WorldWideScience

Sample records for 3d dynamic cell

  1. Local 3D matrix microenvironment regulates cell migration through spatiotemporal dynamics of contractility-dependent adhesions

    Doyle, Andrew D.; Carvajal, Nicole; Jin, Albert; Matsumoto, Kazue; Yamada, Kenneth M.

    2015-11-01

    The physical properties of two-dimensional (2D) extracellular matrices (ECMs) modulate cell adhesion dynamics and motility, but little is known about the roles of local microenvironmental differences in three-dimensional (3D) ECMs. Here we generate 3D collagen gels of varying matrix microarchitectures to characterize their regulation of 3D adhesion dynamics and cell migration. ECMs containing bundled fibrils demonstrate enhanced local adhesion-scale stiffness and increased adhesion stability through balanced ECM/adhesion coupling, whereas highly pliable reticular matrices promote adhesion retraction. 3D adhesion dynamics are locally regulated by ECM rigidity together with integrin/ECM association and myosin II contractility. Unlike 2D migration, abrogating contractility stalls 3D migration regardless of ECM pore size. We find force is not required for clustering of activated integrins on 3D native collagen fibrils. We propose that efficient 3D migration requires local balancing of contractility with ECM stiffness to stabilize adhesions, which facilitates the detachment of activated integrins from ECM fibrils.

  2. A 3D GCL compatible cell-centered Lagrangian scheme for solving gas dynamics equations

    Georges, Gabriel; Breil, Jérôme; Maire, Pierre-Henri

    2016-01-01

    Solving the gas dynamics equations under the Lagrangian formalism enables to simulate complex flows with strong shock waves. This formulation is well suited to the simulation of multi-material compressible fluid flows such as those encountered in the domain of High Energy Density Physics (HEDP). These types of flows are characterized by complex 3D structures such as hydrodynamic instabilities (Richtmyer-Meshkov, Rayleigh-Taylor, etc.). Recently, the 3D extension of different Lagrangian schemes has been proposed and appears to be challenging. More precisely, the definition of the cell geometry in the 3D space through the treatment of its non-planar faces and the limiting of a reconstructed field in 3D in the case of a second-order extension are of great interest. This paper proposes two new methods to solve these problems. A systematic and symmetric geometrical decomposition of polyhedral cells is presented. This method enables to define a discrete divergence operator leading to the respect of the Geometric Conservation Law (GCL). Moreover, a multi-dimensional minmod limiter is proposed. This new limiter constructs, from nodal gradients, a cell gradient which enables to ensure the monotonicity of the numerical solution even in presence of strong discontinuity. These new ingredients are employed into a cell-centered Lagrangian scheme. Robustness and accuracy are assessed against various representative test cases.

  3. Parallel 3-D particle-in-cell modelling of charged ultrarelativistic beam dynamics

    Boronina, Marina A.; Vshivkov, Vitaly A.

    2015-12-01

    > ) in supercolliders. We use the 3-D set of Maxwell's equations for the electromagnetic fields, and the Vlasov equation for the distribution function of the beam particles. The model incorporates automatically the longitudinal effects, which can play a significant role in the cases of super-high densities. We present numerical results for the dynamics of two focused ultrarelativistic beams with a size ratio 10:1:100. The results demonstrate high efficiency of the proposed computational methods and algorithms, which are applicable to a variety of problems in relativistic plasma physics.

  4. Dynamic 3D cell rearrangements guided by a fibronectin matrix underlie somitogenesis.

    Gabriel G Martins

    Full Text Available Somites are transient segments formed in a rostro-caudal progression during vertebrate development. In chick embryos, segmentation of a new pair of somites occurs every 90 minutes and involves a mesenchyme-to-epithelium transition of cells from the presomitic mesoderm. Little is known about the cellular rearrangements involved, and, although it is known that the fibronectin extracellular matrix is required, its actual role remains elusive. Using 3D and 4D imaging of somite formation we discovered that somitogenesis consists of a complex choreography of individual cell movements. Epithelialization starts medially with the formation of a transient epithelium of cuboidal cells, followed by cell elongation and reorganization into a pseudostratified epithelium of spindle-shaped epitheloid cells. Mesenchymal cells are then recruited to this medial epithelium through accretion, a phenomenon that spreads to all sides, except the lateral side of the forming somite, which epithelializes by cell elongation and intercalation. Surprisingly, an important contribution to the somite epithelium also comes from the continuous egression of mesenchymal cells from the core into the epithelium via its apical side. Inhibition of fibronectin matrix assembly first slows down the rate, and then halts somite formation, without affecting pseudopodial activity or cell body movements. Rather, cell elongation, centripetal alignment, N-cadherin polarization and egression are impaired, showing that the fibronectin matrix plays a role in polarizing and guiding the exploratory behavior of somitic cells. To our knowledge, this is the first 4D in vivo recording of a full mesenchyme-to-epithelium transition. This approach brought new insights into this event and highlighted the importance of the extracellular matrix as a guiding cue during morphogenesis.

  5. A Novel Flow-Perfusion Bioreactor Supports 3D Dynamic Cell Culture

    Alexander M. Sailon

    2009-01-01

    Full Text Available Background. Bone engineering requires thicker three-dimensional constructs than the maximum thickness supported by standard cell-culture techniques (2 mm. A flow-perfusion bioreactor was developed to provide chemotransportation to thick (6 mm scaffolds. Methods. Polyurethane scaffolds, seeded with murine preosteoblasts, were loaded into a novel bioreactor. Control scaffolds remained in static culture. Samples were harvested at days 2, 4, 6, and 8 and analyzed for cellular distribution, viability, metabolic activity, and density at the periphery and core. Results. By day 8, static scaffolds had a periphery cell density of 67%±5.0%, while in the core it was 0.3%±0.3%. Flow-perfused scaffolds demonstrated peripheral cell density of 94%±8.3% and core density of 76%±3.1% at day 8. Conclusions. Flow perfusion provides chemotransportation to thick scaffolds. This system may permit high throughput study of 3D tissues in vitro and enable prefabrication of biological constructs large enough to solve clinical problems.

  6. 3D-dynamic visualization of complex molecular cell biology processes : 1-year university students' understanding of visualizations of signal transduction

    Jacobsson, Johan Lars Henrik

    2008-01-01

    This study deals with the use of 3D-dynamic visualizations for teaching complex molecular cell biology concepts. The focus is on signal transduction, which is a concept that constitutes an important part of biological systems. 3D-dynamic visualizations (animations) were produced and shown for a total of 24 students attending a course in molecular cell biology at Karlstad University, Sweden. Data were collected by questionnaires and interviews which were structured around the understandability...

  7. 3D Dynamic Echocardiography with a Digitizer

    Oshiro, Osamu; Matani, Ayumu; Chihara, Kunihiro

    1998-05-01

    In this paper,a three-dimensional (3D) dynamic ultrasound (US) imaging system,where a US brightness-mode (B-mode) imagetriggered with an R-wave of electrocardiogram (ECG)was obtained with an ultrasound diagnostic deviceand the location and orientation of the US probewere simultaneously measured with a 3D digitizer, is described.The obtained B-mode imagewas then projected onto a virtual 3D spacewith the proposed interpolation algorithm using a Gaussian operator.Furthermore, a 3D image was presented on a cathode ray tube (CRT)and stored in virtual reality modeling language (VRML).We performed an experimentto reconstruct a 3D heart image in systole using this system.The experimental results indicatethat the system enables the visualization ofthe 3D and internal structure of a heart viewed from any angleand has potential for use in dynamic imaging,intraoperative ultrasonography and tele-medicine.

  8. Osteoinduction and survival of osteoblasts and bone-marrow stromal cells in 3D biphasic calcium phosphate scaffolds under static and dynamic culture conditions

    Rath, Subha N.; Strobel, Leonie A; Arkudas, Andreas; Beier, Justus P.; Maier, Anne-Kathrin; Greil, Peter; Horch, Raymund E.; Kneser, Ulrich

    2012-01-01

    In many tissue engineering approaches, the basic difference between in vitro and in vivo conditions for cells within three-dimensional (3D) constructs is the nutrition flow dynamics. To achieve comparable results in vitro, bioreactors are advised for improved cell survival, as they are able to provide a controlled flow through the scaffold. We hypothesize that a bioreactor would enhance long-term differentiation conditions of osteogenic cells in 3D scaffolds. To achieve this either primary ra...

  9. The reactor dynamics code DYN3D

    The article provides an overview on the code DYN3D which is a three-dimensional core model for steady-state, dynamic and depletion calculations in reactor cores with quadratic or hexagonal fuel assembly geometry being developed by the Helmholtz-Zentrum Dresden-Rossendorf for more than 20 years. The current paper gives an overview on the basic DYN3D models and the available code couplings. The verification and validation status is shortly outlined. The paper concludes with the current developments of the DYN3D code. For more detailed information the reader is referred to the publications cited in the corresponding chapters.

  10. From Dynamic Live Cell Imaging to 3D Ultrastructure: Novel Integrated Methods for High Pressure Freezing and Correlative Light-Electron Microscopy.

    Spiegelhalter, Coralie; Tosch, Valérie; Hentsch, Didier; Koch, Marc; Kessler, Pascal; Schwab, Yannick; Laporte, Jocelyn

    2010-01-01

    BACKGROUND: In cell biology, the study of proteins and organelles requires the combination of different imaging approaches, from live recordings with light microscopy (LM) to electron microscopy (EM). METHODOLOGY: To correlate dynamic events in adherent cells with both ultrastructural and 3D information, we developed a method for cultured cells that combines confocal time-lapse images of GFP-tagged proteins with electron microscopy. With laser micro-patterned culture substrate, we created coo...

  11. Rendering of 3D Dynamic Virtual Environments

    Catanese, Salvatore; Fiumara, Giacomo; Pagano, Francesco

    2011-01-01

    In this paper we present a framework for the rendering of dynamic 3D virtual environments which can be integrated in the development of videogames. It includes methods to manage sounds and particle effects, paged static geometries, the support of a physics engine and various input systems. It has been designed with a modular structure to allow future expansions. We exploited some open-source state-of-the-art components such as OGRE, PhysX, ParticleUniverse, etc.; all of them have been properly integrated to obtain peculiar physical and environmental effects. The stand-alone version of the application is fully compatible with Direct3D and OpenGL APIs and adopts OpenAL APIs to manage audio cards. Concluding, we devised a showcase demo which reproduces a dynamic 3D environment, including some particular effects: the alternation of day and night infuencing the lighting of the scene, the rendering of terrain, water and vegetation, the reproduction of sounds and atmospheric agents.

  12. INCORPORATING DYNAMIC 3D SIMULATION INTO PRA

    Steven R Prescott; Curtis Smith

    2011-07-01

    provide superior results and insights. We also couple the state model with the dynamic 3D simulation analysis representing events (such as flooding) to determine which (if any) components fail. Not only does the simulation take into account any failed items from the state model, but any failures caused by the simulation are incorporated back into the state model and factored into the overall results. Using this method we incorporate accurate 3D simulation results, eliminate static-based PRA issues, and have time ordered failure information.

  13. Dynamic stall and 3D effects

    Bjoerck, A.; Thor, S.E. [Aeronautical Research Inst. of Sweden, Bromma (Sweden)

    1996-12-01

    The JOULE II project `Dynamic stall and 3D effects` started in January 1994 and was completed in September 1995. The objective of the project has been to increase the understanding of the three-dimensional and unsteady aerodynamics of stall controlled HAWT`s. The objectives have also been to develop `engineering models` suitable for inclusion into aero-elastic codes. The project included the participation of 13 parties within Europe. This paper describes an overview of the work carried out within the project and key results. 3 refs, 4 figs

  14. Dynamics of 3D isolated thermal filaments

    Walkden, N R; Militello, F; Omotani, J T

    2016-01-01

    Simulations have been carried out to establish how electron thermal physics, introduced in the form of a dynamic electron temperature, affects isolated filament motion and dynamics in 3D. It is found that thermal effects impact filament motion in two major ways when the filament has a significant temperature perturbation compared to its density perturbation: They lead to a strong increase in filament propagation in the bi-normal direction and a significant decrease in net radial propagation. Both effects arise from the temperature dependence of the sheath current which leads to a non-uniform floating potential, with the latter effect supplemented by faster pressure loss. The reduction in radial velocity can only occur when the filament cross-section loses angular symmetry. The behaviour is observed across different filament sizes and suggests that filaments with much larger temperature perturbations than density perturbations are more strongly confined to the near SOL region.

  15. Simulating coronal condensation dynamics in 3D

    Moschou, S P; Xia, C; Fang, X

    2015-01-01

    We present numerical simulations in 3D settings where coronal rain phenomena take place in a magnetic configuration of a quadrupolar arcade system. Our simulation is a magnetohydrodynamic simulation including anisotropic thermal conduction, optically thin radiative losses, and parametrised heating as main thermodynamical features to construct a realistic arcade configuration from chromospheric to coronal heights. The plasma evaporation from chromospheric and transition region heights eventually causes localised runaway condensation events and we witness the formation of plasma blobs due to thermal instability, that evolve dynamically in the heated arcade part and move gradually downwards due to interchange type dynamics. Unlike earlier 2.5D simulations, in this case there is no large scale prominence formation observed, but a continuous coronal rain develops which shows clear indications of Rayleigh-Taylor or interchange instability, that causes the denser plasma located above the transition region to fall do...

  16. Overall Dynamic Properties of 3-D periodic elastic composites

    Srivastava, Ankit

    2011-01-01

    A method for the homogenization of 3-D periodic elastic composites is presented. It allows for the evaluation of the averaged overall frequency dependent dynamic material constitutive tensors relating the averaged dynamic ?eld variable tensors of velocity, strain, stress, and linear momentum. The formulation is based on micromechanical modeling of a representative unit cell of a composite proposed by Nemat-Nasser & Hori (1993), Nemat-Nasser et. al. (1982) and Mura (1987) and is the 3-D generalization of the 1-D elastodynamic homogenization scheme presented by Nemat-Nasser & Srivastava (2011). We show that for 3-D periodic composites the overall compliance (stiffness) tensor is hermitian, irrespective of whether the corresponding unit cell is geometrically or materially symmetric.Overall mass density is shown to be a tensor and, like the overall compliance tensor, always hermitian. The average strain and linear momentum tensors are, however, coupled and the coupling tensors are shown to be each others'...

  17. 3D Cell Culture in Alginate Hydrogels

    Therese Andersen

    2015-03-01

    Full Text Available This review compiles information regarding the use of alginate, and in particular alginate hydrogels, in culturing cells in 3D. Knowledge of alginate chemical structure and functionality are shown to be important parameters in design of alginate-based matrices for cell culture. Gel elasticity as well as hydrogel stability can be impacted by the type of alginate used, its concentration, the choice of gelation technique (ionic or covalent, and divalent cation chosen as the gel inducing ion. The use of peptide-coupled alginate can control cell–matrix interactions. Gelation of alginate with concomitant immobilization of cells can take various forms. Droplets or beads have been utilized since the 1980s for immobilizing cells. Newer matrices such as macroporous scaffolds are now entering the 3D cell culture product market. Finally, delayed gelling, injectable, alginate systems show utility in the translation of in vitro cell culture to in vivo tissue engineering applications. Alginate has a history and a future in 3D cell culture. Historically, cells were encapsulated in alginate droplets cross-linked with calcium for the development of artificial organs. Now, several commercial products based on alginate are being used as 3D cell culture systems that also demonstrate the possibility of replacing or regenerating tissue.

  18. From dynamic live cell imaging to 3D ultrastructure: novel integrated methods for high pressure freezing and correlative light-electron microscopy.

    Coralie Spiegelhalter

    Full Text Available BACKGROUND: In cell biology, the study of proteins and organelles requires the combination of different imaging approaches, from live recordings with light microscopy (LM to electron microscopy (EM. METHODOLOGY: To correlate dynamic events in adherent cells with both ultrastructural and 3D information, we developed a method for cultured cells that combines confocal time-lapse images of GFP-tagged proteins with electron microscopy. With laser micro-patterned culture substrate, we created coordinates that were conserved at every step of the sample preparation and visualization processes. Specifically designed for cryo-fixation, this method allowed a fast freezing of dynamic events within seconds and their ultrastructural characterization. We provide examples of the dynamic oligomerization of GFP-tagged myotubularin (MTM1 phosphoinositides phosphatase induced by osmotic stress, and of the ultrastructure of membrane tubules dependent on amphiphysin 2 (BIN1 expression. CONCLUSION: Accessible and versatile, we show that this approach is efficient to routinely correlate functional and dynamic LM with high resolution morphology by EM, with immuno-EM labeling, with 3D reconstruction using serial immuno-EM or tomography, and with scanning-EM.

  19. High-dose radiotherapy in inoperable nonsmall cell lung cancer: comparison of volumetric modulated arc therapy, dynamic IMRT and 3D conformal radiotherapy.

    Bree, Ingrid de; van Hinsberg, Mariëlle G E; van Veelen, Lieneke R

    2012-01-01

    Conformal 3D radiotherapy (3D-CRT) combined with chemotherapy for inoperable non-small cell lung cancer (NSCLC) to the preferable high dose is often not achievable because of dose-limiting organs. This reduces the probability of regional tumor control. Therefore, the surplus value of using intensity-modulated radiation therapy (IMRT) techniques, specifically volumetric modulated arc therapy (RapidArc [RA]) and dynamic IMRT (d-IMRT) has been investigated. RA and d-IMRT plans were compared with 3D-CRT treatment plans for 20 patients eligible for concurrent high-dose chemoradiotherapy, in whom a dose of 60 Gy was not achievable. Comparison of dose delivery in the target volume and organs at risk was carried out by evaluating 3D dose distributions and dose-volume histograms. Quality of the dose distribution was assessed using the inhomogeneity and conformity index. For most patients, a higher dose to the target volume can be delivered using RA or d-IMRT; in 15% of the patients a dose ≥60 Gy was possible. Both IMRT techniques result in a better conformity of the dose (p < 0.001). There are no significant differences in homogeneity of dose in the target volume. IMRT techniques for NSCLC patients allow higher dose to the target volume, thus improving regional tumor control. PMID:22459649

  20. High-dose radiotherapy in inoperable nonsmall cell lung cancer: Comparison of volumetric modulated arc therapy, dynamic IMRT and 3D conformal radiotherapy

    Bree, Ingrid de, E-mail: i.de.bree@zrti.nl [Zeeuws Radiotherapeutisch Instituut, Vlissingen (Netherlands); Hinsberg, Marieelle G.E. van; Veelen, Lieneke R. van [Zeeuws Radiotherapeutisch Instituut, Vlissingen (Netherlands)

    2012-01-01

    Conformal 3D radiotherapy (3D-CRT) combined with chemotherapy for inoperable non-small cell lung cancer (NSCLC) to the preferable high dose is often not achievable because of dose-limiting organs. This reduces the probability of regional tumor control. Therefore, the surplus value of using intensity-modulated radiation therapy (IMRT) techniques, specifically volumetric modulated arc therapy (RapidArc [RA]) and dynamic IMRT (d-IMRT) has been investigated. RA and d-IMRT plans were compared with 3D-CRT treatment plans for 20 patients eligible for concurrent high-dose chemoradiotherapy, in whom a dose of 60 Gy was not achievable. Comparison of dose delivery in the target volume and organs at risk was carried out by evaluating 3D dose distributions and dose-volume histograms. Quality of the dose distribution was assessed using the inhomogeneity and conformity index. For most patients, a higher dose to the target volume can be delivered using RA or d-IMRT; in 15% of the patients a dose {>=}60 Gy was possible. Both IMRT techniques result in a better conformity of the dose (p < 0.001). There are no significant differences in homogeneity of dose in the target volume. IMRT techniques for NSCLC patients allow higher dose to the target volume, thus improving regional tumor control.

  1. High-dose radiotherapy in inoperable nonsmall cell lung cancer: Comparison of volumetric modulated arc therapy, dynamic IMRT and 3D conformal radiotherapy

    Conformal 3D radiotherapy (3D-CRT) combined with chemotherapy for inoperable non–small cell lung cancer (NSCLC) to the preferable high dose is often not achievable because of dose-limiting organs. This reduces the probability of regional tumor control. Therefore, the surplus value of using intensity-modulated radiation therapy (IMRT) techniques, specifically volumetric modulated arc therapy (RapidArc [RA]) and dynamic IMRT (d-IMRT) has been investigated. RA and d-IMRT plans were compared with 3D-CRT treatment plans for 20 patients eligible for concurrent high-dose chemoradiotherapy, in whom a dose of 60 Gy was not achievable. Comparison of dose delivery in the target volume and organs at risk was carried out by evaluating 3D dose distributions and dose-volume histograms. Quality of the dose distribution was assessed using the inhomogeneity and conformity index. For most patients, a higher dose to the target volume can be delivered using RA or d-IMRT; in 15% of the patients a dose ≥60 Gy was possible. Both IMRT techniques result in a better conformity of the dose (p < 0.001). There are no significant differences in homogeneity of dose in the target volume. IMRT techniques for NSCLC patients allow higher dose to the target volume, thus improving regional tumor control.

  2. Laser printing of cells into 3D scaffolds

    One of the most promising approaches in tissue engineering is the application of 3D scaffolds, which provide cell support and guidance in the initial tissue formation stage. The porosity of the scaffold and internal pore organization influence cell migration and play a major role in its biodegradation dynamics, nutrient diffusion and mechanical stability. In order to control cell migration and cellular interactions within the scaffold, novel technologies capable of producing 3D structures in accordance with predefined design are required. The two-photon polymerization (2PP) technique, used in this report for the fabrication of scaffolds, allows the realization of arbitrary 3D structures with submicron spatial resolution. Highly porous 3D scaffolds, produced by 2PP of acrylated poly(ethylene glycol), are seeded with cells by means of laser-induced forward transfer (LIFT). In this laser printing approach, a propulsive force, resulting from laser-induced shock wave, is used to propel individual cells or cell groups from a donor substrate towards the receiver substrate. We demonstrate that with this technique printing of multiple cell types into 3D scaffolds is possible. Combination of LIFT and 2PP provides a route for the realization of 3D multicellular tissue constructs and artificial ECM engineered on the microscale.

  3. 3D Molecular dynamics simulations using spheropolytopes

    Galindo-Torres, Sergio-Andres; Alonso-Marroquin, Fernando; Wang, Yucang

    2008-01-01

    We present a simple and efficient method to simulate three-dimensional, complex-shaped, interacting bodies. The particle shape is represented by Minkowski operators. A time-continuous interaction between these bodies is derived using simple concepts of computational geometry. The model (particles + interactions) is efficient, accurate and easy to implement, and it complies with the conservation laws of physics. 3D simulations of hopper flow shows that the non-convexity of the particles strong...

  4. 3D blob dynamics in toroidal geometry

    Nielsen, Anders Henry; Reiser, Dirk

    DIESEL code is an extension of the ESEL code [1]. It solves a simple interchange model in full 3D tokamak geometry, where the toroidal direction is divided into a number of drift planes. On each drift plane the equations are solved in a domain corresponding to the full 2D cross section of the tokamak and...... communicate parallel with the nearest drift planes using parameterized velocities, the ion sound speed, Cs for the density equation and the Alfvén speed VA for the vorticity equation. Results show that a decrease of Alfvénic interaction of electric potential and current density leads to the expected radial...

  5. Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

    Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF6.

  6. A microfluidic device for 2D to 3D and 3D to 3D cell navigation

    Shamloo, Amir; Amirifar, Leyla

    2016-01-01

    Microfluidic devices have received wide attention and shown great potential in the field of tissue engineering and regenerative medicine. Investigating cell response to various stimulations is much more accurate and comprehensive with the aid of microfluidic devices. In this study, we introduced a microfluidic device by which the matrix density as a mechanical property and the concentration profile of a biochemical factor as a chemical property could be altered. Our microfluidic device has a cell tank and a cell culture chamber to mimic both 2D to 3D and 3D to 3D migration of three types of cells. Fluid shear stress is negligible on the cells and a stable concentration gradient can be obtained by diffusion. The device was designed by a numerical simulation so that the uniformity of the concentration gradients throughout the cell culture chamber was obtained. Adult neural cells were cultured within this device and they showed different branching and axonal navigation phenotypes within varying nerve growth factor (NGF) concentration profiles. Neural stem cells were also cultured within varying collagen matrix densities while exposed to NGF concentrations and they experienced 3D to 3D collective migration. By generating vascular endothelial growth factor concentration gradients, adult human dermal microvascular endothelial cells also migrated in a 2D to 3D manner and formed a stable lumen within a specific collagen matrix density. It was observed that a minimum absolute concentration and concentration gradient were required to stimulate migration of all types of the cells. This device has the advantage of changing multiple parameters simultaneously and is expected to have wide applicability in cell studies.

  7. A microfluidic device for 2D to 3D and 3D to 3D cell navigation

    Microfluidic devices have received wide attention and shown great potential in the field of tissue engineering and regenerative medicine. Investigating cell response to various stimulations is much more accurate and comprehensive with the aid of microfluidic devices. In this study, we introduced a microfluidic device by which the matrix density as a mechanical property and the concentration profile of a biochemical factor as a chemical property could be altered. Our microfluidic device has a cell tank and a cell culture chamber to mimic both 2D to 3D and 3D to 3D migration of three types of cells. Fluid shear stress is negligible on the cells and a stable concentration gradient can be obtained by diffusion. The device was designed by a numerical simulation so that the uniformity of the concentration gradients throughout the cell culture chamber was obtained. Adult neural cells were cultured within this device and they showed different branching and axonal navigation phenotypes within varying nerve growth factor (NGF) concentration profiles. Neural stem cells were also cultured within varying collagen matrix densities while exposed to NGF concentrations and they experienced 3D to 3D collective migration. By generating vascular endothelial growth factor concentration gradients, adult human dermal microvascular endothelial cells also migrated in a 2D to 3D manner and formed a stable lumen within a specific collagen matrix density. It was observed that a minimum absolute concentration and concentration gradient were required to stimulate migration of all types of the cells. This device has the advantage of changing multiple parameters simultaneously and is expected to have wide applicability in cell studies. (paper)

  8. Correlative Microscopy for 3D Structural Analysis of Dynamic Interactions

    Jun, Sangmi; Zhao, Gongpu; Ning, Jiying; Gibson, Gregory A.; Watkins, Simon C.; Zhang, Peijun

    2013-01-01

    Cryo-electron tomography (cryoET) allows 3D visualization of cellular structures at molecular resolution in a close-to-physiological state1. However, direct visualization of individual viral complexes in their host cellular environment with cryoET is challenging2, due to the infrequent and dynamic nature of viral entry, particularly in the case of HIV-1. While time-lapse live-cell imaging has yielded a great deal of information about many aspects of the life cycle of HIV-13-7, the resolution ...

  9. 3d Lorentzian, dynamically triangulated quantum gravity

    Ambjørn, J.; Jurkiewicz, J.(Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, ul. prof. Stanislawa Lojasiewicza 11, Krakow, PL 30-348, Poland); Loll, R

    2006-01-01

    The model of Lorentzian three-dimensional dynamical triangulations provides a non-perturbative definition of three-dimensional quantum gravity. The theory has two phases: a weak-coupling phase with quantum fluctuations around a ``semiclassical'' background geometry which is generated dynamically despite the fact that the formulation is explicitly background-independent, and a strong-coupling phase where ``classical'' space disintegrates into a foam of baby universes.

  10. Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis

    Tajbakhsh, Jian, E-mail: tajbakhshj@cshs.org [Chromatin Biology Laboratory, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Stefanovski, Darko [Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19348 (United States); Tang, George [Chromatin Biology Laboratory, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Wawrowsky, Kolja [Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Liu, Naiyou; Fair, Jeffrey H. [Department of Surgery and UF Health Comprehensive Transplant Center, University of Florida College of Medicine, Gainesville, FL 32608 (United States)

    2015-03-15

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. In summary: 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC{sup +}/5mC{sup −}, 5hmC{sup +}/5mC{sup +}, and 5hmC{sup −}/5mC{sup +} cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC{sup +}/5mC{sup +} cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably

  11. Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. In summary: 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC+/5mC−, 5hmC+/5mC+, and 5hmC−/5mC+ cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC+/5mC+ cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably delineating chromatin domains in remodeling. We

  12. Dynamic 3D echocardiography in virtual reality

    Simoons Maarten L

    2005-12-01

    Full Text Available Abstract Background This pilot study was performed to evaluate whether virtual reality is applicable for three-dimensional echocardiography and if three-dimensional echocardiographic 'holograms' have the potential to become a clinically useful tool. Methods Three-dimensional echocardiographic data sets from 2 normal subjects and from 4 patients with a mitral valve pathological condition were included in the study. The three-dimensional data sets were acquired with the Philips Sonos 7500 echo-system and transferred to the BARCO (Barco N.V., Kortrijk, Belgium I-space. Ten independent observers assessed the 6 three-dimensional data sets with and without mitral valve pathology. After 10 minutes' instruction in the I-Space, all of the observers could use the virtual pointer that is necessary to create cut planes in the hologram. Results The 10 independent observers correctly assessed the normal and pathological mitral valve in the holograms (analysis time approximately 10 minutes. Conclusion this report shows that dynamic holographic imaging of three-dimensional echocardiographic data is feasible. However, the applicability and use-fullness of this technology in clinical practice is still limited.

  13. Critical bifurcation surfaces of 3D discrete dynamics

    Michael Sonis

    2000-01-01

    Full Text Available This paper deals with the analytical representation of bifurcations of each 3D discrete dynamics depending on the set of bifurcation parameters. The procedure of bifurcation analysis proposed in this paper represents the 3D elaboration and specification of the general algorithm of the n-dimensional linear bifurcation analysis proposed by the author earlier. It is proven that 3D domain of asymptotic stability (attraction of the fixed point for a given 3D discrete dynamics is bounded by three critical bifurcation surfaces: the divergence, flip and flutter surfaces. The analytical construction of these surfaces is achieved with the help of classical Routh–Hurvitz conditions of asymptotic stability. As an application the adjustment process proposed by T. Puu for the Cournot oligopoly model is considered in detail.

  14. Multizone paper platform for 3D cell cultures.

    Ratmir Derda

    Full Text Available In vitro 3D culture is an important model for tissues in vivo. Cells in different locations of 3D tissues are physiologically different, because they are exposed to different concentrations of oxygen, nutrients, and signaling molecules, and to other environmental factors (temperature, mechanical stress, etc. The majority of high-throughput assays based on 3D cultures, however, can only detect the average behavior of cells in the whole 3D construct. Isolation of cells from specific regions of 3D cultures is possible, but relies on low-throughput techniques such as tissue sectioning and micromanipulation. Based on a procedure reported previously ("cells-in-gels-in-paper" or CiGiP, this paper describes a simple method for culture of arrays of thin planar sections of tissues, either alone or stacked to create more complex 3D tissue structures. This procedure starts with sheets of paper patterned with hydrophobic regions that form 96 hydrophilic zones. Serial spotting of cells suspended in extracellular matrix (ECM gel onto the patterned paper creates an array of 200 micron-thick slabs of ECM gel (supported mechanically by cellulose fibers containing cells. Stacking the sheets with zones aligned on top of one another assembles 96 3D multilayer constructs. De-stacking the layers of the 3D culture, by peeling apart the sheets of paper, "sections" all 96 cultures at once. It is, thus, simple to isolate 200-micron-thick cell-containing slabs from each 3D culture in the 96-zone array. Because the 3D cultures are assembled from multiple layers, the number of cells plated initially in each layer determines the spatial distribution of cells in the stacked 3D cultures. This capability made it possible to compare the growth of 3D tumor models of different spatial composition, and to examine the migration of cells in these structures.

  15. Fabrication of Nanostructured Poly-ε-caprolactone 3D Scaffolds for 3D Cell Culture Technology

    Schipani, Rossana

    2015-04-21

    Tissue engineering is receiving tremendous attention due to the necessity to overcome the limitations related to injured or diseased tissues or organs. It is the perfect combination of cells and biomimetic-engineered materials. With the appropriate biochemical factors, it is possible to develop new effective bio-devices that are capable to improve or replace biological functions. Latest developments in microfabrication methods, employing mostly synthetic biomaterials, allow the production of three-dimensional (3D) scaffolds that are able to direct cell-to-cell interactions and specific cellular functions in order to drive tissue regeneration or cell transplantation. The presented work offers a rapid and efficient method of 3D scaffolds fabrication by using optical lithography and micro-molding techniques. Bioresorbable polymer poly-ε-caprolactone (PCL) was the material used thanks to its high biocompatibility and ability to naturally degrade in tissues. 3D PCL substrates show a particular combination in the designed length scale: cylindrical shaped pillars with 10μm diameter, 10μm height, arranged in a hexagonal lattice with spacing of 20μm were obtained. The sidewalls of the pillars were nanostructured by attributing a 3D architecture to the scaffold. The suitability of these devices as cell culture technology supports was evaluated by plating NIH/3T3 mouse embryonic fibroblasts and human Neural Stem Cells (hNSC) on them. Scanning Electron Microscopy (SEM) analysis was carried out in order to examine the micro- and nano-patterns on the surface of the supports. In addition, after seeding of cells, SEM and immunofluorescence characterization of the fabricated systems were performed to check adhesion, growth and proliferation. It was observed that cells grow and develop healthy on the bio-polymeric devices by giving rise to well-interconnected networks. 3D PCL nano-patterned pillared scaffold therefore may have considerable potential as effective tool for

  16. Stem cell reprogramming: A 3D boost

    Abilez, Oscar J.; Wu, Joseph C.

    2016-03-01

    Biophysical factors in an optimized three-dimensional microenvironment enhance the reprogramming efficiency of human somatic cells into pluripotent stem cells when compared to traditional cell-culture substrates.

  17. NIKE3D, Static and Dynamic Response of 3-D Solids

    1 - Description of program or function: NIKE3D is a vectorized, fully implicit, three-dimensional, finite-element program for analyzing the finite-strain, static and dynamic response of inelastic solids, shells, and beams. Capabilities currently available include sliding interfaces, body force loads due to base acceleration, body force loads due to spinning (geometry dependent), concentrated nodal loads, pressure boundary conditions (geometry dependent), displacement boundary conditions, thermal stresses, plot-file generation, and problem restart. 2 - Method of solution: Spatial discretization is accomplished using eight-node solid elements that are integrated using a two-point Gauss quadrature rule, four-node shell elements that use a 2x2 Gauss integration in the surface and from 1 to 5 integration points through the thickness, and two-node thick beam elements using from 1 to 5 integration points in each local direction of the cross section at the center of the beam. Elastic, orthotropic elastic, elastic-plastic, thermo-elastic-plastic, soil and crushable foam, linear viscoelastic, thermo-orthotropic elastic, and thermo-elastic- creep material models are implemented. An incremental-interactive numerical algorithm, based on the Green-Naghdi and Jaumann stress rate formulations, is implemented in NIKE3D. Five iterative schemes are available including the BFGS quasi-Newton method, Broyden's quasi-Newton method, modified Newton-Raphson, full Newton, and full Newton with line search

  18. d3D-CTA (dynamic 3D-CTA) for cerebral infarction using multi-detector row CT (MDCT)

    Since three-dimensional-CT angiography (3D-CTA) can demonstrate occlusion or stenosis of the arteries, it has been employed for the diagnosis of patients with cerebral infarction. However, it does not provide information on the blood-flow dynamics. We therefore developed a new technique, d3D-CTA (dynamic 3D-CTA), that yields 3D images of the vessels and hemodynamics. We assessed whether or not our technique could be applied to patients with cerebral infarction. We subjected 41 patients with cerebral infarction to d3D-CTA (17 lacunar infarctions, 14 cardioembolisms and 10 atherosclerotic infarctions). d3D-CTA was performed using a multi-detector row CT scanner with 64 detectors. Contrast medium was injected at a speed of 6 ml/s (a total volume of 30 ml). The scanning was performed for 30 sec with a scan delay of 5 sec. In all cases, we successfully developed d3D-CTA. The d3D-CTA provided us with information on the vascular structures, hemodynamics and cerebral perfusion. Although our technique, d3D-CTA, has some disadvantages such as a limited scan range (32 mm) and relatively high radiation dose, it does facilitate the acquisition of information on the vascular anatomy, flow dynamics on 3D images and cerebral perfusion. We conclude that d3D-CTA can be applied for the diagnosis and treatment of patients with cerebral infarction. (author)

  19. Long-term 3D map maintenance in dynamic environments

    Pomerleau, François; Krüsi, Philipp; Colas, Francis; Furgale, Paul; Siegwart, Roland

    2014-01-01

    New applications of mobile robotics in dynamic urban areas require more than the single-session geometric maps that have dominated simultaneous localization and mapping (SLAM) research to date; maps must be updated as the environment changes and include a semantic layer (such as road network information) to aid motion planning in dynamic environments. We present an algorithm for long-term localization and mapping in real time using a three-dimensional (3D) laser scanner. The system infers the...

  20. Asymptotic dynamics in 3D gravity with torsion

    Blagojevic, M; Vasilic, M.

    2003-01-01

    We study the nature of boundary dynamics in the teleparallel 3D gravity. The asymptotic field equations with anti-de Sitter boundary conditions yield only two non-trivial boundary modes, related to a conformal field theory with classical central charge. After showing that the teleparallel gravity can be formulated as a Chern-Simons theory, we identify dynamical structure at the boundary as the Liouville theory.

  1. Multitasking the code ARC3D. [for computational fluid dynamics

    Barton, John T.; Hsiung, Christopher C.

    1986-01-01

    The CRAY multitasking system was developed in order to utilize all four processors and sharply reduce the wall clock run time. This paper describes the techniques used to modify the computational fluid dynamics code ARC3D for this run and analyzes the achieved speedup. The ARC3D code solves either the Euler or thin-layer N-S equations using an implicit approximate factorization scheme. Results indicate that multitask processing can be used to achieve wall clock speedup factors of over three times, depending on the nature of the program code being used. Multitasking appears to be particularly advantageous for large-memory problems running on multiple CPU computers.

  2. DYNA3D, 3-D Finite Elements for Dynamic Response of Inelastic Solids

    1 - Description of program or function: DYNA3D is an explicit, three- dimensional, finite element program for analyzing the large deformation dynamic response of inelastic solids and structures. DYNA3D contain 30 material models and 10 equations of state (EOS) to cover a wide range of material behavior. The material models implemented are: elastic, orthotropic elastic, kinematic/isotropic plasticity, thermo-elastoplastic, soil and crushable foam, linear viscoelastic, Blatz-Ko rubber, high explosive burn, hydrodynamic without deviatoric stresses, elastoplastic hydrodynamic, temperature dependent elastoplastic, isotropic elastoplastic, isotropic elastoplastic with failure, soil and crushable foam with failure, Johnson/Cook plasticity model, pseudo TENSOR geological model, elastoplastic with fracture, power law isotropic plasticity, strain rate dependent plasticity, rigid, thermal orthotropic, composite damage model, thermal orthotropic with 12 curves, piecewise linear isotropic plasticity, and inviscid two invariant geologic cap, orthotropic crushable model, Moonsy-Rivlin rubber, resultant plasticity, closed form update shell plasticity, and Frazer-Nash rubber model. The IBM 3090 version does not contain the last two models mentioned. The hydrodynamic material models determine only the deviatoric stresses. Pressure is determined by one of ten equations of state including linear polynomial, JWL high explosive, Sack 'Tuesday' high explosive, Gruneisen, ratio of polynomials, linear polynomial with energy deposition, ignition and growth of reaction in HE, tabulated compaction, tabulated, and TENSOR pore collapse. DYNA3D generates three binary output databases. One contains information for complete states at infrequent intervals; 50 to 100 states is typical. The second contains information for a subset of nodes and elements at frequent intervals; 1,000 to 10,000 states is typical. The last contains interfaces data for contact surfaces. 2 - Method of solution: A contact

  3. Propagating torsion in 3D gravity and dynamical mass generation

    In this paper, fermions are minimally coupled to 3D gravity with dynamical torsion. A Kalb-Ramond field is also introduced and non-minimally coupled to the fermions in a gauge-invariant way. We show that a 1-loop mass generation mechanism takes place for both the 2-form gauge field and the torsion. As for the fermions, no mass is dynamically generated: at 1-loop, there is only a fermion mass shift proportional to the Yukawa coupling whenever these fermions have a non-vanishing tree-level mass

  4. Dynamic Heterogeneity of DNA Methylation and Hydroxymethylation in Embryonic Stem Cell Populations Captured by Single-Cell 3D High-Content Analysis

    Tajbakhsh, Jian; Stefanovski, Darko; Tang, George; Wawrowsky, Kolja; Liu, Naiyou; FAIR, JEFFREY H.

    2015-01-01

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (F...

  5. Causal Dynamical Triangulation of 3D Tensor Model

    Kawabe, Hiroshi

    2016-01-01

    We extend the string field theory of the two dimensional (2D) generalized causal dynamical triangulation (GCDT) with the Ishibashi-Kawai (IK-) type interaction formulated by the matrix model, to the three dimensional (3D) model of the surface field theory. Based on the loop gas model, we construct a tensor model for the discretized surface field and then apply it the stochastic quantization method. In the double scaling limit, the model is characterized by two scaling dimensions $D$ and $D_N$, the power indices of the minimal length as the scaling parameter. The continuum GCDT model with the IK-type interaction is realized with the similar restriction in the $D_N$-$D$ space, to the 2D model. The distinct property in the 3D model is that the quantum effect contains the IK-type interaction only, while the ordinary splitting interaction is excluded.

  6. Cyto-3D-print to attach mitotic cells.

    Castroagudin, Michelle R; Zhai, Yujia; Li, Zhi; Marnell, Michael G; Glavy, Joseph S

    2016-08-01

    The Cyto-3D-print is an adapter that adds cytospin capability to a standard centrifuge. Like standard cytospinning, Cyto-3D-print increases the surface attachment of mitotic cells while giving a higher degree of adaptability to other slide chambers than available commercial devices. The use of Cyto-3D-print is cost effective, safe, and applicable to many slide designs. It is durable enough for repeated use and made of biodegradable materials for environment-friendly disposal. PMID:26464272

  7. Digital microfabrication of user-defined 3D microstructures in cell-laden hydrogels.

    Soman, Pranav; Chung, Peter H; Zhang, A Ping; Chen, Shaochen

    2013-11-01

    Complex 3D interfacial arrangements of cells are found in several in vivo biosystems such as blood vasculature, renal glomeruli, and intestinal villi. Current tissue engineering techniques fail to develop suitable 3D microenvironments to evaluate the concurrent effects of complex topography and cell encapsulation. There is a need to develop new fabrication approaches that control cell density and distribution within complex 3D features. In this work, we present a dynamic projection printing process that allows rapid construction of complex 3D structures using custom-defined computer-aided-design (CAD) files. Gelatin-methacrylate (GelMA) constructs featuring user-defined spiral, pyramid, flower, and dome micro-geometries were fabricated with and without encapsulated cells. Encapsulated cells demonstrate good cell viability across all geometries both on the scaffold surface and internal to the structures. Cells respond to geometric cues individually as well as collectively throughout the larger-scale patterns. Time-lapse observations also reveal the dynamic nature of mechanical interactions between cells and micro-geometry. When compared to conventional cell-seeding, cell encapsulation within complex 3D patterned scaffolds provides long-term control over proliferation, cell morphology, and geometric guidance. Overall, this biofabrication technique offers a flexible platform to evaluate cell interactions with complex 3D micro-features, with the ability to scale-up towards high-throughput screening platforms. PMID:23686741

  8. 3-D DYNAMIC RESPONSE OF TRANSVERSELY ISOTROPIC SATURATED SOILS

    WANG Xiao-gang; HUANG Yi

    2005-01-01

    A study on dynamic response of transversely isotropic saturated poroelastic media under a circular non-axisymmetrical harmonic source has been presented by Huang Yi et al.using the technique of Fourier expansion and Hankel transform. However, the method may not always be valid. The work is extended to the general case being in the rectangular coordinate. The purpose is to study the 3-d dynamic response of transversely isotropic saturated soils under a general source distributing in arbitrary rectangular zoon on the medium surface. Based on Biot's theory for fluid-saturated porous media, the 3-d wave motion equations in rectangular coordinate for transversely isotropic saturated poroelastic media were transformed into the two uncoupling governing differential equations of 6-order and 2-order respectively by means of the displacement functions. Then, using the technique of double Fourier transform, the governing differential equations were easily solved. Integral solutions of soil skeleton displacements and pore pressure as well as the total stresses for poroelastic media were obtained. Furthermore, a systematic study on half-space problem in saturated soils was performed. Integral solutions for surface displacements under the general harmonic source distributing on arbitrary surface zone,considering both case of drained surface and undrained surface,were presented.

  9. Distributed 3D Information Visualization - Towards Integration of the Dynamic 3D Graphics and Web Services

    Vucinic, Dean; Deen, Danny; Oanta, Emil; Batarilo, Zvonimir; Lacor, Chris

    This paper focuses on visualization and manipulation of graphical content in distributed network environments. The developed graphical middleware and 3D desktop prototypes were specialized for situational awareness. This research was done in the LArge Scale COllaborative decision support Technology (LASCOT) project, which explored and combined software technologies to support human-centred decision support system for crisis management (earthquake, tsunami, flooding, airplane or oil-tanker incidents, chemical, radio-active or other pollutants spreading, etc.). The performed state-of-the-art review did not identify any publicly available large scale distributed application of this kind. Existing proprietary solutions rely on the conventional technologies and 2D representations. Our challenge was to apply the "latest" available technologies, such Java3D, X3D and SOAP, compatible with average computer graphics hardware. The selected technologies are integrated and we demonstrate: the flow of data, which originates from heterogeneous data sources; interoperability across different operating systems and 3D visual representations to enhance the end-users interactions.

  10. 3D Dynamic Earthquake Fracture Simulation (Test Case)

    Korkusuz Öztürk, Yasemin; Meral Özel, Nurcan; Ando, Ryosuke

    2016-04-01

    A 3D dynamic earthquake fracture simulation is being developed for the fault structures which are non-planar to understand heterogeneous stress states in the Marmara Sea. Locating in a seismic gap, a large earthquake is expected in the center of the Sea of Marmara. Concerning the fact that more than 14 million inhabitants of İstanbul, located very closely to the Marmara Sea, the importance of the analysis of the Central Marmara Sea is extremely high. A few 3D dynamic earthquake fracture studies have been already done in the Sea of Marmara for pure right lateral strike-slip stress regimes (Oglesby and Mai, 2012; Aochi and Ulrich, 2015). In this study, a 3D dynamic earthquake fracture model with heterogeneous stress patches from the TPV5, a SCEC code validation case, is adapted. In this test model, the fault and the ground surfaces are gridded by a scalene triangulation technique using GMSH program. For a grid size changing between 0.616 km and 1.050 km the number of elements for the fault surface is 1984 and for the ground surface is 1216. When these results are compared with Kaneko's results for TPV5 from SPECFEM3D, reliable findings could be observed for the first 6.5 seconds (stations on the fault) although a stability problem is encountered after this time threshold. To solve this problem grid sizes are made smaller, so the number of elements increase 7986 for the fault surface and 4867 for the ground surface. On the other hand, computational problems arise in that case, since the computation time is directly proportional to the number of total elements and the required memory also increases with the square of that. Therefore, it is expected that this method can be adapted for less coarse grid cases, regarding the main difficulty coming from the necessity of an effective supercomputer and run time limitations. The main objective of this research is to obtain 3D dynamic earthquake rupture scenarios, concerning not only planar and non-planar faults but also

  11. Bioimpedance monitoring of 3D cell culturing-Complementary electrode configurations for enhanced spatial sensitivity

    Canali, Chiara; Heiskanen, Arto; Muhammad, Haseena Bashir;

    2015-01-01

    configurations. By switching between the different combinations of electrode couples, it was possible to generate a multiplexing-like approach, which allowed for collecting spatially distributed information within the 3D space. Computational finite element (FE) analysis and electrochemical impedance...... at the corners of the 3D culture chamber. By combining a number of electrode configurations, complementary spatially distributed information on a large 3D cell culture can be obtained with maximised sensitivity in the entire 3D space. The experimental results show that cell proliferation can be monitored within...... spectroscopic (EIS) characterisation were used to determine the configurations' sensitivity field localisation. The 2T setup gives insight into the interfacial phenomena at both electrode surfaces and covers the central part of the 3D cell culture volume, while the four 3T modes provide focus on the dynamics...

  12. Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture

    Han, Ju; Chang, Hang; Giricz, Orsi; Lee, Genee; Baehner, Frederick; Gray, Joe; Bissell, Mina; Kenny, Paraic; Parvin, Bahram

    2010-02-01

    Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype). Next, associations with molecular features were realized through (i) differential analysis within each morphological cluster, and (ii) regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPAR? has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPAR? has been validated through two supporting biological assays.

  13. Molecular predictors of 3D morphogenesis by breast cancer cell lines in 3D culture.

    Ju Han

    2010-02-01

    Full Text Available Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype. Next, associations with molecular features were realized through (i differential analysis within each morphological cluster, and (ii regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPARgamma has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPARgamma has been validated through two supporting biological assays.

  14. Scaling in Gravitational Clustering, 2D and 3D Dynamics

    Munshi, D; Melott, A L; Schäffer, R

    1999-01-01

    Perturbation Theory (PT) applied to a cosmological density field with Gaussian initial fluctuations suggests a specific hierarchy for the correlation functions when the variance is small. In particular quantitative predictions have been made for the moments and the shape of the one-point probability distribution function (PDF) of the top-hat smoothed density. In this paper we perform a series of systematic checks of these predictions against N-body computations both in 2D and 3D with a wide range of featureless power spectra. In agreement with previous studies, we found that the reconstructed PDF-s work remarkably well down to very low probabilities, even when the variance approaches unity. Our results for 2D reproduce the features for the 3D dynamics. In particular we found that the PT predictions are more accurate for spectra with less power on small scales. The nonlinear regime has been explored with various tools, PDF-s, moments and Void Probability Function (VPF). These studies have been done with unprec...

  15. Modeling Tree Crown Dynamics with 3D Partial Differential Equations

    Robert eBeyer

    2014-07-01

    Full Text Available We characterize a tree's spatial foliage distribution by the local leaf area density. Considering this spatially continuous variable allows to describe the spatiotemporal evolution of the tree crown by means of 3D partial differential equations. These offer a framework to rigorously take locally and adaptively acting effects into account, notably the growth towards light. Biomass production through photosynthesis and the allocation to foliage and wood are readily included in this model framework. The system of equations stands out due to its inherent dynamic property of self-organization and spontaneous adaptation, generating complex behavior from even only a few parameters. The density-based approach yields spatially structured tree crowns without relying on detailed geometry. We present the methodological fundamentals of such a modeling approach and discuss further prospects and applications.

  16. Bioimpedance monitoring of 3D cell culturing--complementary electrode configurations for enhanced spatial sensitivity.

    Canali, Chiara; Heiskanen, Arto; Muhammad, Haseena Bashir; Høyum, Per; Pettersen, Fred-Johan; Hemmingsen, Mette; Wolff, Anders; Dufva, Martin; Martinsen, Ørjan Grøttem; Emnéus, Jenny

    2015-01-15

    A bioimpedance platform is presented as a promising tool for non-invasive real-time monitoring of the entire process of three-dimensional (3D) cell culturing in a hydrogel scaffold. In this study, the dynamics involved in the whole process of 3D cell culturing, starting from polymerisation of a bare 3D gelatin scaffold, to human mesenchymal stem cell (MSC) encapsulation and proliferation, was monitored over time. The platform consists of a large rectangular culture chamber with four embedded vertical gold plate electrodes that were exploited in two- and three terminal (2T and 3T) measurement configurations. By switching between the different combinations of electrode couples, it was possible to generate a multiplexing-like approach, which allowed for collecting spatially distributed information within the 3D space. Computational finite element (FE) analysis and electrochemical impedance spectroscopic (EIS) characterisation were used to determine the configurations' sensitivity field localisation. The 2T setup gives insight into the interfacial phenomena at both electrode surfaces and covers the central part of the 3D cell culture volume, while the four 3T modes provide focus on the dynamics at the corners of the 3D culture chamber. By combining a number of electrode configurations, complementary spatially distributed information on a large 3D cell culture can be obtained with maximised sensitivity in the entire 3D space. The experimental results show that cell proliferation can be monitored within the tested biomimetic environment, paving the way to further developments in bioimpedance tracking of 3D cell cultures and tissue engineering. PMID:25058941

  17. 3D Reconstruction of Coronary Artery Vascular Smooth Muscle Cells.

    Tong Luo

    Full Text Available The 3D geometry of individual vascular smooth muscle cells (VSMCs, which are essential for understanding the mechanical function of blood vessels, are currently not available. This paper introduces a new 3D segmentation algorithm to determine VSMC morphology and orientation.A total of 112 VSMCs from six porcine coronary arteries were used in the analysis. A 3D semi-automatic segmentation method was developed to reconstruct individual VSMCs from cell clumps as well as to extract the 3D geometry of VSMCs. A new edge blocking model was introduced to recognize cell boundary while an edge growing was developed for optimal interpolation and edge verification. The proposed methods were designed based on Region of Interest (ROI selected by user and interactive responses of limited key edges. Enhanced cell boundary features were used to construct the cell's initial boundary for further edge growing. A unified framework of morphological parameters (dimensions and orientations was proposed for the 3D volume data. Virtual phantom was designed to validate the tilt angle measurements, while other parameters extracted from 3D segmentations were compared with manual measurements to assess the accuracy of the algorithm. The length, width and thickness of VSMCs were 62.9±14.9 μm, 4.6±0.6 μm and 6.2±1.8 μm (mean±SD. In longitudinal-circumferential plane of blood vessel, VSMCs align off the circumferential direction with two mean angles of -19.4±9.3° and 10.9±4.7°, while an out-of-plane angle (i.e., radial tilt angle was found to be 8±7.6° with median as 5.7°.A 3D segmentation algorithm was developed to reconstruct individual VSMCs of blood vessel walls based on optical image stacks. The results were validated by a virtual phantom and manual measurement. The obtained 3D geometries can be utilized in mathematical models and leads a better understanding of vascular mechanical properties and function.

  18. Fabrication and optimization of alginate hydrogel constructs for use in 3D neural cell culture

    Two-dimensional (2D) culture systems provide useful information about many biological processes. However, some applications including tissue engineering, drug transport studies, and analysis of cell growth and dynamics are better studied using three-dimensional (3D) culture systems. 3D culture systems can potentially offer higher degrees of organization and control of cell growth environments, more physiologically relevant diffusion characteristics, and permit the formation of more extensive 3D networks of cell-cell interactions. A 3D culture system has been developed using alginate as a cell scaffold, capable of maintaining the viability and function of a variety of neural cell types. Alginate was functionalized by the covalent attachment of a variety of whole proteins and peptide epitopes selected to provide sites for cell attachment. Alginate constructs were used to entrap a variety of neural cell types including astroglioma cells, astrocytes, microglia and neurons. Neural cells displayed process outgrowth over time in culture. Cell-seeded scaffolds were characterized in terms of their biochemical and biomechanical properties, effects on seeded neural cells, and suitability for use as 3D neural cell culture models.

  19. Fabrication and optimization of alginate hydrogel constructs for use in 3D neural cell culture

    Frampton, J P; Hynd, M R; Shain, W [Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY 12210 (United States); Shuler, M L, E-mail: jf7674@albany.edu [Department of Biomedical Engineering, 270 Olin Hall, Cornell University, Ithaca, NY 14850 (United States)

    2011-02-15

    Two-dimensional (2D) culture systems provide useful information about many biological processes. However, some applications including tissue engineering, drug transport studies, and analysis of cell growth and dynamics are better studied using three-dimensional (3D) culture systems. 3D culture systems can potentially offer higher degrees of organization and control of cell growth environments, more physiologically relevant diffusion characteristics, and permit the formation of more extensive 3D networks of cell-cell interactions. A 3D culture system has been developed using alginate as a cell scaffold, capable of maintaining the viability and function of a variety of neural cell types. Alginate was functionalized by the covalent attachment of a variety of whole proteins and peptide epitopes selected to provide sites for cell attachment. Alginate constructs were used to entrap a variety of neural cell types including astroglioma cells, astrocytes, microglia and neurons. Neural cells displayed process outgrowth over time in culture. Cell-seeded scaffolds were characterized in terms of their biochemical and biomechanical properties, effects on seeded neural cells, and suitability for use as 3D neural cell culture models.

  20. Coupling of the computational fluid dynamics code ANSYS CFX with the 3D neutron kinetic core model DYN3D

    The computational fluid dynamics code ANSYS CFX has been coupled with the neutron-kinetic core model DYN3D. ANSYS CFX calculates the fluid dynamics and related transport phenomena in the reactors coolant and provides the corresponding data to DYN3D. In the fluid flow simulation of the coolant, the core itself is modeled within the porous body approach. DYN3D calculates the neutron kinetics and the fuel behavior including the heat transfer to the coolant. The physical data interface between the codes is the volumetric heat release rate into the coolant. In the prototype that is currently available, the coupling is restricted to single-phase flow problems. In the time domain an explicit coupling of the codes has been implemented so far. Steady-state and transient verification calculations for two small-size test problems confirm the correctness of the implementation of the prototype coupling. The first test problem was a mini-core consisting of nine real-size fuel assemblies with quadratic cross section. Comparison was performed with the DYN3D stand-alone code. In the steady state, the effective multiplication factor obtained by the DYN3D/ANSYS CFX codes hows a deviation of 9.8 pcm from the DYN3D stand-alone solution. This difference can be attributed to the use of different water property packages in the two codes. The transient test case simulated the withdrawal of the control rod from the central fuel assembly at hot zero power in the same mini-core. Power increase during the introduction of positive reactivity and power reduction due to fuel temperature increase are calculated in the same manner by the coupled and the stand-alone codes. The maximum values reached during the power rise differ by about 1 MW at a power level of 50 MW. Beside the different water property packages, these differences are caused by the use of different flow solvers. The same calculations were carried for a mini-core with seven real-size fuel assemblies with hexagonal cross section in

  1. A novel mechanotactic 3D modeling of cell morphology

    Cell morphology plays a critical role in many biological processes, such as cell migration, tissue development, wound healing and tumor growth. Recent investigations demonstrate that, among other stimuli, cells adapt their shapes according to their substrate stiffness. Until now, the development of this process has not been clear. Therefore, in this work, a new three-dimensional (3D) computational model for cell morphology has been developed. This model is based on a previous cell migration model presented by the same authors. The new model considers that during cell–substrate interaction, cell shape is governed by internal cell deformation, which leads to an accurate prediction of the cell shape according to the mechanical characteristic of its surrounding micro-environment. To study this phenomenon, the model has been applied to different numerical cases. The obtained results, which are qualitatively consistent with well-known related experimental works, indicate that cell morphology not only depends on substrate stiffness but also on the substrate boundary conditions. A cell located within an unconstrained soft substrate (several kPa) with uniform stiffness is unable to adhere to its substrate or to send out pseudopodia. When the substrate stiffness increases to tens of kPa (intermediate and rigid substrates), the cell can adequately adhere to its substrate. Subsequently, as the traction forces exerted by the cell increase, the cell elongates and its shape changes. Within very stiff (hard) substrates, the cell cannot penetrate into its substrate or send out pseudopodia. On the other hand, a cell is found to be more elongated within substrates with a constrained surface. However, this elongation decreases when the cell approaches it. It can be concluded that the higher the net traction force, the greater the cell elongation, the larger the cell membrane area, and the less random the cell alignment. (paper)

  2. Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming.

    Krijger, Peter Hugo Lodewijk; Di Stefano, Bruno; de Wit, Elzo; Limone, Francesco; van Oevelen, Chris; de Laat, Wouter; Graf, Thomas

    2016-05-01

    Forced expression of reprogramming factors can convert somatic cells into induced pluripotent stem cells (iPSCs). Here we studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale topologically associated domain (TAD) repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic-cell-specific genome structures while establishing an embryonic stem-cell-like 3D genome. Yet, early passage iPSCs carry topological hallmarks that enable recognition of their cell of origin. These hallmarks are not remnants of somatic chromosome topologies. Instead, the distinguishing topological features are acquired during reprogramming, as we also find for cell-of-origin-dependent gene expression patterns. PMID:26971819

  3. Self-Assembled Peptide Gels for 3D Cell Culture

    Tang, Claire

    2010-01-01

    Under specific conditions short peptides modified with an N-terminal fluorenyl-9-methoxycarbonyl (Fmoc) group can self-assemble into hydrogel scaffolds similar in properties to the natural extracellular matrix. Fmoc-diphenylalanine (Fmoc-FF) for instance, has been shown to form hydrogels at physiological pH that have the ability to support 2D and 3D cell culture. The aim of this investigation is to provide further understanding of the self-assembly mechanism of such systems in order to progre...

  4. Surface modified alginate microcapsules for 3D cell culture

    Chen, Yi-Wen; Kuo, Chiung Wen; Chueh, Di-Yen; Chen, Peilin

    2016-06-01

    Culture as three dimensional cell aggregates or spheroids can offer an ideal platform for tissue engineering applications and for pharmaceutical screening. Such 3D culture models, however, may suffer from the problems such as immune response and ineffective and cumbersome culture. This paper describes a simple method for producing microcapsules with alginate cores and a thin shell of poly(L-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG) to encapsulate mouse induced pluripotent stem (miPS) cells, generating a non-fouling surface as an effective immunoisolation barrier. We demonstrated the trapping of the alginate microcapsules in a microwell array for the continuous observation and culture of a large number of encapsulated miPS cells in parallel. miPS cells cultured in the microcapsules survived well and proliferated to form a single cell aggregate. Droplet formation of monodisperse microcapsules with controlled size combined with flow cytometry provided an efficient way to quantitatively analyze the growth of encapsulated cells in a high-throughput manner. The simple and cost-effective coating technique employed to produce the core-shell microcapsules could be used in the emerging field of cell therapy. The microwell array would provide a convenient, user friendly and high-throughput platform for long-term cell culture and monitoring.

  5. Quasi-3d aerodynamic code for analyzing dynamic flap response

    Ramos García, Néstor; Sørensen, Jens Nørkær; Shen, Wen Zhong

    2011-01-01

    A computational model for predicting the aerodynamic behavior of wind turbine airfoil profiles subjected to steady and unsteady motions has been developed. The model is based on a viscous-inviscid interaction technique using strong coupling between the viscous and inviscid parts. The inviscid part is modeled using a panel method whereas the viscous part is modeled by using the integral form of the the laminar and turbulent boundary layer equations and with extensions for 3-D rotational effect...

  6. Finding Apparent Horizons in Dynamic 3D Numerical Spacetimes

    Anninos, P.; Camarda, K.; Libson, J.; Masso, J.; Seidel, E; Suen, W.

    1996-01-01

    We have developed a general method for finding apparent horizons in 3D numerical relativity. Instead of solving for the partial differential equation describing the location of the apparent horizons, we expand the closed 2D surfaces in terms of symmetric trace--free tensors and solve for the expansion coefficients using a minimization procedure. Our method is applied to a number of different spacetimes, including numerically constructed spacetimes containing highly distorted axisymmetric blac...

  7. DREAM3D simulations of inner-belt dynamics

    Cunningham, Gregory Scott [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-05-26

    A 1973 paper by Lyons and Thorne explains the two-belt structure for electrons in the inner magnetosphere as a balance between inward radial diffusion and loss to the atmosphere, where the loss to the atmosphere is enabled by pitch-angle scattering from Coulomb and wave-particle interactions. In the 1973 paper, equilibrium solutions to a decoupled set of 1D radial diffusion equations, one for each value of the first invariant of motion, μ, were computed to produce the equilibrium two-belt structure. Each 1D radial diffusion equation incorporated an L-and μ-dependent `lifetime' due to the Coulomb and wave-particle interactions. This decoupling of the problem is appropriate under the assumption that radial diffusion is slow in comparison to pitch-angle scattering. However, for some values of μ and L the lifetime associated with pitch-angle scattering is comparable to the timescale associated with radial diffusion, suggesting that the true equilibrium solutions might reflect `coupled modes' involving pitch-angle scattering and radial diffusion and thus requiring a 3D diffusion model. In the work we show here, we have computed the equilibrium solutions using our 3D diffusion model, DREAM3D, that allows for such coupling. We find that the 3D equilibrium solutions are quite similar to the solutions shown in the 1973 paper when we use the same physical models for radial diffusion and pitch-angle scattering from hiss. However, we show that the equilibrium solutions are quite sensitive to various aspects of the physics model employed in the 1973 paper that can be improved, suggesting that additional work needs to be done to understand the two-belt structure.

  8. Enhanced 3D fluorescence live cell imaging on nanoplasmonic substrate

    Gartia, Manas Ranjan [Department of Nuclear, Plasma and Radiological Engineering, University of Illinois, Urbana, IL 61801 (United States); Hsiao, Austin; Logan Liu, G [Department of Bioengineering, University of Illinois, Urbana, IL 61801 (United States); Sivaguru, Mayandi [Institute for Genomic Biology, University of Illinois, Urbana, IL 61801 (United States); Chen Yi, E-mail: loganliu@illinois.edu [Department of Electrical and Computer Engineering, University of Illinois, Urbana, IL 61801 (United States)

    2011-09-07

    We have created a randomly distributed nanocone substrate on silicon coated with silver for surface-plasmon-enhanced fluorescence detection and 3D cell imaging. Optical characterization of the nanocone substrate showed it can support several plasmonic modes (in the 300-800 nm wavelength range) that can be coupled to a fluorophore on the surface of the substrate, which gives rise to the enhanced fluorescence. Spectral analysis suggests that a nanocone substrate can create more excitons and shorter lifetime in the model fluorophore Rhodamine 6G (R6G) due to plasmon resonance energy transfer from the nanocone substrate to the nearby fluorophore. We observed three-dimensional fluorescence enhancement on our substrate shown from the confocal fluorescence imaging of chinese hamster ovary (CHO) cells grown on the substrate. The fluorescence intensity from the fluorophores bound on the cell membrane was amplified more than 100-fold as compared to that on a glass substrate. We believe that strong scattering within the nanostructured area coupled with random scattering inside the cell resulted in the observed three-dimensional enhancement in fluorescence with higher photostability on the substrate surface.

  9. 3D numerical simulations of vesicle and inextensible capsule dynamics

    Farutin, Alexander; Biben, Thierry; Misbah, Chaouqi

    2014-10-01

    Vesicles are locally-inextensible fluid membranes, capsules are endowed with in-plane shear elasticity mimicking the cytoskeleton of red blood cells (RBCs), but are extensible, while RBCs are inextensible. We use boundary integral (BI) methods based on the Green function techniques to model and solve numerically their dynamics. We regularize the single layer integral by subtraction of exact identities for the terms involving the normal and the tangential components of the force. The stability and precision of BI calculation is enhanced by taking advantage of additional quadrature nodes located in vertices of an auxiliary mesh, constructed by a standard refinement procedure from the main mesh. We extend the partition of unity technique to boundary integral calculation on triangular meshes. The proposed algorithm offers the same treatment of near-singular integration regardless whether the source and the target points belong to the same surface or not. Bending forces are calculated by using expressions derived from differential geometry. Membrane incompressibility is handled by using two penalization parameters per suspended entity: one for deviation of the global area from prescribed value and another for the sum of squares of local strains defined on each vertex. Extensible or inextensible capsules, a model of RBC, are studied by storing the position in the reference configuration for each vertex. The elastic force is then calculated by direct variation of the elastic energy. Various nonequilibrium physical examples on vesicles and capsules will be presented and the convergence and precision tests highlighted. Overall, a good convergence is observed with numerical error inversely proportional to the number of vertices used for surface discretization, the highest order of convergence allowed by piece-wise linear interpolation of the surface.

  10. Quasi-3d aerodynamic code for analyzing dynamic flap response

    Ramos García, Néstor

    is modeled using a panel method whereas the viscous part is modeled by using the integral form of the the laminar and turbulent boundary layer equations and with extensions for 3-D rotational effects. Laminar to turbulent transition can be forced with a boundary layer trip or computed with a modified...... reduced frequencies and oscillation amplitudes, and generally a good agreement is obtained. The capability of the code to simulate a trailing edge flap under steady or unsteady flow conditions has been proven. A parametric study on rotational effects induced by Coriolis and centrifugal forces in the......A computational model for predicting the aerodynamic behavior of wind turbine airfoil profiles subjected to steady and unsteady motions has been developed. The model is based on a viscous-inviscid interaction technique using strong coupling between the viscous and inviscid parts. The inviscid part...

  11. Computational Modelling of Piston Ring Dynamics in 3D

    Dlugoš Jozef

    2014-12-01

    Full Text Available Advanced computational models of a piston assembly based on the level of virtual prototypes require a detailed description of piston ring behaviour. Considering these requirements, the piston rings operate in regimes that cannot, in general, be simplified into an axisymmetric model. The piston and the cylinder liner do not have a perfect round shape, mainly due to machining tolerances and external thermo-mechanical loads. If the ring cannot follow the liner deformations, a local loss of contact occurs resulting in blow-by and increased consumption of lubricant oil in the engine. Current computational models are unable to implement such effects. The paper focuses on the development of a flexible 3D piston ring model based on the Timoshenko beam theory using the multibody system (MBS. The MBS model is compared to the finite element method (FEM solution.

  12. Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations

    Jung, Jaewoon; Kobayashi, Chigusa; Imamura, Toshiyuki; Sugita, Yuji

    2016-03-01

    Three-dimensional Fast Fourier Transform (3D FFT) plays an important role in a wide variety of computer simulations and data analyses, including molecular dynamics (MD) simulations. In this study, we develop hybrid (MPI+OpenMP) parallelization schemes of 3D FFT based on two new volumetric decompositions, mainly for the particle mesh Ewald (PME) calculation in MD simulations. In one scheme, (1d_Alltoall), five all-to-all communications in one dimension are carried out, and in the other, (2d_Alltoall), one two-dimensional all-to-all communication is combined with two all-to-all communications in one dimension. 2d_Alltoall is similar to the conventional volumetric decomposition scheme. We performed benchmark tests of 3D FFT for the systems with different grid sizes using a large number of processors on the K computer in RIKEN AICS. The two schemes show comparable performances, and are better than existing 3D FFTs. The performances of 1d_Alltoall and 2d_Alltoall depend on the supercomputer network system and number of processors in each dimension. There is enough leeway for users to optimize performance for their conditions. In the PME method, short-range real-space interactions as well as long-range reciprocal-space interactions are calculated. Our volumetric decomposition schemes are particularly useful when used in conjunction with the recently developed midpoint cell method for short-range interactions, due to the same decompositions of real and reciprocal spaces. The 1d_Alltoall scheme of 3D FFT takes 4.7 ms to simulate one MD cycle for a virus system containing more than 1 million atoms using 32,768 cores on the K computer.

  13. Results of comparative RBMK neutron computation using VNIIEF codes (cell computation, 3D statics, 3D kinetics). Final report

    In conformity with the protocol of the Workshop under Contract open-quotes Assessment of RBMK reactor safety using modern Western Codesclose quotes VNIIEF performed a neutronics computation series to compare western and VNIIEF codes and assess whether VNIIEF codes are suitable for RBMK type reactor safety assessment computation. The work was carried out in close collaboration with M.I. Rozhdestvensky and L.M. Podlazov, NIKIET employees. The effort involved: (1) cell computations with the WIMS, EKRAN codes (improved modification of the LOMA code) and the S-90 code (VNIIEF Monte Carlo). Cell, polycell, burnup computation; (2) 3D computation of static states with the KORAT-3D and NEU codes and comparison with results of computation with the NESTLE code (USA). The computations were performed in the geometry and using the neutron constants presented by the American party; (3) 3D computation of neutron kinetics with the KORAT-3D and NEU codes. These computations were performed in two formulations, both being developed in collaboration with NIKIET. Formulation of the first problem maximally possibly agrees with one of NESTLE problems and imitates gas bubble travel through a core. The second problem is a model of the RBMK as a whole with imitation of control and protection system controls (CPS) movement in a core

  14. File list: Pol.ALL.20.Polr3d.AllCell [Chip-atlas[Archive

    Full Text Available Pol.ALL.20.Polr3d.AllCell mm9 RNA polymerase Polr3d All cell types SRX301459,SRX373...73041 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.ALL.20.Polr3d.AllCell.bed ...

  15. File list: Pol.ALL.05.Polr3d.AllCell [Chip-atlas[Archive

    Full Text Available Pol.ALL.05.Polr3d.AllCell mm9 RNA polymerase Polr3d All cell types SRX373040,SRX373...04148 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.ALL.05.Polr3d.AllCell.bed ...

  16. File list: Pol.ALL.50.Polr3d.AllCell [Chip-atlas[Archive

    Full Text Available Pol.ALL.50.Polr3d.AllCell mm9 RNA polymerase Polr3d All cell types SRX301459,SRX373...04147 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.ALL.50.Polr3d.AllCell.bed ...

  17. File list: Pol.ALL.10.Polr3d.AllCell [Chip-atlas[Archive

    Full Text Available Pol.ALL.10.Polr3d.AllCell mm9 RNA polymerase Polr3d All cell types SRX373040,SRX301...04147 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.ALL.10.Polr3d.AllCell.bed ...

  18. Controlling Shear Stress in 3D Bioprinting is a Key Factor to Balance Printing Resolution and Stem Cell Integrity.

    Blaeser, Andreas; Duarte Campos, Daniela Filipa; Puster, Uta; Richtering, Walter; Stevens, Molly M; Fischer, Horst

    2016-02-01

    A microvalve-based bioprinting system for the manufacturing of high-resolution, multimaterial 3D-structures is reported. Applying a straightforward fluid-dynamics model, the shear stress at the nozzle site can precisely be controlled. Using this system, a broad study on how cell viability and proliferation potential are affected by different levels of shear stress is conducted. Complex, multimaterial 3D structures are printed with high resolution. This work pioneers the investigation of shear stress-induced cell damage in 3D bioprinting and might help to comprehend and improve the outcome of cell-printing studies in the future. PMID:26626828

  19. Introducing a new 3D dynamical model for barred galaxies

    Jung, Christof

    2015-01-01

    The regular or chaotic dynamics of an analytical realistic three dimensional model composed of a spherically symmetric central nucleus, a bar and a flat disk is investigated. For describing the properties of the bar we introduce a new simple dynamical model and we explore the influence on the character of orbits of all the involved parameters of it, such as the mass and the scale length of the bar, the major semi-axis and the angular velocity of the bar as well as the energy. Regions of phase space with ordered and chaotic motion are identified in dependence on these parameters and for breaking the rotational symmetry. First we study in detail the dynamics in the invariant plane $z = p_z = 0$ using the Poincar\\'e map as a basic tool and then we study the full 3 dimensional case using the SALI method as principal tool for distinguishing between order and chaos. We also present strong evidence obtained through the numerical simulations that our new bar model can realistically describe the formation and the evol...

  20. Uncovering cancer cell behavioral phenotype in 3-D in vitro metastatic landscapes

    Liu, Liyu; Sun, Bo; Duclos, Guillaume; Kam, Yoonseok; Gatenby, Robert; Stone, Howard; Austin, Robert

    2012-02-01

    One well-known fact is that cancer cell genetics determines cell metastatic potentials. However, from a physics point of view, genetics as cell properties cannot directly act on metastasis. An agent is needed to unscramble the genetics first before generating dynamics for metastasis. Exactly this agent is cell behavioral phenotype, which is rarely studied due to the difficulties of real-time cell tracking in in vivo tissue. Here we have successfully constructed a micro in vitro environment with collagen based Extracellular Matrix (ECM) structures for cell 3-D metastasis. With stable nutrition (glucose) gradient inside, breast cancer cell MDA-MB-231 is able to invade inside the collagen from the nutrition poor site towards the nutrition rich site. Continuous confocal microscopy captures images of the cells every 12 hours and tracks their positions in 3-D space. The micro fluorescent beads pre-mixed inside the ECM demonstrate that invasive cells have altered the structures through mechanics. With the observation and the analysis of cell collective behaviors, we argue that game theory may exist between the pioneering cells and their followers in the metastatic cell group. The cell collaboration may explain the high efficiency of metastasis.

  1. Characterizations of individual mouse red blood cells parasitized by Babesia microti using 3-D holographic microscopy

    Park, HyunJoo; Kim, Kyoohyun; Cho, Shin-Hyeong; Lee, Won-Ja; Kim, Youngchan; Lee, SangEun; Park, YongKeun

    2015-01-01

    Babesia microti causes emergency human babesiosis. However, little is known about the alterations in B. microti invaded red blood cells (Bm-RBCs) at the individual cell level. Through quantitative phase imaging techniques based on laser interferometry, we present the simultaneous measurements of structural, chemical, and mechanical modifications in individual mouse Bm-RBCs. 3-D refractive index maps of individual RBCs and in situ parasite vacuoles are imaged, from which total contents and concentration of dry mass are also precisely quantified. In addition, we examine the dynamic membrane fluctuation of Bm-RBCs, which provide information on cell membrane deformability.

  2. Development of a version of the reactor dynamics code DYN3D applicable for High Temperature Reactors; Entwicklung einer Version des Reaktordynamikcodes DYN3D fuer Hochtemperaturreaktoren. Abschlussbericht

    Rohde, Ulrich; Apanasevich, Pavel; Baier, Silvio; Duerigen, Susan; Fridman, Emil; Grahn, Alexander; Kliem, Soeren; Merk, Bruno

    2012-07-15

    Based on the reactor dynamics code DYN3D for the simulation of transient processes in Light Water Reactors, a code version DYN3D-HTR for application to graphitemoderated, gas-cooled block-type high temperature reactors has been developed. This development comprises: - the methodical improvement of the 3D steady-state neutron flux calculation for the hexagonal geometry of the HTR fuel element blocks - the development of methods for the generation of homogenised cross section data taking into account the double heterogeneity of the fuel element block structure - the implementation of a 3D model for heat conduction and heat transport in the graphite matrix. The nodal method for neutron flux calculation based on SP3 transport approximation was extended to hexagonal fuel element geometry, where the hexagons are subdivided into triangles, thus the method had finally to be derived for triangular geometry. In triangular geometry, a subsequent subdivision of the hexagonal elements can be considered, and therefore, the effect of systematic mesh refinement can be studied. The algorithm was verified by comparison with Monte Carlo reference solutions, on the node-wise level, as well as also on the pin-wise level. New procedures were developed for the homogenization of the double-heterogeneous fuel element structures. One the one hand, the so-called Reactivity equivalent Physical Transformation (RPT), the two-step homogenization method based on 2D deterministic lattice calculations, was extended to cells with different temperatures of the materials. On the other hand, the progress in development of Monte Carlo methods for spectral calculations, in particular the development of the code SERPENT, opened a new, fully consistent 3D approach, where all details of the structures on fuel particle, fuel compact and fuel block level can be taken into account within one step. Moreover, a 3D heat conduction and heat transport model was integrated into DYN3D to be able to simulate radial

  3. 3D Printing of Scaffold for Cells Delivery: Advances in Skin Tissue Engineering

    Deepti Singh

    2016-01-01

    Full Text Available Injury or damage to tissue and organs is a major health problem, resulting in about half of the world’s annual healthcare expenditure every year. Advances in the fields of stem cells (SCs and biomaterials processing have provided a tremendous leap for researchers to manipulate the dynamics between these two, and obtain a skin substitute that can completely heal the wounded areas. Although wound healing needs a coordinated interplay between cells, extracellular proteins and growth factors, the most important players in this process are the endogenous SCs, which activate the repair cascade by recruiting cells from different sites. Extra cellular matrix (ECM proteins are activated by these SCs, which in turn aid in cellular migrations and finally secretion of growth factors that can seal and heal the wounds. The interaction between ECM proteins and SCs helps the skin to sustain the rigors of everyday activity, and in an attempt to attain this level of functionality in artificial three-dimensional (3D constructs, tissue engineered biomaterials are fabricated using more advanced techniques such as bioprinting and laser assisted printing of the organs. This review provides a concise summary of the most recent advances that have been made in the area of polymer bio-fabrication using 3D bio printing used for encapsulating stem cells for skin regeneration. The focus of this review is to describe, in detail, the role of 3D architecture and arrangement of cells within this system that can heal wounds and aid in skin regeneration.

  4. Gel de plaquetas: arcabouço 3D para cultura celular Platelet gel: 3D scaffold for cell culture

    Andrei Moroz

    2009-01-01

    Full Text Available INTRODUÇÃO: O reparo tissular é o objetivo final da cirurgia. A cultura celular requer arcabouço mecânico que dê suporte ao crescimento celular e difusão dos nutrientes. O uso do plasma rico em plaquetas (PRP como um arcabouço 3D possui diversas vantagens: é material biológico, de fácil absorção pós-transplante, rico em fatores de crescimento, em especial PDGF- ββ e TGF-β que estimula síntese de matriz extracelular na cartilagem. OBJETIVO: Desenvolver arcabouço 3D à base de PRP. MATERIAIS E MÉTODOS: Duas formas foram idealizadas: Sphere e Carpet. Condições estéreis foram utilizadas. O gel de plaquetas permaneceu em cultura celular, observado diariamente em microscópio invertido. RESULTADOS: Ambos arcabouços obtiveram sucesso, com aspectos positivos e negativos. DISCUSSÃO: A forma Sphere não aderiu ao plástico. Observou-se retração do gel e investigação ao microscópio dificultada devido às áreas opacas no campo visual. A forma Carpet não aderiu ao plástico e apresentou-se translúcida. O tempo de estudo foi de 20 dias. CONCLUSÕES: A produção de um arcabouço 3D PRP foi um sucesso, e trata-se de uma alternativa que necessita ser mais utilizado e investigado para que se consolide em uma rota eficiente e confiável na tecnologia de engenharia tissular, particularmente em cultura de tecido cartilaginoso.INTRODUCTION: Tissue repair has been the ultimate goal of surgery. Cell culture requires a mechanical scaffold that supports cell growth and nutrient diffusion. Using platelet-rich plasma (PRP as a 3D scaffold presents various advantages: it is a biological material, easily absorbed after transplantation, rich in growth factors, in particular, PDGF-ββ and TGF-β that stimulate extracellular matrix synthesis in cartilage culture. OBJECTIVE: To develop a PRP 3D scaffold. Material and METHODS: Two forms were idealized: Sphere and Carpet. Sterile conditions were used. The platelet gel remained in culture

  5. Multicellular tumor spheroid models to explore cell cycle checkpoints in 3D

    MultiCellular Tumor Spheroid (MCTS) mimics the organization of a tumor and is considered as an invaluable model to study cancer cell biology and to evaluate new antiproliferative drugs. Here we report how the characteristics of MCTS in association with new technological developments can be used to explore the regionalization and the activation of cell cycle checkpoints in 3D. Cell cycle and proliferation parameters were investigated in Capan-2 spheroids by immunofluorescence staining, EdU incorporation and using cells engineered to express Fucci-red and -green reporters. We describe in details the changes in proliferation and cell cycle parameters during spheroid growth and regionalization. We report the kinetics and regionalized aspects of cell cycle arrest in response to checkpoint activation induced by EGF starvation, lovastatin treatment and etoposide-induced DNA damage. Our data present the power and the limitation of spheroids made of genetically modified cells to explore cell cycle checkpoints. This study paves the way for the investigation of molecular aspects and dynamic studies of the response to novel antiproliferative agents in 3D models

  6. 3D-Printing Crystallographic Unit Cells for Learning Materials Science and Engineering

    Rodenbough, Philip P.; Vanti, William B.; Chan, Siu-Wai

    2015-01-01

    Introductory materials science and engineering courses universally include the study of crystal structure and unit cells, which are by their nature highly visual 3D concepts. Traditionally, such topics are explored with 2D drawings or perhaps a limited set of difficult-to-construct 3D models. The rise of 3D printing, coupled with the wealth of…

  7. Radiobiology goes 3D: How ECM and cell morphology impact on cell survival after irradiation

    Translational research is essential to find new therapeutic approaches to improve cancer patient survival. Despite extensive efforts in preclinical studies, many novel therapies fail to turn out to be translational from bench to beside. Therefore, new models better reflecting the conditions in vivo are needed to generate results, which transfer reliably into the clinic. The use of three-dimensional (3D) cell culture models has provided new emerging insights into the understanding of cellular behavior upon cancer therapies. Interestingly, cells cultured in a 3D extracellular matrix are more radio- and chemoresistant than cells grown under conventional 2D conditions. In this review, we summarize and discuss underlying mechanisms of this phenomenon including integrin-mediated cell-matrix interactions, cell shape, nuclear organization and chromatin structure. Identifying the molecular differences between 2D and 3D cultured cells will offer the opportunity to improve our research and widen our therapeutic possibilities against cancer.

  8. Simulation of Missing Pellet Surface thermal behavior with 3D dynamic gap element

    Most of the fuel performance codes that are able to simulate a multidimensional analysis are used to calculate the radial temperature distribution and perform a multidimensional mechanical analysis based on a one-dimensional (1D) temperature result. The FRAPCON-FRAPTRAN code system incorporates a 1D thermal module and two-dimensional (2D) mechanical module when FEM option is activated. In this method, the multidimensional gap conductance model is not required because one-dimensional thermal analysis is carried out. On the other hand, a gap conductance model for a multi-dimension should be developed in the code to perform a multidimensional thermal analysis. ALCYONE developed by CEA introduces an equivalent heat convection coefficient that represents the multidimensional gap conductance. However, the code does not employ dynamic gap conductance which is a function of gap thickness and gap characteristics in direct. The BISON code, which has been developed by INL (Idaho National Laboratory), employed a thermo-mechanical contact method that is specifically designed for tightly-coupled implicit solutions that employ Jacobian-free solution methods. Owing to tightly-coupled implicit solutions, the BISON code solves gap conductance and gap thickness simultaneously with given boundary conditions. In this paper, 3D dynamic gap element has been proposed to resolve convergence issue and nonlinear characteristic of multidimensional gap conductance. To evaluate 3D dynamic gap element module, 3D thermomechanical module using FORTRAN77 has been implemented incorporating 3D dynamic gap element. To demonstrate effect of 3D dynamic gap element, thermal behavior of missing pellet surface (MPS) has been simulated by the developed module. LWR fuel performance codes should incorporate thermo-mechanical loop to solve gap conductance problem, iteratively. However, gap conductance in multidimensional model is difficult issue owing to its nonlinearity and convergence characteristics. In

  9. 3D-printed microfluidic chips with patterned, cell-laden hydrogel constructs.

    Knowlton, Stephanie; Yu, Chu Hsiang; Ersoy, Fulya; Emadi, Sharareh; Khademhosseini, Ali; Tasoglu, Savas

    2016-01-01

    Three-dimensional (3D) printing offers potential to fabricate high-throughput and low-cost fabrication of microfluidic devices as a promising alternative to traditional techniques which enables efficient design iterations in the development stage. In this study, we demonstrate a single-step fabrication of a 3D transparent microfluidic chip using two alternative techniques: a stereolithography-based desktop 3D printer and a two-step fabrication using an industrial 3D printer based on polyjet technology. This method, compared to conventional fabrication using relatively expensive materials and labor-intensive processes, presents a low-cost, rapid prototyping technique to print functional 3D microfluidic chips. We enhance the capabilities of 3D-printed microfluidic devices by coupling 3D cell encapsulation and spatial patterning within photocrosslinkable gelatin methacryloyl (GelMA). The platform presented here serves as a 3D culture environment for long-term cell culture and growth. Furthermore, we have demonstrated the ability to print complex 3D microfluidic channels to create predictable and controllable fluid flow regimes. Here, we demonstrate the novel use of 3D-printed microfluidic chips as controllable 3D cell culture environments, advancing the applicability of 3D printing to engineering physiological systems for future applications in bioengineering. PMID:27321481

  10. Dynamic echo-planar MR imaging of the diaphragm for a 3D dynamic analysis

    The purpose of this study was to prove the feasibility of 3D reconstructions of the diaphragm during the respiratory cycle using EPI sequences (EPI acquisition, 270 ms/image, on a healthy subject breathing spontaneously and at 0.1 Hz). Continuously recorded respiratory signal allowed for retrospective synchronization with respiratory phases for reconstruction of successive diaphragm surfaces using a specifically designed software. Displacements, area and volume changes of the diaphragm were quantified. Our measurements were comparable with the data in the literature. Reconstructed surfaces allowed in vivo diaphragm dynamic evaluation in terms of displacements, area and volume variations. EPI has adequate spatial and temporal resolution for studying diaphragm dynamics during natural breathing. (orig.)

  11. Dynamic scattering theory for dark-field electron holography of 3D strain fields

    Lubk, Axel; Javon, Elsa; Cherkashin, Nikolay; Reboh, Shay; Gatel, Christophe; HYTCH, Martin

    2014-01-01

    Abstract: Dark-held electron holography maps strain in crystal lattices into reconstructed phases over large fields of view. Here we investigate the details of the lattice strain-reconstructed phase relationship by applying dynamic scattering theory both analytically and numerically. We develop efficient analytic linear projection rules for 3D strain fields, facilitating a straight-forward calculation of reconstructed phases from 3D strained materials. They are used in the following to quanti...

  12. Human disc cells in monolayer vs 3D culture: cell shape, division and matrix formation

    Hanley Edward N

    2000-10-01

    Full Text Available Abstract Background The relationship between cell shape, proliferation, and extracellular matrix (ECM production, important aspects of cell behavior, is examined in a little-studied cell type, the human annulus cell from the intervertebral disc, during monolayer vs three-dimensional (3D culture. Results Three experimental studies showed that cells respond specifically to culture microenvironments by changes in cell shape, mitosis and ECM production: 1 Cell passages showed extensive immunohistochemical evidence of Type I and II collagens only in 3D culture. Chondroitin sulfate and keratan sulfate were abundant in both monolayer and 3D cultures. 2 Cells showed significantly greater proliferation in monolayer in the presence of platelet-derived growth factor compared to cells in 3D. 3 Cells on Matrigel™-coated monolayer substrates became rounded and formed nodular colonies, a finding absent during monolayer growth. Conclusions The cell's in vivo interactions with the ECM can regulate shape, gene expression and other cell functions. The shape of the annulus cell changes markedly during life: the young, healthy disc contains spindle shaped cells and abundant collagen. With aging and degeneration, many cells assume a strikingly different appearance, become rounded and are surrounded by unusual accumulations of ECM products. In vitro manipulation of disc cells provides an experimental window for testing how disc cells from given individuals respond when they are grown in environments which direct cells to have either spindle- or rounded-shapes. In vitro assessment of the response of such cells to platelet-derived growth factor and to Matrigel™ showed a continued influence of cell shape even in the presence of a growth factor stimulus. These findings contribute new information to the important issue of the influence of cell shape on cell behavior.

  13. Detection of In Vivo Dynamic 3-D Motion Patterns in the Wrist Joint

    B. Carelsen; R. Jonges; S.D. Strackee; M. Maas; P. van Kemenade; C.A. Grimbergen; M. van Herk; G.J. Streekstra

    2009-01-01

    We present a method for measurement dynamic in vivo carpal motion patterns. The method consists of a 4-D rotational X-ray (RX) with improved image quality and image processing for accurate detection in vivo wrist motion measurements. Dynamic 3-D imaging yields a number of volume reconstructions of t

  14. Evolution, Interaction, and Intrinsic Properties of Dislocations in Intermetallics: Anisotropic 3D Dislocation Dynamics Approach

    Qian Chen

    2008-08-18

    The generation, motion, and interaction of dislocations play key roles during the plastic deformation process of crystalline solids. 3D Dislocation Dynamics has been employed as a mesoscale simulation algorithm to investigate the collective and cooperative behavior of dislocations. Most current research on 3D Dislocation Dynamics is based on the solutions available in the framework of classical isotropic elasticity. However, due to some degree of elastic anisotropy in almost all crystalline solids, it is very necessary to extend 3D Dislocation Dynamics into anisotropic elasticity. In this study, first, the details of efficient and accurate incorporation of the fully anisotropic elasticity into 3D discrete Dislocation Dynamics by numerically evaluating the derivatives of Green's functions are described. Then the intrinsic properties of perfect dislocations, including their stability, their core properties and disassociation characteristics, in newly discovered rare earth-based intermetallics and in conventional intermetallics are investigated, within the framework of fully anisotropic elasticity supplemented with the atomistic information obtained from the ab initio calculations. Moreover, the evolution and interaction of dislocations in these intermetallics as well as the role of solute segregation are presented by utilizing fully anisotropic 3D dislocation dynamics. The results from this work clearly indicate the role and the importance of elastic anisotropy on the evolution of dislocation microstructures, the overall ductility and the hardening behavior in these systems.

  15. Reprogramming mediated radio-resistance of 3D-grown cancer cells

    In vitro 3D growth of tumors is a new cell culture model that more closely mimics the features of the in vivo environment and is being used increasingly in the field of biological and medical research. It has been demonstrated that cancer cells cultured in 3D matrices are more radio-resistant compared with cells in monolayers. However, the mechanisms causing this difference remain unclear. Here we show that cancer cells cultured in a 3D microenvironment demonstrated an increase in cells with stem cell properties. This was confirmed by the finding that cells in 3D cultures upregulated the gene and protein expression of the stem cell reprogramming factors such as OCT4, SOX2, NANOG, LIN28 and miR-302a, compared with cells in monolayers. Moreover, the expression of β-catenin, a regulating molecule of reprogramming factors, also increased in 3D-grown cancer cells. These findings suggest that cancer cells were reprogrammed to become stem cell-like cancer cells in a 3D growth culture microenvironment. Since cancer stem cell-like cells demonstrate an increased radio-resistance and chemo-resistance, our results offer a new perspective as to why. Our findings shed new light on understanding the features of the 3D growth cell model and its application in basic research into clinical radiotherapy and medicine. (author)

  16. Validation of Continuously Tagged MRI for the Measurement of Dynamic 3D Skeletal Muscle Tissue Deformation

    Moerman, Kevin M; Simms, Ciaran K; Lamerichs, Rolf M; Stoker, Jaap; Nederveen, Aart J

    2016-01-01

    A SPAMM tagged MRI methodology is presented allowing continuous (3.3-3.6 Hz) sampling of 3D dynamic soft tissue deformation using non-segmented 3D acquisitions. The 3D deformation is reconstructed by the combination of 3 mutually orthogonal tagging directions, thus requiring only 3 repeated motion cycles. In addition a fully automatic post-processing framework is presented employing Gabor scale-space and filter-bank analysis for tag extrema segmentation and triangulated surface fitting aided by Gabor filter bank derived surface normals. Deformation is derived following tracking of tag surface triplet triangle intersections. The dynamic deformation measurements were validated using indentation tests (~20 mm deep at 12 mm/s) on a silicone gel soft tissue phantom containing contrasting markers which provide a reference measure of deformation. In addition, the techniques were evaluated in-vivo for dynamic skeletal muscle tissue deformation measurement during indentation of the biceps region of the upper arm in a ...

  17. Hot embossing for fabrication of a microfluidic 3D cell culture platform

    Jeon, Jessie S.; Chung, Seok; Kamm, Roger D.; Charest, Joseph L.

    2011-01-01

    Clinically relevant studies of cell function in vitro require a physiologically-representative microenvironment possessing aspects such as a 3D extracellular matrix (ECM) and controlled biochemical and biophysical parameters. A polydimethylsiloxane (PDMS) microfluidic system with a 3D collagen gel has previously served for analysis of factors inducing different responses of cells in a 3D microenvironment under controlled biochemical and biophysical parameters. In the present study, applying t...

  18. Hot embossing for fabrication of a microfluidic 3D cell culture

    Jeon, Jessie S.; Chung, Seok; Kamm, Roger Dale; Charest, Joseph L.

    2010-01-01

    Clinically relevant studies of cell function in vitro require a physiologically-representative microenvironment possessing aspects such as a 3D extracellular matrix (ECM) and controlled biochemical and biophysical parameters. A polydimethylsiloxane (PDMS) microfluidic system with a 3D collagen gel has previously served for analysis of factors inducing different responses of cells in a 3D microenvironment under controlled biochemical and biophysical parameters. In the present study, applying t...

  19. Static and dynamic stability analysis using 3D-DDA with incision body scheme

    Wang Jianquan; Lin Gao; Liu Jun

    2006-01-01

    Discontinuous deformation analysis (DDA) provides a powerful numerical tool for the analysis of discontinuous media. This method has been widely applied to the 2D analysis of discontinuous deformation. However, it is hindered from analyzing 3D rock engineering problems mainly due to the lack of reliable 3D contact detection algorithms for polyhedra.Contact detection is a key in 3-D DDA analysis. The limitations and advantages of existing contact detection schemes are discussed in this paper, and a new approach, called the incision body (IB), is proposed, taking into account the advantages of the existing methods. A computer code 3DIB, which uses the IB scheme as a 3D contact detection algorithm, was programmed with Visual C++. Static and dynamic stability analysis for three realistic engineering problems has been carried out. Furthermore, the focus is on studying the stability of a gravity dam on jointed rock foundation and dynamic stability of a fractured gravity dam subject to earthquake shaking. The simulation results show that the program 3DIB and incision body scheme are capable of detecting 3D block contacts correctly and hence simulating the open-close and slide process of jointed block masses. In addition, the code 3DIB could provide an effective tool for evaluating the safety of 3D dam structures, which is quite important for engineering problems.

  20. Drug penetration and metabolism in 3D cell cultures treated in a 3D printed fluidic device: assessment of irinotecan via MALDI imaging mass spectrometry.

    LaBonia, Gabriel J; Lockwood, Sarah Y; Heller, Andrew A; Spence, Dana M; Hummon, Amanda B

    2016-06-01

    Realistic in vitro models are critical in the drug development process. In this study, a novel in vitro platform is employed to assess drug penetration and metabolism. This platform, which utilizes a 3D printed fluidic device, allows for dynamic dosing of three dimensional cell cultures, also known as spheroids. The penetration of the chemotherapeutic irinotecan into HCT 116 colon cancer spheroids was examined with MALDI imaging mass spectrometry (IMS). The active metabolite of irinotecan, SN-38, was also detected. After twenty-four hours of treatment, SN-38 was concentrated to the outside of the spheroid, a region of actively dividing cells. The irinotecan prodrug localization contrasted with SN-38 and was concentrated to the necrotic core of the spheroids, a region containing mostly dead and dying cells. These results demonstrate that this unique in vitro platform is an effective means to assess drug penetration and metabolism in 3D cell cultures. This innovative system can have a transformative impact on the preclinical evaluation of drug candidates due to its cost effectiveness and high throughput. PMID:27198560

  1. Impedance Spectroscopic Characterisation of Porosity in 3D Cell Culture Scaffolds with Different Channel Networks

    Canali, Chiara; Mohanty, Soumyaranjan; Heiskanen, Arto;

    2015-01-01

    We present the application of electrochemical impedance spectroscopy (EIS) as a method for discriminating between different polydimethylsiloxane (PDMS) scaffolds for three-dimensional (3D) cell cultures. The validity of EIS characterisation for scaffolds having different degree of porosity...... serve as means of single-frequency measurements for fast scaffold characterization combined with in vitro monitoring of 3D cell cultures....

  2. Final results of the sixth three-dimensional AER dynamic Benchmark problem calculation. Solution of problem with DYN3D and RELAP5-3D codes

    The paper gives a brief survey of the 6th three-dimensional AER dynamic benchmark calculation results received with the codes DYN3D and RELAP5-3D at NRI Rez. This benchmark was defined at the 10th AER Symposium. Its initiating event is a double ended break in the steam line of steam generator No. 1 in a WWER-440/213 plant at the end of the first fuel cycle and in hot full power conditions. Stationary and burnup calculations as well as tuning of initial state before the transient were performed with the code DYN3D. Transient calculations were made with the system code RELAP5-3D. The KASSETA library was used for the generation of reactor core neutronic parameters. The detailed six loops model of NPP Dukovany was adopted for the 6th AER dynamic benchmark purposes. The RELAP5-3D full core neutronic model was connected with 37 coolant channels thermal-hydraulic model of the core, 6-sector nodalization of reactor downcomer, lower and upper plenum was used. Mixing in lower and upper plenum was simulated. The first part of paper contains a brief characteristic of RELAP5 -3D system code and a short description of NPP input deck and reactor core model. The second part shows the time dependencies of important global and local parameters (Authors)

  3. 3D dynamic simulation of crack propagation in extracorporeal shock wave lithotripsy

    Some experimental observations of Shock Wave Lithotripsy(SWL), which include 3D dynamic crack propagation, are simulated with the aim of reproducing fragmentation of kidney stones with SWL. Extracorporeal shock wave lithotripsy (ESWL) is the fragmentation of kidney stones by focusing an ultrasonic pressure pulse onto the stones. 3D models with fine discretization are used to accurately capture the high amplitude shear shock waves. For solving the resulting large scale dynamic crack propagation problem, PDS-FEM is used; it provides numerically efficient failure treatments. With a distributed memory parallel code of PDS-FEM, experimentally observed 3D photoelastic images of transient stress waves and crack patterns in cylindrical samples are successfully reproduced. The numerical crack patterns are in good agreement with the experimental ones, quantitatively. The results shows that the high amplitude shear waves induced in solid, by the lithotriptor generated shock wave, play a dominant role in stone fragmentation.

  4. Intelligent Autonomous Primary 3D Feature Extraction in Vehicle System Dynamics' Analysis: Theory and Application

    Annamária R. Várkonyi-Kóczy

    2008-01-01

    Full Text Available 3D model reconstruction plays a very important role in computer vision as wellas in different engineering applications. The determination of the 3D model from multipleimages is of key importance. One of the most important difficulties in autonomous 3Dreconstruction is the (automatic selection of the ‘significant’ points which carryinformation about the shape of the 3D bodies i.e. are characteristic from the model point ofview. Another problem to be solved is the point correspondence matching in differentimages.In this paper a 3D reconstruction technique is introduced, which is capable to determinethe 3D model of a scene without any external (human intervention. The method is based onrecent results of image processing, epipolar geometry, and intelligent and soft techniques.Possible applications of the presented algorithm in vehicle system dynamics are alsopresented. The results can be applied advantageously at other engineering fields, like carcrashanalysis, robot guiding, object recognition, supervision of 3D scenes, etc,. as well.

  5. On the Dynamic Programming Approach for the 3D Navier-Stokes Equations

    The dynamic programming approach for the control of a 3D flow governed by the stochastic Navier-Stokes equations for incompressible fluid in a bounded domain is studied. By a compactness argument, existence of solutions for the associated Hamilton-Jacobi-Bellman equation is proved. Finally, existence of an optimal control through the feedback formula and of an optimal state is discussed

  6. Simplified 3D model of a PWR reactor vessel using fluid dynamics code ANSYS CFX computational

    This paper presents the results from the calculation of the steady state simulation with model of CFD (computational fluid dynamic) operating under conditions of operation at full power (Hot Full Power). Development and the CFD model results show the usefulness of these codes for calculating 3D of the variable thermohydraulics of these reactors.

  7. Development of 3-D Hydrogel Culture Systems With On-Demand Cell Separation

    Hamilton, Sharon K.; Bloodworth, Nathaniel C.; Massad, Christopher S.; Hammoudi, Taymour M.; Suri, Shalu; Yang, Peter J.; Lu, Hang; Temenoff, Johnna S.

    2013-01-01

    Recently there has been an increased interest in the effects of paracrine signaling between groups of cells, particularly in the context of better understanding how stem cells contribute to tissue repair. Most current 3-D co-culture methods lack the ability to effectively separate 2 cell populations after the culture period, which is important for simultaneously analyzing the reciprocal effects of each cell type on the other. Here, we detail the development of a 3-D hydrogel co-culture system...

  8. Influence of the 3D inverse dynamic method on the joint forces and moments during gait

    Dumas, R; Nicol, E.; Cheze, L.

    2007-01-01

    The joint forces and moments are commonly used in gait analysis. They can be computed by four different 3D inverse dynamic methods proposed in the literature, either based on vectors and Euler angles, wrenches and quaternions, homogeneous matrices, or generalized coordinates and forces. In order to analyze the influence of the inverse dynamic method, the joint forces and moments were computed during gait on nine healthy subjects. A ratio was computed between the relative dispersions (due to t...

  9. Comment on "Numerical Study on Aging Dynamics in the 3D Ising Spin Glass Model"

    Marinari, Enzo; Parisi, Giorgio; Ruiz-Lorenzo, Juan J.

    1999-01-01

    We show that the dynamical behavior of the 3D Ising spin glass with Gaussian couplings is not compatible with a droplet dynamics. We show that this is implied from the data of reference cond-mat/9904143, that, when analyzed in an accurate way, give multiple evidences of this fact. Our study is based on the analysis of the overlap-overlap correlation function, at different values of the separation r and of the time t.

  10. Label free cell tracking in 3D tissue engineering constructs with high resolution imaging

    Smith, W. A.; Lam, K.-P.; Dempsey, K. P.; Mazzocchi-Jones, D.; Richardson, J. B.; Yang, Y.

    2014-02-01

    Within the field of tissue engineering there is an emphasis on studying 3-D live tissue structures. Consequently, to investigate and identify cellular activities and phenotypes in a 3-D environment for all in vitro experiments, including shape, migration/proliferation and axon projection, it is necessary to adopt an optical imaging system that enables monitoring 3-D cellular activities and morphology through the thickness of the construct for an extended culture period without cell labeling. This paper describes a new 3-D tracking algorithm developed for Cell-IQ®, an automated cell imaging platform, which has been equipped with an environmental chamber optimized to enable capturing time-lapse sequences of live cell images over a long-term period without cell labeling. As an integral part of the algorithm, a novel auto-focusing procedure was developed for phase contrast microscopy equipped with 20x and 40x objectives, to provide a more accurate estimation of cell growth/trajectories by allowing 3-D voxels to be computed at high spatiotemporal resolution and cell density. A pilot study was carried out in a phantom system consisting of horizontally aligned nanofiber layers (with precise spacing between them), to mimic features well exemplified in cellular activities of neuronal growth in a 3-D environment. This was followed by detailed investigations concerning axonal projections and dendritic circuitry formation in a 3-D tissue engineering construct. Preliminary work on primary animal neuronal cells in response to chemoattractant and topographic cue within the scaffolds has produced encouraging results.

  11. Dynamic WIFI-Based Indoor Positioning in 3D Virtual World

    Chan, S.; G. Sohn; Wang, L.; Lee, W.

    2013-01-01

    A web-based system based on the 3DTown project was proposed using Google Earth plug-in that brings information from indoor positioning devices and real-time sensors into an integrated 3D indoor and outdoor virtual world to visualize the dynamics of urban life within the 3D context of a city. We addressed limitation of the 3DTown project with particular emphasis on video surveillance camera used for indoor tracking purposes. The proposed solution was to utilize wireless local area net...

  12. Dynamic scattering theory for dark-field electron holography of 3D strain fields.

    Lubk, Axel; Javon, Elsa; Cherkashin, Nikolay; Reboh, Shay; Gatel, Christophe; Hÿtch, Martin

    2014-01-01

    Dark-field electron holography maps strain in crystal lattices into reconstructed phases over large fields of view. Here we investigate the details of the lattice strain-reconstructed phase relationship by applying dynamic scattering theory both analytically and numerically. We develop efficient analytic linear projection rules for 3D strain fields, facilitating a straight-forward calculation of reconstructed phases from 3D strained materials. They are used in the following to quantify the influence of various experimental parameters like strain magnitude, specimen thickness, excitation error and surface relaxation. PMID:24012934

  13. 3D Dislocation dynamics modelling of interactions between prismatic loops and mobile dislocations in pure iron

    Novokshanov, Roman [Department of Materials, University of Oxford, Oxford (United Kingdom)], E-mail: novoksha@maths.ox.ac.uk; Roberts, Steve [Department of Materials, University of Oxford, Oxford (United Kingdom)

    2009-04-30

    3D Dislocation dynamics simulations have been carried out to model the interaction between prismatic loops and dislocations in pure iron subject to uniaxial loading conditions. The primary goal was to understand the mechanism of interaction of an a/2 <1 1 1> interstitial loop and a mobile dislocation. The secondary goal was to investigate the dependence of the critical stress needed for dislocations to overcome the obstacles as a function of size of loops and their orientation with respect to the glide plane. The simulations have shown a complicated 3D interaction resulting in the mobile dislocation bowing around a loop, either reacting with the loop dislocation or leaving it behind unchanged.

  14. 3D wake dynamics of the VAWT: experimental and numerical investigation

    Ferreira, C.; Hofemann, C.; Dixon, K.; Kuik, G. A. M.; Van Bussel, G.J.W.

    2010-01-01

    The Vertical Axis Wind Turbine, in its 2D form, is characterized by a complex unsteady aerodynamic flow, including dynamic stall and blade vortex interaction. Adding to this complexity, the 3D flow causes spanwise effects and the presence of trailing vorticity and tip vortices. The objective of the current paper is to bring insight into the 3D development of the near wake of a H-VAWT, understanding: • The spanwise blade load distribution in the upwind and the downwind blade passages. • The tr...

  15. Screening for Stromal and Matrix Effects in 3D Microenvironments of Breast Cancer Cells

    Montanez-Sauri, Sara I.

    Breast cancer progression ensures through the acquisition of genetic mutations, the uncontrollable growth of cells, and their progression to invasion. Studies have shown that the surrounding three-dimensional (3D) microenvironment can also influence breast cancer cell progression by controlling the morphology, differentiation, proliferation, and migration of cells. However, most of the currently available in vitro screening platforms are based on the two-dimensional (2D) culture of cells, and do not provide cells with the complex 3D microenvironment that exists in vivo. Therefore, there is a need for more biologically relevant in vitro platforms to help decipher the complexity of the microenvironment and its influence in breast cancer. In this dissertation we present an automated microfluidic platform that allows to efficiently screen for the effect of multiple matrix and stromal microenvironment in 3D cultures of breast cancer cells. Several extracellular matrix (ECM) compositions and stromal cells are included in the 3D microenvironments to examine their influence on breast cancer cell behavior. The screening results suggest that collagen gels with fibronectin might be influencing paracrine signals between breast cancer cells and stromal cells. The ability of the platform to culture and treat cells in 3D microenvironments offers a powerful screening tool for the identification of compounds and interactions using more in vivo-like 3D microenvironments. The identification of these mechanisms will increase our current understanding of breast cancer, and will aid in the identification of potential therapeutics.

  16. 3D porous biomimetically modified hydrogels supporting stem cells adhesion

    Studenovská, Hana; Vodička, Petr; Proks, Vladimír; Juhásová, Jana; Motlík, Jan; Rypáček, František

    Dublin : National University of Ireland , 2011. s. 119, psiii-630. [Annual Conference of the European Society for Biomaterials /24./. 04.09.2011-08.09.2011, Dublin] R&D Projects: GA MŠk 1M0538 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z50450515 Keywords : porous hydrogel * cell adhesion * polypeptide Subject RIV: FH - Neurology

  17. Towards high resolution mapping of 3-D mesoscale dynamics from observations

    B. Buongiorno Nardelli

    2012-10-01

    Full Text Available The MyOcean R&D project MESCLA (MEsoSCaLe dynamical Analysis through combined model, satellite and in situ data was devoted to the high resolution 3-D retrieval of tracer and velocity fields in the oceans, based on the combination of in situ and satellite observations and quasi-geostrophic dynamical models. The retrieval techniques were also tested and compared with the output of a primitive equation model, with particular attention to the accuracy of the vertical velocity field as estimated through the Q vector formulation of the omega equation. The project focused on a test case, covering the region where the Gulf Stream separates from the US East Coast. This work demonstrated that innovative methods for the high resolution mapping of 3-D mesoscale dynamics from observations can be used to build the next generations of operational observation-based products.

  18. 3D-Modelling of polycrystalline silicon solar cells

    Dugas, J.; Oualid, J.

    1987-01-01

    This work is concerned with the effect of grain boundaries (gb) on the main parameters which characterize polycrystalline silicon solar cells. The variation with illumination of the grain boundary effective recombination velocity has been calculated by means of a self-consistent procedure which takes into account the bending of the minority carrier quasi-Fermi level in the space-charge region and in the gb quasi-neutral region. Abaci have been plotted which allow to predict the photovoltaic p...

  19. Rapid Assembly of Heterogeneous 3D Cell Microenvironments in a Microgel Array.

    Li, Yiwei; Chen, Pu; Wang, Yachao; Yan, Shuangqian; Feng, Xiaojun; Du, Wei; Koehler, Stephan A; Demirci, Utkan; Liu, Bi-Feng

    2016-05-01

    Heterogeneous 3D cell microenvironment arrays are rapidly assembled by combining surface-wettability-guided assembly and microdroplet-array-based operations. This approach enables precise control over individual shapes, sizes, chemical concentrations, cell density, and 3D spatial distribution of multiple components. This technique provides a cost-effective solution to meet the increasing demand of stem cell research, tissue engineering, and drug screening. PMID:26991071

  20. Design of 3D printed insert for hanging culture of Caco-2 cells

    A Caco-2 cell culture on Transwell, an alternative testing to animal or human testing used in evaluating drug intestinal permeability, incorrectly estimated the absorption of actively transported drugs due to the low expression of membrane transporters. Similarly, three-dimensional (3D) cultures of Caco-2 cells, which have been recommended to be more physiological relevant, were not superior to the Transwell culture in either accuracy or convenience in drug permeability testing. Using rapid 3D printing prototyping techniques, this study proposed a hanging culture of Caco-2 cells that performed with high accuracy in predicting drug permeability in humans. As found, hanging cultured Caco-2 cells formed a confluent monolayer and maintained high cell viability on the 3D printed insert. Compared with the normal culture on Transwell, the Caco-2 cells on the 3D printed insert presented ∼30–100% higher brush border enzyme activity and ∼2–7 folds higher activity of P-glycoprotein/multidrug resistance-associated protein 2 during 21 days of incubation. For the eight membrane transporter substrates, the predictive curve of the 3D printing culture exhibited better linearity (R2 = 0.92) to the human oral adsorption than that of the Transwell culture (R2 = 0.84), indicating better prediction by the 3D printing culture. In this regard, the 3D printed insert for hanging culture could be potentially developed as a convenient and low-cost tool for testing drug oral absorption. (paper)

  1. Towards the development of a 3D full cell and external busbars thermo-electric model

    Taking advantage of the increasing power of computers, it is now practical to consider building a 3D full cell and external busbars thermo-electric model. In the present study, a 3D full cell quarter thermo-electric model and a 3D cathode half plus liquid zone and busbars thermo-electric model have been developed and solved using a PIll 800 MHz computer. Developing a 3D full cell and external busbars thermo-electric model will constitute a step further towards the development of a fully 'multi-physic' unified aluminium reduction cell model. Already, a full cell thermo-electric model will be able to interact with a MHD model by providing it with accurate liquid zone current density and potshell temperature data and by receiving from it local liquid/ledge interface heat transfer coefficients. (author)

  2. Fibroblasts Lead the Way: A Unified View of 3D Cell Motility.

    Petrie, Ryan J; Yamada, Kenneth M

    2015-11-01

    Primary human fibroblasts are remarkably adaptable, able to migrate in differing types of physiological 3D tissue and on rigid 2D tissue culture surfaces. The crawling behavior of these and other vertebrate cells has been studied intensively, which has helped generate the concept of the cell motility cycle as a comprehensive model of 2D cell migration. However, this model fails to explain how cells force their large nuclei through the confines of a 3D matrix environment and why primary fibroblasts can use more than one mechanism to move in 3D. Recent work shows that the intracellular localization of myosin II activity is governed by cell-matrix interactions to both force the nucleus through the extracellular matrix (ECM) and dictate the type of protrusions used to migrate in 3D. PMID:26437597

  3. Further validation and development of the 3-dimensional dynamics code TRAB-3D

    TRAB-3D, the newest member of VTT's code system for LWR dynamics calculations, is a coupled neutronics-thermal hydraulics code for transient and accident analyses of BWR reactors. The code is largely based on the ID code TRAB and the 3D hexagonal code HEXTRAN which have long been used in safety analyses of Finnish and foreign reactors. In TRAB-3D the two-group neutron diffusion equations are solved in three dimensions in a rectangular fuel assembly geometry by a new method which is similar to the nodal expansion method developed earlier at VTT for hexagonal geometry. The accuracy of the method is shown by comparison with 2D fine-mesh calculations and with 3D calculation for the Olkiluoto reactor with the POLCA-4 code. Capabilities of the code in dynamic analyses is validated with the OECD/NEA LWR benchmark problems and with transient calculations for the Olkiluoto reactor. Further development of the code includes a pin power reconstruction method which makes use of precomputed power distributions within fuel assemblies

  4. XPO1 Inhibition Preferentially Disrupts the 3D Nuclear Organization of Telomeres in Tumor Cells.

    Taylor-Kashton, Cheryl; Lichtensztejn, Daniel; Baloglu, Erkan; Senapedis, William; Shacham, Sharon; Kauffman, Michael G; Kotb, Rami; Mai, Sabine

    2016-12-01

    Previous work has shown that the three-dimensional (3D) nuclear organization of telomeres is altered in cancer cells and the degree of alterations coincides with aggressiveness of disease. Nuclear pores are essential for spatial genome organization and gene regulation and XPO1 (exportin 1/CRM1) is the key nuclear export protein. The Selective Inhibitor of Nuclear Export (SINE) compounds developed by Karyopharm Therapeutics (KPT-185, KPT-330/selinexor, and KPT-8602) inhibit XPO1 nuclear export function. In this study, we investigated whether XPO1 inhibition has downstream effects on the 3D nuclear organization of the genome. This was assessed by measuring the 3D telomeric architecture of normal and tumor cells in vitro and ex vivo. Our data demonstrate for the first time a rapid and preferential disruption of the 3D nuclear organization of telomeres in tumor cell lines and in primary cells ex vivo derived from treatment-naïve newly diagnosed multiple myeloma patients. Normal primary cells in culture as well as healthy lymphocyte control cells from the same patients were minimally affected. Using both lymphoid and non-lymphoid tumor cell lines, we found that the downstream effects on the 3D nuclear telomere structure are independent of tumor type. We conclude that the 3D nuclear organization of telomeres is a sensitive indicator of cellular response when treated with XPO1 inhibitors. J. Cell. Physiol. 231: 2711-2719, 2016. © 2016 Wiley Periodicals, Inc. PMID:26991404

  5. Characteristics of tumor and host cells in 3-D simulated microgravity environment

    Chopra, V.; Dinh, T.; Wood, T.; Pellis, N.; Hannigan, E.

    Co-cultures of three-dimensional (3-D) constructs of one cell type with dispersed cells of a second cell type in low-shear rotating suspension cultures in simulated microgravity environment have been used to investigate invasive properties of normal and malignant cell types. We have shown that the epithelial and endothelial cells undergo a switch in characteristics when grown in an in vitro 3-D environment, that mimics the in vivo host environment as compared with conventional two-dimensional (2-D) monolayer cultures. Histological preparations and immunohistochemical staining procedures of cocultured harvests demonstrated various markers of interest: like collagen vimentin, mucin, elastin, fibrin, fibrinogen, cytokeratin, adhesion molecules and various angiogenic factors by tumor cells from gynecological cancer patients along with fibroblasts, endothelial cells and patient-derived mononuclear cells (n=8). The growth rate was enhanced 10-15 folds by 3-D cocultures of patient-derived cells as compared with 2-D monolayer cultures and 3-D monocultures. The production of interleukin-2, interleukin-6, interleukin -8, vascular endothelial cell growth factor, basic fibroblast growth factor, and angiogenin was studied by using ELISA and RT- PCR. Human umbilical vein-derived endothelial cell (HUVEC) were used to study the mitogenic response of the conditioned medium collected from 3-D monocultures and cocultures during proliferation and migration assays. The conditioned medium collected from 3-D cocultures of cancer cells also 1) increased the expression of message levels of vascular endothelial growth factor and its receptor flt-1 and KDR was observed by HUVEC, and 2) increased the expression of intracellular and vascular cell adhesion molecules on the surface of HUVEC, when measured by using Live cell ELISA assays and immunofluorescent staining as compared with 3-D monocultures of normal epithelial cells. There was an increase in production of 1) enzymatic activity that

  6. Neural cell 3D microtissue formation is marked by cytokines' up-regulation.

    Yinzhi Lai

    Full Text Available Cells cultured in three dimensional (3D scaffolds as opposed to traditional two-dimensional (2D substrates have been considered more physiologically relevant based on their superior ability to emulate the in vivo environment. Combined with stem cell technology, 3D cell cultures can provide a promising alternative for use in cell-based assays or biosensors in non-clinical drug discovery studies. To advance 3D culture technology, a case has been made for identifying and validating three-dimensionality biomarkers. With this goal in mind, we conducted a transcriptomic expression comparison among neural progenitor cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and as 3D neurospheres (in vivo surrogate. Up-regulation of cytokines as a group in 3D and neurospheres was observed. A group of 13 cytokines were commonly up-regulated in cells cultured in polystyrene scaffolds and neurospheres, suggesting potential for any or a combination from this list to serve as three-dimensionality biomarkers. These results are supportive of further cytokine identification and validation studies with cells from non-neural tissue.

  7. Cell force measurements in 3D microfabricated environments based on compliant cantilevers.

    Marelli, Mattia; Gadhari, Neha; Boero, Giovanni; Chiquet, Matthias; Brugger, Jürgen

    2014-01-21

    We report the fabrication, functionalization and testing of microdevices for cell culture and cell traction force measurements in three-dimensions (3D). The devices are composed of bent cantilevers patterned with cell-adhesive spots not lying on the same plane, and thus suspending cells in 3D. The cantilevers are soft enough to undergo micrometric deflections when cells pull on them, allowing cell forces to be measured by means of optical microscopy. Since individual cantilevers are mechanically independent of each other, cell traction forces are determined directly from cantilever deflections. This proves the potential of these new devices as a tool for the quantification of cell mechanics in a system with well-defined 3D geometry and mechanical properties. PMID:24217771

  8. Computational fluid dynamics simulations of blood flow regularized by 3D phase contrast MRI

    Rispoli, Vinicius C; Nielsen, Jon; Nayak, Krishna S;

    2015-01-01

    BACKGROUND: Phase contrast magnetic resonance imaging (PC-MRI) is used clinically for quantitative assessment of cardiovascular flow and function, as it is capable of providing directly-measured 3D velocity maps. Alternatively, vascular flow can be estimated from model-based computation fluid...... approach in regularizing 3D flow fields is evaluated. METHODS: The proposed algorithm incorporates both a Newtonian fluid physics model and a linear PC-MRI signal model. The model equations are solved numerically using a modified CFD algorithm. The numerical solution corresponds to the optimal solution of...... dynamics (CFD) calculations. CFD provides arbitrarily high resolution, but its accuracy hinges on model assumptions, while velocity fields measured with PC-MRI generally do not satisfy the equations of fluid dynamics, provide limited resolution, and suffer from partial volume effects. The purpose of this...

  9. First application of the 3D-MHB on dynamic compressive behavior of UHPC

    Cadoni Ezio

    2015-01-01

    Full Text Available In order to study the dynamic behaviour of material in confined conditions a new machine was conceived and called 3D-Modified Hopkinson Bar (3D-MHB. It is a Modified Hopkinson Bar apparatus designed to apply dynamic loading in materials having a tri-axial stress state. It consists of a pulse generator system (with pre-tensioned bar and brittle joint, 1 input bar, and 5 output bars. The first results obtained on Ultra High Performance Concrete in compression with three different mono-axial compression states are presented. The results show how the pre-stress states minimize the boundary condition and a more uniform response is obtained.

  10. BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models

    Bilgin, Cemal Cagatay; Fontenay, Gerald; Cheng, Qingsu; Chang, Hang; Han, Ju; Parvin, Bahram

    2016-01-01

    BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i) morphogenesis of a panel of human mammary epithelial cell lines (HMEC), and (ii) heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation. PMID:26978075

  11. BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models.

    Cemal Cagatay Bilgin

    Full Text Available BioSig3D is a computational platform for high-content screening of three-dimensional (3D cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i morphogenesis of a panel of human mammary epithelial cell lines (HMEC, and (ii heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation.

  12. BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models.

    Bilgin, Cemal Cagatay; Fontenay, Gerald; Cheng, Qingsu; Chang, Hang; Han, Ju; Parvin, Bahram

    2016-01-01

    BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i) morphogenesis of a panel of human mammary epithelial cell lines (HMEC), and (ii) heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation. PMID:26978075

  13. Development of 3D dynamic gap element for simulation of asymmetric fuel behavior

    The accurate modeling of heat transfer across the gap between fuel pellets and the protective cladding is essential to understanding the fuel performance, including cladding stress and behavior under irradiated conditions. To establish a heat transfer model through a gap in the fuel performance code, the gap conductance based on the Ross and Stoute model was employed in most previous works. In this model, the gap conductance that determines the temperature gradient within the gap is a function of gap thickness, which is dependent on mechanical behavior. Recently, many researchers have been developing fuel performance codes based on the finite element method (FE) to calculate the temperature, stress, and strain in 2D or 3D. The gap conductance model for FE can be a challenging issue in terms of convergence and nonlinearity because the elements that are positioned in a gap have a different gap conductance, and the boundary conditions of the gap vary at each iteration step. In this paper, the specified 3D dynamic gap element has been proposed and implemented to simulate asymmetric thermo-mechanical fuel behavior. A thermo-mechanical 3D finite element module incorporating a gap element has been implemented using FORTRAN77. To evaluate the proposed 3D gap element, the missing pellet surface (MPS), which results in an asymmetric heat transfer in the pellet and cladding, was simulated. As a result, the maximum temperature of a pellet for the MPS problem calculated with the specified 3D gap element is much higher than the temperature calculated with a uniform gap conductance model that a multidimensional fuel performance code employs. The results demonstrate that a 3D simulation is essential to evaluate the temperature and stress of the pellet and cladding for an asymmetric geometry simulation. (author)

  14. Particle optics in the TIT-RFQ calculated using a 3D particle-in-cell code

    Beam dynamics in an RFQ at the Tokyo Institute of Technology was analyzed using a 3D particle-in-cell computer code. In this calculation not only space charge force between each macroparticles but also 3D image charge field were included. Beam transmission performance was calculated for two types of vane-tip design with different tip curvature radii. These results are compared with ones obtained with the idealized linear two-term potential. The old vane tip design with a small tip curvature radius has given very poor beam transmission efficiency which cannot be accepted for the actual machine. (author)

  15. Parallel 3D Finite Element Particle-in-Cell Simulations with Pic3P

    Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Ng, C.; Schussman, G.; Ko, K.; /SLAC; Ben-Zvi, I.; Kewisch, J.; /Brookhaven

    2009-06-19

    SLAC's Advanced Computations Department (ACD) has developed the parallel 3D Finite Element electromagnetic Particle-In-Cell code Pic3P. Designed for simulations of beam-cavity interactions dominated by space charge effects, Pic3P solves the complete set of Maxwell-Lorentz equations self-consistently and includes space-charge, retardation and boundary effects from first principles. Higher-order Finite Element methods with adaptive refinement on conformal unstructured meshes lead to highly efficient use of computational resources. Massively parallel processing with dynamic load balancing enables large-scale modeling of photoinjectors with unprecedented accuracy, aiding the design and operation of next-generation accelerator facilities. Applications include the LCLS RF gun and the BNL polarized SRF gun.

  16. RV functional imaging: 3-D echo-derived dynamic geometry and flow field simulations.

    Pasipoularides, Ares D; Shu, Ming; Womack, Michael S; Shah, Ashish; Von Ramm, Olaf; Glower, Donald D

    2003-01-01

    We describe a novel functional imaging approach for quantitative analysis of right ventricular (RV) blood flow patterns in specific experimental animals (or humans) using real-time, three-dimensional (3-D) echocardiography (RT3D). The method is independent of the digital imaging modality used. It comprises three parts. First, a semiautomated segmentation aided by intraluminal contrast medium locates the RV endocardial surface. Second, a geometric scheme for dynamic RV chamber reconstruction applies a time interpolation procedure to the RT3D data to quantify wall geometry and motion at 400 Hz. A volumetric prism method validated the dynamic geometric reconstruction against simultaneous sonomicrometric canine measurements. Finally, the RV endocardial border motion information is used for mesh generation on a computational fluid dynamics solver to simulate development of the early RV diastolic inflow field. Boundary conditions (tessellated endocardial surface nodal velocities) for the solver are directly derived from the endocardial geometry and motion information. The new functional imaging approach may yield important kinematic information on the distribution of instantaneous velocities in the RV diastolic flow field of specific normal or diseased hearts. PMID:12388220

  17. Feasibility of radiation dose reduction using AIDR-3D in dynamic pulmonary CT perfusion

    Aim: To assess the feasibility of radiation dose reduction with adaptive iterative dose reduction (AIDR-6 3D) reconstruction in dynamic pulmonary CT perfusion. Materials and methods: CTP examinations of 10 patients acquired at 100 kVp/50 mAs were reconstructed with filtered back projection (FBP) and AIDR-3D. Artificial noise was added to raw data (pre-reconstruction projection data) to simulate lower tube current scanning. Radiodensity (in Hounsfield units), noise, and perfusion values were compared. Results: There was no significant difference in noise between the full and simulated reduced tube current with AIDR-3D reconstruction (p = 1). There was significantly lower noise in lung tissue with AIDR-3D images when compared to reconstructions without AIDR-3D (p = 0.005) and no significant change in the radiodensity (p = 1; mean difference <6 HU). Mean perfusion values increased significantly at lower tube currents (25 and 12.5 mAs), compared to 50 mAs (p = 0.005). This effect was significantly greater in larger patients compared to thin patients. Conclusion: AIDR-3D produced significantly lower noise images than FBP-based algorithms and maintained consistent noise levels in lung at 12.5 mAs, indicating this algorithm is suitable for reduced dose lung perfusion imaging. Iterative reconstruction allows significant radiation dose reduction of up to fourfold in smaller patients, and up to twofold in the medium/large size patients. The increase in perfusion values at 25% simulated tube currents is attributed to attenuation bias. -- Highlights: •Dynamic CT provides functional data but at the cost of a higher radiation dose. •Doses can be reduced by decreasing tube current but increases image noise. •Significant dose reduction is feasible when images are reconstructed with AIDR-3D. •There is a limit to how low the dose can be reduced

  18. Cell Proliferation on Macro/Nano Surface Structure and Collagen Immobilization of 3D Polycaprolactone Scaffolds.

    Park, Young-Ouk; Myung, Sung-Woon; Kook, Min-Suk; Jung, Sang-Chul; Kim, Byung-Hoon

    2016-02-01

    In this study, 3D polycaprolactone (PCL) scaffolds were fabricated by 3D printing technique. The macro/nano morphology of, 3D PCL scaffolds surface was etched with oxygen plasma. Acrylic acid (AA) plasma-polymerization was performed to functionalize the macro/nano surface with carboxyl groups and then collagen was immobilized with plasma-polymerized 3D PCL scaffolds. After O2 plasma and AA plasma-polymerization, contact angles were decreased. The FE-SEM and AFM results showed that O2 plasma is increased the surface roughness. The MTT assay results showed that proliferation of the M3CT3-E1 cells increased on the oxygen plasma treated and collagen immobilized 3D PCL scaffolds. PMID:27433597

  19. PRONTO3D users` instructions: A transient dynamic code for nonlinear structural analysis

    Attaway, S.W.; Mello, F.J.; Heinstein, M.W.; Swegle, J.W.; Ratner, J.A. [Sandia National Labs., Albuquerque, NM (United States); Zadoks, R.I. [Univ. of Texas, El Paso, TX (United States)

    1998-06-01

    This report provides an updated set of users` instructions for PRONTO3D. PRONTO3D is a three-dimensional, transient, solid dynamics code for analyzing large deformations of highly nonlinear materials subjected to extremely high strain rates. This Lagrangian finite element program uses an explicit time integration operator to integrate the equations of motion. Eight-node, uniform strain, hexahedral elements and four-node, quadrilateral, uniform strain shells are used in the finite element formulation. An adaptive time step control algorithm is used to improve stability and performance in plasticity problems. Hourglass distortions can be eliminated without disturbing the finite element solution using either the Flanagan-Belytschko hourglass control scheme or an assumed strain hourglass control scheme. All constitutive models in PRONTO3D are cast in an unrotated configuration defined using the rotation determined from the polar decomposition of the deformation gradient. A robust contact algorithm allows for the impact and interaction of deforming contact surfaces of quite general geometry. The Smooth Particle Hydrodynamics method has been embedded into PRONTO3D using the contact algorithm to couple it with the finite element method.

  20. Optimization of a 3D Dynamic Culturing System for In Vitro Modeling of Frontotemporal Neurodegeneration-Relevant Pathologic Features

    Tunesi, Marta; Fusco, Federica; Fiordaliso, Fabio; Corbelli, Alessandro; Biella, Gloria; Raimondi, Manuela T.

    2016-01-01

    Frontotemporal lobar degeneration (FTLD) is a severe neurodegenerative disorder that is diagnosed with increasing frequency in clinical setting. Currently, no therapy is available and in addition the molecular basis of the disease are far from being elucidated. Consequently, it is of pivotal importance to develop reliable and cost-effective in vitro models for basic research purposes and drug screening. To this respect, recent results in the field of Alzheimer’s disease have suggested that a tridimensional (3D) environment is an added value to better model key pathologic features of the disease. Here, we have tried to add complexity to the 3D cell culturing concept by using a microfluidic bioreactor, where cells are cultured under a continuous flow of medium, thus mimicking the interstitial fluid movement that actually perfuses the body tissues, including the brain. We have implemented this model using a neuronal-like cell line (SH-SY5Y), a widely exploited cell model for neurodegenerative disorders that shows some basic features relevant for FTLD modeling, such as the release of the FTLD-related protein progranulin (PRGN) in specific vesicles (exosomes). We have efficiently seeded the cells on 3D scaffolds, optimized a disease-relevant oxidative stress experiment (by targeting mitochondrial function that is one of the possible FTLD-involved pathological mechanisms) and evaluated cell metabolic activity in dynamic culture in comparison to static conditions, finding that SH-SY5Y cells cultured in 3D scaffold are susceptible to the oxidative damage triggered by a mitochondrial-targeting toxin (6-OHDA) and that the same cells cultured in dynamic conditions kept their basic capacity to secrete PRGN in exosomes once recovered from the bioreactor and plated in standard 2D conditions. We think that a further improvement of our microfluidic system may help in providing a full device where assessing basic FTLD-related features (including PRGN dynamic secretion) that may

  1. 3D Hopkinson bar: new experiments for dynamic testing on soils

    Semblat, J F; Gary, G

    2009-01-01

    The direct analysis of the dynamic response of materials is possible using Split Hopkinson pressure bar method. For soils, it has to be adapted since the specimen has generally poor mechanical properties. An original experimental arrangement called "Three-Dimensional Split Hopkinson Pressure Bar" (3D SHPB) is proposed. It allows the measurement of the complete three-dimensional dynamic response of soils. Different types of confinement systems are used. The results on different loading paths are compared with other works on sand and clay. The analysis at grain-size level gives further elements on the comminution process.

  2. Dynamic WIFI-Based Indoor Positioning in 3D Virtual World

    Chan, S.; Sohn, G.; Wang, L.; Lee, W.

    2013-11-01

    A web-based system based on the 3DTown project was proposed using Google Earth plug-in that brings information from indoor positioning devices and real-time sensors into an integrated 3D indoor and outdoor virtual world to visualize the dynamics of urban life within the 3D context of a city. We addressed limitation of the 3DTown project with particular emphasis on video surveillance camera used for indoor tracking purposes. The proposed solution was to utilize wireless local area network (WLAN) WiFi as a replacement technology for localizing objects of interest due to the wide spread availability and large coverage area of WiFi in indoor building spaces. Indoor positioning was performed using WiFi without modifying existing building infrastructure or introducing additional access points (AP)s. A hybrid probabilistic approach was used for indoor positioning based on previously recorded WiFi fingerprint database in the Petrie Science and Engineering building at York University. In addition, we have developed a 3D building modeling module that allows for efficient reconstruction of outdoor building models to be integrated with indoor building models; a sensor module for receiving, distributing, and visualizing real-time sensor data; and a web-based visualization module for users to explore the dynamic urban life in a virtual world. In order to solve the problems in the implementation of the proposed system, we introduce approaches for integration of indoor building models with indoor positioning data, as well as real-time sensor information and visualization on the web-based system. In this paper we report the preliminary results of our prototype system, demonstrating the system's capability for implementing a dynamic 3D indoor and outdoor virtual world that is composed of discrete modules connected through pre-determined communication protocols.

  3. 1-integrin and MT1-MMP promote tumor cell migration in 2D but not in 3D fibronectin microenvironments

    Corall, Silke; Haraszti, Tamas; Bartoschik, Tanja; Spatz, Joachim Pius; Ludwig, Thomas; Cavalcanti-Adam, Elisabetta Ada

    2014-03-01

    Cell migration is a crucial event for physiological processes, such as embryonic development and wound healing, as well as for pathological processes, such as cancer dissemination and metastasis formation. Cancer cell migration is a result of the concerted action of matrix metalloproteinases (MMPs), expressed by cancer cells to degrade the surrounding matrix, and integrins, the transmembrane receptors responsible for cell binding to matrix proteins. While it is known that cell-microenvironment interactions are essential for migration, the role of the physical state of such interactions remains still unclear. In this study we investigated human fibrosarcoma cell migration in two-dimensional (2D) and three-dimensional (3D) fibronectin (FN) microenvironments. By using antibody blocking approach and cell-binding site mutation, we determined that -integrin is the main mediator of fibrosarcoma cell migration in 2D FN, whereas in 3D fibrillar FN, the binding of - and -integrins is not necessary for cell movement in the fibrillar network. Furthermore, while the general inhibition of MMPs with GM6001 has no effect on cell migration in both 2D and 3D FN matrices, we observed opposing effect after targeted silencing of a membrane-bound MMP, namely MT1-MMP. In 2D fibronectin, silencing of MT1-MMP results in decreased migration speed and loss of directionality, whereas in 3D FN matrices, cell migration speed is increased and integrin-mediated signaling for actin dynamics is promoted. Our results suggest that the fibrillar nature of the matrix governs the migratory behavior of fibrosarcoma cells. Therefore, to hinder migration and dissemination of diseased cells, matrix molecules should be directly targeted, rather than specific subtypes of receptors at the cell membrane.

  4. Micromorph silicon tandem solar cells with fully integrated 3D photonic crystal intermediate reflectors

    Üpping, J.; Bielawny, A.; Fahr, S.; Rockstuhl, C.; Lederer, F.; Steidl, L.; Zentel, R.; Beckers, T.; Lambertz, A.; Carius, R.; Wehrspohn, R. B.

    2010-05-01

    A 3D photonic intermediate reflector for textured micromorph silicon tandem solar cells has been investigated. In thin-film silicon tandem solar cells consisting of amorphous and microcrystalline silicon with two junctions of a-Si/c-Si, efficiency enhancements can be achieved by increasing the current density in the a-Si top cell providing an optimized current matching at high current densities. For an ideal photon-management between top and bottom cell, a spectrally-selective intermediate reflective layer (IRL) is necessary. We present the first fully-integrated 3D photonic thin-film IRL device incorporated on a planar substrate. Using a ZnO inverted opal structure the external quantum efficiency of the top cell in the spectral region of interest could be enhanced. As an outlook we present the design and the preparation of a 3D self organized photonic crystal structure in a textured micromorph tandem solar cell.

  5. 3D photonic crystal interlayers for micromorph thin film silicon tandem cell

    Uepping, Johannes; Bielawny, Andreas; Otto, Martin; Wehrspohn, Ralf B. [Institute of Physics, University of Halle, Wittenberg (Germany); Steidl, Lorenz; Zentel, Rudolf [Dept. of Chemistry, University of Mainz (Germany); Lee, Seung-Mo; Knez, Mato [Max Planck Institute of Microstructure Physics, Halle (Germany); Beckers, Thomas; Carius, Reinhard [Institute of Energy Research, IEF-5 Photovoltaics, Forschungszentrum Juelich GmbH (Germany)

    2010-07-01

    A 3D photonic intermediate reflector for textured micromorph silicon tandem solar cells has been investigated. In thin-film silicon tandem solar cells consisting of amorphous and microcrystalline silicon with two junctions of a-Si/{mu}c-Si, efficiency enhancements can be achieved by increasing the current density in the a-Si top cell. It is one goal to provide an optimized current matching at high current densities. For an ideal photon-management between top and bottom cell, a spectrally selective intermediate reflective layer (IRL) is necessary. We show results toward the first fully integrated 3D photonic thin-film IRL device incorporated in a state-of-the-art textured tandem solar cell. The design and the preparation of a 3D self organized inverted opal photonic crystal structure in a textured micromorph tandem solar cell is presented.

  6. Research of Chaotic Dynamics of 3D Autonomous Quadratic Systems by Their Reduction to Special 2D Quadratic Systems

    2015-01-01

    New results about the existence of chaotic dynamics in the quadratic 3D systems are derived. These results are based on the method allowing studying dynamics of 3D system of autonomous quadratic differential equations with the help of reduction of this system to the special 2D quadratic system of differential equations.

  7. Dynamic scattering theory for dark-field electron holography of 3D strain fields

    Lubk, Axel, E-mail: Axel.Lubk@yahoo.de [CEMES-CNRS 29, rue Jeanne Marvig B.P. 94347 F-31055 Toulouse Cedex (France); Institute of Structure Physics, Technische Universität Dresden, 01062 Dresden (Germany); TEMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Javon, Elsa [CEMES-CNRS 29, rue Jeanne Marvig B.P. 94347 F-31055 Toulouse Cedex (France); TEMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Cherkashin, Nikolay [CEMES-CNRS 29, rue Jeanne Marvig B.P. 94347 F-31055 Toulouse Cedex (France); Reboh, Shay [CEMES-CNRS 29, rue Jeanne Marvig B.P. 94347 F-31055 Toulouse Cedex (France); CEA-Leti, 17rue des Martyrs, 38054 Grenoble (France); Gatel, Christophe; Hÿtch, Martin [CEMES-CNRS 29, rue Jeanne Marvig B.P. 94347 F-31055 Toulouse Cedex (France)

    2014-01-15

    Dark-field electron holography maps strain in crystal lattices into reconstructed phases over large fields of view. Here we investigate the details of the lattice strain–reconstructed phase relationship by applying dynamic scattering theory both analytically and numerically. We develop efficient analytic linear projection rules for 3D strain fields, facilitating a straight-forward calculation of reconstructed phases from 3D strained materials. They are used in the following to quantify the influence of various experimental parameters like strain magnitude, specimen thickness, excitation error and surface relaxation. - Author-Highlights: • We derive a simple dynamic scattering formalism for dark field electron holography based on a perturbative two-beam theory. • The formalism facilitates the projection of 3D strain fields by a simple weighting integral. • The weighted projection depends analytically on the diffraction order, the excitation error and the specimen thickness. • The weighting integral formalism represents an important prerequisite towards the development of tomographic strain reconstruction techniques.

  8. Dynamic scattering theory for dark-field electron holography of 3D strain fields

    Dark-field electron holography maps strain in crystal lattices into reconstructed phases over large fields of view. Here we investigate the details of the lattice strain–reconstructed phase relationship by applying dynamic scattering theory both analytically and numerically. We develop efficient analytic linear projection rules for 3D strain fields, facilitating a straight-forward calculation of reconstructed phases from 3D strained materials. They are used in the following to quantify the influence of various experimental parameters like strain magnitude, specimen thickness, excitation error and surface relaxation. - Author-Highlights: • We derive a simple dynamic scattering formalism for dark field electron holography based on a perturbative two-beam theory. • The formalism facilitates the projection of 3D strain fields by a simple weighting integral. • The weighted projection depends analytically on the diffraction order, the excitation error and the specimen thickness. • The weighting integral formalism represents an important prerequisite towards the development of tomographic strain reconstruction techniques

  9. Hot embossing for fabrication of a microfluidic 3D cell culture platform.

    Jeon, Jessie S; Chung, Seok; Kamm, Roger D; Charest, Joseph L

    2011-04-01

    Clinically relevant studies of cell function in vitro require a physiologically-representative microenvironment possessing aspects such as a 3D extracellular matrix (ECM) and controlled biochemical and biophysical parameters. A polydimethylsiloxane (PDMS) microfluidic system with a 3D collagen gel has previously served for analysis of factors inducing different responses of cells in a 3D microenvironment under controlled biochemical and biophysical parameters. In the present study, applying the known commercially-viable manufacturing methods to a cyclic olefin copolymer (COC) material resulted in a microfluidic device with enhanced 3D gel capabilities, controlled surface properties, and improved potential to serve high-volume applications. Hot embossing and roller lamination molded and sealed the microfluidic device. A combination of oxygen plasma and thermal treatments enhanced the sealing, ensured proper placement of the 3D gel, and created controlled and stable surface properties within the device. Culture of cells in the new device indicated no adverse effects of the COC material or processing as compared to previous PDMS devices. The results demonstrate a methodology to transition microfluidic devices for 3D cell culture from scientific research to high-volume applications with broad clinical impact. PMID:21113663

  10. A 3D generic inverse dynamic method using wrench notation and quaternion algebra.

    Dumas, R; Aissaoui, R; de Guise, J A

    2004-06-01

    In the literature, conventional 3D inverse dynamic models are limited in three aspects related to inverse dynamic notation, body segment parameters and kinematic formalism. First, conventional notation yields separate computations of the forces and moments with successive coordinate system transformations. Secondly, the way conventional body segment parameters are defined is based on the assumption that the inertia tensor is principal and the centre of mass is located between the proximal and distal ends. Thirdly, the conventional kinematic formalism uses Euler or Cardanic angles that are sequence-dependent and suffer from singularities. In order to overcome these limitations, this paper presents a new generic method for inverse dynamics. This generic method is based on wrench notation for inverse dynamics, a general definition of body segment parameters and quaternion algebra for the kinematic formalism. PMID:15512759

  11. Hand Gesture Spotting Based on 3D Dynamic Features Using Hidden Markov Models

    Elmezain, Mahmoud; Al-Hamadi, Ayoub; Michaelis, Bernd

    In this paper, we propose an automatic system that handles hand gesture spotting and recognition simultaneously in stereo color image sequences without any time delay based on Hidden Markov Models (HMMs). Color and 3D depth map are used to segment hand regions. The hand trajectory will determine in further step using Mean-shift algorithm and Kalman filter to generate 3D dynamic features. Furthermore, k-means clustering algorithm is employed for the HMMs codewords. To spot meaningful gestures accurately, a non-gesture model is proposed, which provides confidence limit for the calculated likelihood by other gesture models. The confidence measures are used as an adaptive threshold for spotting meaningful gestures. Experimental results show that the proposed system can successfully recognize isolated gestures with 98.33% and meaningful gestures with 94.35% reliability for numbers (0-9).

  12. Nonlinear dynamics of Airy-Vortex 3D wave packets: Emission of vortex light waves

    Driben, Rodislav

    2014-01-01

    The dynamics of 3D Airy-vortex wave packets is studied under the action of strong self-focusing Kerr nonlinearity. Emissions of nonlinear 3D waves out of the main wave packets with the topological charges were demonstrated. Due to the conservation of the total angular momentum, charges of the emitted waves are equal to those carried by the parental light structure. The rapid collapse imposes a severe limitation on the propagation of multidimensional waves in Kerr media. However, the structure of the Airy beam carrier allows the coupling of light from the leading, most intense peak into neighboring peaks and consequently strongly postpones the collapse. The dependence of the critical input amplitude for the appearance of a fast collapse on the beam width is studied for wave packets with zero and non-zero topological charges. Wave packets carrying angular momentum are found to be much more resistant to the rapid collapse, especially those having small width.

  13. Radial electric field 3D modeling for wire arrays driving dynamic hohlraums on Z

    The anode-cathode structure of the Z-machine wire array results in a higher negative radial electric field (Er) on the wires near the cathode relative to the anode. The magnitude of this field has been shown to anti-correlate with the axial radiation top/bottom symmetry in the DH (Dynamic Hohlraum). Using 3D modeling, the structure of this field is revealed for different wire-array configurations and for progressive mechanical alterations, providing insight for minimizing the negative Er on the wire array in the anode-to-cathode region of the DH. Also, the 3D model is compared to Sasorov's approximation, which describes Er at the surface of the wire in terms of wire-array parameters

  14. Radial electric field 3D modeling for wire arrays driving dynamic hohlraums on Z.

    Mock, Raymond Cecil

    2007-06-01

    The anode-cathode structure of the Z-machine wire array results in a higher negative radial electric field (Er) on the wires near the cathode relative to the anode. The magnitude of this field has been shown to anti-correlate with the axial radiation top/bottom symmetry in the DH (Dynamic Hohlraum). Using 3D modeling, the structure of this field is revealed for different wire-array configurations and for progressive mechanical alterations, providing insight for minimizing the negative Er on the wire array in the anode-to-cathode region of the DH. Also, the 3D model is compared to Sasorov's approximation, which describes Er at the surface of the wire in terms of wire-array parameters.

  15. Dynamic Characteristic Analysis of Linear DC Motor by 3D EMCN Considering Input Voltage

    Ha, Kyung Ho; Yeom, Sang Bu [Changwon National University, Changwon(Korea); Hong, JUNG Pyo; Hur Jin; Kang Do Hyunc [Hanyang University(Seoul Campus), Seoul(Korea)

    2002-02-01

    In order to design the Linear DC Motor (LDM) With improved characteristics, transient and steady state analysis are required. Furthermore, 3D analysis is also needed to analyze the precise characteristics like thrust, time harmonics. This paper deals with the transient and dynamic characteristic analysis if LDM by coupling of external circuit and motion equation using 3D Equivalent Magnetic Circuit Network Method (EMCN). For the three dimensional analysis of electric machine, EMCN is very effective method that ensures high accuracy similar to FEM and short computation time. Also, The modeling by EMCN easily allows the mover to move with respect to the Sartre at each time Also, and the spatial moving step is determined by the solution of the mechanical motion equation and the computed electromagnetic thrust. The results are compared with experimental ones to clarify the usefulness and verify the accuracy of the proposed method. (author). 11 refs., 20 figs., 2 tabs.

  16. Label-free characterization of white blood cells by measuring 3D refractive index maps

    Yoon, Jonghee; Park, HyunJoo; Choi, Chulhee; Jang, Seongsoo; Park, YongKeun

    2015-01-01

    The characterization of white blood cells (WBCs) is crucial for blood analyses and disease diagnoses. However, current standard techniques rely on cell labeling, a process which imposes significant limitations. Here we present three-dimensional (3D) optical measurements and the label-free characterization of mouse WBCs using optical diffraction tomography. 3D refractive index (RI) tomograms of individual WBCs are constructed from multiple two-dimensional quantitative phase images of samples illuminated at various angles of incidence. Measurements of the 3D RI tomogram of WBCs enable the separation of heterogeneous populations of WBCs using quantitative morphological and biochemical information. Time-lapse tomographic measurements also provide the 3D trajectory of micrometer-sized beads ingested by WBCs. These results demonstrate that optical diffraction tomography can be a useful and versatile tool for the study of WBCs.

  17. High sensitivity plasmonic biosensor based on nanoimprinted quasi 3D nanosquares for cell detection.

    Zhu, Shuyan; Li, Hualin; Yang, Mengsu; Pang, Stella W

    2016-07-22

    Quasi three-dimensional (3D) plasmonic nanostructures consisting of Au nanosquares on top of SU-8 nanopillars and Au nanoholes on the bottom were developed and fabricated using nanoimprint lithography with simultaneous thermal and UV exposure. These 3D plasmonic nanostructures were used to detect cell concentration of lung cancer A549 cells, retinal pigment epithelial (RPE) cells, and breast cancer MCF-7 cells. Nanoimprint technology has the advantage of producing high uniformity plasmonic nanostructures for such biosensors. Multiple resonance modes were observed in these quasi 3D plasmonic nanostructures. The hybrid coupling of localized surface plasmon resonances and Fabry-Perot cavity modes in the quasi 3D nanostructures resulted in high sensitivity of 496 nm/refractive index unit. The plasmonic resonance peak wavelength and sensitivity could be tuned by varying the Au thickness. Resonance peak shifts for different cells at the same concentration were distinct due to their different cell area and confluency. The cell concentration detection limit covered a large range of 5 × 10(2) to 1 × 10(7) cells ml(-1) with these new plasmonic nanostructures. They also provide a large resonance peak shift of 51 nm for as little as 0.08 cells mm(-2) of RPE cells for high sensitivity cell detection. PMID:27275952

  18. High sensitivity plasmonic biosensor based on nanoimprinted quasi 3D nanosquares for cell detection

    Zhu, Shuyan; Li, Hualin; Yang, Mengsu; Pang, Stella W.

    2016-07-01

    Quasi three-dimensional (3D) plasmonic nanostructures consisting of Au nanosquares on top of SU-8 nanopillars and Au nanoholes on the bottom were developed and fabricated using nanoimprint lithography with simultaneous thermal and UV exposure. These 3D plasmonic nanostructures were used to detect cell concentration of lung cancer A549 cells, retinal pigment epithelial (RPE) cells, and breast cancer MCF-7 cells. Nanoimprint technology has the advantage of producing high uniformity plasmonic nanostructures for such biosensors. Multiple resonance modes were observed in these quasi 3D plasmonic nanostructures. The hybrid coupling of localized surface plasmon resonances and Fabry–Perot cavity modes in the quasi 3D nanostructures resulted in high sensitivity of 496 nm/refractive index unit. The plasmonic resonance peak wavelength and sensitivity could be tuned by varying the Au thickness. Resonance peak shifts for different cells at the same concentration were distinct due to their different cell area and confluency. The cell concentration detection limit covered a large range of 5 × 102 to 1 × 107 cells ml‑1 with these new plasmonic nanostructures. They also provide a large resonance peak shift of 51 nm for as little as 0.08 cells mm‑2 of RPE cells for high sensitivity cell detection.

  19. 3D kinematic and dynamic analysis of the front crawl tumble turn in elite male swimmers.

    Puel, F; Morlier, J; Avalos, M; Mesnard, M; Cid, M; Hellard, P

    2012-02-01

    The aim of this study was to identify kinematic and dynamic variables related to the best tumble turn times (3mRTT, the turn time from 3-m in to 3-m out, independent variable) in ten elite male swimmers using a three-dimensional (3D) underwater analysis protocol and the Lasso (least absolute shrinkage and selection operator) as statistical method. For each swimmer, the best-time turn was analyzed with five stationary and synchronized underwater cameras. The 3D reconstruction was performed using the Direct Linear Transformation algorithm. An underwater piezoelectric 3D force platform completed the set-up to compute dynamic variables. Data were smoothed by the Savitzky-Golay filtering method. Three variables were considered relevant in the best Lasso model (3mRTT=2.58-0.425 RD+0.204 VPe+0.0046 TD): the head-wall distance where rotation starts (RD), the horizontal speed at the force peak (VPe), and the 3D length of the path covered during the turn (TD). Furthermore, bivariate analysis showed that upper body (CUBei) and lower limb extension indexes at first contact (CLLei) were also linked to the turn time (r=-0.65 and pvariables). Thus the best turn times were associated with a long RD, slower VPe and reduced TD. By an early transverse rotation, male elite swimmers reach the wall with a slightly flexed posture that results in fast extension. These swimmers opt for a movement that is oriented forward and they focus on reducing the distance covered. PMID:22176710

  20. MULTILEVEL (3D) MICROFLUIDIC TECHNOLOGY FOR AN INNOVATIVE MAGNETIC CELL SEPARATION PLATFORM

    Fouet, Marc; Cargou, Sébastien; Courson, Rémi; Blatché, Charline; Montrose, A.; Reybier, K; Gué, Anne-Marie

    2014-01-01

    We demonstrate a new concept of devices, which by combining 3D fluid engineering and localized mag-netic actuation enables the full integration of a cell tagging and magnetic separation device. We used a low cost, commercially available dry film (EMS Inc, Ohio, USA) that fits microfluidic requirements and gives the possibility to build easily 3D microfluidic structures. The labelling of blood monocytes with su-perparamagnetic particles was performed "up stream" with the aim of a microparticle...

  1. Enhancement of neurite outgrowth in neuron cancer stem cells by growth on 3-D collagen scaffolds

    Highlights: ► Neuron cancer stem cells (NCSCs) behave high multiply of growth on collagen scaffold. ► Enhancement of NCSCs neurite outgrowth on porous collagen scaffold. ► 3-D collagen culture of NCSCs shows an advance differentiation than 2-D culture. -- Abstract: Collagen is one component of the extracellular matrix that has been widely used for constructive remodeling to facilitate cell growth and differentiation. The 3-D distribution and growth of cells within the porous scaffold suggest a clinical significance for nerve tissue engineering. In the current study, we investigated proliferation and differentiation of neuron cancer stem cells (NCSCs) on a 3-D porous collagen scaffold that mimics the natural extracellular matrix. We first generated green fluorescence protein (GFP) expressing NCSCs using a lentiviral system to instantly monitor the transitions of morphological changes during growth on the 3-D scaffold. We found that proliferation of GFP-NCSCs increased, and a single cell mass rapidly grew with unrestricted expansion between days 3 and 9 in culture. Moreover, immunostaining with neuronal nuclei (NeuN) revealed that NCSCs grown on the 3-D collagen scaffold significantly enhanced neurite outgrowth. Our findings confirmed that the 80 μm porous collagen scaffold could enhance attachment, viability and differentiation of the cancer neural stem cells. This result could provide a new application for nerve tissue engineering and nerve regeneration.

  2. Self-assembling Fmoc dipeptide hydrogel for in situ 3D cell culturing

    Akpe Victor; Rydholm Susanna; Liebmann Thomas; Brismar Hjalmar

    2007-01-01

    Abstract Background Conventional cell culture studies have been performed on 2D surfaces, resulting in flat, extended cell growth. More relevant studies are desired to better mimic 3D in vivo tissue growth. Such realistic environments should be the aim of any cell growth study, requiring new methods for culturing cells in vitro. Cell biology is also tending toward miniaturization for increased efficiency and specificity. This paper discusses the application of a self-assembling peptide-derive...

  3. Fast isotropic banding-free bSSFP imaging using 3D dynamically phase-cycled radial bSSFP (3D DYPR-SSFP)

    Aims: Dynamically phase-cycled radial balanced steady-state free precession (DYPR-SSFP) is a method for efficient banding artifact removal in bSSFP imaging. Based on a varying radiofrequency (RF) phase-increment in combination with a radial trajectory, DYPR-SSFP allows obtaining a banding-free image out of a single acquired k-space. The purpose of this work is to present an extension of this technique, enabling fast three-dimensional isotropic banding-free bSSFP imaging. Methods: While banding artifact removal with DYPR-SSFP relies on the applied dynamic phase-cycle, this aspect can lead to artifacts, at least when the number of acquired projections lies below a certain limit. However, by using a 3D radial trajectory with quasi-random view ordering for image acquisition, this problem is intrinsically solved, enabling 3D DYPR-SSFP imaging at or even below the Nyquist criterion. The approach is validated for brain and knee imaging at 3 Tesla. Results: Volumetric, banding-free images were obtained in clinically acceptable scan times with an isotropic resolution up to 0.56 mm. Conclusion: The combination of DYPR-SSFP with a 3D radial trajectory allows banding-free isotropic volumetric bSSFP imaging with no expense of scan time. Therefore, this is a promising candidate for clinical applications such as imaging of cranial nerves or articular cartilage.

  4. Fast isotropic banding-free bSSFP imaging using 3D dynamically phase-cycled radial bSSFP (3D DYPR-SSFP)

    Benkert, Thomas; Blaimer, Martin; Breuer, Felix A. [Research Center Magnetic Resonance Bavaria (MRB), Wuerzburg (Germany); Ehses, Philipp [Tuebingen Univ. (Germany). Dept. of Neuroimaging; Max Planck Institute for Biological Cybernetics, Tuebingen (Germany). High-Field MR Center; Jakob, Peter M. [Research Center Magnetic Resonance Bavaria (MRB), Wuerzburg (Germany); Wuerzburg Univ. (Germany). Dept. of Experimental Physics 5

    2016-05-01

    Aims: Dynamically phase-cycled radial balanced steady-state free precession (DYPR-SSFP) is a method for efficient banding artifact removal in bSSFP imaging. Based on a varying radiofrequency (RF) phase-increment in combination with a radial trajectory, DYPR-SSFP allows obtaining a banding-free image out of a single acquired k-space. The purpose of this work is to present an extension of this technique, enabling fast three-dimensional isotropic banding-free bSSFP imaging. Methods: While banding artifact removal with DYPR-SSFP relies on the applied dynamic phase-cycle, this aspect can lead to artifacts, at least when the number of acquired projections lies below a certain limit. However, by using a 3D radial trajectory with quasi-random view ordering for image acquisition, this problem is intrinsically solved, enabling 3D DYPR-SSFP imaging at or even below the Nyquist criterion. The approach is validated for brain and knee imaging at 3 Tesla. Results: Volumetric, banding-free images were obtained in clinically acceptable scan times with an isotropic resolution up to 0.56 mm. Conclusion: The combination of DYPR-SSFP with a 3D radial trajectory allows banding-free isotropic volumetric bSSFP imaging with no expense of scan time. Therefore, this is a promising candidate for clinical applications such as imaging of cranial nerves or articular cartilage.

  5. 3D photonic crystal interlayers for micromorph thin film silicon tandem cell

    Bielawny, Andreas; Uepping, Johannes; Miclea, Paul T.; Wehrspohn, Ralf B. [Institute of Physics, University of Halle, Wittenberg (Germany); Rockstuhl, Carsten; Lederer, Falk [Institue of Physics, Solid States Optics, University of Jena (Germany); Peters, Marius [Freiburg Centre for Material Research, University of Freiburg (Germany); Steidl, Lorenz; Zentel, Rudolf [Dept. of Chemistry, Pharmacy and Earth Science, University of Mainz (Germany); Lee, Seung-Mo; Knez, Mato [Max Planck Institute of Microstructure Physics, Halle (Germany); Lambertz, Andreas; Carius, Reinhard [Institute of Energy Research, IEF-5 Photovoltaics, Forschungszentrum Juelich GmbH (Germany)

    2009-07-01

    The concept of 3D photonic intermediate reflectors for micromorph silicon tandem cells has been investigated toward first prototype cells. The reflector enhances the absorption of spectrally selected light in the top cell and decreases the current mismatch between both junctions. Our device is an inverted opal structure made of ZnO and built using self organized nanoparticles and atomic layer deposition coating methods. This 3D photonic crystal intermediate layer is less dependent of the angle of incidence than other state of the art thickness dependent massive interlayers. We present design rules, preparation and characterization of a 3D photonic thin film device. A first prototype is compared to a state of the art reference silicon tandem cell.

  6. Quantification of Diaphragm Mechanics in Pompe Disease Using Dynamic 3D MRI.

    Katja Mogalle

    Full Text Available Diaphragm weakness is the main reason for respiratory dysfunction in patients with Pompe disease, a progressive metabolic myopathy affecting respiratory and limb-girdle muscles. Since respiratory failure is the major cause of death among adult patients, early identification of respiratory muscle involvement is necessary to initiate treatment in time and possibly prevent irreversible damage. In this paper we investigate the suitability of dynamic MR imaging in combination with state-of-the-art image analysis methods to assess respiratory muscle weakness.The proposed methodology relies on image registration and lung surface extraction to quantify lung kinematics during breathing. This allows for the extraction of geometry and motion features of the lung that characterize the independent contribution of the diaphragm and the thoracic muscles to the respiratory cycle.Results in 16 3D+t MRI scans (10 Pompe patients and 6 controls of a slow expiratory maneuver show that kinematic analysis from dynamic 3D images reveals important additional information about diaphragm mechanics and respiratory muscle involvement when compared to conventional pulmonary function tests. Pompe patients with severely reduced pulmonary function showed severe diaphragm weakness presented by minimal motion of the diaphragm. In patients with moderately reduced pulmonary function, cranial displacement of posterior diaphragm parts was reduced and the diaphragm dome was oriented more horizontally at full inspiration compared to healthy controls.Dynamic 3D MRI provides data for analyzing the contribution of both diaphragm and thoracic muscles independently. The proposed image analysis method has the potential to detect less severe diaphragm weakness and could thus be used to determine the optimal start of treatment in adult patients with Pompe disease in prospect of increased treatment response.

  7. Quantification of Diaphragm Mechanics in Pompe Disease Using Dynamic 3D MRI

    Mogalle, Katja; Perez-Rovira, Adria; Ciet, Pierluigi; Wens, Stephan C. A.; van Doorn, Pieter A.; Tiddens, Harm A. W. M.; van der Ploeg, Ans T.; de Bruijne, Marleen

    2016-01-01

    Background Diaphragm weakness is the main reason for respiratory dysfunction in patients with Pompe disease, a progressive metabolic myopathy affecting respiratory and limb-girdle muscles. Since respiratory failure is the major cause of death among adult patients, early identification of respiratory muscle involvement is necessary to initiate treatment in time and possibly prevent irreversible damage. In this paper we investigate the suitability of dynamic MR imaging in combination with state-of-the-art image analysis methods to assess respiratory muscle weakness. Methods The proposed methodology relies on image registration and lung surface extraction to quantify lung kinematics during breathing. This allows for the extraction of geometry and motion features of the lung that characterize the independent contribution of the diaphragm and the thoracic muscles to the respiratory cycle. Results Results in 16 3D+t MRI scans (10 Pompe patients and 6 controls) of a slow expiratory maneuver show that kinematic analysis from dynamic 3D images reveals important additional information about diaphragm mechanics and respiratory muscle involvement when compared to conventional pulmonary function tests. Pompe patients with severely reduced pulmonary function showed severe diaphragm weakness presented by minimal motion of the diaphragm. In patients with moderately reduced pulmonary function, cranial displacement of posterior diaphragm parts was reduced and the diaphragm dome was oriented more horizontally at full inspiration compared to healthy controls. Conclusion Dynamic 3D MRI provides data for analyzing the contribution of both diaphragm and thoracic muscles independently. The proposed image analysis method has the potential to detect less severe diaphragm weakness and could thus be used to determine the optimal start of treatment in adult patients with Pompe disease in prospect of increased treatment response. PMID:27391236

  8. Signatures of topological phase transition in 3 d topological insulators from dynamical axion response

    Makhfudz, Imam

    2016-04-01

    Axion electrodynamics, first proposed in the context of particle physics, manifests itself in condensed matter physics in the topological field theory description of 3 d topological insulators and gives rise to magnetoelectric effect, where applying magnetic (electric) field B (E ) induces polarization (magnetization) p (m ) . We use linear response theory to study the associated topological current using the Fu-Kane-Mele model of 3 d topological insulators in the presence of time-dependent uniform weak magnetic field. By computing the dynamical current susceptibility χij jpjp(ω ) , we discover from its static limit an `order parameter' of the topological phase transition between weak topological (or ordinary) insulator and strong topological insulator, found to be continuous. The χij jpjp(ω ) shows a sign-changing singularity at a critical frequency with suppressed strength in the topological insulating state. Our results can be verified in current noise experiment on 3 d TI candidate materials for the detection of such topological phase transition.

  9. Salinity effects on cracking morphology and dynamics in 3-D desiccating clays

    DeCarlo, Keita F.; Shokri, Nima

    2014-04-01

    Saline conditions induce not only chemical but physical changes in swelling clays, and have a significant influence on the crack dynamics and morphology of desiccating clays. In this study, we used X-ray microtomography to experimentally investigate the effects of sodium chloride on the morphology and dynamics of desiccation cracks in three-dimensional mixtures of sand-bentonite slurry under varying rheological conditions. Rectangular glass containers were packed with slurries of different salt concentrations, with the top boundary exposed to air for evaporation. The growth and propagation of the cracking network that subsequently formed was visualized in 3-D at multiple intervals. The characterization of cracking and branching behavior shows a high extent of localized surficial crack networks at low salinity, with a transition to less extensive but more centralized crack networks with increased salinity. The observed behavior was described in the context of the physicochemical properties of the montmorillonite clay, where shifts from an "entangled" (large platelet spacing, small pore structure) to a "stacked" (small platelet spacing, open pore structure) network influence fluid distribution and thus extent of cracking and branching behavior. This is further corroborated by vertical profiles of water distribution, which shows localized desiccation fronts that shift to uniform desaturation with increasing salt concentration. Our results provide new insights regarding the formation, dynamics, and patterns of desiccation cracks formed during evaporation from 3-D saline clay structures, which will be useful in hydrological applications including water management, land surface evaporation, and subsurface contaminant transport.

  10. Magnetic resonance velocity mapping of 3D cerebrospinal fluid flow dynamics in hydrocephalus: preliminary results

    Stadlbauer, Andreas [Landesklinikum St. Poelten, MR Physics Group, Department of Radiology, St. Poelten (Austria); University of Erlangen-Nuremberg, Department of Neurosurgery, Erlangen (Germany); Salomonowitz, Erich [Landesklinikum St. Poelten, MR Physics Group, Department of Radiology, St. Poelten (Austria); Brenneis, Christian [Landesklinikum St. Poelten, Department of Neurology, St. Poelten (Austria); Ungersboeck, Karl [Landesklinikum St. Poelten, Department of Neurosurgery, St. Poelten (Austria); Riet, Wilma van der [European MRI Consultancy (EMRIC), Strasbourg (France); Buchfelder, Michael; Ganslandt, Oliver [University of Erlangen-Nuremberg, Department of Neurosurgery, Erlangen (Germany)

    2012-01-15

    To investigate the detectability of CSF flow alterations in the ventricular system of patients with hydrocephalus using time-resolved 3D MR velocity mapping. MR velocity mapping was performed in 21 consecutive hydrocephalus patients and 21 age-matched volunteers using a 3D phase-contrast (PC) sequence. Velocity vectors and particle path lines were calculated for visualisation of flow dynamics. CSF flow was classified as ''hypomotile flow'' if it showed attenuated dynamics and as ''hypermotile flow'' if it showed increased dynamics compared with volunteers. Diagnostic efficacy was compared with routine 2D cine PC-MRI. Seven patients showed hypomotile CSF flow: six had non-communicating hydrocephalus due to aqueductal stenosis. One showed oscillating flow between the lateral ventricles after craniotomy for intracranial haemorrhage. Seven patients showed normal flow: six had hydrocephalus ex vacuo due to brain atrophy. One patient who underwent ventriculostomy 10 years ago showed a flow path through the opening. Seven patients showed hypermotile flow: three had normal pressure hydrocephalus, three had dementia, and in one the diagnosis remained unclear. The diagnostic efficacy of velocity mapping was significantly higher except for that of aqueductal stenosis. Our approach may be useful for diagnosis, therapy planning, and follow-up of different kinds of hydrocephalus. (orig.)

  11. 3D discrete dislocation dynamics applied to a motion of low-angle tilt boundaries

    Záležák, Tomáš; Dlouhý, Antonín

    Zurich: Trans Tech Publications, 2014 - (Šandera, P.), s. 87-91. (Key Engineering Materials. 592-593). ISBN 978-3-03785-934-6. ISSN 1013-9826. [MSMF 7 - International Conference on Materials Structure & Micromechanics of Fracture /7./. Brno (CZ), 01.07.2013-03.07.2013] R&D Projects: GA MŠk EE2.3.20.0214 Institutional support: RVO:68081723 Keywords : 3D discrete dislocation dynamics * low-angle dislocation boundaries * particle strengthening * high temperature deformation * Orowan stress Subject RIV: JG - Metallurgy

  12. Time resolved 3D momentum imaging of ultrafast dynamics by coherent VUV-XUV radiation

    Sturm, F. P.; Wright, T. W.; Ray, D.; Zalyubovskaya, I.; Shivaram, N.; Slaughter, D. S.; Ranitovic, P.; Belkacem, A.; Weber, Th.

    2016-06-01

    We present a new experimental setup for measuring ultrafast nuclear and electron dynamics of molecules after photo-excitation and ionization. We combine a high flux femtosecond vacuum ultraviolet (VUV) and extreme ultraviolet (XUV) source with an internally cold molecular beam and a 3D momentum imaging particle spectrometer to measure electrons and ions in coincidence. We describe a variety of tools developed to perform pump-probe studies in the VUV-XUV spectrum and to modify and characterize the photon beam. First benchmark experiments are presented to demonstrate the capabilities of the system.

  13. 3D Discrete Dislocation Dynamics Applied to Interactions between Dislocation Walls and Particles

    Záležák, Tomáš; Dlouhý, Antonín

    2012-01-01

    Roč. 122, č. 3 (2012), s. 450-452. ISSN 0587-4246. [ International Symposium on Physics of Materials /12./ - ISPMA 12. Prague, 04.09.2011-08.09.2011] R&D Projects: GA ČR GD106/09/H035; GA ČR GA202/09/2073; GA MŠk OC 162 Institutional research plan: CEZ:AV0Z20410507 Keywords : 3D discrete dislocation dynamics * tilt boundary * migration * diffusion * pecipitation hardening Subject RIV: JG - Metallurgy Impact factor: 0.531, year: 2012

  14. Time resolved 3D momentum imaging of ultrafast dynamics by coherent VUV-XUV radiation.

    Sturm, F P; Wright, T W; Ray, D; Zalyubovskaya, I; Shivaram, N; Slaughter, D S; Ranitovic, P; Belkacem, A; Weber, Th

    2016-06-01

    We present a new experimental setup for measuring ultrafast nuclear and electron dynamics of molecules after photo-excitation and ionization. We combine a high flux femtosecond vacuum ultraviolet (VUV) and extreme ultraviolet (XUV) source with an internally cold molecular beam and a 3D momentum imaging particle spectrometer to measure electrons and ions in coincidence. We describe a variety of tools developed to perform pump-probe studies in the VUV-XUV spectrum and to modify and characterize the photon beam. First benchmark experiments are presented to demonstrate the capabilities of the system. PMID:27370429

  15. 3D chitosan-gelatin-chondroitin porous scaffold improves osteogenic differentiation of mesenchymal stem cells

    A porous 3D scaffold was developed to support and enhance the differentiation process of mesenchymal stem cells (MSC) into osteoblasts in vitro. The 3D scaffold was made with chitosan, gelatin and chondroitin and it was crosslinked by EDAC. The scaffold physicochemical properties were evaluated. SEM revealed the high porosity and interconnection of pores in the scaffold; rheological measurements show that the scaffold exhibits a characteristic behavior of strong gels. The elastic modulus found in compressive tests of the crosslinked scaffold was about 50 times higher than the non-crosslinked one. After 21 days, the 3D matrix submitted to hydrolytic degradation loses above 40% of its weight. MSC were collected from rat bone marrow and seeded in chitosan-gelatin-chondroitin 3D scaffolds and in 2D culture plates as well. MSC were differentiated into osteoblasts for 21 days. Cell proliferation and alkaline phosphatase activity were followed weekly during the osteogenic process. The osteogenic differentiation of MSC was improved in 3D culture as shown by MTT assay and alkaline phosphatase activity. On the 21st day, bone markers, osteopontin and osteocalcin, were detected by the PCR analysis. This study shows that the chitosan-gelatin-chondroitin 3D structure provides a good environment for the osteogenic process and enhances cellular proliferation

  16. Cell volume and geometric parameters determination in living cells using confocal microscopy and 3D reconstruction

    sprotocols

    2015-01-01

    Authors: David Hevia, Aida Rodriguez-Garcia, Marta Alonso-Gervós, Isabel Quirós-González, Henar M Cimadevilla, Carmen Gómez-Cordovés, Rosa M Sainz & Juan C Mayo ### Abstract The protocol reported here describes a simple, easy, fast and reproducible method aimed to know the geometric parameters of living cells based on confocal laser scanning microscopy combined with 3D reconstruction software. Briefly, the method is based on intrinsic fluorescence properties of acridine orange (AO...

  17. Determination of Drug Toxicity Using 3D Spheroids Constructed From an Immortal Human Hepatocyte Cell Line

    Fey, S. J.; Wrzesinski, Krzysztof

    2012-01-01

    Numerous publications have documented that the immortal cells grown in three-dimensional (3D) cultures possess physiological behavior, which is more reminiscent of their parental organ than when the same cells are cultivated using classical two-dimensional (2D) culture techniques. The goal of this...

  18. 3D-printed concentrator arrays for external light trapping on thin film solar cells

    van Dijk, Lourens; Marcus, E. A. Pepijn; Oostra, A. Jolt; Schropp, Ruud E. I.; Di Vece, Marcel

    2015-01-01

    After our recent demonstration of a 3D-printed external light trap on a small solar cell, we now consider its potential for large solar panels. An external light trap consists of a parabolic concentrator and a spacer that redirects the photons that are reflected by the solar cell back towards the so

  19. 3D Image-Guided Automatic Pipette Positioning for Single Cell Experiments in vivo

    Brian Long; Lu Li; Ulf Knoblich; Hongkui Zeng; Hanchuan Peng

    2015-01-01

    We report a method to facilitate single cell, image-guided experiments including in vivo electrophysiology and electroporation. Our method combines 3D image data acquisition, visualization and on-line image analysis with precise control of physical probes such as electrophysiology microelectrodes in brain tissue in vivo. Adaptive pipette positioning provides a platform for future advances in automated, single cell in vivo experiments.

  20. Endothelial cells stimulate growth of normal and cancerous breast epithelial cells in 3D culture

    Magnusson Magnus K

    2010-07-01

    Full Text Available Abstract Background Epithelial-stromal interaction provides regulatory signals that maintain correct histoarchitecture and homeostasis in the normal breast and facilitates tumor progression in breast cancer. However, research on the regulatory role of the endothelial component in the normal and malignant breast gland has largely been neglected. The aim of the study was to investigate the effects of endothelial cells on growth and differentiation of human breast epithelial cells in a three-dimensional (3D co-culture assay. Methods Breast luminal and myoepithelial cells and endothelial cells were isolated from reduction mammoplasties. Primary cells and established normal and malignant breast cell lines were embedded in reconstituted basement membrane in direct co-culture with endothelial cells and by separation of Transwell filters. Morphogenic and phenotypic profiles of co-cultures was evaluated by phase contrast microscopy, immunostaining and confocal microscopy. Results In co-culture, endothelial cells stimulate proliferation of both luminal- and myoepithelial cells. Furthermore, endothelial cells induce a subpopulation of luminal epithelial cells to form large acini/ducts with a large and clear lumen. Endothelial cells also stimulate growth and cloning efficiency of normal and malignant breast epithelial cell lines. Transwell and gradient co-culture studies show that endothelial derived effects are mediated - at least partially - by soluble factors. Conclusion Breast endothelial cells - beside their role in transporting nutrients and oxygen to tissues - are vital component of the epithelial microenvironment in the breast and provide proliferative signals to the normal and malignant breast epithelium. These growth promoting effects of endothelial cells should be taken into consideration in breast cancer biology.

  1. Digital Image Analysis of Cells : Applications in 2D, 3D and Time

    Pinidiyaarachchi, Amalka

    2009-01-01

    Light microscopes are essential research tools in biology and medicine. Cell and tissue staining methods have improved immensely over the years and microscopes are now equipped with digital image acquisition capabilities. The image data produced require development of specialized analysis methods. This thesis presents digital image analysis methods for cell image data in 2D, 3D and time sequences. Stem cells have the capability to differentiate into specific cell types. The mechanism behind di...

  2. 3D Dynamic Representation for Urban Sprawl Modelling: Example of India’s Delhi-Mumbai corridor

    Gadal, Sébastien; Fournier, Stéphane; Prouteau, Emeric

    2010-01-01

    3D dynamic geo-visualisation models reflect changes in urban land areas and make a new contribution to the spatiotemporal representation of land use processes and the production of geographic knowledge. They facilitate understanding of the process of urbanisation and the resulting transformations of land use. The 3D dynamic visualisation model of the Delhi-Mumbai corridor in India illustrates how it is now possible to integrate the temporal, spatial dynamic and geographic dimensions of a proc...

  3. An Innovative Cell Microincubator for Drug Discovery Based on 3D Silicon Structures

    Francesca Aredia

    2016-01-01

    Full Text Available We recently employed three-dimensional (3D silicon microstructures (SMSs consisting in arrays of 3 μm-thick silicon walls separated by 50 μm-deep, 5 μm-wide gaps, as microincubators for monitoring the biomechanical properties of tumor cells. They were here applied to investigate the in vitro behavior of HT1080 human fibrosarcoma cells driven to apoptosis by the chemotherapeutic drug Bleomycin. Our results, obtained by fluorescence microscopy, demonstrated that HT1080 cells exhibited a great ability to colonize the narrow gaps. Remarkably, HT1080 cells grown on 3D-SMS, when treated with the DNA damaging agent Bleomycin under conditions leading to apoptosis, tended to shrink, reducing their volume and mimicking the normal behavior of apoptotic cells, and were prone to leave the gaps. Finally, we performed label-free detection of cells adherent to the vertical silicon wall, inside the gap of 3D-SMS, by exploiting optical low coherence reflectometry using infrared, low power radiation. This kind of approach may become a new tool for increasing automation in the drug discovery area. Our results open new perspectives in view of future applications of the 3D-SMS as the core element of a lab-on-a-chip suitable for screening the effect of new molecules potentially able to kill tumor cells.

  4. Development and Validation of a 3D Clinostat for the Study of Cells during Microgravity Simulation.

    Russomano, T; Cardoso, R; Falcao, F; Dalmarco, G; V Dos Santos, C; F Dos Santos, L; G de Azevedo, D; Dos Santos, M; Martinelli, L; Motta, J; Forraz, N; McGuckin, C

    2005-01-01

    The clinostat was originally used to find out why plant roots appear to grow predominantly toward the center of the Earth. Over the last 2-3 decades, slow- and fast-rotating 2D and 3D clinostats have been used to assess cellular adaptation to this environment. A cell culture is placed in a spin module of the clinostat platform and its rotation is set empirically (2-3 rpm). The machine is then allowed to run for a specified period (hours to days) after which the cultures are removed and assayed for specific properties, such as cell growth, size and shape, distribution of receptors, integrity of the cytoskeleton or gene expression. A 3D clinostat was developed by the Microgravity Laboratory/IPCT-PUCRS group and validated by the Stem Cell Group of Kingston University London, which used 4 different types of human cancer cells and cord blood stem cells (CBSC). After rotation for 19h at 37degC, 5%CO2 humidified atmosphere, the 3D clinostat significantly improved proliferation potential of all tested cell populations when compared to static cultures. After only 5 days, high definition microscopic analysis revealed that all CBSC adhered and expanded onto the BDtrade 3D collagen composite scaffolds, and cross-developed into hepatocyte-like cells upon stimulation. PMID:17282243

  5. High Content Imaging (HCI on Miniaturized Three-Dimensional (3D Cell Cultures

    Pranav Joshi

    2015-12-01

    Full Text Available High content imaging (HCI is a multiplexed cell staining assay developed for better understanding of complex biological functions and mechanisms of drug action, and it has become an important tool for toxicity and efficacy screening of drug candidates. Conventional HCI assays have been carried out on two-dimensional (2D cell monolayer cultures, which in turn limit predictability of drug toxicity/efficacy in vivo; thus, there has been an urgent need to perform HCI assays on three-dimensional (3D cell cultures. Although 3D cell cultures better mimic in vivo microenvironments of human tissues and provide an in-depth understanding of the morphological and functional features of tissues, they are also limited by having relatively low throughput and thus are not amenable to high-throughput screening (HTS. One attempt of making 3D cell culture amenable for HTS is to utilize miniaturized cell culture platforms. This review aims to highlight miniaturized 3D cell culture platforms compatible with current HCI technology.

  6. Heterogeneous Differentiation of Human Mesenchymal Stem Cells in 3D Extracellular Matrix Composites

    Jung, Jangwook P.; Bache-Wiig, Meredith K.; Provenzano, Paolo P.; Ogle, Brenda M.

    2016-01-01

    Abstract Extracellular matrix (ECM) proteins are structural elements of tissue and also potent signaling molecules. Previously, our laboratory showed that ECM of 2D coatings can trigger differentiation of bone marrow-derived mesenchymal stem cells (MSCs) into mesodermal lineages in an ECM-specific manner over 14 days, in some cases comparable to chemical induction. To test whether a similar effect was possible in a 3D, tissue-like environment, we designed a synthetic-natural biomaterial composite. The composite can present whole-molecule ECM proteins to cells, even those that do not spontaneously form hydrogels ex vivo, in 3D. To this end, we entrapped collagen type I, laminin-111, or fibronectin in ECM composites with MSCs and directly compared markers of mesodermal differentiation including cardiomyogenic (ACTC1), osteogenic (SPP1), adipogenic (PPARG), and chondrogenic (SOX9) in 2D versus 3D. We found the 3D condition largely mimicked the 2D condition such that the addition of type I collagen was the most potent inducer of differentiation to all lineages tested. One notable difference between 2D and 3D was pronounced adipogenic differentiation in 3D especially in the presence of exogenous collagen type I. In particular, PPARG gene expression was significantly increased ∼16-fold relative to chemical induction, in 3D and not in 2D. Unexpectedly, 3D engagement of ECM proteins also altered immunomodulatory function of MSCs in that expression of IL-6 gene was elevated relative to basal levels in 2D. In fact, levels of IL-6 gene expression in 3D composites containing exogenously supplied collagen type I or fibronectin were statistically similar to levels attained in 2D with tumor necrosis factor-α (TNF-α) stimulation and these levels were sustained over a 2-week period. Thus, this novel biomaterial platform allowed us to compare the biochemical impact of whole-molecule ECM proteins in 2D versus 3D indicating enhanced adipogenic differentiation and IL-6 expression

  7. TRAIL protein localization in human primary T cells by 3D microscopy using 3D interactive surface plot: a new method to visualize plasma membrane.

    Gras, Christophe; Smith, Nikaïa; Sengmanivong, Lucie; Gandini, Mariana; Kubelka, Claire Fernandes; Herbeuval, Jean-Philippe

    2013-01-31

    The apoptotic ligand TNF-related apoptosis ligand (TRAIL) is expressed on the membrane of immune cells during HIV infection. The intracellular stockade of TRAIL in human primary CD4(+) T cells is not known. Here we investigated whether primary CD4(+) T cells expressed TRAIL in their intracellular compartment and whether TRAIL is relocalized on the plasma membrane under HIV activation. We found that TRAIL protein was stocked in intracellular compartment in non activated CD4(+) T cells and that the total level of TRAIL protein was not increased under HIV-1 stimulation. However, TRAIL was massively relocalized on plasma membrane when cells were cultured with HIV. Using three dimensional (3D) microscopy we localized TRAIL protein in human T cells and developed a new method to visualize plasma membrane without the need of a membrane marker. This method used the 3D interactive surface plot and bright light acquired images. PMID:23085529

  8. 3D dynamics of hydrous thermal-chemical plumes in subduction zones

    Zhu, G.; Gerya, T.; Yuen, D.; Connolly, J. A. D.

    2009-04-01

    Mantle wedges are identified as sites of intense thermal convection and thermal-chemical Rayleigh-Taylor instabilities ("cold plumes") controlling distribution and intensity of magmatic activity in subduction zones. To investigate 3D hydrous partially molten cold plumes forming in the mantle wedge in response to slab dehydration, we perform 3D petrological-thermomechanical numerical simulations of the intraoceanic one-sided subduction with spontaneously bending retreating slab characterized by weak hydrated upper interface. I3ELVIS code is used which is developed based on multigrid approach combined with marker-in-cell method with conservative finite-difference schemes. We investigated regional 800 km wide and 200 km deep 3D subduction models with variable 200 to 800 km lateral dimension along the trench using uniform numerical staggered grid with 405x101x101 nodal points and up to 50 million markers. Our results show three patterns (roll(sheet)-, zig-zag- and finger-like) of Rayleigh-Taylor instabilities can develop above the subducting slab, which are controlled by effective viscosity of partially molten rocks. Spatial and temporal periodicity of plumes correlate well with that of volcanic activity in natural intraoceanic arcs such as Japan. High laterally variable surface heat flow predicted in the arc region in response to thermal-chemical plumes activity is also consistent with natural observations.

  9. Computer-controlled dynamic mode multidirectional UV lithography for 3D microfabrication

    Computer-controlled dynamic mode multidirectional ultraviolet (UV) lithography has been demonstrated using a collimated UV light source, a substrate-holding stage equipped with two stepper motors (one for tilting and the other for rotation), a controller with programming software and a laptop computer. The tilting and rotational angles of the stage in motion are accurately controlled during UV exposure as programmed by the user to produce complex three-dimensional (3D) microstructures. Process parameters include the initial and final tilting and rotational angles of the stage, and the relative angular velocities of the two motors in addition to the normal fabrication process parameters of UV lithography such as optical dose, baking time, and developing time and condition. Symmetric patterns can be generated by a simple synchronous mode dynamic operation, where both the angular velocities of the tilting motion and the rotating motion are set equal or harmonically related. More complex and non-symmetric patterns can be obtained using a piecewise synchronous mode, where the relationship between the angular velocities of the two motors is described not with a single coefficient but with a set of coefficients. 3D structures fabricated from the synchronous mode operation include the four-leaf clover horn and the cardiac horn while the ones from the piecewise synchronous mode are a vertical triangular slab, a screwed wind vane and arbitrary shape horns. Ray trace simulation has been performed using a mathematical tool in a spherical coordinate system and the simulated 3D patterns show good agreement with the fabricated ones.

  10. Investigating dynamic stall, 3-D and rotational effects on wind turbine blades by means of an unsteady quasi-3D Navier-Stokes solver

    Chaviaropoulos, P.K. [CRES-Center for Renewable Energy Sources, Pikermi Attiki (Greece)

    1997-08-01

    The blade element codes provide surprisingly accurate predictions of the aerodynamic loads provided that they are `fed` with proper lift and drag - incidence curves for the profiles mounted on the rotor blades. The evident question is how one can obtain such data. It is common experience that the use of the mostly available steady two-dimensional profile data may lead to serious discrepancies between measured and simulated loads. Although several correction techniques have been proposed as a remedy during the last years, from simplified dynamic stall models suitably tuned for wind turbines to 3-D correction schemes for profile data, the problem is by no means over-passed. Especially for the three-dimensional effects it seems that part of the difficulty is due to our limited understanding of the physical mechanism which is responsible for the extra loading of the inner part of the blades. Recognizing the importance of the above aspects two relevant Joule projects have been launched, the concluded `Dynamic Stall and 3-D Effects` JOU2-CT93-0345 and the ongoing `VISCWIND` JOR3-CT95-0007 project. Part of the activities in the first and all the activities in the second project are devoted to the identification and quantification of the dynamic stall and three-dimensional effects experienced by the wind turbine blades using Navier-Stokes computations. The contribution of CRES in these two projects is briefly presented in this paper. (EG)

  11. On-chip clearing of arrays of 3-D cell cultures and micro-tissues.

    Grist, S M; Nasseri, S S; Poon, T; Roskelley, C; Cheung, K C

    2016-07-01

    Three-dimensional (3-D) cell cultures are beneficial models for mimicking the complexities of in vivo tissues, especially in tumour studies where transport limitations can complicate response to cancer drugs. 3-D optical microscopy techniques are less involved than traditional embedding and sectioning, but are impeded by optical scattering properties of the tissues. Confocal and even two-photon microscopy limit sample imaging to approximately 100-200 μm depth, which is insufficient to image hypoxic spheroid cores. Optical clearing methods have permitted high-depth imaging of tissues without physical sectioning, but they are difficult to implement for smaller 3-D cultures due to sample loss in solution exchange. In this work, we demonstrate a microfluidic platform for high-throughput on-chip optical clearing of breast cancer spheroids using the SeeDB, Clear(T2), and ScaleSQ clearing methods. Although all three methods are able to effectively clear the spheroids, we find that SeeDB and ScaleSQ more effectively clear the sample than Clear(T2); however, SeeDB induces green autofluorescence while ScaleS causes sample expansion. Our unique on-chip implementation permits clearing arrays of 3-D cultures using perfusion while monitoring the 3-D cultures throughout the process, enabling visualization of the clearing endpoint as well as monitoring of transient changes that could induce image artefacts. Our microfluidic device is compatible with on-chip 3-D cell culture, permitting the use of on-chip clearing at the endpoint after monitoring the same spheroids during their culture. This on-chip method has the potential to improve readout from 3-D cultures, facilitating their use in cell-based assays for high-content drug screening and other applications. PMID:27493703

  12. Grounding line dynamics inferred from a 3D full-Stokes model solving the contact problem

    Favier, Lionel; Gagliardini, Olivier; Durand, Gael; Zwinger, Thomas

    2010-05-01

    The mass balance of marine ice-sheets, such as the West Antarctic Ice Sheet, is mostly controlled by their grounding line dynamics. Most numerical models simulating marine ice-sheets involve simplifications and do not include all the stress gradients. First results obtained with a 3D full-Stokes model for the grounded ice-sheet / floating ice-shelf transition, using the finite-element code Elmer/Ice, are presented. The initial geometry, which takes into account a dome and a calving front, has been laterally extruded from a previously investigated 2D flowline geometry. The grounding line migration is computed by solving the contact problem between the ice and the rigid downward sloping bedrock, where a non linear friction law is applied in the two horizontal directions. The evolutions of the sea-air and sea-ice interfaces are determined by the solution of a local transport equation. The consistency between the 3D model and the analogous results of the flowline model is shown by comparing the results in the basic extruded case, with no normal flux through lateral boundaries. Thereafter, spatially non uniform perturbations are introduced, to simulate the grounding line dynamics under fully three-dimensional perturbations.

  13. Dynamics of Phase Transitions: The 3D 3-state Potts model

    Berg, B A; Velytsky, A; Berg, Bernd A.; Meyer-Ortmanns, Hildegard; Velytsky, Alexander

    2004-01-01

    In studies of the QCD deconfining phase transition or cross-over by means of heavy ion experiments, one ought to be concerned about non-equilibrium effects due to heating and cooling of the system. In this paper we extend our previous study of Glauber dynamics of 2D Potts models to the 3D 3-state Potts model, which serves as an effective model for some QCD properties. We investigate the linear theory of spinodal decomposition in some detail. It describes the early time evolution of the 3D model under a quench from the disordered into the ordered phase well, but fails in 2D. Further, the quench leads to competing vacuum domains, which are difficult to equilibrate, even in the presence of a small external magnetic field. From our hysteresis study we find, as before, a dynamics dominated by spinodal decomposition. There is evidence that some effects survive in the case of a cross-over. But the infinite volume extrapolation is difficult to control, even with lattices as large as 120^3.

  14. 3D Multisource Full‐Waveform Inversion using Dynamic Random Phase Encoding

    Boonyasiriwat, Chaiwoot

    2010-10-17

    We have developed a multisource full‐waveform inversion algorithm using a dynamic phase encoding strategy with dual‐randomization—both the position and polarity of simultaneous sources are randomized and changed every iteration. The dynamic dual‐randomization is used to promote the destructive interference of crosstalk noise resulting from blending a large number of common shot gathers into a supergather. We compare our multisource algorithm with various algorithms in a numerical experiment using the 3D SEG/EAGE overthrust model and show that our algorithm provides a higher‐quality velocity tomogram than the other methods that use only monorandomization. This suggests that increasing the degree of randomness in phase encoding should improve the quality of the inversion result.

  15. Formation of '3D' multiplanet systems by dynamical disruption of multiple-resonance configurations

    Libert, A -S

    2012-01-01

    Assuming that giant planets are formed in thin protoplanetary discs, a '3D' system can form, provided that the mutual inclination is excited by some dynamical mechanism. Resonant interactions and close planetary encounters are thought to be the primary inclination-excitation mechanisms, resulting in a resonant and non-resonant system, respectively. Here we propose an alternative formation scenario, starting from a system composed of three giant planets in a nearly coplanar configuration. As was recently shown for the case of the Solar system, planetary migration in the gas disc (Type II migration) can force the planets to become trapped in a multiply resonant state. We simulate this process, assuming different values for the planetary masses and mass ratios. We show that such a triple resonance generally becomes unstable as the resonance excites the eccentricities of all planets and planet-planet scattering sets in. One of the three planets is typically ejected from the system, leaving behind a dynamically 'h...

  16. Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

    Chwalowski, Pawel; Quon, Eliot; Brynildsen, Scott E.

    2016-01-01

    This paper presents results from an exploratory two-year effort of applying Computational Fluid Dynamics (CFD) to analyze the empty-tunnel flow in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). The TDT is a continuous-flow, closed circuit, 16- x 16-foot slotted-test-section wind tunnel, with capabilities to use air or heavy gas as a working fluid. In this study, experimental data acquired in the empty tunnel using the R-134a test medium was used to calibrate the computational data. The experimental calibration data includes wall pressures, boundary-layer profiles, and the tunnel centerline Mach number profiles. Subsonic and supersonic flow regimes were considered, focusing on Mach 0.5, 0.7 and Mach 1.1 in the TDT test section. This study discusses the computational domain, boundary conditions, and initial conditions selected and the resulting steady-state analyses using NASA's FUN3D CFD software.

  17. Dynamic mechanical properties of 3D fiber-deposited PEOT/PBT scaffolds: An experimental and numerical analysis

    Moroni, L.; Poort, G.; Keulen, van F.; Wijn, de J.R.; Blitterswijk, van C.A.

    2006-01-01

    Mechanical properties of three-dimensional (3D) scaffolds can be appropriately modulated through novel fabrication techniques like 3D fiber deposition (3DF), by varying scaffold's pore size and shape. Dynamic stiffness, in particular, can be considered as an important property to optimize the scaffo

  18. Self-assembling Fmoc dipeptide hydrogel for in situ 3D cell culturing

    Liebmann, Thomas; Rydholm, Susanna; Akpe, Victor; Brismar, Hjalmar

    2007-01-01

    Background Conventional cell culture studies have been performed on 2D surfaces, resulting in flat, extended cell growth. More relevant studies are desired to better mimic 3D in vivo tissue growth. Such realistic environments should be the aim of any cell growth study, requiring new methods for culturing cells in vitro. Cell biology is also tending toward miniaturization for increased efficiency and specificity. This paper discusses the application of a self-assembling peptide-derived hydrogel for use as a 3D cell culture scaffold at the microscale. Results Phenylalanine derivative hydrogel formation was seen to occur in multiple dispersion media. Cells were immobilized in situ within microchambers designed for cell analysis. Use of the highly biocompatible hydrogel components and simplistic procedures significantly reduced the cytotoxic effects seen with alternate 3D culture materials and microstructure loading methods. Cells were easily immobilized, sustained and removed from microchambers. Differences in growth morphology were seen in the cultured cells, owing to the 3-dimentional character of the gel structure. Degradation improved the removal of hydrogel from the microstructures, permitting reuse of the analysis platforms. Conclusion Self-assembling diphenylalanine derivative hydrogel provided a method to dramatically reduce the typical difficulties of microculture formation. Effective generation of patterned 3D cultures will lead to improved cell study results by better modeling in vivo growth environments and increasing efficiency and specificity of cell studies. Use of simplified growth scaffolds such as peptide-derived hydrogel should be seen as highly advantageous and will likely become more commonplace in cell culture methodology. PMID:18070345

  19. Study of a Microfluidic Chip Integrating Single Cell Trap and 3D Stable Rotation Manipulation

    Liang Huang

    2016-08-01

    Full Text Available Single cell manipulation technology has been widely applied in biological fields, such as cell injection/enucleation, cell physiological measurement, and cell imaging. Recently, a biochip platform with a novel configuration of electrodes for cell 3D rotation has been successfully developed by generating rotating electric fields. However, the rotation platform still has two major shortcomings that need to be improved. The primary problem is that there is no on-chip module to facilitate the placement of a single cell into the rotation chamber, which causes very low efficiency in experiment to manually pipette single 10-micron-scale cells into rotation position. Secondly, the cell in the chamber may suffer from unstable rotation, which includes gravity-induced sinking down to the chamber bottom or electric-force-induced on-plane movement. To solve the two problems, in this paper we propose a new microfluidic chip with manipulation capabilities of single cell trap and single cell 3D stable rotation, both on one chip. The new microfluidic chip consists of two parts. The top capture part is based on the least flow resistance principle and is used to capture a single cell and to transport it to the rotation chamber. The bottom rotation part is based on dielectrophoresis (DEP and is used to 3D rotate the single cell in the rotation chamber with enhanced stability. The two parts are aligned and bonded together to form closed channels for microfluidic handling. Using COMSOL simulation and preliminary experiments, we have verified, in principle, the concept of on-chip single cell traps and 3D stable rotation, and identified key parameters for chip structures, microfluidic handling, and electrode configurations. The work has laid a solid foundation for on-going chip fabrication and experiment validation.

  20. Self-assembling Fmoc dipeptide hydrogel for in situ 3D cell culturing

    Akpe Victor

    2007-12-01

    Full Text Available Abstract Background Conventional cell culture studies have been performed on 2D surfaces, resulting in flat, extended cell growth. More relevant studies are desired to better mimic 3D in vivo tissue growth. Such realistic environments should be the aim of any cell growth study, requiring new methods for culturing cells in vitro. Cell biology is also tending toward miniaturization for increased efficiency and specificity. This paper discusses the application of a self-assembling peptide-derived hydrogel for use as a 3D cell culture scaffold at the microscale. Results Phenylalanine derivative hydrogel formation was seen to occur in multiple dispersion media. Cells were immobilized in situ within microchambers designed for cell analysis. Use of the highly biocompatible hydrogel components and simplistic procedures significantly reduced the cytotoxic effects seen with alternate 3D culture materials and microstructure loading methods. Cells were easily immobilized, sustained and removed from microchambers. Differences in growth morphology were seen in the cultured cells, owing to the 3-dimentional character of the gel structure. Degradation improved the removal of hydrogel from the microstructures, permitting reuse of the analysis platforms. Conclusion Self-assembling diphenylalanine derivative hydrogel provided a method to dramatically reduce the typical difficulties of microculture formation. Effective generation of patterned 3D cultures will lead to improved cell study results by better modeling in vivo growth environments and increasing efficiency and specificity of cell studies. Use of simplified growth scaffolds such as peptide-derived hydrogel should be seen as highly advantageous and will likely become more commonplace in cell culture methodology.

  1. Mechano-sensing and cell migration: a 3D model approach

    Cell migration is essential for tissue development in different physiological and pathological conditions. It is a complex process orchestrated by chemistry, biological factors, microstructure and surrounding mechanical properties. Focusing on the mechanical interactions, cells do not only exert forces on the matrix that surrounds them, but they also sense and react to mechanical cues in a process called mechano-sensing. Here, we hypothesize the involvement of mechano-sensing in the regulation of directional cell migration through a three-dimensional (3D) matrix. For this purpose, we develop a 3D numerical model of individual cell migration, which incorporates the mechano-sensing process of the cell as the main mechanism regulating its movement. Consistent with this hypothesis, we found that factors, such as substrate stiffness, boundary conditions and external forces, regulate specific and distinct cell movements

  2. Population and Evolutionary Dynamics based on Predator-Prey Relationships in a 3D Physical Simulation.

    Ito, Takashi; Pilat, Marcin L; Suzuki, Reiji; Arita, Takaya

    2016-01-01

    Recent studies have reported that population dynamics and evolutionary dynamics, occurring at different time scales, can be affected by each other. Our purpose is to explore the interaction between population and evolutionary dynamics using an artificial life approach based on a 3D physically simulated environment in the context of predator-prey and morphology-behavior coevolution. The morphologies and behaviors of virtual prey creatures are evolved using a genetic algorithm based on the predation interactions between predators and prey. Both population sizes are also changed, depending on the fitness. We observe two types of cyclic behaviors, corresponding to short-term and long-term dynamics. The former can be interpreted as a simple population dynamics of Lotka-Volterra type. It is shown that the latter cycle is based on the interaction between the changes in the prey strategy against predators and the long-term change in both population sizes, resulting partly from a tradeoff between their defensive success and the cost of defense. PMID:26934093

  3. Surface 3D nanostructuring by tightly focused laser pulse: simulations by Lagrangian code and molecular dynamics

    Inogamov, Nail A.; Zhakhovsky, Vasily V.

    2016-02-01

    There are many important applications in which the ultrashort diffraction-limited and therefore tightly focused laser pulses irradiates metal films mounted on dielectric substrate. Here we present the detailed picture of laser peeling and 3D structure formation of the thin (relative to a depth of a heat affected zone in the bulk targets) gold films on glass substrate. The underlying physics of such diffraction-limited laser peeling was not well understood previously. Our approach is based on a physical model which takes into consideration the new calculations of the two-temperature (2T) equation of state (2T EoS) and the two-temperature transport coefficients together with the coupling parameter between electron and ion subsystems. The usage of the 2T EoS and the kinetic coefficients is required because absorption of an ultrashort pulse with duration of 10-1000 fs excites electron subsystem of metal and transfers substance into the 2T state with hot electrons (typical electron temperatures 1-3 eV) and much colder ions. It is shown that formation of submicrometer-sized 3D structures is a result of the electron-ion energy transfer, melting, and delamination of film from substrate under combined action of electron and ion pressures, capillary deceleration of the delaminated liquid metal or semiconductor, and ultrafast freezing of molten material. We found that the freezing is going in non-equilibrium regime with strongly overcooled liquid phase. In this case the Stefan approximation is non-applicable because the solidification front speed is limited by the diffusion rate of atoms in the molten material. To solve the problem we have developed the 2T Lagrangian code including all this reach physics in. We also used the high-performance combined Monte- Carlo and molecular dynamics code for simulation of surface 3D nanostructuring at later times after completion of electron-ion relaxation.

  4. Making and Remaking Dynamic 3D Structures by Shining Light on Flat Liquid Crystalline Vitrimer Films without a Mold.

    Yang, Yang; Pei, Zhiqiang; Li, Zhen; Wei, Yen; Ji, Yan

    2016-02-24

    Making dynamic three-dimensional (3D) structures capable of reversible shape changes or locomotion purely out of dry polymers is very difficult. Meanwhile, no previous dynamic 3D structures can be remade into new configurations while being resilient to mechanical damages and low temperature. Here, we show that light-activated transesterification in carbon nanotube dispersed liquid crystalline vitrimers enables flexible design and easy building of dynamic 3D structures out of flat films upon irradiation of light without screws, glues, or molds. Shining light also enables dynamic 3D structures to be quickly modified on demand, restored from distortion, repaired if broken, in situ healed when microcrack appears, assembled for more sophisticated structures, reconfigured, and recycled after use. Furthermore, the fabrication, reconfiguration, actuation, reparation, and assembly as well as healing can be performed even at extremely low temperatures (e.g., -130 °C). PMID:26840838

  5. 3D staggered Lagrangian hydrodynamics scheme with cell-centered Riemann solver-based artificial viscosity

    The aim of the present work is the 3D extension of a general formalism to derive a staggered discretization for Lagrangian hydrodynamics on unstructured grids. The classical compatible discretization is used; namely, momentum equation is discretized using the fundamental concept of subcell forces. Specific internal energy equation is obtained using total energy conservation. The subcell force is derived by invoking the Galilean invariance and thermodynamic consistency. A general form of the subcell force is provided so that a cell entropy inequality is satisfied. The subcell force consists of a classical pressure term plus a tensorial viscous contribution proportional to the difference between the node velocity and the cell-centered velocity. This cell-centered velocity is an extra degree of freedom solved with a cell-centered approximate Riemann solver. The second law of thermodynamics is satisfied by construction of the local positive definite subcell tensor involved in the viscous term. A particular expression of this tensor is proposed. A more accurate extension of this discretization both in time and space is also provided using a piecewise linear reconstruction of the velocity field and a predictor-corrector time discretization. Numerical tests are presented in order to assess the efficiency of this approach in 3D. Sanity checks show that the 3D extension of the 2D approach reproduces 1D and 2D results. Finally, 3D problems such as Sedov, Noh, and Saltzman are simulated. (authors)

  6. 3D patterned stem cell differentiation using thermo-responsive methylcellulose hydrogel molds

    Lee, Wonjae; Park, Jon

    2016-07-01

    Tissue-specific patterned stem cell differentiation serves as the basis for the development, remodeling, and regeneration of the multicellular structure of the native tissues. We herein proposed a cytocompatible 3D casting process to recapitulate this patterned stem cell differentiation for reconstructing multicellular tissues in vitro. We first reconstituted the 2D culture conditions for stem cell fate control within 3D hydrogel by incorporating the sets of the diffusible signal molecules delivered through drug-releasing microparticles. Then, utilizing thermo-responsivity of methylcellulose (MC), we developed a cytocompatible casting process to mold these hydrogels into specific 3D configurations, generating the targeted spatial gradients of diffusible signal molecules. The liquid phase of the MC solution was viscous enough to adopt the shapes of 3D impression patterns, while the gelated MC served as a reliable mold for patterning the hydrogel prepolymers. When these patterned hydrogels were integrated together, the stem cells in each hydrogel distinctly differentiated toward individually defined fates, resulting in the formation of the multicellular tissue structure bearing the very structural integrity and characteristics as seen in vascularized bones and osteochondral tissues.

  7. 3D patterned stem cell differentiation using thermo-responsive methylcellulose hydrogel molds

    Lee, Wonjae; Park, Jon

    2016-01-01

    Tissue-specific patterned stem cell differentiation serves as the basis for the development, remodeling, and regeneration of the multicellular structure of the native tissues. We herein proposed a cytocompatible 3D casting process to recapitulate this patterned stem cell differentiation for reconstructing multicellular tissues in vitro. We first reconstituted the 2D culture conditions for stem cell fate control within 3D hydrogel by incorporating the sets of the diffusible signal molecules delivered through drug-releasing microparticles. Then, utilizing thermo-responsivity of methylcellulose (MC), we developed a cytocompatible casting process to mold these hydrogels into specific 3D configurations, generating the targeted spatial gradients of diffusible signal molecules. The liquid phase of the MC solution was viscous enough to adopt the shapes of 3D impression patterns, while the gelated MC served as a reliable mold for patterning the hydrogel prepolymers. When these patterned hydrogels were integrated together, the stem cells in each hydrogel distinctly differentiated toward individually defined fates, resulting in the formation of the multicellular tissue structure bearing the very structural integrity and characteristics as seen in vascularized bones and osteochondral tissues. PMID:27381562

  8. Estimation of Pulmonary Motion in Healthy Subjects and Patients with Intrathoracic Tumors Using 3D-Dynamic MRI: Initial Results

    Plathow, Christian; Schoebinger, Max; Meinzer, Heinz Peter [German Cancer Research Center, Heidelberg (Germany); Herth, Felix; Tuengerthal, Siegfried [Clinic of Thoracic Disease, Heidelberg (Germany); Kauczor, Hans Ulrich [University of Heidelberg, Heidelberg (Germany)

    2009-12-15

    To estimate a new technique for quantifying regional lung motion using 3D-MRI in healthy volunteers and to apply the technique in patients with intra- or extrapulmonary tumors. Intraparenchymal lung motion during a whole breathing cycle was quantified in 30 healthy volunteers using 3D-dynamic MRI (FLASH [fast low angle shot] 3D, TRICKS [time-resolved interpolated contrast kinetics]). Qualitative and quantitative vector color maps and cumulative histograms were performed using an introduced semiautomatic algorithm. An analysis of lung motion was performed and correlated with an established 2D-MRI technique for verification. As a proof of concept, the technique was applied in five patients with non-small cell lung cancer (NSCLC) and 5 patients with malignant pleural mesothelioma (MPM). The correlation between intraparenchymal lung motion of the basal lung parts and the 2D-MRI technique was significant (r = 0.89, p < 0.05). Also, the vector color maps quantitatively illustrated regional lung motion in all healthy volunteers. No differences were observed between both hemithoraces, which was verified by cumulative histograms. The patients with NSCLC showed a local lack of lung motion in the area of the tumor. In the patients with MPM, there was global diminished motion of the tumor bearing hemithorax, which improved significantly after chemotherapy (CHT) (assessed by the 2D- and 3D-techniques) (p < 0.01). Using global spirometry, an improvement could also be shown (vital capacity 2.9 {+-} 0.5 versus 3.4 L {+-} 0.6, FEV1 0.9 {+-} 0.2 versus 1.4 {+-} 0.2 L) after CHT, but this improvement was not significant. A 3D-dynamic MRI is able to quantify intraparenchymal lung motion. Local and global parenchymal pathologies can be precisely located and might be a new tool used to quantify even slight changes in lung motion (e.g. in therapy monitoring, follow-up studies or even benign lung diseases)

  9. Estimation of Pulmonary Motion in Healthy Subjects and Patients with Intrathoracic Tumors Using 3D-Dynamic MRI: Initial Results

    To estimate a new technique for quantifying regional lung motion using 3D-MRI in healthy volunteers and to apply the technique in patients with intra- or extrapulmonary tumors. Intraparenchymal lung motion during a whole breathing cycle was quantified in 30 healthy volunteers using 3D-dynamic MRI (FLASH [fast low angle shot] 3D, TRICKS [time-resolved interpolated contrast kinetics]). Qualitative and quantitative vector color maps and cumulative histograms were performed using an introduced semiautomatic algorithm. An analysis of lung motion was performed and correlated with an established 2D-MRI technique for verification. As a proof of concept, the technique was applied in five patients with non-small cell lung cancer (NSCLC) and 5 patients with malignant pleural mesothelioma (MPM). The correlation between intraparenchymal lung motion of the basal lung parts and the 2D-MRI technique was significant (r = 0.89, p < 0.05). Also, the vector color maps quantitatively illustrated regional lung motion in all healthy volunteers. No differences were observed between both hemithoraces, which was verified by cumulative histograms. The patients with NSCLC showed a local lack of lung motion in the area of the tumor. In the patients with MPM, there was global diminished motion of the tumor bearing hemithorax, which improved significantly after chemotherapy (CHT) (assessed by the 2D- and 3D-techniques) (p < 0.01). Using global spirometry, an improvement could also be shown (vital capacity 2.9 ± 0.5 versus 3.4 L ± 0.6, FEV1 0.9 ± 0.2 versus 1.4 ± 0.2 L) after CHT, but this improvement was not significant. A 3D-dynamic MRI is able to quantify intraparenchymal lung motion. Local and global parenchymal pathologies can be precisely located and might be a new tool used to quantify even slight changes in lung motion (e.g. in therapy monitoring, follow-up studies or even benign lung diseases)

  10. Mutual information as a measure of image quality for 3D dynamic lung imaging with EIT

    We report on a pilot study of dynamic lung electrical impedance tomography (EIT) at the University of Manchester. Low-noise EIT data at 100 frames per second were obtained from healthy male subjects during controlled breathing, followed by magnetic resonance imaging (MRI) subsequently used for spatial validation of the EIT reconstruction. The torso surface in the MR image and electrode positions obtained using MRI fiducial markers informed the construction of a 3D finite element model extruded along the caudal-distal axis of the subject. Small changes in the boundary that occur during respiration were accounted for by incorporating the sensitivity with respect to boundary shape into a robust temporal difference reconstruction algorithm. EIT and MRI images were co-registered using the open source medical imaging software, 3D Slicer. A quantitative comparison of quality of different EIT reconstructions was achieved through calculation of the mutual information with a lung-segmented MR image. EIT reconstructions using a linear shape correction algorithm reduced boundary image artefacts, yielding better contrast of the lungs, and had 10% greater mutual information compared with a standard linear EIT reconstruction. (paper)

  11. Dynamical study of 2D and 3D barred galaxy models

    Manos, T

    2008-01-01

    We study the dynamics of 2D and 3D barred galaxy analytical models, focusing on the distinction between regular and chaotic orbits with the help of the Smaller ALigment Index (SALI), a very powerful tool for this kind of problems. We present briefly the method and we calculate the fraction of chaotic and regular orbits in several cases. In the 2D model, taking initial conditions on a Poincar\\'{e} $(y,p_y)$ surface of section, we determine the fraction of regular and chaotic orbits. In the 3D model, choosing initial conditions on a cartesian grid in a region of the $(x, z, p_y)$ space, which in coordinate space covers the inner disc, we find how the fraction of regular orbits changes as a function of the Jacobi constant. Finally, we outline that regions near the $(x,y)$ plane are populated mainly by regular orbits. The same is true for regions that lie either near to the galactic center, or at larger relatively distances from it.

  12. Correlative 3D imaging of Whole Mammalian Cells with Light and Electron Microscopy

    Murphy, Gavin E.; Narayan, Kedar; Lowekamp, Bradley C.; Hartnell, Lisa M.; Heymann, Jurgen A. W.; Fu, Jing; Subramaniam, Sriram

    2011-01-01

    We report methodological advances that extend the current capabilities of ion-abrasion scanning electron microscopy (IA–SEM), also known as focused ion beam scanning electron microscopy, a newly emerging technology for high resolution imaging of large biological specimens in 3D. We establish protocols that enable the routine generation of 3D image stacks of entire plastic-embedded mammalian cells by IA-SEM at resolutions of ~10 to 20 nm at high contrast and with minimal artifacts from the foc...

  13. Quantitative data analysis methods for 3D microstructure characterization of Solid Oxide Cells

    Jørgensen, Peter Stanley

    . Alignment of the individual image slices is performed by automatic detection of ducial marks. Uneven illumination is corrected by tting hypersurfaces to the spatial intensity variation in the 3D image data. Routine use of quantitative three dimensional analysis of microstructure is generally restricted by...... for gaining further fundamental understanding of how microstructure affects performance. In this work, methods for automatic 3D characterization of microstructure are studied: from the acquisition of 3D image data by focused ion beam tomography to the extraction of quantitative measures that......The performance of electrochemical ceramic devices such as solid oxide fuel and electrolyser cells depends on the distribution of constituent phases on the micro or nano scale, also known as the microstructure. The microstructure governs key properties such as ion, electron and gas transport...

  14. MAPLE deposition of 3D micropatterned polymeric substrates for cell culture

    Paun, Irina Alexandra, E-mail: irina.paun@physics.pub.ro [National Institute for Laser, Plasma and Radiation Physics, RO-077125, Magurele, Bucharest (Romania); Faculty of Applied Sciences, University Politehnica of Bucharest, RO-060042, Bucharest (Romania); Mihailescu, Mona [Faculty of Applied Sciences, University Politehnica of Bucharest, RO-060042, Bucharest (Romania); Calenic, Bogdan [Department of Biochemistry, Faculty of Dentistry, UMF Carol Davila, Bucharest (Romania); Luculescu, Catalin Romeo [National Institute for Laser, Plasma and Radiation Physics, RO-077125, Magurele, Bucharest (Romania); Greabu, Maria [Department of Biochemistry, Faculty of Dentistry, UMF Carol Davila, Bucharest (Romania); Dinescu, Maria, E-mail: dinescum@nipne.ro [National Institute for Laser, Plasma and Radiation Physics, RO-077125, Magurele, Bucharest (Romania)

    2013-08-01

    3D micropatterned poly(lactide-co-glycolide)/polyurethane (PLGA/PU) substrates were produced by MAPLE deposition through masks and used for regulating the behavior of oral keratinocyte stem cells in response to topography. Flat PLGA/PU substrates were produced for comparison. 3D imaging of the PLGA/PU substrates and of the cultured cells was performed by Digital Holographic Microscopy. The micropatterns were in the shape of squares of 50 × 50 and 80 × 80 μm{sup 2} areas, ∼1.8 μm in height and separated by 20 μm wide channels. It was found that substrate topography guided the adhesion of the cultured cells: on the smooth substrates the cells adhered randomly and showed no preferred orientation; in contrast, on the micropatterned substrates the cells adhered preferentially onto the squares and not in the separating channels. Furthermore, key properties of the cells (size, viability, proliferation rate and stem cell marker expression) did not show any dependence on substrate topography. The size of the cultured cells, their viability, the proportions of actively/slow proliferating cells, as well as the stem cell markers expressions, were similar for both flat and micropatterned substrates. Finally, it was found that the cells cultured on the PLGA/PU substrates deposited by MAPLE exhibited similar properties as the controls (i.e. cells cultured on glass slides), indicating the capability of the former to preserve the properties of the keratinocyte stem cells.

  15. MAPLE deposition of 3D micropatterned polymeric substrates for cell culture

    3D micropatterned poly(lactide-co-glycolide)/polyurethane (PLGA/PU) substrates were produced by MAPLE deposition through masks and used for regulating the behavior of oral keratinocyte stem cells in response to topography. Flat PLGA/PU substrates were produced for comparison. 3D imaging of the PLGA/PU substrates and of the cultured cells was performed by Digital Holographic Microscopy. The micropatterns were in the shape of squares of 50 × 50 and 80 × 80 μm2 areas, ∼1.8 μm in height and separated by 20 μm wide channels. It was found that substrate topography guided the adhesion of the cultured cells: on the smooth substrates the cells adhered randomly and showed no preferred orientation; in contrast, on the micropatterned substrates the cells adhered preferentially onto the squares and not in the separating channels. Furthermore, key properties of the cells (size, viability, proliferation rate and stem cell marker expression) did not show any dependence on substrate topography. The size of the cultured cells, their viability, the proportions of actively/slow proliferating cells, as well as the stem cell markers expressions, were similar for both flat and micropatterned substrates. Finally, it was found that the cells cultured on the PLGA/PU substrates deposited by MAPLE exhibited similar properties as the controls (i.e. cells cultured on glass slides), indicating the capability of the former to preserve the properties of the keratinocyte stem cells.

  16. Fabrication of Dye-Sensitized Solar Cells with a 3D Nanostructured Electrode

    Guo-Yang Chen

    2010-01-01

    Full Text Available A novel Dye-Sensitized Solar Cell (DSSC scheme for better solar conversion efficiency is proposed. The distinctive characteristic of this novel scheme is that the conventional thin film electrode is replaced by a 3D nanostructured indium tin oxide (ITO electrode, which was fabricated using RF magnetron sputtering with an anodic aluminum oxide (AAO template. The template was prepared by immersing the barrier-layer side of an AAO film into a 30 wt% phosphoric acid solution to produce a contrasting surface. RF magnetron sputtering was then used to deposit a 3D nanostructured ITO thin film on the template. The crystallinity and conductivity of the 3D ITO films were further enhanced by annealing. Titanium dioxide nanoparticles were electrophoretically deposited on the 3D ITO film after which the proposed DSSC was formed by filling vacant spaces in the 3D nanostructured ITO electrode with dye. The measured solar conversion efficiency of the device was 0.125%. It presents a 5-fold improvement over that of conventional spin-coated TiO2 film electrode DSSCs.

  17. Computational Graph Model for 3D Cells Tracking in Zebra Fish Datasets

    Zhang, Lelin; Xiong, Hongkai; Zhao, Yang; Zhang, Kai; Zhou, Xiaobo

    2007-11-01

    This paper leads to a novel technique for tracking and identification of zebra-fish cells in 3D image sequences, extending graph-based multi-objects tracking algorithm to 3D applications. As raised in previous work of 2D graph-based method, separated cells are modeled as vertices that connected by edges. Then the tracking work is simplified to that of vertices matching between graphs generated from consecutive frames. Graph-based tracking is composed of three steps: graph generation, initial source vertices selection and graph saturation. To satisfy demands in this work separated cell records are segmented from original datasets using 3D level-set algorithms. Besides, advancements are achieved in each of the step including graph regulations, multi restrictions on source vertices and enhanced flow quantifications. Those strategies make a good compensation for graph-based multi-objects tracking method in 2D space. Experiments are carried out in 3D datasets sampled from zebra fish, results of which shows that this enhanced method could be potentially applied to tracking of objects with diverse features.

  18. Organic MEMS/NEMS-based high-efficiency 3D ITO-less flexible photovoltaic cells

    A novel approach based on three-dimensional (3D) architecture for polymeric photovoltaic cells made up of an array of sub-micron and nano-pillars which not only increase the area of the light absorbing surface, but also improve the carrier collection efficiency of bulk-heterojunction organic solar cells is presented. The approach also introduces coating of 3D anodes with a new solution-processable highly conductive transparent polymer (Orgacon™) that replaces expensive vacuum-deposited ITO (indium tin oxide) as well as the additional hole-collecting layer of conventional PEDOT:PSS (poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate)). In addition, the described procedure is well suited to roll-to-roll high-throughput manufacturing. The high aspect-ratio 3D pillars which form the basis for this new architecture are patterned through micro-electromechanical-system- and nano-electromechanical-system-based processes. For the particular case of P3HT (poly(3-hexylthiophene)) and PCBM (phenyl-C61-butyric acid methyl ester) active material, efficiencies in excess of 6% have been achieved for these photovoltaic cells of 3D architecture using ITO-less flexible PET (polyethylene terephthalate) substrates. This increase in efficiency turns out to be more than twice higher than those achieved for their 2D counterparts. (paper)

  19. Multiscale modeling of mechanosensing channels on vesicles and cell membranes in 3D constricted flows and shear flows

    Peng, Zhangli; Pak, On Shun; Young, Yuan-Nan; Liu, Allen; Stone, Howard

    2015-11-01

    We investigate the gating of mechanosensing channels (Mscls) on vesicles and cell membranes under different flow conditions using a multiscale approach. At the cell level (microns), the membrane tension is calculated using a 3D two-component whole-cell membrane model based on dissipative particle dynamics (DPD), including the cortex cytoskeleton and its interactions with the lipid bilayer. At the Mscl level (nanometers), we predict the relation between channel gating and the membrane tension obtained from a cell-level model using a semi-analytical model based on the bilayer hydrophobic mismatch energy. We systematically study the gating of Mscls of vesicles and cell membranes in constricted channel flows and shear flows, and explore the dependence of the gating on flow rate, cell shape and size. The results provide guidance for future experiments in inducing Mscl opening for various purposes such as drug delivery.

  20. 3D particle tracking velocimetry using dynamic discrete tomography for plasma physics applications

    Moseev, Dmitry; Alpers, Andreas; Gritzmann, Peter;

    2013-01-01

    3D particle tracking velocimetry (PTV) is a diagnostic technique which is widely used for studying flows, combustion, and plasmas. Current tomographic particle tracking methods are based on the multiplicative algebraic reconstruction technique and used for reconstructing the distribution of multi......-pixel sized particles as greylevel images. Reconstructions obtained by these methods do not necessarily match the experimental data. We propose a new algorithm which can be used for tracking dust particles in tokamaks and stellarators, as well as in low-temperature and complex plasmas. The dynamic discrete...... tomography algorithm is efficient for data from two projection directions and exact. The non-uniqueness can be detected and tracked individually. The algorithm performance is proportional to N3 on average where N is the number of particles in the reconstruction. There is a room for further improvement of the...

  1. Self-Consistent 3D Modeling of Electron Cloud Dynamics and Beam Response

    We present recent advances in the modeling of beam electron-cloud dynamics, including surface effects such as secondary electron emission, gas desorption, etc, and volumetric effects such as ionization of residual gas and charge-exchange reactions. Simulations for the HCX facility with the code WARP/POSINST will be described and their validity demonstrated by benchmarks against measurements. The code models a wide range of physical processes and uses a number of novel techniques, including a large-timestep electron mover that smoothly interpolates between direct orbit calculation and guiding-center drift equations, and a new computational technique, based on a Lorentz transformation to a moving frame, that allows the cost of a fully 3D simulation to be reduced to that of a quasi-static approximation

  2. Development of an environment for 3D visualization of riser dynamics

    Bernardes Junior, Joao Luiz; Martins, Clovis de Arruda [Universidade de Sao Paulo (USP), SP (Brazil). Escola Politecnica]. E-mails: joao.bernardes@poli.usp.br; cmartins@usp.br

    2006-07-01

    This paper describes the merging of Virtual Reality and Scientific Visualization techniques in the development of Riser View, a multi platform 3D environment for real time, interactive visualization of riser dynamics. Its features, architecture, unusual collision detection algorithm and how up was customized for the project are discussed. Using Open GL through VRK, the software is able to make use of the resources available in most modern Graphics. Acceleration Hardware to improve performance. IUP/LED allows for native loo-and-feel in MS-Windows or Linux platform. The paper discusses conflicts that arise between scientific visualization and aspects such as realism and immersion, and how the visualization is prioritized. (author)

  3. A 3D dynamical biomechanical tongue model to study speech motor control

    Gérard, J M; Perrier, P; Payan, Y; Gerard, Jean-Michel; Wilhelms-Tricarico, Reiner; Perrier, Pascal; Payan, Yohan

    2003-01-01

    A 3D biomechanical dynamical model of human tongue is presented, that is elaborated in the aim to test hypotheses about speech motor control. Tissue elastic properties are accounted for in Finite Element Modeling (FEM). The FEM mesh was designed in order to facilitate the implementation of muscle arrangement within the tongue. Therefore, its structure was determined on the basis of accurate anatomical data about the tongue. Mechanically, the hypothesis of hyperelasticity was adopted with the Mooney-Rivlin formulation of the strain energy function. Muscles are modeled as general force generators that act on anatomically specified sets of nodes of the FEM structure. The 8 muscles that are known to be largely involved in the production of basic speech movements are modeled. The model and the solving of the Lagrangian equations of movement are implemented using the ANSYSTM software. Simulations of the influence of muscle activations onto the tongue shape are presented and analyzed.

  4. Human dental pulp stem cells produce mineralized matrix in 2D and 3D cultures

    M. Riccio; Resca, E.; Maraldi, T; Pisciotta, A.; Ferrari, A; Bruzzesi, G.; De Pol, A.

    2010-01-01

    The aim of this study was to characterize the in vitro osteogenic differentiation of dental pulp stem cells (DPSCs) in 2D cultures and 3D biomaterials. DPSCs, separated from dental pulp by enzymatic digestion, and isolated by magnetic cell sorting were differentiated toward osteogenic lineage on 2D surface by using an osteogenic medium. During the differentiation process, DPSCs express specific bone proteins like Runx-2, Osx, OPN and OCN with a sequential expression, analogous to those occurr...

  5. 3D-printing of Redox flow batteries for energy storage: a rapid prototype laboratory cell

    Arenas-Martinez, L.F.; Walsh, F.C.; Ponce de Leon, C.

    2015-01-01

    Although interest in redox flow batteries (RFBs) for energy storage has grown over the last few years, implementation of RFB technology has been slow and challenging. Recent developments in 3D-printing of materials enable a transforming technology for fast, reproducible and documented cell manufacture. This technology can give an improved engineering approach to cell design and fabrication, needed to fulfil requirements for lower cost, longer lifetime hardware capable of efficient reliable pe...

  6. Development of bioartificial myocardium by electrostimulation of 3D collagen scaffolds seeded with stem cells

    Alain Carpentier; Juan C. Chachques; Fabien Legrand; Samira Benadda; Nermine Lila; Kanwal Haneef

    2012-01-01

    Electrostimulation (ES) can be defined as a safe physical method to induce stem cell differentiation. The aim of this study is to evaluate the effectiveness of ES on bone marrow mesenchymal stem cells (BMSCs) seeded in collagen scaffolds in terms of proliferation and differentiation into cardiomyocytes. BMSCs were isolated from Wistar rats and seeded into 3D collagen type 1 templates measuring 25 x 25 x 6 mm. Bipolar in vitro ES was performed during 21 days. Electrical im...

  7. 3D Reconstruction of Human Laryngeal Dynamics Based on Endoscopic High-Speed Recordings.

    Semmler, Marion; Kniesburges, Stefan; Birk, Veronika; Ziethe, Anke; Patel, Rita; Dollinger, Michael

    2016-07-01

    Standard laryngoscopic imaging techniques provide only limited two-dimensional insights into the vocal fold vibrations not taking the vertical component into account. However, previous experiments have shown a significant vertical component in the vibration of the vocal folds. We present a 3D reconstruction of the entire superior vocal fold surface from 2D high-speed videoendoscopy via stereo triangulation. In a typical camera-laser set-up the structured laser light pattern is projected on the vocal folds and captured at 4000 fps. The measuring device is suitable for in vivo application since the external dimensions of the miniaturized set-up barely exceed the size of a standard rigid laryngoscope. We provide a conservative estimate on the resulting resolution based on the hardware components and point out the possibilities and limitations of the miniaturized camera-laser set-up. In addition to the 3D vocal fold surface, we extended previous approaches with a G2-continuous model of the vocal fold edge. The clinical applicability was successfully established by the reconstruction of visual data acquired from 2D in vivo high-speed recordings of a female and a male subject. We present extracted dynamic parameters like maximum amplitude and velocity in the vertical direction. The additional vertical component reveals deeper insights into the vibratory dynamics of the vocal folds by means of a non-invasive method. The successful miniaturization allows for in vivo application giving access to the most realistic model available and hence enables a comprehensive understanding of the human phonation process. PMID:26829782

  8. Defining an optimal surface chemistry for pluripotent stem cell culture in 2D and 3D

    Zonca, Michael R., Jr.

    Surface chemistry is critical for growing pluripotent stem cells in an undifferentiated state. There is great potential to engineer the surface chemistry at the nanoscale level to regulate stem cell adhesion. However, the challenge is to identify the optimal surface chemistry of the substrata for ES cell attachment and maintenance. Using a high-throughput polymerization and screening platform, a chemically defined, synthetic polymer grafted coating that supports strong attachment and high expansion capacity of pluripotent stem cells has been discovered using mouse embryonic stem (ES) cells as a model system. This optimal substrate, N-[3-(Dimethylamino)propyl] methacrylamide (DMAPMA) that is grafted on 2D synthetic poly(ether sulfone) (PES) membrane, sustains the self-renewal of ES cells (up to 7 passages). DMAPMA supports cell attachment of ES cells through integrin beta1 in a RGD-independent manner and is similar to another recently reported polymer surface. Next, DMAPMA has been able to be transferred to 3D by grafting to synthetic, polymeric, PES fibrous matrices through both photo-induced and plasma-induced polymerization. These 3D modified fibers exhibited higher cell proliferation and greater expression of pluripotency markers of mouse ES cells than 2D PES membranes. Our results indicated that desirable surfaces in 2D can be scaled to 3D and that both surface chemistry and structural dimension strongly influence the growth and differentiation of pluripotent stem cells. Lastly, the feasibility of incorporating DMAPMA into a widely used natural polymer, alginate, has been tested. Novel adhesive alginate hydrogels have been successfully synthesized by either direct polymerization of DMAPMA and methacrylic acid blended with alginate, or photo-induced DMAPMA polymerization on alginate nanofibrous hydrogels. In particular, DMAPMA-coated alginate hydrogels support strong ES cell attachment, exhibiting a concentration dependency of DMAPMA. This research provides a

  9. Cell counting in human endobronchial biopsies--disagreement of 2D versus 3D morphometry.

    Vlad A Bratu

    Full Text Available QUESTION: Inflammatory cell numbers are important endpoints in clinical studies relying on endobronchial biopsies. Assumption-based bidimensional (2D counting methods are widely used, although theoretically design-based stereologic three-dimensional (3D methods alone offer an unbiased quantitative tool. We assessed the method agreement between 2D and 3D counting designs in practice when applied to identical samples in parallel. MATERIALS AND METHODS: Biopsies from segmental bronchi were collected from healthy non-smokers (n = 7 and smokers (n = 7, embedded and sectioned exhaustively. Systematic uniform random samples were immunohistochemically stained for macrophages (CD68 and T-lymphocytes (CD3, respectively. In identical fields of view, cell numbers per volume unit (NV were assessed using the physical disector (3D, and profiles per area unit (NA were counted (2D. For CD68+ cells, profiles with and without nucleus were separately recorded. In order to enable a direct comparison of the two methods, the zero-dimensional CD68+/CD3+-ratio was calculated for each approach. Method agreement was tested by Bland-Altmann analysis. RESULTS: In both groups, mean CD68+/CD3+ ratios for NV and NA were significantly different (non-smokers: 0.39 and 0.68, p<0.05; smokers: 0.49 and 1.68, p<0.05. When counting only nucleated CD68+ profiles, mean ratios obtained by 2D and 3D counting were similar, but the regression-based Bland-Altmann analysis indicated a bias of the 2D ratios proportional to their magnitude. This magnitude dependent deviation differed between the two groups. CONCLUSIONS: 2D counts of cell and nuclear profiles introduce a variable size-dependent bias throughout the measurement range. Because the deviation between the 3D and 2D data was different in the two groups, it precludes establishing a 'universal conversion formula'.

  10. A 3D printed nano bone matrix for characterization of breast cancer cell and osteoblast interactions

    Zhu, Wei; Castro, Nathan J.; Cui, Haitao; Zhou, Xuan; Boualam, Benchaa; McGrane, Robert; Glazer, Robert I.; Zhang, Lijie Grace

    2016-08-01

    Bone metastasis is one of the most prevalent complications of late-stage breast cancer, in which the native bone matrix components, including osteoblasts, are intimately involved in tumor progression. The development of a successful in vitro model would greatly facilitate understanding the underlying mechanism of breast cancer bone invasion as well as provide a tool for effective discovery of novel therapeutic strategies. In the current study, we fabricated a series of in vitro bone matrices composed of a polyethylene glycol hydrogel and nanocrystalline hydroxyapatite of varying concentrations to mimic the native bone microenvironment for the investigation of breast cancer bone metastasis. A stereolithography-based three-dimensional (3D) printer was used to fabricate the bone matrices with precisely controlled architecture. The interaction between breast cancer cells and osteoblasts was investigated in the optimized bone matrix. Using a Transwell® system to separate the two cell lines, breast cancer cells inhibited osteoblast proliferation, while osteoblasts stimulated breast cancer cell growth, whereas, both cell lines increased IL-8 secretion. Breast cancer cells co-cultured with osteoblasts within the 3D bone matrix formed multi-cellular spheroids in comparison to two-dimensional monolayers. These findings validate the use of our 3D printed bone matrices as an in vitro metastasis model, and highlights their potential for investigating breast cancer bone metastasis.

  11. 3D nanochannel electroporation for high-throughput cell transfection with high uniformity and dosage control

    Chang, Lingqian; Bertani, Paul; Gallego-Perez, Daniel; Yang, Zhaogang; Chen, Feng; Chiang, Chiling; Malkoc, Veysi; Kuang, Tairong; Gao, Keliang; Lee, L. James; Lu, Wu

    2015-12-01

    Of great interest to modern medicine and biomedical research is the ability to inject individual target cells with the desired genes or drug molecules. Some advances in cell electroporation allow for high throughput, high cell viability, or excellent dosage control, yet no platform is available for the combination of all three. In an effort to solve this problem, here we show a ``3D nano-channel electroporation (NEP) chip'' on a silicon platform designed to meet these three criteria. This NEP chip can simultaneously deliver the desired molecules into 40 000 cells per cm2 on the top surface of the device. Each 650 nm pore aligns to a cell and can be used to deliver extremely small biological elements to very large plasmids (>10 kbp). When compared to conventional bulk electroporation (BEP), the NEP chip shows a 20 fold improvement in dosage control and uniformity, while still maintaining high cell viability (>90%) even in cells such as cardiac cells which are characteristically difficult to transfect. This high-throughput 3D NEP system provides an innovative and medically valuable platform with uniform and reliable cellular transfection, allowing for a steady supply of healthy, engineered cells.Of great interest to modern medicine and biomedical research is the ability to inject individual target cells with the desired genes or drug molecules. Some advances in cell electroporation allow for high throughput, high cell viability, or excellent dosage control, yet no platform is available for the combination of all three. In an effort to solve this problem, here we show a ``3D nano-channel electroporation (NEP) chip'' on a silicon platform designed to meet these three criteria. This NEP chip can simultaneously deliver the desired molecules into 40 000 cells per cm2 on the top surface of the device. Each 650 nm pore aligns to a cell and can be used to deliver extremely small biological elements to very large plasmids (>10 kbp). When compared to conventional bulk

  12. Transforming 2d Cadastral Data Into a Dynamic Smart 3d Model

    Tsiliakou, E.; Labropoulos, T.; Dimopoulou, E.

    2013-08-01

    3D property registration has become an imperative need in order to optimally reflect all complex cases of the multilayer reality of property rights and restrictions, revealing their vertical component. This paper refers to the potentials and multiple applications of 3D cadastral systems and explores the current state-of-the art, especially the available software with which 3D visualization can be achieved. Within this context, the Hellenic Cadastre's current state is investigated, in particular its data modeling frame. Presenting the methodologies and specifications addressing the registration of 3D properties, the operating cadastral system's shortcomings and merits are pointed out. Nonetheless, current technological advances as well as the availability of sophisticated software packages (proprietary or open source) call for 3D modeling. In order to register and visualize the complex reality in 3D, Esri's CityEngine modeling software has been used, which is specialized in the generation of 3D urban environments, transforming 2D GIS Data into Smart 3D City Models. The application of the 3D model concerns the Campus of the National Technical University of Athens, in which a complex ownership status is established along with approved special zoning regulations. The 3D model was built using different parameters based on input data, derived from cadastral and urban planning datasets, as well as legal documents and architectural plans. The process resulted in a final 3D model, optimally describing the cadastral situation and built environment and proved to be a good practice example of 3D visualization.

  13. A 3-D Model of a Perennial Ryegrass Primary Cell Wall and Its Enzymatic Degradation

    Indrakumar Vetharaniam; Kelly, William J.; Graeme T. Attwood; Harris, Philip J.

    2014-01-01

    We have developed a novel 3-D, agent-based model of cell-wall digestion to improve our understanding of ruminal cell-wall digestion. It offers a capability to study cell walls and their enzymatic modification, by providing a representation of cellulose microfibrils and non-cellulosic polysaccharides and by simulating their spatial and catalytic interactions with enzymes. One can vary cell-wall composition and the types and numbers of enzyme molecules, allowing the model to be applied to a ran...

  14. 3D cell culture systems modeling tumor growth determinants in cancer target discovery.

    Thoma, Claudio R; Zimmermann, Miriam; Agarkova, Irina; Kelm, Jens M; Krek, Wilhelm

    2014-04-01

    Phenotypic heterogeneity of cancer cells, cell biological context, heterotypic crosstalk and the microenvironment are key determinants of the multistep process of tumor development. They sign responsible, to a significant extent, for the limited response and resistance of cancer cells to molecular-targeted therapies. Better functional knowledge of the complex intra- and intercellular signaling circuits underlying communication between the different cell types populating a tumor tissue and of the systemic and local factors that shape the tumor microenvironment is therefore imperative. Sophisticated 3D multicellular tumor spheroid (MCTS) systems provide an emerging tool to model the phenotypic and cellular heterogeneity as well as microenvironmental aspects of in vivo tumor growth. In this review we discuss the cellular, chemical and physical factors contributing to zonation and cellular crosstalk within tumor masses. On this basis, we further describe 3D cell culture technologies for growth of MCTS as advanced tools for exploring molecular tumor growth determinants and facilitating drug discovery efforts. We conclude with a synopsis on technological aspects for on-line analysis and post-processing of 3D MCTS models. PMID:24636868

  15. Melanin Transfer in Human 3D Skin Equivalents Generated Exclusively from Induced Pluripotent Stem Cells.

    Karl Gledhill

    Full Text Available The current utility of 3D skin equivalents is limited by the fact that existing models fail to recapitulate the cellular complexity of human skin. They often contain few cell types and no appendages, in part because many cells found in the skin are difficult to isolate from intact tissue and cannot be expanded in culture. Induced pluripotent stem cells (iPSCs present an avenue by which we can overcome this issue due to their ability to be differentiated into multiple cell types in the body and their unlimited growth potential. We previously reported generation of the first human 3D skin equivalents from iPSC-derived fibroblasts and iPSC-derived keratinocytes, demonstrating that iPSCs can provide a foundation for modeling a complex human organ such as skin. Here, we have increased the complexity of this model by including additional iPSC-derived melanocytes. Epidermal melanocytes, which are largely responsible for skin pigmentation, represent the second most numerous cell type found in normal human epidermis and as such represent a logical next addition. We report efficient melanin production from iPSC-derived melanocytes and transfer within an entirely iPSC-derived epidermal-melanin unit and generation of the first functional human 3D skin equivalents made from iPSC-derived fibroblasts, keratinocytes and melanocytes.

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

    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

  17. A digital holography set-up for 3D vortex flow dynamics

    Lebon, Benoît; Perret, Gaële; Coëtmellec, Sébastien; Godard, Gilles; Gréhan, Gérard; Lebrun, Denis; Brossard, Jérôme

    2016-06-01

    In the present paper, a digital in-line holography (DIH) set-up, with a converging beam, is used to take three-dimensional (3D) velocity measurements of vortices. The vortices are formed periodically at the edges of a submerged horizontal plate submitted to regular waves. They take the form of vortex filaments that extend from side to side of the channel. They undergo strongly three-dimensional instability mechanisms that remain very complicated to characterize experimentally. The experiments are performed in a 10 × 0.3 × 0.3 m3 wave flume. The DIH set-up is performed using a modulated laser diode emitting at the wavelength of 640 nm and a lensless CCD camera. The beam crosses the channel side to side. To reveal the flow dynamics, 30-μm hydrogen bubbles are generated at the edge of the plate to serve as tracers. Their locations are recorded on the holograms multiple times to access the dynamics of the flow. This method leads to an accuracy in the order of 100 μm on the axial location. Those measurements have been validated with stereo-PIV measurements. A very good agreement is found on time-averaged velocity fields between the two techniques.

  18. The Shock Dynamics of Heterogeneous YSO Jets: 3-D Simulations Meet Multi-Epoch Observations

    Hansen, E C; Hartigan, P; Lebedev, S V

    2016-01-01

    High resolution observations of Young Stellar Object (YSO) jets show them to be composed of many small-scale knots or clumps. In this paper we report results of 3-D numerical simulations designed to study how such clumps interact and create morphologies and kinematic patterns seen in emission line observations. Our simulations focus on clump scale dynamics by imposing velocity differences between spherical, over-dense regions which then lead to the formation of bow shocks as faster clumps overtake slower material. We show that much of the spatial structure apparent in emission line images of jets arises from the dynamics and interactions of these bow shocks. Our simulations show a variety of time-dependent features, including bright knots associated with Mach stems where the shocks intersect, a "frothy" emission structure that arises from the presence of the Non-linear Thin Shell Instability (NTSI) along the surfaces of the bow shocks, and the merging and fragmentation of clumps. Our simulations use a new non...

  19. 3D photonic crystal intermediate reflector for micromorph thin-film tandem solar cell

    Uepping, Johannes; Miclea, Paul T.; Wehrspohn, Ralf B. [Institute of Physics, Martin-Luther-University of Halle-Wittenberg, Heinrich-Damerow-Str. 4, 06120 Halle (Germany); Rockstuhl, Carsten; Lederer, Falk [Institute of Condensed Matter Theory and Solid States Optics, Friedrich Schiller University Jena, 07743 Jena (Germany); Peters, Marius [Freiburg Centre for Material Research, University of Freiburg, 79104 Freiburg (Germany); Steidl, Lorenz; Zentel, Rudolf [Dept. of Chemistry, Pharmacy and Earth Science, Johannes Gutenberg University of Mainz, Duesbergweg 10-14 (Germany); Lee, Seung-Mo; Knez, Mato [Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle (Germany); Lambertz, Andreas; Carius, Reinhard [Institute of Energy Research, IEF-5 Photovoltaics, Forschungszentrum Juelich GmbH, 52425 Juelich (Germany); Bielawny, Andreas

    2008-12-15

    The concept of 3D photonic intermediate reflectors for micromorph silicon tandem solar cells has been investigated. In thin-film silicon tandem solar cells consisting of amorphous and microcrystalline silicon with two junctions of a-Si/{mu}c-Si, efficiency enhancements can be achieved by increasing the current density in the a-Si top cell. It is one goal to provide an optimized current matching at high current densities. For an ideal photon-management between top and bottom cell, a spectrally selective intermediate reflective layer (IRL) is necessary, which is less dependent of the angle of incidence than state-of-the-art thickness dependent massive interlayers. The design, preparation and characterization of a 3D photonic thin-film filter device for this purpose has been pursued straight forward in simulation and experimental realization. The inverted opal is capable of providing a suitable optical band stop with high reflectance and the necessary long wavelength transmittance as well and provides further options for improved light trapping. We have determined numerically the relative efficiency enhancement of an a-Si/{mu}c-Si tandem solar cell using a conductive 3D-photonic crystal. We have further fabricated such structures by ZnO-replication of polymeric opals using chemical vapour deposition and atomic layer deposition techniques and present the results of their characterization. Thin film photonic IRL have been prepared at the rear side of a-Si solar cells. Completed with a back contact, this is the first step to integrate this novel technology into an a-Si/{mu}c-Si tandem solar cell process. The spectral response of the cell is presented and compared with reference cells. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  20. Modeling the Dynamic Damage Process of the SiC3d/Al Interpenetrating Phase Composites

    In the current study, a 3D mesoscopic structure FE-Model of interpenetrating SiC3d/Al composite is built based on the digital image-based modeling technique together with optimized methods of three-dimensional mesh generation. Subsequently, the finite element method is proposed to simulate the dynamic damage process of the interpenetrating phase composites SiC3d/Al under dynamic axial crushing. The cracking process in micro 3D space is clearly presented in the current study. It is shown that the cracks initialization and propagation mainly appear in the region of interface between ceramic and metallic phase. Moreover, the ceramic phase attributes to the model's damage predominantly. The method proposed in this paper would be of help in the microstructure design of Interpenetrating Phase Composites.

  1. Total 3D imaging of phase objects using defocusing microscopy: application to red blood cells

    Roma, P M S; Amaral, F T; Agero, U; Mesquita, O N

    2014-01-01

    We present Defocusing Microscopy (DM), a bright-field optical microscopy technique able to perform total 3D imaging of transparent objects. By total 3D imaging we mean the determination of the actual shapes of the upper and lower surfaces of a phase object. We propose a new methodology using DM and apply it to red blood cells subject to different osmolality conditions: hypotonic, isotonic and hypertonic solutions. For each situation the shape of the upper and lower cell surface-membranes (lipid bilayer/cytoskeleton) are completely recovered, displaying the deformation of RBCs surfaces due to adhesion on the glass-substrate. The axial resolution of our technique allowed us to image surface-membranes separated by distances as small as 300 nm. Finally, we determine volume, superficial area, sphericity index and RBCs refractive index for each osmotic condition.

  2. Determination of key parameters of SEU occurrence using 3-D full cell SRAM simulations

    A 3-D entire SRAM cell, based on a 0.35-microm current CMOS technology, is simulated in this work with a DEVICE simulator. The transient current, resulting from a heavy ion strike in the most sensitive region of the cell, is studied as a function of the LET value, the cell layout and the ion penetration depth. A definition of the critical charge is proposed and two new methods are presented to compute this basic amount of charge only using SPICE simulations. Numerical applications are performed with two different generations of submicron CMOS technologies, including the determination of the sensitive thicknesses

  3. In-chip fabrication of free-form 3D constructs for directed cell migration analysis

    Olsen, Mark Holm; Hjortø, Gertrud Malene; Hansen, Morten;

    2013-01-01

    Free-form constructs with three-dimensional (3D) microporosity were fabricated by two-photon polymerization inside the closed microchannel of an injection-molded, commercially available polymer chip for analysis of directed cell migration. Acrylate constructs were produced as woodpile topologies...... with a range of pore sizes from 5 × 5 μm to 15 × 15 μm and prefilled with fibrillar collagen. Dendritic cells seeded into the polymer chip in a concentration gradient of the chemoattractant CCL21 efficiently negotiated the microporous maze structure for pore sizes of 8 × 8 μm or larger. The cells...

  4. Controlled Positioning of Cells in Biomaterials—Approaches Towards 3D Tissue Printing

    Sandra Hofmann

    2011-08-01

    Full Text Available Current tissue engineering techniques have various drawbacks: they often incorporate uncontrolled and imprecise scaffold geometries, whereas the current conventional cell seeding techniques result mostly in random cell placement rather than uniform cell distribution. For the successful reconstruction of deficient tissue, new material engineering approaches have to be considered to overcome current limitations. An emerging method to produce complex biological products including cells or extracellular matrices in a controlled manner is a process called bioprinting or biofabrication, which effectively uses principles of rapid prototyping combined with cell-loaded biomaterials, typically hydrogels. 3D tissue printing is an approach to manufacture functional tissue layer-by-layer that could be transplanted in vivo after production. This method is especially advantageous for stem cells since a controlled environment can be created to influence cell growth and differentiation. Using printed tissue for biotechnological and pharmacological needs like in vitro drug-testing may lead to a revolution in the pharmaceutical industry since animal models could be partially replaced by biofabricated tissues mimicking human physiology and pathology. This would not only be a major advancement concerning rising ethical issues but would also have a measureable impact on economical aspects in this industry of today, where animal studies are very labor-intensive and therefore costly. In this review, current controlled material and cell positioning techniques are introduced highlighting approaches towards 3D tissue printing.

  5. Coculture System with an Organotypic Brain Slice and 3D Spheroid of Carcinoma Cells

    Chuang, Han-Ning; Lohaus, Raphaela; Hanisch, Uwe-Karsten; Binder, Claudia

    2013-01-01

    Patients with cerebral metastasis of carcinomas have a poor prognosis. However, the process at the metastatic site has barely been investigated, in particular the role of the resident (stromal) cells. Studies in primary carcinomas demonstrate the influence of the microenvironment on metastasis, even on prognosis1,2. Especially the tumor associated macrophages (TAM) support migration, invasion and proliferation3. Interestingly, the major target sites of metastasis possess tissue-specific macrophages, such as Kupffer cells in the liver or microglia in the CNS. Moreover, the metastatic sites also possess other tissue-specific cells, like astrocytes. Recently, astrocytes were demonstrated to foster proliferation and persistence of cancer cells4,5. Therefore, functions of these tissue-specific cell types seem to be very important in the process of brain metastasis6,7. Despite these observations, however, up to now there is no suitable in vivo/in vitro model available to directly visualize glial reactions during cerebral metastasis formation, in particular by bright field microscopy. Recent in vivo live imaging of carcinoma cells demonstrated their cerebral colonization behavior8. However, this method is very laborious, costly and technically complex. In addition, these kinds of animal experiments are restricted to small series and come with a substantial stress for the animals (by implantation of the glass plate, injection of tumor cells, repetitive anaesthesia and long-term fixation). Furthermore, in vivo imaging is thus far limited to the visualization of the carcinoma cells, whereas interactions with resident cells have not yet been illustrated. Finally, investigations of human carcinoma cells within immunocompetent animals are impossible8. For these reasons, we established a coculture system consisting of an organotypic mouse brain slice and epithelial cells embedded in matrigel (3D cell sphere). The 3D carcinoma cell spheres were placed directly next to the brain

  6. Non-crimp 3D woven composites unit cell: from geometric modelling to damage simulation

    Bedogni, Enrico

    2013-01-01

    In the last twenty years, the research on composite materials has increased and many progresses have been made. However, there are still unresolved issues concerning the geometric modelling of a material at the meso-level (i.e. on a unit cell) and its damage simulation. In particular, the complexity of the internal geometry of some composite materials, such as 3D textiles, yields to new challenges for the research community. A correct definition of the internal structure in all the important ...

  7. Digital holography for recovering 3D shape of red blood cells

    Memmolo, P.; Miccio, L.; Merola, F.; Gennari, O.; Netti, P.; Ferraro, Pietro

    2015-07-01

    Full morphometric data analysis and 3D rendering of Red Blood Cells (RBCs) is provided by means of Digital Holography (DH) in combination with Optical Tweezers (OT). The proposed method is compared with a geometrical model of RBC in order to evaluate its accuracy and tested for many kinds of RBCs, from healthy ones with double-concavity to that with abnormal shapes. Applications in diagnostics are foreseen.

  8. A Prospective Study of Breast Dynamic Morphological Changes after Dual-plane Augmentation Mammaplasty with 3D Scanning Technique

    Ji, Kai; Luan, Jie; LIU, CHUNJUN; Mu, Dali; Mu, Lanhua; Xin, Minqiang; Sun, Jingjing; Yin, Shilu; Chen, Lin

    2014-01-01

    Background The dual-plane technique has been widely used in augmentation mammaplasty procedures. However, there are some concerns about aesthetic contour maintenance for long time after muscle releasing. This study aims to track and analyze breast dynamic morphological changes after dual-plane breast augmentation with three-dimensional (3D) scanning technique. Methods Thirteen dual-plane anatomic implant augmentation patients underwent 3D scanning preoperatively (pre-OP) and postoperatively i...

  9. 3D airflow dynamics over transverse ridges Mpekweni, South Africa: implications for dune field migration behaviour

    Jackson, Derek; Cooper, Andrew; Green, Andrew; Beyers, Meiring; Wiles, Errol; Benallack, Keegan

    2016-04-01

    Un-vegetated dune fields provide excellent opportunities to examine airflow dynamics over various types and scales of dune landforms. The three dimensional surface over which lower boundary layers travel, help adjust surface airflow and consequently the aeolian response of the dunes themselves. The use of computational fluid dynamic (CFD) modelling in recent studies now enables investigation of the 3D behaviour of airflow over complex terrain, providing new insights into heterogeneous surface flow and aeolian response of dune surfaces on a large (dunefield) scale. Using a largely un-vegetated coastal dune field site at Mpekweni, Eastern Cape, South Africa, a detailed (0.1m gridded) terrestrial laser scanning survey was conducted to create a high resolution topographical surface. Using local wind flow measurements and local met station records as input, CFD modelling was performed for a number of scenarios involving variable direction and magnitude to examine surface flow patterns across multiple dune forms. Near surface acceleration, expansion and separation of airflow inducing convergence and divergence (steering) of flow velocity streamlines are investigated. Flow acceleration over dune crests/brink lines is a key parameter in driving dune migration and slip face dynamics. Dune aspect ratio (height to length) is also important in determining the degree of crestal flow acceleration, with an increase in flow associated with increasing aspect ratios. Variations in dune height appear to be the most important parameter in driving general flow acceleration. The results from the study provide new insights into dune migration behaviour at this site as well as surface flow behaviour across multiple dune configurations and length scales within un-vegetated dune fields.

  10. Human dental pulp stem cells produce mineralized matrix in 2D and 3D cultures

    M. Riccio

    2010-11-01

    Full Text Available The aim of this study was to characterize the in vitro osteogenic differentiation of dental pulp stem cells (DPSCs in 2D cultures and 3D biomaterials. DPSCs, separated from dental pulp by enzymatic digestion, and isolated by magnetic cell sorting were differentiated toward osteogenic lineage on 2D surface by using an osteogenic medium. During the differentiation process, DPSCs express specific bone proteins like Runx-2, Osx, OPN and OCN with a sequential expression, analogous to those occurring during osteoblast differentiation, and produce extracellular calcium deposits. In order to differentiate cells in a 3D space that mimes the physiological environment, DPSCs were cultured in two distinct bioscaffolds, MatrigelTM and Collagen sponge. With the addition of a third dimension, osteogenic differentiation and mineralized extracellular matrix production significantly improved. In particular, in MatrigelTM DPSCs differentiated with osteoblast/osteocyte characteristics and connected by gap junction, and therefore formed calcified nodules with a 3D intercellular network. Furthermore, DPSCs differentiated in collagen sponge actively secrete human type I collagen micro-fibrils and form calcified matrix containing trabecular-like structures. These neo-formed DPSCs-scaffold devices may be used in regenerative surgical applications in order to resolve pathologies and traumas characterized by critical size bone defects.

  11. How the venetian blind percept emerges from the laminar cortical dynamics of 3D vision

    Stephen eGrossberg

    2014-01-01

    The 3D LAMINART model of 3D vision and figure-ground perception is used to explain and simulate a key example of the Venetian blind effect and to show how it is related to other well-known perceptual phenomena such as Panum's limiting case. The model proposes how lateral geniculate nucleus (LGN) and hierarchically organized laminar circuits in cortical areas V1, V2, and V4 interact to control processes of 3D boundary formation and surface filling-in that simulate many properties of 3D vision ...

  12. Perfusion Stirred-Tank Bioreactors for 3D Differentiation of Human Neural Stem Cells.

    Simão, Daniel; Arez, Francisca; Terasso, Ana P; Pinto, Catarina; Sousa, Marcos F Q; Brito, Catarina; Alves, Paula M

    2016-01-01

    Therapeutic breakthroughs in neurological disorders have been hampered by the lack of accurate central nervous system (CNS) models. The development of these models allows the study of the disease onset/progression mechanisms and the preclinical evaluation of new therapeutics. This has traditionally relied on genetically engineered animal models that often diverge considerably from the human phenotype (developmental, anatomic, and physiological) and 2D in vitro cell models, which fail to recapitulate the characteristics of the target tissue (cell-cell and cell-matrix interactions, cell polarity, etc.). Recapitulation of CNS phenotypic and functional features in vitro requires the implementation of advanced culture strategies, such as 3D culture systems, which enable to mimic the in vivo structural and molecular complexity. Models based on differentiation of human neural stem cells (hNSC) in 3D cultures have great potential as complementary tools in preclinical research, bridging the gap between human clinical studies and animal models. The development of robust and scalable processes for the 3D differentiation of hNSC can improve the accuracy of early stage development in preclinical research. In this context, the use of software-controlled stirred-tank bioreactors (STB) provides an efficient technological platform for hNSC aggregation and differentiation. This system enables to monitor and control important physicochemical parameters for hNSC culture, such as dissolved oxygen. Importantly, the adoption of a perfusion operation mode allows a stable flow of nutrients and differentiation/neurotrophic factors, while clearing the toxic by-products. This contributes to a setting closer to the physiological, by mimicking the in vivo microenvironment. In this chapter, we address the technical requirements and procedures for the implementation of 3D differentiation strategies of hNSC, by operating STB under perfusion mode for long-term cultures. This strategy is suitable

  13. Toward a 3D dynamic model of a faulty duplex ball bearing

    Kogan, Gideon; Klein, Renata; Kushnirsky, Alex; Bortman, Jacob

    2015-03-01

    Bearings are vital components for safe and proper operation of machinery. Increasing efficiency of bearing diagnostics usually requires training of health and usage monitoring systems via expensive and time-consuming ground calibration tests. The main goal of this research, therefore, is to improve bearing dynamics modeling tools in order to reduce the time and budget needed to implement the health and usage monitoring approach. The proposed three-dimensional ball bearing dynamic model is based on the classic dynamic and kinematic equations. Interactions between the bodies are simulated using non-linear springs combined with dampers described by Hertz-type contact relation. The force friction is simulated using the hyperbolic-tangent function. The model allows simulation of a wide range of mechanical faults. It is validated by comparison to known bearing behavior and to experimental results. The model results are verified by demonstrating numerical convergence. The model results for the two cases of single and duplex angular ball bearings with axial deformation in the outer ring are presented. The qualitative investigation provides insight into bearing dynamics, the sensitivity study generalizes the qualitative findings for similar cases, and the comparison to the test results validates model reliability. The article demonstrates the variety of the cases that the 3D bearing model can simulate and the findings to which it may lead. The research allowed the identification of new patterns generated by single and duplex bearings with axially deformed outer race. It also enlightened the difference between single and duplex bearing manifestation. In the current research the dynamic model enabled better understanding of the physical behavior of the faulted bearings. Therefore, it is expected that the modeling approach has the potential to simplify and improve the development process of diagnostic algorithms. • A deformed outer race of a single axially loaded bearing is

  14. Differences in growth properties of endometrial cancer in three dimensional (3D) culture and 2D cell monolayer

    Chitcholtan, Kenny, E-mail: kenny.chitcholtan@otago.ac.nz [Department of Obstetrics and Gynaecology, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011 (New Zealand); Asselin, Eric, E-mail: Eric.Asselin@uqtr.ca [Department of Chemistry and Biology, University of Quebec, at Trois-Rivières, C.P. 500, Trois-Rivières, Quebec, Canada G9A 5H7 (Canada); Parent, Sophie, E-mail: Sophie.Parent@uqtr.ca [Department of Chemistry and Biology, University of Quebec, at Trois-Rivières, C.P. 500, Trois-Rivières, Quebec, Canada G9A 5H7 (Canada); Sykes, Peter H., E-mail: peter.sykes@otago.ac.nz [Department of Obstetrics and Gynaecology, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011 (New Zealand); Evans, John J., E-mail: john.evans@otago.ac.nz [Department of Obstetrics and Gynaecology, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011 (New Zealand); Centre of Neuroendocrinology and The MacDiarmid Institute of Advanced Materials and Nanotechnology, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011 (New Zealand)

    2013-01-01

    Three-dimensional (3D) in vitro models have an invaluable role in understanding the behaviour of tumour cells in a well defined microenvironment. This is because some aspects of tumour characteristics cannot be fully recapitulated in a cell monolayer (2D). In the present study, we compared growth patterns, expression of signalling molecules, and metabolism-associated proteins of endometrial cancer cell lines in 3D and 2D cell cultures. Cancer cells formed spherical structures in 3D reconstituted basement membrane (3D rBM), and the morphological appearance was cell line dependent. Cell differentiation was observed after 8 days in the 3D rBM. There was reduced proliferation, detected by less expression of PCNA in 3D rBM than in 2D cell monolayers. The addition of exogenous epidermal growth factor (EGF) to cancer cells induced phosphorylation of EGFR and Akt in both cell culture conditions. The uptake of glucose was selectively altered in the 3D rBM, but there was a lack of association with Glut-1 expression. The secretion of vascular endothelial growth factor (VEGF) and prostaglandin E{sub 2} (PGE{sub 2}) was selectively altered in 3D rBM, and it was cell line dependent. Our data demonstrated that 3D rBM as an in vitro model can influence proliferation and metabolism of endometrial cancer cell behaviour compared to 2D cell monolayer. Changes are specific to individual cell types. The use of 3D rBM is, therefore, important in the in vitro study of targeted anticancer therapies.

  15. Differences in growth properties of endometrial cancer in three dimensional (3D) culture and 2D cell monolayer

    Three-dimensional (3D) in vitro models have an invaluable role in understanding the behaviour of tumour cells in a well defined microenvironment. This is because some aspects of tumour characteristics cannot be fully recapitulated in a cell monolayer (2D). In the present study, we compared growth patterns, expression of signalling molecules, and metabolism-associated proteins of endometrial cancer cell lines in 3D and 2D cell cultures. Cancer cells formed spherical structures in 3D reconstituted basement membrane (3D rBM), and the morphological appearance was cell line dependent. Cell differentiation was observed after 8 days in the 3D rBM. There was reduced proliferation, detected by less expression of PCNA in 3D rBM than in 2D cell monolayers. The addition of exogenous epidermal growth factor (EGF) to cancer cells induced phosphorylation of EGFR and Akt in both cell culture conditions. The uptake of glucose was selectively altered in the 3D rBM, but there was a lack of association with Glut-1 expression. The secretion of vascular endothelial growth factor (VEGF) and prostaglandin E2 (PGE2) was selectively altered in 3D rBM, and it was cell line dependent. Our data demonstrated that 3D rBM as an in vitro model can influence proliferation and metabolism of endometrial cancer cell behaviour compared to 2D cell monolayer. Changes are specific to individual cell types. The use of 3D rBM is, therefore, important in the in vitro study of targeted anticancer therapies.

  16. Probabilistic Voxel-Fe model for single cell motility in 3D

    Borau, Carlos; Polacheck, William J; Kamm, Roger D; García-Aznar, José Manuel

    2015-01-01

    Background Cells respond to a variety of external stimuli regulated by the environment conditions. Mechanical, chemical and biological factors are of great interest and have been deeply studied. Furthermore, mathematical and computational models have been rapidly growing over the past few years, permitting researches to run complex scenarios saving time and resources. Usually these models focus on specific features of cell migration, making them only suitable to study restricted phenomena. Methods Here we present a versatile finite element (FE) cell-scale 3D migration model based on probabilities depending in turn on ECM mechanical properties, chemical, fluid and boundary conditions. Results With this approach we are able to capture important outcomes of cell migration such as: velocities, trajectories, cell shape and aspect ratio, cell stress or ECM displacements. Conclusions The modular form of the model will allow us to constantly update and redefine it as advancements are made in clarifying how cellular events take place. PMID:26290806

  17. Exploration of Novel Inhibitors for Bruton's Tyrosine Kinase by 3D QSAR Modeling and Molecular Dynamics Simulation.

    Rohit Bavi

    Full Text Available Bruton's tyrosine kinase (BTK is a cytoplasmic, non-receptor tyrosine kinase which is expressed in most of the hematopoietic cells and plays an important role in many cellular signaling pathways. B cell malignancies are dependent on BCR signaling, thus making BTK an efficient therapeutic target. Over the last few years, significant efforts have been made in order to develop BTK inhibitors to treat B-cell malignancies, and autoimmunity or allergy/hypersensitivity but limited success has been achieved. Here in this study, 3D QSAR pharmacophore models were generated for Btk based on known IC50 values and experimental energy scores with extensive validations. The five features pharmacophore model, Hypo1, includes one hydrogen bond acceptor lipid, one hydrogen bond donor, and three hydrophobic features, which has the highest correlation coefficient (0.98, cost difference (112.87, and low RMS (1.68. It was further validated by the Fisher's randomization method and test set. The well validated Hypo1 was used as a 3D query to search novel Btk inhibitors with different chemical scaffold using high throughput virtual screening technique. The screened compounds were further sorted by applying ADMET properties, Lipinski's rule of five and molecular docking studies to refine the retrieved hits. Furthermore, molecular dynamic simulation was employed to study the stability of docked conformation and to investigate the binding interactions in detail. Several important hydrogen bonds with Btk were revealed, which includes the gatekeeper residues Glu475 and Met 477 at the hinge region. Overall, this study suggests that the proposed hits may be more effective inhibitors for cancer and autoimmune therapy.

  18. 3D hepatic cultures simultaneously maintain primary hepatocyte and liver sinusoidal endothelial cell phenotypes.

    Yeonhee Kim

    Full Text Available Developing in vitro engineered hepatic tissues that exhibit stable phenotype is a major challenge in the field of hepatic tissue engineering. However, the rapid dedifferentiation of hepatic parenchymal (hepatocytes and non-parenchymal (liver sinusoidal endothelial, LSEC cell types when removed from their natural environment in vivo remains a major obstacle. The primary goal of this study was to demonstrate that hepatic cells cultured in layered architectures could preserve or potentially enhance liver-specific behavior of both cell types. Primary rat hepatocytes and rat LSECs (rLSECs were cultured in a layered three-dimensional (3D configuration. The cell layers were separated by a chitosan-hyaluronic acid polyelectrolyte multilayer (PEM, which served to mimic the Space of Disse. Hepatocytes and rLSECs exhibited several key phenotypic characteristics over a twelve day culture period. Immunostaining for the sinusoidal endothelial 1 antibody (SE-1 demonstrated that rLSECs cultured in the 3D hepatic model maintained this unique feature over twelve days. In contrast, rLSECs cultured in monolayers lost their phenotype within three days. The unique stratified structure of the 3D culture resulted in enhanced heterotypic cell-cell interactions, which led to improvements in hepatocyte functions. Albumin production increased three to six fold in the rLSEC-PEM-Hepatocyte cultures. Only rLSEC-PEM-Hepatocyte cultures exhibited increasing CYP1A1/2 and CYP3A activity. Well-defined bile canaliculi were observed only in the rLSEC-PEM-Hepatocyte cultures. Together, these data suggest that rLSEC-PEM-Hepatocyte cultures are highly suitable models to monitor the transformation of toxins in the liver and their transport out of this organ. In summary, these results indicate that the layered rLSEC-PEM-hepatocyte model, which recapitulates key features of hepatic sinusoids, is a potentially powerful medium for obtaining comprehensive knowledge on liver metabolism

  19. 3D Hepatic Cultures Simultaneously Maintain Primary Hepatocyte and Liver Sinusoidal Endothelial Cell Phenotypes

    Kim, Yeonhee; Rajagopalan, Padmavathy

    2010-01-01

    Developing in vitro engineered hepatic tissues that exhibit stable phenotype is a major challenge in the field of hepatic tissue engineering. However, the rapid dedifferentiation of hepatic parenchymal (hepatocytes) and non-parenchymal (liver sinusoidal endothelial, LSEC) cell types when removed from their natural environment in vivo remains a major obstacle. The primary goal of this study was to demonstrate that hepatic cells cultured in layered architectures could preserve or potentially enhance liver-specific behavior of both cell types. Primary rat hepatocytes and rat LSECs (rLSECs) were cultured in a layered three-dimensional (3D) configuration. The cell layers were separated by a chitosan-hyaluronic acid polyelectrolyte multilayer (PEM), which served to mimic the Space of Disse. Hepatocytes and rLSECs exhibited several key phenotypic characteristics over a twelve day culture period. Immunostaining for the sinusoidal endothelial 1 antibody (SE-1) demonstrated that rLSECs cultured in the 3D hepatic model maintained this unique feature over twelve days. In contrast, rLSECs cultured in monolayers lost their phenotype within three days. The unique stratified structure of the 3D culture resulted in enhanced heterotypic cell-cell interactions, which led to improvements in hepatocyte functions. Albumin production increased three to six fold in the rLSEC-PEM-Hepatocyte cultures. Only rLSEC-PEM-Hepatocyte cultures exhibited increasing CYP1A1/2 and CYP3A activity. Well-defined bile canaliculi were observed only in the rLSEC-PEM-Hepatocyte cultures. Together, these data suggest that rLSEC-PEM-Hepatocyte cultures are highly suitable models to monitor the transformation of toxins in the liver and their transport out of this organ. In summary, these results indicate that the layered rLSEC-PEM-hepatocyte model, which recapitulates key features of hepatic sinusoids, is a potentially powerful medium for obtaining comprehensive knowledge on liver metabolism, detoxification and

  20. 3D X-rays application for precision measurement of the cell structure of extruded polystyrene

    Lim, J. Y.; Kim, K. Y.; Shin, H. S.; Yeom, S.; Lee, S. E.

    2015-12-01

    While the thermal performance of existing insulation materials have been determined by blister gases, the thermal performance of future insulation materials will be dependent on the cell size and independent foam content as we use eco-friendly blister gases with a higher thermal conductivity. However, with the current technology we are only able to guess the whole cell size and independent foam content through SEM applied 2D fragmentary scanning but are still far from the level of accurate cell structure data extraction. Under this situation, we utilized X-ray CT scanned 3D images to identify and shape the cell structure and proposed a method of inferring the whole distribution and independent foam content as accurately as possible. According to X-ray CT scanning images and SEM images, the shape was similar but according to tracer applied CT scanning images, the cell size distribution was 380∼400 pm within the range of the general insulation diameter distribution which had the highest reliability. As for extrusion foaming polystyrene, we need additional image processing to identify the independent foam content as its density is too low. So, it is recommended to raise the 3D cell structure completeness of XPS by improving the scanning accuracy.

  1. Enhanced high dynamic range 3D shape measurement based on generalized phase-shifting algorithm

    Wang, Minmin; Zhou, Canlin; Zhang, Chaorui; Si, Shuchun; Li, Hui; Lei, Zhenkun; Li, YanJie

    2016-01-01

    It is a challenge for Phase Measurement Profilometry (PMP) to measure objects with a large range of reflectivity variation across the surface. Saturated or dark pixels in the deformed fringe patterns captured by the camera will lead to phase fluctuations and errors. Jiang et al. proposed a high dynamic range real-time 3D shape measurement method without changing camera exposures. Three inverted phase-shifted fringe patterns are used to complement three regular phase-shifted fringe patterns for phase retrieval when any of the regular fringe patterns are saturated. But Jiang's method still has some drawbacks: (1) The phases in saturated pixels are respectively estimated by different formulas for different cases. It is shortage of an universal formula; (2) it cannot be extended to four-step phase-shifting algorithm because inverted fringe patterns are the repetition of regular fringe patterns; (3) only three unsaturated intensity values at every pixel of fringe patterns are chosen for phase demodulation, lying i...

  2. Dynamical effects of subducting ridges: Insights from 3-D laboratory models

    Martinod, Joseph; Faccenna, Claudio; Labanieh, Shasa; Regard, Vincent; 10.1111/j.1365-246X.2005.02797.x

    2010-01-01

    We model the subduction of buoyant ridges and plateaus to study their effect on slab dynamics. Oceanic ridges parallel to the trench have a stronger effect on the process of subduction because they simultaneously affect a longer trench segment. Large buoyant slab segments sink more slowly into the asthenosphere, and their subduction result in a diminution of the velocity of subduction of the plate. We observe a steeping of the slab below those buoyant anomalies, resulting in smaller radius of curvature of the slab, that augments the energy dissipated in folding the plate and further diminishes the velocity of subduction. When the 3D geometry of a buoyant plateau is modelled, the dip of the slab above the plateau decreases, as a result of the larger velocity of subduction of the dense "normal" oceanic plate on both sides of the plateau. Such a perturbation of the dip of the slab maintains long time after the plateau has been entirely incorporated into the subduction zone. We compare experiments with the presen...

  3. Introducing ZEUS-MP A 3D, Parallel, Multiphysics Code for Astrophysical Fluid Dynamics

    Norman, M L

    2000-01-01

    We describe ZEUS-MP: a Multi-Physics, Massively-Parallel, Message-Passing code for astrophysical fluid dynamics simulations in 3 dimensions. ZEUS-MP is a follow-on to the sequential ZEUS-2D and ZEUS-3D codes developed and disseminated by the Laboratory for Computational Astrophysics (lca.ncsa.uiuc.edu) at NCSA. V1.0 released 1/1/2000 includes the following physics modules: ideal hydrodynamics, ideal MHD, and self-gravity. Future releases will include flux-limited radiation diffusion, thermal heat conduction, two-temperature plasma, and heating and cooling functions. The covariant equations are cast on a moving Eulerian grid with Cartesian, cylindrical, and spherical polar coordinates currently supported. Parallelization is done by domain decomposition and implemented in F77 and MPI. The code is portable across a wide range of platforms from networks of workstations to massively parallel processors. Some parallel performance results are presented as well as an application to turbulent star formation.

  4. Spectral history modeling in the reactor dynamics code DYN3D

    A new method of treating spectral history effects in reactor core calculations was developed and verified in this dissertation. The nature of history effects is a dependence of fuel properties not only on the burnup, but also on the local spectral conditions during burnup. The basic idea of the proposed method is the use of the plutonium-239 concentration as the spectral history indicator. The method was implemented in the reactor dynamics code DYN3D and provides a correction for nodal cross sections according to the local spectral history. A verification of the new method was performed by single-assembly calculations in comparison with results of the lattice code HELIOS. The application of plutonium-based history correction significantly improves the cross section estimation accuracy both for UOX and MOX fuel, with quadratic and hexagonal geometry. The new method was applied to evaluate the influence of history effects on full-core calculation results. Analysis of a PWR equilibrium fuel cycle has shown a significant effect on the axial power distribution during a whole cycle, which causes axial temperature and burnup redistributions. The observed neutron flux redistribution improves neutron economy, so the fuel cycle is longer than in calculations without history corrections. Analyses of hypothetical control rod ejection accidents have shown a minor influence of history effects on the transient course and safety relevant parameters.

  5. Heritable Genetic Changes in Cells Recovered From Irradiated 3D Tissue Constructs

    Michael Cornforth

    2012-03-26

    Combining contemporary cytogenetic methods with DNA CGH microarray technology and chromosome flow-sorting increases substantially the ability to resolve exchange breakpoints associated with interstitial deletions and translocations, allowing the consequences of radiation damage to be directly measured at low doses, while also providing valuable insights into molecular mechanisms of misrepair processes that, in turn, identify appropriate biophysical models of risk at low doses. Specific aims apply to cells recovered from 3D tissue constructs of human skin and, for the purpose of comparison, the same cells irradiated in traditional 2D cultures. The project includes research complementary to NASA/HRP space radiation project.

  6. Mechanical Properties of 3-D Printed Cellular Foams with triangular cells

    Bunga, Pratap Kumar

    In the present work, poly lactic acid (PLA) is used as a model system to investigate the mechanical behavior of 3-D printed foams with triangular cells. Solid PLA tension and compression specimens and foams made of PLA were fabricated using fused deposition 3-D printing technique. The solid PLA tension specimens were characterized for their densities and found to be about 10% lower in density as compared to their bulk counter parts. The triangular foams had a relative density of about 64%. The relationships between the structure of the foams and its deformation behavior under compression along two in-plane directions were characterized. Furthermore, simple finite element models were developed to understand the observed deformation behavior of triangular foams.

  7. A novel asymmetric 3D in-vitro assay for the study of tumor cell invasion

    The induction of tumor cell invasion is an important step in tumor progression. Due to the cost and slowness of in-vivo invasion assays, there is need for quantitative in-vitro invasion assays that mimic as closely as possible the tumor environment and in which conditions can be rigorously controlled. We have established a novel asymmetric 3D in-vitro invasion assay by embedding a monolayer of tumor cells between two layers of collagen. The cells were then allowed to invade the upper and lower layers of collagen. To visualize invading cells the gels were sectioned perpendicular to the monolayer so that after seeding the monolayer appears as a thin line precisely defining the origin of invasion. The number of invading tumor cells, their proliferation rate, the distance they traverse and the direction of invasion could then be determined quantitatively. The assay was used to compare the invasive properties of several tumor cell types and the results compare well with those obtained by previously described assays. Lysyl-oxidase like protein-2 (Loxl2) is a potent inducer of invasiveness. Using our assay we show for the first time that inhibition of endogenous Loxl2 expression in several types of tumor cells strongly inhibits their invasiveness. We also took advantage of the asymmetric nature of the assay in order to show that fibronectin enhances the invasiveness of breast cancer cells more potently than laminin. The asymmetric properties of the assay were also used to demonstrate that soluble factors derived from fibroblasts can preferentially attract invading breast cancer cells. Our assay displays several advantages over previous invasion assays as it is allows the quantitative analysis of directional invasive behavior of tumor cells in a 3D environment mimicking the tumor microenvironment. It should be particularly useful for the study of the effects of components of the tumor microenvironment on tumor cell invasiveness

  8. Universal lab-on-a-chip platform for complex, perfused 3D cell cultures

    Sonntag, F.; Schmieder, F.; Ströbel, J.; Grünzner, S.; Busek, M.; Günther, K.; Steege, T.; Polk, C.; Klotzbach, U.

    2016-03-01

    The miniaturization, rapid prototyping and automation of lab-on-a-chip technology play nowadays a very important role. Lab-on-a-chip technology is successfully implemented not only for environmental analysis and medical diagnostics, but also as replacement of animals used for the testing of substances in the pharmaceutical and cosmetics industries. For that purpose the Fraunhofer IWS and partners developed a lab-on-a-chip platform for perfused cell-based assays in the last years, which includes different micropumps, valves, channels, reservoirs and customized cell culture modules. This technology is already implemented for the characterization of different human cell cultures and organoids, like skin, liver, endothelium, hair follicle and nephron. The advanced universal lab-on-a-chip platform for complex, perfused 3D cell cultures is divided into a multilayer basic chip with integrated micropump and application-specific 3D printed cell culture modules. Moreover a technology for surface modification of the printed cell culture modules by laser micro structuring and a complex and flexibly programmable controlling device based on an embedded Linux system was developed. A universal lab-on-a-chip platform with an optional oxygenator and a cell culture module for cubic scaffolds as well as first cell culture experiments within the cell culture device will be presented. The module is designed for direct interaction with robotic dispenser systems. This offers the opportunity to combine direct organ printing of cells and scaffolds with the microfluidic cell culture module. The characterization of the developed system was done by means of Micro-Particle Image Velocimetry (μPIV) and an optical oxygen measuring system.

  9. A method for the evaluation of thousands of automated 3D stem cell segmentations.

    Bajcsy, P; Simon, M; Florczyk, S J; Simon, C G; Juba, D; Brady, M C

    2015-12-01

    There is no segmentation method that performs perfectly with any dataset in comparison to human segmentation. Evaluation procedures for segmentation algorithms become critical for their selection. The problems associated with segmentation performance evaluations and visual verification of segmentation results are exaggerated when dealing with thousands of three-dimensional (3D) image volumes because of the amount of computation and manual inputs needed. We address the problem of evaluating 3D segmentation performance when segmentation is applied to thousands of confocal microscopy images (z-stacks). Our approach is to incorporate experimental imaging and geometrical criteria, and map them into computationally efficient segmentation algorithms that can be applied to a very large number of z-stacks. This is an alternative approach to considering existing segmentation methods and evaluating most state-of-the-art algorithms. We designed a methodology for 3D segmentation performance characterization that consists of design, evaluation and verification steps. The characterization integrates manual inputs from projected surrogate 'ground truth' of statistically representative samples and from visual inspection into the evaluation. The novelty of the methodology lies in (1) designing candidate segmentation algorithms by mapping imaging and geometrical criteria into algorithmic steps, and constructing plausible segmentation algorithms with respect to the order of algorithmic steps and their parameters, (2) evaluating segmentation accuracy using samples drawn from probability distribution estimates of candidate segmentations and (3) minimizing human labour needed to create surrogate 'truth' by approximating z-stack segmentations with 2D contours from three orthogonal z-stack projections and by developing visual verification tools. We demonstrate the methodology by applying it to a dataset of 1253 mesenchymal stem cells. The cells reside on 10 different types of biomaterial

  10. Estimation of single cell volume from 3D confocal images using automatic data processing

    Chorvatova, A.; Cagalinec, M.; Mateasik, A.; Chorvat, D., Jr.

    2012-06-01

    Cardiac cells are highly structured with a non-uniform morphology. Although precise estimation of their volume is essential for correct evaluation of hypertrophic changes of the heart, simple and unified techniques that allow determination of the single cardiomyocyte volume with sufficient precision are still limited. Here, we describe a novel approach to assess the cell volume from confocal microscopy 3D images of living cardiac myocytes. We propose a fast procedure based on segementation using active deformable contours. This technique is independent on laser gain and/or pinhole settings and it is also applicable on images of cells stained with low fluorescence markers. Presented approach is a promising new tool to investigate changes in the cell volume during normal, as well as pathological growth, as we demonstrate in the case of cell enlargement during hypertension in rats.

  11. 3D-4D Interlinkage Of B-S Amplitudes Unified View Of QQbar And QQQ Dynamics

    Mitra, A N

    2000-01-01

    This article has a 3-fold objective: i) to provide a panoramic view of several types of 3D vs 4D approaches in Field Theory (Tamm-Dancoff, Bethe Salpeter Equation (BSE), Quasi-potentials, Light-Front Dynamics, etc) for strong interaction dunamics; ii) to focus on the role of the Markov-Yukawa Transversality Principle (MYTP) as a novel paradigm for an exact 3D-4D interlinkage between the corresponding BSE amplitudes; iii) Stress on a closely parallel treatment of $q{\\bar q}$ and qqq BSE's stemming from a common 4-fermion Lagrangian mediated by gluon (vector)-like exchange. The two-way interlinkage offered by MYTP between the 3D and 4D BSE forms via a Lorentz-covariant 3D support to the BS kernel, gives it a unique status which distinguishes it from most other 3D approaches to strong interaction dynamics, which give at most a one-way connection. Two specific types of MYTP which provide 3D support to the BSE kernel, are considered: a) Covariant Instantaneity Ansatz (CIA); b) Covariant LF/NP ansatz (Cov.LF). Both...

  12. Longitudinal, label-free, quantitative tracking of cell death and viability in a 3D tumor model with OCT

    Jung, Yookyung; Klein, Oliver J.; Wang, Hequn; Evans, Conor L.

    2016-06-01

    Three-dimensional in vitro tumor models are highly useful tools for studying tumor growth and treatment response of malignancies such as ovarian cancer. Existing viability and treatment assessment assays, however, face shortcomings when applied to these large, complex, and heterogeneous culture systems. Optical coherence tomography (OCT) is a noninvasive, label-free, optical imaging technique that can visualize live cells and tissues over time with subcellular resolution and millimeters of optical penetration depth. Here, we show that OCT is capable of carrying out high-content, longitudinal assays of 3D culture treatment response. We demonstrate the usage and capability of OCT for the dynamic monitoring of individual and combination therapeutic regimens in vitro, including both chemotherapy drugs and photodynamic therapy (PDT) for ovarian cancer. OCT was validated against the standard LIVE/DEAD Viability/Cytotoxicity Assay in small tumor spheroid cultures, showing excellent correlation with existing standards. Importantly, OCT was shown to be capable of evaluating 3D spheroid treatment response even when traditional viability assays failed. OCT 3D viability imaging revealed synergy between PDT and the standard-of-care chemotherapeutic carboplatin that evolved over time. We believe the efficacy and accuracy of OCT in vitro drug screening will greatly contribute to the field of cancer treatment and therapy evaluation.

  13. Many-faced cells and many-edged faces in 3D Poisson–Voronoi tessellations

    Motivated by recent new Monte Carlo data we investigate a heuristic asymptotic theory that applies to n-faced 3D Poisson–Voronoi cells in the limit of large n. We show how this theory may be extended to n-edged cell faces. It predicts the leading order large-n behavior of the average volume and surface area of the n-faced cell, and of the average area and perimeter of the n-edged face. Such a face is shown to be surrounded by a toroidal region of volume n/λ (with λ the seed density) that is void of seeds. Two neighboring cells sharing an n-edged face are found to have their seeds at a typical distance that scales as n−1/6 and whose probability law we determine. We present a new data set of 4 × 109 Monte Carlo generated 3D Poisson–Voronoi cells, larger than any before. Full compatibility is found between the Monte Carlo data and the theory. Deviations from the asymptotic predictions are explained in terms of subleading corrections whose powers in n we estimate from the data. (paper)

  14. Many-faced cells and many-edged faces in 3D Poisson-Voronoi tessellations

    Hilhorst, H. J.; Lazar, E. A.

    2014-10-01

    Motivated by recent new Monte Carlo data we investigate a heuristic asymptotic theory that applies to n-faced 3D Poisson-Voronoi cells in the limit of large n. We show how this theory may be extended to n-edged cell faces. It predicts the leading order large-n behavior of the average volume and surface area of the n-faced cell, and of the average area and perimeter of the n-edged face. Such a face is shown to be surrounded by a toroidal region of volume n/λ (with λ the seed density) that is void of seeds. Two neighboring cells sharing an n-edged face are found to have their seeds at a typical distance that scales as n-1/6 and whose probability law we determine. We present a new data set of 4 × 109 Monte Carlo generated 3D Poisson-Voronoi cells, larger than any before. Full compatibility is found between the Monte Carlo data and the theory. Deviations from the asymptotic predictions are explained in terms of subleading corrections whose powers in n we estimate from the data.

  15. The leading-edge simulation software for 3D EM and charged particle dynamics, and its applications

    The latest 3D electromagnetic and charged particle dynamics simulation software enables scientists and engineers to develop accelerators and its components in less time at a lower cost as compared to testing experientially, even when only personal computers are available. These simulations provide solutions for various applications in industry, medicine and research, including non-destructive inspection, radiation cancer treatment, medical device sterilization and synchrotron radiation. Additionally, we are benefiting from advances in computer hardware technology, especially GPU computing. This paper reviews the current status of the latest 3D EM and charged particle dynamics simulation software and its applications. (author)

  16. 3D measurements of live cells via digital holographic microscopy and terahertz spectroscopy

    Park, Jun Yong; Oser, Dorian; Iapozzuto, Peter; Norbury, Sean; Mahajan, Supriya; Khmaladze, Alexander; Sharikova, Anna

    2016-03-01

    This is a study of the central nervous system (CNS) cells, including brain micro vascular endothelial cells (BMV) that constitute the blood brain barrier, and C6 glial cells that are the predominant cell in the brain. The cells are exposed to various chemicals by non-invasive, label-free methods. Digital holographic microscopy (DHM) is a technique that records an interference pattern between an object and reference waves, so that the computationally reconstructed holographic image contains both amplitude and phase information, and 3D images are obtained. The measurement of cell cultures by digital holographic microscopy yields information about cell death mechanisms, since these processes are correlated with individual cell volume. Our in-house DHM combines a visible (red) laser source with a conventional microscope base, and LabVIEW-run data processing. Terahertz spectral signatures are associated with structural changes in molecules and provide complementary information about cells. Both CNS cells BMV and C6 cells are treated with the drug "Methamphetamine" (METH), which induces apoptosis in neuronal cells and exhibits decrease in cell volume, a characteristic of cells undergoing apoptosis (induced cell death). METH can cause CNS cell death by cross-talk between mitochondria-, endoplasmic reticulum-, and receptor-mediated apoptotic events, all of which results in drug induced changes in neuroplasticity and significant neuropathology. Doxorubicin (DOX), a popular anticancer drug, is used as a control. We observe that METH treatment resulted in more pronounced cell volume shrinkage in both the BMV and C6 cells, as compared to DOX-induced cell apoptosis.

  17. Beam dynamics study of RFQ for CADS with a 3D space-charge-effect

    The ADS (accelerator driven subcritical system) project was proposed by the Chinese Academy of Sciences. The initial proton beams delivered from an electron cyclotron resonance ion source can be effectively accelerated by 162.5 MHz 4.2 m long room temperature radio-frequency-quadrupoles (RFQ) operating in CW mode. To test the feasibility of this physical design, a new Fortran code for RFQ beam dynamics study, which is space charge dominated, was developed. This program is based on Particle-In-Cell (PIC) technique in the time domain. Using the RFQ structure designed for the CADS project, the beam dynamics behavior is performed. The well-known simulation code TRACK is used for benchmarks. The results given by these two codes show good agreements. Numerical techniques as well as the results of beam dynamics studies are presented in this paper. (authors)

  18. Beam dynamics study of RFQ for CADS with a 3D space-charge-effect

    Li, Chao; Zhang, Zhi-Lei; Qi, Xin; Xu, Xian-Bo; He, Yuan; Yang, Lei

    2014-03-01

    The ADS (accelerator driven subcritical system) project was proposed by the Chinese Academy of Sciences. The initial proton beams delivered from an electron cyclotron resonance ion source can be effectively accelerated by 162.5 MHz 4.2 m long room temperature radio-frequency-quadrupoles (RFQ) operating in CW mode. To test the feasibility of this physical design, a new Fortran code for RFQ beam dynamics study, which is space charge dominated, was developed. This program is based on Particle-In-Cell (PIC) technique in the time domain. Using the RFQ structure designed for the CADS project, the beam dynamics behavior is performed. The well-known simulation code TRACK is used for benchmarks. The results given by these two codes show good agreements. Numerical techniques as well as the results of beam dynamics studies are presented in this paper.

  19. Low-level laser therapy in 3D cell culture model using gingival fibroblasts.

    Basso, Fernanda G; Soares, Diana G; de Souza Costa, Carlos Alberto; Hebling, Josimeri

    2016-07-01

    Besides extensive data about the effects of low-level laser therapy (LLLT) on different cell types, so far, these results were obtained from monolayer cell culture models, which have limitations in terms of cell morphology and phenotype expression. Therefore, for better in vitro evaluation of the effects of LLLT, this study was performed with a 3D cell culture model, where gingival fibroblasts were seeded in collagen matrix. Cells isolated from a healthy patient were seeded in wells of 24-well plates with culture medium (DMEM) supplemented with 10 % fetal bovine serum and collagen type I solution. After 5 days, a serum-free DMEM was added to the matrices with cells that were subjected or not to three consecutive irradiations of LLLT by means of the LaserTABLE diode device (780 nm, 25 mW) at 0.5, 1.5, and 3 J/cm(2). Twenty-four hours after the last irradiation, cell viability and morphology as well as gene expression of growth factors were assessed. Histological evaluation of matrices demonstrated uniform distribution and morphology of gingival fibroblasts within the collagen matrix. LLLT at 3 J/cm(2) increased gingival fibroblast viability. Enhanced gene expression of hCOL-I and hEGF was observed for 0.5 J/cm(2), while no significant changes were detected for the other irradiation densities tested. In conclusion, LLLT promoted biostimulation of gingival fibroblasts seeded in a 3D cell culture model, demonstrating that this model can be applied for phototherapy studies and that LLLT could penetrate the collagen matrix to increase cell functions related to tissue repair. PMID:27126408

  20. Characterizing interstate vibrational coherent dynamics of surface adsorbed catalysts by fourth-order 3D SFG spectroscopy

    Li, Yingmin; Wang, Jiaxi; Clark, Melissa L.; Kubiak, Clifford P.; Xiong, Wei

    2016-04-01

    We report the first fourth-order 3D SFG spectroscopy of a monolayer of the catalyst Re(diCN-bpy)(CO)3Cl on a gold surface. Besides measuring the vibrational coherences of single vibrational modes, the fourth-order 3D SFG spectrum also measures the dynamics of interstate coherences and vibrational coherences states between two vibrational modes. By comparing the 3D SFG to the corresponding 2D and third-order 3D IR spectroscopy of the same molecules in solution, we found that the interstate coherences exist in both liquid and surface systems, suggesting that the interstate coherence is not disrupted by surface interactions. However, by analyzing the 3D spectral lineshape, we found that the interstate coherences also experience non-negligible homogenous dephasing dynamics that originate from surface interactions. This unique ability of determining interstate vibrational coherence dynamics of the molecular monolayer can help in understanding of how energy flows within surface catalysts and other molecular monolayers.

  1. Direct 3D-printing of cell-laden constructs in microfluidic architectures.

    Liu, Justin; Hwang, Henry H; Wang, Pengrui; Whang, Grace; Chen, Shaochen

    2016-04-21

    Microfluidic platforms have greatly benefited the biological and medical fields, however standard practices require a high cost of entry in terms of time and energy. The utilization of three-dimensional (3D) printing technologies has greatly enhanced the ability to iterate and build functional devices with unique functions. However, their inability to fabricate within microfluidic devices greatly increases the cost of producing several different devices to examine different scientific questions. In this work, a variable height micromixer (VHM) is fabricated using projection 3D-printing combined with soft lithography. Theoretical and flow experiments demonstrate that altering the local z-heights of VHM improved mixing at lower flow rates than simple geometries. Mixing of two fluids occurs as low as 320 μL min(-1) in VHM whereas the planar zigzag region requires a flow rate of 2.4 mL min(-1) before full mixing occurred. Following device printing, to further demonstrate the ability of this projection-based method, complex, user-defined cell-laden scaffolds are directly printed inside the VHM. The utilization of this unique ability to produce 3D tissue models within a microfluidic system could offer a unique platform for medical diagnostics and disease modeling. PMID:26980159

  2. Effects of electromagnetic field frequencies on chondrocytes in 3D cell-printed composite constructs.

    Yi, Hee-Gyeong; Kang, Kyung Shin; Hong, Jung Min; Jang, Jinah; Park, Moon Nyeo; Jeong, Young Hun; Cho, Dong-Woo

    2016-07-01

    In cartilage tissue engineering, electromagnetic field (EMF) therapy has been reported to have a modest effect on promoting cartilage regeneration. However, these studies were conducted using different frequencies of EMF to stimulate chondrocytes. Thus, it is necessary to investigate the effect of EMF frequency on cartilage formation. In addition to the stimulation, a scaffold is required to satisfy the characteristics of cartilage such as its hydrated and dense extracellular matrix, and a mechanical resilience to applied loads. Therefore, we 3D-printed a composite construct composed of a polymeric framework and a chondrocyte-laden hydrogel. Here, we observed frequency-dependent positive and negative effects on chondrogenesis using a 3D cell-printed cartilage tissue. We found that a frequency of 45 Hz promoted gene expression and secretion of extracellular matrix molecules of chondrocytes. In contrast, a frequency of 7.5 Hz suppressed chondrogenic differentiation in vitro. Additionally, the EMF-treated composite constructs prior to implantation showed consistent results with those of in vitro, suggesting that in vitro pre-treatment with different EMF frequencies provides different capabilities for the enhancement of cartilage formation in vivo. This correlation between EMF frequency and 3D-printed chondrocytes suggests the necessity for optimization of EMF parameters when this physical stimulus is applied to engineered cartilage. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1797-1804, 2016. PMID:26991030

  3. Standardized 3D Bioprinting of Soft Tissue Models with Human Primary Cells.

    Rimann, Markus; Bono, Epifania; Annaheim, Helene; Bleisch, Matthias; Graf-Hausner, Ursula

    2016-08-01

    Cells grown in 3D are more physiologically relevant than cells cultured in 2D. To use 3D models in substance testing and regenerative medicine, reproducibility and standardization are important. Bioprinting offers not only automated standardizable processes but also the production of complex tissue-like structures in an additive manner. We developed an all-in-one bioprinting solution to produce soft tissue models. The holistic approach included (1) a bioprinter in a sterile environment, (2) a light-induced bioink polymerization unit, (3) a user-friendly software, (4) the capability to print in standard labware for high-throughput screening, (5) cell-compatible inkjet-based printheads, (6) a cell-compatible ready-to-use BioInk, and (7) standard operating procedures. In a proof-of-concept study, skin as a reference soft tissue model was printed. To produce dermal equivalents, primary human dermal fibroblasts were printed in alternating layers with BioInk and cultured for up to 7 weeks. During long-term cultures, the models were remodeled and fully populated with viable and spreaded fibroblasts. Primary human dermal keratinocytes were seeded on top of dermal equivalents, and epidermis-like structures were formed as verified with hematoxylin and eosin staining and immunostaining. However, a fully stratified epidermis was not achieved. Nevertheless, this is one of the first reports of an integrative bioprinting strategy for industrial routine application. PMID:25609254

  4. 3D cut-cell modelling for high-resolution atmospheric simulations

    Yamazaki, H; Nikiforakis, N

    2015-01-01

    With the recent, rapid development of computer technology, the resolution of atmospheric numerical models has increased substantially. As a result, steep gradients in mountainous terrain are now being resolved in high-resolution models. This results in large truncation errors in those models using terrain-following coordinates. In this study, a new 3D Cartesian coordinate non-hydrostatic atmospheric model is developed. A cut-cell representation of topography based on finite-volume discretization is combined with a cell-merging approach, in which small cut-cells are merged with neighboring cells either vertically or horizontally. In addition, a block-structured mesh-refinement technique achieves a variable resolution on the model grid with the finest resolution occurring close to the terrain surface. The model successfully reproduces a flow over a 3D bell-shaped hill that shows a good agreement with the flow predicted by the linear theory. The ability of the model to simulate flows over steep terrain is demons...

  5. Assessing Drug Efficacy in a Miniaturized Pancreatic Cancer In Vitro 3D Cell Culture Model.

    Shelper, Todd B; Lovitt, Carrie J; Avery, Vicky M

    2016-09-01

    Pancreatic cancer continues to have one of the poorest prognoses among all cancers. The drug discovery efforts for this disease have largely failed, with no significant improvement in survival outcomes for advanced pancreatic cancer patients over the past 20 years. Traditional in vitro cell culture techniques have been used extensively in both basic and early drug discovery; however, these systems offer poor models to assess emerging therapeutics. More predictive cell-based models, which better capture the cellular heterogeneity and complexities of solid pancreatic tumors, are urgently needed not only to improve drug discovery success but also to provide insight into the tumor biology. Pancreatic tumors are characterized by a unique micro-environment that is surrounded by a dense stroma. A complex network of interactions between extracellular matrix (ECM) components and the effects of cell-to-cell contacts may enhance survival pathways within in vivo tumors. This biological and physical complexity is lost in traditional cell monolayer models. To explore the predictive potential of a more complex cellular system, a three-dimensional (3D) micro-tumor assay was evaluated. Efficacy of six current chemotherapeutics was determined against a panel of primary and metastatic pancreatic tumor cell lines in a miniaturized ECM-based 3D cell culture system. Suitability for potential use in high-throughput screening applications was assessed, including ascertaining the effects that miniaturization and automation had on assay robustness. Cellular health was determined by utilizing an indirect population-based metabolic activity assay and a direct imaging-based cell viability assay. PMID:27552143

  6. How the venetian blind percept emerges from the laminar cortical dynamics of 3D vision.

    Cao, Yongqiang; Grossberg, Stephen

    2014-01-01

    The 3D LAMINART model of 3D vision and figure-ground perception is used to explain and simulate a key example of the Venetian blind effect and to show how it is related to other well-known perceptual phenomena such as Panum's limiting case. The model proposes how lateral geniculate nucleus (LGN) and hierarchically organized laminar circuits in cortical areas V1, V2, and V4 interact to control processes of 3D boundary formation and surface filling-in that simulate many properties of 3D vision percepts, notably consciously seen surface percepts, which are predicted to arise when filled-in surface representations are integrated into surface-shroud resonances between visual and parietal cortex. Interactions between layers 4, 3B, and 2/3 in V1 and V2 carry out stereopsis and 3D boundary formation. Both binocular and monocular information combine to form 3D boundary and surface representations. Surface contour surface-to-boundary feedback from V2 thin stripes to V2 pale stripes combines computationally complementary boundary and surface formation properties, leading to a single consistent percept, while also eliminating redundant 3D boundaries, and triggering figure-ground perception. False binocular boundary matches are eliminated by Gestalt grouping properties during boundary formation. In particular, a disparity filter, which helps to solve the Correspondence Problem by eliminating false matches, is predicted to be realized as part of the boundary grouping process in layer 2/3 of cortical area V2. The model has been used to simulate the consciously seen 3D surface percepts in 18 psychophysical experiments. These percepts include the Venetian blind effect, Panum's limiting case, contrast variations of dichoptic masking and the correspondence problem, the effect of interocular contrast differences on stereoacuity, stereopsis with polarity-reversed stereograms, da Vinci stereopsis, and perceptual closure. These model mechanisms have also simulated properties of 3D neon

  7. Adipogenic differentiation of laser-printed 3D tissue grafts consisting of human adipose-derived stem cells

    Gruene, M; Deiwick, A; Koch, L; Schlie, S; Unger, C; Chichkov, B N [Nanotechnology Department, Laser Zentrum Hannover e.V., Hollerithallee 8, 30419 Hannover (Germany); Pflaum, M; Wilhelmi, M; Haverich, A, E-mail: m.gruene@lzh.de [Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, 30625 Hannover (Germany)

    2011-03-15

    Laser-assisted bioprinting (LaBP) allows the realization of computer-generated 3D tissue grafts consisting of cells embedded in a hydrogel environment. In this study, human adipose-derived stem cells (hASCs) were printed in a free-scalable 3D grid pattern by means of LaBP. We demonstrate that neither the proliferation ability nor the differentiation behaviour of the stem cells was affected by the LaBP procedure. Furthermore, the 3D grafts were differentiated down the adipogenic lineage pathway for 10 days. We verify by quantitative assessments of adipogenic markers that the 3D grafts resemble cell lineages present in natural adipose tissue. Additionally, we provide the proof that even pre-differentiated hASCs could be utilized for the generation of 3D tissue grafts. These results indicate that the biofabrication of living grafts resembling their complex native origin is within reach.

  8. Adipogenic differentiation of laser-printed 3D tissue grafts consisting of human adipose-derived stem cells

    Laser-assisted bioprinting (LaBP) allows the realization of computer-generated 3D tissue grafts consisting of cells embedded in a hydrogel environment. In this study, human adipose-derived stem cells (hASCs) were printed in a free-scalable 3D grid pattern by means of LaBP. We demonstrate that neither the proliferation ability nor the differentiation behaviour of the stem cells was affected by the LaBP procedure. Furthermore, the 3D grafts were differentiated down the adipogenic lineage pathway for 10 days. We verify by quantitative assessments of adipogenic markers that the 3D grafts resemble cell lineages present in natural adipose tissue. Additionally, we provide the proof that even pre-differentiated hASCs could be utilized for the generation of 3D tissue grafts. These results indicate that the biofabrication of living grafts resembling their complex native origin is within reach.

  9. Isotropic 3D Nuclear Morphometry of Normal, Fibrocystic and Malignant Breast Epithelial Cells Reveals New Structural Alterations

    Nandakumar, Vivek; Kelbauskas, Laimonas; Hernandez, Kathryn F.; Lintecum, Kelly M.; Senechal, Patti; Bussey, Kimberly J.; Davies, Paul C.W.; Johnson, Roger H.; Meldrum, Deirdre R.

    2012-01-01

    Background Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading ...

  10. Enabling Flexible Polymer Tandem Solar Cells by 3D Ptychographic Imaging

    Dam, Henrik Friis; Andersen, Thomas Rieks; Pedersen, Emil Bøje Lind;

    2015-01-01

    one after the other by wet processing leaves plenty of room for error and the process development calls for an analytical technique that enables 3D reconstruction of the layer stack with the possibility to probe thickness, density, and chemistry of the individual layers in the stack. The use of......The realization of a complete tandem polymer solar cell under ambient conditions using only printing and coating methods on a flexible substrate results in a fully scalable process but also requires accurate control during layer formation to succeed. The serial process where the layers are added...

  11. 3-D slug flow heat transfer analysis of coupled coolant cells in finite LMFBR bundles

    A three-dimensional single region slug flow heat transfer analysis for finite LMFBR rod bundles using a classical analytical solution method has been performed. According to the isolated single cell analysis, the results show that the peripheral clad temperature variation as well as the thermal entrance length are strongly dependent upon the degree of irregularity displayed by various coolant geometries. Since under the present LMFBR conditions, fully-developed temperature fields may hardly be established in such characteristic rod bundle regions, a 3-D heat transfer analysis seems to be mandatory. This implies that the results of fully developed heat transfer analyses are by far too conservative

  12. A harmonic polynomial cell (HPC) method for 3D Laplace equation with application in marine hydrodynamics

    We propose a new efficient and accurate numerical method based on harmonic polynomials to solve boundary value problems governed by 3D Laplace equation. The computational domain is discretized by overlapping cells. Within each cell, the velocity potential is represented by the linear superposition of a complete set of harmonic polynomials, which are the elementary solutions of Laplace equation. By its definition, the method is named as Harmonic Polynomial Cell (HPC) method. The characteristics of the accuracy and efficiency of the HPC method are demonstrated by studying analytical cases. Comparisons will be made with some other existing boundary element based methods, e.g. Quadratic Boundary Element Method (QBEM) and the Fast Multipole Accelerated QBEM (FMA-QBEM) and a fourth order Finite Difference Method (FDM). To demonstrate the applications of the method, it is applied to some studies relevant for marine hydrodynamics. Sloshing in 3D rectangular tanks, a fully-nonlinear numerical wave tank, fully-nonlinear wave focusing on a semi-circular shoal, and the nonlinear wave diffraction of a bottom-mounted cylinder in regular waves are studied. The comparisons with the experimental results and other numerical results are all in satisfactory agreement, indicating that the present HPC method is a promising method in solving potential-flow problems. The underlying procedure of the HPC method could also be useful in other fields than marine hydrodynamics involved with solving Laplace equation

  13. In-cell maintenance by manipulator arm with 3D workspace information recreated by laser rangefinder

    Highlights: → We developed a remote control system for maintenance of in-cell type fuel fabrication equipment. → The system display recreated three-dimensional information of the workspace from data obtained by laser rangefinder and conventional cameras. It has allowed us to operate a manipulator arm remotely with several control modes. → We implemented remote handling experiments using mock up equipment. Performance was compared for remote operation conducted using several different display and operation modes. → It was observed that integration of 3D information from the laser rangefinder reduced operation time and reinforced visual information during remote operation. - Abstract: We developed a remote control system for maintenance of in-cell type fuel fabrication equipment. The system display recreated three-dimensional information of the workspace from data obtained by laser rangefinder and conventional cameras. It has allowed us to operate a manipulator arm remotely with several control modes. In order to evaluate the effectiveness and usefulness of developed system, we implemented remote handling experiments using mock up equipment. Performance was compared for remote operation conducted using several different display and operation modes. We confirmed that the system is able to maintain in-cell fuel fabrication equipment in each display and operation mode. Times required to complete the remote operations were collected and compared in each mode. It was observed that integration of 3D information from the laser rangefinder reduced operation time and reinforced visual information during remote operation.

  14. A harmonic polynomial cell (HPC) method for 3D Laplace equation with application in marine hydrodynamics

    Shao, Yan-Lin, E-mail: yanlin.shao@dnvgl.com; Faltinsen, Odd M.

    2014-10-01

    We propose a new efficient and accurate numerical method based on harmonic polynomials to solve boundary value problems governed by 3D Laplace equation. The computational domain is discretized by overlapping cells. Within each cell, the velocity potential is represented by the linear superposition of a complete set of harmonic polynomials, which are the elementary solutions of Laplace equation. By its definition, the method is named as Harmonic Polynomial Cell (HPC) method. The characteristics of the accuracy and efficiency of the HPC method are demonstrated by studying analytical cases. Comparisons will be made with some other existing boundary element based methods, e.g. Quadratic Boundary Element Method (QBEM) and the Fast Multipole Accelerated QBEM (FMA-QBEM) and a fourth order Finite Difference Method (FDM). To demonstrate the applications of the method, it is applied to some studies relevant for marine hydrodynamics. Sloshing in 3D rectangular tanks, a fully-nonlinear numerical wave tank, fully-nonlinear wave focusing on a semi-circular shoal, and the nonlinear wave diffraction of a bottom-mounted cylinder in regular waves are studied. The comparisons with the experimental results and other numerical results are all in satisfactory agreement, indicating that the present HPC method is a promising method in solving potential-flow problems. The underlying procedure of the HPC method could also be useful in other fields than marine hydrodynamics involved with solving Laplace equation.

  15. Fabrication and evaluation of electrohydrodynamic jet 3D printed polycaprolactone/chitosan cell carriers using human embryonic stem cell-derived fibroblasts.

    Wu, Yang; Sriram, Gopu; Fawzy, Amr S; Fuh, Jerry Yh; Rosa, Vinicius; Cao, Tong; Wong, Yoke San

    2016-08-01

    Biological function of adherent cells depends on the cell-cell and cell-matrix interactions in three-dimensional space. To understand the behavior of cells in 3D environment and their interactions with neighboring cells and matrix requires 3D culture systems. Here, we present a novel 3D cell carrier scaffold that provides an environment for routine 3D cell growth in vitro We have developed thin, mechanically stable electrohydrodynamic jet (E-jet) 3D printed polycaprolactone and polycaprolactone/Chitosan macroporous scaffolds with precise fiber orientation for basic 3D cell culture application. We have evaluated the application of this technology by growing human embryonic stem cell-derived fibroblasts within these 3D scaffolds. Assessment of cell viability and proliferation of cells seeded on polycaprolactone and polycaprolactone/Chitosan 3D-scaffolds show that the human embryonic stem cell-derived fibroblasts could adhere and proliferate on the scaffolds over time. Further, using confocal microscopy we demonstrate the ability to use fluorescence-labelled cells that could be microscopically monitored in real-time. Hence, these 3D printed polycaprolactone and polycaprolactone/Chitosan scaffolds could be used as a cell carrier for in vitro 3D cell culture-, bioreactor- and tissue engineering-related applications in the future. PMID:27252227

  16. Dielectrophoresis-assisted 3D nanoelectroporation for non-viral cell transfection in adoptive immunotherapy.

    Chang, Lingqian; Gallego-Perez, Daniel; Zhao, Xi; Bertani, Paul; Yang, Zhaogang; Chiang, Chi-Ling; Malkoc, Veysi; Shi, Junfeng; Sen, Chandan K; Odonnell, Lynn; Yu, Jianhua; Lu, Wu; Lee, L James

    2015-08-01

    Current transfection technologies lead to significant inter-clonal variations. Previously we introduced a unique electrotransfection technology, Nanochannel-Electroporation (NEP), which can precisely and benignly transfect small cell populations (~100-200 cells) with single-cell resolution. Here we report on the development of a novel 3D NEP system for large scale transfection. A properly-engineered array of nanochannels, capable of handling/transfecting ~60 000 cells cm(-2), was fabricated using cleanroom technologies. Positive dielectrophoresis was used to selectively position cells on the nanochannels, thus allowing highly efficient transfection. Single-cell dosage control was demonstrated using both small and large molecules, and different cell types. The potential clinical relevance of this system was tested with difficult-to-transfect natural killer cell suspensions, and plasmids encoding for the chimeric antigen receptor (CAR), a model of high relevance for adoptive immunotherapy. Our results show significantly higher CAR transfection efficiencies for the DEP-NEP system (>70% vs. <30%), as well as enhanced cell viabilities. PMID:26105628

  17. Simulation of dynamic behaviour of a digital displacement motor using transient 3d computational fluid dynamics analysis

    Rømer, Daniel; Johansen, Per; Pedersen, Henrik C.;

    2013-01-01

    A fast rotating 1500 rpm radial piston digital displacement motor connected to a 350 bar high pressure manifold is simulated by means of transient 3D CFD analysis of a single pressure chamber. The analysis includes dynamic piston and valve movement, influencing the boundaries of the fluid domain....... Movement of the low and high pressure valves is coupled to fluid forces and valve actuation is included to control the valve movement according to the pressure cycle of the digital displacement motor. The fluid domain is meshed using a structured/unstructured non-conformal mesh, which is updated throughout...... the simulation using layering zones as required by the moving fluid boundaries. The effect of cavitation at low pressures is included by implementing a pressure dependent density, based on an effective bulk modulus model. In addition, pressure dependent oil viscosity is included in the analysis. As a...

  18. Usefulness of 3-D dynamic pulmonary xenon-133 SPECT for thoracoscopic lung volume reduction surgery in patients with pulmonary emphysema

    Six patients with pulmonary emphysema scheduled to undergo thoracoscopic lung volume reduction surgery (TLVRS) were evaluated by three-dimensional (3-D) dynamic pulmonary xenon-133 SPECT. Serial 30-second dynamic SPECT data for equilibrium and washout (for 5 min) were acquired using a continuous repetitive rotating acquisition mode with a triple-detector SPECT system. SPECT data were reconstructed to 3-D images with a color, surface-rendering technique, and a 3-D fusion image of the 3-min washout image over the equilibrium image was obtained. Regional ventilation was visually assessed on the fusion 3-D images and quantified by xenon-133 half-washout time (T1/2) and mean transit time (MTT). The 3-D fusion image localized and lateralized the worst diseased sites with xenon-133 retention. Xenon-133 retention, T1/2 and MTT were reduced on these images in five patients with improved pulmonary function tests following TLVRS. However, xenon-133 retention was greater in one with asynchronous diaphragm movement after TLVRS. This modality will assist TLVRS in determining the lung-resection target and in evaluating the treatment effect. (author)

  19. How the Venetian Blind Percept Emergesfrom the Laminar Cortical Dynamics of 3D Vision

    Stephen eGrossberg

    2014-08-01

    Full Text Available The 3D LAMINART model of 3D vision and figure-ground perception is used to explain and simulate a key example of the Venetian blind effect and show how it is related to other well-known perceptual phenomena such as Panum's limiting case. The model shows how identified neurons that interact in hierarchically organized laminar circuits of the visual cortex can simulate many properties of 3D vision percepts, notably consciously seen surface percepts, which are predicted to arise when filled-in surface representations are integrated into surface-shroud resonances between visual and parietal cortex. The model describes how monocular and binocular oriented filtering interacts with later stages of 3D boundary formation and surface filling-in in the lateral geniculate nucleus (LGN and cortical areas V1, V2, and V4. It proposes how interactions between layers 4, 3B, and 2/3 in V1 and V2 contribute to stereopsis, and how binocular and monocular information combine to form 3D boundary and surface representations. The model suggests how surface-to-boundary feedback from V2 thin stripes to pale stripes enables computationally complementary boundary and surface formation properties to generate a single consistent percept, eliminate redundant 3D boundaries, and trigger figure-ground perception. The model also shows how false binocular boundary matches may be eliminated by Gestalt grouping properties. In particular, a disparity filter, which helps to solve the Correspondence Problem by eliminating false matches, is predicted to be realized as part of the boundary grouping process in layer 2/3 of cortical area V2. The model has been used to simulate the consciously seen 3D surface percepts in 18 psychophysical experiments. These percepts include the Venetian blind effect, Panum's limiting case, contrast variations of dichoptic masking and the correspondence problem, the effect of interocular contrast differences on stereoacuity, stereopsis with polarity

  20. Engineering a perfusable 3D human liver platform from iPS cells.

    Schepers, Arnout; Li, Cheri; Chhabra, Arnav; Seney, Benjamin Tschudy; Bhatia, Sangeeta

    2016-07-01

    In vitro models of human tissue are crucial to our ability to study human disease as well as develop safe and effective drug therapies. Models of single organs in static and microfluidic culture have been established and shown utility for modeling some aspects of health and disease; however, these systems lack multi-organ interactions that are critical to some aspects of drug metabolism and toxicity. Thus, as part of a consortium of researchers, we have developed a liver chip that meets the following criteria: (1) employs human iPS cells from a patient of interest, (2) cultures cells in perfusable 3D organoids, and (3) is robust to variations in perfusion rate so as to be compatible in series with other specialized tissue chips (e.g. heart, lung). In order to achieve this, we describe methods to form hepatocyte aggregates from primary and iPS-derived cells, alone and in co-culture with support cells. This necessitated a novel culture protocol for the interrupted differentiation of iPS cells that permits their removal from a plated surface and aggregation while maintaining phenotypic hepatic functions. In order to incorporate these 3D aggregates in a perfusable platform, we next encapsulated the cells in a PEG hydrogel to prevent aggregation and overgrowth once on chip. We adapted a C-trap chip architecture from the literature that enabled robust loading with encapsulated organoids and culture over a range of flow rates. Finally, we characterize the liver functions of this iHep organoid chip under perfusion and demonstrate a lifetime of at least 28 days. We envision that such this strategy can be generalized to other microfluidic tissue models and provides an opportunity to query patient-specific liver responses in vitro. PMID:27296616

  1. Accessible bioprinting: adaptation of a low-cost 3D-printer for precise cell placement and stem cell differentiation.

    Reid, John A; Mollica, Peter A; Johnson, Garett D; Ogle, Roy C; Bruno, Robert D; Sachs, Patrick C

    2016-01-01

    The precision and repeatability offered by computer-aided design and computer-numerically controlled techniques in biofabrication processes is quickly becoming an industry standard. However, many hurdles still exist before these techniques can be used in research laboratories for cellular and molecular biology applications. Extrusion-based bioprinting systems have been characterized by high development costs, injector clogging, difficulty achieving small cell number deposits, decreased cell viability, and altered cell function post-printing. To circumvent the high-price barrier to entry of conventional bioprinters, we designed and 3D printed components for the adaptation of an inexpensive 'off-the-shelf' commercially available 3D printer. We also demonstrate via goal based computer simulations that the needle geometries of conventional commercially standardized, 'luer-lock' syringe-needle systems cause many of the issues plaguing conventional bioprinters. To address these performance limitations we optimized flow within several microneedle geometries, which revealed a short tapered injector design with minimal cylindrical needle length was ideal to minimize cell strain and accretion. We then experimentally quantified these geometries using pulled glass microcapillary pipettes and our modified, low-cost 3D printer. This systems performance validated our models exhibiting: reduced clogging, single cell print resolution, and maintenance of cell viability without the use of a sacrificial vehicle. Using this system we show the successful printing of human induced pluripotent stem cells (hiPSCs) into Geltrex and note their retention of a pluripotent state 7 d post printing. We also show embryoid body differentiation of hiPSC by injection into differentiation conducive environments, wherein we observed continuous growth, emergence of various evaginations, and post-printing gene expression indicative of the presence of all three germ layers. These data demonstrate an

  2. One-step fabrication of 3D silver paste electrodes into microfluidic devices for enhanced droplet-based cell sorting

    Lang Rao

    2015-05-01

    Full Text Available 3D microelectrodes are one-step fabricated into a microfluidic droplet separator by filling conductive silver paste into PDMS microchambers. The advantages of 3D silver paste electrodes in promoting droplet sorting accuracy are systematically demonstrated by theoretical calculation, numerical simulation and experimental validation. The employment of 3D electrodes also helps to decrease the droplet sorting voltage, guaranteeing that cells encapsulated in droplets undergo chip-based sorting processes are at better metabolic status for further potential cellular assays. At last, target droplet containing single cell are selectively sorted out from others by an appropriate electric pulse. This method provides a simple and inexpensive alternative to fabricate 3D electrodes, and it is expected our 3D electrode-integrated microfluidic droplet separator platform can be widely used in single cell operation and analysis.

  3. Has 3-D conformal radiotherapy (3D CRT) improved the local tumour control for stage I non-small cell lung cancer?

    Aims and background: The high local failure rates observed after radiotherapy in stage I non-small cell lung cancer (NSCLC) may be improved by the use of 3-dimensional conformal radiotherapy (3D CRT). Materials and methods: The case-records of 113 patients who were treated with curative 3D CRT between 1991 and 1999 were analysed. No elective nodal irradiation was performed, and doses of 60 Gy or more, in once-daily fractions of between 2 and 3 Gy, were prescribed. Results: The median actuarial survival of patients was 20 months, with 1-, 3- and 5-year survival of 71, 25 and 12%, respectively. Local disease progression was the cause of death in 30% of patients, and 22% patients died from distant metastases. Grade 2-3 acute radiation pneumonitis (SWOG) was observed in 6.2% of patients. The median actuarial local progression-free survival (LPFS) was 27 months, with 85 and 43% of patients free from local progression at 1 and 3 years, respectively. Endobronchial tumour extension significantly influenced LPFS, both on univariate (P=0.023) and multivariate analysis (P=0.023). The median actuarial cause-specific survival (CSS) was 19 months, and the respective 1- and 3-year rates were 72 and 30%. Multivariate analysis showed T2 classification (P=0.017) and the presence of endobronchial tumour extension (P=0.029) to be adverse prognostic factors for CSS. On multivariate analysis, T-stage significantly correlated with distant failure (P=0.005). Conclusions: Local failure rates remain substantial despite the use of 3D CRT for stage I NSCLC. Additional improvements in local control can come about with the use of radiation dose escalation and approaches to address the problem of tumour mobility

  4. Adaptive geometric tessellation for 3D reconstruction of anisotropically developing cells in multilayer tissues from sparse volumetric microscopy images.

    Anirban Chakraborty

    Full Text Available The need for quantification of cell growth patterns in a multilayer, multi-cellular tissue necessitates the development of a 3D reconstruction technique that can estimate 3D shapes and sizes of individual cells from Confocal Microscopy (CLSM image slices. However, the current methods of 3D reconstruction using CLSM imaging require large number of image slices per cell. But, in case of Live Cell Imaging of an actively developing tissue, large depth resolution is not feasible in order to avoid damage to cells from prolonged exposure to laser radiation. In the present work, we have proposed an anisotropic Voronoi tessellation based 3D reconstruction framework for a tightly packed multilayer tissue with extreme z-sparsity (2-4 slices/cell and wide range of cell shapes and sizes. The proposed method, named as the 'Adaptive Quadratic Voronoi Tessellation' (AQVT, is capable of handling both the sparsity problem and the non-uniformity in cell shapes by estimating the tessellation parameters for each cell from the sparse data-points on its boundaries. We have tested the proposed 3D reconstruction method on time-lapse CLSM image stacks of the Arabidopsis Shoot Apical Meristem (SAM and have shown that the AQVT based reconstruction method can correctly estimate the 3D shapes of a large number of SAM cells.

  5. Dynamic lens and monovision 3D displays to improve viewer comfort

    Johnson, Paul V; Kim, Joowan; Saunter, Christopher D; Love, Gordon D; Banks, Martin S

    2016-01-01

    Stereoscopic 3D (S3D) displays provide an additional sense of depth compared to non-stereoscopic displays by sending slightly different images to the two eyes. But conventional S3D displays do not reproduce all natural depth cues. In particular, focus cues are incorrect causing mismatches between accommodation and vergence: The eyes must accommodate to the display screen to create sharp retinal images even when binocular disparity drives the eyes to converge to other distances. This mismatch causes visual discomfort and reduces visual performance. We propose and assess two new techniques that are designed to reduce the vergence-accommodation conflict and thereby decrease discomfort and increase visual performance. These techniques are much simpler to implement than previous conflict-reducing techniques.

  6. Order reconstruction phenomena and temperature-driven dynamics in a 3D zenithally bistable device

    Raisch, A.

    2014-07-01

    We model the zenithally bistable device (ZBD) in three dimensions (3D), within the Landau-de Gennes theory, and find three stable static states in 3D without an applied field: the vertically aligned nematic (VAN) state, the hybrid aligned nematic (HAN) state and a third, high-tilt state, which we call the THAN state, with an interior and a surface defect. We recover the order reconstruction (OR) phenomenon around the defects in the HAN and THAN states and the 3D THAN and HAN solutions exhibit stable biaxial cylinders connecting defects on opposite faces of the ZBD device. We demonstrate a two-way temperature-driven switching between high-tilt and low-tilt states through controlled heating and cooling procedures in two dimensions (2D), with no applied fields. © CopyrightEPLA, 2014.

  7. Temperature distributions in the laser-heated diamond anvil cell from 3-D numerical modeling

    We present TempDAC, a 3-D numerical model for calculating the steady-state temperature distribution for continuous wave laser-heated experiments in the diamond anvil cell. TempDAC solves the steady heat conduction equation in three dimensions over the sample chamber, gasket, and diamond anvils and includes material-, temperature-, and direction-dependent thermal conductivity, while allowing for flexible sample geometries, laser beam intensity profile, and laser absorption properties. The model has been validated against an axisymmetric analytic solution for the temperature distribution within a laser-heated sample. Example calculations illustrate the importance of considering heat flow in three dimensions for the laser-heated diamond anvil cell. In particular, we show that a “flat top” input laser beam profile does not lead to a more uniform temperature distribution or flatter temperature gradients than a wide Gaussian laser beam

  8. Additive manufactured polymeric 3D scaffolds with tailored surface topography influence mesenchymal stromal cells activity.

    Neves, Sara C; Mota, Carlos; Longoni, Alessia; Barrias, Cristina C; Granja, Pedro L; Moroni, Lorenzo

    2016-06-01

    Additive manufactured three-dimensional (3D) scaffolds with tailored surface topography constitute a clear advantage in tissue regeneration strategies to steer cell behavior. 3D fibrous scaffolds of poly(ethylene oxide terephthalate)/poly(butylene terephthalate) block copolymer presenting different fiber surface features were successfully fabricated by additive manufacturing combined with wet-spinning, in a single step, without any post-processing. The optimization of the processing parameters, mainly driven by different solvent/non-solvent combinations, led to four distinct scaffold types, with average surface roughness values ranging from 0.071 ± 0.012 μm to 1.950 ± 0.553 μm, average pore sizes in the x- and y-axis between 351.1 ± 33.6 μm and 396.1 ± 32.3 μm, in the z-axis between 36.5 ± 5.3 μm and 70.7 ± 8.8 μm, average fiber diameters between 69.4 ± 6.1 μm and 99.0 ± 9.4 μm, and porosity values ranging from 60.2 ± 0.8% to 71.7 ± 2.6%. Human mesenchymal stromal cells (hMSCs) cultured on these scaffolds adhered, proliferated, and produced endogenous extracellular matrix. The effect of surface roughness and topography on hMSCs differentiation was more evident for cells seeded at lower density, where the percentage of cells in direct contact with the surface was higher compared to more densely seeded scaffolds. Under osteogenic conditions, lower surface roughness values (0.227 ± 0.035 μm) had a synergistic effect on hMSCs behavior, while chondrogenesis was favored on rougher surfaces (1.950 ± 0.553 μm). PMID:27219645

  9. 3D Dynamics of Magnetopause Reconnection Using Hall-MHD Global Simulations

    Maynard, K.; Germaschewski, K.; Raeder, J.; Bhattacharjee, A.

    2011-12-01

    Magnetic reconnection at Earth's magnetopause and in the magnetotail is of crucial importance for the dynamics of the global magnetosphere and space weather. Even though the plasma conditions in the magnetosphere are largely in the collisionless regime, most of the existing research using global computational models employ single-fluid magnetohydrodynamics (MHD) with artificial resistivity. Studies of reconnection in simplified, two-dimensional geometries have established that two-fluid and kinetic effects can dramatically alter dynamics and reconnection rates when compared with single-fluid models. These enhanced models also introduce particular signatures, for example a quadrupolar out-of-plane magnetic field component that has already been observed in space by satellite measurements. However, results from simplified geometries cannot be translated directly to the dynamics of three-dimensional magnetospheric reconnection. For instance, magnetic flux originating from the solar wind and arriving at the magnetopause can either reconnect or be advected around the magnetosphere. In this study, we use a new version of the OpenGGCM code that incorporates the Hall term in a Generalized Ohm's Law to study magnetopause reconnection under synthetic solar wind conditions and investigate how reconnection rates and dynamics of flux transfer events depend on the strength of the Hall term. The OpenGGCM, a global model of Earth's magnetosphere, has recently been ported to exploit modern computing architectures like the Cell processor and SIMD capabilities of conventional processors using an automatic code generator. These enhancements provide us with the performance needed to include the computationally expensive Hall physics.

  10. 3D Dynamic Modeling of the Head-Neck Complex for Fast Eye and Head Orientation Movements Research

    Daniel A. Sierra

    2011-01-01

    Full Text Available A 3D dynamic computer model for the movement of the head-neck complex is presented. It incorporates anatomically correct information about the diverse elements forming the system. The skeleton is considered as a set of interconnected rigid 3D bodies following the Newton-Euler laws of movement. The muscles are modeled using Enderle's linear model, which shows equivalent dynamic characteristics to Loeb's virtual muscle model. The soft tissues, namely, the ligaments, intervertebral disks, and facet joints, are modeled considering their physiological roles and dynamics. In contrast with other head and neck models developed for safety research, the model is aimed to study the neural control of the complex during fast eye and head movements, such as saccades and gaze shifts. In particular, the time-optimal hypothesis and the feedback control ones are discussed.

  11. Complete factorial design experiment for 3D load cell instrumented crank validation.

    Omar, Valle-Casas; Rafael, Dalazen; Vinicius, Cene; Alexandre, Balbinot

    2015-08-01

    Developing of instrumentation systems for sport medicine is a promising area, that's why this research evaluates the design of a new instrumented crank arm prototype for a race bicycle projecting an experiment for indoor - outdoor comparison. This study investigated the viability of an instrumentation 3D load cell for force measurement crank, implementing a design of experiment. A Complete factorial design experiment was developed for data validation, with an Analysis of Variance (ANOVA) throwing significant results for controlled factors with response variables rms, mean and variance. A software routine allowed to obtained system variables metrics for Symmetry and Cadence analysis, which came out from Effective force bilateral comparing and speed computation. Characterization allowed achieving calibration curves that were used for data conversion in force projection channels with a linearity error of 0.29% (perpendicular), 0.55% (parallel) and 0.10% (lateral). Interactions of factors resulted significant mainly for indoor tests in symmetry and cadence was significant in interactions generally for outdoor tests. Implemented system was able to generate Effective Force graph for 3D plot symmetry analysis, torque and power symmetry for specialist's analysis. PMID:26737085

  12. A MULTISCALE APPROACH TO THE REPRESENTATION OF 3D IMAGES, WITH APPLICATION TO POLYMER SOLAR CELLS

    Ralf Thiedmann

    2011-03-01

    Full Text Available A multiscale approach to the description of geometrically complex 3D image data is proposed which distinguishes between morphological features on a ‘macro-scale’ and a ‘micro-scale’. Since our method is mainly tailored to nanostructures observed in composite materials consisting of two different phases, an appropriate binarization of grayscale images is required first. Then, a morphological smoothing is applied to extract the structural information from binarized image data on the ‘macro-scale’. A stochastic algorithm is developed for the morphologically smoothed images whose goal is to find a suitable representation of the macro-scale structure by unions of overlapping spheres. Such representations can be interpreted as marked point patterns. They lead to an enormous reduction of data and allow the application of well-known tools from point-process theory for their analysis and structural modeling. All those voxels which have been ‘misspecified’ by the morphological smoothing and subsequent representation by unions of overlapping spheres are interpreted as ‘micro-scale’ structure. The exemplary data sets considered in this paper are 3D grayscale images of photoactive layers in hybrid solar cells gained by electron tomography. These composite materials consist of two phases: a polymer phase and a zinc oxide phase. The macro-scale structure of the latter is represented by unions of overlapping spheres.

  13. A Parallelized 3D Particle-In-Cell Method With Magnetostatic Field Solver And Its Applications

    Hsu, Kuo-Hsien; Chen, Yen-Sen; Wu, Men-Zan Bill; Wu, Jong-Shinn

    2008-10-01

    A parallelized 3D self-consistent electrostatic particle-in-cell finite element (PIC-FEM) code using an unstructured tetrahedral mesh was developed. For simulating some applications with external permanent magnet set, the distribution of the magnetostatic field usually also need to be considered and determined accurately. In this paper, we will firstly present the development of a 3D magnetostatic field solver with an unstructured mesh for the flexibility of modeling objects with complex geometry. The vector Poisson equation for magnetostatic field is formulated using the Galerkin nodal finite element method and the resulting matrix is solved by parallel conjugate gradient method. A parallel adaptive mesh refinement module is coupled to this solver for better resolution. Completed solver is then verified by simulating a permanent magnet array with results comparable to previous experimental observations and simulations. By taking the advantage of the same unstructured grid format of this solver, the developed PIC-FEM code could directly and easily read the magnetostatic field for particle simulation. In the upcoming conference, magnetron is simulated and presented for demonstrating the capability of this code.

  14. A miniature microbial fuel cell with conducting nanofibers-based 3D porous biofilm

    Jiang, Huawei; Halverson, Larry J.; Dong, Liang

    2015-12-01

    Miniature microbial fuel cell (MFC) technology has received growing interest due to its potential applications in high-throughput screening of bacteria and mutants to elucidate mechanisms of electricity generation. This paper reports a novel miniature MFC with an improved output power density and short startup time, utilizing electrospun conducting poly(3,4-ethylenedioxythiophene) (PEDOT) nanofibers as a 3D porous anode within a 12 μl anolyte chamber. This device results in 423 μW cm-3 power density based on the volume of the anolyte chamber, using Shewanella oneidensis MR-1 as a model biocatalyst without any optimization of bacterial culture. The device also excels in a startup time of only 1hr. The high conductivity of the electrospun nanofibers makes them suitable for efficient electron transfer. The mean pore size of the conducting nanofibers is several micrometers, which is favorable for bacterial penetration and colonization of surfaces of the nanofibers. We demonstrate that S. oneidensis can fully colonize the interior region of this nanofibers-based porous anode. This work represents a new attempt to explore the use of electrospun PEDOT nanofibers as a 3D anode material for MFCs. The presented miniature MFC potentially will provide a high-sensitivity, high-throughput tool to screen suitable bacterial species and mutant strains for use in large-size MFCs.

  15. 3D Printing Bioceramic Porous Scaffolds with Good Mechanical Property and Cell Affinity.

    Chih-Hao Chang

    Full Text Available Artificial bone grafting is widely used in current orthopedic surgery for bone defect problems. Unfortunately, surgeons remain unsatisfied with the current commercially available products. One of the major complaints is that these products cannot provide sufficient mechanical strength to support the human skeletal structure. In this study, we aimed to develop a bone scaffold with better mechanical property and good cell affinity by 3D printing (3DP techniques. A self-developed 3D printer with laser-aided gelling (LAG process was used to fabricate bioceramic scaffolds with inter-porous structures. To improve the mechanical property of the bioceramic parts after heating, CaCO3 was added to the silica ceramic slurry. CaCO3 was blended into a homogenous SiO2-sol dispersion at weight ratios varying from 0/100 to 5/95 to 9/91 (w/w. Bi-component CaCO3/SiO2-sol was prepared as a biocomposite for the 3DP scaffold. The well-mixed biocomposite was used to fabricate the bioceramic green part using the LAG method. The varied scaffolds were sintered at different temperatures ranging from 900 to 1500°C, and the mechanical property was subsequently analyzed. The scaffolds showed good property with the composite ratio of 5:95 CaCO3:SiO2 at a sintering temperature of 1300°C. The compressive strength was 47 MPa, and the porosity was 34%. The topography of the sintered 3DP bioceramic scaffold was examined by SEM, EDS and XRD. The silica bioceramic presented no cytotoxicity and good MG-63 osteoblast-like cell affinity, demonstrating good biocompatibility. Therefore, the new silica biocomposite is viable for fabricating 3DP bone bioceramics with improved mechanical property and good cell affinity.

  16. 3-D-conformal radiation therapy for pediatric giant cell tumors of the skull base

    Hug, E.B. [Massachusetts General Hospital, Boston, MA (United States). Dept. of Radiation Oncology; Harvard Univ., Cambridge, MA (United States). Cyclotron Lab.; Dartmouth Hitchcock Medical Center, Lebanon, NH (United States). Section of Radiation Oncology; Muenter, M.W.; Vries, A. de [Massachusetts General Hospital, Boston, MA (United States). Dept. of Radiation Oncology; Adams, J.A.; Munzenrider, J.E. [Massachusetts General Hospital, Boston, MA (United States). Dept. of Radiation Oncology; Harvard Univ., Cambridge, MA (United States). Cyclotron Lab.; Rosenberg, A.E. [Massachusetts General Hospital, Boston, MA (United States). Dept. of Pathology

    2002-05-01

    Background: Giant cell tumors (GCT) of the base of skull are rare neoplasms. This report reviews the treatment of four pediatric patients presenting with aggressive giant cell tumor, using fractionated and combined, conformal proton and photon radiation therapy at Massachusetts General Hospital and Harvard Cyclotron Laboratory. Patients and Methods: Three female patients and one adolescent male, ages 10-15 years, had undergone prior, extensive surgical resection(s) and were treated for either primary (two patients) or recurrent (two patients) disease. Gross residual tumor was evident in three patients and microscopic disease suspected in one patient. Combined proton and photon radiation theory was based on three-dimensional (3-D) planning, consisting of fractionated treatment, one fraction per day at 1.8 CGE (cobalt-gray equivalent) to total target doses of 57.6, 57.6, 59.4, and 61.2 Gy/CGE. Results: With observation times of 3.1 years, 3.3, 5.3, and 5.8 years, all four patients were alive and well and remained locally controlled without evidence of recurrent disease. Except for one patient with partial pituitary insufficiency following radiotherapy for sellar recurrent disease, thus far no late effects attributable to radiation therapy have been observed. Conclusions: 3-D conformal radiation therapy offers a realistic chance of tumor control for aggressive giant cell tumor in the skull base, either postoperatively or at time of recurrence. Conformal treatment techniques allow the safe delivery of relatively high radiation doses in the pediatric patient without apparent increase of side effects. (orig.)

  17. Dual targeting of EGFR and focal adhesion kinase in 3D grown HNSCC cell cultures

    Purpose: Epidermal growth factor receptor (EGFR) and focal adhesion kinase (FAK) show frequent overexpression and hyperactivity in various human malignancies including head and neck squamous cell carcinomas (HNSCC). To examine effects of dual EGFR/FAK inhibition on cellular radiosensitivity of HNSCC cells in a more physiological environment, we employed a previously established laminin-rich extracellular matrix (lrECM) based three-dimensional (3D) cell culture model. Materials and methods: UTSCC15 and SAS HNSCC cell lines stably transfected with EGFR-CFP or CFP were used. Single or combined EGFR (Cetuximab, siRNA) and FAK (TAE226, siRNA) inhibition were accomplished prior to measuring clonogenic survival and protein expression and phosphorylation. Immunofluorescence enabled visualization of EGFR-CFP and FAK. Results: Cetuximab resulted in higher radiosensitization in EGFR-CFP overexpressing cell lines than CFP controls. Single EGFR or FAK inhibition mediated radiosensitization, while dual EGFR/FAK targeting further augmented this effect. Despite signaling alterations upon Cetuximab and siRNA knockdown, analysis of protein expression and phosphorylation indicates EGFR and FAK signaling coexistence without obvious overlap. Conclusions: Combined EGFR/FAK targeting yielded stronger radiosensitization than either approach alone, which might be based on non-overlapping downstream signaling. Whether dual targeting of EGFR and FAK can reasonably be combined with radiotherapy and chemotherapy needs clarification.

  18. Metabolic response of lung cancer cells to radiation in a paper-based 3D cell culture system.

    Simon, Karen A; Mosadegh, Bobak; Minn, Kyaw Thu; Lockett, Matthew R; Mohammady, Marym R; Boucher, Diane M; Hall, Amy B; Hillier, Shawn M; Udagawa, Taturo; Eustace, Brenda K; Whitesides, George M

    2016-07-01

    This work demonstrates the application of a 3D culture system-Cells-in-Gels-in-Paper (CiGiP)-in evaluating the metabolic response of lung cancer cells to ionizing radiation. The 3D tissue-like construct-prepared by stacking multiple sheets of paper containing cell-embedded hydrogels-generates a gradient of oxygen and nutrients that decreases monotonically in the stack. Separating the layers of the stack after exposure enabled analysis of the cellular response to radiation as a function of oxygen and nutrient availability; this availability is dictated by the distance between the cells and the source of oxygenated medium. As the distance between the cells and source of oxygenated media increased, cells show increased levels of hypoxia-inducible factor 1-alpha, decreased proliferation, and reduced sensitivity to ionizing radiation. Each of these cellular responses are characteristic of cancer cells observed in solid tumors. With this setup we were able to differentiate three isogenic variants of A549 cells based on their metabolic radiosensitivity; these three variants have known differences in their metastatic behavior in vivo. This system can, therefore, capture some aspects of radiosensitivity of populations of cancer cells related to mass-transport phenomenon, carry out systematic studies of radiation response in vitro that decouple effects from migration and proliferation of cells, and regulate the exposure of oxygen to subpopulations of cells in a tissue-like construct either before or after irradiation. PMID:27116031

  19. A Multifunctional 3D Co-Culture System for Studies of Mammary Tissue Morphogenesis and Stem Cell Biology

    Campbell, Jonathan J.; Davidenko, Natalia; Caffarel, Maria M.; Cameron, Ruth E.; Watson, Christine J

    2011-01-01

    Studies on the stem cell niche and the efficacy of cancer therapeutics require complex multicellular structures and interactions between different cell types and extracellular matrix (ECM) in three dimensional (3D) space. We have engineered a 3D in vitro model of mammary gland that encompasses a defined, porous collagen/hyaluronic acid (HA) scaffold forming a physiologically relevant foundation for epithelial and adipocyte co-culture. Polarized ductal and acinar structures form within this sc...

  20. Isotropic 3D nuclear morphometry of normal, fibrocystic and malignant breast epithelial cells reveals new structural alterations.

    Vivek Nandakumar

    Full Text Available BACKGROUND: Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading criteria. METHODOLOGY: We applied micro-optical computed tomographic imaging and automated 3D nuclear morphometry to quantify and compare morphological variations between human cell lines derived from normal, benign fibrocystic or malignant breast epithelium. To reproduce the appearance and contrast in clinical cytopathology images, we stained cells with hematoxylin and eosin and obtained 3D images of 150 individual stained cells of each cell type at sub-micron, isotropic resolution. Applying volumetric image analyses, we computed 42 3D morphological and textural descriptors of cellular and nuclear structure. PRINCIPAL FINDINGS: We observed four distinct nuclear shape categories, the predominant being a mushroom cap shape. Cell and nuclear volumes increased from normal to fibrocystic to metastatic type, but there was little difference in the volume ratio of nucleus to cytoplasm (N/C ratio between the lines. Abnormal cell nuclei had more nucleoli, markedly higher density and clumpier chromatin organization compared to normal. Nuclei of non-tumorigenic, fibrocystic cells exhibited larger textural variations than metastatic cell nuclei. At p<0.0025 by ANOVA and Kruskal-Wallis tests, 90% of our computed descriptors statistically differentiated control from abnormal cell populations, but only 69% of these features statistically differentiated the fibrocystic from the metastatic cell populations. CONCLUSIONS: Our results provide a new perspective on nuclear

  1. Atypical pyramidal cells in epileptic human cortex: CFLS and 3-D reconstructions.

    Belichencko, P; Dahlström, A; von Essen, C; Lindström, S; Nordborg, C; Sourander, P

    1992-09-01

    Epileptic temporal cortices, removed from 3 patients with intractable partial epilepsy (IPE) during neurosurgery, were studied. Pyramidal neurons (40-50 per slice) in laminae III, V and white matter, were injected with lucifer yellow. Samples were examined in a confocal laser scanning microscope (Biorad 600) and individual cells scanned at 0.1-1 microns incremental levels. 2-D maximal linear projection was used for overview. Frames (50-60) of scanned neurons were transformed into 3-D volumes, using VoxelView software on a Silicone Graphics workstation and rotated. All samples contained neurons with duplicated apical dendrites, additional basal dendrites or were misplaced in a horizontal position in the white matter. The relation between these preliminary observations and the disease is discussed. PMID:1421134

  2. Epithelial-to-mesenchymal transition in pancreatic ductal adenocarcinoma: Characterization in a 3D-cell culture model

    Gagliano, Nicoletta; Celesti, Giuseppe; Tacchini, Lorenza; Pluchino, Stefano; Sforza, Chiarella; Rasile, Marco; Valerio, Vincenza; Laghi, Luigi; Conte, Vincenzo; Procacci, Patrizia

    2016-01-01

    AIM: To analyze the effect of three-dimensional (3D)-arrangement on the expression of epithelial-to-mesenchymal transition markers in pancreatic adenocarcinoma (PDAC) cells. METHODS: HPAF-II, HPAC, and PL45 PDAC cells were cultured in either 2D-monolayers or 3D-spheroids. Ultrastructure was analyzed by transmission electron microscopy. The expression of E-cadherin, β-catenin, N-cadherin, collagen type I (COL-I), vimentin, α-smooth muscle actin (αSMA), and podoplanin was assayed by confocal microscopy in cells cultured on 12-mm diameter round coverslips and in 3D-spheroids. Gene expression for E-cadherin, Snail, Slug, Twist, Zeb1, and Zeb2 was quantified by real-time PCR. E-cadherin protein level and its electrophoretic pattern were studied by Western blot in cell lysates obtained from cells grown in 2D-monolayers and 3D-spheroids. RESULTS: The E-cadherin/β-catenin complex was expressed in a similar way in plasma membrane cell boundaries in both 2D-monolayers and 3D-spheroids. E-cadherin increased in lysates obtained from 3D-spheroids, while cleavage fragments were more evident in 2D-monolayers. N-cadherin expression was observed in very few PDAC cells grown in 2D-monolayers, but was more evident in 3D-spheroids. Some cells expressing COL-I were observed in 3D-spheroids. Podoplanin, expressed in collectively migrating cells, and αSMA were similarly expressed in both experimental conditions. The concomitant maintenance of the E-cadherin/β-catenin complex at cell boundaries supports the hypothesis of a collective migration for these cells, which is consistent with podoplanin expression. CONCLUSION: We show that a 3D-cell culture model could provide deeper insight into understanding the biology of PDAC and allow for the detection of marked differences in the phenotype of PDAC cells grown in 3D-spheroids. PMID:27182158

  3. Versatile, immersive, creative and dynamic virtual 3-D healthcare learning environments: a review of the literature.

    Hansen, Margaret M

    2008-01-01

    The author provides a critical overview of three-dimensional (3-D) virtual worlds and "serious gaming" that are currently being developed and used in healthcare professional education and medicine. The relevance of this e-learning innovation for teaching students and professionals is debatable and variables influencing adoption, such as increased knowledge, self-directed learning, and peer collaboration, by academics, healthcare professionals, and business executives are examined while looking at various Web 2.0/3.0 applications. There is a need for more empirical research in order to unearth the pedagogical outcomes and advantages associated with this e-learning technology. A brief description of Roger's Diffusion of Innovations Theory and Siemens' Connectivism Theory for today's learners is presented as potential underlying pedagogical tenets to support the use of virtual 3-D learning environments in higher education and healthcare. PMID:18762473

  4. Novel carbocyclic curcumin analog CUR3d modulates genes involved in multiple apoptosis pathways in human hepatocellular carcinoma cells.

    Bhullar, Khushwant S; Jha, Amitabh; Rupasinghe, H P Vasantha

    2015-12-01

    Anticancer activity of a novel curcumin analog (E)-2-(4-hydroxy-3-methoxybenzylidene)-5-((E)-3-(4-hydroxy-3-methoxyphenyl)acryloyl)cyclopentanone (CUR3d) was studied using a human hepatocellular carcinoma cell line (HepG2). The results showed that CUR3d completely inhibits the tumor cell proliferation in a dose- and time-dependent manner. CUR3d at 100 μmol/L activated the pro-apoptotic caspase-3 along with downregulation of anti-apoptotic BIRC5 and Bcl2. CUR3d treatment controlled the cancer cell growth by downregulating the expression of PI3K/Akt (Akt1, Akt2) pathway along with NF-κB. CUR3d down-regulated the members of epidermal growth receptor family (EGFR, ERBB3, ERBB2) and insulin like growth receptors (IGF1, IGF-1R, IGF2). This correlated with the downregulation of G-protein (RHOA, RHOB) and RAS (ATF2, HRAS, KRAS, NRAS) pathway signaling. CUR3d also arrested cell cycle via inhibition of CDK2, CDK4, CDK5, CDK9, MDM2, MDM4 and TERT genes. Cell cycle essential aurora kinases (AURKα, AURKβ) and polo-like kinases (PLK1, PLK2, PLK3) were also modulated by CUR3d. Topoisomerases (TOP2α, TOP2β), important factors in cancer cell immortality, as well as HIF-1α were downregulated following CUR3d treatment. The expression of protein kinase-C family (PRKC-A, PRKC-D, PRKC-E) was also attenuated by CUR3d. The downregulation of histone deacetylases (Class I, II, IV) and PARP I further strengthened the anticancer efficacy of CUR3d. Downregulation of carcinogenic cathepsins (CTSB, CTSD) and heat shock proteins exhibited CUR3d's potency as a potential immunological adjuvant. Finally, the non-toxic manifestation of CUR3d in healthy liver and lung cells along with downregulation of drug resistant gene ABCC1 further warrant need for advance investigations. PMID:26409325

  5. Versatile, Immersive, Creative and Dynamic Virtual 3-D Healthcare Learning Environments: A Review of the Literature

    Hansen, Margaret M

    2008-01-01

    The author provides a critical overview of three-dimensional (3-D) virtual worlds and “serious gaming” that are currently being developed and used in healthcare professional education and medicine. The relevance of this e-learning innovation for teaching students and professionals is debatable and variables influencing adoption, such as increased knowledge, self-directed learning, and peer collaboration, by academics, healthcare professionals, and business executives are examined while lookin...

  6. Motion Field Estimation for a Dynamic Scene Using a 3D LiDAR

    Qingquan Li; Liang Zhang; Qingzhou Mao; Qin Zou; Pin Zhang; Shaojun Feng; Washington Ochieng

    2014-01-01

    This paper proposes a novel motion field estimation method based on a 3D light detection and ranging (LiDAR) sensor for motion sensing for intelligent driverless vehicles and active collision avoidance systems. Unlike multiple target tracking methods, which estimate the motion state of detected targets, such as cars and pedestrians, motion field estimation regards the whole scene as a motion field in which each little element has its own motion state. Compared to multiple target tracking, seg...

  7. Solid friction at high sliding velocities: an explicit 3D dynamical SPH approach

    Maveyraud, C.; Benz, W.; Ouillon, G.; Sornette, A.; Sornette, D.

    1998-01-01

    We present realistic 3D numerical simulations of elastic bodies sliding on top of each other in a regime of velocities ranging from meters to tens of meters per second using the so-called Smoothed Particle Hydrodynamics (SPH) method. Our investigations are restricted to regimes of pressure and roughness where only elastic deformations occur between asperities at the contact surface between the slider block and the substrate. In this regime, solid friction is due to the generation of vibration...

  8. Using Polymer Confinement for Stem Cell Differentiation: 3D Printed vs Molded Scaffolds

    Rafailovich, Miriam

    Additive manufacturing technologies are increasingly being used to replace standard extrusion or molding methods in engineering polymeric biomedical implants, which can be further seeded with cells for tissue regeneration. The principal advantage of this new technology is the ability to print directly from a scan and hence produce parts which are an ideal fit for an individual, eliminating much of the sizing and fitting associated with standard manufacturing methods. The question though arises whether devices which may be macroscopically similar, serve identical functions and are produced from the same material, interact in the same manner with cells and living tissue. Here we show that fundamental differences can exist between 3-D printed and extruded scaffolds which can impact stem cell differentiation and lineage selection. We will show how polymer confinement inherent in these methods affect the printed features on multiple length scales. We will also and how the differentiation of stem cells is affected by substrate heterogeneity in both morphological and mechanical features. NSF-Inspire award # 1344267.

  9. Antibody-free isolation of rare cancer cells from blood based on 3D lateral dielectrophoresis.

    Cheng, I-Fang; Huang, Wei-Lun; Chen, Tzu-Ying; Liu, Chien-Wei; Lin, Yu-De; Su, Wu-Chou

    2015-07-21

    We present an antibody-free approach for the high-purity and high-throughput dielectrophoretic (DEP) isolation of circulating tumour cells (CTCs) from blood in a microfluidic chip. A hydrodynamic sheath flow is designed upstream in the chip to direct the suspension samples to the channel side walls, thus providing a queue to allow DEP-induced lateral displacements. High-throughput continuous cancer cell sorting (maximum flow rate: ~2.4 mL h(-1), linear velocity: ~4 mm s(-1)) is achieved with a sustained 3D lateral DEP (LDEP) particle force normal to the continuous through-flow. This design allows the continuous fractionation of micro/nanosized particles into different downstream subchannels based on the differences in their different critical negative DEP strengths/mobilities. The main advantage of this separation strategy is that increasing the channel length can effectively increase the throughput proportionally. The effective separation of rare cancer cells (<0.001%) from diluted human blood in a handheld chip is demonstrated. An enrichment factor of 10(5) and a recovery rate of ~85% from a 0.001% cancer cell sample are achieved at an optimal flow rate of 20 μL min(-1) passing through a 6 cm long LDEP channel with an appropriate voltage at a frequency of 10 kHz. A higher throughput of 2.4 mL h(-1) is also achieved with a 13 cm long metal-based microchannel. PMID:26085231

  10. Motion field estimation for a dynamic scene using a 3D LiDAR.

    Li, Qingquan; Zhang, Liang; Mao, Qingzhou; Zou, Qin; Zhang, Pin; Feng, Shaojun; Ochieng, Washington

    2014-01-01

    This paper proposes a novel motion field estimation method based on a 3D light detection and ranging (LiDAR) sensor for motion sensing for intelligent driverless vehicles and active collision avoidance systems. Unlike multiple target tracking methods, which estimate the motion state of detected targets, such as cars and pedestrians, motion field estimation regards the whole scene as a motion field in which each little element has its own motion state. Compared to multiple target tracking, segmentation errors and data association errors have much less significance in motion field estimation, making it more accurate and robust. This paper presents an intact 3D LiDAR-based motion field estimation method, including pre-processing, a theoretical framework for the motion field estimation problem and practical solutions. The 3D LiDAR measurements are first projected to small-scale polar grids, and then, after data association and Kalman filtering, the motion state of every moving grid is estimated. To reduce computing time, a fast data association algorithm is proposed. Furthermore, considering the spatial correlation of motion among neighboring grids, a novel spatial-smoothing algorithm is also presented to optimize the motion field. The experimental results using several data sets captured in different cities indicate that the proposed motion field estimation is able to run in real-time and performs robustly and effectively. PMID:25207868

  11. Motion Field Estimation for a Dynamic Scene Using a 3D LiDAR

    Qingquan Li

    2014-09-01

    Full Text Available This paper proposes a novel motion field estimation method based on a 3D light detection and ranging (LiDAR sensor for motion sensing for intelligent driverless vehicles and active collision avoidance systems. Unlike multiple target tracking methods, which estimate the motion state of detected targets, such as cars and pedestrians, motion field estimation regards the whole scene as a motion field in which each little element has its own motion state. Compared to multiple target tracking, segmentation errors and data association errors have much less significance in motion field estimation, making it more accurate and robust. This paper presents an intact 3D LiDAR-based motion field estimation method, including pre-processing, a theoretical framework for the motion field estimation problem and practical solutions. The 3D LiDAR measurements are first projected to small-scale polar grids, and then, after data association and Kalman filtering, the motion state of every moving grid is estimated. To reduce computing time, a fast data association algorithm is proposed. Furthermore, considering the spatial correlation of motion among neighboring grids, a novel spatial-smoothing algorithm is also presented to optimize the motion field. The experimental results using several data sets captured in different cities indicate that the proposed motion field estimation is able to run in real-time and performs robustly and effectively.

  12. Motion Field Estimation for a Dynamic Scene Using a 3D LiDAR

    Li, Qingquan; Zhang, Liang; Mao, Qingzhou; Zou, Qin; Zhang, Pin; Feng, Shaojun; Ochieng, Washington

    2014-01-01

    This paper proposes a novel motion field estimation method based on a 3D light detection and ranging (LiDAR) sensor for motion sensing for intelligent driverless vehicles and active collision avoidance systems. Unlike multiple target tracking methods, which estimate the motion state of detected targets, such as cars and pedestrians, motion field estimation regards the whole scene as a motion field in which each little element has its own motion state. Compared to multiple target tracking, segmentation errors and data association errors have much less significance in motion field estimation, making it more accurate and robust. This paper presents an intact 3D LiDAR-based motion field estimation method, including pre-processing, a theoretical framework for the motion field estimation problem and practical solutions. The 3D LiDAR measurements are first projected to small-scale polar grids, and then, after data association and Kalman filtering, the motion state of every moving grid is estimated. To reduce computing time, a fast data association algorithm is proposed. Furthermore, considering the spatial correlation of motion among neighboring grids, a novel spatial-smoothing algorithm is also presented to optimize the motion field. The experimental results using several data sets captured in different cities indicate that the proposed motion field estimation is able to run in real-time and performs robustly and effectively. PMID:25207868

  13. Exploring natural silk protein sericin for regenerative medicine: an injectable, photoluminescent, cell-adhesive 3D hydrogel

    Wang, Zheng; Zhang, Yeshun; Zhang, Jinxiang; Huang, Lei; Liu, Jia; Li, Yongkui; Zhang, Guozheng; Kundu, Subhas C.; Wang, Lin

    2014-11-01

    Sericin, a major component of silk, has a long history of being discarded as a waste during silk processing. The value of sericin for tissue engineering is underestimated and its potential application in regenerative medicine has just begun to be explored. Here we report the successful fabrication and characterization of a covalently-crosslinked 3D pure sericin hydrogel for delivery of cells and drugs. This hydrogel is injectable, permitting its implantation through minimally invasive approaches. Notably, this hydrogel is found to exhibit photoluminescence, enabling bioimaging and in vivo tracking. Moreover, this hydrogel system possesses excellent cell-adhesive capability, effectively promoting cell attachment, proliferation and long-term survival of various types of cells. Further, the sericin hydrogel releases bioactive reagents in a sustained manner. Additionally, this hydrogel demonstrates good elasticity, high porosity, and pH-dependent degradation dynamics, which are advantageous for this sericin hydrogel to serve as a delivery vehicle for cells and therapeutic drugs. With all these unique features, it is expected that this sericin hydrogel will have wide utility in the areas of tissue engineering and regenerative medicine.

  14. CARS and SHG microscopy to follow the collagen production in living human corneal fibroblasts and mesenchymal stem cells in fibrin gel 3D cultures

    Mortati, Leonardo; Sassi, Maria Paola

    2011-01-01

    Coherent anti-Stokes Raman scattering (CARS) microscopy is combined with second harmonic generation (SHG) technique in order to follow the early stage of stem cell differentiation within a 3D scaffold. CARS microscopy can detect lipid membranes and droplet compartments in living cells and SHG microscopy enables a strong imaging contrast for molecules with a non-centrosymmetric ordered structure like collagen. One of the first evidence of hMSCs differentiation is the formation of an extracellular matrix (ECM) where the collagen protein is its main component. This work demonstrated the multimodal CARS and SHG microscopy as a powerful non-invasive label free technique to investigate the collagen production dynamic in living cell 3D cultures. Its ability to image the cell morphology and the produced collagen distribution on a long term (4 weeks) experiment allowed to obtain important information about the cell-scaffold interaction and the ECM production. The very low limit reached in detecting collagen has permit...

  15. Improved Human Bone Marrow Mesenchymal Stem Cell Osteogenesis in 3D Bioprinted Tissue Scaffolds with Low Intensity Pulsed Ultrasound Stimulation.

    Zhou, Xuan; Castro, Nathan J; Zhu, Wei; Cui, Haitao; Aliabouzar, Mitra; Sarkar, Kausik; Zhang, Lijie Grace

    2016-01-01

    3D printing and ultrasound techniques are showing great promise in the evolution of human musculoskeletal tissue repair and regeneration medicine. The uniqueness of the present study was to combine low intensity pulsed ultrasound (LIPUS) and advanced 3D printing techniques to synergistically improve growth and osteogenic differentiation of human mesenchymal stem cells (MSC). Specifically, polyethylene glycol diacrylate bioinks containing cell adhesive Arginine-Glycine-Aspartic acid-Serene (RGDS) peptide and/or nanocrystalline hydroxyapatite (nHA) were used to fabricate 3D scaffolds with different geometric patterns via novel table-top stereolithography 3D printer. The resultant scaffolds provide a highly porous and interconnected 3D environment to support cell proliferation. Scaffolds with small square pores were determined to be the optimal geometric pattern for MSC attachment and growth. The optimal LIPUS working parameters were determined to be 1.5 MHz, 20% duty cycle with 150 mW/cm(2) intensity. Results demonstrated that RGDS peptide and nHA containing 3D printed scaffolds under LIPUS treatment can greatly promote MSC proliferation, alkaline phosphatase activity, calcium deposition and total protein content. These results illustrate the effectiveness of the combination of LIPUS and biomimetic 3D printing scaffolds as a valuable combinatorial tool for improved MSC function, thus make them promising for future clinical and various regenerative medicine application. PMID:27597635

  16. Development of bioartificial myocardium by electrostimulation of 3D collagen scaffolds seeded with stem cells

    Alain Carpentier

    2012-06-01

    Full Text Available Electrostimulation (ES can be defined as a safe physical method to induce stem cell differentiation. The aim of this study is to evaluate the effectiveness of ES on bone marrow mesenchymal stem cells (BMSCs seeded in collagen scaffolds in terms of proliferation and differentiation into cardiomyocytes. BMSCs were isolated from Wistar rats and seeded into 3D collagen type 1 templates measuring 25 x 25 x 6 mm. Bipolar in vitro ES was performed during 21 days. Electrical impedance and cell proliferation were measured. Expression of cardiac markers was assessed by immunocytochemistry. Viscoelasticity of collagen matrix was evaluated. Electrical impedance assessments showed a low resistance of 234±41 Ohms which indicates good electrical conductivity of collagen matrix. Cell proliferation at 570 nm as significantly increased in ES groups after seven day (ES 0.129±0.03 vs non-stimulated control matrix 0.06±0.01, P=0.002 and after 21 days, (ES 0.22±0.04 vs control 0.13±0.01, P=0.01. Immunocytochemistry of BMSCs after 21 days ES showed positive staining of cardiac markers, troponin I, connexin 43, sarcomeric alpha-actinin, slow myosin, fast myosin and desmin. Staining for BMSCs marker CD29 after 21 days was negative. Electrostimulation of cell-seeded collagen matrix changed stem cell morphology and bio- chemical characteristics, increasing the expression of cardiac markers. Thus, MSC-derived differentiated cells by electrostimulation grafted in biological scaffolds might result in a convenient tissue engineering source for myocardial diseases.

  17. Pulmonary hilar lymph nodes in lung cancer: assessment with 3D-dynamic contrast-enhanced MR imaging

    Purpose: We performed 3D-dynamic MRI on patients with primary lung cancer to identify its usefulness for detecting hilar adenopathy shown at surgery. Methods and materials: 30 consecutive patients with peripheral lung cancer underwent preoperative 3D-dynamic Gd-DTPA-enhanced MRI. Two thoracic radiologists blinded to histopathologic findings reviewed those studies independently for hilar adenopathy visualization. The results were correlated with surgical and histopathologic findings. Interreader agreement for the detection of hilar adenopathy was assessed by means of the κ statistic. Results: Dynamic MRI demonstrated hilar adenopathy, with or without metastasis revealed at surgery, in all of 15 patients. Adenopathy without metastasis was shown in four patients. Dynamic MRI also revealed metastatic adenopathy in 11 of 12 patients with pathologically proven metastasis. There was only one case with lymph node metastasis that did not have adenopathy either on MRI or even at surgery. The diagnostic accuracy of dynamic MRI for adenopathy with or without metastases revealed at surgery were as follows; sensitivity, 100%; specificity, 100%; positive predictive value, 100%; and negative predictive value, 100%, respectively. The diagnostic accuracy of dynamic MRI for hilar lymph nodes metastasis were as follows; sensitivity, 92%; specificity, 78%; positive predictive value, 73%; and negative predictive value, 93%. Interreader agreement was substantial (κ=0.73) for detection of hilar adenopathy. Conclusion: Hilar adenopathy on 3D-dynamic MRI correlated well with that of surgical finding on patients with primary lung cancer. It may have the potential to make an accurate preoperative evaluation of hilar lymph node metastasis from lung cancer

  18. Engineering hyaluronic acid hydrogel degradation to control cellular interactions and adult stem cell fate in 3D

    Khetan, Sudhir

    The design and implementation of extracellular matrix (ECM)-mimetic hydrogels for tissue engineering (TE) applications requires an intensive understanding of cell-material interactions, including matrix remodeling and stem cell differentiation. However, the influence of microenvironmental cues, e.g., matrix biodegradability, on cell behavior in vitro has not been well studied in the case of direct cell encapsulation within 3-dimensional (3D) hydrogels. To address these issues, a facile sequential crosslinking technique was developed that provides spatial and temporal control of 3D hydrogel degradability to investigate the importance of material design on cell behavior. Specifically, hydrogels were synthesized from hyaluronic acid (HA) macromers in a sequential process: (1) a primary Michael-type addition crosslinking using cell adhesive and matrix metalloprotease (MMP)-degradable oligopeptides to consume a portion of total reactive groups and resulting in "-UV" hydrogels permissive to cell-mediated degradation, followed by (2) a secondary, light initiated free-radical crosslinking to consume remaining reactive groups and "switch" the network to a non-degradable structure ("+UV") via the addition of non-degradable kinetic chains. Using this approach, we demonstrated control of encapsulated hMSC spreading by varying the crosslink type (i.e., the relative hydrogel biodegradability), including with spatial control. Upon incubation with bipotential soluble differentiation factors, these same degradation-mediated spreading cues resulted in an hMSC differentiation fate switch within -UV versus +UV environments. Follow-up studies demonstrated that degradation-mediated traction generation, rather than matrix mechanics or cell morphology, is the critical biophysical signal determining hMSC fate. Sequentially crosslinked HA hydrogels were also studied for the capacity to support remodeling by in vivo and ex vivo tissues, including with spatial control, toward tissue

  19. Improving organic tandem solar cells based on water-processed nanoparticles by quantitative 3D nanoimaging.

    Pedersen, E B L; Angmo, D; Dam, H F; Thydén, K T S; Andersen, T R; Skjønsfjell, E T B; Krebs, F C; Holler, M; Diaz, A; Guizar-Sicairos, M; Breiby, D W; Andreasen, J W

    2015-08-28

    Organic solar cells have great potential for upscaling due to roll-to-roll processing and a low energy payback time, making them an attractive sustainable energy source for the future. Active layers coated with water-dispersible Landfester particles enable greater control of the layer formation and easier access to the printing industry, which has reduced the use of organic solvents since the 1980s. Through ptychographic X-ray computed tomography (PXCT), we image quantitatively a roll-to-roll coated photovoltaic tandem stack consisting of one bulk heterojunction active layer and one Landfester particle active layer. We extract the layered morphology with structural and density information including the porosity present in the various layers and the silver electrode with high resolution in 3D. The Landfester particle layer is found to have an undesired morphology with negatively correlated top- and bottom interfaces, wide thickness distribution and only partial surface coverage causing electric short circuits through the layer. By top coating a polymer material onto the Landfester nanoparticles we eliminate the structural defects of the layer such as porosity and roughness, and achieve the increased performance larger than 1 V expected for a tandem cell. This study highlights that quantitative imaging of weakly scattering stacked layers of organic materials has become feasible by PXCT, and that this information cannot be obtained by other methods. In the present study, this technique specifically reveals the need to improve the coatability and layer formation of Landfester nanoparticles, thus allowing improved solar cells to be produced. PMID:26220159

  20. X-ray tomography: Biological cells in 3-D at better than 50 nm resolution

    Full text: X-ray microscopy can be used to image whole, hydrated, specimens with a spatial resolution 5-10 times better than that obtained using visible light microscopy. X-ray imaging at photon energies below the K- absorption edge of oxygen, referred to as the water window, exploits the strong natural contrast for organic material embedded in a mostly water matrix. With a transmission X-ray microscope using Fresnel zone plate optics, specimens up to 10 microns thick can be examined. The highest X-ray transmission in hydrated samples is obtained at a wavelength of 2.4 nm but, due to the low numerical aperture of zone plate lenses operated in st order diffraction mode the structures resolved are much larger than the X-ray wavelength. Because of the low NA of X-ray lenses (NA=0.05), combined with the effect of polychromatic illumination and a wavelength dependant focal length, the effective depth of ld is large (6-10 microns). The experiments presented here were performed at the Advanced Light Source using the full ld transmission X-ray microscope, XM-1. This microscope employs a bend magnet X-ray source and zone plate condenser and objective lenses. The condenser zone plate acts as a monochromator and the X-ray images are recorded directly on a cooled, back-thinned 1024x1024 pixel CCD camera. The sample holder was a rotationally symmetric glass tube; the region containing the sample was 10 microns in diameter with a wall thickness of 200 nm. Live yeast cells were loaded into the tube, rapidly frozen by a blast of liquid nitrogen-cooled helium gas, and maintained at 140 deg C by a steady flow of cold helium. The image sequence spanned 180 deg and consisted of 45 images spaced by 4 deg. The images were aligned to a common axis and computed tomographic reconstruction was used to obtain the 3-D X-ray linear absorption coefficient. Volume rendering and animation of reconstructed data was performed using the 3-D program, Amira. Acquisition time for 90 images was 3 min

  1. WARP3D-Release 10.8: Dynamic Nonlinear Analysis of Solids using a Preconditioned Conjugate Gradient Software Architecture

    Koppenhoefer, Kyle C.; Gullerud, Arne S.; Ruggieri, Claudio; Dodds, Robert H., Jr.; Healy, Brian E.

    1998-01-01

    This report describes theoretical background material and commands necessary to use the WARP3D finite element code. WARP3D is under continuing development as a research code for the solution of very large-scale, 3-D solid models subjected to static and dynamic loads. Specific features in the code oriented toward the investigation of ductile fracture in metals include a robust finite strain formulation, a general J-integral computation facility (with inertia, face loading), an element extinction facility to model crack growth, nonlinear material models including viscoplastic effects, and the Gurson-Tver-gaard dilatant plasticity model for void growth. The nonlinear, dynamic equilibrium equations are solved using an incremental-iterative, implicit formulation with full Newton iterations to eliminate residual nodal forces. The history integration of the nonlinear equations of motion is accomplished with Newmarks Beta method. A central feature of WARP3D involves the use of a linear-preconditioned conjugate gradient (LPCG) solver implemented in an element-by-element format to replace a conventional direct linear equation solver. This software architecture dramatically reduces both the memory requirements and CPU time for very large, nonlinear solid models since formation of the assembled (dynamic) stiffness matrix is avoided. Analyses thus exhibit the numerical stability for large time (load) steps provided by the implicit formulation coupled with the low memory requirements characteristic of an explicit code. In addition to the much lower memory requirements of the LPCG solver, the CPU time required for solution of the linear equations during each Newton iteration is generally one-half or less of the CPU time required for a traditional direct solver. All other computational aspects of the code (element stiffnesses, element strains, stress updating, element internal forces) are implemented in the element-by- element, blocked architecture. This greatly improves

  2. Bioengineering a 3D integumentary organ system from iPS cells using an in vivo transplantation model.

    Takagi, Ryoji; Ishimaru, Junko; Sugawara, Ayaka; Toyoshima, Koh-Ei; Ishida, Kentaro; Ogawa, Miho; Sakakibara, Kei; Asakawa, Kyosuke; Kashiwakura, Akitoshi; Oshima, Masamitsu; Minamide, Ryohei; Sato, Akio; Yoshitake, Toshihiro; Takeda, Akira; Egusa, Hiroshi; Tsuji, Takashi

    2016-04-01

    The integumentary organ system is a complex system that plays important roles in waterproofing, cushioning, protecting deeper tissues, excreting waste, and thermoregulation. We developed a novel in vivo transplantation model designated as a clustering-dependent embryoid body transplantation method and generated a bioengineered three-dimensional (3D) integumentary organ system, including appendage organs such as hair follicles and sebaceous glands, from induced pluripotent stem cells. This bioengineered 3D integumentary organ system was fully functional following transplantation into nude mice and could be properly connected to surrounding host tissues, such as the epidermis, arrector pili muscles, and nerve fibers, without tumorigenesis. The bioengineered hair follicles in the 3D integumentary organ system also showed proper hair eruption and hair cycles, including the rearrangement of follicular stem cells and their niches. Potential applications of the 3D integumentary organ system include an in vitro assay system, an animal model alternative, and a bioengineered organ replacement therapy. PMID:27051874

  3. Pin cell discontinuity factors in the transient 3-D discrete ordinates code TORT-TD

    Even with the rapid increase of computing power, whole core transient and accident analyses based on the direct solution of the 3-D neutron transport equation with a large number of energy groups and a detailed heterogeneous description of the core still remain computationally challenging. Current industrial methods for reactor core calculations therefore involve a two step approach in which lattice (assembly) depletion transport methods are used to prepare energy collapsed and fuel assembly or pin cell homogenized cross sections for subsequent whole core transport calculations. Spatial homogenization, in principal, requires the knowledge of both the actual boundary condition (local core environment) of the fuel assembly and the exact heterogeneous flux distribution (reference solution) of the whole core problem within that fuel assembly. Since, in particular, the latter is not known a priori, an infinite medium (zero net current) condition is used in the lattice calculations. It is well known that this approximation may lead to undesirable errors in cores in which large flux gradients are present across the fuel assemblies. This is the case in cores that have high heterogeneity and/or strong local absorbers, e.g. PWRs with partial MOX loading and inserted control rod clusters. There are two major approaches to mitigate spatial homogenization errors, superhomogenization (SPH) factors, and discontinuity factors within the scope of equivalence theory (ET) and generalized equivalence theory (GET). Although discontinuity factors are usually applied at the level of fuel assembly node size (assembly discontinuity factors, ADF), the methodology can be extended to pin cell homogenized whole core calculations involving pin cell discontinuity factors (PDF). There are also further developments for both the diffusion and the simplified transport (SP3) equation. In this paper, PDFs are introduced into the time-dependent 3-D discrete ordinates code TORT-TD in order to reduce the

  4. Heritable Genetic Changes in Cells Recovered From Irradiated 3D Tissue Contracts. Final report

    Cornforth, Michael N. [The University of Texas Medical Branch at Galveston, TX (United States)

    2013-05-03

    Combining contemporary cytogenetic methods with DNA CGH microarray technology and chromosome flow-sorting increases substantially the ability to resolve exchange breakpoints associated with interstitial deletions and translocations, allowing the consequences of radiation damage to be directly measured at low doses, while also providing valuable insights into molecular mechanisms of misrepair processes that, in turn, identify appropriate biophysical models of risk at low doses. The aims of this work apply to cells recovered from 3D tissue constructs of human skin and, for the purpose of comparison, the same cells irradiated in traditional 2D cultures. These aims are: to analyze by multi-flour fluorescence in situ hybridization (mFISH) the chromosomes in clonal descendents of individual human fibroblasts that were previously irradiated; to examine irradiated clones from Aim 1 for submicroscopic deletions by subjecting their DNA to comparative genomic hybridization (CGH) microarray analysis; and to flow-sort aberrant chromosomes from clones containing stable radiation-induced translocations and map the breakpoints to within an average resolution of 100 kb using the technique of 'array painting'.

  5. Tuning Cell Differentiation into a 3D Scaffold Presenting a Pore Shape Gradient for Osteochondral Regeneration.

    Di Luca, Andrea; Lorenzo-Moldero, Ivan; Mota, Carlos; Lepedda, Antonio; Auhl, Dietmar; Van Blitterswijk, Clemens; Moroni, Lorenzo

    2016-07-01

    Osteochondral regeneration remains nowadays a major problem since the outcome of current techniques is not satisfactory in terms of functional tissue formation and development. A possible solution is the combination of human mesenchymal stem cells (hMSCs) with additive manufacturing technologies to fabricate scaffolds with instructive properties. In this study, the differentiation of hMSCs within a scaffold presenting a gradient in pore shape is presented. The variation in pore shape is determined by varying the angle formed by the fibers of two consequent layers. The fiber deposition patterns are 0-90, which generate squared pores, 0-45, 0-30, and 0-15, that generate rhomboidal pores with an increasing major axis as the deposition angle decreases. Within the gradient construct, squared pores support a better chondrogenic differentiation whereas cells residing in the rhomboidal pores display a better osteogenic differentiation. When cultured under osteochondral conditions the trend in both osteogenic and chondrogenic markers is maintained. Engineering the pore shape, thus creating axial gradients in structural properties, seems to be an instructive strategy to fabricate functional 3D scaffolds that are able to influence hMSCs differentiation for osteochondral tissue regeneration. PMID:27109461

  6. Heritable Genetic Changes in Cells Recovered From Irradiated 3D Tissue Contracts. Final report

    Combining contemporary cytogenetic methods with DNA CGH microarray technology and chromosome flow-sorting increases substantially the ability to resolve exchange breakpoints associated with interstitial deletions and translocations, allowing the consequences of radiation damage to be directly measured at low doses, while also providing valuable insights into molecular mechanisms of misrepair processes that, in turn, identify appropriate biophysical models of risk at low doses. The aims of this work apply to cells recovered from 3D tissue constructs of human skin and, for the purpose of comparison, the same cells irradiated in traditional 2D cultures. These aims are: to analyze by multi-flour fluorescence in situ hybridization (mFISH) the chromosomes in clonal descendents of individual human fibroblasts that were previously irradiated; to examine irradiated clones from Aim 1 for submicroscopic deletions by subjecting their DNA to comparative genomic hybridization (CGH) microarray analysis; and to flow-sort aberrant chromosomes from clones containing stable radiation-induced translocations and map the breakpoints to within an average resolution of 100 kb using the technique of 'array painting'

  7. Magnetic L-edge EXAFS of 3 d elements multiple-scattering analysis and spin dynamics

    Wende, H; Arvanitis, D; Wilhelm, F; Lemke, L; Ankudinov, A; Rehr, J J; Freeland, J W; Idzerda, Yu; Baberschke, K

    1999-01-01

    Magnetic EXAFS (MEXAFS) adds magnetic selectivity to the well established EXAFS technique opening the door to the exploration of local magnetic structure and disorder. Of particular interest is the behavior of 3d transition metal $9 systems. By utilizing the enhanced L /sub 3,2/ MEXAFS signal, which is one order of magnitude larger than the K-edge MEXAFS, we performed a temperature dependent study of polycrystalline and epitaxially grown Fe and Co films. By $9 analyzing single and multiple scattering contributions to the helicity dependent data, it is found that there are enhanced multiple scattering contributions in the magnetic case. In addition, we discuss the temperature dependence of $9 the MEXAFS data which is linked to spin fluctuations. (12 refs).

  8. Dynamic complex optical fields for optical manipulation, 3D microscopy, and photostimulation of neurotransmitters

    Daria, Vincent R.; Stricker, Christian; Bekkers, John; Redman, Steve; Bachor, Hans

    2010-08-01

    We demonstrate a multi-functional system capable of multiple-site two-photon excitation of photo-sensitive compounds as well as transfer of optical mechanical properties on an array of mesoscopic particles. We use holographic projection of a single Ti:Sapphire laser operating in femtosecond pulse mode to show that the projected three-dimensional light patterns have sufficient spatiotemporal photon density for multi-site two-photon excitation of biological fluorescent markers and caged neurotransmitters. Using the same laser operating in continuous-wave mode, we can use the same light patterns for non-invasive transfer of both linear and orbital angular momentum on a variety of mesoscopic particles. The system also incorporates high-speed scanning using acousto-optic modulators to rapidly render 3D images of neuron samples via two-photon microscopy.

  9. Development and validation of the 3-D PWR core dynamics SIMTRAN code

    We discuss the main features and results of the SIMTRAN development and validation work. Included in the first are the extension of the nodal neutronic solution to account for intranodal shape and spectrum, due to both heterogeneities and flux gradients, the implicit scheme for spatial kinetics with six delayed neutron precursors and the integration of the neutronic and thermohydraulic solutions on an staggered time mesh. Validation results are discussed for the NEACRP 3-D PWR Core Transient Benchmark and an actual transient with sudden increase of core flow occurred in the Vandellos-II 3-loop PWR NPP. Agreement with the reference numerical solution and measured plant data is shown for both problems. (orig./DG)

  10. Functional 3D Neural Mini-Tissues from Printed Gel-Based Bioink and Human Neural Stem Cells.

    Gu, Qi; Tomaskovic-Crook, Eva; Lozano, Rodrigo; Chen, Yu; Kapsa, Robert M; Zhou, Qi; Wallace, Gordon G; Crook, Jeremy M

    2016-06-01

    Direct-write printing of stem cells within biomaterials presents an opportunity to engineer tissue for in vitro modeling and regenerative medicine. Here, a first example of constructing neural tissue by printing human neural stem cells that are differentiated in situ to functional neurons and supporting neuroglia is reported. The supporting biomaterial incorporates a novel clinically relevant polysaccharide-based bioink comprising alginate, carboxymethyl-chitosan, and agarose. The printed bioink rapidly gels by stable cross-linking to form a porous 3D scaffold encapsulating stem cells for in situ expansion and differentiation. Differentiated neurons form synaptic contacts, establish networks, are spontaneously active, show a bicuculline-induced increased calcium response, and are predominantly gamma-aminobutyric acid expressing. The 3D tissues will facilitate investigation of human neural development, function, and disease, and may be adaptable for engineering other 3D tissues from different stem cell types. PMID:27028356

  11. Geocadabra Construction Box: A dynamic geometry interface within a 3D visualization teaching-learning trajectory for elementary learners

    Jacqueline Sack

    2013-07-01

    Full Text Available This study focuses on the integration of a 3-D dynamic geometry interface to enhance the 3-D visualization capacity of 8-9-year-old children who attend an after-school program. Each year, all third grade children, who attend a dual-language urban elementary school, are invited to participate, typically beginning with 20-25 participants. The program runs for one hour per week for the duration of the academic year. The research team (a university researcher and one or more classroom teachers uses design research principles (Cobb, et al., 2003 to develop and refine teaching-learning trajectories for the program. They use socially mediated instructional strategies, constantly challenging learners to find multiple solutions and explanations to a wide variety ofspatial problems. Learners work with figures made from wooden cubes, 2-D pictures that resemble these figures, and with iconic representations (such as top-view numeric or top, side and front plane views that do not directly resemble the figures. Through the integration of Geocadabra (Lecluse, 2005, the 3-D dynamic digital interface, learners move easily among the different representations and then can mentally abstract properties of these figures. They were able to visualize and accurately enumerate cubes of a complex 2-D conventional picture, but were also able to determine multiple solutions for given sets of front, side and top view diagrams, which do not always correlate with only one 3-D solution. With the current curricular focus on predominantly symbolic numeration, systematic integration of visualization, even as a representation tool for number work, into the elementary curriculum is problematic.

  12. Using the UM dynamical cores to reproduce idealised 3-D flows

    N. J. Mayne

    2014-12-01

    Full Text Available We demonstrate that both the current (New Dynamics, and next generation (ENDGame dynamical cores of the UK Met Office global circulation model, the UM, reproduce consistently, the long-term, large-scale flows found in several published idealised tests. The cases presented are the Held–Suarez test, a simplified model of Earth (including a stratosphere, and a hypothetical tidally locked Earth. Furthermore, we show that using simplifications to the dynamical equations, which are expected to be justified for the physical domains and flow regimes we have studied, and which are supported by the ENDGame dynamical core, also produces matching long-term, large-scale flows. Finally, we present evidence for differences in the detail of the planetary flows and circulations resulting from improvements in the ENDGame formulation over New Dynamics.

  13. Mesenchymal stem cells enhance ovarian cancer cell infiltration through IL6 secretion in an amniochorionic membrane based 3D model

    Touboul Cyril

    2013-01-01

    Full Text Available Abstract Background The early peritoneal invasion of epithelial ovarian cancer (EOC by tumoral aggregates presents in ascites is a major concern. The role of the microenvironment seems to be important in this process but the lack of adequate models to study cellular interactions between cancer cells and stromal cells does not allow to uncover the molecular pathways involved. Our goal was to study the interactions between ovarian cancer cells (OCC and mesenchymal stem cells (MSC using a 3D model. Methods We used millimetric pieces of amniochorionic membrane - referred to as amniotic membrane scaffold (AMS - to create 3D peritoneal nodules mimicking EOC early invasion. We were able to measure the distribution and the depth of infiltration using confocal microsopy. We extracted MSC from the amniochorionic membrane using the markers CD34-, CD45-, CD73+, CD90+, CD105+ and CD29+ at the Fluorescence Activated Cell Sorting (FACS analysis. We used transwell and wound healing tests to test OCC migration and invasion in vitro. Results Here we show that OCC tumors were located in regions rich in MSC (70%. The tumors infiltrated deeper within AMS in regions rich in MSC (p Conclusions The use of tridimensional models using AMS could be a useful tool to decipher early molecular events in ovarian cancer metastasis. Cytokine inhibitors interrupting the cross-talk between OCCs and MSCs such as IL6 should be investigated as a new therapeutic approach in ovarian cancer.

  14. Analyzing Biological Performance of 3D-Printed, Cell-Impregnated Hybrid Constructs for Cartilage Tissue Engineering.

    Izadifar, Zohreh; Chang, Tuanjie; Kulyk, William; Chen, Xiongbiao; Eames, B Frank

    2016-03-01

    Three-dimensional (3D) bioprinting of hybrid constructs is a promising biofabrication method for cartilage tissue engineering because a synthetic polymer framework and cell-impregnated hydrogel provide structural and biological features of cartilage, respectively. During bioprinting, impregnated cells may be subjected to high temperatures (caused by the adjacent melted polymer) and process-induced mechanical forces, potentially compromising cell function. This study addresses these biofabrication issues, evaluating the heat distribution of printed polycaprolactone (PCL) strands and the rheological property and structural stability of alginate hydrogels at various temperatures and concentrations. The biocompatibility of parameters from these studies was tested by culturing 3D hybrid constructs bioprinted with primary cells from embryonic chick cartilage. During initial two-dimensional culture expansion of these primary cells, two morphologically and molecularly distinct cell populations ("rounded" and "fibroblastic") were isolated. The biological performance of each population was evaluated in 3D hybrid constructs separately. The cell viability, proliferation, and cartilage differentiation were observed at high levels in hybrid constructs of both cell populations, confirming the validity of these 3D bioprinting parameters for effective cartilage tissue engineering. Statistically significant performance variations were observed, however, between the rounded and fibroblastic cell populations. Molecular and morphological data support the notion that such performance differences may be attributed to the relative differentiation state of rounded versus fibroblastic cells (i.e., differentiated chondrocytes vs. chondroprogenitors, respectively), which is a relevant issue for cell-based tissue engineering strategies. Taken together, our study demonstrates that bioprinting 3D hybrid constructs of PCL and cell-impregnated alginate hydrogel is a promising approach for

  15. Surface Acoustic Waves (SAW-Based Biosensing for Quantification of Cell Growth in 2D and 3D Cultures

    Tao Wang

    2015-12-01

    Full Text Available Detection and quantification of cell viability and growth in two-dimensional (2D and three-dimensional (3D cell cultures commonly involve harvesting of cells and therefore requires a parallel set-up of several replicates for time-lapse or dose–response studies. Thus, developing a non-invasive and touch-free detection of cell growth in longitudinal studies of 3D tumor spheroid cultures or of stem cell regeneration remains a major unmet need. Since surface acoustic waves (SAWs permit mass loading-based biosensing and have been touted due to their many advantages including low cost, small size and ease of assembly, we examined the potential of SAW-biosensing to detect and quantify cell growth. Herein, we demonstrate that a shear horizontal-surface acoustic waves (SH-SAW device comprising two pairs of resonators consisting of interdigital transducers and reflecting fingers can be used to quantify mass loading by the cells in suspension as well as within a 3D cell culture platform. A 3D COMSOL model was built to simulate the mass loading response of increasing concentrations of cells in suspension in the polydimethylsiloxane (PDMS well in order to predict the characteristics and optimize the design of the SH-SAW biosensor. The simulated relative frequency shift from the two oscillatory circuit systems (one of which functions as control were found to be concordant to experimental data generated with RAW264.7 macrophage and A549 cancer cells. In addition, results showed that SAW measurements per se did not affect viability of cells. Further, SH-SAW biosensing was applied to A549 cells cultured on a 3D electrospun nanofiber scaffold that generate tumor spheroids (tumoroids and the results showed the device's ability to detect changes in tumor spheroid growth over the course of eight days. Taken together, these results demonstrate the use of SH-SAW device for detection and quantification of cell growth changes over time in 2D suspension cultures and in

  16. Cast and 3D printed ion exchange membranes for monolithic microbial fuel cell fabrication

    Philamore, Hemma; Rossiter, Jonathan; Walters, Peter; Winfield, Jonathan; Ieropoulos, Ioannis

    2015-09-01

    We present novel solutions to a key challenge in microbial fuel cell (MFC) technology; greater power density through increased relative surface area of the ion exchange membrane that separates the anode and cathode electrodes. The first use of a 3D printed polymer and a cast latex membrane are compared to a conventionally used cation exchange membrane. These new techniques significantly expand the geometric versatility available to ion exchange membranes in MFCs, which may be instrumental in answering challenges in the design of MFCs including miniaturisation, cost and ease of fabrication. Under electrical load conditions selected for optimal power transfer, peak power production (mean 10 batch feeds) was 11.39 μW (CEM), 10.51 μW (latex) and 0.92 μW (Tangoplus). Change in conductivity and pH of anolyte were correlated with MFC power production. Digital and environmental scanning electron microscopy show structural changes to and biological precipitation on membrane materials following long term use in an MFC. The cost of the novel membranes was lower than the conventional CEM. The efficacy of two novel membranes for ion exchange indicates that further characterisation of these materials and their fabrication techniques, shows great potential to significantly increase the range and type of MFCs that can be produced.

  17. Digital holography as a method for 3D imaging and estimating the biovolume of motile cells.

    Merola, F; Miccio, L; Memmolo, P; Di Caprio, G; Galli, A; Puglisi, R; Balduzzi, D; Coppola, G; Netti, P; Ferraro, P

    2013-12-01

    Sperm morphology is regarded as a significant prognostic factor for fertilization, as abnormal sperm structure is one of the most common factors in male infertility. Furthermore, obtaining accurate morphological information is an important issue with strong implications in zoo-technical industries, for example to perform sorting of species X from species Y. A challenging step forward would be the availability of a fast, high-throughput and label-free system for the measurement of physical parameters and visualization of the 3D shape of such biological specimens. Here we show a quantitative imaging approach to estimate simply and quickly the biovolume of sperm cells, combining the optical tweezers technique with digital holography, in a single and integrated set-up for a biotechnology assay process on the lab-on-a-chip scale. This approach can open the way for fast and high-throughput analysis in label-free microfluidic based "cytofluorimeters" and prognostic examination based on sperm morphology, thus allowing advancements in reproductive science. PMID:24129638

  18. Telomere-surrounding regions are transcription-permissive 3D nuclear compartments in human cells

    Positioning of genes relative to nuclear heterochromatic compartments is thought to help regulate their transcriptional activity. Given that human subtelomeric regions are rich in highly expressed genes, we asked whether human telomeres are related to transcription-permissive nuclear compartments. To address this question, we investigated in the nuclei of normal human lymphocytes the spatial relations of two constitutively expressed genes (ACTB and RARA) and three nuclear transcripts (ACTB, IL2RA and TCRB) to telomeres and centromeres, as a function of gene activity and transcription levels. We observed that genes and gene transcripts locate close to telomere clusters and away from chromocenters upon activation of transcription. These findings, together with the observation that SC35 domains, which are enriched in pre-mRNA processing factors, are in close proximity to telomeres, indicate that telomere-neighboring regions are permissive to gene expression in human cells. Therefore, the associations of telomeres observed in the interphase nucleus might contribute, as opposed to chromocenters, for the establishment of transcription-permissive 3D nuclear compartments

  19. Prospective use of the 3D printing technology for the microstructural engineering of Solid Oxide Fuel Cell components

    Hernandez-Rodriguez, E. M.; Acosta-Mora, P.; Mendez-Ramos, J.; Borges Chinea, E.; Esparza Ferrera, P.; Canales-Vazquez, J.; Nunez, P.; Ruiz-Morales, J.

    2014-07-01

    A cost-effective micro-manufacturing process to accurately build 3D microstructures for their prospective use in the fabrication of Solid Oxide Fuel Cells components has been tested. The 3D printing method, based on the stereo lithography, allows solidifying layer by layer a dispersion of ceramic material in a liquid photosensitive organic monomer. A simple projector, a computer-controlled z-stage and a few PowerPoint slides may be used for the fabrication of a wide range of complex 3D microstructures in few minutes. In this work, 3D ceramic microstructures based on the yttria-stabilized zirconia (YSZ) were successfully fabricated. The micro structured ceramic components produced were stable after sintering at 1400 degree centigrade for 4 h. Impedance measurements show that the fabrication process does not have any detrimental effect on the electrical properties of the structured material. (Author)

  20. Prospective use of the 3D printing technology for the microstructural engineering of Solid Oxide Fuel Cell components

    A cost-effective micro-manufacturing process to accurately build 3D microstructures for their prospective use in the fabrication of Solid Oxide Fuel Cells components has been tested. The 3D printing method, based on the stereo lithography, allows solidifying layer by layer a dispersion of ceramic material in a liquid photosensitive organic monomer. A simple projector, a computer-controlled z-stage and a few PowerPoint slides may be used for the fabrication of a wide range of complex 3D microstructures in few minutes. In this work, 3D ceramic microstructures based on the yttria-stabilized zirconia (YSZ) were successfully fabricated. The micro structured ceramic components produced were stable after sintering at 1400 degree centigrade for 4 h. Impedance measurements show that the fabrication process does not have any detrimental effect on the electrical properties of the structured material. (Author)

  1. 3D cell cultures of human head and neck squamous cell carcinoma cells are radiosensitized by the focal adhesion kinase inhibitor TAE226

    Background and purpose: Focal adhesion kinase (FAK), a main player in integrin signaling and survival, is frequently overexpressed in human cancers and therefore postulated as potential target in cancer therapy. The aim of this study was to evaluate the radiosensitizing potential of the FAK inhibitor TAE226 in three-dimensional (3D) tumor cell cultures. Materials and methods: Head and neck squamous cell carcinoma (HNSCC) cells (FaDu, UT-SCC15, UT-SCC45), lung cancer cells (A549), colorectal carcinoma cells (DLD-1, HCT-116) and pancreatic tumor cells (MiaPaCa2, Panc1) were treated with different concentrations of TAE226 (0-1 μm; 1 or 24 h) without or in combination with irradiation (0-6 Gy, X-ray, single dose). Subsequently, 3D clonogenic survival assays (laminin-rich extracellular matrix) and Western blotting (expression/phosphorylation, e.g. FAK, Akt, ERK1/2) were performed. Results: All investigated 3D cell cultures showed a dose-dependent reduction in clonogenic survival by TAE226. Intriguingly, TAE226 only significantly radiosensitized 3D HNSCC cell cultures accompanied by a pronounced dephosphorylation of FAK, Akt and ERK1/2. Conclusions: Our data demonstrate TAE226 as potent FAK inhibitor that enhances the cellular radiosensitivity particularly of HNSCC cells grown in a 3D cell culture model. Future in vitro and in vivo investigations will clarify, to which extent this approach might be clinically relevant for radiotherapy of HNSCC.

  2. Immunogenicity and T cell recognition in swine of foot-and-mouth disease virus polymerase 3D

    Immunization of domestic pigs with a vaccinia virus (VV) recombinant expressing foot-and-mouth disease virus (FMDV) 3D protein conferred partial protection against challenge with infectious virus. The severity reduction of the clinical symptoms developed by the challenged animals occurred in the absence of significant levels of anti-3D circulating antibodies. This observation suggested that the partial protection observed was mediated by the induction of a 3D-specific cellular immune response. To gain information on the T cell recognition of FMDV 3D protein, we conducted in vitro proliferative assays using lymphocytes from outbred pigs experimentally infected with FMDV and 90 overlapping peptides spanning the complete 3D sequence. The use of pools of two to three peptides allowed the identification of T cell epitopes that were efficiently recognized by lymphocytes from at least four of the five animals analyzed. This recognition was heterotypic because anti-peptide responses increased upon reinfection of animals with a FMDV isolate from a different serotype. The results obtained with individual peptides confirmed the antigenicity observed with peptide pools. Detection of cytokine mRNAs by RT-PCR in lymphocytes stimulated in vitro by individual 3D peptides revealed that IFN-γ mRNA was the most consistently induced, suggesting that the activated T cells belong to the Th 1 subset. These results indicate that 3D protein contains epitopes that can be efficiently recognized by porcine T lymphocytes from different infected animals, both upon primary and secondary (heterotypic) FMDV infection. These epitopes can extend the repertoire of viral T cell epitopes to be included in subunit and synthetic FMD vaccines

  3. Simplified 3D model of a PWR reactor vessel using fluid dynamics code ANSYS CFX computational; Modelo simplificado 3D de la vasija de un reactor PWR mediante el codigo de dinamica de fluidos computacional ANSYS CFX

    Martinez, M.; Miro, R.; Barrachina, T.; Verdu, G.

    2011-07-01

    This paper presents the results from the calculation of the steady state simulation with model of CFD (computational fluid dynamic) operating under conditions of operation at full power (Hot Full Power). Development and the CFD model results show the usefulness of these codes for calculating 3D of the variable thermohydraulics of these reactors.

  4. Calcium Electroporation: Evidence for Differential Effects in Normal and Malignant Cell Lines, Evaluated in a 3D Spheroid Model

    Frandsen, Stine Krog; Gibot, Laure; Madi, Moinecha; Gehl, Julie; Rols, Marie-Pierre

    2015-01-01

    Background Calcium electroporation describes the use of high voltage electric pulses to introduce supraphysiological calcium concentrations into cells. This promising method is currently in clinical trial as an anti-cancer treatment. One very important issue is the relation between tumor cell kill efficacy–and normal cell sensitivity. Methods Using a 3D spheroid cell culture model we have tested the effect of calcium electroporation and electrochemotherapy using bleomycin on three different h...

  5. Cation Exchange in Dynamic 3D Porous Magnets: Improvement of the Physical Properties.

    Grancha, Thais; Acosta, Alvaro; Cano, Joan; Ferrando-Soria, Jesús; Seoane, Beatriz; Gascon, Jorge; Pasán, Jorge; Armentano, Donatella; Pardo, Emilio

    2015-11-16

    We report two novel three-dimensional porous coordination polymers (PCPs) of formulas Li4{Mn4[Cu2(Me3mpba)2]3}·68H2O (2) and K4{Mn4[Cu2(Me3mpba)2]3}·69H2O (3) obtained-via alkali cation exchange in a single-crystal to single-crystal process-from the earlier reported anionic manganese(II)-copper(II) PCP of formula Na4{Mn4[Cu2(Me3mpba)2]3}·60H2O (1) [Me3mpba(4-) = N,N'-2,4,6-trimethyl-1,3-phenylenebis(oxamate)]. This postsynthetic process succeeds where the direct synthesis in solution from the corresponding building blocks fails and affords significantly more robust PCPs with enhanced magnetic properties [long-range 3D magnetic ordering temperatures for the dehydrated phases (1'-3') of 2.0 (1'), 12.0 (2'), and 20.0 K (3')]. Changes in the adsorptive properties upon postsynthetic exchange suggest that the nature, electrostatic properties, mobility, and location of the cations within the framework are crucial for the enhanced structural stability. Overall, these results further confirm the potential of postsynthetic methods (including cation exchange) to obtain PCPs with novel or enhanced physical properties while maintaining unaltered their open-framework structures. PMID:26492551

  6. 3D Dynamical Modeling of Wind Accretion in Cyg X-3

    Okazaki, Atsuo T

    2014-01-01

    Cyg X-3 is a high mass X-ray binary consisting of a Wolf-Rayet star and a compact object in a very short orbital period of 4.8h. The only confirmed microquasar with high energy gamma-ray emission, Cyg X-3 provides a unique opportunity to study the relationship between the accretion power and the power in high energy emission. Because of a compact orbit and a slow Wolf-Rayet wind, the flow structure around the compact object is thought to be strongly affected by the orbital motion, details of which can be obtained only by numerical simulations. In this paper, we report on the results from 3D hydrodynamic simulations of the wind accretion in Cyg X-3. For simplicity we adopt an anti-gravity-like force that emulates the radiative acceleration consistent with the beta-velocity wind. Due to the rapid orbital motion, the flow around the compact object has large density gradients. As a result, the accretion rate onto the compact object is significantly lower than that of the Bondi-Hoyle-Lyttleton rate. We also calcul...

  7. 3-D parallel program for numerical calculation of gas dynamics problems with heat conductivity on distributed memory computational systems (CS)

    Sofronov, I.D.; Voronin, B.L.; Butnev, O.I. [VNIIEF (Russian Federation)] [and others

    1997-12-31

    The aim of the work performed is to develop a 3D parallel program for numerical calculation of gas dynamics problem with heat conductivity on distributed memory computational systems (CS), satisfying the condition of numerical result independence from the number of processors involved. Two basically different approaches to the structure of massive parallel computations have been developed. The first approach uses the 3D data matrix decomposition reconstructed at temporal cycle and is a development of parallelization algorithms for multiprocessor CS with shareable memory. The second approach is based on using a 3D data matrix decomposition not reconstructed during a temporal cycle. The program was developed on 8-processor CS MP-3 made in VNIIEF and was adapted to a massive parallel CS Meiko-2 in LLNL by joint efforts of VNIIEF and LLNL staffs. A large number of numerical experiments has been carried out with different number of processors up to 256 and the efficiency of parallelization has been evaluated in dependence on processor number and their parameters.

  8. Constraining the Absolute Orientation of Eta Carinae's Binary Orbit: A 3-D Dynamical Model for the Broad [Fe III] Emission

    Madura, Thomas I; Owocki, Stanley P; Groh, Jose H; Okazaki, Atsuo T; Russell, Christopher M P

    2011-01-01

    We present a three-dimensional (3-D) dynamical model for the broad [Fe III] emission observed in Eta Carinae using the Hubble Space Telescope/Space Telescope Imaging Spectrograph (HST/STIS). This model is based on full 3-D Smoothed Particle Hydrodynamics (SPH) simulations of Eta Car's binary colliding winds. Radiative transfer codes are used to generate synthetic spectro-images of [Fe III] emission line structures at various observed orbital phases and STIS slit position angles (PAs). Through a parameter study that varies the orbital inclination i, the PA {\\theta} that the orbital plane projection of the line-of-sight makes with the apastron side of the semi-major axis, and the PA on the sky of the orbital axis, we are able, for the first time, to tightly constrain the absolute 3-D orientation of the binary orbit. To simultaneously reproduce the blue-shifted emission arcs observed at orbital phase 0.976, STIS slit PA = +38 degrees, and the temporal variations in emission seen at negative slit PAs, the binary ...

  9. A 3D cell-centered Lagrangian scheme applied to the simulation of 3D non-stationary Rayleigh-Taylor Instability in supernova remnants

    Georges, G.; Breil, J.; Ribeyre, X.; Le Bel, E.

    2015-12-01

    Several astronomical flows can be studied thanks to the gas dynamics equations under the Lagrangian formalism. Here we propose to study the plerion dynamic, i.e. supernova remnants blown-up by a central pulsar as well as the Rayleigh-Taylor Instability (RTI) development at the inner interface of this gas shell. The scheme used is a multi-dimensional second order cell-centered Lagrangian scheme. It satisfies the Geometric Conservation Law (GCL), a semi-discrete entropy inequality and it conserves globally the momentum and the total energy. The convergence of the scheme towards the analytical solution is tested for the plerion test case and in the case of an axi-symmetric perturbation. Finally, the scheme is used to study the perturbation growth on the shell inner face perturbed with spherical harmonics.

  10. A New Crank Arm-Based Load Cell for the 3D Analysis of the Force Applied by a Cyclist

    Alexandre Balbinot

    2014-12-01

    Full Text Available This report describes a new crank arm-based force platform designed to evaluate the three-dimensional force applied to the pedals by cyclists in real conditions. The force platform was designed to be fitted on a conventional competition bicycle crankset while data is transmitted wirelessly through a BluetoothTM module and also stored on a SD card. A 3D solid model is created in the SolidWorks (Dassault Systèmes SOLIDWORKS Corp. to analyze the static and dynamic characteristics of the crank arm by using the finite elements technique. Each crankset arm is used as a load cell based on strain gauges configured as three Wheatstone bridges. The signals are conditioned on a printed circuit board attached directly to the structure. The load cell showed a maximum nonlinearity error between 0.36% and 0.61% and a maximum uncertainty of 2.3% referred to the sensitivity of each channel. A roller trainer equipped with an optical encoder was also developed, allowing the measurement of the wheel’s instantaneous velocity.

  11. Imaging- and Flow Cytometry-based Analysis of Cell Position and the Cell Cycle in 3D Melanoma Spheroids.

    Beaumont, Kimberley A; Anfosso, Andrea; Ahmed, Farzana; Weninger, Wolfgang; Haass, Nikolas K

    2015-01-01

    Three-dimensional (3D) tumor spheroids are utilized in cancer research as a more accurate model of the in vivo tumor microenvironment, compared to traditional two-dimensional (2D) cell culture. The spheroid model is able to mimic the effects of cell-cell interaction, hypoxia and nutrient deprivation, and drug penetration. One characteristic of this model is the development of a necrotic core, surrounded by a ring of G1 arrested cells, with proliferating cells on the outer layers of the spheroid. Of interest in the cancer field is how different regions of the spheroid respond to drug therapies as well as genetic or environmental manipulation. We describe here the use of the fluorescence ubiquitination cell cycle indicator (FUCCI) system along with cytometry and image analysis using commercial software to characterize the cell cycle status of cells with respect to their position inside melanoma spheroids. These methods may be used to track changes in cell cycle status, gene/protein expression or cell viability in different sub-regions of tumor spheroids over time and under different conditions. PMID:26779761

  12. Simulation of a simple RCCS experiment with RELAP5-3D system code and computational fluid dynamics computer program

    A small scale experimental facility was designed to study the thermal hydraulic phenomena in the Reactor Cavity Cooling System (RCCS). The facility was scaled down from the full scale RCCS system by applying scaling laws. A set of RELAP5-3D simulations were performed to confirm the scaling calculations, and to refine and optimize the facility's configuration, instrumentation selection, and layout. Computational Fluid Dynamics (CFD) calculations using StarCCM+ were performed in order to study the flow patterns and two-phase water behavior in selected locations of the facility where expected complex flow structure occurs. (author)

  13. 3D CFD Electrochemical And Heat Transfer Model Of An Internally Manifolded Solid Oxide Electrolysis Cell

    A three-dimensional computational fluid dynamics (CFD) electrochemical model has been created to model high-temperature electrolysis cell performance and steam electrolysis in an internally manifolded planar solid oxide electrolysis cell (SOEC) stack. This design is being evaluated at the Idaho National Laboratory for hydrogen production from nuclear power and process heat. Mass, momentum, energy, and species conservation and transport are provided via the core features of the commercial CFD code FLUENT. A solid-oxide fuel cell (SOFC) model adds the electrochemical reactions and loss mechanisms and computation of the electric field throughout the cell. The FLUENT SOFC user-defined subroutine was modified for this work to allow for operation in the SOEC mode. Model results provide detailed profiles of temperature, operating potential, steam-electrode gas composition, oxygen-electrode gas composition, current density and hydrogen production over a range of stack operating conditions. Single-cell and five-cell results will be presented. Flow distribution through both models is discussed. Flow enters from the bottom, distributes through the inlet plenum, flows across the cells, gathers in the outlet plenum and flows downward making an upside-down ''U'' shaped flow pattern. Flow and concentration variations exist downstream of the inlet holes. Predicted mean outlet hydrogen and steam concentrations vary linearly with current density, as expected. Effects of variations in operating temperature, gas flow rate, oxygen-electrode and steam-electrode current density, and contact resistance from the base case are presented. Contour plots of local electrolyte temperature, current density, and Nernst potential indicate the effects of heat transfer, reaction cooling/heating, and change in local gas composition. Results are discussed for using this design in the electrolysis mode. Discussion of thermal neutral voltage, enthalpy of reaction, hydrogen production, cell thermal

  14. 3D Case Studies of Monitoring Dynamic Structural Tests using Long Exposure Imagery

    McCarthy, D. M. J.; Chandler, J. H.; Palmeri, A.

    2014-06-01

    Structural health monitoring uses non-destructive testing programmes to detect long-term degradation phenomena in civil engineering structures. Structural testing may also be carried out to assess a structure's integrity following a potentially damaging event. Such investigations are increasingly carried out with vibration techniques, in which the structural response to artificial or natural excitations is recorded and analysed from a number of monitoring locations. Photogrammetry is of particular interest here since a very high number of monitoring locations can be measured using just a few images. To achieve the necessary imaging frequency to capture the vibration, it has been necessary to reduce the image resolution at the cost of spatial measurement accuracy. Even specialist sensors are limited by a compromise between sensor resolution and imaging frequency. To alleviate this compromise, a different approach has been developed and is described in this paper. Instead of using high-speed imaging to capture the instantaneous position at each epoch, long-exposure images are instead used, in which the localised image of the object becomes blurred. The approach has been extended to create 3D displacement vectors for each target point via multiple camera locations, which allows the simultaneous detection of transverse and torsional mode shapes. The proposed approach is frequency invariant allowing monitoring of higher modal frequencies irrespective of a sampling frequency. Since there is no requirement for imaging frequency, a higher image resolution is possible for the most accurate spatial measurement. The results of a small scale laboratory test using off-the-shelf consumer cameras are demonstrated. A larger experiment also demonstrates the scalability of the approach.

  15. The microenvironment determines the breast cancer cells' phenotype: organization of MCF7 cells in 3D cultures

    Stromal-epithelial interactions mediate breast development, and the initiation and progression of breast cancer. In the present study, we developed 3-dimensional (3D) in vitro models to study breast cancer tissue organization and the role of the microenvironment in phenotypic determination. The human breast cancer MCF7 cells were grown alone or co-cultured with primary human breast fibroblasts. Cells were embedded in matrices containing either type I collagen or a combination of reconstituted basement membrane proteins and type I collagen. The cultures were carried out for up to 6 weeks. For every time point (1-6 weeks), the gels were fixed and processed for histology, and whole-mounted for confocal microscopy evaluation. The epithelial structures were characterized utilizing immunohistochemical techniques; their area and proliferation index were measured using computerized morphometric analysis. Statistical differences between groups were analyzed by ANOVA, Dunnett's T3 post-hoc test and chi-square. Most of the MCF7 cells grown alone within a collagen matrix died during the first two weeks; those that survived organized into large, round and solid clusters. The presence of fibroblasts in collagen gels reduced MCF7 cell death, induced cell polarity, and the formation of round and elongated epithelial structures containing a lumen. The addition of reconstituted basement membrane to collagen gels by itself had also survival and organizational effects on the MCF7 cells. Regardless of the presence of fibroblasts, the MCF7 cells both polarized and formed a lumen. The addition of fibroblasts to the gel containing reconstituted basement membrane and collagen induced the formation of elongated structures. Our results indicate that a matrix containing both type I collagen and reconstituted basement membrane, and the presence of normal breast fibroblasts constitute the minimal permissive microenvironment to induce near-complete tumor phenotype reversion. These human

  16. Development of dynamic 3-D surface profilometry using stroboscopic interferometric measurement and vertical scanning techniques

    The main objective of this technical advance is to provide a single optical interferometric framework and methodology to be capable of delivering both nano-scale static and dynamic surface profilometry. Microscopic interferometry is a powerful technique for static and dynamic characterization of micro (opto) electromechanical systems (M (O) EMS). In view of this need, a microscopic prototype based on white-light stroboscopic interferometry and the white light vertical scanning principle, was developed to achieve dynamic full-field profilometry and characterization of MEMS devices. The system primarily consists of an optical microscope, on which a Mirau interferometric objective embedded with a piezoelectric vertical translator, a high-power LED light module with dual operation modes and light synchronizing electronics unit are integrated. A micro cantilever beam used in AFM was measured to verify the system capability in accurate characterization of dynamic behaviours of the device. The full-field second-mode vibration at a vibratory frequency of 68.60 kHz can be fully characterized and 3-5 nm of vertical measurement resolution as well as tens of micrometers of vertical measurement range can be easily achieved

  17. Development of 3D in vitro platform technology to engineer mesenchymal stem cells

    Hosseinkhani H

    2012-06-01

    Full Text Available Hossein Hosseinkhani,1 Po-Da Hong,1 Dah-Shyong Yu,2 Yi-Ru Chen,3 Diana Ickowicz,4 Ira-Yudovin Farber,4 Abraham J Domb41Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology (TAIWANTECH, 2Nanomedicine Research Center, National Defense Medical Center, Taipei, Taiwan, 3Department of Biomedical Engineering, National Yang-Ming University, Taipei, Taiwan, 4Institute of Drug Research, The Center for Nanoscience and Nanotechnology, School of Pharmacy-Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, IsraelAbstract: This study aims to develop a three-dimensional in vitro culture system to genetically engineer mesenchymal stem cells (MSC to express bone morphogenic protein-2. We employed nanofabrication technologies borrowed from the spinning industry, such as electrospinning, to mass-produce identical building blocks in a variety of shapes and sizes to fabricate electrospun nanofiber sheets comprised of composites of poly (glycolic acid and collagen. Homogenous nanoparticles of cationic biodegradable natural polymer were formed by simple mixing of an aqueous solution of plasmid DNA encoded bone morphogenic protein-2 with the same volume of cationic polysaccharide, dextran-spermine. Rat bone marrow MSC were cultured on electrospun nanofiber sheets comprised of composites of poly (glycolic acid and collagen prior to the incorporation of the nanoparticles into the nanofiber sheets. Bone morphogenic protein-2 was significantly detected in MSC cultured on nanofiber sheets incorporated with nanoparticles after 2 days compared with MSC cultured on nanofiber sheets incorporated with naked plasmid DNA. We conclude that the incorporation of nanoparticles into nanofiber sheets is a very promising strategy to genetically engineer MSC and can be used for further applications in regenerative medicine therapy.Keywords: 3D culture, nanoparticles, nanofibers, polycations, tissue engineering

  18. Synthesis of TiO2 nanotube arrays and its application in mini-3D dye-sensitized solar cells

    Here we report a mini-three-dimensional dye-sensitized solar cell (3D DSSC) based on TiO2 nanotube arrays (TNAs). TNAs were directly grown on spiral-shaped titanium wire via a facile potentiostatic anodization. Furthermore, the TNAs film was characterized by scanning electron microscopy, x-ray diffraction and transmission electron microscopy, indicating that the annealed TNAs were composed of single-crystalline anatase particles. Unlike conventional flat DSSC, this mini-3D DSSC could easily hold liquid electrolyte due to the capillary force which facilitated sealing the cell. This mini-3D DSSC showed an energy conversion efficiency of 4.1% under the AM 1.5 condition, which was much higher compared with that (3.2%) of the backside illuminated TNAs based DSSC of the same projected area.

  19. 3D simulations of Einstein's equations: symmetric hyperbolicity, live gauges and dynamic control of the constraints

    Tiglio, M H; Neilsen, D W; Tiglio, Manuel; Lehner, Luis; Neilsen, David

    2003-01-01

    We present three-dimensional simulations of Einstein equations implementing a symmetric hyperbolic system of equations with dynamical lapse. The numerical implementation makes use of techniques that guarantee linear numerical stability for the associated initial-boundary value problem. The code is first tested with a gauge wave solution, where rather larger amplitudes and for significantly longer times are obtained with respect to other state of the art implementations. Additionally, by minimizing a suitably defined energy for the constraints in terms of free constraint-functions in the formulation one can dynamically single out preferred values of these functions for the problem at hand. We apply the technique to fully three-dimensional simulations of a stationary black hole spacetime with excision of the singularity, considerably extending the lifetime of the simulations.

  20. 3D Dynamic Response of Layered Unsaturated Soils to Harmonic Loads

    XU Ming-jiang; WEI De-min

    2010-01-01

    Considering compression of solid grain and pore fluids,viscous-coupling interactions and inertial force of fluids,dynamic governing equations for unsaturated soils are established by adopting an exact constitutive formula of saturation.These equations are highly versatile and completely compatible with Biot's wave equations for the special case of fully saturated soils.The governing equations in Cartesian coordinates are firstly transformed into a group of state differential equations by introducing the state vector.Then the transfer matrix for layered media are derived by means of a double Fourier transform.Using the transfer matrix followed by boundary and continuity conditions between strata,solutions of steady-state dynamic response for multi-layered unsaturated soils are obtained.Numerical examples show that the echoes generated by boundary and stratum interfaces make the displacement amplitude of the ground surface fluctuate with distance;the relative position of soft and hard strata has a significant influence on displacement.

  1. A method of improving the dynamic response of 3D force/torque sensors

    Osypiuk, Rafał; Piskorowski, Jacek; Kubus, Daniel

    2016-02-01

    In the paper attention is drawn to adverse dynamic properties of filters implemented in commercial measurement systems, force/torque sensors, which are increasingly used in industrial robotics. To remedy the problem, it has been proposed to employ a time-variant filter with appropriately modulated parameters, owing to which it is possible to suppress the amplitude of the transient response and, at the same time, to increase the pulsation of damped oscillations; this results in the improvement of dynamic properties in terms of reducing the duration of transients. This property plays a key role in force control and in the fundamental problem of the robot establishing contact with rigid environment. The parametric filters have been verified experimentally and compared with filters available for force/torque sensors manufactured by JR3. The obtained results clearly indicate the advantages of the proposed solution, which may be an interesting alternative to the classic methods of filtration.

  2. A Dynamic Imaging Database for 3-D Morphologic Analysis and Clinical Assessment in Diagnostic Radiology

    Niculescu, Gabriela; Toni, Louay; Foran, David J.; Nosher, John L.; DeMarco, J. Kevin

    2002-01-01

    Modern imaging techniques such as MRI and CT have become invaluable clinical and research tools for visualizing internal organs and anatomic structures, non-invasively. We present a dynamic imaging database for performing comparative morphologic studies in diagnostic radiology to facilitate clinical assessment. The prototype system utilizes a double elliptic Fourier transform to characterize shape in three dimensions. A prototype system was used to evaluate neuroanatomy from MR brain scans of...

  3. Non-linear dynamic analysis of ancient masonry structures by 3D rigid block models

    Orduña, Agustin; Ayala, A. Gustavo

    2015-12-01

    This work presents a formulation for non-linear dynamic analysis of unreinforced masonry structures using rigid block models. This procedure is akin to the distinct element family of methods, nevertheless, we assume that small displacements occur and, therefore, the formulation does not involve the search for new contacts between blocks. This proposal is also related to the rigid element method, although, in this case we use full three-dimensional models and a more robust interface formulation.

  4. 3D Discrete Dislocation Dynamics: Influence of Segment Mobility on Critical Shear Stress

    Záležák, Tomáš; Dlouhý, Antonín

    2015-01-01

    Roč. 128, č. 4 (2015), s. 654-656. ISSN 0587-4246. [ISPMA 13 - International Symposium on Physics of Materials /13./. Praha, 31.08.2014-04.09.2014] R&D Projects: GA MŠk(CZ) EE2.3.20.0214; GA ČR(CZ) GA14-22834S Institutional support: RVO:68081723 Keywords : metal matrix composites * discrete dislocation dynamics * high temperature creep Subject RIV: JG - Metallurgy Impact factor: 0.530, year: 2014

  5. Virgo Cluster and field dwarf ellipticals in 3D - II. Internal dynamics points to tidal harassment?

    Ryś, A.; van de Ven, G.; Falcón-Barroso, J.

    2014-03-01

    We present the dynamical analysis of a sample of 12 dwarf elliptical (dE) galaxies for which we have obtained SAURON large-scale two-dimensional spectroscopic data. We construct Jeans axisymmetric models and obtain total dynamical masses enclosed within one effective radius. We use the obtained values to show that the validity of the dynamical scaling relations of massive early-type galaxies can be extended to these low-mass systems, except that dEs seem to contain relatively larger fraction of dark matter in their inner parts. We then demonstrate that dE galaxies have lower angular momenta than the present-day analogues of their presumed late-type progenitors, and we show that dE circular velocity curves are steeper than the rotation curves of galaxies with equal and up to an order of magnitude higher luminosity. This requires a transformation mechanism that is not only able to lower the angular momentum but also one that needs to account for increased stellar concentration. Additionally, we match the dark matter fraction of our galaxies to their location in the Virgo Cluster and see that galaxies in the cluster outskirts tend to have a higher dark-to-stellar matter ratio. Transformation due to tidal harassment is able to explain all of the above, unless the dE progenitors were already compact and had lower angular momenta at higher redshifts.

  6. Virgo Cluster and field dwarf ellipticals in 3D - II. Internal dynamics points to tidal harassment?

    Ryś, Agnieszka; Falcón-Barroso, Jesús

    2013-01-01

    We present the dynamical analysis of a sample of 12 dwarf elliptical (dE) galaxies for which we have obtained SAURON large-scale two-dimensional spectroscopic data. We construct Jeans axisymmetric models and obtain total dynamical masses enclosed within one effective radius. We use the obtained values to show that the validity of the dynamical scaling relations of massive early-type galaxies can be extended to these low-mass systems, except that dEs seem to contain relatively larger fraction of dark matter in their inner parts. We then demonstrate that dE galaxies have lower angular momenta than the present-day analogues of their presumed late-type progenitors and we show that dE circular velocity curves are steeper than the rotation curves of galaxies with equal and up to an order of magnitude higher luminosity. This requires a transformation mechanism that is not only able to lower the angular momentum but also one that needs to account for increased stellar concentration. Additionally, we match the dark ma...

  7. Numerical simulation of 3D unsteady flow in a rotating pump by dynamic mesh technique

    In this paper, the numerical simulation of unsteady flow for three kinds of typical rotating pumps, roots blower, roto-jet pump and centrifugal pump, were performed using the three-dimensional Dynamic Mesh technique. In the unsteady simulation, all the computational domains, as stationary, were set in one inertial reference frame. The motions of the solid boundaries were defined by the Profile file in FLUENT commercial code, in which the rotational orientation and speed of the rotors were specified. Three methods (Spring-based Smoothing, Dynamic Layering and Local Re-meshing) were used to achieve mesh deformation and re-meshing. The unsteady solutions of flow field and pressure distribution were solved. After a start-up stage, the flow parameters exhibit time-periodic behaviour corresponding to blade passing frequency of rotor. This work shows that Dynamic Mesh technique could achieve numerical simulation of three-dimensional unsteady flow field in various kinds of rotating pumps and have a strong versatility and broad application prospects

  8. Increased GFAP immunoreactivity by astrocytes in response to contact with dorsal root ganglia cells in a 3D culture model

    East, Emma; Golding, Jon; Phillips, James

    2007-01-01

    Failure of repair mechanisms in the injured CNS is widely attributed to the inhibitory environment of the lesion site, most notably the formation of the glial scar which forms a physical and physiological barrier to axon regeneration. We developed an in vitro 3D cell culture model to investigate the response of astrocytes to cells found at the inhibitory interfaces formed following damage to the spinal cord. CellTrackerTM labelled dissociated DRGs were seeded onto astrocy...

  9. 3D Ultrastructural Organization of Whole Chlamydomonas reinhardtii Cells Studied by Nanoscale Soft X-Ray Tomography

    Hummel, Eric; Guttmann, Peter; Werner, Stephan; Tarek, Basel; SCHNEIDER, Gerd; Kunz, Michael; Frangakis, Achilleas S.; Westermann, Benedikt

    2012-01-01

    The complex architecture of their structural elements and compartments is a hallmark of eukaryotic cells. The creation of high resolution models of whole cells has been limited by the relatively low resolution of conventional light microscopes and the requirement for ultrathin sections in transmission electron microscopy. We used soft x-ray tomography to study the 3D ultrastructural organization of whole cells of the unicellular green alga Chlamydomonas reinhardtii at unprecedented spatial re...

  10. 3D ultrastructural organization of whole Chlamydomonas reinhardtii cells studied by nanoscale soft x-ray tomography

    Hummel, Eric; Guttmann, Peter; Werner, Stephan; Tarek, Basel; SCHNEIDER, Gerd; Kunz, Michael; Frangakis, Achilleas S.; Westermann, Benedikt

    2012-01-01

    The complex architecture of their structural elements and compartments is a hallmark of eukaryotic cells. The creation of high resolution models of whole cells has been limited by the relatively low resolution of conventional light microscopes and the requirement for ultrathin sections in transmission electron microscopy. We used soft x-ray tomography to study the 3D ultrastructural organization of whole cells of the unicellular green alga Chlamydomonas reinhardtii at unprecedented spatial re...

  11. Infrared imaging of MDA-MB-231 breast cancer cell line phenotypes in 2D and 3D cultures.

    Smolina, Margarita; Goormaghtigh, Erik

    2015-04-01

    One current challenge in the field of breast cancer infrared imaging is the identification of carcinoma cell subtypes in the tissue. Neither sequencing nor immunochemistry is currently able to provide a cell by cell thorough classification. The latter is needed to build accurate statistical models capable of recognizing the diversity of breast cancer cell lines that may be present in a tissue section. One possible approach for overcoming this problem is to obtain the IR spectral signature of well-characterized tumor cell lines in culture. Cultures in three-dimensional matrices appear to generate an environment that mimics better the in vivo environment. There are, at present, series of breast cancer cell lines that have been thoroughly characterized in two- and three-dimensional (2D and 3D) cultures by full transcriptomics analyses. In this work, we describe the methods used to grow, to process, and to characterize a triple-negative breast cancer cell line, MDA-MB-231, in 3D laminin-rich extracellular matrix (lrECM) culture and compare it with traditional monolayer cultures and tissue sections. While unsupervised analyses did not completely separate spectra of cells grown in 2D from 3D lrECM cultures, a supervised statistical analysis resulted in an almost perfect separation. When IR spectral responses of epithelial tumor cells from clinical triple-negative breast carcinoma samples were added to these data, a principal component analysis indicated that they cluster closer to the spectra of 3D culture cells than to the spectra of cells grown on a flat plastic substrata. This result is encouraging because of correlating well-characterized cell line features with clinical biopsies. PMID:25568895

  12. The effect of porosity on cell ingrowth into accurately defined, laser-made, polylactide-based 3D scaffolds

    Danilevicius, Paulius; Georgiadi, Leoni [Foundation for Research and Technology Hellas (FORTH), Institute of Electronic Structure and Laser (IESL), N Plastira 100, 70013 Heraklion (Greece); Pateman, Christopher J.; Claeyssens, Frederik [Kroto Research Institute, Department of Materials Science and Engineering, University of Sheffield, Broad Lane, Sheffield S3 7HQ (United Kingdom); Chatzinikolaidou, Maria, E-mail: mchatzin@materials.uoc.gr [Foundation for Research and Technology Hellas (FORTH), Institute of Electronic Structure and Laser (IESL), N Plastira 100, 70013 Heraklion (Greece); Department of Materials Science and Technology, University of Crete, PO Box 2208, 71303 Heraklion (Greece); Farsari, Maria, E-mail: mfarsari@iesl.forth.gr [Foundation for Research and Technology Hellas (FORTH), Institute of Electronic Structure and Laser (IESL), N Plastira 100, 70013 Heraklion (Greece)

    2015-05-01

    Highlights: • We studied the porosity of laser-made 3D scaffolds on MC3T3-E1 pre-osteoblastic cells. • We made polylactide 3D scaffolds with pores 25–110 μm. - Abstract: The aim of this study is to demonstrate the accuracy required for the investigation of the role of solid scaffolds’ porosity in cell proliferation. We therefore present a qualitative investigation into the effect of porosity on MC3T3-E1 pre-osteoblastic cell ingrowth of three-dimensional (3D) scaffolds fabricated by direct femtosecond laser writing. The material we used is a purpose made photosensitive pre-polymer based on polylactide. We designed and fabricated complex, geometry-controlled 3D scaffolds with pore sizes ranging from 25 to 110 μm, representing porosities 70%, 82%, 86%, and 90%. The 70% porosity scaffolds did not support cell growth initially and in the long term. For the other porosities, we found a strong adhesion of the pre-osteoblastic cells from the first hours after seeding and a remarkable proliferation increase after 3 weeks and up to 8 weeks. The 86% porosity scaffolds exhibited a higher efficiency compared to 82% and 90%. In addition, bulk material degradation studies showed that the employed, highly-acrylated polylactide is degradable. These findings support the potential use of the proposed material and the scaffold fabrication technique in bone tissue engineering.

  13. Dynamically Self-consistent Simulations of the 3D Gravity and Magnetic Fields to be Measured by Juno at Jupiter

    Glatzmaier, G.

    2013-12-01

    In 2016 NASA's Juno spacecraft will begin making high fidelity gravity and magnetic measurements near the surface of Jupiter that will provide clues to Jupiter's internal structure and dynamics. To prepare for the interpretation of these data, we are producing 3D dynamo simulations that self-consistently solve for the gravity and magnetic fields throughout the interior and exterior of our simulated gas giant. Knowing the trajectories of the 34 11-day polar orbits Juno will make around Jupiter as Jupiter rotates, we calculate the three components of the gravity and magnetic fields that Juno would measure as a function of time for two different simulated giant planet dynamos: one having latitudinally banded zonal winds that exist only in a shallow surface layer and one with banded zonal winds that extend deep below the surface. The different dynamo solutions are obtained by making different specifications for poorly known quantities, like the amplitude and radial dependence of the effective viscous diffusivity within Jupiter. By identifying fundamental differences in the 3D data that Juno would collect for these two scenarios, we will provide a dynamically self-consistent test for inferring the structure and amplitude of the zonal winds in Jupiter's interior. For example, a latitudinally banded pattern of magnetic field measured by Juno would suggest that strong zonal winds extend well below the surface to where the electrical conductivity is high enough for the generation of Jupiter's magnetic field.

  14. Multi-coupling dynamic model and 3d simulation program for in-situ leaching of uranium mining

    The in-situ leaching of uranium mining is a very complicated non-linear dynamic system, which involves couplings and positive/negative feedback among many factors and processes. A comprehensive, coupled multi-factors and processes dynamic model and simulation method was established to study the in-situ leaching of uranium mining. The model accounts for most coupling among various processes as following: (1) rock texture mechanics and its evolution, (2)the incremental stress rheology of rock deformation, (3) 3-D viscoelastic/ plastic multi-deformation processes, (4) hydrofracturing, (5) tensorial (anisotropic) fracture and rock permeability, (6) water-rock interactions and mass-transport (both advective and diffusive), (7) dissolution-induced chemical compaction, (8) multi-phase fluid flow. A 3-D simulation program was compiled based on Fortran and C++. An example illustrating the application of this model to simulating acidification, production and terminal stage of in situ leaching of uranium mining is presented for the some mine in Xinjiang, China. This model and program can be used for theoretical study, mine design, production management, the study of contaminant transport and restoration in groundwater of in-situ leaching of uranium mining. (authors)

  15. Effect of biomimetic 3D environment of an injectable polymeric scaffold on MG-63 osteoblastic-cell response

    Solid PLGA microspheres were fabricated and characterized in terms of their in vitro degradation behaviour. Microsphere scaffolds were then modified covalently by P-15 (GTPGPQGIAGQRGVV) to obtain a 3D bioactive collagen surrogate matrix for bone filling applications. These scaffolds were characterized for surface topography, hydrophilicity and evaluated for their effect on osteoblastic activity of MG-63 cell line vis-a-vis 2D monolayer culture. AFM and contact angle experiments indicated enhanced nano-level roughness and hydrophilicity on P-15 modification. Modified scaffolds showed enhanced cell attachment, proliferation, extracellular matrix formation, mineralization and collagen type-I expression when compared to unmodified microspheres, prerequisite for bone filling applications. On long term in vitro cell culture, however, decreased cell viability was observed which may be attributed to the acidic microenvironment generated due to polymer degradation and reduction in nutrient diffusion through the copious ECM formed in 3D scaffolds. Though a higher cell count could be obtained in 2D monolayer cell culture, it was overshadowed by weak cell attachment, poor phenotypic characteristics, decreased cell viability and low mineralization levels, over 28 day cell culture studies. Results indicate that P-15 modified microsphere scaffolds may provide a natural, biomimetic 3D environment and may be successfully exploited for non-invasive bone filling applications.

  16. Progress in the Peeling-Ballooning Model of ELMs: Numerical Studies of 3D Nonlinear ELM Dynamics

    Snyder, P B; Wilson, H R; Xu, X Q

    2004-12-13

    Nonlinear simulations with the 3D electromagnetic two-fluid BOUT code are employed to study the dynamics of edge localized modes (ELMs) driven by intermediate wavelength peeling-ballooning modes. It is found that the early behavior of the modes is similar to expectations from linear, ideal peeling-ballooning mode theory, with the modes growing linearly at a fraction of the Alfven frequency. In the non-linear phase, the modes grow explosively, forming a number of extended filaments which propagate rapidly from the outer closed flux region into the open flux region toward the outer wall. Similarities to non-linear linear ballooning theory, as well as additional complexities are observed. Comparison to observations reveals a number of similarities. Implications of the simulations and proposals for the dynamics of the full ELM crash are discussed.

  17. PROGRESS IN THE PEELING-BALLOONING MODEL OF ELMS: NUMERICAL STUDIES OF 3D NONLINEAR ELM DYNAMICS

    SNYDER,P.B; WILSON,H.R; XU,X.Q

    2004-11-01

    Nonlinear simulations with the 3D electromagnetic two-fluid BOUT code are employed to study the dynamics of edge localized modes (ELMs) driven by intermediate wavelength peeling-ballooning modes. It is found that the early behavior of the modes is similar to expectations from linear, ideal peeling-ballooning mode theory, with the modes growing linearly at a fraction of the Alfven frequency. In the nonlinear phase, the modes grow explosively, forming a number of extended filaments which propagate rapidly from the outer closed flux region into the open flux region toward the outboard wall. Similarities to non-linear ballooning theory, as well as additional complexities are observed. Comparison to observations reveals a number of similarities. Implications of the simulations and proposals for the dynamics of the full ELM crash are discussed.

  18. PROGRESS IN THE PEELING-BALLOONING MODEL OF ELMS: NUMERICAL STUDIES OF 3D NONLINEAR ELM DYNAMICS

    Nonlinear simulations with the 3D electromagnetic two-fluid BOUT code are employed to study the dynamics of edge localized modes (ELMs) driven by intermediate wavelength peeling-ballooning modes. It is found that the early behavior of the modes is similar to expectations from linear, ideal peeling-ballooning mode theory, with the modes growing linearly at a fraction of the Alfven frequency. In the nonlinear phase, the modes grow explosively, forming a number of extended filaments which propagate rapidly from the outer closed flux region into the open flux region toward the outboard wall. Similarities to non-linear ballooning theory, as well as additional complexities are observed. Comparison to observations reveals a number of similarities. Implications of the simulations and proposals for the dynamics of the full ELM crash are discussed

  19. Designing a binding interface for control of cancer cell adhesion via 3D topography and metabolic oligosaccharide engineering.

    Du, Jian; Che, Pao-Lin; Wang, Zhi-Yun; Aich, Udayanath; Yarema, Kevin J

    2011-08-01

    This study combines metabolic oligosaccharide engineering (MOE), a technology where the glycocalyx of living cells is endowed with chemical features not normally found in sugars, with custom-designed three-dimensional biomaterial substrates to enhance the adhesion of cancer cells and control their morphology and gene expression. Specifically, Ac(5)ManNTGc, a thiol-bearing analog of N-acetyl-d-mannosamine (ManNAc) was used to introduce thiolated sialic acids into the glycocalyx of human Jurkat T-lymphoma derived cells. In parallel 2D films and 3D electrospun nanofibrous scaffolds were prepared from polyethersulfone (PES) and (as controls) left unmodified or aminated. Alternately, the materials were malemided or gold-coated to provide bio-orthogonal binding partners for the thiol groups newly expressed on the cell surface. Cell attachment was modulated by both the topography of the substrate surface and by the chemical compatibility of the binding interface between the cell and the substrate; a substantial increase in binding for normally non-adhesive Jurkat line for 3D scaffold compared to 2D surfaces with an added degree of adhesion resulting from chemoselective binding to malemidede-derivatived or gold-coated surfaces. In addition, the morphology of the cells attached to the 3D scaffolds via MOE-mediated adhesion was dramatically altered and the expression of genes involved in cell adhesion changed in a time-dependent manner. This study showed that cell adhesion could be enhanced, gene expression modulated, and cell fate controlled by introducing the 3D topograhical cues into the growth substrate and by creating a glycoengineered binding interface where the chemistry of both the cell surface and biomaterials scaffold was controlled to facilitate a new mode of carbohydrate-mediated adhesion. PMID:21549424

  20. An analysis of migration of low-angle dislocation boundaries with 3D discrete dislocation dynamics

    Záležák, Tomáš; Dlouhý, Antonín

    Brno : Ústav fyziky materiálů AV ČR, v. v. i., 2015 - (Dlouhý, A.; Kunz, L.). s. 43-43 ISBN 978-80-87434-07-9. [ICSMA-17 International Conference on the Strength of Materials /17./. 09.08.2015-14.08.2015, Brno] R&D Projects: GA ČR(CZ) GA14-22834S; GA ČR GJ15-21292Y; GA MŠk(CZ) EE2.3.20.0214 Institutional support: RVO:68081723 Keywords : discrete dislocation dynamics * high temperature creep * critical shear stress * precipitate strenghtened materials * metal matrix composites Subject RIV: JI - Composite Materials

  1. Microfluidics 3D gel-island chip for single cell isolation and lineage-dependent drug responses study.

    Zhang, Zhixiong; Chen, Yu-Chih; Cheng, Yu-Heng; Luan, Yi; Yoon, Euisik

    2016-07-01

    3D cell culture in the extracellular matrix (ECM), which not only provides structural support to cellular constituents, but also initiates regulatory biochemical cues for a variety of important cell functions in tissue, has become more and more important in understanding cancer pathology and drug testing. Although the ECM-gel has been used in cell culture both in bulk and on-chip, previous studies focused on collective cell behavior rather than single-cell heterogeneity. To track the behavior of each individual cell, we have developed a gel-island chip, which can form thousands of islands containing single cells encapsulated by the desired ECM. Optimized by Poisson's distribution, the device can attain 34% single cell capture efficiency of the exact number of single cells per island. A good culture media exchange rate and high cell viability can be achieved in the gel-islands. The cells in the islands can be automatically counted for high-throughput analysis. As a proof of concept, we monitored the proliferation and differentiation of single Notch+ (stem-like) T47D breast cancer cells. The 3D collagen gel environment was found to be favorable for the stem-like phenotype through better self-renewal and de-differentiation (Notch- to Notch+ transition). More interestingly, we found that the Notch- de-differentiated cells were more resistant to doxorubicin and cisplatin than the Notch+ cells. Combining the 3D ECM culture and single cell resolution, the presented platform can automatically analyze the individual cell behaviors of hundreds of cells using a small amount of drug and reagents. PMID:27270563

  2. 3D high-content screening for the identification of compounds that target cells in dormant tumor spheroid regions

    Wenzel, Carsten; Riefke, Björn; Gründemann, Stephan; Krebs, Alice; Christian, Sven; Prinz, Florian; Osterland, Marc; Golfier, Sven; Räse, Sebastian [Bayer Pharma AG, Global Drug Discovery, Muellerstrasse 178, 13353 Berlin (Germany); Ansari, Nariman [Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt (Germany); Esner, Milan; Bickle, Marc [Max Planck Institute of Molecular Cell Biology and Genetics, High-Throughput Technology Development Studio (TDS), Dresden (Germany); Pampaloni, Francesco; Mattheyer, Christian; Stelzer, Ernst H. [Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt (Germany); Parczyk, Karsten; Prechtl, Stefan [Bayer Pharma AG, Global Drug Discovery, Muellerstrasse 178, 13353 Berlin (Germany); Steigemann, Patrick, E-mail: Patrick.Steigemann@bayer.com [Bayer Pharma AG, Global Drug Discovery, Muellerstrasse 178, 13353 Berlin (Germany)

    2014-04-15

    Cancer cells in poorly vascularized tumor regions need to adapt to an unfavorable metabolic microenvironment. As distance from supplying blood vessels increases, oxygen and nutrient concentrations decrease and cancer cells react by stopping cell cycle progression and becoming dormant. As cytostatic drugs mainly target proliferating cells, cancer cell dormancy is considered as a major resistance mechanism to this class of anti-cancer drugs. Therefore, substances that target cancer cells in poorly vascularized tumor regions have the potential to enhance cytostatic-based chemotherapy of solid tumors. With three-dimensional growth conditions, multicellular tumor spheroids (MCTS) reproduce several parameters of the tumor microenvironment, including oxygen and nutrient gradients as well as the development of dormant tumor regions. We here report the setup of a 3D cell culture compatible high-content screening system and the identification of nine substances from two commercially available drug libraries that specifically target cells in inner MCTS core regions, while cells in outer MCTS regions or in 2D cell culture remain unaffected. We elucidated the mode of action of the identified compounds as inhibitors of the respiratory chain and show that induction of cell death in inner MCTS core regions critically depends on extracellular glucose concentrations. Finally, combinational treatment with cytostatics showed increased induction of cell death in MCTS. The data presented here shows for the first time a high-content based screening setup on 3D tumor spheroids for the identification of substances that specifically induce cell death in inner tumor spheroid core regions. This validates the approach to use 3D cell culture screening systems to identify substances that would not be detectable by 2D based screening in otherwise similar culture conditions. - Highlights: • Establishment of a novel method for 3D cell culture based high-content screening. • First reported high

  3. 3D high-content screening for the identification of compounds that target cells in dormant tumor spheroid regions

    Cancer cells in poorly vascularized tumor regions need to adapt to an unfavorable metabolic microenvironment. As distance from supplying blood vessels increases, oxygen and nutrient concentrations decrease and cancer cells react by stopping cell cycle progression and becoming dormant. As cytostatic drugs mainly target proliferating cells, cancer cell dormancy is considered as a major resistance mechanism to this class of anti-cancer drugs. Therefore, substances that target cancer cells in poorly vascularized tumor regions have the potential to enhance cytostatic-based chemotherapy of solid tumors. With three-dimensional growth conditions, multicellular tumor spheroids (MCTS) reproduce several parameters of the tumor microenvironment, including oxygen and nutrient gradients as well as the development of dormant tumor regions. We here report the setup of a 3D cell culture compatible high-content screening system and the identification of nine substances from two commercially available drug libraries that specifically target cells in inner MCTS core regions, while cells in outer MCTS regions or in 2D cell culture remain unaffected. We elucidated the mode of action of the identified compounds as inhibitors of the respiratory chain and show that induction of cell death in inner MCTS core regions critically depends on extracellular glucose concentrations. Finally, combinational treatment with cytostatics showed increased induction of cell death in MCTS. The data presented here shows for the first time a high-content based screening setup on 3D tumor spheroids for the identification of substances that specifically induce cell death in inner tumor spheroid core regions. This validates the approach to use 3D cell culture screening systems to identify substances that would not be detectable by 2D based screening in otherwise similar culture conditions. - Highlights: • Establishment of a novel method for 3D cell culture based high-content screening. • First reported high

  4. Intrinsic FGF2 and FGF5 promotes angiogenesis of human aortic endothelial cells in 3D microfluidic angiogenesis system.

    Seo, Ha-Rim; Jeong, Hyo Eun; Joo, Hyung Joon; Choi, Seung-Cheol; Park, Chi-Yeon; Kim, Jong-Ho; Choi, Ji-Hyun; Cui, Long-Hui; Hong, Soon Jun; Chung, Seok; Lim, Do-Sun

    2016-01-01

    The human body contains different endothelial cell types and differences in their angiogenic potential are poorly understood. We compared the functional angiogenic ability of human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs) using a three-dimensional (3D) microfluidic cell culture system. HAECs and HUVECs exhibited similar cellular characteristics in a 2D culture system; however, in the 3D microfluidic angiogenesis system, HAECs exhibited stronger angiogenic potential than HUVECs. Interestingly, the expression level of fibroblast growth factor (FGF)2 and FGF5 under vascular endothelial growth factor (VEGF)-A stimulation was significantly higher in HAECs than in HUVECs. Moreover, small interfering RNA-mediated knockdown of FGF2 and FGF5 more significantly attenuated vascular sprouting induced from HAECs than HUVECs. Our results suggest that HAECs have greater angiogenic potential through FGF2 and FGF5 upregulation and could be a compatible endothelial cell type to achieve robust angiogenesis. PMID:27357248

  5. Dynamic 3D shape of the plantar surface of the foot using coded structured light: a technical report

    Thabet, Ali Kassem

    2014-01-23

    Background The foot provides a crucial contribution to the balance and stability of the musculoskeletal system, and accurate foot measurements are important in applications such as designing custom insoles/footwear. With better understanding of the dynamic behavior of the foot, dynamic foot reconstruction techniques are surfacing as useful ways to properly measure the shape of the foot. This paper presents a novel design and implementation of a structured-light prototype system providing dense three dimensional (3D) measurements of the foot in motion. The input to the system is a video sequence of a foot during a single step; the output is a 3D reconstruction of the plantar surface of the foot for each frame of the input. Methods Engineering and clinical tests were carried out to test the accuracy and repeatability of the system. Accuracy experiments involved imaging a planar surface from different orientations and elevations and measuring the fitting errors of the data to a plane. Repeatability experiments were done using reconstructions from 27 different subjects, where for each one both right and left feet were reconstructed in static and dynamic conditions over two different days. Results The static accuracy of the system was found to be 0.3 mm with planar test objects. In tests with real feet, the system proved repeatable, with reconstruction differences between trials one week apart averaging 2.4 mm (static case) and 2.8 mm (dynamic case). Conclusion The results obtained in the experiments show positive accuracy and repeatability results when compared to current literature. The design also shows to be superior to the systems available in the literature in several factors. Further studies need to be done to quantify the reliability of the system in clinical environments.

  6. The 3D dynamics of the Cosserat rod as applied to continuum robotics

    Jones, Charles Rees

    2011-12-01

    In the effort to simulate the biologically inspired continuum robot's dynamic capabilities, researchers have been faced with the daunting task of simulating---in real-time---the complete three dimensional dynamics of the "beam-like" structure which includes the three "stiff" degrees-of-freedom transverse and dilational shear. Therefore, researchers have traditionally limited the difficulty of the problem with simplifying assumptions. This study, however, puts forward a solution which makes no simplifying assumptions and trades off only the real-time requirement of the desired solution. The solution is a Finite Difference Time Domain method employing an explicit single step method with cheap right hands sides. The cheap right hand sides are the result of a rather ingenious formulation of the classical beam called the Cosserat rod by, first, the Cosserat brothers and, later, Stuart S. Antman which results in five nonlinear but uncoupled equations that require only multiplication and addition. The method is therefore suitable for hardware implementation thus moving the real-time requirement from a software solution to a hardware solution.

  7. 3D radiative hydrodynamic simulations of protostellar collapse with H-C-O dynamical chemistry

    Dzyurkevich, Natalia; Lesaffre, Pierre; Semenov, Dimitry

    2016-01-01

    Combining the co-evolving chemistry, hydrodynamics and radiative transfer is an important step for star formation studies. It allows both a better link to observations and a self-consistent monitoring of the magnetic dissipation in the collapsing core. Our aim is to follow a chemo-dynamical evolution of collapsing dense cores with a reduced gas-grain chemical network. We present the results of radiative hydrodynamic (RHD) simulations of 1 M$_\\odot$ isolated dense core collapse. The physical setup includes RHD and dynamical evolution of a chemical network. To perform those simulations, we merged the multi-dimensional adaptive-mesh-refinement code RAMSES and the thermo-chemistry Paris-Durham shock code. We simulate the formation of the first hydro-static core (FHSC) and the co-evolution of 56 species describing mainly H-C-O chemistry. Accurate benchmarking is performed, testing the reduced chemical network against a well-establiched complex network. We show that by using a compact set of reactions, one can matc...

  8. 3D dislocation dynamics: stress-strain behavior and hardening mechanisms in fcc and bcc metals

    A dislocation dynamics (DD) model for plastic deformation, connecting the macroscopic mechanical properties to basic physical laws governing dislocation mobility and related interaction mechanisms, has been developed. In this model there is a set of critical reactions that determine the overall results of the simulations, such as the stress-strain curve. These reactions are annihilation, formation of jogs, junctions, and dipoles and cross-slip. In this paper, we discuss these reactions and the manner in which they influence the simulated stress-strain behavior of fcc and bcc metals. In particular, we examine the formation (zipping) and strength of dipoles and junctions, and effect of jogs, using the dislocation dynamics model. We show that the strengths (unzipping) of these reactions for various configurations can be determined by direct evaluation of the elastic interactions. Next, we investigate the phenomenon of hardening in metals subjected to cascade damage. The investigated microstructure consists of small dislocation loops decorating the mobile dislocations. Preliminary results reveal that these loops act as hardening agents, trapping the dislocations and resulting in increased yield stress

  9. 双手和双腕关节3D LAVA和FAME MR动态增强扫描对比%Study of bilateral hands and wrists with MR dynamic contrast-enhanced imaging with comparison of 3D LAVA sequence and 3D FAME sequence

    张森; 刘霞; 李绪斌; 杜湘珂

    2011-01-01

    目的:通过对比分析双手、双腕关节3D LAVA和FAME MR动态增强扫描图像质量差异,探讨双手、双腕关节理想的MR动态增强成像序列.方法:对34例以双手、双腕多关节肿痛初诊患者行MR动态增强扫描,其中9例行3D FAME动态增强扫描,25例行3D AVA动态增强扫描.采用3分法对比评估两种成像方法图像质量.结果:25例3D LAVA动态增强扫描患者中图像质量3分22例,2分3例;9例3D FAME动态增强扫患者中2分6例,1分3例.3DLAVA动态增强扫描获得优良图像(2分及以上)明显多于3D FAME动态增强扫描(P= 0.014).结论:双手、双腕关节3D LAVA动态增强扫描图像质量优于3D FAME动态增强扫描,是一种理想的双手、双腕关节MR动态增强成像序列.%Objective:To investigate an ideal MR dynamic contrast-enhanced imaging sequence for bilateral hands and wrists by comparing liver acquisition with 3D volume acceleration (LAVA) sequence with 3D fast acquisition with multiphase enhanced fast GRE (FAME) sequence. Methods: Thirty-four patients with polyarthralgia including involvement of hands and wrists during their first visit had MR dynamic contrast-enhanced imaging performed. 3D FAME sequence was used in 9 cases and 3D LAVA sequence in 25 cases. Image quality was evaluated with a 3-point system. Results: Of the 25 cases with 3D LAVA sequence,3 points were scored in 22 cases and 2 points were scored in 3 cases. Of the 9 cases with 3D FAME sequence,2 points were scored in 6 cases and 1 point was scored in 3 cases. 3D LAVA sequence was superior to 3D FAME sequence in image quality by achieving more good images (P = 0. 014). Conclusion: The image quality of images achieved with 3D LAVA sequence was better than that of 3D FAME sequence. 3D LAVA sequence might be an ideal MR dynamic contrast-enhanced imaging sequence for bilateral hands and wrists.

  10. 3D Ultrastructural organization of whole Chlamydomonas reinhardtii cells studied by nanoscale soft x-ray tomography.

    Eric Hummel

    Full Text Available The complex architecture of their structural elements and compartments is a hallmark of eukaryotic cells. The creation of high resolution models of whole cells has been limited by the relatively low resolution of conventional light microscopes and the requirement for ultrathin sections in transmission electron microscopy. We used soft x-ray tomography to study the 3D ultrastructural organization of whole cells of the unicellular green alga Chlamydomonas reinhardtii at unprecedented spatial resolution. Intact frozen hydrated cells were imaged using the natural x-ray absorption contrast of the sample without any staining. We applied different fiducial-based and fiducial-less alignment procedures for the 3D reconstructions. The reconstructed 3D volumes of the cells show features down to 30 nm in size. The whole cell tomograms reveal ultrastructural details such as nuclear envelope membranes, thylakoids, basal apparatus, and flagellar microtubule doublets. In addition, the x-ray tomograms provide quantitative data from the cell architecture. Therefore, nanoscale soft x-ray tomography is a new valuable tool for numerous qualitative and quantitative applications in plant cell biology.

  11. AlgiMatrix™ Based 3D Cell Culture System as an In-Vitro Tumor Model for Anticancer Studies

    Godugu, Chandraiah; Patel, Apurva R.; Desai, Utkarsh; Andey, Terrick; Sams, Alexandria; Singh, Mandip

    2013-01-01

    Background Three-dimensional (3D) in-vitro cultures are recognized for recapitulating the physiological microenvironment and exhibiting high concordance with in-vivo conditions. Taking the advantages of 3D culture, we have developed the in-vitro tumor model for anticancer drug screening. Methods Cancer cells grown in 6 and 96 well AlgiMatrix™ scaffolds resulted in the formation of multicellular spheroids in the size range of 100–300 µm. Spheroids were grown in two weeks in cultures without co...

  12. Comparison of hemodynamics of intracranial aneurysms between MR fluid dynamics using 3D cine phase-contrast MRI and MR-based computational fluid dynamics

    Hemodynamics is thought to play a very important role in the initiation, growth, and rupture of intracranial aneurysms. The purpose of our study was to compare hemodynamics of intracranial aneurysms of MR fluid dynamics (MRFD) using 3D cine PC MR imaging (4D-Flow) at 1.5 T and MR-based computational fluid dynamics (CFD). 4D-Flow was performed for five intracranial aneurysms by a 1.5 T MR scanner. 3D TOF MR angiography was performed for geometric information. The blood flow in the aneurysms was modeled using CFD simulation based on the finite element method. We used MR angiographic data as the vascular models and MR flow information as boundary conditions in CFD. 3D velocity vector fields, 3D streamlines, shearing velocity maps, wall shear stress (WSS) distribution maps and oscillatory shear index (OSI) distribution maps were obtained by MRFD and CFD and were compared. There was a moderate to high degree of correlation in 3D velocity vector fields and a low to moderate degree of correlation in WSS of aneurysms between MRFD and CFD using regression analysis. The patterns of 3D streamlines were similar between MRFD and CFD. The small and rotating shearing velocities and higher OSI were observed at the top of the spiral flow in the aneurysms. The pattern and location of shearing velocity in MRFD and CFD were similar. The location of high oscillatory shear index obtained by MRFD was near to that obtained by CFD. MRFD and CFD of intracranial aneurysms correlated fairly well. (orig.)

  13. A molecular dynamics implementation of the 3D Mercedes-Benz water model

    Hynninen, T.; Dias, C. L.; Mkrtchyan, A.; Heinonen, V.; Karttunen, M.; Foster, A. S.; Ala-Nissila, T.

    2012-02-01

    The three-dimensional Mercedes-Benz model was recently introduced to account for the structural and thermodynamic properties of water. It treats water molecules as point-like particles with four dangling bonds in tetrahedral coordination, representing H-bonds of water. Its conceptual simplicity renders the model attractive in studies where complex behaviors emerge from H-bond interactions in water, e.g., the hydrophobic effect. A molecular dynamics (MD) implementation of the model is non-trivial and we outline here the mathematical framework of its force-field. Useful routines written in modern Fortran are also provided. This open source code is free and can easily be modified to account for different physical context. The provided code allows both serial and MPI-parallelized execution. Program summaryProgram title: CASHEW (Coarse Approach Simulator for Hydrogen-bonding Effects in Water) Catalogue identifier: AEKM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 20 501 No. of bytes in distributed program, including test data, etc.: 551 044 Distribution format: tar.gz Programming language: Fortran 90 Computer: Program has been tested on desktop workstations and a Cray XT4/XT5 supercomputer. Operating system: Linux, Unix, OS X Has the code been vectorized or parallelized?: The code has been parallelized using MPI. RAM: Depends on size of system, about 5 MB for 1500 molecules. Classification: 7.7 External routines: A random number generator, Mersenne Twister ( http://www.math.sci.hiroshima-u.ac.jp/m-mat/MT/VERSIONS/FORTRAN/mt95.f90), is used. A copy of the code is included in the distribution. Nature of problem: Molecular dynamics simulation of a new geometric water model. Solution method: New force-field for

  14. A multifunctional 3D co-culture system for studies of mammary tissue morphogenesis and stem cell biology.

    Jonathan J Campbell

    Full Text Available Studies on the stem cell niche and the efficacy of cancer therapeutics require complex multicellular structures and interactions between different cell types and extracellular matrix (ECM in three dimensional (3D space. We have engineered a 3D in vitro model of mammary gland that encompasses a defined, porous collagen/hyaluronic acid (HA scaffold forming a physiologically relevant foundation for epithelial and adipocyte co-culture. Polarized ductal and acinar structures form within this scaffold recapitulating normal tissue morphology in the absence of reconstituted basement membrane (rBM hydrogel. Furthermore, organoid developmental outcome can be controlled by the ratio of collagen to HA, with a higher HA concentration favouring acinar morphological development. Importantly, this culture system recapitulates the stem cell niche as primary mammary stem cells form complex organoids, emphasising the utility of this approach for developmental and tumorigenic studies using genetically altered animals or human biopsy material, and for screening cancer therapeutics for personalised medicine.

  15. Separation efficiency of a hydrodynamic separator using a 3D computational fluid dynamics multiscale approach.

    Schmitt, Vivien; Dufresne, Matthieu; Vazquez, Jose; Fischer, Martin; Morin, Antoine

    2014-01-01

    The aim of this study is to investigate the use of computational fluid dynamics (CFD) to predict the solid separation efficiency of a hydrodynamic separator. The numerical difficulty concerns the discretization of the geometry to simulate both the global behavior and the local phenomena that occur near the screen. In this context, a CFD multiscale approach was used: a global model (at the scale of the device) is used to observe the hydrodynamic behavior within the device; a local model (portion of the screen) is used to determine the local phenomena that occur near the screen. The Eulerian-Lagrangian approach was used to model the particle trajectories in both models. The global model shows the influence of the particles' characteristics on the trapping efficiency. A high density favors the sedimentation. In contrast, particles with small densities (1,040 kg/m(3)) are steered by the hydrodynamic behavior and can potentially be trapped by the separator. The use of the local model allows us to observe the particle trajectories near the screen. A comparison between two types of screens (perforated plate vs expanded metal) highlights the turbulent effects created by the shape of the screen. PMID:24622557

  16. 3D dislocation dynamics study of plastic instability in irradiated copper

    The onset of plastic instability in neutron irradiated copper is investigated by computer simulation of the dynamics of the elastic interaction between dislocation loops emitted from Frank-Read (F-R) sources and irradiation-induced defect clusters. We show that small prismatic defect clusters produced directly from collision cascades are trapped in the stress field of slip dislocations, and that mobile clusters are absorbed in the dislocation core, when they approach within ∼6 nm. Sessile vacancy clusters are also absorbed within this 'stand-off' distance because of an induced surface tension on their stacking fault. The interaction between prismatic defect clusters in 'decorations' and dislocations is shown to provide significant resistance to the initiation of plastic deformation in irradiated copper (source hardening). Sessile stacking fault tetrahedra are also shown to resist dislocation motion by localized forces before they are absorbed and removed by activated dislocation sources. The significance of these mechanisms to initiation of localized deformation and plastic instability are discussed

  17. Dose distribution of IMRT and 3D-CRT on treating central non-small-cell lung cancer

    3D-CRT and IMRT were used in the radiation therapy of Central Non-small-cell lung cancer (NSCLC), and the dose difference of the methods was estimated. Thirty-two patients suffering with II class NSCLC were selected. Based on CT images, each patient was given 1 3D-CRT (3 dimensional conformal radiotherapy) and 2 IMRT(intensity modulated radiation therapy) treatment plans (5 fields and 7 fields), respectively, and the dose distribution was evaluated too. The results showed that PTVDmean and the PTVmax, PTVDmax (%) and CI of IMRT were both higher than those of 3D-CRT, but the uniformity was not as good as 3D-CRT. All indexes of lung and spinal cord treated with IMRT were lower than that treated with 3D-CRT. Moreover, there was no significance of the difference between 5 fields and 7 fields. In a conclusion, IMRT could not only decrease the target dose of NSCLC, but it can protect normal tissue from radiation damage effectively. And when IMRT was used, 5 fields might be enough. (authors)

  18. Parallel phase-shifting digital holography and its application to high-speed 3D imaging of dynamic object

    Awatsuji, Yasuhiro; Xia, Peng; Wang, Yexin; Matoba, Osamu

    2016-03-01

    Digital holography is a technique of 3D measurement of object. The technique uses an image sensor to record the interference fringe image containing the complex amplitude of object, and numerically reconstructs the complex amplitude by computer. Parallel phase-shifting digital holography is capable of accurate 3D measurement of dynamic object. This is because this technique can reconstruct the complex amplitude of object, on which the undesired images are not superimposed, form a single hologram. The undesired images are the non-diffraction wave and the conjugate image which are associated with holography. In parallel phase-shifting digital holography, a hologram, whose phase of the reference wave is spatially and periodically shifted every other pixel, is recorded to obtain complex amplitude of object by single-shot exposure. The recorded hologram is decomposed into multiple holograms required for phase-shifting digital holography. The complex amplitude of the object is free from the undesired images is reconstructed from the multiple holograms. To validate parallel phase-shifting digital holography, a high-speed parallel phase-shifting digital holography system was constructed. The system consists of a Mach-Zehnder interferometer, a continuous-wave laser, and a high-speed polarization imaging camera. Phase motion picture of dynamic air flow sprayed from a nozzle was recorded at 180,000 frames per second (FPS) have been recorded by the system. Also phase motion picture of dynamic air induced by discharge between two electrodes has been recorded at 1,000,000 FPS, when high voltage was applied between the electrodes.

  19. Identifying cell and molecular stress after radiation in a three-dimensional (3-D) model of oral mucositis

    Research highlights: → We irradiated a 3-D human oral cell culture of keratinocytes and fibroblasts with 12 and 2 Gy. → 6 h after irradiation the histopathology and apoptosis of the 3-D culture were evaluated. Microarrays were used to assess the gene expression in the irradiated 3-D tissue. → 12 Gy induced significant histopathologic changes and cellular apoptosis. → 12 Gy significantly affected genes of the NF-kB pathway, inflammatory cytokines and DAMPs. -- Abstract: Mucositis is a debilitating adverse effect of chemotherapy and radiation treatment. It is important to develop a simple and reliable in vitro model, which can routinely be used to screen new drugs for prevention and treatment of mucositis. Furthermore, identifying cell and molecular stresses especially in the initiation phase of mucositis in this model will help towards this end. We evaluated a three-dimensional (3-D) human oral cell culture that consisted of oral keratinocytes and fibroblasts as a model of oral mucositis. The 3-D cell culture model was irradiated with 12 or 2 Gy. Six hours after the irradiation we evaluated microscopic sections of the cell culture for evidence of morphologic changes including apoptosis. We used microarrays to compare the expression of several genes from the irradiated tissue with identical genes from tissue that was not irradiated. We found that irradiation with 12 Gy induced significant histopathologic effects including cellular apoptosis. Irradiation significantly affected the expression of several genes of the NF-kB pathway and several inflammatory cytokines, such as IL-1B, 1L-8, NF-kB1, and FOS compared to tissue that was not irradiated. We identified significant upregulation of several genes that belong to damage-associated molecular patterns (DAMPs) such as HMB1, S100A13, SA10014, and SA10016 in the 3-D tissues that received 12 Gy but not in tissues that received 2 Gy. In conclusion, this model quantifies radiation damage and this is an important first

  20. Identifying cell and molecular stress after radiation in a three-dimensional (3-D) model of oral mucositis

    Lambros, Maria Polikandritou, E-mail: mlambros@westernu.edu [Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766 (United States); Parsa, Cyrus [Department of Clinical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, Pomona, CA 91766 (United States); Mulamalla, HariChandana [Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766 (United States); Orlando, Robert [Department of Clinical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, Pomona, CA 91766 (United States); Lau, Bernard [Center for Advancement of Drug Research and Evaluation (CADRE), Western University of Health Sciences, Pomona, CA 91766 (United States); Huang, Ying [Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766 (United States); Center for Advancement of Drug Research and Evaluation (CADRE), Western University of Health Sciences, Pomona, CA 91766 (United States); Pon, Doreen [Department of Pharmacy Practice and Administration, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766 (United States); Chow, Moses [Department of Pharmacy Practice and Administration, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766 (United States); Center for Advancement of Drug Research and Evaluation (CADRE), Western University of Health Sciences, Pomona, CA 91766 (United States)

    2011-02-04

    Research highlights: {yields} We irradiated a 3-D human oral cell culture of keratinocytes and fibroblasts with 12 and 2 Gy. {yields} 6 h after irradiation the histopathology and apoptosis of the 3-D culture were evaluated. Microarrays were used to assess the gene expression in the irradiated 3-D tissue. {yields} 12 Gy induced significant histopathologic changes and cellular apoptosis. {yields} 12 Gy significantly affected genes of the NF-kB pathway, inflammatory cytokines and DAMPs. -- Abstract: Mucositis is a debilitating adverse effect of chemotherapy and radiation treatment. It is important to develop a simple and reliable in vitro model, which can routinely be used to screen new drugs for prevention and treatment of mucositis. Furthermore, identifying cell and molecular stresses especially in the initiation phase of mucositis in this model will help towards this end. We evaluated a three-dimensional (3-D) human oral cell culture that consisted of oral keratinocytes and fibroblasts as a model of oral mucositis. The 3-D cell culture model was irradiated with 12 or 2 Gy. Six hours after the irradiation we evaluated microscopic sections of the cell culture for evidence of morphologic changes including apoptosis. We used microarrays to compare the expression of several genes from the irradiated tissue with identical genes from tissue that was not irradiated. We found that irradiation with 12 Gy induced significant histopathologic effects including cellular apoptosis. Irradiation significantly affected the expression of several genes of the NF-kB pathway and several inflammatory cytokines, such as IL-1B, 1L-8, NF-kB1, and FOS compared to tissue that was not irradiated. We identified significant upregulation of several genes that belong to damage-associated molecular patterns (DAMPs) such as HMB1, S100A13, SA10014, and SA10016 in the 3-D tissues that received 12 Gy but not in tissues that received 2 Gy. In conclusion, this model quantifies radiation damage and this

  1. Micro 3D cell culture systems for cellular behavior studies: Culture matrices, devices, substrates, and in-situ sensing methods.

    Choi, Jonghoon; Lee, Eun Kyu; Choo, Jaebum; Yuh, Junhan; Hong, Jong Wook

    2015-09-01

    Microfabricated systems equipped with 3D cell culture devices and in-situ cellular biosensing tools can be a powerful bionanotechnology platform to investigate a variety of biomedical applications. Various construction substrates such as plastics, glass, and paper are used for microstructures. When selecting a construction substrate, a key consideration is a porous microenvironment that allows for spheroid growth and mimics the extracellular matrix (ECM) of cell aggregates. Various bio-functionalized hydrogels are ideal candidates that mimic the natural ECM for 3D cell culture. When selecting an optimal and appropriate microfabrication method, both the intended use of the system and the characteristics and restrictions of the target cells should be carefully considered. For highly sensitive and near-cell surface detection of excreted cellular compounds, SERS-based microsystems capable of dual modal imaging have the potential to be powerful tools; however, the development of optical reporters and nanoprobes remains a key challenge. We expect that the microsystems capable of both 3D cell culture and cellular response monitoring would serve as excellent tools to provide fundamental cellular behavior information for various biomedical applications such as metastasis, wound healing, high throughput screening, tissue engineering, regenerative medicine, and drug discovery and development. PMID:26358782

  2. 3D Plant Cell Architecture of Arabidopsis thaliana (Brassicaceae Using Focused Ion Beam–Scanning Electron Microscopy

    Bhawana

    2014-06-01

    Full Text Available Premise of the study: Focused ion beam–scanning electron microscopy (FIB-SEM combines the ability to sequentially mill the sample surface and obtain SEM images that can be used to create 3D renderings with micron-level resolution. We have applied FIB-SEM to study Arabidopsis cell architecture. The goal was to determine the efficacy of this technique in plant tissue and cellular studies and to demonstrate its usefulness in studying cell and organelle architecture and distribution. Methods: Seed aleurone, leaf mesophyll, stem cortex, root cortex, and petal lamina from Arabidopsis were fixed and embedded for electron microscopy using protocols developed for animal tissues and modified for use with plant cells. Each sample was sectioned using the FIB and imaged with SEM. These serial images were assembled to produce 3D renderings of each cell type. Results: Organelles such as nuclei and chloroplasts were easily identifiable, and other structures such as endoplasmic reticula, lipid bodies, and starch grains were distinguishable in each tissue. Discussion: The application of FIB-SEM produced 3D renderings of five plant cell types and offered unique views of their shapes and internal content. These results demonstrate the usefulness of FIB-SEM for organelle distribution and cell architecture studies.

  3. Aquilion ONE / ViSION Edition CT scanner realizing 3D dynamic observation with low-dose scanning

    Computed tomography (CT) scanners have been continuously advancing as essential diagnostic imaging equipment for the diagnosis and treatment of a variety of diseases, including the three major disease classes of cerebrovascular disease, cardiovascular disease, and cancer. Through the development of helical CT scanners and multislice CT scanners, Toshiba Medical Systems Corporation has developed the Aquilion ONE, a CT scanner with a scanning range of up to 160 mm per rotation that can obtain three-dimensional (3D) images of the brain, heart, and other organs in a single rotation. We have now developed the Aquilion ONE / ViSION Edition, a next-generation 320-row multislice CT scanner incorporating the latest technologies that achieves a shorter scanning time and significant reduction in dose compared with conventional products. This product with its low-dose scanning technology will contribute to the practical realization of new diagnosis and treatment modalities employing four-dimensional (4D) data based on 3D dynamic observations through continuous rotations. (author)

  4. NIKE2D, Analysis of Static and Dynamic Response of 3-D Solids

    1 - Description of program or function: NIKE2D is a vectorized, implicit, finite-deformation, large strain, finite-element code for analyzing the response of two-dimensional axisymmetric, plane stress solids. A variety of loading conditions can be handled including traction boundary conditions, displacement boundary conditions, concentrated nodal point loads, body force loads due to base accelerations, and body force loads due to base accelerations, and body force loads due to spinning. Slide-lines with interface friction are available. Elastic, orthotropic-elastic, elastic-plastic, soil and crushable foam, thermo-elastic-plastic, linear viscoelastic thermo-orthotropic elastic, elastic-creep, and strain rate dependent material models are implemented. Nearly incompressible behavior that arises in plasticity problems and elasticity problems with Poisson's ratio approaching 0.5 is accounted for in the element formulation to preclude mesh lock-ups and the associated anomalous stress states. 2 - Method of solution: Four-node iso-parametric elements are used for the spatial discretization, and profile (bandwidth) minimization is optional. An incremental-interactive numerical algorithm, based on the Green-Naghdi stress rate formulation is implemented in NIKE2D. Arc length methods are used to solve problems that involve snap through buckling, plastic instabilities, and related problems where equilibrium is difficult to achieve. Forces due to surface tractions (pressure and shear) and spinning are calculated based on the current configuration and are recalculated for each equilibrium interaction using the current estimate of the configuration. No limit exists on the number of load-time histories that can be defined, and any loading function may reference any time history. Body force loads may be applied in static and dynamic analyses. The automatic rezoning in NIKE2D consists of three phases: generate nodal values on the old mesh for all variables to be re-mapped; rezone

  5. Development of non-contact 3D measurement system for HALF cells

    We strive to develop a 3D coordinate measuring machine, which can measure the shape of parts of accelerator cavity with without contact and rapidly. Currently, the ILC (International Linear Collider) project is progressing through international collaboration. The major goal of ILC is to produce and investigate Higgs bosons. ILC consists of two linear accelerators facing each other, and will hurl some 10 billion electrons and positrons toward each other at nearly the speed of light. The cavity is an important component to accelerate particles to near light speed. A cavity's inner 3D shape influences the accelerating performance. Therefore, it is important to measure the shape of the parts of a cavity. We are developing a highly accurate and non-contact shape measuring machine using triangulation method. (author)

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

    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

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

    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

  8. The Effects of GDF-5 and Uniaxial Strain on Mesenchymal Stem Cells in 3-D Culture

    Farng, Eugene; Urdaneta, Alfonso R.; Barba, David; Esmende, Sean; McAllister, David R.

    2008-01-01

    Recent endeavors in tissue engineering have attempted to identify the optimal parameters to create an artificial ligament. Both mechanical and biochemical stimulation have been used by others to independently modulate growth and differentiation, although few studies have explored their interactions. We applied previously described fabrication techniques to create a highly porous (90%–95% porosity, 212–300 μm), 3-D, bioabsorbable polymer scaffold (polycaprolactone). Scaffolds were coated with ...

  9. Non-linear dynamics of viscous bilayers subjected to an electric field: 3D phase field simulations

    Dritselis, Christos; Karapetsas, George; Bontozoglou, Vasilis

    2014-11-01

    The scope of this work is to investigate the non-linear dynamics of the electro-hydrodynamic instability of a bilayer of immiscible liquids. We consider the case of two viscous films which is separated from the top electrode by air. We assume that the liquids are perfect dielectrics and consider the case of both flat and patterned electrodes. We develop a computational model using the diffuse interface method and carry out 3D numerical simulations fully accounting for the flow and electric field in all phases. We perform a parametric study and investigate the influence of the electric properties of fluids, applied voltage and various geometrical characteristics of the mask. The authors acknowledge the support by the General Secretariat of Research and Technology of Greece under the action ``Supporting Postdoctoral Researchers'' (Grant Number PE8/906), co-funded by the European Social Fund and National Resources.

  10. Modelling crystal plasticity by 3D dislocation dynamics and the finite element method: The Discrete-Continuous Model revisited

    Vattré, A.; Devincre, B.; Feyel, F.; Gatti, R.; Groh, S.; Jamond, O.; Roos, A.

    2014-02-01

    A unified model coupling 3D dislocation dynamics (DD) simulations with the finite element (FE) method is revisited. The so-called Discrete-Continuous Model (DCM) aims to predict plastic flow at the (sub-)micron length scale of materials with complex boundary conditions. The evolution of the dislocation microstructure and the short-range dislocation-dislocation interactions are calculated with a DD code. The long-range mechanical fields due to the dislocations are calculated by a FE code, taking into account the boundary conditions. The coupling procedure is based on eigenstrain theory, and the precise manner in which the plastic slip, i.e. the dislocation glide as calculated by the DD code, is transferred to the integration points of the FE mesh is described in full detail. Several test cases are presented, and the DCM is applied to plastic flow in a single-crystal Nickel-based superalloy.

  11. The effect of rheological approximations on the dynamics and topography in 3D subduction-collision models

    Pusok, Adina E.; Kaus, Boris J. P.; Popov, Anton A.

    2016-04-01

    Most of the major mountain belts and orogenic plateaus are found within the overlying plate of active or fossil subduction and/or collision zones. Moreover, they evolve differently from one another as the result of specific combinations of surface and mantle processes. These differences arise for several reasons, such as different rheological properties, different amounts of regional isostatic compensation, and different mechanisms by which forces are applied to the convergent plates. Previous 3D geodynamic models of subduction/collision processes have used various rheological approximations, making numerical results difficult to compare, since there is no clear image on the extent of these approximations on the dynamics. Here, we employ the code LaMEM to perform high-resolution long-term 3D simulations of subduction/continental collision in an integrated lithospheric and upper-mantle scale model. We test the effect of rheological approximations on mantle and lithosphere dynamics in a geometrically simplified model setup that resembles a tectonic map of the India-Asia collision zone. We use the "sticky-air" approach to allow for the development of topography and the dynamics of subduction and collision is entirely driven by slab-pull (i.e. "free subduction"). The models exhibit a wide range of behaviours depending on the rheological law employed: from linear to temperature-dependent visco-elasto-plastic rheology that takes into account both diffusion and dislocation creep. For example, we find that slab dynamics varies drastically between end member models: in viscous approximations, slab detachment is slow following a viscous thinning, while for a non-linear visco-elasto-plastic rheology, slab detachment is relatively fast, inducing strong mantle flow in the slab window. We also examine the stress states in the subducting and overriding plates and topography evolution in the upper plate, and we discuss the implications on lithosphere dynamics at convergent margins

  12. Characterizing microscale aluminum composite layer properties on silicon solar cells with hybrid 3D scanning force measurements

    Bae, Sung-Kuk; Choi, Beomjoon; Chung, Haseung; Shin, Seungwon; Song, Hee-Eun; Seo, Jung Hwan

    2016-03-01

    This article presents a novel technique to estimate the mechanical properties of the aluminum composite layer on silicon solar cells by using a hybrid 3-dimensional laser scanning force measurement (3-D LSFM) system. The 3-D LSFM system measures the material properties of sub-layers constituting a solar cell. This measurement is critical for realizing high-efficient ultra-thin solar cells. The screen-printed aluminum layer, which significantly affects the bowing phenomenon, is separated from the complete solar cell by removing the silicon (Si) layer with deep reactive ion etching. An elastic modulus of ~15.1 GPa and a yield strength of ~35.0 MPa for the aluminum (Al) composite layer were obtained by the 3-D LSFM system. In experiments performed for 6-inch Si solar cells, the bowing distances decreased from 12.02 to 1.18 mm while the Si layer thicknesses increased from 90 to 190 μm. These results are in excellent agreement with the theoretical predictions for ultra-thin Si thickness (90 μm) based on the obtained Al composite layer properties.

  13. A photopolymerizable hydrogel for 3-D culture of human embryonic stem cell-derived cardiomyocytes and rat neonatal cardiac cells.

    Shapira-Schweitzer, Keren; Habib, Manhal; Gepstein, Lior; Seliktar, Dror

    2009-02-01

    The purpose of this study was to assess the in vitro ability of two types of cardiomyocytes (cardiomyocytes derived from human embryonic stem cells (hESC-CM) and rat neonatal cardiomyocytes (rN-CM)) to survive and generate a functional cardiac syncytium in a three-dimensional in situ polymerizable hydrogel environment. Each cell type was cultured in a PEGylated fibrinogen (PF) hydrogel for up to two weeks while maturation and cardiac function were documented in terms of spontaneous contractile behavior and biomolecular organization. Quantitative contractile parameters including contraction amplitude and synchronization were measured by non-invasive image analysis. The rN-CM demonstrated the fastest maturation and the most significant spontaneous contraction. The hESC-CM maturation occurred between 10-14 days in culture, and exhibited less contraction amplitude and synchronization in comparison to the rN-CMs. The maturation of both cell types within the hydrogels was confirmed by cardiac-specific biomolecular markers, including alpha-sarcomeric actin, actinin, and connexin-43. Cellular responsiveness to isoproterenol, carbamylcholine and heptanol provided further evidence of the cardiac maturation in the 3-D PF hydrogel as well as identified a potential to use this system for in vitro drug screening. These findings indicate that the PF hydrogel biomaterial can be used as an in situ polymerizable biomaterial for stem cells and their cardiomyocyte derivatives. PMID:19027751

  14. FEM modeling for 3D dynamic analysis of deep-ocean mining pipeline and its experimental verification

    2007-01-01

    3D dynamic analysis models of 1000 m deep-ocean mining pipeline, including steel lift pipe, pump, buffer and flexible hose, were established by finite element method (FEM). The coupling effect of steel lift pipe and flexible hose, and main external loads of pipeline were considered in the models, such as gravity, buoyancy, hydrodynamic forces, internal and external fluid pressures, concentrated suspension buoyancy on the flexible hose, torsional moment and axial force induced by pump working.Some relevant FEM models and solution techniques were developed, according to various 3D transient behaviors of integrated deep-ocean mining pipeline, including towing motions of track-keeping operation and launch process of pipeline. Meanwhile, an experimental verification system in towing water tank that had similar characteristics of designed mining pipeline was developed to verify the accuracy of the FEM models and dynamic simulation. The experiment results show that the experimental records and simulation results of stress of pipe are coincided. Based on the further simulations of 1 000 m deep-ocean mining pipeline, the simulation results show that, to form configuration of a saddle shape, the total concentrated suspension buoyancy of flexible hose should be 95%-105% of the gravity of flexible hose in water, the first suspension point occupies 1/3 of the total buoyancy, and the second suspension point occupies 2/3 of the total buoyancy. When towing velocity of mining system is less than 0.5 m/s, the towing track of buffer is coincided with the setting route of ship on the whole and the configuration of flexible hose is also kept well.

  15. Real-time in situ characterization of interface dynamics in microstructure formation during 3D-directional solidification of transparent alloys

    Bergeon, N.; Trivedi, R.; Billia, B.; Echebarria, B.; Karma, A.; Liu, S.; Weiss, C.

    The properties of structural materials are to a large extent determined by the solid microstructure so that the understanding of the fundamental physics of microstructure formation is critical in the engineering of materials. Also, microstructure selection occurs during the dynamical growth process so that in situ observation of spatio-temporal evolution of the solid-liquid interface shape is necessary. Under terrestrial conditions, convection effects dominates in bulk samples which prevent precise characterization of microstructure selection. As the glass ampoule conducts heat better than transparent materials, e.g. succinonitrile, the sample near the wall is cooler and convection arises. This leads to concave interface and non-uniform morphological instability starting at the center, while the region near the wall remains smooth. Diffusion-controlled experiments in thin samples give microstructures that are neither 2D nor 3D. When the spacing between glass plates is smaller than the spacing, the cell shape near the tip is 3D, and becomes 2D away from the tip. Preliminary rigorous phase-field results show that in 3D tube geometry (reasonable approximation for a hexagonal array), axisymmetric cells only exist over a narrow range of spacing whereas in 2D steady-state shapes span a wide range of spacing. A benchmark experimental study in bulk samples is thus required under low gravity conditions. In the frame of the joint work of DSIP and MISOL3D projects, respectively selected by NASA and CNES, microgravity experiments in a model transparent system are planned on ISS using the Directional Solidification Insert in the DECLIC facility. The critical aspects of hardware design, the key fundamental issues identified through 1g-experiments, the proposed study on ISS, and the results of rigorous theoretical modeling will be presented. The cellular/dendritic interface morphologies will be examined by systematically varying the process parameters, yielding insight into the

  16. Single Molecule 3D Orientation in Time and Space: A 6D Dynamic Study on Fluorescently Labeled Lipid Membranes.

    Börner, Richard; Ehrlich, Nicky; Hohlbein, Johannes; Hübner, Christian G

    2016-05-01

    Interactions between single molecules profoundly depend on their mutual three-dimensional orientation. Recently, we demonstrated a technique that allows for orientation determination of single dipole emitters using a polarization-resolved distribution of fluorescence into several detection channels. As the method is based on the detection of single photons, it additionally allows for performing fluorescence correlation spectroscopy (FCS) as well as dynamical anisotropy measurements thereby providing access to fast orientational dynamics down to the nanosecond time scale. The 3D orientation is particularly interesting in non-isotropic environments such as lipid membranes, which are of great importance in biology. We used giant unilamellar vesicles (GUVs) labeled with fluorescent dyes down to a single molecule concentration as a model system for both, assessing the robustness of the orientation determination at different timescales and quantifying the associated errors. The vesicles provide a well-defined spherical surface, such that the use of fluorescent lipid dyes (DiO) allows to establish a a wide range of dipole orientations experimentally. To complement our experimental data, we performed Monte Carlo simulations of the rotational dynamics of dipoles incorporated into lipid membranes. Our study offers a comprehensive view on the dye orientation behavior in a lipid membrane with high spatiotemporal resolution representing a six-dimensional fluorescence detection approach. PMID:26972111

  17. 3D Digital Modelling

    Hundebøl, Jesper

    wave of new building information modelling tools demands further investigation, not least because of industry representatives' somewhat coarse parlance: Now the word is spreading -3D digital modelling is nothing less than a revolution, a shift of paradigm, a new alphabet... Research qeustions. Based...... on empirical probes (interviews, observations, written inscriptions) within the Danish construction industry this paper explores the organizational and managerial dynamics of 3D Digital Modelling. The paper intends to - Illustrate how the network of (non-)human actors engaged in the promotion (and arrest) of 3......D Modelling (in Denmark) stabilizes - Examine how 3D Modelling manifests itself in the early design phases of a construction project with a view to discuss the effects hereof for i.a. the management of the building process. Structure. The paper introduces a few, basic methodological concepts...

  18. Improving organic tandem solar cells based on water-processed nanoparticles by quantitative 3D nanoimaging

    Pedersen, Emil Bøje Lind; Angmo, Dechan; Dam, Henrik Friis;

    2015-01-01

    particle active layer. We extract the layered morphology with structural and density information including the porosity present in the various layers and the silver electrode with high resolution in 3D. The Landfester particle layer is found to have an undesired morphology with negatively correlated top...... easier access to the printing industry, which has reduced the use of organic solvents since the 1980s. Through ptychographic X-ray computed tomography (PXCT), we image quantitatively a roll-to-roll coated photovoltaic tandem stack consisting of one bulk heterojunction active layer and one Landfester...

  19. Epstein-Barr virus (EBV) infection of murine L cells expressing recombinant human EBV/C3d receptor.

    Ahearn, J M; Hayward, S D; Hickey, J C; Fearon, D T

    1988-01-01

    The normal host range of Epstein-Barr virus (EBV) is limited to primate B lymphocytes and certain epithelial cells that express the C3d/EBV receptor [complement receptor 2 (CR2, CD21)]. In the present study, expansion of the tissue tropism of EBV has been accomplished by stably transfecting the murine fibroblast L cell line with pMT.CR2. neo.1, a eukaryotic expression vector promoting the transcription of a complementary DNA insert encoding human CR2. High CR2-expressing transfected L cells w...

  20. Fully 3D Particle-in-Cell Simulation of Double Post-Hole Convolute on PTS Facility

    Zhao, Hailong; Dong, Ye; Zhou, Haijing; Zou, Wenkang; Institute of Fluid Physics Collaboration; Institute of Applied Physics; Computational Mathematics Collaboration

    2015-11-01

    In order to get better understand of energy transforming and converging process during High Energy Density Physics (HEDP) experiments, fully 3D particle-in-cell (PIC) simulation code NEPTUNE3D was used to provide numerical approach towards parameters which could hardly be acquired through diagnostics. Cubic region (34cm × 34cm × 18cm) including the double post-hole convolute (DPHC) on the primary test stand (PTS) facility was chosen to perform a series of fully 3D PIC simulations, calculating ability of codes were tested and preliminary simulation results about DPHC on PTS facility were discussed. Taking advantages of 3D simulation codes and large-scale parallel computation, massive data (~ 250GB) could be acquired in less than 5 hours and clear process of current transforming and electron emission in DPHC were demonstrated with the help of visualization tools. Cold-chamber tests were performed during which only cathode electron emission was considered without temperature rise or ion emission, current loss efficiency was estimated to be 0.46% ~ 0.48% by comparisons between output magnetic field profiles with or without electron emission. Project supported by the National Natural Science Foundation of China (Grant No. 11205145, 11305015, 11475155).

  1. Cellular differentiation in 3D-bioprinted mesenchymal stem cell-loaded hydrogels with varying structural and mechanical properties

    Duarte Campos, Daniela Filipa

    2016-01-01

    Hydrogels are a promising alternative to rigid biomaterials typically used in the field of bone tissue engineering for the treatment of musculoskeletal disorders. By hydrogel-based 3D-bioprinting, the native ornamentation of cells and matrix from bone tissue could be resembled. Herein, it was hypothesized the combination of polysaccharides (agarose, alginate) with biological components (collagen, fibrinogen) would increase mechanical stiffness of printed constructs as well as support the prin...

  2. Design, construction and testing of a COC 3D flow-over flow-through bioreactor for hepatic cell culture

    Windels, Jindrich; Verplancke, Rik; Jahanshahi, Amir; Heimann, Marcus; Leite, Sofia B.; Roosens, Tiffany; van Grunsven, Leo A; Barbe, Laurent; Prill, Sebastian; Jaeger, Magnus; Duschl, Claus; Vanfleteren, Jan

    2015-01-01

    In this poster, we present the joint development efforts for a 3D microfluidic bioreactor for hepatic cell cultures. Cyclic Olefin Copolymer (COC) was selected for constructing the bioreactor, since the material has good chemical resistance, low adsorption and good optical properties, including low auto-fluorescence. A downside of COC is that it is much more difficult to structure than more traditional microfluidic materials, such as PDMS, PMMA, … Two parallel approaches were developed for...

  3. Exploring natural silk protein sericin for regenerative medicine: an injectable, photoluminescent, cell-adhesive 3D hydrogel

    Wang, Zheng; Zhang, Yeshun; Zhang, Jinxiang; Huang, Lei; Liu, Jia; Li, Yongkui; Zhang, Guozheng; Kundu, Subhas C.; Wang, Lin

    2014-01-01

    Sericin, a major component of silk, has a long history of being discarded as a waste during silk processing. The value of sericin for tissue engineering is underestimated and its potential application in regenerative medicine has just begun to be explored. Here we report the successful fabrication and characterization of a covalently-crosslinked 3D pure sericin hydrogel for delivery of cells and drugs. This hydrogel is injectable, permitting its implantation through minimally invasive approac...

  4. Ammonium accumulation and cell death in a rat 3D brain cell model of glutaric aciduria type I.

    Paris Jafari

    Full Text Available Glutaric aciduria type I (glutaryl-CoA dehydrogenase deficiency is an inborn error of metabolism that usually manifests in infancy by an acute encephalopathic crisis and often results in permanent motor handicap. Biochemical hallmarks of this disease are elevated levels of glutarate and 3-hydroxyglutarate in blood and urine. The neuropathology of this disease is still poorly understood, as low lysine diet and carnitine supplementation do not always prevent brain damage, even in early-treated patients. We used a 3D in vitro model of rat organotypic brain cell cultures in aggregates to mimic glutaric aciduria type I by repeated administration of 1 mM glutarate or 3-hydroxyglutarate at two time points representing different developmental stages. Both metabolites were deleterious for the developing brain cells, with 3-hydroxyglutarate being the most toxic metabolite in our model. Astrocytes were the cells most strongly affected by metabolite exposure. In culture medium, we observed an up to 11-fold increase of ammonium in the culture medium with a concomitant decrease of glutamine. We further observed an increase in lactate and a concomitant decrease in glucose. Exposure to 3-hydroxyglutarate led to a significantly increased cell death rate. Thus, we propose a three step model for brain damage in glutaric aciduria type I: (i 3-OHGA causes the death of astrocytes, (ii deficiency of the astrocytic enzyme glutamine synthetase leads to intracerebral ammonium accumulation, and (iii high ammonium triggers secondary death of other brain cells. These unexpected findings need to be further investigated and verified in vivo. They suggest that intracerebral ammonium accumulation might be an important target for the development of more effective treatment strategies to prevent brain damage in patients with glutaric aciduria type I.

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

    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

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

    Ko, Jae Hyung [Regenerative Medicine Research Center, Dalim Tissen Co., LTD., 383-93, Yonnam-Dong, Mapo-gu, Seoul (Korea, Republic of); Kim, Yang Hee [Regenerative Medicine Research Center, Dalim Tissen Co., LTD., 383-93, Yonnam-Dong, Mapo-gu, Seoul (Korea, Republic of); Asan Institute for Life Science, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul (Korea, Republic of); Jeong, Seong Hee; Lee, Song [Asan Institute for Life Science, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul (Korea, Republic of); Park, Si-Nae [Regenerative Medicine Research Center, Dalim Tissen Co., LTD., 383-93, Yonnam-Dong, Mapo-gu, Seoul (Korea, Republic of); Shim, In Kyong, E-mail: shimiink@gmail.com [Asan Institute for Life Science, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul (Korea, Republic of); Kim, Song Cheol, E-mail: drksc@amc.seoul.kr [Asan Institute for Life Science, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul (Korea, Republic of); Department of Surgery, University of Ulsan College of Medicine & Asan Medical Center, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul (Korea, Republic of)

    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.

  7. Double targeting of Survivin and XIAP radiosensitizes 3D grown human colorectal tumor cells and decreases migration

    Background and purpose: In the present study, we aimed to investigate the effect of single and double knockdown of the inhibitor of apoptosis proteins (IAP) Survivin and X-linked IAP (XIAP) on three-dimensional (3D) clonogenic survival, migration capacity and underlying signaling pathways. Materials and methods: Colorectal cancer cell lines (HCT-15, SW48, SW480, SW620) were subjected to siRNA-mediated single or Survivin/XIAP double knockdown followed by 3D colony forming assays, cell cycle analysis, Caspase activity assays, migration assays, matrigel transmigration assays and Western blotting (Survivin, XIAP, Focal adhesion kinase (FAK), p-FAK Y397, Akt1, p-Akt1 S473, Extracellular signal-regulated kinase (ERK1/2), p-ERK1/2 T202/Y204, Glycogen synthase kinase (GSK)3β, p-GSK3β S9, nuclear factor (NF)-κB p65). Results: While basal cell survival was altered cell line-dependently, Survivin or XIAP single and Survivin/XIAP double knockdown enhanced cellular radiosensitivity of all tested cancer cell lines grown in 3D. Particularly double knockdown conditions revealed accumulation of cells in G2/M, increased subG1 fraction, elevated Caspase 3/7 activity, and reduced migration. Intracellular signaling showed dephosphorylation of FAK and Akt1 upon Survivin and/or Survivin/XIAP silencing. Conclusions: Our results strengthen the notion of Survivin and XIAP to act as radiation resistance factors and further indicate that these apoptosis-regulating proteins are also functioning in cell cycling and cell migration

  8. Assessment of dynamic contrast enhancement of the small bowel in active Crohn's disease using 3D MR enterography

    Purpose: To retrospectively compare the dynamic contrast enhancement of the small bowel segments with and without active Crohn's disease at 3D MR enterography (MRE). Materials and methods: Thirteen patients (five men, eight women; mean age 41.2 years; range 29-56) were imaged on a 1.5-T MR scanner (Sonata, Siemens Medical) with standard MR sequences after having ingested 1000 ml of a 3% mannitol solution. Subsequently, high resolution 3D gradient-echo (volumetric interpolated breath-hold examination = VIBE) data sets were obtained pre-contrast and 20-40 s, 60-80 s, and 120-140 s after i.v. Gd-DOTA administration (0.2 mmol/kg). Signal enhancement was measured on single slices both in normal and histologically confirmed (12/13) inflamed small bowel wall segments as well as in the aorta, the psoas muscle, and the background to calculate signal-to-noise (SNR) and contrast-to-noise ratios (CNR). Results: Small bowel wall enhancement was significantly higher (p < 0.05) in inflamed compared to normal segments at 20-40 s (SNR inflamed: 58.7 ± 33.8 vs normal: 36.0 ± 19.8; p = 0.048; CNR inflamed: 34.8 ± 23.4 vs normal: 16.3 ± 11.2; p = 0.017) and at 60-80 s (SNR: 60.3 ± 25.1 vs 41.9 ± 20.0; p = 0.049; CNR: 34.9 ± 15.1 vs 19.3 ± 13.2; p = 0.01) after i.v. contrast administration, respectively. Even at 120-140 s CNR was still increased in inflamed segments (33.7 ± 16.0 vs 18.1 ± 13.2; p = 0.04), while differences in SNR did not attain statistical significance (63.0 ± 26.2 vs 45.3 ± 23.3; p = 0.15). Conclusion: In active Crohn's disease, histologically confirmed inflamed small bowel wall segments demonstrate a significantly increased early uptake of gadolinium on 3D VIBE sequences compared to normal small bowel segments.

  9. Revealing plot scale heterogeneity in soil moisture dynamics under contrasting vegetation assemblages using 3D electrical resistivity tomography (ERT) surveys

    Dick, Jonathan; Tetzlaff, Doerthe; Bradford, John; Soulsby, Chris

    2016-04-01

    Soil moisture is a fundamental component of the water cycle that influences many hydrological processes, such as flooding, solute transport, biogeochemical processes, and land-atmosphere interactions. The relationship between vegetation and soil moisture is complex and reciprocal. Soil moisture may affect vegetation distribution due to its function as the primary source of water, in turn the structure of vegetation canopies regulate water partitioning into interception, throughfall and steam flow. Such spatial differences in inputs, together with complex patterns of water uptake from distributed root networks can create marked heterogeneity in soil moisture dynamics at small scales. Traditional methods of monitoring soil moisture have revolved around limited point measurements, but improved geophysical techniques have facilitated a trend towards more spatially distributed measurements to help understand this heterogeneity. Here, we present a study using 3D ERT surveys in a 3.2km upland catchment in the Scottish Highlands where increasing afforestation (for climate change adaptation, biofuels and conservation) has the potential to increase interception losses and reduce soil moisture storage. The study combined 3D surveys, traditional point measurements and laboratory analysis of soil cores to assess the plot scale soil moisture dynamics in podzolic soils under forest stands of 15m high Scots pine (Pinus sylvestris) and adjacent non-forest plots dominated by heather (Calluna vulgaris) shrubs (forest and non-forest vegetation communities the Scottish Highlands. Results showed differences in the soil moisture dynamics under the different vegetation types, with heterogeneous patterns in the forested site mainly correlated with canopy cover and mirroring interception losses. Temporal variability in the forested site was greater, probably due to the interception, and increased evapotranspiration losses relative to the heather site. The smaller moisture changes in the

  10. Revealing plot scale heterogeneity in soil moisture dynamics under contrasting vegetation assemblages using 3D electrical resistivity tomography (ERT) surveys

    Dick, Jonathan; Tetzlaff, Doerthe; Bradford, John; Soulsby, Chris

    2016-04-01

    Soil moisture is a fundamental component of the water cycle that influences many hydrological processes, such as flooding, solute transport, biogeochemical processes, and land-atmosphere interactions. The relationship between vegetation and soil moisture is complex and reciprocal. Soil moisture may affect vegetation distribution due to its function as the primary source of water, in turn the structure of vegetation canopies regulate water partitioning into interception, throughfall and steam flow. Such spatial differences in inputs, together with complex patterns of water uptake from distributed root networks can create marked heterogeneity in soil moisture dynamics at small scales. Traditional methods of monitoring soil moisture have revolved around limited point measurements, but improved geophysical techniques have facilitated a trend towards more spatially distributed measurements to help understand this heterogeneity. Here, we present a study using 3D ERT surveys in a 3.2km upland catchment in the Scottish Highlands where increasing afforestation (for climate change adaptation, biofuels and conservation) has the potential to increase interception losses and reduce soil moisture storage. The study combined 3D surveys, traditional point measurements and laboratory analysis of soil cores to assess the plot scale soil moisture dynamics in podzolic soils under forest stands of 15m high Scots pine (Pinus sylvestris) and adjacent non-forest plots dominated by heather (Calluna vulgaris) shrubs (<0.5m high). These dominant species are typical of forest and non-forest vegetation communities the Scottish Highlands. Results showed differences in the soil moisture dynamics under the different vegetation types, with heterogeneous patterns in the forested site mainly correlated with canopy cover and mirroring interception losses. Temporal variability in the forested site was greater, probably due to the interception, and increased evapotranspiration losses relative to the

  11. Large Scale 3-D Dislocation Dynamics and Atomistic Simulations of Flow and Strain-Hardening Behavior of Metallic Micropillars

    Rao, Satish

    2015-03-01

    Experimental studies show strong strengthening effects for micrometer-scale FCC as well as two-phase superalloy crystals, even at high initial dislocation densities. This talk shows results from large-scale 3-D discrete dislocation simulations (DDS) used to explicitly model the deformation behavior of FCC Ni (flow stress and strain-hardening) as well as superalloy microcrystals for diameters ranging from 1 - 20 microns. The work shows that two size-sensitive athermal hardening processes, beyond forest and precipitation hardening, are sufficient to develop the dimensional scaling of the flow stress, stochastic stress variation, flow intermittency and, high initial strain-hardening rates, similar to experimental observations for various materials. In addition, 3D dislocation dynamics simulations are used to investigate strain-hardening characteristics and dislocation microstructure evolution with strain in large 20 micron size Ni microcrystals (bulk-like) under three different loading axes: 111, 001 and 110. Three different multi-slip loading axes, , and , are explored for shear strains of ~0.03 and final dislocation densities of ~1013/m2. The orientation dependence of initial strain hardening rates and dislocation microstructure evolution with strain are discussed. The simulated strain hardening results are compared with experimental data under similar loading conditions from bulk single-crystal Ni. Finally, atomistic simulation results on the operation of single arm sources in Ni bipillars with a large angle grain boundary is discussed. The atomistic simulation results are compared with experimental mechanical behavior data on Cu bipillars with a similar large angle grain boundary. This work was supported by AFOSR (Dr. David Stargel), and by a grant of computer time from the DOD High Performance Computing Modernization Program, at the Aeronautical Systems Center/Major Shared Resource Center.

  12. Comparison between 3D dynamics filter technique, field-in-field, electronic compensator in breast cancer; Comparacao entre tecnica 3D com filtro dinamico, field-in-field e compensacao eletronica para cancer de mama

    Trindade, Cassia; Silva, Leonardo P.; Martins, Lais P.; Garcia, Paulo L.; Santos, Maira R.; Bastista, Delano V.S.; Vieira, Anna Myrian M.T.L.; Rocha, Igor M., E-mail: cassiatr@gmail.com [Instituto Nacional de Cancer (INCA), Rio de Janeiro, RJ (Brazil)

    2012-12-15

    The radiotherapy has been used in a wild scale in breast cancer treatment. With this high demand, new technologies have been developed to improve the dose distribution in the target while reducing the dose delivered in critical organs. In this study, performed with one clinical case, three planning were done for comparison: 3D technique with dynamic filter, 3D with field-in-field technique (forward-planned IMRT) and 3D technique using electronic compensator (ECOMP). The planning were done with a 6MV photon beam using the Eclipse software, version 8.6 (Varian Medical Systems). The PTV was drawn covering the whole breast and the critical organs were: the lung on the irradiated side, the heart, the contralateral breast and the anterior descending coronary artery (LAD). The planning using the compensator technique permitted more homogeneous dose distribution in the target volume. The V20 value of the lung on the irradiated side was 8,3% for the electronic compensator technique, 8,9% for the field-in-field technique and 8,2% for the dynamic filter technique. For the heart the dose range was 15.7 - 139.9 cGy, 16.3 - 148.4 cGy for the dynamic filter technique and 19.6 - 157.0 cGy for the field-in-field technique. The dose gradient was 11% with compensator electronic, 15% dynamic filter technique and 13% with field-in-field. The application of electronic technique in breast cancer treatment allows better dose distribution while reduces dose in critical organs, but in the same time requires a quality assurance. (author)

  13. RIMBAY – a multi-physics 3-D ice-dynamics model for comprehensive applications: model-description and examples

    M. Thoma

    2013-06-01

    Full Text Available Glaciers and ice caps exhibit currently the largest cryospheric contributions to sea level rise. Modelling the dynamics and mass balance of the major ice sheets is therefore an important issue to investigate the current state and the future response of the cryosphere in response to changing environmental conditions, namely global warming. This requires a powerful, easy-to-use, scalable multi-physics ice dynamics model. Based on the well-known and established ice sheet model of Pattyn (2003 we develop the modular multi-physics thermomechanic ice model RIMBAY, in which we improve the original version in several aspects like a shallow-ice–shallow-shelf coupler and a full 3-D-grounding-line migration scheme based on Schoof's (2007 heuristic analytical approach. We summarise the Full–Stokes equations and several approximations implemented within this model and we describe the different numerical discretisations. The results are cross-validated against previous publications dealing with ice modelling, and some additional artificial set-ups demonstrate the robustness of the different solvers and their internal coupling. RIMBAY is designed for an easy adaption to new scientific issues. Hence, we demonstrate in very different set-ups the applicability and functionality of RIMBAY in Earth system science in general and ice modelling in particular.

  14. RIMBAY - a multi-approximation 3D ice-dynamics model for comprehensive applications: model description and examples

    Thoma, M.; Grosfeld, K.; Barbi, D.; Determann, J.; Goeller, S.; Mayer, C.; Pattyn, F.

    2014-01-01

    Glaciers and ice caps exhibit currently the largest cryospheric contributions to sea level rise. Modelling the dynamics and mass balance of the major ice sheets is therefore an important issue to investigate the current state and the future response of the cryosphere in response to changing environmental conditions, namely global warming. This requires a powerful, easy-to-use, versatile multi-approximation ice dynamics model. Based on the well-known and established ice sheet model of Pattyn (2003) we develop the modular multi-approximation thermomechanic ice model RIMBAY, in which we improve the original version in several aspects like a shallow ice-shallow shelf coupler and a full 3D-grounding-line migration scheme based on Schoof's (2007) heuristic analytical approach. We summarise the full Stokes equations and several approximations implemented within this model and we describe the different numerical discretisations. The results are cross-validated against previous publications dealing with ice modelling, and some additional artificial set-ups demonstrate the robustness of the different solvers and their internal coupling. RIMBAY is designed for an easy adaption to new scientific issues. Hence, we demonstrate in very different set-ups the applicability and functionality of RIMBAY in Earth system science in general and ice modelling in particular.

  15. A fully defined and scalable 3D culture system for human pluripotent stem cell expansion and differentiation

    Lei, Yuguo; Schaffer, David V.

    2013-12-01

    Human pluripotent stem cells (hPSCs), including human embryonic stem cells and induced pluripotent stem cells, are promising for numerous biomedical applications, such as cell replacement therapies, tissue and whole-organ engineering, and high-throughput pharmacology and toxicology screening. Each of these applications requires large numbers of cells of high quality; however, the scalable expansion and differentiation of hPSCs, especially for clinical utilization, remains a challenge. We report a simple, defined, efficient, scalable, and good manufacturing practice-compatible 3D culture system for hPSC expansion and differentiation. It employs a thermoresponsive hydrogel that combines easy manipulation and completely defined conditions, free of any human- or animal-derived factors, and entailing only recombinant protein factors. Under an optimized protocol, the 3D system enables long-term, serial expansion of multiple hPSCs lines with a high expansion rate (∼20-fold per 5-d passage, for a 1072-fold expansion over 280 d), yield (∼2.0 × 107 cells per mL of hydrogel), and purity (∼95% Oct4+), even with single-cell inoculation, all of which offer considerable advantages relative to current approaches. Moreover, the system enabled 3D directed differentiation of hPSCs into multiple lineages, including dopaminergic neuron progenitors with a yield of ∼8 × 107 dopaminergic progenitors per mL of hydrogel and ∼80-fold expansion by the end of a 15-d derivation. This versatile system may be useful at numerous scales, from basic biological investigation to clinical development.

  16. AlgiMatrix™ based 3D cell culture system as an in-vitro tumor model for anticancer studies.

    Chandraiah Godugu

    Full Text Available BACKGROUND: Three-dimensional (3D in-vitro cultures are recognized for recapitulating the physiological microenvironment and exhibiting high concordance with in-vivo conditions. Taking the advantages of 3D culture, we have developed the in-vitro tumor model for anticancer drug screening. METHODS: Cancer cells grown in 6 and 96 well AlgiMatrix™ scaffolds resulted in the formation of multicellular spheroids in the size range of 100-300 µm. Spheroids were grown in two weeks in cultures without compromising the growth characteristics. Different marketed anticancer drugs were screened by incubating them for 24 h at 7, 9 and 11 days in 3D cultures and cytotoxicity was measured by AlamarBlue® assay. Effectiveness of anticancer drug treatments were measured based on spheroid number and size distribution. Evaluation of apoptotic and anti-apoptotic markers was done by immunohistochemistry and RT-PCR. The 3D results were compared with the conventional 2D monolayer cultures. Cellular uptake studies for drug (Doxorubicin and nanoparticle (NLC were done using spheroids. RESULTS: IC(50 values for anticancer drugs were significantly higher in AlgiMatrix™ systems compared to 2D culture models. The cleaved caspase-3 expression was significantly decreased (2.09 and 2.47 folds respectively for 5-Fluorouracil and Camptothecin in H460 spheroid cultures compared to 2D culture system. The cytotoxicity, spheroid size distribution, immunohistochemistry, RT-PCR and nanoparticle penetration data suggested that in vitro tumor models show higher resistance to anticancer drugs and supporting the fact that 3D culture is a better model for the cytotoxic evaluation of anticancer drugs in vitro. CONCLUSION: The results from our studies are useful to develop a high throughput in vitro tumor model to study the effect of various anticancer agents and various molecular pathways affected by the anticancer drugs and formulations.

  17. Automated quantitative analysis of 3D morphology and mean corpuscular hemoglobin in human red blood cells stored in different periods.

    Moon, Inkyu; Yi, Faliu; Lee, Yeon H; Javidi, Bahram; Boss, Daniel; Marquet, Pierre

    2013-12-16

    Quantitative phase (QP) images of red blood cells (RBCs), which are obtained by off-axis digital holographic microscopy, can provide quantitative information about three-dimensional (3D) morphology of human RBCs and the characteristic properties such as mean corpuscular hemoglobin (MCH) and MCH surface density (MCHSD). In this paper, we investigate modifications of the 3D morphology and MCH in RBCs induced by the period of storage time for the purpose of classification of RBCs with different periods of storage by using off-axis digital holographic microscopy. The classification of RBCs based on the duration of storage is highly relevant because a long storage of blood before transfusion may alter the functionality of RBCs and, therefore, cause complications in patients. To analyze any changes in the 3D morphology and MCH of RBCs due to storage, we use data sets from RBC samples stored for 8, 13, 16, 23, 27, 30, 34, 37, 40, 47, and 57 days, respectively. The data sets consist of more than 3,300 blood cells in eleven classes, with more than 300 blood cells per class. The classes indicate the storage period of RBCs and are listed in chronological order. Using the RBCs donated by healthy persons, the off-axis digital holographic microscopy reconstructs several quantitative phase images of RBC samples stored for eleven different periods. We employ marker-controlled watershed transform to remove the background in the RBC quantitative phase images obtained by the off-axis digital holographic microscopy. More than 300 single RBCs are extracted from the segmented quantitative phase images for each class. Such a large number of RBC samples enable us to obtain statistical distributions of the characteristic properties of RBCs after a specific period of storage. Experimental results show that the 3D morphology of the RBCs, in contrast to MCH, is essentially related to the aging of the RBCs. PMID:24514667

  18. Controlled positioning of cells in biomaterials - approaches towards 3D tissue printing

    Sandra Hofmann; Ralph Müller; Silke Wüst

    2011-01-01

    Current tissue engineering techniques have various drawbacks: they often incorporate uncontrolled and imprecise scaffold geometries, whereas the current conventional cell seeding techniques result mostly in random cell placement rather than uniform cell distribution. For the successful reconstruction of deficient tissue, new material engineering approaches have to be considered to overcome current limitations. An emerging method to produce complex biological products including cells or extrac...

  19. Dynamic, ecological, accessible and 3D Virtual Worlds-based Libraries using OpenSim and Sloodle along with mobile location and NFC for checking in

    Ruben Gonzalez Crespo

    2012-12-01

    Full Text Available This paper proposes the implementation of a 3D virtual library, using open platforms such as OpenSimulator and Sloodle, applied to the integration of virtual learning environments. It also proposes their application to the creation of open libraries to share and disseminate the new dynamic nature of knowledge, in the understanding that 3D virtual worlds may contribute to the future of libraries as part of green initiatives to achieve an ecologic and sustainable planet.

  20. Dynamic, ecological, accessible and 3D Virtual Worlds-based Libraries using OpenSim and Sloodle along with mobile location and NFC for checking in

    Ruben Gonzalez Crespo; Pontifical University of Salamanca; Roberto Ferro Escobar; Nicolás Torres

    2012-01-01

    This paper proposes the implementation of a 3D virtual library, using open platforms such as OpenSimulator and Sloodle, applied to the integration of virtual learning environments. It also proposes their application to the creation of open libraries to share and disseminate the new dynamic nature of knowledge, in the understanding that 3D virtual worlds may contribute to the future of libraries as part of green initiatives to achieve an ecologic and sustainable planet.

  1. Effect of Aflatoxin B1 on Growth of Bovine Mammary Epithelial Cells in 3D and Monolayer Culture System

    Babak Qasemi-Panahi

    2013-02-01

    Full Text Available Purpose: Many studies have been showed transfer of aflatoxins, toxins produced by Aspergillus flvaus and Aspergillus parasiticus fungi, into milk. These toxins are transferred into the milk through digestive system by eating contaminated food. Due to the toxicity of these materials, it seems that it has side effects on the growth of mammary cells. Therefore, the present work aimed to investigate possible toxic effects of aflatoxin B1 (AFB1 on bovine mammary epithelial cells in monolayer and three-dimensional cultures. Methods: Specimens of the mammary tissue of bovine were sized out in size 2×2 cm in slaughterhouse. After disinfection and washing in sterile PBS, primary cell culture was performed by enzymatic digestion of tissue with collagenase. When proper numbers of cells were achieved in monolayer culture, cells were seeded in a 24-well culture plate for three-dimensional (3D culture in Matrigel matrix. After 21 days of 3D culture and reaching the required number of cells, the concentrations of 15, 25 and 35 μL of AFB1 were added to the culture in quadruplicate and incubated for 8 hours. Cellular cytotoxicity was examined using standard colorimetric assay and finally, any change in the morphology of the cells was studied by microscopic technique. Results: Microscopic investigations showed necrosis of the AFB1-exposed cells compared to the control cells. Also, bovine mammary epithelial cells were significantly affected by AFB1 in dose and time dependent manner in cell viability assays. Conclusion: According to the results, it seems that AFB1 can induce cytotoxicity and necrosis in bovine mammary epithelial cells.

  2. 3D printed sample holder for in-operando EPR spectroscopy on high temperature polymer electrolyte fuel cells

    Niemöller, Arvid; Jakes, Peter; Kayser, Steffen; Lin, Yu; Lehnert, Werner; Granwehr, Josef

    2016-08-01

    Electrochemical cells contain electrically conductive components, which causes various problems if such a cell is analyzed during operation in an EPR resonator. The optimum cell design strongly depends on the application and it is necessary to make certain compromises that need to be individually arranged. Rapid prototyping presents a straightforward option to implement a variable cell design that can be easily adapted to changing requirements. In this communication, it is demonstrated that sample containers produced by 3D printing are suitable for EPR applications, with a particular emphasis on electrochemical applications. The housing of a high temperature polymer electrolyte fuel cell (HT-PEFC) with a phosphoric acid doped polybenzimidazole membrane was prepared from polycarbonate by 3D printing. Using a custom glass Dewar, this fuel cell could be operated at temperatures up to 140 °C in a standard EPR cavity. The carbon-based gas diffusion layer showed an EPR signal with a characteristic Dysonian line shape, whose evolution could be monitored in-operando in a non-invasive manner.

  3. 3D printed sample holder for in-operando EPR spectroscopy on high temperature polymer electrolyte fuel cells.

    Niemöller, Arvid; Jakes, Peter; Kayser, Steffen; Lin, Yu; Lehnert, Werner; Granwehr, Josef

    2016-08-01

    Electrochemical cells contain electrically conductive components, which causes various problems if such a cell is analyzed during operation in an EPR resonator. The optimum cell design strongly depends on the application and it is necessary to make certain compromises that need to be individually arranged. Rapid prototyping presents a straightforward option to implement a variable cell design that can be easily adapted to changing requirements. In this communication, it is demonstrated that sample containers produced by 3D printing are suitable for EPR applications, with a particular emphasis on electrochemical applications. The housing of a high temperature polymer electrolyte fuel cell (HT-PEFC) with a phosphoric acid doped polybenzimidazole membrane was prepared from polycarbonate by 3D printing. Using a custom glass Dewar, this fuel cell could be operated at temperatures up to 140°C in a standard EPR cavity. The carbon-based gas diffusion layer showed an EPR signal with a characteristic Dysonian line shape, whose evolution could be monitored in-operando in a non-invasive manner. PMID:27323280

  4. 3D dynamic simulations of spontaneous rupture propagation governed by different constitutive laws with rake rotation allowed

    M. Cocco

    2005-06-01

    Full Text Available In this work we present a 3D Finite Difference numerical method to model the dynamic spontaneous propagation of an earthquake rupture on planar faults in an elastic half-space. We implement the Traction-at-Split-Nodes fault boundary condition for a system of faults, either vertical or oblique, using different constitutive laws. We can adopt both a slip-weakening law to prescribe the traction evolution within the breakdown zone or rate- and state-dependent friction laws, which involve the choice of an evolution relation for the state variable. Our numerical procedure allows the use of oblique and heterogeneous distribution of initial stress and allows the rake rotation. This implies that the two components of slip velocity and total dynamic traction are coupled together to satisfy, in norm, the adopted constitutive law. The simulations presented in this study show that the rupture acceleration to super-shear crack speeds occurs along the direction of the imposed initial stress; the rupture front velocity along the perpendicular direction is slower than that along the pre-stress direction. Depending on the position on the fault plane the orientation of instantaneous total dynamic traction can change with time with respect to the imposed initial stress direction. These temporal rake rotations depend on the amplitude of initial stress and on its distribution on the fault plane. They also depend on the curvature and direction of the rupture front with respect to the imposed initial stress direction: this explains why rake rotations are mostly located near the rupture front and within the cohesive zone.

  5. Mesenchymal stem cell-induced 3D displacement field of cell-adhesion matrices with differing elasticities.

    Morita, Yasuyuki; Kawase, Naoki; Ju, Yang; Yamauchi, Takashi

    2016-07-01

    Cells maintain homeostasis and perform various functions by interacting mechanically with a cell-adhesive matrix. Regarding cellular differentiation, it has been found that matrix elasticity can determine the differentiation lineage of mesenchymal stem cells (MSCs). Direct quantitative measurements of the mechanical interaction between MSCs and matrix for differentiation, however, have yet to be reported. Herein, the displacement field of the cell-adhesive matrix was observed quantitatively using a digital volume correlation (DVC) method. Maximum displacement and cellular traction stress were analyzed when the MSC differentiated into a neuron-like cell or an osteoblast-like cell on a soft or hard elastic matrix, respectively. The function of non-muscle myosin II (NMM II), which plays an important role in intracellular cytoskeletal dynamics, was investigated during cellular differentiation. The mechanical interaction (maximum displacement and subjected area of the matrix) between the cell and matrix was dependent on matrix elasticity. It has also been shown that the mechanical interaction between the intracellular cytoskeleton and cell-adhesion matrix is indispensable for cellular differentiation. This work provides the first quantitative visualization of the mechanical interaction between MSCs and the cell-adhesion matrix for differentiation. PMID:26945874

  6. Super-resolved 3-D imaging of live cells organelles from bright-field photon transmission micrographs

    Rychtarikova, Renata; Shi, Kevin; Malakhova, Daria; Machacek, Petr; Smaha, Rebecca; Urban, Jan; Stys, Dalibor

    2016-01-01

    Current biological and medical research is aimed at obtaining a detailed spatiotemporal map of a live cell's interior to describe and predict cell's physiological state. We present here an algorithm for complete 3-D modelling of cellular structures from a z-stack of images obtained using label-free wide-field bright-field light-transmitted microscopy. The method visualizes 3-D objects with a volume equivalent to the area of a camera pixel multiplied by the z-height. The computation is based on finding pixels of unchanged intensities between two consecutive images of an object spread function. These pixels represent strongly light-diffracting, light-absorbing, or light-emitting objects. To accomplish this, variables derived from R\\'{e}nyi entropy are used to suppress camera noise. Using this algorithm, the detection limit of objects is only limited by the technical specifications of the microscope setup--we achieve the detection of objects of the size of one camera pixel. This method allows us to obtain 3-D re...

  7. Electricity Generation with the Novel 3D Electrode from Swim Wastewater in a Dual-chamber Microbial Fuel Cell

    Lai Mei-Feng

    2016-01-01

    Full Text Available The swine wastewater has the characteristics of high concentration of organic matter, suspended solids and more high ammonia nitrogen, odor, complex pollution ingredient and large emissions. Microbial fuel cells (MFC is an electrochemical and biological systems related to chemical energy into electrical energy. A two-chambered cubic microbial fuel cell was used to evaluate the effect of a novel 3D electrode which made of iron and copper on the electricity generation. The swine wastewater containing total chemical oxygen demand (TCOD 3300±300 mg/L was used as the feedstock in anode chamber, and the potassium ferricyanide was used as electron acceptor in cathode chamber. The MFC reactor was incubated with the initial pH 7.0 in a air-shaker with a temperature (ca. 35°C and 100 rpm in fed-batch mode. A fixed external resistance (R of 100 Ω was connected between the electrodes and the closed circuit potentials of the MFCs were recorded every 2 min. The results show that using iron 3D electrode has the peak electricity generation of 176 mV at the first two day and maintained the stable electricity voltage of 110 mV during the 5th to 15th days. The COD removal efficiency could reach 80%. Using copper 3D electrode only can generate the peak electricity of 33.1 mV and stable electricity of 27 mV with the COD removal efficiency of 70%.

  8. A new method to address unmet needs for extracting individual cell migration features from a large number of cells embedded in 3D volumes.

    Ivan Adanja

    Full Text Available BACKGROUND: In vitro cell observation has been widely used by biologists and pharmacologists for screening molecule-induced effects on cancer cells. Computer-assisted time-lapse microscopy enables automated live cell imaging in vitro, enabling cell behavior characterization through image analysis, in particular regarding cell migration. In this context, 3D cell assays in transparent matrix gels have been developed to provide more realistic in vitro 3D environments for monitoring cell migration (fundamentally different from cell motility behavior observed in 2D, which is related to the spread of cancer and metastases. METHODOLOGY/PRINCIPAL FINDINGS: In this paper we propose an improved automated tracking method that is designed to robustly and individually follow a large number of unlabeled cells observed under phase-contrast microscopy in 3D gels. The method automatically detects and tracks individual cells across a sequence of acquired volumes, using a template matching filtering method that in turn allows for robust detection and mean-shift tracking. The robustness of the method results from detecting and managing the cases where two cell (mean-shift trackers converge to the same point. The resulting trajectories quantify cell migration through statistical analysis of 3D trajectory descriptors. We manually validated the method and observed efficient cell detection and a low tracking error rate (6%. We also applied the method in a real biological experiment where the pro-migratory effects of hyaluronic acid (HA were analyzed on brain cancer cells. Using collagen gels with increased HA proportions, we were able to evidence a dose-response effect on cell migration abilities. CONCLUSIONS/SIGNIFICANCE: The developed method enables biomedical researchers to automatically and robustly quantify the pro- or anti-migratory effects of different experimental conditions on unlabeled cell cultures in a 3D environment.

  9. Dynamic analysis of radial force density in brushless DC motor using 3-D equivalent magnetic circuit network method

    Hur, J.; Chun, Y.D.; Lee, J.; Hyun, D.S. [Hanyang Univ., Seoul (Korea, Republic of). Dept. of Electrical Engineering

    1998-09-01

    The distribution of radial force density in brushless permanent magnet DC motor is not uniform in axial direction. The analysis of radial force density has to consider the 3-D shape of teeth and overhand, because the radial force density causes vibration and acts on the surface of teeth inconstantly. For the analysis, a new 3-D equivalent magnetic circuit network method is used to account the rotor movement without remesh. The radial force density is calculated and analyzed by Maxwell stress tensor and discrete Fourier transform (DFT) respectively. The results of 3-D equivalent magnetic circuit method have been compared with the results of 3-D FEM.

  10. 3D game environments create professional 3D game worlds

    Ahearn, Luke

    2008-01-01

    The ultimate resource to help you create triple-A quality art for a variety of game worlds; 3D Game Environments offers detailed tutorials on creating 3D models, applying 2D art to 3D models, and clear concise advice on issues of efficiency and optimization for a 3D game engine. Using Photoshop and 3ds Max as his primary tools, Luke Ahearn explains how to create realistic textures from photo source and uses a variety of techniques to portray dynamic and believable game worlds.From a modern city to a steamy jungle, learn about the planning and technological considerations for 3D modelin

  11. A New Crank Arm-Based Load Cell for the 3D Analysis of the Force Applied by a Cyclist

    Alexandre Balbinot; Cleiton Milani; Jussan da Silva Bahia Nascimento

    2014-01-01

    This report describes a new crank arm-based force platform designed to evaluate the three-dimensional force applied to the pedals by cyclists in real conditions. The force platform was designed to be fitted on a conventional competition bicycle crankset while data is transmitted wirelessly through a BluetoothTM module and also stored on a SD card. A 3D solid model is created in the SolidWorks (Dassault Systèmes SOLIDWORKS Corp.) to analyze the static and dynamic characteristics of the crank a...

  12. Quantitative 3-D imaging of eukaryotic cells using soft x-ray tomography

    Parkinson, Dilworth Y.; McDermott, Gerry; Etkin, Laurence D.; Le Gros, Mark A.; Larabell, Carolyn A.

    2008-01-01

    Imaging has long been one of the principal techniques used in biological and biomedical research. Indeed, the field of cell biology grew out of the first electron microscopy images of organelles in a cell. Since this landmark event, much work has been carried out to image and classify the organelles in eukaryotic cells using electron microscopy. Fluorescently labeled organelles can now be tracked in live cells, and recently, powerful light microscope techniques have pushed the limit of optica...

  13. 3D Imaging of mammalian cells with ion-abrasion scanning electron microscopy

    Heymann, Jurgen A. W.; Shi, Dan; Kim, Sang; Bliss, Donald; Milne, Jacqueline L. S.; Subramaniam, Sriram

    2008-01-01

    Understanding the hierarchical organization of molecules and organelles within the interior of large eukaryotic cells is a challenge of fundamental interest in cell biology. We are using ion-abrasion scanning electron microscopy (IA-SEM) to visualize this hierarchical organization in an approach that combines focused ion-beam milling with scanning electron microscopy. Here, we extend our previous studies on imaging yeast cells to image subcellular architecture in human melanoma cells and mela...

  14. A new 3D tracking method for cell mechanics investigation exploiting the capabilities of digital holography in microscopy

    Miccio, L.; Memmolo, P.; Merola, F.; Fusco, S.; Netti, P. A.; Ferraro, P.

    2014-03-01

    A method for 3D tracking has been developed exploiting Digital Holography features in Microscopy (DHM). In the framework of self-consistent platform for manipulation and measurement of biological specimen we use DHM for quantitative and completely label free analysis of samples with low amplitude contrast. Tracking capability extend the potentiality of DHM allowing to monitor the motion of appropriate probes and correlate it with sample properties. Complete 3D tracking has been obtained for the probes avoiding the amplitude refocusing in traditional tracking processes. Moreover, in biology and biomedical research fields one of the main topic is the understanding of morphology and mechanics of cells and microorganisms. Biological samples present low amplitude contrast that limits the information that can be retrieved through optical bright-field microscope measurements. The main effect on light propagating in such objects is in phase. This is known as phase-retardation or phase-shift. DHM is an innovative and alternative approach in microscopy, it's a good candidate for no-invasive and complete specimen analysis because its main characteristic is the possibility to discern between intensity and phase information performing quantitative mapping of the Optical Path Length. In this paper, the flexibility of DH is employed to analyze cell mechanics of unstained cells subjected to appropriate stimuli. DHM is used to measure all the parameters useful to understand the deformations induced by external and controlled stresses on in-vitro cells. Our configuration allows 3D tracking of micro-particles and, simultaneously, furnish quantitative phase-contrast maps. Experimental results are presented and discussed for in vitro cells.

  15. Control of Retinal Ganglion Cell Positioning and Neurite Growth: Combining 3D Printing with Radial Electrospun Scaffolds.

    Kador, Karl E; Grogan, Shawn P; Dorthé, Erik W; Venugopalan, Praseeda; Malek, Monisha F; Goldberg, Jeffrey L; D'lima, Darryl D

    2016-02-01

    Retinal ganglion cells (RGCs) are responsible for the transfer of signals from the retina to the brain. As part of the central nervous system, RGCs are unable to regenerate following injury, and implanted cells have limited capacity to orient and integrate in vivo. During development, secreted guidance molecules along with signals from extracellular matrix and the vasculature guide cell positioning, for example, around the fovea, and axon outgrowth; however, these changes are temporally regulated and are not the same in the adult. Here, we combine electrospun cell transplantation scaffolds capable of RGC neurite guidance with thermal inkjet 3D cell printing techniques capable of precise positioning of RGCs on the scaffold surface. Optimal printing parameters are developed for viability, electrophysiological function and, neurite pathfinding. Different media, commonly used to promote RGC survival and growth, were tested under varying conditions. When printed in growth media containing both brain-derived neurotrophic factor (BDNF) and ciliary neurotrophic factor (CNTF), RGCs maintained survival and normal electrophysiological function, and displayed radial axon outgrowth when printed onto electrospun scaffolds. These results demonstrate that 3D printing technology may be combined with complex electrospun surfaces in the design of future retinal models or therapies. PMID:26729061

  16. Role of Mechanical Cues in Cell Differentiation and Proliferation: A 3D Numerical Model

    Mousavi, Seyed Jamaleddin; Hamdy Doweidar, Mohamed

    2015-01-01

    Cell differentiation, proliferation and migration are essential processes in tissue regeneration. Experimental evidence confirms that cell differentiation or proliferation can be regulated according to the extracellular matrix stiffness. For instance, mesenchymal stem cells (MSCs) can differentiate to neuroblast, chondrocyte or osteoblast within matrices mimicking the stiffness of their native substrate. However, the precise mechanisms by which the substrate stiffness governs cell differentiation or proliferation are not well known. Therefore, a mechano-sensing computational model is here developed to elucidate how substrate stiffness regulates cell differentiation and/or proliferation during cell migration. In agreement with experimental observations, it is assumed that internal deformation of the cell (a mechanical signal) together with the cell maturation state directly coordinates cell differentiation and/or proliferation. Our findings indicate that MSC differentiation to neurogenic, chondrogenic or osteogenic lineage specifications occurs within soft (0.1-1 kPa), intermediate (20-25 kPa) or hard (30-45 kPa) substrates, respectively. These results are consistent with well-known experimental observations. Remarkably, when a MSC differentiate to a compatible phenotype, the average net traction force depends on the substrate stiffness in such a way that it might increase in intermediate and hard substrates but it would reduce in a soft matrix. However, in all cases the average net traction force considerably increases at the instant of cell proliferation because of cell-cell interaction. Moreover cell differentiation and proliferation accelerate with increasing substrate stiffness due to the decrease in the cell maturation time. Thus, the model provides insights to explain the hypothesis that substrate stiffness plays a key role in regulating cell fate during mechanotaxis. PMID:25933372

  17. Role of Mechanical Cues in Cell Differentiation and Proliferation: A 3D Numerical Model.

    Seyed Jamaleddin Mousavi

    Full Text Available Cell differentiation, proliferation and migration are essential processes in tissue regeneration. Experimental evidence confirms that cell differentiation or proliferation can be regulated according to the extracellular matrix stiffness. For instance, mesenchymal stem cells (MSCs can differentiate to neuroblast, chondrocyte or osteoblast within matrices mimicking the stiffness of their native substrate. However, the precise mechanisms by which the substrate stiffness governs cell differentiation or proliferation are not well known. Therefore, a mechano-sensing computational model is here developed to elucidate how substrate stiffness regulates cell differentiation and/or proliferation during cell migration. In agreement with experimental observations, it is assumed that internal deformation of the cell (a mechanical signal together with the cell maturation state directly coordinates cell differentiation and/or proliferation. Our findings indicate that MSC differentiation to neurogenic, chondrogenic or osteogenic lineage specifications occurs within soft (0.1-1 kPa, intermediate (20-25 kPa or hard (30-45 kPa substrates, respectively. These results are consistent with well-known experimental observations. Remarkably, when a MSC differentiate to a compatible phenotype, the average net traction force depends on the substrate stiffness in such a way that it might increase in intermediate and hard substrates but it would reduce in a soft matrix. However, in all cases the average net traction force considerably increases at the instant of cell proliferation because of cell-cell interaction. Moreover cell differentiation and proliferation accelerate with increasing substrate stiffness due to the decrease in the cell maturation time. Thus, the model provides insights to explain the hypothesis that substrate stiffness plays a key role in regulating cell fate during mechanotaxis.

  18. Diagnosis of breast cancer extent and enhancement patterns using 3D-dynamic MR imaging. Correlation with intraductal component

    The usefulness of 3D-dynamic MR imaging with fat suppression and magnetization transfer contrast for assessing breast cancer extent and tumor profile was evaluated in 74 breasts with 67 malignant and 7 benign lesions. We classified breast cancer by the intraductal component of the main tumor. Five histological types were assigned: type 1 (DS 0) invasive carcinoma without intraductal component, type 2 (DS 1): intraductal component is less than 50% of whole tumor, type 3 (DS 2): intraductal component is nearly equal to 50%, type 4 (DS 3): intraductal component is more than 50%, type 5 (DS 4): pure DSIC or DCIS associated with microinvasive foci. Histologic results and preoperative MR imaging were analyzed regarding tumor size and enhancement pattern for the various tumor types (DS 0, 1, 2, 3 and 4). The three tumors occult to MR imaging were two DCIS and one Paget's disease. The other 64 breast cancers were detected on MR imaging. Tumor size measured with MR imaging correlated closely with histologic measurement in DS 0, 1 and 2, whereas less accuracy was noted in DS 3 and 4. Rapid enhancement was frequently seen in DS 0, 1, 2 and 3. Peripheral enhancement was highly specific for breast cancer. However, peripheral enhancement was not found in all cases of DS 4. Linear and nodular enhancement was frequently seen in DS 3 and 4. MR imaging was useful in predicting the intraductal component. (author)

  19. 3D Gas Dynamic Simulation of the Interaction Between the Exoplanet WASP-12b and Its Host Star

    Bisikalo, D; Ionov, D; Shematovich, V; Lammer, H; Fossati, L

    2012-01-01

    HST transit observations in the near-UV performed in 2009 made WASP-12b one of the most "mysterious" exoplanets; the system presents an early-ingress, which can be explained by the presence of optically thick matter located ahead of the planet at a distance of 4-5 planet radii. This work follows previous attempts to explain this asymmetry with an exospheric outflow or a bow shock, induced by a planetary magnetic field, and provides a numerical solution of the early-ingress, though we did not perform any radiative transfer calculation. We performed pure 3D gas dynamic simulations of the plasma interaction between WASP-12b and its host star, and describe the flow pattern in the system. In particular, we show that the overfilling of the planet's Roche lobe leads to a noticeable outflow from the upper atmosphere in the direction of the L1 and L2 points. Due to the conservation of the angular momentum, the flow to the L1 point is deflected in the direction of the planet's orbital motion, while the flow towards L2 ...

  20. Radionuclide Transport and Uptake in Coastal Aquatic Ecosystems: A Comparison of a 3D Dynamic Model and a Compartment Model

    In safety assessments of underground radioactive waste repositories, understanding radionuclide fate in ecosystems is necessary to determine the impacts of potential releases. Here, the reliability of two mechanistic models (the compartmental K-model and the 3D dynamic D-model) in describing the fate of radionuclides released into a Baltic Sea bay is tested. Both are based on ecosystem models that simulate the cycling of organic matter (carbon). Radionuclide transfer is linked to adsorption and flows of carbon in food chains. Accumulation of Th-230, Cs-135, and Ni-59 in biological compartments was comparable between the models and site measurements despite differences in temporal resolution, biological state variables, and partition coefficients. Both models provided confidence limits for their modeled concentration ratios, an improvement over models that only estimate means. The D-model enables estimates at high spatio-temporal resolution. The K-model, being coarser but faster, allows estimates centuries ahead. Future developments could integrate the two models to take advantage of their respective strengths

  1. Optimization design of the coating furnace by 3-d simulation of spouted bed dynamics in the coater

    Liu, Malin, E-mail: liumalin@tsinghua.edu.cn; Liu, Bing; Shao, Youlin; Wang, Jing

    2014-05-01

    The 3-d Euler–Euler CFD simulation was adopted to study the particle dynamics in the spouted bed under different operation conditions and different gas inlet structures (traditional single-nozzle inlet, modified single-nozzle inlet, multi-nozzle inlet and swirl flow design inlet). The maximum spouted height is mainly determined by the gas velocity. The simulation results were in good agreement with the experimental results in spouted bed with traditional single-nozzle inlet. The gas velocity increase will also reduce the volume of particle clusters in spouted bed with multi-nozzle inlet. By comparing simulation results, the multi-nozzle inlet and special swirl flow design inlet is better than single nozzle inlet for obtaining a more uniform fluidization state, which can disperse the gas to increase the gas–particle contact efficiency. The specially swirl flow design can reduce the accumulation of solid particles close to the wall further, especially at the bottom of the spouted bed. The experimental study should be given to validate the superiority of this newly swirl flow design inlet before the industrial application in the future.

  2. Readily Accessible Multiplane Microscopy: 3D Tracking the HIV-1 Genome in Living Cells.

    Itano, Michelle S; Bleck, Marina; Johnson, Daniel S; Simon, Sanford M

    2016-02-01

    Human immunodeficiency virus (HIV)-1 infection and the associated disease AIDS are a major cause of human death worldwide with no vaccine or cure available. The trafficking of HIV-1 RNAs from sites of synthesis in the nucleus, through the cytoplasm, to sites of assembly at the plasma membrane are critical steps in HIV-1 viral replication, but are not well characterized. Here we present a broadly accessible microscopy method that captures multiple focal planes simultaneously, which allows us to image the trafficking of HIV-1 genomic RNAs with high precision. This method utilizes a customization of a commercial multichannel emission splitter that enables high-resolution 3D imaging with single-macromolecule sensitivity. We show with high temporal and spatial resolution that HIV-1 genomic RNAs are most mobile in the cytosol, and undergo confined mobility at sites along the nuclear envelope and in the nucleus and nucleolus. These provide important insights regarding the mechanism by which the HIV-1 RNA genome is transported to the sites of assembly of nascent virions. PMID:26567131

  3. Modelling of river plume dynamics in Öre estuary (Baltic Sea) with Telemac-3D hydrodynamic model

    Sokolov, Alexander

    2016-04-01

    The main property of river plumes is their buoyancy, fresh water discharged by rivers is less dense than the receiving, saline waters. To study the processes of plume formation in case of river discharge into a brackish estuary where salinity is low (3.5 - 5 psu) a three dimensional hydrodynamic model was applied to the Öre estuary in the Baltic Sea. This estuary is a small fjord-like bay in the north part of the Baltic Sea. Size of the bay is about 8 by 8 km with maximum depth of 35 metres. River Öre has a small average freshwater discharge of 35 m3/s. But in spring during snowmelt the discharge can be many times higher. For example, in April 2015 the discharge increased from 8 m3/s to 160 m3/s in 18 days. To study river plume dynamics a finite element based three dimensional baroclinic model TELEMAC - 3D is used. The TELEMAC modelling suite is developed by the National Laboratory of Hydraulics and Environment (LNHE) of Electricité de France (EDF). Modelling domain was approximated by an unstructured mesh with element size varies from 50 to 500 m. In vertical direction a sigma-coordinate with 20 layers was used. Open sea boundary conditions were obtained from the Baltic Sea model HIROMB-BOOS using COPERNICUS marine environment monitoring service. Comparison of modelling results with observations obtained by BONUS COCOA project's field campaign in Öre estuary in 2015 shows that the model plausible simulate river plume dynamics. Modelling of age of freshwater is also discussed. This work resulted from the BONUS COCOA project was supported by BONUS (Art 185), funded jointly by the EU and the Swedish Research Council Formas.

  4. Development of a 3D coculture system to study adipocyte and lymph node cell interactions

    Daya, S.; Loughlin, J.; MacQueen, H.

    2006-01-01

    We have developed a long term 3-dimensional coculture system with adipocytes and lymph node cells for the purpose of investigating interactions between these cells in vitro. Present experimental work with the culture system is aimed at introducing lymph node cells, in proportions similar to those found in intact lymph nodes, among differentiated adipocytes and observing interactions and the establishment of a spatial relationship between them. Co-cultures will be used to investigate the ly...

  5. 3D Texture Analysis in Renal Cell Carcinoma Tissue Image Grading

    Tae-Yun Kim; Nam-Hoon Cho; Goo-Bo Jeong; Ewert Bengtsson; Heung-Kook Choi

    2014-01-01

    One of the most significant processes in cancer cell and tissue image analysis is the efficient extraction of features for grading purposes. This research applied two types of three-dimensional texture analysis methods to the extraction of feature values from renal cell carcinoma tissue images, and then evaluated the validity of the methods statistically through grade classification. First, we used a confocal laser scanning microscope to obtain image slices of four grades of renal cell carcin...

  6. Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy.

    Höhn, K; Fuchs, J; Fröber, A; Kirmse, R; Glass, B; Anders-Össwein, M; Walther, P; Kräusslich, H-G; Dietrich, C

    2015-08-01

    In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily be identified and imaged by state of the art 3D confocal fluorescence microscopy and are precisely referenced with respect to an imprinted coordinate system on the surface of the resin block. This allows precise guidance of the focused ion beam assisted scanning electron microscopy and limits the volume to be imaged to the structure of interest. This, in turn, minimizes the total acquisition time necessary to conduct the time consuming ultrastructural scanning electron microscope imaging while eliminating the risk to miss parts of the target structure. We illustrate the value of this workflow for targeting virus compartments, which are formed in HIV-pulsed mature human dendritic cells. PMID:25786567

  7. Enabling Lorentz boosted frame particle-in-cell simulations of laser wakefield acceleration in quasi-3D geometry

    Yu, Peicheng; Xu, Xinlu; Davidson, Asher; Tableman, Adam; Dalichaouch, Thamine; Li, Fei; Meyers, Michael D.; An, Weiming; Tsung, Frank S.; Decyk, Viktor K.; Fiuza, Frederico; Vieira, Jorge; Fonseca, Ricardo A.; Lu, Wei; Silva, Luis O.; Mori, Warren B.

    2016-07-01

    When modeling laser wakefield acceleration (LWFA) using the particle-in-cell (PIC) algorithm in a Lorentz boosted frame, the plasma is drifting relativistically at βb c towards the laser, which can lead to a computational speedup of ∼ γSUB>/bSUB>2 = (1 -space-time distribution of the LWFA data in the lab and boosted frame, we propose to use a moving window to follow the drifting plasma, instead of following the laser driver as is done in the LWFA lab frame simulations, in order to further reduce the computational loads. We describe the details of how the NCI is mitigated for the quasi-3D geometry, the setups for simulations which combine the Lorentz boosted frame, quasi-3D geometry, and the use of a moving window, and compare the results from these simulations against their corresponding lab frame cases. Good agreement is obtained among these sample simulations, particularly when there is no self-trapping, which demonstrates it is possible to combine the Lorentz boosted frame and the quasi-3D algorithms when modeling LWFA. We also discuss the preliminary speedups achieved in these sample simulations.

  8. Fabrication of solution processed 3D nanostructured CuInGaS2 thin film solar cells

    In this study we demonstrate the fabrication of CuInGaS2 (CIGS) thin film solar cells with a three-dimensional (3D) nanostructure based on indium tin oxide (ITO) nanorod films and precursor solutions (Cu, In and Ga nitrates in alcohol). To obtain solution processed 3D nanostructured CIGS thin film solar cells, two different precursor solutions were applied to complete gap filling in ITO nanorods and achieve the desirable absorber film thickness. Specifically, a coating of precursor solution without polymer binder material was first applied to fill the gap between ITO nanorods followed by deposition of the second precursor solution in the presence of a binder to generate an absorber film thickness of ∼1.3 μm. A solar cell device with a (Al, Ni)/AZO/i-ZnO/CdS/CIGS/ITO nanorod/glass structure was constructed using the CIGS film, and the highest power conversion efficiency was measured to be ∼6.3% at standard irradiation conditions, which was 22.5% higher than the planar type of CIGS solar cell on ITO substrate fabricated using the same precursor solutions. (paper)

  9. Electric transport in 3D photonic crystal intermediate reflectors for micromorph thin-film tandem solar cells

    Üpping, J.; Bielawny, A.; Lee, S.; Knez, M.; Carius, R.; Wehrspohn, R. B.

    2009-08-01

    The progress of 3D photonic intermediate reflectors for micromorph silicon tandem cells towards a first prototype cell is presented. Intermediate reflectors enhance the absorption of spectrally-selected light in the top cell and decrease the current mismatch between both junctions. A numerical method to predict filter properties for optimal current matching is presented. Our device is an inverted opal structure made of ZnO and fabricated using self-organized nanoparticles and atomic layer deposition for conformal coating. In particular, the influence of ZnO-doping and replicated cracks during drying of the opal is discussed with respect to conductivity and optical properties. A first prototype is compared to a state-of-the-art reference cell.

  10. Biofabrication of tissue constructs by 3D bioprinting of cell-laden microcarriers

    Bioprinting allows the fabrication of living constructs with custom-made architectures by spatially controlled deposition of multiple bioinks. This is important for the generation of tissue, such as osteochondral tissue, which displays a zonal composition in the cartilage domain supported by the underlying subchondral bone. Challenges in fabricating functional grafts of clinically relevant size include the incorporation of cues to guide specific cell differentiation and the generation of sufficient cells, which is hard to obtain with conventional cell culture techniques. A novel strategy to address these demands is to combine bioprinting with microcarrier technology. This technology allows for the extensive expansion of cells, while they form multi-cellular aggregates, and their phenotype can be controlled. In this work, living constructs were fabricated via bioprinting of cell-laden microcarriers. Mesenchymal stromal cell (MSC)-laden polylactic acid microcarriers, obtained via static culture or spinner flask expansion, were encapsulated in gelatin methacrylamide-gellan gum bioinks, and the printability of the composite material was studied. This bioprinting approach allowed for the fabrication of constructs with high cell concentration and viability. Microcarrier encapsulation improved the compressive modulus of the hydrogel constructs, facilitated cell adhesion, and supported osteogenic differentiation and bone matrix deposition by MSCs. Bilayered osteochondral models were fabricated using microcarrier-laden bioink for the bone compartment. These findings underscore the potential of this new microcarrier-based biofabrication approach for bone and osteochondral constructs. (paper)

  11. Osteogenic Differentiation of Miniature Pig Mesenchymal Stem Cells in 2D and 3D Environment

    Juhásová, Jana; Juhás, Štefan; Klíma, Jiří; Strnádel, Ján; Holubová, Monika; Motlík, Jan

    2011-01-01

    Roč. 60, č. 3 (2011), s. 559-571. ISSN 0862-8408 R&D Projects: GA MŠk 1M0538; GA MŠk 2B06130 Institutional research plan: CEZ:AV0Z50450515 Keywords : miniature pig * mesenchymal stem cells * cell differentiation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.555, year: 2011

  12. Dose distribution and tumor control probability in out-of-field lymph node stations in intensity modulated radiotherapy (IMRT) vs 3D-conformal radiotherapy (3D-CRT) of non-small-cell lung cancer: an in silico analysis

    The advent of IMRT and image-guided radiotherapy (IGRT) in combination with involved-field radiotherapy (IF-RT) in inoperable non-small-cell lung cancer results in a decreased incidental dose deposition in elective nodal stations. While incidental nodal irradiation is considered a relevant by-product of 3D-CRT to control microscopic disease this planning study analyzed the impact of IMRT on dosimetric parameters and tumor control probabilities (TCP) in elective nodal s