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Sample records for 3d dynamic cell

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

    Science.gov (United States)

    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

    Science.gov (United States)

    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. Brownian nanoimaging of interface dynamics and ligand-receptor binding at cell surfaces in 3-D.

    Science.gov (United States)

    Kuznetsov, Igor R; Evans, Evan A

    2013-04-01

    We describe a method for nanoimaging interfacial dynamics and ligand-receptor binding at surfaces of live cells in 3-D. The imaging probe is a 1-μm diameter glass bead confined by a soft laser trap to create a "cloud" of fluctuating states. Using a facile on-line method of video image analysis, the probe displacements are reported at ~10 ms intervals with bare precisions (±SD) of 4-6 nm along the optical axis (elevation) and 2 nm in the transverse directions. We demonstrate how the Brownian distributions are analyzed to characterize the free energy potential of each small probe in 3-D taking into account the blur effect of its motions during CCD image capture. Then, using the approach to image interactions of a labeled probe with lamellae of leukocytic cells spreading on cover-glass substrates, we show that deformations of the soft distribution in probe elevations provide both a sensitive long-range sensor for defining the steric topography of a cell lamella and a fast telemetry for reporting rare events of probe binding with its surface receptors. Invoking established principles of Brownian physics and statistical thermodynamics, we describe an off-line method of super resolution that improves precision of probe separations from a non-reactive steric boundary to ~1 nm.

  4. Dynamic, large-scale profiling of transcription factor activity from live cells in 3D culture.

    Directory of Open Access Journals (Sweden)

    Michael S Weiss

    Full Text Available BACKGROUND: Extracellular activation of signal transduction pathways and their downstream target transcription factors (TFs are critical regulators of cellular processes and tissue development. The intracellular signaling network is complex, and techniques that quantify the activities of numerous pathways and connect their activities to the resulting phenotype would identify the signals and mechanisms regulating tissue development. The ability to investigate tissue development should capture the dynamic pathway activity and requires an environment that supports cellular organization into structures that mimic in vivo phenotypes. Taken together, our objective was to develop cellular arrays for dynamic, large-scale quantification of TF activity as cells organized into spherical structures within 3D culture. METHODOLOGY/PRINCIPAL FINDINGS: TF-specific and normalization reporter constructs were delivered in parallel to a cellular array containing a well-established breast cancer cell line cultured in Matrigel. Bioluminescence imaging provided a rapid, non-invasive, and sensitive method to quantify luciferase levels, and was applied repeatedly on each sample to monitor dynamic activity. Arrays measuring 28 TFs identified up to 19 active, with 13 factors changing significantly over time. Stimulation of cells with β-estradiol or activin A resulted in differential TF activity profiles evolving from initial stimulation of the ligand. Many TFs changed as expected based on previous reports, yet arrays were able to replicate these results in a single experiment. Additionally, arrays identified TFs that had not previously been linked with activin A. CONCLUSIONS/SIGNIFICANCE: This system provides a method for large-scale, non-invasive, and dynamic quantification of signaling pathway activity as cells organize into structures. The arrays may find utility for investigating mechanisms regulating normal and abnormal tissue growth, biomaterial design, or as a

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  7. 3D-dynamic visualization of complex molecular cell biology processes : 1-year university students' understanding of visualizations of signal transduction

    OpenAIRE

    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...

  8. 3D culture for cardiac cells.

    Science.gov (United States)

    Zuppinger, Christian

    2016-07-01

    This review discusses historical milestones, recent developments and challenges in the area of 3D culture models with cardiovascular cell types. Expectations in this area have been raised in recent years, but more relevant in vitro research, more accurate drug testing results, reliable disease models and insights leading to bioartificial organs are expected from the transition to 3D cell culture. However, the construction of organ-like cardiac 3D models currently remains a difficult challenge. The heart consists of highly differentiated cells in an intricate arrangement.Furthermore, electrical “wiring”, a vascular system and multiple cell types act in concert to respond to the rapidly changing demands of the body. Although cardiovascular 3D culture models have been predominantly developed for regenerative medicine in the past, their use in drug screening and for disease models has become more popular recently. Many sophisticated 3D culture models are currently being developed in this dynamic area of life science. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.

  9. Recognition of 3D facial expression dynamics

    NARCIS (Netherlands)

    Sandbach, G.; Zafeiriou, S.; Pantic, Maja; Rueckert, D.

    2012-01-01

    In this paper we propose a method that exploits 3D motion-based features between frames of 3D facial geometry sequences for dynamic facial expression recognition. An expressive sequence is modelled to contain an onset followed by an apex and an offset. Feature selection methods are applied in order

  10. High-Throughput Cancer Cell Sphere Formation for Characterizing the Efficacy of Photo Dynamic Therapy in 3D Cell Cultures

    Science.gov (United States)

    Chen, Yu-Chih; Lou, Xia; Zhang, Zhixiong; Ingram, Patrick; Yoon, Euisik

    2015-07-01

    Photodynamic therapy (PDT), wherein light sensitive non-toxic agents are locally and selectively activated using light, has emerged as an appealing alternative to traditional cancer chemotherapy. Yet to date, PDT efficacy has been mostly characterized using 2D cultures. Compared to 2D cultures, 3D sphere culture generates unique spatial distributions of nutrients and oxygen for the cells that better mimics the in-vivo conditions. Using a novel polyHEMA (non-adherent polymer) fabrication process, we developed a microfluidic sphere formation platform that can (1) generate 1,024 uniform (size variation cancer spheres within a 2 cm by 2 cm core area, (2) culture spheres for more than 2 weeks, and (3) allow the retrieval of spheres. Using the presented platform, we have successfully characterized the different responses in 2D and 3D cell culture to PDT. Furthermore, we investigated the treatment resistance effect in cancer cells induced by tumor associated fibroblasts (CAF). Although the CAFs can enhance the resistance to traditional chemotherapy agents, no significant difference in PDT was observed. The preliminary results suggest that the PDT can be an attractive alternative cancer therapy, which is less affected by the therapeutic resistance induced by cancer associated cells.

  11. The reactor dynamics code DYN3D

    Energy Technology Data Exchange (ETDEWEB)

    Kliem, Soeren; Bilodid, Yuri; Fridman, Emil; Baier, Silvio; Grahn, Alexander; Gommlich, Andre; Nikitin, Evgeny; Rohde, Ulrich [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany)

    2016-05-15

    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.

  12. The reactor dynamics code DYN3D

    International Nuclear Information System (INIS)

    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.

  13. Rendering of 3D Dynamic Virtual Environments

    CERN Document Server

    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.

  14. 3D blob dynamics in toroidal geometry

    DEFF Research Database (Denmark)

    Nielsen, Anders Henry; Reiser, Dirk

    In this paper we study the simple case of the dynamics of a density perturbation localized in the edge region of a medium sized tokamak in a full 3D geometry. The 2D evolution of such a perturbation has been studied in details on the low-field side, where the gradient of the magnetic field always...... dynamics in a full 3D tokamak geometry including the edge and SOL region as well. Previous studies with the ATTEMPT code proved that density blobs appear for typical parameters in the TEXTOR tokamak. The code has been prepared for flux driven simulations with detailed control of the blob initial state....... The 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...

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

    Science.gov (United States)

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

    2012-10-01

    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 rat osteoblasts or bone marrow stromal cells (BMSC) were implanted on uniform-sized biphasic calcium phosphate (BCP) scaffolds produced by a 3D printing method. Three types of culture conditions were applied: static culture without osteoinduction (Group A); static culture with osteoinduction (Group B); dynamic culture with osteoinduction (Group C). After 3 and 6 weeks, the scaffolds were analysed by alkaline phosphatase (ALP), dsDNA amount, SEM, fluorescent labelled live-dead assay, and real-time RT-PCR in addition to weekly alamarBlue assays. With osteoinduction, increased ALP values and calcium deposition are observed; however, under static conditions, a significant decrease in the cell number on the biomaterial is observed. Interestingly, the bioreactor system not only reversed the decreased cell numbers but also increased their differentiation potential. We conclude from this study that a continuous flow bioreactor not only preserves the number of osteogenic cells but also keeps their differentiation ability in balance providing a suitable cell-seeded scaffold product for applications in regenerative medicine.

  16. INCORPORATING DYNAMIC 3D SIMULATION INTO PRA

    Energy Technology Data Exchange (ETDEWEB)

    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.

  17. Dynamic stall and 3D effects

    Energy Technology Data Exchange (ETDEWEB)

    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

  18. A dynamic 3D foot reconstruction system.

    Science.gov (United States)

    Thabet, Ali K; Trucco, Emanuele; Salvi, Joaquim; Wang, Weijie; Abboud, Rami J

    2011-01-01

    Foot problems are varied and range from simple disorders through to complex diseases and joint deformities. Wherever possible, the use of insoles, or orthoses, is preferred over surgery. Current insole design techniques are based on static measurements of the foot, despite the fact that orthoses are prevalently used in dynamic conditions while walking or running. This paper presents the design and implementation of a structured-light prototype system providing dense three dimensional (3D) measurements of the foot in motion, and its use to show that foot measurements in dynamic conditions differ significantly from their static counterparts. 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. Engineering and clinical tests were carried out for the validation of the system. The accuracy of the system was found to be 0.34 mm with planar test objects. In tests with real feet, the system proved repeatable, with reconstruction differences between trials one week apart averaging 2.44 mm (static case) and 2.81 mm (dynamic case). Furthermore, a study was performed to compare the effective length of the foot between static and dynamic reconstructions using the 4D system. Results showed an average increase of 9 mm for the dynamic case. This increase is substantial for orthotics design, cannot be captured by a static system, and its subject-specific measurement is crucial for the design of effective foot orthoses.

  19. Dynamics of 3D isolated thermal filaments

    CERN Document Server

    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.

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

    CERN Document Server

    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'...

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

    Science.gov (United States)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    International Nuclear Information System (INIS)

    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.

  4. Laser printing of cells into 3D scaffolds

    International Nuclear Information System (INIS)

    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.

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

    International Nuclear Information System (INIS)

    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)

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

    Science.gov (United States)

    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. 3d Lorentzian, dynamically triangulated quantum gravity

    OpenAIRE

    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.

  8. Tissuelike 3D Assemblies of Human Broncho-Epithelial Cells

    Science.gov (United States)

    Goodwin, Thomas J.

    2010-01-01

    Three-dimensional (3D) tissuelike assemblies (TLAs) of human broncho-epithelial (HBE) cells have been developed for use in in vitro research on infection of humans by respiratory viruses. The 2D monolayer HBE cell cultures heretofore used in such research lack the complex cell structures and interactions characteristic of in vivo tissues and, consequently, do not adequately emulate the infection dynamics of in-vivo microbial adhesion and invasion. In contrast, the 3D HBE TLAs are characterized by more-realistic reproductions of the geometrical and functional complexity, differentiation of cells, cell-to-cell interactions, and cell-to-matrix interactions characteristic of human respiratory epithelia. Hence, the 3D HBE TLAs are expected to make it possible to perform at least some of the research in vitro under more-realistic conditions, without need to infect human subjects. The TLAs are grown on collagen-coated cyclodextran microbeads under controlled conditions in a nutrient liquid in the simulated microgravitational environment of a bioreactor of the rotating- wall-vessel type. Primary human mesenchymal bronchial-tracheal cells are used as a foundation matrix, while adult human bronchial epithelial immortalized cells are used as the overlying component. The beads become coated with cells, and cells on adjacent beads coalesce into 3D masses. The resulting TLAs have been found to share significant characteristics with in vivo human respiratory epithelia including polarization, tight junctions, desmosomes, and microvilli. The differentiation of the cells in these TLAs into tissues functionally similar to in vivo tissues is confirmed by the presence of compounds, including villin, keratins, and specific lung epithelium marker compounds, and by the production of tissue mucin. In a series of initial infection tests, TLA cultures were inoculated with human respiratory syncytial viruses and parainfluenza type 3 viruses. Infection was confirmed by photomicrographs that

  9. Dynamic 3D echocardiography in virtual reality

    Directory of Open Access Journals (Sweden)

    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.

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

    International Nuclear Information System (INIS)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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

  12. Dynamic contrast-enhanced 3D photoacoustic imaging

    Science.gov (United States)

    Wong, Philip; Kosik, Ivan; Carson, Jeffrey J. L.

    2013-03-01

    Photoacoustic imaging (PAI) is a hybrid imaging modality that integrates the strengths from both optical imaging and acoustic imaging while simultaneously overcoming many of their respective weaknesses. In previous work, we reported on a real-time 3D PAI system comprised of a 32-element hemispherical array of transducers. Using the system, we demonstrated the ability to capture photoacoustic data, reconstruct a 3D photoacoustic image, and display select slices of the 3D image every 1.4 s, where each 3D image resulted from a single laser pulse. The present study aimed to exploit the rapid imaging speed of an upgraded 3D PAI system by evaluating its ability to perform dynamic contrast-enhanced imaging. The contrast dynamics can provide rich datasets that contain insight into perfusion, pharmacokinetics and physiology. We captured a series of 3D PA images of a flow phantom before and during injection of piglet and rabbit blood. Principal component analysis was utilized to classify the data according to its spatiotemporal information. The results suggested that this technique can be used to separate a sequence of 3D PA images into a series of images representative of main features according to spatiotemporal flow dynamics.

  13. Critical bifurcation surfaces of 3D discrete dynamics

    Directory of Open Access Journals (Sweden)

    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. 3D in vitro cell culture models of tube formation.

    Science.gov (United States)

    Zegers, Mirjam M

    2014-07-01

    Building the complex architecture of tubular organs is a highly dynamic process that involves cell migration, polarization, shape changes, adhesion to neighboring cells and the extracellular matrix, physicochemical characteristics of the extracellular matrix and reciprocal signaling with the mesenchyme. Understanding these processes in vivo has been challenging as they take place over extended time periods deep within the developing organism. Here, I will discuss 3D in vitro models that have been crucial to understand many of the molecular and cellular mechanisms and key concepts underlying branching morphogenesis in vivo. PMID:24613912

  15. 3D particle tracking velocimetry using dynamic discrete tomography

    NARCIS (Netherlands)

    Alpers, A.; Gritzmann, P.; Moseev, D.; Salewski, M.

    2015-01-01

    Particle tracking velocimetry in 3D is becoming an increasingly important imaging tool in the study of fluid dynamics and combustion as well as plasmas. We introduce a dynamic discrete tomography algorithm for reconstructing particle trajectories from projections. The algorithm is efficient for data

  16. 3D particle tracking velocimetry using dynamic discrete tomography

    DEFF Research Database (Denmark)

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

    2015-01-01

    Particle tracking velocimetry in 3D is becoming an increasingly important imaging tool in the study of fluid dynamics and combustion as well as plasmas. We introduce a dynamic discrete tomography algorithm for reconstructing particle trajectories from projections. The algorithm is efficient...

  17. An Evaluative Review of Simulated Dynamic Smart 3d Objects

    Science.gov (United States)

    Romeijn, H.; Sheth, F.; Pettit, C. J.

    2012-07-01

    Three-dimensional (3D) modelling of plants can be an asset for creating agricultural based visualisation products. The continuum of 3D plants models ranges from static to dynamic objects, also known as smart 3D objects. There is an increasing requirement for smarter simulated 3D objects that are attributed mathematically and/or from biological inputs. A systematic approach to plant simulation offers significant advantages to applications in agricultural research, particularly in simulating plant behaviour and the influences of external environmental factors. This approach of 3D plant object visualisation is primarily evident from the visualisation of plants using photographed billboarded images, to more advanced procedural models that come closer to simulating realistic virtual plants. However, few programs model physical reactions of plants to external factors and even fewer are able to grow plants based on mathematical and/or biological parameters. In this paper, we undertake an evaluation of plant-based object simulation programs currently available, with a focus upon the components and techniques involved in producing these objects. Through an analytical review process we consider the strengths and weaknesses of several program packages, the features and use of these programs and the possible opportunities in deploying these for creating smart 3D plant-based objects to support agricultural research and natural resource management. In creating smart 3D objects the model needs to be informed by both plant physiology and phenology. Expert knowledge will frame the parameters and procedures that will attribute the object and allow the simulation of dynamic virtual plants. Ultimately, biologically smart 3D virtual plants that react to changes within an environment could be an effective medium to visually represent landscapes and communicate land management scenarios and practices to planners and decision-makers.

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

    KAUST Repository

    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

  19. Multizone paper platform for 3D cell cultures.

    Directory of Open Access Journals (Sweden)

    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.

  20. Stem cell reprogramming: A 3D boost

    Science.gov (United States)

    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.

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

    International Nuclear Information System (INIS)

    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

  2. 3D particle tracking velocimetry using dynamic discrete tomography

    CERN Document Server

    Alpers, Andreas; Moseev, Dmitry; Salewski, Mirko

    2013-01-01

    Particle tracking velocimetry in 3D is becoming an increasingly important imaging tool in the study of fluid dynamics, combustion as well as plasmas. We introduce a dynamic discrete tomography algorithm for reconstructing particle trajectories from projections. The algorithm is efficient for data from two projection directions and exact in the sense that it finds a solution consistent with the experimental data. Non-uniqueness of solutions can be detected and solutions can be tracked individually.

  3. Asymptotic dynamics in 3D gravity with torsion

    OpenAIRE

    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.

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

    Science.gov (United States)

    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.

  5. Causal Dynamical Triangulation of 3D Tensor Model

    CERN Document Server

    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. Dynamic 3D computed tomography scanner for vascular imaging

    Science.gov (United States)

    Lee, Mark K.; Holdsworth, David W.; Fenster, Aaron

    2000-04-01

    A 3D dynamic computed-tomography (CT) scanner was developed for imaging objects undergoing periodic motion. The scanner system has high spatial and sufficient temporal resolution to produce quantitative tomographic/volume images of objects such as excised arterial samples perfused under physiological pressure conditions and enables the measurements of the local dynamic elastic modulus (Edyn) of the arteries in the axial and longitudinal directions. The system was comprised of a high resolution modified x-ray image intensifier (XRII) based computed tomographic system and a computer-controlled cardiac flow simulator. A standard NTSC CCD camera with a macro lens was coupled to the electro-optically zoomed XRII to acquire dynamic volumetric images. Through prospective cardiac gating and computer synchronized control, a time-resolved sequence of 20 mm thick high resolution volume images of porcine aortic specimens during one simulated cardiac cycle were obtained. Performance evaluation of the scanners illustrated that tomographic images can be obtained with resolution as high as 3.2 mm-1 with only a 9% decrease in the resolution for objects moving at velocities of 1 cm/s in 2D mode and static spatial resolution of 3.55 mm-1 with only a 14% decrease in the resolution in 3D mode for objects moving at a velocity of 10 cm/s. Application of the system for imaging of intact excised arterial specimens under simulated physiological flow/pressure conditions enabled measurements of the Edyn of the arteries with a precision of +/- kPa for the 3D scanner. Evaluation of the Edyn in the axial and longitudinal direction produced values of 428 +/- 35 kPa and 728 +/- 71 kPa, demonstrating the isotropic and homogeneous viscoelastic nature of the vascular specimens. These values obtained from the Dynamic CT systems were not statistically different (p less than 0.05) from the values obtained by standard uniaxial tensile testing and volumetric measurements.

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

    Science.gov (United States)

    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

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

    Institute of Scientific and Technical Information of China (English)

    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

    Science.gov (United States)

    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)

    Science.gov (United States)

    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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

    CERN Document Server

    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...

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

    Directory of Open Access Journals (Sweden)

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. Modeling tree crown dynamics with 3D partial differential equations.

    Science.gov (United States)

    Beyer, Robert; Letort, Véronique; Cournède, Paul-Henry

    2014-01-01

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

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

    Science.gov (United States)

    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

  19. Analysis and dynamic 3D visualization of cerebral blood flow combining 3D and 4D MR image sequences

    Science.gov (United States)

    Forkert, Nils Daniel; Säring, Dennis; Fiehler, Jens; Illies, Till; Möller, Dietmar; Handels, Heinz

    2009-02-01

    In this paper we present a method for the dynamic visualization of cerebral blood flow. Spatio-temporal 4D magnetic resonance angiography (MRA) image datasets and 3D MRA datasets with high spatial resolution were acquired for the analysis of arteriovenous malformations (AVMs). One of the main tasks is the combination of the information of the 3D and 4D MRA image sequences. Initially, in the 3D MRA dataset the vessel system is segmented and a 3D surface model is generated. Then, temporal intensity curves are analyzed voxelwise in the 4D MRA image sequences. A curve fitting of the temporal intensity curves to a patient individual reference curve is used to extract the bolus arrival times in the 4D MRA sequences. After non-linear registration of both MRA datasets the extracted hemodynamic information is transferred to the surface model where the time points of inflow can be visualized color coded dynamically over time. The dynamic visualizations computed using the curve fitting method for the estimation of the bolus arrival times were rated superior compared to those computed using conventional approaches for bolus arrival time estimation. In summary the procedure suggested allows a dynamic visualization of the individual hemodynamic situation and better understanding during the visual evaluation of cerebral vascular diseases.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. 2D- and 3D-culture of cell

    Directory of Open Access Journals (Sweden)

    Khoruzhenko A. I.

    2011-02-01

    Full Text Available The cultivation of mammalian cells in three-dimensional conditions acquires a priority in a variety of biomedical applications. In the areas of toxicology and anticancer drug development it concerns a significant difference of responses to proapoptotic factors of the cells cultured in 2D versus 3D environment. Besides, the clear-cut differences have been found in cell polarity, cytoskeleton structure, distribution of receptors to wide range of hormones, growth factors, etc. in mammalian cells depending on culture conditions. It is resulted in different response of cultured cells to extracellular stimuli. Multicellular spheroids are regarded presently as the most convenient model of solid tumour growth in vitro. The cultivation of thyroid follicles, mammary acini and other structure units, maintaining initial tissue organization, allows studying the behavior, biochemical features and gene profile of differentiated cells. On the other hand, 3D cultures have some limitations in comparison with a well established monolayer culture. The advantages and disadvantages of each type of cultures and their application in biological and medical researches will be discussed in this review

  2. Rapid fabrication of complex 3D extracellular microenvironments by dynamic optical projection stereolithography.

    Science.gov (United States)

    Zhang, A Ping; Qu, Xin; Soman, Pranav; Hribar, Kolin C; Lee, Jin W; Chen, Shaochen; He, Sailing

    2012-08-16

    The topographic features of the extracelluar matrix (ECM) lay the foundation for cellular behavior. A novel biofabrication method using a digital-mirror device (DMD), called dynamic optical projection stereolithography (DOPsL) is demonstrated. This robust and versatile platform can generate complex biomimetic scaffolds within seconds. Such 3D scaffolds have promising potentials for studying cell interactions with microenvironments in vitro and in vivo.

  3. 3D in vitro cell culture models of tube formation

    NARCIS (Netherlands)

    Zegers, M.M.P.

    2014-01-01

    Building the complex architecture of tubular organs is a highly dynamic process that involves cell migration, polarization, shape changes, adhesion to neighboring cells and the extracellular matrix, physicochemical characteristics of the extracellular matrix and reciprocal signaling with the mesench

  4. 3D Chromosome Regulatory Landscape of Human Pluripotent Cells.

    Science.gov (United States)

    Ji, Xiong; Dadon, Daniel B; Powell, Benjamin E; Fan, Zi Peng; Borges-Rivera, Diego; Shachar, Sigal; Weintraub, Abraham S; Hnisz, Denes; Pegoraro, Gianluca; Lee, Tong Ihn; Misteli, Tom; Jaenisch, Rudolf; Young, Richard A

    2016-02-01

    In this study, we describe the 3D chromosome regulatory landscape of human naive and primed embryonic stem cells. To devise this map, we identified transcriptional enhancers and insulators in these cells and placed them within the context of cohesin-associated CTCF-CTCF loops using cohesin ChIA-PET data. The CTCF-CTCF loops we identified form a chromosomal framework of insulated neighborhoods, which in turn form topologically associating domains (TADs) that are largely preserved during the transition between the naive and primed states. Regulatory changes in enhancer-promoter interactions occur within insulated neighborhoods during cell state transition. The CTCF anchor regions we identified are conserved across species, influence gene expression, and are a frequent site of mutations in cancer cells, underscoring their functional importance in cellular regulation. These 3D regulatory maps of human pluripotent cells therefore provide a foundation for future interrogation of the relationships between chromosome structure and gene control in development and disease. PMID:26686465

  5. 3D surface topology guides stem cell adhesion and differentiation.

    Science.gov (United States)

    Viswanathan, Priyalakshmi; Ondeck, Matthew G; Chirasatitsin, Somyot; Ngamkham, Kamolchanok; Reilly, Gwendolen C; Engler, Adam J; Battaglia, Giuseppe

    2015-06-01

    Polymerized high internal phase emulsion (polyHIPE) foams are extremely versatile materials for investigating cell-substrate interactions in vitro. Foam morphologies can be controlled by polymerization conditions to result in either open or closed pore structures with different levels of connectivity, consequently enabling the comparison between 2D and 3D matrices using the same substrate with identical surface chemistry conditions. Additionally, here we achieve the control of pore surface topology (i.e. how different ligands are clustered together) using amphiphilic block copolymers as emulsion stabilizers. We demonstrate that adhesion of human mesenchymal progenitor (hES-MP) cells cultured on polyHIPE foams is dependent on foam surface topology and chemistry but is independent of porosity and interconnectivity. We also demonstrate that the interconnectivity, architecture and surface topology of the foams has an effect on the osteogenic differentiation potential of hES-MP cells. Together these data demonstrate that the adhesive heterogeneity of a 3D scaffold could regulate not only mesenchymal stem cell attachment but also cell behavior in the absence of soluble growth factors.

  6. A novel mechanotactic 3D modeling of cell morphology

    International Nuclear Information System (INIS)

    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)

  7. Peptide hydrogels – versatile matrices for 3D cell culture in cancer medicine

    Directory of Open Access Journals (Sweden)

    Peter eWorthington

    2015-04-01

    Full Text Available Traditional two-dimensional (2D cell culture systems have contributed tremendously to our understanding of cancer biology but have significant limitations in mimicking in vivo conditions such as the tumor microenvironment. In vitro, three-dimensional (3D cell culture models represent a more accurate, intermediate platform between simplified 2D culture models and complex and expensive in vivo models. 3D in vitro models can overcome 2D in vitro limitations caused by the oversupply of nutrients, and unphysiological cell-cell and cell-material interactions, and allow for dynamic interactions between cells, stroma, and extracellular matrix. In addition, 3D cultures allow for the development of concentration gradients, including oxygen, metabolites and growth factors, with chemical gradients playing an integral role in many cellular functions ranging from development to signaling in normal epithelia and cancer environments in vivo. Currently, the most common matrices used for 3D culture are biologically derived materials such as matrigel and collagen. However, in recent years, more defined, synthetic materials have become available as scaffolds for 3D culture with the advantage of forming well-defined, designed, tunable materials to control matrix charge, stiffness, porosity, nanostructure, degradability and adhesion properties, in addition to other material and biological properties. One important area of synthetic materials currently available for 3D cell culture are short sequence, self-assembling peptide hydrogels. In addition to the review of recent work towards the control of material, structure, and mechanical properties, we will also discuss the biochemical functionalization of peptide hydrogels and how this functionalization, coupled with desired hydrogel material characteristics, affects tumor cell behavior in 3D culture.

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

    OpenAIRE

    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...

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

    Science.gov (United States)

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

    2016-01-01

    Summary 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

  10. Surface modified alginate microcapsules for 3D cell culture

    Science.gov (United States)

    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.

  11. DREAM3D simulations of inner-belt dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. Finding Apparent Horizons in Dynamic 3D Numerical Spacetimes

    OpenAIRE

    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...

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

    OpenAIRE

    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...

  14. Phenomenological modelling and simulation of cell clusters in 3D cultures.

    Science.gov (United States)

    González-Valverde, I; Semino, C; García-Aznar, J M

    2016-10-01

    Cell clustering and aggregation are fundamental processes in the development of several tissues and the progression of many diseases. The formation of these aggregates also has a direct impact on the oxygen concentration in their surroundings due to cellular respiration and poor oxygen diffusion through clusters. In this work, we propose a mathematical model that is capable of simulating cell cluster formation in 3D cultures through combining a particle-based and a finite element approach to recreate complex experimental conditions. Cells are modelled considering cell proliferation, cell death and cell-cell mechanical interactions. Additionally, the oxygen concentration profile is calculated through finite element analysis using a reaction-diffusion model that considers cell oxygen consumption and diffusion through the extracellular matrix and the cell clusters. In our model, the local oxygen concentration in the medium determines both cell proliferation and cell death. Numerical predictions are also compared with experimental data from the literature. The simulation results indicate that our model can predict cell clustering, cluster growth and oxygen distribution in 3D cultures. We conclude that the initial cell distribution, cell death and cell proliferation dynamics determine the size and density of clusters. Moreover, these phenomena are directly affected by the oxygen transport in the 3D culture. PMID:27615191

  15. Computational Modelling of Piston Ring Dynamics in 3D

    Directory of Open Access Journals (Sweden)

    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.

  16. 3D photospheric velocity field of a Supergranular cell

    CERN Document Server

    Del Moro, Dario; Berrilli, Francesco

    2007-01-01

    We investigate the plasma flow properties inside a Supergranular (SG) cell, in particular its interaction with small scale magnetic field structures. The SG cell has been identified using the magnetic network (CaII wing brightness) as proxy, applying the TST to high spatial, spectral and temporal resolution observations obtained by IBIS. The full 3D velocity vector field for the SG has been reconstructed at two different photospheric heights. In order to strengthen our findings, we also computed the mean radial flow of the SG by means of cork tracing. We also studied the behaviour of the horizontal and Line of Sight plasma flow cospatial with cluster of bright CaII structures of magnetic origin to better understand the interaction between photospheric convection and small scale magnetic features. The SG cell we investigated seems to be organized with an almost radial flow from its centre to the border. The large scale divergence structure is probably created by a compact region of costant up-flow close to the...

  17. The vibrational dynamics of 3D HOCl above dissociation

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Yi-Der; Reichl, L. E. [Center for Complex Quantum Systems and Department of Physics, The University of Texas at Austin, Austin, Texas 78712 (United States); Jung, Christof [Instituto de Ciencias Fisicas, Universidad Nacional Autonoma de Mexico, Av. Universidad 1001, 62251 Cuernavaca (Mexico)

    2015-03-28

    We explore the classical vibrational dynamics of the HOCl molecule for energies above the dissociation energy of the molecule. Above dissociation, we find that the classical dynamics is dominated by an invariant manifold which appears to stabilize two periodic orbits at energies significantly above the dissociation energy. These stable periodic orbits can hold a large number of quantum states and likely can support a significant quasibound state of the molecule, well above the dissociation energy. The classical dynamics and the lifetime of quantum states on the invariant manifold are determined.

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

    Science.gov (United States)

    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.

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

    Lifescience Database Archive (English)

    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 ...

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

    Lifescience Database Archive (English)

    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 ...

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

    Lifescience Database Archive (English)

    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 ...

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

    Lifescience Database Archive (English)

    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 ...

  3. Low Complexity Connectivity Driven Dynamic Geometry Compression for 3D Tele-Immersion

    NARCIS (Netherlands)

    Mekuria, R.N.; Bulterman, D.C.A.; Cesar Garcia, P.S.

    2014-01-01

    Geometry based 3D Tele-Immersion is a novel emerging media application that involves on the fly reconstructed 3D mesh geometry. To enable real-time communication of such live reconstructed mesh geometry over a bandwidth limited link, fast dynamic geometry compression is needed. However, most tools a

  4. A dynamic approach to the recognition of 3D facial expressions and their temporal models

    NARCIS (Netherlands)

    Sandbach, Georgia; Zafeiriou, Stefanos; Pantic, Maja; Rueckert, Daniel

    2011-01-01

    In this paper we propose a method that exploits 3D motion-based features between frames of 3D facial geometry sequences for dynamic facial expression recognition. An expressive sequence is modeled to contain an onset followed by an apex and an offset. Feature selection methods are applied in order t

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

    Science.gov (United States)

    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.

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

    CERN Document Server

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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

  8. 3D video-based deformation measurement of the pelvis bone under dynamic cyclic loading

    Directory of Open Access Journals (Sweden)

    Freslier Marie

    2011-07-01

    Full Text Available Abstract Background Dynamic three-dimensional (3D deformation of the pelvic bones is a crucial factor in the successful design and longevity of complex orthopaedic oncological implants. The current solutions are often not very promising for the patient; thus it would be interesting to measure the dynamic 3D-deformation of the whole pelvic bone in order to get a more realistic dataset for a better implant design. Therefore we hypothesis if it would be possible to combine a material testing machine with a 3D video motion capturing system, used in clinical gait analysis, to measure the sub millimetre deformation of a whole pelvis specimen. Method A pelvis specimen was placed in a standing position on a material testing machine. Passive reflective markers, traceable by the 3D video motion capturing system, were fixed to the bony surface of the pelvis specimen. While applying a dynamic sinusoidal load the 3D-movement of the markers was recorded by the cameras and afterwards the 3D-deformation of the pelvis specimen was computed. The accuracy of the 3D-movement of the markers was verified with 3D-displacement curve with a step function using a manual driven 3D micro-motion-stage. Results The resulting accuracy of the measurement system depended on the number of cameras tracking a marker. The noise level for a marker seen by two cameras was during the stationary phase of the calibration procedure ± 0.036 mm, and ± 0.022 mm if tracked by 6 cameras. The detectable 3D-movement performed by the 3D-micro-motion-stage was smaller than the noise level of the 3D-video motion capturing system. Therefore the limiting factor of the setup was the noise level, which resulted in a measurement accuracy for the dynamic test setup of ± 0.036 mm. Conclusion This 3D test setup opens new possibilities in dynamic testing of wide range materials, like anatomical specimens, biomaterials, and its combinations. The resulting 3D-deformation dataset can be used for a better

  9. 3D Printing of Scaffold for Cells Delivery: Advances in Skin Tissue Engineering

    Directory of Open Access Journals (Sweden)

    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.

  10. A unified viscous-spring artificial boundary for 3-D static and dynamic applications

    Institute of Scientific and Technical Information of China (English)

    LIU Jingbo; LI Bin

    2005-01-01

    A method to develop unified artificial boundaries for problems coupling static effect and dynamic effect is proposed. Based on the dynamic viscous-spring artificial boundary and the fundamental solution of static problems in elastic half space, a unified viscous-spring artificial boundary for 3-D static and dynamic applications is established.

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

    Directory of Open Access Journals (Sweden)

    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

  12. 3D-Printing Crystallographic Unit Cells for Learning Materials Science and Engineering

    Science.gov (United States)

    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…

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

    International Nuclear Information System (INIS)

    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

  14. Investigation of Dynamic Crack Coalescence Using a Gypsum-Like 3D Printing Material

    Science.gov (United States)

    Jiang, Chao; Zhao, Gao-Feng; Zhu, Jianbo; Zhao, Yi-Xin; Shen, Luming

    2016-10-01

    Dynamic crack coalescence attracts great attention in rock mechanics. However, specimen preparation in experimental study is a time-consuming and difficult procedure. In this work, a gypsum-like material by powder bed and inkjet 3D printing technique was applied to produce specimens with preset cracks for split Hopkinson pressure bar (SHPB) test. From micro X-ray CT test, it was found that the 3D printing technique could successfully prepare specimens that contain preset cracks with width of 0.2 mm. Basic mechanical properties of the 3D printing material, i.e., the elastic modulus, the Poisson's ratio, the density, the compressive strength, the indirect tensile strength, and the fracture toughness, were obtained and reported. Unlike 3D printed specimens using polylactic acid, these gypsum-like specimens can produce failure patterns much closer to those observed in classical rock mechanical tests. Finally, the dynamic crack coalescence of the 3D printed specimens with preset cracks were captured using a high-speed camera during SHPB tests. Failure patterns of these 3D printed specimens are similar to the specimens made by Portland cement concrete. Our results indicate that sample preparation by 3D printing is highly competitive due to its quickness in prototyping, precision and flexibility on the geometry, and high material homogeneity.

  15. Observing molecular dynamics with time-resolved 3D momentum imaging

    Science.gov (United States)

    Sturm, F. P.; Wright, T.; Bocharova, I.; Ray, D.; Shivaram, N.; Cryan, J.; Belkacem, A.; Weber, T.; Dörner, R.

    2014-05-01

    Photo-excitation and ionization trigger rich dynamics in molecular systems which play a key role in many important processes in nature such as vision, photosynthesis or photoprotection. Observing those reactions in real-time without significantly disturbing the molecules by a strong electric field has been a great challenge. Recent experiments using Time-of-Flight and Velocity Map Imaging techniques have revealed important information on the dynamics of small molecular systems upon photo-excitation. We have developed an apparatus for time-resolved momentum imaging of electrons and ions in all three spatial dimensions that employs two-color femtosecond laser pulses in the vacuum and extreme ultraviolet (VUV, XUV) for probing molecular dynamics. Our COLTRIMS style reaction microscope can measure electrons and ions in coincidence and reconstruct the momenta of the reaction fragments in 3D. We use a high power 800 nm laser in a loose focusing geometry gas cell to efficinetly drive High Harmonic Generation. The resulting photon flux is sufficient to perform 2-photon pump-probe experiments using VUV and XUV pulses for both pump and probe. With this setup we investigate non-Born-Oppenheimer dynamics in small molecules such as C2H4 and CO2 on a femtosecond time scale. Supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.

  16. 3D-printed microfluidic chips with patterned, cell-laden hydrogel constructs.

    Science.gov (United States)

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

    2016-06-01

    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

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

    NARCIS (Netherlands)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Qian [Iowa State Univ., Ames, IA (United States)

    2008-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    International Nuclear Information System (INIS)

    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)

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

    CERN Document Server

    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 ...

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

    Institute of Scientific and Technical Information of China (English)

    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.

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

    Science.gov (United States)

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

    2016-01-01

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

  4. Regulation of mesenchymal stem cell 3D microenvironment: From macro to microfluidic bioreactors.

    Science.gov (United States)

    Sart, Sébastien; Agathos, Spiros N; Li, Yan; Ma, Teng

    2016-01-01

    Human mesenchymal stem cells (hMSCs) have emerged as an important cell type in cell therapy and tissue engineering. In these applications, maintaining the therapeutic properties of hMSCs requires tight control of the culture environments and the structural cell organizations. Bioreactor systems are essential tools to achieve these goals in the clinical-scale expansion and tissue engineering applications. This review summarizes how different bioreactors provide cues to regulate the structure and the chemico-mechanical microenvironment of hMSCs with a focus on 3D organization. In addition to conventional bioreactors, recent advances in microfluidic bioreactors as a novel approach to better control the hMSC microenvironment are also discussed. These advancements highlight the key role of bioreactor systems in preserving hMSC's functional properties by providing dynamic and temporal regulation of in vitro cellular microenvironment.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    Blinowski, Grzegorz; Kamiński, Maciej; Wawer, Dariusz

    2014-08-01

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

  7. 3D wake dynamics of the VAWT: experimental and numerical investigation

    NARCIS (Netherlands)

    Ferreira, C.; Hofemann, C.; Dixon, K.; Van 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

  8. Effect of Ductile Agents on the Dynamic Behavior of SiC3D Network Composites

    Science.gov (United States)

    Zhu, Jingbo; Wang, Yangwei; Wang, Fuchi; Fan, Qunbo

    2016-10-01

    Co-continuous SiC ceramic composites using pure aluminum, epoxy, and polyurethane (PU) as ductile agents were developed. The dynamic mechanical behavior and failure mechanisms were investigated experimentally using the split Hopkinson pressure bar (SHPB) method and computationally by finite element (FE) simulations. The results show that the SiC3D/Al composite has the best overall performance in comparison with SiC3D/epoxy and SiC3D/PU composites. FE simulations are generally consistent with experimental data. These simulations provide valuable help in predicting mechanical strength and in interpreting the experimental results and failure mechanisms. They may be combined with micrographs for fracture characterizations of the composites. We found that interactions between the SiC phase and ductile agents under dynamic compression in the SHPB method are complex, and that interfacial condition is an important parameter that determines the mechanical response of SiC3D composites with a characteristic interlocking structure during dynamic compression. However, the effect of the mechanical properties of ductile agents on dynamic behavior of the composites is a second consideration in the production of the composites.

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

    OpenAIRE

    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...

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

    Science.gov (United States)

    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.

  11. Local 3D matrix confinement determines division axis through cell shape.

    Science.gov (United States)

    He, Lijuan; Chen, Weitong; Wu, Pei-Hsun; Jimenez, Angela; Wong, Bin Sheng; San, Angela; Konstantopoulos, Konstantinos; Wirtz, Denis

    2016-02-01

    How the division axis is determined in mammalian cells embedded in three-dimensional (3D) matrices remains elusive, despite that many types of cells divide in 3D environments. Cells on two-dimensional (2D) substrates typically round up completely to divide. Here, we show that in 3D collagen matrices, mammalian cells such as HT1080 human fibrosarcoma and MDA-MB-231 breast cancer cells exhibit division modes distinct from their Counterparts on 2D substrates, with a markedly higher fraction of cells remaining highly elongated through mitosis in 3D matrices. The long axis of elongated mitotic cells accurately predicts the division axis, independently of matrix density and cell-matrix interactions. This 3D-specific elongated division mode is determined by the local confinement produced by the matrix and the ability of cells to protrude and locally remodel the matrix via β1 integrin. Elongated division is readily recapitulated using collagen-coated microfabricated channels. Cells depleted of β1 integrin still divide in the elongated mode in microchannels, suggesting that 3D confinement is sufficient to induce the elongated cell-division phenotype.

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

    Directory of Open Access Journals (Sweden)

    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.

  13. Nonpolarized signaling reveals two distinct modes of 3D cell migration.

    Science.gov (United States)

    Petrie, Ryan J; Gavara, Núria; Chadwick, Richard S; Yamada, Kenneth M

    2012-04-30

    We search in this paper for context-specific modes of three-dimensional (3D) cell migration using imaging for phosphatidylinositol (3,4,5)-trisphosphate (PIP3) and active Rac1 and Cdc42 in primary fibroblasts migrating within different 3D environments. In 3D collagen, PIP3 and active Rac1 and Cdc42 were targeted to the leading edge, consistent with lamellipodia-based migration. In contrast, elongated cells migrating inside dermal explants and the cell-derived matrix (CDM) formed blunt, cylindrical protrusions, termed lobopodia, and Rac1, Cdc42, and PIP3 signaling was nonpolarized. Reducing RhoA, Rho-associated protein kinase (ROCK), or myosin II activity switched the cells to lamellipodia-based 3D migration. These modes of 3D migration were regulated by matrix physical properties. Specifically, experimentally modifying the elasticity of the CDM or collagen gels established that nonlinear elasticity supported lamellipodia-based migration, whereas linear elasticity switched cells to lobopodia-based migration. Thus, the relative polarization of intracellular signaling identifies two distinct modes of 3D cell migration governed intrinsically by RhoA, ROCK, and myosin II and extrinsically by the elastic behavior of the 3D extracellular matrix.

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

    International Nuclear Information System (INIS)

    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)

  15. Cell compatible encapsulation of filaments into 3D hydrogels.

    Science.gov (United States)

    Schirmer, Katharina S U; Gorkin, Robert; Beirne, Stephen; Stewart, Elise; Thompson, Brianna C; Quigley, Anita F; Kapsa, Robert M I; Wallace, Gordon G

    2016-06-01

    Tissue engineering scaffolds for nerve regeneration, or artificial nerve conduits, are particularly challenging due to the high level of complexity the structure of the nerve presents. The list of requirements for artificial nerve conduits is long and includes the ability to physically guide nerve growth using physical and chemical cues as well as electrical stimulation. Combining these characteristics into a conduit, while maintaining biocompatibility and biodegradability, has not been satisfactorily achieved by currently employed fabrication techniques. Here we present a method combining pultrusion and wet-spinning techniques facilitating incorporation of pre-formed filaments into ionically crosslinkable hydrogels. This new biofabrication technique allows the incorporation of conducting or drug-laden filaments, controlled guidance channels and living cells into hydrogels, creating new improved conduit designs. PMID:27213861

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

    Science.gov (United States)

    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

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

    DEFF Research Database (Denmark)

    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...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    DEFF Research Database (Denmark)

    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 (netwo...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  4. Novel function of complement C3d as an autologous helper T-cell target.

    Science.gov (United States)

    Knopf, Paul M; Rivera, Daniel S; Hai, Si-Han; McMurry, Julie; Martin, William; De Groot, Anne S

    2008-01-01

    The C3d fragment of complement component C3 has been shown to enhance immune responses to antigens that lack T-cell epitopes such as bacterial polysaccharides. C3d binds to the B-cell complement receptor 2 (CR2 or CD21); this binding serves as a co-activation signal to the B cell when the polysaccharide antigen portion binds simultaneously to the B-cell receptor (surface Ig). Bringing together receptor-associated signal transduction molecules CD19 and Igalpha/beta, respectively, results in a lower threshold of activation. Paradoxically, C3d has also been shown to enhance antibody titers in the CD21 knockout (KO) mouse model as well as increase Th1 and Th2 cytokine secretion, suggesting that that an auxiliary CR2-independent pathway of immune activation may exist. We hypothesized that in addition to its molecular adjuvant property that enhances signal 1 during B-cell activation (co-signal 1), C3d also contains T-cell epitopes that are able to stimulate autoreactive C3d peptide-specific helper T cells which we term 'co-signal 2'. Using the EpiMatrix T-cell epitope-mapping algorithm, we identified 11 putative T-cell epitopes in C3d, a very high epitope density for a 302 amino-acid sequence. Eight of these epitope candidates were synthesized and shown to bind a variety of class II HLA-DR molecules of different haplotypes, and to stimulate C3d peptide-specific T cells to secrete pro-inflammatory cytokines in vitro. Further, we demonstrate a C3d-peptide specific increase in CD4(+) intracellular IFN-gamma(+) T cells in peripheral blood mononuclear cells (PBMCs) exposed to C3d peptides in vitro. We believe that the discovery of these autologous T cells autoreactive for C3d provides evidence supporting the 'co-signal 2' hypothesis and may offer a novel explanation of the CD21 KO paradox. PMID:18180801

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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

  7. 3D Hopkinson bar: new experiments for dynamic testing on soils

    CERN Document Server

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    OpenAIRE

    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.

  11. Measurement of particle trajectories, dynamics, surface adhesion and detachment in near-wall shear flows using 3D velocimetry

    Science.gov (United States)

    Guasto, Jeffrey; Schmidt, Brian; Lawrence, Michael; Breuer, Kenneth

    2007-11-01

    Three-dimensional total internal reflection velocimetry (3D-TIRV) is used to measure the trajectories of fluorescent tracer particles within 200 nm of a wall. Diffusion and shear-induced motion can result in mean velocity measurement errors, and by taking measurements using different particle sizes and sampling times, we quantify these effects and compare with theory. We also use 3D-TIRV to observe and characterize the adhesion, surface rolling and release dynamics of particles that can adhere to the surface through the action of biological binding proteins. Particles coated with P-Selectin are allowed to adhere to and detach from a PSGL-1-coated microchannel surface, modeling the interaction between leukocytes (white blood cells) and blood vessels, respectively. Binding affinities, bond strengths and hydrodynamic interactions are inferred from the trajectory data.

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

    Science.gov (United States)

    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.

  13. 3D photonic crystal interlayers for micromorph thin film silicon tandem cell

    Energy Technology Data Exchange (ETDEWEB)

    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.

  14. 1-integrin and MT1-MMP promote tumor cell migration in 2D but not in 3D fibronectin microenvironments

    Science.gov (United States)

    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.

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

    CERN Document Server

    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.

  16. Nonlinear dynamics of Airy-vortex 3D wave packets: emission of vortex light waves.

    Science.gov (United States)

    Driben, Rodislav; Meier, Torsten

    2014-10-01

    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. Because of 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 nonzero topological charges. Wave packets carrying angular momentum are found to be much more resistant to the rapid collapse.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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).

  19. The computer simulation of 3d gas dynamics in a gas centrifuge

    Science.gov (United States)

    Borman, V. D.; Bogovalov, S. V.; Borisevich, V. D.; Tronin, I. V.; Tronin, V. N.

    2016-09-01

    We argue on the basis of the results of 2D analysis of the gas flow in gas centrifuges that a reliable calculation of the circulation of the gas and gas content in the gas centrifuge is possible only in frameworks of 3D numerical simulation of gas dynamics in the gas centrifuge (hereafter GC). The group from National research nuclear university, MEPhI, has created a computer code for 3D simulation of the gas flow in GC. The results of the computer simulations of the gas flows in GC are presented. A model Iguassu centrifuge is explored for the simulations. A nonaxisymmetric gas flow is produced due to interaction of the hypersonic rotating flow with the scoops for extraction of the product and waste flows from the GC. The scoops produce shock waves penetrating into a working camera of the GC and form spiral waves there.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. 3D kinematic and dynamic analysis of the front crawl tumble turn in elite male swimmers.

    Science.gov (United States)

    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

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

    CERN Document Server

    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.

  3. FHR3 Blocks C3d-Mediated Coactivation of Human B Cells.

    Science.gov (United States)

    Buhlmann, Denise; Eberhardt, Hannes U; Medyukhina, Anna; Prodinger, Wolfgang M; Figge, Marc Thilo; Zipfel, Peter F; Skerka, Christine

    2016-07-15

    The autoimmune renal disease deficient for complement factor H-related (CFHR) genes and autoantibody-positive form of hemolytic uremic syndrome is characterized by the presence of autoantibodies specific for the central complement regulator, factor H, combined with a homozygous deficiency, mostly in CFHR3 and CFHR1 Because FHR3 and FHR1 bind to C3d and inactivated C3b, which are ligands for complement receptor type 2 (CR2/CD21), the aim of the current study was to examine whether FHR3-C3d or FHR1-C3d complexes modulate B cell activation. Laser-scanning microscopy and automated image-based analysis showed that FHR3, but not FHR1 or factor H, blocked B cell activation by the BCR coreceptor complex (CD19/CD21/CD81). FHR3 bound to C3d, thereby inhibiting the interaction between C3d and CD21 and preventing colocalization of the coreceptor complex with the BCR. FHR3 neutralized the adjuvant effect of C3d on B cells, as shown by inhibited intracellular CD19 and Akt phosphorylation in Raji cells, as well as Ca(2+) release in peripheral B cells. In cases of CFHR3/CFHR1 deficiency, the FHR3 binding sites on C3d are occupied by factor H, which lacks B cell-inhibitory functions. These data provide evidence that FHR3, which is absent in patients with the autoimmune form of hemolytic uremic syndrome, is involved in B cell regulation. PMID:27279373

  4. Stem cells catalyze cartilage formation by neonatal articular chondrocytes in 3D biomimetic hydrogels

    Science.gov (United States)

    Lai, Janice H.; Kajiyama, Glen; Smith, Robert Lane; Maloney, William; Yang, Fan

    2013-12-01

    Cartilage loss is a leading cause of disability among adults and effective therapy remains elusive. Neonatal chondrocytes (NChons) are an attractive allogeneic cell source for cartilage repair, but their clinical translation has been hindered by scarce donor availability. Here we examine the potential for catalyzing cartilage tissue formation using a minimal number of NChons by co-culturing them with adipose-derived stem cells (ADSCs) in 3D hydrogels. Using three different co-culture models, we demonstrated that the effects of co-culture on cartilage tissue formation are dependent on the intercellular distance and cell distribution in 3D. Unexpectedly, increasing ADSC ratio in mixed co-culture led to increased synergy between NChons and ADSCs, and resulted in the formation of large neocartilage nodules. This work raises the potential of utilizing stem cells to catalyze tissue formation by neonatal chondrocytes via paracrine signaling, and highlights the importance of controlling cell distribution in 3D matrices to achieve optimal synergy.

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

    Science.gov (United States)

    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.

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

    OpenAIRE

    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...

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    International Nuclear Information System (INIS)

    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.

  9. Highly ordered large-scale neuronal networks of individual cells - toward single cell to 3D nanowire intracellular interfaces.

    Science.gov (United States)

    Kwiat, Moria; Elnathan, Roey; Pevzner, Alexander; Peretz, Asher; Barak, Boaz; Peretz, Hagit; Ducobni, Tamir; Stein, Daniel; Mittelman, Leonid; Ashery, Uri; Patolsky, Fernando

    2012-07-25

    The use of artificial, prepatterned neuronal networks in vitro is a promising approach for studying the development and dynamics of small neural systems in order to understand the basic functionality of neurons and later on of the brain. The present work presents a high fidelity and robust procedure for controlling neuronal growth on substrates such as silicon wafers and glass, enabling us to obtain mature and durable neural networks of individual cells at designed geometries. It offers several advantages compared to other related techniques that have been reported in recent years mainly because of its high yield and reproducibility. The procedure is based on surface chemistry that allows the formation of functional, tailormade neural architectures with a micrometer high-resolution partition, that has the ability to promote or repel cells attachment. The main achievements of this work are deemed to be the creation of a large scale neuronal network at low density down to individual cells, that develop intact typical neurites and synapses without any glia-supportive cells straight from the plating stage and with a relatively long term survival rate, up to 4 weeks. An important application of this method is its use on 3D nanopillars and 3D nanowire-device arrays, enabling not only the cell bodies, but also their neurites to be positioned directly on electrical devices and grow with registration to the recording elements underneath.

  10. Hypoxia Created Human Mesenchymal Stem Cell Sheet for Prevascularized 3D Tissue Construction.

    Science.gov (United States)

    Zhang, Lijun; Xing, Qi; Qian, Zichen; Tahtinen, Mitchell; Zhang, Zhaoqiang; Shearier, Emily; Qi, Shaohai; Zhao, Feng

    2016-02-01

    3D tissue based on human mesenchymal stem cell (hMSC) sheets offers many interesting opportunities for regenerating multiple types of connective tissues. Prevascularizing hMSC sheets with endothelial cells (ECs) will improve 3D tissue performance by supporting cell survival and accelerating integration with host tissue. It is hypothesized that hypoxia cultured hMSC sheets can promote microvessel network formation and preserve stemness of hMSCs. This study investigates the vascularization of hMSC sheets under different oxygen tensions. It is found that the HN condition, in which hMSC sheets formed under physiological hypoxia (2% O2 ) and then cocultured with ECs under normoxia (20% O2 ), enables longer and more branched microvessel network formation. The observation is corroborated by higher levels of angiogenic factors in coculture medium. Additionally, the hypoxic hMSC sheet is more uniform and less defective, which facilitates fabrication of 3D prevascularized tissue construct by layering the prevascularized hMSC sheets and maturing in rotating wall vessel bioreactor. The hMSCs in the 3D construct still maintain multilineage differentiation ability, which indicates the possible application of the 3D construct for various connective tissues regeneration. These results demonstrate that hypoxia created hMSC sheets benefit the microvessel growth and it is feasible to construct 3D prevascularized tissue construct using the prevascularized hMSC sheets.

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

    OpenAIRE

    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...

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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.

  15. 3D photonic crystal interlayers for micromorph thin film silicon tandem cell

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.)

  17. Dynamics of gecko locomotion: a force-measuring array to measure 3D reaction forces.

    Science.gov (United States)

    Dai, Zhendong; Wang, Zhouyi; Ji, Aihong

    2011-03-01

    Measuring the interaction between each foot of an animal and the substrate is one of the most effective ways to understand the dynamics of legged locomotion. Here, a new facility - the force-measuring array (FMA) - was developed and applied to measure 3D reaction forces of geckos on different slope surfaces. The FMA consists of 16 3D sensors with resolution to the mN level. At the same time the locomotion behaviour of geckos freely moving on the FMA was recorded by high speed camera. The reaction forces acting on the gecko's individual feet measured by the FMA and correlated with locomotion behaviour provided enough information to reveal the mechanical and dynamic secrets of gecko locomotion. Moreover, dynamic forces were also measured by a force platform and correlated with locomotion behaviour. The difference between the forces measured by the two methods is discussed. From the results we conclude that FMA is the best way to obtain true reaction forces acting on the gecko's individual feet.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  20. Development and validation of a 3-D model to predict knee joint loading during dynamic movement.

    Science.gov (United States)

    McLean, S G; Su, A; van den Bogert, A J

    2003-12-01

    The purpose of this study was to develop a subject-specific 3-D model of the lower extremity to predict neuromuscular control effects on 3-D knee joint loading during movements that can potentially cause injury to the anterior cruciate ligament (ACL) in the knee. The simulation consisted of a forward dynamic 3-D musculoskeletal model of the lower extremity, scaled to represent a specific subject. Inputs of the model were the initial position and velocity of the skeletal elements, and the muscle stimulation patterns. Outputs of the model were movement and ground reaction forces, as well as resultant 3-D forces and moments acting across the knee joint. An optimization method was established to find muscle stimulation patterns that best reproduced the subject's movement and ground reaction forces during a sidestepping task. The optimized model produced movements and forces that were generally within one standard deviation of the measured subject data. Resultant knee joint loading variables extracted from the optimized model were comparable to those reported in the literature. The ability of the model to successfully predict the subject's response to altered initial conditions was quantified and found acceptable for use of the model to investigate the effect of altered neuromuscular control on knee joint loading during sidestepping. Monte Carlo simulations (N = 100,000) using randomly perturbed initial kinematic conditions, based on the subject's variability, resulted in peak anterior force, valgus torque and internal torque values of 378 N, 94 Nm and 71 Nm, respectively, large enough to cause ACL rupture. We conclude that the procedures described in this paper were successful in creating valid simulations of normal movement, and in simulating injuries that are caused by perturbed neuromuscular control.

  1. 3D chitosan-gelatin-chondroitin porous scaffold improves osteogenic differentiation of mesenchymal stem cells

    Energy Technology Data Exchange (ETDEWEB)

    Machado, C B [Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais (Brazil); Ventura, J M G [Department of Ceramics and Glass Engineering, University of Aveiro (Portugal); Lemos, A F [Department of Ceramics and Glass Engineering, University of Aveiro (Portugal); Ferreira, J M F [Department of Ceramics and Glass Engineering, University of Aveiro (Portugal); Leite, M F [Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais (Brazil); Goes, A M [Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais (Brazil)

    2007-06-01

    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.

  2. Pulmonary surfactant expression analysis--role of cell-cell interactions and 3-D tissue-like architecture.

    Science.gov (United States)

    Nandkumar, Maya A; Ashna, U; Thomas, Lynda V; Nair, Prabha D

    2015-03-01

    Surfactant production is important in maintaining alveolar function both in vivo and in vitro, but surfactant expression is the primary property lost by alveolar Type II Pneumocytes in culture and its maintenance is a functional requirement. To develop a functional tissue-like model, the in vivo cell-cell interactions and three dimensional architecture has to be reproduced. To this end, 3D button-shaped synthetic gelatin vinyl acetate (GeVAc) co-polymer scaffold was seeded with different types of lung cells. Functionality of the construct was studied under both static and dynamic conditions. The construct was characterized by Environmental Scanning Electron and fluorescent microscopy, and functionality of the system was analyzed by studying mRNA modulations of all four surfactant genes A, B, C, and D by real time-PCR and varying culture conditions. The scaffold supports alveolar cell adhesion and maintenance of cuboidal morphology, and the alveolar-specific property of surfactant synthesis, which would otherwise be rapidly lost in culture. This is a novel 3D system that expresses all 4 surfactants for a culture duration of 3 weeks.

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

    NARCIS (Netherlands)

    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

  4. 3D Image-Guided Automatic Pipette Positioning for Single Cell Experiments in vivo

    OpenAIRE

    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.

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

    OpenAIRE

    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...

  6. 3D Dynamic Representation for Urban Sprawl Modelling: Example of India’s Delhi-Mumbai corridor

    OpenAIRE

    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...

  7. 3D Reconstitution of the Patterned Neural Tube from Embryonic Stem Cells

    Directory of Open Access Journals (Sweden)

    Andrea Meinhardt

    2014-12-01

    Full Text Available Inducing organogenesis in 3D culture is an important aspect of stem cell research. Anterior neural structures have been produced from large embryonic stem cell (ESC aggregates, but the steps involved in patterning such complex structures have been ill defined, as embryoid bodies typically contained many cell types. Here we show that single mouse ESCs directly embedded in Matrigel or defined synthetic matrices under neural induction conditions can clonally form neuroepithelial cysts containing a single lumen in 3D. Untreated cysts were uniformly dorsal and could be ventralized to floor plate (FP. Retinoic acid posteriorized cysts to cervical levels and induced localize FP formation yielding full patterning along the dorsal/ventral (DV axis. Correct spatial organization of motor neurons, interneurons, and dorsal interneurons along the DV axis was observed. This system serves as a valuable tool for studying morphogen action in 3D and as a source of patterned spinal cord tissue.

  8. 3D reconstitution of the patterned neural tube from embryonic stem cells.

    Science.gov (United States)

    Meinhardt, Andrea; Eberle, Dominic; Tazaki, Akira; Ranga, Adrian; Niesche, Marco; Wilsch-Bräuninger, Michaela; Stec, Agnieszka; Schackert, Gabriele; Lutolf, Matthias; Tanaka, Elly M

    2014-12-01

    Inducing organogenesis in 3D culture is an important aspect of stem cell research. Anterior neural structures have been produced from large embryonic stem cell (ESC) aggregates, but the steps involved in patterning such complex structures have been ill defined, as embryoid bodies typically contained many cell types. Here we show that single mouse ESCs directly embedded in Matrigel or defined synthetic matrices under neural induction conditions can clonally form neuroepithelial cysts containing a single lumen in 3D. Untreated cysts were uniformly dorsal and could be ventralized to floor plate (FP). Retinoic acid posteriorized cysts to cervical levels and induced localize FP formation yielding full patterning along the dorsal/ventral (DV) axis. Correct spatial organization of motor neurons, interneurons, and dorsal interneurons along the DV axis was observed. This system serves as a valuable tool for studying morphogen action in 3D and as a source of patterned spinal cord tissue.

  9. Insights from 3D numerical simulations on the dynamics of the India-Asia collision zone

    Science.gov (United States)

    Pusok, A. E.; Kaus, B.; Popov, A.

    2013-12-01

    The dynamics of the India-Asia collision zone remains one of the most remarkable topics of the current research interest: the transition from subduction to collision and uplift, followed by the rise of the abnormally thick Tibetan plateau, and the deformation at its Eastern and Western syntaxes, are processes still not fully understood. Models that have addressed this topic include wholescale underthrusting of Indian lithospheric mantle under Tibet, distributed homogeneous shortening or the thin-sheet model, slip-line field model for lateral extrusion or lower crustal flow models for the exhumation of the Himalayan units and lateral spreading of the Tibetan plateau. Of these, the thin-sheet model has successfully illustrated some of the basic physics of continental collision and has the advantage of a 3D model being reduced to 2D, but one of its major shortcomings is that it cannot simultaneously represent channel flow and gravitational collapse of the mantle lithosphere, since these mechanisms require the lithosphere to interact with the underlying mantle, or to have a vertically non-homogeneous rheology. As a consequence, 3D models are emerging as powerful tools to understand the dynamics of coupled systems. However, because of yet recent developments and various complexities, the current 3D models simulating the dynamics of continent collision zones have relied on certain explicit assumptions, such as replacing part of the asthenosphere with various types of boundary conditions that mimic the effect of mantle flow, in order to focus on the lithospheric/crustal deformation. Here, we employ the parallel 3D code LaMEM (Lithosphere and Mantle Evolution Model), with a finite difference staggered grid solver, which is capable of simulating lithospheric deformation while simultaneously taking mantle flow and a free surface into account. We present qualitative results on lithospheric and upper-mantle scale simulations in which the Indian lithosphere is subducted and

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

    Energy Technology Data Exchange (ETDEWEB)

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

    International Nuclear Information System (INIS)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  13. CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation.

    Science.gov (United States)

    Hodneland, Erlend; Kögel, Tanja; Frei, Dominik Michael; Gerdes, Hans-Hermann; Lundervold, Arvid

    2013-08-09

    : The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening.

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    NARCIS (Netherlands)

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

    2016-01-01

    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 doma

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  19. 3D quantitative visualization of altered LV wall thickening dynamics caused by coronary microembolization

    Science.gov (United States)

    Eusemann, Christian D.; Mohlenkamp, Stefan; Ritman, Erik L.; Robb, Richard A.

    2001-05-01

    Regional heart wall dynamics has been shown to be a sensitive indicator of LV wall ischemia. Rates of local LV wall thickening during a cardiac cycle can be measured and illustrated using functional parametric mappings. This display conveys the spatial distribution of dynamic strain in the myocardium and thereby provides a rapid qualitative appreciation of the severity and extent of the ischemic region. 3D reconstructions were obtained in an anesthetized pig from 8 adjacent, shortaxis, slices of the left ventricle imaged with an Electron Beam Computer Tomograph at 11 time points through one complete cardiac cycle. The 3D reconstructions were obtained before and after injection of 100 micrometer microspheres into the Left Anterior Descending (LAD) coronary artery. This injection causes microembolization of LAD artery branches within the heart wall. The image processing involved radially dividing the tomographic images of the myocardium into small subdivisions with color encoding of the local magnitude of regional thickness or regional velocities of LV wall thickening throughout the cardiac cycle. We compared the effectiveness of animation of wall thickness encoded in color versus a static image of computed rate of wall thickness change in color. The location, extent and severity of regional wall akinesis or dyskinesis, as determined from these displays, can then be compared to the region of embolization as indicated by the distribution of altered LV wall perfusion.

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

    CERN Document Server

    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.

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

    Science.gov (United States)

    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

  2. 3D Multisource Full‐Waveform Inversion using Dynamic Random Phase Encoding

    KAUST Repository

    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.

  3. Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

    Science.gov (United States)

    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.

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

    NARCIS (Netherlands)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    International Nuclear Information System (INIS)

    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

  10. Ornamenting 3D printed scaffolds with cell-laid extracellular matrix for bone tissue regeneration.

    Science.gov (United States)

    Pati, Falguni; Song, Tae-Ha; Rijal, Girdhari; Jang, Jinah; Kim, Sung Won; Cho, Dong-Woo

    2015-01-01

    3D printing technique is the most sophisticated technique to produce scaffolds with tailorable physical properties. But, these scaffolds often suffer from limited biological functionality as they are typically made from synthetic materials. Cell-laid mineralized ECM was shown to be potential for improving the cellular responses and drive osteogenesis of stem cells. Here, we intend to improve the biological functionality of 3D-printed synthetic scaffolds by ornamenting them with cell-laid mineralized extracellular matrix (ECM) that mimics a bony microenvironment. We developed bone graft substitutes by using 3D printed scaffolds made from a composite of polycaprolactone (PCL), poly(lactic-co-glycolic acid) (PLGA), and β-tricalcium phosphate (β-TCP) and mineralized ECM laid by human nasal inferior turbinate tissue-derived mesenchymal stromal cells (hTMSCs). A rotary flask bioreactor was used to culture hTMSCs on the scaffolds to foster formation of mineralized ECM. A freeze/thaw cycle in hypotonic buffer was used to efficiently decellularize (97% DNA reduction) the ECM-ornamented scaffolds while preserving its main organic and inorganic components. The ECM-ornamented 3D printed scaffolds supported osteoblastic differentiation of newly-seeded hTMSCs by upregulating four typical osteoblastic genes (4-fold higher RUNX2; 3-fold higher ALP; 4-fold higher osteocalcin; and 4-fold higher osteopontin) and increasing calcium deposition compared to bare 3D printed scaffolds. In vivo, in ectopic and orthotopic models in rats, ECM-ornamented scaffolds induced greater bone formation than that of bare scaffolds. These results suggest a valuable method to produce ECM-ornamented 3D printed scaffolds as off-the-shelf bone graft substitutes that combine tunable physical properties with physiological presentation of biological signals.

  11. 3D culture broadly regulates tumor cell hypoxia response and angiogenesis via pro-inflammatory pathways.

    Science.gov (United States)

    DelNero, Peter; Lane, Maureen; Verbridge, Scott S; Kwee, Brian; Kermani, Pouneh; Hempstead, Barbara; Stroock, Abraham; Fischbach, Claudia

    2015-07-01

    Oxygen status and tissue dimensionality are critical determinants of tumor angiogenesis, a hallmark of cancer and an enduring target for therapeutic intervention. However, it is unclear how these microenvironmental conditions interact to promote neovascularization, due in part to a lack of comprehensive, unbiased data sets describing tumor cell gene expression as a function of oxygen levels within three-dimensional (3D) culture. Here, we utilized alginate-based, oxygen-controlled 3D tumor models to study the interdependence of culture context and the hypoxia response. Microarray gene expression analysis of tumor cells cultured in 2D versus 3D under ambient or hypoxic conditions revealed striking interdependence between culture dimensionality and hypoxia response, which was mediated in part by pro-inflammatory signaling pathways. In particular, interleukin-8 (IL-8) emerged as a major player in the microenvironmental regulation of the hypoxia program. Notably, this interaction between dimensionality and oxygen status via IL-8 increased angiogenic sprouting in a 3D endothelial invasion assay. Taken together, our data suggest that pro-inflammatory pathways are critical regulators of tumor hypoxia response within 3D environments that ultimately impact tumor angiogenesis, potentially providing important therapeutic targets. Furthermore, these results highlight the importance of pathologically relevant tissue culture models to study the complex physical and chemical processes by which the cancer microenvironment mediates new vessel formation.

  12. Microrheology and ROCK signaling of human endothelial cells embedded in a 3D matrix.

    Science.gov (United States)

    Panorchan, Porntula; Lee, Jerry S H; Kole, Thomas P; Tseng, Yiider; Wirtz, Denis

    2006-11-01

    Cell function is profoundly affected by the geometry of the extracellular environment confining the cell. Whether and how cells plated on a two-dimensional matrix or embedded in a three-dimensional (3D) matrix mechanically sense the dimensionality of their environment is mostly unknown, partly because individual cells in an extended matrix are inaccessible to conventional cell-mechanics probes. Here we develop a functional assay based on multiple particle tracking microrheology coupled with ballistic injection of nanoparticles to measure the local intracellular micromechanical properties of individual cells embedded inside a matrix. With our novel assay, we probe the mechanical properties of the cytoplasm of individual human umbilical vein endothelial cells (HUVECs) embedded in a 3D peptide hydrogel in the presence or absence of vascular endothelial growth factor (VEGF). We found that VEGF treatment, which enhances endothelial migration, increases the compliance and reduces the elasticity of the cytoplasm of HUVECs in a matrix. This VEGF-induced softening response of the cytoplasm is abrogated by specific Rho-kinase (ROCK) inhibition. These results establish combined particle-tracking microrheology and ballistic injection as the first method able to probe the micromechanical properties and mechanical response to agonists and/or drug treatments of individual cells inside a matrix. These results suggest that ROCK plays an essential role in the regulation of the intracellular mechanical response to VEGF of endothelial cells in a 3D matrix.

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

    Energy Technology Data Exchange (ETDEWEB)

    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)

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

    International Nuclear Information System (INIS)

    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)

  15. Planning and Control for Passive Dynamics Based Walking of 3D Biped Robots

    Institute of Scientific and Technical Information of China (English)

    Xiang Luo; Wenlong Xu

    2012-01-01

    Efficient walking is one of the main goals of research on biped robots.Passive Dynamics Based Walking (PDBW) has been proven to be an efficient pattern in numerous previous approaches to 2D biped walking.The goal of this study is to develop a feasible method for the application of PDBW to 3D robots.First a hybrid control method is presented,where a previously proposed two-point-foot walking pattern is employed to generate a PDBW gait in the sagittal plane and,in the frontal plane,a systematic balance control algorithm is applied including online planning of the landing point of the swing leg and feedback control of the stance foot.Then a multi-space planning structure is proposed to implement the proposed method on a 13-link 3D robot.Related kinematics and planning details of the robot are presented.Furthermore,a simulation of the 13-link biped robot verifies that stable and highly efficient walking can be achieved by the proposed control method.In addition,a number of features of the biped walking,including the transient powers and torques of the joints are explored.

  16. Description of patellar movement by 3D parameters obtained from dynamic CT acquisition

    Science.gov (United States)

    de Sá Rebelo, Marina; Moreno, Ramon Alfredo; Gobbi, Riccardo Gomes; Camanho, Gilberto Luis; de Ávila, Luiz Francisco Rodrigues; Demange, Marco Kawamura; Pecora, Jose Ricardo; Gutierrez, Marco Antonio

    2014-03-01

    The patellofemoral joint is critical in the biomechanics of the knee. The patellofemoral instability is one condition that generates pain, functional impairment and often requires surgery as part of orthopedic treatment. The analysis of the patellofemoral dynamics has been performed by several medical image modalities. The clinical parameters assessed are mainly based on 2D measurements, such as the patellar tilt angle and the lateral shift among others. Besides, the acquisition protocols are mostly performed with the leg laid static at fixed angles. The use of helical multi slice CT scanner can allow the capture and display of the joint's movement performed actively by the patient. However, the orthopedic applications of this scanner have not yet been standardized or widespread. In this work we present a method to evaluate the biomechanics of the patellofemoral joint during active contraction using multi slice CT images. This approach can greatly improve the analysis of patellar instability by displaying the physiology during muscle contraction. The movement was evaluated by computing its 3D displacements and rotations from different knee angles. The first processing step registered the images in both angles based on the femuŕs position. The transformation matrix of the patella from the images was then calculated, which provided the rotations and translations performed by the patella from its position in the first image to its position in the second image. Analysis of these parameters for all frames provided real 3D information about the patellar displacement.

  17. A 3D dynamical model of the colliding winds in binary systems

    CERN Document Server

    Parkin, E R

    2008-01-01

    We present a 3D dynamical model of the orbital induced curvature of the wind-wind collision region in binary star systems. Momentum balance equations are used to determine the position and shape of the contact discontinuity between the stars, while further downstream the gas is assumed to behave ballistically. An archimedean spiral structure is formed by the motion of the stars, with clear resemblance to high resolution images of the so-called ``pinwheel nebulae''. A key advantage of this approach over grid or smoothed particle hydrodynamic models is its significantly reduced computational cost, while it also allows the study of the structure obtained in an eccentric orbit. The model is relevant to symbiotic systems and Gamma-ray binaries, as well as systems with O-type and Wolf-Rayet stars. As an example application, we simulate the X-ray emission from hypothetical O+O and WR+O star binaries, and describe a method of ray tracing through the 3D spiral structure to account for absorption by the circumstellar m...

  18. 3D patterned stem cell differentiation using thermo-responsive methylcellulose hydrogel molds

    Science.gov (United States)

    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.

  19. 3D staggered Lagrangian hydrodynamics scheme with cell-centered Riemann solver-based artificial viscosity

    International Nuclear Information System (INIS)

    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)

  20. Interfacing polymeric scaffolds with primary pancreatic ductal adenocarcinoma cells to develop 3D cancer models

    NARCIS (Netherlands)

    Ricci, C.; Mota, C.M.; Moscato, S.; Alessandro, D' D.; Ugel, S.; Sartoris, S.; Bronte, V.; Boggi, U.; Campani, D.; Funel, N.; Moroni, L.; Danti, S.

    2014-01-01

    We analyzed the interactions between human primary cells from pancreatic ductal adenocarcinoma (PDAC) and polymeric scaffolds to develop 3D cancer models useful for mimicking the biology of this tumor. Three scaffold types based on two biocompatible polymeric formulations, such as poly(vinyl alcohol

  1. 3D patterned stem cell differentiation using thermo-responsive methylcellulose hydrogel molds

    Science.gov (United States)

    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

  2. 3D particle tracking velocimetry using dynamic discrete tomography for plasma physics applications

    DEFF Research Database (Denmark)

    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...

  3. Fast 3D Pattern Synthesis with Polarization and Dynamic Range Ratio Control for Conformal Antenna Arrays

    Directory of Open Access Journals (Sweden)

    Massimiliano Comisso

    2014-01-01

    Full Text Available This paper proposes an iterative algorithm for the 3D synthesis of the electric far-field pattern of a conformal antenna array in the presence of requirements on both the polarization and the dynamic range ratio (DRR of the excitations. Thanks to the use of selectable weights, the algorithm allows a versatile control of the DRR and of the polarization in a given angular region and requires a low CPU time to provide the array excitations. Furthermore, a modified version of the algorithm is developed to enable the optimization of the polarization state by phase-only control. Numerical results are presented to verify the usefulness of the proposed approach for the joint pattern and polarization synthesis of conformal arrays with reduced or even unitary DRR.

  4. Dynamic Characteristics of a Model and Prototype for 3D-RC Structure

    Directory of Open Access Journals (Sweden)

    Moniuddin Md. Khaja

    2016-06-01

    Full Text Available Infill walls provide durable and economical partitions that have relatively excellent thermal and sound insulation with high fire resistance. Monolithic infilled walls are provided within RC structures without being analyzed as a combination of concrete and brick elements, although in reality they act as a single unit during earthquakes. The performance of such structures during earthquakes has proved to be superior in comparison to bare frames in terms of stiffness, strength and energy dissipation. To know the dynamic characteristics of monolithic infill wall panels and masonry infill, modal, response spectrum and time history analyses have been carried out on a model and prototype of a 3D RC structure for a comparative study.

  5. 3D Myocardial Contraction Imaging Based on Dynamic Grid Interpolation: Theory and Simulation Analysis

    Science.gov (United States)

    Bu, Shuhui; Shiina, Tsuyoshi; Yamakawa, Makoto; Takizawa, Hotaka

    Accurate assessment of local myocardial contraction is important for diagnosis of ischemic heart disease, because decreases of myocardial motion often appear in the early stages of the disease. Three-dimensional (3-D) assessment of the stiffness distribution is required for accurate diagnosis of ischemic heart disease. Since myocardium motion occurs radially within the left ventricle wall and the ultrasound beam propagates axially, conventional approaches, such as tissue Doppler imaging and strain-rate imaging techniques, cannot provide us with enough quantitative information about local myocardial contraction. In order to resolve this problem, we propose a novel myocardial contraction imaging system which utilizes the weighted phase gradient method, the extended combined autocorrelation method, and the dynamic grid interpolation (DGI) method. From the simulation results, we conclude that the strain image's accuracy and contrast have been improved by the proposed method.

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

    CERN Document Server

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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)

  8. 3D Dynamic Finite Element Analysis of the Nonuniform Residual Stress in Ultrasonic Impact Treatment Process

    Science.gov (United States)

    Hu, Shengsun; Guo, Chaobo; Wang, Dongpo; Wang, Zhijiang

    2016-09-01

    The nonuniform distributions of the residual stress were simulated by a 3D finite element model to analyze the elastic-plastic dynamic ultrasonic impact treatment (UIT) process of multiple impacts on the 2024 aluminum alloy. The evolution of the stress during the impact process was discussed. The successive impacts during the UIT process improve the uniformity of the plastic deformation and decrease the maximum compressive residual stress beneath the former impact indentations. The influences of different controlled parameters, including the initial impact velocity, pin diameter, pin tip, device moving, and offset distances, on the residual stress distributions were analyzed. The influences of the controlled parameters on the residual stress distributions are apparent in the offset direction due to the different surface coverage in different directions. The influences can be used to understand the UIT process and to obtain the desired residual stress by optimizing the controlled parameters.

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

    International Nuclear Information System (INIS)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

  11. 3D Reconstruction of Human Laryngeal Dynamics Based on Endoscopic High-Speed Recordings.

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    OpenAIRE

    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...

  14. Orbital Data Confirms Dynamic Fractal Firework Universe Having 3D-spiral Code

    CERN Document Server

    Savov, E P

    2005-01-01

    The understanding of the universe is confused by the unknown nature of about 95% of its matter, required to confine the motions of space objects in cosmic structures. The proposed self-similar transformations of one all-building basic matter suggest that the universe is dynamic fractal that has 3D-spiral code. Its dynamic fractal elements create unifying force described by equation of the unifying interaction, drawn in the new fundamental dynamic fractal framework. The equation of unifying interaction converges into the inverse square laws and the principle of uncertainty at laboratory scales. It is further confirmed with calculations based on the orbital data of bodies moving around the nucleus of the Milky Way Galaxy, the centers of the Earth and the Sun and also orbiting the 87 Sylvia asteroid. Some of the testable predictions say that 87 Sylvia will have density > 1.2 g/cm2 and variations in gravity force less or comparable to 5.4 x 10exp(-4) m/s2, having space scales less or comparable to 10exp(3) km, wi...

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

    Directory of Open Access Journals (Sweden)

    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'.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  19. 3D nanochannel electroporation for high-throughput cell transfection with high uniformity and dosage control

    Science.gov (United States)

    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

  20. Rab3D is critical for secretory granule maturation in PC12 cells.

    Directory of Open Access Journals (Sweden)

    Tanja Kögel

    Full Text Available Neuropeptide- and hormone-containing secretory granules (SGs are synthesized at the trans-Golgi network (TGN as immature secretory granules (ISGs and complete their maturation in the F-actin-rich cell cortex. This maturation process is characterized by acidification-dependent processing of cargo proteins, condensation of the SG matrix and removal of membrane and proteins not destined to mature secretory granules (MSGs. Here we addressed a potential role of Rab3 isoforms in these maturation steps by expressing their nucleotide-binding deficient mutants in PC12 cells. Our data show that the presence of Rab3D(N135I decreases the restriction of maturing SGs to the F-actin-rich cell cortex, blocks the removal of the endoprotease furin from SGs and impedes the processing of the luminal SG protein secretogranin II. This strongly suggests that Rab3D is implicated in the subcellular localization and maturation of ISGs.

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

    OpenAIRE

    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...

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

    Directory of Open Access Journals (Sweden)

    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.

  3. Slanted channel microfluidic chip for 3D fluorescence imaging of cells in flow.

    Science.gov (United States)

    Jagannadh, Veerendra Kalyan; Mackenzie, Mark D; Pal, Parama; Kar, Ajoy K; Gorthi, Sai Siva

    2016-09-19

    Three-dimensional cellular imaging techniques have become indispensable tools in biological research and medical diagnostics. Conventional 3D imaging approaches employ focal stack collection to image different planes of the cell. In this work, we present the design and fabrication of a slanted channel microfluidic chip for 3D fluorescence imaging of cells in flow. The approach employs slanted microfluidic channels fabricated in glass using ultrafast laser inscription. The slanted nature of the microfluidic channels ensures that samples come into and go out of focus, as they pass through the microscope imaging field of view. This novel approach enables the collection of focal stacks in a straight-forward and automated manner, even with off-the-shelf microscopes that are not equipped with any motorized translation/rotation sample stages. The presented approach not only simplifies conventional focal stack collection, but also enhances the capabilities of a regular widefield fluorescence microscope to match the features of a sophisticated confocal microscope. We demonstrate the retrieval of sectioned slices of microspheres and cells, with the use of computational algorithms to enhance the signal-to-noise ratio (SNR) in the collected raw images. The retrieved sectioned images have been used to visualize fluorescent microspheres and bovine sperm cell nucleus in 3D while using a regular widefield fluorescence microscope. We have been able to achieve sectioning of approximately 200 slices per cell, which corresponds to a spatial translation of ∼ 15 nm per slice along the optical axis of the microscope.

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

    Science.gov (United States)

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

    2014-10-21

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

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

    Science.gov (United States)

    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.

  6. Holographic display system for dynamic synthesis of 3D light fields with increased space bandwidth product.

    Science.gov (United States)

    Agour, Mostafa; Falldorf, Claas; Bergmann, Ralf B

    2016-06-27

    We present a new method for the generation of a dynamic wave field with high space bandwidth product (SBP). The dynamic wave field is generated from several wave fields diffracted by a display which comprises multiple spatial light modulators (SLMs) each having a comparably low SBP. In contrast to similar approaches in stereoscopy, we describe how the independently generated wave fields can be coherently superposed. A major benefit of the scheme is that the display system may be extended to provide an even larger display. A compact experimental configuration which is composed of four phase-only SLMs to realize the coherent combination of independent wave fields is presented. Effects of important technical parameters of the display system on the wave field generated across the observation plane are investigated. These effects include, e.g., the tilt of the individual SLM and the gap between the active areas of multiple SLMs. As an example of application, holographic reconstruction of a 3D object with parallax effects is demonstrated. PMID:27410593

  7. Earthquake Source Parameters Relationships from 3D Rough Fault Dynamic Rupture

    Science.gov (United States)

    Yao, Q.; Day, S. M.; Shi, Z.

    2015-12-01

    Fault surface roughness has a strong influence on the distribution of stress around the fault, and affects the dynamics of the earthquake process. In particular, roughness influences the distribution of the parameters conventionally used to describe fault slip in, for example, kinematic modeling of strong ground motion. We explore the effect of the fault roughness on earthquake source parameters through the statistical analysis of a large suite of 3D rupture simulations. We have built a database of more than 1000 simulated dynamic ruptures based on different rough fault profiles and relative-strength (S) ratios, and have quantitatively analyzed the correlation between earthquake source parameter pairs.. In the subshear propagation-speed regime, we find the following relationships: (1) Rise time, total slip and peak slip rate each decrease with increasing roughness. (2) Rupture velocity is weakly positively related to slip, and the relationship is stronger with increasing roughness. We also explore how peak slip rate, rise time and different pairs of source parameters correlations are affected by fault roughness. This work may give useful guidance for use in kinematic rupture-source generators and help improve methods for ground strong motion prediction.

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

    CERN Document Server

    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...

  9. A general approach for time-supersampling of 3D-PIV data by the vortex-in-cell method

    Science.gov (United States)

    Scarano, Fulvio; Schneiders, Jan; Dwight, Richard; Aerospace Engineering/Aerodynamics Team

    2013-11-01

    Advancements of tomographic PIV [1] have led into 3D time-resolved experiments to study the dynamical evolution of 3D turbulent flows [2]. The known bottleneck of Tomo-PIV is the high laser power required to illuminate large volumes in airflows, which becomes critical beyond 10 kHz. Time-super-sampling is an approach to reduce the sampling rate, proven for frozen turbulence where the advection model yields a significant increase of temporal resolution [3]. Instead, in separated flows, the advection principle yields unacceptable distortions. The use of Navier-Stokes numerical calculations with the vortex-in-cell (VIC) method is proposed herein. The assumption is made of inviscid incompressible flow [4]. The spatial-resolution of the data is exploited to increase the temporal resolution. The dynamical evolution of the vorticity and velocity field between subsequent snapshots in the 3D domain is numerically evaluated. The verification with fully time resolved data of a circular jet indicates a substantial increase of temporal resolution. Interestingly, data sampled below the Nyquist limit could be reconstructed faithfully, indicating the potential of VIC in alleviating requirements on PIV measurement rate. Work supported by the European Research Council grant 202887.

  10. The influence of printing parameters on cell survival rate and printability in microextrusion-based 3D cell printing technology.

    Science.gov (United States)

    Zhao, Yu; Li, Yang; Mao, Shuangshuang; Sun, Wei; Yao, Rui

    2015-11-02

    Three-dimensional (3D) cell printing technology has provided a versatile methodology to fabricate cell-laden tissue-like constructs and in vitro tissue/pathological models for tissue engineering, drug testing and screening applications. However, it still remains a challenge to print bioinks with high viscoelasticity to achieve long-term stable structure and maintain high cell survival rate after printing at the same time. In this study, we systematically investigated the influence of 3D cell printing parameters, i.e. composition and concentration of bioink, holding temperature and holding time, on the printability and cell survival rate in microextrusion-based 3D cell printing technology. Rheological measurements were utilized to characterize the viscoelasticity of gelatin-based bioinks. Results demonstrated that the bioink viscoelasticity was increased when increasing the bioink concentration, increasing holding time and decreasing holding temperature below gelation temperature. The decline of cell survival rate after 3D cell printing process was observed when increasing the viscoelasticity of the gelatin-based bioinks. However, different process parameter combinations would result in the similar rheological characteristics and thus showed similar cell survival rate after 3D bioprinting process. On the other hand, bioink viscoelasticity should also reach a certain point to ensure good printability and shape fidelity. At last, we proposed a protocol for 3D bioprinting of temperature-sensitive gelatin-based hydrogel bioinks with both high cell survival rate and good printability. This research would be useful for biofabrication researchers to adjust the 3D bioprinting process parameters quickly and as a referable template for designing new bioinks.

  11. Culturing and applications of rotating wall vessel bioreactor derived 3D epithelial cell models.

    Science.gov (United States)

    Radtke, Andrea L; Herbst-Kralovetz, Melissa M

    2012-04-03

    Cells and tissues in the body experience environmental conditions that influence their architecture, intercellular communications, and overall functions. For in vitro cell culture models to accurately mimic the tissue of interest, the growth environment of the culture is a critical aspect to consider. Commonly used conventional cell culture systems propagate epithelial cells on flat two-dimensional (2-D) impermeable surfaces. Although much has been learned from conventional cell culture systems, many findings are not reproducible in human clinical trials or tissue explants, potentially as a result of the lack of a physiologically relevant microenvironment. Here, we describe a culture system that overcomes many of the culture condition boundaries of 2-D cell cultures, by using the innovative rotating wall vessel (RWV) bioreactor technology. We and others have shown that organotypic RWV-derived models can recapitulate structure, function, and authentic human responses to external stimuli similarly to human explant tissues (1-6). The RWV bioreactor is a suspension culture system that allows for the growth of epithelial cells under low physiological fluid shear conditions. The bioreactors come in two different formats, a high-aspect rotating vessel (HARV) or a slow-turning lateral vessel (STLV), in which they differ by their aeration source. Epithelial cells are added to the bioreactor of choice in combination with porous, collagen-coated microcarrier beads (Figure 1A). The cells utilize the beads as a growth scaffold during the constant free fall in the bioreactor (Figure 1B). The microenvironment provided by the bioreactor allows the cells to form three-dimensional (3-D) aggregates displaying in vivo-like characteristics often not observed under standard 2-D culture conditions (Figure 1D). These characteristics include tight junctions, mucus production, apical/basal orientation, in vivo protein localization, and additional epithelial cell-type specific properties

  12. 3D nanochannel electroporation for high-throughput cell transfection with high uniformity and dosage control.

    Science.gov (United States)

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

    2016-01-01

    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 cm(2) 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. PMID:26309218

  13. 3D nanochannel electroporation for high-throughput cell transfection with high uniformity and dosage control.

    Science.gov (United States)

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

    2016-01-01

    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 cm(2) 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.

  14. 3D photonic crystal intermediate reflector for micromorph thin-film tandem solar cell

    Energy Technology Data Exchange (ETDEWEB)

    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.)

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

    CERN Document Server

    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.

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

    DEFF Research Database (Denmark)

    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...... that a precise dose can be provided in a manner similar to in vivo studies. This avoided correction of the actual dose given based on a protein determination after treatment (when some cells may have lysed). Conversion of published in vitro LC50 data (mM) for six common drugs (acetaminophen, amiodarone...

  17. 3D airflow dynamics over transverse ridges Mpekweni, South Africa: implications for dune field migration behaviour

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    OpenAIRE

    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 ...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    OpenAIRE

    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 ...

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  5. 3D culture of adult mouse neural stem cells within functionalized self-assembling peptide scaffolds

    Directory of Open Access Journals (Sweden)

    Cunha C

    2011-05-01

    Full Text Available Carla Cunha1,2, Silvia Panseri3,4, Omar Villa1,2, Diego Silva1,2, Fabrizio Gelain1,21Department of Biotechnology and Biosciences, University of Milano-Bicocca; 2Center for Nanomedicine and Tissue Engineering, CNTE – A.O. Ospedale Niguarda Ca' Granda, Milan; 3Laboratory of Biomechanics and Technology Innovation, Rizzoli Orthopaedic Institute, Bologna; 4Laboratory of Nano-Biomagnetism, Institute of Science and Technology for Ceramics, National Research Council, Faenza, ItalyAbstract: Three-dimensional (3D in vitro models of cell culture aim to fill the gap between the standard two-dimensional cell studies and the in vivo environment. Especially for neural tissue regeneration approaches where there is little regenerative capacity, these models are important for mimicking the extracellular matrix in providing support, allowing the natural flow of oxygen, nutrients, and growth factors, and possibly favoring neural cell regrowth. We have previously demonstrated that a new self-assembling nanostructured biomaterial, based on matrigel, was able to support adult neural stem cell (NSC culture. In this study, we developed a new 3D cell culture system that takes advantage of the nano- and microfiber assembling process, under physiologic conditions, of these biomaterials. The assembled scaffold forms an intricate and biologically active matrix that displays specifically designed functional motifs: RGD (Arg-Gly-Asp, BMHP1 (bone marrow homing peptide 1, and BMHP2, for the culture of adult NSCs. These scaffolds were prepared at different concentrations, and microscopic examination of the cell-embedded scaffolds showed that NSCs are viable and they proliferate and differentiate within the nanostructured environment of the scaffold. Such a model has the potential to be tailored to develop ad hoc designed peptides for specific cell lines.Keywords: biomaterials, tissue engineering, 3D in vitro model

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

    CERN Document Server

    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...

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

    CERN Document Server

    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...

  8. Spectral history modeling in the reactor dynamics code DYN3D

    International Nuclear Information System (INIS)

    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.

  9. Automatic Reconstruction of Fault Networks from Seismicity Catalogs: 3D Optimal Anisotropic Dynamic Clustering

    CERN Document Server

    Ouillon, G; Sornette, D; Ouillon, Guy; Ducorbier, Caroline; Sornette, Didier

    2007-01-01

    We propose a new pattern recognition method that is able to reconstruct the 3D structure of the active part of a fault network using the spatial location of earthquakes. The method is a generalization of the so-called dynamic clustering method, that originally partitions a set of datapoints into clusters, using a global minimization criterion over the spatial inertia of those clusters. The new method improves on it by taking into account the full spatial inertia tensor of each cluster, in order to partition the dataset into fault-like, anisotropic clusters. Given a catalog of seismic events, the output is the optimal set of plane segments that fits the spatial structure of the data. Each plane segment is fully characterized by its location, size and orientation. The main tunable parameter is the accuracy of the earthquake localizations, which fixes the resolution, i.e. the residual variance of the fit. The resolution determines the number of fault segments needed to describe the earthquake catalog, the better...

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

    Science.gov (United States)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. Effect of a Material Contrast on a Dynamic Rupture: 3-D

    Science.gov (United States)

    Harris, R. A.; Day, S. M.

    2003-12-01

    We use numerical simulations of spontaneously propagating ruptures to examine the effect of a material contrast on earthquake dynamics. We specifically study the case of a lateral contrast whereby the fault is the boundary between two different rock-types. This scenario was previously studied in two-dimensions by Harris and Day [BSSA, 1997], and Andrews and Ben-Zion [JGR, 1997], in addition to subsequent 2-D studies, but it has not been known if the two-dimensional results are applicable to the real three-dimensional world. The addition of the third dimension implies a transition from pure mode II (i.e., plane-strain) to mixed-mode crack dynamics, which is more complicated since in mode II the shear and normal stresses are coupled whereas in mode III (i.e., anti-plane strain) they are not coupled. We use a slip-weakening fracture criterion and examine the effect on an earthquake rupture of material contrasts of up to 50 percent across the fault zone. We find a surprisingly good agreement between our earlier 2-D results, and our 3-D results for along-strike propagation. We find that the analytical solution presented in Harris and Day [BSSA, 1997] does an excellent job at predicting the bilateral, along-strike rupture velocities for the three-dimensional situation. In contrast, the along-dip propagation behaves much as expected for a purely mode-III rupture, with the rupture velocities up-dip and down-dip showing the expected symmetries.

  13. 3D hepatic cultures simultaneously maintain primary hepatocyte and liver sinusoidal endothelial cell phenotypes.

    Directory of Open Access Journals (Sweden)

    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

  14. Image informatics for studying signal transduction in cells interacting with 3D matrices

    Science.gov (United States)

    Tzeranis, Dimitrios S.; Guo, Jin; Chen, Chengpin; Yannas, Ioannis V.; Wei, Xunbin; So, Peter T. C.

    2014-03-01

    Cells sense and respond to chemical stimuli on their environment via signal transduction pathways, complex networks of proteins whose interactions transmit chemical information. This work describes an implementation of image informatics, imaging-based methodologies for studying signal transduction networks. The methodology developed focuses on studying signal transduction networks in cells that interact with 3D matrices. It utilizes shRNA-based knock down of network components, 3D high-content imaging of cells inside the matrix by spectral multi-photon microscopy, and single-cell quantification using features that describe both cell morphology and cell-matrix adhesion pattern. The methodology is applied in a pilot study of TGFβ signaling via the SMAD pathway in fibroblasts cultured inside porous collagen-GAG scaffolds, biomaterials similar to the ones used clinically to induce skin regeneration. Preliminary results suggest that knocking down all rSMAD components affects fibroblast response to TGFβ1 and TGFβ3 isoforms in different ways, and suggest a potential role for SMAD1 and SMAD5 in regulating TGFβ isoform response. These preliminary results need to be verified with proteomic results that can provide solid evidence about the particular role of individual components of the SMAD pathway.

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

    DEFF Research Database (Denmark)

    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...... of the CFD analysis, the dynamic response of the pressure chamber and valve movement of a digital displacement motor is presented, along with the total efficiency of a multi-chamber motor at full and partial displacement. Simulation predicts that pressure over- and undershoot may be reduced to a few percent....... 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...

  16. Reconstruction of 3D ion beam micro-tomography data for applications in Cell Biology

    Energy Technology Data Exchange (ETDEWEB)

    Habchi, C. [Universite de Bordeaux, Centre d' Etudes Nucleaires de Bordeaux Gradignan, UMR 5797, Gradignan F-33175 (France)], E-mail: habchi@cenbg.in2p3.fr; Nguyen, D.T.; Barberet, Ph. [Universite de Bordeaux, Centre d' Etudes Nucleaires de Bordeaux Gradignan, UMR 5797, Gradignan F-33175 (France); Incerti, S. [CNRS/IN2P3, Centre d' Etudes Nucleaires de Bordeaux Gradignan, UMR 5797, Gradignan F-33175 (France); Moretto, Ph. [Universite de Bordeaux, Centre d' Etudes Nucleaires de Bordeaux Gradignan, UMR 5797, Gradignan F-33175 (France); Sakellariou, A. [Research School of Physical Sciences and Engineering, Australian National University, Canberra ACT 0200 (Australia); Seznec, H. [CNRS/IN2P3, Centre d' Etudes Nucleaires de Bordeaux Gradignan, UMR 5797, Gradignan F-33175 (France)

    2009-06-15

    The DISRA (Discrete Image Space Reconstruction Algorithm) reconstruction code, created by A. Sakellariou, was conceived for the ideal case of complete three-dimensional (3D) PIXET (Particle Induced X-ray Emission Tomography) data. This implies two major difficulties for biological samples: first, the long duration of such experiments and second, the subsequent damage that occurs on such fragile specimens. For this reason, the DISRA code was extended at CENBG in order to probe isolated PIXET slices, taking into account the sample structure and mass density provided by 3D STIMT (Scanning Transmission Ion Microscopy Tomography) in the volume of interest. This modified version was tested on a phantom sample and first results on human cancer cells are also presented.

  17. Reconstruction of 3D ion beam micro-tomography data for applications in Cell Biology

    Science.gov (United States)

    Habchi, C.; Nguyen, D. T.; Barberet, Ph.; Incerti, S.; Moretto, Ph.; Sakellariou, A.; Seznec, H.

    2009-06-01

    The DISRA (Discrete Image Space Reconstruction Algorithm) reconstruction code, created by A. Sakellariou, was conceived for the ideal case of complete three-dimensional (3D) PIXET (Particle Induced X-ray Emission Tomography) data. This implies two major difficulties for biological samples: first, the long duration of such experiments and second, the subsequent damage that occurs on such fragile specimens. For this reason, the DISRA code was extended at CENBG in order to probe isolated PIXET slices, taking into account the sample structure and mass density provided by 3D STIMT (Scanning Transmission Ion Microscopy Tomography) in the volume of interest. This modified version was tested on a phantom sample and first results on human cancer cells are also presented.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  3. Fabrication of 3-D Reconstituted Organoid Arrays by DNA-Programmed Assembly of Cells (DPAC).

    Science.gov (United States)

    Todhunter, Michael E; Weber, Robert J; Farlow, Justin; Jee, Noel Y; Cerchiari, Alec E; Gartner, Zev J

    2016-01-01

    Tissues are the organizational units of function in metazoan organisms. Tissues comprise an assortment of cellular building blocks, soluble factors, and extracellular matrix (ECM) composed into specific three-dimensional (3-D) structures. The capacity to reconstitute tissues in vitro with the structural complexity observed in vivo is key to understanding processes such as morphogenesis, homeostasis, and disease. In this article, we describe DNA-programmed assembly of cells (DPAC), a method to fabricate viable, functional arrays of organoid-like tissues within 3-D ECM gels. In DPAC, dissociated cells are chemically functionalized with degradable oligonucleotide "Velcro," allowing rapid, specific, and reversible cell adhesion to a two-dimensional (2-D) template patterned with complementary DNA. An iterative assembly process builds up organoids, layer-by-layer, from this initial 2-D template and into the third dimension. Cleavage of the DNA releases the completed array of tissues that are captured and fully embedded in ECM gels for culture and observation. DPAC controls the size, shape, composition, and spatial heterogeneity of organoids and permits positioning of constituent cells with single-cell resolution even within cultures several centimeters long. © 2016 by John Wiley & Sons, Inc. PMID:27622567

  4. An Innovative Hybrid 3D Analytic-Numerical Approach for System Level Modelling of PEM Fuel Cells

    Directory of Open Access Journals (Sweden)

    Gregor Tavčar

    2013-10-01

    Full Text Available The PEM fuel cell model presented in this paper is based on modelling species transport and coupling electrochemical reactions to species transport in an innovative way. Species transport is modelled by obtaining a 2D analytic solution for species concentration distribution in the plane perpendicular to the gas-flow and coupling consecutive 2D solutions by means of a 1D numerical gas-flow model. The 2D solution is devised on a jigsaw puzzle of multiple coupled domains which enables the modelling of parallel straight channel fuel cells with realistic geometries. Electrochemical and other nonlinear phenomena are coupled to the species transport by a routine that uses derivative approximation with prediction-iteration. A hybrid 3D analytic-numerical fuel cell model of a laboratory test fuel cell is presented and evaluated against a professional 3D computational fluid dynamic (CFD simulation tool. This comparative evaluation shows very good agreement between results of the presented model and those of the CFD simulation. Furthermore, high accuracy results are achieved at computational times short enough to be suitable for system level simulations. This computational efficiency is owed to the semi-analytic nature of its species transport modelling and to the efficient computational coupling of electrochemical kinetics and species transport.

  5. Current automated 3D cell detection methods are not a suitable replacement for manual stereologic cell counting

    Directory of Open Access Journals (Sweden)

    Christoph eSchmitz

    2014-05-01

    Full Text Available Stereologic cell counting has had a major impact on the field of neuroscience. A major bottleneck in stereologic cell counting is that the user must manually decide whether or not each cell is counted according to three-dimensional (3D stereologic counting rules by visual inspection within hundreds of microscopic fields-of-view per investigated brain or brain region. Reliance on visual inspection forces stereologic cell counting to be very labor-intensive and time-consuming, and is the main reason why biased, non-stereologic two-dimensional (2D cell counting approaches have remained in widespread use. We present an evaluation of the performance of modern automated cell detection and segmentation algorithms as a potential alternative to the manual approach in stereologic cell counting. The image data used in this study were 3D microscopic images of thick brain tissue sections prepared with a variety of commonly used nuclear and cytoplasmic stains. The evaluation compared the numbers and locations of cells identified unambiguously and counted exhaustively by an expert observer with those found by three automated 3D cell detection algorithms: nuclei segmentation from the FARSIGHT toolkit, nuclei segmentation by 3D multiple level set methods, and the 3D object counter plug-in for ImageJ. Of these methods, FARSIGHT performed best, with true-positive detection rates between 38–99% and false-positive rates from 3.6–82%. The results demonstrate that the current automated methods suffer from lower detection rates and higher false-positive rates than are acceptable for obtaining valid estimates of cell numbers. Thus, at present, stereologic cell counting with manual decision for object inclusion according to unbiased stereologic counting rules remains the only adequate method for unbiased cell quantification in histologic tissue sections.

  6. 3D measurements of live cells via digital holographic microscopy and terahertz spectroscopy

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  9. 3D cut-cell modelling for high-resolution atmospheric simulations

    CERN Document Server

    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...

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  14. The 3-D dynamics of slab break-off and implications for continental collision zones

    Science.gov (United States)

    van Hunen, Jeroen; Allen, Mark

    2010-05-01

    Some of the world best studied mountain ranges are a result of continental collision, such as the Himalayas, Zagros mountains, and the Alps. Continental collision forms the last stage of the closure of an oceanic basin, and leads to the slow-down or complete cessation of the subduction process. Previously subducted slab material will experience a period of thermal warming (Gerya et al., 2004) and/or a larger tensile stress, and will eventually weaken, yield and sink into the mantle. This process has potentially important implications for the thermal and stress regime of the overlying convergence zone, and has been held responsible for various phenomena such as late-stage magmatism (Davies and von Blanckenburg, 1995) and surface uplift or depression (van der Meulen et al., 1998, Buiter et al., 2002). Even though the collision process itself is relatively short-lived compared to the preceding oceanic subduction, its remnants are often preserved, and probably provide a valuable window into the plate tectonic process during the Proterozoic and perhaps the Archaean (e.g. Calvert et al., 1995). The three-dimensional nature of this break-off process has previously been discussed with conceptual models. E.g. slab break-off has been suggested to propagate laterally through an advancing tear (Wortel and Spakman, 2000). In this study we present 3D numerical results of the evolution of slab break-off. We focus on the development and evolution of a laterally migrating slab tear, and present results on the sensitivity of this process to the geometry of the closing oceanic basin, the tensile stresses in and the rheological properties of the slab, and the thermal state of the surrounding mantle. By comparing our numerical results to previously published analogue results (Regard et al., 2004) and various tomographic, structural, and magmatic observations of well-studied subduction collision systems, we are able to extract valuable insights in to the dynamics and strength of

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

    Science.gov (United States)

    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

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

    DEFF Research Database (Denmark)

    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......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...

  17. Tuning 3D Collagen Matrix Stiffness Independently of Collagen Concentration Modulates Endothelial Cell Behavior

    Science.gov (United States)

    Mason, Brooke N.; Starchenko, Alina; Williams, Rebecca M.; Bonassar, Lawrence J.; Reinhart-King, Cynthia A.

    2012-01-01

    Numerous studies have described the effects of matrix stiffening on cell behavior using two dimensional (2D) synthetic surfaces; however less is known about the effects of matrix stiffening on cells embedded in three dimensional (3D) in vivo-like matrices. A primary limitation in investigating the effects of matrix stiffness in 3D is the lack of materials that can be tuned to control stiffness independently of matrix density. Here, we use collagen-based scaffolds where the mechanical properties are tuned using non-enzymatic glycation of the collagen in solution, prior to polymerization. Collagen solutions glycated prior to polymerization result in collagen gels with a 3-fold increase in compressive modulus without significant changes to the collagen architecture. Using these scaffolds, we show that endothelial cell spreading increases with matrix stiffness, as does the number and length of angiogenic sprouts and the overall spheroid outgrowth. Differences in sprout length are maintained even when the receptor for advanced glycation endproducts is inhibited. Our results demonstrate the ability to de-couple matrix stiffness from matrix density and structure in collagen gels, and that increased matrix stiffness results in increased sprouting and outgrowth. PMID:22902816

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Directory of Open Access Journals (Sweden)

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

    International Nuclear Information System (INIS)

    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)

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

    Science.gov (United States)

    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

  2. AC electric field induced dipole-based on-chip 3D cell rotation.

    Science.gov (United States)

    Benhal, Prateek; Chase, J Geoffrey; Gaynor, Paul; Oback, Björn; Wang, Wenhui

    2014-08-01

    The precise rotation of suspended cells is one of the many fundamental manipulations used in a wide range of biotechnological applications such as cell injection and enucleation in nuclear transfer (NT) cloning. Noticeably scarce among the existing rotation techniques is the three-dimensional (3D) rotation of cells on a single chip. Here we present an alternating current (ac) induced electric field-based biochip platform, which has an open-top sub-mm square chamber enclosed by four sidewall electrodes and two bottom electrodes, to achieve rotation about the two axes, thus 3D cell rotation. By applying an ac potential to the four sidewall electrodes, an in-plane (yaw) rotating electric field is generated and in-plane rotation is achieved. Similarly, by applying an ac potential to two opposite sidewall electrodes and the two bottom electrodes, an out-of-plane (pitch) rotating electric field is generated and rolling rotation is achieved. As a prompt proof-of-concept, bottom electrodes were constructed with transparent indium tin oxide (ITO) using the standard lift-off process and the sidewall electrodes were constructed using a low-cost micro-milling process and then assembled to form the chip. Through experiments, we demonstrate rotation of bovine oocytes of ~120 μm diameter about two axes, with the capability of controlling the rotation direction and the rate for each axis through control of the ac potential amplitude, frequency, and phase shift, and cell medium conductivity. The maximum observed rotation rate reached nearly 140° s⁻¹, while a consistent rotation rate reached up to 40° s⁻¹. Rotation rate spectra for zona pellucida-intact and zona pellucida-free oocytes were further compared and found to have no effective difference. This simple, transparent, cheap-to-manufacture, and open-top platform allows additional functional modules to be integrated to become a more powerful cell manipulation system.

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

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

    2016-06-01

    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

  6. Multiplexing encoding method for full-color dynamic 3D holographic display.

    Science.gov (United States)

    Xue, Gaolei; Liu, Juan; Li, Xin; Jia, Jia; Zhang, Zhao; Hu, Bin; Wang, Yongtian

    2014-07-28

    The multiplexing encoding method is proposed and demonstrated for reconstructing colorful images accurately by using single phase-only spatial light modulator (SLM). It will encode the light waves at different wavelengths into one pure-phase hologram at the same time based on the analytic formulas. The three-dimensional (3D) images can be reconstructed clearly when the light waves at different wavelengths are incident into the encoding hologram. Numerical simulations and optical experiments for 2D and 3D colorful images are performed. The results show that the colorful reconstructed images with high quality are achieved successfully. The proposed multiplexing method is a simple and fast encoding approach and the size of the system is small and compact. It is expected to be used for realizing full-color 3D holographic display in future.

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

    KAUST Repository

    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.

  8. High power density microbial fuel cell with flexible 3D graphene-nickel foam as anode

    Science.gov (United States)

    Wang, Hanyu; Wang, Gongming; Ling, Yichuan; Qian, Fang; Song, Yang; Lu, Xihong; Chen, Shaowei; Tong, Yexiang; Li, Yat

    2013-10-01

    The structure and electrical conductivity of anode play a significant role in the power generation of microbial fuel cells (MFCs). In this study, we developed a three-dimensional (3D) reduced graphene oxide-nickel (denoted as rGO-Ni) foam as an anode for MFC through controlled deposition of rGO sheets onto the nickel foam substrate. The loading amount of rGO sheets and electrode surface area can be controlled by the number of rGO loading cycles. 3D rGO-Ni foam anode provides not only a large accessible surface area for microbial colonization and electron mediators, but also a uniform macro-porous scaffold for effective mass diffusion of the culture medium. Significantly, at a steady state of the power generation, the MFC device with flexible rGO-Ni electrodes produced an optimal volumetric power density of 661 W m-3 calculated based on the volume of anode material, or 27 W m-3 based on the volume of the anode chamber. These values are substantially higher than that of plain nickel foam, and other conventional carbon based electrodes (e.g., carbon cloth, carbon felt, and carbon paper) measured in the same conditions. To our knowledge, this is the highest volumetric power density reported for mL-scale MFC device with a pure strain of Shewanella oneidensis MR-1. We also demonstrated that the MFC device can be operated effectively in a batch-mode at least for a week. These new 3D rGO-Ni electrodes show great promise for improving the power generation of MFC devices.The structure and electrical conductivity of anode play a significant role in the power generation of microbial fuel cells (MFCs). In this study, we developed a three-dimensional (3D) reduced graphene oxide-nickel (denoted as rGO-Ni) foam as an anode for MFC through controlled deposition of rGO sheets onto the nickel foam substrate. The loading amount of rGO sheets and electrode surface area can be controlled by the number of rGO loading cycles. 3D rGO-Ni foam anode provides not only a large accessible

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

    International Nuclear Information System (INIS)

    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

  10. 3D Dynamics of Magnetopause Reconnection Using Hall-MHD Global Simulations

    Science.gov (United States)

    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.

  11. A Dynamic Platform for Developing 3D Facial Avatars in a Networked Virtual Environment

    Directory of Open Access Journals (Sweden)

    Anis Zarrad

    2016-01-01

    Full Text Available Avatar facial expression and animation in 3D collaborative virtual environment (CVE systems are reconstructed through a complex manipulation of muscles, bones, and wrinkles in 3D space. The need for a fast and easy reconstruction approach has emerged in the recent years due to its application in various domains: 3D disaster management, virtual shopping, and military training. In this work we proposed a new script language based on atomic parametric action to easily produce real-time facial animation. To minimize use of the game engine, we introduced script-based component where the user introduces simple short script fragments to feed the engine with a new animation on the fly. During runtime, when an embedded animation is required, an xml file is created and injected into the game engine without stopping or restarting the engine. The resulting animation method preserves the real-time performance because the modification occurs not through the modification of the 3D code that describes the CVE and its objects but rather through modification of the action scenario that rules when an animation happens or might happen in that specific situation.

  12. 3D Dynamic Modeling of the Head-Neck Complex for Fast Eye and Head Orientation Movements Research

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

  16. 3D structure determination of a protein in living cells using paramagnetic NMR spectroscopy.

    Science.gov (United States)

    Pan, Bin-Bin; Yang, Feng; Ye, Yansheng; Wu, Qiong; Li, Conggang; Huber, Thomas; Su, Xun-Cheng

    2016-08-11

    Determining the three-dimensional structure of a protein in living cells remains particularly challenging. We demonstrated that the integration of site-specific tagging proteins and GPS-Rosetta calculations provides a fast and effective way of determining the structures of proteins in living cells, and in principle the interactions and dynamics of protein-ligand complexes. PMID:27470136

  17. 3D Printing Bioceramic Porous Scaffolds with Good Mechanical Property and Cell Affinity.

    Directory of Open Access Journals (Sweden)

    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.

  18. 3D Printing Bioceramic Porous Scaffolds with Good Mechanical Property and Cell Affinity.

    Science.gov (United States)

    Chang, Chih-Hao; Lin, Chih-Yang; Liu, Fwu-Hsing; Chen, Mark Hung-Chih; Lin, Chun-Pin; Ho, Hong-Nerng; Liao, Yunn-Shiuan

    2015-01-01

    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.

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

    Science.gov (United States)

    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

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

    OpenAIRE

    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...

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

    OpenAIRE

    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...

  2. Motion field estimation for a dynamic scene using a 3D LiDAR.

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

  5. SURVIVAL OF LIVER CELLS, IMMOBILIZED ON 3D-MATRIXES, IN LIVER FAILURE MODEL

    Directory of Open Access Journals (Sweden)

    M. Y. Shagidulin

    2011-01-01

    Full Text Available It was examined a new method for correction of hepatic failure by transplantation of liver support biounit (liver cells, immobilized on biocompatible and biodegradable 3D-matrixes ElastoPOB® into small intestine mesentery. It was determined that after modeling of acute hepatic failure on dogs by 65–70% liver resection and transplantation liver support biounit the restoration of disturbed biochemical indecies (such as total protein, lactate, cytolytic ensymes-ALT, AST, ALP, LDH, fibrinogen, protrombine index and others took place more rapidly on 9–14th day instead of 18th day in control. It was made a preposition about efficiency of the suggested method for correction both acute hepatic failure because even 90 days after transplantation of liver support biounit alive hepatocytes and neogenic plethoric vessels, growing through matrix were revealed. 

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

    Science.gov (United States)

    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

  7. Effect of bioink properties on printability and cell viability for 3D bioplotting of embryonic stem cells.

    Science.gov (United States)

    Ouyang, Liliang; Yao, Rui; Zhao, Yu; Sun, Wei

    2016-01-01

    3D cell printing is an emerging technology for fabricating complex cell-laden constructs with precise and pre-designed geometry, structure and composition to overcome the limitations of 2D cell culture and conventional tissue engineering scaffold technology. This technology enables spatial manipulation of cells and biomaterials, also referred to as 'bioink', and thus allows study of cellular interactions in a 3D microenvironment and/or in the formation of functional tissues and organs. Recently, many efforts have been made to develop new bioinks and to apply more cell sources for better biocompatibility and biofunctionality. However, the influences of printing parameters on the shape fidelity of 3D constructs as well as on cell viability after the cell printing process have been poorly characterized. Furthermore, parameter optimization based on a specific cell type might not be suitable for other types of cells, especially cells with high sensibility. In this study, we systematically studied the influence of bioink properties and printing parameters on bioink printability and embryonic stem cell (ESC) viability in the process of extrusion-based cell printing, also known as bioplotting. A novel method was established to determine suitable conditions for bioplotting ESCs to achieve both good printability and high cell viability. The rheological properties of gelatin/alginate bioinks were evaluated to determine the gelation properties under different bioink compositions, printing temperatures and holding times. The bioink printability was characterized by a newly developed semi-quantitative method. The results demonstrated that bioinks with longer gelation times would result in poorer printability. The live/dead assay showed that ESC viability increased with higher printing temperatures and lower gelatin concentrations. Furthermore, an exponential relationship was obtained between ESC viability and induced shear stress. By defining the proper printability and

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

    Science.gov (United States)

    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. Consolidation and dynamics of 3D unsaturated porous seabed under rigid caisson breakwater loaded by hydrostatic pressure and wave

    Institute of Scientific and Technical Information of China (English)

    YE JianHong; JENG DongSheng; CHAN A H C

    2012-01-01

    In this study,based on the dynamic Biot's theory "u-p" approximation,a 3D finite element method (FEM) numerical soil model is developed,in which the Generalized Newmark-β method is adopted to determine the time integration.The developed 3D FEM soil model is a part of the coupled model PORO-WSSI 3D for 3D wave-seabed-marine structures interaction problem,and is validated by the analytical solution proposed by Wang (2000) for a laterally infinite seabed loaded by a uniform force.By adopting the developed 3D soil model,the consolidation of seabed under a caisson breakwater and hydrostatic pressure is investigated.The numerical results show that the caisson breakwater built on seabed has very significant effect on the stresses/displacements fields in the seabed foundation after the transient deformation and primary consolidation are completed.The parametric study indicates that the Young's modulus E of seabed is the most important parameter to affect the settlement of breakwater,and the displacement fields in seabed foundation.Taking the consolidation status as the initial condition,the interaction between ocean wave,caisson breakwater and seabed foundation is briefly investigated.The 3D ocean wave is determined by solving the Navier-Stokes equations with finite volume method (FVM).The numerical results indicate that there is intensive interaction between ocean wave,caisson breakwater and seabed foundation; and the breakwater indeed can effectively block the wave energy propagating to the coastline.

  10. Improved Human Bone Marrow Mesenchymal Stem Cell Osteogenesis in 3D Bioprinted Tissue Scaffolds with Low Intensity Pulsed Ultrasound Stimulation.

    Science.gov (United States)

    Zhou, Xuan; Castro, Nathan J; Zhu, Wei; Cui, Haitao; Aliabouzar, Mitra; Sarkar, Kausik; Zhang, Lijie Grace

    2016-09-06

    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.

  11. Improved Human Bone Marrow Mesenchymal Stem Cell Osteogenesis in 3D Bioprinted Tissue Scaffolds with Low Intensity Pulsed Ultrasound Stimulation.

    Science.gov (United States)

    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

  12. Improved Human Bone Marrow Mesenchymal Stem Cell Osteogenesis in 3D Bioprinted Tissue Scaffolds with Low Intensity Pulsed Ultrasound Stimulation

    Science.gov (United States)

    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/cm2 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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

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

    2012-06-01

    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 × 25 × 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). Immunocytoche mistry 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 biochemical 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.

  15. Exploring natural silk protein sericin for regenerative medicine: an injectable, photoluminescent, cell-adhesive 3D hydrogel

    Science.gov (United States)

    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.

  16. CARS and SHG microscopy to follow the collagen production in living human corneal fibroblasts and mesenchymal stem cells in fibrin gel 3D cultures

    CERN Document Server

    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...

  17. Interfacing polymeric scaffolds with primary pancreatic ductal adenocarcinoma cells to develop 3D cancer models.

    Science.gov (United States)

    Ricci, Claudio; Mota, Carlos; Moscato, Stefania; D'Alessandro, Delfo; Ugel, Stefano; Sartoris, Silvia; Bronte, Vincenzo; Boggi, Ugo; Campani, Daniela; Funel, Niccola; Moroni, Lorenzo; Danti, Serena

    2014-01-01

    We analyzed the interactions between human primary cells from pancreatic ductal adenocarcinoma (PDAC) and polymeric scaffolds to develop 3D cancer models useful for mimicking the biology of this tumor. Three scaffold types based on two biocompatible polymeric formulations, such as poly(vinyl alcohol)/gelatin (PVA/G) mixture and poly(ethylene oxide terephthalate)/poly(butylene terephthalate) (PEOT/PBT) copolymer, were obtained via different techniques, namely, emulsion and freeze-drying, compression molding followed by salt leaching, and electrospinning. In this way, primary PDAC cells interfaced with different pore topographies, such as sponge-like pores of different shape and size or nanofiber interspaces. The aim of this study was to investigate the influence played by the scaffold architecture over cancerous cell growth and function. In all scaffolds, primary PDAC cells showed good viability and synthesized tumor-specific metalloproteinases (MMPs) such as MMP-2, and MMP-9. However, only sponge-like pores, obtained via emulsion-based and salt leaching-based techniques allowed for an organized cellular aggregation very similar to the native PDAC morphological structure. Differently, these cell clusters were not observed on PEOT/PBT electrospun scaffolds. MMP-2 and MMP-9, as active enzymes, resulted to be increased in PVA/G and PEOT/PBT sponges, respectively. These findings suggested that spongy scaffolds supported the generation of pancreatic tumor models with enhanced aggressiveness. In conclusion, primary PDAC cells showed diverse behaviors while interacting with different scaffold types that can be potentially exploited to create stage-specific pancreatic cancer models likely to provide new knowledge on the modulation and drug susceptibility of MMPs.

  18. Improving organic tandem solar cells based on water-processed nanoparticles by quantitative 3D nanoimaging.

    Science.gov (United States)

    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

  19. X-ray tomography: Biological cells in 3-D at better than 50 nm resolution

    International Nuclear Information System (INIS)

    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

  20. Magnetohydrodynamics dynamical relaxation of coronal magnetic fields. IV. 3D tilted nulls

    CERN Document Server

    Fuentes-Fernandez, Jorge

    2013-01-01

    In this paper we study current accumulations in 3D "tilted" nulls formed by a folding of the spine and fan. A non-zero component of current parallel to the fan is required such that the null's fan plane and spine are not perpendicular. Our aims are to provide valid magnetohydrostatic equilibria and to describe the current accumulations in various cases involving finite plasma pressure.To create our equilibrium current structures we use a full, non-resistive, magnetohydrodynamic (MHD) code so that no reconnection is allowed. A series of experiments are performed in which a perturbed 3D tilted null relaxes towards an equilibrium via real, viscous damping forces. Changes to the initial plasma pressure and to magnetic parameters are investigated systematically.An initially tilted fan is associated with a non-zero Lorentz force that drives the fan and spine to collapse towards each other, in a similar manner to the collapse of a 2D X-point. In the final equilibrium state for an initially radial null with only the ...

  1. Heart wall motion analysis by dynamic 3D strain rate imaging from tissue Doppler echocardiography

    Science.gov (United States)

    Hastenteufel, Mark; Wolf, Ivo; de Simone, Raffaele; Mottl-Link, Sibylle; Meinzer, Hans-Peter

    2002-04-01

    The knowledge about the complex three-dimensional (3D) heart wall motion pattern, particular in the left ventricle, provides valuable information about potential malfunctions, e.g., myocardial ischemia. Nowadays, echocardiography (cardiac ultrasound) is the predominant technique for evaluation of cardiac function. Beside morphology, tissue velocities can be obtained by Doppler techniques (tissue Doppler imaging, TDI). Strain rate imaging (SRI) is a new technique to diagnose heart vitality. It provides information about the contraction ability of the myocardium. Two-dimensional color Doppler echocardiography is still the most important clinical method for estimation of morphology and function. Two-dimensional methods leads to a lack of information due to the three-dimensional overall nature of the heart movement. Due to this complex three-dimensional motion pattern of the heart, the knowledge about velocity and strain rate distribution over the whole ventricle can provide more valuable diagnostic information about motion disorders. For the assessment of intracardiac blood flow three-dimensional color Doppler has already shown its clinical utility. We have developed methods to produce strain rate images by means of 3D tissue Doppler echocardiography. The tissue Doppler and strain rate images can be visualized and quantified by different methods. The methods are integrated into an interactively usable software environment, making them available in clinical everyday life. Our software provides the physician with a valuable tool for diagnosis of heart wall motion.

  2. High-speed dynamic 3D photoacoustic imaging of sentinel lymph node in a murine model using an ultrasound array.

    Science.gov (United States)

    Song, Liang; Kim, Chulhong; Maslov, Konstantin; Shung, K Kirk; Wang, Lihong V

    2009-08-01

    Noninvasive photoacoustic sentinel lymph node (SLN) mapping with high spatial resolution has the potential to improve the false negative rate and eliminate the use of radioactive tracers in SLN identification. In addition, the demonstrated high spatial resolution may enable physicians to replace SLN biopsy with fine needle aspiration biopsy, and thus reduce the risk of associated morbidity. The primary goal of this study is to demonstrate the feasibility of high-speed 3D photoacoustic imaging of the uptake and clearance dynamics of Evans blue dye in SLNs. The photoacoustic imaging system was developed with a 30 MHz ultrasound array and a kHz repetition rate laser system. It acquires one 3D photoacoustic image of 166 B-scan frames in 1 s, with axial, lateral, and elevational resolutions of 25, 70, and 200 microm, respectively. With optic-fiber based light delivery, the entire system is compact and is convenient to use. Upon injection of Evans blue, a blue dye currently used in clinical SLN biopsy, SLNs in mice and rats were accurately and noninvasively mapped in vivo using our imaging system. In our experiments, the SLNs were found to be located at approximately 0.65 mm below the skin surface in mice and approximately 1.2 mm in rats. In some cases, lymph vessels and lymphatic valves were also imaged. The dye dynamics--accumulation and clearance--in SLNs were quantitatively monitored by sequential 3D imaging with temporal resolution of as high as approximately 6 s. The demonstrated capability suggests that high-speed 3D photoacoustic imaging should facilitate the understanding of the dynamics of various dyes in SLNs and potentially help identify SLNs with high accuracy. PMID:19746805

  3. WARP3D-Release 10.8: Dynamic Nonlinear Analysis of Solids using a Preconditioned Conjugate Gradient Software Architecture

    Science.gov (United States)

    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

  4. Dynamics of Mantle Circulation Associated with Slab Window Formation: Insights from 3D Laboratory Models

    Science.gov (United States)

    Guillaume, B.; Funiciello, F.; Moroni, M.; Faccenna, C.; Martinod, J.

    2009-12-01

    Slab window can form either by the intersection of a spreading ridge with a subduction zone or because of internal deformation of the slab that leads to its disruption. The main consequences of this phenomenon are the modifications of the physical, chemical and thermal conditions in the backarc mantle that in turn affect the tectonic and magmatic evolution of the overriding plate. We performed laboratory models of a two-layer linear viscous slab (silicone putty)-upper mantle (glucose syrup) system to quantitatively investigate the pattern of mantle circulation within the slab window (using Feature Tracking image analysis technique) and its influence on the kinematics of the system. Two different geometries have been tested considering a window located (a) at slab edges or (b) within the slab. Kinematic consequences of slab window have been explored to understand the dynamics of the mantle-slab interaction. Configuration (a) implies a reduction of the slab width (W) during subduction and is characterized by toroidal fluxes around the slab edges. The abrupt opening of lateral slab windows produces an acceleration of the trench retreat and subduction velocity, such as 40% for a three-fold width reduction. We interpret this behavior as mostly due to the decrease in the toroidal flow inside subduction windows, scaling with W2. Configuration (b) has been designed to explore the pattern of mantle flow within the window in the case of a laterally constrained subduction system. Slab window, which had a width (Ww) fixed to 15 % of the slab width, opened in the trench-perpendicular direction. It produced the formation of two toroidal mantle cells, centered on the slab midpoint and laterally growing as the slab window enlarged. Particles extruded through the slab window did not mix with particles located in the mantle wedge, the boundary between both reaching distances from the trench up to 3×Ww in the trench-perpendicular direction, and up to 1.5×Ww from the window edge in

  5. Heritable Genetic Changes in Cells Recovered From Irradiated 3D Tissue Contracts. Final report

    Energy Technology Data Exchange (ETDEWEB)

    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'.

  6. Tuning Cell Differentiation into a 3D Scaffold Presenting a Pore Shape Gradient for Osteochondral Regeneration.

    Science.gov (United States)

    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

  7. Dynamic complex optical fields for optical manipulation, 3D microscopy, and photostimulation of neurotransmitters

    Science.gov (United States)

    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.

  8. Efficient Numerical Modeling of 3D, Half-Space, Slow-Slip and Quasi-Dynamic Earthquake Ruptures

    Science.gov (United States)

    Bradley, A. M.; Segall, P.

    2011-12-01

    Motivated by the hypothesis that dilatancy plays a critical role in faulting in subduction zones, we are developing FDRA2 (Fault Dynamics with the Radiation-damping Approximation), a software package to simulate three-dimensional quasi-dynamic faulting that includes rate-state friction, thermal pressurization, and dilatancy (following Segall and Rice [1995]) in a finite-width shear zone. This work builds on the two-dimensional simulations performed by FDRA1 (Bradley and Segall [AGU 2010], Segall and Bradley [submitted]). These simulations show that at lower background effective normal stress (\\bar σ), slow slip events occur spontaneously, whereas at higher \\bar σ , slip is inertially limited. At intermediate \\bar σ , dynamic events are followed by quiescent periods and then long durations of repeating slow slip events. Models with depth-dependent properties produce sequences similar to those observed in Cascadia. Like FDRA1, FDRA2 solves partial differential equations in pressure and temperature on profiles normal to the fault. The diffusion equations are discretized in space using finite differences on a nonuniform mesh having greater density near the fault. The full system of equations is a semiexplicit index-1 differential algebraic equation (DAE) in slip, slip rate, state, fault zone porosity, pressure, and temperature. We integrate state, porosity, and slip explicitly; solve the momentum balance equation on the fault for slip rate; and integrate pressure and temperature implicitly. Adaptive time steps are limited by accuracy and the stability criterion governing explicit integration of hyperbolic, but not the more stringent one governing parabolic, PDE. To compute elasticity in a 3D half-space, FDRA2 compresses the large, dense matrix arising from the boundary element method using an H-matrix. The work to perform a matrix-vector product scales almost linearly, rather than quadratically, in the number of fault cells. A new technique to relate the error

  9. Thunderstorms in my computer : The effect of visual dynamics and sound in a 3D environment

    NARCIS (Netherlands)

    Houtkamp, J.; Schuurink, E.L.; Toet, A.

    2008-01-01

    We assessed the effects of the addition of dynamic visual elements and sounds to a levee patroller training game on the appraisal of the environment and weather conditions, the engagement of the users and their performance. Results show that the combination of visual dynamics and sounds best conveys

  10. Geocadabra Construction Box: A dynamic geometry interface within a 3D visualization teaching-learning trajectory for elementary learners

    Directory of Open Access Journals (Sweden)

    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.

  11. Using the UM dynamical cores to reproduce idealised 3D flows

    CERN Document Server

    Mayne, N J; Acreman, David M; Smith, Chris; Wood, Nigel; Amundsen, David Skålid; Thuburn, John; Jackson, David R

    2013-01-01

    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.

  12. Simulation and Analysis of Dynamic Characteristics of3D Assembly Circuit Module with Finite Element Method

    Institute of Scientific and Technical Information of China (English)

    黄春跃; 周德俭; 黄红艳

    2004-01-01

    Based on the modal analysis theory and by using the dynamics finite element analysis model of a three-dimensional assembly circuit module, dynamic characteristics of circuit module have been studied, including both natural characteristics analysis and dynamic responses analysis. Using a subspace method, modal analysis is first carried out. The first 6 orders of natural frequencies and vibration modes are obtained. Influence of the number of the Z-shaped metal slices on dynamic characteristics of the entire structure is also studied.Harmonic response analysis is then conducted. The steady-state response when the circuit module is subjected to harmonic excitation is determined. A curve of the response values against frequencies is obtained. As a result, the optimal number of Z-shaped metal slices can be determined, and it can be assured that the three-dimensional assembly circuit module has good performance in terms of the dynamic characteristics.

  13. Using the UM dynamical cores to reproduce idealised 3-D flows

    Directory of Open Access Journals (Sweden)

    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.

  14. A Bio-Acoustic Levitational (BAL) Assembly Method for Engineering of Multilayered, 3D Brain-Like Constructs, Using Human Embryonic Stem Cell Derived Neuro-Progenitors.

    Science.gov (United States)

    Bouyer, Charlène; Chen, Pu; Güven, Sinan; Demirtaş, Tuğrul Tolga; Nieland, Thomas J F; Padilla, Frédéric; Demirci, Utkan

    2016-01-01

    A bio-acoustic levitational assembly method for engineering of multilayered, 3D brainlike constructs is presented. Acoustic radiation forces are used to levitate neuroprogenitors derived from human embryonic stem cells in 3D multilayered fibrin tissue constructs. The neuro-progenitor cells are subsequently differentiated in neural cells, resulting in a 3D neuronal construct with inter and intralayer neurite elongations.

  15. Integrating Dynamic Data and Sensors with Semantic 3D City Models in the Context of Smart Cities

    Science.gov (United States)

    Chaturvedi, K.; Kolbe, T. H.

    2016-10-01

    Smart cities provide effective integration of human, physical and digital systems operating in the built environment. The advancements in city and landscape models, sensor web technologies, and simulation methods play a significant role in city analyses and improving quality of life of citizens and governance of cities. Semantic 3D city models can provide substantial benefits and can become a central information backbone for smart city infrastructures. However, current generation semantic 3D city models are static in nature and do not support dynamic properties and sensor observations. In this paper, we propose a new concept called Dynamizer allowing to represent highly dynamic data and providing a method for injecting dynamic variations of city object properties into the static representation. The approach also provides direct capability to model complex patterns based on statistics and general rules and also, real-time sensor observations. The concept is implemented as an Application Domain Extension for the CityGML standard. However, it could also be applied to other GML-based application schemas including the European INSPIRE data themes and national standards for topography and cadasters like the British Ordnance Survey Mastermap or the German cadaster standard ALKIS.

  16. Functional 3D Neural Mini-Tissues from Printed Gel-Based Bioink and Human Neural Stem Cells.

    Science.gov (United States)

    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

  17. Mesenchymal stem cells enhance ovarian cancer cell infiltration through IL6 secretion in an amniochorionic membrane based 3D model

    Directory of Open Access Journals (Sweden)

    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.

  18. Prospective use of the 3D printing technology for the microstructural engineering of Solid Oxide Fuel Cell components

    Energy Technology Data Exchange (ETDEWEB)

    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)

  19. Prospective use of the 3D printing technology for the microstructural engineering of Solid Oxide Fuel Cell components

    International Nuclear Information System (INIS)

    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. 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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. Surface Acoustic Waves (SAW-Based Biosensing for Quantification of Cell Growth in 2D and 3D Cultures

    Directory of Open Access Journals (Sweden)

    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

  2. An impedance method for spatial sensing of 3D cell constructs – towards applications in tissue engineering

    DEFF Research Database (Denmark)

    Canali, Chiara; Mazzoni, Chiara; Larsen, Layla Bashir;

    2015-01-01

    ) cells were encapsulated in gelatin to form artificial 3D cell constructs and detected when placed in different positions inside large gelatin scaffolds. Taken together, these results open new perspectives for impedance-based sensing technologies for non-invasive monitoring in tissue engineering...

  3. Response of microscale cell/matrix constructs to successive force application in a 3D environment

    Science.gov (United States)

    Liu, Alan; Chen, Christopher; Reich, Daniel

    2014-03-01

    Mechanical dilation of arteries by pulsatile blood flow is directly opposed by coordinated contraction of a band of smooth muscle tissue that envelops the vessels. This mechanical adaptation of smooth muscle cells to external loading is a critical feature of normal blood vessel function. While most previous studies on biomechanical systems have focused on single cells or large excised tissue, we utilize a device to apply forces to engineered smooth muscle microtissues. This device consists of arrayed pairs of elastomeric micro-cantilevers capable of magnetic actuation. Tissues are formed through self-assembly following the introduction of cell-infused collagen gel to the array. With this system, we are able to dynamically stretch and relax these sub-millimeter sized tissues. The timing and magnitude of the force application can be precisely controlled and thus can be used to mimic a wide range of physiological behavior. In particular, we will discuss results that show that the interval between successive force applications mediates the both the subsequent mechanical and active dynamics of the cell/matrix composite system. Understanding this process will lead to better understanding of the interplay between cell and extracellular matrix responses to mechanical stimulus at a novel length scale.

  4. Intersegmental dynamics of 3D upper arm and forearm longitudinal axis rotations during baseball pitching.

    Science.gov (United States)

    Naito, Kozo; Takagi, Hiroyasu; Yamada, Norimasa; Hashimoto, Shinichi; Maruyama, Takeo

    2014-12-01

    The shoulder internal rotation (IR) and forearm pronation (PR) are important elements for baseball pitching, however, how rapid rotations of IR and PR are produced by muscular torques and inter-segmental forces is not clear. The aim of this study is to clarify how IR and PR angular velocities are maximized, depending on muscular torque and interactive torque effects, and gain a detailed knowledge about inter-segmental interaction within a multi-joint linked chain. The throwing movements of eight collegiate baseball pitchers were recorded by a motion capture system, and induced-acceleration analysis was used to assess the respective contributions of the muscular (MUS) and interactive torques associated with gyroscopic moment (GYR), and Coriolis (COR) and centrifugal forces (CEN) to maximum angular velocities of IR (MIRV) and PR (MPRV). The results showed that the contribution of MUS account for 98.0% of MIRV, while that contribution to MPRV was indicated as negative (-48.1%). It was shown that MPRV depends primarily on the interactive torques associated with GYR and CEN, but the effects of GYR, COR and CEN on MIRV are negligible. In conclusion, rapid PR motion during pitching is created by passive-effect, and is likely a natural movement which arises from 3D throwing movement. Applying the current analysis to IR and PR motions is helpful in providing the implications for improving performance and considering conditioning methods for pitchers. PMID:25303496

  5. Introducing zeus-mp: a 3d, parallel, multiphysics code for astrophysical fluid dynamics

    Directory of Open Access Journals (Sweden)

    Michael L. Norman

    2000-01-01

    Full Text Available Describimos ZEUS-MP: un c odigo Multi-F sica, Masivamente-Paralelo, Pasa-Mensajes para simulaciones tridimensionales de din amica de uidos astrof sicos. ZEUS-MP es la continuaci on de los c odigos ZEUS-2D y ZEUS-3D, desarrollados y diseminados por el Laboratorio de Astrof sica Computacional (lca.ncsa.uiuc.edu del NCSA. La versi on V1.0, liberada el 1/1/2000, contiene los siguientes m odulos: hidrodin amica ideal, MHD ideal y auto-gravedad. Las pr oximas versiones tendr an difusi on radiativa de ujo limitado, conducci on de calor, plasma de dos temperaturas y funciones de enfriamiento y calentamiento. Las ecuaciones covariantes est an avanzadas en una malla Euleriana m ovil en coordenadas Cartesianas, cil ndricas y polares esf ericas. La paralelizaci on es hecha por descomposici on del dominio y est a implementada en F77 y MPI. El c odigo es portable en un amplio rango de plataformas, desde redes de estaciones de trabajo hasta procesadores de paralelismo masivo. Se presentan algunos resultados de la e ciencia en paralelo junto con una aplicaci on a formaci on estelar turbulenta.

  6. Dynamic 3-D chemical agent cloud mapping using a sensor constellation deployed on mobile platforms

    Science.gov (United States)

    Cosofret, Bogdan R.; Konno, Daisei; Rossi, David; Marinelli, William J.; Seem, Pete

    2014-05-01

    The need for standoff detection technology to provide early Chem-Bio (CB) threat warning is well documented. Much of the information obtained by a single passive sensor is limited to bearing and angular extent of the threat cloud. In order to obtain absolute geo-location, range to threat, 3-D extent and detailed composition of the chemical threat, fusion of information from multiple passive sensors is needed. A capability that provides on-the-move chemical cloud characterization is key to the development of real-time Battlespace Awareness. We have developed, implemented and tested algorithms and hardware to perform the fusion of information obtained from two mobile LWIR passive hyperspectral sensors. The implementation of the capability is driven by current Nuclear, Biological and Chemical Reconnaissance Vehicle operational tactics and represents a mission focused alternative of the already demonstrated 5-sensor static Range Test Validation System (RTVS).1 The new capability consists of hardware for sensor pointing and attitude information which is made available for streaming and aggregation as part of the data fusion process for threat characterization. Cloud information is generated using 2-sensor data ingested into a suite of triangulation and tomographic reconstruction algorithms. The approaches are amenable to using a limited number of viewing projections and unfavorable sensor geometries resulting from mobile operation. In this paper we describe the system architecture and present an analysis of results obtained during the initial testing of the system at Dugway Proving Ground during BioWeek 2013.

  7. Ordering Single Cells and Single Embryos in 3D Confinement: A New Device for High Content Screening.

    Science.gov (United States)

    Wollrab, Viktoria; Caballero, David; Thiagarajan, Raghavan; Riveline, Daniel

    2016-01-01

    Biological cells are usually observed on flat (2D) surfaces. This condition is not physiological, and phenotypes and shapes are highly variable. Screening based on cells in such environments have therefore serious limitations: cell organelles show extreme phenotypes, cell morphologies and sizes are heterogeneous and/or specific cell organelles cannot be properly visualized. In addition, cells in vivo are located in a 3D environment; in this situation, cells show different phenotypes mainly because of their interaction with the surrounding extracellular matrix of the tissue. In order to standardize and generate order of single cells in a physiologically-relevant 3D environment for cell-based assays, we report here the microfabrication and applications of a device for in vitro 3D cell culture. This device consists of a 2D array of microcavities (typically 10(5) cavities/cm(2)), each filled with single cells or embryos. Cell position, shape, polarity and internal cell organization become then normalized showing a 3D architecture. We used replica molding to pattern an array of microcavities, 'eggcups', onto a thin polydimethylsiloxane (PDMS) layer adhered on a coverslip. Cavities were covered with fibronectin to facilitate adhesion. Cells were inserted by centrifugation. Filling percentage was optimized for each system allowing up to 80%. Cells and embryos viability was confirmed. We applied this methodology for the visualization of cellular organelles, such as nucleus and Golgi apparatus, and to study active processes, such as the closure of the cytokinetic ring during cell mitosis. This device allowed the identification of new features, such as periodic accumulations and inhomogeneities of myosin and actin during the cytokinetic ring closure and compacted phenotypes for Golgi and nucleus alignment. We characterized the method for mammalian cells, fission yeast, budding yeast, C. elegans with specific adaptation in each case. Finally, the characteristics of this

  8. Immunogenicity and T cell recognition in swine of foot-and-mouth disease virus polymerase 3D

    International Nuclear Information System (INIS)

    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

  9. A 3D culture system enhances the ability of human bone marrow stromal cells to support the growth of limbal stem/progenitor cells

    Directory of Open Access Journals (Sweden)

    Sheyla González

    2016-03-01

    Full Text Available The standard method of cultivating limbal epithelial progenitor/stem cells (LSCs on a monolayer of mouse 3T3 feeder cells possesses the risk of cross-contamination in clinical applications. Human feeder cells have been used to eliminate this risk; however, efficiency from xenobiotic-free cultures on a monolayer appears to be lower than in the standard method using 3T3 cells. We investigated whether bone marrow stromal cells (BMSCs, also known as bone marrow-derived mesenchymal stem cells, could serve as feeder cells for the expansion of LSCs in the 3-dimensional (3D system. Primary single human LSCs on a monolayer of 3T3s served as the control. Very poor growth was observed when single LSCs were cultured on BMSCs. When LSC clusters were cultured on a BMSC monolayer (CC-BM, 3D culture system (3D CC-BM and fibrin 3D system (fibrin 3D CC-BM, the 3D CC-BM method supported a greater LSC expansion. The 3D CC-BM system produced a 2.5-fold higher cell growth rate than the control (p  0.05, whereas the proportion of K12+ cells was lower (p < 0.05. These results indicate that BMSCs can efficiently support the expansion of the LSC population in the 3D culture.

  10. Constraining the Absolute Orientation of Eta Carinae's Binary Orbit: A 3-D Dynamical Model for the Broad [Fe III] Emission

    CERN Document Server

    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 ...

  11. 3-D parallel program for numerical calculation of gas dynamics problems with heat conductivity on distributed memory computational systems (CS)

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    DEFF Research Database (Denmark)

    Jørgensen, Peter Stanley

    the microstructure. The methods are exemplied by the analysis of Ni-YSZ and LSC-CGO electrode samples. Automatic methods for preprocessing the raw 3D image data are developed. The preprocessing steps correct for errors introduced by the image acquisition by the focused ion beam serial sectioning. Alignment...... 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 characterize...... 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 the time consuming...

  13. Calcium Electroporation: Evidence for Differential Effects in Normal and Malignant Cell Lines, Evaluated in a 3D Spheroid Model

    OpenAIRE

    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...

  14. Simulation of a simple RCCS experiment with RELAP5-3D system code and computational fluid dynamics computer program

    International Nuclear Information System (INIS)

    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)

  15. 3D Case Studies of Monitoring Dynamic Structural Tests using Long Exposure Imagery

    Science.gov (United States)

    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.

  16. Development of dynamic 3-D surface profilometry using stroboscopic interferometric measurement and vertical scanning techniques

    International Nuclear Information System (INIS)

    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. A New Crank Arm-Based Load Cell for the 3D Analysis of the Force Applied by a Cyclist

    Directory of Open Access Journals (Sweden)

    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.

  18. NASA-approved rotary bioreactor enhances proliferation of human epidermal stem cells and supports formation of 3D epidermis-like structure.

    Directory of Open Access Journals (Sweden)

    Xiao-hua Lei

    Full Text Available The skin is susceptible to different injuries and diseases. One major obstacle in skin tissue engineering is how to develop functional three-dimensional (3D substitute for damaged skin. Previous studies have proved a 3D dynamic simulated microgravity (SMG culture system as a "stimulatory" environment for the proliferation and differentiation of stem cells. Here, we employed the NASA-approved rotary bioreactor to investigate the proliferation and differentiation of human epidermal stem cells (hEpSCs. hEpSCs were isolated from children foreskins and enriched by collecting epidermal stem cell colonies. Cytodex-3 micro-carriers and hEpSCs were co-cultured in the rotary bioreactor and 6-well dish for 15 days. The result showed that hEpSCs cultured in rotary bioreactor exhibited enhanced proliferation and viability surpassing those cultured in static conditions. Additionally, immunostaining analysis confirmed higher percentage of ki67 positive cells in rotary bioreactor compared with the static culture. In contrast, comparing with static culture, cells in the rotary bioreactor displayed a low expression of involucrin at day 10. Histological analysis revealed that cells cultured in rotary bioreactor aggregated on the micro-carriers and formed multilayer 3D epidermis structures. In conclusion, our research suggests that NASA-approved rotary bioreactor can support the proliferation of hEpSCs and provide a strategy to form multilayer epidermis structure.

  19. Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis

    Directory of Open Access Journals (Sweden)

    Wang Yan

    2008-12-01

    Full Text Available Abstract Background The prediction of conformational B-cell epitopes is one of the most important goals in immunoinformatics. The solution to this problem, even if approximate, would help in designing experiments to precisely map the residues of interaction between an antigen and an antibody. Consequently, this area of research has received considerable attention from immunologists, structural biologists and computational biologists. Phage-displayed random peptide libraries are powerful tools used to obtain mimotopes that are selected by binding to a given monoclonal antibody (mAb in a similar way to the native epitope. These mimotopes can be considered as functional epitope mimics. Mimotope analysis based methods can predict not only linear but also conformational epitopes and this has been the focus of much research in recent years. Though some algorithms based on mimotope analysis have been proposed, the precise localization of the interaction site mimicked by the mimotopes is still a challenging task. Results In this study, we propose a method for B-cell epitope prediction based on mimotope analysis called Pep-3D-Search. Given the 3D structure of an antigen and a set of mimotopes (or a motif sequence derived from the set of mimotopes, Pep-3D-Search can be used in two modes: mimotope or motif. To evaluate the performance of Pep-3D-Search to predict epitopes from a set of mimotopes, 10 epitopes defined by crystallography were compared with the predicted results from a Pep-3D-Search: the average Matthews correlation oefficient (MCC, sensitivity and precision were 0.1758, 0.3642 and 0.6948. Compared with other available prediction algorithms, Pep-3D-Search showed comparable MCC, specificity and precision, and could provide novel, rational results. To verify the capability of Pep-3D-Search to align a motif sequence to a 3D structure for predicting epitopes, 6 test cases were used. The predictive performance of Pep-3D-Search was demonstrated to be

  20. Lamellipodin promotes invasive 3D cancer cell migration via regulated interactions with Ena/VASP and SCAR/WAVE

    Science.gov (United States)

    Carmona, Guillaume; Perera, Upamali; Gillett, Cheryl; Naba, Alexandra; Law, Ah-Lai; Sharma, Ved P.; Wang, Jian; Wyckoff, Jeffrey; Balsamo, Michele; Mosis, Fuad; De Piano, Mario; Monypenny, James; Woodman, Natalie; McConnell, Russell E.; Mouneimne, Ghassan; Van Hemelrijck, Mieke; Cao, Yihai; Condeelis, John; Hynes, Richard O.; Gertler, Frank B.; Krause, Matthias

    2016-01-01

    Cancer invasion is a hallmark of metastasis. The mesenchymal mode of cancer cell invasion is mediated by elongated membrane protrusions driven by the assembly of branched F-actin networks. How deregulation of actin regulators promotes cancer cell invasion is still enigmatic. We report that increased expression and membrane localization of the actin regulator Lamellipodin correlates with reduced metastasis-free survival and poor prognosis in breast cancer patients. In agreement we find that Lamellipodin depletion reduced lung metastasis in an orthotopic mouse breast cancer model. Invasive 3D cancer cell migration as well as invadopodia formation, and matrix degradation were impaired upon Lamellipodin depletion. Mechanistically, we show that Lamellipodin promotes invasive 3D cancer cell migration via both actin-elongating Ena/VASP proteins and the Scar/WAVE complex, which stimulates actin branching. In contrast, Lamellipodin interaction with Scar/WAVE but not Ena/VASP is required for random 2D cell migration. We identify a phosphorylation-dependent mechanism that regulates selective recruitment of these effectors to Lamellipodin: Abl-mediated Lamellipodin phosphorylation promotes its association with both Scar/WAVE and Ena/VASP, while Src-dependent phosphorylation enhances binding to Scar/WAVE but not Ena/VASP. Through these selective, regulated interactions Lamellipodin mediates directional sensing of EGF gradients and invasive 3D migration of breast cancer cells. Our findings imply that increased Lamellipodin levels enhance Ena/VASP and Scar/WAVE activities at the plasma membrane to promote 3D invasion and metastasis. PMID:26996666

  1. 3D Dynamic Response of Layered Unsaturated Soils to Harmonic Loads

    Institute of Scientific and Technical Information of China (English)

    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.

  2. A method of improving the dynamic response of 3D force/torque sensors

    Science.gov (United States)

    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.

  3. The microenvironment determines the breast cancer cells' phenotype: organization of MCF7 cells in 3D cultures

    Directory of Open Access Journals (Sweden)

    Soto Ana M

    2010-06-01

    Full Text Available Abstract Background 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. Methods 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. Results 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. Conclusions 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

  4. The microenvironment determines the breast cancer cells' phenotype: organization of MCF7 cells in 3D cultures

    International Nuclear Information System (INIS)

    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

  5. A Dynamic Imaging Database for 3-D Morphologic Analysis and Clinical Assessment in Diagnostic Radiology

    OpenAIRE

    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...

  6. 3-D finite element computation and dynamic modal analysis on ultrasonic vibration systems

    Institute of Scientific and Technical Information of China (English)

    倪金刚; 张学仁; 聂景旭(Department of Jet Propulsion 405; Beijing University of Aeronautics and Astronautics; Beijing 100083; China)

    1996-01-01

    Stress and modal analyses are performed on an ultrasonic vibration system by means of a 3-dimensional finite element computation and dynamic modal analysis code "Algor" The system consists of an edge-cracked specimen linked elastically with one or two amplifying horns which come into resonant longitudinal vibration at 20kHz.Operating principle of the ultrasonic fatigue machines and experimental procedures for ultrasonic fatigue crack growth studies are briefly presented.

  7. Virgo Cluster and field dwarf ellipticals in 3D - II. Internal dynamics points to tidal harassment?

    Science.gov (United States)

    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.

  8. Virgo Cluster and field dwarf ellipticals in 3D - II. Internal dynamics points to tidal harassment?

    CERN Document Server

    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...

  9. Numerical simulation of 3D unsteady flow in a rotating pump by dynamic mesh technique

    International Nuclear Information System (INIS)

    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

  10. Haptic perception of force magnitude and its relation to postural arm dynamics in 3D.

    Science.gov (United States)

    van Beek, Femke E; Bergmann Tiest, Wouter M; Mugge, Winfred; Kappers, Astrid M L

    2015-12-08

    In a previous study, we found the perception of force magnitude to be anisotropic in the horizontal plane. In the current study, we investigated this anisotropy in three dimensional space. In addition, we tested our previous hypothesis that the perceptual anisotropy was directly related to anisotropies in arm dynamics. In experiment 1, static force magnitude perception was studied using a free magnitude estimation paradigm. This experiment revealed a significant and consistent anisotropy in force magnitude perception, with forces exerted perpendicular to the line between hand and shoulder being perceived as 50% larger than forces exerted along this line. In experiment 2, postural arm dynamics were measured using stochastic position perturbations exerted by a haptic device and quantified through system identification. By fitting a mass-damper-spring model to the data, the stiffness, damping and inertia parameters could be characterized in all the directions in which perception was also measured. These results show that none of the arm dynamics parameters were oriented either exactly perpendicular or parallel to the perceptual anisotropy. This means that endpoint stiffness, damping or inertia alone cannot explain the consistent anisotropy in force magnitude perception.

  11. Development of 3D in vitro platform technology to engineer mesenchymal stem cells

    Directory of Open Access Journals (Sweden)

    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

  12. Revealing plot scale heterogeneity in soil moisture dynamics under contrasting vegetation assemblages using 3D electrical resistivity tomography (ERT) surveys

    Science.gov (United States)

    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 (stresses with planned increased afforestation which may be compounded by climate change projections of decreasing precipitation during the growing season.

  13. Multiplex profiling of cellular invasion in 3D cell culture models.

    Directory of Open Access Journals (Sweden)

    Gerald Burgstaller

    Full Text Available To-date, most invasion or migration assays use a modified Boyden chamber-like design to assess migration as single-cell or scratch assays on coated or uncoated planar plastic surfaces. Here, we describe a 96-well microplate-based, high-content, three-dimensional cell culture assay capable of assessing invasion dynamics and molecular signatures thereof. On applying our invasion assay, we were able to demonstrate significant effects on the invasion capacity of fibroblast cell lines, as well as primary lung fibroblasts. Administration of epidermal growth factor resulted in a substantial increase of cellular invasion, thus making this technique suitable for high-throughput pharmacological screening of novel compounds regulating invasive and migratory pathways of primary cells. Our assay also correlates cellular invasiveness to molecular events. Thus, we argue of having developed a powerful and versatile toolbox for an extensive profiling of invasive cells in a 96-well format. This will have a major impact on research in disease areas like fibrosis, metastatic cancers, or chronic inflammatory states.

  14. The effect of porosity on cell ingrowth into accurately defined, laser-made, polylactide-based 3D scaffolds

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. Sustained PDGF-BB release from PHBHHx loaded nanoparticles in 3D hydrogel/stem cell model.

    Science.gov (United States)

    Dong, Cui-Ling; Webb, William R; Peng, Qiang; Tang, James Z; Forsyth, Nicholas R; Chen, Guo-Qiang; El Haj, Alicia J

    2015-01-01

    This study aimed to design a growth factor loaded copolyester of 3-hydroxybutyrate and 3-hydroxyhexanoate (PHBHHx) nanoparticles containing 3D collagen matrix to achieve growth factor sustained release for long-term stimulation of human mesenchymal stem cells (hMSCs) proliferation/differentiation for tissue engineer application. Platelet-derived growth factor-BB (PDGF-BB), which is known to enhance hMSCs proliferation in human serum, was selected as a model growth factor, and biodegradable copolyester of PHBHHx was chosen to be the sustained release vehicle. PDGF-BB phospholipid complex encapsulated PHBHHx nanoparticles were fabricated, and their effect on hMSCs proliferation was investigated via assays of CCK-8 and live-dead staining to cells inoculated in 2D tissue culture plates and 3D collagen gel scaffolds, respectively. The resulting spherical PHBHHx nanoparticles were stable in terms of their mean particle size, polydispersity index and zeta potential before and after lyophilization. In vitro study revealed a sustained release of PDGF-BB with a low burst release. Furthermore, sustained released PDGF-BB was revealed to significantly promote hMSCs proliferation in both cell monolayer and cell seeded 3D collagen scaffolds inoculated in serum-free media. Therefore, the 3D collagen matrices with locally sustained release growth factor nanoparticles hold promise to be used for stem cell tissue engineering.

  16. 3D Ultrastructural Organization of Whole Chlamydomonas reinhardtii Cells Studied by Nanoscale Soft X-Ray Tomography

    OpenAIRE

    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...

  17. 3D ultrastructural organization of whole Chlamydomonas reinhardtii cells studied by nanoscale soft x-ray tomography

    OpenAIRE

    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...

  18. Infrared imaging of MDA-MB-231 breast cancer cell line phenotypes in 2D and 3D cultures.

    Science.gov (United States)

    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

  19. Progress in the Peeling-Ballooning Model of ELMs: Numerical Studies of 3D Nonlinear ELM Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. PROGRESS IN THE PEELING-BALLOONING MODEL OF ELMS: NUMERICAL STUDIES OF 3D NONLINEAR ELM DYNAMICS

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. PROGRESS IN THE PEELING-BALLOONING MODEL OF ELMS: NUMERICAL STUDIES OF 3D NONLINEAR ELM DYNAMICS

    International Nuclear Information System (INIS)

    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

  2. 3D mapping of buried underworld infrastructure using dynamic Bayesian network based multi-sensory image data fusion

    Science.gov (United States)

    Dutta, Ritaban; Cohn, Anthony G.; Muggleton, Jen M.

    2013-05-01

    The successful operation of buried infrastructure within urban environments is fundamental to the conservation of modern living standards. In this paper a novel multi-sensor image fusion framework has been proposed and investigated using dynamic Bayesian network for automatic detection of buried underworld infrastructure. Experimental multi-sensors images were acquired for a known buried plastic water pipe using Vibro-acoustic sensor based location methods and Ground Penetrating Radar imaging system. Computationally intelligent conventional image processing techniques were used to process three types of sensory images. Independently extracted depth and location information from different images regarding the target pipe were fused together using dynamic Bayesian network to predict the maximum probable location and depth of the pipe. The outcome from this study was very encouraging as it was able to detect the target pipe with high accuracy compared with the currently existing pipe survey map. The approach was also applied successfully to produce a best probable 3D buried asset map.

  3. Increased extracellular matrix density decreases MCF10A breast cell acinus formation in 3D culture conditions.

    Science.gov (United States)

    Lance, Amanda; Yang, Chih-Chao; Swamydas, Muthulekha; Dean, Delphine; Deitch, Sandy; Burg, Karen J L; Dréau, Didier

    2016-01-01

    The extracellular matrix (ECM) contributes to the generation and dynamic of normal breast tissue, in particular to the generation of polarized acinar and ductal structures. In vitro 3D culture conditions, including variations in the composition of the ECM, have been shown to directly influence the formation and organization of acinus-like and duct-like structures. Furthermore, the density of the ECM appears to also play a role in the normal mammary tissue and tumour formation. Here we show that the density of the ECM directly influences the number, organization and function of breast acini. Briefly, non-malignant human breast MCF10A cells were incubated in increasing densities of a Matrigel®-collagen I matrix. Elastic moduli near and distant to the acinus structures were measured by atomic force microscopy, and the number of acinus structures was determined. Immunochemistry was used to investigate the expression levels of E-cadherin, laminin, matrix metalloproteinase-14 and ß-casein in MCF10A cells. The modulus of the ECM was significantly increased near the acinus structures and the number of acinus structures decreased with the increase in Matrigel-collagen I density. As evaluated by the expression of laminin, the organization of the acinus structures present was altered as the density of the ECM increased. Increases in both E-cadherin and MMP14 expression by MCF10A cells as ECM density increased were also observed. In contrast, MCF10A cells expressed lower ß-casein levels as the ECM density increased. Taken together, these observations highlight the key role of ECM density in modulating the number, organization and function of breast acini.

  4. 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

    Institute of Scientific and Technical Information of China (English)

    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.

  5. 3D radiative hydrodynamic simulations of protostellar collapse with H-C-O dynamical chemistry

    CERN Document Server

    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...

  6. A preliminary study of 3D difference scheme with energy dynamic equilibrium

    Institute of Scientific and Technical Information of China (English)

    Chiping Wu; Yongxing Zhang; Zhongzhen Ji; Wenxing Sun; Zede Guo; Weiping Jin

    2005-01-01

    In this paper, a difference scheme with energy dynamic equilibrium (DS-EDE) is presented, which can be used for the simulation of long-term atmosphere and sea motion.Based on three dimensional nonlinear evolution equations for atmosphere and sea motion, a three dimensional compact upwind scheme (CUWS) is constructed, as the basis of the DS-EDE. The DS-EDE satisfies the following condition of energy dynamic equilibrium (EDE): the total work of exter nal forces on the region boundary is equal to the sum of the total effective variation of the kinetic energy and the energy dissipation in the average flow motion and the effective variation of the potential energy per unit time within the region of interest. It really reflects the basic mechanism of the action of external forces and dissipation in atmosphere and sea movement. Therefore, the DS-EDE developed in this paper is a suitable model for simulating long-term atmosphere and sea movement with forcing and dissipation.

  7. Dynamic 3D shape of the plantar surface of the foot using coded structured light: a technical report

    KAUST Repository

    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.

  8. Effect of biomimetic 3D environment of an injectable polymeric scaffold on MG-63 osteoblastic-cell response

    International Nuclear Information System (INIS)

    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.

  9. Designing a binding interface for control of cancer cell adhesion via 3D topography and metabolic oligosaccharide engineering.

    Science.gov (United States)

    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

  10. Solvent-modified dynamic porosity in chiral 3D kagome frameworks.

    Science.gov (United States)

    Keene, Tony D; Rankine, Damien; Evans, Jack D; Southon, Peter D; Kepert, Cameron J; Aitken, Jade B; Sumby, Christopher J; Doonan, Christian J

    2013-06-14

    Dynamically porous metal-organic frameworks (MOFs) with a chiral quartz-based structure have been synthesized from the multidentate ligand 2,2'-dihydroxybiphenyl-4,4'-dicarboxylate (H2diol). Compounds [Ni(II)(H2diol)(S)2]·xS (where S = DMF or DEF) show marked changes in 77 K N2 uptake between partially desolvated [Ni(II)(H2diol)(S)2] (only the pore solvent is removed) and fully desolvated [Ni(II)(H2diol)] forms. Furthermore, [Ni(II)(H2diol)(DMF)2] displays additional solvent-dependent porosity through the rotation of DMF molecules attached to the axial coordination sites of the Ni(II) centre. A unique feature of the four coordinate Ni(II) centre in [Ni(II)(H2diol)] is the dynamic response to its chemical environment. Exposure of [Ni(II)(H2diol)] to H2O and MeOH vapour leads to coordination of both axial sites of the Ni centres and to the generation of a solvated framework, whereas exposure to EtOH, DMF, acetone, and MeCN does not lead to any change in metal coordination or structure metrics. MeOH vapour adsorption was able to be tracked by time-dependent magnetometry as the solvated and desolvated structures have different magnetic moments. Solvated and desolvated forms of the MOF show remarkable differences in their thermal expansivities; [Ni(II)(H2diol)(DMF)2]·DMF displays marked positive thermal expansion (PTE) in the c-axis, yet near to zero thermal expansion, between 90 and 450 K, is observed for [Ni(II)(H2diol)]. These new MOF architectures demonstrate a dynamic structural and colourimetric response to selected adsorbates via a unique mechanism that involves a reversible change in the coordination environment of the metal centre. These coordination changes are mediated throughout the MOF by rotational mobility about the biaryl bond of the ligand.

  11. MORPHOLOGY AND DYNAMICS OF SOLAR PROMINENCES FROM 3D MHD SIMULATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Terradas, J.; Soler, R.; Oliver, R.; Ballester, J. L. [Departament de Física, Universitat de les Illes Balears, E-07122 Palma de Mallorca (Spain); Luna, M., E-mail: jaume.terradas@uib.es [Instituto de Astrofísica de Canarias, E-38200 La Laguna, Tenerife (Spain)

    2015-01-20

    In this paper we present a numerical study of the time evolution of solar prominences embedded in sheared magnetic arcades. The prominence is represented by a density enhancement in a background-stratified atmosphere and is connected to the photosphere through the magnetic field. By solving the ideal magnetohydrodynamic equations in three dimensions, we study the dynamics for a range of parameters representative of real prominences. Depending on the parameters considered, we find prominences that are suspended above the photosphere, i.e., detached prominences, but also configurations resembling curtain or hedgerow prominences whose material continuously connects to the photosphere. The plasma-β is an important parameter that determines the shape of the structure. In many cases magnetic Rayleigh-Taylor instabilities and oscillatory phenomena develop. Fingers and plumes are generated, affecting the whole prominence body and producing vertical structures in an essentially horizontal magnetic field. However, magnetic shear is able to reduce or even to suppress this instability.

  12. 3D high-content screening for the identification of compounds that target cells in dormant tumor spheroid regions

    Energy Technology Data Exchange (ETDEWEB)

    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

  13. Impact of the 3D microenvironment on phenotype, gene expression, and EGFR inhibition of colorectal cancer cell lines.

    Directory of Open Access Journals (Sweden)

    Anna C Luca

    Full Text Available Three-dimensional (3D tumor cell cultures grown in laminin-rich-extracellular matrix (lrECM are considered to reflect human tumors more realistic as compared to cells grown as monolayer on plastic. Here, we systematically investigated the impact of ECM on phenotype, gene expression, EGFR signaling pathway, and on EGFR inhibition in commonly used colorectal cancer (CRC cell lines. LrECM on-top (3D culture assays were performed with the CRC cell lines SW-480, HT-29, DLD-1, LOVO, CACO-2, COLO-205 and COLO-206F. Morphology of lrECM cultivated CRC cell lines was determined by phase contrast and confocal laser scanning fluorescence microscopy. Proliferation of cells was examined by MTT assay, invasive capacity of the cell lines was assayed using Matrigel-coated Boyden chambers, and migratory activity was determined employing the Fence assay. Differential gene expression was analyzed at the transcriptional level by the Agilent array platform. EGFR was inhibited by using the specific small molecule inhibitor AG1478. A specific spheroid growth pattern was observed for all investigated CRC cell lines. DLD-1, HT-29 and SW-480 and CACO-2 exhibited a clear solid tumor cell formation, while LOVO, COLO-205 and COLO-206F were characterized by forming grape-like structures. Although the occurrence of a spheroid morphology did not correlate with an altered migratory, invasive, or proliferative capacity of CRC cell lines, gene expression was clearly altered in cells grown on lrECM as compared to 2D cultures. Interestingly, in KRAS wild-type cell lines, inhibition of EGFR was less effective in lrECM (3D cultures as compared to 2D cell cultures. Thus, comparing both 2D and 3D cell culture models, our data support the influence of the ECM on cancer growth. Compared to conventional 2D cell culture, the lrECM (3D cell culture model offers the opportunity to investigate permanent CRC cell lines under more physiological conditions, i.e. in the context of molecular

  14. Microfluidics 3D gel-island chip for single cell isolation and lineage-dependent drug responses study.

    Science.gov (United States)

    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

  15. 3D Ultrastructural organization of whole Chlamydomonas reinhardtii cells studied by nanoscale soft x-ray tomography.

    Directory of Open Access Journals (Sweden)

    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.

  16. A molecular dynamics implementation of the 3D Mercedes-Benz water model

    Science.gov (United States)

    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

  17. AlgiMatrix™ Based 3D Cell Culture System as an In-Vitro Tumor Model for Anticancer Studies

    OpenAIRE

    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...

  18. Comparison of predicting drag methods using computational fluid dynamics in 2d/3d viscous flow

    Institute of Scientific and Technical Information of China (English)

    ZHU; ZiQiang; WANG; XiaoLu; LIU; Jie; LIU; Zhou

    2007-01-01

    As a result of the necessity of aircraft engineering design and the progress of computational fluid dynamics (CFD), techniques of accurately predicting aerodynamic drag are being increasingly explored. According to the momentum balance, the drag can be represented by an integral over a cross-flow plane (called wake integration method) at an arbitrary distance behind the configuration. A formulation to reduce the size of the wake cross plane region required for calculating the drag is developed by using cutoff parameters of vorticity and entropy. This increases the calculation accuracy and decreases the computation time required. Numerical experiments are made to obtain the threshold values of these cutoff parameters. The wake integration method is applied to predict drags of some examples including airfoil, a variety of wings and wing-body combination. Numerical results are compared with those of traditional surface integration method, showing that the predicting drag values with the wake integration method are closer to the experimental data. The results also show that drag prediction within engineering accuracy is possible by using CFD and the numerical drag optimization of complex aircraft configurations is possible, too.

  19. Parallel phase-shifting digital holography and its application to high-speed 3D imaging of dynamic object

    Science.gov (United States)

    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.

  20. Dose distribution of IMRT and 3D-CRT on treating central non-small-cell lung cancer

    International Nuclear Information System (INIS)

    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)

  1. A multifunctional 3D co-culture system for studies of mammary tissue morphogenesis and stem cell biology.

    Directory of Open Access Journals (Sweden)

    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.

  2. Structural design, layout analysis and routing strategy for constructing IC standard cells using emerging 3D vertical MOSFETs

    Science.gov (United States)

    Liu, Hongyi; Hong, Chuyang; Han, Ting; Zhou, Jun; Chen, Yijian

    2016-03-01

    As optical lithography and conventional transistor structure are approaching their physical limits, 3D vertical gate-all-around (GAA) nanowire MOSFETs and double-surrounding-gate (DSG) MOSFETs are two promising device candidates for post-FinFET logic scaling owing to their superior gate control and scaling potential. However, source, drain and gate of a vertical nanowire MOSFET and DSG MOSFETs are located in different physical layers. Consequently, structural design of IC devices/circuits, layout arrangement for high-density vertical nanowires/interconnects, and routing strategy are non-trivial challenges. In this paper, we shall discuss these critical issues for constructing standard cells using 3D vertical GAA nanowire MOSFETs and DSG MOSFETs. We redesigned the standard cells in Nangate Open Cell Library for 5nm node using vertical GAA nanowire MOSFETs and DSG MOSFETs. Experimental results verify the functionality of the proposed standard cell layout design approach.

  3. Hepatic Differentiation of Human Induced Pluripotent Stem Cells in a Perfused 3D Porous Polymer Scaffold for Liver Tissue Engineering

    DEFF Research Database (Denmark)

    Hemmingsen, Mette; Muhammad, Haseena Bashir; Mohanty, Soumyaranjan;

    differentiation of hIPS-derived definitive endoderm (DE) cells in a 3D porous polymer scaffold built-in a perfusable bioreactor. The use of a microfluidic bioreactor array enables the culture of 16 independent tissues in one experimental run and thereby an optimization study to be performed....... to limitations of primary hepatocytes regarding availability and maintenance of functionality, stem cells and especially human induced pluripotent stem cells (hIPS cells) are an attractive cell source for liver tissue engineering. The aim of this part of NanoBio4Trans is to optimize culture and hepatic...

  4. Combined dynamic contrast-enhancement and serial 3D-subtraction analysis in magnetic resonance imaging of osteoid osteomas

    Energy Technology Data Exchange (ETDEWEB)

    Kalle, T. von; Winkler, P. [Klinikum Stuttgart Olgahospital, Department of Paediatric Radiology, Stuttgart (Germany); Langendoerfer, M.; Fernandez, F.F. [Klinikum Stuttgart Olgahospital, Department of Paediatric Orthopaedics, Stuttgart (Germany)

    2009-10-15

    The purpose of this study was to retrospectively correlate the results of dynamic contrast-enhanced magnetic resonance imaging (MRI) with histological and clinical diagnoses in patients with osteoid osteomas. Fifty-four patients with the MR diagnosis of osteoid osteoma were studied. MRI (1.5 Tesla) consisted of thin-section STIR sequences, dynamic 3D T1 gradient echo sequences during application of contrast material, and high-resolution postcontrast T1 spin echo sequences with fat saturation (maximum voxel size 0.6 x 0.6 x 3.0 mm). Evaluation was focused on serial image subtraction during the early phase after contrast injection and on time-intensity curves. The surrounding edema was helpful in finding the nidus in each lesion. In 49 of 54 patients (90.7%), the diagnosis of osteoid osteoma was certain or highly probable (sensitivity 1.0, positive predictive value 0.91). A total of 38 of 54 osteoid osteomas were histologically proven. Five MRI diagnoses were regarded as false positives. A similar proportion has been reported for computed tomography. Tailored high-resolution MR examinations with dynamic contrast enhancement can reliably diagnose osteoid osteomas and exactly localize the nidus without radiation exposure. We propose a stepwise approach with STIR sequences, dynamic contrast-enhanced scanning, and high-resolution postcontrast T1 spin echo sequences with fat saturation. (orig.)

  5. 3D high-content screening for the identification of compounds that target cells in dormant tumor spheroid regions.

    Science.gov (United States)

    Wenzel, Carsten; Riefke, Björn; Gründemann, Stephan; Krebs, Alice; Christian, Sven; Prinz, Florian; Osterland, Marc; Golfier, Sven; Räse, Sebastian; Ansari, Nariman; Esner, Milan; Bickle, Marc; Pampaloni, Francesco; Mattheyer, Christian; Stelzer, Ernst H; Parczyk, Karsten; Prechtl, Stefan; Steigemann, Patrick

    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.

  6. Aquilion ONE / ViSION Edition CT scanner realizing 3D dynamic observation with low-dose scanning

    International Nuclear Information System (INIS)

    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)

  7. Identifying cell and molecular stress after radiation in a three-dimensional (3-D) model of oral mucositis

    International Nuclear Information System (INIS)

    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

  8. Identifying cell and molecular stress after radiation in a three-dimensional (3-D) model of oral mucositis

    Energy Technology Data Exchange (ETDEWEB)

    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

  9. Characterization of 3D filament dynamics in a MAST SOL flux tube geometry

    Science.gov (United States)

    Walkden, N. R.; Dudson, B. D.; Fishpool, G.

    2013-10-01

    Non-linear simulations of filament propagation in a realistic MAST SOL flux tube geometry using the BOUT++ fluid modelling framework show an isolation of the dynamics of the filament in the divertor region from the midplane region due to three features of the magnetic geometry; the variation of magnetic curvature along the field line, the expansion of the flux tube and strong magnetic shear. Of the three effects, the latter two lead to a midplane ballooning feature of the filament, whilst the former leads to a ballooning around the X-points. In simulations containing all three effects the filament is observed to balloon at the midplane, suggesting that the role of curvature variation is sub-dominant to the flux expansion and magnetic shear. The magnitudes of these effects are all strongest near the X-point which leads to the formation of parallel density gradients. The filaments simulated, which represent filaments in MAST, are identified as resistive ballooning, meaning that their motion is inertially limited, not sheath limited. Parallel density gradients can drive the filament towards a Boltzmann response when the collisionalityof the plasma is low. The results here show that the formation of parallel density gradients is a natural and inevitable consequence of a realistic magnetic geometry and therefore the transition to the Boltzmann response is a consequence of the use of realistic magnetic geometry and does not require initializing specifically varying background profiles as in slab simulations. The filaments studied here are stable to the linear resistive drift-wave instability but are subject to the non-linear effects associated with the Boltzmann response, particularly Boltzmann spinning. The Boltzmann response causes the filament to spin on an axis. In later stages of its evolution a non-linear turbulent state develops where the vorticity evolves into a turbulent eddy field on the same length scale as the parallel current. The transition from interchange

  10. Micro 3D cell culture systems for cellular behavior studies: Culture matrices, devices, substrates, and in-situ sensing methods.

    Science.gov (United States)

    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

  11. 3D Plant Cell Architecture of Arabidopsis thaliana (Brassicaceae Using Focused Ion Beam–Scanning Electron Microscopy

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  14. Non-linear dynamics of viscous bilayers subjected to an electric field: 3D phase field simulations

    Science.gov (United States)

    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.

  15. The effect of rheological approximations on the dynamics and topography in 3D subduction-collision models

    Science.gov (United States)

    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

  16. FEM modeling for 3D dynamic analysis of deep-ocean mining pipeline and its experimental verification

    Institute of Scientific and Technical Information of China (English)

    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.

  17. Laser 3D printing with sub-microscale resolution of porous elastomeric scaffolds for supporting human bone stem cells.

    Science.gov (United States)

    Petrochenko, Peter E; Torgersen, Jan; Gruber, Peter; Hicks, Lucas A; Zheng, Jiwen; Kumar, Girish; Narayan, Roger J; Goering, Peter L; Liska, Robert; Stampfl, Jürgen; Ovsianikov, Aleksandr

    2015-04-01

    A reproducible method is needed to fabricate 3D scaffold constructs that results in periodic and uniform structures with precise control at sub-micrometer and micrometer length scales. In this study, fabrication of scaffolds by two-photon polymerization (2PP) of a biodegradable urethane and acrylate-based photoelastomer is demonstrated. This material supports 2PP processing with sub-micrometer spatial resolution. The high photoreactivity of the biophotoelastomer permits 2PP processing at a scanning speed of 1000 mm s(-1), facilitating rapid fabrication of relatively large structures (>5 mm(3)). These structures are custom printed for in vitro assay screening in 96-well plates and are sufficiently flexible to enable facile handling and transplantation. These results indicate that stable scaffolds with porosities of greater than 60% can be produced using 2PP. Human bone marrow stromal cells grown on 3D scaffolds exhibit increased growth and proliferation compared to smooth 2D scaffold controls. 3D scaffolds adsorb larger amounts of protein than smooth 2D scaffolds due to their larger surface area; the scaffolds also allow cells to attach in multiple planes and to completely infiltrate the porous scaffolds. The flexible photoelastomer material is biocompatible in vitro and is associated with facile handling, making it a viable candidate for further study of complex 3D-printed scaffolds.

  18. Characterizing microscale aluminum composite layer properties on silicon solar cells with hybrid 3D scanning force measurements

    Science.gov (United States)

    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.

  19. Single Molecule 3D Orientation in Time and Space: A 6D Dynamic Study on Fluorescently Labeled Lipid Membranes.

    Science.gov (United States)

    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

  20. 3D Dynamics of the Near-Surface Layer of the Ocean in the Presence of Freshwater Influx

    Science.gov (United States)

    Dean, C.; Soloviev, A.

    2015-12-01

    Freshwater inflow due to convective rains or river runoff produces lenses of freshened water in the near surface layer of the ocean. These lenses are localized in space and typically involve both salinity and temperature anomalies. Due to significant density anomalies, strong pressure gradients develop, which result in lateral spreading of freshwater lenses in a form resembling gravity currents. Gravity currents inherently involve three-dimensional dynamics. The gravity current head can include the Kelvin-Helmholtz billows with vertical density inversions. In this work, we have conducted a series of numerical experiments using computational fluid dynamics tools. These numerical simulations were designed to elucidate the relationship between vertical mixing and horizontal advection of salinity under various environmental conditions and potential impact on the pollution transport including oil spills. The near-surface data from the field experiments in the Gulf of Mexico during the SCOPE experiment were available for validation of numerical simulations. In particular, we observed a freshwater layer within a few-meter depth range and, in some cases, a density inversion at the edge of the freshwater lens, which is consistent with the results of numerical simulations. In conclusion, we discuss applicability of these results to the interpretation of Aquarius and SMOS sea surface salinity satellite measurements. The results of this study indicate that 3D dynamics of the near-surface layer of the ocean are essential in the presence of freshwater inflow.

  1. Real-time in situ characterization of interface dynamics in microstructure formation during 3D-directional solidification of transparent alloys

    Science.gov (United States)

    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

  2. Lamellipodin promotes invasive 3D cancer cell migration via regulated interactions with Ena/VASP and SCAR/WAVE.

    Science.gov (United States)

    Carmona, G; Perera, U; Gillett, C; Naba, A; Law, A-L; Sharma, V P; Wang, J; Wyckoff, J; Balsamo, M; Mosis, F; De Piano, M; Monypenny, J; Woodman, N; McConnell, R E; Mouneimne, G; Van Hemelrijck, M; Cao, Y; Condeelis, J; Hynes, R O; Gertler, F B; Krause, M

    2016-09-29

    Cancer invasion is a hallmark of metastasis. The mesenchymal mode of cancer cell invasion is mediated by elongated membrane protrusions driven by the assembly of branched F-actin networks. How deregulation of actin regulators promotes cancer cell invasion is still enigmatic. We report that increased expression and membrane localization of the actin regulator Lamellipodin correlate with reduced metastasis-free survival and poor prognosis in breast cancer patients. In agreement, we find that Lamellipodin depletion reduced lung metastasis in an orthotopic mouse breast cancer model. Invasive 3D cancer cell migration as well as invadopodia formation and matrix degradation was impaired upon Lamellipodin depletion. Mechanistically, we show that Lamellipodin promotes invasive 3D cancer cell migration via both actin-elongating Ena/VASP proteins and the Scar/WAVE complex, which stimulates actin branching. In contrast, Lamellipodin interaction with Scar/WAVE but not with Ena/VASP is required for random 2D cell migration. We identified a phosphorylation-dependent mechanism that regulates selective recruitment of these effectors to Lamellipodin: Abl-mediated Lamellipodin phosphorylation promotes its association with both Scar/WAVE and Ena/VASP, whereas Src-dependent phosphorylation enhances binding to Scar/WAVE but not to Ena/VASP. Through these selective, regulated interactions Lamellipodin mediates directional sensing of epidermal growth factor (EGF) gradients and invasive 3D migration of breast cancer cells. Our findings imply that increased Lamellipodin levels enhance Ena/VASP and Scar/WAVE activities at the plasma membrane to promote 3D invasion and metastasis.

  3. A photopolymerizable hydrogel for 3-D culture of human embryonic stem cell-derived cardiomyocytes and rat neonatal cardiac cells.

    Science.gov (United States)

    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

  4. Synthesis and Characterization of a Photoelectrode with a Novel 3D Structure for Dye-Sensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    Kun-Ching Cho

    2014-01-01

    Full Text Available This study designs a novel dye-sensitized solar cell (DSSC in which the photoanode is derived from its three-dimensional (3D structure. The inside of the cell has a positive illumination structure, with the purposes of increasing the area of photoelectrode thin film and of increasing the illuminated area within a fixed area in order to achieve the objective of enhancing the photoelectric conversion efficiency of cell. For the cell structure experiment, the study uses graphite paper, carbon and platinum as counter electrode materials, and then conducts measurement with cell heights of 3 mm, 5 mm, and 7 mm. The electrolyte used is a gel polymer electrolyte. The assembly of the cell is divided into vertical assembly, inclined assembly, and tandem assembly. In the 3D tandem cell experiment, the counter electrode material is platinum. Experimental results show that when cell height is 7 mm and illuminated area is 0.28 cm2, open-loop voltage is 0.662 V, short-circuit current density is 18.42 mA/cm2, fill factor is 0.31, and the photoelectric conversion efficiency is 3.85%, which is 1.65 times that under vertical assembly (2.34% and 2.15 times that of the flat cell (1.79%.

  5. 3D exploration of light scattering from live cells in the presence of gold nanomarkers using holographic microscopy

    CERN Document Server

    Joud, Fadwa; Bun, P; Verpillat, Frédéric; Suck, Sarah Y; Tessier, G; Atlan, Michael; Desbiolles, Pierre; Coppey-Moisan, Maite; Abboud, Marie; Gross, Michel

    2011-01-01

    In this paper, we explore the 3D structure of light scattering from dark-field illuminated live 3T3 cells in the presence of 40 nm gold nanomarkers. For this purpose, we use a high resolution holographic microscope combining the off-axis heterodyne geometry and the phase-shifting acquisition of the digital holograms. A comparative study of the 3D reconstructions of the scattered fields allows us to locate the gold markers which yield, contrarily to the cell structures, well defined bright scattering patterns that are not angularly titled and clearly located along the optical axis (z). This characterization is an unambiguous signature of the presence of gold biological nanomarkers, and validates the capability of digital holographic microscopy to discriminate them from background signals in live ce

  6. Viral Infection at High Magnification: 3D Electron Microscopy Methods to Analyze the Architecture of Infected Cells.

    Science.gov (United States)

    Romero-Brey, Inés; Bartenschlager, Ralf

    2015-12-01

    As obligate intracellular parasites, viruses need to hijack their cellular hosts and reprogram their machineries in order to replicate their genomes and produce new virions. For the direct visualization of the different steps of a viral life cycle (attachment, entry, replication, assembly and egress) electron microscopy (EM) methods are extremely helpful. While conventional EM has given important information about virus-host cell interactions, the development of three-dimensional EM (3D-EM) approaches provides unprecedented insights into how viruses remodel the intracellular architecture of the host cell. During the last years several 3D-EM methods have been developed. Here we will provide a description of the main approaches and examples of innovative applications.

  7. Epstein-Barr virus (EBV) infection of murine L cells expressing recombinant human EBV/C3d receptor.

    OpenAIRE

    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...

  8. Fast dynamic 3D MR spectroscopic imaging with compressed sensing and multiband excitation pulses for hyperpolarized 13C studies.

    Science.gov (United States)

    Larson, Peder E Z; Hu, Simon; Lustig, Michael; Kerr, Adam B; Nelson, Sarah J; Kurhanewicz, John; Pauly, John M; Vigneron, Daniel B

    2011-03-01

    Hyperpolarized 13C MR spectroscopic imaging can detect not only the uptake of the pre-polarized molecule but also its metabolic products in vivo, thus providing a powerful new method to study cellular metabolism. Imaging the dynamic perfusion and conversion of these metabolites provides additional tissue information but requires methods for efficient hyperpolarization usage and rapid acquisitions. In this work, we have developed a time-resolved 3D MR spectroscopic imaging method for acquiring hyperpolarized 13C data by combining compressed sensing methods for acceleration and multiband excitation pulses to efficiently use the magnetization. This method achieved a 2 sec temporal resolution with full volumetric coverage of a mouse, and metabolites were observed for up to 60 sec following injection of hyperpolarized [1-(13)C]-pyruvate. The compressed sensing acquisition used random phase encode gradient blips to create a novel random undersampling pattern tailored to dynamic MR spectroscopic imaging with sampling incoherency in four (time, frequency, and two spatial) dimensions. The reconstruction was also tailored to dynamic MR spectroscopic imaging by applying a temporal wavelet sparsifying transform to exploit the inherent temporal sparsity. Customized multiband excitation pulses were designed with a lower flip angle for the [1-(13)C]-pyruvate substrate given its higher concentration than its metabolic products ([1-(13)C]-lactate and [1-(13)C]-alanine), thus using less hyperpolarization per excitation. This approach has enabled the monitoring of perfusion and uptake of the pyruvate, and the conversion dynamics to lactate and alanine throughout a volume with high spatial and temporal resolution. PMID:20939089

  9. 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

    Energy Technology Data Exchange (ETDEWEB)

    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)

  10. Revealing plot scale heterogeneity in soil moisture dynamics under contrasting vegetation assemblages using 3D electrical resistivity tomography (ERT) surveys

    Science.gov (United States)

    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. Scanning transmission and computer-aided volumic electron microscopy: 3-D modeling of entire cells by electronic imaging

    Science.gov (United States)

    Bron, Christophe; Gremillet, Philip; Launay, D.; Jourlin, Michel; Gautschi, H. P.; Baechi, Thomas; Schuepbach, Joerg

    1990-05-01

    The digital processing of electron microscopic images from serial sections containing laser-induced topographical references allows a 3-D reconstruction at a depth resolution of 30 to 40 nm of entire cells by the use of image analysis methods, as already demonstrated for Transmission Electron Microscopy (TEM) coupled with a video camera. We decided to use a Scanning Transmission Electron Microscope (STEM) to get higher contrast and better resolution at medium magnification. The scanning of our specimens at video frequencies is an attractive and easy way to link a STEM with an image processing system but the hysteresis of the electronic spools responsible for the magnetic deviation of the scanning electron beam induces deformations of images which have to be modelized and corrected before registration. Computer algorithms developed for image analysis and treatment correct the artifacts caused by the use of STEM and by serial sectioning to automatically reconstruct the third dimension of the cells. They permit the normalization of the images through logarithmic processing of the original grey level infonnation. The automatic extraction of cell limits allows to link the image analysis and treatments with image synthesis methods by minimal human intervention. The surface representation and the registered images provide an ultrastructural data base from which quantitative 3-D morphological parameters, as well as otherwise impossible visualizations, can be computed. This 3-D image processing named C.A.V.U.M. for Computer Aided Volumic Ultra-Microscopy offers a new tool for the documentation and analysis of cell ultrastructure and for 3-D morphometric studies at EM magnifications. Further, a virtual observer can be computed in such a way as to simulate a visit of the reconstructed object.

  12. Exploring natural silk protein sericin for regenerative medicine: an injectable, photoluminescent, cell-adhesive 3D hydrogel

    OpenAIRE

    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...

  13. Cellular differentiation in 3D-bioprinted mesenchymal stem cell-loaded hydrogels with varying structural and mechanical properties

    OpenAIRE

    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...

  14. Tuning the Mechanical Properties of Poly(Ethylene Glycol) Microgel-Based Scaffolds to Increase 3D Schwann Cell Proliferation.

    Science.gov (United States)

    Zhou, Wenda; Stukel, Jessica M; Cebull, Hannah L; Willits, Rebecca Kuntz

    2016-04-01

    2D in vitro studies have demonstrated that Schwann cells prefer scaffolds with mechanical modulus approximately 10× higher than the modulus preferred by nerves, limiting the ability of many scaffolds to promote both neuron extension and Schwann cell proliferation. Therefore, the goals of this work are to develop and characterize microgel-based scaffolds that are tuned over the stiffness range relevant to neural tissue engineering and investigate Schwann cell morphology, viability, and proliferation within 3D scaffolds. Using thiol-ene reaction, microgels with surface thiols are produced and crosslinked into hydrogels using a multiarm vinylsulfone (VS). By varying the concentration of VS, scaffold stiffness ranges from 0.13 to 0.76 kPa. Cell morphology in all groups demonstrates that cells are able to spread and interact with the scaffold through day 5. Although the viability in all groups is high, proliferation of Schwann cells within the scaffold of G* = 0.53 kPa is significantly higher than other groups. This result is ≈ 5× lower than previously reported optimal stiffnesses on 2D surfaces, demonstrating the need for correlation of 3D cell response to mechanical modulus. As proliferation is the first step in Schwann cell integration into peripheral nerve conduits, these scaffolds demonstrate that the stiffness is a critical parameter to optimizing the regenerative process.

  15. RIMBAY – a multi-physics 3-D ice-dynamics model for comprehensive applications: model-description and examples

    Directory of Open Access Journals (Sweden)

    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.

  16. RIMBAY - a multi-approximation 3D ice-dynamics model for comprehensive applications: model description and examples

    Science.gov (United States)

    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.

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

    International Nuclear Information System (INIS)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  19. Ammonium accumulation and cell death in a rat 3D brain cell model of glutaric aciduria type I.

    Directory of Open Access Journals (Sweden)

    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.

  20. A fully defined and scalable 3D culture system for human pluripotent stem cell expansion and differentiation

    Science.gov (United States)

    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.

  1. AlgiMatrix™ based 3D cell culture system as an in-vitro tumor model for anticancer studies.

    Directory of Open Access Journals (Sweden)

    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.

  2. Dynamic, ecological, accessible and 3D Virtual Worlds-based Libraries using OpenSim and Sloodle along with mobile location and NFC for checking in

    OpenAIRE

    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.

  3. Dynamic, ecological, accessible and 3D Virtual Worlds-based Libraries using OpenSim and Sloodle along with mobile location and NFC for checking in

    Directory of Open Access Journals (Sweden)

    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.

  4. Controlled positioning of cells in biomaterials - approaches towards 3D tissue printing

    OpenAIRE

    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...

  5. 3D dynamic simulations of spontaneous rupture propagation governed by different constitutive laws with rake rotation allowed

    Directory of Open Access Journals (Sweden)

    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.

  6. 3D game environments create professional 3D game worlds

    CERN Document Server

    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

  7. Super-resolved 3-D imaging of live cells organelles from bright-field photon transmission micrographs

    CERN Document Server

    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...

  8. Electricity Generation with the Novel 3D Electrode from Swim Wastewater in a Dual-chamber Microbial Fuel Cell

    Directory of Open Access Journals (Sweden)

    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%.

  9. 3D printed sample holder for in-operando EPR spectroscopy on high temperature polymer electrolyte fuel cells.

    Science.gov (United States)

    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.

  10. 3D printed sample holder for in-operando EPR spectroscopy on high temperature polymer electrolyte fuel cells

    Science.gov (United States)

    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.

  11. 3D printed sample holder for in-operando EPR spectroscopy on high temperature polymer electrolyte fuel cells.

    Science.gov (United States)

    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

  12. A new method to address unmet needs for extracting individual cell migration features from a large number of cells embedded in 3D volumes.

    Directory of Open Access Journals (Sweden)

    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.

  13. Quantitative 3-D imaging of eukaryotic cells using soft x-ray tomography

    OpenAIRE

    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...

  14. 3D Imaging of mammalian cells with ion-abrasion scanning electron microscopy

    OpenAIRE

    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...

  15. A new 3D tracking method for cell mechanics investigation exploiting the capabilities of digital holography in microscopy

    Science.gov (United States)

    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.

  16. Dynamic simulation and modeling of the motion modes produced during the 3D controlled manipulation of biological micro/nanoparticles based on the AFM.

    Science.gov (United States)

    Saraee, Mahdieh B; Korayem, Moharam H

    2015-08-01

    Determining the motion modes and the exact position of a particle displaced during the manipulation process is of special importance. This issue becomes even more important when the studied particles are biological micro/nanoparticles and the goals of manipulation are the transfer of these particles within body cells, repair of cancerous cells and the delivery of medication to damaged cells. However, due to the delicate nature of biological nanoparticles and their higher vulnerability, by obtaining the necessary force of manipulation for the considered motion mode, we can prevent the sample from interlocking with or sticking to the substrate because of applying a weak force or avoid damaging the sample due to the exertion of excessive force. In this paper, the dynamic behaviors and the motion modes of biological micro/nanoparticles such as DNA, yeast, platelet and bacteria due to the 3D manipulation effect have been investigated. Since the above nanoparticles generally have a cylindrical shape, the cylindrical contact models have been employed in an attempt to more precisely model the forces exerted on the nanoparticle during the manipulation process. Also, this investigation has performed a comprehensive modeling and simulation of all the possible motion modes in 3D manipulation by taking into account the eccentricity of the applied load on the biological nanoparticle. The obtained results indicate that unlike the macroscopic scale, the sliding of nanoparticle on substrate in nano-scale takes place sooner than the other motion modes and that the spinning about the vertical and transverse axes and the rolling of nanoparticle occur later than the other motion modes. The simulation results also indicate that the applied force necessary for the onset of nanoparticle movement and the resulting motion mode depend on the size and aspect ratio of the nanoparticle.

  17. Role of Mechanical Cues in Cell Differentiation and Proliferation: A 3D Numerical Model.

    Directory of Open Access Journals (Sweden)

    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. Role of Mechanical Cues in Cell Differentiation and Proliferation: A 3D Numerical Model

    Science.gov (United States)

    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 sof