Shiow; Dai, Lien-Guo; Hsu, Shan-hui

    2016-03-01

    Conventional 3D printing may not readily incorporate bioactive ingredients for controlled release because the process often involves the use of heat, organic solvent, or crosslinkers that reduce the bioactivity of the ingredients. Water-based 3D printing materials with controlled bioactivity for customized cartilage tissue engineering is developed in this study. The printing ink contains the water dispersion of synthetic biodegradable polyurethane (PU) elastic nanoparticles, hyaluronan, and bioactive ingredients TGFβ3 or a small molecule drug Y27632 to replace TGFβ3. Compliant scaffolds are printed from the ink at low temperature. These scaffolds promote the self-aggregation of mesenchymal stem cells (MSCs) and, with timely release of the bioactive ingredients, induce the chondrogenic differentiation of MSCs and produce matrix for cartilage repair. Moreover, the growth factor-free controlled release design may prevent cartilage hypertrophy. Rabbit knee implantation supports the potential of the novel 3D printing scaffolds in cartilage regeneration. We consider that the 3D printing composite scaffolds with controlled release bioactivity may have potential in customized tissue engineering.

  16. Statistical Atlas Construction via Weighted Functional Boxplots

    PubMed Central

    Hong, Yi; Davis, Brad; Marron, J.S.; Kwitt, Roland; Singh, Nikhil; Kimbell, Julia S.; Pitkin, Elizabeth; Superfine, Richard; Davis, Stephanie D.; Zdanski, Carlton J.; Niethammer, Marc

    2014-01-01

    Atlas-building from population data is widely used in medical imaging. However, the emphasis of atlas-building approaches is typically to estimate a spatial alignment to compute a mean / median shape or image based on population data. In this work, we focus on the statistical characterization of the population data, once spatial alignment has been achieved. We introduce and propose the use of the weighted functional boxplot. This allows the generalization of concepts such as the median, percentiles, or outliers to spaces where the data objects are functions, shapes, or images, and allows spatio-temporal atlas-building based on kernel regression. In our experiments, we demonstrate the utility of the approach to construct statistical atlases for pediatric upper airways and corpora callosa revealing their growth patterns. We also define a score system based on the pediatric airway atlas to quantitatively measure the severity of subglottic stenosis (SGS) in the airway. This scoring allows the classification of pre- and post-surgery SGS subjects and radiographically normal controls. Experimental results show the utility of atlas information to assess the effect of airway surgery in children. PMID:24747271

  17. Statistical atlas construction via weighted functional boxplots.

    PubMed

    Hong, Yi; Davis, Brad; Marron, J S; Kwitt, Roland; Singh, Nikhil; Kimbell, Julia S; Pitkin, Elizabeth; Superfine, Richard; Davis, Stephanie D; Zdanski, Carlton J; Niethammer, Marc

    2014-05-01

    Atlas-building from population data is widely used in medical imaging. However, the emphasis of atlas-building approaches is typically to estimate a spatial alignment to compute a mean/median shape or image based on population data. In this work, we focus on the statistical characterization of the population data, once spatial alignment has been achieved. We introduce and propose the use of the weighted functional boxplot. This allows the generalization of concepts such as the median, percentiles, or outliers to spaces where the data objects are functions, shapes, or images, and allows spatio-temporal atlas-building based on kernel regression. In our experiments, we demonstrate the utility of the approach to construct statistical atlases for pediatric upper airways and corpora callosa revealing their growth patterns. We also define a score system based on the pediatric airway atlas to quantitatively measure the severity of subglottic stenosis (SGS) in the airway. This scoring allows the classification of pre- and post-surgery SGS subjects and radiographically normal controls. Experimental results show the utility of atlas information to assess the effect of airway surgery in children.

  18. 3D printing of HEK 293FT cell-laden hydrogel into macroporous constructs with high cell viability and normal biological functions.

    PubMed

    Ouyang, Liliang; Yao, Rui; Chen, Xi; Na, Jie; Sun, Wei

    2015-02-18

    3D printing has evolved into a versatile technology for fabricating tissue-engineered constructs with spatially controlled cells and biomaterial distribution to allow biomimicking of in vivo tissues. In this paper, we reported a novel study of 3D printing of cell lines derived from human embryonic kidney tissue into a macroporous tissue-like construct. Nozzle temperature, chamber temperature and the composition of the matrix material were studied to achieve high cell viability (>90%) after 3D printing and construct formation. Long-term construct stability with a clear grid structure up to 30 days was observed. Cells continued to grow as cellular spheroids with strong cell-cell interactions. Two transfected cell lines of HEK 293FT were also 3D printed and showed normal biological functions, i.e. protein synthesis and gene activation in responding to small molecule stimulus. With further refinement, this 3D cell printing technology may lead to a practical fabrication of functional embryonic tissues in vitro.

  19. Pyro-EHD ink-jet printing for direct functionalization of 3D lab-on-chip devices

    NASA Astrophysics Data System (ADS)

    Coppola, S.; Vespini, V.; Bianco, V.; Mecozzi, L.; Olivieri, F.; Todino, M.; Paturzo, M.; Grilli, S.; Ferraro, P.

    2016-03-01

    A challenging request in the fabrication of microfluidics and biomedical microsystems is a flexible ink-jet printing for breaking the rigidity of classical lithography. A pyroelectric-EHD system is presented. The system has proved challenging spatial resolution down to nanoscale, printing of high ordered patterns, capability of dispensing bio-ink as DNA and protein array for biosensing fabrication, single cells printing and direct printing of nanoparticles. With the method proposed high viscous polymers could be easily printed at high resolution in 2D or in 3D configuration. The pyro-EHD process has been proved for the fabrication of biodegradable microneedles for trasndermal drug delivery and 3D optical waveguides.

  20. A framework for geometry acquisition, 3-D printing, simulation, and measurement of head-related transfer functions with a focus on hearing-assistive devices

    PubMed Central

    Harder, Stine; Paulsen, Rasmus R.; Larsen, Martin; Laugesen, Søren; Mihocic, Michael; Majdak, Piotr

    2017-01-01

    Individual head-related transfer functions (HRTFs) are essential in applications like fitting hearing-assistive devices (HADs) for providing accurate sound localization performance. Individual HRTFs are usually obtained through intricate acoustic measurements. This paper investigates the use of a three-dimensional (3D) head model for acquisition of individual HRTFs. Two aspects were investigated; whether a 3D-printed model can replace measurements on a human listener and whether numerical simulations can replace acoustic measurements. For this purpose, HRTFs were acoustically measured for four human listeners and for a 3D printed head model of one of these listeners. Further, HRTFs were simulated by applying the finite element method to the 3D head model. The monaural spectral features and spectral distortions were very similar between re-measurements and between human and printed measurements, however larger deviations were observed between measurement and simulation. The binaural cues were in agreement among all HRTFs of the same listener, indicating that the 3D model is able to provide localization cues potentially accessible to HAD users. Hence, the pipeline of geometry acquisition, printing, and acoustic measurements or simulations, seems to be a promising step forward towards in-silico design of HADs. PMID:28239188

  1. Changes in foot pressure elicited by 3D air balance exercise and pelvic stability exercise for functional leg-length discrepancy in adult women

    PubMed Central

    Lee, Byung-Hoon; Kim, Jeong-Ja; Kim, Chan-Kyu

    2015-01-01

    [Purpose] This study was conducted to examine the effect of pelvic stabilization exercise and 3D equipment exercise on adult women with Functional Leg-Length Discrepancy (FLLD). [Subjects and Methods] Twenty female students in their 20’s having FLLD without Structural Leg Length Discrepancy were selected. Exercise was performed for 50 min per session, three times a week, for six weeks. The Pelvic stabilization exercise (PSE) group performed pelvic stabilization exercises for 50 minutes, and the 3D exercise (3DE) group performed 3D Air Balance exercise for 10 minutes after performing the pelvic stabilization exercise program for 40 minutes. [Results] The PSE group showed statistically significant differences in tape measure method (TMM) and maximum pressure between pre-test and post-test, and 3DE showed statistically significant differences in TMM, the difference in maximum pressure, the difference in average pressure, and the difference in support area. At the end of the 6-week intervention, TMM, difference in maximum pressure, difference in average pressure, and difference in support area showed significantly greater reduction in the 3DE group. [Conclusion] The results show that 3D stabilization exercise was more effective at improving the stabilization of the deep muscles surrounding the pelvis and left-right muscular balance. We consider that 3D exercise should be included in exercise programs for improving pelvic cavity and spinal stability in the future. PMID:25931758

  2. A comparison of US- versus MR-based 3-D Prostate Shapes Using Radial Basis Function Interpolation and Statistical Shape Models.

    PubMed

    Tao, Ran; Tavakoli, Mahdi; Sloboda, Ron; Usmani, Nawaid

    2015-03-01

    This paper presents a comparison of three-dimensional (3-D) segmentations of the prostate, based on two-dimensional (2-D) manually segmented contours, obtained using ultrasound (US) and magnetic resonance (MR) imaging data collected from 40 patients diagnosed with localized prostate cancer and scheduled to receive brachytherapy treatment. The approach we propose here for 3-D prostate segmentation first uses radial basis function interpolation to construct a 3-D point distribution model for each prostate. Next, a modified principal axis transformation is utilized for rigid registration of the US and MR images of the same prostate in preparation for the following shape comparison. Then, statistical shape models are used to capture the segmented 3-D prostate geometries for the subsequent cross-modality comparison. Our study includes not only cross-modality geometric comparisons in terms of prostate volumes and dimensions, but also an investigation of interchangeability of the two imaging modalities in terms of automatic contour segmentation at the pre-implant planning stage of prostate brachytherapy treatment. By developing a new scheme to compare the two imaging modalities in terms of the segmented 3-D shapes, we have taken a first step necessary for building coupled US-MR segmentation strategies for prostate brachytherapy pre-implant planning, which at present is predominantly informed by US images only.

  3. Europeana and 3D

    NASA Astrophysics Data System (ADS)

    Pletinckx, D.

    2011-09-01

    The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.

  4. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  5. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  6. The interplay of fibronectin functionalization and TGF-β1 presence on fibroblast proliferation, differentiation and migration in 3D matrices.

    PubMed

    Sapudom, Jiranuwat; Rubner, Stefan; Martin, Steve; Thoenes, Stephan; Anderegg, Ulf; Pompe, Tilo

    2015-09-01

    Defined biomimetic three-dimensional (3D) matrices are needed to decipher the complex cellular signalling during wound healing at high resolution in vitro. Soluble factors like TGF-β1 and adhesion promoting structural components of the extracellular matrix (ECM) are known to be key regulators of fibroblast behaviour. The ECM component fibronectin (FN) bears a complex function as adhesion promoter, fibrillar element and soluble factor binder. However, its implementation in biomimetic 3D matrices is frequently ill defined. To study the impact of FN on fibroblast cellular function under differentiating conditions (TGF-β1 stimulation), we functionalized 3D collagen I matrices with FN using two strategies: co-assembly and adsorptive immobilization. In comparison to co-assembly, adsorptive immobilization provided no alteration in collagen microstructure as well as mechanical properties. Moreover, this approach provided a controllable FN amount and a homogenous distribution of FN throughout collagen networks. A strong interplay of FN amount and TGF-β1 stimulation on fibroblast function was found in terms of proliferation, migration and myofibroblast differentiation. High levels of FN alone reduced proliferation and showed no effect on differentiation of fibroblasts, but increased migration. In contrast, fibroblast stimulation with high amounts of FN together with TGF-β1 increased proliferation. Independent of FN, the TGF-β1 stimulation enhanced mRNA expression of matrix components like collagen type I alpha 1 chain (Coll I(a1), FN with extra domain A (EDA-FN) and reduced cell migration. The latter cell behaviour indicated a FN independent differentiation into a myofibroblast phenotype. Overall, our 3D biomimetic matrices allow dissecting the overlapping action of the ECM protein FN and the soluble factor TGF-β1 on fibroblast proliferation, migration and differentiation in 3D microenvironments. Furthermore, this model enables the mimicking of important steps of the

  7. On Boundary Misorientation Distribution Functions and How to Incorporate them into 3D Models of Microstructural Evolution

    SciTech Connect

    Godfrey, A.W.; Holm, E.A.; Hughes, D.A.; Miodownik, M.

    1998-12-23

    The fundamental difficulties incorporating experimentally obtained-boundary disorientation distributions (BMD) into 3D microstructural models are discussed. An algorithm is described which overcomes these difficulties. The boundary misorientations are treated as a statistical ensemble which is evolved toward the desired BMD using a Monte Carlo method. The application of this algorithm to a number complex arbitrary BMDs shows that the approach is effective for both conserved and non-conserved textures. The algorithm is successfully used to create the BMDs observed in deformation microstructure containing both incidental dislocation boundaries (IDBs) and geometrically necessary boundaries (GNBs).

  8. PLOT3D user's manual

    NASA Technical Reports Server (NTRS)

    Walatka, Pamela P.; Buning, Pieter G.; Pierce, Larry; Elson, Patricia A.

    1990-01-01

    PLOT3D is a computer graphics program designed to visualize the grids and solutions of computational fluid dynamics. Seventy-four functions are available. Versions are available for many systems. PLOT3D can handle multiple grids with a million or more grid points, and can produce varieties of model renderings, such as wireframe or flat shaded. Output from PLOT3D can be used in animation programs. The first part of this manual is a tutorial that takes the reader, keystroke by keystroke, through a PLOT3D session. The second part of the manual contains reference chapters, including the helpfile, data file formats, advice on changing PLOT3D, and sample command files.

  9. DC Potentials Applied to an End-cap Electrode of a 3-D Ion Trap for Enhanced MSn Functionality

    PubMed Central

    Prentice, Boone M.; Xu, Wei; Ouyang, Zheng; McLuckey, Scott A.

    2010-01-01

    The effects of the application of various DC magnitudes and polarities to an end-cap of a 3-D quadrupole ion trap throughout a mass spectrometry experiment were investigated. Application of a monopolar DC field was achieved by applying a DC potential to the exit end-cap electrode, while maintaining the entrance end-cap electrode at ground potential. Control over the monopolar DC magnitude and polarity during time periods associated with ion accumulation, mass analysis, ion isolation, ion/ion reaction, and ion activation can have various desirable effects. Included amongst these are increased ion capture efficiency, increased ion ejection efficiency during mass analysis, effective isolation of ions using lower AC resonance ejection amplitudes, improved temporal control of the overlap of oppositely charged ion populations, and the performance of “broad-band” collision induced dissociation (CID). These results suggest general means to improve the performance of the 3-D ion trap in a variety of mass spectrometry and tandem mass spectrometry experiments. PMID:21927573

  10. Incorporation of the purified epstein barr virus/C3d receptor (CR2) into liposomes and demonstration of its dual ligand binding functions

    SciTech Connect

    Mold, C.; Cooper, N.R.; Nemerow, G.R.

    1986-06-01

    The 145-kDA molecule that has been identified as the C3d receptor CR2 was isolated from lysates of Raji cells by affinity chromatography by using the monoclonal antibody (MoAb)HB-5. The purified protein was incorporated into /sup 14/C-phosphatidylcholine liposomes by deoxycholate dialysis followed by flotation on discontinuous sucrose gradients. Incorporation of the receptor was verified by testing the gradient fractions for CR2 by an enzyme-linked immunosorbent assay. Liposomes were shown to be unilamellar vesicles ranging in diameter from 25 to 100 nm by electron microscopy. The external orientation of CR2 in the membranes was demonstrated by immunoelectron microscopy. The functional activities of liposomes containing CR2 and liposomes without protein were compared. CR2 liposomes bound to EC3d, but not to E, and this binding was inhibited by the anti-CR2 MoAb OKB7 and by a MoAb specific for C3d. Control liposomes failed to bind to either E or EC3D. The ability of CR2 to function as a receptor for Epstein Barr virus (EBV) was tested in two ways. First, CR2 liposomes bound to B95-8, a cell line expressing EBV membrane antigens, but not to B95-8 cells treated with the viral DNA polymerase inhibitor phosphonoformic acid. Second, liposomes containing CR2 were shown by ultracentrifugal analyses to bind directly to purified EBV, and this binding was also inhibited by OKB7. Control liposomes did not bind to B95-8 cells or to EBV. These findings show that CR2 purified from detergent extracts of Raji cells can be reconstituted into lipid membranes with maintenance of its dual functions as a receptor for C3d and EBV.

  11. Analyzing Structure and Function of Vascularization in Engineered Bone Tissue by Video-Rate Intravital Microscopy and 3D Image Processing

    PubMed Central

    Pang, Yonggang; Tsigkou, Olga; Spencer, Joel A.; Lin, Charles P.; Neville, Craig

    2015-01-01

    Vascularization is a key challenge in tissue engineering. Three-dimensional structure and microcirculation are two fundamental parameters for evaluating vascularization. Microscopic techniques with cellular level resolution, fast continuous observation, and robust 3D postimage processing are essential for evaluation, but have not been applied previously because of technical difficulties. In this study, we report novel video-rate confocal microscopy and 3D postimage processing techniques to accomplish this goal. In an immune-deficient mouse model, vascularized bone tissue was successfully engineered using human bone marrow mesenchymal stem cells (hMSCs) and human umbilical vein endothelial cells (HUVECs) in a poly (d,l-lactide-co-glycolide) (PLGA) scaffold. Video-rate (30 FPS) intravital confocal microscopy was applied in vitro and in vivo to visualize the vascular structure in the engineered bone and the microcirculation of the blood cells. Postimage processing was applied to perform 3D image reconstruction, by analyzing microvascular networks and calculating blood cell viscosity. The 3D volume reconstructed images show that the hMSCs served as pericytes stabilizing the microvascular network formed by HUVECs. Using orthogonal imaging reconstruction and transparency adjustment, both the vessel structure and blood cells within the vessel lumen were visualized. Network length, network intersections, and intersection densities were successfully computed using our custom-developed software. Viscosity analysis of the blood cells provided functional evaluation of the microcirculation. These results show that by 8 weeks, the blood vessels in peripheral areas function quite similarly to the host vessels. However, the viscosity drops about fourfold where it is only 0.8 mm away from the host. In summary, we developed novel techniques combining intravital microscopy and 3D image processing to analyze the vascularization in engineered bone. These techniques have broad

  12. 3d-3d correspondence revisited

    DOE PAGES

    Chung, Hee -Joong; Dimofte, Tudor; Gukov, Sergei; ...

    2016-04-21

    In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d N = 2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. As a result, we also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  13. Structure-Function Studies of Blood and Air Capillaries in Chicken Lung Using 3D Electron Microscopy

    PubMed Central

    West, John B.; Fu, Zhenxing; Deerinck, Thomas J.; Mackey, Mason R.; Obayashi, James T.; Ellisman, Mark H.

    2010-01-01

    Avian pulmonary capillaries differ from those of mammals in three important ways. The blood-gas barrier is much thinner, it is more uniform in thickness, and the capillaries are far more rigid when their transmural pressure is altered. The thinness of the barrier is surprising because it predisposes the capillaries to stress failure. A possible mechanism for these differences is that avian pulmonary capillaries, unlike mammalian, are supported from the outside by air capillaries, but the details of the support are poorly understood. To clarify this we studied the blood and air capillaries in chicken lung using transmission electron microscopy (EM) and two relatively new techniques that allow 3D visualization: electron tomography and serial block-face scanning EM. These studies show that the pulmonary capillaries are flanked by epithelial bridges composed of two extremely thin epithelial cells with large surface areas. The junctions of the bridges with the capillary walls show thickening of the epithelial cells and an accumulation of extracellular matrix. Collapse of the pulmonary capillaries when the pressure outside them is increased is apparently prevented by the guy wire-like action of the epithelial bridges. The enlarged junctions between the bridges and the walls could provide a mechanism that limits the hoop stress in the capillary walls when the pressure inside them is increased. The support of the pulmonary capillaries may also be explained by an interdependence mechanism whereby the capillaries are linked to a rigid assemblage of air capillaries. These EM studies show the supporting structures in greater detail than has previously been possible, particularly in 3D, and they allow a more complete analysis of the mechanical forces affecting avian pulmonary capillaries. PMID:20038456

  14. Axial 3D region of interest reconstruction using weighted cone beam BPF/DBPF algorithm cascaded with adequately oriented orthogonal butterfly filtering

    NASA Astrophysics Data System (ADS)

    Tang, Shaojie; Tang, Xiangyang

    2016-03-01

    Axial cone beam (CB) computed tomography (CT) reconstruction is still the most desirable in clinical applications. As the potential candidates with analytic form for the task, the back projection-filtration (BPF) and the derivative backprojection filtered (DBPF) algorithms, in which Hilbert filtering is the common algorithmic feature, are originally derived for exact helical and axial reconstruction from CB and fan beam projection data, respectively. These two algorithms have been heuristically extended for axial CB reconstruction via adoption of virtual PI-line segments. Unfortunately, however, streak artifacts are induced along the Hilbert filtering direction, since these algorithms are no longer accurate on the virtual PI-line segments. We have proposed to cascade the extended BPF/DBPF algorithm with orthogonal butterfly filtering for image reconstruction (namely axial CB-BPP/DBPF cascaded with orthogonal butterfly filtering), in which the orientation-specific artifacts caused by post-BP Hilbert transform can be eliminated, at a possible expense of losing the BPF/DBPF's capability of dealing with projection data truncation. Our preliminary results have shown that this is not the case in practice. Hence, in this work, we carry out an algorithmic analysis and experimental study to investigate the performance of the axial CB-BPP/DBPF cascaded with adequately oriented orthogonal butterfly filtering for three-dimensional (3D) reconstruction in region of interest (ROI).

  15. 3D Ta/TaO x /TiO2/Ti synaptic array and linearity tuning of weight update for hardware neural network applications

    NASA Astrophysics Data System (ADS)

    Wang, I.-Ting; Chang, Chih-Cheng; Chiu, Li-Wen; Chou, Teyuh; Hou, Tuo-Hung

    2016-09-01

    The implementation of highly anticipated hardware neural networks (HNNs) hinges largely on the successful development of a low-power, high-density, and reliable analog electronic synaptic array. In this study, we demonstrate a two-layer Ta/TaO x /TiO2/Ti cross-point synaptic array that emulates the high-density three-dimensional network architecture of human brains. Excellent uniformity and reproducibility among intralayer and interlayer cells were realized. Moreover, at least 50 analog synaptic weight states could be precisely controlled with minimal drifting during a cycling endurance test of 5000 training pulses at an operating voltage of 3 V. We also propose a new state-independent bipolar-pulse-training scheme to improve the linearity of weight updates. The improved linearity considerably enhances the fault tolerance of HNNs, thus improving the training accuracy.

  16. Combinatorial 3D Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

    Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin

    2015-03-01

    We present a class of elastic structures which exhibit 3D-folding motion. Our structures consist of cubic lattices of anisotropic unit cells that can be tiled in a complex combinatorial fashion. We design and 3d-print this complex ordered mechanism, in which we combine elastic hinges and defects to tailor the mechanics of the material. Finally, we use this large design space to encode smart functionalities such as surface patterning and multistability.

  17. 3D and Education

    NASA Astrophysics Data System (ADS)

    Meulien Ohlmann, Odile

    2013-02-01

    Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible relations of moving objects with subjects? Does this transform our model of exchange with others? What kind of interaction this has with our everyday life? Then come more practical questions: How to learn creating 3D visualization, to learn 3D grammar, 3D language, 3D thinking? What for? At what level? In which matter? for whom?

  18. The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.

    PubMed

    Chen, Brian Y; Fofanov, Viacheslav Y; Bryant, Drew H; Dodson, Bradley D; Kristensen, David M; Lisewski, Andreas M; Kimmel, Marek; Lichtarge, Olivier; Kavraki, Lydia E

    2007-01-01

    The development of new and effective drugs is strongly affected by the need to identify drug targets and to reduce side effects. Resolving these issues depends partially on a thorough understanding of the biological function of proteins. Unfortunately, the experimental determination of protein function is expensive and time consuming. To support and accelerate the determination of protein functions, algorithms for function prediction are designed to gather evidence indicating functional similarity with well studied proteins. One such approach is the MASH pipeline, described in the first half of this paper. MASH identifies matches of geometric and chemical similarity between motifs, representing known functional sites, and substructures of functionally uncharacterized proteins (targets). Observations from several research groups concur that statistically significant matches can indicate functionally related active sites. One major subproblem is the design of effective motifs, which have many matches to functionally related targets (sensitive motifs), and few matches to functionally unrelated targets (specific motifs). Current techniques select and combine structural, physical, and evolutionary properties to generate motifs that mirror functional characteristics in active sites. This approach ignores incidental similarities that may occur with functionally unrelated proteins. To address this problem, we have developed Geometric Sieving (GS), a parallel distributed algorithm that efficiently refines motifs, designed by existing methods, into optimized motifs with maximal geometric and chemical dissimilarity from all known protein structures. In exhaustive comparison of all possible motifs based on the active sites of 10 well-studied proteins, we observed that optimized motifs were among the most sensitive and specific.

  19. 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.

  20. Utility of real-time prospective motion correction (PROMO) on 3D T1-weighted imaging in automated brain structure measurements

    PubMed Central

    Watanabe, Keita; Kakeda, Shingo; Igata, Natsuki; Watanabe, Rieko; Narimatsu, Hidekuni; Nozaki, Atsushi; Dan Rettmann; Abe, Osamu; Korogi, Yukunori

    2016-01-01

    PROspective MOtion correction (PROMO) can prevent motion artefacts. The aim of this study was to determine whether brain structure measurements of motion-corrected images with PROMO were reliable and equivalent to conventional images without motion artefacts. The following T1-weighted images were obtained in healthy subjects: (A) resting scans with and without PROMO and (B) two types of motion scans (“side-to-side” and “nodding” motions) with and without PROMO. The total gray matter volumes and cortical thicknesses were significantly decreased in motion scans without PROMO as compared to the resting scans without PROMO (p < 0.05). Conversely, Bland–Altman analysis indicated no bias between motion scans with PROMO, which have good image quality, and resting scans without PROMO. In addition, there was no bias between resting scans with and without PROMO. The use of PROMO facilitated more reliable brain structure measurements in subjects moving during data acquisition. PMID:27917950

  1. Utility of real-time prospective motion correction (PROMO) on 3D T1-weighted imaging in automated brain structure measurements

    NASA Astrophysics Data System (ADS)

    Watanabe, Keita; Kakeda, Shingo; Igata, Natsuki; Watanabe, Rieko; Narimatsu, Hidekuni; Nozaki, Atsushi; Dan Rettmann; Abe, Osamu; Korogi, Yukunori

    2016-12-01

    PROspective MOtion correction (PROMO) can prevent motion artefacts. The aim of this study was to determine whether brain structure measurements of motion-corrected images with PROMO were reliable and equivalent to conventional images without motion artefacts. The following T1-weighted images were obtained in healthy subjects: (A) resting scans with and without PROMO and (B) two types of motion scans (“side-to-side” and “nodding” motions) with and without PROMO. The total gray matter volumes and cortical thicknesses were significantly decreased in motion scans without PROMO as compared to the resting scans without PROMO (p < 0.05). Conversely, Bland–Altman analysis indicated no bias between motion scans with PROMO, which have good image quality, and resting scans without PROMO. In addition, there was no bias between resting scans with and without PROMO. The use of PROMO facilitated more reliable brain structure measurements in subjects moving during data acquisition.

  2. Adaptive-weighted cubic B-spline using lookup tables for fast and efficient axial resampling of 3D confocal microscopy images.

    PubMed

    Indhumathi, C; Cai, Y Y; Guan, Y Q; Opas, M; Zheng, J

    2012-01-01

    Confocal laser scanning microscopy has become a most powerful tool to visualize and analyze the dynamic behavior of cellular molecules. Photobleaching of fluorochromes is a major problem with confocal image acquisition that will lead to intensity attenuation. Photobleaching effect can be reduced by optimizing the collection efficiency of the confocal image by fast z-scanning. However, such images suffer from distortions, particularly in the z dimension, which causes disparities in the x, y, and z directions of the voxels with the original image stacks. As a result, reliable segmentation and feature extraction of these images may be difficult or even impossible. Image interpolation is especially needed for the correction of undersampling artifact in the axial plane of three-dimensional images generated by a confocal microscope to obtain cubic voxels. In this work, we present an adaptive cubic B-spline-based interpolation with the aid of lookup tables by deriving adaptive weights based on local gradients for the sampling nodes in the interpolation formulae. Thus, the proposed method enhances the axial resolution of confocal images by improving the accuracy of the interpolated value simultaneously with great reduction in computational cost. Numerical experimental results confirm the effectiveness of the proposed interpolation approach and demonstrate its superiority both in terms of accuracy and speed compared to other interpolation algorithms.

  3. NON-INVASIVE 3D FACIAL ANALYSIS AND SURFACE ELECTROMYOGRAPHY DURING FUNCTIONAL PRE-ORTHODONTIC THERAPY: A PRELIMINARY REPORT

    PubMed Central

    Tartaglia, Gianluca M.; Grandi, Gaia; Mian, Fabrizio; Sforza, Chiarella; Ferrario, Virgilio F.

    2009-01-01

    Objectives: Functional orthodontic devices can modify oral function thus permitting more adequate growth processes. The assessment of their effects should include both facial morphology and muscle function. This preliminary study investigated whether a preformed functional orthodontic device could induce variations in facial morphology and function along with correction of oral dysfunction in a group of orthodontic patients in the mixed and early permanent dentitions. Material and Methods: The three-dimensional coordinates of 50 facial landmarks (forehead, eyes, nose, cheeks, mouth, jaw and ears) were collected in 10 orthodontic male patients aged 8-13 years, and in 89 healthy reference boys of the same age. Soft tissue facial angles, distances, and ratios were computed. Surface electromyography of the masseter and temporalis muscles was performed, and standardized symmetry, muscular torque and activity were calculated. Soft-tissue facial modifications were analyzed non-invasively before and after a 6-month treatment with a functional device. Comparisons were made with z-scores and paired Student's t-tests. Results: The 6-month treatment stimulated mandibular growth in the anterior and inferior directions, with significant variations in three-dimensional facial divergence and facial convexity. The modifications were larger in the patients than in reference children. In several occasions, the discrepancies relative to the norm became not significant after treatment. No significant variations in standardized muscular activity were found. Conclusions: Preliminary results showed that the continuous and correct use of the functional device induced measurable intraoral (dental arches) and extraoral (face) morphological modifications. The device did not modify the functional equilibrium of the masticatory muscles. PMID:19936531

  4. High-efficiency and wideband interlayer grating couplers in multilayer Si/SiO2/SiN platform for 3D integration of optical functionalities.

    PubMed

    Sodagar, Majid; Pourabolghasem, Reza; Eftekhar, Ali A; Adibi, Ali

    2014-07-14

    We have designed interlayer grating couplers with single/double metallic reflectors for Si/SiO(2)/SiN multilayer material platform. Out-of-plane diffractive grating couplers separated by 1.6 μm thick buffer SiO(2) layer are vertically stacked against each other in Si and SiN layers. Geometrical optimization using genetic algorithm coupled with electromagnetic simulations using two-dimensional (2D) finite element method (FEM) results in coupler designs with high peak coupling efficiency of up to 89% for double- mirror and 64% for single-mirror structures at telecom wavelength. Also, 3-dB bandwidths of 40 nm and 50 nm are theoretically predicted for the two designs, respectively. We have fabricated the grating coupler structure with single mirror. Measured values for insertion loss and 3-dB bandwidth in the fabricated single-mirror coupler confirms the theoretical results. This opens up the possibility of low-loss 3D dense integration of optical functionalities in hybrid material platforms.

  5. Optical full-depth refocusing of 3-D objects based on subdivided-elemental images and local periodic δ-functions in integral imaging.

    PubMed

    Ai, Ling-Yu; Dong, Xiao-Bin; Jang, Jae-Young; Kim, Eun-Soo

    2016-05-16

    We propose a new approach for optical refocusing of three-dimensional (3-D) objects on their real depth without a pickup-range limitation based on subdivided-elemental image arrays (sub-EIAs) and local periodic δ-function arrays (L-PDFAs). The captured EIA from the 3-D objects locating out of the pickup-range, is divided into a number of sub-EIAs depending on the object distance from the lens array. Then, by convolving these sub-EIAs with each L-PDFA whose spatial period corresponds to the specific object's depth, as well as whose size is matched to that of the sub-EIA, arrays of spatially-filtered sub-EIAs (SF-sub-EIAs) for each object depth can be uniquely extracted. From these arrays of SF-sub-EIAs, 3-D objects can be optically reconstructed to be refocused on their real depth. Operational principle of the proposed method is analyzed based on ray-optics. In addition, to confirm the feasibility of the proposed method in the practical application, experiments with test objects are carried out and the results are comparatively discussed with those of the conventional method.

  6. 3D Imaging.

    ERIC Educational Resources Information Center

    Hastings, S. K.

    2002-01-01

    Discusses 3 D imaging as it relates to digital representations in virtual library collections. Highlights include X-ray computed tomography (X-ray CT); the National Science Foundation (NSF) Digital Library Initiatives; output peripherals; image retrieval systems, including metadata; and applications of 3 D imaging for libraries and museums. (LRW)

  7. Collagen/heparin sulfate scaffolds fabricated by a 3D bioprinter improved mechanical properties and neurological function after spinal cord injury in rats.

    PubMed

    Chen, Chong; Zhao, Ming-Liang; Zhang, Ren-Kun; Lu, Gang; Zhao, Chang-Yu; Fu, Feng; Sun, Hong-Tao; Zhang, Sai; Tu, Yue; Li, Xiao-Hong

    2017-01-25

    Effective treatments promoting axonal regeneration and functional recovery for spinal cord injury (SCI) are still in the early stages of development. Most approaches have been focused on providing supportive substrates for guiding neurons and overcoming the physical and chemical barriers to healing that arise after SCI. Although collagen has become a promising natural substrate with good compatibility, its low mechanical properties restrict its potential applications. The mechanical properties mainly rely on the composition and pore structure of scaffolds. For the composition of a scaffold, we used heparin sulfate to react with collagen by crosslinking. For the structure, we adopted a three-dimensional (3D) printing technology to fabricate a scaffold with a uniform pore distributions. We observed that the internal structure of the scaffold printed with a 3D bioprinter was regular and porous. We also found that both the compression modulus and strengths of the scaffold were significantly enhanced by the collagen/heparin sulfate composition compared to a collagen scaffold. Meanwhile, the collagen/heparin sulfate scaffold presented good biocompatibility when it was co-cultured with neural stem cells in vitro. We also demonstrated that heparin sulfate modification significantly improved bFGF immobilization and absorption to the collagen by examining the release kinetics of bFGF from scaffolds. Two months after implantating the scaffold into transection lesions in T10 of the spinal cord in rats, the collagen/heparin sulfate group demonstrated significant recovery of locomotor function and according to electrophysiological examinations. Parallel to functional recovery, collagen/heparin sulfate treatment further ameliorated the pathological process and markedly increased the number of neurofilament (NF) positive cells compared to collagen treatment alone. These data suggested that a collagen/heparin sulfate scaffold fabricated by a 3D bioprinter could enhance the

  8. Novel 3D Culture Systems for Studies of Human Liver Function and Assessments of the Hepatotoxicity of Drugs and Drug Candidates.

    PubMed

    Lauschke, Volker M; Hendriks, Delilah F G; Bell, Catherine C; Andersson, Tommy B; Ingelman-Sundberg, Magnus

    2016-12-19

    The liver is an organ with critical importance for drug treatment as the disposition and response to a given drug is often determined by its hepatic metabolism. Patient-specific factors can entail increased susceptibility to drug-induced liver injury, which constitutes a major risk for drug development programs causing attrition of promising drug candidates or costly withdrawals in postmarketing stages. Hitherto, mainly animal studies and 2D hepatocyte systems have been used for the examination of human drug metabolism and toxicity. Yet, these models are far from satisfactory due to extensive species differences and because hepatocytes in 2D cultures rapidly dedifferentiate resulting in the loss of their hepatic phenotype and functionality. With the increasing comprehension that 3D cell culture systems more accurately reflect in vivo physiology, in the recent decade more and more research has focused on the development and optimization of various 3D culture strategies in an attempt to preserve liver properties in vitro. In this contribution, we critically review these developments, which have resulted in an arsenal of different static and perfused 3D models. These systems include sandwich-cultured hepatocytes, spheroid culture platforms, and various microfluidic liver or multiorgan biochips. Importantly, in many of these models hepatocytes maintain their phenotype for prolonged times, which allows probing the potential of newly developed chemical entities to cause chronic hepatotoxicity. Moreover, some platforms permit the investigation of drug action in specific genetic backgrounds or diseased hepatocytes, thereby significantly expanding the repertoire of tools to detect drug-induced liver injuries. It is concluded that the development of 3D liver models has hitherto been fruitful and that systems are now at hand whose sensitivity and specificity in detecting hepatotoxicity are superior to those of classical 2D culture systems. For the future, we highlight the

  9. Executive functions predict weight loss in a medically supervised weight loss programme

    PubMed Central

    Bond, D.; Gunstad, J.; Pera, V.; Rathier, L.; Tremont, G.

    2016-01-01

    Summary Background Deficits in executive functions are related to poorer weight loss after bariatric surgery; however, less is known about the role that these deficits may play during participation in nonsurgical weight loss programmes. This study examined associations between objectively measured executive functions and weight loss during participation in a medically supervised weight loss programme. Methods Twenty‐three adult patients (age 50.4 ± 15.1, BMI 44.2 ± 8.8, 68% female, 92% White) enrolled in a medically supervised weight loss programme, involving prescription of a very low calorie diet and strategies to change eating and activity behaviours, underwent comprehensive computerized testing of executive functions at baseline. Weight was obtained at baseline and 8 weeks. Demographic and clinical information were obtained through medical chart review. Results Participants lost an average of 9.8 ± 3.4% of their initial body weight at 8 weeks. Fewer correct responses on a set‐shifting task and faster reaction time on a response inhibition task were associated with lower weight loss percentage at 8 weeks after adjusting for age, education and depressive symptoms. There were no associations between performance on tests of working memory or planning and weight loss. Conclusions This study shows that worse performance on a set‐shifting task (indicative of poorer cognitive flexibility) and faster reaction times on a response inhibition test (indicative of higher impulsivity) are associated with lower weight loss among participants in a medically supervised weight loss programme. Pre‐treatment assessment of executive functions may be useful in identifying individuals who may be at risk for suboptimal treatment outcomes. Future research is needed to replicate these findings in larger samples and identify underlying mechanisms. PMID:28090338

  10. Development of microgravity, full body functional reach envelope using 3-D computer graphic models and virtual reality technology

    NASA Technical Reports Server (NTRS)

    Lindsey, Patricia F.

    1994-01-01

    In microgravity conditions mobility is greatly enhanced and body stability is difficult to achieve. Because of these difficulties, optimum placement and accessibility of objects and controls can be critical to required tasks on board shuttle flights or on the proposed space station. Anthropometric measurement of the maximum reach of occupants of a microgravity environment provide knowledge about maximum functional placement for tasking situations. Calculations for a full body, functional reach envelope for microgravity environments are imperative. To this end, three dimensional computer modeled human figures, providing a method of anthropometric measurement, were used to locate the data points that define the full body, functional reach envelope. Virtual reality technology was utilized to enable an occupant of the microgravity environment to experience movement within the reach envelope while immersed in a simulated microgravity environment.

  11. 3D Printed Bionic Nanodevices.

    PubMed

    Kong, Yong Lin; Gupta, Maneesh K; Johnson, Blake N; McAlpine, Michael C

    2016-06-01

    The ability to three-dimensionally interweave biological and functional materials could enable the creation of bionic devices possessing unique and compelling geometries, properties, and functionalities. Indeed, interfacing high performance active devices with biology could impact a variety of fields, including regenerative bioelectronic medicines, smart prosthetics, medical robotics, and human-machine interfaces. Biology, from the molecular scale of DNA and proteins, to the macroscopic scale of tissues and organs, is three-dimensional, often soft and stretchable, and temperature sensitive. This renders most biological platforms incompatible with the fabrication and materials processing methods that have been developed and optimized for functional electronics, which are typically planar, rigid and brittle. A number of strategies have been developed to overcome these dichotomies. One particularly novel approach is the use of extrusion-based multi-material 3D printing, which is an additive manufacturing technology that offers a freeform fabrication strategy. This approach addresses the dichotomies presented above by (1) using 3D printing and imaging for customized, hierarchical, and interwoven device architectures; (2) employing nanotechnology as an enabling route for introducing high performance materials, with the potential for exhibiting properties not found in the bulk; and (3) 3D printing a range of soft and nanoscale materials to enable the integration of a diverse palette of high quality functional nanomaterials with biology. Further, 3D printing is a multi-scale platform, allowing for the incorporation of functional nanoscale inks, the printing of microscale features, and ultimately the creation of macroscale devices. This blending of 3D printing, novel nanomaterial properties, and 'living' platforms may enable next-generation bionic systems. In this review, we highlight this synergistic integration of the unique properties of nanomaterials with the

  12. Radiologic-Pathologic Analysis of Contrast-enhanced and Diffusion-weighted MR Imaging in Patients with HCC after TACE: Diagnostic Accuracy of 3D Quantitative Image Analysis

    PubMed Central

    Chapiro, Julius; Wood, Laura D.; Lin, MingDe; Duran, Rafael; Cornish, Toby; Lesage, David; Charu, Vivek; Schernthaner, Rüdiger; Wang, Zhijun; Tacher, Vania; Savic, Lynn Jeanette; Kamel, Ihab R.

    2014-01-01

    Purpose To evaluate the diagnostic performance of three-dimensional (3Dthree-dimensional) quantitative enhancement-based and diffusion-weighted volumetric magnetic resonance (MR) imaging assessment of hepatocellular carcinoma (HCChepatocellular carcinoma) lesions in determining the extent of pathologic tumor necrosis after transarterial chemoembolization (TACEtransarterial chemoembolization). Materials and Methods This institutional review board–approved retrospective study included 17 patients with HCChepatocellular carcinoma who underwent TACEtransarterial chemoembolization before surgery. Semiautomatic 3Dthree-dimensional volumetric segmentation of target lesions was performed at the last MR examination before orthotopic liver transplantation or surgical resection. The amount of necrotic tumor tissue on contrast material–enhanced arterial phase MR images and the amount of diffusion-restricted tumor tissue on apparent diffusion coefficient (ADCapparent diffusion coefficient) maps were expressed as a percentage of the total tumor volume. Visual assessment of the extent of tumor necrosis and tumor response according to European Association for the Study of the Liver (EASLEuropean Association for the Study of the Liver) criteria was performed. Pathologic tumor necrosis was quantified by using slide-by-slide segmentation. Correlation analysis was performed to evaluate the predictive values of the radiologic techniques. Results At histopathologic examination, the mean percentage of tumor necrosis was 70% (range, 10%–100%). Both 3Dthree-dimensional quantitative techniques demonstrated a strong correlation with tumor necrosis at pathologic examination (R2 = 0.9657 and R2 = 0.9662 for quantitative EASLEuropean Association for the Study of the Liver and quantitative ADCapparent diffusion coefficient, respectively) and a strong intermethod agreement (R2 = 0.9585). Both methods showed a significantly lower discrepancy with pathologically measured necrosis (residual

  13. 3D carotid plaque MR Imaging

    PubMed Central

    Parker, Dennis L.

    2015-01-01

    SYNOPSIS There has been significant progress made in 3D carotid plaque magnetic resonance imaging techniques in recent years. 3D plaque imaging clearly represents the future in clinical use. With effective flow suppression techniques, choices of different contrast weighting acquisitions, and time-efficient imaging approaches, 3D plaque imaging offers flexible imaging plane and view angle analysis, large coverage, multi-vascular beds capability, and even can be used in fast screening. PMID:26610656

  14. Functional Loss of Semaphorin 3C and/or Semaphorin 3D and Their Epistatic Interaction with Ret Are Critical to Hirschsprung Disease Liability

    PubMed Central

    Jiang, Qian; Arnold, Stacey; Heanue, Tiffany; Kilambi, Krishna Praneeth; Doan, Betty; Kapoor, Ashish; Ling, Albee Yun; Sosa, Maria X.; Guy, Moltu; Jiang, Qingguang; Burzynski, Grzegorz; West, Kristen; Bessling, Seneca; Griseri, Paola; Amiel, Jeanne; Fernandez, Raquel M.; Verheij, Joke B.G.M.; Hofstra, Robert M.W.; Borrego, Salud; Lyonnet, Stanislas; Ceccherini, Isabella; Gray, Jeffrey J.; Pachnis, Vassilis; McCallion, Andrew S.; Chakravarti, Aravinda

    2015-01-01

    Innervation of the gut is segmentally lost in Hirschsprung disease (HSCR), a consequence of cell-autonomous and non-autonomous defects in enteric neuronal cell differentiation, proliferation, migration, or survival. Rare, high-penetrance coding variants and common, low-penetrance non-coding variants in 13 genes are known to underlie HSCR risk, with the most frequent variants in the ret proto-oncogene (RET). We used a genome-wide association (220 trios) and replication (429 trios) study to reveal a second non-coding variant distal to RET and a non-coding allele on chromosome 7 within the class 3 Semaphorin gene cluster. Analysis in Ret wild-type and Ret-null mice demonstrates specific expression of Sema3a, Sema3c, and Sema3d in the enteric nervous system (ENS). In zebrafish embryos, sema3 knockdowns show reduction of migratory ENS precursors with complete ablation under conjoint ret loss of function. Seven candidate receptors of Sema3 proteins are also expressed within the mouse ENS and their expression is also lost in the ENS of Ret-null embryos. Sequencing of SEMA3A, SEMA3C, and SEMA3D in 254 HSCR-affected subjects followed by in silico protein structure modeling and functional analyses identified five disease-associated alleles with loss-of-function defects in semaphorin dimerization and binding to their cognate neuropilin and plexin receptors. Thus, semaphorin 3C/3D signaling is an evolutionarily conserved regulator of ENS development whose dys-regulation is a cause of enteric aganglionosis. PMID:25839327

  15. Using anisotropic 3D Minkowski functionals for trabecular bone characterization and biomechanical strength prediction in proximal femur specimens

    NASA Astrophysics Data System (ADS)

    Nagarajan, Mahesh B.; De, Titas; Lochmüller, Eva-Maria; Eckstein, Felix; Wismüller, Axel

    2014-04-01

    The ability of Anisotropic Minkowski Functionals (AMFs) to capture local anisotropy while evaluating topological properties of the underlying gray-level structures has been previously demonstrated. We evaluate the ability of this approach to characterize local structure properties of trabecular bone micro-architecture in ex vivo proximal femur specimens, as visualized on multi-detector CT, for purposes of biomechanical bone strength prediction. To this end, volumetric AMFs were computed locally for each voxel of volumes of interest (VOI) extracted from the femoral head of 146 specimens. The local anisotropy captured by such AMFs was quantified using a fractional anisotropy measure; the magnitude and direction of anisotropy at every pixel was stored in histograms that served as a feature vectors that characterized the VOIs. A linear multi-regression analysis algorithm was used to predict the failure load (FL) from the feature sets; the predicted FL was compared to the true FL determined through biomechanical testing. The prediction performance was measured by the root mean square error (RMSE) for each feature set. The best prediction performance was obtained from the fractional anisotropy histogram of AMF Euler Characteristic (RMSE = 1.01 ± 0.13), which was significantly better than MDCT-derived mean BMD (RMSE = 1.12 ± 0.16, p<0.05). We conclude that such anisotropic Minkowski Functionals can capture valuable information regarding regional trabecular bone quality and contribute to improved bone strength prediction, which is important for improving the clinical assessment of osteoporotic fracture risk.

  16. Computational chemistry study of 3D-structure-function relationships for enzymes based on Markov models for protein electrostatic, HINT, and van der Waals potentials.

    PubMed

    Concu, Riccardo; Podda, Gianni; Uriarte, Eugenio; González-Díaz, Humberto

    2009-07-15

    In a significant work, Dobson and Doig (J Mol Biol 2003, 330, 771) illustrated protein prediction as enzymatic or not from spatial structure without resorting to alignments. They used 52 protein features and a nonlinear support vector machine model to classify more than 1000 proteins collected from the PDB with a 77% overall accuracy. The most useful features were: the secondary-structure content, the amino acid frequencies, the number of disulphide bonds, and the largest cleft size. Working on the same dataset used by D&D, in this article we reported a good and simple model, based on the Markov chain models (MCM), to classify protein 3D structures as enzymatic or not, taking into consideration the spatial structure without resorting to alignments. Here we define, for the first time, a general MCM to calculate the electrostatic potential, molecular vibrations, van der Waals (vdw) interactions, and hydrophobic interactions (HINT) and use them in comparative studies of potential fields and/or protein function prediction. The dataset is composed of 1371 proteins divided into 689 enzymes and 682 nonenzymes, all proteins were collected from the PDB. The best model we found was a linear model carried out with the linear discriminant analysis; it was able to classify 74.18% of the proteins using only two electrostatic potentials. In the work described here, we define 3D-HINT potentials (mu(k)) and use them for the first time to derive a classifier for protein enzymes. We analyzed ROC curves, domain of applicability, parametric assumptions, desirability maps, and also tested other nonlinear artificial neural network models which did not improve the linear model. In closing, this MCM allows a fast calculation and comparison of different potentials deriving into accurate protein 3D structure-function relationships, notably simpler than the previous.

  17. Application of the Minkowski functionals in 3D to high-resolution MR images of trabecular bone: prediction of the biomechanical strength by nonlinear topological measures

    NASA Astrophysics Data System (ADS)

    Boehm, Holger F.; Link, Thomas M.; Monetti, Roberto A.; Mueller, Dirk; Rummeny, Ernst J.; Newitt, David; Majumdar, Sharmila; Raeth, Christoph W.

    2004-05-01

    Multi-dimensional convex objects can be characterized with respect to shape, structure, and the connectivity of their components using a set of morphological descriptors known as the Minkowski functionals. In a 3D Euclidian space, these correspond to volume, surface area, mean integral curvature, and the Euler-Poincaré characteristic. We introduce the Minkowski functionals to medical image processing for the morphological analysis of trabecular bone tissue. In the context of osteoporosis-a metabolic disorder leading to a weakening of bone due to deterioration of micro-architecture-the structure of bone increasingly gains attention in the quantification of bone quality. The trabecular architecture of healthy cancellous bone consists of a complex 3D system of inter-connected mineralised elements whereas in osteoporosis the micro-structure is dominated by gaps and disconnections. At present, the standard parameter for diagnosis and assessment of fracture risk in osteoporosis is the bone mineral density (BMD) - a bulk measure of mineralisation irrespective of structural texture characteristics. With the development of modern imaging modalities (high resolution MRI, micro-CT) with spatial resolutions allowing to depict individual trabeculae bone micro-architecture has successfully been analysed using linear, 2- dimensional structural measures adopted from standard histo-morphometry. The preliminary results of our study demonstrate that due to the complex - i.e. the non-linear - network of trabecular bone structures non-linear measures in 3D are superior to linear ones in predicting mechanical properties of trabecular bone from structural information extracted from high resolution MR image data.

  18. Software to compute elastostatic Green's functions for sources in 3D homogeneous elastic layers above a (visco)elastic halfspace

    NASA Astrophysics Data System (ADS)

    Bradley, A. M.; Segall, P.

    2012-12-01

    We describe software, in development, to calculate elastostatic displacement Green's functions and their derivatives for point and polygonal dislocations in three-dimensional homogeneous elastic layers above an elastic or a viscoelastic halfspace. The steps to calculate a Green's function for a point source at depth zs are as follows. 1. A grid in wavenumber space is chosen. 2. A six-element complex rotated stress-displacement vector x is obtained at each grid point by solving a two-point boundary value problem (2P-BVP). If the halfspace is viscoelastic, the solution is inverse Laplace transformed. 3. For each receiver, x is propagated to the receiver depth zr (often zr = 0) and then, 4, inverse Fourier transformed, with the Fourier component corresponding to the receiver's horizontal position. 5. The six elements are linearly combined into displacements and their derivatives. The dominant work is in step 2. The grid is chosen to represent the wavenumber-space solution with as few points as possible. First, the wavenumber space is transformed to increase sampling density near 0 wavenumber. Second, a tensor-product grid of Chebyshev points of the first kind is constructed in each quadrant of the transformed wavenumber space. Moment-tensor-dependent symmetries further reduce work. The numerical solution of the 2P-BVP problem in step 2 involves solving a linear equation A x = b. Half of the elements of x are of geophysical interest; the subset depends on whether zr ≤ zs. Denote these \\hat x. As wavenumber k increases, \\hat x can become inaccurate in finite precision arithmetic for two reasons: 1. The condition number of A becomes too large. 2. The norm-wise relative error (NWRE) in \\hat x is large even though it is small in x. To address this problem, a number of researchers have used determinants to obtain x. This may be the best approach for 6-dimensional or smaller 2P-BVP, where the combinatorial increase in work is still moderate. But there is an alternative

  19. AE3D

    SciTech Connect

    Spong, Donald A

    2016-06-20

    AE3D solves for the shear Alfven eigenmodes and eigenfrequencies in a torodal magnetic fusion confinement device. The configuration can be either 2D (e.g. tokamak, reversed field pinch) or 3D (e.g. stellarator, helical reversed field pinch, tokamak with ripple). The equations solved are based on a reduced MHD model and sound wave coupling effects are not currently included.

  20. Normal-mode function representation of global 3-D data sets: open-access software for the atmospheric research community

    NASA Astrophysics Data System (ADS)

    Žagar, N.; Kasahara, A.; Terasaki, K.; Tribbia, J.; Tanaka, H.

    2015-04-01

    This article presents new software for the analysis of global dynamical fields in (re)analyses, weather forecasts and climate models. A new diagnostic tool, developed within the MODES project, allows one to diagnose properties of balanced and inertio-gravity (IG) circulations across many scales. In particular, the IG spectrum, which has only recently become observable, can be studied simultaneously in the mass and wind fields while considering the whole model depth in contrast to the majority of studies. The paper includes the theory of normal-mode function (NMF) expansion, technical details of the Fortran 90 code, examples of namelists which control the software execution and outputs of the software application on the ERA Interim reanalysis data set. The applied libraries and default compiler are from the open-source domain. A limited understanding of Fortran suffices for the successful implementation of the software. The presented application of the software to the ERA Interim data set reveals several aspects of the large-scale circulation after it has been partitioned into the linearly balanced and IG components. The global energy distribution is dominated by the balanced energy while the IG modes contribute around 10% of the total wave energy. However, on sub-synoptic scales, IG energy dominates and it is associated with the main features of tropical variability on all scales. The presented energy distribution and features of the zonally averaged and equatorial circulation provide a reference for the validation of climate models.

  1. Molecular cloning of XYL3 (D-xylulokinase) from Pichia stipitis and characterization of its physiological function.

    PubMed

    Jin, Yong-Su; Jones, Sharon; Shi, Nian-Qing; Jeffries, Thomas W

    2002-03-01

    XYL3, which encodes a D-xylulokinase (EC 2.7.1.17), was isolated from Pichia stipitis CBS 6054 genomic DNA by using primers designed against conserved motifs. Disruption of XYL3 eliminated D-xylulokinase activity, but D-ribulokinase activity was still present. Southern analysis of P. stipitis genomic DNA with XYL3 as a probe confirmed the disruption and did not reveal additional related genes. Disruption of XYL3 stopped ethanol production from xylose, but the resulting mutant still assimilated xylose slowly and formed xylitol and arabinitol. These results indicate that XYL3 is critical for ethanol production from xylose but that P. stipitis has another pathway for xylose assimilation. Expression of XYL3 using its P. stipitis promoter increased Saccharomyces cerevisiae D-xylulose consumption threefold and enabled the transformants to produce ethanol from a mixture of xylose and xylulose, whereas the parental strain only accumulated xylitol. In vitro, D-xylulokinase activity in recombinant S. cerevisiae was sixfold higher with a multicopy than with a single-copy XYL3 plasmid, but ethanol production decreased with increased copy number. These results confirmed the function of XYL3 in S. cerevisiae.

  2. Functional, biochemical and 3D studies of Mycobacterium tuberculosis protein peptides for an effective anti-tuberculosis vaccine.

    PubMed

    Ocampo, Marisol; Patarroyo, Manuel A; Vanegas, Magnolia; Alba, Martha P; Patarroyo, Manuel E

    2014-05-01

    Tuberculosis (TB) is an air-born, transmissible disease, having an estimated 9.4 million new TB cases worldwide in 2009. Eventual control of this disease by developing a safe and efficient new vaccine able to detain its spread will have an enormous impact on public health policy. Selecting potential antigens to be included in a multi-epitope, minimal subunit-based, chemically-synthesized vaccine containing the minimum sequences needed for blocking mycobacterial interaction with host cells is a complex task due to the multiple mechanisms involved in M. tuberculosis infection and the mycobacterium's immune evasion mechanisms. Our methodology, described here takes into account a highly robust, specific, sensitive and functional approach to the search for potential epitopes to be included in an anti-TB vaccine; it has been based on identifying short mycobacterial protein fragments using synthetic peptides having high affinity interaction with alveolar epithelial cells (A549) and monocyte-derived macrophages (U937) which are able to block the microorganism's entry to target cells in in vitro assays. This manuscript presents a review of the results obtained with some of the MTB H37Rv proteins studied to date, aimed at using these high activity binding peptides (HABPs) as platforms to be included in a minimal subunit-based, multiepitope, chemically-synthesized, antituberculosis vaccine.

  3. A 3-D crustal and uppermost mantle model of the western US from receiver functions and surface wave dispersion derived from ambient noise and teleseismic earthquakes

    NASA Astrophysics Data System (ADS)

    Shen, W.; Schulte-Pelkum, V.; Ritzwoller, M. H.

    2011-12-01

    The joint inversion of surface wave dispersion and receiver functions was proven feasible on a station by station basis more than a decade ago. Joint application to a large number of stations across a broad region such as western US is more challenging, however, because of the different resolutions of the two methods. Improvements in resolution in surface wave studies derived from ambient noise and array-based methods applied to earthquake data now allow surface wave dispersion and receiver functions to be inverted simultaneously across much of the Earthscope/USArray Transportable Array (TA), and we have developed a Monte-Carlo procedure for this purpose. As a proof of concept we applied this procedure to a region containing 186 TA stations in the intermountain west, including a variety of tectonic settings such as the Colorado Plateau, the Basin and Range, the Rocky Mountains, and the Great Plains. This work has now been expanded to encompass all TA stations in the western US. Our approach includes three main components. (1) We enlarge the Earthscope Automated Receiver Survey (EARS) receiver function database by adding more events within a quality control procedure. A back-azimuth-independent receiver function and its associated uncertainties are constructed using a harmonic stripping algorithm. (2) Rayleigh wave dispersion curves are generated from the eikonal tomography applied to ambient noise cross-correlation data and Helmoholtz tomography applied to teleseismic surface wave data to yield dispersion maps from 8 sec to 80 sec period. (3) We apply a Metropolis Monte Carlo algorithm to invert for the average velocity structure beneath each station. Simple kriging is applied to interpolate to the discrete results into a continuous 3-D model. This method has now been applied to over 1,000 TA stations in the western US. We show that the receiver functions and surface wave dispersion data can be reconciled beneath more than 80% of the stations using a smooth

  4. Cell-based approach for 3D reconstruction of lymphatic capillaries in vitro reveals distinct functions of HGF and VEGF-C in lymphangiogenesis.

    PubMed

    Gibot, Laure; Galbraith, Todd; Kloos, Bryan; Das, Suvendu; Lacroix, Dan A; Auger, François A; Skobe, Mihaela

    2016-02-01

    Regeneration of lymphatic vessels is important for treatment of various disorders of lymphatic system and for restoration of lymphatic function after surgery. We have developed a method for generating a human 3D lymphatic vascular construct. In this system, human lymphatic endothelial cells, co-cultured with fibroblasts, spontaneously organized into a stable 3D lymphatic capillary network without the use of any exogenous factors. In vitro-generated lymphatic capillaries exhibited the major molecular and ultra-structural features of native, human lymphatic microvasculature: branches in the three dimensions, wide lumen, blind ends, overlapping borders, adherens and tight junctions, anchoring filaments, lack of mural cells, and poorly developed basement membrane. Furthermore, we show that fibroblast-derived VEGF-C and HGF cooperate in the formation of lymphatic vasculature by activating ERK1/2 signaling, and demonstrate distinct functions of HGF/c-Met and VEGF-C/VEGFR-3 in lymphangiogenesis. This lymphatic vascular construct is expected to facilitate studies of lymphangiogenesis in vitro and it holds promise as a strategy for regeneration of lymphatic vessels and treatment of lymphatic disorders in various conditions.

  5. Identification of the critical residues for the function of vacuolar H⁺-pyrophosphatase by mutational analysis based on the 3D structure.

    PubMed

    Asaoka, Mariko; Segami, Shoji; Maeshima, Masayoshi

    2014-12-01

    H(+)-translocating pyrophosphatase (H(+)-PPase) converts energy from hydrolysis of inorganic pyrophosphate (PPi) to active H(+) translocation across membranes. From the 3D structure resolved by crystallography, 17 amino acid residues in several domains of mung bean (Vigna radiata) enzyme were selected and substituted with alanine individually. The mutant enzymes were expressed in yeast cells to evaluate their biochemical role. The highly conserved residues in the substrate-binding site (T249, D269, D507 and N534) were shown to be essential for PPi hydrolysis and H(+) pump. The amino acid substitution of residues in the H(+) translocation pathway (I545, L555, N738, V746 and L749) resulted in mild decrease in the PPase activity and strong suppression of the H(+) pump. These results suggest that the decoupling of PPi hydrolysis and active H(+) translocation occurred in these five mutants including I545A. The alanine substitution of the C124 and C132, which form an intra-molecular disulfide bond, did not affect the enzyme activity. The modifications of the other residues in the vacuolar lumen loop, and M15 had relatively mild effect on the enzyme function. Functional roles of the 17 residues are discussed with consideration of the 3D structural information.

  6. A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy Studies.

    PubMed

    Marquart, Gregory D; Tabor, Kathryn M; Brown, Mary; Strykowski, Jennifer L; Varshney, Gaurav K; LaFave, Matthew C; Mueller, Thomas; Burgess, Shawn M; Higashijima, Shin-Ichi; Burgess, Harold A

    2015-01-01

    Transgenic methods enable the selective manipulation of neurons for functional mapping of neuronal circuits. Using confocal microscopy, we have imaged the cellular-level expression of 109 transgenic lines in live 6 day post fertilization larvae, including 80 Gal4 enhancer trap lines, 9 Cre enhancer trap lines and 20 transgenic lines that express fluorescent proteins in defined gene-specific patterns. Image stacks were acquired at single micron resolution, together with a broadly expressed neural marker, which we used to align enhancer trap reporter patterns into a common 3-dimensional reference space. To facilitate use of this resource, we have written software that enables searching for transgenic lines that label cells within a selectable 3-dimensional region of interest (ROI) or neuroanatomical area. This software also enables the intersectional expression of transgenes to be predicted, a feature which we validated by detecting cells with co-expression of Cre and Gal4. Many of the imaged enhancer trap lines show intrinsic brain-specific expression. However, to increase the utility of lines that also drive expression in non-neuronal tissue we have designed a novel UAS reporter, that suppresses expression in heart, muscle, and skin through the incorporation of microRNA binding sites in a synthetic 3' untranslated region. Finally, we mapped the site of transgene integration, thus providing molecular identification of the expression pattern for most lines. Cumulatively, this library of enhancer trap lines provides genetic access to 70% of the larval brain and is therefore a powerful and broadly accessible tool for the dissection of neural circuits in larval zebrafish.

  7. Flow shear stress regulates endothelial barrier function and expression of angiogenic factors in a 3D microfluidic tumor vascular model

    PubMed Central

    Buchanan, Cara F; Verbridge, Scott S; Vlachos, Pavlos P; Rylander, Marissa Nichole

    2014-01-01

    Endothelial cells lining blood vessels are exposed to various hemodynamic forces associated with blood flow. These include fluid shear, the tangential force derived from the friction of blood flowing across the luminal cell surface, tensile stress due to deformation of the vessel wall by transvascular flow, and normal stress caused by the hydrodynamic pressure differential across the vessel wall. While it is well known that these fluid forces induce changes in endothelial morphology, cytoskeletal remodeling, and altered gene expression, the effect of flow on endothelial organization within the context of the tumor microenvironment is largely unknown. Using a previously established microfluidic tumor vascular model, the objective of this study was to investigate the effect of normal (4 dyn/cm2), low (1 dyn/cm2), and high (10 dyn/cm2) microvascular wall shear stress (WSS) on tumor-endothelial paracrine signaling associated with angiogenesis. It is hypothesized that high WSS will alter the endothelial phenotype such that vascular permeability and tumor-expressed angiogenic factors are reduced. Results demonstrate that endothelial permeability decreases as a function of increasing WSS, while co-culture with tumor cells increases permeability relative to mono-cultures. This response is likely due to shear stress-mediated endothelial cell alignment and tumor-VEGF-induced permeability. In addition, gene expression analysis revealed that high WSS (10 dyn/cm2) significantly down-regulates tumor-expressed MMP9, HIF1, VEGFA, ANG1, and ANG2, all of which are important factors implicated in tumor angiogenesis. This result was not observed in tumor mono-cultures or static conditioned media experiments, suggesting a flow-mediated paracrine signaling mechanism exists with surrounding tumor cells that elicits a change in expression of angiogenic factors. Findings from this work have significant implications regarding low blood velocities commonly seen in the tumor vasculature

  8. A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy Studies

    PubMed Central

    Marquart, Gregory D.; Tabor, Kathryn M.; Brown, Mary; Strykowski, Jennifer L.; Varshney, Gaurav K.; LaFave, Matthew C.; Mueller, Thomas; Burgess, Shawn M.; Higashijima, Shin-ichi; Burgess, Harold A.

    2015-01-01

    Transgenic methods enable the selective manipulation of neurons for functional mapping of neuronal circuits. Using confocal microscopy, we have imaged the cellular-level expression of 109 transgenic lines in live 6 day post fertilization larvae, including 80 Gal4 enhancer trap lines, 9 Cre enhancer trap lines and 20 transgenic lines that express fluorescent proteins in defined gene-specific patterns. Image stacks were acquired at single micron resolution, together with a broadly expressed neural marker, which we used to align enhancer trap reporter patterns into a common 3-dimensional reference space. To facilitate use of this resource, we have written software that enables searching for transgenic lines that label cells within a selectable 3-dimensional region of interest (ROI) or neuroanatomical area. This software also enables the intersectional expression of transgenes to be predicted, a feature which we validated by detecting cells with co-expression of Cre and Gal4. Many of the imaged enhancer trap lines show intrinsic brain-specific expression. However, to increase the utility of lines that also drive expression in non-neuronal tissue we have designed a novel UAS reporter, that suppresses expression in heart, muscle, and skin through the incorporation of microRNA binding sites in a synthetic 3′ untranslated region. Finally, we mapped the site of transgene integration, thus providing molecular identification of the expression pattern for most lines. Cumulatively, this library of enhancer trap lines provides genetic access to 70% of the larval brain and is therefore a powerful and broadly accessible tool for the dissection of neural circuits in larval zebrafish. PMID:26635538

  9. A study on the flip angle for an optimal T1-weighted image based on the 3D-THRIVE MRI technique: Focusing on the detection of a hepatocellular carcinoma (HCC)

    NASA Astrophysics Data System (ADS)

    Dong, Kyung-Rae; Goo, Eun-Hoe; Lee, Jae-Seung; Chung, Woon-Kwan; Kim, Young-Jae

    2014-04-01

    This study examined the optimal flip angle (FA) for a T1-weighted image in the detection of a hepatocellular carcinoma (HCC). A 3D-T1-weighted high-resolution isotropic volume examination (THRIVE) technique was used to determine the dependence of the signal to noise ratio (SNR) and the contrast-to-noise ratio (CNR) on the change in FA. This study targeted 40 liver cancer patients (25 men and 15 women aged 50 to 70 years with a mean age of 60.32 ± 6.2 years) who visited this hospital to undergo an abdominal MRI examination from January to June 2013. A 3.0 Tesla MRI machine (Philips, Medical System, Achieva) and a MRI receiver coil for data reception with a 16-channel multicoil were used in this study. The THRIVE (repetition time (TR): 8.1 ms, echo time (TE): 3.7 ms, matrix: 172 × 172, slice thickness: 4 mm, gap: 2 mm, field of view (FOV): 350 mm, and band width (BW): 380.1 Hz) technique was applied as a pulse sequence. The time required for the examination was 19 seconds, and the breath-hold technique was used. Axial images were obtained at five FAs: 5, 10, 15, 20 and 25°. The signal intensities of the liver, the lesion and the background noise were measured based on the acquired images before the SNR and the CNR were calculated. To evaluate the image at the FA, we used SPSS for Windows ver. 17.0 to conduct a one-way ANOVA test. A Bonferroni test was conducted as a post-hoc test. The SNRs of the hemorrhagic HCC in the 3D-THRIVE technique were 35.50 ± 4.12, 97.00 ± 10.24, 66.09 ± 7.29, 53.84 ± 5.43, and 42.92 ± 5.11 for FAs of 5, 10, 15, 20, and 25°, respectively (p = 0.0430), whereas the corresponding CNRs were 30.50 ± 3.84, 43.00 ± 5.42, 36.54 ± 4.09, 32.30 ± 2.79, and 31.69 ± 3.21 (p = 0.0003). At a small FA of 10, the SNR and the CNR showed the highest values. As the FA was increased, the SNR and the CNR values showed a decreasing tendency. In conclusion, the optimal T1-weighted image FA should be set to 10° to detect a HCC by using the 3D

  10. 3D multifocus astigmatism and compressed sensing (3D MACS) based superresolution reconstruction

    PubMed Central

    Huang, Jiaqing; Sun, Mingzhai; Gumpper, Kristyn; Chi, Yuejie; Ma, Jianjie

    2015-01-01

    Single molecule based superresolution techniques (STORM/PALM) achieve nanometer spatial resolution by integrating the temporal information of the switching dynamics of fluorophores (emitters). When emitter density is low for each frame, they are located to the nanometer resolution. However, when the emitter density rises, causing significant overlapping, it becomes increasingly difficult to accurately locate individual emitters. This is particularly apparent in three dimensional (3D) localization because of the large effective volume of the 3D point spread function (PSF). The inability to precisely locate the emitters at a high density causes poor temporal resolution of localization-based superresolution technique and significantly limits its application in 3D live cell imaging. To address this problem, we developed a 3D high-density superresolution imaging platform that allows us to precisely locate the positions of emitters, even when they are significantly overlapped in three dimensional space. Our platform involves a multi-focus system in combination with astigmatic optics and an ℓ1-Homotopy optimization procedure. To reduce the intrinsic bias introduced by the discrete formulation of compressed sensing, we introduced a debiasing step followed by a 3D weighted centroid procedure, which not only increases the localization accuracy, but also increases the computation speed of image reconstruction. We implemented our algorithms on a graphic processing unit (GPU), which speeds up processing 10 times compared with central processing unit (CPU) implementation. We tested our method with both simulated data and experimental data of fluorescently labeled microtubules and were able to reconstruct a 3D microtubule image with 1000 frames (512×512) acquired within 20 seconds. PMID:25798314

  11. Photoemission spectra and density functional theory calculations of 3d transition metal-aqua complexes (Ti-Cu) in aqueous solution.

    PubMed

    Yepes, Diana; Seidel, Robert; Winter, Bernd; Blumberger, Jochen; Jaque, Pablo

    2014-06-19

    Photoelectron spectroscopy measurements and density functional calculations are combined to determine the lowest electron binding energies of first-row transition-metal aqua ions, titanium through copper, with 3d(1) through 3d(9) electronic configurations, in their most common oxidation states. Vertical ionization energies are found to oscillate considerably between 6.76 and 9.65 eV for the dications and between 7.05 and 10.28 eV for the respective trivalent cations. The metal cations are modeled as [M(H2O)n](q+) clusters (q = 2, 3, and 4; n = 6 and 18) surrounded by continuum solvent. The performance of 10 exchange-correlation functionals, two GGAs, three MGGAs, two HGGAs and three HMGGAs, combined with the MDF10(ECP)/6-31+G(d,p) basis set is assessed for 11 M-O bond distances, 10 vertical ionization energies, 6 adiabatic ionization energies, and the associated reorganization free energies. We find that for divalent cations the HGGA and HMGGA functionals in combination with the 18 water model show the best agreement with experimental vertical ionization energies and geometries; for trivalent ions, the MGGA functionals perform best. The corresponding reorganization free energies (λo) of the oxidized ions are significantly underestimated with all DFT functionals and cluster models. This indicates that the structural reorganization of the solvation shell upon ionization is not adequately accounted for by the simple solvation models used, emphasizing the importance of extended sampling of thermally accessible solvation structures for an accurate computation of this quantity. The photoelectron spectroscopy measurements reported herein provide a comprehensive set of transition-metal redox energetic quantities for future electronic structure benchmarks.

  12. In Vivo 3D Analysis of Thoracic Kinematics: Changes in Size and Shape During Breathing and Their Implications for Respiratory Function in Recent Humans and Fossil Hominins.

    PubMed

    Bastir, Markus; García-Martínez, Daniel; Torres-Tamayo, Nicole; Sanchis-Gimeno, Juan Alberto; O'Higgins, Paul; Utrilla, Cristina; Torres Sánchez, Isabel; García Río, Francisco

    2017-02-01

    The human ribcage expands and contracts during respiration as a result of the interaction between the morphology of the ribs, the costo-vertebral articulations and respiratory muscles. Variations in these factors are said to produce differences in the kinematics of the upper thorax and the lower thorax, but the extent and nature of any such differences and their functional implications have not yet been quantified. Applying geometric morphometrics we measured 402 three-dimensional (3D) landmarks and semilandmarks of 3D models built from computed tomographic scans of thoraces of 20 healthy adult subjects in maximal forced inspiration (FI) and expiration (FE). We addressed the hypothesis that upper and lower parts of the ribcage differ in kinematics and compared different models of functional compartmentalization. During inspiration the thorax superior to the level of the sixth ribs undergoes antero-posterior expansion that differs significantly from the medio-lateral expansion characteristic of the thorax below this level. This supports previous suggestions for dividing the thorax into a pulmonary and diaphragmatic part. While both compartments differed significantly in mean size and shape during FE and FI the size changes in the lower compartment were significantly larger. Additionally, for the same degree of kinematic shape change, the pulmonary thorax changes less in size than the diaphragmatic thorax. Therefore, variations in the form and function of the diaphragmatic thorax will have a strong impact on respiratory function. This has important implications for interpreting differences in thorax shape in terms of respiratory functional differences within and among recent humans and fossil hominins. Anat Rec, 300:255-264, 2017. © 2016 Wiley Periodicals, Inc.

  13. Brain function predictors and outcome of weight loss and weight loss maintenance.

    PubMed

    Szabo-Reed, Amanda N; Breslin, Florence J; Lynch, Anthony M; Patrician, Trisha M; Martin, Laura E; Lepping, Rebecca J; Powell, Joshua N; Yeh, Hung-Wen Henry; Befort, Christie A; Sullivan, Debra; Gibson, Cheryl; Washburn, Richard; Donnelly, Joseph E; Savage, Cary R

    2015-01-01

    Obesity rates are associated with public health consequences and rising health care costs. Weight loss interventions, while effective, do not work for everyone, and weight regain is a significant problem. Eating behavior is influenced by a convergence of processes in the brain, including homeostatic factors and motivational processing that are important contributors to overeating. Initial neuroimaging studies have identified brain regions that respond differently to visual food cues in obese and healthy weight individuals that are positively correlated with reports of hunger in obese participants. While these findings provide mechanisms of overeating, many important questions remain. It is not known whether brain activation patterns change after weight loss, or if they change differentially based on amount of weight lost. Also, little is understood regarding biological processes that contribute to long-term weight maintenance. This study will use neuroimaging in participants while viewing food and non-food images. Functional Magnetic Resonance Imaging will take place before and after completion of a twelve-week weight loss intervention. Obese participants will be followed though a 6-month maintenance period. The study will address three aims: 1. Characterize brain activation underlying food motivation and impulsive behaviors in obese individuals. 2. Identify brain activation changes and predictors of weight loss. 3. Identify brain activation predictors of weight loss maintenance. Findings from this study will have implications for understanding mechanisms of obesity, weight loss, and weight maintenance. Results will be significant to public health and could lead to a better understanding of how differences in brain activation relate to obesity.

  14. Brain function predictors and outcome of weight loss and weight loss maintenance

    PubMed Central

    Szabo-Reed, Amanda N.; Breslin, Florence J.; Lynch, Anthony M.; Patrician, Trisha M.; Martin, Laura E.; Lepping, Rebecca J.; Powell, Joshua N.; Yeh, Hung-Wen (Henry); Befort, Christie A.; Sullivan, Debra; Gibson, Cheryl; Washburn, Richard; Donnelly, Joseph E.; Savage, Cary R.

    2015-01-01

    Obesity rates are associated with public health consequences and rising health care costs. Weight loss interventions, while effective, do not work for everyone, and weight regain is a significant problem. Eating behavior is influenced by a convergence of processes in the brain, including homeostatic factors and motivational processing that are important contributors to overeating. Initial neuroimaging studies have identified brain regions that respond differently to visual food cues in obese and healthy weight individuals that are positively correlated with reports of hunger in obese participants. While these findings provide mechanisms of overeating, many important questions remain. It is not known whether brain activation patterns change after weight loss, or if they change differentially based on amount of weight lost. Also, little is understood regarding biological processes that contribute to long-term weight maintenance. This study will use neuroimaging in participants while viewing food and non-food images. Functional Magnetic Resonance Imaging will take place before and after completion of a twelve-week weight loss intervention. Obese participants will be followed though a 6-month maintenance period. The study will address three aims: 1. Characterize brain activation underlying food motivation and impulsive behaviors in obese individuals. 2. Identify brain activation changes and predictors of weight loss. 3. Identify brain activation predictors of weight loss maintenance. Findings from this study will have implications for understanding mechanisms of obesity, weight loss, and weight maintenance. Results will be significant to public health and could lead to a better understanding of how differences in brain activation relate to obesity. PMID:25533729

  15. Test of high-resolution 3D P-wave velocity model of Poland by back-azimuthal sections of teleseismic receiver function

    NASA Astrophysics Data System (ADS)

    Wilde-Piorko, Monika; Polkowski, Marcin; Grad, Marek

    2015-04-01

    Geological and seismic structure under area of Poland is well studied by over one hundred thousand boreholes, over thirty deep seismic refraction and wide angle reflection profiles and by vertical seismic profiling, magnetic, gravity, magnetotelluric and thermal methods. Compilation of these studies allowed to create a high-resolution 3D P-wave velocity model down to 60 km depth in the area of Poland (Polkowski et al. 2014). Model also provides details about the geometry of main layers of sediments (Tertiary and Quaternary, Cretaceous, Jurassic, Triassic, Permian, old Paleozoic), consolidated/crystalline crust (upper, middle and lower) and uppermost mantle. This model gives an unique opportunity for calculation synthetic receiver function and compering it with observed receiver function calculated for permanent and temporary seismic stations. Modified ray-tracing method (Langston, 1977) can be used directly to calculate the response of the structure with dipping interfaces to the incoming plane wave with fixed slowness and back-azimuth. So, 3D P-wave velocity model has been interpolated to 2.5D P-wave velocity model beneath each seismic station and back-azimuthal sections of components of receiver function have been calculated. Vp/Vs ratio is assumed to be 1.8, 1.67, 1.73, 1.77 and 1.8 in the sediments, upper/middle/lower consolidated/crystalline crust and uppermost mantle, respectively. Densities were calculated with combined formulas of Berteussen (1977) and Gardner et al. (1974). Additionally, to test a visibility of the lithosphere-asthenosphere boundary phases at receiver function sections models have been extended to 250 km depth based on P4-mantle model (Wilde-Piórko et al., 2010). National Science Centre Poland provided financial support for this work by NCN grant DEC-2011/02/A/ST10/00284 and by NCN grant UMO-2011/01/B/ST10/06653.

  16. MIMO radar 3D imaging based on combined amplitude and total variation cost function with sequential order one negative exponential form.

    PubMed

    Ma, Changzheng; Yeo, Tat Soon; Zhao, Yongbo; Feng, Junjie

    2014-05-01

    In inverse synthetic aperture radar (ISAR) imaging, a target is usually regarded as consist of a few strong (specular) scatterers and the distribution of these strong scatterers is sparse in the imaging volume. In this paper, we propose to incorporate the sparse signal recovery method in 3D multiple-input multiple-output radar imaging algorithm. Sequential order one negative exponential (SOONE) function, which forms homotopy between 1 and 0 norms, is proposed to measure the sparsity. Gradient projection is used to solve a constrained nonconvex SOONE function minimization problem and recover the sparse signal. However, while the gradient projection method is computationally simple, it is not robust when a matrix in the algorithm is ill conditioned. We thus further propose using diagonal loading and singular value decomposition methods to improve the robustness of the algorithm. In order to handle targets with large flat surfaces, a combined amplitude and total-variation objective function is also proposed to regularize the shapes of the flat surfaces. Simulation results show that the proposed gradient projection of SOONE function method is better than orthogonal matching pursuit, CoSaMp, l1-magic, Bayesian method with Laplace prior, smoothed l0 method, and l1-ls in high SNR cases for recovery of ± 1 random spikes sparse signal. The quality of the simulated 3D images and real data ISAR images obtained using the new method is better than that of the conventional correlation method and minimum l2 norm method, and competitive to the aforementioned sparse signal recovery algorithms.

  17. A sediment structure model for describing the 3D spatial distribution of soil hydraulic properties of an artificial catchment using pedotransfer functions

    NASA Astrophysics Data System (ADS)

    Maurer, T.; Bartsch, R.; Schneider, A.; Gerke, H. H.

    2012-04-01

    Modelling the spatial heterogeneity of catchments is a prerequisite for the understanding of flow processes and the application of hydrological models. The initial structure represents also the starting point for catchment and ecosystem development. The quality of hydrologic modeling is often limited due to a lack of data or an oversimplification of aquifer properties. Predictions can be significantly improved by using spatial models that reproduce specific structural characteristics. Current geostatistical methods are unable the capture spatially complex conditions, e.g. abrupt changes in structures. More deterministic structure generator approaches are currently been discussed in hydrogeology for exploration. Process-based structure generators deduce structural characteristics e.g. from the known formation processes of the aquifer. The objective was to describe the spatial distribution of soil hydraulic properties in a catchment based on generated 3D sediments distributions. The approach was tested for the artificially constructed "Hühnerwasser" ("Chicken Creek") catchment. The catchment is located in the post-lignite mining area of Welzow-Süd in Lower Lusatia, Brandenburg, Germany. Here, the initial sediment distribution was governed primarily by dumping processes of the large-scale mining technology and the geological conditions at the excavation site. For the initially organic matter-free sandy sediments, the structure model generated the distributions of soil texture and soil bulk density within dumping spoil cones. These were represented by 2D cross sections with compacted central parts and particle-segregated flanks. The 3D geometry of the catchment was generated by sequencing of these basic structural elements along identified stacker trajectories, finally yielding a discretized 3D volume model using the GOCAD software. Based on these data, spatial distributions of hydraulic properties were calculated using well-established pedotransfer functions

  18. Time-Dependent Distribution Functions in C-Mod Calculated with the CQL3D-Hybrid-FOW, AORSA Full-Wave, and DC Lorentz Codes

    NASA Astrophysics Data System (ADS)

    Harvey, R. W. (Bob); Petrov, Yu. V.; Jaeger, E. F.; Berry, L. A.; Bonoli, P. T.; Bader, A.

    2015-11-01

    A time-dependent simulation of C-Mod pulsed ICRF power is made calculating minority hydrogen ion distribution functions with the CQL3D-Hybrid-FOW finite-orbit-width Fokker-Planck code. ICRF fields are calculated with the AORSA full wave code, and RF diffusion coefficients are obtained from these fields using the DC Lorentz gyro-orbit code. Prior results with a zero-banana-width simulation using the CQL3D/AORSA/DC time-cycles showed a pronounced enhancement of the H distribution in the perpendicular velocity direction compared to results obtained from Stix's quasilinear theory, in general agreement with experiment. The present study compares the new FOW results, including relevant gyro-radius effects, to determine the importance of these effects on the the NPA synthetic diagnostic time-dependence. The new NPA results give increased agreement with experiment, particularly in the ramp-down time after the ICRF pulse. Funded, through subcontract with Massachusetts Institute of Technology, by USDOE sponsored SciDAC Center for Simulation of Wave-Plasma Interactions.

  19. A complex 3D human tissue culture system based on mammary stromal cells and silk scaffolds for modeling breast morphogenesis and function.

    PubMed

    Wang, Xiuli; Sun, Lin; Maffini, Maricel V; Soto, Ana; Sonnenschein, Carlos; Kaplan, David L

    2010-05-01

    Epithelial-stromal interactions play a crucial role in normal embryonic development and carcinogenesis of the human breast while the underlying mechanisms of these events remain poorly understood. To address this issue, we constructed a physiologically relevant, three-dimensional (3D) culture surrogate of complex human breast tissue that included a tri-culture system made up of human mammary epithelial cells (MCF10A), human fibroblasts and adipocytes, i.e., the two dominant breast stromal cell types, in a Matrigel/collagen mixture on porous silk protein scaffolds. The presence of stromal cells inhibited MCF10A cell proliferation and induced both alveolar and ductal morphogenesis and enhanced casein expression. In contrast to the immature polarity exhibited by co-cultures with either fibroblasts or adipocytes, the alveolar structures formed by the tri-cultures exhibited proper polarity similar to that observed in breast tissue in vivo. Only alveolar structures with reverted polarity were observed in MCF10A monocultures. Consistent with their phenotypic appearance, more functional differentiation of epithelial cells was also observed in the tri-cultures, where casein alpha- and -beta mRNA expression was significantly increased. This in vitro tri-culture breast tissue system sustained on silk scaffold effectively represents a more physiologically relevant 3D microenvironment for mammary epithelial cells and stromal cells than either co-cultures or monocultures. This experimental model provides an important first step for bioengineering an informative human breast tissue system, with which to study normal breast morphogenesis and neoplastic transformation.

  20. 3-D Seismic Interpretation

    NASA Astrophysics Data System (ADS)

    Moore, Gregory F.

    2009-05-01

    This volume is a brief introduction aimed at those who wish to gain a basic and relatively quick understanding of the interpretation of three-dimensional (3-D) seismic reflection data. The book is well written, clearly illustrated, and easy to follow. Enough elementary mathematics are presented for a basic understanding of seismic methods, but more complex mathematical derivations are avoided. References are listed for readers interested in more advanced explanations. After a brief introduction, the book logically begins with a succinct chapter on modern 3-D seismic data acquisition and processing. Standard 3-D acquisition methods are presented, and an appendix expands on more recent acquisition techniques, such as multiple-azimuth and wide-azimuth acquisition. Although this chapter covers the basics of standard time processing quite well, there is only a single sentence about prestack depth imaging, and anisotropic processing is not mentioned at all, even though both techniques are now becoming standard.

  1. Radiochromic 3D Detectors

    NASA Astrophysics Data System (ADS)

    Oldham, Mark

    2015-01-01

    Radiochromic materials exhibit a colour change when exposed to ionising radiation. Radiochromic film has been used for clinical dosimetry for many years and increasingly so recently, as films of higher sensitivities have become available. The two principle advantages of radiochromic dosimetry include greater tissue equivalence (radiologically) and the lack of requirement for development of the colour change. In a radiochromic material, the colour change arises direct from ionising interactions affecting dye molecules, without requiring any latent chemical, optical or thermal development, with important implications for increased accuracy and convenience. It is only relatively recently however, that 3D radiochromic dosimetry has become possible. In this article we review recent developments and the current state-of-the-art of 3D radiochromic dosimetry, and the potential for a more comprehensive solution for the verification of complex radiation therapy treatments, and 3D dose measurement in general.

  2. Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function.

    PubMed

    Serohijos, Adrian W R; Hegedus, Tamás; Aleksandrov, Andrei A; He, Lihua; Cui, Liying; Dokholyan, Nikolay V; Riordan, John R

    2008-03-04

    Deletion of phenylalanine-508 (Phe-508) from the N-terminal nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR), a member of the ATP-binding cassette (ABC) transporter family, disrupts both its folding and function and causes most cystic fibrosis. Most mutant nascent chains do not pass quality control in the ER, and those that do remain thermally unstable, only partially functional, and are rapidly endocytosed and degraded. Although the lack of the Phe-508 peptide backbone diminishes the NBD1 folding yield, the absence of the aromatic side chain is primarily responsible for defective CFTR assembly and channel gating. However, the site of interdomain contact by the side chain is unknown as is the high-resolution 3D structure of the complete protein. Here we present a 3D structure of CFTR, constructed by molecular modeling and supported biochemically, in which Phe-508 mediates a tertiary interaction between the surface of NBD1 and a cytoplasmic loop (CL4) in the C-terminal membrane-spanning domain (MSD2). This crucial cytoplasmic membrane interface, which is dynamically involved in regulation of channel gating, explains the known sensitivity of CFTR assembly to many disease-associated mutations in CL4 as well as NBD1 and provides a sharply focused target for small molecules to treat CF. In addition to identifying a key intramolecular site to be repaired therapeutically, our findings advance understanding of CFTR structure and function and provide a platform for focused biochemical studies of other features of this unique ABC ion channel.

  3. Measurement of residual stresses using fracture mechanics weight functions

    SciTech Connect

    Fan, Y.

    2000-10-01

    A residual stress measurement method has been developed to quantify through-the-thickness residual stresses. Accurate measurement of residual stresses is crucial for many engineering structures. Fabrication processes such as welding and machining generate residual stresses that are difficult to predict. Residual stresses affect the integrity of structures through promoting failures due to brittle fracture, fatigue, stress corrosion cracking, and wear. In this work, the weight function theory of fracture mechanics is used to measure residual stresses. The weight function theory is an important development in computational fracture mechanics. Stress intensity factors for arbitrary stress distribution on the crack faces can be accurately and efficiently computed for predicting crack growth. This paper demonstrates that the weight functions are equally useful in measuring residual stresses. In this method, an artificial crack is created by a thin cut in a structure containing residual stresses. The cut relieves the residual stresses normal to the crack-face and allows the relieved residual stresses to deform the structure. Strain gages placed adjacent to the cut measure the relieved strains corresponding to incrementally increasing depths of the cut. The weight functions of the cracked body relate the measured strains to the residual stresses normal to the cut within the structure. The procedure details, such as numerical integration of the singular functions in applying the weight function method, will be discussed.

  4. Solar Wind Halo Formation by the Scattering of the Strahl via Direct Cluster/PEACE Observations of the 3D Velocity Distribution Function

    NASA Technical Reports Server (NTRS)

    Figueroa-Vinas, Adolfo; Gurgiolo, Chris A.; Nieves-Chinchilla, Teresa; Goldstein, Melvyn L.

    2010-01-01

    It has been suggested by a number of authors that the solar wind electron halo can be formed by the scattering of the strahl. On frequent occasions we have observed in electron angular skymaps (Phi/Theta-plots) of the electron 3D velocity distribution functions) a bursty-filament of particles connecting the strahl to the solar wind core-halo. These are seen over a very limited energy range. When the magnetic field is well off the nominal solar wind flow direction such filaments are inconsistent with any local forces and are probably the result of strong scattering. Furthermore, observations indicates that the strahl component is frequently and significantly anisotropic (Tper/Tpal approx.2). This provides a possible free energy source for the excitation of whistler waves as a possible scattering mechanism. The empirical observational evidence between the halo and the strahl suggests that the strahl population may be, at least in part, the source of the halo component.

  5. Venus in 3D

    NASA Technical Reports Server (NTRS)

    Plaut, Jeffrey J.

    1993-01-01

    Stereographic images of the surface of Venus which enable geologists to reconstruct the details of the planet's evolution are discussed. The 120-meter resolution of these 3D images make it possible to construct digital topographic maps from which precise measurements can be made of the heights, depths, slopes, and volumes of geologic structures.

  6. Models for predicting objective function weights in prostate cancer IMRT

    SciTech Connect

    Boutilier, Justin J. Lee, Taewoo; Craig, Tim; Sharpe, Michael B.; Chan, Timothy C. Y.

    2015-04-15

    Purpose: To develop and evaluate the clinical applicability of advanced machine learning models that simultaneously predict multiple optimization objective function weights from patient geometry for intensity-modulated radiation therapy of prostate cancer. Methods: A previously developed inverse optimization method was applied retrospectively to determine optimal objective function weights for 315 treated patients. The authors used an overlap volume ratio (OV) of bladder and rectum for different PTV expansions and overlap volume histogram slopes (OVSR and OVSB for the rectum and bladder, respectively) as explanatory variables that quantify patient geometry. Using the optimal weights as ground truth, the authors trained and applied three prediction models: logistic regression (LR), multinomial logistic regression (MLR), and weighted K-nearest neighbor (KNN). The population average of the optimal objective function weights was also calculated. Results: The OV at 0.4 cm and OVSR at 0.1 cm features were found to be the most predictive of the weights. The authors observed comparable performance (i.e., no statistically significant difference) between LR, MLR, and KNN methodologies, with LR appearing to perform the best. All three machine learning models outperformed the population average by a statistically significant amount over a range of clinical metrics including bladder/rectum V53Gy, bladder/rectum V70Gy, and dose to the bladder, rectum, CTV, and PTV. When comparing the weights directly, the LR model predicted bladder and rectum weights that had, on average, a 73% and 74% relative improvement over the population average weights, respectively. The treatment plans resulting from the LR weights had, on average, a rectum V70Gy that was 35% closer to the clinical plan and a bladder V70Gy that was 29% closer, compared to the population average weights. Similar results were observed for all other clinical metrics. Conclusions: The authors demonstrated that the KNN and MLR

  7. 3D False Color Computed Tomography for Diagnosis and Follow-Up of Permanent Denervated Human Muscles Submitted to Home-Based Functional Electrical Stimulation.

    PubMed

    Carraro, Ugo; Edmunds, Kyle J; Gargiulo, Paolo

    2015-03-11

    This report outlines the use of a customized false-color 3D computed tomography (CT) protocol for the imaging of the rectus femoris of spinal cord injury (SCI) patients suffering from complete and permanent denervation, as characterized by complete Conus and Cauda Equina syndrome. This muscle imaging method elicits the progression of the syndrome from initial atrophy to eventual degeneration, as well as the extent to which patients' quadriceps could be recovered during four years of home-based functional electrical stimulation (h-b FES). Patients were pre-selected from several European hospitals and functionally tested by, and enrolled in the EU Commission Shared Cost Project RISE (Contract n. QLG5-CT-2001-02191) at the Department of Physical Medicine, Wilhelminenspital, Vienna, Austria. Denervated muscles were electrically stimulated using a custom-designed stimulator, large surface electrodes, and customized progressive stimulation settings. Spiral CT images and specialized computational tools were used to isolate the rectus femoris muscle and produce 3D and 2D reconstructions of the denervated muscles. The cross sections of the muscles were determined by 2D Color CT, while muscle volumes were reconstructed by 3D Color CT. Shape, volume, and density changes were measured over the entirety of each rectus femoris muscle. Changes in tissue composition within the muscle were visualized by associating different colors to specified Hounsfield unit (HU) values for fat, (yellow: [-200; -10]), loose connective tissue or atrophic muscle, (cyan: [-9; 40]), and normal muscle, fascia and tendons included, (red: [41; 200]). The results from this analysis are presented as the average HU values within the rectus femoris muscle reconstruction, as well as the percentage of these tissues with respect to the total muscle volume. Results from this study demonstrate that h-b FES induces a compliance-dependent recovery of muscle volume and size of muscle fibers, as evidenced by the

  8. 3D False Color Computed Tomography for Diagnosis and Follow-Up of Permanent Denervated Human Muscles Submitted to Home-Based Functional Electrical Stimulation

    PubMed Central

    Carraro, Ugo; Edmunds, Kyle J.

    2015-01-01

    This report outlines the use of a customized false-color 3D computed tomography (CT) protocol for the imaging of the rectus femoris of spinal cord injury (SCI) patients suffering from complete and permanent denervation, as characterized by complete Conus and Cauda Equina syndrome. This muscle imaging method elicits the progression of the syndrome from initial atrophy to eventual degeneration, as well as the extent to which patients' quadriceps could be recovered during four years of home-based functional electrical stimulation (h-b FES). Patients were pre-selected from several European hospitals and functionally tested by, and enrolled in the EU Commission Shared Cost Project RISE (Contract n. QLG5-CT-2001-02191) at the Department of Physical Medicine, Wilhelminenspital, Vienna, Austria. Denervated muscles were electrically stimulated using a custom-designed stimulator, large surface electrodes, and customized progressive stimulation settings. Spiral CT images and specialized computational tools were used to isolate the rectus femoris muscle and produce 3D and 2D reconstructions of the denervated muscles. The cross sections of the muscles were determined by 2D Color CT, while muscle volumes were reconstructed by 3D Color CT. Shape, volume, and density changes were measured over the entirety of each rectus femoris muscle. Changes in tissue composition within the muscle were visualized by associating different colors to specified Hounsfield unit (HU) values for fat, (yellow: [-200; -10]), loose connective tissue or atrophic muscle, (cyan: [-9; 40]), and normal muscle, fascia and tendons included, (red: [41; 200]). The results from this analysis are presented as the average HU values within the rectus femoris muscle reconstruction, as well as the percentage of these tissues with respect to the total muscle volume. Results from this study demonstrate that h-b FES induces a compliance-dependent recovery of muscle volume and size of muscle fibers, as evidenced by the

  9. 3D photoacoustic imaging

    NASA Astrophysics Data System (ADS)

    Carson, Jeffrey J. L.; Roumeliotis, Michael; Chaudhary, Govind; Stodilka, Robert Z.; Anastasio, Mark A.

    2010-06-01

    Our group has concentrated on development of a 3D photoacoustic imaging system for biomedical imaging research. The technology employs a sparse parallel detection scheme and specialized reconstruction software to obtain 3D optical images using a single laser pulse. With the technology we have been able to capture 3D movies of translating point targets and rotating line targets. The current limitation of our 3D photoacoustic imaging approach is its inability ability to reconstruct complex objects in the field of view. This is primarily due to the relatively small number of projections used to reconstruct objects. However, in many photoacoustic imaging situations, only a few objects may be present in the field of view and these objects may have very high contrast compared to background. That is, the objects have sparse properties. Therefore, our work had two objectives: (i) to utilize mathematical tools to evaluate 3D photoacoustic imaging performance, and (ii) to test image reconstruction algorithms that prefer sparseness in the reconstructed images. Our approach was to utilize singular value decomposition techniques to study the imaging operator of the system and evaluate the complexity of objects that could potentially be reconstructed. We also compared the performance of two image reconstruction algorithms (algebraic reconstruction and l1-norm techniques) at reconstructing objects of increasing sparseness. We observed that for a 15-element detection scheme, the number of measureable singular vectors representative of the imaging operator was consistent with the demonstrated ability to reconstruct point and line targets in the field of view. We also observed that the l1-norm reconstruction technique, which is known to prefer sparseness in reconstructed images, was superior to the algebraic reconstruction technique. Based on these findings, we concluded (i) that singular value decomposition of the imaging operator provides valuable insight into the capabilities of

  10. Comparison of outcomes of tricuspid annuloplasty with 3D-rigid versus flexible prosthetic ring for functional tricuspid regurgitation secondary to rheumatic mitral valve disease

    PubMed Central

    Wang, Haiping; Wang, Xin; Lv, Zhenqian; Liu, Xiaojun

    2016-01-01

    Background Annuloplasty bands and rings are widely used for repairing functional tricuspid regurgitation (FTR). However, the question regarding which is the ideal annuloplasty device remains unclear. The aim of this study was to compare the efficacy and mid-term durability of tricuspid ring annuloplasty for FTR secondary to rheumatic mitral valve disease using flexible Cosgrove-Edwards band and the rigid Edwards MC3 ring (Edwards Lifesciences, LLC, Irvine, CA, USA). Methods We retrospectively collected the clinical data of those who underwent mitral valve replacement (MVR) in concomitant with tricuspid ring annuloplasty from 2009 to 2013. The flexible band was used in 46 patients (flexible group), and the 3D rigid ring was used in 60 patients (rigid group). Echocardiographic evaluation of tricuspid function was performed preoperatively and postoperatively. Results The grade of TR was significantly improved compared to preoperative values in two groups. There was no significant difference regarding postoperative TR grade between the two groups at 1 week and 2–3 months but there was statistical significant difference at postoperative 6–12 months, and 2–3 years. During the follow up period, 25 of 46 patients (54.3%) in flexible group and 22 of 60 patients (30.3%) in rigid group developed recurrent TR. Freedom from recurrent TR in flexible group is significant lower than rigid group in each postoperative follow up period. Conclusions These findings suggest that 3D rigid ring annuloplasty might be more effective for tricuspid ring annuloplasty in FTR in mid-term postoperative periods when compared to flexible band. PMID:28066587

  11. Spatio-temporal validation of long-term 3D hydrological simulations of a forested catchment using empirical orthogonal functions and wavelet coherence analysis

    NASA Astrophysics Data System (ADS)

    Fang, Zhufeng; Bogena, Heye; Kollet, Stefan; Koch, Julian; Vereecken, Harry

    2015-10-01

    Soil moisture plays a key role in the water and energy balance in soil, vegetation and atmosphere systems. According to Wood et al. (2011) there is a grand need to increase global-scale hyper-resolution water-energy-biogeochemistry land surface modelling capabilities. These modelling capabilities should also recognize epistemic uncertainties, as well as the nonlinearity and hysteresis in its dynamics. Unfortunately, it is not clear how to parameterize hydrological processes as a function of scale, and how to test deterministic models with regard to epistemic uncertainties. In this study, high resolution long-term simulations were conducted in the highly instrumented TERENO hydrological observatory of the Wüstebach catchment. Soil hydraulic parameters were derived using inverse modelling with the Hydrus-1D model using the global optimization scheme SCE-UA and soil moisture data from a wireless soil moisture sensor network. The estimated parameters were then used for 3D simulations of water transport using the integrated parallel simulation platform ParFlow-CLM. The simulated soil moisture dynamics, as well as evapotranspiration (ET) and runoff, were compared with long-term field observations to illustrate how well the model was able to reproduce the water budget dynamics. We investigated different anisotropies of hydraulic conductivity to analyze how fast lateral flow processes above the underlying bedrock affect the simulation results. For a detail investigation of the model results we applied the empirical orthogonal function (EOF) and wavelet coherence methods. The EOF analysis of temporal-spatial patterns of simulated and observed soil moisture revealed that introduction of heterogeneity in the soil porosity effectively improves estimates of soil moisture patterns. Our wavelet coherence analysis indicates that wet and dry seasons have significant effect on temporal correlation between observed and simulated soil moisture and ET. Our study demonstrates the

  12. Improving compact gravity inversion based on new weighting functions

    NASA Astrophysics Data System (ADS)

    Ghalehnoee, Mohammad Hossein; Ansari, Abdolhamid; Ghorbani, Ahmad

    2016-11-01

    We have developed a method to estimate the geometry, location and densities of anomalies coming from two-dimensional gravity data based on compact gravity inversion technique. Compact gravity inversion is simple, fast and user friendly but severely depends on the number of model parameters, i.e. by increasing the model parameters, the anomalies tend to concentrate near the surface. To overcome this ambiguity new weighting functions based on density contrast, depth, and compactness models have been introduced. Variable compactness factors have been defined here to get either a sharp or a smooth model based on the depth of the source or existence of prior information. Depth weighting derived from one station of gravity data whereas the effect of gravity data is two- and three-dimensional. To compensate this limitation an innovating weighting function namely kernel function has been introduced which multiplies with weight and compactness matrixes to yield a general model weighting function. The method is tested using three different sets of synthetic examples: a body at various depths (20, 40, 80 and 140 m), two bodies at the same depth but various distances to estimate lateral resolution and three bodies with negative and positive density contrast in different depths. The method is also applied to three real gravity data of Woodlawn massive sulfide body, sulfides mineralization of British Colombia and iron ore body of Missouri. The method produces solutions consistent with the known geologic attributes of the gravity sources, illustrating its potential practicality.

  13. Visual Semantic Based 3D Video Retrieval System Using HDFS

    PubMed Central

    Kumar, C.Ranjith; Suguna, S.

    2016-01-01

    This paper brings out a neoteric frame of reference for visual semantic based 3d video search and retrieval applications. Newfangled 3D retrieval application spotlight on shape analysis like object matching, classification and retrieval not only sticking up entirely with video retrieval. In this ambit, we delve into 3D-CBVR (Content Based Video Retrieval) concept for the first time. For this purpose, we intent to hitch on BOVW and Mapreduce in 3D framework. Instead of conventional shape based local descriptors, we tried to coalesce shape, color and texture for feature extraction. For this purpose, we have used combination of geometric & topological features for shape and 3D co-occurrence matrix for color and texture. After thriving extraction of local descriptors, TB-PCT (Threshold Based- Predictive Clustering Tree) algorithm is used to generate visual codebook and histogram is produced. Further, matching is performed using soft weighting scheme with L2 distance function. As a final step, retrieved results are ranked according to the Index value and acknowledged to the user as a feedback .In order to handle prodigious amount of data and Efficacious retrieval, we have incorporated HDFS in our Intellection. Using 3D video dataset, we future the performance of our proposed system which can pan out that the proposed work gives meticulous result and also reduce the time intricacy. PMID:28003793

  14. Visual Semantic Based 3D Video Retrieval System Using HDFS.

    PubMed

    Kumar, C Ranjith; Suguna, S

    2016-08-01

    This paper brings out a neoteric frame of reference for visual semantic based 3d video search and retrieval applications. Newfangled 3D retrieval application spotlight on shape analysis like object matching, classification and retrieval not only sticking up entirely with video retrieval. In this ambit, we delve into 3D-CBVR (Content Based Video Retrieval) concept for the first time. For this purpose, we intent to hitch on BOVW and Mapreduce in 3D framework. Instead of conventional shape based local descriptors, we tried to coalesce shape, color and texture for feature extraction. For this purpose, we have used combination of geometric & topological features for shape and 3D co-occurrence matrix for color and texture. After thriving extraction of local descriptors, TB-PCT (Threshold Based- Predictive Clustering Tree) algorithm is used to generate visual codebook and histogram is produced. Further, matching is performed using soft weighting scheme with L2 distance function. As a final step, retrieved results are ranked according to the Index value and acknowledged to the user as a feedback .In order to handle prodigious amount of data and Efficacious retrieval, we have incorporated HDFS in our Intellection. Using 3D video dataset, we future the performance of our proposed system which can pan out that the proposed work gives meticulous result and also reduce the time intricacy.

  15. Comparison of 3D-Printed Poly-ɛ-Caprolactone Scaffolds Functionalized with Tricalcium Phosphate, Hydroxyapatite, Bio-Oss, or Decellularized Bone Matrix.

    PubMed

    Nyberg, Ethan; Rindone, Alexandra; Dorafshar, Amir; Grayson, Warren L

    2017-02-07

    Three-dimensional (3D)-printing facilitates rapid, custom manufacturing of bone scaffolds with a wide range of material choices. Recent studies have demonstrated the potential for 3D-printing bioactive (i.e., osteo-inductive) scaffolds for use in bone regeneration applications. In this study, we 3D-printed porous poly-ɛ-caprolactone (PCL) scaffolds using a fused deposition modeling (FDM) process and functionalized them with mineral additives that have been widely used commercially and clinically: tricalcium phosphate (TCP), hydroxyapatite (HA), Bio-Oss (BO), or decellularized bone matrix (DCB). We assessed the "print quality" of the composite scaffolds and found that the print quality of PCL-TCP, PCL-BO, and PCL-DCB measured ∼0.7 and was statistically lower than PCL and PCL-HA scaffolds (∼0.8). We found that the incorporation of mineral particles did not significantly decrease the compressive modulus of the graft, which was on the order of 260 MPa for solid blocks and ranged from 32 to 83 MPa for porous scaffolds. Raman spectroscopy revealed the surfaces of the scaffolds maintained the chemical profile of their dopants following the printing process. We evaluated the osteo-inductive properties of each scaffold composite by culturing adipose-derived stromal/stem cells in vitro and assessing their differentiation into osteoblasts. The calcium content (normalized to DNA) increased significantly in PCL-TCP (p < 0.05), PCL-BO (p < 0.001), and PCL-DCB (p < 0.0001) groups relative to PCL only. The calcium content also increased in PCL-HA but was not statistically significant (p > 0.05). Collagen 1 expression was 10-fold greater than PCL in PCL-BO and PCL-DCB (p < 0.05) and osteocalcin expression was 10-fold greater in PCL-BO and PCL-DCB (p < 0.05) as measured by quantitative-real time-polymerase chain reaction. This study suggests that PCL-BO and PCL-DCB hybrid material may be advantageous for bone healing applications over PCL-HA or PCL

  16. Identification of novel histone deacetylase 1 inhibitors by combined pharmacophore modeling, 3D-QSAR analysis, in silico screening and Density Functional Theory (DFT) approaches

    NASA Astrophysics Data System (ADS)

    Choubey, Sanjay K.; Mariadasse, Richard; Rajendran, Santhosh; Jeyaraman, Jeyakanthan

    2016-12-01

    Overexpression of HDAC1, a member of Class I histone deacetylase is reported to be implicated in breast cancer. Epigenetic alteration in carcinogenesis has been the thrust of research for few decades. Increased deacetylation leads to accelerated cell proliferation, cell migration, angiogenesis and invasion. HDAC1 is pronounced as the potential drug target towards the treatment of breast cancer. In this study, the biochemical potential of 6-aminonicotinamide derivatives was rationalized. Five point pharmacophore model with one hydrogen-bond acceptor (A3), two hydrogen-bond donors (D5, D6), one ring (R12) and one hydrophobic group (H8) was developed using 6-aminonicotinamide derivatives. The pharmacophore hypothesis yielded a 3D-QSAR model with correlation-coefficient (r2 = 0.977, q2 = 0.801) and it was externally validated with (r2pred = 0.929, r2cv = 0.850 and r2m = 0.856) which reveals the statistical significance of the model having high predictive power. The model was then employed as 3D search query for virtual screening against compound libraries (Zinc, Maybridge, Enamine, Asinex, Toslab, LifeChem and Specs) in order to identify novel scaffolds which can be experimentally validated to design future drug molecule. Density Functional Theory (DFT) at B3LYP/6-31G* level was employed to explore the electronic features of the ligands involved in charge transfer reaction during receptor ligand interaction. Binding free energy (ΔGbind) calculation was done using MM/GBSA which defines the affinity of ligands towards the receptor.

  17. Synthesis of functionalized 3D porous graphene using both ionic liquid and SiO2 spheres as "spacers" for high-performance application in supercapacitors.

    PubMed

    Li, Tingting; Li, Na; Liu, Jiawei; Cai, Kai; Foda, Mohamed F; Lei, Xiaomin; Han, Heyou

    2015-01-14

    In this work, a high-capacity supercapacitor material based on functionalized three-dimensional (3D) porous graphene was fabricated by low temperature hydrothermal treatment of graphene oxide (GO) using both ionic liquid (IL) and SiO2 spheres as "spacers". In the synthesis, the introduction of dual "spacers" effectively enlarged the interspace between graphene sheets and suppressed their re-stacking. In addition, the IL also acted as a structure-directing agent playing a crucial role in inducing the formation of unique 3D architectures. Consequently, fast electron/ion transport channels were successfully constructed and numerous oxygen-containing groups on graphene sheets were effectively reserved, which had unique advantages in decreasing ion diffusion resistance and providing additional pseudocapacitance. As expected, the obtained material exhibited superior specific capacitance and rate capability compared to single "spacer" designed electrodes and simultaneously maintained excellent cycling stability. In particular, there was nearly no loss of its initial capacitance after 3000 cycles. In addition, we further assembled a symmetric two-electrode device using the material, which showed outstanding flexibility and low equivalent series resistance (ESR). More importantly, it was capable of yielding a maximum power density of about 13.3 kW kg(-1) with an energy density of about 7.0 W h kg(-1) at a voltage of 1.0 V in 1 M H2SO4 electrolyte. All these impressive results demonstrate that the material obtained by this approach is greatly promising for application in high-performance supercapacitors.

  18. 3D structural conformation and functional domains of polysialyltransferase ST8Sia IV required for polysialylation of neural cell adhesion molecules.

    PubMed

    Zhou, Guo-Ping; Huang, Ri-Bo; Troy, Frederic A

    2015-01-01

    Synthesis of α2,8-polysialic acid (polySia) glycans are catalyzed by two highly homologous mammalian polysialyltransferases (polySTs), ST8Sia II (STX) and ST8Sia IV (PST), which are two members of the ST8Sia gene family of sialytransferases. During polysialylation, both STX and PST catalyze the transfer of multiple Sia residues from the activated sugar nucleotide precursor, CMP-Neu5Ac (Sia), to terminal Sia residues on N- and Olinked oligosaccharide chains on acceptor glycoproteins, including the neural cell adhesion molecule (NCAM), which is the major carrier protein of polySia. Based on our new findings and previously published studies, this review summarizes the present concepts regarding the molecular mechanism underlying regulation of protein-specific polysialylation of NCAM that includes the following: (1) Determination of the catalytic domains and specific regions within ST8Sia IV for recognizing and catalyzing the efficient polysialylation of NCAM; (2) Identification of key amino acid residues within the PSTD motif of ST8Sia IV that are essential for polysialylation; (3) Verification of key amino acids in the PBR domain of ST8Sia IV required for NCAM-specific polysialylation; and (4) a 3D conformational study of ST8Sia IV based on the Phyre2 server to discover the relationship between the structure and its functional domains of the polyST. Based on these results, our 3D model of ST8Sia IV was used to identify and characterize the catalytic domains and amino acid residues critical for catalyzing polysialylation, and have provided new structural information for supporting a detailed mechanism of polyST-NCAM interaction required for polysialylation of NCAM, findings that have not been previously reported.

  19. A mechanistic approach to explore novel HDAC1 inhibitor using pharmacophore modeling, 3D- QSAR analysis, molecular docking, density functional and molecular dynamics simulation study.

    PubMed

    Choubey, Sanjay K; Jeyaraman, Jeyakanthan

    2016-11-01

    Deregulated epigenetic activity of Histone deacetylase 1 (HDAC1) in tumor development and carcinogenesis pronounces it as promising therapeutic target for cancer treatment. HDAC1 has recently captured the attention of researchers owing to its decisive role in multiple types of cancer. In the present study a multistep framework combining ligand based 3D-QSAR, molecular docking and Molecular Dynamics (MD) simulation studies were performed to explore potential compound with good HDAC1 binding affinity. Four different pharmacophore hypotheses Hypo1 (AADR), Hypo2 (AAAH), Hypo3 (AAAR) and Hypo4 (ADDR) were obtained. The hypothesis Hypo1 (AADR) with two hydrogen bond acceptors (A), one hydrogen bond donor (D) and one aromatics ring (R) was selected to build 3D-QSAR model on the basis of statistical parameter. The pharmacophore hypothesis produced a statistically significant QSAR model, with co-efficient of correlation r(2)=0.82 and cross validation correlation co-efficient q(2)=0.70. External validation result displays high predictive power with r(2) (o) value of 0.88 and r(2) (m) value of 0.58 to carry out further in silico studies. Virtual screening result shows ZINC70450932 as the most promising lead where HDAC1 interacts with residues Asp99, His178, Tyr204, Phe205 and Leu271 forming seven hydrogen bonds. A high docking score (-11.17kcal/mol) and lower docking energy -37.84kcal/mol) displays the binding efficiency of the ligand. Binding free energy calculation was done using MM/GBSA to access affinity of ligands towards protein. Density Functional Theory was employed to explore electronic features of the ligands describing intramolcular charge transfer reaction. Molecular dynamics simulation studies at 50ns display metal ion (Zn)-ligand interaction which is vital to inhibit the enzymatic activity of the protein.

  20. Numerical Solution of 3D Poisson-Nernst-Planck Equations Coupled with Classical Density Functional Theory for Modeling Ion and Electron Transport in a Confined Environment

    SciTech Connect

    Meng, Da; Zheng, Bin; Lin, Guang; Sushko, Maria L.

    2014-08-29

    We have developed efficient numerical algorithms for the solution of 3D steady-state Poisson-Nernst-Planck equations (PNP) with excess chemical potentials described by the classical density functional theory (cDFT). The coupled PNP equations are discretized by finite difference scheme and solved iteratively by Gummel method with relaxation. The Nernst-Planck equations are transformed into Laplace equations through the Slotboom transformation. Algebraic multigrid method is then applied to efficiently solve the Poisson equation and the transformed Nernst-Planck equations. A novel strategy for calculating excess chemical potentials through fast Fourier transforms is proposed which reduces computational complexity from O(N2) to O(NlogN) where N is the number of grid points. Integrals involving Dirac delta function are evaluated directly by coordinate transformation which yields more accurate result compared to applying numerical quadrature to an approximated delta function. Numerical results for ion and electron transport in solid electrolyte for Li ion batteries are shown to be in good agreement with the experimental data and the results from previous studies.

  1. Study on characteristics of 3-D translating-pulsating source green function of deep-water havelock form and its fast integration method

    NASA Astrophysics Data System (ADS)

    Xu, Yong; Dong, Wen-Cai

    2011-09-01

    The singularities, oscillatory performances and the contributing factors to the 3-D translating-pulsating source Green function of deep-water Havelock form which consists of a local disturbance part and a far-field wave-like part, are analyzed systematically. Relative numerical integral methods about the two parts are presented in this paper. An improved method based on LOBATTO rule is used to eliminate singularities caused respectively by infinite discontinuity and jump discontinuous node from the local disturbance part function, which makes the improvement of calculation efficiency and accuracy possible. And variable substitution is applied to remove the singularity existing at the end of the integral interval of the far-field wave-like part function. Two auxiliary techniques such as valid interval calculation and local refinement of integral steps technique in narrow zones near false singularities are applied so as to avoid unnecessary integration of invalid interval and improve integral accordance. Numerical test results have proved the efficiency and accuracy in these integral methods that thus can be applied to calculate hydrodynamic performance of floating structures moving in waves.

  2. More on volume dependence of spectral weight functions

    SciTech Connect

    Niu Zhiyuan; Du Dechuan; Guo Baozhong; Li Ning; Liu Hang; Liu Chuan

    2010-09-01

    Spectral weight functions are easily obtained from two-point correlation functions, and they might be used to distinguish single-particle from multiparticle states in a finite-volume lattice calculation, a problem crucial for many lattice QCD simulations. In previous studies, it has been shown that the spectral weight function for a broad resonance shares the typical volume dependence of a two-particle scattering state, i.e. proportional to 1/L{sup 3} in a large cubic box of size L, while the narrow resonance case requires further investigation. In this paper, a generalized formula is found for the spectral weight function which incorporates both the narrow and broad resonance cases. Within Luescher's formalism, it is shown that the volume dependence of the spectral weight function exhibits a single-particle behavior for an extremely narrow resonance and a two-particle behavior for a broad resonance. The corresponding formulas for both A{sub 1}{sup +} and T{sub 1}{sup -} channels are derived. The potential application of these formulas in the extraction of resonance parameters are also discussed.

  3. Hardware Trust Implications of 3-D Integration

    DTIC Science & Technology

    2010-12-01

    enhancing a commod- ity processor with a variety of security functions. This paper examines the 3-D design approach and provides an analysis concluding...of key components. The question addressed by this paper is, “Can a 3-D control plane provide useful secure services when it is conjoined with an...untrust- worthy computation plane?” Design-level investigation of this question yields a definite yes. This paper explores 3- D applications and their

  4. A Christoffel function weighted least squares algorithm for collocation approximations

    DOE PAGES

    Narayan, Akil; Jakeman, John D.; Zhou, Tao

    2016-11-28

    Here, we propose, theoretically investigate, and numerically validate an algorithm for the Monte Carlo solution of least-squares polynomial approximation problems in a collocation framework. Our investigation is motivated by applications in the collocation approximation of parametric functions, which frequently entails construction of surrogates via orthogonal polynomials. A standard Monte Carlo approach would draw samples according to the density defining the orthogonal polynomial family. Our proposed algorithm instead samples with respect to the (weighted) pluripotential equilibrium measure of the domain, and subsequently solves a weighted least-squares problem, with weights given by evaluations of the Christoffel function. We present theoretical analysis tomore » motivate the algorithm, and numerical results that show our method is superior to standard Monte Carlo methods in many situations of interest.« less

  5. A Christoffel function weighted least squares algorithm for collocation approximations

    SciTech Connect

    Narayan, Akil; Jakeman, John D.; Zhou, Tao

    2016-11-28

    Here, we propose, theoretically investigate, and numerically validate an algorithm for the Monte Carlo solution of least-squares polynomial approximation problems in a collocation framework. Our investigation is motivated by applications in the collocation approximation of parametric functions, which frequently entails construction of surrogates via orthogonal polynomials. A standard Monte Carlo approach would draw samples according to the density defining the orthogonal polynomial family. Our proposed algorithm instead samples with respect to the (weighted) pluripotential equilibrium measure of the domain, and subsequently solves a weighted least-squares problem, with weights given by evaluations of the Christoffel function. We present theoretical analysis to motivate the algorithm, and numerical results that show our method is superior to standard Monte Carlo methods in many situations of interest.

  6. Dynamics of pickup ion velocity distribution function in Titan's plasma environment (TA encounter): 3D hybrid kinetic modeling and comparison with CAPS observations

    NASA Astrophysics Data System (ADS)

    Simpson, D. G.; Lipatov, A. S.; Sittler, E. C.; Hartle, R. E.; Cooper, J. F.

    2013-12-01

    Wave-particle interactions play a very important role in the plasma dynamics near Titan: mass loading, excitation of the low-frequency waves and the formation of the particle velocity distribution function, e.g. ring/shell-like distributions, etc. The kinetic approach is important for estimation of the collision processes e.g. a charge exchange. The particle velocity distribution function also plays a key role for understanding the observed particle fluxes. In this report we discuss the ion velocity distribution function dynamics from 3D hybrid modeling. The modeling is based on recent analysis of the Cassini Plasma Spectrometer (CAPS) ion measurements during the TA flyby. In our model the background ions, all pickup ions, and ionospheric ions are considered as particles, whereas the electrons are described as a fluid. Inhomogeneous photoionization, electron-impact ionization and charge exchange are included in our model. The temperatures of the background electrons and pickup electrons were also included into the generalized Ohm's law. We also take into account the collisions between the ions and neutrals. We use Chamberlain profiles for the exosphere's components and include a simple ionosphere model with M=28 ions that were generated inside the ionosphere. The moon is considered as a weakly conducting body. Our modeling shows that interaction between background plasma and pickup ions H+, H2+, CH4+ and N2+ has a more complicated structure than was observed in the T9 flyby and modeling due to the large gyroradius of the background O+ ions [1,2,3,4]. Special attention will be paid to comparing the simulated pickup ion velocity distribution with CAPS TA observations. We also compare our kinetic modeling with other hybrid and MHD modeling of Titan's environment. References [1] Sittler, E.C., et al., Energy Deposition Processes in Titan's Upper Atmosphere and Its Induced Magnetosphere. In: Titan from Cassini-Huygens, Brown, R.H., Lebreton J.P., Waite, J.H., Eds

  7. In vitro generation of mechanically functional cartilage grafts based on adult human stem cells and 3D-woven poly(epsilon-caprolactone) scaffolds.

    PubMed

    Valonen, Piia K; Moutos, Franklin T; Kusanagi, Akihiko; Moretti, Matteo G; Diekman, Brian O; Welter, Jean F; Caplan, Arnold I; Guilak, Farshid; Freed, Lisa E

    2010-03-01

    Three-dimensionally woven poly(epsilon-caprolactone) (PCL) scaffolds were combined with adult human mesenchymal stem cells (hMSC) to engineer mechanically functional cartilage constructs in vitro. The specific objectives were to: (i) produce PCL scaffolds with cartilage-like mechanical properties, (ii) demonstrate that hMSCs formed cartilage after 21 days of culture on PCL scaffolds, and (iii) study effects of scaffold structure (loosely vs. tightly woven), culture vessel (static dish vs. oscillating bioreactor), and medium composition (chondrogenic additives with or without serum). Aggregate moduli of 21-day constructs approached normal articular cartilage for tightly woven PCL cultured in bioreactors, were lower for tightly woven PCL cultured statically, and lowest for loosely woven PCL cultured statically (p<0.05). Construct DNA, total collagen, and glycosaminoglycans (GAG) increased in a manner dependent on time, culture vessel, and medium composition. Chondrogenesis was verified histologically by rounded cells within a hyaline-like matrix that immunostained for collagen type II but not type I. Bioreactors yielded constructs with higher collagen content (p<0.05) and more homogenous matrix than static controls. Chondrogenic additives yielded constructs with higher GAG (p<0.05) and earlier expression of collagen II mRNA if serum was not present in medium. These results show feasibility of functional cartilage tissue engineering from hMSC and 3D-woven PCL scaffolds.

  8. Robust extrapolation scheme for fast estimation of 3D ising field partition functions: application to within-subject fMRI data analysis.

    PubMed

    Risser, Laurent; Vincent, Thomas; Ciuciu, Philippe; Idier, Jérôme

    2009-01-01

    In this paper, we present a fast numerical scheme to estimate Partition Functions (PF) of 3D Ising fields. Our strategy is applied to the context of the joint detection-estimation of brain activity from functional Magnetic Resonance Imaging (fMRI) data, where the goal is to automatically recover activated regions and estimate region-dependent hemodynamic filters. For any region, a specific binary Markov random field may embody spatial correlation over the hidden states of the voxels by modeling whether they are activated or not. To make this spatial regularization fully adaptive, our approach is first based upon a classical path-sampling method to approximate a small subset of reference PFs corresponding to prespecified regions. Then, the proposed extrapolation method allows us to approximate the PFs associated with the Ising fields defined over the remaining brain regions. In comparison with preexisting approaches, our method is robust to topological inhomogeneities in the definition of the reference regions. As a result, it strongly alleviates the computational burden and makes spatially adaptive regularization of whole brain fMRI datasets feasible.

  9. Identification of source velocities on 3D structures in non-anechoic environments: Theoretical background and experimental validation of the inverse patch transfer functions method

    NASA Astrophysics Data System (ADS)

    Aucejo, M.; Totaro, N.; Guyader, J.-L.

    2010-08-01

    In noise control, identification of the source velocity field remains a major problem open to investigation. Consequently, methods such as nearfield acoustical holography (NAH), principal source projection, the inverse frequency response function and hybrid NAH have been developed. However, these methods require free field conditions that are often difficult to achieve in practice. This article presents an alternative method known as inverse patch transfer functions, designed to identify source velocities and developed in the framework of the European SILENCE project. This method is based on the definition of a virtual cavity, the double measurement of the pressure and particle velocity fields on the aperture surfaces of this volume, divided into elementary areas called patches and the inversion of impedances matrices, numerically computed from a modal basis obtained by FEM. Theoretically, the method is applicable to sources with complex 3D geometries and measurements can be carried out in a non-anechoic environment even in the presence of other stationary sources outside the virtual cavity. In the present paper, the theoretical background of the iPTF method is described and the results (numerical and experimental) for a source with simple geometry (two baffled pistons driven in antiphase) are presented and discussed.

  10. Full source tensor inversions of San Jacinto fault zone earthquakes using 3D Green's functions with the gCAP method

    NASA Astrophysics Data System (ADS)

    Ross, Z.; Ben-Zion, Y.; Zhu, L.; Graves, R. W.

    2015-12-01

    We perform a full source tensor inversion of several M > 4 earthquakes that occurred in the San Jacinto fault zone in southern California, with an emphasis on resolving signatures of volumetric source changes. A previous study on these events with Green's functions based on a 1D velocity model identified statistically significant explosive isotropic components (Ross et al. 2015). Here we use the SCEC 3D Community Velocity Model to derive Green's functions with source-receiver reciprocity and finite-difference calculations based on the code of Graves (1996). About 50 stations are used at epicentral distances of up to 55 km. The inversions are performed using the 'generalized Cut and Paste' method, which includes CLVD and isotropic components (Zhu and Ben-Zion 2013). The derived source tensors are compared to the results of the previous study based on the simplified 1D velocity model. The results are analyzed with bootstrap analysis to estimate uncertainties involved. Additional tests are performed using synthetic waveforms to study the effects of neglecting various features on the source inversions.

  11. In vitro generation of mechanically functional cartilage grafts based on adult human stem cells and 3D-woven poly(ε-caprolactone) scaffolds

    PubMed Central

    Valonen, P.K.; Moutos, F.T.; Kusanagi, A.; Moretti, M.; Diekman, B.O.; Welter, J.F.; Caplan, A.I.; Guilak, F.

    2009-01-01

    Three-dimensionally woven poly(ε-caprolactone)(PCL) scaffolds were combined with adult human mesenchymal stem cells (hMSC) to engineer mechanically functional cartilage constructs in vitro. The specific objectives were to: (i) produce PCL scaffolds with cartilage-like mechanical properties, (ii) demonstrate that hMSCs formed cartilage after 21-days of culture on PCL scaffolds, and (iii) study effects of scaffold structure (loosely vs. tightly woven), culture vessel (static dish vs. oscillating bioreactor), and medium composition (chondrogenic additives with or without serum). Aggregate moduli of 21-day constructs approached normal articular cartilage for tightly woven PCL cultured in bioreactors, were lower for tightly woven PCL cultured statically, and lowest for loosely woven PCL cultured statically (p<0.05). Construct DNA, total collagen, and glyocosaminoglycans (GAG) increased in a manner dependent on time, culture vessel, and medium composition. Chondrogenesis was verified histologically by rounded cells within a hyaline-like matrix that immunostained for collagen type II but not type I. Bioreactors yielded constructs with higher collagen content (p<0.05) and more homogenous matrix than static controls. Chondrogenic additives yielded constructs with higher GAG (p<0.05) and earlier expression of collagen II mRNA if serum was not present in medium. These results show feasibility of functional cartilage tissue engineering from hMSC and 3D woven PCL scaffolds. PMID:20034665

  12. Conversion of uniform graphene oxide/polypyrrole composites into functionalized 3D carbon nanosheet frameworks with superior supercapacitive and sodium-ion storage properties

    NASA Astrophysics Data System (ADS)

    Wang, Huanwen; Zhang, Yu; Sun, Wenping; Tan, Hui Teng; Franklin, Joseph B.; Guo, Yuanyuan; Fan, Haosen; Ulaganathan, Mani; Wu, Xing-Long; Luo, Zhong-Zhen; Madhavi, Srinivasan; Yan, Qingyu

    2016-03-01

    Two-dimensional (2D) graphene oxide/polypyrrole (GO/PPy) hybrid materials derived from in-situ polymerization are used as precursors for constructing functionalized three-dimensional (3D) porous nitrogen-doped carbon nanosheet frameworks (FT-PNCNFs) through a one-step activation strategy. In the formation process of FT-PNCNFs, PPY is directly converted into hierarchical porous nitrogen-doped carbon layers, while GO is simultaneously reduced to become electrically conductive. The complementary functions of individual components endow the FT-PNCNFs with excellent properties for both supercapacitors (SCs) and sodium ion batteries (SIBs) applications. When tested in symmetrical SC, the FT-PNCNFs demonstrate superior energy storage behaviour. At an extremely high scan rate of 3000 mV s-1, the cyclic voltammetry (CV) curve retains an inspiring quasi-rectangle shape in KOH solution. Meanwhile, high capacitances (∼247 F g-1 at 10 mV s-1; ∼146 F g-1 at 3000 mV s-1) and good cycling stability (∼95% retention after 8000 cycles) are achieved. In addition, an attractive SIB anode performance could be achieved. The FT-PNCNFs electrode delivers a reversible capacity of 187 mAh g-1 during 160th cycle at 100 mA g-1. Its reversible capacity retains 144 mAh g-1 after extending the number of cycles to 500 at 500 mA g-1.

  13. TACO3D. 3-D Finite Element Heat Transfer Code

    SciTech Connect

    Mason, W.E.

    1992-03-04

    TACO3D is a three-dimensional, finite-element program for heat transfer analysis. An extension of the two-dimensional TACO program, it can perform linear and nonlinear analyses and can be used to solve either transient or steady-state problems. The program accepts time-dependent or temperature-dependent material properties, and materials may be isotropic or orthotropic. A variety of time-dependent and temperature-dependent boundary conditions and loadings are available including temperature, flux, convection, and radiation boundary conditions and internal heat generation. Additional specialized features treat enclosure radiation, bulk nodes, and master/slave internal surface conditions (e.g., contact resistance). Data input via a free-field format is provided. A user subprogram feature allows for any type of functional representation of any independent variable. A profile (bandwidth) minimization option is available. The code is limited to implicit time integration for transient solutions. TACO3D has no general mesh generation capability. Rows of evenly-spaced nodes and rows of sequential elements may be generated, but the program relies on separate mesh generators for complex zoning. TACO3D does not have the ability to calculate view factors internally. Graphical representation of data in the form of time history and spatial plots is provided through links to the POSTACO and GRAPE postprocessor codes.

  14. Quasi-3D space charge simulation

    SciTech Connect

    Yang, Xi; /Fermilab

    2007-04-01

    The longitudinal space charge effect is simulated by binning the longitudinal beam profile in order to calculate the force on the bins using the binned particle distribution via FFT, and applying momentum kick based upon this space charge force to macro-particles. Usually, the longitudinal space charge kick is calculated once per turn since the longitudinal profile doesn't change much in a single turn. Besides, the longitudinal profile is used as a weighting factor for the transverse space charge force. The transverse space charge effect is simulated by projecting the 3-D beam to a 2-D Gaussian distribution in order to use the complex error function to compute the transverse space charge force, and applying this space charge force to macro-particles. One transverse space charge calculation per scale length of the beam shape variation requires at least ten transverse space charge force calculations per betatron oscillation.

  15. Twin Peaks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    The two hills in the distance, approximately one to two kilometers away, have been dubbed the 'Twin Peaks' and are of great interest to Pathfinder scientists as objects of future study. 3D glasses are necessary to identify surface detail. The white areas on the left hill, called the 'Ski Run' by scientists, may have been formed by hydrologic processes.

    The IMP is a stereo imaging system with color capability provided by 24 selectable filters -- twelve filters per 'eye.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  16. 3D Audio System

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Ames Research Center research into virtual reality led to the development of the Convolvotron, a high speed digital audio processing system that delivers three-dimensional sound over headphones. It consists of a two-card set designed for use with a personal computer. The Convolvotron's primary application is presentation of 3D audio signals over headphones. Four independent sound sources are filtered with large time-varying filters that compensate for motion. The perceived location of the sound remains constant. Possible applications are in air traffic control towers or airplane cockpits, hearing and perception research and virtual reality development.

  17. The problem of frequency weighting functions and standards for birds

    NASA Astrophysics Data System (ADS)

    Dooling, Robert; Brittan-Powell, Elizabeth; Lauer, Amanda; Dent, Micheal; Noirot, Isabelle

    2005-09-01

    Frequency weighting functions in humans are widely used as a single-figure guess to assess noise problems and aid in making decisions with regard to noise limitations when no other data exist. However, this use of frequency weightings invariably results in a loss of precision in assessing the likelihood of a sound to produce hearing damage or sound annoyance. There is a growing interest in developing frequency weighting functions in animals presumably to assist in judging the risk of hearing damage, interference with acoustic communication, or habitat suitability. Laboratory studies reveal many parallels between humans and animals on a variety of psychoacoustic measures, such as equal loudness contours. However, differences between humans and animals on specific tests argue against using standards developed for humans to gauge the effect of noise on animals. Here we review data which show this same problem exists among birds. That is, the differences in the effects of noise among bird species can be as large as the differences between humans and birds. These results suggest that whereas frequency weighting functions and acoustic standards for a specific species might be useful, generalizing across species is likely not practical.

  18. 3D Printing of Molecular Models

    ERIC Educational Resources Information Center

    Gardner, Adam; Olson, Arthur

    2016-01-01

    Physical molecular models have played a valuable role in our understanding of the invisible nano-scale world. We discuss 3D printing and its use in producing models of the molecules of life. Complex biomolecular models, produced from 3D printed parts, can demonstrate characteristics of molecular structure and function, such as viral self-assembly,…

  19. Global magnetosphere-like 3D structure formation in kinetics by hot magnetized plasma flow characterized by shape of the particle distribution function

    NASA Astrophysics Data System (ADS)

    Gubchenko, Vladimir

    The task was to provide an analytical elementary magnetosphere-like model in kinetics for verification of the 3D EM PIC codes created for space/aerospace and HED plasmas applications. Kinetic approach versus cold MHD approach takes into account different behavior in the EM fields of resonant and non resonant particles in the velocity phase space, which appears via shape characteristics of the particle velocity distribution function (PVDF) and via the spatial dispersion effect forming the collisionless dissipation in the EM fields. The external flow is a hot collisionless plasma characterized by the particle velocity distribution function (PVDF) with different shapes: Maxwellian, kappa, etc. The flow is in a “hot regime”: it can be supersonic but its velocity remains less the thermal velocity of the electrons. The “internal” part of the magnetosphere formed by trapped particles is the prescribed 3D stationary magnetization considered as a spherical “quasiparticle” with internal magnetodipole and toroidal moments represented as a broadband EM driver. We obtain after the linearization of Vlasov/Maxwell equations a self-consistent 3D large scale kinetic solution of the classic problem. Namely, we: model the “outer” part of the magnetosphere formed by external hot plasma flow of the flyby particles. Solution of the Vlasov equation expressed via a tensor of dielectric permittivity of nonmagnetized and magnetized flowing plasma. Here, we obtain the direct kinetic dissipative effect of the magnetotail formation and the opposite diamagnetic effect of the magnetosphere “dipolization”. We get MHD wave cone in flow magnetized by external guiding magnetic (GM) field. Magnetosphere in our consideration is a 3D dissipative “wave” package structure of the skinned EM fields formed by the “waves” excited at frequency bands where we obtain negative values and singularities (resonances) of squared EM refractive index of the cold plasma. The hot regime

  20. 3D Surgical Simulation

    PubMed Central

    Cevidanes, Lucia; Tucker, Scott; Styner, Martin; Kim, Hyungmin; Chapuis, Jonas; Reyes, Mauricio; Proffit, William; Turvey, Timothy; Jaskolka, Michael

    2009-01-01

    This paper discusses the development of methods for computer-aided jaw surgery. Computer-aided jaw surgery allows us to incorporate the high level of precision necessary for transferring virtual plans into the operating room. We also present a complete computer-aided surgery (CAS) system developed in close collaboration with surgeons. Surgery planning and simulation include construction of 3D surface models from Cone-beam CT (CBCT), dynamic cephalometry, semi-automatic mirroring, interactive cutting of bone and bony segment repositioning. A virtual setup can be used to manufacture positioning splints for intra-operative guidance. The system provides further intra-operative assistance with the help of a computer display showing jaw positions and 3D positioning guides updated in real-time during the surgical procedure. The CAS system aids in dealing with complex cases with benefits for the patient, with surgical practice, and for orthodontic finishing. Advanced software tools for diagnosis and treatment planning allow preparation of detailed operative plans, osteotomy repositioning, bone reconstructions, surgical resident training and assessing the difficulties of the surgical procedures prior to the surgery. CAS has the potential to make the elaboration of the surgical plan a more flexible process, increase the level of detail and accuracy of the plan, yield higher operative precision and control, and enhance documentation of cases. Supported by NIDCR DE017727, and DE018962 PMID:20816308

  1. Martian terrain - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    An area of rocky terrain near the landing site of the Sagan Memorial Station can be seen in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. This image is part of a 3D 'monster' panorama of the area surrounding the landing site.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  2. 3D pharmacophore-based virtual screening, docking and density functional theory approach towards the discovery of novel human epidermal growth factor receptor-2 (HER2) inhibitors.

    PubMed

    Gogoi, Dhrubajyoti; Baruah, Vishwa Jyoti; Chaliha, Amrita Kashyap; Kakoti, Bibhuti Bhushan; Sarma, Diganta; Buragohain, Alak Kumar

    2016-12-21

    Human epidermal growth factor receptor 2 (HER2) is one of the four members of the epidermal growth factor receptor (EGFR) family and is expressed to facilitate cellular proliferation across various tissue types. Therapies targeting HER2, which is a transmembrane glycoprotein with tyrosine kinase activity, offer promising prospects especially in breast and gastric/gastroesophageal cancer patients. Persistence of both primary and acquired resistance to various routine drugs/antibodies is a disappointing outcome in the treatment of many HER2 positive cancer patients and is a challenge that requires formulation of new and improved strategies to overcome the same. Identification of novel HER2 inhibitors with improved therapeutics index was performed with a highly correlating (r=0.975) ligand-based pharmacophore model (Hypo1) in this study. Hypo1 was generated from a training set of 22 compounds with HER2 inhibitory activity and this well-validated hypothesis was subsequently used as a 3D query to screen compounds in a total of four databases of which two were natural product databases. Further, these compounds were analyzed for compliance with Veber's drug-likeness rule and optimum ADMET parameters. The selected compounds were then subjected to molecular docking and Density Functional Theory (DFT) analysis to discern their molecular interactions at the active site of HER2. The findings thus presented would be an important starting point towards the development of novel HER2 inhibitors using well-validated computational techniques.

  3. 3D origami electrochemical device for sensitive Pb(2+) testing based on DNA functionalized iron-porphyrinic metal-organic framework.

    PubMed

    Wang, Xiu; Yang, Chunlei; Zhu, Shaojun; Yan, Mei; Ge, Shenguang; Yu, Jinghua

    2017-01-15

    A highly sensitive electrochemical (EC) biosensor combined with a 3D origami device for detection of Pb(2+)was developed based on novel Au nanoparticles modified paper working electrode (Au-PWE) as sensor platform and DNA functionalized iron-porphyrinic metal-organic framework ((Fe-P)n-MOF-Au-GR) hybrids as signal probes. In the presence of Pb(2+), GR could be specifically cleaved at the ribonucleotide (rA) site, which produced the short (Fe-P)n-MOF-linked oligonucleotide fragment to hybridize with hairpin DNA immobilized on the surface of Au-PWE. Because of the mimic peroxidase property of (Fe-P)n-MOF, enzymatically amplified electrochemical signal was obtained to offer the sensitive detection of Pb(2+). In addition, benefiting from the Pb(2+) dependent GR, the proposed assay could selectively detect Pb(2+) in the presence of other metal ions. This method showed a good linear relationship between the current response and the Pb(2+) concentration ranging from 0.03 to 1000nmolL(-1) with a detection limit of 0.02nmolL(-1). The Au-PWE based electrochemical sensor along with the (Fe-P)n-MOF-Au-GR probe exhibited the advantages of low-cost, simple fabrication, high sensitivity and selectivity, providing potential application of real-time Pb(2+) detection both in environmental and biological samples.

  4. Solar Wind Halo Formation by the Scattering of the Strahl: Direct Cluster/PEACE Observations of the 3D Velocity Distribution Function

    NASA Astrophysics Data System (ADS)

    Vinas, A. F.; Gurgiolo, C. A.; Nieves-Chinchilla, T.; Wendel, D. E.; Goldstein, M. L.; Fazakerley, A. N.

    2010-12-01

    The current hypothesis of the formation of the solar wind halo electrons is that they are produced from scattering of the strahl. This hypothesis is strengthened by direct observations of the strahl electrons being scattered into the halo in an isolated event. On frequent occasions we have observed in electron angular skymaps (Phi/Theta-plots) of the electron 3D velocity distribution functions, a bursty-filament of particles connecting the strahl to the solar wind core-halo. These are seen over a limited energy range. The observation implies that the formation of the halo is not a continuous process but occurs in bursts in regions where conditions for wave growth providing the scattering are optimum. Sometimes, observations indicates that the strahl component is anisotropic (Tper/Tpal ~ 2). This provides a possible free energy source for the excitation of whistler waves as a possible scattering mechanism, however this condition is not always observed. The empirical observational evidence between the halo and the strahl suggests that the strahl population may be, at least in part, the source of the halo component.

  5. Source inversion analysis of the 2011 Tohoku-Oki earthquake using Green's functions calculated from a 3-D heterogeneous structure model

    NASA Astrophysics Data System (ADS)

    Suzuki, W.; Aoi, S.; Maeda, T.; Sekiguchi, H.; Kunugi, T.

    2013-12-01

    Source inversion analysis using near-source strong-motion records with an assumption of 1-D underground structure models has revealed the overall characteristics of the rupture process of the 2011 Tohoku-Oki mega-thrust earthquake. This assumption for the structure model is acceptable because the seismic waves radiated during the Tohoku-Oki event were rich in the very-low-frequency contents lower than 0.05 Hz, which are less affected by the small-scale heterogeneous structure. The analysis using more reliable Green's functions even in the higher-frequency range considering complex structure of the subduction zone will illuminate more detailed rupture process in space and time and the transition of the frequency dependence of the wave radiation for the Tohoku-Oki earthquake. In this study, we calculate the near-source Green's functions using a 3-D underground structure model and perform the source inversion analysis using them. The 3-D underground structure model used in this study is the Japan Integrated Velocity Structure Model (Headquarters for Earthquake Research Promotion, 2012). A curved fault model on the Pacific plate interface is discretized into 287 subfaults at ~20 km interval. The Green's functions are calculated using GMS (Aoi et al., 2004), which is a simulation program package for the seismic wave field by the finite difference method using discontinuous grids (Aoi and Fujiwara, 1999). Computational region is 136-146.2E in longitude, 34-41.6N in latitude, and 0-100 km in depth. The horizontal and vertical grid intervals are 200 m and 100 m, respectively, for the shallower region and those for the deeper region are tripled. The number of the total grids is 2.1 billion. We derive 300-s records by calculating 36,000 steps with a time interval of 0.0083 second (120 Hz sampling). It takes nearly one hour to compute one case using 48 Graphics Processing Units (GPU) on TSUBAME2.0 supercomputer owned by Tokyo Institute of Technology. In total, 574 cases are

  6. Synthesis and Exploratory Catalysis of 3d Metals: Group-Transfer Reactions, and the Activation and Functionalization of Small Molecules Including Greenhouse Gases

    SciTech Connect

    Mindiola, Daniel J.

    2014-05-07

    Our work over the past three years has resulted in the development of electron rich and low-coordinate vanadium fragments, molecular nitrides of vanadium and parent imide systems of titanium, and the synthesis of phosphorus containing molecules of the 3d transition metal series. Likewise, with financial support from BES Division in DOE (DE-FG02-07ER15893), we now completed the full characterization of the first single molecular magnet (SMM) of Fe(III). We demonstrated that this monomeric form of Fe(III) has an unusual slow relaxation of the magnetization under zero applied field. To make matters more interesting, this system also undergoes a rare example of an intermediate to high-spin transition (an S = 3/2 to S = 5/2 transition). In 2010 we reported the synthesis of the first neutral and low-coordinate vanadium complexes having the terminal nitride functionality. We have now completed a full study to understand formation of the nitride ligand from the metastable azide precursor, and have also explored the reactivity of the nitride ligand in the context of incomplete and complete N-atom transfer. During the 2010-2013 period we also discovered a facile approach to assemble low-coordinate and low-valent vanadium(II) complexes and exploit their multielectron chemistry ranging from 1-3 electrons. Consequently, we can now access 3d ligand frameworks such as cyclo-P3 (and its corresponding radical anion), nitride radical anions and cations, low-coordinate vanadium oxo’s, and the first example of a vanadium thionitrosyl complex. A cis-divacant iron(IV) imido having some ligand centered radical has been also discovered, and we are in the process of elucidating its electronic structure (in particular the sign of zero field splitting and the origin of its magnitude), bonding and reactivity. We have also revisited some paramagnetic and classic metallocene compounds with S >1/2 ground states in order to understand their reactivity patterns and electronic structure. Lastly

  7. In vitro assessment of Function Graded (FG) artificial Hip joint stem in terms of bone/cement stresses: 3D Finite Element (FE) study

    PubMed Central

    2013-01-01

    Background Stress shielding in the cemented hip prosthesis occurs due to the mismatching in the mechanical properties of metallic stem and bone. This mismatching in properties is considered as one of the main reasons for implant loosening. Therefore, a new stem material in orthopedic surgery is still required. In the present study, 3D finite element modeling is used for evaluating the artificial hip joint stem that is made of Function Graded (FG) material in terms of joint stress distributions and stem length. Method 3D finite element models of different stems made of two types of FG materials and traditional stems made of Cobalt Chromium alloy (CoCrMo) and Titanium alloy (Ti) were developed using the ANSYS Code. The effects on the total artificial hip joint stresses (Shear stress and Von Mises stresses at bone cement, Von Mises stresses at bone and stem) due to using the proposed FG materials stems were investigated. The effects on the total artificial hip joint system stresses due to using different stem lengths were investigated. Results Using FG stem (with low stiffness at stem distal end and high stiffness at its proximal end) resulted in a significant reduction in shear stress at the bone cement/stem interface. Also, the Von Mises stresses at the bone cement and stem decrease significantly when using FG material instead of CoCrMo and Ti alloy. The stresses’ distribution along the bone cement length when using FG material was found to be more uniform along the whole bone cement compared with other stem materials. These more uniform stresses will help in the reduction of the artificial hip joint loosening rate and improve its short and long term performance. Conclusion FE results showed that using FG stem increases the resultant stresses at the femur bone (reduces stress shielding) compared to metallic stem. The results showed that the stem length has significant effects on the resultant shear and Von Mises stresses at bone, stem and bone cement for all types

  8. Optimum weight design of functionally graded material gears

    NASA Astrophysics Data System (ADS)

    Jing, Shikai; Zhang, He; Zhou, Jingtao; Song, Guohua

    2015-11-01

    Traditional gear weight optimization methods consider gear tooth number, module, face width or other dimension parameters of gear as design variables. However, due to the complicated form and geometric features peculiar to the gear, there will be large amounts of design parameters in gear design, and the influences of gear parameters changing on gear trains, transmission system and the whole equipment have to be taken into account, which increases the complexity of optimization problem. This paper puts forward to apply functionally graded materials (FGMs) to gears and then conduct the optimization. According to the force situation of gears, the material distribution form of FGM gears is determined. Then based on the performance parameters analysis of FGMs and the practical working demands for gears, a multi-objective optimization model is formed. Finally by using the goal driven optimization (GDO) method, the optimal material distribution is achieved, which makes gear weight and the maximum deformation be minimum and the maximum bending stress do not exceed the allowable stress. As an example, the applying of FGM to automotive transmission gear is conducted to illustrate the optimization design process and the result shows that under the condition of keeping the normal working performance of gear, the method achieves in greatly reducing the gear weight. This research proposes a FGM gears design method that is able to largely reduce the weight of gears by optimizing the microscopic material parameters instead of changing the macroscopic dimension parameters of gears, which reduces the complexity of gear weight optimization problem.

  9. 3D field harmonics

    SciTech Connect

    Caspi, S.; Helm, M.; Laslett, L.J.

    1991-03-30

    We have developed an harmonic representation for the three dimensional field components within the windings of accelerator magnets. The form by which the field is presented is suitable for interfacing with other codes that make use of the 3D field components (particle tracking and stability). The field components can be calculated with high precision and reduced cup time at any location (r,{theta},z) inside the magnet bore. The same conductor geometry which is used to simulate line currents is also used in CAD with modifications more readily available. It is our hope that the format used here for magnetic fields can be used not only as a means of delivering fields but also as a way by which beam dynamics can suggest correction to the conductor geometry. 5 refs., 70 figs.

  10. The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation.

    PubMed

    Wu, Shirley; Liang, Mike P; Altman, Russ B

    2008-01-16

    Structural genomics efforts have led to increasing numbers of novel, uncharacterized protein structures with low sequence identity to known proteins, resulting in a growing need for structure-based function recognition tools. Our method, SeqFEATURE, robustly models protein functions described by sequence motifs using a structural representation. We built a library of models that shows good performance compared to other methods. In particular, SeqFEATURE demonstrates significant improvement over other methods when sequence and structural similarity are low.

  11. Absorption and scattering 2-D volcano images from numerically calculated space-weighting functions

    NASA Astrophysics Data System (ADS)

    Del Pezzo, Edoardo; Ibañez, Jesus; Prudencio, Janire; Bianco, Francesca; De Siena, Luca

    2016-08-01

    Short-period small magnitude seismograms mainly comprise scattered waves in the form of coda waves (the tail part of the seismogram, starting after S waves and ending when the noise prevails), spanning more than 70 per cent of the whole seismogram duration. Corresponding coda envelopes provide important information about the earth inhomogeneity, which can be stochastically modeled in terms of distribution of scatterers in a random medium. In suitable experimental conditions (i.e. high earth heterogeneity), either the two parameters describing heterogeneity (scattering coefficient), intrinsic energy dissipation (coefficient of intrinsic attenuation) or a combination of them (extinction length and seismic albedo) can be used to image Earth structures. Once a set of such parameter couples has been measured in a given area and for a number of sources and receivers, imaging their space distribution with standard methods is straightforward. However, as for finite-frequency and full-waveform tomography, the essential problem for a correct imaging is the determination of the weighting function describing the spatial sensitivity of observable data to scattering and absorption anomalies. Due to the nature of coda waves, the measured parameter couple can be seen as a weighted space average of the real parameters characterizing the rock volumes illuminated by the scattered waves. This paper uses the Monte Carlo numerical solution of the Energy Transport Equation to find approximate but realistic 2-D space-weighting functions for coda waves. Separate images for scattering and absorption based on these sensitivity functions are then compared with those obtained with commonly used sensitivity functions in an application to data from an active seismic experiment carried out at Deception Island (Antarctica). Results show that these novel functions are based on a reliable and physically grounded method to image magnitude and shape of scattering and absorption anomalies. Their

  12. Cryptographic Properties of the Hidden Weighted Bit Function

    DTIC Science & Technology

    2013-12-23

    40 and revisited by D. Knuth in Vol. 4 of The Art of Computer Programming, is a function that seems to be the simplest one with exponential Binary...SUPPLEMENTARY NOTES 14. ABSTRACT The hidden weighted bit function (HWBF), introduced by R. Bryant in IEEE Trans. Comp. 40 and revisited by D. Knuth in...but has a VLSI implementation with low area-time complexity [2]. In [19], Knuth reproved Bryant’s theorem stating that the HWBF has a large BDD size

  13. CART peptides: regulators of body weight, reward and other functions

    PubMed Central

    Rogge, G.; Jones, D.; Hubert, G. W.; Lin, Y.; Kuhar, M. J.

    2015-01-01

    Over the past decade or so, CART (cocaine- and amphetamine-regulated transcript) peptides have emerged as major neurotransmitters and hormones. CART peptides are widely distributed in the CNS and are involved in regulating many processes, including food intake and the maintenance of body weight, reward and endocrine functions. Recent studies have produced a wealth of information about the location, regulation, processing and functions of CART peptides, but additional studies aimed at elucidating the physiological effects of the peptides and at characterizing the CART receptor(s) are needed to take advantage of possible therapeutic applications. PMID:18802445

  14. 3D printed bionic ears.

    PubMed

    Mannoor, Manu S; Jiang, Ziwen; James, Teena; Kong, Yong Lin; Malatesta, Karen A; Soboyejo, Winston O; Verma, Naveen; Gracias, David H; McAlpine, Michael C

    2013-06-12

    The ability to three-dimensionally interweave biological tissue with functional electronics could enable the creation of bionic organs possessing enhanced functionalities over their human counterparts. Conventional electronic devices are inherently two-dimensional, preventing seamless multidimensional integration with synthetic biology, as the processes and materials are very different. Here, we present a novel strategy for overcoming these difficulties via additive manufacturing of biological cells with structural and nanoparticle derived electronic elements. As a proof of concept, we generated a bionic ear via 3D printing of a cell-seeded hydrogel matrix in the anatomic geometry of a human ear, along with an intertwined conducting polymer consisting of infused silver nanoparticles. This allowed for in vitro culturing of cartilage tissue around an inductive coil antenna in the ear, which subsequently enables readout of inductively-coupled signals from cochlea-shaped electrodes. The printed ear exhibits enhanced auditory sensing for radio frequency reception, and complementary left and right ears can listen to stereo audio music. Overall, our approach suggests a means to intricately merge biologic and nanoelectronic functionalities via 3D printing.

  15. 3D Printed Bionic Ears

    PubMed Central

    Mannoor, Manu S.; Jiang, Ziwen; James, Teena; Kong, Yong Lin; Malatesta, Karen A.; Soboyejo, Winston O.; Verma, Naveen; Gracias, David H.; McAlpine, Michael C.

    2013-01-01

    The ability to three-dimensionally interweave biological tissue with functional electronics could enable the creation of bionic organs possessing enhanced functionalities over their human counterparts. Conventional electronic devices are inherently two-dimensional, preventing seamless multidimensional integration with synthetic biology, as the processes and materials are very different. Here, we present a novel strategy for overcoming these difficulties via additive manufacturing of biological cells with structural and nanoparticle derived electronic elements. As a proof of concept, we generated a bionic ear via 3D printing of a cell-seeded hydrogel matrix in the precise anatomic geometry of a human ear, along with an intertwined conducting polymer consisting of infused silver nanoparticles. This allowed for in vitro culturing of cartilage tissue around an inductive coil antenna in the ear, which subsequently enables readout of inductively-coupled signals from cochlea-shaped electrodes. The printed ear exhibits enhanced auditory sensing for radio frequency reception, and complementary left and right ears can listen to stereo audio music. Overall, our approach suggests a means to intricately merge biologic and nanoelectronic functionalities via 3D printing. PMID:23635097

  16. Function estimation by feedforward sigmoidal networks with bounded weights

    SciTech Connect

    Rao, N.S.V.; Protopoescu, V.; Qiao, H.

    1996-05-01

    The authors address the problem of PAC (probably and approximately correct) learning functions f : [0, 1]{sup d} {r_arrow} [{minus}K, K] based on iid (independently and identically distributed) sample generated according to an unknown distribution, by using feedforward sigmoidal networks. They use two basic properties of the neural networks with bounded weights, namely: (a) they form a Euclidean class, and (b) for hidden units of the form tanh ({gamma}z) they are Lipschitz functions. Either property yields sample sizes for PAC function learning under any Lipschitz cost function. The sample size based on the first property is tighter compared to the known bounds based on VC-dimension. The second estimate yields a sample size that can be conveniently adjusted by a single parameter, {gamma}, related to the hidden nodes.

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

    SciTech Connect

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

    2015-08-24

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

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

    DOE PAGES

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

    2015-08-24

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

  19. 3D structure of macropore networks within natural and de-embarked estuary saltmarsh sediments: towards an improved understanding of network structural control over hydrologic function

    NASA Astrophysics Data System (ADS)

    Carr, Simon; Spencer, Kate; James, Tempest; Lucy, Diggens

    2015-04-01

    Saltmarshes are globally important environments which, though occupying < 4% of the Earth's surface, provide a range of ecosystem services. Yet, they are threatened by sea level rise, human population growth, urbanization and pollution resulting in degradation. To compensate for this habitat loss many coastal restoration projects have been implemented over the last few decades, largely driven by legislative requirements for improved biodiversity e.g. the EU Habitats Directive and Birds Directive. However, there is growing evidence that restored saltmarshes, recreated through the return to tidal inundation of previously drained and defended low-lying coastal land, do not have the same species composition even after 100 years and while environmental enhancement has been achieved, there may be consequences for ecosystem functioning This study presents the findings of a comparative analysis of detailed sediment structure and hydrological functioning of equivalent natural and de-embanked saltmarsh sediments at Orplands Farm, Essex, UK. 3D x-ray CT scanning of triplicate undisturbed sediment cores recovered in 2013 have been used to derive detailed volumetric reconstructions of macropore structure and networks, and to infer differences in bulk microporosity between natural and de-embanked saltmarshes. These volumes have been further visualised for qualitative analysis of the main sediment components, and extraction of key macropore space parameters for quantified analysis including total porosity and connectivity, as well as structure, organisation and efficiency (tortuosity) of macropore networks. Although total porosity was significantly greater within the de-embanked saltmarsh sediments, pore networks in these samples were less organised and more tortuous, and were also inferred to have significantly lower micro-porosity than those of the natural saltmarsh. These datasets are applied to explain significant differences in the hydraulic behaviour and functioning

  20. Positional Awareness Map 3D (PAM3D)

    NASA Technical Reports Server (NTRS)

    Hoffman, Monica; Allen, Earl L.; Yount, John W.; Norcross, April Louise

    2012-01-01

    The Western Aeronautical Test Range of the National Aeronautics and Space Administration s Dryden Flight Research Center needed to address the aging software and hardware of its current situational awareness display application, the Global Real-Time Interactive Map (GRIM). GRIM was initially developed in the late 1980s and executes on older PC architectures using a Linux operating system that is no longer supported. Additionally, the software is difficult to maintain due to its complexity and loss of developer knowledge. It was decided that a replacement application must be developed or acquired in the near future. The replacement must provide the functionality of the original system, the ability to monitor test flight vehicles in real-time, and add improvements such as high resolution imagery and true 3-dimensional capability. This paper will discuss the process of determining the best approach to replace GRIM, and the functionality and capabilities of the first release of the Positional Awareness Map 3D.

  1. Intraoral 3D scanner

    NASA Astrophysics Data System (ADS)

    Kühmstedt, Peter; Bräuer-Burchardt, Christian; Munkelt, Christoph; Heinze, Matthias; Palme, Martin; Schmidt, Ingo; Hintersehr, Josef; Notni, Gunther

    2007-09-01

    Here a new set-up of a 3D-scanning system for CAD/CAM in dental industry is proposed. The system is designed for direct scanning of the dental preparations within the mouth. The measuring process is based on phase correlation technique in combination with fast fringe projection in a stereo arrangement. The novelty in the approach is characterized by the following features: A phase correlation between the phase values of the images of two cameras is used for the co-ordinate calculation. This works contrary to the usage of only phase values (phasogrammetry) or classical triangulation (phase values and camera image co-ordinate values) for the determination of the co-ordinates. The main advantage of the method is that the absolute value of the phase at each point does not directly determine the coordinate. Thus errors in the determination of the co-ordinates are prevented. Furthermore, using the epipolar geometry of the stereo-like arrangement the phase unwrapping problem of fringe analysis can be solved. The endoscope like measurement system contains one projection and two camera channels for illumination and observation of the object, respectively. The new system has a measurement field of nearly 25mm × 15mm. The user can measure two or three teeth at one time. So the system can by used for scanning of single tooth up to bridges preparations. In the paper the first realization of the intraoral scanner is described.

  2. 'Diamond' in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

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

    Opportunity has bored nearly a dozen holes into the inner walls of 'Endurance Crater.' On sols 177 and 178 (July 23 and July 24, 2004), the rover worked double-duty on Diamond Jenness. Surface debris and the bumpy shape of the rock resulted in a shallow and irregular hole, only about 2 millimeters (0.08 inch) deep. The final depth was not enough to remove all the bumps and leave a neat hole with a smooth floor. This extremely shallow depression was then examined by the rover's alpha particle X-ray spectrometer.

    On Sol 178, Opportunity's 'robotic rodent' dined on Diamond Jenness once again, grinding almost an additional 5 millimeters (about 0.2 inch). The rover then applied its Moessbauer spectrometer to the deepened hole. This double dose of Diamond Jenness enabled the science team to examine the rock at varying layers. Results from those grindings are currently being analyzed.

    The image mosaic is about 6 centimeters (2.4 inches) across.

  3. Prominent rocks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Many prominent rocks near the Sagan Memorial Station are featured in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. Wedge is at lower left; Shark, Half-Dome, and Pumpkin are at center. Flat Top, about four inches high, is at lower right. The horizon in the distance is one to two kilometers away.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  4. iSocial: delivering the Social Competence Intervention for Adolescents (SCI-A) in a 3D virtual learning environment for youth with high functioning autism.

    PubMed

    Stichter, Janine P; Laffey, James; Galyen, Krista; Herzog, Melissa

    2014-02-01

    One consistent area of need for students with autism spectrum disorders is in the area of social competence. However, the increasing need to provide qualified teachers to deliver evidence-based practices in areas like social competence leave schools, such as those found in rural areas, in need of support. Distance education and in particular, 3D Virtual Learning, holds great promise for supporting schools and youth to gain social competence through knowledge and social practice in context. iSocial, a distance education, 3D virtual learning environment implemented the 31-lesson social competence intervention for adolescents across three small cohorts totaling 11 students over a period of 4 months. Results demonstrated that the social competence curriculum was delivered with fidelity in the 3D virtual learning environment. Moreover, learning outcomes suggest that the iSocial approach shows promise for social competence benefits for youth.

  5. 3D ultrafast ultrasound imaging in vivo.

    PubMed

    Provost, Jean; Papadacci, Clement; Arango, Juan Esteban; Imbault, Marion; Fink, Mathias; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

    2014-10-07

    Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in 3D based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32  ×  32 matrix-array probe. Its ability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3D Shear-Wave Imaging, 3D Ultrafast Doppler Imaging, and, finally, 3D Ultrafast combined Tissue and Flow Doppler Imaging. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3D Ultrafast Doppler was used to obtain 3D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, at thousands of volumes per second, the complex 3D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, as well as the 3D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3D Ultrafast Ultrasound Imaging for the 3D mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra--and inter-observer variability.

  6. 3D ultrafast ultrasound imaging in vivo

    NASA Astrophysics Data System (ADS)

    Provost, Jean; Papadacci, Clement; Esteban Arango, Juan; Imbault, Marion; Fink, Mathias; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

    2014-10-01

    Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in 3D based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32  ×  32 matrix-array probe. Its ability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3D Shear-Wave Imaging, 3D Ultrafast Doppler Imaging, and, finally, 3D Ultrafast combined Tissue and Flow Doppler Imaging. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3D Ultrafast Doppler was used to obtain 3D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, at thousands of volumes per second, the complex 3D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, as well as the 3D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3D Ultrafast Ultrasound Imaging for the 3D mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra—and inter-observer variability.

  7. Do community-weighted mean functional traits reflect optimal strategies?

    PubMed Central

    Muscarella, Robert; Uriarte, María

    2016-01-01

    The notion that relationships between community-weighted mean (CWM) traits (i.e. plot-level trait values weighted by species abundances) and environmental conditions reflect selection towards locally optimal phenotypes is challenged by the large amount of interspecific trait variation typically found within ecological communities. Reconciling these contrasting patterns is a key to advancing predictive theories of functional community ecology. We combined data on geographical distributions and three traits (wood density, leaf mass per area and maximum height) of 173 tree species in Puerto Rico. We tested the hypothesis that species are more likely to occur where their trait values are more similar to the local CWM trait values (the ‘CWM-optimality’ hypothesis) by comparing species occurrence patterns (as a proxy for fitness) with the functional composition of forest plots across a precipitation gradient. While 70% of the species supported CWM-optimality for at least one trait, nearly 25% significantly opposed it for at least one trait, thereby contributing to local functional diversity. The majority (85%) of species that opposed CWM-optimality did so only for one trait and few species opposed CWM-optimality in multivariate trait space. Our study suggests that constraints to local functional variation act more strongly on multivariate phenotypes than on univariate traits. PMID:27030412

  8. Do community-weighted mean functional traits reflect optimal strategies?

    PubMed

    Muscarella, Robert; Uriarte, María

    2016-03-30

    The notion that relationships between community-weighted mean (CWM) traits (i.e. plot-level trait values weighted by species abundances) and environmental conditions reflect selection towards locally optimal phenotypes is challenged by the large amount of interspecific trait variation typically found within ecological communities. Reconciling these contrasting patterns is a key to advancing predictive theories of functional community ecology. We combined data on geographical distributions and three traits (wood density, leaf mass per area and maximum height) of 173 tree species in Puerto Rico. We tested the hypothesis that species are more likely to occur where their trait values are more similar to the local CWM trait values (the'CWM-optimality' hypothesis) by comparing species occurrence patterns (as a proxy for fitness) with the functional composition of forest plots across a precipitation gradient. While 70% of the species supported CWM-optimality for at least one trait, nearly 25% significantly opposed it for at least one trait, thereby contributing to local functional diversity. The majority (85%) of species that opposed CWM-optimality did so only for one trait and few species opposed CWM-optimality in multivariate trait space. Our study suggests that constraints to local functional variation act more strongly on multivariate phenotypes than on univariate traits.

  9. Metabolically active functional food ingredients for weight control.

    PubMed

    Kovacs, E M R; Mela, D J

    2006-02-01

    The scale of the obesity epidemic creates a pressing consumer need as well as an enormous business opportunity for successful development and marketing of food products with added benefits for weight control. A number of proposed functional food ingredients have been shown to act post-absorptively to influence substrate utilization or thermogenesis. Characteristics and supporting data on conjugated linoleic acid, diglycerides, medium-chain triglycerides, green tea, ephedrine, caffeine, capsaicin and calcium, are reviewed here, giving examples of how these could act to alter energy expenditure or appetite control. Consideration is also given to other factors, in addition to efficacy, which must be satisfied to get such ingredients into foods. We conclude that, for each of the safe, putatively metabolically active agents, there remain gaps in clinical evidence or knowledge of mechanisms, which need to be addressed in order to specify the dietary conditions and food product compositions where these ingredients could be of most benefit for weight control.

  10. Quantitative Evaluation of 3D Mouse Behaviors and Motor Function in the Open-Field after Spinal Cord Injury Using Markerless Motion Tracking

    PubMed Central

    Sheets, Alison L.; Lai, Po-Lun; Fisher, Lesley C.; Basso, D. Michele

    2013-01-01

    Thousands of scientists strive to identify cellular mechanisms that could lead to breakthroughs in developing ameliorative treatments for debilitating neural and muscular conditions such as spinal cord injury (SCI). Most studies use rodent models to test hypotheses, and these are all limited by the methods available to evaluate animal motor function. This study’s goal was to develop a behavioral and locomotor assessment system in a murine model of SCI that enables quantitative kinematic measurements to be made automatically in the open-field by applying markerless motion tracking approaches. Three-dimensional movements of eight naïve, five mild, five moderate, and four severe SCI mice were recorded using 10 cameras (100 Hz). Background subtraction was used in each video frame to identify the animal’s silhouette, and the 3D shape at each time was reconstructed using shape-from-silhouette. The reconstructed volume was divided into front and back halves using k-means clustering. The animal’s front Center of Volume (CoV) height and whole-body CoV speed were calculated and used to automatically classify animal behaviors including directed locomotion, exploratory locomotion, meandering, standing, and rearing. More detailed analyses of CoV height, speed, and lateral deviation during directed locomotion revealed behavioral differences and functional impairments in animals with mild, moderate, and severe SCI when compared with naïve animals. Naïve animals displayed the widest variety of behaviors including rearing and crossing the center of the open-field, the fastest speeds, and tallest rear CoV heights. SCI reduced the range of behaviors, and decreased speed (r = .70 p<.005) and rear CoV height (r = .65 p<.01) were significantly correlated with greater lesion size. This markerless tracking approach is a first step toward fundamentally changing how rodent movement studies are conducted. By providing scientists with sensitive, quantitative measurement

  11. Determination of focal mechanisms of intermediate-magnitude earthquakes in Mexico, based on Greens functions calculated for a 3D Earth model

    NASA Astrophysics Data System (ADS)

    Rodrigo Rodríguez Cardozo, Félix; Hjörleifsdóttir, Vala

    2015-04-01

    One important ingredient in the study of the complex active tectonics in Mexico is the analysis of earthquake focal mechanisms, or the seismic moment tensor. They can be determined trough the calculation of Green functions and subsequent inversion for moment-tensor parameters. However, this calculation is gets progressively more difficult as the magnitude of the earthquakes decreases. Large earthquakes excite waves of longer periods that interact weakly with laterally heterogeneities in the crust. For these earthquakes, using 1D velocity models to compute the Greens fucntions works well. The opposite occurs for smaller and intermediate sized events, where the relatively shorter periods excited interact strongly with lateral heterogeneities in the crust and upper mantle and requires more specific or regional 3D models. In this study, we calculate Greens functions for earthquakes in Mexico using a laterally heterogeneous seismic wave speed model, comprised of mantle model S362ANI (Kustowski et al 2008) and crustal model CRUST 2.0 (Bassin et al 1990). Subsequently, we invert the observed seismograms for the seismic moment tensor using a method developed by Liu et al (2004) an implemented by Óscar de La Vega (2014) for earthquakes in Mexico. By following a brute force approach, in which we include all observed Rayleigh and Love waves of the Mexican National Seismic Network (Servicio Sismológico Naciona, SSN), we obtain reliable focal mechanisms for events that excite a considerable amount of low frequency waves (Mw > 4.8). However, we are not able to consistently estimate focal mechanisms for smaller events using this method, due to high noise levels in many of the records. Excluding the noisy records, or noisy parts of the records manually, requires interactive edition of the data, using an efficient tool for the editing. Therefore, we developed a graphical user interface (GUI), based on python and the python library ObsPy, that allows the edition of observed and

  12. Text Classification by Combining Different Distance Functions with Weights

    NASA Astrophysics Data System (ADS)

    Yamada, Takahiro; Ishii, Naohiro; Nakashima, Toyoshiro

    The text classification is an important subject in the data mining. For the text classification, several methods have been developed up to now, as the nearest neighbor analysis, the latent semantic analysis, etc. The k-nearest neighbor (kNN) classification is a well-known simple and effective method for the classification of data in many domains. In the use of the kNN, the distance function is important to measure the distance and the similarity between data. To improve the performance of the classifier by the kNN, a new approach to combine multiple distance functions is proposed here. The weighting factors of elements in the distance function, are computed by GA for the effectiveness of the measurement. Further, an ensemble processing was developed for the improvement of the classification accuracy. Finally, it is shown by experiments that the methods, developed here, are effective in the text classification.

  13. Hierarchical 3D ZnIn2S4/graphene nano-heterostructures: their in situ fabrication with dual functionality in solar hydrogen production and as anodes for lithium ion batteries.

    PubMed

    Kale, Sayali B; Kalubarme, Ramchandra S; Mahadadalkar, Manjiri A; Jadhav, Harsharaj S; Bhirud, Ashwini P; Ambekar, Jalinder D; Park, Chan-Jin; Kale, Bharat B

    2015-12-21

    Hierarchical 3D ZnIn2S4/graphene (ZnIn2S4/Gr) nano-heterostructures were successfully synthesized using an in-situ hydrothermal method. The dual functionality of these nano-heterostructures i.e. for solar hydrogen production and lithium ion batteries has been demonstrated for the first time. The ZnIn2S4/Gr nano-heterostructures were optimized by varying the concentrations of graphene for utmost hydrogen production. An inspection of the structure shows the existence of layered hexagonal ZnIn2S4 wrapped in graphene. The reduction of graphene oxide (GO) to graphene was confirmed by Raman and XPS analyses. The morphological analysis demonstrated that ultrathin ZnIn2S4 nanopetals are dispersed on graphene sheets. The optical study reveals the extended absorption edge to the visible region due to the presence of graphene and hence is used as a photocatalyst to transform H2S into eco-friendly hydrogen using solar light. The ZnIn2S4/Gr nano-heterostructure that is comprised of graphene and ZnIn2S4 in a weight ratio of 1 : 99 exhibits enhanced photocatalytically stable hydrogen production i.e. ∼6365 μmole h(-1) under visible light irradiation using just 0.2 g of nano-heterostructure, which is much higher as compared to bare hierarchical 3D ZnIn2S4. The heightened photocatalytic activity is attributed to the enhanced charge carrier separation due to graphene which acts as an excellent electron collector and transporter. Furthermore, the usage of nano-heterostructures and pristine ZnIn2S4 as anodes in lithium ion batteries confers the charge capacities of 590 and 320 mA h g(-1) after 220 cycles as compared to their initial reversible capacities of 645 and 523 mA h g(-1), respectively. These nano-heterostructures show high reversible capacity, excellent cycling stability, and high-rate capability indicating their potential as promising anode materials for LIBs. The excellent performance is due to the nanostructuring of ZnIn2S4 and the presence of a graphene layer, which

  14. 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.

  15. 3D Ultrafast Ultrasound Imaging In Vivo

    PubMed Central

    Provost, Jean; Papadacci, Clement; Arango, Juan Esteban; Imbault, Marion; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

    2014-01-01

    Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative real-time imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in three dimensions based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32×32 matrix-array probe. Its capability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3-D Shear-Wave Imaging, 3-D Ultrafast Doppler Imaging and finally 3D Ultrafast combined Tissue and Flow Doppler. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3-D Ultrafast Doppler was used to obtain 3-D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, for the first time, the complex 3-D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, and the 3-D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3-D Ultrafast Ultrasound Imaging for the 3-D real-time mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra- and inter-observer variability. PMID:25207828

  16. 3D Visualization Development of SIUE Campus

    NASA Astrophysics Data System (ADS)

    Nellutla, Shravya

    Geographic Information Systems (GIS) has progressed from the traditional map-making to the modern technology where the information can be created, edited, managed and analyzed. Like any other models, maps are simplified representations of real world. Hence visualization plays an essential role in the applications of GIS. The use of sophisticated visualization tools and methods, especially three dimensional (3D) modeling, has been rising considerably due to the advancement of technology. There are currently many off-the-shelf technologies available in the market to build 3D GIS models. One of the objectives of this research was to examine the available ArcGIS and its extensions for 3D modeling and visualization and use them to depict a real world scenario. Furthermore, with the advent of the web, a platform for accessing and sharing spatial information on the Internet, it is possible to generate interactive online maps. Integrating Internet capacity with GIS functionality redefines the process of sharing and processing the spatial information. Enabling a 3D map online requires off-the-shelf GIS software, 3D model builders, web server, web applications and client server technologies. Such environments are either complicated or expensive because of the amount of hardware and software involved. Therefore, the second objective of this research was to investigate and develop simpler yet cost-effective 3D modeling approach that uses available ArcGIS suite products and the free 3D computer graphics software for designing 3D world scenes. Both ArcGIS Explorer and ArcGIS Online will be used to demonstrate the way of sharing and distributing 3D geographic information on the Internet. A case study of the development of 3D campus for the Southern Illinois University Edwardsville is demonstrated.

  17. 3-D Medicine.

    ERIC Educational Resources Information Center

    Reese, Susan

    2001-01-01

    Describes the Visible Human Project of the National Library of Medicine that links the print library of functional-physiological knowledge with the image library of structural-anatomical knowledge into one unified resource. (JOW)

  18. The role of susceptibility weighted imaging in functional MRI.

    PubMed

    Haacke, E Mark; Ye, Yongquan

    2012-08-15

    The development of functional brain magnetic resonance imaging (fMRI) has been a boon for neuroscientists and radiologists alike. It provides for fundamental information on brain function and better diagnostic tools to study disease. In this paper, we will review some of the early concepts in high resolution gradient echo imaging with a particular emphasis on susceptibility weighted imaging (SWI) and MR angiography (MRA). We begin with the history of our own experience in this area, followed by a discussion of the role of high resolution in studying the vasculature of the brain and how this relates to the BOLD (blood oxygenation level dependent) signal. We introduce the role of SWI and susceptibility mapping (SWIM) in fMRI and close with recommendations for future high resolution experiments.

  19. Electric-dipole allowed and intercombination transitions among the 3d 5, 3d 44s and 3d 44p levels of Fe IV

    NASA Astrophysics Data System (ADS)

    Deb, Narayan C.; Hibbert, Alan

    2010-07-01

    Oscillator strengths and transition rates for the electric-dipole (E1) allowed and intercombination transitions among 3d 5, 3d 44s and 3d 44p levels of Fe IV are calculated using the CIV3 code of Hibbert and coworkers. Using the Hartree-Fock functions up to 3d orbitals we have also optimized 4s, 4p, 4d, 4f, 5s, 5p and 5d orbitals of which 4s and 4p are taken to be spectroscopic and the remaining orbitals represent corrections to the spectroscopic orbitals or the correlation effects. The J-dependent levels of 108 LS states are included in the calculation and the relativistic effects are accounted for via the Breit-Pauli operator. Configurations are chosen in two steps: (a) two promotions were allowed from the 3p, 3d, 4s and 4p subshells, using all the orbitals; and (b) selective promotions from the 3s subshell are included, but only to the 3s and 4s orbitals. The ab initio fine-structure levels are then fine tuned to reproduce observed energy levels as closely as possible, and the resulting wavefunctions are used to calculate oscillator strengths and transition rates for all possible E1 transitions. For many of these transitions, the present results show good agreement between the length and velocity forms while for some transitions, some large disagreements are found with other available results. The complete list of weighted oscillator strengths, transition rates, and line strengths for transitions among the fine structure levels of the three lowest configurations are presented in ascending order of wavelength.

  20. 3D bioprinting of tissues and organs.

    PubMed

    Murphy, Sean V; Atala, Anthony

    2014-08-01

    Additive manufacturing, otherwise known as three-dimensional (3D) printing, is driving major innovations in many areas, such as engineering, manufacturing, art, education and medicine. Recent advances have enabled 3D printing of biocompatible materials, cells and supporting components into complex 3D functional living tissues. 3D bioprinting is being applied to regenerative medicine to address the need for tissues and organs suitable for transplantation. Compared with non-biological printing, 3D bioprinting involves additional complexities, such as the choice of materials, cell types, growth and differentiation factors, and technical challenges related to the sensitivities of living cells and the construction of tissues. Addressing these complexities requires the integration of technologies from the fields of engineering, biomaterials science, cell biology, physics and medicine. 3D bioprinting has already been used for the generation and transplantation of several tissues, including multilayered skin, bone, vascular grafts, tracheal splints, heart tissue and cartilaginous structures. Other applications include developing high-throughput 3D-bioprinted tissue models for research, drug discovery and toxicology.

  1. Peptide-directed self-assembly of functionalized polymeric nanoparticles part I: design and self-assembly of peptide-copolymer conjugates into nanoparticle fibers and 3D scaffolds.

    PubMed

    Ding, Xiaochu; Janjanam, Jagadeesh; Tiwari, Ashutosh; Thompson, Martin; Heiden, Patricia A

    2014-06-01

    A robust self-assembly of nanoparticles into fibers and 3D scaffolds is designed and fabricated by functionalizing a RAFT-polymerized amphiphilic triblock copolymer with designer ionic complementary peptides so that the assembled core-shell polymeric nanoparticles are directed by peptide assembly into continuous "nanoparticle fibers," ultimately leading to 3D fiber scaffolds. The assembled nanostructure is confirmed by FESEM and optical microscopy. The assembly is not hindered when a protein (insulin) is incorporated within the nanoparticles as an active ingredient. MTS cytotoxicity tests on SW-620 cell lines show that the peptides, copolymers, and peptide-copolymer conjugates are biocompatible. The methodology of self-assembled nanoparticle fibers and 3D scaffolds is intended to combine the advantages of a flexible hydrogel scaffold with the versatility of controlled release nanoparticles to offer unprecedented ability to incorporate desired drug(s) within a self-assembled scaffold system with individual control over the release of each drug.

  2. Joint Inversion of Gravity and Gravity Tensor Data Using the Structural Index as Weighting Function Rate Decay

    NASA Astrophysics Data System (ADS)

    Ialongo, S.; Cella, F.; Fedi, M.; Florio, G.

    2011-12-01

    distribution, well defining a central uplift area, ring structures and low density sediments. REFERENCES Cella F., and Fedi M., 2011, Inversion of potential field data using the structural index as weighting function rate decay, Geophysical Prospecting, doi: 10.1111/j.1365-2478.2011.00974.x Fedi M., Hansen P. C., and Paoletti V., 2005 Analysis of depth resolution in potential-field inversion. Geophysics, 70, NO. 6 Li, Y., 2001, 3-D inversion of gravity gradiometry data: 71st Annual Meeting, SEG, Expanded Abstracts, 1470-1473. Zhdanov, M. S., Ellis, R. G., and Mukherjee, S., 2004, Regularized focusing inversion of 3-D gravity tensor data: Geophysics, 69, 925-937.

  3. DNA biosensing with 3D printing technology.

    PubMed

    Loo, Adeline Huiling; Chua, Chun Kiang; Pumera, Martin

    2017-01-16

    3D printing, an upcoming technology, has vast potential to transform conventional fabrication processes due to the numerous improvements it can offer to the current methods. To date, the employment of 3D printing technology has been examined for applications in the fields of engineering, manufacturing and biological sciences. In this study, we examined the potential of adopting 3D printing technology for a novel application, electrochemical DNA biosensing. Metal 3D printing was utilized to construct helical-shaped stainless steel electrodes which functioned as a transducing platform for the detection of DNA hybridization. The ability of electroactive methylene blue to intercalate into the double helix structure of double-stranded DNA was then exploited to monitor the DNA hybridization process, with its inherent reduction peak serving as an analytical signal. The designed biosensing approach was found to demonstrate superior selectivity against a non-complementary DNA target, with a detection range of 1-1000 nM.

  4. 3D Printing for Tissue Engineering.

    PubMed

    Richards, Dylan Jack; Tan, Yu; Jia, Jia; Yao, Hai; Mei, Ying

    2013-10-01

    Tissue engineering aims to fabricate functional tissue for applications in regenerative medicine and drug testing. More recently, 3D printing has shown great promise in tissue fabrication with a structural control from micro- to macro-scale by using a layer-by-layer approach. Whether through scaffold-based or scaffold-free approaches, the standard for 3D printed tissue engineering constructs is to provide a biomimetic structural environment that facilitates tissue formation and promotes host tissue integration (e.g., cellular infiltration, vascularization, and active remodeling). This review will cover several approaches that have advanced the field of 3D printing through novel fabrication methods of tissue engineering constructs. It will also discuss the applications of synthetic and natural materials for 3D printing facilitated tissue fabrication.

  5. 3D Printing for Tissue Engineering

    PubMed Central

    Jia, Jia; Yao, Hai; Mei, Ying

    2016-01-01

    Tissue engineering aims to fabricate functional tissue for applications in regenerative medicine and drug testing. More recently, 3D printing has shown great promise in tissue fabrication with a structural control from micro- to macro-scale by using a layer-by-layer approach. Whether through scaffold-based or scaffold-free approaches, the standard for 3D printed tissue engineering constructs is to provide a biomimetic structural environment that facilitates tissue formation and promotes host tissue integration (e.g., cellular infiltration, vascularization, and active remodeling). This review will cover several approaches that have advanced the field of 3D printing through novel fabrication methods of tissue engineering constructs. It will also discuss the applications of synthetic and natural materials for 3D printing facilitated tissue fabrication. PMID:26869728

  6. 3D Spectroscopy in Astronomy

    NASA Astrophysics Data System (ADS)

    Mediavilla, Evencio; Arribas, Santiago; Roth, Martin; Cepa-Nogué, Jordi; Sánchez, Francisco

    2011-09-01

    Preface; Acknowledgements; 1. Introductory review and technical approaches Martin M. Roth; 2. Observational procedures and data reduction James E. H. Turner; 3. 3D Spectroscopy instrumentation M. A. Bershady; 4. Analysis of 3D data Pierre Ferruit; 5. Science motivation for IFS and galactic studies F. Eisenhauer; 6. Extragalactic studies and future IFS science Luis Colina; 7. Tutorials: how to handle 3D spectroscopy data Sebastian F. Sánchez, Begona García-Lorenzo and Arlette Pécontal-Rousset.

  7. Spherical 3D isotropic wavelets

    NASA Astrophysics Data System (ADS)

    Lanusse, F.; Rassat, A.; Starck, J.-L.

    2012-04-01

    Context. Future cosmological surveys will provide 3D large scale structure maps with large sky coverage, for which a 3D spherical Fourier-Bessel (SFB) analysis in spherical coordinates is natural. Wavelets are particularly well-suited to the analysis and denoising of cosmological data, but a spherical 3D isotropic wavelet transform does not currently exist to analyse spherical 3D data. Aims: The aim of this paper is to present a new formalism for a spherical 3D isotropic wavelet, i.e. one based on the SFB decomposition of a 3D field and accompany the formalism with a public code to perform wavelet transforms. Methods: We describe a new 3D isotropic spherical wavelet decomposition based on the undecimated wavelet transform (UWT) described in Starck et al. (2006). We also present a new fast discrete spherical Fourier-Bessel transform (DSFBT) based on both a discrete Bessel transform and the HEALPIX angular pixelisation scheme. We test the 3D wavelet transform and as a toy-application, apply a denoising algorithm in wavelet space to the Virgo large box cosmological simulations and find we can successfully remove noise without much loss to the large scale structure. Results: We have described a new spherical 3D isotropic wavelet transform, ideally suited to analyse and denoise future 3D spherical cosmological surveys, which uses a novel DSFBT. We illustrate its potential use for denoising using a toy model. All the algorithms presented in this paper are available for download as a public code called MRS3D at http://jstarck.free.fr/mrs3d.html

  8. 3D Elevation Program—Virtual USA in 3D

    USGS Publications Warehouse

    Lukas, Vicki; Stoker, J.M.

    2016-04-14

    The U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) uses a laser system called ‘lidar’ (light detection and ranging) to create a virtual reality map of the Nation that is very accurate. 3D maps have many uses with new uses being discovered all the time.  

  9. The GLOBE 3D Genome Platform - towards a novel system-biological paper tool to integrate the huge complexity of genome organization and function.

    PubMed

    Knoch, Tobias A; Lesnussa, Michael; Kepper, Nick; Eussen, Hubert B; Grosveld, Frank G

    2009-01-01

    Genomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the general sequential, three-dimensional and regulatory organization. Here, we present the GLOBE 3D Genome Platform a completely novel grid based virtual "paper" tool and in fact the first system-biological genome browser integrating the holistic complexity of genomes in a single easy comprehensible platform: Based on a detailed study of biophysical and IT requirements, every architectural level from sequence to morphology of one or several genomes can be approached in a real and in a symbolic representation simultaneously and navigated by continuous scale-free zooming within a unique three-dimensional OpenGL and grid driven environment. In principle an unlimited number of multi-dimensional data sets can be visualized, customized in terms of arrangement, shape, colour, and texture etc. as well as accessed and annotated individually or in groups using internal or external data bases/facilities. Any information can be searched and correlated by importing or calculating simple relations in real-time using grid resources. A general correlation and application platform for more complex correlative analysis and a front-end for system-biological simulations both using again the huge capabilities of grid infrastructures is currently under development. Hence, the GLOBE 3D Genome Platform is an example of a grid based approach towards a virtual desktop for genomic work combining the three fundamental distributed resources: i) visual data representation, ii) data access and management, and iii) data analysis and creation. Thus, the GLOBE 3D Genome Platform is the novel system-biology oriented information system urgently needed to access, present, annotate, and to simulate the holistic genome

  10. Location and moment tensor inversion of small earthquakes using 3D Green's functions in models with rugged topography: application to the Longmenshan fault zone

    NASA Astrophysics Data System (ADS)

    Zhou, Li; Zhang, Wei; Shen, Yang; Chen, Xiaofei; Zhang, Jie

    2016-06-01

    With dense seismic arrays and advanced imaging methods, regional three-dimensional (3D) Earth models have become more accurate. It is now increasingly feasible and advantageous to use a 3D Earth model to better locate earthquakes and invert their source mechanisms by fitting synthetics to observed waveforms. In this study, we develop an approach to determine both the earthquake location and source mechanism from waveform information. The observed waveforms are filtered in different frequency bands and separated into windows for the individual phases. Instead of picking the arrival times, the traveltime differences are measured by cross-correlation between synthetic waveforms based on the 3D Earth model and observed waveforms. The earthquake location is determined by minimizing the cross-correlation traveltime differences. We then fix the horizontal location of the earthquake and perform a grid search in depth to determine the source mechanism at each point by fitting the synthetic and observed waveforms. This new method is verified by a synthetic test with noise added to the synthetic waveforms and a realistic station distribution. We apply this method to a series of M W3.4-5.6 earthquakes in the Longmenshan fault (LMSF) zone, a region with rugged topography between the eastern margin of the Tibetan plateau and the western part of the Sichuan basin. The results show that our solutions result in improved waveform fits compared to the source parameters from the catalogs we used and the location can be better constrained than the amplitude-only approach. Furthermore, the source solutions with realistic topography provide a better fit to the observed waveforms than those without the topography, indicating the need to take the topography into account in regions with rugged topography.

  11. Scalable 3D GIS environment managed by 3D-XML-based modeling

    NASA Astrophysics Data System (ADS)

    Shi, Beiqi; Rui, Jianxun; Chen, Neng

    2008-10-01

    Nowadays, the namely 3D GIS technologies become a key factor in establishing and maintaining large-scale 3D geoinformation services. However, with the rapidly increasing size and complexity of the 3D models being acquired, a pressing needed for suitable data management solutions has become apparent. This paper outlines that storage and exchange of geospatial data between databases and different front ends like 3D models, GIS or internet browsers require a standardized format which is capable to represent instances of 3D GIS models, to minimize loss of information during data transfer and to reduce interface development efforts. After a review of previous methods for spatial 3D data management, a universal lightweight XML-based format for quick and easy sharing of 3D GIS data is presented. 3D data management based on XML is a solution meeting the requirements as stated, which can provide an efficient means for opening a new standard way to create an arbitrary data structure and share it over the Internet. To manage reality-based 3D models, this paper uses 3DXML produced by Dassault Systemes. 3DXML uses opening XML schemas to communicate product geometry, structure and graphical display properties. It can be read, written and enriched by standard tools; and allows users to add extensions based on their own specific requirements. The paper concludes with the presentation of projects from application areas which will benefit from the functionality presented above.

  12. 3-D imaging of the CNS.

    PubMed

    Runge, V M; Gelblum, D Y; Wood, M L

    1990-01-01

    3-D gradient echo techniques, and in particular FLASH, represent a significant advance in MR imaging strategy allowing thin section, high resolution imaging through a large region of interest. Anatomical areas of application include the brain, spine, and extremities, although the majority of work to date has been performed in the brain. Superior T1 contrast and thus sensitivity to the presence of GdDTPA is achieved with 3-D FLASH when compared to 2-D spin echo technique. There is marked arterial and venous enhancement following Gd DTPA administration on 3-D FLASH, a less common finding with 2-D spin echo. Enhancement of the falx and tentorium is also more prominent. From a single data acquisition, requiring less than 11 min of scan time, high resolution reformatted sagittal, coronal, and axial images can obtained in addition to sections in any arbitrary plane. Tissue segmentation techniques can be applied and lesions displayed in three dimensions. These results may lead to the replacement of 2-D spin echo with 3-D FLASH for high resolution T1-weighted MR imaging of the CNS, particularly in the study of mass lesions and structural anomalies. The application of similar T2-weighted gradient echo techniques may follow, however the signal-to-noise ratio which can be achieved remains a potential limitation.

  13. 3D PLUS HI-REL DDR2 Termination Regulator Module- A Building Block Function for High Reliability SDRAM DDR2 System Architecture

    NASA Astrophysics Data System (ADS)

    Perrot, Nicolas; Dubus, Patrick; Garcia-Sanchez, Esther

    2015-09-01

    Memory system architectures using DDR2 technology need to be compliant with JEDEC JESD8-15A standard [1]. Therefore a bus termination regulator able to sink and source current while regulating VTT voltage is used for this purpose. Such module has been developed by 3D PLUS and is the first space qualified DDR Termination Regulator (DDR2-TR) available on the market. It is based on an innovative Bang-Bang regulation principle, chosen for its speed performance and to guarantee an output voltage that remains within the predefined limits regardless of any output current transients. The output filter type is selected to make the module rugged to any overload condition without complex protection circuits. The module has been specifically designed for low input voltage, low noise and high reliability systems where space is a key consideration. The module uses the 3D PLUS SIP (System-In-Package) technology embedding 3 stacked PCBs. No external filters or decoupling capacitors are needed.

  14. Making claims: functional foods for managing appetite and weight.

    PubMed

    Blundell, John

    2010-01-01

    Functional food products promote claims such as 'freedom from hunger' and 'feel fuller for longer'. A legislative framework has been established by the European Food Safety Authority to evaluate the validity of such claims: a claim must be substantiated by scientific evidence and should be clearly understood by consumers. Since consumed foods influence appetite by means of a system of physiological satiety signals, functional foods could in principle act by increasing the potency and/or duration of these signals. Importantly, what constitutes a useful action: a reduction in hunger, an increase in fullness, a change in food intake at a meal, an adjustment in daily energy balance or a reduction in body weight? Any claim should not go beyond the scientific evidence of an effect, and methods exist to scientifically evaluate claims. The wording of a claim is, therefore, critical. The difference between a proof of concept and a guarantee of success is an important point that needs to be conveyed to the consumer.

  15. 3D World Building System

    ScienceCinema

    None

    2016-07-12

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  16. 3D Buckligami: Digital Matter

    NASA Astrophysics Data System (ADS)

    van Hecke, Martin; de Reus, Koen; Florijn, Bastiaan; Coulais, Corentin

    2014-03-01

    We present a class of elastic structures which exhibit collective buckling in 3D, and create these by a 3D printing/moulding technique. Our structures consist of cubic lattice of anisotropic unit cells, and we show that their mechanical properties are programmable via the orientation of these unit cells.

  17. 3D World Building System

    SciTech Connect

    2013-10-30

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  18. LLNL-Earth3D

    SciTech Connect

    2013-10-01

    Earth3D is a computer code designed to allow fast calculation of seismic rays and travel times through a 3D model of the Earth. LLNL is using this for earthquake location and global tomography efforts and such codes are of great interest to the Earth Science community.

  19. Market study: 3-D eyetracker

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A market study of a proposed version of a 3-D eyetracker for initial use at NASA's Ames Research Center was made. The commercialization potential of a simplified, less expensive 3-D eyetracker was ascertained. Primary focus on present and potential users of eyetrackers, as well as present and potential manufacturers has provided an effective means of analyzing the prospects for commercialization.

  20. 3D fast wavelet network model-assisted 3D face recognition

    NASA Astrophysics Data System (ADS)

    Said, Salwa; Jemai, Olfa; Zaied, Mourad; Ben Amar, Chokri

    2015-12-01

    In last years, the emergence of 3D shape in face recognition is due to its robustness to pose and illumination changes. These attractive benefits are not all the challenges to achieve satisfactory recognition rate. Other challenges such as facial expressions and computing time of matching algorithms remain to be explored. In this context, we propose our 3D face recognition approach using 3D wavelet networks. Our approach contains two stages: learning stage and recognition stage. For the training we propose a novel algorithm based on 3D fast wavelet transform. From 3D coordinates of the face (x,y,z), we proceed to voxelization to get a 3D volume which will be decomposed by 3D fast wavelet transform and modeled after that with a wavelet network, then their associated weights are considered as vector features to represent each training face . For the recognition stage, an unknown identity face is projected on all the training WN to obtain a new vector features after every projection. A similarity score is computed between the old and the obtained vector features. To show the efficiency of our approach, experimental results were performed on all the FRGC v.2 benchmark.

  1. PLOT3D Export Tool for Tecplot

    NASA Technical Reports Server (NTRS)

    Alter, Stephen

    2010-01-01

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

  2. Olfactory and gustatory functions and its relation to body weight.

    PubMed

    Skrandies, Wolfgang; Zschieschang, Romy

    2015-04-01

    In the present study we investigated the influence of body weight as defined by BMI on gustatory and olfactory perception. A total of 66 healthy adults (41 females; 25 males) participated in psychophysical measurements using the "Sniffin' Sticks" test and "Taste Strips" test. Odor thresholds as well as discrimination and identification performance were determined. Tests of gustatory function involved the identification and thresholds of sweet, sour, salty, or bitter taste. In this study, all subjects were healthy participants in a middle age range (between 20 and 56 years of age). Persons with an extreme BMI value were excluded. Subjects were classified according to their BMI in four groups: (1) 15-19.9 kg/m, (2) 20-24.9 kg/m, (3) 25-29.9 kg/m, and (4) >30 kg/m. We did not observe an overall effect of BMI on general sensory sensitivity. There was a significant influence of BMI on olfactory thresholds (F(3,62)=2.79; p<0.047) which increased with increasing BMI. In a similar line, the gustatory thresholds for "salty" were significantly higher with higher BMI (F(3,62)=3.06; p<0.035). Olfactory discrimination and identification was not affected by BMI. Thresholds for odor and sweet or salty taste were also correlated. Our data show that body weight influences gustatory and olfactory perception in healthy adults. Increasing BMI is associated with a decrease in olfactory and taste sensitivity. These findings may have implications for the understanding of pathophysiological mechanisms in patients.

  3. Euro3D Science Conference

    NASA Astrophysics Data System (ADS)

    Walsh, J. R.

    2004-02-01

    The Euro3D RTN is an EU funded Research Training Network to foster the exploitation of 3D spectroscopy in Europe. 3D spectroscopy is a general term for spectroscopy of an area of the sky and derives its name from its two spatial + one spectral dimensions. There are an increasing number of instruments which use integral field devices to achieve spectroscopy of an area of the sky, either using lens arrays, optical fibres or image slicers, to pack spectra of multiple pixels on the sky (``spaxels'') onto a 2D detector. On account of the large volume of data and the special methods required to reduce and analyse 3D data, there are only a few centres of expertise and these are mostly involved with instrument developments. There is a perceived lack of expertise in 3D spectroscopy spread though the astronomical community and its use in the armoury of the observational astronomer is viewed as being highly specialised. For precisely this reason the Euro3D RTN was proposed to train young researchers in this area and develop user tools to widen the experience with this particular type of data in Europe. The Euro3D RTN is coordinated by Martin M. Roth (Astrophysikalisches Institut Potsdam) and has been running since July 2002. The first Euro3D science conference was held in Cambridge, UK from 22 to 23 May 2003. The main emphasis of the conference was, in keeping with the RTN, to expose the work of the young post-docs who are funded by the RTN. In addition the team members from the eleven European institutes involved in Euro3D also presented instrumental and observational developments. The conference was organized by Andy Bunker and held at the Institute of Astronomy. There were over thirty participants and 26 talks covered the whole range of application of 3D techniques. The science ranged from Galactic planetary nebulae and globular clusters to kinematics of nearby galaxies out to objects at high redshift. Several talks were devoted to reporting recent observations with newly

  4. 3D vision system assessment

    NASA Astrophysics Data System (ADS)

    Pezzaniti, J. Larry; Edmondson, Richard; Vaden, Justin; Hyatt, Bryan; Chenault, David B.; Kingston, David; Geulen, Vanilynmae; Newell, Scott; Pettijohn, Brad

    2009-02-01

    In this paper, we report on the development of a 3D vision system consisting of a flat panel stereoscopic display and auto-converging stereo camera and an assessment of the system's use for robotic driving, manipulation, and surveillance operations. The 3D vision system was integrated onto a Talon Robot and Operator Control Unit (OCU) such that direct comparisons of the performance of a number of test subjects using 2D and 3D vision systems were possible. A number of representative scenarios were developed to determine which tasks benefited most from the added depth perception and to understand when the 3D vision system hindered understanding of the scene. Two tests were conducted at Fort Leonard Wood, MO with noncommissioned officers ranked Staff Sergeant and Sergeant First Class. The scenarios; the test planning, approach and protocols; the data analysis; and the resulting performance assessment of the 3D vision system are reported.

  5. 3D printing in dentistry.

    PubMed

    Dawood, A; Marti Marti, B; Sauret-Jackson, V; Darwood, A

    2015-12-01

    3D printing has been hailed as a disruptive technology which will change manufacturing. Used in aerospace, defence, art and design, 3D printing is becoming a subject of great interest in surgery. The technology has a particular resonance with dentistry, and with advances in 3D imaging and modelling technologies such as cone beam computed tomography and intraoral scanning, and with the relatively long history of the use of CAD CAM technologies in dentistry, it will become of increasing importance. Uses of 3D printing include the production of drill guides for dental implants, the production of physical models for prosthodontics, orthodontics and surgery, the manufacture of dental, craniomaxillofacial and orthopaedic implants, and the fabrication of copings and frameworks for implant and dental restorations. This paper reviews the types of 3D printing technologies available and their various applications in dentistry and in maxillofacial surgery.

  6. 3D steerable wavelets in practice.

    PubMed

    Chenouard, Nicolas; Unser, Michael

    2012-11-01

    We introduce a systematic and practical design for steerable wavelet frames in 3D. Our steerable wavelets are obtained by applying a 3D version of the generalized Riesz transform to a primary isotropic wavelet frame. The novel transform is self-reversible (tight frame) and its elementary constituents (Riesz wavelets) can be efficiently rotated in any 3D direction by forming appropriate linear combinations. Moreover, the basis functions at a given location can be linearly combined to design custom (and adaptive) steerable wavelets. The features of the proposed method are illustrated with the processing and analysis of 3D biomedical data. In particular, we show how those wavelets can be used to characterize directional patterns and to detect edges by means of a 3D monogenic analysis. We also propose a new inverse-problem formalism along with an optimization algorithm for reconstructing 3D images from a sparse set of wavelet-domain edges. The scheme results in high-quality image reconstructions which demonstrate the feature-reduction ability of the steerable wavelets as well as their potential for solving inverse problems.

  7. Spatioangular Prefiltering for Multiview 3D Displays.

    PubMed

    Ramachandra, Vikas; Hirakawa, Keigo; Zwicker, Matthias; Nguyen, Truong

    2011-05-01

    In this paper, we analyze the reproduction of light fields on multiview 3D displays. A three-way interaction between the input light field signal (which is often aliased), the joint spatioangular sampling grids of multiview 3D displays, and the interview light leakage in modern multiview 3D displays is characterized in the joint spatioangular frequency domain. Reconstruction of light fields by all physical 3D displays is prone to light leakage, which means that the reconstruction low-pass filter implemented by the display is too broad in the angular domain. As a result, 3D displays excessively attenuate angular frequencies. Our analysis shows that this reduces sharpness of the images shown in the 3D displays. In this paper, stereoscopic image recovery is recast as a problem of joint spatioangular signal reconstruction. The combination of the 3D display point spread function and human visual system provides the narrow-band low-pass filter which removes spectral replicas in the reconstructed light field on the multiview display. The nonideality of this filter is corrected with the proposed prefiltering. The proposed light field reconstruction method performs light field antialiasing as well as angular sharpening to compensate for the nonideal response of the 3D display. The union of cosets approach which has been used earlier by others is employed here to model the nonrectangular spatioangular sampling grids on a multiview display in a generic fashion. We confirm the effectiveness of our approach in simulation and in physical hardware, and demonstrate improvement over existing techniques.

  8. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  9. Fourier-based reconstruction for fully 3-D PET: optimization of interpolation parameters.

    PubMed

    Matej, Samuel; Kazantsev, Ivan G

    2006-07-01

    Fourier-based approaches for three-dimensional (3-D) reconstruction are based on the relationship between the 3-D Fourier transform (FT) of the volume and the two-dimensional (2-D) FT of a parallel-ray projection of the volume. The critical step in the Fourier-based methods is the estimation of the samples of the 3-D transform of the image from the samples of the 2-D transforms of the projections on the planes through the origin of Fourier space, and vice versa for forward-projection (reprojection). The Fourier-based approaches have the potential for very fast reconstruction, but their straightforward implementation might lead to unsatisfactory results if careful attention is not paid to interpolation and weighting functions. In our previous work, we have investigated optimal interpolation parameters for the Fourier-based forward and back-projectors for iterative image reconstruction. The optimized interpolation kernels were shown to provide excellent quality comparable to the ideal sinc interpolator. This work presents an optimization of interpolation parameters of the 3-D direct Fourier method with Fourier reprojection (3D-FRP) for fully 3-D positron emission tomography (PET) data with incomplete oblique projections. The reprojection step is needed for the estimation (from an initial image) of the missing portions of the oblique data. In the 3D-FRP implementation, we use the gridding interpolation strategy, combined with proper weighting approaches in the transform and image domains. We have found that while the 3-D reprojection step requires similar optimal interpolation parameters as found in our previous studies on Fourier-based iterative approaches, the optimal interpolation parameters for the main 3D-FRP reconstruction stage are quite different. Our experimental results confirm that for the optimal interpolation parameters a very good image accuracy can be achieved even without any extra spectral oversampling, which is a common practice to decrease errors

  10. Unassisted 3D camera calibration

    NASA Astrophysics Data System (ADS)

    Atanassov, Kalin; Ramachandra, Vikas; Nash, James; Goma, Sergio R.

    2012-03-01

    With the rapid growth of 3D technology, 3D image capture has become a critical part of the 3D feature set on mobile phones. 3D image quality is affected by the scene geometry as well as on-the-device processing. An automatic 3D system usually assumes known camera poses accomplished by factory calibration using a special chart. In real life settings, pose parameters estimated by factory calibration can be negatively impacted by movements of the lens barrel due to shaking, focusing, or camera drop. If any of these factors displaces the optical axes of either or both cameras, vertical disparity might exceed the maximum tolerable margin and the 3D user may experience eye strain or headaches. To make 3D capture more practical, one needs to consider unassisted (on arbitrary scenes) calibration. In this paper, we propose an algorithm that relies on detection and matching of keypoints between left and right images. Frames containing erroneous matches, along with frames with insufficiently rich keypoint constellations, are detected and discarded. Roll, pitch yaw , and scale differences between left and right frames are then estimated. The algorithm performance is evaluated in terms of the remaining vertical disparity as compared to the maximum tolerable vertical disparity.

  11. 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

  12. 3D Scan Systems Integration

    DTIC Science & Technology

    2007-11-02

    AGENCY USE ONLY (Leave Blank) 2. REPORT DATE 5 Feb 98 4. TITLE AND SUBTITLE 3D Scan Systems Integration REPORT TYPE AND DATES COVERED...2-89) Prescribed by ANSI Std. Z39-1 298-102 [ EDO QUALITY W3PECTEDI DLA-ARN Final Report for US Defense Logistics Agency on DDFG-T2/P3: 3D...SCAN SYSTEMS INTEGRATION Contract Number SPO100-95-D-1014 Contractor Ohio University Delivery Order # 0001 Delivery Order Title 3D Scan Systems

  13. Effect of real-time weighted integration system for rapid calculation of functional images in clinical positron emission tomography

    SciTech Connect

    Iida, Hidehiro; Bloomfield, P.M.; Miura, Shuichi

    1995-03-01

    A system has been developed to rapidly calculate images of parametric rate constants, without acquiring dynamic frame data for clinical positron emission tomography (PET). This method is based on the weighted-integration algorithms for the two- and three-compartment models, and hardware developments (real-time operation and a large cache memory system) in a PET scanner, Headtome-IV, which enables the acquisition of multiple sinograms with independent weight integration functions. Following the administration of the radio-tracer, the scan is initiated to collect multiple time-weighted, integrated sinograms with three different weight functions. These sinograms are reconstructed and the images, with the arterial blood data, are inserted into the operational equations to provide parametric rate constant images. The implementation of this method has been checked in H{sub 2} {sup 15}O and {sup 18}F-fluorophenylalanine ({sup 18}FPhe) studies based on a two-compartment model, and in a {sup 18}F-fluorodeoxyglucose ({sup 18}FDG) study based on the three-compartment model. A volunteer study, completed for each compound, yielded results consistent with those produced by existing nonlinear fitting methods. Thus, this system has been developed capable of generating rapidly quantitative, physiological images, without dynamic data acquisition, which will be of great advantage to PET in the clinical environment. This system would also be of great advantage in the new generation high-resolution PET tomography, which acquire data in a 3-D, septaless mode.

  14. Transformation from a 2D stacked layer to 3D interpenetrated framework by changing the spacer functionality: synthesis, structure, adsorption, and magnetic properties.

    PubMed

    Maji, Tapas Kumar; Ohba, Masaaki; Kitagawa, Susumu

    2005-12-12

    Two novel coordination polymers of Cu(II), viz. [Cu(bipy)(1,4-napdc)(H2O)2]n and {[Cu(bpe)1.5(1,4-napdc)](H2O)}n (bipy=4,4'-bipyridine; bpe=1,2-bis(4-pyridyl)ethane; 1,4-napdc2-=1,4-naphthalenedicarboxylate), have been synthesized and structurally characterized by changing only the pillar motifs. Both the compounds crystallize by slow evaporation from the ammoniacal solution of the as-synthesized solid. Framework 1 crystallizes in monoclinic crystal system, space group P2/n (No. 13), with a=11.028(19) A, b=11.16(3) A, c=7.678(13) A, beta=103.30(5) degrees, and Z=2. Framework 2 crystallizes in triclinic system, space group, P (No. 2), a=10.613(4) A, b=10.828(10) A, c=13.333(9) A, alpha=85.25(9) degrees, beta=82.59(6) degrees, gamma=60.37(5) degrees, and Z=2. The structure determination reveals that has a 2D network based on rectangular grids, where each Cu(II) is in 4+2 coordination mode. The 2D networks stacked in a staggered manner through the pi-pi interaction to form a 3D supramolecular network. In the case of, a {Cu(bpe)1.5}n ladder connected by 1,4-napdc2- results a 2D cuboidal bilayer network and each bilayer network is interlocked by two adjacent identical network (upper and lower) forming 3-fold interpenetrated 3D framework with small channel along the c-axis, which accommodates two water molecules. The TGA and XRPD measurements reveal that both the frameworks are stable after dehydration. Adsorption measurements (N2, CO2, and different solvents, like H2O, MeOH, etc.) were carried out for both frameworks. Framework shows type-II sorption profile with N2 in contrast to H2O and MeOH, which are chemisorbed in the framework. In case of, only H2O molecules can diffuse into the micropore, whereas N2, CO2, and MeOH cannot be adsorbed, as corroborated by the smaller channel aperture. The low-temperature (300-2 K) magnetic measurement of and reveals that both are weakly antiferromagnetically coupled (J=-1.85 cm-1, g=2.02; J=-0.153 cm-1, g=2.07), which is correlated

  15. 3D polymer scaffold arrays.

    PubMed

    Simon, Carl G; Yang, Yanyin; Dorsey, Shauna M; Ramalingam, Murugan; Chatterjee, Kaushik

    2011-01-01

    We have developed a combinatorial platform for fabricating tissue scaffold arrays that can be used for screening cell-material interactions. Traditional research involves preparing samples one at a time for characterization and testing. Combinatorial and high-throughput (CHT) methods lower the cost of research by reducing the amount of time and material required for experiments by combining many samples into miniaturized specimens. In order to help accelerate biomaterials research, many new CHT methods have been developed for screening cell-material interactions where materials are presented to cells as a 2D film or surface. However, biomaterials are frequently used to fabricate 3D scaffolds, cells exist in vivo in a 3D environment and cells cultured in a 3D environment in vitro typically behave more physiologically than those cultured on a 2D surface. Thus, we have developed a platform for fabricating tissue scaffold libraries where biomaterials can be presented to cells in a 3D format.

  16. Autofocus for 3D imaging

    NASA Astrophysics Data System (ADS)

    Lee-Elkin, Forest

    2008-04-01

    Three dimensional (3D) autofocus remains a significant challenge for the development of practical 3D multipass radar imaging. The current 2D radar autofocus methods are not readily extendable across sensor passes. We propose a general framework that allows a class of data adaptive solutions for 3D auto-focus across passes with minimal constraints on the scene contents. The key enabling assumption is that portions of the scene are sparse in elevation which reduces the number of free variables and results in a system that is simultaneously solved for scatterer heights and autofocus parameters. The proposed method extends 2-pass interferometric synthetic aperture radar (IFSAR) methods to an arbitrary number of passes allowing the consideration of scattering from multiple height locations. A specific case from the proposed autofocus framework is solved and demonstrates autofocus and coherent multipass 3D estimation across the 8 passes of the "Gotcha Volumetric SAR Data Set" X-Band radar data.

  17. Enhanced human bone marrow mesenchymal stem cell functions in novel 3D cartilage scaffolds with hydrogen treated multi-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Holmes, Benjamin; Castro, Nathan J.; Li, Jian; Keidar, Michael; Zhang, Lijie Grace

    2013-09-01

    Cartilage tissue is a nanostructured tissue which is notoriously hard to regenerate due to its extremely poor inherent regenerative capacity and complex stratified architecture. Current treatment methods are highly invasive and may have many complications. Thus, the goal of this work is to use nanomaterials and nano/microfabrication methods to create novel biologically inspired tissue engineered cartilage scaffolds to facilitate human bone marrow mesenchymal stem cell (MSC) chondrogenesis. To this end we utilized electrospinning to design and fabricate a series of novel 3D biomimetic nanostructured scaffolds based on hydrogen (H2) treated multi-walled carbon nanotubes (MWCNTs) and biocompatible poly(L-lactic acid) (PLLA) polymers. Specifically, a series of electrospun fibrous PLLA scaffolds with controlled fiber dimension were fabricated in this study. In vitro MSC studies showed that stem cells prefer to attach in the scaffolds with smaller fiber diameter. More importantly, the MWCNT embedded scaffolds showed a drastic increase in mechanical strength and a compressive Young’s modulus matching to natural cartilage. Furthermore, our MSC differentiation results demonstrated that incorporation of the H2 treated carbon nanotubes and poly-L-lysine coating can induce more chondrogenic differentiations of MSCs than controls. After two weeks of culture, PLLA scaffolds with H2 treated MWCNTs and poly-L-lysine can achieve the highest glycosaminoglycan synthesis, making them promising for further exploration for cartilage regeneration.

  18. Evaluation of a 3D point spread function (PSF) model derived from Monte Carlo simulation for a small animal PET scanner

    NASA Astrophysics Data System (ADS)

    Yao, Rutao; Ramachandra, Ranjith M.; Panse, Ashish; Balla, Deepika; Yan, Jianhua; Carson, Richard E.

    2010-04-01

    We previously designed a component based 3-D PSF model to obtain a compact yet accurate system matrix for a dedicated human brain PET scanner. In this work, we adapted the model to a small animal PET scanner. Based on the model, we derived the system matrix for back-to-back gamma source in air, fluorine-18 and iodine-124 source in water by Monte Carlo simulation. The characteristics of the PSF model were evaluated and the performance of the newly derived system matrix was assessed by comparing its reconstructed images with the established reconstruction program provided on the animal PET scanner. The new system matrix showed strong PSF dependency on the line-of-response (LOR) incident angle and LOR depth. This confirmed the validity of the two components selected for the model. The effect of positron range on the system matrix was observed by comparing the PSFs of different isotopes. A simulated and an experimental hot-rod phantom study showed that the reconstruction with the proposed system matrix achieved better resolution recovery as compared to the algorithm provided by the manufacturer. Quantitative evaluation also showed better convergence to the expected contrast value at similar noise level. In conclusion, it has been shown that the system matrix derivation method is applicable to the animal PET system studied, suggesting that the method may be used for other PET systems and different isotope applications.

  19. A computer-controlled near-field electrospinning setup and its graphic user interface for precision patterning of functional nanofibers on 2D and 3D substrates.

    PubMed

    Bisht, Gobind; Nesterenko, Sergiy; Kulinsky, Lawrence; Madou, Marc

    2012-08-01

    Electrospinning is a versatile technique for production of nanofibers. However, it lacks the precision and control necessary for fabrication of nanofiber-based devices. The positional control of the nanofiber placement can be dramatically improved using low-voltage near-field electrospinning (LV-NFES). LV-NFES allows nanofibers to be patterned on 2D and 3D substrates. However, use of NFES requires low working distance between the electrospinning nozzle and substrate, manual jet initiation, and precise substrate movement to control fiber deposition. Environmental factors such as humidity also need to be controlled. We developed a computer-controlled automation strategy for LV-NFES to improve performance and reliability. With this setup, the user is able to control the relevant sensor and actuator parameters through a custom graphic user interface application programmed on the C#.NET platform. The stage movement can be programmed as to achieve any desired nanofiber pattern and thickness. The nanofiber generation step is initiated through a software-controlled linear actuator. Parameter setting files can be saved into an Excel sheet and can be used subsequently in running multiple experiments. Each experiment is automatically video recorded and stamped with the pertinent real-time parameters. Humidity is controlled with ±3% accuracy through a feedback loop. Further improvements, such as real-time droplet size control for feed rate regulation are in progress.

  20. Enhanced human bone marrow mesenchymal stem cell functions in novel 3D cartilage scaffolds with hydrogen treated multi-walled carbon nanotubes.

    PubMed

    Holmes, Benjamin; Castro, Nathan J; Li, Jian; Keidar, Michael; Zhang, Lijie Grace

    2013-09-13

    Cartilage tissue is a nanostructured tissue which is notoriously hard to regenerate due to its extremely poor inherent regenerative capacity and complex stratified architecture. Current treatment methods are highly invasive and may have many complications. Thus, the goal of this work is to use nanomaterials and nano/microfabrication methods to create novel biologically inspired tissue engineered cartilage scaffolds to facilitate human bone marrow mesenchymal stem cell (MSC) chondrogenesis. To this end we utilized electrospinning to design and fabricate a series of novel 3D biomimetic nanostructured scaffolds based on hydrogen (H2) treated multi-walled carbon nanotubes (MWCNTs) and biocompatible poly(L-lactic acid) (PLLA) polymers. Specifically, a series of electrospun fibrous PLLA scaffolds with controlled fiber dimension were fabricated in this study. In vitro MSC studies showed that stem cells prefer to attach in the scaffolds with smaller fiber diameter. More importantly, the MWCNT embedded scaffolds showed a drastic increase in mechanical strength and a compressive Young's modulus matching to natural cartilage. Furthermore, our MSC differentiation results demonstrated that incorporation of the H2 treated carbon nanotubes and poly-L-lysine coating can induce more chondrogenic differentiations of MSCs than controls. After two weeks of culture, PLLA scaffolds with H2 treated MWCNTs and poly-L-lysine can achieve the highest glycosaminoglycan synthesis, making them promising for further exploration for cartilage regeneration.

  1. PLOT3D/AMES, DEC VAX VMS VERSION USING DISSPLA (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  2. PLOT3D/AMES, DEC VAX VMS VERSION USING DISSPLA (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P. G.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  3. 3D bioprinting and its in vivo applications.

    PubMed

    Hong, Nhayoung; Yang, Gi-Hoon; Lee, JaeHwan; Kim, GeunHyung

    2017-01-20

    The purpose of 3D bioprinting technology is to design and create functional 3D tissues or organs in situ for in vivo applications. 3D cell-printing, or additive biomanufacturing, allows the selection of biomaterials and cells (bioink), and the fabrication of cell-laden structures in high resolution. 3D cell-printed structures have also been used for applications such as research models, drug delivery and discovery, and toxicology. Recently, numerous attempts have been made to fabricate tissues and organs by using various 3D printing techniques. However, challenges such as vascularization are yet to be solved. This article reviews the most commonly used 3D cell-printing techniques with their advantages and drawbacks. Furthermore, up-to-date achievements of 3D bioprinting in in vivo applications are introduced, and prospects for the future of 3D cell-printing technology are discussed. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2017.

  4. Constructing Arguments with 3-D Printed Models

    ERIC Educational Resources Information Center

    McConnell, William; Dickerson, Daniel

    2017-01-01

    In this article, the authors describe a fourth-grade lesson where 3-D printing technologies were not only a stimulus for engagement but also served as a modeling tool providing meaningful learning opportunities. Specifically, fourth-grade students construct an argument that animals' external structures function to support survival in a particular…

  5. PLOT3D/AMES, GENERIC UNIX VERSION USING DISSPLA (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  6. PLOT3D/AMES, GENERIC UNIX VERSION USING DISSPLA (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  7. Full-color holographic 3D printer

    NASA Astrophysics Data System (ADS)

    Takano, Masami; Shigeta, Hiroaki; Nishihara, Takashi; Yamaguchi, Masahiro; Takahashi, Susumu; Ohyama, Nagaaki; Kobayashi, Akihiko; Iwata, Fujio

    2003-05-01

    A holographic 3D printer is a system that produces a direct hologram with full-parallax information using the 3-dimensional data of a subject from a computer. In this paper, we present a proposal for the reproduction of full-color images with the holographic 3D printer. In order to realize the 3-dimensional color image, we selected the 3 laser wavelength colors of red (λ=633nm), green (λ=533nm), and blue (λ=442nm), and we built a one-step optical system using a projection system and a liquid crystal display. The 3-dimensional color image is obtained by synthesizing in a 2D array the multiple exposure with these 3 wavelengths made on each 250mm elementary hologram, and moving recording medium on a x-y stage. For the natural color reproduction in the holographic 3D printer, we take the approach of the digital processing technique based on the color management technology. The matching between the input and output colors is performed by investigating first, the relation between the gray level transmittance of the LCD and the diffraction efficiency of the hologram and second, by measuring the color displayed by the hologram to establish a correlation. In our first experimental results a non-linear functional relation for single and multiple exposure of the three components were found. These results are the first step in the realization of a natural color 3D image produced by the holographic color 3D printer.

  8. 3D bioprinting for engineering complex tissues.

    PubMed

    Mandrycky, Christian; Wang, Zongjie; Kim, Keekyoung; Kim, Deok-Ho

    2016-01-01

    Bioprinting is a 3D fabrication technology used to precisely dispense cell-laden biomaterials for the construction of complex 3D functional living tissues or artificial organs. While still in its early stages, bioprinting strategies have demonstrated their potential use in regenerative medicine to generate a variety of transplantable tissues, including skin, cartilage, and bone. However, current bioprinting approaches still have technical challenges in terms of high-resolution cell deposition, controlled cell distributions, vascularization, and innervation within complex 3D tissues. While no one-size-fits-all approach to bioprinting has emerged, it remains an on-demand, versatile fabrication technique that may address the growing organ shortage as well as provide a high-throughput method for cell patterning at the micrometer scale for broad biomedical engineering applications. In this review, we introduce the basic principles, materials, integration strategies and applications of bioprinting. We also discuss the recent developments, current challenges and future prospects of 3D bioprinting for engineering complex tissues. Combined with recent advances in human pluripotent stem cell technologies, 3D-bioprinted tissue models could serve as an enabling platform for high-throughput predictive drug screening and more effective regenerative therapies.

  9. Extra dimensions: 3D in PDF documentation

    SciTech Connect

    Graf, Norman A.

    2011-01-11

    Experimental science is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universal 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide, non-technical audience. We discuss how the field of radiation imaging could benefit from incorporating full 3D information about not only the detectors, but also the results of the experimental analyses, in its electronic publications. In this article, we present examples drawn from high-energy physics, mathematics and molecular biology which take advantage of this functionality. Furthermore, we demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input.

  10. Extra dimensions: 3D in PDF documentation

    DOE PAGES

    Graf, Norman A.

    2011-01-11

    Experimental science is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universalmore » 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide, non-technical audience. We discuss how the field of radiation imaging could benefit from incorporating full 3D information about not only the detectors, but also the results of the experimental analyses, in its electronic publications. In this article, we present examples drawn from high-energy physics, mathematics and molecular biology which take advantage of this functionality. Furthermore, we demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input.« less

  11. 3D Printed Multimaterial Microfluidic Valve

    PubMed Central

    Patrick, William G.; Sharma, Sunanda; Kong, David S.; Oxman, Neri

    2016-01-01

    We present a novel 3D printed multimaterial microfluidic proportional valve. The microfluidic valve is a fundamental primitive that enables the development of programmable, automated devices for controlling fluids in a precise manner. We discuss valve characterization results, as well as exploratory design variations in channel width, membrane thickness, and membrane stiffness. Compared to previous single material 3D printed valves that are stiff, these printed valves constrain fluidic deformation spatially, through combinations of stiff and flexible materials, to enable intricate geometries in an actuated, functionally graded device. Research presented marks a shift towards 3D printing multi-property programmable fluidic devices in a single step, in which integrated multimaterial valves can be used to control complex fluidic reactions for a variety of applications, including DNA assembly and analysis, continuous sampling and sensing, and soft robotics. PMID:27525809

  12. Recent EFIT Developments and 3D Extension

    NASA Astrophysics Data System (ADS)

    Lao, L. L.; Chu, M. S.; St. John, H. E.; Strait, E. J.; Montgomery, A. L.; Perkins, F. W.

    2006-10-01

    Recent developments of the equilibrium reconstruction code EFIT and its 3D extension to model toroidally asymmetric effects due to error and externally applied perturbation magnetic fields are presented. These include a new more complete uncertainty matrix for magnetic diagnostics based on detailed knowledge about their fabrication, installation, calibration, and operation. A new algorithm to efficiently compute high bootstrap-fraction equilibria that explicitly separates out the Pfirsch-Schluter and bootstrap contributions to the poloidal current stream function is also being developed. Other on-going and planned developments include a new computational structure based on Fortran 90/95 with a unified interface that can conveniently accommodate different tokamak devices and grid sizes, as well as a computational link that allows easy integration with transport and stability physics modules for integrated modeling. EFIT reconstruction capability is also being extended to 3D based on perturbation solutions to the 3D Grad-Shafranov equilibrium equation.

  13. Combining Microwave Functions To Reduce Weight Of Spacecraft

    NASA Technical Reports Server (NTRS)

    Palaszewski, Bryan A.; Dickinson, Richard M.

    1989-01-01

    Report discusses integration of sources of microwave power for microwave-arcjet propulsive systems and such microwave instruments as synthetic-aperture radar and radiometers in spacecraft. Integration essential feature of Combined Microwave Science and Propulsion (COMAPP) concept, which incorporates new approach to design of spacecraft for exploration of planets. One of principal objectives in COMAPP to reduce overall weight of spacecraft and to maximize portion of weight devoted to scientific instrumentation.

  14. From 3D view to 3D print

    NASA Astrophysics Data System (ADS)

    Dima, M.; Farisato, G.; Bergomi, M.; Viotto, V.; Magrin, D.; Greggio, D.; Farinato, J.; Marafatto, L.; Ragazzoni, R.; Piazza, D.

    2014-08-01

    In the last few years 3D printing is getting more and more popular and used in many fields going from manufacturing to industrial design, architecture, medical support and aerospace. 3D printing is an evolution of bi-dimensional printing, which allows to obtain a solid object from a 3D model, realized with a 3D modelling software. The final product is obtained using an additive process, in which successive layers of material are laid down one over the other. A 3D printer allows to realize, in a simple way, very complex shapes, which would be quite difficult to be produced with dedicated conventional facilities. Thanks to the fact that the 3D printing is obtained superposing one layer to the others, it doesn't need any particular work flow and it is sufficient to simply draw the model and send it to print. Many different kinds of 3D printers exist based on the technology and material used for layer deposition. A common material used by the toner is ABS plastics, which is a light and rigid thermoplastic polymer, whose peculiar mechanical properties make it diffusely used in several fields, like pipes production and cars interiors manufacturing. I used this technology to create a 1:1 scale model of the telescope which is the hardware core of the space small mission CHEOPS (CHaracterising ExOPlanets Satellite) by ESA, which aims to characterize EXOplanets via transits observations. The telescope has a Ritchey-Chrétien configuration with a 30cm aperture and the launch is foreseen in 2017. In this paper, I present the different phases for the realization of such a model, focusing onto pros and cons of this kind of technology. For example, because of the finite printable volume (10×10×12 inches in the x, y and z directions respectively), it has been necessary to split the largest parts of the instrument in smaller components to be then reassembled and post-processed. A further issue is the resolution of the printed material, which is expressed in terms of layers

  15. Superplot3d: an open source GUI tool for 3d trajectory visualisation and elementary processing.

    PubMed

    Whitehorn, Luke J; Hawkes, Frances M; Dublon, Ian An

    2013-09-30

    When acquiring simple three-dimensional (3d) trajectory data it is common to accumulate large coordinate data sets. In order to examine integrity and consistency of object tracking, it is often necessary to rapidly visualise these data. Ordinarily, to achieve this the user must either execute 3d plotting functions in a numerical computing environment or manually inspect data in two dimensions, plotting each individual axis.Superplot3d is an open source MATLAB script which takes tab delineated Cartesian data points in the form x, y, z and time and generates an instant visualization of the object's trajectory in free-rotational three dimensions. Whole trajectories may be instantly presented, allowing for rapid inspection. Executable from the MATLAB command line (or deployable as a compiled standalone application) superplot3d also provides simple GUI controls to obtain rudimentary trajectory information, allow specific visualization of trajectory sections and perform elementary processing.Superplot3d thus provides a framework for non-programmers and programmers alike, to recreate recently acquired 3d object trajectories in rotatable 3d space. It is intended, via the use of a preference driven menu to be flexible and work with output from multiple tracking software systems. Source code and accompanying GUIDE .fig files are provided for deployment and further development.

  16. Assessing 3D tunnel position in ACL reconstruction using a novel single image 3D-2D registration

    NASA Astrophysics Data System (ADS)

    Kang, X.; Yau, W. P.; Otake, Y.; Cheung, P. Y. S.; Hu, Y.; Taylor, R. H.

    2012-02-01

    The routinely used procedure for evaluating tunnel positions following anterior cruciate ligament (ACL) reconstructions based on standard X-ray images is known to pose difficulties in terms of obtaining accurate measures, especially in providing three-dimensional tunnel positions. This is largely due to the variability in individual knee joint pose relative to X-ray plates. Accurate results were reported using postoperative CT. However, its extensive usage in clinical routine is hampered by its major requirement of having CT scans of individual patients, which is not available for most ACL reconstructions. These difficulties are addressed through the proposed method, which aligns a knee model to X-ray images using our novel single-image 3D-2D registration method and then estimates the 3D tunnel position. In the proposed method, the alignment is achieved by using a novel contour-based 3D-2D registration method wherein image contours are treated as a set of oriented points. However, instead of using some form of orientation weighting function and multiplying it with a distance function, we formulate the 3D-2D registration as a probability density estimation using a mixture of von Mises-Fisher-Gaussian (vMFG) distributions and solve it through an expectation maximization (EM) algorithm. Compared with the ground-truth established from postoperative CT, our registration method in an experiment using a plastic phantom showed accurate results with errors of (-0.43°+/-1.19°, 0.45°+/-2.17°, 0.23°+/-1.05°) and (0.03+/-0.55, -0.03+/-0.54, -2.73+/-1.64) mm. As for the entry point of the ACL tunnel, one of the key measurements, it was obtained with high accuracy of 0.53+/-0.30 mm distance errors.

  17. YouDash3D: exploring stereoscopic 3D gaming for 3D movie theaters

    NASA Astrophysics Data System (ADS)

    Schild, Jonas; Seele, Sven; Masuch, Maic

    2012-03-01

    Along with the success of the digitally revived stereoscopic cinema, events beyond 3D movies become attractive for movie theater operators, i.e. interactive 3D games. In this paper, we present a case that explores possible challenges and solutions for interactive 3D games to be played by a movie theater audience. We analyze the setting and showcase current issues related to lighting and interaction. Our second focus is to provide gameplay mechanics that make special use of stereoscopy, especially depth-based game design. Based on these results, we present YouDash3D, a game prototype that explores public stereoscopic gameplay in a reduced kiosk setup. It features live 3D HD video stream of a professional stereo camera rig rendered in a real-time game scene. We use the effect to place the stereoscopic effigies of players into the digital game. The game showcases how stereoscopic vision can provide for a novel depth-based game mechanic. Projected trigger zones and distributed clusters of the audience video allow for easy adaptation to larger audiences and 3D movie theater gaming.

  18. PLOT3D/AMES, UNIX SUPERCOMPUTER AND SGI IRIS VERSION (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  19. PLOT3D/AMES, UNIX SUPERCOMPUTER AND SGI IRIS VERSION (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  20. Geometric-model-free tracking of extended targets using 3D lidar measurements

    NASA Astrophysics Data System (ADS)

    Steinemann, Philipp; Klappstein, Jens; Dickmann, Juergen; von Hundelshausen, Felix; Wünsche, Hans-Joachim

    2012-06-01

    Tracking of extended targets in high definition, 360-degree 3D-LIDAR (Light Detection and Ranging) measurements is a challenging task and a current research topic. It is a key component in robotic applications, and is relevant to path planning and collision avoidance. This paper proposes a new method without a geometric model to simultaneously track and accumulate 3D-LIDAR measurements of an object. The method itself is based on a particle filter and uses an object-related local 3D grid for each object. No geometric object hypothesis is needed. Accumulation allows coping with occlusions. The prediction step of the particle filter is governed by a motion model consisting of a deterministic and a probabilistic part. Since this paper is focused on tracking ground vehicles, a bicycle model is used for the deterministic part. The probabilistic part depends on the current state of each particle. A function for calculating the current probability density function for state transition is developed. It is derived in detail and based on a database consisting of vehicle dynamics measurements over several hundreds of kilometers. The adaptive probability density function narrows down the gating area for measurement data association. The second part of the proposed method addresses weighting the particles with a cost function. Different 3D-griddependent cost functions are presented and evaluated. Evaluations with real 3D-LIDAR measurements show the performance of the proposed method. The results are also compared to ground truth data.

  1. Speaking Volumes About 3-D

    NASA Technical Reports Server (NTRS)

    2002-01-01

    In 1999, Genex submitted a proposal to Stennis Space Center for a volumetric 3-D display technique that would provide multiple users with a 360-degree perspective to simultaneously view and analyze 3-D data. The futuristic capabilities of the VolumeViewer(R) have offered tremendous benefits to commercial users in the fields of medicine and surgery, air traffic control, pilot training and education, computer-aided design/computer-aided manufacturing, and military/battlefield management. The technology has also helped NASA to better analyze and assess the various data collected by its satellite and spacecraft sensors. Genex capitalized on its success with Stennis by introducing two separate products to the commercial market that incorporate key elements of the 3-D display technology designed under an SBIR contract. The company Rainbow 3D(R) imaging camera is a novel, three-dimensional surface profile measurement system that can obtain a full-frame 3-D image in less than 1 second. The third product is the 360-degree OmniEye(R) video system. Ideal for intrusion detection, surveillance, and situation management, this unique camera system offers a continuous, panoramic view of a scene in real time.

  2. CASTLE3D - A Computer Aided System for Labelling Archaeological Excavations in 3D

    NASA Astrophysics Data System (ADS)

    Houshiar, H.; Borrmann, D.; Elseberg, J.; Nüchter, A.; Näth, F.; Winkler, S.

    2015-08-01

    one label. Further information such as color, orientation and archaeological notes are added to the label to improve the documentation. The available 3D information allows for easy measurements in the data. The full 3D information of a region of interest can be segmented from the entire data. By joining this data from different georeferenced views the full 3D shape of findings is stored. All the generated documentation in CASTLE3D is exported to an XML format and serves as input for other systems and databases. Apart from presenting the functionalities of CASTLE3D we evaluate its documentation process in a sample project. For this purpose we export the data to the Adiuvabit database (http://adiuvabit.de) where more information is added for further analysis. The documentation process is compared to traditional documentation methods and it is shown how the automated system helps in accelerating the documentation process and decreases errors to a minimum.

  3. 3D aerosol climatology over East Asia derived from CALIOP observations

    NASA Astrophysics Data System (ADS)

    Zhou, Yongbo; Sun, Xuejin; Zhang, Chuanliang; Zhang, Riwei; Li, Yan; Li, Haoran

    2017-03-01

    The seasonal mean extinction coefficient profile (ECP), single scattering albedo (SSA), and scattering phase function (SPF) derived from the CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization) version 3 Level 2 5-km aerosol profile product (2011-2014) were compiled into a three-dimensional (3D) aerosol climatology for East Asia. The SSA and SPF were calculated as the weighted averages of the scattering properties of the CALIOP aerosol subtypes. The weights were set to the occurrence frequencies of the subtypes. The single scattering properties of each subtype were extrapolated from the volume-based size distribution and complex refractive indexes based on Mie calculations. For the high-loading episodes (aerosol optical depth ≥ 0.6), the exponential ECP structures were most frequently observed over the farmland and desert areas, along with the uplifted ECP structures over the marine and coastal areas. Besides the desert areas, high-loading episodes also occurred over areas with frequent agricultural and industry activities. Unlike the conventional half-3D aerosol climatology (vertically constant SSA and SPF), this newly generated climatology specified SSA and SPF in the full-3D space (full-3D aerosol climatology). Errors on the shortwave radiative heating rate (SW RHR) due to the half-3D aerosol climatology approximation were quantified. The SW RHR errors were around ±1 K/day, implying that the half-3D aerosol climatology should be used with caution in climate modeling. This study is among the first to generate a full-3D aerosol climatology from the CALIOP data. This full-3D aerosol climatology is potentially useful for aerosol remote sensing and climate modeling.

  4. Evaluation of 3D radio-frequency electromagnetic fields for any matching and coupling conditions by the use of basis functions.

    PubMed

    Tiberi, Gianluigi; Fontana, Nunzia; Monorchio, Agostino; Stara, Riccardo; Retico, Alessandra; Tosetti, Michela

    2015-12-01

    A procedure for evaluating radio-frequency electromagnetic fields in anatomical human models for any matching and coupling conditions is introduced. The procedure resorts to the extraction of basis functions: such basis functions, which represent the fields produced by each individual port without any residual coupling, are derived through an algebraic procedure which uses the S parameter matrix and the fields calculated in one (only) full-wave simulation. The basis functions are then used as building-blocks for calculating the fields for any other S parameter matrix. The proposed approach can be used both for volume coil driven in quadrature and for parallel transmission configuration.

  5. Evaluation of 3D radio-frequency electromagnetic fields for any matching and coupling conditions by the use of basis functions

    NASA Astrophysics Data System (ADS)

    Tiberi, Gianluigi; Fontana, Nunzia; Monorchio, Agostino; Stara, Riccardo; Retico, Alessandra; Tosetti, Michela

    2015-12-01

    A procedure for evaluating radio-frequency electromagnetic fields in anatomical human models for any matching and coupling conditions is introduced. The procedure resorts to the extraction of basis functions: such basis functions, which represent the fields produced by each individual port without any residual coupling, are derived through an algebraic procedure which uses the S parameter matrix and the fields calculated in one (only) full-wave simulation. The basis functions are then used as building-blocks for calculating the fields for any other S parameter matrix. The proposed approach can be used both for volume coil driven in quadrature and for parallel transmission configuration.

  6. PLOT3D/AMES, SGI IRIS VERSION (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  7. PLOT3D/AMES, SGI IRIS VERSION (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  8. Macrophage podosomes go 3D.

    PubMed

    Van Goethem, Emeline; Guiet, Romain; Balor, Stéphanie; Charrière, Guillaume M; Poincloux, Renaud; Labrousse, Arnaud; Maridonneau-Parini, Isabelle; Le Cabec, Véronique

    2011-01-01

    Macrophage tissue infiltration is a critical step in the immune response against microorganisms and is also associated with disease progression in chronic inflammation and cancer. Macrophages are constitutively equipped with specialized structures called podosomes dedicated to extracellular matrix (ECM) degradation. We recently reported that these structures play a critical role in trans-matrix mesenchymal migration mode, a protease-dependent mechanism. Podosome molecular components and their ECM-degrading activity have been extensively studied in two dimensions (2D), but yet very little is known about their fate in three-dimensional (3D) environments. Therefore, localization of podosome markers and proteolytic activity were carefully examined in human macrophages performing mesenchymal migration. Using our gelled collagen I 3D matrix model to obligate human macrophages to perform mesenchymal migration, classical podosome markers including talin, paxillin, vinculin, gelsolin, cortactin were found to accumulate at the tip of F-actin-rich cell protrusions together with β1 integrin and CD44 but not β2 integrin. Macrophage proteolytic activity was observed at podosome-like protrusion sites using confocal fluorescence microscopy and electron microscopy. The formation of migration tunnels by macrophages inside the matrix was accomplished by degradation, engulfment and mechanic compaction of the matrix. In addition, videomicroscopy revealed that 3D F-actin-rich protrusions of migrating macrophages were as dynamic as their 2D counterparts. Overall, the specifications of 3D podosomes resembled those of 2D podosome rosettes rather than those of individual podosomes. This observation was further supported by the aspect of 3D podosomes in fibroblasts expressing Hck, a master regulator of podosome rosettes in macrophages. In conclusion, human macrophage podosomes go 3D and take the shape of spherical podosome rosettes when the cells perform mesenchymal migration. This work

  9. Petal, terrain & airbags - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Portions of the lander's deflated airbags and a petal are at the lower area of this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. The metallic object at lower right is part of the lander's low-gain antenna. This image is part of a 3D 'monster

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  10. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2004-04-05

    This project consists of two activities. Task A, Simulations and Measurements, combines all the material model development and associated numerical work with the materials-oriented experimental activities. The goal of this effort is to provide an improved understanding of dynamic material properties and to provide accurate numerical representations of those properties for use in analysis codes. Task B, ALE3D Development, involves general development activities in the ALE3D code with the focus of improving simulation capabilities for problems of mutual interest to DoD and DOE. Emphasis is on problems involving multi-phase flow, blast loading of structures and system safety/vulnerability studies.

  11. Weight change and functional limitations among older adults in North Carolina.

    PubMed

    Carson, April P; Holmes, DaJuanicia N; Howard, Daniel L

    2010-12-01

    There is emerging evidence that weight change during older adulthood is associated with decreased physical function; however, less is known about the association between weight change during middle to older adulthood and physical function. This study assessed the association of weight change between middle and older adulthood and functional limitations among 2,531 older African-American and white participants, ages 65 and older at baseline (1987), from the Piedmont Health Survey of the Elderly. Weight gainers had ≥8% increase in weight, weight losers had >8% decrease in weight, and weight maintainers had <8% increase or decrease between age 50 and baseline. Functional limitations were categorized as none (0), mild (1-3), or severe (4 or more) using items from the activities of daily living scale by Katz and the extremity function scale by Nagi. Modified Poisson regression was used to assess these associations in crude and adjusted analyses. Weight gain and weight loss between age 50 and baseline were associated with severe functional limitations (prevalence ratio (PR) = 1.19, 95% CI: 1.04, 1.36 and PR = 1.58, 95% CI: 1.41, 1.78, respectively) compared to weight maintainers after adjustment for age, race, and gender. These associations were attenuated after additional adjustment for health characteristics, while weaker associations were noted for mild functional limitations. In summary, weight gain and weight loss between middle and older adulthood were associated with severe functional limitations among older adults in North Carolina. Additional research is needed to explore weight change across the life course and its possible effects on physical function later in life.

  12. Advanced Visualization and Analysis of Climate Data using DV3D and UV-CDAT

    NASA Astrophysics Data System (ADS)

    Maxwell, T. P.

    2012-12-01

    This paper describes DV3D, a Vistrails package of high-level modules for the Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT) interactive visual exploration system that enables exploratory analysis of diverse and rich data sets stored in the Earth System Grid Federation (ESGF). DV3D provides user-friendly workflow interfaces for advanced visualization and analysis of climate data at a level appropriate for scientists. The application builds on VTK, an open-source, object-oriented library, for visualization and analysis. DV3D provides the high-level interfaces, tools, and application integrations required to make the analysis and visualization power of VTK readily accessible to users without exposing burdensome details such as actors, cameras, renderers, and transfer functions. It can run as a desktop application or distributed over a set of nodes for hyperwall or distributed visualization applications. DV3D is structured as a set of modules which can be linked to create workflows in Vistrails. Figure 1 displays a typical DV3D workflow as it would appear in the Vistrails workflow builder interface of UV-CDAT and, on the right, the visualization spreadsheet output of the workflow. Each DV3D module encapsulates a complex VTK pipeline with numerous supporting objects. Each visualization module implements a unique interactive 3D display. The integrated Vistrails visualization spreadsheet offers multiple synchronized visualization displays for desktop or hyperwall. The currently available displays include volume renderers, volume slicers, 3D isosurfaces, 3D hovmoller, and various vector plots. The DV3D GUI offers a rich selection of interactive query, browse, navigate, and configure options for all displays. All configuration operations are saved as Vistrails provenance. DV3D's seamless integration with UV-CDAT's climate data management system (CDMS) and other climate data analysis tools provides a wide range of climate data analysis operations, e

  13. The World of 3-D.

    ERIC Educational Resources Information Center

    Mayshark, Robin K.

    1991-01-01

    Students explore three-dimensional properties by creating red and green wall decorations related to Christmas. Students examine why images seem to vibrate when red and green pieces are small and close together. Instructions to conduct the activity and construct 3-D glasses are given. (MDH)

  14. 3D Printing: Exploring Capabilities

    ERIC Educational Resources Information Center

    Samuels, Kyle; Flowers, Jim

    2015-01-01

    As 3D printers become more affordable, schools are using them in increasing numbers. They fit well with the emphasis on product design in technology and engineering education, allowing students to create high-fidelity physical models to see and test different iterations in their product designs. They may also help students to "think in three…

  15. SNL3dFace

    SciTech Connect

    Russ, Trina; Koch, Mark; Koudelka, Melissa; Peters, Ralph; Little, Charles; Boehnen, Chris; Peters, Tanya

    2007-07-20

    This software distribution contains MATLAB and C++ code to enable identity verification using 3D images that may or may not contain a texture component. The code is organized to support system performance testing and system capability demonstration through the proper configuration of the available user interface. Using specific algorithm parameters the face recognition system has been demonstrated to achieve a 96.6% verification rate (Pd) at 0.001 false alarm rate. The system computes robust facial features of a 3D normalized face using Principal Component Analysis (PCA) and Fisher Linear Discriminant Analysis (FLDA). A 3D normalized face is obtained by alighning each face, represented by a set of XYZ coordinated, to a scaled reference face using the Iterative Closest Point (ICP) algorithm. The scaled reference face is then deformed to the input face using an iterative framework with parameters that control the deformed surface regulation an rate of deformation. A variety of options are available to control the information that is encoded by the PCA. Such options include the XYZ coordinates, the difference of each XYZ coordinates from the reference, the Z coordinate, the intensity/texture values, etc. In addition to PCA/FLDA feature projection this software supports feature matching to obtain similarity matrices for performance analysis. In addition, this software supports visualization of the STL, MRD, 2D normalized, and PCA synthetic representations in a 3D environment.

  16. Making Inexpensive 3-D Models

    ERIC Educational Resources Information Center

    Manos, Harry

    2016-01-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the "TPT" theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity…

  17. Arginine–glycine–aspartic acid–polyethylene glycol–polyamidoamine dendrimer conjugate improves liver-cell aggregation and function in 3-D spheroid culture

    PubMed Central

    Chen, Zhanfei; Lian, Fen; Wang, Xiaoqian; Chen, Yanling; Tang, Nanhong

    2016-01-01

    The polyamidoamine (PAMAM) dendrimer, a type of macromolecule material, has been used in spheroidal cell culture and drug delivery in recent years. However, PAMAM is not involved in the study of hepatic cell-spheroid culture or its biological activity, particularly in detoxification function. Here, we constructed a PAMAM-dendrimer conjugate decorated by an integrin ligand: arginine–glycine–aspartic acid (RGD) peptide. Our studies demonstrate that RGD–polyethylene glycol (PEG)–PAMAM conjugates can promote singly floating hepatic cells to aggregate together in a sphere-like growth with a weak reactive oxygen species. Moreover, RGD-PEG-PAMAM conjugates can activate the AKT–MAPK pathway in hepatic cells to promote cell proliferation and improve basic function and ammonia metabolism. Together, our data support the hepatocyte sphere treated by RGD-PEG-PAMAM conjugates as a potential source of hepatic cells for a biological artificial liver system. PMID:27621619

  18. Arginine-glycine-aspartic acid-polyethylene glycol-polyamidoamine dendrimer conjugate improves liver-cell aggregation and function in 3-D spheroid culture.

    PubMed

    Chen, Zhanfei; Lian, Fen; Wang, Xiaoqian; Chen, Yanling; Tang, Nanhong

    The polyamidoamine (PAMAM) dendrimer, a type of macromolecule material, has been used in spheroidal cell culture and drug delivery in recent years. However, PAMAM is not involved in the study of hepatic cell-spheroid culture or its biological activity, particularly in detoxification function. Here, we constructed a PAMAM-dendrimer conjugate decorated by an integrin ligand: arginine-glycine-aspartic acid (RGD) peptide. Our studies demonstrate that RGD-polyethylene glycol (PEG)-PAMAM conjugates can promote singly floating hepatic cells to aggregate together in a sphere-like growth with a weak reactive oxygen species. Moreover, RGD-PEG-PAMAM conjugates can activate the AKT-MAPK pathway in hepatic cells to promote cell proliferation and improve basic function and ammonia metabolism. Together, our data support the hepatocyte sphere treated by RGD-PEG-PAMAM conjugates as a potential source of hepatic cells for a biological artificial liver system.

  19. Comparative Analysis of Virtual 3-D Visual Display Systems Contributions to Cross-Functional Team Collaboration in a Product Design Review Environment

    DTIC Science & Technology

    1998-01-01

    76 subject interacted with the VE. These researchers also have explored application of neurolinguistic programming to quantify the sense of presence...model that a user forms of how a computer system or program works. It can be conceived as the users’ understanding of the relationships of between the...revise the program strategy. 36 Another important objective of design reviews is to integrate knowledge from various functional areas into one common

  20. Investigating the mechanical function of the cervix during pregnancy using finite element models derived from high-resolution 3D MRI.

    PubMed

    Fernandez, M; House, M; Jambawalikar, S; Zork, N; Vink, J; Wapner, R; Myers, K

    2016-01-01

    Preterm birth is a strong contributor to perinatal mortality, and preterm infants that survive are at risk for long-term morbidities. During most of pregnancy, appropriate mechanical function of the cervix is required to maintain the developing fetus in utero. Premature cervical softening and subsequent cervical shortening are hypothesized to cause preterm birth. Presently, there is a lack of understanding of the structural and material factors that influence the mechanical function of the cervix during pregnancy. In this study we build finite element models of the pregnant uterus, cervix, and fetal membrane based on magnetic resonance imagining data in order to examine the mechanical function of the cervix under the physiologic loading conditions of pregnancy. We calculate the mechanical loading state of the cervix for two pregnant patients: 22 weeks gestational age with a normal cervical length and 28 weeks with a short cervix. We investigate the influence of (1) anatomical geometry, (2) cervical material properties, and (3) fetal membrane material properties, including its adhesion properties, on the mechanical loading state of the cervix under physiologically relevant intrauterine pressures. Our study demonstrates that membrane-uterus interaction, cervical material modeling, and membrane mechanical properties are factors that must be deliberately and carefully handled in order to cons