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Sample records for 3d tumor models

  1. Heralding a new paradigm in 3D tumor modeling.

    PubMed

    Fong, Eliza L S; Harrington, Daniel A; Farach-Carson, Mary C; Yu, Hanry

    2016-11-01

    Numerous studies to date have contributed to a paradigm shift in modeling cancer, moving from the traditional two-dimensional culture system to three-dimensional (3D) culture systems for cancer cell culture. This led to the inception of tumor engineering, which has undergone rapid advances over the years. In line with the recognition that tumors are not merely masses of proliferating cancer cells but rather, highly complex tissues consisting of a dynamic extracellular matrix together with stromal, immune and endothelial cells, significant efforts have been made to better recapitulate the tumor microenvironment in 3D. These approaches include the development of engineered matrices and co-cultures to replicate the complexity of tumor-stroma interactions in vitro. However, the tumor engineering and cancer biology fields have traditionally relied heavily on the use of cancer cell lines as a cell source in tumor modeling. While cancer cell lines have contributed to a wealth of knowledge in cancer biology, the use of this cell source is increasingly perceived as a major contributing factor to the dismal failure rate of oncology drugs in drug development. Backing this notion is the increasing evidence that tumors possess intrinsic heterogeneity, which predominantly homogeneous cancer cell lines poorly reflect. Tumor heterogeneity contributes to therapeutic resistance in patients. To overcome this limitation, cancer cell lines are beginning to be replaced by primary tumor cell sources, in the form of patient-derived xenografts and organoids cultures. Moving forward, we propose that further advances in tumor engineering would require that tumor heterogeneity (tumor variants) be taken into consideration together with tumor complexity (tumor-stroma interactions). In this review, we provide a comprehensive overview of what has been achieved in recapitulating tumor complexity, and discuss the importance of incorporating tumor heterogeneity into 3D in vitro tumor models. This

  2. Model-based risk assessment for motion effects in 3D radiotherapy of lung tumors

    NASA Astrophysics Data System (ADS)

    Werner, René; Ehrhardt, Jan; Schmidt-Richberg, Alexander; Handels, Heinz

    2012-02-01

    Although 4D CT imaging becomes available in an increasing number of radiotherapy facilities, 3D imaging and planning is still standard in current clinical practice. In particular for lung tumors, respiratory motion is a known source of uncertainty and should be accounted for during radiotherapy planning - which is difficult by using only a 3D planning CT. In this contribution, we propose applying a statistical lung motion model to predict patients' motion patterns and to estimate dosimetric motion effects in lung tumor radiotherapy if only 3D images are available. Being generated based on 4D CT images of patients with unimpaired lung motion, the model tends to overestimate lung tumor motion. It therefore promises conservative risk assessment regarding tumor dose coverage. This is exemplarily evaluated using treatment plans of lung tumor patients with different tumor motion patterns and for two treatment modalities (conventional 3D conformal radiotherapy and step-&- shoot intensity modulated radiotherapy). For the test cases, 4D CT images are available. Thus, also a standard registration-based 4D dose calculation is performed, which serves as reference to judge plausibility of the modelbased 4D dose calculation. It will be shown that, if combined with an additional simple patient-specific breathing surrogate measurement (here: spirometry), the model-based dose calculation provides reasonable risk assessment of respiratory motion effects.

  3. Digital holographic microscopy for imaging growth and treatment response in 3D tumor models

    NASA Astrophysics Data System (ADS)

    Li, Yuyu; Petrovic, Ljubica; Celli, Jonathan P.; Yelleswarapu, Chandra S.

    2014-03-01

    While three-dimensional tumor models have emerged as valuable tools in cancer research, the ability to longitudinally visualize the 3D tumor architecture restored by these systems is limited with microscopy techniques that provide only qualitative insight into sample depth, or which require terminal fixation for depth-resolved 3D imaging. Here we report the use of digital holographic microscopy (DHM) as a viable microscopy approach for quantitative, non-destructive longitudinal imaging of in vitro 3D tumor models. Following established methods we prepared 3D cultures of pancreatic cancer cells in overlay geometry on extracellular matrix beds and obtained digital holograms at multiple timepoints throughout the duration of growth. The holograms were digitally processed and the unwrapped phase images were obtained to quantify nodule thickness over time under normal growth, and in cultures subject to chemotherapy treatment. In this manner total nodule volumes are rapidly estimated and demonstrated here to show contrasting time dependent changes during growth and in response to treatment. This work suggests the utility of DHM to quantify changes in 3D structure over time and suggests the further development of this approach for time-lapse monitoring of 3D morphological changes during growth and in response to treatment that would otherwise be impractical to visualize.

  4. Longitudinal Measurement of Extracellular Matrix Rigidity in 3D Tumor Models Using Particle-tracking Microrheology

    PubMed Central

    El-Hamidi, Hamid; Celli, Jonathan P.

    2014-01-01

    The mechanical microenvironment has been shown to act as a crucial regulator of tumor growth behavior and signaling, which is itself remodeled and modified as part of a set of complex, two-way mechanosensitive interactions. While the development of biologically-relevant 3D tumor models have facilitated mechanistic studies on the impact of matrix rheology on tumor growth, the inverse problem of mapping changes in the mechanical environment induced by tumors remains challenging. Here, we describe the implementation of particle-tracking microrheology (PTM) in conjunction with 3D models of pancreatic cancer as part of a robust and viable approach for longitudinally monitoring physical changes in the tumor microenvironment, in situ. The methodology described here integrates a system of preparing in vitro 3D models embedded in a model extracellular matrix (ECM) scaffold of Type I collagen with fluorescently labeled probes uniformly distributed for position- and time-dependent microrheology measurements throughout the specimen. In vitro tumors are plated and probed in parallel conditions using multiwell imaging plates. Drawing on established methods, videos of tracer probe movements are transformed via the Generalized Stokes Einstein Relation (GSER) to report the complex frequency-dependent viscoelastic shear modulus, G*(ω). Because this approach is imaging-based, mechanical characterization is also mapped onto large transmitted-light spatial fields to simultaneously report qualitative changes in 3D tumor size and phenotype. Representative results showing contrasting mechanical response in sub-regions associated with localized invasion-induced matrix degradation as well as system calibration, validation data are presented. Undesirable outcomes from common experimental errors and troubleshooting of these issues are also presented. The 96-well 3D culture plating format implemented in this protocol is conducive to correlation of microrheology measurements with therapeutic

  5. 3D cell culture systems modeling tumor growth determinants in cancer target discovery.

    PubMed

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

    2014-04-01

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

  6. Generation of a tumor spheroid in a microgravity environment as a 3D model of melanoma.

    PubMed

    Marrero, Bernadette; Messina, Jane L; Heller, Richard

    2009-10-01

    An in vitro 3D model was developed utilizing a synthetic microgravity environment to facilitate studying the cell interactions. 2D monolayer cell culture models have been successfully used to understand various cellular reactions that occur in vivo. There are some limitations to the 2D model that are apparent when compared to cells grown in a 3D matrix. For example, some proteins that are not expressed in a 2D model are found up-regulated in the 3D matrix. In this paper, we discuss techniques used to develop the first known large, free-floating 3D tissue model used to establish tumor spheroids. The bioreactor system known as the High Aspect Ratio Vessel (HARVs) was used to provide a microgravity environment. The HARVs promoted aggregation of keratinocytes (HaCaT) that formed a construct that served as scaffolding for the growth of mouse melanoma. Although there is an emphasis on building a 3D model with the proper extracellular matrix and stroma, we were able to develop a model that excluded the use of matrigel. Immunohistochemistry and apoptosis assays provided evidence that this 3D model supports B16.F10 cell growth, proliferation, and synthesis of extracellular matrix. Immunofluorescence showed that melanoma cells interact with one another displaying observable cellular morphological changes. The goal of engineering a 3D tissue model is to collect new information about cancer development and develop new potential treatment regimens that can be translated to in vivo models while reducing the use of laboratory animals. PMID:19533253

  7. Anti-tumor activity of obinutuzumab and rituximab in a follicular lymphoma 3D model

    PubMed Central

    Decaup, E; Jean, C; Laurent, C; Gravelle, P; Fruchon, S; Capilla, F; Marrot, A; Al Saati, T; Frenois, F-X; Laurent, G; Klein, C; Varoqueaux, N; Savina, A; Fournié, J-J; Bezombes, C

    2013-01-01

    Follicular lymphomas (FLs) account for 35–40% of all adult lymphomas. Treatment typically involves chemotherapy combined with the anti-CD20 monoclonal antibody (MAb) rituximab (RTX). The development of the type II anti-CD20 MAb obinutuzumab (GA101) aims to further improve treatment. Here, using FL cells we show that RTX and GA101 display a similar activity on RL cells cultured in 2D. However, 2D culture cannot mimic tumor spatial organization and conventional 2D models may not reflect the effects of antibodies as they occur in vivo. Thus, we created a non-Hodgkin's lymphoma (NHL) 3D culture system, termed multicellular aggregates of lymphoma cells (MALC), and used it to compare RTX and GA101 activity. Our results show that both antibodies display greater activity towards FL cells in 3D culture compared with 2D culture. Moreover, we observed that in the 3D model GA101 was more effective than RTX both in inhibiting MALC growth through induction of (lysosomal) cell death and senescence and in inhibiting intracellular signaling pathways, such as mammalian target of rapamycin, Akt, PLCgamma (Phospholipase C gamma) and Syk. Altogether, our study demonstrates that spatial organization strongly influences the response to antibody treatment, supporting the use of 3D models for the testing of therapeutic agents in NHL. PMID:23933705

  8. Capturing tumor complexity in vitro: Comparative analysis of 2D and 3D tumor models for drug discovery

    PubMed Central

    Stock, Kristin; Estrada, Marta F.; Vidic, Suzana; Gjerde, Kjersti; Rudisch, Albin; Santo, Vítor E.; Barbier, Michaël; Blom, Sami; Arundkar, Sharath C.; Selvam, Irwin; Osswald, Annika; Stein, Yan; Gruenewald, Sylvia; Brito, Catarina; van Weerden, Wytske; Rotter, Varda; Boghaert, Erwin; Oren, Moshe; Sommergruber, Wolfgang; Chong, Yolanda; de Hoogt, Ronald; Graeser, Ralph

    2016-01-01

    Two-dimensional (2D) cell cultures growing on plastic do not recapitulate the three dimensional (3D) architecture and complexity of human tumors. More representative models are required for drug discovery and validation. Here, 2D culture and 3D mono- and stromal co-culture models of increasing complexity have been established and cross-comparisons made using three standard cell carcinoma lines: MCF7, LNCaP, NCI-H1437. Fluorescence-based growth curves, 3D image analysis, immunohistochemistry and treatment responses showed that end points differed according to cell type, stromal co-culture and culture format. The adaptable methodologies described here should guide the choice of appropriate simple and complex in vitro models. PMID:27364600

  9. Capturing tumor complexity in vitro: Comparative analysis of 2D and 3D tumor models for drug discovery.

    PubMed

    Stock, Kristin; Estrada, Marta F; Vidic, Suzana; Gjerde, Kjersti; Rudisch, Albin; Santo, Vítor E; Barbier, Michaël; Blom, Sami; Arundkar, Sharath C; Selvam, Irwin; Osswald, Annika; Stein, Yan; Gruenewald, Sylvia; Brito, Catarina; van Weerden, Wytske; Rotter, Varda; Boghaert, Erwin; Oren, Moshe; Sommergruber, Wolfgang; Chong, Yolanda; de Hoogt, Ronald; Graeser, Ralph

    2016-01-01

    Two-dimensional (2D) cell cultures growing on plastic do not recapitulate the three dimensional (3D) architecture and complexity of human tumors. More representative models are required for drug discovery and validation. Here, 2D culture and 3D mono- and stromal co-culture models of increasing complexity have been established and cross-comparisons made using three standard cell carcinoma lines: MCF7, LNCaP, NCI-H1437. Fluorescence-based growth curves, 3D image analysis, immunohistochemistry and treatment responses showed that end points differed according to cell type, stromal co-culture and culture format. The adaptable methodologies described here should guide the choice of appropriate simple and complex in vitro models. PMID:27364600

  10. Recapitulating the Tumor Ecosystem Along the Metastatic Cascade Using 3D Culture Models

    PubMed Central

    Kim, Jiyun; Tanner, Kandice

    2015-01-01

    Advances in cancer research have shown that a tumor can be likened to a foreign species that disrupts delicately balanced ecological interactions, compromising the survival of normal tissue ecosystems. In efforts to mitigate tumor expansion and metastasis, experimental approaches from ecology are becoming more frequently and successfully applied by researchers from diverse disciplines to reverse engineer and re-engineer biological systems in order to normalize the tumor ecosystem. We present a review on the use of 3D biomimetic platforms to recapitulate biotic and abiotic components of the tumor ecosystem, in efforts to delineate the underlying mechanisms that drive evolution of tumor heterogeneity, tumor dissemination, and acquisition of drug resistance. PMID:26284194

  11. A computational model for estimating tumor margins in complementary tactile and 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Shamsil, Arefin; Escoto, Abelardo; Naish, Michael D.; Patel, Rajni V.

    2016-03-01

    Conventional surgical methods are effective for treating lung tumors; however, they impose high trauma and pain to patients. Minimally invasive surgery is a safer alternative as smaller incisions are required to reach the lung; however, it is challenging due to inadequate intraoperative tumor localization. To address this issue, a mechatronic palpation device was developed that incorporates tactile and ultrasound sensors capable of acquiring surface and cross-sectional images of palpated tissue. Initial work focused on tactile image segmentation and fusion of position-tracked tactile images, resulting in a reconstruction of the palpated surface to compute the spatial locations of underlying tumors. This paper presents a computational model capable of analyzing orthogonally-paired tactile and ultrasound images to compute the surface circumference and depth margins of a tumor. The framework also integrates an error compensation technique and an algebraic model to align all of the image pairs and to estimate the tumor depths within the tracked thickness of a palpated tissue. For validation, an ex vivo experimental study was conducted involving the complete palpation of 11 porcine liver tissues injected with iodine-agar tumors of varying sizes and shapes. The resulting tactile and ultrasound images were then processed using the proposed model to compute the tumor margins and compare them to fluoroscopy based physical measurements. The results show a good negative correlation (r = -0.783, p = 0.004) between the tumor surface margins and a good positive correlation (r = 0.743, p = 0.009) between the tumor depth margins.

  12. Modeling stromal determinants of 3D tumor growth to inform PDT-mediated combination treatments

    NASA Astrophysics Data System (ADS)

    Rizvi, I.; Anbil, S.; Celli, J. P.; Alagic, N.; Massodi, I.; Hasan, T.

    2013-03-01

    Advanced stage ovarian carcinoma is characterized by poor prognosis and peritoneal micronodules that exhibit treatment resistance. This is partially due to interactions between multifocal disease and the tumor microenvironment, which includes tumor endothelial cells (TECs) and extracellular matrix components (ECM). Here we describe the development of a three-dimensional model of ovarian cancer that incorporates TECs and ECM. A comparison of several methodologies to generate endothelialized ovarian micronodules along with a preliminary physical characterization is described. This model will allow for detailed investigation of tumor-stroma interactions and how they impact disease progression and treatment response.

  13. Development of drug loaded nanoparticles for tumor targeting. Part 2: Enhancement of tumor penetration through receptor mediated transcytosis in 3D tumor models

    NASA Astrophysics Data System (ADS)

    El-Dakdouki, Mohammad H.; Puré, Ellen; Huang, Xuefei

    2013-04-01

    We report that receptor mediated transcytosis can be utilized to facilitate tumor penetration by drug loaded nanoparticles (NPs). We synthesized hyaluronan (HA) coated silica nanoparticles (SNPs) containing a highly fluorescent core to target CD44 expressed on the cancer cell surface. Although prior studies have primarily focused on CD44 mediated endocytosis to facilitate cellular uptake of HA-NPs by cancer cells, we discovered that, once internalized, the HA-SNPs could be transported out of the cells with their cargo. The exported NPs could be taken up by neighboring cells. This enabled the HA-SNPs to penetrate deeper inside tumors and reach a much greater number of tumor cells in 3D tumor models, presumably through tandem cycles of CD44 mediated endocytosis and exocytosis. When doxorubicin (DOX) was loaded onto the NPs, better penetration of multilayered tumor cells was observed with much improved cytotoxicities against both drug sensitive and drug resistant cancer spheroids compared to the free drug. Thus, targeting receptors such as CD44 that can readily undergo recycling between the cell surface and interior of the cells can become a useful strategy to enhance the tumor penetration potential of NPs and the efficiency of drug delivery through receptor mediated transcytosis.We report that receptor mediated transcytosis can be utilized to facilitate tumor penetration by drug loaded nanoparticles (NPs). We synthesized hyaluronan (HA) coated silica nanoparticles (SNPs) containing a highly fluorescent core to target CD44 expressed on the cancer cell surface. Although prior studies have primarily focused on CD44 mediated endocytosis to facilitate cellular uptake of HA-NPs by cancer cells, we discovered that, once internalized, the HA-SNPs could be transported out of the cells with their cargo. The exported NPs could be taken up by neighboring cells. This enabled the HA-SNPs to penetrate deeper inside tumors and reach a much greater number of tumor cells in 3D tumor

  14. Hydrogels to Model 3D in vitro Microenvironment of Tumor Vascularization

    PubMed Central

    Song, Hyun-Ho Greco; Park, Kyung Min; Gerecht, Sharon

    2014-01-01

    A growing number of failing clinical trials for cancer therapy is substantiating the need to upgrade the current practice in culturing tumor cells and modeling tumor angiogenesis in vitro. Many attempts have been made to engineer vasculature in vitro by utilizing hydrogels, but the application of these tools in simulating in vivo tumor angiogenesis is still very new. In this review, we explore current use of hydrogels and their design parameters to engineer vasculogenesis and angiogenesis and to evaluate the angiogenic capability of cancerous cells and tissues. When coupled with other technologies such as lithography and three-dimensional printing, one can even create an advanced microvessel model as microfluidic channels to more accurately capture the native angiogenesis process. PMID:24969477

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

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

    2016-01-01

    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. PMID:27248849

  17. Designing PDT-based combinations to overcome chemoresistance in heterocellular 3D tumor models (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Rizvi, Imran; Briars, Emma A.; Bulin, Anne-Laure; Anbil, Sriram; Vecchio, Daniela; Alkhateeb, Ahmed; Hanna, William R.; Celli, Jonathan P.; Hasan, Tayyaba

    2016-03-01

    A major barrier to treating advanced-stage cancers is heterogeneity in the responsiveness of metastatic disease to conventional therapies leading to resistance and treatment failure. Photodynamic therapy (PDT) has been shown to synergize with conventional agents and to overcome the evasion pathways that cause resistance. Developing PDT-based combinations that target resistant tumor populations and cooperate mechanistically with conventional agents is an increasingly promising approach to improve therapeutic efficacy while minimizing toxicity, particularly in complex disease sites. Identifying the molecular, cellular, and microenvironmental cues that lead to heterogeneity and treatment resistance is critical to developing strategies to target unresponsive regions of stubborn disease. Cell-based research platforms that integrate key microenvironmental cues are emerging as increasingly important tools to improve the translational efficiency of new agents, and to design combination regimens. Among the challenges associated with developing and scaling complex cell-based screening platforms is the need to integrate, and balance, biological relevance with appropriate, high-content imaging routines that provide meaningful quantitative readouts of therapeutic response. The benefits and challenges associated with deriving meaningful insights from complex cell-based models will be presented, with a particular emphasis on overcoming chemoresistance mediated by physical stress and communication with stromal partners (e.g. tumor endothelial cells, which are emerging as dynamic regulators of treatment resistance) using PDT-based combinations.

  18. Inhibition of Lysyl Oxidases Improves Drug Diffusion and Increases Efficacy of Cytotoxic Treatment in 3D Tumor Models

    PubMed Central

    Schütze, Friedrich; Röhrig, Florian; Vorlová, Sandra; Gätzner, Sabine; Kuhn, Anja; Ergün, Süleyman; Henke, Erik

    2015-01-01

    Tumors are characterized by a rigid, highly cross-linked extracellular matrix (ECM), which impedes homogeneous drug distribution and potentially protects malignant cells from exposure to therapeutics. Lysyl oxidases are major contributors to tissue stiffness and the elevated expression of these enzymes observed in most cancers might influence drug distribution and efficacy. We examined the effect of lysyl oxidases on drug distribution and efficacy in 3D in vitro assay systems. In our experiments elevated lysyl oxidase activity was responsible for reduced drug diffusion under hypoxic conditions and consequently impaired cytotoxicity of various chemotherapeutics. This effect was only observed in 3D settings but not in 2D-cell culture, confirming that lysyl oxidases affect drug efficacy by modification of the ECM and do not confer a direct desensitizing effect. Both drug diffusion and efficacy were strongly enhanced by inhibition of lysyl oxidases. The results from the in vitro experiments correlated with tumor drug distribution in vivo, and predicted response to therapeutics in murine tumor models. Our results demonstrate that lysyl oxidase activity modulates the physical barrier function of ECM for small molecule drugs influencing their therapeutic efficacy. Targeting this process has the potential to significantly enhance therapeutic efficacy in the treatment of malignant diseases. PMID:26620400

  19. Co-culture of 3D tumor spheroids with fibroblasts as a model for epithelial–mesenchymal transition in vitro

    SciTech Connect

    Kim, Sun-Ah; Lee, Eun Kyung; Kuh, Hyo-Jeong

    2015-07-15

    Epithelial–mesenchymal transition (EMT) acts as a facilitator of metastatic dissemination in the invasive margin of malignant tumors where active tumor–stromal crosstalks take place. Co-cultures of cancer cells with cancer-associated fibroblasts (CAFs) are often used as in vitro models of EMT. We established a tumor–fibroblast proximity co-culture using HT-29 tumor spheroids (TSs) with CCD-18co fibroblasts. When co-cultured with TSs, CCD-18co appeared activated, and proliferative activity as well as cell migration increased. Expression of fibronectin increased whereas laminin and type I collagen decreased in TSs co-cultured with fibroblasts compared to TSs alone, closely resembling the margin of in vivo xenograft tissue. Active TGFβ1 in culture media significantly increased in TS co-cultures but not in 2D co-cultures of cancer cells–fibroblasts, indicating that 3D context-associated factors from TSs may be crucial to crosstalks between cancer cells and fibroblasts. We also observed in TSs co-cultured with fibroblasts increased expression of α-SMA, EGFR and CTGF; reduced expression of membranous β-catenin and E-cadherin, together suggesting an EMT-like changes similar to a marginal region of xenograft tissue in vivo. Overall, our in vitro TS–fibroblast proximity co-culture mimics the EMT-state of the invasive margin of in vivo tumors in early metastasis. - Highlights: • An adjacent co-culture of tumor spheroids and fibroblasts is presented as EMT model. • Activation of fibroblasts and increased cell migration were shown in co-culture. • Expression of EMT-related factors in co-culture was similar to that in tumor tissue. • Crosstalk between spheroids and fibroblasts was demonstrated by secretome analysis.

  20. A GPU-based framework for modeling real-time 3D lung tumor conformal dosimetry with subject-specific lung tumor motion

    NASA Astrophysics Data System (ADS)

    Min, Yugang; Santhanam, Anand; Neelakkantan, Harini; Ruddy, Bari H.; Meeks, Sanford L.; Kupelian, Patrick A.

    2010-09-01

    In this paper, we present a graphics processing unit (GPU)-based simulation framework to calculate the delivered dose to a 3D moving lung tumor and its surrounding normal tissues, which are undergoing subject-specific lung deformations. The GPU-based simulation framework models the motion of the 3D volumetric lung tumor and its surrounding tissues, simulates the dose delivery using the dose extracted from a treatment plan using Pinnacle Treatment Planning System, Phillips, for one of the 3DCTs of the 4DCT and predicts the amount and location of radiation doses deposited inside the lung. The 4DCT lung datasets were registered with each other using a modified optical flow algorithm. The motion of the tumor and the motion of the surrounding tissues were simulated by measuring the changes in lung volume during the radiotherapy treatment using spirometry. The real-time dose delivered to the tumor for each beam is generated by summing the dose delivered to the target volume at each increase in lung volume during the beam delivery time period. The simulation results showed the real-time capability of the framework at 20 discrete tumor motion steps per breath, which is higher than the number of 4DCT steps (approximately 12) reconstructed during multiple breathing cycles.

  1. 3D modeling of effects of increased oxygenation and activity concentration in tumors treated with radionuclides and antiangiogenic drugs

    SciTech Connect

    Lagerloef, Jakob H.; Kindblom, Jon; Bernhardt, Peter

    2011-08-15

    Purpose: Formation of new blood vessels (angiogenesis) in response to hypoxia is a fundamental event in the process of tumor growth and metastatic dissemination. However, abnormalities in tumor neovasculature often induce increased interstitial pressure (IP) and further reduce oxygenation (pO{sub 2}) of tumor cells. In radiotherapy, well-oxygenated tumors favor treatment. Antiangiogenic drugs may lower IP in the tumor, improving perfusion, pO{sub 2} and drug uptake, by reducing the number of malfunctioning vessels in the tissue. This study aims to create a model for quantifying the effects of altered pO{sub 2}-distribution due to antiangiogenic treatment in combination with radionuclide therapy. Methods: Based on experimental data, describing the effects of antiangiogenic agents on oxygenation of GlioblastomaMultiforme (GBM), a single cell based 3D model, including 10{sup 10} tumor cells, was developed, showing how radionuclide therapy response improves as tumor oxygenation approaches normal tissue levels. The nuclides studied were {sup 90}Y, {sup 131}I, {sup 177}Lu, and {sup 211}At. The absorbed dose levels required for a tumor control probability (TCP) of 0.990 are compared for three different log-normal pO{sub 2}-distributions: {mu}{sub 1} = 2.483, {sigma}{sub 1} = 0.711; {mu}{sub 2} = 2.946, {sigma}{sub 2} = 0.689; {mu}{sub 3} = 3.689, and {sigma}{sub 3} = 0.330. The normal tissue absorbed doses will, in turn, depend on this. These distributions were chosen to represent the expected oxygen levels in an untreated hypoxic tumor, a hypoxic tumor treated with an anti-VEGF agent, and in normal, fully-oxygenated tissue, respectively. The former two are fitted to experimental data. The geometric oxygen distributions are simulated using two different patterns: one Monte Carlo based and one radially increasing, while keeping the log-normal volumetric distributions intact. Oxygen and activity are distributed, according to the same pattern. Results: As tumor pO{sub 2

  2. Computer-aided classification of liver tumors in 3D ultrasound images with combined deformable model segmentation and support vector machine

    NASA Astrophysics Data System (ADS)

    Lee, Myungeun; Kim, Jong Hyo; Park, Moon Ho; Kim, Ye-Hoon; Seong, Yeong Kyeong; Cho, Baek Hwan; Woo, Kyoung-Gu

    2014-03-01

    In this study, we propose a computer-aided classification scheme of liver tumor in 3D ultrasound by using a combination of deformable model segmentation and support vector machine. For segmentation of tumors in 3D ultrasound images, a novel segmentation model was used which combined edge, region, and contour smoothness energies. Then four features were extracted from the segmented tumor including tumor edge, roundness, contrast, and internal texture. We used a support vector machine for the classification of features. The performance of the developed method was evaluated with a dataset of 79 cases including 20 cysts, 20 hemangiomas, and 39 hepatocellular carcinomas, as determined by the radiologist's visual scoring. Evaluation of the results showed that our proposed method produced tumor boundaries that were equal to or better than acceptable in 89.8% of cases, and achieved 93.7% accuracy in classification of cyst and hemangioma.

  3. Novel chemical scaffolds of the tumor marker AKR1B10 inhibitors discovered by 3D QSAR pharmacophore modeling

    PubMed Central

    Kumar, Raj; Son, Minky; Bavi, Rohit; Lee, Yuno; Park, Chanin; Arulalapperumal, Venkatesh; Cao, Guang Ping; Kim, Hyong-ha; Suh, Jung-keun; Kim, Yong-seong; Kwon, Yong Jung; Lee, Keun Woo

    2015-01-01

    Aim: Recent evidence suggests that aldo-keto reductase family 1 B10 (AKR1B10) may be a potential diagnostic or prognostic marker of human tumors, and that AKR1B10 inhibitors offer a promising choice for treatment of many types of human cancers. The aim of this study was to identify novel chemical scaffolds of AKR1B10 inhibitors using in silico approaches. Methods: The 3D QSAR pharmacophore models were generated using HypoGen. A validated pharmacophore model was selected for virtual screening of 4 chemical databases. The best mapped compounds were assessed for their drug-like properties. The binding orientations of the resulting compounds were predicted by molecular docking. Density functional theory calculations were carried out using B3LYP. The stability of the protein-ligand complexes and the final binding modes of the hit compounds were analyzed using 10 ns molecular dynamics (MD) simulations. Results: The best pharmacophore model (Hypo 1) showed the highest correlation coefficient (0.979), lowest total cost (102.89) and least RMSD value (0.59). Hypo 1 consisted of one hydrogen-bond acceptor, one hydrogen-bond donor, one ring aromatic and one hydrophobic feature. This model was validated by Fischer's randomization and 40 test set compounds. Virtual screening of chemical databases and the docking studies resulted in 30 representative compounds. Frontier orbital analysis confirmed that only 3 compounds had sufficiently low energy band gaps. MD simulations revealed the binding modes of the 3 hit compounds: all of them showed a large number of hydrogen bonds and hydrophobic interactions with the active site and specificity pocket residues of AKR1B10. Conclusion: Three compounds with new structural scaffolds have been identified, which have stronger binding affinities for AKR1B10 than known inhibitors. PMID:26051108

  4. Extracellular matrix composition and rigidity regulate invasive behavior and response to PDT in 3D pancreatic tumor models

    NASA Astrophysics Data System (ADS)

    Cramer, Gwendolyn; El-Hamidi, Hamid; Jafari, Seyedehrojin; Jones, Dustin P.; Celli, Jonathan P.

    2016-03-01

    The composition and mechanical compliance of the extracellular matrix (ECM) have been shown to serve as regulators of tumor growth and invasive behavior. These effects may be particularly relevant in tumors of the pancreas, noted for a profound desmoplastic reaction and an abundance of stroma rich in ECM. In view of recent progress in the clinical implementation of photodynamic therapy (PDT) for pancreatic tumors, in this report we examine how ECM composition and rheological properties impact upon invasive behavior and response to PDT in 3D multicellular pancreatic tumor spheroids in ECM environments with characterized rheological properties. Tumor spheroids were cultured initially in attachment-free conditions to form millimeter-sized spheroids that were transplanted into reconstituted ECM microenvironments (Matrigel and Type I Collagen) that were characterized using bulk oscillatory shear rheology. Analysis of growth behavior shows that the soft collagen ECM promoted growth and extensive invasion and this microenvironment was used in subsequent assessment of PDT and chemotherapy response. Evaluation of treatment response revealed that primary tumor nodule growth is inhibited more effectively with PDT, while verteporfin PDT response is significantly enhanced in the ECM-infiltrating populations that are non-responsive to oxaliplatin chemotherapy. This finding is potentially significant, suggesting the potential for PDT to target these clinically problematic invasive populations that are associated with aggressive metastatic progression and chemoresistance. Experiments to further validate and identify the mechanistic basis of this observation are ongoing.

  5. Microfluidic 3D models of cancer

    PubMed Central

    Sung, Kyung Eun; Beebe, David J.

    2014-01-01

    Despite advances in medicine and biomedical sciences, cancer still remains a major health issue. Complex interactions between tumors and their microenvironment contribute to tumor initiation and progression and also contribute to the development of drug resistant tumor cell populations. The complexity and heterogeneity of tumors and their microenvironment make it challenging to both study and treat cancer. Traditional animal cancer models and in vitro cancer models are limited in their ability to recapitulate human structures and functions, thus hindering the identification of appropriate drug targets and therapeutic strategies. The development and application of microfluidic 3D cancer models has the potential to overcome some of the limitations inherent to traditional models. This review summarizes the progress in microfluidic 3D cancer models, their benefits, and their broad application to basic cancer biology, drug screening, and drug discovery. PMID:25017040

  6. Microfluidic 3D models of cancer.

    PubMed

    Sung, Kyung Eun; Beebe, David J

    2014-12-15

    Despite advances in medicine and biomedical sciences, cancer still remains a major health issue. Complex interactions between tumors and their microenvironment contribute to tumor initiation and progression and also contribute to the development of drug resistant tumor cell populations. The complexity and heterogeneity of tumors and their microenvironment make it challenging to both study and treat cancer. Traditional animal cancer models and in vitro cancer models are limited in their ability to recapitulate human structures and functions, thus hindering the identification of appropriate drug targets and therapeutic strategies. The development and application of microfluidic 3D cancer models have the potential to overcome some of the limitations inherent to traditional models. This review summarizes the progress in microfluidic 3D cancer models, their benefits, and their broad application to basic cancer biology, drug screening, and drug discovery.

  7. Making Inexpensive 3-D Models

    ERIC Educational Resources Information Center

    Manos, Harry

    2016-01-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the "TPT" theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity…

  8. Bioengineered 3D brain tumor model to elucidate the effects of matrix stiffness on glioblastoma cell behavior using PEG-based hydrogels.

    PubMed

    Wang, Christine; Tong, Xinming; Yang, Fan

    2014-07-01

    Glioblastoma (GBM) is the most common and aggressive form of primary brain tumor with a median survival of 12-15 months, and the mechanisms underlying GBM tumor progression remain largely elusive. Given the importance of tumor niche signaling in driving GBM progression, there is a strong need to develop in vitro models to facilitate analysis of brain tumor cell-niche interactions in a physiologically relevant and controllable manner. Here we report the development of a bioengineered 3D brain tumor model to help elucidate the effects of matrix stiffness on GBM cell fate using poly(ethylene-glycol) (PEG)-based hydrogels with brain-mimicking biochemical and mechanical properties. We have chosen PEG given its bioinert nature and tunable physical property, and the resulting hydrogels allow tunable matrix stiffness without changing the biochemical contents. To facilitate cell proliferation and migration, CRGDS and a MMP-cleavable peptide were chemically incorporated. Hyaluronic acid (HA) was also incorporated to mimic the concentration in the brain extracellular matrix. Using U87 cells as a model GBM cell line, we demonstrate that such biomimetic hydrogels support U87 cell growth, spreading, and migration in 3D over the course of 3 weeks in culture. Gene expression analyses showed U87 cells actively deposited extracellular matrix and continued to upregulate matrix remodeling genes. To examine the effects of matrix stiffness on GBM cell fate in 3D, we encapsulated U87 cells in soft (1 kPa) or stiff (26 kPa) hydrogels, which respectively mimics the matrix stiffness of normal brain or GBM tumor tissues. Our results suggest that changes in matrix stiffness induce differential GBM cell proliferation, morphology, and migration modes in 3D. Increasing matrix stiffness led to delayed U87 cell proliferation inside hydrogels, but cells formed denser spheroids with extended cell protrusions. Cells cultured in stiff hydrogels also showed upregulation of HA synthase 1 and matrix

  9. 3D tumor spheroid models for in vitro therapeutic screening: a systematic approach to enhance the biological relevance of data obtained

    PubMed Central

    Zanoni, Michele; Piccinini, Filippo; Arienti, Chiara; Zamagni, Alice; Santi, Spartaco; Polico, Rolando; Bevilacqua, Alessandro; Tesei, Anna

    2016-01-01

    The potential of a spheroid tumor model composed of cells in different proliferative and metabolic states for the development of new anticancer strategies has been amply demonstrated. However, there is little or no information in the literature on the problems of reproducibility of data originating from experiments using 3D models. Our analyses, carried out using a novel open source software capable of performing an automatic image analysis of 3D tumor colonies, showed that a number of morphology parameters affect the response of large spheroids to treatment. In particular, we found that both spheroid volume and shape may be a source of variability. We also compared some commercially available viability assays specifically designed for 3D models. In conclusion, our data indicate the need for a pre-selection of tumor spheroids of homogeneous volume and shape to reduce data variability to a minimum before use in a cytotoxicity test. In addition, we identified and validated a cytotoxicity test capable of providing meaningful data on the damage induced in large tumor spheroids of up to diameter in 650 μm by different kinds of treatments. PMID:26752500

  10. A 3D in vitro model of patient-derived prostate cancer xenograft for controlled interrogation of in vivo tumor-stromal interactions.

    PubMed

    Fong, Eliza L S; Wan, Xinhai; Yang, Jun; Morgado, Micaela; Mikos, Antonios G; Harrington, Daniel A; Navone, Nora M; Farach-Carson, Mary C

    2016-01-01

    Patient-derived xenograft (PDX) models better represent human cancer than traditional cell lines. However, the complex in vivo environment makes it challenging to employ PDX models to investigate tumor-stromal interactions, such as those that mediate prostate cancer (PCa) bone metastasis. Thus, we engineered a defined three-dimensional (3D) hydrogel system capable of supporting the co-culture of PCa PDX cells and osteoblastic cells to recapitulate the PCa-osteoblast unit within the bone metastatic microenvironment in vitro. Our 3D model not only maintained cell viability but also preserved the typical osteogenic phenotype of PCa PDX cells. Additionally, co-culture cellularity was maintained over that of either cell type cultured alone, suggesting that the PCa-osteoblast cross-talk supports PCa progression in bone, as is hypothesized to occur in patients with prostatic bone metastasis. Strikingly, osteoblastic cells co-cultured with PCa PDX tumoroids organized around the tumoroids, closely mimicking the architecture of PCa metastases in bone. Finally, tumor-stromal signaling mediated by the fibroblast growth factor axis tightly paralleled that in the in vivo counterpart. Together, these findings indicate that this 3D PCa PDX model recapitulates important pathological properties of PCa bone metastasis, and validate the use of this model for controlled and systematic interrogation of complex in vivo tumor-stromal interactions.

  11. 3D discrete angiogenesis dynamic model and stochastic simulation for the assessment of blood perfusion coefficient and impact on heat transfer between nanoparticles and malignant tumors.

    PubMed

    Yifat, Jonathan; Gannot, Israel

    2015-03-01

    Early detection of malignant tumors plays a crucial role in the survivability chances of the patient. Therefore, new and innovative tumor detection methods are constantly searched for. Tumor-specific magnetic-core nano-particles can be used with an alternating magnetic field to detect and treat tumors by hyperthermia. For the analysis of the method effectiveness, the bio-heat transfer between the nanoparticles and the tissue must be carefully studied. Heat diffusion in biological tissue is usually analyzed using the Pennes Bio-Heat Equation, where blood perfusion plays an important role. Malignant tumors are known to initiate an angiogenesis process, where endothelial cell migration from neighboring vasculature eventually leads to the formation of a thick blood capillary network around them. This process allows the tumor to receive its extensive nutrition demands and evolve into a more progressive and potentially fatal tumor. In order to assess the effect of angiogenesis on the bio-heat transfer problem, we have developed a discrete stochastic 3D model & simulation of tumor-induced angiogenesis. The model elaborates other angiogenesis models by providing high resolution 3D stochastic simulation, capturing of fine angiogenesis morphological features, effects of dynamic sprout thickness functions, and stochastic parent vessel generator. We show that the angiogenesis realizations produced are well suited for numerical bio-heat transfer analysis. Statistical study on the angiogenesis characteristics was derived using Monte Carlo simulations. According to the statistical analysis, we provide analytical expression for the blood perfusion coefficient in the Pennes equation, as a function of several parameters. This updated form of the Pennes equation could be used for numerical and analytical analyses of the proposed detection and treatment method.

  12. 3D discrete angiogenesis dynamic model and stochastic simulation for the assessment of blood perfusion coefficient and impact on heat transfer between nanoparticles and malignant tumors.

    PubMed

    Yifat, Jonathan; Gannot, Israel

    2015-03-01

    Early detection of malignant tumors plays a crucial role in the survivability chances of the patient. Therefore, new and innovative tumor detection methods are constantly searched for. Tumor-specific magnetic-core nano-particles can be used with an alternating magnetic field to detect and treat tumors by hyperthermia. For the analysis of the method effectiveness, the bio-heat transfer between the nanoparticles and the tissue must be carefully studied. Heat diffusion in biological tissue is usually analyzed using the Pennes Bio-Heat Equation, where blood perfusion plays an important role. Malignant tumors are known to initiate an angiogenesis process, where endothelial cell migration from neighboring vasculature eventually leads to the formation of a thick blood capillary network around them. This process allows the tumor to receive its extensive nutrition demands and evolve into a more progressive and potentially fatal tumor. In order to assess the effect of angiogenesis on the bio-heat transfer problem, we have developed a discrete stochastic 3D model & simulation of tumor-induced angiogenesis. The model elaborates other angiogenesis models by providing high resolution 3D stochastic simulation, capturing of fine angiogenesis morphological features, effects of dynamic sprout thickness functions, and stochastic parent vessel generator. We show that the angiogenesis realizations produced are well suited for numerical bio-heat transfer analysis. Statistical study on the angiogenesis characteristics was derived using Monte Carlo simulations. According to the statistical analysis, we provide analytical expression for the blood perfusion coefficient in the Pennes equation, as a function of several parameters. This updated form of the Pennes equation could be used for numerical and analytical analyses of the proposed detection and treatment method. PMID:24462603

  13. Making Inexpensive 3-D Models

    NASA Astrophysics Data System (ADS)

    Manos, Harry

    2016-03-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the TPT theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity well tailored to specific class lessons. Most of the supplies are readily available in the home or at school: rubbing alcohol, a rag, two colors of spray paint, art brushes, and masking tape. The cost of these supplies, if you don't have them, is less than 20.

  14. 3-D individual cell based computational modeling of tumor cell–macrophage paracrine signaling mediated by EGF and CSF-1 gradients†

    PubMed Central

    Knutsdottir, Hildur; Condeelis, John S.; Palsson, Eirikur

    2016-01-01

    High density of macrophages in mammary tumors has been associated with a higher risk of metastasis and thus increased mortality in women. The EGF/CSF-1 paracrine signaling increases the number of invasive tumor cells by both recruiting tumor cells further away and manipulating the macrophages’ innate ability to open up a passage into blood vessels thus promoting intravasation and finally metastasis. A 3-D individual-cell-based model is introduced, to better understand the tumor cell–macrophage interactions, and to explore how changing parameters of the paracrine signaling system affects the number of invasive tumor cells. The simulation data and videos of the cell movements correlated well with findings from both in vitro and in vivo experimental results. The model demonstrated how paracrine signaling is necessary to achieve co-migration of tumor cells and macrophages towards a specific signaling source. We showed how the paracrine signaling enhances the number of both invasive tumor cells and macrophages. The simulations revealed that for the in vitro experiments the imposed no-flux boundary condition might be affecting the results, and that changing the setup might lead to different experimental findings. In our simulations, the 3 : 1 tumor cell/macrophage ratio, observed in vivo, was robust for many parameters but sensitive to EGF signal strength and fraction of macrophages in the tumor. The model can be used to identify new agents for targeted therapy and we suggest that a successful strategy to prevent or limit invasion of tumor cells would be to block the tumor cell–macrophage paracrine signaling. This can be achieved by either blocking the EGF or CSF-1 receptors or supressing the EGF or CSF-1 signal. PMID:26686751

  15. A robust framework for soft tissue simulations with application to modeling brain tumor mass effect in 3D MR images.

    PubMed

    Hogea, Cosmina; Biros, George; Abraham, Feby; Davatzikos, Christos

    2007-12-01

    We present a framework for black-box and flexible simulation of soft tissue deformation for medical imaging and surgical planning applications. Our main motivation in the present work is to develop robust algorithms that allow batch processing for registration of brains with tumors to statistical atlases of normal brains and construction of brain tumor atlases. We describe a fully Eulerian formulation able to handle large deformations effortlessly, with a level-set-based approach for evolving fronts. We use a regular grid-fictitious domain method approach, in which we approximate coefficient discontinuities, distributed forces and boundary conditions. This approach circumvents the need for unstructured mesh generation, which is often a bottleneck in the modeling and simulation pipeline. Our framework employs penalty approaches to impose boundary conditions and uses a matrix-free implementation coupled with a multigrid-accelerated Krylov solver. The overall scheme results in a scalable method with minimal storage requirements and optimal algorithmic complexity. We illustrate the potential of our framework to simulate realistic brain tumor mass effects at reduced computational cost, for aiding the registration process towards the construction of brain tumor atlases. PMID:18029982

  16. A Combined 3D Tissue Engineered In Vitro/In Silico Lung Tumor Model for Predicting Drug Effectiveness in Specific Mutational Backgrounds.

    PubMed

    Göttlich, Claudia; Müller, Lena C; Kunz, Meik; Schmitt, Franziska; Walles, Heike; Walles, Thorsten; Dandekar, Thomas; Dandekar, Gudrun; Nietzer, Sarah L

    2016-01-01

    In the present study, we combined an in vitro 3D lung tumor model with an in silico model to optimize predictions of drug response based on a specific mutational background. The model is generated on a decellularized porcine scaffold that reproduces tissue-specific characteristics regarding extracellular matrix composition and architecture including the basement membrane. We standardized a protocol that allows artificial tumor tissue generation within 14 days including three days of drug treatment. Our article provides several detailed descriptions of 3D read-out screening techniques like the determination of the proliferation index Ki67 staining's, apoptosis from supernatants by M30-ELISA and assessment of epithelial to mesenchymal transition (EMT), which are helpful tools for evaluating the effectiveness of therapeutic compounds. We could show compared to 2D culture a reduction of proliferation in our 3D tumor model that is related to the clinical situation. Despite of this lower proliferation, the model predicted EGFR-targeted drug responses correctly according to the biomarker status as shown by comparison of the lung carcinoma cell lines HCC827 (EGFR -mutated, KRAS wild-type) and A549 (EGFR wild-type, KRAS-mutated) treated with the tyrosine-kinase inhibitor (TKI) gefitinib. To investigate drug responses of more advanced tumor cells, we induced EMT by long-term treatment with TGF-beta-1 as assessed by vimentin/pan-cytokeratin immunofluorescence staining. A flow-bioreactor was employed to adjust culture to physiological conditions, which improved tissue generation. Furthermore, we show the integration of drug responses upon gefitinib treatment or TGF-beta-1 stimulation - apoptosis, proliferation index and EMT - into a Boolean in silico model. Additionally, we explain how drug responses of tumor cells with a specific mutational background and counterstrategies against resistance can be predicted. We are confident that our 3D in vitro approach especially with its

  17. Emergent Stratification in Solid Tumors Selects for Reduced Cohesion of Tumor Cells: A Multi-Cell, Virtual-Tissue Model of Tumor Evolution Using CompuCell3D.

    PubMed

    Swat, Maciej H; Thomas, Gilberto L; Shirinifard, Abbas; Clendenon, Sherry G; Glazier, James A

    2015-01-01

    Tumor cells and structure both evolve due to heritable variation of cell behaviors and selection over periods of weeks to years (somatic evolution). Micro-environmental factors exert selection pressures on tumor-cell behaviors, which influence both the rate and direction of evolution of specific behaviors, especially the development of tumor-cell aggression and resistance to chemotherapies. In this paper, we present, step-by-step, the development of a multi-cell, virtual-tissue model of tumor somatic evolution, simulated using the open-source CompuCell3D modeling environment. Our model includes essential cell behaviors, microenvironmental components and their interactions. Our model provides a platform for exploring selection pressures leading to the evolution of tumor-cell aggression, showing that emergent stratification into regions with different cell survival rates drives the evolution of less cohesive cells with lower levels of cadherins and higher levels of integrins. Such reduced cohesivity is a key hallmark in the progression of many types of solid tumors.

  18. Crowdsourcing Based 3d Modeling

    NASA Astrophysics Data System (ADS)

    Somogyi, A.; Barsi, A.; Molnar, B.; Lovas, T.

    2016-06-01

    Web-based photo albums that support organizing and viewing the users' images are widely used. These services provide a convenient solution for storing, editing and sharing images. In many cases, the users attach geotags to the images in order to enable using them e.g. in location based applications on social networks. Our paper discusses a procedure that collects open access images from a site frequently visited by tourists. Geotagged pictures showing the image of a sight or tourist attraction are selected and processed in photogrammetric processing software that produces the 3D model of the captured object. For the particular investigation we selected three attractions in Budapest. To assess the geometrical accuracy, we used laser scanner and DSLR as well as smart phone photography to derive reference values to enable verifying the spatial model obtained from the web-album images. The investigation shows how detailed and accurate models could be derived applying photogrammetric processing software, simply by using images of the community, without visiting the site.

  19. Longitudinal, Quantitative Monitoring of Therapeutic Response in 3D In Vitro Tumor Models with OCT for High-Content Therapeutic Screening

    PubMed Central

    Klein, O. J.; Jung, Y. K.; Evans, C. L.

    2013-01-01

    In vitro three-dimensional models of cancer have the ability to recapitulate many features of tumors found in vivo, including cell-cell and cell-matrix interactions, microenvironments that become hypoxic and acidic, and other barriers to effective therapy. These model tumors can be large, highly complex, heterogeneous, and undergo time-dependent growth and treatment response processes that are difficult to track and quantify using standard imaging tools. Optical coherence tomography is an optical ranging technique that is ideally suited for visualizing, monitoring, and quantifying the growth and treatment response dynamics occurring in these informative model systems. By optimizing both optical coherence tomography and 3D culture systems, it is possible to continuously and non-perturbatively monitor advanced in vitro models without the use of labels over the course of hours and days. In this article, we describe approaches and methods for creating and carrying out quantitative therapeutic screens with in vitro 3D cultures using optical coherence tomography to gain insights into therapeutic mechanisms and build more effective treatment regimens. PMID:24013042

  20. A 3D Poly(ethylene glycol)-based Tumor Angiogenesis Model to Study the Influence of Vascular Cells on Lung Tumor Cell Behavior

    PubMed Central

    Roudsari, Laila C.; Jeffs, Sydney E.; Witt, Amber S.; Gill, Bartley J.; West, Jennifer L.

    2016-01-01

    Tumor angiogenesis is critical to tumor growth and metastasis, yet much is unknown about the role vascular cells play in the tumor microenvironment. In vitro models that mimic in vivo tumor neovascularization facilitate exploration of this role. Here we investigated lung adenocarcinoma cancer cells (344SQ) and endothelial and pericyte vascular cells encapsulated in cell-adhesive, proteolytically-degradable poly(ethylene) glycol-based hydrogels. 344SQ in hydrogels formed spheroids and secreted proangiogenic growth factors that significantly increased with exposure to transforming growth factor beta 1 (TGF-β1), a potent tumor progression-promoting factor. Vascular cells in hydrogels formed tubule networks with localized activated TGF-β1. To study cancer cell-vascular cell interactions, we engineered a 2-layer hydrogel with 344SQ and vascular cell layers. Large, invasive 344SQ clusters (area > 5,000 μm2, circularity < 0.25) developed at the interface between the layers, and were not evident further from the interface or in control hydrogels without vascular cells. A modified model with spatially restricted 344SQ and vascular cell layers confirmed that observed cluster morphological changes required close proximity to vascular cells. Additionally, TGF-β1 inhibition blocked endothelial cell-driven 344SQ migration. Our findings suggest vascular cells contribute to tumor progression and establish this culture system as a platform for studying tumor vascularization. PMID:27596933

  1. A 3D Poly(ethylene glycol)-based Tumor Angiogenesis Model to Study the Influence of Vascular Cells on Lung Tumor Cell Behavior

    NASA Astrophysics Data System (ADS)

    Roudsari, Laila C.; Jeffs, Sydney E.; Witt, Amber S.; Gill, Bartley J.; West, Jennifer L.

    2016-09-01

    Tumor angiogenesis is critical to tumor growth and metastasis, yet much is unknown about the role vascular cells play in the tumor microenvironment. In vitro models that mimic in vivo tumor neovascularization facilitate exploration of this role. Here we investigated lung adenocarcinoma cancer cells (344SQ) and endothelial and pericyte vascular cells encapsulated in cell-adhesive, proteolytically-degradable poly(ethylene) glycol-based hydrogels. 344SQ in hydrogels formed spheroids and secreted proangiogenic growth factors that significantly increased with exposure to transforming growth factor beta 1 (TGF-β1), a potent tumor progression-promoting factor. Vascular cells in hydrogels formed tubule networks with localized activated TGF-β1. To study cancer cell-vascular cell interactions, we engineered a 2-layer hydrogel with 344SQ and vascular cell layers. Large, invasive 344SQ clusters (area > 5,000 μm2, circularity < 0.25) developed at the interface between the layers, and were not evident further from the interface or in control hydrogels without vascular cells. A modified model with spatially restricted 344SQ and vascular cell layers confirmed that observed cluster morphological changes required close proximity to vascular cells. Additionally, TGF-β1 inhibition blocked endothelial cell-driven 344SQ migration. Our findings suggest vascular cells contribute to tumor progression and establish this culture system as a platform for studying tumor vascularization.

  2. A 3D Poly(ethylene glycol)-based Tumor Angiogenesis Model to Study the Influence of Vascular Cells on Lung Tumor Cell Behavior.

    PubMed

    Roudsari, Laila C; Jeffs, Sydney E; Witt, Amber S; Gill, Bartley J; West, Jennifer L

    2016-01-01

    Tumor angiogenesis is critical to tumor growth and metastasis, yet much is unknown about the role vascular cells play in the tumor microenvironment. In vitro models that mimic in vivo tumor neovascularization facilitate exploration of this role. Here we investigated lung adenocarcinoma cancer cells (344SQ) and endothelial and pericyte vascular cells encapsulated in cell-adhesive, proteolytically-degradable poly(ethylene) glycol-based hydrogels. 344SQ in hydrogels formed spheroids and secreted proangiogenic growth factors that significantly increased with exposure to transforming growth factor beta 1 (TGF-β1), a potent tumor progression-promoting factor. Vascular cells in hydrogels formed tubule networks with localized activated TGF-β1. To study cancer cell-vascular cell interactions, we engineered a 2-layer hydrogel with 344SQ and vascular cell layers. Large, invasive 344SQ clusters (area > 5,000 μm(2), circularity < 0.25) developed at the interface between the layers, and were not evident further from the interface or in control hydrogels without vascular cells. A modified model with spatially restricted 344SQ and vascular cell layers confirmed that observed cluster morphological changes required close proximity to vascular cells. Additionally, TGF-β1 inhibition blocked endothelial cell-driven 344SQ migration. Our findings suggest vascular cells contribute to tumor progression and establish this culture system as a platform for studying tumor vascularization. PMID:27596933

  3. Probing tumor-stroma interactions and response to photodynamic therapy in a 3D pancreatic cancer-fibroblast co-culture model

    NASA Astrophysics Data System (ADS)

    Glidden, Michael D.; Massodi, Iqbal; Rizvi, Imran; Celli, Jonathan P.; Hasan, Tayyaba

    2012-02-01

    Pancreatic ductal adenocarcinoma is a lethal disease that is often unresectable by the time of diagnosis and is typically non-responsive to chemo- and radiotherapy, resulting in a five year survival of only 3%. Tumors of the pancreas are characterized by a dense fibrous stroma rich in extracellular matrix proteins, which is implicated in poor therapeutic response, though its precise roles remain poorly understood. Indeed, while the use of therapeutics that target the stroma is an emerging paradigm in the clinical management of this disease, the primary focus of such efforts is to enhance drug penetration through dense fibrous stroma and it is unclear to what extent the characteristically rigid stroma of pancreatic tumors imparts drug resistance by acting as a complex signaling partner, or merely as a physical barrier for drug delivery. Here we use 3D in vitro co-cultures of pancreatic cancer cells and normal human fibroblasts as a model system to study heterotypic interactions between these populations. Leveraging this in vitro model along with image-based methods for quantification of growth and therapeutic endpoints, we characterize these co-cultures and examine the role of verteporfin-based photodynamic therapy (PDT) for targeting tumor-fibroblast interactions in pancreatic tumors.

  4. Overcoming therapeutic resistance in pancreatic cancer is not a simple mix of PDT and chemotherapy: Evaluation of PDT-chemotherapy combinations in 3D tumor models

    NASA Astrophysics Data System (ADS)

    Celli, Jonathan P.; Petrovic, Ljubica; Massdodi, Iqbal; Rizvi, Imran; Hasan, Tayyaba

    2013-03-01

    The dismal survival statistics for pancreatic cancer are due in large part to the notoriously poor response of these tumors to conventional therapies. Here we examine the ability of photodynamic therapy (PDT), using the photosensitizer verteporfin to enhance of the efficacy of traditional chemotherapy agents and/or eradicate populations that are nonresponsive to these agents. Using an in vitro 3D tumor model of pancreatic cancer combined with an imaging-based methodology for quantifying therapeutic response, we specifically examine PDT combination treatments with gemcitabine and oxaliplatin. We show that our 3D cell culture model recapitulates a more clinically-relevant dose response to gemcitabine, with minimal cytotoxic response even at high doses. The same cultures exhibit modest response to PDT treatments, but are also less responsive to this modality relative to our previous reports of monolayer dose response in the same cells. In combination we found no evidence of any enhancement in efficacy of either PDT or gemcitabine treatment regardless of dose or sequence (PDT before gemcitabine, or gemcitabine before PDT). However, when oxaliplatin chemotherapy was administered immediately after treatment with 2.5J/cm2 verteporfin PDT, there was an observable enhancement in response that appears to exceed the additive combination of either treatment alone and suggesting there may be a synergistic interaction. This observation is consistent with previous reports of enhanced efficacy in combinations of PDT with platinum-based chemotherapy. The contrast in results between the combinations examined here underscores the need for rational design of mechanism-based PDT combinations.

  5. 3D Printing of Molecular Models

    ERIC Educational Resources Information Center

    Gardner, Adam; Olson, Arthur

    2016-01-01

    Physical molecular models have played a valuable role in our understanding of the invisible nano-scale world. We discuss 3D printing and its use in producing models of the molecules of life. Complex biomolecular models, produced from 3D printed parts, can demonstrate characteristics of molecular structure and function, such as viral self-assembly,…

  6. Three-dimensional (3D) tumor spheroid invasion assay.

    PubMed

    Vinci, Maria; Box, Carol; Eccles, Suzanne A

    2015-01-01

    Invasion of surrounding normal tissues is generally considered to be a key hallmark of malignant (as opposed to benign) tumors. For some cancers in particular (e.g., brain tumors such as glioblastoma multiforme and squamous cell carcinoma of the head and neck - SCCHN) it is a cause of severe morbidity and can be life-threatening even in the absence of distant metastases. In addition, cancers which have relapsed following treatment unfortunately often present with a more aggressive phenotype. Therefore, there is an opportunity to target the process of invasion to provide novel therapies that could be complementary to standard anti-proliferative agents. Until now, this strategy has been hampered by the lack of robust, reproducible assays suitable for a detailed analysis of invasion and for drug screening. Here we provide a simple micro-plate method (based on uniform, self-assembling 3D tumor spheroids) which has great potential for such studies. We exemplify the assay platform using a human glioblastoma cell line and also an SCCHN model where the development of resistance against targeted epidermal growth factor receptor (EGFR) inhibitors is associated with enhanced matrix-invasive potential. We also provide two alternative methods of semi-automated quantification: one using an imaging cytometer and a second which simply requires standard microscopy and image capture with digital image analysis. PMID:25993495

  7. Breast tumor angiogenesis analysis using 3D power Doppler ultrasound

    NASA Astrophysics Data System (ADS)

    Chang, Ruey-Feng; Huang, Sheng-Fang; Lee, Yu-Hau; Chen, Dar-Ren; Moon, Woo Kyung

    2006-03-01

    Angiogenesis is the process that correlates to tumor growth, invasion, and metastasis. Breast cancer angiogenesis has been the most extensively studied and now serves as a paradigm for understanding the biology of angiogenesis and its effects on tumor outcome and patient prognosis. Most studies on characterization of angiogenesis focus on pixel/voxel counts more than morphological analysis. Nevertheless, in cancer, the blood flow is greatly affected by the morphological changes, such as the number of vessels, branching pattern, length, and diameter. This paper presents a computer-aided diagnostic (CAD) system that can quantify vascular morphology using 3-D power Doppler ultrasound (US) on breast tumors. We propose a scheme to extract the morphological information from angiography and to relate them to tumor diagnosis outcome. At first, a 3-D thinning algorithm helps narrow down the vessels into their skeletons. The measurements of vascular morphology significantly rely on the traversing of the vascular trees produced from skeletons. Our study of 3-D assessment of vascular morphological features regards vessel count, length, bifurcation, and diameter of vessels. Investigations into 221 solid breast tumors including 110 benign and 111 malignant cases, the p values using the Student's t-test for all features are less than 0.05 indicating that the proposed features are deemed statistically significant. Our scheme focuses on the vascular architecture without involving the technique of tumor segmentation. The results show that the proposed method is feasible, and have a good agreement with the diagnosis of the pathologists.

  8. BEAMS3D Neutral Beam Injection Model

    SciTech Connect

    Lazerson, Samuel

    2014-04-14

    With the advent of applied 3D fi elds in Tokamaks and modern high performance stellarators, a need has arisen to address non-axisymmetric effects on neutral beam heating and fueling. We report on the development of a fully 3D neutral beam injection (NBI) model, BEAMS3D, which addresses this need by coupling 3D equilibria to a guiding center code capable of modeling neutral and charged particle trajectories across the separatrix and into the plasma core. Ionization, neutralization, charge-exchange, viscous velocity reduction, and pitch angle scattering are modeled with the ADAS atomic physics database [1]. Benchmark calculations are presented to validate the collisionless particle orbits, neutral beam injection model, frictional drag, and pitch angle scattering effects. A calculation of neutral beam heating in the NCSX device is performed, highlighting the capability of the code to handle 3D magnetic fields.

  9. VALIDATION OF IMPROVED 3D ATR MODEL

    SciTech Connect

    Soon Sam Kim; Bruce G. Schnitzler

    2005-11-01

    A full-core Monte Carlo based 3D model of the Advanced Test Reactor (ATR) was previously developed. [1] An improved 3D model has been developed by the International Criticality Safety Benchmark Evaluation Project (ICSBEP) to eliminate homogeneity of fuel plates of the old model, incorporate core changes into the new model, and to validate against a newer, more complicated core configuration. This new 3D model adds capability for fuel loading design and azimuthal power peaking studies of the ATR fuel elements.

  10. Modeling Cellular Processes in 3-D

    PubMed Central

    Mogilner, Alex; Odde, David

    2011-01-01

    Summary Recent advances in photonic imaging and fluorescent protein technology offer unprecedented views of molecular space-time dynamics in living cells. At the same time, advances in computing hardware and software enable modeling of ever more complex systems, from global climate to cell division. As modeling and experiment become more closely integrated, we must address the issue of modeling cellular processes in 3-D. Here, we highlight recent advances related to 3-D modeling in cell biology. While some processes require full 3-D analysis, we suggest that others are more naturally described in 2-D or 1-D. Keeping the dimensionality as low as possible reduces computational time and makes models more intuitively comprehensible; however, the ability to test full 3-D models will build greater confidence in models generally and remains an important emerging area of cell biological modeling. PMID:22036197

  11. 3D facial expression modeling for recognition

    NASA Astrophysics Data System (ADS)

    Lu, Xiaoguang; Jain, Anil K.; Dass, Sarat C.

    2005-03-01

    Current two-dimensional image based face recognition systems encounter difficulties with large variations in facial appearance due to the pose, illumination and expression changes. Utilizing 3D information of human faces is promising for handling the pose and lighting variations. While the 3D shape of a face does not change due to head pose (rigid) and lighting changes, it is not invariant to the non-rigid facial movement and evolution, such as expressions and aging effect. We propose a facial surface matching framework to match multiview facial scans to a 3D face model, where the (non-rigid) expression deformation is explicitly modeled for each subject, resulting in a person-specific deformation model. The thin plate spline (TPS) is applied to model the deformation based on the facial landmarks. The deformation is applied to the 3D neutral expression face model to synthesize the corresponding expression. Both the neutral and the synthesized 3D surface models are used to match a test scan. The surface registration and matching between a test scan and a 3D model are achieved by a modified Iterative Closest Point (ICP) algorithm. Preliminary experimental results demonstrate that the proposed expression modeling and recognition-by-synthesis schemes improve the 3D matching accuracy.

  12. Digital relief generation from 3D models

    NASA Astrophysics Data System (ADS)

    Wang, Meili; Sun, Yu; Zhang, Hongming; Qian, Kun; Chang, Jian; He, Dongjian

    2016-09-01

    It is difficult to extend image-based relief generation to high-relief generation, as the images contain insufficient height information. To generate reliefs from three-dimensional (3D) models, it is necessary to extract the height fields from the model, but this can only generate bas-reliefs. To overcome this problem, an efficient method is proposed to generate bas-reliefs and high-reliefs directly from 3D meshes. To produce relief features that are visually appropriate, the 3D meshes are first scaled. 3D unsharp masking is used to enhance the visual features in the 3D mesh, and average smoothing and Laplacian smoothing are implemented to achieve better smoothing results. A nonlinear variable scaling scheme is then employed to generate the final bas-reliefs and high-reliefs. Using the proposed method, relief models can be generated from arbitrary viewing positions with different gestures and combinations of multiple 3D models. The generated relief models can be printed by 3D printers. The proposed method provides a means of generating both high-reliefs and bas-reliefs in an efficient and effective way under the appropriate scaling factors.

  13. NUBEAM developments and 3d halo modeling

    NASA Astrophysics Data System (ADS)

    Gorelenkova, M. V.; Medley, S. S.; Kaye, S. M.

    2012-10-01

    Recent developments related to the 3D halo model in NUBEAM code are described. To have a reliable halo neutral source for diagnostic simulation, the TRANSP/NUBEAM code has been enhanced with full implementation of ADAS atomic physic ground state and excited state data for hydrogenic beams and mixed species plasma targets. The ADAS codes and database provide the density and temperature dependence of the atomic data, and the collective nature of the state excitation process. To be able to populate 3D halo output with sufficient statistical resolution, the capability to control the statistics of fast ion CX modeling and for thermal halo launch has been added to NUBEAM. The 3D halo neutral model is based on modification and extension of the ``beam in box'' aligned 3d Cartesian grid that includes the neutral beam itself, 3D fast neutral densities due to CX of partially slowed down fast ions in the beam halo region, 3D thermal neutral densities due to CX deposition and fast neutral recapture source. More details on the 3D halo simulation design will be presented.

  14. The CIFIST 3D model atmosphere grid.

    NASA Astrophysics Data System (ADS)

    Ludwig, H.-G.; Caffau, E.; Steffen, M.; Freytag, B.; Bonifacio, P.; Kučinskas, A.

    Grids of stellar atmosphere models and associated synthetic spectra are numerical products which have a large impact in astronomy due to their ubiquitous application in the interpretation of radiation from individual stars and stellar populations. 3D model atmospheres are now on the verge of becoming generally available for a wide range of stellar atmospheric parameters. We report on efforts to develop a grid of 3D model atmospheres for late-type stars within the CIFIST Team at Paris Observatory. The substantial demands in computational and human labor for the model production and post-processing render this apparently mundane task a challenging logistic exercise. At the moment the CIFIST grid comprises 77 3D model atmospheres with emphasis on dwarfs of solar and sub-solar metallicities. While the model production is still ongoing, first applications are already worked upon by the CIFIST Team and collaborators.

  15. 3D Modeling Engine Representation Summary Report

    SciTech Connect

    Steven Prescott; Ramprasad Sampath; Curtis Smith; Timothy Yang

    2014-09-01

    Computers have been used for 3D modeling and simulation, but only recently have computational resources been able to give realistic results in a reasonable time frame for large complex models. This summary report addressed the methods, techniques, and resources used to develop a 3D modeling engine to represent risk analysis simulation for advanced small modular reactor structures and components. The simulations done for this evaluation were focused on external events, specifically tsunami floods, for a hypothetical nuclear power facility on a coastline.

  16. BEAMS3D Neutral Beam Injection Model

    NASA Astrophysics Data System (ADS)

    McMillan, Matthew; Lazerson, Samuel A.

    2014-09-01

    With the advent of applied 3D fields in Tokamaks and modern high performance stellarators, a need has arisen to address non-axisymmetric effects on neutral beam heating and fueling. We report on the development of a fully 3D neutral beam injection (NBI) model, BEAMS3D, which addresses this need by coupling 3D equilibria to a guiding center code capable of modeling neutral and charged particle trajectories across the separatrix and into the plasma core. Ionization, neutralization, charge-exchange, viscous slowing down, and pitch angle scattering are modeled with the ADAS atomic physics database. Elementary benchmark calculations are presented to verify the collisionless particle orbits, NBI model, frictional drag, and pitch angle scattering effects. A calculation of neutral beam heating in the NCSX device is performed, highlighting the capability of the code to handle 3D magnetic fields. Notice: this manuscript has been authored by Princeton University under Contract Number DE-AC02-09CH11466 with the US Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.

  17. 3D culture broadly regulates tumor cell hypoxia response and angiogenesis via pro-inflammatory pathways

    PubMed Central

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

    2015-01-01

    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. PMID:25934456

  18. 3D culture broadly regulates tumor cell hypoxia response and angiogenesis via pro-inflammatory pathways.

    PubMed

    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.

  19. Evolution of Archaea in 3D modeling

    NASA Astrophysics Data System (ADS)

    Pikuta, Elena V.; Tankosic, Dragana; Sheldon, Rob

    2012-11-01

    The analysis of all groups of Archaea performed in two-dimensions have demonstrated a specific distribution of Archaean species as a function of pH/temperature, temperature/salinity and pH/salinity. Work presented here is an extension of this analysis with a three dimensional (3D) modeling in logarithmic scale. As it was shown in 2D representation, the "Rules of the Diagonal" have been expressed even more clearly in 3D modeling. In this article, we used a 3D Mesh modeling to show the range of distribution of each separate group of Archaea as a function of pH, temperature, and salinity. Visible overlap and links between different groups indicate a direction of evolution in Archaea. The major direction in ancestral life (vector of evolution) has been indicated: from high temperature, acidic, and low-salinity system towards low temperature, alkaline and high salinity systems. Specifics of the geometrical coordinates and distribution of separate groups of Archaea in 3 D scale were analyzed with a mathematical description of the functions. Based on the obtained data, a new model for the origin and evolution of life on Earth is proposed. The geometry of this model is described by a hyperboloid of one sheet. Conclusions of this research are consistent with previous results derived from the two-dimensional diagrams. This approach is suggested as a new method for analyzing any biological group in accordance to its environmental parameters.

  20. The impact of including spatially longitudinal heterogeneities of vessel oxygen content and vascular fraction in 3D tumor oxygenation models on predicted radiation sensitivity

    SciTech Connect

    Lagerlöf, Jakob H.; Kindblom, Jon; Bernhardt, Peter

    2014-04-15

    Purpose: Oxygen distribution models have been used to analyze the influences of oxygen tensions on tissue response after radiotherapy. These distributions are often generated assuming constant oxygen tension in the blood vessels. However, as red blood cells progress through the vessels, oxygen is continuously released into the plasma and the surrounding tissue, resulting in longitudinally varying oxygen levels in the blood vessels. In the present study, the authors investigated whether a tumor oxygenation model that incorporated longitudinally varying oxygen levels would provide different predictions of necrotic fractions and radiosensitivity compared to commonly used models with a constant oxygen pressure. Methods: Our models simulated oxygen diffusion based on a Green's function approach and oxygen consumption according to the Michaelis-Menten equation. The authors constructed tumor models with different vascular fractions (VFs), from which they generated depth oxygenation curves and a look-up table of oxygen pressure gradients. The authors evaluated models of spherical tumors of various sizes, from 1 to 10{sup 4} mg. The authors compared the results from a model with constant vessel oxygen (CVO) pressure to those from models with longitudinal variations in oxygen saturation and either a constant VF (CVF) or variable VF (VVF) within the tumor tissue. The authors monitored the necrotic fractions, defined as tumor regions with an oxygen pressure below 1 mmHg. Tumor radiation sensitivity was expressed as D{sub 99,} the homogeneous radiation dose required for a tumor control probability of 0.99. Results: In the CVO saturation model, no necrosis was observed, and decreasing the VF could only decrease the D{sub 99} by up to 10%. Furthermore, the D{sub 99} vs VF dependence was similar for different tumor masses. Compared to the CVO model, the extended CVF and VVF models provided clearly different results, including pronounced effects of VF and tumor size on the necrotic

  1. Individualized Surgical Approach Planning for Petroclival Tumors Using a 3D Printer.

    PubMed

    Muelleman, Thomas John; Peterson, Jeremy; Chowdhury, Naweed Iffat; Gorup, Jason; Camarata, Paul; Lin, James

    2016-06-01

    Objectives To determine the utility of three-dimensional (3D) printed models in individualized petroclival tumor resection planning by measuring the fidelity of printed anatomical structures and comparing tumor exposure afforded by different approaches. Design Case series and review of the literature. Setting Tertiary care center. Participants Three patients with petroclival lesions. Main Outcome Measures Subjective opinion of access by neuro-otologists and neurosurgeons as well as surface area of tumor exposure. Results Surgeons found the 3D models of each patient's skull and tumor useful for preoperative planning. Limitations of individual surgical approaches not identified through preoperative imaging were apparent after 3D models were evaluated. Significant variability in exposure was noted between models for similar or identical approaches. A notable drawback is that our printing process did not replicate mastoid air cells. Conclusions We found that 3D modeling is useful for individualized preoperative planning for approaching petroclival tumors. Our printing techniques did produce authentic replicas of the tumors in relation to bony structures. PMID:27175320

  2. Individualized Surgical Approach Planning for Petroclival Tumors Using a 3D Printer.

    PubMed

    Muelleman, Thomas John; Peterson, Jeremy; Chowdhury, Naweed Iffat; Gorup, Jason; Camarata, Paul; Lin, James

    2016-06-01

    Objectives To determine the utility of three-dimensional (3D) printed models in individualized petroclival tumor resection planning by measuring the fidelity of printed anatomical structures and comparing tumor exposure afforded by different approaches. Design Case series and review of the literature. Setting Tertiary care center. Participants Three patients with petroclival lesions. Main Outcome Measures Subjective opinion of access by neuro-otologists and neurosurgeons as well as surface area of tumor exposure. Results Surgeons found the 3D models of each patient's skull and tumor useful for preoperative planning. Limitations of individual surgical approaches not identified through preoperative imaging were apparent after 3D models were evaluated. Significant variability in exposure was noted between models for similar or identical approaches. A notable drawback is that our printing process did not replicate mastoid air cells. Conclusions We found that 3D modeling is useful for individualized preoperative planning for approaching petroclival tumors. Our printing techniques did produce authentic replicas of the tumors in relation to bony structures.

  3. 3-D Teaching Models for All

    ERIC Educational Resources Information Center

    Bradley, Joan; Farland-Smith, Donna

    2010-01-01

    Allowing a student to "see" through touch what other students see through a microscope can be a challenging task. Therefore, author Joan Bradley created three-dimensional (3-D) models with one student's visual impairment in mind. They are meant to benefit all students and can be used to teach common high school biology topics, including the…

  4. Do-It-Yourself: 3D Models of Hydrogenic Orbitals through 3D Printing

    ERIC Educational Resources Information Center

    Griffith, Kaitlyn M.; de Cataldo, Riccardo; Fogarty, Keir H.

    2016-01-01

    Introductory chemistry students often have difficulty visualizing the 3-dimensional shapes of the hydrogenic electron orbitals without the aid of physical 3D models. Unfortunately, commercially available models can be quite expensive. 3D printing offers a solution for producing models of hydrogenic orbitals. 3D printing technology is widely…

  5. Quantification of tumor morphology via 3D histology: application to oral cavity cancers

    NASA Astrophysics Data System (ADS)

    Doyle, Scott; Brandwein-Gensler, Margaret; Tomaszewski, John

    2016-03-01

    Traditional histopathology quantifies disease through the study of glass slides, i.e. two-dimensional samples that are representative of the overall process. We hypothesize that 3D reconstruction can enhance our understanding of histopathologic interpretations. To test this hypothesis, we perform a pilot study of the risk model for oral cavity cancer (OCC), which stratifies patients into low-, intermediate-, and high-risk for locoregional disease-free survival. Classification is based on study of hematoxylin and eosin (H and E) stained tissues sampled from the resection specimens. In this model, the Worst Pattern of Invasion (WPOI) is assessed, representing specific architectural features at the interface between cancer and non-cancer tissue. Currently, assessment of WPOI is based on 2D sections of tissue, representing complex 3D structures of tumor growth. We believe that by reconstructing a 3D model of tumor growth and quantifying the tumor-host interface, we can obtain important diagnostic information that is difficult to assess in 2D. Therefore, we introduce a pilot study framework for visualizing tissue architecture and morphology in 3D from serial sections of histopathology. This framework can be used to enhance predictive models for diseases where severity is determined by 3D biological structure. In this work we utilize serial H and E-stained OCC resections obtained from 7 patients exhibiting WPOI-3 (low risk of recurrence) through WPOI-5 (high risk of recurrence). A supervised classifier automatically generates a map of tumor regions on each slide, which are then co-registered using an elastic deformation algorithm. A smooth 3D model of the tumor region is generated from the registered maps, which is suitable for quantitative tumor interface morphology feature extraction. We report our preliminary models created with this system and suggest further enhancements to traditional histology scoring mechanisms that take spatial architecture into consideration.

  6. Debris Dispersion Model Using Java 3D

    NASA Technical Reports Server (NTRS)

    Thirumalainambi, Rajkumar; Bardina, Jorge

    2004-01-01

    This paper describes web based simulation of Shuttle launch operations and debris dispersion. Java 3D graphics provides geometric and visual content with suitable mathematical model and behaviors of Shuttle launch. Because the model is so heterogeneous and interrelated with various factors, 3D graphics combined with physical models provides mechanisms to understand the complexity of launch and range operations. The main focus in the modeling and simulation covers orbital dynamics and range safety. Range safety areas include destruct limit lines, telemetry and tracking and population risk near range. If there is an explosion of Shuttle during launch, debris dispersion is explained. The shuttle launch and range operations in this paper are discussed based on the operations from Kennedy Space Center, Florida, USA.

  7. Beyond 3D culture models of cancer

    PubMed Central

    Tanner, Kandice; Gottesman, Michael M.

    2016-01-01

    The mechanisms underlying the spatiotemporal evolution of tumor ecosystems present a challenge in evaluating drug efficacy. In this Perspective, we address the use of three-dimensional in vitro culture models to delineate the dynamic interplay between the tumor and the host microenvironment in an effort to attain realistic platforms for assessing pharmaceutical efficacy in patients. PMID:25877888

  8. Collaborative annotation of 3D crystallographic models.

    PubMed

    Hunter, J; Henderson, M; Khan, I

    2007-01-01

    This paper describes the AnnoCryst system-a tool that was designed to enable authenticated collaborators to share online discussions about 3D crystallographic structures through the asynchronous attachment, storage, and retrieval of annotations. Annotations are personal comments, interpretations, questions, assessments, or references that can be attached to files, data, digital objects, or Web pages. The AnnoCryst system enables annotations to be attached to 3D crystallographic models retrieved from either private local repositories (e.g., Fedora) or public online databases (e.g., Protein Data Bank or Inorganic Crystal Structure Database) via a Web browser. The system uses the Jmol plugin for viewing and manipulating the 3D crystal structures but extends Jmol by providing an additional interface through which annotations can be created, attached, stored, searched, browsed, and retrieved. The annotations are stored on a standardized Web annotation server (Annotea), which has been extended to support 3D macromolecular structures. Finally, the system is embedded within a security framework that is capable of authenticating users and restricting access only to trusted colleagues.

  9. 3-D model-based vehicle tracking.

    PubMed

    Lou, Jianguang; Tan, Tieniu; Hu, Weiming; Yang, Hao; Maybank, Steven J

    2005-10-01

    This paper aims at tracking vehicles from monocular intensity image sequences and presents an efficient and robust approach to three-dimensional (3-D) model-based vehicle tracking. Under the weak perspective assumption and the ground-plane constraint, the movements of model projection in the two-dimensional image plane can be decomposed into two motions: translation and rotation. They are the results of the corresponding movements of 3-D translation on the ground plane (GP) and rotation around the normal of the GP, which can be determined separately. A new metric based on point-to-line segment distance is proposed to evaluate the similarity between an image region and an instantiation of a 3-D vehicle model under a given pose. Based on this, we provide an efficient pose refinement method to refine the vehicle's pose parameters. An improved EKF is also proposed to track and to predict vehicle motion with a precise kinematics model. Experimental results with both indoor and outdoor data show that the algorithm obtains desirable performance even under severe occlusion and clutter.

  10. 3-D model-based vehicle tracking.

    PubMed

    Lou, Jianguang; Tan, Tieniu; Hu, Weiming; Yang, Hao; Maybank, Steven J

    2005-10-01

    This paper aims at tracking vehicles from monocular intensity image sequences and presents an efficient and robust approach to three-dimensional (3-D) model-based vehicle tracking. Under the weak perspective assumption and the ground-plane constraint, the movements of model projection in the two-dimensional image plane can be decomposed into two motions: translation and rotation. They are the results of the corresponding movements of 3-D translation on the ground plane (GP) and rotation around the normal of the GP, which can be determined separately. A new metric based on point-to-line segment distance is proposed to evaluate the similarity between an image region and an instantiation of a 3-D vehicle model under a given pose. Based on this, we provide an efficient pose refinement method to refine the vehicle's pose parameters. An improved EKF is also proposed to track and to predict vehicle motion with a precise kinematics model. Experimental results with both indoor and outdoor data show that the algorithm obtains desirable performance even under severe occlusion and clutter. PMID:16238061

  11. Sensing and compressing 3-D models

    SciTech Connect

    Krumm, J.

    1998-02-01

    The goal of this research project was to create a passive and robust computer vision system for producing 3-D computer models of arbitrary scenes. Although the authors were unsuccessful in achieving the overall goal, several components of this research have shown significant potential. Of particular interest is the application of parametric eigenspace methods for planar pose measurement of partially occluded objects in gray-level images. The techniques presented provide a simple, accurate, and robust solution to the planar pose measurement problem. In addition, the representational efficiency of eigenspace methods used with gray-level features were successfully extended to binary features, which are less sensitive to illumination changes. The results of this research are presented in two papers that were written during the course of this project. The papers are included in sections 2 and 3. The first section of this report summarizes the 3-D modeling efforts.

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

    NASA Astrophysics Data System (ADS)

    Chen, Jimin; Jiang, Yijian; Li, Yangsheng

    2016-04-01

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

  13. Robust hashing for 3D models

    NASA Astrophysics Data System (ADS)

    Berchtold, Waldemar; Schäfer, Marcel; Rettig, Michael; Steinebach, Martin

    2014-02-01

    3D models and applications are of utmost interest in both science and industry. With the increment of their usage, their number and thereby the challenge to correctly identify them increases. Content identification is commonly done by cryptographic hashes. However, they fail as a solution in application scenarios such as computer aided design (CAD), scientific visualization or video games, because even the smallest alteration of the 3D model, e.g. conversion or compression operations, massively changes the cryptographic hash as well. Therefore, this work presents a robust hashing algorithm for 3D mesh data. The algorithm applies several different bit extraction methods. They are built to resist desired alterations of the model as well as malicious attacks intending to prevent correct allocation. The different bit extraction methods are tested against each other and, as far as possible, the hashing algorithm is compared to the state of the art. The parameters tested are robustness, security and runtime performance as well as False Acceptance Rate (FAR) and False Rejection Rate (FRR), also the probability calculation of hash collision is included. The introduced hashing algorithm is kept adaptive e.g. in hash length, to serve as a proper tool for all applications in practice.

  14. Fallon FORGE 3D Geologic Model

    DOE Data Explorer

    Doug Blankenship

    2016-03-01

    An x,y,z scattered data file for the 3D geologic model of the Fallon FORGE site. Model created in Earthvision by Dynamic Graphic Inc. The model was constructed with a grid spacing of 100 m. Geologic surfaces were extrapolated from the input data using a minimum tension gridding algorithm. The data file is tabular data in a text file, with lithology data associated with X,Y,Z grid points. All the relevant information is in the file header (the spatial reference, the projection etc.) In addition all the fields in the data file are identified in the header.

  15. 3D Models of Symbiotic Binaries

    NASA Astrophysics Data System (ADS)

    Mohamed, S.; Booth, R.; Podsiadlowski, Ph.; Ramstedt, S.; Vlemmings, W.; Maercker, M.

    2015-12-01

    Symbiotic binaries consist of a cool, mass-losing giant and an accreting, compact companion. We present 3D Smoothed Particle Hydrodynamics (SPH) models of two such interacting binaries, RS Oph and Mira AB. RS Oph is also a recurrent nova system, thus we model multiple quiescent mass transfer-nova outburst cycles. The resulting circumstellar structures of both systems are highly complex with the formation of spirals, arcs, shells, equatorial and bipolar outflows. We compare the models to recent observations and discuss the implications of our results for related systems, e.g., bipolar nebulae and jets, chemically peculiar stars, and the progenitors of Type Ia supernovae.

  16. 3D model of bow shocks

    NASA Astrophysics Data System (ADS)

    Gustafsson, M.; Ravkilde, T.; Kristensen, L. E.; Cabrit, S.; Field, D.; Pineau Des Forêts, G.

    2010-04-01

    Context. Shocks produced by outflows from young stars are often observed as bow-shaped structures in which the H2 line strength and morphology are characteristic of the physical and chemical environments and the velocity of the impact. Aims: We present a 3D model of interstellar bow shocks propagating in a homogeneous molecular medium with a uniform magnetic field. The model enables us to estimate the shock conditions in observed flows. As an example, we show how the model can reproduce rovibrational H2 observations of a bow shock in OMC1. Methods: The 3D model is constructed by associating a planar shock with every point on a 3D bow skeleton. The planar shocks are modelled with a highly sophisticated chemical reaction network that is essential for predicting accurate shock widths and line emissions. The shock conditions vary along the bow surface and determine the shock type, the local thickness, and brightness of the bow shell. The motion of the cooling gas parallel to the bow surface is also considered. The bow shock can move at an arbitrary inclination to the magnetic field and to the observer, and we model the projected morphology and radial velocity distribution in the plane-of-sky. Results: The morphology of a bow shock is highly dependent on the orientation of the magnetic field and the inclination of the flow. Bow shocks can appear in many different guises and do not necessarily show a characteristic bow shape. The ratio of the H2 v = 2-1 S(1) line to the v = 1-0 S(1) line is variable across the flow and the spatial offset between the peaks of the lines may be used to estimate the inclination of the flow. The radial velocity comes to a maximum behind the apparent apex of the bow shock when the flow is seen at an inclination different from face-on. Under certain circumstances the radial velocity of an expanding bow shock can show the same signatures as a rotating flow. In this case a velocity gradient perpendicular to the outflow direction is a projection

  17. Composite model of a 3-D image

    NASA Technical Reports Server (NTRS)

    Dukhovich, I. J.

    1980-01-01

    This paper presents a composite model of a moving (3-D) image especially useful for the sequential image processing and encoding. A non-linear predictor based on the composite model is described. The performance of this predictor is used as a measure of the validity of the model for a real image source. The minimization of a total mean square prediction error provides an inequality which determines a condition for the profitable use of the composite model and can serve as a decision device for the selection of the number of subsources within the model. The paper also describes statistical properties of the prediction error and contains results of computer simulation of two non-linear predictors in the case of perfect classification between subsources.

  18. 3D Model of Surfactant Replacement Therapy

    NASA Astrophysics Data System (ADS)

    Grotberg, James; Tai, Cheng-Feng; Filoche, Marcel

    2015-11-01

    Surfactant Replacement Therapy (SRT) involves instillation of a liquid-surfactant mixture directly into the lung airway tree. Though successful in neonatal applications, its use in adults had early success followed by failure. We present the first mathematical model of 3D SRT where a liquid plug propagates through the tree from forced inspiration. In two separate modeling steps, the plug first deposits a coating film on the airway wall which subtracts from its volume, a ``coating cost''. Then the plug splits unevenly at the airway bifurcation due to gravity. The steps are repeated until a plug ruptures or reaches the tree endpoint alveoli/acinus. The model generates 3D images of the resulting acinar distribution and calculates two global indexes, efficiency and homogeneity. Simulating published literature, the earlier successful adult SRT studies show comparatively good index values, while the later failed studies do not. Those unsuccessful studies used smaller dose volumes with higher concentration mixtures, apparently assuming a well mixed compartment. The model shows that adult lungs are not well mixed in SRT due to the coating cost and gravity effects. Returning to the higher dose volume protocols could save many thousands of lives annually in the US. Supported by NIH Grants HL85156, HL84370 and Agence Nationale de la Recherche, ANR no. 2010-BLAN-1119-05.

  19. MOSSFRAC: An anisotropic 3D fracture model

    SciTech Connect

    Moss, W C; Levatin, J L

    2006-08-14

    Despite the intense effort for nearly half a century to construct detailed numerical models of plastic flow and plastic damage accumulation, models for describing fracture, an equally important damage mechanism still cannot describe basic fracture phenomena. Typical fracture models set the stress tensor to zero for tensile fracture and set the deviatoric stress tensor to zero for compressive fracture. One consequence is that the simple case of the tensile fracture of a cylinder under combined compressive radial and tensile axial loads is not modeled correctly. The experimental result is a cylinder that can support compressive radial loads, but no axial load, whereas, the typical numerical result is a cylinder with all stresses equal to zero. This incorrect modeling of fracture locally also has a global effect, because material that is fracturing produces stress release waves, which propagate from the fracture and influence the surrounding material. Consequently, it would be useful to have a model that can describe the stress relief and the resulting anisotropy due to fracture. MOSSFRAC is a material model that simulates three-dimensional tensile and shear fracture in initially isotropic elastic-plastic materials, although its framework is also amenable to initially anisotropic materials. It differs from other models by accounting for the effects of cracks on the constitutive response of the material, so that the previously described experiment, as well as complicated fracture scenarios are simulated more accurately. The model is implemented currently in the LLNL hydrocodes DYNA3D, PARADYN, and ALE3D. The purpose of this technical note is to present a complete qualitative description of the model and quantitative descriptions of salient features.

  20. Synergistic anti-tumor efficacy of immunogenic adenovirus ONCOS-102 (Ad5/3-D24-GM-CSF) and standard of care chemotherapy in preclinical mesothelioma model.

    PubMed

    Kuryk, Lukasz; Haavisto, Elina; Garofalo, Mariangela; Capasso, Cristian; Hirvinen, Mari; Pesonen, Sari; Ranki, Tuuli; Vassilev, Lotta; Cerullo, Vincenzo

    2016-10-15

    Malignant mesothelioma (MM) is a rare cancer type caused mainly by asbestos exposure. The median overall survival time of a mesothelioma cancer patient is less than 1-year from diagnosis. Currently there are no curative treatment modalities for malignant mesothelioma, however treatments such as surgery, chemotherapy and radiotherapy can help to improve patient prognosis and increase life expectancy. Pemetrexed-Cisplatin is the only standard of care (SoC) chemotherapy for malignant mesothelioma, but the median PFS/OS (progression-free survival/overall survival) from the initiation of treatment is only up to 12 months. Therefore, new treatment strategies against malignant mesothelioma are in high demand. ONCOS-102 is a dual targeting, chimeric oncolytic adenovirus, coding for human GM-CSF. The safety and immune activating properties of ONCOS-102 have already been assessed in phase 1 study (NCT01598129). In this preclinical study, we evaluated the antineoplastic activity of combination treatment with SoC chemotherapy (Pemetrexed, Cisplatin, Carboplatin) and ONCOS-102 in xenograft BALB/c model of human malignant mesothelioma. We demonstrated that ONCOS-102 is able to induce immunogenic cell death of human mesothelioma cell lines in vitro and showed anti-tumor activity in the treatment of refractory H226 malignant pleural mesothelioma (MPM) xenograft model. While chemotherapy alone showed no anti-tumor activity in the mesothelioma mouse model, ONCOS-102 was able to slow down tumor growth. Interestingly, a synergistic anti-tumor effect was seen when ONCOS-102 was combined with chemotherapy regimens. These findings give a rationale for the clinical testing of ONCOS-102 in combination with first-line chemotherapy in patients suffering from malignant mesothelioma. PMID:27287512

  1. 3D Stratigraphic Modeling of Central Aachen

    NASA Astrophysics Data System (ADS)

    Dong, M.; Neukum, C.; Azzam, R.; Hu, H.

    2010-05-01

    Since 1980s, advanced computer hardware and software technologies, as well as multidisciplinary research have provided possibilities to develop advanced three dimensional (3D) simulation software for geosciences application. Some countries, such as USA1) and Canada2) 3), have built up regional 3D geological models based on archival geological data. Such models have played huge roles in engineering geology2), hydrogeology2) 3), geothermal industry1) and so on. In cooperating with the Municipality of Aachen, the Department of Engineering Geology of RWTH Aachen University have built up a computer-based 3D stratigraphic model of 50 meter' depth for the center of Aachen, which is a 5 km by 7 km geologically complex area. The uncorrelated data from multi-resources, discontinuous nature and unconformable connection of the units are main challenges for geological modeling in this area. The reliability of 3D geological models largely depends on the quality and quantity of data. Existing 1D and 2D geological data were collected, including 1) approximately 6970 borehole data of different depth compiled in Microsoft Access database and MapInfo database; 2) a Digital Elevation Model (DEM); 3) geological cross sections; and 4) stratigraphic maps in 1m, 2m and 5m depth. Since acquired data are of variable origins, they were managed step by step. The main processes are described below: 1) Typing errors of borehole data were identified and the corrected data were exported to Variowin2.2 to distinguish duplicate points; 2) The surface elevation of borehole data was compared to the DEM, and differences larger than 3m were eliminated. Moreover, where elevation data missed, it was read from the DEM; 3) Considerable data were collected from municipal constructions, such as residential buildings, factories, and roads. Therefore, many boreholes are spatially clustered, and only one or two representative points were picked out in such areas; After above procedures, 5839 boreholes with -x

  2. Efficacy of a Cell-Cycle Decoying Killer Adenovirus on 3-D Gelfoam®-Histoculture and Tumor-Sphere Models of Chemo-Resistant Stomach Carcinomatosis Visualized by FUCCI Imaging

    PubMed Central

    Yano, Shuya; Takehara, Kiyoto; Tazawa, Hiroshi; Kishimoto, Hiroyuki; Urata, Yasuo; Kagawa, Shunsuke; Fujiwara, Toshiyoshi; Hoffman, Robert M.

    2016-01-01

    Stomach cancer carcinomatosis peritonitis (SCCP) is a recalcitrant disease. The goal of the present study was to establish an in vitro-in vivo-like imageable model of SCCP to develop cell-cycle-based therapeutics of SCCP. We established 3-D Gelfoam® histoculture and tumor-sphere models of SCCP. FUCCI-expressing MKN-45 stomach cancer cells were transferred to express the fluorescence ubiquinized cell-cycle indicator (FUCCI). FUCCI-expressing MKN-45 cells formed spheres on agarose or on Gelfoam® grew into tumor-like structures with G0/G1 cancer cells in the center and S/G2 cancer cells located in the surface as indicated by FUCCI imaging when the cells fluoresced red or green, respectively. We treated FUCCI-expressing cancer cells forming SCCP tumors in Gelfoam® histoculture with OBP-301, cisplatinum (CDDP), or paclitaxel. CDDP or paclitaxel killed only cycling cancer cells and were ineffective against G1/G2 MKN-45 cells in tumors growing on Gelfoam®. In contrast, the telomerase-dependent adenovirus OBP-301 decoyed the MKN-45 cells in tumors on Gelfoam® to cycle from G0/G1 phase to S/G2 phase and reduced their viability. CDDP- or paclitaxel-treated MKN-45 tumors remained quiescent and did not change in size. In contrast, OB-301 reduced the size of the MKN-45 tumors on Gelfoam®. We examined the cell cycle-related proteins using Western blotting. CDDP increased the expression of p53 and p21 indicating cell cycle arrest. In contrast, OBP-301 decreased the expression of p53 and p21 Furthermore, OBP-301 increased the expression of E2F and pAkt as further indication of cell cycle decoy. This 3-D Gelfoam® histoculture and FUCCI imaging are powerful tools to discover effective therapy of SCCP such as OBP-301. PMID:27673332

  3. SB3D User Manual, Santa Barbara 3D Radiative Transfer Model

    SciTech Connect

    O'Hirok, William

    1999-01-01

    SB3D is a three-dimensional atmospheric and oceanic radiative transfer model for the Solar spectrum. The microphysics employed in the model are the same as used in the model SBDART. It is assumed that the user of SB3D is familiar with SBDART and IDL. SB3D differs from SBDART in that computations are conducted on media in three-dimensions rather than a single column (i.e. plane-parallel), and a stochastic method (Monte Carlo) is employed instead of a numerical approach (Discrete Ordinates) for estimating a solution to the radiative transfer equation. Because of these two differences between SB3D and SBDART, the input and running of SB3D is more unwieldy and requires compromises between model performance and computational expense. Hence, there is no one correct method for running the model and the user must develop a sense to the proper input and configuration of the model.

  4. 3D in vitro bioengineered tumors based on collagen I hydrogels

    PubMed Central

    Szot, Christopher S.; Buchanan, Cara F.; Freeman, Joseph W.; Rylander, Marissa N.

    2011-01-01

    Cells cultured within a three-dimensional (3D) in vitro environment have the ability to acquire phenotypes and respond to stimuli analogous to in vivo biological systems. This approach has been utilized in tissue engineering and can also be applied to the development of a physiologically relevant in vitro tumor model. In this study, collagen I hydrogels cultured with MDA-MB-231 human breast cancer cells were bioengineered as a platform for in vitro solid tumor development. The cell–cell and cell-matrix interactions present during in vivo tissue progression were encouraged within the 3D hydrogel architecture, and the biocompatibility of collagen I supported unconfined cellular proliferation. The development of necrosis beyond a depth of ~150–200 μm and the expression of hypoxia-inducible factor (HIF)-1α were demonstrated in the in vitro bioengineered tumors. Oxygen and nutrient diffusion limitations through the collagen I matrix as well as competition for available nutrients resulted in growing levels of intra-cellular hypoxia, quantified by a statistically significant (p < 0.01) upregulation of HIF-1α gene expression. The bioengineered tumors also demonstrated promising angiogenic potential with a statistically significant (p < 0.001) upregulation of vascular endothelial growth factor (VEGF)-A gene expression. In addition, comparable gene expression analysis demonstrated a statistically significant increase of HIF-1α (p < 0.05) and VEGF-A (p < 0.001) by MDA-MB-231 cells cultured in the 3D collagen I hydrogels compared to cells cultured in a monolayer on two-dimensional tissue culture polystyrene. The results presented in this study demonstrate the capacity of collagen I hydrogels to facilitate the development of 3D in vitro bioengineered tumors that are representative of the pre-vascularized stages of in vivo solid tumor progression. PMID:21782234

  5. 3-D physical models of amitosis (cytokinesis).

    PubMed

    Cheng, Kang; Zou, Changhua

    2005-01-01

    Based on Newton's laws, extended Coulomb's law and published biological data, we develop our 3-D physical models of natural and normal amitosis (cytokinesis), for prokaryotes (bacterial cells) in M phase. We propose following hypotheses: Chromosome rings exclusion: No normally and naturally replicated chromosome rings (RCR) can occupy the same prokaryote, a bacterial cell. The RCR produce spontaneous and strong electromagnetic fields (EMF), that can be alternated environmentally, in protoplasm and cortex. The EMF is approximately a repulsive quasi-static electric (slowly variant and mostly electric) field (EF). The EF forces between the RCR are strong enough, and orderly accumulate contractile proteins that divide the procaryotes in the cell cortex of division plane or directly split the cell compartment envelope longitudinally. The radial component of the EF forces could also make furrows or cleavages of procaryotes. The EF distribution controls the protoplasm partition and completes the amitosis (cytokinesis). After the cytokinesis, the spontaneous and strong EF disappear because the net charge accumulation becomes weak, in the protoplasm. The exclusion is because the two sets of informative objects (RCR) have identical DNA codes information and they are electro magnetically identical, therefore they repulse from each other. We also compare divisions among eukaryotes, prokaryotes, mitochondria and chloroplasts and propose our hypothesis: The principles of our models are applied to divisions of mitochondria and chloroplasts of eucaryotes too because these division mechanisms are closer than others in a view of physics. Though we develop our model using 1 division plane (i.e., 1 cell is divided into 2 cells) as an example, the principle of our model is applied to the cases with multiple division planes (i.e., 1 cell is divided into multiple cells) too.

  6. 3D Models of Stellar Interactions

    NASA Astrophysics Data System (ADS)

    Mohamed, S.; Podsiadlowski, Ph.; Booth, R.; Maercker, M.; Ramstedt, S.; Vlemmings, W.; Harries, T.; Mackey, J.; Langer, N.; Corradi, R.

    2014-04-01

    Symbiotic binaries consist of a cool, evolved mass-losing giant and an accreting compact companion. As symbiotic nebulae show similar morphologies to those in planetary nebulae (so much so that it is often difficult to distinguish between the two), they are ideal laboratories for understanding the role a binary companion plays in shaping the circumstellar envelopes in these evolved systems. We will present 3D Smoothed Particle Hydrodynamics (SPH) models of interacting binaries, e.g. R Aquarii and Mira, and discuss the formation of spiral outflows, arcs, shells and equatorial density enhancements.We will also discuss the implications of the former for planetary nebulae, e.g. the Egg Nebula and Cat's Eye, and the latter for the formation of bipolar geometries, e.g. M2-9. We also investigate accretion and angular momentum evolution in symbiotic binaries which may be important to understand the formation of jets and more episodic mass-loss features we see in circumstellar envelopes and the orbital characteristics of binary central stars of planetary nebulae.

  7. Multi-view and 3D deformable part models.

    PubMed

    Pepik, Bojan; Stark, Michael; Gehler, Peter; Schiele, Bernt

    2015-11-01

    As objects are inherently 3D, they have been modeled in 3D in the early days of computer vision. Due to the ambiguities arising from mapping 2D features to 3D models, 3D object representations have been neglected and 2D feature-based models are the predominant paradigm in object detection nowadays. While such models have achieved outstanding bounding box detection performance, they come with limited expressiveness, as they are clearly limited in their capability of reasoning about 3D shape or viewpoints. In this work, we bring the worlds of 3D and 2D object representations closer, by building an object detector which leverages the expressive power of 3D object representations while at the same time can be robustly matched to image evidence. To that end, we gradually extend the successful deformable part model [1] to include viewpoint information and part-level 3D geometry information, resulting in several different models with different level of expressiveness. We end up with a 3D object model, consisting of multiple object parts represented in 3D and a continuous appearance model. We experimentally verify that our models, while providing richer object hypotheses than the 2D object models, provide consistently better joint object localization and viewpoint estimation than the state-of-the-art multi-view and 3D object detectors on various benchmarks (KITTI [2] , 3D object classes [3] , Pascal3D+ [4] , Pascal VOC 2007 [5] , EPFL multi-view cars[6] ). PMID:26440264

  8. Improved Anti-Tumoral Therapeutic Efficacy of 4-Hydroxynonenal Incorporated in Novel Lipid Nanocapsules in 2D and 3D Models.

    PubMed

    Pizzimenti, Stefania; Daga, Martina; Ciamporcero, Eric; Toaldo, Cristina; Pettazzoni, Piergiorgio; Osella-Abate, Simona; Novelli, Mauro; Minelli, Rosalba; Bisazza, Agnese; Gamba, Paola; Testa, Gabriella; Ullio, Chiara; Ferruti, Paolo; Ranucci, Elisabetta; Bernengo, Maria Grazia; Ferretti, Carlo; Dianzani, Chiara; Biasi, Fiorella; Barrera, Giuseppina; Cavalli, Roberta

    2015-12-01

    4-hydroxynonenal (HNE), a lipid peroxidation product, is a promising anti-neoplastic drug due to its remarkable anti-cancer activities. However, this possibility has not been explored, because the delivery of HNE is very challenging as a result of its low solubility and its poor stability. This study intentionally designed a new type of lipid nanocapsules specifically for HNE delivery. They consist of a medium chain triglyceride liquid oil core surrounded by a polymer shell. A β-cyclodextrin-poly(4-acryloylmorpholine) conjugate was selected as the shell component. HNE-loaded nanocapsules were about 350 nm in size with a negative surface charge. They were stable for two years when stored in suspensions at 4 degrees C. In vitro experiments showed that HNE was released from the nanocapsules at a considerable rate. Nanocapsule uptake into cells was evaluated using a fluorescent formulation that revealed rapid internalisation. Cytotoxicity studies demonstrated the safety of the formulation. Enhanced anti-tumoral activity against various cell lines, depending on increased HNE stability, was obtained by using HNE-loaded nanocapsules. In particular, we have demonstrated an increase in anti-proliferative, pro-apoptotic and differentiative activity in several tumour cell lines from different tissues. Moreover, we evaluated the effects of these new nanocapsules on a three-dimensional human reconstructed model of skin melanoma. Interestingly, the encouraging results obtained with topical administration on the epidermal surface could open new perspectives in melanoma treatments. PMID:26510311

  9. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

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

    2016-07-01

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

  10. 3D-GNOME: an integrated web service for structural modeling of the 3D genome

    PubMed Central

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

    2016-01-01

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

  11. Volume change determination of metastatic lung tumors in CT images using 3-D template matching

    NASA Astrophysics Data System (ADS)

    Ambrosini, Robert D.; Wang, Peng; O'Dell, Walter G.

    2009-02-01

    The ability of a clinician to properly detect changes in the size of lung nodules over time is a vital element to both the diagnosis of malignant growths and the monitoring of the response of cancerous lesions to therapy. We have developed a novel metastasis sizing algorithm based on 3-D template matching with spherical tumor appearance models that were created to match the expected geometry of the tumors of interest while accounting for potential spatial offsets of nodules in the slice thickness direction. The spherical template that best-fits the overall volume of each lung metastasis was determined through the optimization of the 3-D normalized cross-correlation coefficients (NCCC) calculated between the templates and the nodules. A total of 17 different lung metastases were extracted manually from real patient CT datasets and reconstructed in 3-D using spherical harmonics equations to generate simulated nodules for testing our algorithm. Each metastasis 3-D shape was then subjected to 10%, 25%, 50%, 75% and 90% scaling of its volume to allow for 5 possible volume change combinations relative to the original size per each reconstructed nodule and inserted back into CT datasets with appropriate blurring and noise addition. When plotted against the true volume change, the nodule volume changes calculated by our algorithm for these 85 data points exhibited a high degree of accuracy (slope = 0.9817, R2 = 0.9957). Our results demonstrate that the 3-D template matching method can be an effective, fast, and accurate tool for automated sizing of metastatic tumors.

  12. 3D fast wavelet network model-assisted 3D face recognition

    NASA Astrophysics Data System (ADS)

    Said, Salwa; Jemai, Olfa; Zaied, Mourad; Ben Amar, Chokri

    2015-12-01

    In last years, the emergence of 3D shape in face recognition is due to its robustness to pose and illumination changes. These attractive benefits are not all the challenges to achieve satisfactory recognition rate. Other challenges such as facial expressions and computing time of matching algorithms remain to be explored. In this context, we propose our 3D face recognition approach using 3D wavelet networks. Our approach contains two stages: learning stage and recognition stage. For the training we propose a novel algorithm based on 3D fast wavelet transform. From 3D coordinates of the face (x,y,z), we proceed to voxelization to get a 3D volume which will be decomposed by 3D fast wavelet transform and modeled after that with a wavelet network, then their associated weights are considered as vector features to represent each training face . For the recognition stage, an unknown identity face is projected on all the training WN to obtain a new vector features after every projection. A similarity score is computed between the old and the obtained vector features. To show the efficiency of our approach, experimental results were performed on all the FRGC v.2 benchmark.

  13. Anatomy-based 3D skeleton extraction from femur model.

    PubMed

    Gharenazifam, Mina; Arbabi, Ehsan

    2014-11-01

    Using 3D models of bones can highly improve accuracy and reliability of orthopaedic evaluation. However, it may impose excessive computational load. This article proposes a fully automatic method for extracting a compact model of the femur from its 3D model. The proposed method works by extracting a 3D skeleton based on the clinical parameters of the femur. Therefore, in addition to summarizing a 3D model of the bone, the extracted skeleton would preserve important clinical and anatomical information. The proposed method has been applied on 3D models of 10 femurs and the results have been evaluated for different resolutions of data.

  14. 3D Modeling Techniques for Print and Digital Media

    NASA Astrophysics Data System (ADS)

    Stephens, Megan Ashley

    In developing my thesis, I looked to gain skills using ZBrush to create 3D models, 3D scanning, and 3D printing. The models created compared the hearts of several vertebrates and were intended for students attending Comparative Vertebrate Anatomy. I used several resources to create a model of the human heart and was able to work from life while creating heart models from other vertebrates. I successfully learned ZBrush and 3D scanning, and successfully printed 3D heart models. ZBrush allowed me to create several intricate models for use in both animation and print media. The 3D scanning technique did not fit my needs for the project, but may be of use for later projects. I was able to 3D print using two different techniques as well.

  15. Design, synthesis, anti-tumor activity, and molecular modeling of quinazoline and pyrido[2,3-d]pyrimidine derivatives targeting epidermal growth factor receptor.

    PubMed

    Hou, Ju; Wan, Shanhe; Wang, Guangfa; Zhang, Tingting; Li, Zhonghuang; Tian, Yuanxin; Yu, Yonghuan; Wu, Xiaoyun; Zhang, Jiajie

    2016-08-01

    Three series of novel quinazoline and pyrido[2,3-d]pyrimidine derivatives were designed, synthesized and evaluated for their ability to inhibit EGFR tyrosine kinase and a panel of five human cancer cell lines (MCF-7, A549, BT-474, SK-BR-3, and MDA-MB-231). Bioassay results indicated that five of these prepared compounds (12c-12e and 13c-13d) exhibited remarkably higher inhibitory activities against EGFR and SK-BR-3 cell line. Compounds 12c and 12e displayed the most potent EGFR inhibitory activity (IC50 = 2.97 nM and 3.58 nM, respectively) and good anti-proliferative effect against SK-BR-3 cell with the IC50 values of 3.10 μM and 5.87 μM, respectively. Furthermore, molecular docking and molecular dynamics simulation studies verified that compound 12c and 12e shared similar binding pattern with gefitinib in the binding pocket of EGFR. MM-GBSA binding free energy revealed that the compound 12c and 12e have almost the same inhibitory activity against EGFR as gefitinib, and that the dominating effect of van der Waals interactions drives the binding process. PMID:27132165

  16. Low-cost photodynamic therapy devices for global health settings: Characterization of battery-powered LED performance and smartphone imaging in 3D tumor models.

    PubMed

    Hempstead, Joshua; Jones, Dustin P; Ziouche, Abdelali; Cramer, Gwendolyn M; Rizvi, Imran; Arnason, Stephen; Hasan, Tayyaba; Celli, Jonathan P

    2015-01-01

    A lack of access to effective cancer therapeutics in resource-limited settings is implicated in global cancer health disparities between developed and developing countries. Photodynamic therapy (PDT) is a light-based treatment modality that has exhibited safety and efficacy in the clinic using wavelengths and irradiances achievable with light-emitting diodes (LEDs) operated on battery power. Here we assess low-cost enabling technology to extend the clinical benefit of PDT to regions with little or no access to electricity or medical infrastructure. We demonstrate the efficacy of a device based on a 635 nm high-output LED powered by three AA disposable alkaline batteries, to achieve strong cytotoxic response in monolayer and 3D cultures of A431 squamous carcinoma cells following photosensitization by administering aminolevulinic acid (ALA) to induce the accumulation of protoporphyrin IX (PpIX). Here we characterize challenges of battery-operated device performance, including battery drain and voltage stability specifically over relevant PDT dose parameters. Further motivated by the well-established capacity of PDT photosensitizers to serve as tumour-selective fluorescence contrast agents, we demonstrate the capability of a consumer smartphone with low-cost add-ons to measure concentration-dependent PpIX fluorescence. This study lays the groundwork for the on-going development of image-guided ALA-PDT treatment technologies for global health applications. PMID:25965295

  17. Design, synthesis, anti-tumor activity, and molecular modeling of quinazoline and pyrido[2,3-d]pyrimidine derivatives targeting epidermal growth factor receptor.

    PubMed

    Hou, Ju; Wan, Shanhe; Wang, Guangfa; Zhang, Tingting; Li, Zhonghuang; Tian, Yuanxin; Yu, Yonghuan; Wu, Xiaoyun; Zhang, Jiajie

    2016-08-01

    Three series of novel quinazoline and pyrido[2,3-d]pyrimidine derivatives were designed, synthesized and evaluated for their ability to inhibit EGFR tyrosine kinase and a panel of five human cancer cell lines (MCF-7, A549, BT-474, SK-BR-3, and MDA-MB-231). Bioassay results indicated that five of these prepared compounds (12c-12e and 13c-13d) exhibited remarkably higher inhibitory activities against EGFR and SK-BR-3 cell line. Compounds 12c and 12e displayed the most potent EGFR inhibitory activity (IC50 = 2.97 nM and 3.58 nM, respectively) and good anti-proliferative effect against SK-BR-3 cell with the IC50 values of 3.10 μM and 5.87 μM, respectively. Furthermore, molecular docking and molecular dynamics simulation studies verified that compound 12c and 12e shared similar binding pattern with gefitinib in the binding pocket of EGFR. MM-GBSA binding free energy revealed that the compound 12c and 12e have almost the same inhibitory activity against EGFR as gefitinib, and that the dominating effect of van der Waals interactions drives the binding process.

  18. Low-cost photodynamic therapy devices for global health settings: Characterization of battery-powered LED performance and smartphone imaging in 3D tumor models.

    PubMed

    Hempstead, Joshua; Jones, Dustin P; Ziouche, Abdelali; Cramer, Gwendolyn M; Rizvi, Imran; Arnason, Stephen; Hasan, Tayyaba; Celli, Jonathan P

    2015-05-12

    A lack of access to effective cancer therapeutics in resource-limited settings is implicated in global cancer health disparities between developed and developing countries. Photodynamic therapy (PDT) is a light-based treatment modality that has exhibited safety and efficacy in the clinic using wavelengths and irradiances achievable with light-emitting diodes (LEDs) operated on battery power. Here we assess low-cost enabling technology to extend the clinical benefit of PDT to regions with little or no access to electricity or medical infrastructure. We demonstrate the efficacy of a device based on a 635 nm high-output LED powered by three AA disposable alkaline batteries, to achieve strong cytotoxic response in monolayer and 3D cultures of A431 squamous carcinoma cells following photosensitization by administering aminolevulinic acid (ALA) to induce the accumulation of protoporphyrin IX (PpIX). Here we characterize challenges of battery-operated device performance, including battery drain and voltage stability specifically over relevant PDT dose parameters. Further motivated by the well-established capacity of PDT photosensitizers to serve as tumour-selective fluorescence contrast agents, we demonstrate the capability of a consumer smartphone with low-cost add-ons to measure concentration-dependent PpIX fluorescence. This study lays the groundwork for the on-going development of image-guided ALA-PDT treatment technologies for global health applications.

  19. Low-cost photodynamic therapy devices for global health settings: Characterization of battery-powered LED performance and smartphone imaging in 3D tumor models

    NASA Astrophysics Data System (ADS)

    Hempstead, Joshua; Jones, Dustin P.; Ziouche, Abdelali; Cramer, Gwendolyn M.; Rizvi, Imran; Arnason, Stephen; Hasan, Tayyaba; Celli, Jonathan P.

    2015-05-01

    A lack of access to effective cancer therapeutics in resource-limited settings is implicated in global cancer health disparities between developed and developing countries. Photodynamic therapy (PDT) is a light-based treatment modality that has exhibited safety and efficacy in the clinic using wavelengths and irradiances achievable with light-emitting diodes (LEDs) operated on battery power. Here we assess low-cost enabling technology to extend the clinical benefit of PDT to regions with little or no access to electricity or medical infrastructure. We demonstrate the efficacy of a device based on a 635 nm high-output LED powered by three AA disposable alkaline batteries, to achieve strong cytotoxic response in monolayer and 3D cultures of A431 squamous carcinoma cells following photosensitization by administering aminolevulinic acid (ALA) to induce the accumulation of protoporphyrin IX (PpIX). Here we characterize challenges of battery-operated device performance, including battery drain and voltage stability specifically over relevant PDT dose parameters. Further motivated by the well-established capacity of PDT photosensitizers to serve as tumour-selective fluorescence contrast agents, we demonstrate the capability of a consumer smartphone with low-cost add-ons to measure concentration-dependent PpIX fluorescence. This study lays the groundwork for the on-going development of image-guided ALA-PDT treatment technologies for global health applications.

  20. Low-cost photodynamic therapy devices for global health settings: Characterization of battery-powered LED performance and smartphone imaging in 3D tumor models

    PubMed Central

    Hempstead, Joshua; Jones, Dustin P.; Ziouche, Abdelali; Cramer, Gwendolyn M.; Rizvi, Imran; Arnason, Stephen; Hasan, Tayyaba; Celli, Jonathan P.

    2015-01-01

    A lack of access to effective cancer therapeutics in resource-limited settings is implicated in global cancer health disparities between developed and developing countries. Photodynamic therapy (PDT) is a light-based treatment modality that has exhibited safety and efficacy in the clinic using wavelengths and irradiances achievable with light-emitting diodes (LEDs) operated on battery power. Here we assess low-cost enabling technology to extend the clinical benefit of PDT to regions with little or no access to electricity or medical infrastructure. We demonstrate the efficacy of a device based on a 635 nm high-output LED powered by three AA disposable alkaline batteries, to achieve strong cytotoxic response in monolayer and 3D cultures of A431 squamous carcinoma cells following photosensitization by administering aminolevulinic acid (ALA) to induce the accumulation of protoporphyrin IX (PpIX). Here we characterize challenges of battery-operated device performance, including battery drain and voltage stability specifically over relevant PDT dose parameters. Further motivated by the well-established capacity of PDT photosensitizers to serve as tumour-selective fluorescence contrast agents, we demonstrate the capability of a consumer smartphone with low-cost add-ons to measure concentration-dependent PpIX fluorescence. This study lays the groundwork for the on-going development of image-guided ALA-PDT treatment technologies for global health applications. PMID:25965295

  1. The 3D rocket combustor acoustics model

    NASA Technical Reports Server (NTRS)

    Priem, Richard J.; Breisacher, Kevin J.

    1992-01-01

    The theory and procedures for determining the characteristics of pressure oscillations in rocket engines with prescribed burning rate oscillations are presented. Analyses including radial and hub baffles and absorbers can be performed in one, two, and three dimensions. Pressure and velocity oscillations calculated using this procedure are presented for the SSME to show the influence of baffles and absorbers on the burning rate oscillations required to achieve neutral stability. Comparisons are made between the results obtained utilizing 1-D, 2-D, and 3-D assumptions with regards to capturing the physical phenomena of interest and computational requirements.

  2. Stochastic Modeling of Calcium in 3D Geometry

    PubMed Central

    Mazel, Tomáš; Raymond, Rebecca; Raymond-Stintz, Mary; Jett, Stephen; Wilson, Bridget S.

    2009-01-01

    Release of inflammatory mediators by mast cells in type 1 immediate-hypersensitivity allergic reactions relies on antigen-dependent increases in cytosolic calcium. Here, we used a series of electron microscopy images to build a 3D reconstruction representing a slice through a rat tumor mast cell, which then served as a basis for stochastic modeling of inositol-trisphosphate-mediated calcium responses. The stochastic approach was verified by reaction-diffusion modeling within the same geometry. Local proximity of the endoplasmic reticulum to either the plasma membrane or mitochondria is predicted to differentially impact local inositol trisphosphate receptor transport. The explicit consideration of organelle spatial relationships represents an important step toward building a comprehensive, realistic model of cellular calcium dynamics. PMID:19254531

  3. 3D In Vitro Model for Breast Cancer Research Using Magnetic Levitation and Bioprinting Method.

    PubMed

    Leonard, Fransisca; Godin, Biana

    2016-01-01

    Tumor microenvironment composition and architecture are known as a major factor in orchestrating the tumor growth and its response to various therapies. In this context, in vivo studies are necessary to evaluate the responses. However, while tumor cells can be of human origin, tumor microenvironment in the in vivo models is host-based. On the other hand, in vitro studies in a flat monoculture of tumor cells (the most frequently used in vitro tumor model) are unable to recapitulate the complexity of tumor microenvironment. Three-dimensional (3D) in vitro cell cultures of tumor cells have been proven to be an important experimental tool in understanding mechanisms of tumor growth, response to therapeutics, and transport of nutrients/drugs. We have recently described a novel tool to create 3D co-cultures of tumor cells and cells in the tumor microenvironment. Our method utilizes magnetic manipulation/levitation of the specific ratios of tumor cells and cells in the tumor microenvironment (from human or animal origin) aiding in the formation of tumor spheres with defined cellular composition and density, as quickly as within 24 h. This chapter describes the experimental protocols developed to model the 3D structure of the cancer environment using the above method. PMID:26820961

  4. Heating properties of non-invasive hyperthermia treatment for abdominal deep tumors by 3-D FEM.

    PubMed

    Morita, E; Kato, K; Ono, S; Shindo, Y; Tsuchiya, K; Kubo, M

    2009-01-01

    This paper discusses the heating properties of a new type of hyperthermia system composed of a re-entrant type resonant cavity applicator for deep tumors of the abdominal region. In this method, a human body is placed in the gap of two inner electrodes and is non-invasively heated with electromagnetic fields stimulated in the cavity. Here, we calculated temperature distributions of a simple human abdominal phantom model that we constructed to examine the heating properties of the developed hyperthermia system. First, the proposed heating method and a simple abdominal model to calculate the temperature distribution are presented. Second, the computer simulation results of temperature distribution by 3-D FEM are presented. From these results, it was found that the proposed simple human abdominal phantom model composed of muscle, fat and lung was useful to test the heating properties of our heating method. Our heating method was also effective to non-invasively heat abdominal deep tumors.

  5. 3D Face modeling using the multi-deformable method.

    PubMed

    Hwang, Jinkyu; Yu, Sunjin; Kim, Joongrock; Lee, Sangyoun

    2012-01-01

    In this paper, we focus on the problem of the accuracy performance of 3D face modeling techniques using corresponding features in multiple views, which is quite sensitive to feature extraction errors. To solve the problem, we adopt a statistical model-based 3D face modeling approach in a mirror system consisting of two mirrors and a camera. The overall procedure of our 3D facial modeling method has two primary steps: 3D facial shape estimation using a multiple 3D face deformable model and texture mapping using seamless cloning that is a type of gradient-domain blending. To evaluate our method's performance, we generate 3D faces of 30 individuals and then carry out two tests: accuracy test and robustness test. Our method shows not only highly accurate 3D face shape results when compared with the ground truth, but also robustness to feature extraction errors. Moreover, 3D face rendering results intuitively show that our method is more robust to feature extraction errors than other 3D face modeling methods. An additional contribution of our method is that a wide range of face textures can be acquired by the mirror system. By using this texture map, we generate realistic 3D face for individuals at the end of the paper. PMID:23201976

  6. 3D Face Modeling Using the Multi-Deformable Method

    PubMed Central

    Hwang, Jinkyu; Yu, Sunjin; Kim, Joongrock; Lee, Sangyoun

    2012-01-01

    In this paper, we focus on the problem of the accuracy performance of 3D face modeling techniques using corresponding features in multiple views, which is quite sensitive to feature extraction errors. To solve the problem, we adopt a statistical model-based 3D face modeling approach in a mirror system consisting of two mirrors and a camera. The overall procedure of our 3D facial modeling method has two primary steps: 3D facial shape estimation using a multiple 3D face deformable model and texture mapping using seamless cloning that is a type of gradient-domain blending. To evaluate our method's performance, we generate 3D faces of 30 individuals and then carry out two tests: accuracy test and robustness test. Our method shows not only highly accurate 3D face shape results when compared with the ground truth, but also robustness to feature extraction errors. Moreover, 3D face rendering results intuitively show that our method is more robust to feature extraction errors than other 3D face modeling methods. An additional contribution of our method is that a wide range of face textures can be acquired by the mirror system. By using this texture map, we generate realistic 3D face for individuals at the end of the paper. PMID:23201976

  7. Biologically relevant 3D tumor arrays: treatment response and the importance of stromal partners

    NASA Astrophysics Data System (ADS)

    Rizvi, Imran; Celli, Jonathan P.; Xu, Feng; Evans, Conor L.; Abu-Yousif, Adnan O.; Muzikansky, Alona; Elrington, Stefan A.; Pogue, Brian W.; Finkelstein, Dianne M.; Demirci, Utkan; Hasan, Tayyaba

    2011-02-01

    The development and translational potential of therapeutic strategies for cancer is limited, in part, by a lack of biological models that capture important aspects of tumor growth and treatment response. It is also becoming increasingly evident that no single treatment will be curative for this complex disease. Rationally-designed combination regimens that impact multiple targets provide the best hope of significantly improving clinical outcomes for cancer patients. Rapidly identifying treatments that cooperatively enhance treatment efficacy from the vast library of candidate interventions is not feasible, however, with current systems. There is a vital, unmet need to create cell-based research platforms that more accurately mimic the complex biology of human tumors than monolayer cultures, while providing the ability to screen therapeutic combinations more rapidly than animal models. We have developed a highly reproducible in vitro three-dimensional (3D) tumor model for micrometastatic ovarian cancer (OvCa), which in conjunction with quantitative image analysis routines to batch-process large datasets, serves as a high throughput reporter to screen rationally-designed combination regimens. We use this system to assess mechanism-based combination regimens with photodynamic therapy (PDT), which sensitizes OvCa to chemo and biologic agents, and has shown promise in clinic trials. We show that PDT synergistically enhances carboplatin efficacy in a sequence dependent manner. In printed heterocellular cultures we demonstrate that proximity of fibroblasts enhances 3D tumor growth and investigate co-cultures with endothelial cells. The principles described here could inform the design and evaluation of mechanism-based therapeutic options for a broad spectrum of metastatic solid tumors.

  8. Assessing the RELAPS-3D Heat Conduction Enclosure Model

    SciTech Connect

    McCann, Larry D.

    2008-09-30

    Three heat conduction problems that have exact solutions are modeled with RELAP5-3D using the conduction enclosure model. These comparisons are designed to be used in the RELAP5-3D development assessment scheduled to be completed in 2009. It is shown that with proper input choices and adequate model detail the exact solutions can be matched. In addition, this analysis identified an error and the required correction in the cylindrical and spherical heat conductor models in RELAP5-3D which will be corrected in a future version of RELAP5-3D.

  9. Comparing a quasi-3D to a full 3D nearshore circulation model: SHORECIRC and ROMS

    USGS Publications Warehouse

    Haas, K.A.; Warner, J.C.

    2009-01-01

    Predictions of nearshore and surf zone processes are important for determining coastal circulation, impacts of storms, navigation, and recreational safety. Numerical modeling of these systems facilitates advancements in our understanding of coastal changes and can provide predictive capabilities for resource managers. There exists many nearshore coastal circulation models, however they are mostly limited or typically only applied as depth integrated models. SHORECIRC is an established surf zone circulation model that is quasi-3D to allow the effect of the variability in the vertical structure of the currents while maintaining the computational advantage of a 2DH model. Here we compare SHORECIRC to ROMS, a fully 3D ocean circulation model which now includes a three dimensional formulation for the wave-driven flows. We compare the models with three different test applications for: (i) spectral waves approaching a plane beach with an oblique angle of incidence; (ii) monochromatic waves driving longshore currents in a laboratory basin; and (iii) monochromatic waves on a barred beach with rip channels in a laboratory basin. Results identify that the models are very similar for the depth integrated flows and qualitatively consistent for the vertically varying components. The differences are primarily the result of the vertically varying radiation stress utilized by ROMS and the utilization of long wave theory for the radiation stress formulation in vertical varying momentum balance by SHORECIRC. The quasi-3D model is faster, however the applicability of the fully 3D model allows it to extend over a broader range of processes, temporal, and spatial scales. ?? 2008 Elsevier Ltd.

  10. a Fast Method for Measuring the Similarity Between 3d Model and 3d Point Cloud

    NASA Astrophysics Data System (ADS)

    Zhang, Zongliang; Li, Jonathan; Li, Xin; Lin, Yangbin; Zhang, Shanxin; Wang, Cheng

    2016-06-01

    This paper proposes a fast method for measuring the partial Similarity between 3D Model and 3D point Cloud (SimMC). It is crucial to measure SimMC for many point cloud-related applications such as 3D object retrieval and inverse procedural modelling. In our proposed method, the surface area of model and the Distance from Model to point Cloud (DistMC) are exploited as measurements to calculate SimMC. Here, DistMC is defined as the weighted distance of the distances between points sampled from model and point cloud. Similarly, Distance from point Cloud to Model (DistCM) is defined as the average distance of the distances between points in point cloud and model. In order to reduce huge computational burdens brought by calculation of DistCM in some traditional methods, we define SimMC as the ratio of weighted surface area of model to DistMC. Compared to those traditional SimMC measuring methods that are only able to measure global similarity, our method is capable of measuring partial similarity by employing distance-weighted strategy. Moreover, our method is able to be faster than other partial similarity assessment methods. We demonstrate the superiority of our method both on synthetic data and laser scanning data.

  11. A 3D Geometry Model Search Engine to Support Learning

    ERIC Educational Resources Information Center

    Tam, Gary K. L.; Lau, Rynson W. H.; Zhao, Jianmin

    2009-01-01

    Due to the popularity of 3D graphics in animation and games, usage of 3D geometry deformable models increases dramatically. Despite their growing importance, these models are difficult and time consuming to build. A distance learning system for the construction of these models could greatly facilitate students to learn and practice at different…

  12. 3D MRI-based tumor delineation of ocular melanoma and its comparison with conventional techniques.

    PubMed

    Daftari, Inder k; Aghaian, Elsa; O'Brien, Joan M; Dillon, William; Phillips, Theodore L

    2005-11-01

    The aim of this study is to (1) compare the delineation of the tumor volume for ocular melanoma on high-resolution three-dimensional (3D) T2-weighted fast spin echo magnetic resonance imaging (MRI) images with conventional techniques of A- and B-scan ultrasound, transcleral illumination, and placement of tantalum markers around tumor base and (2) to evaluate whether the surgically placed marker ring tumor delineation can be replaced by 3D MRI based tumor delineation. High-resolution 3D T2-weighted fast spin echo (3D FSE) MRI scans were obtained for 60 consecutive ocular melanoma patients using a 1.5 T MRI (GE Medical Systems, Milwaukee, WI), in a standard head coil. These patients were subsequently treated with proton beam therapy at the UC Davis Cyclotron, Davis, CA. The tumor was delineated by placement of tantalum rings (radio-opaque markers) around the tumor periphery as defined by pupillary transillumination during surgery. A point light source, placed against the sclera, was also used to confirm ring agreement with indirect ophthalmoscopy. When necessary, intraoperative ultrasound was also performed. The patients were planned using EYEPLAN software and the tumor volumes were obtained. For analysis, the tumors were divided into four categories based on tumor height and basal diameter. In order to assess the impact of high-resolution 3D T2 FSE MRI, the tumor volumes were outlined on the MRI scans by two independent observers and the tumor volumes calculated for each patient. Six (10%) of 60 patients had tumors, which were not visible on 3D MRI images. These six patients had tumors with tumor heights < or = 3 mm. A small intraobserver variation with a mean of (-0.22 +/- 4)% was seen in tumor volumes delineated by 3D T2 FSE MR images. The ratio of tumor volumes measured on MRI to EYEPLAN for the largest to the smallest tumor volumes varied between 0.993 and 1.02 for 54 patients. The tumor volumes measured directly on 3D T2 FSE MRI ranged from 4.03 to 0.075 cm3

  13. Fringe projection 3D microscopy with the general imaging model.

    PubMed

    Yin, Yongkai; Wang, Meng; Gao, Bruce Z; Liu, Xiaoli; Peng, Xiang

    2015-03-01

    Three-dimensional (3D) imaging and metrology of microstructures is a critical task for the design, fabrication, and inspection of microelements. Newly developed fringe projection 3D microscopy is presented in this paper. The system is configured according to camera-projector layout and long working distance lenses. The Scheimpflug principle is employed to make full use of the limited depth of field. For such a specific system, the general imaging model is introduced to reach a full 3D reconstruction. A dedicated calibration procedure is developed to realize quantitative 3D imaging. Experiments with a prototype demonstrate the accessibility of the proposed configuration, model, and calibration approach.

  14. Complete 3D model reconstruction from multiple views

    NASA Astrophysics Data System (ADS)

    Lin, Huei-Yung; Subbarao, Murali; Park, Soon-Yong

    2002-02-01

    New algorithms are presented for automatically acquiring the complete 3D model of single and multiple objects using rotational stereo. The object is placed on a rotation stage. Stereo images for several viewing directions are taken by rotating the object by known angles. Partial 3D shapes and the corresponding texture maps are obtained using rotational stereo and shape from focus. First, for each view, shape from focus is used to obtain a rough 3D shape and the corresponding focused image. Then, the rough 3D shape and focused images are used in rotational stereo to obtain a more accurate measurement of 3D shape. The rotation axis is calibrated using three fixed points on a planar object and refined during surface integration. The complete 3D model is reconstructed by integrating partial 3D shapes and the corresponding texture maps of the object from multiple views. New algorithms for range image registration, surface integration and texture mapping are presented. Our method can generate 3D models very fast and preserve the texture of objects. A new prototype vision system named Stonybrook VIsion System 2 (SVIS-2) has been built and used in the experiments. In the experiments, 4 viewing directions at 90-degree intervals are used. SVIS-2 can acquire the 3D model of objects within a 250 mm x 250 mm x 250 mm cubic workspace placed about 750 mm from the camera. Both computational algorithms and experimental results on several objects are presented.

  15. An Automated 3d Indoor Topological Navigation Network Modelling

    NASA Astrophysics Data System (ADS)

    Jamali, A.; Rahman, A. A.; Boguslawski, P.; Gold, C. M.

    2015-10-01

    Indoor navigation is important for various applications such as disaster management and safety analysis. In the last decade, indoor environment has been a focus of wide research; that includes developing techniques for acquiring indoor data (e.g. Terrestrial laser scanning), 3D indoor modelling and 3D indoor navigation models. In this paper, an automated 3D topological indoor network generated from inaccurate 3D building models is proposed. In a normal scenario, 3D indoor navigation network derivation needs accurate 3D models with no errors (e.g. gap, intersect) and two cells (e.g. rooms, corridors) should touch each other to build their connections. The presented 3D modeling of indoor navigation network is based on surveying control points and it is less dependent on the 3D geometrical building model. For reducing time and cost of indoor building data acquisition process, Trimble LaserAce 1000 as surveying instrument is used. The modelling results were validated against an accurate geometry of indoor building environment which was acquired using Trimble M3 total station.

  16. Highway 3D model from image and lidar data

    NASA Astrophysics Data System (ADS)

    Chen, Jinfeng; Chu, Henry; Sun, Xiaoduan

    2014-05-01

    We present a new method of highway 3-D model construction developed based on feature extraction in highway images and LIDAR data. We describe the processing road coordinate data that connect the image frames to the coordinates of the elevation data. Image processing methods are used to extract sky, road, and ground regions as well as significant objects (such as signs and building fronts) in the roadside for the 3D model. LIDAR data are interpolated and processed to extract the road lanes as well as other features such as trees, ditches, and elevated objects to form the 3D model. 3D geometry reasoning is used to match the image features to the 3D model. Results from successive frames are integrated to improve the final model.

  17. An Automatic Registration Algorithm for 3D Maxillofacial Model

    NASA Astrophysics Data System (ADS)

    Qiu, Luwen; Zhou, Zhongwei; Guo, Jixiang; Lv, Jiancheng

    2016-09-01

    3D image registration aims at aligning two 3D data sets in a common coordinate system, which has been widely used in computer vision, pattern recognition and computer assisted surgery. One challenging problem in 3D registration is that point-wise correspondences between two point sets are often unknown apriori. In this work, we develop an automatic algorithm for 3D maxillofacial models registration including facial surface model and skull model. Our proposed registration algorithm can achieve a good alignment result between partial and whole maxillofacial model in spite of ambiguous matching, which has a potential application in the oral and maxillofacial reparative and reconstructive surgery. The proposed algorithm includes three steps: (1) 3D-SIFT features extraction and FPFH descriptors construction; (2) feature matching using SAC-IA; (3) coarse rigid alignment and refinement by ICP. Experiments on facial surfaces and mandible skull models demonstrate the efficiency and robustness of our algorithm.

  18. Extending 3D city models with legal information

    NASA Astrophysics Data System (ADS)

    Frank, A. U.; Fuhrmann, T.; Navratil, G.

    2012-10-01

    3D city models represent existing physical objects and their topological and functional relations. In everyday life the rights and responsibilities connected to these objects, primarily legally defined rights and obligations but also other socially and culturally established rights, are of importance. The rights and obligations are defined in various laws and it is often difficult to identify the rules applicable for a certain case. The existing 2D cadastres show civil law rights and obligations and plans to extend them to provide information about public law restrictions for land use are in several countries under way. It is tempting to design extensions to the 3D city models to provide information about legal rights in 3D. The paper analyses the different types of information that are needed to reduce conflicts and to facilitate decisions about land use. We identify the role 3D city models augmented with planning information in 3D can play, but do not advocate a general conversion from 2D to 3D for the legal cadastre. Space is not anisotropic and the up/down dimension is practically very different from the two dimensional plane - this difference must be respected when designing spatial information systems. The conclusions are: (1) continue the current regime for ownership of apartments, which is not ownership of a 3D volume, but co-ownership of a building with exclusive use of some rooms; such exclusive use rights could be shown in a 3D city model; (2) ownership of 3D volumes for complex and unusual building situations can be reported in a 3D city model, but are not required everywhere; (3) indicate restrictions for land use and building in 3D city models, with links to the legal sources.

  19. RELAP5-3D Compressor Model

    SciTech Connect

    James E. Fisher; Cliff B. Davis; Walter L. Weaver

    2005-06-01

    A compressor model has been implemented in the RELAP5-3D© code. The model is similar to that of the existing pump model, and performs the same function on a gas as the pump performs on a single-phase or two-phase fluid. The compressor component consists of an inlet junction and a control volume, and optionally, an outlet junction. This feature permits cascading compressor components in series. The equations describing the physics of the compressor are derived from first principles. These equations are used to obtain the head, the torque, and the energy dissipation. Compressor performance is specified using a map, specific to the design of the machine, in terms of the ratio of outlet-to-inlet total (or stagnation) pressure and adiabatic efficiency as functions of rotational velocity and flow rate. The input quantities are specified in terms of dimensionless variables, which are corrected to stagnation density and stagnation sound speed. A small correction was formulated for the input of efficiency to account for the error introduced by assumption of constant density when integrating the momentum equation. Comparison of the results of steady-state operation of the compressor model to those of the MIT design calculation showed excellent agreement for both pressure ratio and power.

  20. A 3D model of Pluto's atmosphere

    NASA Astrophysics Data System (ADS)

    Vangvichith, M.; Forget, F.; Wordsworth, R.

    2011-10-01

    For the first time, we have built a GCM of Pluto's atmosphere, adapted from the model of Triton's, recently developed[9] . In fact, Pluto and Triton have a lot of similarities (atmospheric, orbital). This GCM will allow to better understand the complex mechanism of the planet and to study the variation of the thermal profile during time.

  1. Venusian Applications of 3D Convection Modeling

    NASA Technical Reports Server (NTRS)

    Bonaccorso, Timary Annie

    2011-01-01

    This study models mantle convection on Venus using the 'cubed sphere' code OEDIPUS, which models one-sixth of the planet in spherical geometry. We are attempting to balance internal heating, bottom mantle viscosity, and temperature difference across Venus' mantle, in order to create a realistic model that matches with current planetary observations. We also have begun to run both lower and upper mantle simulations to determine whether layered (as opposed to whole-mantle) convection might produce more efficient heat transfer, as well as to model coronae formation in the upper mantle. Upper mantle simulations are completed using OEDIPUS' Cartesian counterpart, JOCASTA. This summer's central question has been how to define a mantle plume. Traditionally, we have defined a hot plume the region with temperature at or above 40% of the difference between the maximum and horizontally averaged temperature, and a cold plume as the region with 40% of the difference between the minimum and average temperature. For less viscous cases (1020 Pa?s), the plumes generated by that definition lacked vigor, displaying buoyancies 1/100th of those found in previous, higher viscosity simulations (1021 Pa?s). As the mantle plumes with large buoyancy flux are most likely to produce topographic uplift and volcanism, the low viscosity cases' plumes may not produce observable deformation. In an effort to eliminate the smallest plumes, we experimented with different lower bound parameters and temperature percentages.

  2. Virtual 3d City Modeling: Techniques and Applications

    NASA Astrophysics Data System (ADS)

    Singh, S. P.; Jain, K.; Mandla, V. R.

    2013-08-01

    3D city model is a digital representation of the Earth's surface and it's related objects such as Building, Tree, Vegetation, and some manmade feature belonging to urban area. There are various terms used for 3D city models such as "Cybertown", "Cybercity", "Virtual City", or "Digital City". 3D city models are basically a computerized or digital model of a city contains the graphic representation of buildings and other objects in 2.5 or 3D. Generally three main Geomatics approach are using for Virtual 3-D City models generation, in first approach, researcher are using Conventional techniques such as Vector Map data, DEM, Aerial images, second approach are based on High resolution satellite images with LASER scanning, In third method, many researcher are using Terrestrial images by using Close Range Photogrammetry with DSM & Texture mapping. We start this paper from the introduction of various Geomatics techniques for 3D City modeling. These techniques divided in to two main categories: one is based on Automation (Automatic, Semi-automatic and Manual methods), and another is Based on Data input techniques (one is Photogrammetry, another is Laser Techniques). After details study of this, finally in short, we are trying to give the conclusions of this study. In the last, we are trying to give the conclusions of this research paper and also giving a short view for justification and analysis, and present trend for 3D City modeling. This paper gives an overview about the Techniques related with "Generation of Virtual 3-D City models using Geomatics Techniques" and the Applications of Virtual 3D City models. Photogrammetry, (Close range, Aerial, Satellite), Lasergrammetry, GPS, or combination of these modern Geomatics techniques play a major role to create a virtual 3-D City model. Each and every techniques and method has some advantages and some drawbacks. Point cloud model is a modern trend for virtual 3-D city model. Photo-realistic, Scalable, Geo-referenced virtual 3

  3. Image based 3D city modeling : Comparative study

    NASA Astrophysics Data System (ADS)

    Singh, S. P.; Jain, K.; Mandla, V. R.

    2014-06-01

    3D city model is a digital representation of the Earth's surface and it's related objects such as building, tree, vegetation, and some manmade feature belonging to urban area. The demand of 3D city modeling is increasing rapidly for various engineering and non-engineering applications. Generally four main image based approaches were used for virtual 3D city models generation. In first approach, researchers were used Sketch based modeling, second method is Procedural grammar based modeling, third approach is Close range photogrammetry based modeling and fourth approach is mainly based on Computer Vision techniques. SketchUp, CityEngine, Photomodeler and Agisoft Photoscan are the main softwares to represent these approaches respectively. These softwares have different approaches & methods suitable for image based 3D city modeling. Literature study shows that till date, there is no complete such type of comparative study available to create complete 3D city model by using images. This paper gives a comparative assessment of these four image based 3D modeling approaches. This comparative study is mainly based on data acquisition methods, data processing techniques and output 3D model products. For this research work, study area is the campus of civil engineering department, Indian Institute of Technology, Roorkee (India). This 3D campus acts as a prototype for city. This study also explains various governing parameters, factors and work experiences. This research work also gives a brief introduction, strengths and weakness of these four image based techniques. Some personal comment is also given as what can do or what can't do from these softwares. At the last, this study shows; it concluded that, each and every software has some advantages and limitations. Choice of software depends on user requirements of 3D project. For normal visualization project, SketchUp software is a good option. For 3D documentation record, Photomodeler gives good result. For Large city

  4. NoSQL Based 3D City Model Management System

    NASA Astrophysics Data System (ADS)

    Mao, B.; Harrie, L.; Cao, J.; Wu, Z.; Shen, J.

    2014-04-01

    To manage increasingly complicated 3D city models, a framework based on NoSQL database is proposed in this paper. The framework supports import and export of 3D city model according to international standards such as CityGML, KML/COLLADA and X3D. We also suggest and implement 3D model analysis and visualization in the framework. For city model analysis, 3D geometry data and semantic information (such as name, height, area, price and so on) are stored and processed separately. We use a Map-Reduce method to deal with the 3D geometry data since it is more complex, while the semantic analysis is mainly based on database query operation. For visualization, a multiple 3D city representation structure CityTree is implemented within the framework to support dynamic LODs based on user viewpoint. Also, the proposed framework is easily extensible and supports geoindexes to speed up the querying. Our experimental results show that the proposed 3D city management system can efficiently fulfil the analysis and visualization requirements.

  5. Modelling Polymer Deformation during 3D Printing

    NASA Astrophysics Data System (ADS)

    McIlroy, Claire; Olmsted, Peter

    Three-dimensional printing has the potential to transform manufacturing processes, yet improving the strength of printed parts, to equal that of traditionally-manufactured parts, remains an underlying issue. The fused deposition modelling technique involves melting a thermoplastic, followed by layer-by-layer extrusion to fabricate an object. The key to ensuring strength at the weld between layers is successful inter-diffusion. However, prior to welding, both the extrusion process and the cooling temperature profile can significantly deform the polymer micro-structure and, consequently, how well the polymers are able to ``re-entangle'' across the weld. In particular, polymer alignment in the flow can cause de-bonding of the layers and create defects. We have developed a simple model of the non-isothermal extrusion process to explore the effects that typical printing conditions and material rheology have on the conformation of a polymer melt. In particular, we incorporate both stretch and orientation using the Rolie-Poly constitutive equation to examine the melt structure as it flows through the nozzle, the subsequent alignment with the build plate and the resulting deformation due to the fixed nozzle height, which is typically less than the nozzle radius.

  6. Modeling 3D facial shape from DNA.

    PubMed

    Claes, Peter; Liberton, Denise K; Daniels, Katleen; Rosana, Kerri Matthes; Quillen, Ellen E; Pearson, Laurel N; McEvoy, Brian; Bauchet, Marc; Zaidi, Arslan A; Yao, Wei; Tang, Hua; Barsh, Gregory S; Absher, Devin M; Puts, David A; Rocha, Jorge; Beleza, Sandra; Pereira, Rinaldo W; Baynam, Gareth; Suetens, Paul; Vandermeulen, Dirk; Wagner, Jennifer K; Boster, James S; Shriver, Mark D

    2014-03-01

    Human facial diversity is substantial, complex, and largely scientifically unexplained. We used spatially dense quasi-landmarks to measure face shape in population samples with mixed West African and European ancestry from three locations (United States, Brazil, and Cape Verde). Using bootstrapped response-based imputation modeling (BRIM), we uncover the relationships between facial variation and the effects of sex, genomic ancestry, and a subset of craniofacial candidate genes. The facial effects of these variables are summarized as response-based imputed predictor (RIP) variables, which are validated using self-reported sex, genomic ancestry, and observer-based facial ratings (femininity and proportional ancestry) and judgments (sex and population group). By jointly modeling sex, genomic ancestry, and genotype, the independent effects of particular alleles on facial features can be uncovered. Results on a set of 20 genes showing significant effects on facial features provide support for this approach as a novel means to identify genes affecting normal-range facial features and for approximating the appearance of a face from genetic markers. PMID:24651127

  7. Modeling 3D Facial Shape from DNA

    PubMed Central

    Claes, Peter; Liberton, Denise K.; Daniels, Katleen; Rosana, Kerri Matthes; Quillen, Ellen E.; Pearson, Laurel N.; McEvoy, Brian; Bauchet, Marc; Zaidi, Arslan A.; Yao, Wei; Tang, Hua; Barsh, Gregory S.; Absher, Devin M.; Puts, David A.; Rocha, Jorge; Beleza, Sandra; Pereira, Rinaldo W.; Baynam, Gareth; Suetens, Paul; Vandermeulen, Dirk; Wagner, Jennifer K.; Boster, James S.; Shriver, Mark D.

    2014-01-01

    Human facial diversity is substantial, complex, and largely scientifically unexplained. We used spatially dense quasi-landmarks to measure face shape in population samples with mixed West African and European ancestry from three locations (United States, Brazil, and Cape Verde). Using bootstrapped response-based imputation modeling (BRIM), we uncover the relationships between facial variation and the effects of sex, genomic ancestry, and a subset of craniofacial candidate genes. The facial effects of these variables are summarized as response-based imputed predictor (RIP) variables, which are validated using self-reported sex, genomic ancestry, and observer-based facial ratings (femininity and proportional ancestry) and judgments (sex and population group). By jointly modeling sex, genomic ancestry, and genotype, the independent effects of particular alleles on facial features can be uncovered. Results on a set of 20 genes showing significant effects on facial features provide support for this approach as a novel means to identify genes affecting normal-range facial features and for approximating the appearance of a face from genetic markers. PMID:24651127

  8. 3D PIC Modeling of Microcavity Discharge

    NASA Astrophysics Data System (ADS)

    Hopkins, Matthew; Manginell, Ronald; Moore, Christopher; Yee, Benjamin; Moorman, Matthew

    2015-09-01

    We present a number of techniques and challenges in simulating the transient behavior of a microcavity discharge. Our microcavities are typically cylindrical with diameters approximately 50 - 100 μm, heights of 50 - 200 μm, pressure near atmospheric, and operate at a few hundred volts. We employ a fully kinetic simulation methodology, the Particle-in-Cell (PIC) method, with interparticle collisions handled via methods based on direct simulation Monte Carlo (DSMC). In particular, we explicitly include kinetic electrons. Some of the challenges we encounter include variations in number densities, external circuit coupling, and time step resolution constraints. By employing dynamic particle weighting (particle weights vary over time by species and location) we can mitigate some of the challenges modeling systems with 107 variations in number densities. Smoothing mechanisms have been used to attempt to mitigate external circuit response. We perform our simulations on hundreds or thousands of processing cores to accommodate the computational work inherent in using relatively small time step sizes (e.g., 50 fs for a 100 ns calculation). In addition, particle weighting issues inherent to three-dimensional low temperature plasma systems will be mentioned. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's NNSA under Contract DE-AC04-94AL85000.

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

    PubMed

    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

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

    PubMed

    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.

  11. Toward 3D-guided prostate biopsy target optimization: an estimation of tumor sampling probabilities

    NASA Astrophysics Data System (ADS)

    Martin, Peter R.; Cool, Derek W.; Romagnoli, Cesare; Fenster, Aaron; Ward, Aaron D.

    2014-03-01

    Magnetic resonance imaging (MRI)-targeted, 3D transrectal ultrasound (TRUS)-guided "fusion" prostate biopsy aims to reduce the ~23% false negative rate of clinical 2D TRUS-guided sextant biopsy. Although it has been reported to double the positive yield, MRI-targeted biopsy still yields false negatives. Therefore, we propose optimization of biopsy targeting to meet the clinician's desired tumor sampling probability, optimizing needle targets within each tumor and accounting for uncertainties due to guidance system errors, image registration errors, and irregular tumor shapes. We obtained multiparametric MRI and 3D TRUS images from 49 patients. A radiologist and radiology resident contoured 81 suspicious regions, yielding 3D surfaces that were registered to 3D TRUS. We estimated the probability, P, of obtaining a tumor sample with a single biopsy. Given an RMS needle delivery error of 3.5 mm for a contemporary fusion biopsy system, P >= 95% for 21 out of 81 tumors when the point of optimal sampling probability was targeted. Therefore, more than one biopsy core must be taken from 74% of the tumors to achieve P >= 95% for a biopsy system with an error of 3.5 mm. Our experiments indicated that the effect of error along the needle axis on the percentage of core involvement (and thus the measured tumor burden) was mitigated by the 18 mm core length.

  12. 3D deformable organ model based liver motion tracking in ultrasound videos

    NASA Astrophysics Data System (ADS)

    Kim, Jung-Bae; Hwang, Youngkyoo; Oh, Young-Taek; Bang, Won-Chul; Lee, Heesae; Kim, James D. K.; Kim, Chang Yeong

    2013-03-01

    This paper presents a novel method of using 2D ultrasound (US) cine images during image-guided therapy to accurately track the 3D position of a tumor even when the organ of interest is in motion due to patient respiration. Tracking is possible thanks to a 3D deformable organ model we have developed. The method consists of three processes in succession. The first process is organ modeling where we generate a personalized 3D organ model from high quality 3D CT or MR data sets captured during three different respiratory phases. The model includes the organ surface, vessel and tumor, which can all deform and move in accord with patient respiration. The second process is registration of the organ model to 3D US images. From 133 respiratory phase candidates generated from the deformable organ model, we resolve the candidate that best matches the 3D US images according to vessel centerline and surface. As a result, we can determine the position of the US probe. The final process is real-time tracking using 2D US cine images captured by the US probe. We determine the respiratory phase by tracking the diaphragm on the image. The 3D model is then deformed according to respiration phase and is fitted to the image by considering the positions of the vessels. The tumor's 3D positions are then inferred based on respiration phase. Testing our method on real patient data, we have found the accuracy of 3D position is within 3.79mm and processing time is 5.4ms during tracking.

  13. Multimodality 3D Tumor Segmentation in HCC patients treated with TACE

    PubMed Central

    Wang, Zhijun; Chapiro, Julius; Schernthaner, Rüdiger; Duran, Rafael; Chen, Rongxin; Geschwind, Jean-François; Lin, MingDe

    2015-01-01

    Rationale and Objectives To validate the concordance of a semi-automated multimodality lesion segmentation technique between contrast-enhanced MRI (CE-MRI), cone-beam CT (CBCT) and multi-detector CT (MDCT) in patients with hepatocellular carcinoma (HCC) treated with transarterial chemoembolization (TACE). Materials and methods This retrospective analysis included 45 patients with unresectable HCC that underwent baseline CE-MRI within one month before the treatment, intraprocedural CBCT during conventional TACE and MDCT within 24 hours post TACE. Fourteen patients were excluded due to atypical lesion morphology, portal vein invasion or small lesion size which precluded sufficient lesion visualization. 31 patients with a total of 40 target lesions were included into the analysis. A tumor segmentation software, based on non-Euclidean geometry and theory of radial basis functions, was used to allow for the segmentation of target lesions in 3D on all three modalities. The algorithm created image-based masks located in a 3D region whose center and size was defined by the user, yielding the nomenclature “semi-automatic”. Based on that, tumor volumes on all three modalities were calculated and compared using a linear regression model (R2 values). Residual plots were used to analyze drift and variance of the values. Results The mean value of tumor volumes was 18.72±19.13cm3 (range, 0.41-59.16cm3) on CE-MRI, 21.26±21.99 cm3 (range, 0.62-86.82 cm3) on CBCT and 19.88±20.88 cm3 (range, 0.45-75.24 cm3) on MDCT. The average volumes of the tumor were not significantly different between CE-MR and DP-CBCT, DP-CBCT and MDCT, MDCT and CE-MR (p=0.577, 0.770 and 0.794 respectively). A strong correlation between volumes on CE-MRI and CBCT, CBCT and MDCT, MDCT and CE-MRI was observed (R2=0.974, 0.992 and 0.983, respectively). When plotting the residuals, no drift was observed for all methods showing deviations of no more than 10% of absolute volumes (in cm3). Conclusion A semi

  14. 3D-model building of the jaw impression

    NASA Astrophysics Data System (ADS)

    Ahmed, Moumen T.; Yamany, Sameh M.; Hemayed, Elsayed E.; Farag, Aly A.

    1997-03-01

    A novel approach is proposed to obtain a record of the patient's occlusion using computer vision. Data acquisition is obtained using intra-oral video cameras. The technique utilizes shape from shading to extract 3D information from 2D views of the jaw, and a novel technique for 3D data registration using genetic algorithms. The resulting 3D model can be used for diagnosis, treatment planning, and implant purposes. The overall purpose of this research is to develop a model-based vision system for orthodontics to replace traditional approaches. This system will be flexible, accurate, and will reduce the cost of orthodontic treatments.

  15. 3D model-based still image object categorization

    NASA Astrophysics Data System (ADS)

    Petre, Raluca-Diana; Zaharia, Titus

    2011-09-01

    This paper proposes a novel recognition scheme algorithm for semantic labeling of 2D object present in still images. The principle consists of matching unknown 2D objects with categorized 3D models in order to infer the semantics of the 3D object to the image. We tested our new recognition framework by using the MPEG-7 and Princeton 3D model databases in order to label unknown images randomly selected from the web. Results obtained show promising performances, with recognition rate up to 84%, which opens interesting perspectives in terms of semantic metadata extraction from still images/videos.

  16. Summary on Several Key Techniques in 3D Geological Modeling

    PubMed Central

    2014-01-01

    Several key techniques in 3D geological modeling including planar mesh generation, spatial interpolation, and surface intersection are summarized in this paper. Note that these techniques are generic and widely used in various applications but play a key role in 3D geological modeling. There are two essential procedures in 3D geological modeling: the first is the simulation of geological interfaces using geometric surfaces and the second is the building of geological objects by means of various geometric computations such as the intersection of surfaces. Discrete geometric surfaces that represent geological interfaces can be generated by creating planar meshes first and then spatially interpolating; those surfaces intersect and then form volumes that represent three-dimensional geological objects such as rock bodies. In this paper, the most commonly used algorithms of the key techniques in 3D geological modeling are summarized. PMID:24772029

  17. Quantification of the accuracy of MRI generated 3D models of long bones compared to CT generated 3D models.

    PubMed

    Rathnayaka, Kanchana; Momot, Konstantin I; Noser, Hansrudi; Volp, Andrew; Schuetz, Michael A; Sahama, Tony; Schmutz, Beat

    2012-04-01

    Orthopaedic fracture fixation implants are increasingly being designed using accurate 3D models of long bones based on computer tomography (CT). Unlike CT, magnetic resonance imaging (MRI) does not involve ionising radiation and is therefore a desirable alternative to CT. This study aims to quantify the accuracy of MRI-based 3D models compared to CT-based 3D models of long bones. The femora of five intact cadaver ovine limbs were scanned using a 1.5 T MRI and a CT scanner. Image segmentation of CT and MRI data was performed using a multi-threshold segmentation method. Reference models were generated by digitising the bone surfaces free of soft tissue with a mechanical contact scanner. The MRI- and CT-derived models were validated against the reference models. The results demonstrated that the CT-based models contained an average error of 0.15 mm while the MRI-based models contained an average error of 0.23 mm. Statistical validation shows that there are no significant differences between 3D models based on CT and MRI data. These results indicate that the geometric accuracy of MRI based 3D models was comparable to that of CT-based models and therefore MRI is a potential alternative to CT for generation of 3D models with high geometric accuracy.

  18. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  19. Performance Evaluation of 3d Modeling Software for Uav Photogrammetry

    NASA Astrophysics Data System (ADS)

    Yanagi, H.; Chikatsu, H.

    2016-06-01

    UAV (Unmanned Aerial Vehicle) photogrammetry, which combines UAV and freely available internet-based 3D modeling software, is widely used as a low-cost and user-friendly photogrammetry technique in the fields such as remote sensing and geosciences. In UAV photogrammetry, only the platform used in conventional aerial photogrammetry is changed. Consequently, 3D modeling software contributes significantly to its expansion. However, the algorithms of the 3D modelling software are black box algorithms. As a result, only a few studies have been able to evaluate their accuracy using 3D coordinate check points. With this motive, Smart3DCapture and Pix4Dmapper were downloaded from the Internet and commercial software PhotoScan was also employed; investigations were performed in this paper using check points and images obtained from UAV.

  20. 3D Multi-Cell Simulation of Tumor Growth and Angiogenesis

    PubMed Central

    Shirinifard, Abbas; Gens, J. Scott; Zaitlen, Benjamin L.; Popławski, Nikodem J.; Swat, Maciej; Glazier, James A.

    2009-01-01

    We present a 3D multi-cell simulation of a generic simplification of vascular tumor growth which can be easily extended and adapted to describe more specific vascular tumor types and host tissues. Initially, tumor cells proliferate as they take up the oxygen which the pre-existing vasculature supplies. The tumor grows exponentially. When the oxygen level drops below a threshold, the tumor cells become hypoxic and start secreting pro-angiogenic factors. At this stage, the tumor reaches a maximum diameter characteristic of an avascular tumor spheroid. The endothelial cells in the pre-existing vasculature respond to the pro-angiogenic factors both by chemotaxing towards higher concentrations of pro-angiogenic factors and by forming new blood vessels via angiogenesis. The tumor-induced vasculature increases the growth rate of the resulting vascularized solid tumor compared to an avascular tumor, allowing the tumor to grow beyond the spheroid in these linear-growth phases. First, in the linear-spherical phase of growth, the tumor remains spherical while its volume increases. Second, in the linear-cylindrical phase of growth the tumor elongates into a cylinder. Finally, in the linear-sheet phase of growth, tumor growth accelerates as the tumor changes from cylindrical to paddle-shaped. Substantial periods during which the tumor grows slowly or not at all separate the exponential from the linear-spherical and the linear-spherical from the linear-cylindrical growth phases. In contrast to other simulations in which avascular tumors remain spherical, our simulated avascular tumors form cylinders following the blood vessels, leading to a different distribution of hypoxic cells within the tumor. Our simulations cover time periods which are long enough to produce a range of biologically reasonable complex morphologies, allowing us to study how tumor-induced angiogenesis affects the growth rate, size and morphology of simulated tumors. PMID:19834621

  1. Automatic Texture Mapping of Architectural and Archaeological 3d Models

    NASA Astrophysics Data System (ADS)

    Kersten, T. P.; Stallmann, D.

    2012-07-01

    Today, detailed, complete and exact 3D models with photo-realistic textures are increasingly demanded for numerous applications in architecture and archaeology. Manual texture mapping of 3D models by digital photographs with software packages, such as Maxon Cinema 4D, Autodesk 3Ds Max or Maya, still requires a complex and time-consuming workflow. So, procedures for automatic texture mapping of 3D models are in demand. In this paper two automatic procedures are presented. The first procedure generates 3D surface models with textures by web services, while the second procedure textures already existing 3D models with the software tmapper. The program tmapper is based on the Multi Layer 3D image (ML3DImage) algorithm and developed in the programming language C++. The studies showing that the visibility analysis using the ML3DImage algorithm is not sufficient to obtain acceptable results of automatic texture mapping. To overcome the visibility problem the Point Cloud Painter algorithm in combination with the Z-buffer-procedure will be applied in the future.

  2. Gis-Based Smart Cartography Using 3d Modeling

    NASA Astrophysics Data System (ADS)

    Malinverni, E. S.; Tassetti, A. N.

    2013-08-01

    3D City Models have evolved to be important tools for urban decision processes and information systems, especially in planning, simulation, analysis, documentation and heritage management. On the other hand existing and in use numerical cartography is often not suitable to be used in GIS because not geometrically and topologically correctly structured. The research aim is to 3D structure and organize a numeric cartography for GIS and turn it into CityGML standardized features. The work is framed around a first phase of methodological analysis aimed to underline which existing standard (like ISO and OGC rules) can be used to improve the quality requirement of a cartographic structure. Subsequently, from this technical specifics, it has been investigated the translation in formal contents, using an owner interchange software (SketchUp), to support some guide lines implementations to generate a GIS3D structured in GML3. It has been therefore predisposed a test three-dimensional numerical cartography (scale 1:500, generated from range data captured by 3D laser scanner), tested on its quality according to the previous standard and edited when and where necessary. Cad files and shapefiles are converted into a final 3D model (Google SketchUp model) and then exported into a 3D city model (CityGML LoD1/LoD2). The GIS3D structure has been managed in a GIS environment to run further spatial analysis and energy performance estimate, not achievable in a 2D environment. In particular geometrical building parameters (footprint, volume etc.) are computed and building envelop thermal characteristics are derived from. Lastly, a simulation is carried out to deal with asbestos and home renovating charges and show how the built 3D city model can support municipal managers with risk diagnosis of the present situation and development of strategies for a sustainable redevelop.

  3. Implementation of virtual models from sheet metal forming simulation into physical 3D colour models using 3D printing

    NASA Astrophysics Data System (ADS)

    Junk, S.

    2016-08-01

    Today the methods of numerical simulation of sheet metal forming offer a great diversity of possibilities for optimization in product development and in process design. However, the results from simulation are only available as virtual models. Because there are any forming tools available during the early stages of product development, physical models that could serve to represent the virtual results are therefore lacking. Physical 3D-models can be created using 3D-printing and serve as an illustration and present a better understanding of the simulation results. In this way, the results from the simulation can be made more “comprehensible” within a development team. This paper presents the possibilities of 3D-colour printing with particular consideration of the requirements regarding the implementation of sheet metal forming simulation. Using concrete examples of sheet metal forming, the manufacturing of 3D colour models will be expounded upon on the basis of simulation results.

  4. Optimization of liquid overlay technique to formulate heterogenic 3D co-cultures models.

    PubMed

    Costa, Elisabete C; Gaspar, Vítor M; Coutinho, Paula; Correia, Ilídio J

    2014-08-01

    Three-dimensional (3D) cell culture models of solid tumors are currently having a tremendous impact in the in vitro screening of candidate anti-tumoral therapies. These 3D models provide more reliable results than those provided by standard 2D in vitro cell cultures. However, 3D manufacturing techniques need to be further optimized in order to increase the robustness of these models and provide data that can be properly correlated with the in vivo situation. Therefore, in the present study the parameters used for producing multicellular tumor spheroids (MCTS) by liquid overlay technique (LOT) were optimized in order to produce heterogeneous cellular agglomerates comprised of cancer cells and stromal cells, during long periods. Spheroids were produced under highly controlled conditions, namely: (i) agarose coatings; (ii) horizontal stirring, and (iii) a known initial cell number. The simultaneous optimization of these parameters promoted the assembly of 3D characteristic cellular organization similar to that found in the in vivo solid tumors. Such improvements in the LOT technique promoted the assembly of highly reproducible, individual 3D spheroids, with a low cost of production and that can be used for future in vitro drug screening assays.

  5. Geometric uncertainty of 2D projection imaging in monitoring 3D tumor motion

    NASA Astrophysics Data System (ADS)

    Suh, Yelin; Dieterich, Sonja; Keall, Paul J.

    2007-07-01

    The purpose of this study was to investigate the accuracy of two-dimensional (2D) projection imaging methods in three-dimensional (3D) tumor motion monitoring. Many commercial linear accelerator types have projection imaging capabilities, and tumor motion monitoring is useful for motion inclusive, respiratory gated or tumor tracking strategies. Since 2D projection imaging is limited in its ability to resolve the motion along the imaging beam axis, there is unresolved motion when monitoring 3D tumor motion. From the 3D tumor motion data of 160 treatment fractions for 46 thoracic and abdominal cancer patients, the unresolved motion due to the geometric limitation of 2D projection imaging was calculated as displacement in the imaging beam axis for different beam angles and time intervals. The geometric uncertainty to monitor 3D motion caused by the unresolved motion of 2D imaging was quantified using the root-mean-square (rms) metric. Geometric uncertainty showed interfractional and intrafractional variation. Patient-to-patient variation was much more significant than variation for different time intervals. For the patient cohort studied, as the time intervals increase, the rms, minimum and maximum values of the rms uncertainty show decreasing tendencies for the lung patients but increasing for the liver and retroperitoneal patients, which could be attributed to patient relaxation. Geometric uncertainty was smaller for coplanar treatments than non-coplanar treatments, as superior-inferior (SI) tumor motion, the predominant motion from patient respiration, could be always resolved for coplanar treatments. Overall rms of the rms uncertainty was 0.13 cm for all treatment fractions and 0.18 cm for the treatment fractions whose average breathing peak-trough ranges were more than 0.5 cm. The geometric uncertainty for 2D imaging varies depending on the tumor site, tumor motion range, time interval and beam angle as well as between patients, between fractions and within a

  6. Multivariate 3D modelling of Scottish soil properties

    NASA Astrophysics Data System (ADS)

    Poggio, Laura; Gimona, Alessandro

    2015-04-01

    Information regarding soil properties across landscapes at national or continental scales is critical for better soil and environmental management and for climate regulation and adaptation policy. The prediction of soil properties variation in space and time and their uncertainty is an important part of environmental modelling. Soil properties, and in particular the 3 fractions of soil texture, exhibit strong co-variation among themselves and therefore taking into account this correlation leads to spatially more accurate results. In this study the continuous vertical and lateral distributions of relevant soil properties in Scottish soils were modelled with a multivariate 3D-GAM+GS approach. The approach used involves 1) modelling the multivariate trend with full 3D spatial correlation, i.e., exploiting the values of the neighbouring pixels in 3D-space, and 2) 3D kriging to interpolate the residuals. The values at each cell for each of the considered depth layers were defined using a hybrid GAM-geostatistical 3D model, combining the fitting of a GAM (generalised Additive Models) to estimate multivariate trend of the variables, using a 3D smoother with related covariates. Gaussian simulations of the model residuals were used as spatial component to account for local details. A dataset of about 26,000 horizons (7,800 profiles) was used for this study. A validation set was randomly selected as 25% of the full dataset. Numerous covariates derived from globally available data, such as MODIS and SRTM, are considered. The results of the 3D-GAM+kriging showed low RMSE values, good R squared and an accurate reproduction of the spatial structure of the data for a range of soil properties. The results have an out-of-sample RMSE between 10 to 15% of the observed range when taking into account the whole profile. The approach followed allows the assessment of the uncertainty of both the trend and the residuals.

  7. Shape: A 3D Modeling Tool for Astrophysics.

    PubMed

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

    2011-04-01

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

  8. A spherical harmonics intensity model for 3D segmentation and 3D shape analysis of heterochromatin foci.

    PubMed

    Eck, Simon; Wörz, Stefan; Müller-Ott, Katharina; Hahn, Matthias; Biesdorf, Andreas; Schotta, Gunnar; Rippe, Karsten; Rohr, Karl

    2016-08-01

    The genome is partitioned into regions of euchromatin and heterochromatin. The organization of heterochromatin is important for the regulation of cellular processes such as chromosome segregation and gene silencing, and their misregulation is linked to cancer and other diseases. We present a model-based approach for automatic 3D segmentation and 3D shape analysis of heterochromatin foci from 3D confocal light microscopy images. Our approach employs a novel 3D intensity model based on spherical harmonics, which analytically describes the shape and intensities of the foci. The model parameters are determined by fitting the model to the image intensities using least-squares minimization. To characterize the 3D shape of the foci, we exploit the computed spherical harmonics coefficients and determine a shape descriptor. We applied our approach to 3D synthetic image data as well as real 3D static and real 3D time-lapse microscopy images, and compared the performance with that of previous approaches. It turned out that our approach yields accurate 3D segmentation results and performs better than previous approaches. We also show that our approach can be used for quantifying 3D shape differences of heterochromatin foci.

  9. Modeling 3-D Effects in the DIII-D Boundary

    NASA Astrophysics Data System (ADS)

    Evans, T. E.; Moyer, R. A.; Reiter, D.; Kasilov, S. V.; Runov, A. M.

    2002-11-01

    Resonant magnetic perturbations δ br from the DIII-D locked and resistive wall mode control coils (C-coil and I-coil, respectively) affect ne and Te profiles in both the pedestal and core. To understand why these δ br perturbations change the plasma profiles we first model the edge magnetic topology with a field line integration code, TRIP3D code. In general, the TRIP3D results indicate that the control coils create stochastic layers with as much as 25% edge magnetic flux connected to the divertors and walls. While heat and particle transport modeling in open stochastic layers is inherently very difficult, Monte Carlo methods appear to provide the most reasonable approach with which to address these issues. As such, we have assessed the possibility of coupling a recently developed Monte Carlo heat transport code, the E3D code, [A.M. Runov et al., Phys. Plasmas 8, 916 (2001)] to TRIP3D. We will discuss how this coupling can best be accomplished and what must be done to benchmark the TRIP3D/E3D ensemble using DIII-D experimental data. We will also discuss the analysis of proposed designs for a dedicated DIII-D stochastic boundary layer coil which produce minimal δ br core perturbations.

  10. Assessment of different 3D culture systems to study tumor phenotype and chemosensitivity in pancreatic ductal adenocarcinoma.

    PubMed

    Zeeberg, Katrine; Cardone, Rosa Angela; Greco, Maria Raffaella; Saccomano, Mara; Nøhr-Nielsen, Asbjørn; Alves, Frauke; Pedersen, Stine Falsig; Reshkin, Stephan Joel

    2016-07-01

    Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant disease with a very poor prognosis, due to the influence of the tumor stroma, which promotes tumor growth, early invasion and chemoradiation resistance. Efforts to develop models for identifying novel anticancer therapeutic compounds have been hampered by the limited ability of in vitro models to mimic these in vivo tumor-stroma interactions. This has led to the development of various three-dimensional (3D) culture platforms recapitulating the in vivo tumor-stroma crosstalk and designed to better understand basic cancer processes and screen drug action. However, a consensus for different experimental 3D platforms is still missing in PDAC. We compared four PDAC cell lines of different malignancy grown in 2D monolayers to three of the more commonly used 3D techniques (ultralow adhesion concave microwells, Matrigel inclusion and organotypic systems) and to tumors derived from their orthotopic implantation in mice. In these 3D platforms, we observed that cells grow with very different tumor morphologies and the organotypic setting most closely resembles the tumor cytoarchitecture obtained by orthotopically implanting the four cell lines in mice. We then analyzed the molecular and cellular responses of one of these cell lines to epidermal growth factor receptor (EGFR) stimulation with EGF and inhibition with erlotinib and found that only in the 3D platforms, and especially the organotypic, cells: i) responded to EGF by changing the expression of signalling components underlying cell-stroma crosstalk and tissue architecture, growth, invasion and drug resistance (E-cadherin, EGFR, ezrin, β1 integrin, NHERF1 and HIF-1α) similar to those reported in vivo; ii) had stimulated growth and increased erlotinib sensitivity in response to EGF, more faithfully mimicking their known in vivo behaviour. Altogether, these results, indicate the organotypic as the most relevant physiological 3D system to study the

  11. A Bayesian approach to real-time 3D tumor localization via monoscopic x-ray imaging during treatment delivery

    SciTech Connect

    Li, Ruijiang; Fahimian, Benjamin P.; Xing, Lei

    2011-07-15

    Purpose: Monoscopic x-ray imaging with on-board kV devices is an attractive approach for real-time image guidance in modern radiation therapy such as VMAT or IMRT, but it falls short in providing reliable information along the direction of imaging x-ray. By effectively taking consideration of projection data at prior times and/or angles through a Bayesian formalism, the authors develop an algorithm for real-time and full 3D tumor localization with a single x-ray imager during treatment delivery. Methods: First, a prior probability density function is constructed using the 2D tumor locations on the projection images acquired during patient setup. Whenever an x-ray image is acquired during the treatment delivery, the corresponding 2D tumor location on the imager is used to update the likelihood function. The unresolved third dimension is obtained by maximizing the posterior probability distribution. The algorithm can also be used in a retrospective fashion when all the projection images during the treatment delivery are used for 3D localization purposes. The algorithm does not involve complex optimization of any model parameter and therefore can be used in a ''plug-and-play'' fashion. The authors validated the algorithm using (1) simulated 3D linear and elliptic motion and (2) 3D tumor motion trajectories of a lung and a pancreas patient reproduced by a physical phantom. Continuous kV images were acquired over a full gantry rotation with the Varian TrueBeam on-board imaging system. Three scenarios were considered: fluoroscopic setup, cone beam CT setup, and retrospective analysis. Results: For the simulation study, the RMS 3D localization error is 1.2 and 2.4 mm for the linear and elliptic motions, respectively. For the phantom experiments, the 3D localization error is < 1 mm on average and < 1.5 mm at 95th percentile in the lung and pancreas cases for all three scenarios. The difference in 3D localization error for different scenarios is small and is not

  12. 3D Slicer as a Tool for Interactive Brain Tumor Segmentation

    PubMed Central

    Kikinis, Ron; Pieper, Steve

    2014-01-01

    User interaction is required for reliable segmentation of brain tumors in clinical practice and in clinical research. By incorporating current research tools, 3D Slicer provides a set of easy to use interactive tools that can be efficiently used for this purpose. PMID:22255945

  13. Improving 3d Spatial Queries Search: Newfangled Technique of Space Filling Curves in 3d City Modeling

    NASA Astrophysics Data System (ADS)

    Uznir, U.; Anton, F.; Suhaibah, A.; Rahman, A. A.; Mioc, D.

    2013-09-01

    The advantages of three dimensional (3D) city models can be seen in various applications including photogrammetry, urban and regional planning, computer games, etc.. They expand the visualization and analysis capabilities of Geographic Information Systems on cities, and they can be developed using web standards. However, these 3D city models consume much more storage compared to two dimensional (2D) spatial data. They involve extra geometrical and topological information together with semantic data. Without a proper spatial data clustering method and its corresponding spatial data access method, retrieving portions of and especially searching these 3D city models, will not be done optimally. Even though current developments are based on an open data model allotted by the Open Geospatial Consortium (OGC) called CityGML, its XML-based structure makes it challenging to cluster the 3D urban objects. In this research, we propose an opponent data constellation technique of space-filling curves (3D Hilbert curves) for 3D city model data representation. Unlike previous methods, that try to project 3D or n-dimensional data down to 2D or 3D using Principal Component Analysis (PCA) or Hilbert mappings, in this research, we extend the Hilbert space-filling curve to one higher dimension for 3D city model data implementations. The query performance was tested using a CityGML dataset of 1,000 building blocks and the results are presented in this paper. The advantages of implementing space-filling curves in 3D city modeling will improve data retrieval time by means of optimized 3D adjacency, nearest neighbor information and 3D indexing. The Hilbert mapping, which maps a subinterval of the [0, 1] interval to the corresponding portion of the d-dimensional Hilbert's curve, preserves the Lebesgue measure and is Lipschitz continuous. Depending on the applications, several alternatives are possible in order to cluster spatial data together in the third dimension compared to its

  14. Aortic valve and ascending aortic root modeling from 3D and 3D+t CT

    NASA Astrophysics Data System (ADS)

    Grbic, Saša; Ionasec, Razvan I.; Zäuner, Dominik; Zheng, Yefeng; Georgescu, Bogdan; Comaniciu, Dorin

    2010-02-01

    Aortic valve disorders are the most frequent form of valvular heart disorders (VHD) affecting nearly 3% of the global population. A large fraction among them are aortic root diseases, such as aortic root aneurysm, often requiring surgical procedures (valve-sparing) as a treatment. Visual non-invasive assessment techniques could assist during pre-selection of adequate patients, planning procedures and afterward evaluation of the same. However state of the art approaches try to model a rather short part of the aortic root, insufficient to assist the physician during intervention planning. In this paper we propose a novel approach for morphological and functional quantification of both the aortic valve and the ascending aortic root. A novel physiological shape model is introduced, consisting of the aortic valve root, leaflets and the ascending aortic root. The model parameters are hierarchically estimated using robust and fast learning-based methods. Experiments performed on 63 CT sequences (630 Volumes) and 20 single phase CT volumes demonstrated an accuracy of 1.45mm and an performance of 30 seconds (3D+t) for this approach. To the best of our knowledge this is the first time a complete model of the aortic valve (including leaflets) and the ascending aortic root, estimated from CT, has been proposed.

  15. STELLOPT Modeling of the 3D Diagnostic Response in ITER

    SciTech Connect

    Lazerson, Samuel A

    2013-05-07

    The ITER three dimensional diagnostic response to an n=3 resonant magnetic perturbation is modeled using the STELLOPT code. The in-vessel coils apply a resonant magnetic perturbation (RMP) fi eld which generates a 4 cm edge displacement from axisymmetry as modeled by the VMEC 3D equilibrium code. Forward modeling of flux loop and magnetic probe response with the DIAGNO code indicates up to 20 % changes in measured plasma signals. Simulated LIDAR measurements of electron temperature indicate 2 cm shifts on the low field side of the plasma. This suggests that the ITER diagnostic will be able to diagnose the 3D structure of the equilibria.

  16. Detecting Distance between Injected Microspheres and Target Tumor via 3D Reconstruction of Tissue Sections

    SciTech Connect

    Carson, James P.; Kuprat, Andrew P.; Colby, Sean M.; Davis, Cassi A.; Basciano, Christopher; Greene, Kevin; Feo, John T.; Kennedy, Andrew

    2012-08-28

    One treatment increasing in use for solid tumors in the liver is radioembolization via the delivery of 90Y microspheres to the vascular bed within or near the location of the tumor. It is desirable as part of the treatment for the microspheres to embed preferentially in or near the tumor. This work details an approach for analyzing the deposition of microspheres with respect to the location of the tumor. The approach used is based upon thin-slice serial sectioning of the tissue sample, followed by high resolution imaging, microsphere detection, and 3-D reconstruction of the tumor surface. Distance from the microspheres to the tumor was calculated using a fast deterministic point inclusion method.

  17. Potential of 3D City Models to assess flood vulnerability

    NASA Astrophysics Data System (ADS)

    Schröter, Kai; Bochow, Mathias; Schüttig, Martin; Nagel, Claus; Ross, Lutz; Kreibich, Heidi

    2016-04-01

    Vulnerability, as the product of exposure and susceptibility, is a key factor of the flood risk equation. Furthermore, the estimation of flood loss is very sensitive to the choice of the vulnerability model. Still, in contrast to elaborate hazard simulations, vulnerability is often considered in a simplified manner concerning the spatial resolution and geo-location of exposed objects as well as the susceptibility of these objects at risk. Usually, area specific potential flood loss is quantified on the level of aggregated land-use classes, and both hazard intensity and resistance characteristics of affected objects are represented in highly simplified terms. We investigate the potential of 3D City Models and spatial features derived from remote sensing data to improve the differentiation of vulnerability in flood risk assessment. 3D City Models are based on CityGML, an application scheme of the Geography Markup Language (GML), which represents the 3D geometry, 3D topology, semantics and appearance of objects on different levels of detail. As such, 3D City Models offer detailed spatial information which is useful to describe the exposure and to characterize the susceptibility of residential buildings at risk. This information is further consolidated with spatial features of the building stock derived from remote sensing data. Using this database a spatially detailed flood vulnerability model is developed by means of data-mining. Empirical flood damage data are used to derive and to validate flood susceptibility models for individual objects. We present first results from a prototype application in the city of Dresden, Germany. The vulnerability modeling based on 3D City Models and remote sensing data is compared i) to the generally accepted good engineering practice based on area specific loss potential and ii) to a highly detailed representation of flood vulnerability based on a building typology using urban structure types. Comparisons are drawn in terms of

  18. Thermal 3D modeling system based on 3-view geometry

    NASA Astrophysics Data System (ADS)

    Yu, Sunjin; Kim, Joongrock; Lee, Sangyoun

    2012-11-01

    In this paper, we propose a novel thermal three-dimensional (3D) modeling system that includes 3D shape, visual, and thermal infrared information and solves a registration problem among these three types of information. The proposed system consists of a projector, a visual camera and, a thermal camera (PVT). To generate 3D shape information, we use a structured light technique, which consists of a visual camera and a projector. A thermal camera is added to the structured light system in order to provide thermal information. To solve the correspondence problem between the three sensors, we use three-view geometry. Finally, we obtain registered PVT data, which includes visual, thermal, and 3D shape information. Among various potential applications such as industrial measurements, biological experiments, military usage, and so on, we have adapted the proposed method to biometrics, particularly for face recognition. With the proposed method, we obtain multi-modal 3D face data that includes not only textural information but also data regarding head pose, 3D shape, and thermal information. Experimental results show that the performance of the proposed face recognition system is not limited by head pose variation which is a serious problem in face recognition.

  19. 3D MHD Models of Active Region Loops

    NASA Technical Reports Server (NTRS)

    Ofman, Leon

    2004-01-01

    Present imaging and spectroscopic observations of active region loops allow to determine many physical parameters of the coronal loops, such as the density, temperature, velocity of flows in loops, and the magnetic field. However, due to projection effects many of these parameters remain ambiguous. Three dimensional imaging in EUV by the STEREO spacecraft will help to resolve the projection ambiguities, and the observations could be used to setup 3D MHD models of active region loops to study the dynamics and stability of active regions. Here the results of 3D MHD models of active region loops are presented, and the progress towards more realistic 3D MHD models of active regions. In particular the effects of impulsive events on the excitation of active region loop oscillations, and the generation, propagations and reflection of EIT waves are shown. It is shown how 3D MHD models together with 3D EUV observations can be used as a diagnostic tool for active region loop physical parameters, and to advance the science of the sources of solar coronal activity.

  20. 3D fluoroscopic image estimation using patient-specific 4DCBCT-based motion models.

    PubMed

    Dhou, S; Hurwitz, M; Mishra, P; Cai, W; Rottmann, J; Li, R; Williams, C; Wagar, M; Berbeco, R; Ionascu, D; Lewis, J H

    2015-05-01

    3D fluoroscopic images represent volumetric patient anatomy during treatment with high spatial and temporal resolution. 3D fluoroscopic images estimated using motion models built using 4DCT images, taken days or weeks prior to treatment, do not reliably represent patient anatomy during treatment. In this study we developed and performed initial evaluation of techniques to develop patient-specific motion models from 4D cone-beam CT (4DCBCT) images, taken immediately before treatment, and used these models to estimate 3D fluoroscopic images based on 2D kV projections captured during treatment. We evaluate the accuracy of 3D fluoroscopic images by comparison to ground truth digital and physical phantom images. The performance of 4DCBCT-based and 4DCT-based motion models are compared in simulated clinical situations representing tumor baseline shift or initial patient positioning errors. The results of this study demonstrate the ability for 4DCBCT imaging to generate motion models that can account for changes that cannot be accounted for with 4DCT-based motion models. When simulating tumor baseline shift and patient positioning errors of up to 5 mm, the average tumor localization error and the 95th percentile error in six datasets were 1.20 and 2.2 mm, respectively, for 4DCBCT-based motion models. 4DCT-based motion models applied to the same six datasets resulted in average tumor localization error and the 95th percentile error of 4.18 and 5.4 mm, respectively. Analysis of voxel-wise intensity differences was also conducted for all experiments. In summary, this study demonstrates the feasibility of 4DCBCT-based 3D fluoroscopic image generation in digital and physical phantoms and shows the potential advantage of 4DCBCT-based 3D fluoroscopic image estimation when there are changes in anatomy between the time of 4DCT imaging and the time of treatment delivery.

  1. Quality of 3D Models Generated by SFM Technology

    NASA Astrophysics Data System (ADS)

    Marčiš, Marián

    2013-12-01

    Using various types of automation in digital photogrammetry is associated with questions such as the accuracy of a 3D model generated on various types of surfaces and textures, the financial costs of the equipment needed, and also the time costs of the processing. This topic deals with the actual technology of computer vision, which allows the automated exterior orientation of images, camera calibration, and the generation of 3D models directly from images of the object itself, based on the automatic detection of significant points. Detailed testing is done using the Agisoft PhotoScan system, and the camera configuration is solved with respect to the accuracy of the 3D model generated and the time consumption of the calculations for the different types of textures and the different settings for the processing.

  2. 3D model of amphioxus steroid receptor complexed with estradiol

    SciTech Connect

    Baker, Michael E.; Chang, David J.

    2009-08-28

    The origins of signaling by vertebrate steroids are not fully understood. An important advance was the report that an estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates. To investigate the evolution of estrogen-binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with estradiol. This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human ER{alpha} are not conserved in the SR, which can explain the low affinity of estradiol for the SR. These differences between the SR and ER{alpha} in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the SR. The 3D model predicts that mutation of Glu-346 to Gln will increase the affinity of testosterone for amphioxus SR and elucidate the evolution of steroid-binding to nuclear receptors.

  3. Detectability of hepatic tumors during 3D post-processed ultrafast cone-beam computed tomography

    NASA Astrophysics Data System (ADS)

    Paul, Jijo; Vogl, Thomas J.; Chacko, Annamma

    2015-10-01

    To evaluate hepatic tumor detection using ultrafast cone-beam computed tomography (UCBCT) cross-sectional and 3D post-processed image datasets. 657 patients were examined using UCBCT during hepatic transarterial chemoembolization (TACE), and data were collected retrospectively from January 2012 to September 2014. Tumor detectability, diagnostic ability, detection accuracy and sensitivity were examined for different hepatic tumors using UCBCT cross-sectional, perfusion blood volume (PBV) and UCBCT-MRI (magnetic resonance imaging) fused image datasets. Appropriate statistical tests were used to compare collected sample data. Fused image data showed the significantly higher (all P  <  0.05) diagnostic ability for hepatic tumors compared to UCBCT or PBV image data. The detectability of small hepatic tumors (<5 mm) was significantly reduced (all P  <  0.05) using UCBCT cross-sectional images compared to MRI or fused image data; however, PBV improved tumor detectability using a color display. Fused image data produced 100% tumor sensitivity due to the simultaneous availability of MRI and UCBCT information during tumor diagnosis. Fused image data produced excellent hepatic tumor sensitivity, detectability and diagnostic ability compared to other datasets assessed. Fused image data is extremely reliable and useful compared to UCBCT cross-sectional or PBV image datasets to depict hepatic tumors during TACE. Partial anatomical visualization on cross-sectional images was compensated by fused image data during tumor diagnosis.

  4. Geospatial Modelling Approach for 3d Urban Densification Developments

    NASA Astrophysics Data System (ADS)

    Koziatek, O.; Dragićević, S.; Li, S.

    2016-06-01

    With growing populations, economic pressures, and the need for sustainable practices, many urban regions are rapidly densifying developments in the vertical built dimension with mid- and high-rise buildings. The location of these buildings can be projected based on key factors that are attractive to urban planners, developers, and potential buyers. Current research in this area includes various modelling approaches, such as cellular automata and agent-based modelling, but the results are mostly linked to raster grids as the smallest spatial units that operate in two spatial dimensions. Therefore, the objective of this research is to develop a geospatial model that operates on irregular spatial tessellations to model mid- and high-rise buildings in three spatial dimensions (3D). The proposed model is based on the integration of GIS, fuzzy multi-criteria evaluation (MCE), and 3D GIS-based procedural modelling. Part of the City of Surrey, within the Metro Vancouver Region, Canada, has been used to present the simulations of the generated 3D building objects. The proposed 3D modelling approach was developed using ESRI's CityEngine software and the Computer Generated Architecture (CGA) language.

  5. Parallel Optimization of 3D Cardiac Electrophysiological Model Using GPU

    PubMed Central

    Xia, Yong; Wang, Kuanquan; Zhang, Henggui

    2015-01-01

    Large-scale 3D virtual heart model simulations are highly demanding in computational resources. This imposes a big challenge to the traditional computation resources based on CPU environment, which already cannot meet the requirement of the whole computation demands or are not easily available due to expensive costs. GPU as a parallel computing environment therefore provides an alternative to solve the large-scale computational problems of whole heart modeling. In this study, using a 3D sheep atrial model as a test bed, we developed a GPU-based simulation algorithm to simulate the conduction of electrical excitation waves in the 3D atria. In the GPU algorithm, a multicellular tissue model was split into two components: one is the single cell model (ordinary differential equation) and the other is the diffusion term of the monodomain model (partial differential equation). Such a decoupling enabled realization of the GPU parallel algorithm. Furthermore, several optimization strategies were proposed based on the features of the virtual heart model, which enabled a 200-fold speedup as compared to a CPU implementation. In conclusion, an optimized GPU algorithm has been developed that provides an economic and powerful platform for 3D whole heart simulations. PMID:26581957

  6. Robust model-based 3d/3D fusion using sparse matching for minimally invasive surgery.

    PubMed

    Neumann, Dominik; Grbic, Sasa; John, Matthias; Navab, Nassir; Hornegger, Joachim; Ionasec, Razvan

    2013-01-01

    Classical surgery is being disrupted by minimally invasive and transcatheter procedures. As there is no direct view or access to the affected anatomy, advanced imaging techniques such as 3D C-arm CT and C-arm fluoroscopy are routinely used for intra-operative guidance. However, intra-operative modalities have limited image quality of the soft tissue and a reliable assessment of the cardiac anatomy can only be made by injecting contrast agent, which is harmful to the patient and requires complex acquisition protocols. We propose a novel sparse matching approach for fusing high quality pre-operative CT and non-contrasted, non-gated intra-operative C-arm CT by utilizing robust machine learning and numerical optimization techniques. Thus, high-quality patient-specific models can be extracted from the pre-operative CT and mapped to the intra-operative imaging environment to guide minimally invasive procedures. Extensive quantitative experiments demonstrate that our model-based fusion approach has an average execution time of 2.9 s, while the accuracy lies within expert user confidence intervals. PMID:24505663

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

    PubMed Central

    2009-01-01

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

  8. 3D printer generated thorax phantom with mobile tumor for radiation dosimetry.

    PubMed

    Mayer, Rulon; Liacouras, Peter; Thomas, Andrew; Kang, Minglei; Lin, Liyong; Simone, Charles B

    2015-07-01

    This article describes the design, construction, and properties of an anthropomorphic thorax phantom with a moving surrogate tumor. This novel phantom permits detection of dose both inside and outside a moving tumor and within the substitute lung tissue material. A 3D printer generated the thorax shell composed of a chest wall, spinal column, and posterior regions of the phantom. Images of a computed tomography scan of the thorax from a patient with lung cancer provided the template for the 3D printing. The plastic phantom is segmented into two materials representing the muscle and bones, and its geometry closely matches a patient. A surrogate spherical plastic tumor controlled by a 3D linear stage simulates a lung tumor's trajectory during normal breathing. Sawdust emulates the lung tissue in terms of average and distribution in Hounsfield numbers. The sawdust also provides a forgiving medium that permits tumor motion and sandwiching of radiochromic film inside the mobile surrogate plastic tumor for dosimetry. A custom cork casing shields the film and tumor and eliminates film bending during extended scans. The phantom, lung tissue surrogate, and radiochromic film are exposed to a seven field plan based on an ECLIPSE plan for 6 MV photons from a Trilogy machine delivering 230 cGy to the isocenter. The dose collected in a sagittal plane is compared to the calculated plan. Gamma analysis finds 8.8% and 5.5% gamma failure rates for measurements of large amplitude trajectory and static measurements relative to the large amplitude plan, respectively. These particular gamma analysis results were achieved using parameters of 3% dose and 3 mm, for regions receiving doses >150 cGy. The plan assumes a stationary detection grid unlike the moving radiochromic film and tissues. This difference was experimentally observed and motivated calculated dose distributions that incorporated the phase of the tumor periodic motion. These calculations modestly improve agreement between

  9. 3D printer generated thorax phantom with mobile tumor for radiation dosimetry

    NASA Astrophysics Data System (ADS)

    Mayer, Rulon; Liacouras, Peter; Thomas, Andrew; Kang, Minglei; Lin, Liyong; Simone, Charles B.

    2015-07-01

    This article describes the design, construction, and properties of an anthropomorphic thorax phantom with a moving surrogate tumor. This novel phantom permits detection of dose both inside and outside a moving tumor and within the substitute lung tissue material. A 3D printer generated the thorax shell composed of a chest wall, spinal column, and posterior regions of the phantom. Images of a computed tomography scan of the thorax from a patient with lung cancer provided the template for the 3D printing. The plastic phantom is segmented into two materials representing the muscle and bones, and its geometry closely matches a patient. A surrogate spherical plastic tumor controlled by a 3D linear stage simulates a lung tumor's trajectory during normal breathing. Sawdust emulates the lung tissue in terms of average and distribution in Hounsfield numbers. The sawdust also provides a forgiving medium that permits tumor motion and sandwiching of radiochromic film inside the mobile surrogate plastic tumor for dosimetry. A custom cork casing shields the film and tumor and eliminates film bending during extended scans. The phantom, lung tissue surrogate, and radiochromic film are exposed to a seven field plan based on an ECLIPSE plan for 6 MV photons from a Trilogy machine delivering 230 cGy to the isocenter. The dose collected in a sagittal plane is compared to the calculated plan. Gamma analysis finds 8.8% and 5.5% gamma failure rates for measurements of large amplitude trajectory and static measurements relative to the large amplitude plan, respectively. These particular gamma analysis results were achieved using parameters of 3% dose and 3 mm, for regions receiving doses >150 cGy. The plan assumes a stationary detection grid unlike the moving radiochromic film and tissues. This difference was experimentally observed and motivated calculated dose distributions that incorporated the phase of the tumor periodic motion. These calculations modestly improve agreement between

  10. 3D Model Generation From the Engineering Drawing

    NASA Astrophysics Data System (ADS)

    Vaský, Jozef; Eliáš, Michal; Bezák, Pavol; Červeňanská, Zuzana; Izakovič, Ladislav

    2010-01-01

    The contribution deals with the transformation of engineering drawings in a paper form into a 3D computer representation. A 3D computer model can be further processed in CAD/CAM system, it can be modified, archived, and a technical drawing can be then generated from it as well. The transformation process from paper form to the data one is a complex and difficult one, particularly owing to the different types of drawings, forms of displayed objects and encountered errors and deviations from technical standards. The algorithm for 3D model generating from an orthogonal vector input representing a simplified technical drawing of the rotational part is described in this contribution. The algorithm was experimentally implemented as ObjectARX application in the AutoCAD system and the test sample as the representation of the rotational part was used for verificaton.

  11. Space Partitioning for Privacy Enabled 3D City Models

    NASA Astrophysics Data System (ADS)

    Filippovska, Y.; Wichmann, A.; Kada, M.

    2016-10-01

    Due to recent technological progress, data capturing and processing of highly detailed (3D) data has become extensive. And despite all prospects of potential uses, data that includes personal living spaces and public buildings can also be considered as a serious intrusion into people's privacy and a threat to security. It becomes especially critical if data is visible by the general public. Thus, a compromise is needed between open access to data and privacy requirements which can be very different for each application. As privacy is a complex and versatile topic, the focus of this work particularly lies on the visualization of 3D urban data sets. For the purpose of privacy enabled visualizations of 3D city models, we propose to partition the (living) spaces into privacy regions, each featuring its own level of anonymity. Within each region, the depicted 2D and 3D geometry and imagery is anonymized with cartographic generalization techniques. The underlying spatial partitioning is realized as a 2D map generated as a straight skeleton of the open space between buildings. The resulting privacy cells are then merged according to the privacy requirements associated with each building to form larger regions, their borderlines smoothed, and transition zones established between privacy regions to have a harmonious visual appearance. It is exemplarily demonstrated how the proposed method generates privacy enabled 3D city models.

  12. 3D shape decomposition and comparison for gallbladder modeling

    NASA Astrophysics Data System (ADS)

    Huang, Weimin; Zhou, Jiayin; Liu, Jiang; Zhang, Jing; Yang, Tao; Su, Yi; Law, Gim Han; Chui, Chee Kong; Chang, Stephen

    2011-03-01

    This paper presents an approach to gallbladder shape comparison by using 3D shape modeling and decomposition. The gallbladder models can be used for shape anomaly analysis and model comparison and selection in image guided robotic surgical training, especially for laparoscopic cholecystectomy simulation. The 3D shape of a gallbladder is first represented as a surface model, reconstructed from the contours segmented in CT data by a scheme of propagation based voxel learning and classification. To better extract the shape feature, the surface mesh is further down-sampled by a decimation filter and smoothed by a Taubin algorithm, followed by applying an advancing front algorithm to further enhance the regularity of the mesh. Multi-scale curvatures are then computed on the regularized mesh for the robust saliency landmark localization on the surface. The shape decomposition is proposed based on the saliency landmarks and the concavity, measured by the distance from the surface point to the convex hull. With a given tolerance the 3D shape can be decomposed and represented as 3D ellipsoids, which reveal the shape topology and anomaly of a gallbladder. The features based on the decomposed shape model are proposed for gallbladder shape comparison, which can be used for new model selection. We have collected 19 sets of abdominal CT scan data with gallbladders, some shown in normal shape and some in abnormal shapes. The experiments have shown that the decomposed shapes reveal important topology features.

  13. Geodiversity: Exploration of 3D geological model space

    NASA Astrophysics Data System (ADS)

    Lindsay, M. D.; Jessell, M. W.; Ailleres, L.; Perrouty, S.; de Kemp, E.; Betts, P. G.

    2013-05-01

    The process of building a 3D model necessitates the reconciliation of field observations, geophysical interpretation, geological data uncertainty and the prevailing tectonic evolution hypotheses and interpretations. Uncertainty is compounded when clustered data points collected at local scales are statistically upscaled to one or two points for use in regional models. Interpretation is required to interpolate between sparse field data points using ambiguous geophysical data in covered terranes. It becomes clear that multiple interpretations are possible during model construction. The various interpretations are considered as potential natural representatives, but pragmatism typically dictates that just a single interpretation is offered by the modelling process. Uncertainties are introduced into the 3D model during construction from a variety of sources and through data set optimisation that produces a single model. Practices such as these are likely to result in a model that does not adequately represent the target geology. A set of geometrical ‘geodiversity’ metrics are used to analyse a 3D model of the Gippsland Basin, southeastern Australia after perturbing geological input data via uncertainty simulation. The resulting sets of perturbed geological observations are used to calculate a suite of geological 3D models that display a range of geological architectures. The concept of biodiversity has been adapted for the geosciences to quantify geometric variability, or geodiversity, between models in order to understand the effect uncertainty has models geometry. Various geometrical relationships (depth, volume, contact surface area, curvature and geological complexity) are used to describe the range of possibilities exhibited throughout the model suite. End-member models geodiversity metrics are classified in a similar manner to taxonomic descriptions. Further analysis of the model suite is performed using principal component analysis (PCA) to determine

  14. Improving Semantic Updating Method on 3d City Models Using Hybrid Semantic-Geometric 3d Segmentation Technique

    NASA Astrophysics Data System (ADS)

    Sharkawi, K.-H.; Abdul-Rahman, A.

    2013-09-01

    Cities and urban areas entities such as building structures are becoming more complex as the modern human civilizations continue to evolve. The ability to plan and manage every territory especially the urban areas is very important to every government in the world. Planning and managing cities and urban areas based on printed maps and 2D data are getting insufficient and inefficient to cope with the complexity of the new developments in big cities. The emergence of 3D city models have boosted the efficiency in analysing and managing urban areas as the 3D data are proven to represent the real world object more accurately. It has since been adopted as the new trend in buildings and urban management and planning applications. Nowadays, many countries around the world have been generating virtual 3D representation of their major cities. The growing interest in improving the usability of 3D city models has resulted in the development of various tools for analysis based on the 3D city models. Today, 3D city models are generated for various purposes such as for tourism, location-based services, disaster management and urban planning. Meanwhile, modelling 3D objects are getting easier with the emergence of the user-friendly tools for 3D modelling available in the market. Generating 3D buildings with high accuracy also has become easier with the availability of airborne Lidar and terrestrial laser scanning equipments. The availability and accessibility to this technology makes it more sensible to analyse buildings in urban areas using 3D data as it accurately represent the real world objects. The Open Geospatial Consortium (OGC) has accepted CityGML specifications as one of the international standards for representing and exchanging spatial data, making it easier to visualize, store and manage 3D city models data efficiently. CityGML able to represents the semantics, geometry, topology and appearance of 3D city models in five well-defined Level-of-Details (LoD), namely LoD0

  15. Using the full scale 3D solid anthropometric model in radiation oncology positioning and verification.

    PubMed

    Sun, Shuh-Ping; Wu, Ching-Jung

    2004-01-01

    This paper describes the full size solid 3D Anthropometric Model using in the positioning and verification process for radiation treatment planning of the skull of cancer patients in radiotherapy. In order to obtain a full scale 3D, solid Anthropometric Model, data is first collected through computed tomography and optical scanning. Through surface reconstruction, a model is made of the patients skull, after which rapid prototyping and rapid tooling is applied to acquire a 1:1 solid model, thus, it can replace the patient for the tumor positioning and verification in radiotherapy. The 3D Anthropometric Model are not only provide a clear picture of the external appearance, but also allow insight into the internal structure of organic bodies, which is of great advantage in radiotherapy. During radiotherapy planning, 3D Anthropometric Model can be used to simulate all kinds of situations on the simulator and the linear accelerator, without the patient needing to be present, so that the medical physicist or dosimetrist will be able to design a precise treatment plan that is tailored to the patient. The 3D Anthropometric Model production system can effectively help us solve problems related to r adiotherapy positioning and verification, helping both radiotherapists and cancer patients. We expect that the application of 3D Anthropometric Model can reduce the time that needs to be spent on pretreatment procedures and enhance the quality of health care for cancer patients.

  16. Enhanced LOD Concepts for Virtual 3d City Models

    NASA Astrophysics Data System (ADS)

    Benner, J.; Geiger, A.; Gröger, G.; Häfele, K.-H.; Löwner, M.-O.

    2013-09-01

    Virtual 3D city models contain digital three dimensional representations of city objects like buildings, streets or technical infrastructure. Because size and complexity of these models continuously grow, a Level of Detail (LoD) concept effectively supporting the partitioning of a complete model into alternative models of different complexity and providing metadata, addressing informational content, complexity and quality of each alternative model is indispensable. After a short overview on various LoD concepts, this paper discusses the existing LoD concept of the CityGML standard for 3D city models and identifies a number of deficits. Based on this analysis, an alternative concept is developed and illustrated with several examples. It differentiates between first, a Geometric Level of Detail (GLoD) and a Semantic Level of Detail (SLoD), and second between the interior building and its exterior shell. Finally, a possible implementation of the new concept is demonstrated by means of an UML model.

  17. Teaching the geological subsurface with 3D models

    NASA Astrophysics Data System (ADS)

    Thorpe, Steve; Ward, Emma

    2014-05-01

    3D geological models have great potential as a resource when teaching geological concepts as it allows the student to visualise and interrogate UK geology. They are especially useful when dealing with the conversion of 2D field, map and GIS outputs into three dimensional geological units, which is a common problem for many students. Today's earth science students use a variety of skills and processes during their learning experience including spatial thinking, image construction, detecting patterns, making predictions and deducing the orientation of themselves. 3D geological models can reinforce spatial thinking strategies and encourage students to think about processes and properties, in turn helping the student to recognise pre-learnt geological principles in the field and to convert what they see at the surface into a picture of what is going on at depth. The British Geological Survey (BGS) has been producing digital 3D geological models for over 10 years. The models produced are revolutionising the working practices, data standards and products of the BGS. Sharing our geoscience information with academia is highlighted throughout the BGS strategy as is instilling practical skills in future geoscience professionals, such as model building and interpretation. In 2009 a project was launched to investigate the potential of the models as a teaching resource. The study included justifying if and how the models help students to learn, how models have been used historically, and how other forms of modelling are being used today. BGS now produce 3D geological models for use by anyone teaching or learning geoscience. They incorporate educational strategies that will develop geospatial skills and alleviate potential problems that some students experience. They are contained within contemporary case studies and show standard geological concepts, structures, sedimentary rocks, cross sections and field techniques. 3D geological models of the Isle of Wight and Ingleborough

  18. 3D Geological Model for "LUSI" - a Deep Geothermal System

    NASA Astrophysics Data System (ADS)

    Sohrabi, Reza; Jansen, Gunnar; Mazzini, Adriano; Galvan, Boris; Miller, Stephen A.

    2016-04-01

    Geothermal applications require the correct simulation of flow and heat transport processes in porous media, and many of these media, like deep volcanic hydrothermal systems, host a certain degree of fracturing. This work aims to understand the heat and fluid transport within a new-born sedimentary hosted geothermal system, termed Lusi, that began erupting in 2006 in East Java, Indonesia. Our goal is to develop conceptual and numerical models capable of simulating multiphase flow within large-scale fractured reservoirs such as the Lusi region, with fractures of arbitrary size, orientation and shape. Additionally, these models can also address a number of other applications, including Enhanced Geothermal Systems (EGS), CO2 sequestration (Carbon Capture and Storage CCS), and nuclear waste isolation. Fractured systems are ubiquitous, with a wide-range of lengths and scales, making difficult the development of a general model that can easily handle this complexity. We are developing a flexible continuum approach with an efficient, accurate numerical simulator based on an appropriate 3D geological model representing the structure of the deep geothermal reservoir. Using previous studies, borehole information and seismic data obtained in the framework of the Lusi Lab project (ERC grant n°308126), we present here the first 3D geological model of Lusi. This model is calculated using implicit 3D potential field or multi-potential fields, depending on the geological context and complexity. This method is based on geological pile containing the geological history of the area and relationship between geological bodies allowing automatic computation of intersections and volume reconstruction. Based on the 3D geological model, we developed a new mesh algorithm to create hexahedral octree meshes to transfer the structural geological information for 3D numerical simulations to quantify Thermal-Hydraulic-Mechanical-Chemical (THMC) physical processes.

  19. 3D printer generated thorax phantom with mobile tumor for radiation dosimetry

    SciTech Connect

    Mayer, Rulon; Liacouras, Peter; Thomas, Andrew; Kang, Minglei; Lin, Liyong; Simone, Charles B.

    2015-07-15

    This article describes the design, construction, and properties of an anthropomorphic thorax phantom with a moving surrogate tumor. This novel phantom permits detection of dose both inside and outside a moving tumor and within the substitute lung tissue material. A 3D printer generated the thorax shell composed of a chest wall, spinal column, and posterior regions of the phantom. Images of a computed tomography scan of the thorax from a patient with lung cancer provided the template for the 3D printing. The plastic phantom is segmented into two materials representing the muscle and bones, and its geometry closely matches a patient. A surrogate spherical plastic tumor controlled by a 3D linear stage simulates a lung tumor’s trajectory during normal breathing. Sawdust emulates the lung tissue in terms of average and distribution in Hounsfield numbers. The sawdust also provides a forgiving medium that permits tumor motion and sandwiching of radiochromic film inside the mobile surrogate plastic tumor for dosimetry. A custom cork casing shields the film and tumor and eliminates film bending during extended scans. The phantom, lung tissue surrogate, and radiochromic film are exposed to a seven field plan based on an ECLIPSE plan for 6 MV photons from a Trilogy machine delivering 230 cGy to the isocenter. The dose collected in a sagittal plane is compared to the calculated plan. Gamma analysis finds 8.8% and 5.5% gamma failure rates for measurements of large amplitude trajectory and static measurements relative to the large amplitude plan, respectively. These particular gamma analysis results were achieved using parameters of 3% dose and 3 mm, for regions receiving doses >150 cGy. The plan assumes a stationary detection grid unlike the moving radiochromic film and tissues. This difference was experimentally observed and motivated calculated dose distributions that incorporated the phase of the tumor periodic motion. These calculations modestly improve agreement between

  20. Tracking people and cars using 3D modeling and CCTV.

    PubMed

    Edelman, Gerda; Bijhold, Jurrien

    2010-10-10

    The aim of this study was to find a method for the reconstruction of movements of people and cars using CCTV footage and a 3D model of the environment. A procedure is proposed, in which video streams are synchronized and displayed in a 3D model, by using virtual cameras. People and cars are represented by cylinders and boxes, which are moved in the 3D model, according to their movements as shown in the video streams. The procedure was developed and tested in an experimental setup with test persons who logged their GPS coordinates as a recording of the ground truth. Results showed that it is possible to implement this procedure and to reconstruct movements of people and cars from video recordings. The procedure was also applied to a forensic case. In this work we experienced that more situational awareness was created by the 3D model, which made it easier to track people on multiple video streams. Based on all experiences from the experimental set up and the case, recommendations are formulated for use in practice.

  1. Performance and Cognitive Assessment in 3-D Modeling

    ERIC Educational Resources Information Center

    Fahrer, Nolan E.; Ernst, Jeremy V.; Branoff, Theodore J.; Clark, Aaron C.

    2011-01-01

    The purpose of this study was to investigate identifiable differences between performance and cognitive assessment scores in a 3-D modeling unit of an engineering drafting course curriculum. The study aimed to provide further investigation of the need of skill-based assessments in engineering/technical graphics courses to potentially increase…

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

    PubMed

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

    2016-07-01

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

  3. Assessment of 3D Models Used in Contours Studies

    ERIC Educational Resources Information Center

    Alvarez, F. J. Ayala; Parra, E. B. Blazquez; Tubio, F. Montes

    2015-01-01

    This paper presents an experimental research focusing on the view of first year students. The aim is to check the quality of implementing 3D models integrated in the curriculum. We search to determine students' preference between the various means facilitated in order to understand the given subject. Students have been respondents to prove the…

  4. Modeling the Properties of 3D Woven Composites

    NASA Technical Reports Server (NTRS)

    Cox, Brian N.

    1995-01-01

    An extensive study has been completed of the internal geometry, the mechanisms of failure, and the micromechanics of local failure events in graphite/epoxy composites with three dimensional (3D) woven reinforcement. This work has led to the development of models for predicting elastic constants, strength, notch sensitivity, and fatigue life. A summary is presented here.

  5. 3d model for site effect assessment at Nice (France)

    NASA Astrophysics Data System (ADS)

    Bertrand, E.; Courrioux, G.; Bourgine, B.; Bour, M.; Guillen, A.; Mouroux, P.; Devaux, E.; Duval, A. M.

    2003-04-01

    Assessment of lithologic site effects is based on an accurate knowledge of properties and geometry of superficial geological formations, i.e. ideally a 3D-4G subsurface model (Geology, Geomorphology, Geophysics, Geotechnics). Such a model has been achieved using a 3D geomodeler ("Geological Editor" developed at BRGM) that allows building 3D volumes of geological formations starting from drill-holes data, sections, and geological maps. This software uses a pseudo-stratigraphic pile in order to reproduce geological history and structural relationships (erosion, deposit). The interpolation is achieved through a 3D potential field. A geostatistical formulation allows to consider data points of a geological limit as equipotential, and sructural dips as gradient inputs for the 3D field interpolation. Then isosurfaces corresponding to each limit are combined using formation relationships to provide volumic models of geological formations. The first task was to identify the relevant geological formations underlying in Nice area. In a first approach Mesozoic bedrock, Pliocene bedrock, and Quaternary alluvial deposits have been distinguished considering their seismic properties. Then alluvions have been subdivided into 9 groups according to their lithology and granulometry. Modelling has been performed considering 2 major erosion surfaces, post-Mesozoic and post-Pliocene. The succession of Quaternary alluviums have been considered as "onlap deposits". Given adjacent lithologies contained in maps and drill holes, these relations lead to logical identification of the roof of formations to be interpolated. The distribution of modeled geological formations can be visualised in 3 dimensions or in 2D sections. Besides the visual interest of 3D representations, the model is first used to build a series of earth columns over a 50m/50m 2D grid. A statistical analysis allowed to identify 73 existing configurations in the Nice district area. Among these, only 15 configurations

  6. Robust 3D reconstruction system for human jaw modeling

    NASA Astrophysics Data System (ADS)

    Yamany, Sameh M.; Farag, Aly A.; Tazman, David; Farman, Allan G.

    1999-03-01

    This paper presents a model-based vision system for dentistry that will replace traditional approaches used in diagnosis, treatment planning and surgical simulation. Dentistry requires accurate 3D representation of the teeth and jaws for many diagnostic and treatment purposes. For example orthodontic treatment involves the application of force systems to teeth over time to correct malocclusion. In order to evaluate tooth movement progress, the orthodontists monitors this movement by means of visual inspection, intraoral measurements, fabrication of plastic models, photographs and radiographs, a process which is both costly and time consuming. In this paper an integrate system has been developed to record the patient's occlusion using computer vision. Data is acquired with an intraoral video camera. A modified shape from shading (SFS) technique, using perspective projection and camera calibration, is used to extract accurate 3D information from a sequence of 2D images of the jaw. A new technique for 3D data registration, using a Grid Closest Point transform and genetic algorithms, is used to register the SFS output. Triangulization is then performed, and a solid 3D model is obtained via a rapid prototype machine.

  7. Use Models like Maps in a 3D SDI

    NASA Astrophysics Data System (ADS)

    Gietzel, Jan; Gabriel, Paul; Schaeben, Helmut; Le, Hai Ha

    2013-04-01

    Digital geological applications have become 3D up to 4D modelling of the underground. The modellers are working very heterogeneously in terms of its applied software systems. On the other hand the 3D/4D modelling of the subsurface has become part of the geological surveys all around the world. This implies a wide spread group of users working in different institutions aiming to work together on one subsurface model. Established 3D/4D-modelling software systems mainly use a file based approach to store data, which is in a high contrast to the needs of a central administrated and network based data transfer approach. At the department of geophysics and geo information sciences at the Technical University Bergakademie Freiberg, the GST system for managing 3D and 4D geosciences data in a databases system was developed and is now continued by the company GiGa infosystems. The GST-Framework includes a storage engine, a web service for sharing and a number of client software including a browser based client interface for visualising, accessing and manipulating geological CAD data. Including a check out system GST supports multi user editing on huge models, designed to manage seamless high resolution models of the subsurface. While working on complex projects various software is used for the creation of the model, the prediction of properties and final simulation. A problem rising from the use of several software is the interoperability of the models. Due to conversion errors different working groups use mainly different raw data. This results in different models, which have to be corrected with additional effort. One platform sharing the models is strongly demanded. One high potential solution is a centralized and software independent storage, which will be presented.

  8. 3D Geological modelling - towards a European level infrastructure

    NASA Astrophysics Data System (ADS)

    Lee, Kathryn A.; van der Krogt, Rob; Busschers, Freek S.

    2013-04-01

    The joint European Geological Surveys are preparing the ground for a "European Geological Data Infrastructure" (EGDI), under the framework of the FP7-project EGDI-Scope. This scoping study, started in June 2012, for a pan-European e-Infrastructure is based on the successes of earlier joint projects including 'OneGeology-Europe' and aims to provide the backbone for serving interoperable, geological data currently held by European Geological Surveys. Also data from past, ongoing and future European projects will be incorporated. The scope will include an investigation of the functional and technical requirements for serving 3D geological models and will look to research the potential for providing a framework to integrate models at different scales, and form a structure for enabling the development of new and innovative model delivery mechanisms. The EGDI-scope project encourages pan-European inter-disciplinary collaboration between all European Geological Surveys. It aims to enhance emerging web based technologies that will facilitate the delivery of geological data to user communities involved in European policy making and international industry, but also to geoscientific research communities and the general public. Therefore, stakeholder input and communication is imperative to the success, as is the collaboration with all the Geological Surveys of Europe. The most important functional and technical requirements for delivery of such information at pan-European level will be derived from exchanges with relevant European stakeholder representatives and providers of geological data. For handling and delivering 3D geological model data the project will need to address a number of strategic issues: • Which are the most important issues and queries for the relevant stakeholders, requiring 3D geological models? How can this be translated to functional requirements for development and design of an integrated European application? • How to handle the very large

  9. Recovering 3D tumor locations from 2D bioluminescence images and registration with CT images

    NASA Astrophysics Data System (ADS)

    Huang, Xiaolei; Metaxas, Dimitris N.; Menon, Lata G.; Mayer-Kuckuk, Philipp; Bertino, Joseph R.; Banerjee, Debabrata

    2006-02-01

    In this paper, we introduce a novel and efficient algorithm for reconstructing the 3D locations of tumor sites from a set of 2D bioluminescence images which are taken by a same camera but after continually rotating the object by a small angle. Our approach requires a much simpler set up than those using multiple cameras, and the algorithmic steps in our framework are efficient and robust enough to facilitate its use in analyzing the repeated imaging of a same animal transplanted with gene marked cells. In order to visualize in 3D the structure of the tumor, we also co-register the BLI-reconstructed crude structure with detailed anatomical structure extracted from high-resolution microCT on a single platform. We present our method using both phantom studies and real studies on small animals.

  10. Quasi-3D Multi-scale Modeling Framework Development

    NASA Astrophysics Data System (ADS)

    Arakawa, A.; Jung, J.

    2008-12-01

    When models are truncated in or near an energetically active range of the spectrum, model physics must be changed as the resolution changes. The model physics of GCMs and that of CRMs are, however, quite different from each other and at present there is no unified formulation of model physics that automatically provides transition between these model physics. The Quasi-3D (Q3D) Multi-scale Modeling Framework (MMF) is an attempt to bridge this gap. Like the recently proposed Heterogeneous Multiscale Method (HMM) (E and Engquist 2003), MMF combines a macroscopic model, GCM, and a microscopic model, CRM. Unlike the traditional multiscale methods such as the multi-grid and adapted mesh refinement techniques, HMM and MMF are for solving multi-physics problems. They share the common objective "to design combined macroscopic-microscopic computational methods that are much more efficient than solving the full microscopic model and at the same time give the information we need" (E et al. 2008). The question is then how to meet this objective in practice, which can be highly problem dependent. In HHM, the efficiency is gained typically by localization of the microscale problem. Following the pioneering work by Grabowski and Smolarkiewicz (1999) and Grabowski (2001), MMF takes advantage of the fact that 2D CRMs are reasonably successful in simulating deep clouds. In this approach, the efficiency is gained by sacrificing the three-dimensionality of cloud-scale motion. It also "localizes" the algorithm through embedding a CRM in each GCM grid box using cyclic boundary condition. The Q3D MMF is an attempt to reduce the expense due to these constraints by partially including the cloud-scale 3D effects and extending the CRM beyond individual GCM grid boxes. As currently formulated, the Q3D MMF is a 4D estimation/prediction framework that combines a GCM with a 3D anelastic cloud-resolving vector vorticity equation model (VVM) applied to a network of horizontal grids. The network

  11. Towards a noninvasive intracranial tumor irradiation using 3d optical imaging and multimodal data registration.

    PubMed

    Posada, R; Daul, Ch; Wolf, D; Aletti, P

    2007-01-01

    Conformal radiotherapy (CRT) results in high-precision tumor volume irradiation. In fractioned radiotherapy (FRT), lesions are irradiated in several sessions so that healthy neighbouring tissues are better preserved than when treatment is carried out in one fraction. In the case of intracranial tumors, classical methods of patient positioning in the irradiation machine coordinate system are invasive and only allow for CRT in one irradiation session. This contribution presents a noninvasive positioning method representing a first step towards the combination of CRT and FRT. The 3D data used for the positioning is point clouds spread over the patient's head (CT-data usually acquired during treatment) and points distributed over the patient's face which are acquired with a structured light sensor fixed in the therapy room. The geometrical transformation linking the coordinate systems of the diagnosis device (CT-modality) and the 3D sensor of the therapy room (visible light modality) is obtained by registering the surfaces represented by the two 3D point sets. The geometrical relationship between the coordinate systems of the 3D sensor and the irradiation machine is given by a calibration of the sensor position in the therapy room. The global transformation, computed with the two previous transformations, is sufficient to predict the tumor position in the irradiation machine coordinate system with only the corresponding position in the CT-coordinate system. Results obtained for a phantom show that the mean positioning error of tumors on the treatment machine isocentre is 0.4 mm. Tests performed with human data proved that the registration algorithm is accurate (0.1 mm mean distance between homologous points) and robust even for facial expression changes.

  12. 3-D HYDRODYNAMIC MODELING IN A GEOSPATIAL FRAMEWORK

    SciTech Connect

    Bollinger, J; Alfred Garrett, A; Larry Koffman, L; David Hayes, D

    2006-08-24

    3-D hydrodynamic models are used by the Savannah River National Laboratory (SRNL) to simulate the transport of thermal and radionuclide discharges in coastal estuary systems. Development of such models requires accurate bathymetry, coastline, and boundary condition data in conjunction with the ability to rapidly discretize model domains and interpolate the required geospatial data onto the domain. To facilitate rapid and accurate hydrodynamic model development, SRNL has developed a pre- and post-processor application in a geospatial framework to automate the creation of models using existing data. This automated capability allows development of very detailed models to maximize exploitation of available surface water radionuclide sample data and thermal imagery.

  13. 3D model of the Bernese Part of the Swiss Molasse Basin: visualization of uncertainties in a 3D model

    NASA Astrophysics Data System (ADS)

    Mock, Samuel; Allenbach, Robin; Reynolds, Lance; Wehrens, Philip; Kurmann-Matzenauer, Eva; Kuhn, Pascal; Michael, Salomè; Di Tommaso, Gennaro; Herwegh, Marco

    2016-04-01

    The Swiss Molasse Basin comprises the western and central part of the North Alpine Foreland Basin. In recent years it has come under closer scrutiny due to its promising geopotentials such as geothermal energy and CO2 sequestration. In order to adress these topics good knowledge of the subsurface is a key prerequisite. For that matter, geological 3D models serve as valuable tools. In collaboration with the Swiss Geological Survey (swisstopo) and as part of the project GeoMol CH, a geological 3D model of the Swiss Molasse Basin in the Canton of Bern has been built. The model covers an area of 1810 km2and reaches depth of up to 6.7 km. It comprises 10 major Cenozoic and Mesozoic units and numerous faults. The 3D model is mainly based on 2D seismic data complemented by information from few deep wells. Additionally, data from geological maps and profiles were used for refinement at shallow depths. In total, 1163 km of reflection seismic data, along 77 seismic lines, have been interpreted by different authors with respect to stratigraphy and structures. Both, horizons and faults, have been interpreted in 2D and modelled in 3D using IHS's Kingdom Suite and Midland Valley's MOVE software packages, respectively. Given the variable degree of subsurface information available, each 3D model is subject of uncertainty. With the primary input data coming from interpretation of reflection seismic data, a variety of uncertainties comes into play. Some of them are difficult to address (e.g. author's style of interpretation) while others can be quantified (e.g. mis-tie correction, well-tie). An important source of uncertainties is the quality of seismic data; this affects the traceability and lateral continuation of seismic reflectors. By defining quality classes we can semi-quantify this source of uncertainty. In order to visualize the quality and density of the input data in a meaningful way, we introduce quality-weighted data density maps. In combination with the geological 3D

  14. Optimizing radioimmunotherapy by matching dose distribution with tumor structure using 3D reconstructions of serial images.

    PubMed

    Flynn, A A; Pedley, R B; Green, A J; Boxer, G M; Boden, R; Begent, R H

    2001-10-01

    The biological effect of radioimmunotherapy (RIT) is most commonly assessed in terms of the absorbed radiation dose. In tumor, conventional dosimetry methods assume a uniform radionuclide and calculate a mean dose throughout the tumor. However, the vasculature of solid tumors tends to be highly irregular and the systemic delivery of antibodies is therefore heterogeneous. Tumor-specific antibodies preferentially localize in the viable, radiosensitive parts of the tumor whereas non-specific antibodies can penetrate into the necrosis where the dose is wasted. As a result, the observed biological effect can be very different to the predicted effect from conventional dose estimates. The purpose of this study is to assess the potential for optimizing the biological effect of RIT by matching the dose-distribution with tumor structure through the selection of appropriate antibodies and radionuclides. Storage phosphor plate technology was used to acquire images of the antibody distribution in serial tumor sections. Images of the distributions of a trivalent (TFM), bivalent (A5B7-IgG), monovalent (MFE-23) and a non-specific antibody (MOPC) were obtained. These images were registered with corresponding images showing tumor morphology. Serial images were reconstructed to form 3D maps of the antibody distribution and tumor structure. Convolution of the image of antibody distribution with beta dose point kernals generated dose-rate distributions for 14C, 131I and 90Y. These were statistically compared with the tumor structure. The highest correlation was obtained for the multivalent antibodies combined with 131I, due to specific retention in viable areas of tumor coupled with the fact that much of the dose was deposted locally. With decreasing avidity the correlation also decreased and with the non-specific antibody this correlation was negative, indicating higher concentrations in the necrotic regions. In conclusion, the dose distribution can be optimized in tumor by selecting

  15. 3D Silicon Microstructures: A New Tool for Evaluating Biological Aggressiveness of Tumor Cells.

    PubMed

    Mazzini, Giuliano; Carpignano, Francesca; Surdo, Salvatore; Aredia, Francesca; Panini, Nicolò; Torchio, Martina; Erba, Eugenio; Danova, Marco; Scovassi, Anna Ivana; Barillaro, Giuseppe; Merlo, Sabina

    2015-10-01

    In this work, silicon micromachined structures (SMS), consisting of arrays of 3- μ m-thick silicon walls separated by 50- μm-deep, 5- μ m-wide gaps, were applied to investigate the behavior of eight tumor cell lines, with different origins and biological aggressiveness, in a three-dimensional (3D) microenvironment. Several cell culture experiments were performed on 3D-SMS and cells grown on silicon were stained for fluorescence microscopy analyses. Most of the tumor cell lines recognized in the literature as highly aggressive (OVCAR-5, A375, MDA-MB-231, and RPMI-7951) exhibited a great ability to enter and colonize the narrow deep gaps of the SMS, whereas less aggressive cell lines (OVCAR-3, Capan-1, MCF7, and NCI-H2126) demonstrated less penetration capability and tended to remain on top of the SMS. Quantitative image analyses of several fluorescence microscopy fields of silicon samples were performed for automatic cell recognition and count, in order to quantify the fraction of cells inside the gaps, with respect to the total number of cells in the examined field. Our results show that higher fractions of cells in the gaps are obtained with more aggressive cell lines, thus supporting in a quantitative way the observation that the behavior of tumor cells on the 3D-SMS depends on their aggressiveness level.

  16. Towards a 3d Spatial Urban Energy Modelling Approach

    NASA Astrophysics Data System (ADS)

    Bahu, J.-M.; Koch, A.; Kremers, E.; Murshed, S. M.

    2013-09-01

    Today's needs to reduce the environmental impact of energy use impose dramatic changes for energy infrastructure and existing demand patterns (e.g. buildings) corresponding to their specific context. In addition, future energy systems are expected to integrate a considerable share of fluctuating power sources and equally a high share of distributed generation of electricity. Energy system models capable of describing such future systems and allowing the simulation of the impact of these developments thus require a spatial representation in order to reflect the local context and the boundary conditions. This paper describes two recent research approaches developed at EIFER in the fields of (a) geo-localised simulation of heat energy demand in cities based on 3D morphological data and (b) spatially explicit Agent-Based Models (ABM) for the simulation of smart grids. 3D city models were used to assess solar potential and heat energy demand of residential buildings which enable cities to target the building refurbishment potentials. Distributed energy systems require innovative modelling techniques where individual components are represented and can interact. With this approach, several smart grid demonstrators were simulated, where heterogeneous models are spatially represented. Coupling 3D geodata with energy system ABMs holds different advantages for both approaches. On one hand, energy system models can be enhanced with high resolution data from 3D city models and their semantic relations. Furthermore, they allow for spatial analysis and visualisation of the results, with emphasis on spatially and structurally correlations among the different layers (e.g. infrastructure, buildings, administrative zones) to provide an integrated approach. On the other hand, 3D models can benefit from more detailed system description of energy infrastructure, representing dynamic phenomena and high resolution models for energy use at component level. The proposed modelling strategies

  17. 3-D model-based tracking for UAV indoor localization.

    PubMed

    Teulière, Céline; Marchand, Eric; Eck, Laurent

    2015-05-01

    This paper proposes a novel model-based tracking approach for 3-D localization. One main difficulty of standard model-based approach lies in the presence of low-level ambiguities between different edges. In this paper, given a 3-D model of the edges of the environment, we derive a multiple hypotheses tracker which retrieves the potential poses of the camera from the observations in the image. We also show how these candidate poses can be integrated into a particle filtering framework to guide the particle set toward the peaks of the distribution. Motivated by the UAV indoor localization problem where GPS signal is not available, we validate the algorithm on real image sequences from UAV flights.

  18. 3-D model-based tracking for UAV indoor localization.

    PubMed

    Teulière, Céline; Marchand, Eric; Eck, Laurent

    2015-05-01

    This paper proposes a novel model-based tracking approach for 3-D localization. One main difficulty of standard model-based approach lies in the presence of low-level ambiguities between different edges. In this paper, given a 3-D model of the edges of the environment, we derive a multiple hypotheses tracker which retrieves the potential poses of the camera from the observations in the image. We also show how these candidate poses can be integrated into a particle filtering framework to guide the particle set toward the peaks of the distribution. Motivated by the UAV indoor localization problem where GPS signal is not available, we validate the algorithm on real image sequences from UAV flights. PMID:25099967

  19. Engineering a High-Throughput 3-D In Vitro Glioblastoma Model

    PubMed Central

    Fan, Yantao; Avci, Naze G.; Nguyen, Duong T.; Dragomir, Andrei; Xu, Feng; Akay, Metin

    2015-01-01

    Glioblastoma multiforme (GBM) is the most common and malignant primary brain tumor in adults because of its highly invasive behavior. The existing treatment for GBM, which involves a combination of resection, chemotherapy, and radiotherapy, has a very limited success rate with a median survival rate of <1 year. This is mainly because of the failure of early detection and effective treatment. We designed a novel 3-D GBM cell culture model based on microwells that could mimic in vitro environment and help to bypass the lack of suitable animal models for preclinical toxicity tests. Microwells were fabricated from simple and inexpensive polyethylene glycol material for the control of in vitro 3-D culture. We applied the 3-D micropatterning system to GBM (U-87) cells using the photolithography technique to control the cell spheroids’ shape, size, and thickness. Our preliminary results suggested that uniform GBM spheroids can be formed in 3-D, and the size of these GBM spheroids depends on the size of microwells. The viability of the spheroids generated in this manner was quantitatively evaluated using live/dead assay and shown to improve over 21 days. We believe that in vitro 3-D cell culture model could help to reduce the time of the preclinical brain tumor growth studies. The proposed novel platform could be useful and cost-effective for high-throughput screening of cancer drugs and assessment of treatment responses. PMID:27170911

  20. 3D Multispectral Light Propagation Model For Subcutaneous Veins Imaging

    SciTech Connect

    Paquit, Vincent C; Price, Jeffery R; Meriaudeau, Fabrice; Tobin Jr, Kenneth William

    2008-01-01

    In this paper, we describe a new 3D light propagation model aimed at understanding the effects of various physiological properties on subcutaneous vein imaging. In particular, we build upon the well known MCML (Monte Carlo Multi Layer) code and present a tissue model that improves upon the current state-of-the-art by: incorporating physiological variation, such as melanin concentration, fat content, and layer thickness; including veins of varying depth and diameter; using curved surfaces from real arm shapes; and modeling the vessel wall interface. We describe our model, present results from the Monte Carlo modeling, and compare these results with those obtained with other Monte Carlo methods.

  1. Generation and use of human 3D-CAD models

    NASA Astrophysics Data System (ADS)

    Grotepass, Juergen; Speyer, Hartmut; Kaiser, Ralf

    2002-05-01

    Individualized Products are one of the ten mega trends of the 21st Century with human modeling as the key issue for tomorrow's design and product development. The use of human modeling software for computer based ergonomic simulations within the production process increases quality while reducing costs by 30- 50 percent and shortening production time. This presentation focuses on the use of human 3D-CAD models for both, the ergonomic design of working environments and made to measure garment production. Today, the entire production chain can be designed, individualized models generated and analyzed in 3D computer environments. Anthropometric design for ergonomics is matched to human needs, thus preserving health. Ergonomic simulation includes topics as human vision, reachability, kinematics, force and comfort analysis and international design capabilities. In German more than 17 billions of Mark are moved to other industries, because clothes do not fit. Individual clothing tailored to the customer's preference means surplus value, pleasure and perfect fit. The body scanning technology is the key to generation and use of human 3D-CAD models for both, the ergonomic design of working environments and made to measure garment production.

  2. Method for modeling post-mortem biometric 3D fingerprints

    NASA Astrophysics Data System (ADS)

    Rajeev, Srijith; Shreyas, Kamath K. M.; Agaian, Sos S.

    2016-05-01

    Despite the advancements of fingerprint recognition in 2-D and 3-D domain, authenticating deformed/post-mortem fingerprints continue to be an important challenge. Prior cleansing and reconditioning of the deceased finger is required before acquisition of the fingerprint. The victim's finger needs to be precisely and carefully operated by a medium to record the fingerprint impression. This process may damage the structure of the finger, which subsequently leads to higher false rejection rates. This paper proposes a non-invasive method to perform 3-D deformed/post-mortem finger modeling, which produces a 2-D rolled equivalent fingerprint for automated verification. The presented novel modeling method involves masking, filtering, and unrolling. Computer simulations were conducted on finger models with different depth variations obtained from Flashscan3D LLC. Results illustrate that the modeling scheme provides a viable 2-D fingerprint of deformed models for automated verification. The quality and adaptability of the obtained unrolled 2-D fingerprints were analyzed using NIST fingerprint software. Eventually, the presented method could be extended to other biometric traits such as palm, foot, tongue etc. for security and administrative applications.

  3. 3D modeling of dual-gate FinFET.

    PubMed

    Mil'shtein, Samson; Devarakonda, Lalitha; Zanchi, Brian; Palma, John

    2012-01-01

    The tendency to have better control of the flow of electrons in a channel of field-effect transistors (FETs) did lead to the design of two gates in junction field-effect transistors, field plates in a variety of metal semiconductor field-effect transistors and high electron mobility transistors, and finally a gate wrapping around three sides of a narrow fin-shaped channel in a FinFET. With the enhanced control, performance trends of all FETs are still challenged by carrier mobility dependence on the strengths of the electrical field along the channel. However, in cases when the ratio of FinFET volume to its surface dramatically decreases, one should carefully consider the surface boundary conditions of the device. Moreover, the inherent non-planar nature of a FinFET demands 3D modeling for accurate analysis of the device performance. Using the Silvaco modeling tool with quantization effects, we modeled a physical FinFET described in the work of Hisamoto et al. (IEEE Tran. Elec. Devices 47:12, 2000) in 3D. We compared it with a 2D model of the same device. We demonstrated that 3D modeling produces more accurate results. As 3D modeling results came close to experimental measurements, we made the next step of the study by designing a dual-gate FinFET biased at Vg1 >Vg2. It is shown that the dual-gate FinFET carries higher transconductance than the single-gate device. PMID:23148493

  4. 3D cartographic modeling of the Alpine arc

    NASA Astrophysics Data System (ADS)

    Vouillamoz, Naomi; Sue, Christian; Champagnac, Jean-Daniel; Calcagno, Philippe

    2012-12-01

    We built a 3D cartography of the Alpine arc, a highly non-cylindrical mountain belt, using the 3D GeoModeller of the BRGM (French geological survey). The model allows to handle the large-scale 3D structure of seventeen major crustal units of the belt (from the lower crust to the sedimentary cover nappes), and two main discontinuities (the Insubric Line and the Crustal Penninic Front). It provides a unique document to better understand their structural relationships and to produce new sections. The study area comprises the western Alpine arc, from the Jura to the Northwest, up to the Bergell granite intrusion and the Lepontine Dome to the East, and is limited to the South by the Ligurian basin. The model is limited vertically 10 km above sea level at the top, and the moho interface at the bottom. We discarded the structural relationships between the Alps sensus stricto and the surrounding geodynamic systems such as the Rhine graben or the connection with the Apennines. The 3D-model is based on the global integration of various data such as the DEM of the Alps, the moho isobaths, the simplified geological and tectonic maps of the belt, the crustal cross-sections ECORS-CROP and NFP-20, and complementary cross-sections specifically built to precise local complexities. The database has first been integrated in a GIS-project to prepare their implementation in the GeoModeller, by homogenizing the different spatial referencing systems. The global model is finally interpolated from all these data, using the potential field method. The final document is a new tri-dimensional cartography that would be used as input for further alpine studies.

  5. Generation of an in vitro 3D PDAC stroma rich spheroid model.

    PubMed

    Ware, Matthew J; Keshishian, Vazrik; Law, Justin J; Ho, Jason C; Favela, Carlos A; Rees, Paul; Smith, Billie; Mohammad, Sayeeduddin; Hwang, Rosa F; Rajapakshe, Kimal; Coarfa, Cristian; Huang, Shixia; Edwards, Dean P; Corr, Stuart J; Godin, Biana; Curley, Steven A

    2016-11-01

    Pancreatic ductal adenocarcinoma (PDAC) is characterized by a prominent desmoplastic/stromal reaction, which contributes to the poor clinical outcome of this disease. Therefore, greater understanding of the stroma development and tumor-stroma interactions is highly required. Pancreatic stellate cells (PSC) are myofibroblast-like cells located in exocrine areas of the pancreas, which as a result of inflammation produced by PDAC migrate and accumulate in the tumor mass, secreting extracellular matrix components and producing the dense PDAC stroma. Currently, only a few orthotopic or ectopic animal tumor models, where PDAC cells are injected into the pancreas or subcutaneous tissue layer, or genetically engineered animals offer tumors that encompass some stromal component. Herein, we report generation of a simple 3D PDAC in vitro micro-tumor model without an addition of external extracellular matrix, which encompasses a rich, dense and active stromal compartment. We have achieved this in vitro model by incorporating PSCs into 3D PDAC cell culture using a modified hanging drop method. It is now known that PSCs are the principal source of fibrosis in the stroma and interact closely with cancer cells to create a tumor facilitatory environment that stimulates local and distant tumor growth. The 3D micro-stroma models are highly reproducible with excellent uniformity, which can be used for PDAC-stroma interaction analysis and high throughput automated drug-screening assays. Additionally, the increased expression of collagenous regions means that molecular based perfusion and cytostaticity of gemcitabine is decreased in our Pancreatic adenocarcinoma stroma spheroids (PDAC-SS) model when compared to spheroids grown without PSCs. We believe this model will allow an improved knowledge of PDAC biology and has the potential to provide an insight into pathways that may be therapeutically targeted to inhibit PSC activation, thereby inhibiting the development of fibrosis in PDAC

  6. Interchain coupling and 3D modeling of trans-polyacetylene

    SciTech Connect

    Bronold, F.; Saxena, A.; Bishop, A.R.

    1992-01-01

    In spite of the success of the SSH model for trans-polyacetylene in interpreting many experimental results (e.g. optical and magnetic properties) there remain some aspects of the real material which are outside the scope of the simple 1D model. Especially ordering phenomena of doped and undoped trans-polyacetylene as well as transport properties (e.g. electronic and thermal conductivity) are beyond a 1D description. There are many attempts to construct a transport theory for this novel class of materials using solitons or polaxons as the basic ingredients. But so far it is not yet clear whether these typical 1D excitations still exist in crystalline transpolyacetylene. Therefore, to clarify the role which intrinsic self-localized nonlinear excitations characteristic of 1D models play in the bulk (3D) material, we study the stability of a polaronic excitation against interchain coupling. As a preliminary step we consider first two coupled t-(CH){sub x}-chains where the {pi}-electrons are allowed to hop from one chain to the other. Then we introduce a 3D generalization of the SSH model and study a polaron in a 3D crystalline environment.

  7. Interchain coupling and 3D modeling of trans-polyacetylene

    SciTech Connect

    Bronold, F.; Saxena, A.; Bishop, A.R.

    1992-09-01

    In spite of the success of the SSH model for trans-polyacetylene in interpreting many experimental results (e.g. optical and magnetic properties) there remain some aspects of the real material which are outside the scope of the simple 1D model. Especially ordering phenomena of doped and undoped trans-polyacetylene as well as transport properties (e.g. electronic and thermal conductivity) are beyond a 1D description. There are many attempts to construct a transport theory for this novel class of materials using solitons or polaxons as the basic ingredients. But so far it is not yet clear whether these typical 1D excitations still exist in crystalline transpolyacetylene. Therefore, to clarify the role which intrinsic self-localized nonlinear excitations characteristic of 1D models play in the bulk (3D) material, we study the stability of a polaronic excitation against interchain coupling. As a preliminary step we consider first two coupled t-(CH){sub x}-chains where the {pi}-electrons are allowed to hop from one chain to the other. Then we introduce a 3D generalization of the SSH model and study a polaron in a 3D crystalline environment.

  8. 3-D Numerical Modeling of a Complex Salt Structure

    SciTech Connect

    House, L.; Larsen, S.; Bednar, J.B.

    2000-02-17

    Reliably processing, imaging, and interpreting seismic data from areas with complicated structures, such as sub-salt, requires a thorough understanding of elastic as well as acoustic wave propagation. Elastic numerical modeling is an essential tool to develop that understanding. While 2-D elastic modeling is in common use, 3-D elastic modeling has been too computationally intensive to be used routinely. Recent advances in computing hardware, including commodity-based hardware, have substantially reduced computing costs. These advances are making 3-D elastic numerical modeling more feasible. A series of example 3-D elastic calculations were performed using a complicated structure, the SEG/EAGE salt structure. The synthetic traces show that the effects of shear wave propagation can be important for imaging and interpretation of images, and also for AVO and other applications that rely on trace amplitudes. Additional calculations are needed to better identify and understand the complex wave propagation effects produced in complicated structures, such as the SEG/EAGE salt structure.

  9. CityGML - Interoperable semantic 3D city models

    NASA Astrophysics Data System (ADS)

    Gröger, Gerhard; Plümer, Lutz

    2012-07-01

    CityGML is the international standard of the Open Geospatial Consortium (OGC) for the representation and exchange of 3D city models. It defines the three-dimensional geometry, topology, semantics and appearance of the most relevant topographic objects in urban or regional contexts. These definitions are provided in different, well-defined Levels-of-Detail (multiresolution model). The focus of CityGML is on the semantical aspects of 3D city models, its structures, taxonomies and aggregations, allowing users to employ virtual 3D city models for advanced analysis and visualization tasks in a variety of application domains such as urban planning, indoor/outdoor pedestrian navigation, environmental simulations, cultural heritage, or facility management. This is in contrast to purely geometrical/graphical models such as KML, VRML, or X3D, which do not provide sufficient semantics. CityGML is based on the Geography Markup Language (GML), which provides a standardized geometry model. Due to this model and its well-defined semantics and structures, CityGML facilitates interoperable data exchange in the context of geo web services and spatial data infrastructures. Since its standardization in 2008, CityGML has become used on a worldwide scale: tools from notable companies in the geospatial field provide CityGML interfaces. Many applications and projects use this standard. CityGML is also having a strong impact on science: numerous approaches use CityGML, particularly its semantics, for disaster management, emergency responses, or energy-related applications as well as for visualizations, or they contribute to CityGML, improving its consistency and validity, or use CityGML, particularly its different Levels-of-Detail, as a source or target for generalizations. This paper gives an overview of CityGML, its underlying concepts, its Levels-of-Detail, how to extend it, its applications, its likely future development, and the role it plays in scientific research. Furthermore, its

  10. Lattice percolation approach to 3D modeling of tissue aging

    NASA Astrophysics Data System (ADS)

    Gorshkov, Vyacheslav; Privman, Vladimir; Libert, Sergiy

    2016-11-01

    We describe a 3D percolation-type approach to modeling of the processes of aging and certain other properties of tissues analyzed as systems consisting of interacting cells. Lattice sites are designated as regular (healthy) cells, senescent cells, or vacancies left by dead (apoptotic) cells. The system is then studied dynamically with the ongoing processes including regular cell dividing to fill vacant sites, healthy cells becoming senescent or dying, and senescent cells dying. Statistical-mechanics description can provide patterns of time dependence and snapshots of morphological system properties. The developed theoretical modeling approach is found not only to corroborate recent experimental findings that inhibition of senescence can lead to extended lifespan, but also to confirm that, unlike 2D, in 3D senescent cells can contribute to tissue's connectivity/mechanical stability. The latter effect occurs by senescent cells forming the second infinite cluster in the regime when the regular (healthy) cell's infinite cluster still exists.

  11. The 3D model control of image processing

    NASA Technical Reports Server (NTRS)

    Nguyen, An H.; Stark, Lawrence

    1989-01-01

    Telerobotics studies remote control of distant robots by a human operator using supervisory or direct control. Even if the robot manipulators has vision or other senses, problems arise involving control, communications, and delay. The communication delays that may be expected with telerobots working in space stations while being controlled from an Earth lab have led to a number of experiments attempting to circumvent the problem. This delay in communication is a main motivating factor in moving from well understood instantaneous hands-on manual control to less well understood supervisory control; the ultimate step would be the realization of a fully autonomous robot. The 3-D model control plays a crucial role in resolving many conflicting image processing problems that are inherent in resolving in the bottom-up approach of most current machine vision processes. The 3-D model control approach is also capable of providing the necessary visual feedback information for both the control algorithms and for the human operator.

  12. 3D root canal modeling for advanced endodontic treatment

    NASA Astrophysics Data System (ADS)

    Hong, Shane Y.; Dong, Janet

    2002-06-01

    More than 14 million teeth receive endodontic (root canal) treatment annually. Before a clinician's inspection and diagnosis, destructive access preparation by removing teeth crown and dentin is usually needed. This paper presents a non-invasive method for accessing internal tooth geometry by building 3-D tooth model from 2-D radiographic and endoscopic images to be used for an automatic prescription system of computer-aided treatment procedure planning, and for the root canal preparation by an intelligent micro drilling machine with on-line monitoring. It covers the techniques specific for dental application in the radiographic images acquirement, image enhancement, image segmentation and feature recognition, distance measurement and calibration, merging 2D image into 3D mathematical model representation and display. Included also are the methods to form references for irregular teeth geometry and to do accurately measurement with self-calibration.

  13. Modeling 3D faces from samplings via compressive sensing

    NASA Astrophysics Data System (ADS)

    Sun, Qi; Tang, Yanlong; Hu, Ping

    2013-07-01

    3D data is easier to acquire for family entertainment purpose today because of the mass-production, cheapness and portability of domestic RGBD sensors, e.g., Microsoft Kinect. However, the accuracy of facial modeling is affected by the roughness and instability of the raw input data from such sensors. To overcome this problem, we introduce compressive sensing (CS) method to build a novel 3D super-resolution scheme to reconstruct high-resolution facial models from rough samples captured by Kinect. Unlike the simple frame fusion super-resolution method, this approach aims to acquire compressed samples for storage before a high-resolution image is produced. In this scheme, depth frames are firstly captured and then each of them is measured into compressed samples using sparse coding. Next, the samples are fused to produce an optimal one and finally a high-resolution image is recovered from the fused sample. This framework is able to recover 3D facial model of a given user from compressed simples and this can reducing storage space as well as measurement cost in future devices e.g., single-pixel depth cameras. Hence, this work can potentially be applied into future applications, such as access control system using face recognition, and smart phones with depth cameras, which need high resolution and little measure time.

  14. STELLOPT modeling of the 3D diagnostic response in ITER

    NASA Astrophysics Data System (ADS)

    Lazerson, S. A.; Chapman, I. T.

    2013-08-01

    The ITER three-dimensional (3D) diagnostic response to an n = 3 resonant magnetic perturbation (RMP) is modeled using the STELLOPT code. The in-vessel coils apply a RMP field which generates a 4 cm edge displacement from axisymmetry as modeled by the VMEC 3D equilibrium code. Forward modeling of flux loop and magnetic probe response with the DIAGNO code indicates up to 20% changes in measured plasma signals. Simulated LIDAR measurements of electron temperature indicate 2 cm shifts on the low-field side of the plasma. This suggests that the ITER diagnostic will be able to diagnose the 3D structure of the equilibria. Notice: This paper has been authored by Princeton University under Contract Number DE-AC02-09CH11466 with the US Department of Energy. The publisher, by accepting the paper for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this Paper, or allow others to do so, for United States Government purposes.

  15. Modelling of 3D fractured geological systems - technique and application

    NASA Astrophysics Data System (ADS)

    Cacace, M.; Scheck-Wenderoth, M.; Cherubini, Y.; Kaiser, B. O.; Bloecher, G.

    2011-12-01

    All rocks in the earth's crust are fractured to some extent. Faults and fractures are important in different scientific and industry fields comprising engineering, geotechnical and hydrogeological applications. Many petroleum, gas and geothermal and water supply reservoirs form in faulted and fractured geological systems. Additionally, faults and fractures may control the transport of chemical contaminants into and through the subsurface. Depending on their origin and orientation with respect to the recent and palaeo stress field as well as on the overall kinematics of chemical processes occurring within them, faults and fractures can act either as hydraulic conductors providing preferential pathways for fluid to flow or as barriers preventing flow across them. The main challenge in modelling processes occurring in fractured rocks is related to the way of describing the heterogeneities of such geological systems. Flow paths are controlled by the geometry of faults and their open void space. To correctly simulate these processes an adequate 3D mesh is a basic requirement. Unfortunately, the representation of realistic 3D geological environments is limited by the complexity of embedded fracture networks often resulting in oversimplified models of the natural system. A technical description of an improved method to integrate generic dipping structures (representing faults and fractures) into a 3D porous medium is out forward. The automated mesh generation algorithm is composed of various existing routines from computational geometry (e.g. 2D-3D projection, interpolation, intersection, convex hull calculation) and meshing (e.g. triangulation in 2D and tetrahedralization in 3D). All routines have been combined in an automated software framework and the robustness of the approach has been tested and verified. These techniques and methods can be applied for fractured porous media including fault systems and therefore found wide applications in different geo-energy related

  16. Advanced 3D image processing techniques for liver and hepatic tumor location and volumetry

    NASA Astrophysics Data System (ADS)

    Chemouny, Stephane; Joyeux, Henri; Masson, Bruno; Borne, Frederic; Jaeger, Marc; Monga, Olivier

    1999-05-01

    To assist radiologists and physicians in diagnosing, and in treatment planning and evaluating in liver oncology, we have developed a fast and accurate segmentation of the liver and its lesions within CT-scan exams. The first step of our method is to reduce spatial resolution of CT images. This will have two effects: obtain near isotropic 3D data space and drastically decrease computational time for further processing. On a second step a 3D non-linear `edge- preserving' smoothing filtering is performed throughout the entire exam. On a third step the 3D regions coming out from the second step are homogeneous enough to allow a quite simple segmentation process, based on morphological operations, under supervisor control, ending up with accurate 3D regions of interest (ROI) of the liver and all the hepatic tumors. On a fourth step the ROIs are eventually set back into the original images, features like volume and location are immediately computed and displayed. The segmentation we get is as precise as a manual one but is much faster.

  17. West Flank Coso, CA FORGE 3D geologic model

    DOE Data Explorer

    Doug Blankenship

    2016-03-01

    This is an x,y,z file of the West Flank FORGE 3D geologic model. Model created in Earthvision by Dynamic Graphic Inc. The model was constructed with a grid spacing of 100 m. Geologic surfaces were extrapolated from the input data using a minimum tension gridding algorithm. The data file is tabular data in a text file, with lithology data associated with X,Y,Z grid points. All the relevant information is in the file header (the spatial reference, the projection etc.) In addition all the fields in the data file are identified in the header.

  18. 3D modelling of the Black Sea ecosystem

    NASA Astrophysics Data System (ADS)

    Capet, A.; Gregoire, M.; Beckers, J.-M.; Joassin, P.; Naithani, J.; Soetart, K.

    2009-04-01

    A coupled physical-biogeochemical model has been developed to simulate the ecosystem of the Black Sea at the end of the 80's when eutrophication and invasion by gelatinous organisms seriously affected the stability and dynamics of the system. The biogeochemical model describes the cycle of carbon, nitrogen, silicate, oxygen and phosphorus through the foodweb from bacteria to gelatinous carnivores and explicitly represents processes in the anoxic layer down to the bottom. For calibration and analyses purposes, the coupled model has first been run in 1D at several places in the Black Sea. The biogeochemical model involves some hundred parameters which have been first calibrated by hand using published values. Then, an identifiability analysis has been performed in order to determine a subset of 15 identifiable parameters. An automatic calibration subroutine has been used to fine tune these parameters. In 1D, the model solution exhibits a complex dynamics with several years of transient adjustment. This complexity is imparted by the explicit modelling of top predators. The model has been calibrated and validated using a large set of data available in the Black Sea TU Ocean Base. The calibrated biogeochemical model is implemented in a 3D hydrodynamical model of the Black Sea. Results of these 3D simulations will be presented and compared with maps of in-situ data reconstructed from available data base using the software DIVA (Data Interpolation and Variational analysis).

  19. Northern California Seismic Attenuation: 3-D Qp and Qs models

    NASA Astrophysics Data System (ADS)

    Eberhart-Phillips, D. M.

    2015-12-01

    The northern California crust exhibits a wide range of rock types and deformation processes which produce pronounced heterogeneity in regional attenuation. Using local earthquakes, 3-D Qp and Qs crustal models have been obtained for this region which includes the San Andreas fault system, the Central Valley, the Sierra Nevada batholith, and the Mendocino subduction volcanic system. Path attenuation t* values were determined from P and S spectra of 959 spatially distributed earthquakes, magnitude 2.5-6.0 from 2005-2014, using 1254 stations from NCEDC networks and IRIS Mendocino and Sierra Nevada temporary arrays. The t* data were used in Q inversions, using existing hypocenters and 3-D velocity models, with basic 10-km node spacing. The uneven data coverage was accounted for with linking of nodes into larger areas in order to provide useful Q images across the 3-D volume. The results at shallow depth (< 2 km) show very low Q in the Sacramento Delta, the Eureka area, and parts of the Bay Area. In the brittle crust, fault zones that have high seismicity exhibit low Q. In the lower crust, low Q is observed along fault zones that have large cumulative displacement and have experienced grain size reduction. Underlying active volcanic areas, low Q features are apparent below 20-km depth. Moderately high Q is associated with igneous rocks of the Sierra Nevada and Salinian block, while the Franciscan subduction complex shows moderately low Q. The most prominent high Q feature is related to the Great Valley Ophiolite.

  20. Effective 3-D surface modeling for geographic information systems

    NASA Astrophysics Data System (ADS)

    Yüksek, K.; Alparslan, M.; Mendi, E.

    2016-01-01

    In this work, we propose a dynamic, flexible and interactive urban digital terrain platform with spatial data and query processing capabilities of geographic information systems, multimedia database functionality and graphical modeling infrastructure. A new data element, called Geo-Node, which stores image, spatial data and 3-D CAD objects is developed using an efficient data structure. The system effectively handles data transfer of Geo-Nodes between main memory and secondary storage with an optimized directional replacement policy (DRP) based buffer management scheme. Polyhedron structures are used in digital surface modeling and smoothing process is performed by interpolation. The experimental results show that our framework achieves high performance and works effectively with urban scenes independent from the amount of spatial data and image size. The proposed platform may contribute to the development of various applications such as Web GIS systems based on 3-D graphics standards (e.g., X3-D and VRML) and services which integrate multi-dimensional spatial information and satellite/aerial imagery.

  1. Right approach to 3D modeling using CAD tools

    NASA Astrophysics Data System (ADS)

    Baddam, Mounica Reddy

    The thesis provides a step-by-step methodology to enable an instructor dealing with CAD tools to optimally guide his/her students through an understandable 3D modeling approach which will not only enhance their knowledge about the tool's usage but also enable them to achieve their desired result in comparatively lesser time. In the known practical field, there is particularly very little information available to apply CAD skills to formal beginners' training sessions. Additionally, advent of new software in 3D domain cumulates updating into a more difficult task. Keeping up to the industry's advanced requirements emphasizes the importance of more skilled hands in the field of CAD development, rather than just prioritizing manufacturing in terms of complex software features. The thesis analyses different 3D modeling approaches specified to the varieties of CAD tools currently available in the market. Utilizing performance-time databases, learning curves have been generated to measure their performance time, feature count etc. Based on the results, improvement parameters have also been provided for (Asperl, 2005).

  2. 3D-printer visualization of neuron models

    PubMed Central

    McDougal, Robert A.; Shepherd, Gordon M.

    2015-01-01

    Neurons come in a wide variety of shapes and sizes. In a quest to understand this neuronal diversity, researchers have three-dimensionally traced tens of thousands of neurons; many of these tracings are freely available through online repositories like NeuroMorpho.Org and ModelDB. Tracings can be visualized on the computer screen, used for statistical analysis of the properties of different cell types, used to simulate neuronal behavior, and more. We introduce the use of 3D printing as a technique for visualizing traced morphologies. Our method for generating printable versions of a cell or group of cells is to expand dendrite and axon diameters and then to transform the tracing into a 3D object with a neuronal surface generating algorithm like Constructive Tessellated Neuronal Geometry (CTNG). We show that 3D printed cells can be readily examined, manipulated, and compared with other neurons to gain insight into both the biology and the reconstruction process. We share our printable models in a new database, 3DModelDB, and encourage others to do the same with cells that they generate using our code or other methods. To provide additional context, 3DModelDB provides a simulatable version of each cell, links to papers that use or describe it, and links to associated entries in other databases. PMID:26175684

  3. 3D-printer visualization of neuron models.

    PubMed

    McDougal, Robert A; Shepherd, Gordon M

    2015-01-01

    Neurons come in a wide variety of shapes and sizes. In a quest to understand this neuronal diversity, researchers have three-dimensionally traced tens of thousands of neurons; many of these tracings are freely available through online repositories like NeuroMorpho.Org and ModelDB. Tracings can be visualized on the computer screen, used for statistical analysis of the properties of different cell types, used to simulate neuronal behavior, and more. We introduce the use of 3D printing as a technique for visualizing traced morphologies. Our method for generating printable versions of a cell or group of cells is to expand dendrite and axon diameters and then to transform the tracing into a 3D object with a neuronal surface generating algorithm like Constructive Tessellated Neuronal Geometry (CTNG). We show that 3D printed cells can be readily examined, manipulated, and compared with other neurons to gain insight into both the biology and the reconstruction process. We share our printable models in a new database, 3DModelDB, and encourage others to do the same with cells that they generate using our code or other methods. To provide additional context, 3DModelDB provides a simulatable version of each cell, links to papers that use or describe it, and links to associated entries in other databases.

  4. Underwater 3d Modeling: Image Enhancement and Point Cloud Filtering

    NASA Astrophysics Data System (ADS)

    Sarakinou, I.; Papadimitriou, K.; Georgoula, O.; Patias, P.

    2016-06-01

    This paper examines the results of image enhancement and point cloud filtering on the visual and geometric quality of 3D models for the representation of underwater features. Specifically it evaluates the combination of effects from the manual editing of images' radiometry (captured at shallow depths) and the selection of parameters for point cloud definition and mesh building (processed in 3D modeling software). Such datasets, are usually collected by divers, handled by scientists and used for geovisualization purposes. In the presented study, have been created 3D models from three sets of images (seafloor, part of a wreck and a small boat's wreck) captured at three different depths (3.5m, 10m and 14m respectively). Four models have been created from the first dataset (seafloor) in order to evaluate the results from the application of image enhancement techniques and point cloud filtering. The main process for this preliminary study included a) the definition of parameters for the point cloud filtering and the creation of a reference model, b) the radiometric editing of images, followed by the creation of three improved models and c) the assessment of results by comparing the visual and the geometric quality of improved models versus the reference one. Finally, the selected technique is tested on two other data sets in order to examine its appropriateness for different depths (at 10m and 14m) and different objects (part of a wreck and a small boat's wreck) in the context of an ongoing research in the Laboratory of Photogrammetry and Remote Sensing.

  5. 3D Geologic Model of the San Diego Area

    NASA Astrophysics Data System (ADS)

    Danskin, W. R.; Cromwell, G.; Glockhoff, C.; Martin, D.

    2015-12-01

    Prior geologic studies of the San Diego area, including northern Baja California, Mexico, focused on site investigations, characterization of rock formations, or earthquake hazards. No comprehensive, quantitative model characterizing the three-dimensional (3D) geology of the entire area has been developed. The lack of such a model limits understanding of large-scale processes, such as development of ancient landforms, and groundwater movement and availability. To evaluate these regional processes, the United States Geological Survey (USGS) conducted a study to better understand the geologic structure of the San Diego area. A cornerstone of this study is the installation and analysis of 77 wells at 12 multiple-depth monitoring-well sites. Geologic information from these wells was combined with lithologic data from 81 oil exploration wells and municipal and private water wells, gravity and seismic interpretations, and paleontological interpretations. These data were analyzed in conjunction with geologic maps and digital elevation models to develop a 3D geologic model of the San Diego area, in particular of the San Diego embayment. Existing interpretations of regional surficial geology, faulting, and tectonic history provided the framework for this model, which was refined by independent evaluation of subsurface geology. Geologic formations were simplified into five sedimentary units (Quaternary, Plio-Pleistocene, Oligocene, Eocene and Cretaceous ages), and one basal crystalline unit (primarily Cretaceous and Jurassic). Complex fault systems are represented in the model by ten fault strands that maintain overall displacement. The 3D geologic model corroborates existing geologic concepts of the San Diego area, refines the extent of subsurface geology, and allows users to holistically evaluate subsurface structures and regional hydrogeology.

  6. Subduction zone guided waves: 3D modelling and attenuation effects

    NASA Astrophysics Data System (ADS)

    Garth, T.; Rietbrock, A.

    2013-12-01

    Waveform modelling is an important tool for understanding complex seismic structures such as subduction zone waveguides. These structures are often simplified to 2D structures for modelling purposes to reduce computational costs. In the case of subduction zone waveguide affects, 2D models have shown that dispersed arrivals are caused by a low velocity waveguide, inferred to be subducted oceanic crust and/or hydrated outer rise normal faults. However, due to the 2D modelling limitations the inferred seismic properties such as velocity contrast and waveguide thickness are still debated. Here we test these limitations with full 3D waveform modelling. For waveguide effects to be observable the waveform must be accurately modelled to relatively high frequencies (> 2 Hz). This requires a small grid spacing due to the high seismic velocities present in subduction zones. A large area must be modelled as well due to the long propagation distances (400 - 600 km) of waves interacting with subduction zone waveguides. The combination of the large model area and small grid spacing required means that these simulations require a large amount of computational resources, only available at high performance computational centres like the UK National super computer HECTOR (used in this study). To minimize the cost of modelling for such a large area, the width of the model area perpendicular to the subduction trench (the y-direction) is made as small as possible. This reduces the overall volume of the 3D model domain. Therefore the wave field is simulated in a model ';corridor' of the subduction zone velocity structure. This introduces new potential sources of error particularly from grazing wave side reflections in the y-direction. Various dampening methods are explored to reduce these grazing side reflections, including perfectly matched layers (PML) and more traditional exponential dampening layers. Defining a corridor model allows waveguide affects to be modelled up to at least 2

  7. 3D flare particle model for ShipIR/NTCS

    NASA Astrophysics Data System (ADS)

    Ramaswamy, Srinivasan; Vaitekunas, David A.

    2016-05-01

    A key component in any soft-kill response to an incoming guided missile is the flare /chaff decoy used to distract or seduce the seeker homing system away from the naval platform. This paper describes a new 3D flare particle model in the naval threat countermeasure simulator (NTCS) of the NATO-standard ship signature model (ShipIR), which provides independent control over the size and radial distribution of its signature. The 3D particles of each flare sub-munition are modelled stochastically and rendered using OpenGL z-buffering, 2D projection, and alpha-blending to produce a unique and time varying signature. A sensitivity analysis on each input parameter provides the data and methods needed to synthesize a model from an IR measurement of a decoy. The new model also eliminated artifacts and deficiencies in our previous model which prevented reliable tracks from the adaptive track gate algorithm already presented by Ramaswamy and Vaitekunas (2015). A sequence of scenarios are used to test and demonstrate the new flare model during a missile engagement.

  8. Digital 3D Borobudur - Integration of 3D surveying and modeling techniques

    NASA Astrophysics Data System (ADS)

    Suwardhi, D.; Menna, F.; Remondino, F.; Hanke, K.; Akmalia, R.

    2015-08-01

    The Borobudur temple (Indonesia) is one of the greatest Buddhist monuments in the world, now listed as an UNESCO World Heritage Site. The present state of the temple is the result of restorations after being exposed to natural disasters several times. Today there is still a growing rate of deterioration of the building stones whose causes need further researches. Monitoring programs, supported at institutional level, have been effectively executed to observe the problem. The paper presents the latest efforts to digitally document the Borobudur Temple and its surrounding area in 3D with photogrammetric techniques. UAV and terrestrial images were acquired to completely digitize the temple, produce DEM, orthoimages and maps at 1:100 and 1:1000 scale. The results of the project are now employed by the local government organizations to manage the heritage area and plan new policies for the conservation and preservation of the UNESCO site. In order to help data management and policy makers, a web-based information system of the heritage area was also built to visualize and easily access all the data and achieved 3D results.

  9. Discrete Method of Images for 3D Radio Propagation Modeling

    NASA Astrophysics Data System (ADS)

    Novak, Roman

    2016-09-01

    Discretization by rasterization is introduced into the method of images (MI) in the context of 3D deterministic radio propagation modeling as a way to exploit spatial coherence of electromagnetic propagation for fine-grained parallelism. Traditional algebraic treatment of bounding regions and surfaces is replaced by computer graphics rendering of 3D reflections and double refractions while building the image tree. The visibility of reception points and surfaces is also resolved by shader programs. The proposed rasterization is shown to be of comparable run time to that of the fundamentally parallel shooting and bouncing rays. The rasterization does not affect the signal evaluation backtracking step, thus preserving its advantage over the brute force ray-tracing methods in terms of accuracy. Moreover, the rendering resolution may be scaled back for a given level of scenario detail with only marginal impact on the image tree size. This allows selection of scene optimized execution parameters for faster execution, giving the method a competitive edge. The proposed variant of MI can be run on any GPU that supports real-time 3D graphics.

  10. Fluorescence in situ hybridization on 3D cultures of tumor cells.

    PubMed

    Meaburn, Karen J

    2010-01-01

    Genomes are spatially highly organized within interphase nuclei. Spatial genome organization is increasingly linked to genome function. Fluorescence in situ hybridization (FISH) allows the visualization of specific regions of the genome for spatial mapping. While most gene localization studies have been performed on cultured cells, genome organization is likely to be different in the context of tissues. Three-dimensional (3D) culture model systems provide a powerful tool to study the contribution of tissue organization to gene expression and organization. However, FISH on 3D cultures is technically more challenging than on monocultures. Here, we describe an optimized protocol for interphase DNA FISH on 3D cultures of the breast epithelial cell line MCF-10A.B2, which forms breast acini and can be used as a model for early breast cancer. PMID:20809324

  11. Fibroblasts Influence Survival and Therapeutic Response in a 3D Co-Culture Model.

    PubMed

    Majety, Meher; Pradel, Leon P; Gies, Manuela; Ries, Carola H

    2015-01-01

    In recent years, evidence has indicated that the tumor microenvironment (TME) plays a significant role in tumor progression. Fibroblasts represent an abundant cell population in the TME and produce several growth factors and cytokines. Fibroblasts generate a suitable niche for tumor cell survival and metastasis under the influence of interactions between fibroblasts and tumor cells. Investigating these interactions requires suitable experimental systems to understand the cross-talk involved. Most in vitro experimental systems use 2D cell culture and trans-well assays to study these interactions even though these paradigms poorly represent the tumor, in which direct cell-cell contacts in 3D spaces naturally occur. Investigating these interactions in vivo is of limited value due to problems regarding the challenges caused by the species-specificity of many molecules. Thus, it is essential to use in vitro models in which human fibroblasts are co-cultured with tumor cells to understand their interactions. Here, we developed a 3D co-culture model that enables direct cell-cell contacts between pancreatic, breast and or lung tumor cells and human fibroblasts/ or tumor-associated fibroblasts (TAFs). We found that co-culturing with fibroblasts/TAFs increases the proliferation in of several types of cancer cells. We also observed that co-culture induces differential expression of soluble factors in a cancer type-specific manner. Treatment with blocking antibodies against selected factors or their receptors resulted in the inhibition of cancer cell proliferation in the co-cultures. Using our co-culture model, we further revealed that TAFs can influence the response to therapeutic agents in vitro. We suggest that this model can be reliably used as a tool to investigate the interactions between a tumor and the TME.

  12. Modeling the GFR with RELAP5-3D

    SciTech Connect

    Cliff B. Davis; Theron D. Marshall; K. D. Weaver

    2005-09-01

    Significant improvements have been made to the RELAP5-3D computer code for analysis of the Gas Fast Reactor (GFR). These improvements consisted of adding carbon dioxide as a working fluid, improving the turbine component, developing a compressor model, and adding the Gnielinski heat transfer correlation. The code improvements were validated, generally through comparisons with independent design calculations. A model of the power conversion unit of the GFR was developed. The model of the power conversion unit was coupled to a reactor model to develop a complete model of the GFR system. The RELAP5 model of the GFR was used to simulate two transients, one initiated by a reactor trip and the other initiated by a loss of load.

  13. Testing Mercury Porosimetry with 3D Printed Porosity Models

    NASA Astrophysics Data System (ADS)

    Hasiuk, F.; Ewing, R. P.; Hu, Q.

    2014-12-01

    Mercury intrusion porosimetry is one of the most widely used techniques to study the porous nature of a geological and man-made materials. In the geosciences, it is commonly used to describe petroleum reservoir and seal rocks as well as to grade aggregates for the design of asphalt and portland cement concretes. It's wide utility stems from its ability to characterize a wide range of pore throat sizes (from nanometers to around a millimeter). The fundamental physical model underlying mercury intrusion porosimetry, the Washburn Equation, is based on the assumption that rock porosity can be described as a bundle of cylindrical tubes. 3D printing technology, also known as rapid prototyping, allows the construction of intricate and accurate models, exactly what is required to build models of rock porosity. We evaluate the applicability of the Washburn Equation by comparing properties (like porosity, pore and pore throat size distribution, and surface area) computed on digital porosity models (built from CT data, CAD designs, or periodic geometries) to properties measured via mercury intrusion porosimetry on 3D printed versions of the same digital porosity models.

  14. Simulation of AIMS measurements using rigorous mask 3D modeling

    NASA Astrophysics Data System (ADS)

    Chou, Chih-Shiang; Huang, Hsu-Ting; Chu, Fu-Sheng; Chu, Yuan-Chih; Huang, Wen-Chun; Liu, Ru-Gun; Gau, Tsai-Sheng

    2015-03-01

    Aerial image measurement system (AIMSTM) has been widely used for wafer level inspection of mask defects. Reported inspection flows include die-to-die (D2D) and die-to-database (D2DB) methods. For patterns that do not repeat in another die, only the D2DB approach is applicable. The D2DB method requires accurate simulation of AIMS measurements for a mask pattern. An optical vectorial model is needed to depict the mask diffraction effect in this simulation. To accurately simulate the imaging results, a rigorous electro-magnetic field (EMF) model is essential to correctly take account of the EMF scattering induced by the mask topography, which is usually called the mask 3D effect. In this study, the mask 3D model we use is rigorous coupled-wave analysis (RCWA), which calculates the diffraction fields from a single plane wave incidence. A hybrid Hopkins-Abbe method with RCWA is used to calculate the EMF diffraction at a desired accuracy level while keeping the computation time practical. We will compare the speed of the hybrid Hopkins-Abbe method to the rigorous Abbe method. The matching between simulation and experiment is more challenging for AIMS than CD-SEM because its measurements provide full intensity information. Parameters in the mask 3D model such as film stack thickness or film optical properties, is optimized during the fitting process. We will report the fitting results of AIMS images for twodimensional structures with various pitches. By accurately simulating the AIMS measurements, it provides a necessary tool to perform the mask inspection using the D2DB approach and to accurately predict the mask defects.

  15. Exploiting Textured 3D Models for Developing Serious Games

    NASA Astrophysics Data System (ADS)

    Kontogianni, G.; Georgopoulos, A.

    2015-08-01

    Digital technologies have affected significantly many fields of computer graphics such as Games and especially the field of the Serious Games. These games are usually used for educational proposes in many fields such as Health Care, Military applications, Education, Government etc. Especially Digital Cultural Heritage is a scientific area that Serious Games are applied and lately many applications appear in the related literature. Realistic 3D textured models which have been produced using different photogrammetric methods could be a useful tool for the creation of Serious Game applications in order to make the final result more realistic and close to the reality. The basic goal of this paper is how 3D textured models which are produced by photogrammetric methods can be useful for developing a more realistic environment of a Serious Game. The application of this project aims at the creation of an educational game for the Ancient Agora of Athens. The 3D models used vary not only as far as their production methods (i.e. Time of Flight laser scanner, Structure from Motion, Virtual historical reconstruction etc.) is concerned, but also as far as their era as some of them illustrated according to their existing situation and some others according to how these monuments looked like in the past. The Unity 3D® game developing environment was used for creating this application, in which all these models were inserted in the same file format. For the application two diachronic virtual tours of the Athenian Agora were produced. The first one illustrates the Agora as it is today and the second one at the 2nd century A.D. Finally the future perspective for the evolution of this game is presented which includes the addition of some questions that the user will be able to answer. Finally an evaluation is scheduled to be performed at the end of the project.

  16. 3D model tools for architecture and archaeology reconstruction

    NASA Astrophysics Data System (ADS)

    Vlad, Ioan; Herban, Ioan Sorin; Stoian, Mircea; Vilceanu, Clara-Beatrice

    2016-06-01

    The main objective of architectural and patrimonial survey is to provide a precise documentation of the status quo of the surveyed objects (monuments, buildings, archaeological object and sites) for preservation and protection, for scientific studies and restoration purposes, for the presentation to the general public. Cultural heritage documentation includes an interdisciplinary approach having as purpose an overall understanding of the object itself and an integration of the information which characterize it. The accuracy and the precision of the model are directly influenced by the quality of the measurements realized on field and by the quality of the software. The software is in the process of continuous development, which brings many improvements. On the other side, compared to aerial photogrammetry, close range photogrammetry and particularly architectural photogrammetry is not limited to vertical photographs with special cameras. The methodology of terrestrial photogrammetry has changed significantly and various photographic acquisitions are widely in use. In this context, the present paper brings forward a comparative study of TLS (Terrestrial Laser Scanner) and digital photogrammetry for 3D modeling. The authors take into account the accuracy of the 3D models obtained, the overall costs involved for each technology and method and the 4th dimension - time. The paper proves its applicability as photogrammetric technologies are nowadays used at a large scale for obtaining the 3D model of cultural heritage objects, efficacious in their assessment and monitoring, thus contributing to historic conservation. Its importance also lies in highlighting the advantages and disadvantages of each method used - very important issue for both the industrial and scientific segment when facing decisions such as in which technology to invest more research and funds.

  17. The Engelbourg's ruins: from 3D TLS point cloud acquisition to 3D virtual and historic models

    NASA Astrophysics Data System (ADS)

    Koehl, Mathieu; Berger, Solveig; Nobile, Sylvain

    2014-05-01

    The Castle of Engelbourg was built at the beginning of the 13th century, at the top of the Schlossberg. It is situated on the territory of the municipality of Thann (France), at the crossroads of Alsace and Lorraine, and dominates the outlet of the valley of Thur. Its strategic position was one of the causes of its systematic destructions during the 17th century, and Louis XIV finished his fate by ordering his demolition in 1673. Today only few vestiges remain, of which a section of the main tower from about 7m of diameter and 4m of wide laying on its slice, unique characteristic in the regional castral landscape. It is visible since the valley, was named "the Eye of the witch", and became a key attraction of the region. The site, which extends over approximately one hectare, is for several years the object of numerous archaeological studies and is at the heart of a project of valuation of the vestiges today. It was indeed a key objective, among the numerous planned works, to realize a 3D model of the site in its current state, in other words, a virtual model "such as seized", exploitable as well from a cultural and tourist point of view as by scientists and in archaeological researches. The team of the ICube/INSA lab had in responsibility the realization of this model, the acquisition of the data until the delivery of the virtual model, thanks to 3D TLS and topographic surveying methods. It was also planned to integrate into this 3D model, data of 2D archives, stemming from series of former excavations. The objectives of this project were the following ones: • Acquisition of 3D digital data of the site and 3D modelling • Digitization of the 2D archaeological data and integration in the 3D model • Implementation of a database connected to the 3D model • Virtual Visit of the site The obtained results allowed us to visualize every 3D object individually, under several forms (point clouds, 3D meshed objects and models, etc.) and at several levels of detail

  18. Discussion of Source Reconstruction Models Using 3D MCG Data

    NASA Astrophysics Data System (ADS)

    Melis, Massimo De; Uchikawa, Yoshinori

    In this study we performed the source reconstruction of magnetocardiographic signals generated by the human heart activity to localize the site of origin of the heart activation. The localizations were performed in a four compartment model of the human volume conductor. The analyses were conducted on normal subjects and on a subject affected by the Wolff-Parkinson-White syndrome. Different models of the source activation were used to evaluate whether a general model of the current source can be applied in the study of the cardiac inverse problem. The data analyses were repeated using normal and vector component data of the MCG. The results show that a distributed source model has the better accuracy in performing the source reconstructions, and that 3D MCG data allow finding smaller differences between the different source models.

  19. Modeling moving systems with RELAP5-3D

    DOE PAGES

    Mesina, G. L.; Aumiller, David L.; Buschman, Francis X.; Kyle, Matt R.

    2015-12-04

    RELAP5-3D is typically used to model stationary, land-based reactors. However, it can also model reactors in other inertial and accelerating frames of reference. By changing the magnitude of the gravitational vector through user input, RELAP5-3D can model reactors on a space station or the moon. The field equations have also been modified to model reactors in a non-inertial frame, such as occur in land-based reactors during earthquakes or onboard spacecraft. Transient body forces affect fluid flow in thermal-fluid machinery aboard accelerating crafts during rotational and translational accelerations. It is useful to express the equations of fluid motion in the acceleratingmore » frame of reference attached to the moving craft. However, careful treatment of the rotational and translational kinematics is required to accurately capture the physics of the fluid motion. Correlations for flow at angles between horizontal and vertical are generated via interpolation where no experimental studies or data exist. The equations for three-dimensional fluid motion in a non-inertial frame of reference are developed. As a result, two different systems for describing rotational motion are presented, user input is discussed, and an example is given.« less

  20. Modeling moving systems with RELAP5-3D

    SciTech Connect

    Mesina, G. L.; Aumiller, David L.; Buschman, Francis X.; Kyle, Matt R.

    2015-12-04

    RELAP5-3D is typically used to model stationary, land-based reactors. However, it can also model reactors in other inertial and accelerating frames of reference. By changing the magnitude of the gravitational vector through user input, RELAP5-3D can model reactors on a space station or the moon. The field equations have also been modified to model reactors in a non-inertial frame, such as occur in land-based reactors during earthquakes or onboard spacecraft. Transient body forces affect fluid flow in thermal-fluid machinery aboard accelerating crafts during rotational and translational accelerations. It is useful to express the equations of fluid motion in the accelerating frame of reference attached to the moving craft. However, careful treatment of the rotational and translational kinematics is required to accurately capture the physics of the fluid motion. Correlations for flow at angles between horizontal and vertical are generated via interpolation where no experimental studies or data exist. The equations for three-dimensional fluid motion in a non-inertial frame of reference are developed. As a result, two different systems for describing rotational motion are presented, user input is discussed, and an example is given.

  1. 3D multispecies collisional model of Ganymede's atmosphere

    NASA Astrophysics Data System (ADS)

    Leblanc, Francois; Leclercq, Ludivine; Oza, Apurva; Schmidt, Carl; Modolo, Ronan; Chaufray, Jean-Yves; Johnson, Robert E.

    2016-10-01

    Ganymede's atmosphere is produced by the interaction of the Sun and of the Jovian magnetosphere with its surface. It is a reflection of Ganymede's surface properties, but also of the complex interaction between the Ganymede and Jupiter magnetospheres. The Exospheric Global Model (EGM) has been developed in order to be able to integrate surface and magnetosphere processes with those in Ganymede's atmosphere. It is a 3D parallelized multi-species collisional model, coupled with LatHys, a hybrid multi-grid 3D multi-species model of Ganymede's magnetosphere (Leclercq et al., Geophys. Res. Let., Submitted, 2016). EGM's description of the species-dependent spatial distribution of Ganymede's atmosphere, its temporal variability during rotation around Jupiter, its connection to the surface, the role of collisions, and respective roles of sublimation and sputtering in producing Ganymede's exosphere, illustrates how modeling combined with in situ and remote sensing of Ganymede's atmosphere can contribute to our understanding of this unique surface-atmosphere-magnetosphere integrated system.

  2. Reassessing Geophysical Models of the Bushveld Complex in 3D

    NASA Astrophysics Data System (ADS)

    Cole, J.; Webb, S. J.; Finn, C.

    2012-12-01

    Conceptual geophysical models of the Bushveld Igneous Complex show three possible geometries for its mafic component: 1) Separate intrusions with vertical feeders for the eastern and western lobes (Cousins, 1959) 2) Separate dipping sheets for the two lobes (Du Plessis and Kleywegt, 1987) 3) A single saucer-shaped unit connected at depth in the central part between the two lobes (Cawthorn et al, 1998) Model three incorporates isostatic adjustment of the crust in response to the weight of the dense mafic material. The model was corroborated by results of a broadband seismic array over southern Africa, known as the Southern African Seismic Experiment (SASE) (Nguuri, et al, 2001; Webb et al, 2004). This new information about the crustal thickness only became available in the last decade and could not be considered in the earlier models. Nevertheless, there is still on-going debate as to which model is correct. All of the models published up to now have been done in 2 or 2.5 dimensions. This is not well suited to modelling the complex geometry of the Bushveld intrusion. 3D modelling takes into account effects of variations in geometry and geophysical properties of lithologies in a full three dimensional sense and therefore affects the shape and amplitude of calculated fields. The main question is how the new knowledge of the increased crustal thickness, as well as the complexity of the Bushveld Complex, will impact on the gravity fields calculated for the existing conceptual models, when modelling in 3D. The three published geophysical models were remodelled using full 3Dl potential field modelling software, and including crustal thickness obtained from the SASE. The aim was not to construct very detailed models, but to test the existing conceptual models in an equally conceptual way. Firstly a specific 2D model was recreated in 3D, without crustal thickening, to establish the difference between 2D and 3D results. Then the thicker crust was added. Including the less

  3. Adaptive mesh refinement techniques for 3-D skin electrode modeling.

    PubMed

    Sawicki, Bartosz; Okoniewski, Michal

    2010-03-01

    In this paper, we develop a 3-D adaptive mesh refinement technique. The algorithm is constructed with an electric impedance tomography forward problem and the finite-element method in mind, but is applicable to a much wider class of problems. We use the method to evaluate the distribution of currents injected into a model of a human body through skin contact electrodes. We demonstrate that the technique leads to a significantly improved solution, particularly near the electrodes. We discuss error estimation, efficiency, and quality of the refinement algorithm and methods that allow for preserving mesh attributes in the refinement process.

  4. 3D simulation of the Cluster-Cluster Aggregation model

    NASA Astrophysics Data System (ADS)

    Li, Chao; Xiong, Hailing

    2014-12-01

    We write a program to implement the Cluster-Cluster Aggregation (CCA) model with java programming language. By using the simulation program, the fractal aggregation growth process can be displayed dynamically in the form of a three-dimensional (3D) figure. Meanwhile, the related kinetics data of aggregation simulation can be also recorded dynamically. Compared to the traditional programs, the program has better real-time performance and is more helpful to observe the fractal growth process, which contributes to the scientific study in fractal aggregation. Besides, because of adopting java programming language, the program has very good cross-platform performance.

  5. 3D in vitro cell culture models of tube formation.

    PubMed

    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

  6. A generic 3D kinetic model of gene expression

    NASA Astrophysics Data System (ADS)

    Zhdanov, Vladimir P.

    2012-04-01

    Recent experiments show that mRNAs and proteins can be localized both in prokaryotic and eukaryotic cells. To describe such situations, I present a 3D mean-field kinetic model aimed primarily at gene expression in prokaryotic cells, including the formation of mRNA, its translation into protein, and slow diffusion of these species. Under steady-state conditions, the mRNA and protein spatial distribution is described by simple exponential functions. The protein concentration near the gene transcribed into mRNA is shown to depend on the protein and mRNA diffusion coefficients and degradation rate constants.

  7. High Resolution 3d Numerical Modelling of Rockfalls

    NASA Astrophysics Data System (ADS)

    Agliardi, F.; Crosta, G. B.

    Accurate modelling of rockfall dynamics is a major issue for engineering geologists and land planners in rockfall prone areas, both for hazard assessment and the design of countermeasures. Numerical modelling of rockfalls has been generally performed in two dimensions. Thus, this is subjected to the crucial "a priori" choice of the rock- fall path and affected by a significant error due to the lateral dispersion of rockfall trajectories. In this study, an original 3D rockfall simulation program, first developed for regional scale distributed analysis, has been tested at a local scale with a very high spatial resolution, in order to show its performance in modelling site-specific prob- lems (runout definition, hazard assessment, design and verification of barriers). The code is based on a "lumped mass" kinematic algorithm allowing to simulate the free fall, impact-rebound and rolling motion of boulders on a three-dimensional topogra- phy described by a DTM. The code allows to run very detailed 3D simulations with almost no limitations in the number of modeled rockfall sources, slope elements and topographic points, using spatially distributed input data. Two case studies from the Mt. S.Martino area (Lecco, Larian Prealps) and the Gembrasca area (Valfurva, Central Alps), both from the mountainous area of the Lombardia Region (Northern Italy) are presented. Both the two examples are particularly intriguing because of the occurrence of well-known historical events (one of which causing fatalities) and the presence of valuable elements at risk (urban areas, transportation corridors) and defensive mea- sures (elasto-plastic barriers and catch walls). The Mt. S.Martino model is based on a DTM with cell size of 5 m, obtained from a 1:5.000 scale contour map, while the Gembrasca one uses an extremely detailed LIDAR-ALTM laser topography with a cell size of 1 m. The location of rockfall sources and the data used to develop and calibrate the two models have been collected

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

    ERIC Educational Resources Information Center

    Rowe, Jeremy; Razdan, Anshuman

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

  9. Canada in 3D - Toward a Sustainable 3D Model for Canadian Geology from Diverse Data Sources

    NASA Astrophysics Data System (ADS)

    Brodaric, B.; Pilkington, M.; Snyder, D. B.; St-Onge, M. R.; Russell, H.

    2015-12-01

    Many big science issues span large areas and require data from multiple heterogeneous sources, for example climate change, resource management, and hazard mitigation. Solutions to these issues can significantly benefit from access to a consistent and integrated geological model that would serve as a framework. However, such a model is absent for most large countries including Canada, due to the size of the landmass and the fragmentation of the source data into institutional and disciplinary silos. To overcome these barriers, the "Canada in 3D" (C3D) pilot project was recently launched by the Geological Survey of Canada. C3D is designed to be evergreen, multi-resolution, and inter-disciplinary: (a) it is to be updated regularly upon acquisition of new data; (b) portions vary in resolution and will initially consist of four layers (surficial, sedimentary, crystalline, and mantle) with intermediary patches of higher-resolution fill; and (c) a variety of independently managed data sources are providing inputs, such as geophysical, 3D and 2D geological models, drill logs, and others. Notably, scalability concerns dictate a decentralized and interoperable approach, such that only key control objects, denoting anchors for the modeling process, are imported into the C3D database while retaining provenance links to original sources. The resultant model is managed in the database, contains full modeling provenance as well as links to detailed information on rock units, and is to be visualized in desktop and online environments. It is anticipated that C3D will become the authoritative state of knowledge for the geology of Canada at a national scale.

  10. Toward realistic radiofrequency ablation of hepatic tumors 3D simulation and planning

    NASA Astrophysics Data System (ADS)

    Villard, Caroline; Soler, Luc; Gangi, Afshin; Mutter, Didier; Marescaux, Jacques

    2004-05-01

    Radiofrequency ablation (RFA) has become an increasingly used technique in the treatment of patients with unresectable hepatic tumors. Evaluation of vascular architecture, post-RFA tissue necrosis prediction, and the choice of a suitable needle placement strategy using conventional radiological techniques remain difficult. In an attempt to enhance the safety of RFA, a 3D simulator and treatment planning tool, that simulates the necrosis of the treated area, and proposes an optimal placement for the needle, has been developed. From enhanced spiral CT scans with 2 mm cuts, 3D reconstructions of patients with liver metastases are automatically generated. Virtual needles can be added to the 3D scene, together with their corresponding zones of necrosis that are displayed as a meshed spheroids representing the 60° C isosurface. The simulator takes into account the cooling effect of local vessels greater than 3mm in diameter, making necrosis shapes more realistic. Using a voxel-based algorithm, RFA spheroids are deformed following the shape of the vessels, extended by an additional cooled area. This operation is performed in real-time, allowing updates while needle is adjusted. This allows to observe whether the considered needle placement strategy would burn the whole cancerous zone or not. Planned needle positioning can also be automatically generated by the software to produce complete destruction of the tumor with a 1 cm margin, with maximum respect of the healthy liver and of all major extrahepatic and intrahepatic structures to avoid. If he wishes, the radiologist can select on the skin an insertion window for the needle, focusing the research of the trajectory.

  11. Comparative 3-D Modeling of tmRNA

    PubMed Central

    Burks, Jody; Zwieb, Christian; Müller, Florian; Wower, Iwona; Wower, Jacek

    2005-01-01

    Background Trans-translation releases stalled ribosomes from truncated mRNAs and tags defective proteins for proteolytic degradation using transfer-messenger RNA (tmRNA). This small stable RNA represents a hybrid of tRNA- and mRNA-like domains connected by a variable number of pseudoknots. Comparative sequence analysis of tmRNAs found in bacteria, plastids, and mitochondria provides considerable insights into their secondary structures. Progress toward understanding the molecular mechanism of template switching, which constitutes an essential step in trans-translation, is hampered by our limited knowledge about the three-dimensional folding of tmRNA. Results To facilitate experimental testing of the molecular intricacies of trans-translation, which often require appropriately modified tmRNA derivatives, we developed a procedure for building three-dimensional models of tmRNA. Using comparative sequence analysis, phylogenetically-supported 2-D structures were obtained to serve as input for the program ERNA-3D. Motifs containing loops and turns were extracted from the known structures of other RNAs and used to improve the tmRNA models. Biologically feasible 3-D models for the entire tmRNA molecule could be obtained. The models were characterized by a functionally significant close proximity between the tRNA-like domain and the resume codon. Potential conformational changes which might lead to a more open structure of tmRNA upon binding to the ribosome are discussed. The method, described in detail for the tmRNAs of Escherichia coli, Bacillus anthracis, and Caulobacter crescentus, is applicable to every tmRNA. Conclusion Improved molecular models of biological significance were obtained. These models will guide in the design of experiments and provide a better understanding of trans-translation. The comparative procedure described here for tmRNA is easily adopted for the modeling the members of other RNA families. PMID:15958166

  12. Inverse rendering of faces with a 3D morphable model.

    PubMed

    Aldrian, Oswald; Smith, William A P

    2013-05-01

    In this paper, we present a complete framework to inverse render faces with a 3D Morphable Model (3DMM). By decomposing the image formation process into geometric and photometric parts, we are able to state the problem as a multilinear system which can be solved accurately and efficiently. As we treat each contribution as independent, the objective function is convex in the parameters and a global solution is guaranteed. We start by recovering 3D shape using a novel algorithm which incorporates generalization error of the model obtained from empirical measurements. We then describe two methods to recover facial texture, diffuse lighting, specular reflectance, and camera properties from a single image. The methods make increasingly weak assumptions and can be solved in a linear fashion. We evaluate our findings on a publicly available database, where we are able to outperform an existing state-of-the-art algorithm. We demonstrate the usability of the recovered parameters in a recognition experiment conducted on the CMU-PIE database. PMID:23520253

  13. Dynamic deformable models for 3D MRI heart segmentation

    NASA Astrophysics Data System (ADS)

    Zhukov, Leonid; Bao, Zhaosheng; Gusikov, Igor; Wood, John; Breen, David E.

    2002-05-01

    Automated or semiautomated segmentation of medical images decreases interstudy variation, observer bias, and postprocessing time as well as providing clincally-relevant quantitative data. In this paper we present a new dynamic deformable modeling approach to 3D segmentation. It utilizes recently developed dynamic remeshing techniques and curvature estimation methods to produce high-quality meshes. The approach has been implemented in an interactive environment that allows a user to specify an initial model and identify key features in the data. These features act as hard constraints that the model must not pass through as it deforms. We have employed the method to perform semi-automatic segmentation of heart structures from cine MRI data.

  14. Azo-Based Iridium(III) Complexes as Multicolor Phosphorescent Probes to Detect Hypoxia in 3D Multicellular Tumor Spheroids

    PubMed Central

    Sun, Lingli; Li, Guanying; Chen, Xiang; Chen, Yu; Jin, Chengzhi; Ji, Liangnian; Chao, Hui

    2015-01-01

    Hypoxia is an important characteristic of malignant solid tumors and is considered as a possible causative factor for serious resistance to chemo- and radiotherapy. The exploration of novel fluorescent probes capable of detecting hypoxia in solid tumors will aid tumor diagnosis and treatment. In this study, we reported the design and synthesis of a series of “off-on” phosphorescence probes for hypoxia detection in adherent and three-dimensional multicellular spheroid models. All of the iridium(III) complexes incorporate an azo group as an azo-reductase reactive moiety to detect hypoxia. Reduction of non-phosphorescent probes Ir1-Ir8 by reductases under hypoxic conditions resulted in the generation of highly phosphorescent corresponding amines for detection of hypoxic regions. Moreover, these probes can penetrate into 3D multicellular spheroids over 100 μm and image the hypoxic regions. Most importantly, these probes display a high selectivity for the detection of hypoxia in 2D cells and 3D multicellular spheroids. PMID:26423609

  15. Topological order in an exactly solvable 3D spin model

    SciTech Connect

    Bravyi, Sergey; Leemhuis, Bernhard; Terhal, Barbara M.

    2011-04-15

    Research highlights: RHtriangle We study exactly solvable spin model with six-qubit nearest neighbor interactions on a 3D face centered cubic lattice. RHtriangle The ground space of the model exhibits topological quantum order. RHtriangle Elementary excitations can be geometrically described as the corners of rectangular-shaped membranes. RHtriangle The ground space can encode 4g qubits where g is the greatest common divisor of the lattice dimensions. RHtriangle Logical operators acting on the encoded qubits are described in terms of closed strings and closed membranes. - Abstract: We study a 3D generalization of the toric code model introduced recently by Chamon. This is an exactly solvable spin model with six-qubit nearest-neighbor interactions on an FCC lattice whose ground space exhibits topological quantum order. The elementary excitations of this model which we call monopoles can be geometrically described as the corners of rectangular-shaped membranes. We prove that the creation of an isolated monopole separated from other monopoles by a distance R requires an operator acting on {Omega}(R{sup 2}) qubits. Composite particles that consist of two monopoles (dipoles) and four monopoles (quadrupoles) can be described as end-points of strings. The peculiar feature of the model is that dipole-type strings are rigid, that is, such strings must be aligned with face-diagonals of the lattice. For periodic boundary conditions the ground space can encode 4g qubits where g is the greatest common divisor of the lattice dimensions. We describe a complete set of logical operators acting on the encoded qubits in terms of closed strings and closed membranes.

  16. Development of an aquifer management model AQMAN3D

    USGS Publications Warehouse

    Puig, Juan Carlos; Rolon-Collazo, L. I.; Pagan-Trinidad, Ishmael; Krishna, J.H.; Quinones-Aponte, Vicente; Gomez-Gomez, Fernando; Morris, G.L.

    1990-01-01

    A computer code that enables the use of the USGS Modular groundwater flow model for aquifermanagement modeling has been developed. Aquifermanagement techniques integrate groundwater flow modeling with linear quadratic optimization methods for the solution of various aquifer management problems. The model AQMAN3D, is a modified version of a previously developed two-dimensional AQMAN model. The idea of coupling the AQMAN model with the MODULAR model arose because actual groundwater flow systems behave in a three dimensional manner, therefore requiring treatment as such, and due to the widespread use of MODULAR. The use of the AQMAN3D model permits the implementation of the technique known as aquifer managementmodeling. A generalized approach to obtain an optimal solution to an aquifer management problem is proposed, and a sample test problem is presented to illustrate the use of the model. Even though the model provides the hydrologist with a new and powerful investigative tool, its applicability is limited to confined or quasiconfined systems.

  17. Geographic Video 3d Data Model And Retrieval

    NASA Astrophysics Data System (ADS)

    Han, Z.; Cui, C.; Kong, Y.; Wu, H.

    2014-04-01

    Geographic video includes both spatial and temporal geographic features acquired through ground-based or non-ground-based cameras. With the popularity of video capture devices such as smartphones, the volume of user-generated geographic video clips has grown significantly and the trend of this growth is quickly accelerating. Such a massive and increasing volume poses a major challenge to efficient video management and query. Most of the today's video management and query techniques are based on signal level content extraction. They are not able to fully utilize the geographic information of the videos. This paper aimed to introduce a geographic video 3D data model based on spatial information. The main idea of the model is to utilize the location, trajectory and azimuth information acquired by sensors such as GPS receivers and 3D electronic compasses in conjunction with video contents. The raw spatial information is synthesized to point, line, polygon and solid according to the camcorder parameters such as focal length and angle of view. With the video segment and video frame, we defined the three categories geometry object using the geometry model of OGC Simple Features Specification for SQL. We can query video through computing the spatial relation between query objects and three categories geometry object such as VFLocation, VSTrajectory, VSFOView and VFFovCone etc. We designed the query methods using the structured query language (SQL) in detail. The experiment indicate that the model is a multiple objective, integration, loosely coupled, flexible and extensible data model for the management of geographic stereo video.

  18. Active Exploration of Large 3D Model Repositories.

    PubMed

    Gao, Lin; Cao, Yan-Pei; Lai, Yu-Kun; Huang, Hao-Zhi; Kobbelt, Leif; Hu, Shi-Min

    2015-12-01

    With broader availability of large-scale 3D model repositories, the need for efficient and effective exploration becomes more and more urgent. Existing model retrieval techniques do not scale well with the size of the database since often a large number of very similar objects are returned for a query, and the possibilities to refine the search are quite limited. We propose an interactive approach where the user feeds an active learning procedure by labeling either entire models or parts of them as "like" or "dislike" such that the system can automatically update an active set of recommended models. To provide an intuitive user interface, candidate models are presented based on their estimated relevance for the current query. From the methodological point of view, our main contribution is to exploit not only the similarity between a query and the database models but also the similarities among the database models themselves. We achieve this by an offline pre-processing stage, where global and local shape descriptors are computed for each model and a sparse distance metric is derived that can be evaluated efficiently even for very large databases. We demonstrate the effectiveness of our method by interactively exploring a repository containing over 100 K models. PMID:26529460

  19. 3D in vitro modeling of the central nervous system.

    PubMed

    Hopkins, Amy M; DeSimone, Elise; Chwalek, Karolina; Kaplan, David L

    2015-02-01

    There are currently more than 600 diseases characterized as affecting the central nervous system (CNS) which inflict neural damage. Unfortunately, few of these conditions have effective treatments available. Although significant efforts have been put into developing new therapeutics, drugs which were promising in the developmental phase have high attrition rates in late stage clinical trials. These failures could be circumvented if current 2D in vitro and in vivo models were improved. 3D, tissue-engineered in vitro systems can address this need and enhance clinical translation through two approaches: (1) bottom-up, and (2) top-down (developmental/regenerative) strategies to reproduce the structure and function of human tissues. Critical challenges remain including biomaterials capable of matching the mechanical properties and extracellular matrix (ECM) composition of neural tissues, compartmentalized scaffolds that support heterogeneous tissue architectures reflective of brain organization and structure, and robust functional assays for in vitro tissue validation. The unique design parameters defined by the complex physiology of the CNS for construction and validation of 3D in vitro neural systems are reviewed here.

  20. 3D in vitro modeling of the central nervous system

    PubMed Central

    Hopkins, Amy M.; DeSimone, Elise; Chwalek, Karolina; Kaplan, David L.

    2015-01-01

    There are currently more than 600 diseases characterized as affecting the central nervous system (CNS) which inflict neural damage. Unfortunately, few of these conditions have effective treatments available. Although significant efforts have been put into developing new therapeutics, drugs which were promising in the developmental phase have high attrition rates in late stage clinical trials. These failures could be circumvented if current 2D in vitro and in vivo models were improved. 3D, tissue-engineered in vitro systems can address this need and enhance clinical translation through two approaches: (1) bottom-up, and (2) top-down (developmental/regenerative) strategies to reproduce the structure and function of human tissues. Critical challenges remain including biomaterials capable of matching the mechanical properties and extracellular matrix (ECM) composition of neural tissues, compartmentalized scaffolds that support heterogeneous tissue architectures reflective of brain organization and structure, and robust functional assays for in vitro tissue validation. The unique design parameters defined by the complex physiology of the CNS for construction and validation of 3D in vitro neural systems are reviewed here. PMID:25461688

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

    PubMed

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

    2006-01-01

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

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

    PubMed

    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. PMID:25101095

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

    PubMed

    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.

  4. Biologically relevant 3D tumor arrays: imaging-based methods for quantification of reproducible growth and analysis of treatment response

    NASA Astrophysics Data System (ADS)

    Celli, Jonathan P.; Rizvi, Imran; Blanden, Adam R.; Abu-Yousif, Adnan O.; Spring, Bryan Q.; Hasan, Tayyaba

    2011-02-01

    Three-dimensional in vitro tumor models have emerged as powerful research tools in cancer biology, though the vast potential of these systems as high-throughput, biologically relevant reporters of treatment response has yet to be adequately explored. Here, building on previous studies, we demonstrate the utility of using 3D models for ovarian and pancreatic cancers in conjunction with quantitative image processing to reveal aspects of growth behavior and treatment response that would not be evident without either modeling or quantitative analysis component. In this report we specifically focus on recent improvements in the imaging component of this integrative research platform and emphasize analysis to establish reproducible growth properties in 3D tumor arrays, a key consideration in establishing the utility of this platform as a reliable reporter of therapeutic response. Building on previous studies using automated segmentation of low magnification image fields containing large numbers of nodules to study size dependent treatment effects, we introduce an improvement to this method using multiresolution decomposition to remove gradient background from transmitted light images for more reliable feature identification. This approach facilitates the development of a new treatment response metric, disruption fraction (Dfrac), which quantifies dose dependent distribution shifts from nodular fragmentation induced by cytotoxic therapies. Using this approach we show that PDT treatment is associated with significant dose-dependent increases in Dfrac, while this is not observed with carboplatin treatment. The ability to quantify this response to therapy could play a key role in design of combination regimens involving these two modalities.

  5. Polygonal Shapes Detection in 3d Models of Complex Architectures

    NASA Astrophysics Data System (ADS)

    Benciolini, G. B.; Vitti, A.

    2015-02-01

    A sequential application of two global models defined on a variational framework is proposed for the detection of polygonal shapes in 3D models of complex architectures. As a first step, the procedure involves the use of the Mumford and Shah (1989) 1st-order variational model in dimension two (gridded height data are processed). In the Mumford-Shah model an auxiliary function detects the sharp changes, i.e., the discontinuities, of a piecewise smooth approximation of the data. The Mumford-Shah model requires the global minimization of a specific functional to simultaneously produce both the smooth approximation and its discontinuities. In the proposed procedure, the edges of the smooth approximation derived by a specific processing of the auxiliary function are then processed using the Blake and Zisserman (1987) 2nd-order variational model in dimension one (edges are processed in the plane). This second step permits to describe the edges of an object by means of piecewise almost-linear approximation of the input edges themselves and to detects sharp changes of the first-derivative of the edges so to detect corners. The Mumford-Shah variational model is used in two dimensions accepting the original data as primary input. The Blake-Zisserman variational model is used in one dimension for the refinement of the description of the edges. The selection among all the boundaries detected by the Mumford-Shah model of those that present a shape close to a polygon is performed by considering only those boundaries for which the Blake-Zisserman model identified discontinuities in their first derivative. The output of the procedure are hence shapes, coming from 3D geometric data, that can be considered as polygons. The application of the procedure is suitable for, but not limited to, the detection of objects such as foot-print of polygonal buildings, building facade boundaries or windows contours. v The procedure is applied to a height model of the building of the Engineering

  6. Advanced prior modeling for 3D bright field electron tomography

    NASA Astrophysics Data System (ADS)

    Sreehari, Suhas; Venkatakrishnan, S. V.; Drummy, Lawrence F.; Simmons, Jeffrey P.; Bouman, Charles A.

    2015-03-01

    Many important imaging problems in material science involve reconstruction of images containing repetitive non-local structures. Model-based iterative reconstruction (MBIR) could in principle exploit such redundancies through the selection of a log prior probability term. However, in practice, determining such a log prior term that accounts for the similarity between distant structures in the image is quite challenging. Much progress has been made in the development of denoising algorithms like non-local means and BM3D, and these are known to successfully capture non-local redundancies in images. But the fact that these denoising operations are not explicitly formulated as cost functions makes it unclear as to how to incorporate them in the MBIR framework. In this paper, we formulate a solution to bright field electron tomography by augmenting the existing bright field MBIR method to incorporate any non-local denoising operator as a prior model. We accomplish this using a framework we call plug-and-play priors that decouples the log likelihood and the log prior probability terms in the MBIR cost function. We specifically use 3D non-local means (NLM) as the prior model in the plug-and-play framework, and showcase high quality tomographic reconstructions of a simulated aluminum spheres dataset, and two real datasets of aluminum spheres and ferritin structures. We observe that streak and smear artifacts are visibly suppressed, and that edges are preserved. Also, we report lower RMSE values compared to the conventional MBIR reconstruction using qGGMRF as the prior model.

  7. High-throughput screening with nanoimprinting 3D culture for efficient drug development by mimicking the tumor environment.

    PubMed

    Yoshii, Yukie; Furukawa, Takako; Waki, Atsuo; Okuyama, Hiroaki; Inoue, Masahiro; Itoh, Manabu; Zhang, Ming-Rong; Wakizaka, Hidekatsu; Sogawa, Chizuru; Kiyono, Yasushi; Yoshii, Hiroshi; Fujibayashi, Yasuhisa; Saga, Tsuneo

    2015-05-01

    Anti-cancer drug development typically utilizes high-throughput screening with two-dimensional (2D) cell culture. However, 2D culture induces cellular characteristics different from tumors in vivo, resulting in inefficient drug development. Here, we report an innovative high-throughput screening system using nanoimprinting 3D culture to simulate in vivo conditions, thereby facilitating efficient drug development. We demonstrated that cell line-based nanoimprinting 3D screening can more efficiently select drugs that effectively inhibit cancer growth in vivo as compared to 2D culture. Metabolic responses after treatment were assessed using positron emission tomography (PET) probes, and revealed similar characteristics between the 3D spheroids and in vivo tumors. Further, we developed an advanced method to adopt cancer cells from patient tumor tissues for high-throughput drug screening with nanoimprinting 3D culture, which we termed Cancer tissue-Originated Uniformed Spheroid Assay (COUSA). This system identified drugs that were effective in xenografts of the original patient tumors. Nanoimprinting 3D spheroids showed low permeability and formation of hypoxic regions inside, similar to in vivo tumors. Collectively, the nanoimprinting 3D culture provides easy-handling high-throughput drug screening system, which allows for efficient drug development by mimicking the tumor environment. The COUSA system could be a useful platform for drug development with patient cancer cells.

  8. Brandenburg 3D - a comprehensive 3D Subsurface Model, Conception of an Infrastructure Node and a Web Application

    NASA Astrophysics Data System (ADS)

    Kerschke, Dorit; Schilling, Maik; Simon, Andreas; Wächter, Joachim

    2014-05-01

    The Energiewende and the increasing scarcity of raw materials will lead to an intensified utilization of the subsurface in Germany. Within this context, geological 3D modeling is a fundamental approach for integrated decision and planning processes. Initiated by the development of the European Geospatial Infrastructure INSPIRE, the German State Geological Offices started digitizing their predominantly analog archive inventory. Until now, a comprehensive 3D subsurface model of Brandenburg did not exist. Therefore the project B3D strived to develop a new 3D model as well as a subsequent infrastructure node to integrate all geological and spatial data within the Geodaten-Infrastruktur Brandenburg (Geospatial Infrastructure, GDI-BB) and provide it to the public through an interactive 2D/3D web application. The functionality of the web application is based on a client-server architecture. Server-sided, all available spatial data is published through GeoServer. GeoServer is designed for interoperability and acts as the reference implementation of the Open Geospatial Consortium (OGC) Web Feature Service (WFS) standard that provides the interface that allows requests for geographical features. In addition, GeoServer implements, among others, the high performance certified compliant Web Map Service (WMS) that serves geo-referenced map images. For publishing 3D data, the OGC Web 3D Service (W3DS), a portrayal service for three-dimensional geo-data, is used. The W3DS displays elements representing the geometry, appearance, and behavior of geographic objects. On the client side, the web application is solely based on Free and Open Source Software and leans on the JavaScript API WebGL that allows the interactive rendering of 2D and 3D graphics by means of GPU accelerated usage of physics and image processing as part of the web page canvas without the use of plug-ins. WebGL is supported by most web browsers (e.g., Google Chrome, Mozilla Firefox, Safari, and Opera). The web

  9. Faceless identification: a model for person identification using the 3D shape and 3D motion as cues

    NASA Astrophysics Data System (ADS)

    Klasen, Lena M.; Li, Haibo

    1999-02-01

    Person identification by using biometric methods based on image sequences, or still images, often requires a controllable and cooperative environment during the image capturing stage. In the forensic case the situation is more likely to be the opposite. In this work we propose a method that makes use of the anthropometry of the human body and human actions as cues for identification. Image sequences from surveillance systems are used, which can be seen as monocular image sequences. A 3D deformable wireframe body model is used as a platform to handle the non-rigid information of the 3D shape and 3D motion of the human body from the image sequence. A recursive method for estimating global motion and local shape variations is presented, using two recursive feedback systems.

  10. Validation of a 3-D hemispheric nested air pollution model

    NASA Astrophysics Data System (ADS)

    Frohn, L. M.; Christensen, J. H.; Brandt, J.; Geels, C.; Hansen, K. M.

    2003-07-01

    Several air pollution transport models have been developed at the National Environmental Research Institute in Denmark over the last decade (DREAM, DEHM, ACDEP and DEOM). A new 3-D nested Eulerian transport-chemistry model: REGIonal high resolutioN Air pollution model (REGINA) is based on modules and parameterisations from these models as well as new methods. The model covers the majority of the Northern Hemisphere with currently one nest implemented. The horizontal resolution in the mother domain is 150 km × 150 km, and the nesting factor is three. A chemical scheme (originally 51 species) has been extended with a detailed description of the ammonia chemistry and implemented in the model. The mesoscale numerical weather prediction model MM5v2 is used as meteorological driver for the model. The concentrations of air pollutants, such as sulphur and nitrogen in various forms, have been calculated, applying zero nesting and one nest. The model setup is currently being validated by comparing calculated values of concentrations to measurements from approximately 100 stations included in the European Monitoring and Evalutation Programme (EMEP). The present paper describes the physical processes and parameterisations of the model together with the modifications of the chemical scheme. Validation of the model calculations by comparison to EMEP measurements for a summer and a winter month is shown and discussed. Furthermore, results from a sensitivity study of the model performance with respect to resolution in emission and meteorology input data is presented. Finally the future prospects of the model are discussed. The overall validation shows that the model performs well with respect to correlation for both monthly and daily mean values.

  11. Defect modelling in an interactive 3-D CAD environment

    NASA Astrophysics Data System (ADS)

    Reilly, D.; Potts, A.; McNab, A.; Toft, M.; Chapman, R. K.

    2000-05-01

    This paper describes enhancement of the NDT Workbench, as presented at QNDE '98, to include theoretical models for the ultrasonic inspection of smooth planar defects, developed by British Energy and BNFL-Magnox Generation. The Workbench is a PC-based software package for the reconstruction, visualization and analysis of 3-D ultrasonic NDT data in an interactive CAD environment. This extension of the Workbeach now provides the user with a well established modelling approach, coupled with a graphical user interface for: a) configuring the model for flaw size, shape, orientation and location; b) flexible specification of probe parameters; c) selection of scanning surface and scan pattern on the CAD component model; d) presentation of the output as a simulated ultrasound image within the component, or as graphical or tabular displays. The defect modelling facilities of the Workbench can be used for inspection procedure assessment and confirmation of data interpretation, by comparison of overlay images generated from real and simulated data. The modelling technique currently implemented is based on the Geometrical Theory of Diffraction, for simulation of strip-like, circular or elliptical crack responses in the time harmonic or time dependent cases. Eventually, the Workbench will also allow modelling using elastodynamic Kirchhoff theory.

  12. 3D model generation using an airborne swarm

    NASA Astrophysics Data System (ADS)

    Clark, R. A.; Punzo, G.; Dobie, G.; MacLeod, C. N.; Summan, R.; Pierce, G.; Macdonald, M.; Bolton, G.

    2015-03-01

    Using an artificial kinematic field to provide co-ordination between multiple inspection UAVs, the authors herein demonstrate full 3D modelling capability based on a photogrammetric system. The operation of the system is demonstrated by generating a full 3D surface model of an intermediate level nuclear waste storage drum. Such drums require periodic inspection to ensure that drum distortion or corrosion is carefully monitored. Performing this inspection with multiple airborne platforms enables rapid inspection of structures that are inaccessible to on-surface remote vehicles and are in human-hazardous environments. A three-dimensional surface-meshed model of the target can then be constructed in post-processing through photogrammetry analysis of the visual inspection data. The inspection environment uses a tracking system to precisely monitor the position of each aerial vehicle within the enclosure. The vehicles used are commercially available Parrot AR. Drone quadcopters, controlled through a computer interface connected over an IEEE 802.11n (WiFi) network, implementing a distributed controller for each vehicle. This enables the autonomous and distributed elements of the control scheme to be retained, while alleviating the vehicles of the control algorithm's computational load. The control scheme relies on a kinematic field defined with the target at its centre. This field defines the trajectory for all the drones in the volume relative to the central target, enabling the drones to circle the target at a set radius while avoiding drone collisions. This function enables complete coverage along the height of the object, which is assured by transitioning to another inspection band only after completing circumferential coverage. Using a swarm of vehicles, the time until complete coverage can be significantly reduced.

  13. 3-D numerical modeling of plume-induced subduction initiation

    NASA Astrophysics Data System (ADS)

    Baes, Marzieh; Gerya, taras; Sobolev, Stephan

    2016-04-01

    Investigation of mechanisms involved in formation of a new subduction zone can help us to better understand plate tectonics. Despite numerous previous studies, it is still unclear how and where an old oceanic plate starts to subduct beneath the other plate. One of the proposed scenarios for nucleation of subduction is plume-induced subduction initiation, which was investigated in detail, using 2-D models, by Ueda et al. (2008). Recently. Gerya et al. (2015), using 3D numerical models, proposed that plume-lithosphere interaction in the Archean led to the subduction initiation and onset of plate tectonic. In this study, we aim to pursue work of Ueda et al. (2008) by incorporation of 3-D thermo-mechanical models to investigate conditions leading to oceanic subduction initiation as a result of thermal-chemical mantle plume-lithosphere interaction in the modern earth. Results of our experiments show four different deformation regimes in response to plume-lithosphere interaction, that are a) self-sustaining subduction initiation where subduction becomes self-sustained, b) freezing subduction initiation where subduction stops at shallow depths, c) slab break-off where subducting circular slab breaks off soon after formation and d) plume underplating where plume does not pass through the lithosphere but spreads beneath it (failed subduction initiation). These different regimes depend on several parameters such as plume's size, composition and temperature, lithospheric brittle/plastic strength, age of the oceanic lithosphere and presence/absence of lithospheric heterogeneities. Results show that subduction initiates and becomes self-sustained when lithosphere is older than 10 Myr and non-dimensional ratio of the plume buoyancy force and lithospheric strength above the plume is higher than 2.

  14. 3D model generation using an airborne swarm

    SciTech Connect

    Clark, R. A.; Punzo, G.; Macdonald, M.; Dobie, G.; MacLeod, C. N.; Summan, R.; Pierce, G.; Bolton, G.

    2015-03-31

    Using an artificial kinematic field to provide co-ordination between multiple inspection UAVs, the authors herein demonstrate full 3D modelling capability based on a photogrammetric system. The operation of the system is demonstrated by generating a full 3D surface model of an intermediate level nuclear waste storage drum. Such drums require periodic inspection to ensure that drum distortion or corrosion is carefully monitored. Performing this inspection with multiple airborne platforms enables rapid inspection of structures that are inaccessible to on-surface remote vehicles and are in human-hazardous environments. A three-dimensional surface-meshed model of the target can then be constructed in post-processing through photogrammetry analysis of the visual inspection data. The inspection environment uses a tracking system to precisely monitor the position of each aerial vehicle within the enclosure. The vehicles used are commercially available Parrot AR. Drone quadcopters, controlled through a computer interface connected over an IEEE 802.11n (WiFi) network, implementing a distributed controller for each vehicle. This enables the autonomous and distributed elements of the control scheme to be retained, while alleviating the vehicles of the control algorithm’s computational load. The control scheme relies on a kinematic field defined with the target at its centre. This field defines the trajectory for all the drones in the volume relative to the central target, enabling the drones to circle the target at a set radius while avoiding drone collisions. This function enables complete coverage along the height of the object, which is assured by transitioning to another inspection band only after completing circumferential coverage. Using a swarm of vehicles, the time until complete coverage can be significantly reduced.

  15. Handheld camera 3D modeling system using multiple reference panels

    NASA Astrophysics Data System (ADS)

    Fujimura, Kouta; Oue, Yasuhiro; Terauchi, Tomoya; Emi, Tetsuichi

    2002-03-01

    A novel 3D modeling system in which a target object is easily captured and modeled by using a hand-held camera with several reference panels is presented in this paper. The reference panels are designed to be able to obtain the camera position and discriminate between each other. A conventional 3D modeling system using a reference panel has several restrictions regarding the target object, specifically the size and its location. Our system uses multiple reference panels, which are set around the target object to remove these restrictions. The main features of this system are as follows: 1) The whole shape and photo-realistic textures of the target object can be digitized based on several still images or a movie captured by using a hand-held camera; as well as each location of the camera that can be calculated using the reference panels. 2) Our system can be provided as a software product only. That means there are no special requirements for hardware; even the reference panels , because they can be printed from image files or software. 3) This system can be applied to digitize a larger object. In the experiments, we developed and used an interactive region selection tool to detect the silhouette on each image instead of using the chroma -keying method. We have tested our system with a toy object. The calculation time is about 10 minutes (except for the capturing the images and extracting the silhouette by using our tool) on a personal computer with a Pentium-III processor (600MHz) and 320MB memory. However, it depends on how complex the images are and how many images you use. Our future plan is to evaluate the system with various kind of objects, specifically, large ones in outdoor environments.

  16. Crashworthiness analysis using advanced material models in DYNA3D

    SciTech Connect

    Logan, R.W.; Burger, M.J.; McMichael, L.D.; Parkinson, R.D.

    1993-10-22

    As part of an electric vehicle consortium, LLNL and Kaiser Aluminum are conducting experimental and numerical studies on crashworthy aluminum spaceframe designs. They have jointly explored the effect of heat treat on crush behavior and duplicated the experimental behavior with finite-element simulations. The major technical contributions to the state of the art in numerical simulation arise from the development and use of advanced material model descriptions for LLNL`s DYNA3D code. Constitutive model enhancements in both flow and failure have been employed for conventional materials such as low-carbon steels, and also for lighter weight materials such as aluminum and fiber composites being considered for future vehicles. The constitutive model enhancements are developed as extensions from LLNL`s work in anisotropic flow and multiaxial failure modeling. Analysis quality as a function of level of simplification of material behavior and mesh is explored, as well as the penalty in computation cost that must be paid for using more complex models and meshes. The lightweight material modeling technology is being used at the vehicle component level to explore the safety implications of small neighborhood electric vehicles manufactured almost exclusively from these materials.

  17. 3D Model of the Neal Hot Springs Geothermal Area

    DOE Data Explorer

    Faulds, James E.

    2013-12-31

    The Neal Hot Springs geothermal system lies in a left-step in a north-striking, west-dipping normal fault system, consisting of the Neal Fault to the south and the Sugarloaf Butte Fault to the north (Edwards, 2013). The Neal Hot Springs 3D geologic model consists of 104 faults and 13 stratigraphic units. The stratigraphy is sub-horizontal to dipping <10 degrees and there is no predominant dip-direction. Geothermal production is exclusively from the Neal Fault south of, and within the step-over, while geothermal injection is into both the Neal Fault to the south of the step-over and faults within the step-over.

  18. 3D Model of the San Emidio Geothermal Area

    DOE Data Explorer

    James E. Faulds

    2013-12-31

    The San Emidio geothermal system is characterized by a left-step in a west-dipping normal fault system that bounds the western side of the Lake Range. The 3D geologic model consists of 5 geologic units and 55 faults. Overlying Jurrassic-Triassic metasedimentary basement is a ~500 m-1000 m thick section of the Miocene lower Pyramid sequence, pre- syn-extensional Quaternary sedimentary rocks and post-extensional Quaternary rocks. 15-30º eastward dip of the stratigraphy is controlled by the predominant west-dipping fault set. Both geothermal production and injection are concentrated north of the step over in an area of closely spaced west dipping normal faults.

  19. Energy flow in passive and active 3D cochlear model

    NASA Astrophysics Data System (ADS)

    Wang, Yanli; Puria, Sunil; Steele, Charles

    2015-12-01

    Energy flow in the cochlea is an important characteristic of the cochlear traveling wave, and many investigators, such as von Békésy and Lighthill, have discussed this phenomenon. Particularly after the discovery of the motility of the outer hair cells (OHCs), the nature of the power gain of the cochlea has been a fundamental research question. In the present work, direct three-dimensional (3D) calculations of the power on cross sections of the cochlea and on the basilar membrane are performed based on a box model of the mouse cochlea. The distributions of the fluid pressure and fluid velocity in the scala vestibuli are presented. The power output from the OHCs and the power loss due to fluid viscous damping are calculated along the length of the cochlea. This work provides a basis for theoretical calculations of the power gain of the OHCs from mechanical considerations.

  20. Energy flow in passive and active 3D cochlear model

    SciTech Connect

    Wang, Yanli; Steele, Charles; Puria, Sunil

    2015-12-31

    Energy flow in the cochlea is an important characteristic of the cochlear traveling wave, and many investigators, such as von Békésy and Lighthill, have discussed this phenomenon. Particularly after the discovery of the motility of the outer hair cells (OHCs), the nature of the power gain of the cochlea has been a fundamental research question. In the present work, direct three-dimensional (3D) calculations of the power on cross sections of the cochlea and on the basilar membrane are performed based on a box model of the mouse cochlea. The distributions of the fluid pressure and fluid velocity in the scala vestibuli are presented. The power output from the OHCs and the power loss due to fluid viscous damping are calculated along the length of the cochlea. This work provides a basis for theoretical calculations of the power gain of the OHCs from mechanical considerations.

  1. 3D modeling and raytracing in RPV elbows and nozzles

    SciTech Connect

    Koshy, M.; Isenberg, J.

    1995-12-31

    Three dimensional geometric modeling and ray tracing are used to develop ultrasound inspection procedures for nozzles safe ends and elbows in nuclear reactor pressure vessels and other structures containing cracks or voids. B-spline and analytic conic sections are used to generate 3D outer surfaces and interfaces between regions of contrasting impedance. Voids representing flaws are implanted in the inspection volume. Ray tracing in comer trap or normal incidence is performed to evaluate coverage in pulse-echo or pitch-catch mode. In one scenario, the coverage obtained from search units is designed to achieve the required degree of coverage. Physical experiments have been conducted in which artificially-generated flaws in inner blend regions of reactor pressure vessels are inspected using ultrasound from 2.25 mhz transducers. Predicted and measured positions of search units from which the flaws can be detected compare favorably.

  2. 3D Printed Molecules and Extended Solid Models for Teaching Symmetry and Point Groups

    ERIC Educational Resources Information Center

    Scalfani, Vincent F.; Vaid, Thomas P.

    2014-01-01

    Tangible models help students and researchers visualize chemical structures in three dimensions (3D). 3D printing offers a unique and straightforward approach to fabricate plastic 3D models of molecules and extended solids. In this article, we prepared a series of digital 3D design files of molecular structures that will be useful for teaching…

  3. Towards Automatic Semantic Labelling of 3D City Models

    NASA Astrophysics Data System (ADS)

    Rook, M.; Biljecki, F.; Diakité, A. A.

    2016-10-01

    The lack of semantic information in many 3D city models is a considerable limiting factor in their use, as a lot of applications rely on semantics. Such information is not always available, since it is not collected at all times, it might be lost due to data transformation, or its lack may be caused by non-interoperability in data integration from other sources. This research is a first step in creating an automatic workflow that semantically labels plain 3D city model represented by a soup of polygons, with semantic and thematic information, as defined in the CityGML standard. The first step involves the reconstruction of the topology, which is used in a region growing algorithm that clusters upward facing adjacent triangles. Heuristic rules, embedded in a decision tree, are used to compute a likeliness score for these regions that either represent the ground (terrain) or a RoofSurface. Regions with a high likeliness score, to one of the two classes, are used to create a decision space, which is used in a support vector machine (SVM). Next, topological relations are utilised to select seeds that function as a start in a region growing algorithm, to create regions of triangles of other semantic classes. The topological relationships of the regions are used in the aggregation of the thematic building features. Finally, the level of detail is detected to generate the correct output in CityGML. The results show an accuracy between 85 % and 99 % in the automatic semantic labelling on four different test datasets. The paper is concluded by indicating problems and difficulties implying the next steps in the research.

  4. 3D Model of the Tuscarora Geothermal Area

    SciTech Connect

    Faulds, James E.

    2013-12-31

    The Tuscarora geothermal system sits within a ~15 km wide left-step in a major west-dipping range-bounding normal fault system. The step over is defined by the Independence Mountains fault zone and the Bull Runs Mountains fault zone which overlap along strike. Strain is transferred between these major fault segments via and array of northerly striking normal faults with offsets of 10s to 100s of meters and strike lengths of less than 5 km. These faults within the step over are one to two orders of magnitude smaller than the range-bounding fault zones between which they reside. Faults within the broad step define an anticlinal accommodation zone wherein east-dipping faults mainly occupy western half of the accommodation zone and west-dipping faults lie in the eastern half of the accommodation zone. The 3D model of Tuscarora encompasses 70 small-offset normal faults that define the accommodation zone and a portion of the Independence Mountains fault zone, which dips beneath the geothermal field. The geothermal system resides in the axial part of the accommodation, straddling the two fault dip domains. The Tuscarora 3D geologic model consists of 10 stratigraphic units. Unconsolidated Quaternary alluvium has eroded down into bedrock units, the youngest and stratigraphically highest bedrock units are middle Miocene rhyolite and dacite flows regionally correlated with the Jarbidge Rhyolite and modeled with uniform cumulative thickness of ~350 m. Underlying these lava flows are Eocene volcanic rocks of the Big Cottonwood Canyon caldera. These units are modeled as intracaldera deposits, including domes, flows, and thick ash deposits that change in thickness and locally pinch out. The Paleozoic basement of consists metasedimenary and metavolcanic rocks, dominated by argillite, siltstone, limestone, quartzite, and metabasalt of the Schoonover and Snow Canyon Formations. Paleozoic formations are lumped in a single basement unit in the model. Fault blocks in the eastern

  5. A new 3D dynamical biomechanical tongue model

    NASA Astrophysics Data System (ADS)

    Gerard, Jean-Michel; Perrier, Pascal; Payan, Yohan; Wilhelms-Tricarico, Reiner

    2001-05-01

    A new dynamical biomechanical tongue model is being developed to study speech motor control. In spite of its computational complexity, a 3D representation was chosen in order to account for various contacts between tongue and external structures such as teeth, palate, and vocal tract walls. A fair representation of tongue muscle anatomy is provided, by designing the finite element mesh from the visible human data set (female subject). Model geometry was then matched to a human speaker, so that simulations can be quantitatively compared to experimental MRI data. A set of 11 muscles is modeled, whose role in speech gestures is well established. Each muscle is defined by a set of elements whose elastic properties change with muscle activation. Muscles forces are applied to the tongue model via macrofibers defined within the mesh by muscle specific sets of nodes. These forces are currently specified as step functions. Boundary conditions are set using zero-displacement nodes simulating attachments of tongue on bony structures. The nonlinear mechanical properties of tongue soft tissues are modeled using a hyperelastic material. Three-dimensional tongue deformations generated by each muscle, using FEM software ANSYS for computation, will be presented. Implications for speech motor control will be proposed.

  6. Modeling Electric Current Flow in 3D Fractured Media

    NASA Astrophysics Data System (ADS)

    Demirel, S.; Roubinet, D.; Irving, J.

    2014-12-01

    The study of fractured rocks is extremely important in a variety of research fields and applications such as hydrogeology, hydrocarbon extraction and long-term storage of toxic waste. As fractures are highly conductive structures in comparison to the surrounding rock, their presence can be either an advantage or a drawback. For hydrocarbon extraction, fractures allow for quick and easy access to the resource whereas for toxic waste storage their presence increases the risk of leakage and migration of pollutants. In both cases, the identification of fracture network characteristics is an essential step. Recently, we have developed an approach for modeling electric current flow in 2D fractured media. This approach is based on a discrete-dual-porosity model where fractures are represented explicitly, the matrix is coarsely discretized into blocks, and current flow exchange between the fractures and matrix is analytically evaluated at the fracture-scale and integrated at the block-scale [1]. Although this approach has shown much promise and has proven its efficiency for 2D simulations, its extension to 3D remains to be addressed. To this end, we assume that fractures can be represented as two-dimensional finite planes embedded in the surrounding matrix, and we express analytically the distribution of electric potential at the fracture scale. This fracture-scale expression takes into account the electric-current-flow exchange with the surrounding matrix and flow conservation is enforced at the fracture intersections. The fracture-matrix exchange is then integrated at the matrix-block scale where the electric current flow conservation at the block boundaries is formulated with a modified finite volume method. With the objective of providing a low-computational-cost modeling approach adapted to 3D simulations in fractured media, our model is (i) validated and compared to existing modeling approaches and, (ii) used to evaluate the impact of the presence of fractures on

  7. Dosimetry in brain tumor phantom at 15 MV 3D conformal radiation therapy

    PubMed Central

    2013-01-01

    Glioblastoma multiforme (GBM) is the most common, aggressive, highly malignant and infiltrative of all brain tumors with low rate of control. The main goal of this work was to evaluate the spatial dose distribution into a GBM simulator inside a head phantom exposed to a 15 MV 3D conformal radiation therapy in order to validate internal doses. A head and neck phantom developed by the Ionizing Radiation Research Group (NRI) was used on the experiments. Such phantom holds the following synthetic structures: brain and spinal cord, skull, cervical and thoracic vertebrae, jaw, hyoid bone, laryngeal cartilages, head and neck muscles and skin. Computer tomography (CT) of the simulator was taken, capturing a set of contrasted references. Therapy Radiation planning (TPS) was performed based on those CT images, satisfying a 200 cGy prescribed dose split in three irradiation fields. The TPS assumed 97% of prescribed dose cover the prescribed treatment volume (PTV). Radiochromic films in a solid water phantom provided dose response as a function of optical density. Spatial dosimetric distribution was generated by radiochromic film samples at coronal, sagittal-anterior and sagittal-posterior positions, inserted into tumor simulator and brain. The spatial dose profiles held 70 to 120% of the prescribed dose. In spite of the stratified profile, as opposed to the smooth dose profile from TPS, the tumor internal doses were within a 5% deviation from 214.4 cGy evaluated by TPS. 83.2% of the points with a gamma value of less than 1 (3%/3mm) for TPS and experimental values, respectively. At the tumor, measured at coronal section, a few dark spots in the film caused the appearance of outlier points in 13-15% of dose deviation percentage. And, as final conclusion, such dosimeter choice and the physical anthropomorphic and anthropometric phantom provided an efficient method for validating radiotherapy protocols. PMID:23829593

  8. A multipurpose 3-D grid of stellar models

    NASA Astrophysics Data System (ADS)

    Maíz Apellániz, J.

    2013-05-01

    The last two decades have produced a proliferation of stellar atmosphere grids, evolutionary tracks, and isochrones which are available to the astronomical community from different internet services. However, it is not straightforward (at least for an inexperienced user) to manipulate those models to answer questions of the type: What is the spectral energy distribution of a 9000 K giant? What about its J-band magnitude for different metallicities? What can I tell about the mass of a star if I know that its unreddened B-V color is -0.05 and its luminosity in solar units is 10^5? The answers to those questions are indeed in the models but a series of transformations and combinations involving different variables and models are required to obtain them. To make the available knowledge more user friendly, I have combined a number of state-of-the-art sources to create a 3-D (effective temperature, luminosity, and metallicity) grid of stellar models for which I provide calibrated SEDs and magnitudes as well as auxiliary variables such as mass and age. Furthermore, I have generated a grid of extinguished magnitudes using the recent Maíz Apellániz et al. (2012) extinction laws and incorporated them into the Bayesian code CHORIZOS (Maíz Apellániz 2004).

  9. 3-D Eutrophication Modeling for Lake Simcoe, Canada

    NASA Astrophysics Data System (ADS)

    Lu, Q.; Duckett, F.; Nairn, R.; Brunton, A.

    2006-12-01

    The Lake Simcoe Region Conservation Authority (LSRCA) and the Province of Ontario are undertaking a series of studies to facilitate management of the pressures of population growth in the Lake Simcoe watershed. With rapid population growth and urban development comes additional land clearing, storm water runoff and the discharge of treated sewage, all of which are sources of increased phosphorus loading to Lake Simcoe. Depressed oxygen levels were linked to phosphorous enrichment of the lake, with the resultant stimulation of algal growth in the sunlit upper waters of the lake, and its subsequent senescence and settling into the hypolimnion where bacterial decomposition consumes oxygen from the stratified waters. This poster describes a 3-D hydrodynamic, thermal and water quality model of Lake Simcoe developed using the Danish Hydraulics Institute (DHI) MIKE3 model. The hydrodynamic module includes wind-driven circulation, temperature variation, development of the thermocline and thermal stratification, and hydraulic forcing from inflowing tributaries. This is linked to the water quality module which simulates the eutrophication processes in the response of the lake to loadings of phosphorus, such as algal growth, the growth of aquatic plants and subsequent oxygen consumption. The model has been calibrated against Acoustic Doppler Current Profiler velocity data, plus measured temperature and water quality data at MOE stations in the lake and water intakes. The model is an important assessment tool for the management of the lake and its watersheds, allowing assessment of the impacts of the urban growth and land use change on the water quality in Lake Simcoe.

  10. Indoor Modelling Benchmark for 3D Geometry Extraction

    NASA Astrophysics Data System (ADS)

    Thomson, C.; Boehm, J.

    2014-06-01

    A combination of faster, cheaper and more accurate hardware, more sophisticated software, and greater industry acceptance have all laid the foundations for an increased desire for accurate 3D parametric models of buildings. Pointclouds are the data source of choice currently with static terrestrial laser scanning the predominant tool for large, dense volume measurement. The current importance of pointclouds as the primary source of real world representation is endorsed by CAD software vendor acquisitions of pointcloud engines in 2011. Both the capture and modelling of indoor environments require great effort in time by the operator (and therefore cost). Automation is seen as a way to aid this by reducing the workload of the user and some commercial packages have appeared that provide automation to some degree. In the data capture phase, advances in indoor mobile mapping systems are speeding up the process, albeit currently with a reduction in accuracy. As a result this paper presents freely accessible pointcloud datasets of two typical areas of a building each captured with two different capture methods and each with an accurate wholly manually created model. These datasets are provided as a benchmark for the research community to gauge the performance and improvements of various techniques for indoor geometry extraction. With this in mind, non-proprietary, interoperable formats are provided such as E57 for the scans and IFC for the reference model. The datasets can be found at: http://indoor-bench.github.io/indoor-bench.

  11. Planetary subsurface investigation by 3D visualization model .

    NASA Astrophysics Data System (ADS)

    Seu, R.; Catallo, C.; Tragni, M.; Abbattista, C.; Cinquepalmi, L.

    Subsurface data analysis and visualization represents one of the main aspect in Planetary Observation (i.e. search for water or geological characterization). The data are collected by subsurface sounding radars as instruments on-board of deep space missions. These data are generally represented as 2D radargrams in the perspective of space track and z axes (perpendicular to the subsurface) but without direct correlation to other data acquisition or knowledge on the planet . In many case there are plenty of data from other sensors of the same mission, or other ones, with high continuity in time and in space and specially around the scientific sites of interest (i.e. candidate landing areas or particular scientific interesting sites). The 2D perspective is good to analyse single acquisitions and to perform detailed analysis on the returned echo but are quite useless to compare very large dataset as now are available on many planets and moons of solar system. The best way is to approach the analysis on 3D visualization model generated from the entire stack of data. First of all this approach allows to navigate the subsurface in all directions and analyses different sections and slices or moreover navigate the iso-surfaces respect to a value (or interval). The last one allows to isolate one or more iso-surfaces and remove, in the visualization mode, other data not interesting for the analysis; finally it helps to individuate the underground 3D bodies. Other aspect is the needs to link the on-ground data, as imaging, to the underground one by geographical and context field of view.

  12. Accurate, low-cost 3D-models of gullies

    NASA Astrophysics Data System (ADS)

    Onnen, Nils; Gronz, Oliver; Ries, Johannes B.; Brings, Christine

    2015-04-01

    Soil erosion is a widespread problem in arid and semi-arid areas. The most severe form is the gully erosion. They often cut into agricultural farmland and can make a certain area completely unproductive. To understand the development and processes inside and around gullies, we calculated detailed 3D-models of gullies in the Souss Valley in South Morocco. Near Taroudant, we had four study areas with five gullies different in size, volume and activity. By using a Canon HF G30 Camcorder, we made varying series of Full HD videos with 25fps. Afterwards, we used the method Structure from Motion (SfM) to create the models. To generate accurate models maintaining feasible runtimes, it is necessary to select around 1500-1700 images from the video, while the overlap of neighboring images should be at least 80%. In addition, it is very important to avoid selecting photos that are blurry or out of focus. Nearby pixels of a blurry image tend to have similar color values. That is why we used a MATLAB script to compare the derivatives of the images. The higher the sum of the derivative, the sharper an image of similar objects. MATLAB subdivides the video into image intervals. From each interval, the image with the highest sum is selected. E.g.: 20min. video at 25fps equals 30.000 single images. The program now inspects the first 20 images, saves the sharpest and moves on to the next 20 images etc. Using this algorithm, we selected 1500 images for our modeling. With VisualSFM, we calculated features and the matches between all images and produced a point cloud. Then, MeshLab has been used to build a surface out of it using the Poisson surface reconstruction approach. Afterwards we are able to calculate the size and the volume of the gullies. It is also possible to determine soil erosion rates, if we compare the data with old recordings. The final step would be the combination of the terrestrial data with the data from our aerial photography. So far, the method works well and we

  13. 3D Printing of Molecular Potential Energy Surface Models

    ERIC Educational Resources Information Center

    Lolur, Phalgun; Dawes, Richard

    2014-01-01

    Additive manufacturing, commonly known as 3D printing, is gaining popularity in a variety of applications and has recently become routinely available. Today, 3D printing services are not only found in engineering design labs and through online companies, but also in university libraries offering student access. In addition, affordable options for…

  14. 3D numerical modeling of India-Asia-like collision

    NASA Astrophysics Data System (ADS)

    -Erika Püsök, Adina; Kaus, Boris; Popov, Anton

    2013-04-01

    above a strong mantle lithosphere - the jelly sandwich model (Burov and Watts, 2006). 3D models are thus needed to investigate these hypotheses. However, fully 3D models of the dynamics of continent collision zones have only been developed very recently, and presently most research groups have relied on certain explicit assumptions for their codes. 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 here report on first lithospheric and upper-mantle scale simulations in which the Indian lithosphere is indented into Asia. Acknowledgements. Funding was provided by the European Research Council under the European Community's Seventh Framework Program (FP7/2007-2013) / ERC Grant agreement #258830. Numerical computations have been performed on JUQUEEN of the Jülich high-performance computing center. • Beaumont, C., Jamieson, R.A., Nguyen, M.H., Medvedev, S.E., 2004. Crustal channel flows: 1. Numerical models with applications to the tectonics of the Himalayan-Tibetan orogeny. J. Geophys. Res. 109, B06406. • Burov, E. & Watts, W.S., 2006. The long-term strength of continental lithosphere: "jelly sandwich" or "crème brûlée"?. GSA Today, 16, doi: 10.1130/1052-5173(2006)1016<1134:TLTSOC>1132.1130.CO;1132. • England P., Houseman, G., 1986. Finite strain calculations of continental deformation. 2. Comparison with the India-Asia collision zone. J. Geophys. Res.- Solid Earth and Planets 91 (B3), 3664-3676. • Jackson, J., 2002. Strength of the continental lithosphere: time to abandon the jelly sandwich?. GSA Today, September, 4-10. • Lechmann, S.M., May, D.A., Kaus, B.J.P., Schmalholz, S.M., 2011. Comparing thin-sheet models with 3D multilayer models for continental collision. Geophy. Int. J. doi: 10.1111/j.1365-246X.2011.05164.x • Royden, L.H., Burchfiel, B

  15. 3D-Digital soil property mapping by geoadditive models

    NASA Astrophysics Data System (ADS)

    Papritz, Andreas

    2016-04-01

    In many digital soil mapping (DSM) applications, soil properties must be predicted not only for a single but for multiple soil depth intervals. In the GlobalSoilMap project, as an example, predictions are computed for the 0-5 cm, 5-15 cm, 15-30 cm, 30-60 cm, 60-100 cm, 100-200 cm depth intervals (Arrouays et al., 2014). Legacy soil data are often used for DSM. It is common for such datasets that soil properties were measured for soil horizons or for layers at varying soil depth and with non-constant thickness (support). This poses problems for DSM: One strategy is to harmonize the soil data to common depth prior to the analyses (e.g. Bishop et al., 1999) and conduct the statistical analyses for each depth interval independently. The disadvantage of this approach is that the predictions for different depths are computed independently from each other so that the predicted depth profiles may be unrealistic. Furthermore, the error induced by the harmonization to common depth is ignored in this approach (Orton et al. 2016). A better strategy is therefore to process all soil data jointly without prior harmonization by a 3D-analysis that takes soil depth and geographical position explicitly into account. Usually, the non-constant support of the data is then ignored, but Orton et al. (2016) presented recently a geostatistical approach that accounts for non-constant support of soil data and relies on restricted maximum likelihood estimation (REML) of a linear geostatistical model with a separable, heteroscedastic, zonal anisotropic auto-covariance function and area-to-point kriging (Kyriakidis, 2004.) Although this model is theoretically coherent and elegant, estimating its many parameters by REML and selecting covariates for the spatial mean function is a formidable task. A simpler approach might be to use geoadditive models (Kammann and Wand, 2003; Wand, 2003) for 3D-analyses of soil data. geoAM extend the scope of the linear model with spatially correlated errors to

  16. 3D-Digital soil property mapping by geoadditive models

    NASA Astrophysics Data System (ADS)

    Papritz, Andreas

    2016-04-01

    In many digital soil mapping (DSM) applications, soil properties must be predicted not only for a single but for multiple soil depth intervals. In the GlobalSoilMap project, as an example, predictions are computed for the 0-5 cm, 5-15 cm, 15-30 cm, 30-60 cm, 60-100 cm, 100-200 cm depth intervals (Arrouays et al., 2014). Legacy soil data are often used for DSM. It is common for such datasets that soil properties were measured for soil horizons or for layers at varying soil depth and with non-constant thickness (support). This poses problems for DSM: One strategy is to harmonize the soil data to common depth prior to the analyses (e.g. Bishop et al., 1999) and conduct the statistical analyses for each depth interval independently. The disadvantage of this approach is that the predictions for different depths are computed independently from each other so that the predicted depth profiles may be unrealistic. Furthermore, the error induced by the harmonization to common depth is ignored in this approach (Orton et al. 2016). A better strategy is therefore to process all soil data jointly without prior harmonization by a 3D-analysis that takes soil depth and geographical position explicitly into account. Usually, the non-constant support of the data is then ignored, but Orton et al. (2016) presented recently a geostatistical approach that accounts for non-constant support of soil data and relies on restricted maximum likelihood estimation (REML) of a linear geostatistical model with a separable, heteroscedastic, zonal anisotropic auto-covariance function and area-to-point kriging (Kyriakidis, 2004.) Although this model is theoretically coherent and elegant, estimating its many parameters by REML and selecting covariates for the spatial mean function is a formidable task. A simpler approach might be to use geoadditive models (Kammann and Wand, 2003; Wand, 2003) for 3D-analyses of soil data. geoAM extend the scope of the linear model with spatially correlated errors to

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

    PubMed

    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

  18. Predicted 3D Model of the Rabies Virus Glycoprotein Trimer.

    PubMed

    Fernando, Bastida-González; Yersin, Celaya-Trejo; José, Correa-Basurto; Paola, Zárate-Segura

    2016-01-01

    The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained. PMID:27294109

  19. Predicted 3D Model of the Rabies Virus Glycoprotein Trimer.

    PubMed

    Fernando, Bastida-González; Yersin, Celaya-Trejo; José, Correa-Basurto; Paola, Zárate-Segura

    2016-01-01

    The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained.

  20. Predicted 3D Model of the Rabies Virus Glycoprotein Trimer

    PubMed Central

    Fernando, Bastida-González; Yersin, Celaya-Trejo; José, Correa-Basurto; Paola, Zárate-Segura

    2016-01-01

    The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained. PMID:27294109

  1. 3D finite element modeling of sliding wear

    NASA Astrophysics Data System (ADS)

    Buentello Hernandez, Rodolfo G.

    Wear is defined as "the removal of material volume through some mechanical process between two surfaces". There are many mechanical situations that can induce wear and each can involve many wear mechanisms. This research focuses on the mechanical wear due to dry sliding between two surfaces. Currently there is a need to identify and compare materials that would endure sliding wear under severe conditions such as high velocities. The high costs associated with the field experimentation of systems subject to high-speed sliding, has prevented the collection of the necessary data required to fully characterize this phenomena. Simulating wear through Finite Elements (FE) would enable its prediction under different scenarios and would reduce experimentation costs. In the aerospace, automotive and weapon industries such a model can aid in material selection, design and/or testing of systems subjected to wear in bearings, gears, brakes, gun barrels, slippers, locomotive wheels, or even rocket test tracks. The 3D wear model presented in this dissertation allows one to reasonably predict high-speed sliding mechanical wear between two materials. The model predictions are reasonable, when compared against those measured on a sled slipper traveling over the Holloman High Speed Tests Track. This slipper traveled a distance of 5,816 meters in 8.14 seconds and reached a maximum velocity of 1,530 m/s.

  2. 3D matrix-based cell cultures: Automated analysis of tumor cell survival and proliferation

    PubMed Central

    EKE, IRIS; HEHLGANS, STEPHANIE; SANDFORT, VEIT; CORDES, NILS

    2016-01-01

    Three-dimensional ex vivo cell cultures mimic physiological in vivo growth conditions thereby significantly contributing to our understanding of tumor cell growth and survival, therapy resistance and identification of novel potent cancer targets. In the present study, we describe advanced three-dimensional cell culture methodology for investigating cellular survival and proliferation in human carcinoma cells after cancer therapy including molecular therapeutics. Single cells are embedded into laminin-rich extracellular matrix and can be treated with cytotoxic drugs, ionizing or UV radiation or any other substance of interest when consolidated and approximating in vivo morphology. Subsequently, cells are allowed to grow for automated determination of clonogenic survival (colony number) or proliferation (colony size). The entire protocol of 3D cell plating takes ~1 h working time and pursues for ~7 days before evaluation. This newly developed method broadens the spectrum of exploration of malignant tumors and other diseases and enables the obtainment of more reliable data on cancer treatment efficacy. PMID:26549537

  3. Pros and Cons of ID vs. 3D Modeling

    NASA Technical Reports Server (NTRS)

    Klimchuk, James A.

    2012-01-01

    Advances in computing capability have led to tremendous improvements in 3D modeling. Entire active regions are being simulated in what might be described as a first principles way, in which plasma heating is treated self consistently rather than through the specification of heating functions. There are limitations to this approach, however, as actual heating mechanisms on the Sun involve spatial scales orders of magnitude smaller than what these simulations can resolve. Other simulations begin to resolve these scales, but they only treat a tiny volume and do not include the all important coupling with larger scales or with other parts of the atmosphere, and so cannot be readily compared with observations. Finally, ID hydrodynamic models capture the field-aligned evolution of the plasma extremely well and are ideally suited for data comparison, but they treat the heating in a totally ad hoc manner. All of these approaches have important contributions to make, but we must be aware of their limitations. I will highlight some of the strengths. and weaknesses of each.

  4. Object-oriented urban 3D spatial data model organization method

    NASA Astrophysics Data System (ADS)

    Li, Jing-wen; Li, Wen-qing; Lv, Nan; Su, Tao

    2015-12-01

    This paper combined the 3d data model with object-oriented organization method, put forward the model of 3d data based on object-oriented method, implemented the city 3d model to quickly build logical semantic expression and model, solved the city 3d spatial information representation problem of the same location with multiple property and the same property with multiple locations, designed the space object structure of point, line, polygon, body for city of 3d spatial database, and provided a new thought and method for the city 3d GIS model and organization management.

  5. Flexible building primitives for 3D building modeling

    NASA Astrophysics Data System (ADS)

    Xiong, B.; Jancosek, M.; Oude Elberink, S.; Vosselman, G.

    2015-03-01

    3D building models, being the main part of a digital city scene, are essential to all applications related to human activities in urban environments. The development of range sensors and Multi-View Stereo (MVS) technology facilitates our ability to automatically reconstruct level of details 2 (LoD2) models of buildings. However, because of the high complexity of building structures, no fully automatic system is currently available for producing building models. In order to simplify the problem, a lot of research focuses only on particular buildings shapes, and relatively simple ones. In this paper, we analyze the property of topology graphs of object surfaces, and find that roof topology graphs have three basic elements: loose nodes, loose edges, and minimum cycles. These elements have interesting physical meanings: a loose node is a building with one roof face; a loose edge is a ridge line between two roof faces whose end points are not defined by a third roof face; and a minimum cycle represents a roof corner of a building. Building primitives, which introduce building shape knowledge, are defined according to these three basic elements. Then all buildings can be represented by combining such building primitives. The building parts are searched according to the predefined building primitives, reconstructed independently, and grouped into a complete building model in a CSG-style. The shape knowledge is inferred via the building primitives and used as constraints to improve the building models, in which all roof parameters are simultaneously adjusted. Experiments show the flexibility of building primitives in both lidar point cloud and stereo point cloud.

  6. Methods for Geometric Data Validation of 3d City Models

    NASA Astrophysics Data System (ADS)

    Wagner, D.; Alam, N.; Wewetzer, M.; Pries, M.; Coors, V.

    2015-12-01

    Geometric quality of 3D city models is crucial for data analysis and simulation tasks, which are part of modern applications of the data (e.g. potential heating energy consumption of city quarters, solar potential, etc.). Geometric quality in these contexts is however a different concept as it is for 2D maps. In the latter case, aspects such as positional or temporal accuracy and correctness represent typical quality metrics of the data. They are defined in ISO 19157 and should be mentioned as part of the metadata. 3D data has a far wider range of aspects which influence their quality, plus the idea of quality itself is application dependent. Thus, concepts for definition of quality are needed, including methods to validate these definitions. Quality on this sense means internal validation and detection of inconsistent or wrong geometry according to a predefined set of rules. A useful starting point would be to have correct geometry in accordance with ISO 19107. A valid solid should consist of planar faces which touch their neighbours exclusively in defined corner points and edges. No gaps between them are allowed, and the whole feature must be 2-manifold. In this paper, we present methods to validate common geometric requirements for building geometry. Different checks based on several algorithms have been implemented to validate a set of rules derived from the solid definition mentioned above (e.g. water tightness of the solid or planarity of its polygons), as they were developed for the software tool CityDoctor. The method of each check is specified, with a special focus on the discussion of tolerance values where they are necessary. The checks include polygon level checks to validate the correctness of each polygon, i.e. closeness of the bounding linear ring and planarity. On the solid level, which is only validated if the polygons have passed validation, correct polygon orientation is checked, after self-intersections outside of defined corner points and edges

  7. Numerical model of sonic boom in 3D kinematic turbulence

    NASA Astrophysics Data System (ADS)

    Coulouvrat, François; Luquet, David; Marchiano, Régis

    2015-10-01

    stratified wind superimposed to a 3D random turbulent realization. Propagation is performed either in the case of a shadow zone or of an atmospheric waveguide. To model the turbulent ABL, the mean flow and the fluctuations are handled separately. The wind fluctuations are generated using the Random Fluctuations Generation method assuming a von Kármán spectrum and a homogeneous and isotropic turbulence. The mean stratified wind is modeled based on the Monin-Obhukov Similarity Theory (MOST). To illustrate the method, the typical case of a sunny day with a strong wind has been chosen. Statistics are obtained on several parameters. It shows the importance of turbulence, which leads to an increase of the mean maximum peak pressure in the shadow zone and to its decrease in the waveguide. Moreover, the formation of random caustics that can lead to an increase of the noise perceived locally is outlined.

  8. Development of topography in 3-D continental-collision models

    NASA Astrophysics Data System (ADS)

    Pusok, A. E.; Kaus, Boris J. P.

    2015-05-01

    Understanding the formation and evolution of high mountain belts, such as the Himalayas and the adjacent Tibetan Plateau, has been the focus of many tectonic and numerical models. Here we employ 3-D numerical simulations to investigate the role that subduction, collision, and indentation play on lithosphere dynamics at convergent margins, and to analyze the conditions under which large topographic plateaus can form in an integrated lithospheric and upper mantle-scale model. Distinct dynamics are obtained for the oceanic subduction side (trench retreat, slab rollback) and the continental-collision side (trench advance, slab detachment, topographic uplift, lateral extrusion). We show that slab pull alone is insufficient to generate high topography in the upper plate, and that external forcing and the presence of strong blocks such as the Tarim Basin are necessary to create and shape anomalously high topographic fronts and plateaus. Moreover, scaling is used to predict four different modes of surface expression in continental-collision models: (I) low-amplitude homogeneous shortening, (II) high-amplitude homogeneous shortening, (III) Alpine-type topography with topographic front and low plateau, and (IV) Tibet-Himalaya-type topography with topographic front and high plateau. Results of semianalytical models suggest that the Argand number governs the formation of high topographic fronts, while the amplitude of plateaus is controlled by the initial buoyancy ratio of the upper plate. Applying these results to natural examples, we show that the Alps belong to regime (III), the Himalaya-Tibet to regime (IV), whereas the Andes-Altiplano fall at the boundary between regimes (III) and (IV).

  9. West Flank Coso, CA FORGE 3D temperature model

    DOE Data Explorer

    Doug Blankenship

    2016-03-01

    x,y,z data of the 3D temperature model for the West Flank Coso FORGE site. Model grid spacing is 250m. The temperature model for the Coso geothermal field used over 100 geothermal production sized wells and intermediate-depth temperature holes. At the near surface of this model, two boundary temperatures were assumed: (1) areas with surface manifestations, including fumaroles along the northeast striking normal faults and northwest striking dextral faults with the hydrothermal field, a temperature of ~104˚C was applied to datum at +1066 meters above sea level elevation, and (2) a near-surface temperature at about 10 meters depth, of 20˚C was applied below the diurnal and annual conductive temperature perturbations. These assumptions were based on heat flow studies conducted at the CVF and for the Mojave Desert. On the edges of the hydrothermal system, a 73˚C/km (4˚F/100’) temperature gradient contour was established using conductive gradient data from shallow and intermediate-depth temperature holes. This contour was continued to all elevation datums between the 20˚C surface and -1520 meters below mean sea level. Because the West Flank is outside of the geothermal field footprint, during Phase 1, the three wells inside the FORGE site were incorporated into the preexisting temperature model. To ensure a complete model was built based on all the available data sets, measured bottom-hole temperature gradients in certain wells were downward extrapolated to the next deepest elevation datum (or a maximum of about 25% of the well depth where conductive gradients are evident in the lower portions of the wells). After assuring that the margins of the geothermal field were going to be adequately modelled, the data was contoured using the Kriging method algorithm. Although the extrapolated temperatures and boundary conditions are not rigorous, the calculated temperatures are anticipated to be within ~6˚C (20˚F), or one contour interval, of the

  10. 3D Simulation Modeling of the Tooth Wear Process

    PubMed Central

    Dai, Ning; Hu, Jian; Liu, Hao

    2015-01-01

    Severe tooth wear is the most common non-caries dental disease, and it can seriously affect oral health. Studying the tooth wear process is time-consuming and difficult, and technological tools are frequently lacking. This paper presents a novel method of digital simulation modeling that represents a new way to study tooth wear. First, a feature extraction algorithm is used to obtain anatomical feature points of the tooth without attrition. Second, after the alignment of non-attrition areas, the initial homogeneous surface is generated by means of the RBF (Radial Basic Function) implicit surface and then deformed to the final homogeneous by the contraction and bounding algorithm. Finally, the method of bilinear interpolation based on Laplacian coordinates between tooth with attrition and without attrition is used to inversely reconstruct the sequence of changes of the 3D tooth morphology during gradual tooth wear process. This method can also be used to generate a process simulation of nonlinear tooth wear by means of fitting an attrition curve to the statistical data of attrition index in a certain region. The effectiveness and efficiency of the attrition simulation algorithm are verified through experimental simulation. PMID:26241942

  11. 3D Simulation Modeling of the Tooth Wear Process.

    PubMed

    Dai, Ning; Hu, Jian; Liu, Hao

    2015-01-01

    Severe tooth wear is the most common non-caries dental disease, and it can seriously affect oral health. Studying the tooth wear process is time-consuming and difficult, and technological tools are frequently lacking. This paper presents a novel method of digital simulation modeling that represents a new way to study tooth wear. First, a feature extraction algorithm is used to obtain anatomical feature points of the tooth without attrition. Second, after the alignment of non-attrition areas, the initial homogeneous surface is generated by means of the RBF (Radial Basic Function) implicit surface and then deformed to the final homogeneous by the contraction and bounding algorithm. Finally, the method of bilinear interpolation based on Laplacian coordinates between tooth with attrition and without attrition is used to inversely reconstruct the sequence of changes of the 3D tooth morphology during gradual tooth wear process. This method can also be used to generate a process simulation of nonlinear tooth wear by means of fitting an attrition curve to the statistical data of attrition index in a certain region. The effectiveness and efficiency of the attrition simulation algorithm are verified through experimental simulation.

  12. Simulation of 3D tumor cell growth using nonlinear finite element method.

    PubMed

    Dong, Shoubing; Yan, Yannan; Tang, Liqun; Meng, Junping; Jiang, Yi

    2016-01-01

    We propose a novel parallel computing framework for a nonlinear finite element method (FEM)-based cell model and apply it to simulate avascular tumor growth. We derive computation formulas to simplify the simulation and design the basic algorithms. With the increment of the proliferation generations of tumor cells, the FEM elements may become larger and more distorted. Then, we describe a remesh and refinement processing of the distorted or over large finite elements and the parallel implementation based on Message Passing Interface to improve the accuracy and efficiency of the simulation. We demonstrate the feasibility and effectiveness of the FEM model and the parallelization methods in simulations of early tumor growth. PMID:26213205

  13. 3D modeling of carbonates petro-acoustic heterogeneities

    NASA Astrophysics Data System (ADS)

    Baden, Dawin; Guglielmi, Yves; Saracco, Ginette; Marié, Lionel; Viseur, Sophie

    2015-04-01

    Characterizing carbonate reservoirs heterogeneity is a challenging issue for Oil & Gas Industry, CO2 sequestration and all kinds of fluid manipulations in natural reservoirs, due to the significant impact of heterogeneities on fluid flow and storage within the reservoir. Although large scale (> meter) heterogeneities such as layers petrophysical contrasts are well addressed by computing facies-based models, low scale (< meter) heterogeneities are often poorly constrained because of the complexity in predicting their spatial arrangement. In this study, we conducted petro-acoustic measurements on cores of different size and diameter (Ø = 1", 1.5" and 5") in order to evaluate anisotropy or heterogeneity in carbonates at different laboratory scales. Different types of heterogeneities which generally occur in carbonate reservoir units (e.g. petrographic, diagenetic, and tectonic related) were sampled. Dry / wet samples were investigated with different ultrasonic apparatus and using different sensors allowing acoustic characterization through a bandwidth varying from 50 to 500 kHz. Comprehensive measurements realized on each samples allowed statistical analyses of petro-acoustic properties such as attenuation, shear and longitudinal wave velocity. The cores properties (geological and acoustic facies) were modeled in 3D using photogrammetry and GOCAD geo-modeler. This method successfully allowed detecting and imaging in three dimensions differential diagenesis effects characterized by the occurrence of decimeter-scale diagenetic horizons in samples assumed to be homogeneous and/or different diagenetic sequences between shells filling and the packing matrix. We then discuss how small interfaces such as cracks, stylolithes and laminations which are also imaged may have guided these differential effects, considering that understanding the processes may be taken as an analogue to actual fluid drainage complexity in deep carbonate reservoir.

  14. A 3D numerical model for Kepler's supernova remnant

    NASA Astrophysics Data System (ADS)

    Toledo-Roy, J. C.; Esquivel, A.; Velázquez, P. F.; Reynoso, E. M.

    2014-07-01

    We present new 3D numerical simulations for Kepler's supernova remnant. In this work we revisit the possibility that the asymmetric shape of the remnant in X-rays is the product of a Type Ia supernova explosion which occurs inside the wind bubble previously created by an AGB companion star. Due to the large peculiar velocity of the system, the interaction of the strong AGB wind with the interstellar medium results in a bow shock structure. In this new model we propose that the AGB wind is anisotropic, with properties such as mass-loss rate and density having a latitude dependence, and that the orientation of the polar axis of the AGB star is not aligned with the direction of motion. The ejecta from the Type Ia supernova explosion is modelled using a power-law density profile, and we let the remnant evolve for 400 yr. We computed synthetic X-ray maps from the numerical results. We find that the estimated size and peculiar X-ray morphology of Kepler's supernova remnant are well reproduced by considering an AGB mass-loss rate of 10-5 M⊙ yr-1, a wind terminal velocity of 10 km s-1, an ambient medium density of 10-3 cm-3 and an explosion energy of 7 × 1050 erg. The obtained total X-ray luminosity of the remnant in this model reaches 6 × 1050 erg, which is within a factor of 2 of the observed value, and the time evolution of the luminosity shows a rate of decrease in recent decades of ˜2.4 per cent yr-1 that is consistent with the observations.

  15. Modeling 3-D Slope Stability of Coastal Bluffs Using 3-D Ground-Water Flow, Southwestern Seattle, Washington

    USGS Publications Warehouse

    Brien, Dianne L.; Reid, Mark E.

    2007-01-01

    Landslides are a common problem on coastal bluffs throughout the world. Along the coastal bluffs of the Puget Sound in Seattle, Washington, landslides range from small, shallow failures to large, deep-seated landslides. Landslides of all types can pose hazards to human lives and property, but deep-seated landslides are of significant concern because their large areal extent can cause extensive property damage. Although many geomorphic processes shape the coastal bluffs of Seattle, we focus on large (greater than 3,000 m3), deepseated, rotational landslides that occur on the steep bluffs along Puget Sound. Many of these larger failures occur in advance outwash deposits of the Vashon Drift (Qva); some failures extend into the underlying Lawton Clay Member of the Vashon Drift (Qvlc). The slope stability of coastal bluffs is controlled by the interplay of three-dimensional (3-D) variations in gravitational stress, strength, and pore-water pressure. We assess 3-D slope-stability using SCOOPS (Reid and others, 2000), a computer program that allows us to search a high-resolution digital-elevation model (DEM) to quantify the relative stability of all parts of the landscape by computing the stability and volume of thousands of potential spherical failures. SCOOPS incorporates topography, 3-D strength variations, and 3-D pore pressures. Initially, we use our 3-D analysis methods to examine the effects of topography and geology by using heterogeneous material properties, as defined by stratigraphy, without pore pressures. In this scenario, the least-stable areas are located on the steepest slopes, commonly in Qva or Qvlc. However, these locations do not agree well with observations of deep-seated landslides. Historically, both shallow colluvial landslides and deep-seated landslides have been observed near the contact between Qva and Qvlc, and commonly occur in Qva. The low hydraulic conductivity of Qvlc impedes ground-water flow, resulting in elevated pore pressures at the

  16. Image-driven, model-based 3D abdominal motion estimation for MR-guided radiotherapy

    NASA Astrophysics Data System (ADS)

    Stemkens, Bjorn; Tijssen, Rob H. N.; de Senneville, Baudouin Denis; Lagendijk, Jan J. W.; van den Berg, Cornelis A. T.

    2016-07-01

    Respiratory motion introduces substantial uncertainties in abdominal radiotherapy for which traditionally large margins are used. The MR-Linac will open up the opportunity to acquire high resolution MR images just prior to radiation and during treatment. However, volumetric MRI time series are not able to characterize 3D tumor and organ-at-risk motion with sufficient temporal resolution. In this study we propose a method to estimate 3D deformation vector fields (DVFs) with high spatial and temporal resolution based on fast 2D imaging and a subject-specific motion model based on respiratory correlated MRI. In a pre-beam phase, a retrospectively sorted 4D-MRI is acquired, from which the motion is parameterized using a principal component analysis. This motion model is used in combination with fast 2D cine-MR images, which are acquired during radiation, to generate full field-of-view 3D DVFs with a temporal resolution of 476 ms. The geometrical accuracies of the input data (4D-MRI and 2D multi-slice acquisitions) and the fitting procedure were determined using an MR-compatible motion phantom and found to be 1.0-1.5 mm on average. The framework was tested on seven healthy volunteers for both the pancreas and the kidney. The calculated motion was independently validated using one of the 2D slices, with an average error of 1.45 mm. The calculated 3D DVFs can be used retrospectively for treatment simulations, plan evaluations, or to determine the accumulated dose for both the tumor and organs-at-risk on a subject-specific basis in MR-guided radiotherapy.

  17. Image-driven, model-based 3D abdominal motion estimation for MR-guided radiotherapy

    NASA Astrophysics Data System (ADS)

    Stemkens, Bjorn; Tijssen, Rob H. N.; de Senneville, Baudouin Denis; Lagendijk, Jan J. W.; van den Berg, Cornelis A. T.

    2016-07-01

    Respiratory motion introduces substantial uncertainties in abdominal radiotherapy for which traditionally large margins are used. The MR-Linac will open up the opportunity to acquire high resolution MR images just prior to radiation and during treatment. However, volumetric MRI time series are not able to characterize 3D tumor and organ-at-risk motion with sufficient temporal resolution. In this study we propose a method to estimate 3D deformation vector fields (DVFs) with high spatial and temporal resolution based on fast 2D imaging and a subject-specific motion model based on respiratory correlated MRI. In a pre-beam phase, a retrospectively sorted 4D-MRI is acquired, from which the motion is parameterized using a principal component analysis. This motion model is used in combination with fast 2D cine-MR images, which are acquired during radiation, to generate full field-of-view 3D DVFs with a temporal resolution of 476 ms. The geometrical accuracies of the input data (4D-MRI and 2D multi-slice acquisitions) and the fitting procedure were determined using an MR-compatible motion phantom and found to be 1.0–1.5 mm on average. The framework was tested on seven healthy volunteers for both the pancreas and the kidney. The calculated motion was independently validated using one of the 2D slices, with an average error of 1.45 mm. The calculated 3D DVFs can be used retrospectively for treatment simulations, plan evaluations, or to determine the accumulated dose for both the tumor and organs-at-risk on a subject-specific basis in MR-guided radiotherapy.

  18. Image-driven, model-based 3D abdominal motion estimation for MR-guided radiotherapy.

    PubMed

    Stemkens, Bjorn; Tijssen, Rob H N; de Senneville, Baudouin Denis; Lagendijk, Jan J W; van den Berg, Cornelis A T

    2016-07-21

    Respiratory motion introduces substantial uncertainties in abdominal radiotherapy for which traditionally large margins are used. The MR-Linac will open up the opportunity to acquire high resolution MR images just prior to radiation and during treatment. However, volumetric MRI time series are not able to characterize 3D tumor and organ-at-risk motion with sufficient temporal resolution. In this study we propose a method to estimate 3D deformation vector fields (DVFs) with high spatial and temporal resolution based on fast 2D imaging and a subject-specific motion model based on respiratory correlated MRI. In a pre-beam phase, a retrospectively sorted 4D-MRI is acquired, from which the motion is parameterized using a principal component analysis. This motion model is used in combination with fast 2D cine-MR images, which are acquired during radiation, to generate full field-of-view 3D DVFs with a temporal resolution of 476 ms. The geometrical accuracies of the input data (4D-MRI and 2D multi-slice acquisitions) and the fitting procedure were determined using an MR-compatible motion phantom and found to be 1.0-1.5 mm on average. The framework was tested on seven healthy volunteers for both the pancreas and the kidney. The calculated motion was independently validated using one of the 2D slices, with an average error of 1.45 mm. The calculated 3D DVFs can be used retrospectively for treatment simulations, plan evaluations, or to determine the accumulated dose for both the tumor and organs-at-risk on a subject-specific basis in MR-guided radiotherapy.

  19. Verification and Validation of the k-kL Turbulence Model in FUN3D and CFL3D Codes

    NASA Technical Reports Server (NTRS)

    Abdol-Hamid, Khaled S.; Carlson, Jan-Renee; Rumsey, Christopher L.

    2015-01-01

    The implementation of the k-kL turbulence model using multiple computational uid dy- namics (CFD) codes is reported herein. The k-kL model is a two-equation turbulence model based on Abdol-Hamid's closure and Menter's modi cation to Rotta's two-equation model. Rotta shows that a reliable transport equation can be formed from the turbulent length scale L, and the turbulent kinetic energy k. Rotta's equation is well suited for term-by-term mod- eling and displays useful features compared to other two-equation models. An important di erence is that this formulation leads to the inclusion of higher-order velocity derivatives in the source terms of the scale equations. This can enhance the ability of the Reynolds- averaged Navier-Stokes (RANS) solvers to simulate unsteady ows. The present report documents the formulation of the model as implemented in the CFD codes Fun3D and CFL3D. Methodology, veri cation and validation examples are shown. Attached and sepa- rated ow cases are documented and compared with experimental data. The results show generally very good comparisons with canonical and experimental data, as well as matching results code-to-code. The results from this formulation are similar or better than results using the SST turbulence model.

  20. 3D Geologic Model of the Southern Great Basin

    NASA Astrophysics Data System (ADS)

    Wagoner, J. L.; Myers, S. C.

    2006-12-01

    We have constructed a regional 3D geologic model of the southern Great Basin, in support of a seismic wave propagation investigation of the 1993 Nonproliferation Experiment (NPE) at the Nevada Test Site (NTS). The model is centered on the NPE and spans longitude -119.5° to -112.6°, latitude 34.5° to 39.8°, and a depth from the surface to 150 km below sea level. Hence, the model includes the southern half of Nevada, as well as parts of eastern California, western Utah, and a portion of northwestern Arizona. The upper crust is constrained by geologic and geophysical studies, and the lower crust and upper mantle are constrained by geophysical studies. The upper crustal geologic units are Quaternary basin fill, Tertiary deposits, pre-Tertiary deposits, intrusive rocks, and calderas. The lower crust and upper mantle are parameterized with 8 layers, including the Moho. Detailed geologic data, including surface maps, borehole data, and geophysical surveys, were used to define the geology at the NTS. Digital geologic outcrop data were available for both Nevada and Arizona, whereas we scanned and hand digitized geologic maps for California and Utah. Published gravity data (2km spacing) were used to determine the thickness of the Cenozoic deposits and constrain the depth of the basins. The free surface is based on a 10m lateral resolution DEM at the NTS and a 90m resolution DEM elsewhere. The gross geophysical structure of the crust and upper mantle is taken from regional surface-wave studies. Variations in crustal thickness are based on receiver function analysis and a compilation of reflection/refraction studies. We used the Earthvision (Dynamic Graphics, Inc.) software to integrate the geologic and geophysical information into a model of x,y,z,p nodes, where p is an integer index representing the geologic unit. For regional seismic simulations we convert this realistic geologic model into elastic parameters. Upper crustal units are treated as seismically homogeneous

  1. Numerical Results of 3-D Modeling of Moon Accumulation

    NASA Astrophysics Data System (ADS)

    Khachay, Yurie; Anfilogov, Vsevolod; Antipin, Alexandr

    2014-05-01

    For the last time for the model of the Moon usually had been used the model of mega impact in which the forming of the Earth and its sputnik had been the consequence of the Earth's collision with the body of Mercurial mass. But all dynamical models of the Earth's accumulation and the estimations after the Pb-Pb system, lead to the conclusion that the duration of the planet accumulation was about 1 milliard years. But isotopic results after the W-Hf system testify about a very early (5-10) million years, dividing of the geochemical reservoirs of the core and mantle. In [1,2] it is shown, that the account of energy dissipating by the decay of short living radioactive elements and first of all Al26,it is sufficient for heating even small bodies with dimensions about (50-100) km up to the iron melting temperature and can be realized a principal new differentiation mechanism. The inner parts of the melted preplanets can join and they are mainly of iron content, but the cold silicate fragments return to the supply zone and additionally change the content of Moon forming to silicates. Only after the increasing of the gravitational radius of the Earth, the growing area of the future Earth's core can save also the silicate envelope fragments [3]. For understanding the further system Earth-Moon evolution it is significant to trace the origin and evolution of heterogeneities, which occur on its accumulation stage.In that paper we are modeling the changing of temperature,pressure,velocity of matter flowing in a block of 3d spherical body with a growing radius. The boundary problem is solved by the finite-difference method for the system of equations, which include equations which describe the process of accumulation, the Safronov equation, the equation of impulse balance, equation Navier-Stocks, equation for above litho static pressure and heat conductivity in velocity-pressure variables using the Businesque approach.The numerical algorithm of the problem solution in velocity

  2. 3D Geological Model of Nihe ore deposit Constrained by Gravity and Magnetic Modeling

    NASA Astrophysics Data System (ADS)

    Qi, Guang; Yan, Jiayong; Lv, Qingtan; Zhao, Jinhua

    2016-04-01

    We present a case study on using integrated geologic model in mineral exploration at depth. Nihe ore deposit in Anhui Province, is deep hidden ore deposit which was discovered in recent years, this finding is the major driving force of deep mineral exploration work in Luzong. Building 3D elaborate geological model has the important significance for prospecting to deep or surround in this area, and can help us better understand the metallogenic law and ore-controlling regularity. A 3D geological model, extending a depth from +200m to -1500m in Nihe ore deposit, has been compiled from surface geological map, cross-section, borehole logs and amounts of geological inference. And then the 3D geological models have been given physical property parameter for calculating the potential field. Modelling the potential response is proposed as means of evaluating the viability of the 3D geological models, and the evidence of making small changes to the uncertain parts of the original 3D geological models. It is expected that the final models not only reproduce supplied prior geological knowledge, but also explain the observed geophysical data. The workflow used to develop the 3D geologic model in this study includes the three major steps, as follows: (1) Determine the basic information of Model: Defining the 3D limits of the model area, the basic geological and structural unit, and the tectonic contact relations and the sedimentary sequences between these units. (2) 3D model construction: Firstly, a series of 2D geological cross sections over the model area are built by using all kinds of prior information, including surface geology, borehole data, seismic sections, and local geologists' knowledge and intuition. Lastly, we put these sections into a 3D environment according to their profile locations to build a 3D model by using geostatistics method. (3) 3D gravity and magnetic modeling: we calculate the potential field responses of the 3D model, and compare the predicted and

  3. Orbiter/External Tank Mate 3-D Solid Modeling

    NASA Technical Reports Server (NTRS)

    Godfrey, G. S.; Brandt, B.; Rorden, D.; Kapr, F.

    2004-01-01

    This research and development project presents an overview of the work completed while attending a summer 2004 American Society of Engineering Education/National Aeronautics and Space Administration (ASEE/NASA) Faculty Fellowship. This fellowship was completed at the Kennedy Space Center, Florida. The scope of the project was to complete parts, assemblies, and drawings that could be used by Ground Support Equipment (GSE) personnel to simulate situations and scenarios commonplace to the space shuttle Orbiter/External Tank (ET) Mate (50004). This mate takes place in the Vehicle Assembly Building (VAB). These simulations could then be used by NASA engineers as decision-making tools. During the summer of 2004, parts were created that defined the Orbiter/ET structural interfaces. Emphasis was placed upon assemblies that included the Orbiter/ET forward attachment (EO-1), aft left thrust strut (EO-2), aft right tripod support structure (EO-3), and crossbeam and aft feedline/umbilical supports. These assemblies are used to attach the Orbiter to the ET. The Orbiter/ET Mate assembly was then used to compare and analyze clearance distances using different Orbiter hang angles. It was found that a 30-minute arc angle change in Orbiter hang angle affected distance at the bipod strut to Orbiter yoke fitting 8.11 inches. A 3-D solid model library was established as a result of this project. This library contains parts, assemblies, and drawings translated into several formats. This library contains a collection of the following files: sti for sterolithography, stp for neutral file work, shrinkwrap for compression. tiff for photoshop work, jpeg for Internet use, and prt and asm for Pro/Engineer use. This library was made available to NASA engineers so that they could access its contents to make angle, load, and clearance analysis studies. These decision-making tools may be used by Pro/Engineer users and non-users.

  4. Automated robust generation of compact 3D statistical shape models

    NASA Astrophysics Data System (ADS)

    Vrtovec, Tomaz; Likar, Bostjan; Tomazevic, Dejan; Pernus, Franjo

    2004-05-01

    Ascertaining the detailed shape and spatial arrangement of anatomical structures is important not only within diagnostic settings but also in the areas of planning, simulation, intraoperative navigation, and tracking of pathology. Robust, accurate and efficient automated segmentation of anatomical structures is difficult because of their complexity and inter-patient variability. Furthermore, the position of the patient during image acquisition, the imaging device and protocol, image resolution, and other factors induce additional variations in shape and appearance. Statistical shape models (SSMs) have proven quite successful in capturing structural variability. A possible approach to obtain a 3D SSM is to extract reference voxels by precisely segmenting the structure in one, reference image. The corresponding voxels in other images are determined by registering the reference image to each other image. The SSM obtained in this way describes statistically plausible shape variations over the given population as well as variations due to imperfect registration. In this paper, we present a completely automated method that significantly reduces shape variations induced by imperfect registration, thus allowing a more accurate description of variations. At each iteration, the derived SSM is used for coarse registration, which is further improved by describing finer variations of the structure. The method was tested on 64 lumbar spinal column CT scans, from which 23, 38, 45, 46 and 42 volumes of interest containing vertebra L1, L2, L3, L4 and L5, respectively, were extracted. Separate SSMs were generated for each vertebra. The results show that the method is capable of reducing the variations induced by registration errors.

  5. Engineering a 3D microfluidic culture platform for tumor-treating field application

    NASA Astrophysics Data System (ADS)

    Pavesi, Andrea; Adriani, Giulia; Tay, Andy; Warkiani, Majid Ebrahimi; Yeap, Wei Hseun; Wong, Siew Cheng; Kamm, Roger D.

    2016-05-01

    The limitations of current cancer therapies highlight the urgent need for a more effective therapeutic strategy. One promising approach uses an alternating electric field; however, the mechanisms involved in the disruption of the cancer cell cycle as well as the potential adverse effects on non-cancerous cells must be clarified. In this study, we present a novel microfluidic device with embedded electrodes that enables the application of an alternating electric field therapy to cancer cells in a 3D extracellular matrix. To demonstrate the potential of our system to aid in designing and testing new therapeutic approaches, cancer cells and cancer cell aggregates were cultured individually or co-cultured with endothelial cells. The metastatic potential of the cancer cells was reduced after electric field treatment. Moreover, the proliferation rate of the treated cancer cells was lower compared with that of the untreated cells, whereas the morphologies and proliferative capacities of the endothelial cells were not significantly affected. These results demonstrate that our novel system can be used to rapidly screen the effect of an alternating electric field on cancer and normal cells within an in vivo-like microenvironment with the potential to optimize treatment protocols and evaluate synergies between tumor-treating field treatment and chemotherapy.

  6. Engineering a 3D microfluidic culture platform for tumor-treating field application

    PubMed Central

    Pavesi, Andrea; Adriani, Giulia; Tay, Andy; Warkiani, Majid Ebrahimi; Yeap, Wei Hseun; Wong, Siew Cheng; Kamm, Roger D.

    2016-01-01

    The limitations of current cancer therapies highlight the urgent need for a more effective therapeutic strategy. One promising approach uses an alternating electric field; however, the mechanisms involved in the disruption of the cancer cell cycle as well as the potential adverse effects on non-cancerous cells must be clarified. In this study, we present a novel microfluidic device with embedded electrodes that enables the application of an alternating electric field therapy to cancer cells in a 3D extracellular matrix. To demonstrate the potential of our system to aid in designing and testing new therapeutic approaches, cancer cells and cancer cell aggregates were cultured individually or co-cultured with endothelial cells. The metastatic potential of the cancer cells was reduced after electric field treatment. Moreover, the proliferation rate of the treated cancer cells was lower compared with that of the untreated cells, whereas the morphologies and proliferative capacities of the endothelial cells were not significantly affected. These results demonstrate that our novel system can be used to rapidly screen the effect of an alternating electric field on cancer and normal cells within an in vivo-like microenvironment with the potential to optimize treatment protocols and evaluate synergies between tumor-treating field treatment and chemotherapy. PMID:27215466

  7. Adaptive enhancement and visualization techniques for 3D THz images of breast cancer tumors

    NASA Astrophysics Data System (ADS)

    Wu, Yuhao; Bowman, Tyler; Gauch, John; El-Shenawee, Magda

    2016-03-01

    This paper evaluates image enhancement and visualization techniques for pulsed terahertz (THz) images of tissue samples. Specifically, our research objective is to effectively differentiate between heterogeneous regions of breast tissues that contain tumors diagnosed as triple negative infiltrating ductal carcinoma (IDC). Tissue slices and blocks of varying thicknesses were prepared and scanned using our lab's THz pulsed imaging system. One of the challenges we have encountered in visualizing the obtained images and differentiating between healthy and cancerous regions of the tissues is that most THz images have a low level of details and narrow contrast, making it difficult to accurately identify and visualize the margins around the IDC. To overcome this problem, we have applied and evaluated a number of image processing techniques to the scanned 3D THz images. In particular, we employed various spatial filtering and intensity transformation techniques to emphasize the small details in the images and adjust the image contrast. For each of these methods, we investigated how varying filter sizes and parameters affect the amount of enhancement applied to the images. Our experimentation shows that several image processing techniques are effective in producing THz images of breast tissue samples that contain distinguishable details, making further segmentation of the different image regions promising.

  8. Use of laser 3D surface digitizer in data collection and 3D modeling of anatomical structures

    NASA Astrophysics Data System (ADS)

    Tse, Kelly; Van Der Wall, Hans; Vu, Dzung H.

    2006-02-01

    A laser digitizer (Konica-Minolta Vivid 910) is used to obtain 3-dimensional surface scans of anatomical structures with a maximum resolution of 0.1mm. Placing the specimen on a turntable allows multiple scans allaround because the scanner only captures data from the portion facing its lens. A computer model is generated using 3D modeling software such as Geomagic. The 3D model can be manipulated on screen for repeated analysis of anatomical features, a useful capability when the specimens are rare or inaccessible (museum collection, fossils, imprints in rock formation.). As accurate measurements can be performed on the computer model, instead of taking measurements on actual specimens only at the archeological excavation site e.g., a variety of quantitative data can be later obtained on the computer model in the laboratory as new ideas come to mind. Our group had used a mechanical contact digitizer (Microscribe) for this purpose, but with the surface digitizer, we have been obtaining data sets more accurately and more quickly.

  9. 3D Spherical Convection Modeling of Venusian Resurfacing Mechanisms

    NASA Astrophysics Data System (ADS)

    Prunty, A. C.; King, S. D.

    2014-12-01

    The surface of Venus is thought to have undergone a global resurfacing event approximately 750 Ma. While several variations and modifications within the proposed resurfacing models exist, two end-member mechanisms can be broadly identified: (1) catastrophic overturns of the lithosphere, and (2) global volcanic resurfacing. We perform high-resolution, 3D spherical convection calculations using CitcomS to determine the conditions in Venus' deep interior necessary for each mechanism to occur. To date, we have focused on modeling episodic overturns of the lithosphere in the stagnant lid regime following the method of van Heck and Tackley (2008), and implementing a temperature-dependent rheology and yield stress. We find in general that lithospheric yielding can occur with a Rayleigh number of the order of 105 and a yield stress of the order of 20 ­- 400 MPa, consistent with the results of van Heck and Tackley. Additionally, we find that the behavior of lithospheric overturn depends strongly on the yield stress. To see this, we systematically increase the Rayleigh number and the yield stress via a priori scaling relationships. We find that models with Rayleigh number between 105 and 108 exhibit some variation of stagnant-lid convection; however, we observe that by varying the yield stress we are able to control the degree to which the overturns consist of the subduction of large, coherent segments of lithosphere as opposed to the formation of a large number of smaller, regional delaminations. We analyze these two modes of overturn by looking at the resultant geoid and topography fields to see if they yield distinguishable signatures. Furthermore, we analyze the spherical harmonic power spectrum of the geoid and topography to determine the extent to which their signatures are contributed from lower mantle anomalies and surface features. We also test the effects of mineral phase transformations and depth­-increasing viscosity on lithospheric overturn behavior by varying

  10. Using 3D Geometric Models to Teach Spatial Geometry Concepts.

    ERIC Educational Resources Information Center

    Bertoline, Gary R.

    1991-01-01

    An explanation of 3-D Computer Aided Design (CAD) usage to teach spatial geometry concepts using nontraditional techniques is presented. The software packages CADKEY and AutoCAD are described as well as their usefulness in solving space geometry problems. (KR)

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  12. Examination of 1D Solar Cell Model Limitations Using 3D SPICE Modeling: Preprint

    SciTech Connect

    McMahon, W. E.; Olson, J. M.; Geisz, J. F.; Friedman, D. J.

    2012-06-01

    To examine the limitations of one-dimensional (1D) solar cell modeling, 3D SPICE-based modeling is used to examine in detail the validity of the 1D assumptions as a function of sheet resistance for a model cell. The internal voltages and current densities produced by this modeling give additional insight into the differences between the 1D and 3D models.

  13. Utility of multimaterial 3D printers in creating models with pathological entities to enhance the training experience of neurosurgeons.

    PubMed

    Waran, Vicknes; Narayanan, Vairavan; Karuppiah, Ravindran; Owen, Sarah L F; Aziz, Tipu

    2014-02-01

    The advent of multimaterial 3D printers allows the creation of neurosurgical models of a more realistic nature, mimicking real tissues. The authors used the latest generation of 3D printer to create a model, with an inbuilt pathological entity, of varying consistency and density. Using this model the authors were able to take trainees through the basic steps, from navigation and planning of skin flap to performing initial steps in a craniotomy and simple tumor excision. As the technology advances, models of this nature may be able to supplement the training of neurosurgeons in a simulated operating theater environment, thus improving the training experience.

  14. 3D Atmospheric Radiative Transfer for Cloud System-Resolving Models: Forward Modelling and Observations

    SciTech Connect

    Howard Barker; Jason Cole

    2012-05-17

    Utilization of cloud-resolving models and multi-dimensional radiative transfer models to investigate the importance of 3D radiation effects on the numerical simulation of cloud fields and their properties.

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

    NASA Astrophysics Data System (ADS)

    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.

  16. Multi Sensor Data Integration for AN Accurate 3d Model Generation

    NASA Astrophysics Data System (ADS)

    Chhatkuli, S.; Satoh, T.; Tachibana, K.

    2015-05-01

    The aim of this paper is to introduce a novel technique of data integration between two different data sets, i.e. laser scanned RGB point cloud and oblique imageries derived 3D model, to create a 3D model with more details and better accuracy. In general, aerial imageries are used to create a 3D city model. Aerial imageries produce an overall decent 3D city models and generally suit to generate 3D model of building roof and some non-complex terrain. However, the automatically generated 3D model, from aerial imageries, generally suffers from the lack of accuracy in deriving the 3D model of road under the bridges, details under tree canopy, isolated trees, etc. Moreover, the automatically generated 3D model from aerial imageries also suffers from undulated road surfaces, non-conforming building shapes, loss of minute details like street furniture, etc. in many cases. On the other hand, laser scanned data and images taken from mobile vehicle platform can produce more detailed 3D road model, street furniture model, 3D model of details under bridge, etc. However, laser scanned data and images from mobile vehicle are not suitable to acquire detailed 3D model of tall buildings, roof tops, and so forth. Our proposed approach to integrate multi sensor data compensated each other's weakness and helped to create a very detailed 3D model with better accuracy. Moreover, the additional details like isolated trees, street furniture, etc. which were missing in the original 3D model derived from aerial imageries could also be integrated in the final model automatically. During the process, the noise in the laser scanned data for example people, vehicles etc. on the road were also automatically removed. Hence, even though the two dataset were acquired in different time period the integrated data set or the final 3D model was generally noise free and without unnecessary details.

  17. Numerical Results of Earth's Core Accumulation 3-D Modelling

    NASA Astrophysics Data System (ADS)

    Khachay, Yurie; Anfilogov, Vsevolod

    2013-04-01

    For a long time as a most convenient had been the model of mega impact in which the early forming of the Earth's core and mantle had been the consequence of formed protoplanet collision with the body of Mercurial mass. But all dynamical models of the Earth's accumulation and the estimations after the Pb-Pb system, lead to the conclusion that the duration of the planet accumulation was about 1 milliard years. But isotopic results after the W-Hf system testify about a very early (5-10) million years, dividing of the geochemical reservoirs of the core and mantle. In [1,3] it is shown, that the account of energy dissipating by the decay of short living radioactive elements and first of all Al,it is sufficient for heating even small bodies with dimensions about (50-100) km up to the iron melting temperature and can be realized a principal new differentiation mechanism. The inner parts of the melted preplanets can join and they are mainly of iron content, but the cold silicate fragments return to the supply zone. Only after the increasing of the gravitational radius, the growing area of the future core can save also the silicate envelope fragments. All existing dynamical accumulation models are constructed by using a spherical-symmetrical model. Hence for understanding the further planet evolution it is significant to trace the origin and evolution of heterogeneities, which occur on the planet accumulation stage. In that paper we are modeling distributions of temperature, pressure, velocity of matter flowing in a block of 3D- spherical body with a growing radius. The boundary problem is solved by the finite-difference method for the system of equations, which include equations which describe the process of accumulation, the Safronov equation, the equation of impulse balance, equation Navier-Stocks, equation for above litho static pressure and heat conductivity in velocity-pressure variables using the Businesque approach. The numerical algorithm of the problem solution in

  18. A novel alternative method for 3D visualisation in Parasitology: the construction of a 3D model of a parasite from 2D illustrations.

    PubMed

    Teo, B G; Sarinder, K K S; Lim, L H S

    2010-08-01

    Three-dimensional (3D) models of the marginal hooks, dorsal and ventral anchors, bars and haptoral reservoirs of a parasite, Sundatrema langkawiense Lim & Gibson, 2009 (Monogenea) were developed using the polygonal modelling method in Autodesk 3ds Max (Version 9) based on two-dimensional (2D) illustrations. Maxscripts were written to rotate the modelled 3D structures. Appropriately orientated 3D haptoral hard-parts were then selected and positioned within the transparent 3D outline of the haptor and grouped together to form a complete 3D haptoral entity. This technique is an inexpensive tool for constructing 3D models from 2D illustrations for 3D visualisation of the spatial relationships between the different structural parts within organisms. PMID:20962723

  19. 3-D visualization and non-linear tissue classification of breast tumors using ultrasound elastography in vivo.

    PubMed

    Sayed, Ahmed; Layne, Ginger; Abraham, Jame; Mukdadi, Osama M

    2014-07-01

    The goal of the study described here was to introduce new methods for the classification and visualization of human breast tumors using 3-D ultrasound elastography. A tumor's type, shape and size are key features that can help the physician to decide the sort and extent of necessary treatment. In this work, tumor type, being either benign or malignant, was classified non-invasively for nine volunteer patients. The classification was based on estimating four parameters that reflect the tumor's non-linear biomechanical behavior, under multi-compression levels. Tumor prognosis using non-linear elastography was confirmed with biopsy as a gold standard. Three tissue classification parameters were found to be statistically significant with a p-value < 0.05, whereas the fourth non-linear parameter was highly significant, having a p-value < 0.001. Furthermore, each breast tumor's shape and size were estimated in vivo using 3-D elastography, and were enhanced using interactive segmentation. Segmentation with level sets was used to isolate the stiff tumor from the surrounding soft tissue. Segmentation also provided a reliable means to estimate tumors volumes. Four volumetric strains were investigated: the traditional normal axial strain, the first principal strain, von Mises strain and maximum shear strain. It was noted that these strains can provide varying degrees of boundary enhancement to the stiff tumor in the constructed elastograms. The enhanced boundary improved the performance of the segmentation process. In summary, the proposed methods can be employed as a 3-D non-invasive tool for characterization of breast tumors, and may provide early prognosis with minimal pain, as well as diminish the risk of late-stage breast cancer.

  20. Bootstrapping mixed correlators in the 3D Ising model

    NASA Astrophysics Data System (ADS)

    Kos, Filip; Poland, David; Simmons-Duffin, David

    2014-11-01

    We study the conformal bootstrap for systems of correlators involving nonidentical operators. The constraints of crossing symmetry and unitarity for such mixed correlators can be phrased in the language of semidefinite programming. We apply this formalism to the simplest system of mixed correlators in 3D CFTs with a ℤ2 global symmetry. For the leading ℤ2-odd operator σ and ℤ2-even operator ɛ, we obtain numerical constraints on the allowed dimensions (Δ σ , Δ ɛ ) assuming that σ and ɛ are the only relevant scalars in the theory. These constraints yield a small closed region in (Δ σ , Δ ɛ ) space compatible with the known values in the 3D Ising CFT.

  1. 3D numerical model for NGC 6888 Nebula

    NASA Astrophysics Data System (ADS)

    Reyes-Iturbide, J.; Velázquez, P. F.; Rosado, M.

    We present 3D numerical simulations of the NGC6888 nebula considering the proper motion and the evolution of the star, from the red supergiant (RSG) to the Wolf-Rayet (WR) phase. Our simulations reproduce the limb-brightened morphology observed in [OIII] and X-ray emission maps. The synthetic maps computed by the numerical simulations show filamentary and clumpy structures produced by instabilities triggered in the interaction between the WR wind and the RSG shell.

  2. 3D high-content screening for the identification of compounds that target cells in dormant tumor spheroid regions

    SciTech Connect

    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. - Highlights: • Establishment of a novel method for 3D cell culture based high-content screening. • First reported high

  3. Virtual and Printed 3D Models for Teaching Crystal Symmetry and Point Groups

    ERIC Educational Resources Information Center

    Casas, Lluís; Estop, Euge`nia

    2015-01-01

    Both, virtual and printed 3D crystal models can help students and teachers deal with chemical education topics such as symmetry and point groups. In the present paper, two freely downloadable tools (interactive PDF files and a mobile app) are presented as examples of the application of 3D design to study point-symmetry. The use of 3D printing to…

  4. ODTLES : a model for 3D turbulent flow based on one-dimensional turbulence modeling concepts.

    SciTech Connect

    McDermott, Randy; Kerstein, Alan R.; Schmidt, Rodney Cannon

    2005-01-01

    This report describes an approach for extending the one-dimensional turbulence (ODT) model of Kerstein [6] to treat turbulent flow in three-dimensional (3D) domains. This model, here called ODTLES, can also be viewed as a new LES model. In ODTLES, 3D aspects of the flow are captured by embedding three, mutually orthogonal, one-dimensional ODT domain arrays within a coarser 3D mesh. The ODTLES model is obtained by developing a consistent approach for dynamically coupling the different ODT line sets to each other and to the large scale processes that are resolved on the 3D mesh. The model is implemented computationally and its performance is tested and evaluated by performing simulations of decaying isotropic turbulence, a standard turbulent flow benchmarking problem.

  5. Short and long time effects of low temperature Plasma Activated Media on 3D multicellular tumor spheroids

    NASA Astrophysics Data System (ADS)

    Judée, Florian; Fongia, Céline; Ducommun, Bernard; Yousfi, Mohammed; Lobjois, Valérie; Merbahi, Nofel

    2016-02-01

    This work investigates the regionalized antiproliferative effects of plasma-activated medium (PAM) on colon adenocarcinoma multicellular tumor spheroid (MCTS), a model that mimics 3D organization and regionalization of a microtumor region. PAM was generated by dielectric barrier plasma jet setup crossed by helium carrier gas. MCTS were transferred in PAM at various times after plasma exposure up to 48 hours and effect on MCTS growth and DNA damage were evaluated. We report the impact of plasma exposure duration and delay before transfer on MCTS growth and DNA damage. Local accumulation of DNA damage revealed by histone H2AX phosphorylation is observed on outermost layers and is dependent on plasma exposure. DNA damage is completely reverted by catalase addition indicating that H2O2 plays major role in observed genotoxic effect while growth inhibitory effect is maintained suggesting that it is due to others reactive species. SOD and D-mannitol scavengers also reduced DNA damage by 30% indicating that and OH* are involved in H2O2 formation. Finally, PAM is able to retain its cytotoxic and genotoxic activity upon storage at +4 °C or ‑80 °C. These results suggest that plasma activated media may be a promising new antitumor strategy for colorectal cancer tumors.

  6. Short and long time effects of low temperature Plasma Activated Media on 3D multicellular tumor spheroids

    PubMed Central

    Judée, Florian; Fongia, Céline; Ducommun, Bernard; Yousfi, Mohammed; Lobjois, Valérie; Merbahi, Nofel

    2016-01-01

    This work investigates the regionalized antiproliferative effects of plasma-activated medium (PAM) on colon adenocarcinoma multicellular tumor spheroid (MCTS), a model that mimics 3D organization and regionalization of a microtumor region. PAM was generated by dielectric barrier plasma jet setup crossed by helium carrier gas. MCTS were transferred in PAM at various times after plasma exposure up to 48 hours and effect on MCTS growth and DNA damage were evaluated. We report the impact of plasma exposure duration and delay before transfer on MCTS growth and DNA damage. Local accumulation of DNA damage revealed by histone H2AX phosphorylation is observed on outermost layers and is dependent on plasma exposure. DNA damage is completely reverted by catalase addition indicating that H2O2 plays major role in observed genotoxic effect while growth inhibitory effect is maintained suggesting that it is due to others reactive species. SOD and D-mannitol scavengers also reduced DNA damage by 30% indicating that and OH* are involved in H2O2 formation. Finally, PAM is able to retain its cytotoxic and genotoxic activity upon storage at +4 °C or −80 °C. These results suggest that plasma activated media may be a promising new antitumor strategy for colorectal cancer tumors. PMID:26898904

  7. Short and long time effects of low temperature Plasma Activated Media on 3D multicellular tumor spheroids

    NASA Astrophysics Data System (ADS)

    Judée, Florian; Fongia, Céline; Ducommun, Bernard; Yousfi, Mohammed; Lobjois, Valérie; Merbahi, Nofel

    2016-02-01

    This work investigates the regionalized antiproliferative effects of plasma-activated medium (PAM) on colon adenocarcinoma multicellular tumor spheroid (MCTS), a model that mimics 3D organization and regionalization of a microtumor region. PAM was generated by dielectric barrier plasma jet setup crossed by helium carrier gas. MCTS were transferred in PAM at various times after plasma exposure up to 48 hours and effect on MCTS growth and DNA damage were evaluated. We report the impact of plasma exposure duration and delay before transfer on MCTS growth and DNA damage. Local accumulation of DNA damage revealed by histone H2AX phosphorylation is observed on outermost layers and is dependent on plasma exposure. DNA damage is completely reverted by catalase addition indicating that H2O2 plays major role in observed genotoxic effect while growth inhibitory effect is maintained suggesting that it is due to others reactive species. SOD and D-mannitol scavengers also reduced DNA damage by 30% indicating that and OH* are involved in H2O2 formation. Finally, PAM is able to retain its cytotoxic and genotoxic activity upon storage at +4 °C or -80 °C. These results suggest that plasma activated media may be a promising new antitumor strategy for colorectal cancer tumors.

  8. Short and long time effects of low temperature Plasma Activated Media on 3D multicellular tumor spheroids.

    PubMed

    Judée, Florian; Fongia, Céline; Ducommun, Bernard; Yousfi, Mohammed; Lobjois, Valérie; Merbahi, Nofel

    2016-01-01

    This work investigates the regionalized antiproliferative effects of plasma-activated medium (PAM) on colon adenocarcinoma multicellular tumor spheroid (MCTS), a model that mimics 3D organization and regionalization of a microtumor region. PAM was generated by dielectric barrier plasma jet setup crossed by helium carrier gas. MCTS were transferred in PAM at various times after plasma exposure up to 48 hours and effect on MCTS growth and DNA damage were evaluated. We report the impact of plasma exposure duration and delay before transfer on MCTS growth and DNA damage. Local accumulation of DNA damage revealed by histone H2AX phosphorylation is observed on outermost layers and is dependent on plasma exposure. DNA damage is completely reverted by catalase addition indicating that H2O2 plays major role in observed genotoxic effect while growth inhibitory effect is maintained suggesting that it is due to others reactive species. SOD and D-mannitol scavengers also reduced DNA damage by 30% indicating that O(2)(-)* and OH* are involved in H2O2 formation. Finally, PAM is able to retain its cytotoxic and genotoxic activity upon storage at +4 °C or -80 °C. These results suggest that plasma activated media may be a promising new antitumor strategy for colorectal cancer tumors. PMID:26898904

  9. Towards a predictive model of chromatin 3D organization.

    PubMed

    Xu, Chenhuan; Corces, Victor G

    2016-09-01

    Architectural proteins mediate interactions between distant regions in the genome to bring together different regulatory elements while establishing a specific three-dimensional organization of the genetic material. Depletion of specific architectural proteins leads to miss regulation of gene expression and alterations in nuclear organization. The specificity of interactions mediated by architectural proteins depends on the nature, number, and orientation of their binding site at individual genomic locations. Knowledge of the mechanisms and rules governing interactions among architectural proteins may provide a code to predict the 3D organization of the genome. PMID:26658098

  10. 3D high-content screening for the identification of compounds that target cells in dormant tumor spheroid regions.

    PubMed

    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.

  11. The use of an in vitro 3D melanoma model to predict in vivo plasmid transfection using electroporation

    PubMed Central

    Marrero, Bernadette; Heller, Richard

    2012-01-01

    A large-scale in vitro 3D tumor model was generated to evaluate gene delivery procedures in vivo. This 3D tumor model consists of a “tissue-like” spheroid that provides a micro-environment supportive of melanoma proliferation, allowing cells to behave similarly to cells in vivo. This functional spheroid measures approximately 1 cm in diameter and can be used to effectively evaluate plasmid transfection when testing various electroporation (EP) electrode applicators. In this study, we identified EP conditions that efficiently transfect green fluorescent protein (GFP) and interleukin 15 (IL-15) plasmids into tumor cells residing in the 3D construct. We found that plasmids delivered using a 6-plate electrode applying 6 pulses with nominal electric field strength of 500 V/cm and pulse-length of 20 ms produced significant increase of GFP (7.3-fold) and IL-15 (3.0–fold) expression compared to controls. This in vitro 3D model demonstrates the predictability of cellular response toward delivery techniques, limits the numbers of animals employed for transfection studies, and may facilitate future developments of clinical trials for cancer therapies in vivo. PMID:22244695

  12. 3D model based visualisation using dynamic models: problems with standard software and extensive strategies

    NASA Astrophysics Data System (ADS)

    Appelt, Veit; Shvetsov, Vladimir

    2006-04-01

    For projects concerning modification of urban structures or landscape, it is essential to have a visualisation before, during and after the planning. It conveys an impression of existing city structures or newly planned buildings roads, railways in 3D reality it helps to gain public acceptance. The design of such constructions makes high demands on geometry and planning technology. The construction project, as a 3D object, must therefore be assessed in whole and only this leads to a comprehensive evaluation of alignment, design and following up safety. On the basis of surveying and planning data, a 3D model fitted together of several information levels.

  13. Autophagy initiation correlates with the autophagic flux in 3D models of mesothelioma and with patient outcome

    PubMed Central

    Follo, Carlo; Barbone, Dario; Richards, William G.; Bueno, Raphael; Broaddus, V. Courtney

    2016-01-01

    ABSTRACT Understanding the role of autophagy in cancer has been limited by the inability to measure this dynamic process in formalin-fixed tissue. We considered that 3-dimensional models including ex vivo tumor, such as we have developed for studying mesothelioma, would provide valuable insights. Using these models, in which we could use lysosomal inhibitors to measure the autophagic flux, we sought a marker of autophagy that would be valid in formalin-fixed tumor and be used to assess the role of autophagy in patient outcome. Autophagy was studied in mesothelioma cell lines, as 2-dimensional (2D) monolayers and 3-dimensional (3D) multicellular spheroids (MCS), and in tumor from 25 chemonaive patients, both as ex vivo 3D tumor fragment spheroids (TFS) and as formalin-fixed tissue. Autophagy was evaluated as autophagic flux by detection of the accumulation of LC3 after lysosomal inhibition and as autophagy initiation by detection of ATG13 puncta. We found that autophagic flux in 3D, but not in 2D, correlated with ATG13 positivity. In each TFS, ATG13 positivity was similar to that of the original tumor. When tested in tissue microarrays of 109 chemonaive patients, higher ATG13 positivity correlated with better prognosis and provided information independent of known prognostic factors. Our results show that ATG13 is a static marker of the autophagic flux in 3D models of mesothelioma and may also reflect autophagy levels in formalin-fixed tumor. If confirmed, this marker would represent a novel prognostic factor for mesothelioma, supporting the notion that autophagy plays an important role in this cancer. PMID:27097020

  14. One-step reconstruction with a 3D-printed, biomechanically evaluated custom implant after complex pelvic tumor resection.

    PubMed

    Wong, K C; Kumta, S M; Geel, N V; Demol, J

    2015-01-01

    Resection of a pelvic tumor is challenging because of its complex three-dimensional (3D) anatomy and deep-seated location with nearby vital structures. The resection is technically demanding if a custom implant is used for reconstruction of the bone defect as the surgeon needs to ensure the resection margin is sufficiently wide and the orientation of intended resection planes must match that of the custom implant. We describe a novel workflow of performing a partial acetabular resection in a patient with pelvic chondrosarcoma and reconstruction with a custom pelvic implant in a one-step operation. A multi-planar bone resection was virtually planned. A computer-aided design implant that both matched the bone defect and biomechanically evaluated was prefabricated with 3D printing technology. The 3D-printed patient-specific instruments (PSIs) were used to reproduce the same planned resection. The histology of the tumor specimen showed a clear resection margin. The errors of the achieved resection and implant position were deviating (1-4 mm) from the planned. The patient could walk unaided with a good hip function. No tumor recurrence and implant loosening were noted at 11 months after surgery. The use of this novel CT-based method for surgical planning, the engineering software for implant design and validation, together with 3D printing technology for implant and PSI fabrication makes it possible to generate a personalized, biomechanically evaluated implant for accurate reconstruction after a pelvic tumor resection in a one-step operation. Further study in a larger population is needed to assess the clinical efficacy of the workflow in complex bone tumor surgery.

  15. Microencapsulation of Neuroblastoma Cells and Mesenchymal Stromal Cells in Collagen Microspheres: A 3D Model for Cancer Cell Niche Study

    PubMed Central

    Yeung, Pan; Sin, Hoi Shun; Chan, Shing; Chan, Godfrey Chi Fung; Chan, Barbara Pui

    2015-01-01

    There is a growing trend for researchers to use in vitro 3D models in cancer studies, as they can better recapitulate the complex in vivo situation. And the fact that the progression and development of tumor are closely associated to its stromal microenvironment has been increasingly recognized. The establishment of such tumor supportive niche is vital in understanding tumor progress and metastasis. The mesenchymal origin of many cells residing in the cancer niche provides the rationale to include MSCs in mimicking the niche in neuroblastoma. Here we co-encapsulate and co-culture NBCs and MSCs in a 3D in vitro model and investigate the morphology, growth kinetics and matrix remodeling in the reconstituted stromal environment. Results showed that the incorporation of MSCs in the model lead to accelerated growth of cancer cells as well as recapitulation of at least partially the tumor microenvironment in vivo. The current study therefore demonstrates the feasibility for the collagen microsphere to act as a 3D in vitro cancer model for various topics in cancer studies. PMID:26657086

  16. Heating properties of the needle type applicator made of shape memory alloy by 3-D anatomical human head model.

    PubMed

    Mimoto, N; Kato, K; Kanazawa, Y; Shindo, Y; Tsuchiya, K; Kubo, M; Uzuka, T; Takahashi, H; Fujii, Y

    2009-01-01

    Since the human brain is protected by the skull, it is not easy to non-invasively heat deep brain tumors with electromagnetic energy for hyperthermia treatments. Generally, needle type applicators were used in clinical practice to heat brain tumors. To expand the heating area of needle type applicators, we have developed a new type of needle made of a shape memory alloy (SMA). In this paper, heating properties of the proposed SMA needle type applicator were discussed. Here, in order to apply the SMA needle type applicator clinically. First, we constructed an anatomical 3-D FEM model from MRI and X-ray CT images using 3D-CAD software. Second, we estimated electric and temperature distributions to confirm the SMA needle type applicator using the FEM soft were JMAG-Studio. From these results, it was confirmed that the proposed method can expand the heating area and control the heating of various sizes of brain tumors.

  17. Implementation of algebraic stress models in a general 3-D Navier-Stokes method (PAB3D)

    NASA Technical Reports Server (NTRS)

    Abdol-Hamid, Khaled S.

    1995-01-01

    A three-dimensional multiblock Navier-Stokes code, PAB3D, which was developed for propulsion integration and general aerodynamic analysis, has been used extensively by NASA Langley and other organizations to perform both internal (exhaust) and external flow analysis of complex aircraft configurations. This code was designed to solve the simplified Reynolds Averaged Navier-Stokes equations. A two-equation k-epsilon turbulence model has been used with considerable success, especially for attached flows. Accurate predicting of transonic shock wave location and pressure recovery in separated flow regions has been more difficult. Two algebraic Reynolds stress models (ASM) have been recently implemented in the code that greatly improved the code's ability to predict these difficult flow conditions. Good agreement with Direct Numerical Simulation (DNS) for a subsonic flat plate was achieved with ASM's developed by Shih, Zhu, and Lumley and Gatski and Speziale. Good predictions were also achieved at subsonic and transonic Mach numbers for shock location and trailing edge boattail pressure recovery on a single-engine afterbody/nozzle model.

  18. Developing and Testing a 3d Cadastral Data Model a Case Study in Australia

    NASA Astrophysics Data System (ADS)

    Aien, A.; Kalantari, M.; Rajabifard, A.; Williamson, I. P.; Shojaei, D.

    2012-07-01

    Population growth, urbanization and industrialization place more pressure on land use with the need for increased space. To extend the use and functionality of the land, complex infrastructures are being built, both vertically and horizontally, layered and stacked. These three-dimensional (3D) developments affect the interests (Rights, Restrictions, and Responsibilities (RRRs)) attached to the underlying land. A 3D cadastre will assist in managing the effects of 3D development on a particular extent of land. There are many elements that contribute to developing a 3D cadastre, such as existing of 3D property legislations, 3D DBMS, 3D visualization. However, data modelling is one of the most important elements of a successful 3D cadastre. As architectural models of houses and high rise buildings help their users visualize the final product, 3D cadastre data model supports 3D cadastre users to understand the structure or behavior of the system and has a template that guides them to construct and implement the 3D cadastre. Many jurisdictions, organizations and software developers have built their own cadastral data model. Land Administration Domain Model (DIS-ISO 19152, The Netherlands) and ePlan (Intergovernmental Committee on Surveying and Mapping, Australia) are examples of existing data models. The variation between these data models is the result of different attitudes towards cadastres. However, there is a basic common thread among them all. Current cadastral data models use a 2D land-parcel concept and extend it to support 3D requirements. These data models cannot adequately manage and represent the spatial extent of 3D RRRs. Most of the current cadastral data models have been influenced by a very broad understanding of 3D cadastral concepts because better clarity in what needs to be represented and analysed in the cadastre needs to be established. This paper presents the first version of a 3D Cadastral Data Model (3DCDM_Version 1.0). 3DCDM models both the legal

  19. A new approach towards image based virtual 3D city modeling by using close range photogrammetry

    NASA Astrophysics Data System (ADS)

    Singh, S. P.; Jain, K.; Mandla, V. R.

    2014-05-01

    3D city model is a digital representation of the Earth's surface and it's related objects such as building, tree, vegetation, and some manmade feature belonging to urban area. The demand of 3D city modeling is increasing day to day for various engineering and non-engineering applications. Generally three main image based approaches are using for virtual 3D city models generation. In first approach, researchers used Sketch based modeling, second method is Procedural grammar based modeling and third approach is Close range photogrammetry based modeling. Literature study shows that till date, there is no complete solution available to create complete 3D city model by using images. These image based methods also have limitations This paper gives a new approach towards image based virtual 3D city modeling by using close range photogrammetry. This approach is divided into three sections. First, data acquisition process, second is 3D data processing, and third is data combination process. In data acquisition process, a multi-camera setup developed and used for video recording of an area. Image frames created from video data. Minimum required and suitable video image frame selected for 3D processing. In second section, based on close range photogrammetric principles and computer vision techniques, 3D model of area created. In third section, this 3D model exported to adding and merging of other pieces of large area. Scaling and alignment of 3D model was done. After applying the texturing and rendering on this model, a final photo-realistic textured 3D model created. This 3D model transferred into walk-through model or in movie form. Most of the processing steps are automatic. So this method is cost effective and less laborious. Accuracy of this model is good. For this research work, study area is the campus of department of civil engineering, Indian Institute of Technology, Roorkee. This campus acts as a prototype for city. Aerial photography is restricted in many country

  20. Detection of Disease Symptoms on Hyperspectral 3d Plant Models

    NASA Astrophysics Data System (ADS)

    Roscher, Ribana; Behmann, Jan; Mahlein, Anne-Katrin; Dupuis, Jan; Kuhlmann, Heiner; Plümer, Lutz

    2016-06-01

    We analyze the benefit of combining hyperspectral images information with 3D geometry information for the detection of Cercospora leaf spot disease symptoms on sugar beet plants. Besides commonly used one-class Support Vector Machines, we utilize an unsupervised sparse representation-based approach with group sparsity prior. Geometry information is incorporated by representing each sample of interest with an inclination-sorted dictionary, which can be seen as an 1D topographic dictionary. We compare this approach with a sparse representation based approach without geometry information and One-Class Support Vector Machines. One-Class Support Vector Machines are applied to hyperspectral data without geometry information as well as to hyperspectral images with additional pixelwise inclination information. Our results show a gain in accuracy when using geometry information beside spectral information regardless of the used approach. However, both methods have different demands on the data when applied to new test data sets. One-Class Support Vector Machines require full inclination information on test and training data whereas the topographic dictionary approach only need spectral information for reconstruction of test data once the dictionary is build by spectra with inclination.

  1. Novel Morphologic and Genetic Analysis of Cancer Cells in a 3D Microenvironment Identifies STAT3 as a Regulator of Tumor Permeability Barrier Function.

    PubMed

    Park, Min Chul; Jeong, Hyobin; Son, Sung Hwa; Kim, YounHa; Han, Daeyoung; Goughnour, Peter C; Kang, Taehee; Kwon, Nam Hoon; Moon, Hyo Eun; Paek, Sun Ha; Hwang, Daehee; Seol, Ho Jun; Nam, Do-Hyun; Kim, Sunghoon

    2016-03-01

    Tumor permeability is a critical determinant of drug delivery and sensitivity, but systematic methods to identify factors that perform permeability barrier functions in the tumor microenvironment are not yet available. Multicellular tumor spheroids have become tractable in vitro models to study the impact of a three-dimensional (3D) environment on cellular behavior. In this study, we characterized the spheroid-forming potential of cancer cells and correlated the resulting spheroid morphologies with genetic information to identify conserved cellular processes associated with spheroid structure. Spheroids generated from 100 different cancer cell lines were classified into four distinct groups based on morphology. In particular, round and compact spheroids exhibited highly hypoxic inner cores and permeability barriers against anticancer drugs. Through systematic and correlative analysis, we reveal JAK-STAT signaling as one of the signature pathways activated in round spheroids. Accordingly, STAT3 inhibition in spheroids generated from the established cancer cells and primary glioblastoma patient-derived cells altered the rounded morphology and increased drug sensitivity. Furthermore, combined administration of the STAT3 inhibitor and 5-fluorouracil to a mouse xenograft model markedly reduced tumor growth compared with monotherapy. Collectively, our findings demonstrate the ability to integrate 3D culture and genetic profiling to determine the factors underlying the integrity of the permeability barrier in the tumor microenvironment, and may help to identify and exploit novel mechanisms of drug resistance. PMID:26676754

  2. Novel Morphologic and Genetic Analysis of Cancer Cells in a 3D Microenvironment Identifies STAT3 as a Regulator of Tumor Permeability Barrier Function.

    PubMed

    Park, Min Chul; Jeong, Hyobin; Son, Sung Hwa; Kim, YounHa; Han, Daeyoung; Goughnour, Peter C; Kang, Taehee; Kwon, Nam Hoon; Moon, Hyo Eun; Paek, Sun Ha; Hwang, Daehee; Seol, Ho Jun; Nam, Do-Hyun; Kim, Sunghoon

    2016-03-01

    Tumor permeability is a critical determinant of drug delivery and sensitivity, but systematic methods to identify factors that perform permeability barrier functions in the tumor microenvironment are not yet available. Multicellular tumor spheroids have become tractable in vitro models to study the impact of a three-dimensional (3D) environment on cellular behavior. In this study, we characterized the spheroid-forming potential of cancer cells and correlated the resulting spheroid morphologies with genetic information to identify conserved cellular processes associated with spheroid structure. Spheroids generated from 100 different cancer cell lines were classified into four distinct groups based on morphology. In particular, round and compact spheroids exhibited highly hypoxic inner cores and permeability barriers against anticancer drugs. Through systematic and correlative analysis, we reveal JAK-STAT signaling as one of the signature pathways activated in round spheroids. Accordingly, STAT3 inhibition in spheroids generated from the established cancer cells and primary glioblastoma patient-derived cells altered the rounded morphology and increased drug sensitivity. Furthermore, combined administration of the STAT3 inhibitor and 5-fluorouracil to a mouse xenograft model markedly reduced tumor growth compared with monotherapy. Collectively, our findings demonstrate the ability to integrate 3D culture and genetic profiling to determine the factors underlying the integrity of the permeability barrier in the tumor microenvironment, and may help to identify and exploit novel mechanisms of drug resistance.

  3. XML-based 3D model visualization and simulation framework for dynamic models

    NASA Astrophysics Data System (ADS)

    Kim, Taewoo; Fishwick, Paul A.

    2002-07-01

    Relatively recent advances in computer technology enable us to create three-dimensional (3D) dynamic models and simulate them within a 3D web environment. The use of such models is especially valuable when teaching simulation, and the concepts behind dynamic models, since the models are made more accessible to the students. Students tend to enjoy a construction process in which they are able to employ their own cultural and aesthetic forms. The challenge is to create a language that allows for a grammar for modeling, while simultaneously permitting arbitrary presentation styles. For further flexibility, we need an effective way to represent and simulate dynamic models that can be shared by modelers over the Internet. We present an Extensible Markup Language (XML)-based framework that will guide a modeler in creating personalized 3D models, visualizing its dynamic behaviors, and simulating the created models. A model author will use XML files to represent geometries and topology of a dynamic model. Model Fusion Engine, written in Extensible Stylesheet Language Transformation (XSLT), expedites the modeling process by automating the creation of dynamic models with the user-defined XML files. Modelers can also link simulation programs with a created model to analyze the characteristics of the model. The advantages of this system lie in the education of modeling and simulating dynamic models, and in the exploitation of visualizing the dynamic model behaviors.

  4. Combination of Virtual Tours, 3d Model and Digital Data in a 3d Archaeological Knowledge and Information System

    NASA Astrophysics Data System (ADS)

    Koehl, M.; Brigand, N.

    2012-08-01

    The site of the Engelbourg ruined castle in Thann, Alsace, France, has been for some years the object of all the attention of the city, which is the owner, and also of partners like historians and archaeologists who are in charge of its study. The valuation of the site is one of the main objective, as well as its conservation and its knowledge. The aim of this project is to use the environment of the virtual tour viewer as new base for an Archaeological Knowledge and Information System (AKIS). With available development tools we add functionalities in particular through diverse scripts that convert the viewer into a real 3D interface. By beginning with a first virtual tour that contains about fifteen panoramic images, the site of about 150 times 150 meters can be completely documented by offering the user a real interactivity and that makes visualization very concrete, almost lively. After the choice of pertinent points of view, panoramic images were realized. For the documentation, other sets of images were acquired at various seasons and climate conditions, which allow documenting the site in different environments and states of vegetation. The final virtual tour was deducted from them. The initial 3D model of the castle, which is virtual too, was also joined in the form of panoramic images for completing the understanding of the site. A variety of types of hotspots were used to connect the whole digital documentation to the site, including videos (as reports during the acquisition phases, during the restoration works, during the excavations, etc.), digital georeferenced documents (archaeological reports on the various constituent elements of the castle, interpretation of the excavations and the searches, description of the sets of collected objects, etc.). The completely personalized interface of the system allows either to switch from a panoramic image to another one, which is the classic case of the virtual tours, or to go from a panoramic photographic image

  5. Evaluation of Model Recognition for Grammar-Based Automatic 3d Building Model Reconstruction

    NASA Astrophysics Data System (ADS)

    Yu, Qian; Helmholz, Petra; Belton, David

    2016-06-01

    In recent years, 3D city models are in high demand by many public and private organisations, and the steadily growing capacity in both quality and quantity are increasing demand. The quality evaluation of these 3D models is a relevant issue both from the scientific and practical points of view. In this paper, we present a method for the quality evaluation of 3D building models which are reconstructed automatically from terrestrial laser scanning (TLS) data based on an attributed building grammar. The entire evaluation process has been performed in all the three dimensions in terms of completeness and correctness of the reconstruction. Six quality measures are introduced to apply on four datasets of reconstructed building models in order to describe the quality of the automatic reconstruction, and also are assessed on their validity from the evaluation point of view.

  6. 3D object retrieval with multitopic model combining relevance feedback and LDA model.

    PubMed

    Leng, Biao; Zeng, Jiabei; Yao, Ming; Xiong, Zhang

    2015-01-01

    View-based 3D model retrieval uses a set of views to represent each object. Discovering the complex relationship between multiple views remains challenging in 3D object retrieval. Recent progress in the latent Dirichlet allocation (LDA) model leads us to propose its use for 3D object retrieval. This LDA approach explores the hidden relationships between extracted primordial features of these views. Since LDA is limited to a fixed number of topics, we further propose a multitopic model to improve retrieval performance. We take advantage of a relevance feedback mechanism to balance the contributions of multiple topic models with specified numbers of topics. We demonstrate our improved retrieval performance over the state-of-the-art approaches.

  7. Towards Precise Metadata-set for Discovering 3D Geospatial Models in Geo-portals

    NASA Astrophysics Data System (ADS)

    Zamyadi, A.; Pouliot, J.; Bédard, Y.

    2013-09-01

    Accessing 3D geospatial models, eventually at no cost and for unrestricted use, is certainly an important issue as they become popular among participatory communities, consultants, and officials. Various geo-portals, mainly established for 2D resources, have tried to provide access to existing 3D resources such as digital elevation model, LIDAR or classic topographic data. Describing the content of data, metadata is a key component of data discovery in geo-portals. An inventory of seven online geo-portals and commercial catalogues shows that the metadata referring to 3D information is very different from one geo-portal to another as well as for similar 3D resources in the same geo-portal. The inventory considered 971 data resources affiliated with elevation. 51% of them were from three geo-portals running at Canadian federal and municipal levels whose metadata resources did not consider 3D model by any definition. Regarding the remaining 49% which refer to 3D models, different definition of terms and metadata were found, resulting in confusion and misinterpretation. The overall assessment of these geo-portals clearly shows that the provided metadata do not integrate specific and common information about 3D geospatial models. Accordingly, the main objective of this research is to improve 3D geospatial model discovery in geo-portals by adding a specific metadata-set. Based on the knowledge and current practices on 3D modeling, and 3D data acquisition and management, a set of metadata is proposed to increase its suitability for 3D geospatial models. This metadata-set enables the definition of genuine classes, fields, and code-lists for a 3D metadata profile. The main structure of the proposal contains 21 metadata classes. These classes are classified in three packages as General and Complementary on contextual and structural information, and Availability on the transition from storage to delivery format. The proposed metadata set is compared with Canadian Geospatial

  8. Optimization of Aqueous Biphasic Tumor Spheroid Microtechnology for Anti-Cancer Drug Testing in 3D Culture

    PubMed Central

    Lemmo, Stephanie; Atefi, Ehsan; Luker, Gary D.; Tavana, Hossein

    2014-01-01

    Tumor spheroids are three-dimensional clusters of cancer cells that exhibit characteristics of poorly perfused tumors and hence present a relevant model for testing the efficacy of anti-cancer compounds. The use of spheroids for drug screening is hindered by technological complexities for high throughput generation of consistent size spheroids individually addressable by drug compounds. Here we present and optimize a simple spheroid technology based on the use of an aqueous two-phase system. Cancer cells confined in a drop of the denser aqueous dextran phase are robotically dispensed into a microwell containing the immersion aqueous polyethylene glycol phase. Cells remain within the drop and form a viable spheroid, without a need for any external stimuli. The size of resulting spheroids is sensitive to volume variations of dispensed drops from the air displacement pipetting head of a commercial liquid handling robot. Therefore, we parametrically optimize the process of dispensing of dextran phase drops. For a given cell density, this optimization reproducibly generates consistent size spheroids in standard 96-well plates. In addition, we evaluate the use of a commercial biochemical assay to examine cellular viability of cancer cell spheroids. Spheroids show a dose-dependent response to cisplatin similar to a monolayer culture. However unlike their two-dimensional counterpart, spheroids exhibit resistance to paclitaxel treatment. This technology, which uses only commercially-available reagents and equipment, can potentially expedite anti-cancer drug discovery. Although the use of robotics makes the ATPS spheroid technology particularly useful for drug screening applications, this approach is compatible with simpler liquid handling techniques such as manual micropipetting and offers a straightforward method of 3D cell culture in research laboratories. PMID:25221631

  9. Why 3D? The Need for Solution Based Modeling in a National Geoscience Organization.

    NASA Astrophysics Data System (ADS)

    Terrington, Ricky; Napier, Bruce; Howard, Andy; Ford, Jon; Hatton, William

    2008-05-01

    In recent years national geoscience organizations have increasingly utilized 3D model data as an output to the stakeholder community. Advances in both software and hardware have led to an increasing use of 3D depictions of geoscience data alongside the standard 2D data formats such as maps and GIS data. By characterizing geoscience data in 3D, knowledge transfer between geoscientists and stakeholders is improved as the mindset and thought processes are communicated more effectively in a 3D model than in a 2D flat file format. 3D models allow the user to understand the conceptual basis of the 2D data and aids the decision making process at local, regional and national scales. Some of these issues include foundation and engineering conditions, ground water vulnerability, aquifer recharge and flow, and resource extraction and storage. The British Geological Survey has established a mechanism and infrastructure through the Digital Geoscience Spatial Model Programme (DGSM) to produce these types of 3D geoscience outputs. This cyber-infrastructure not only allows good data and information management, it enables geoscientists to capture their know-how and implicit and tacit knowledge for their 3D interpretations. A user of this data will then have access to value-added information for the 3D dataset including the knowledge, approach, inferences, uncertainty, wider context and best practice acquired during the 3D interpretation. To complement this cyber-infrastructure, an immersive 3D Visualization Facility was constructed at the British Geological Survey offices in Keyworth, Nottingham and Edinburgh. These custom built facilities allow stereo projection of geoscience data, immersing the users and stakeholders in a wealth of 3D geological data. Successful uses of these facilities include collaborative 3D modeling, demonstrations to public stakeholders and Virtual Field Mapping Reconnaissance.

  10. 3D delivered dose assessment using a 4DCT-based motion model

    SciTech Connect

    Cai, Weixing; Hurwitz, Martina H.; Williams, Christopher L.; Dhou, Salam; Berbeco, Ross I.; Mishra, Pankaj E-mail: jhlewis@lroc.harvard.edu; Lewis, John H. E-mail: jhlewis@lroc.harvard.edu; Seco, Joao

    2015-06-15

    Purpose: The purpose of this work is to develop a clinically feasible method of calculating actual delivered dose distributions for patients who have significant respiratory motion during the course of stereotactic body radiation therapy (SBRT). Methods: A novel approach was proposed to calculate the actual delivered dose distribution for SBRT lung treatment. This approach can be specified in three steps. (1) At the treatment planning stage, a patient-specific motion model is created from planning 4DCT data. This model assumes that the displacement vector field (DVF) of any respiratory motion deformation can be described as a linear combination of some basis DVFs. (2) During the treatment procedure, 2D time-varying projection images (either kV or MV projections) are acquired, from which time-varying “fluoroscopic” 3D images of the patient are reconstructed using the motion model. The DVF of each timepoint in the time-varying reconstruction is an optimized linear combination of basis DVFs such that the 2D projection of the 3D volume at this timepoint matches the projection image. (3) 3D dose distribution is computed for each timepoint in the set of 3D reconstructed fluoroscopic images, from which the total effective 3D delivered dose is calculated by accumulating deformed dose distributions. This approach was first validated using two modified digital extended cardio-torso (XCAT) phantoms with lung tumors and different respiratory motions. The estimated doses were compared to the dose that would be calculated for routine 4DCT-based planning and to the actual delivered dose that was calculated using “ground truth” XCAT phantoms at all timepoints. The approach was also tested using one set of patient data, which demonstrated the application of our method in a clinical scenario. Results: For the first XCAT phantom that has a mostly regular breathing pattern, the errors in 95% volume dose (D95) are 0.11% and 0.83%, respectively for 3D fluoroscopic images

  11. 3D delivered dose assessment using a 4DCT-based motion model

    PubMed Central

    Cai, Weixing; Hurwitz, Martina H.; Williams, Christopher L.; Dhou, Salam; Berbeco, Ross I.; Seco, Joao; Mishra, Pankaj; Lewis, John H.

    2015-01-01

    Purpose: The purpose of this work is to develop a clinically feasible method of calculating actual delivered dose distributions for patients who have significant respiratory motion during the course of stereotactic body radiation therapy (SBRT). Methods: A novel approach was proposed to calculate the actual delivered dose distribution for SBRT lung treatment. This approach can be specified in three steps. (1) At the treatment planning stage, a patient-specific motion model is created from planning 4DCT data. This model assumes that the displacement vector field (DVF) of any respiratory motion deformation can be described as a linear combination of some basis DVFs. (2) During the treatment procedure, 2D time-varying projection images (either kV or MV projections) are acquired, from which time-varying “fluoroscopic” 3D images of the patient are reconstructed using the motion model. The DVF of each timepoint in the time-varying reconstruction is an optimized linear combination of basis DVFs such that the 2D projection of the 3D volume at this timepoint matches the projection image. (3) 3D dose distribution is computed for each timepoint in the set of 3D reconstructed fluoroscopic images, from which the total effective 3D delivered dose is calculated by accumulating deformed dose distributions. This approach was first validated using two modified digital extended cardio-torso (XCAT) phantoms with lung tumors and different respiratory motions. The estimated doses were compared to the dose that would be calculated for routine 4DCT-based planning and to the actual delivered dose that was calculated using “ground truth” XCAT phantoms at all timepoints. The approach was also tested using one set of patient data, which demonstrated the application of our method in a clinical scenario. Results: For the first XCAT phantom that has a mostly regular breathing pattern, the errors in 95% volume dose (D95) are 0.11% and 0.83%, respectively for 3D fluoroscopic images

  12. Integration of 3D photogrammetric outcrop models in the reservoir modelling workflow

    NASA Astrophysics Data System (ADS)

    Deschamps, Remy; Joseph, Philippe; Lerat, Olivier; Schmitz, Julien; Doligez, Brigitte; Jardin, Anne

    2014-05-01

    3D technologies are now widely used in geosciences to reconstruct outcrops in 3D. The technology used for the 3D reconstruction is usually based on Lidar, which provides very precise models. Such datasets offer the possibility to build well-constrained outcrop analogue models for reservoir study purposes. The photogrammetry is an alternate methodology which principles are based in determining the geometric properties of an object from photographic pictures taken from different angles. Outcrop data acquisition is easy, and this methodology allows constructing 3D outcrop models with many advantages such as: - light and fast acquisition, - moderate processing time (depending on the size of the area of interest), - integration of field data and 3D outcrops into the reservoir modelling tools. Whatever the method, the advantages of digital outcrop model are numerous as already highlighted by Hodgetts (2013), McCaffrey et al. (2005) and Pringle et al. (2006): collection of data from otherwise inaccessible areas, access to different angles of view, increase of the possible measurements, attributes analysis, fast rate of data collection, and of course training and communication. This paper proposes a workflow where 3D geocellular models are built by integrating all sources of information from outcrops (surface picking, sedimentological sections, structural and sedimentary dips…). The 3D geomodels that are reconstructed can be used at the reservoir scale, in order to compare the outcrop information with subsurface models: the detailed facies models of the outcrops are transferred into petrophysical and acoustic models, which are used to test different scenarios of seismic and fluid flow modelling. The detailed 3D models are also used to test new techniques of static reservoir modelling, based either on geostatistical approaches or on deterministic (process-based) simulation techniques. A modelling workflow has been designed to model reservoir geometries and properties from

  13. Rethinking Design Process: Using 3D Digital Models as an Interface in Collaborative Session

    ERIC Educational Resources Information Center

    Ding, Suining

    2008-01-01

    This paper describes a pilot study for an alternative design process by integrating a designer-user collaborative session with digital models. The collaborative session took place in a 3D AutoCAD class for a real world project. The 3D models served as an interface for designer-user collaboration during the design process. Students not only learned…

  14. 3D Modeling from Multi-views Images for Cultural Heritage in Wat-Pho, Thailand

    NASA Astrophysics Data System (ADS)

    Soontranon, N.; Srestasathiern, P.; Lawawirojwong, S.

    2015-08-01

    In Thailand, there are several types of (tangible) cultural heritages. This work focuses on 3D modeling of the heritage objects from multi-views images. The images are acquired by using a DSLR camera which costs around 1,500 (camera and lens). Comparing with a 3D laser scanner, the camera is cheaper and lighter than the 3D scanner. Hence, the camera is available for public users and convenient for accessing narrow areas. The acquired images consist of various sculptures and architectures in Wat-Pho which is a Buddhist temple located behind the Grand Palace (Bangkok, Thailand). Wat-Pho is known as temple of the reclining Buddha and the birthplace of traditional Thai massage. To compute the 3D models, a diagram is separated into following steps; Data acquisition, Image matching, Image calibration and orientation, Dense matching and Point cloud processing. For the initial work, small heritages less than 3 meters height are considered for the experimental results. A set of multi-views images of an interested object is used as input data for 3D modeling. In our experiments, 3D models are obtained from MICMAC (open source) software developed by IGN, France. The output of 3D models will be represented by using standard formats of 3D point clouds and triangulated surfaces such as .ply, .off, .obj, etc. To compute for the efficient 3D models, post-processing techniques are required for the final results e.g. noise reduction, surface simplification and reconstruction. The reconstructed 3D models can be provided for public access such as website, DVD, printed materials. The high accurate 3D models can also be used as reference data of the heritage objects that must be restored due to deterioration of a lifetime, natural disasters, etc.

  15. SU-E-J-01: 3D Fluoroscopic Image Estimation From Patient-Specific 4DCBCT-Based Motion Models

    SciTech Connect

    Dhou, S; Hurwitz, M; Lewis, J; Mishra, P

    2014-06-01

    Purpose: 3D motion modeling derived from 4DCT images, taken days or weeks before treatment, cannot reliably represent patient anatomy on the day of treatment. We develop a method to generate motion models based on 4DCBCT acquired at the time of treatment, and apply the model to estimate 3D time-varying images (referred to as 3D fluoroscopic images). Methods: Motion models are derived through deformable registration between each 4DCBCT phase, and principal component analysis (PCA) on the resulting displacement vector fields. 3D fluoroscopic images are estimated based on cone-beam projections simulating kV treatment imaging. PCA coefficients are optimized iteratively through comparison of these cone-beam projections and projections estimated based on the motion model. Digital phantoms reproducing ten patient motion trajectories, and a physical phantom with regular and irregular motion derived from measured patient trajectories, are used to evaluate the method in terms of tumor localization, and the global voxel intensity difference compared to ground truth. Results: Experiments included: 1) assuming no anatomic or positioning changes between 4DCT and treatment time; and 2) simulating positioning and tumor baseline shifts at the time of treatment compared to 4DCT acquisition. 4DCBCT were reconstructed from the anatomy as seen at treatment time. In case 1) the tumor localization error and the intensity differences in ten patient were smaller using 4DCT-based motion model, possible due to superior image quality. In case 2) the tumor localization error and intensity differences were 2.85 and 0.15 respectively, using 4DCT-based motion models, and 1.17 and 0.10 using 4DCBCT-based models. 4DCBCT performed better due to its ability to reproduce daily anatomical changes. Conclusion: The study showed an advantage of 4DCBCT-based motion models in the context of 3D fluoroscopic images estimation. Positioning and tumor baseline shift uncertainties were mitigated by the 4DCBCT

  16. A novel 3D partitioned active shape model for segmentation of brain MR images.

    PubMed

    Zhao, Zheen; Aylward, Stephen R; Teoh, Earn Khwang

    2005-01-01

    A 3D Partitioned Active Shape Model (PASM) is proposed in this paper to address the problems of the 3D Active Shape Models (ASM). When training sets are small. It is usually the case in 3D segmentation, 3D ASMs tend to be restrictive. This is because the allowable region spanned by relatively few eigenvectors cannot capture the full range of shape variability. The 3D PASM overcomes this limitation by using a partitioned representation of the ASM. Given a Point Distribution Model (PDM), the mean mesh is partitioned into a group of small tiles. In order to constrain deformation of tiles, the statistical priors of tiles are estimated by applying Principal Component Analysis to each tile. To avoid the inconsistency of shapes between tiles, training samples are projected as curves in one hyperspace instead of point clouds in several hyperspaces. The deformed points are then fitted into the allowable region of the model by using a curve alignment scheme. The experiments on 3D human brain MRIs show that when the numbers of the training samples are limited, the 3D PASMs significantly improve the segmentation results as compared to 3D ASMs and 3D Hierarchical ASMs.

  17. A topological framework for interactive queries on 3D models in the Web.

    PubMed

    Figueiredo, Mauro; Rodrigues, José I; Silvestre, Ivo; Veiga-Pires, Cristina

    2014-01-01

    Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications.

  18. A Topological Framework for Interactive Queries on 3D Models in the Web

    PubMed Central

    Figueiredo, Mauro; Rodrigues, José I.; Silvestre, Ivo; Veiga-Pires, Cristina

    2014-01-01

    Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications. PMID:24977236

  19. Initial Comparison Between a 3D MHD Model and the HAFv2 Kinematic 3D Model: The October/November 2003 Events from the Sun to 6 AU

    SciTech Connect

    Intriligator, Devrie S.; Detman, Thomas; Fry, Craig D.; Sun Wei; Deehr, Charles; Intriligator, James

    2005-08-01

    A first-generation 3D kinematic, space weather forecasting solar wind model (HAFv2) has been used to show the importance of solar generated disturbances in Voyager 1 and Voyager 2 observations in the outer heliosphere. We extend this work by using a 3D MHD model (HHMS) that, like HAFv2, incorporates a global, pre-event, inhomogeneous, background solar wind plasma and interplanetary magnetic field. Initial comparisons are made between the two models of the solar wind out to 6 AU and with in-situ observations at the ACE spacecraft before and after the October/November 2003 solar events.

  20. Use of 3D Printed Models in Medical Education: A Randomized Control Trial Comparing 3D Prints versus Cadaveric Materials for Learning External Cardiac Anatomy

    ERIC Educational Resources Information Center

    Lim, Kah Heng Alexander; Loo, Zhou Yaw; Goldie, Stephen J.; Adams, Justin W.; McMenamin, Paul G.

    2016-01-01

    Three-dimensional (3D) printing is an emerging technology capable of readily producing accurate anatomical models, however, evidence for the use of 3D prints in medical education remains limited. A study was performed to assess their effectiveness against cadaveric materials for learning external cardiac anatomy. A double blind randomized…

  1. Indoor 3D Route Modeling Based On Estate Spatial Data

    NASA Astrophysics Data System (ADS)

    Zhang, H.; Wen, Y.; Jiang, J.; Huang, W.

    2014-04-01

    Indoor three-dimensional route model is essential for space intelligence navigation and emergency evacuation. This paper is motivated by the need of constructing indoor route model automatically and as far as possible. By comparing existing building data sources, this paper firstly explained the reason why the estate spatial management data is chosen as the data source. Then, an applicable method of construction three-dimensional route model in a building is introduced by establishing the mapping relationship between geographic entities and their topological expression. This data model is a weighted graph consist of "node" and "path" to express the spatial relationship and topological structure of a building components. The whole process of modelling internal space of a building is addressed by two key steps: (1) each single floor route model is constructed, including path extraction of corridor using Delaunay triangulation algorithm with constrained edge, fusion of room nodes into the path; (2) the single floor route model is connected with stairs and elevators and the multi-floor route model is eventually generated. In order to validate the method in this paper, a shopping mall called "Longjiang New City Plaza" in Nanjing is chosen as a case of study. And the whole building space is constructed according to the modelling method above. By integrating of existing path finding algorithm, the usability of this modelling method is verified, which shows the indoor three-dimensional route modelling method based on estate spatial data in this paper can support indoor route planning and evacuation route design very well.

  2. Inspection, 3D modelling, and rapid prototyping of cultural heritage by means of a 3D optical digitiser

    NASA Astrophysics Data System (ADS)

    Docchio, F.; Sansoni, G.; Trebeschi, M.

    2005-06-01

    This paper presents the activity carried out to perform the three-dimensional acquisition of the "Vittoria Alata", a 2m-high, bronze statue, symbol of our City, located at the Civici Musei di Arte e Storia (S. Giulia) of Brescia. The acquisition of the statue has been performed by using a three-dimensional vision system based on active triangulation and on the projection of non-coherent light. This system, called OPL-3D, represents one of the research products of our Laboratory, which has been active for years in the development of techniques and systems for the contactless acquisition of free-form, complex shapes. The study, originally motivated by the need to explore a new hypothesis on the origin of the "Vittoria Alata", led to its complete digitization and description in terms of both polygonal and NURBS-based models. A suite of copies of the whole statue has been obtained in the framework of the collaboration between the City Museum and the EOS Electro Optical Systems GmbH, located in Munich, Germany. As a first step, one 30 cm-high replica of the whole statue has been produced using a low-resolution triangle model of the statue (3.5 millions of triangles). As a second step, two 1:1 scale copies of the statue have been produced. For them, the Laboratory has provided the high resolution STL file (16 millions of triangles). The paper discusses in detail the hardware and the software facilities used to implement the whole process, and gives a comprehensive description of the results.

  3. 3-D Geometric Modeling for the 21st Century.

    ERIC Educational Resources Information Center

    Ault, Holly K.

    1999-01-01

    Describes new geometric computer models used in contemporary computer-aided design (CAD) software including wire frame, surface, solid, and parametric models. Reviews their use in engineering design and discusses the impact of these new technologies on the engineering design graphics curriculum. (Author/CCM)

  4. Computational 3-D Model of the Human Respiratory System

    EPA Science Inventory

    We are developing a comprehensive, morphologically-realistic computational model of the human respiratory system that can be used to study the inhalation, deposition, and clearance of contaminants, while being adaptable for age, race, gender, and health/disease status. The model ...

  5. 3-D consistency dynamic constitutive model of concrete

    NASA Astrophysics Data System (ADS)

    Xiao, Shiyun; Li, Hongnan; Lin, Gao

    2010-06-01

    Based on the consistency-viscoplastic constitutive model, the static William-Warnke model with threeparameters is modified and a consistency-viscoplastic William-Warnke model with three-parameters is developed that considers the effect of strain rates. Then, the tangent modulus of the consistency viscoplastic model is introduced and an implicit backward Elure iterative algorithm is developed. Comparisons between the numerical simulations and experimental data show that the consistency model properly provides the uniaxial and biaxial dynamic behaviors of concrete. To study the effect of strain rates on the dynamic response of concrete structures, the proposed model is used in the analysis of the dynamic response of a simply-supported beam and the results show that the strain rate has a significant effect on the displacement and stress magnitudes and distributions. Finally, the seismic responses of a 278 m high arch dam are obtained and compared by using the linear elastic model, as well as rate-independent and rate-dependent William-Warnke three-parameter models. The results indicate that the strain rate affects the first principal stresses, and the maximal equivalent viscoplastic strain rate of the arch dam. Numerical calculations and analyses reveal that considering the strain rate is important in the safety assessments of arch dams located in seismically active areas.

  6. ORPHEE 3D: Static and dynamic tridimensional BHA computer models

    SciTech Connect

    Birades, M.

    1986-01-01

    Elf Aquitaine, within an ARTEP research project granted by EEC, has developed two three-dimensional mathematical models to predict the directional behavior of bottom hole assemblies (BHAs). Both models simulate BHAs by finite element methods. The first model describes dynamically their transient behavior step by step during short time intervals which are continuously adjusted to attain the required precision. Displacements and lateral forces, computed for each step, integrate friction against the borehole wall through a sophisticated shock algorithm. The second model computes a static equilibrium of the BHA while assuming simplified friction forces at the contact points between the wellbore and the BHA. The lateral forces and displacements are found to be an average of the highly varying ones computed by the dynamic model and the static computer run is much faster.

  7. A Gaussian Mixture Model-Based Continuous Boundary Detection for 3D Sensor Networks

    PubMed Central

    Chen, Jiehui; Salim, Mariam B.; Matsumoto, Mitsuji

    2010-01-01

    This paper proposes a high precision Gaussian Mixture Model-based novel Boundary Detection 3D (BD3D) scheme with reasonable implementation cost for 3D cases by selecting a minimum number of Boundary sensor Nodes (BNs) in continuous moving objects. It shows apparent advantages in that two classes of boundary and non-boundary sensor nodes can be efficiently classified using the model selection techniques for finite mixture models; furthermore, the set of sensor readings within each sensor node’s spatial neighbors is formulated using a Gaussian Mixture Model; different from DECOMO [1] and COBOM [2], we also formatted a BN Array with an additional own sensor reading to benefit selecting Event BNs (EBNs) and non-EBNs from the observations of BNs. In particular, we propose a Thick Section Model (TSM) to solve the problem of transition between 2D and 3D. It is verified by simulations that the BD3D 2D model outperforms DECOMO and COBOM in terms of average residual energy and the number of BNs selected, while the BD3D 3D model demonstrates sound performance even for sensor networks with low densities especially when the value of the sensor transmission range (r) is larger than the value of Section Thickness (d) in TSM. We have also rigorously proved its correctness for continuous geometric domains and full robustness for sensor networks over 3D terrains. PMID:22163619

  8. Synthesis of image sequences for Korean sign language using 3D shape model

    NASA Astrophysics Data System (ADS)

    Hong, Mun-Ho; Choi, Chang-Seok; Kim, Chang-Seok; Jeon, Joon-Hyeon

    1995-05-01

    This paper proposes a method for offering information and realizing communication to the deaf-mute. The deaf-mute communicates with another person by means of sign language, but most people are unfamiliar with it. This method enables to convert text data into the corresponding image sequences for Korean sign language (KSL). Using a general 3D shape model of the upper body leads to generating the 3D motions of KSL. It is necessary to construct the general 3D shape model considering the anatomical structure of the human body. To obtain a personal 3D shape model, this general model is to adjust to the personal base images. Image synthesis for KSL consists of deforming a personal 3D shape model and texture-mapping the personal images onto the deformed model. The 3D motions for KSL have the facial expressions and the 3D movements of the head, trunk, arms and hands and are parameterized for easily deforming the model. These motion parameters of the upper body are extracted from a skilled signer's motion for each KSL and are stored to the database. Editing the parameters according to the inputs of text data yields to generate the image sequences of 3D motions.

  9. Services Oriented Smart City Platform Based On 3d City Model Visualization

    NASA Astrophysics Data System (ADS)

    Prandi, F.; Soave, M.; Devigili, F.; Andreolli, M.; De Amicis, R.

    2014-04-01

    The rapid technological evolution, which is characterizing all the disciplines involved within the wide concept of smart cities, is becoming a key factor to trigger true user-driven innovation. However to fully develop the Smart City concept to a wide geographical target, it is required an infrastructure that allows the integration of heterogeneous geographical information and sensor networks into a common technological ground. In this context 3D city models will play an increasingly important role in our daily lives and become an essential part of the modern city information infrastructure (Spatial Data Infrastructure). The work presented in this paper describes an innovative Services Oriented Architecture software platform aimed at providing smartcities services on top of 3D urban models. 3D city models are the basis of many applications and can became the platform for integrating city information within the Smart-Cites context. In particular the paper will investigate how the efficient visualisation of 3D city models using different levels of detail (LODs) is one of the pivotal technological challenge to support Smart-Cities applications. The goal is to provide to the final user realistic and abstract 3D representations of the urban environment and the possibility to interact with a massive amounts of semantic information contained into the geospatial 3D city model. The proposed solution, using OCG standards and a custom service to provide 3D city models, lets the users to consume the services and interact with the 3D model via Web in a more effective way.

  10. Management and services for large-scale virtual 3D urban model data based on network

    NASA Astrophysics Data System (ADS)

    He, Zhengwei; Chen, Jing; Wu, Huayi

    2008-10-01

    The buildings in modern city are complex and diverse, and the quantity is huge. These bring very big challenge for constructing 3D GIS under network circumstance and eventually realizing the Digital Earth. After analyzed the characteristic of network service about massive 3D urban building model data, this paper focuses on the organization and management of spatial data and the network services strategy, proposes a progressive network transmission schema based on the spatial resolution and the component elements of 3D building model data. Next, this paper put forward multistage-link three-dimensional spatial data organization model and encoding method of spatial index based on fully level quadtree structure. Then, a virtual earth platform, called GeoGlobe, was developed using above theory. Experimental results show that above 3D spatial data management model and service theory can availably provide network services for large-scale 3D urban model data. The application results and user experience good .

  11. Assessing a 3D smoothed seismicity model of induced earthquakes

    NASA Astrophysics Data System (ADS)

    Zechar, Jeremy; Király, Eszter; Gischig, Valentin; Wiemer, Stefan

    2016-04-01

    As more energy exploration and extraction efforts cause earthquakes, it becomes increasingly important to control induced seismicity. Risk management schemes must be improved and should ultimately be based on near-real-time forecasting systems. With this goal in mind, we propose a test bench to evaluate models of induced seismicity based on metrics developed by the CSEP community. To illustrate the test bench, we consider a model based on the so-called seismogenic index and a rate decay; to produce three-dimensional forecasts, we smooth past earthquakes in space and time. We explore four variants of this model using the Basel 2006 and Soultz-sous-Forêts 2004 datasets to make short-term forecasts, test their consistency, and rank the model variants. Our results suggest that such a smoothed seismicity model is useful for forecasting induced seismicity within three days, and giving more weight to recent events improves forecast performance. Moreover, the location of the largest induced earthquake is forecast well by this model. Despite the good spatial performance, the model does not estimate the seismicity rate well: it frequently overestimates during stimulation and during the early post-stimulation period, and it systematically underestimates around shut-in. In this presentation, we also describe a robust estimate of information gain, a modification that can also benefit forecast experiments involving tectonic earthquakes.

  12. 3D Modeling of CMEs observed with STEREO

    NASA Astrophysics Data System (ADS)

    Bosman, E.; Bothmer, V.

    2012-04-01

    From January 2007 until end of 2010, 565 typical large-scale coronal mass ejections (CMEs) have been identified in the SECCHI/COR2 synoptic movies of the STEREO Mission. A subset comprising 114 CME events, selected based on the CME's brightness appearance in the SECCHI/COR2 images, has been modeled through the Graduated Cylindrical Shell (GCS) Model developed by Thernisien et al. (2006). This study presents an overview of the GCS forward-modeling results and an interpretation of the CME characteristics in relationship to their solar source region properties and solar cycle appearances.

  13. 3D active workspace of human hand anatomical model

    PubMed Central

    Dragulescu, Doina; Perdereau, Véronique; Drouin, Michel; Ungureanu, Loredana; Menyhardt, Karoly

    2007-01-01

    Background If the model of the human hand is created with accuracy by respecting the type of motion provided by each articulation and the dimensions of articulated bones, it can function as the real organ providing the same motions. Unfortunately, the human hand is hard to model due to its kinematical chains submitted to motion constraints. On the other hand, if an application does not impose a fine manipulation it is not necessary to create a model as complex as the human hand is. But always the hand model has to perform a certain space of motions in imposed workspace architecture no matter what the practical application does. Methods Based on Denavit-Hartenberg convention, we conceived the kinematical model of the human hand, having in mind the structure and the behavior of the natural model. We obtained the kinematical equations describing the motion of every fingertip with respect to the general coordinate system, placed on the wrist. For every joint variable, a range of motion was established. Dividing these joint variables to an appropriate number of intervals and connecting them, the complex surface bordering the active hand model workspace was obtained. Results Using MATLAB 7.0, the complex surface described by fingertips, when hand articulations are all simultaneously moving, was obtained. It can be seen that any point on surface has its own coordinates smaller than the maximum length of the middle finger in static position. Therefore, a sphere having the centre in the origin of the general coordinate system and the radius which equals this length covers the represented complex surface. Conclusion We propose a human hand model that represents a new solution compared to the existing ones. This model is capable to make special movements like power grip and dexterous manipulations. During them, the fingertips do not exceed the active workspace encapsulated by determined surfaces. The proposed kinematical model can help to choose which model joints could be

  14. 3-D photoacoustic and pulse echo imaging of prostate tumor progression in the mouse window chamber

    PubMed Central

    Bauer, Daniel R.; Olafsson, Ragnar; Montilla, Leonardo G.; Witte, Russell S.

    2011-01-01

    Understanding the tumor microenvironment is critical to characterizing how cancers operate and predicting their response to treatment. We describe a novel, high-resolution coregistered photoacoustic (PA) and pulse echo (PE) ultrasound system used to image the tumor microenvironment. Compared to traditional optical systems, the platform provides complementary contrast and important depth information. Three mice are implanted with a dorsal skin flap window chamber and injected with PC-3 prostate tumor cells transfected with green fluorescent protein. The ensuing tumor invasion is mapped during three weeks or more using simultaneous PA and PE imaging at 25 MHz, combined with optical and fluorescent techniques. Pulse echo imaging provides details of tumor structure and the surrounding environment with 100-μm3 resolution. Tumor size increases dramatically with an average volumetric growth rate of 5.35 mm3∕day, correlating well with 2-D fluorescent imaging (R = 0.97, p < 0.01). Photoacoustic imaging is able to track the underlying vascular network and identify hemorrhaging, while PA spectroscopy helps classify blood vessels according to their optical absorption spectrum, suggesting variation in blood oxygen saturation. Photoacoustic and PE imaging are safe, translational modalities that provide enhanced depth resolution and complementary contrast to track the tumor microenvironment, evaluate new cancer therapies, and develop molecular contrast agents in vivo. PMID:21361696

  15. 3-D photoacoustic and pulse echo imaging of prostate tumor progression in the mouse window chamber

    NASA Astrophysics Data System (ADS)

    Bauer, Daniel R.; Olafsson, Ragnar; Montilla, Leonardo G.; Witte, Russell S.

    2011-02-01

    Understanding the tumor microenvironment is critical to characterizing how cancers operate and predicting their response to treatment. We describe a novel, high-resolution coregistered photoacoustic (PA) and pulse echo (PE) ultrasound system used to image the tumor microenvironment. Compared to traditional optical systems, the platform provides complementary contrast and important depth information. Three mice are implanted with a dorsal skin flap window chamber and injected with PC-3 prostate tumor cells transfected with green fluorescent protein. The ensuing tumor invasion is mapped during three weeks or more using simultaneous PA and PE imaging at 25 MHz, combined with optical and fluorescent techniques. Pulse echo imaging provides details of tumor structure and the surrounding environment with 100-μm3 resolution. Tumor size increases dramatically with an average volumetric growth rate of 5.35 mm3/day, correlating well with 2-D fluorescent imaging (R = 0.97, p < 0.01). Photoacoustic imaging is able to track the underlying vascular network and identify hemorrhaging, while PA spectroscopy helps classify blood vessels according to their optical absorption spectrum, suggesting variation in blood oxygen saturation. Photoacoustic and PE imaging are safe, translational modalities that provide enhanced depth resolution and complementary contrast to track the tumor microenvironment, evaluate new cancer therapies, and develop molecular contrast agents in vivo.

  16. Automated mask creation from a 3D model using Faethm.

    SciTech Connect

    Schiek, Richard Louis; Schmidt, Rodney Cannon

    2007-11-01

    We have developed and implemented a method which given a three-dimensional object can infer from topology the two-dimensional masks needed to produce that object with surface micro-machining. The masks produced by this design tool can be generic, process independent masks, or if given process constraints, specific for a target process. This design tool calculates the two-dimensional mask set required to produce a given three-dimensional model by investigating the vertical topology of the model.

  17. Ozone Measurements and a 3D Chemical Transport Model

    NASA Technical Reports Server (NTRS)

    Stolarski, Richard S.; Douglass, Anne R.; Frith, Stacey; Steenrod, Steven; Polansky, Brian

    2004-01-01

    We have used our three-dimensional chemical transport model (CTM) to calculate the expected reponse of stratospheric composition over the past 30 years to forcing by chlorine and bromine compounds, solar ultraviolet, and volcanic aerosols. The CTM uses off-line winds and temperatures fiom a 50-year run of the finite volume general circulation model (FVGCM). We compare the total column ozone and the ozone profile fiom the CTM output to a variety of data sources. These include a merged total ozone data set from TOMS and SBUV using the new version 8 algorithm. Total ozone fiom the CTM are compared to ground-station measurements of total ozone at specific locations. Ozone profiles are compared to satellite meausrements fiom SBUV, SAGE, and HALOE. Profiles are also compared to ozonesondes over several locations. The results of the comparisons are quantified by using a time-series statistical analysis to determine trends, solar cycle, and volcanic reponse in both the model and in the data. Initial results indicate that the model responds to forcings in a way that is similar to the observed atmospheric response. The model does seem to be more sensitive to the chlorine and bromine perturbation ihan is the data. Further details and comparisons wiii be discussed.

  18. Inhomogeneous Media 3D EM Modeling with Integral Equation Method

    NASA Astrophysics Data System (ADS)

    di, Q.; Wang, R.; An, Z.; Fu, C.; Xu, C.

    2010-12-01

    In general, only the half space of earth is considered in electromagnetic exploration. However, for the long bipole source, because the length is close to the height of ionosphere and also most offsets between source and receivers are equal or larger than the height of ionosphere, the effect of ionosphere on the electromagnetic (EM) field should be considered when observation is carried at a very far (about several thousands kilometers) location away from the source. At this point the problem becomes one which should contain ionosphere, atmosphere and earth that is “earth-ionosphere” case. There are a few of literatures to report the electromagnetic field results which is including ionosphere, atmosphere and earth media at the same time. We firstly calculate the electromagnetic fields with the traditional controlled source (CSEM) configuration using integral equation (IE) method for a three layers earth-ionosphere model. The modeling results agree well with the half space analytical results because the effect of ionosphere for this small scale bipole source can be ignorable. The comparison of small scale three layers earth-ionosphere modeling and half space analytical resolution shows that the IE method can be used to modeling the EM fields for long bipole large offset configuration. In order to discuss EM fields’ characteristics for complicate earth-ionosphere media excited by long bipole source in the far-field and wave-guide zones, we first modeled the decay characters of electromagnetic fields for three layers earth-ionosphere model. Because of the effect of ionosphere, the earth-ionosphere electromagnetic fields’ decay curves with given frequency show that there should be an extra wave guide zone for long bipole artificial source, and there are many different characters between this extra zone and far field zone. They are: 1) the amplitudes of EM fields decay much slower; 2) the polarization patterns change; 3) the positions better to measure Zxy and

  19. A Cartesian scheme for compressible multimaterial models in 3D

    NASA Astrophysics Data System (ADS)

    de Brauer, Alexia; Iollo, Angelo; Milcent, Thomas

    2016-05-01

    We model the three-dimensional interaction of compressible materials separated by sharp interfaces. We simulate fluid and hyperelastic solid flows in a fully Eulerian framework. The scheme is the same for all materials and can handle large deformations and frictionless contacts. Necessary conditions for hyperbolicity of the hyperelastic neohookean model in three dimensions are proved thanks to an explicit computation of the characteristic speeds. We present stiff multimaterial interactions including air-helium and water-air shock interactions, projectile-shield impacts in air and rebounds.

  20. Modeling and simulation of charge collection properties for 3D-trench electrode detector

    NASA Astrophysics Data System (ADS)

    Ding, Hao; Chen, Jianwei; Li, Zheng; Yan, Shaoan

    2015-10-01

    3D-trench electrode detectors were simulated in this paper. Charge collection of 3D-trench electrode detector was simulated using the full 3D device simulation. The induced current and collected charge caused by drifting carriers, generated by a minimum ionizing particle (MIP) incident through the detector, have been modeled and calculated. The results indicate that the total collected charge in irradiated detector change with particle incident position and radiation fluence. In addition, we have estimated the average total collected charge generated by a MIP incident in 3D-trench electrode detector.

  1. 3D modelling of stellar auroral radio emission

    NASA Astrophysics Data System (ADS)

    Leto, P.; Trigilio, C.; Buemi, C. S.; Umana, G.; Ingallinera, A.; Cerrigone, L.

    2016-06-01

    The electron cyclotron maser is the coherent emission process that gives rise to the radio lighthouse effect observed in the hot magnetic chemically peculiar star CU Virginis. It has also been proposed to explain the highly circularly polarized radio pulses observed in some ultracool dwarfs with spectral type earlier than M7. Coherent events of this kind resemble auroral radio emission from the magnetized planets of the Solar system. In this article, we present a three-dimensional model able to simulate the timing and profile of the pulses emitted by those stars characterized by a dipolar magnetic field by following the hypothesis of the laminar source model, used to explain the beaming of terrestrial auroral kilometric radiation. This model proves to be a powerful tool with which to understand the auroral radio emission phenomenon, allowing us to derive some general conclusions about the effects of the model's free parameters on the features of coherent pulses and to learn more about the detectability of such pulsed radio emission.

  2. New 3D parallel SGILD modeling and inversion

    SciTech Connect

    Xie, G.; Li, J.; Majer, E.

    1998-09-01

    In this paper, a new parallel modeling and inversion algorithm using a Stochastic Global Integral and Local Differential equation (SGILD) is presented. The authors derived new acoustic integral equations and differential equation for statistical moments of the parameters and field. The new statistical moments integral equation on the boundary and local differential equations in domain will be used together to obtain mean wave field and its moments in the modeling. The new moments global Jacobian volume integral equation and the local Jacobian differential equations in domain will be used together to update the mean parameters and their moments in the inversion. A new parallel multiple hierarchy substructure direct algorithm or direct-iteration hybrid algorithm will be used to solve the sparse matrices and one smaller full matrix from domain to the boundary, in parallel. The SGILD modeling and imaging algorithm has many advantages over the conventional imaging approaches. The SGILD algorithm can be used for the stochastic acoustic, electromagnetic, and flow modeling and inversion, and are important for the prediction of oil, gas, coal, and geothermal energy reservoirs in geophysical exploration.

  3. 3-D orbital evolution model of outer asteroid belt

    NASA Technical Reports Server (NTRS)

    Solovaya, Nina A.; Gerasimov, Igor A.; Pittich, Eduard M.

    1992-01-01

    The evolution of minor planets in the outer part of the asteroid belt is considered. In the framework of the semi-averaged elliptic restricted three-dimensional three-body model, the boundary of regions of the Hill's stability is found. As was shown in our work, the Jacobian integral exists.

  4. 3D pharmacophore models for thromboxane A(2) receptor antagonists.

    PubMed

    Wei, Jing; Liu, Yixi; Wang, Songqing

    2009-10-01

    Thromboxane A(2) (TXA(2)) is an endogenous arachidonic acid derivative closely correlated to thrombosis and other cardiovascular diseases. The action of TXA(2) can be effectively inhibited with TXA(2) receptor antagonists (TXRAs). Previous studies have attempted to describe the interactions between the TXA(2) receptor and its ligands, but their conclusions are still controversial. In this study, ligand-based computational drug design is used as a new and effective way to investigate the structure-activity relationship of TXRAs. Three-dimensional pharmacophore models of TXRAs were built with HypoGenRefine and HipHop modules in CATALYST software. The optimal HypoGenRefine model was developed on the basis of 25 TXRAs. It consists of two hydrophobic groups, one aromatic ring, one hydrogen-bond acceptor and four excluded volumes. The optimal HipHop model contains two hydrophobic groups and two hydrogen-bond acceptors. These models describe the key structure-activity relationship of TXRAs, can predict their activities, and can thus be used to design novel antagonists. PMID:19263096

  5. 3D pharmacophore models for thromboxane A(2) receptor antagonists.

    PubMed

    Wei, Jing; Liu, Yixi; Wang, Songqing

    2009-10-01

    Thromboxane A(2) (TXA(2)) is an endogenous arachidonic acid derivative closely correlated to thrombosis and other cardiovascular diseases. The action of TXA(2) can be effectively inhibited with TXA(2) receptor antagonists (TXRAs). Previous studies have attempted to describe the interactions between the TXA(2) receptor and its ligands, but their conclusions are still controversial. In this study, ligand-based computational drug design is used as a new and effective way to investigate the structure-activity relationship of TXRAs. Three-dimensional pharmacophore models of TXRAs were built with HypoGenRefine and HipHop modules in CATALYST software. The optimal HypoGenRefine model was developed on the basis of 25 TXRAs. It consists of two hydrophobic groups, one aromatic ring, one hydrogen-bond acceptor and four excluded volumes. The optimal HipHop model contains two hydrophobic groups and two hydrogen-bond acceptors. These models describe the key structure-activity relationship of TXRAs, can predict their activities, and can thus be used to design novel antagonists.

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

    PubMed Central

    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. PMID:25482337

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

    PubMed

    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.

  8. A 3D Convective Model for the Jovian Wind Bands

    NASA Astrophysics Data System (ADS)

    Mayr, H. G.; Chan, K. L.

    2004-11-01

    In an earlier paper (Mayr et al. 1984, Earth, Moon, & Planets, 30, 245), we proposed that Jupiter's alternating wind bands are a manifestation of the global interaction between rotation and convection in a shallow layer. The model, however, was obtained from linearization of the 2D equations of motions. At HKUST/Hong Kong, we are now trying to study this problem by rigorous numerical simulation. Using a three-dimensional spectral numerical code, we compute models for the outermost layer of Jupiter's convective envelope. Two cases have been studied. In one the atmospheric pressure varies from 1 to 23 bar, and in the other from 1 to 115 bar. The physical parameters (internal energy flux, rotation rate) are chosen to be close to those expected, but solar heating, chemistry, as well as dynamical influences from deeper layers are ignored. The models generate wind field patterns that contain alternating jet streams with resemblance to the Jovian bands. Instantaneous values of the mean zonal flow at the equator reach 80 m/sec. Yet the mean meridional flows are less than 1% of such value. The meridional temperature profile at the cloud top level also shows a double hump structure of a few degrees (as observed) in the subtropics. Though there is not complete quantitative agreement (caused perhaps by neglected effects like solar radiation), these models demonstrate, in principle, the feasibility of generating a Jovian type wind pattern through the interaction of fast rotation and convection in a thin shell. KLC thanks RGC/Hong Kong for support.

  9. Multiple-Relaxation-Time Lattice Boltzmann Models in 3D

    NASA Technical Reports Server (NTRS)

    dHumieres, Dominique; Ginzburg, Irina; Krafczyk, Manfred; Lallemand, Pierre; Luo, Li-Shi; Bushnell, Dennis M. (Technical Monitor)

    2002-01-01

    This article provides a concise exposition of the multiple-relaxation-time lattice Boltzmann equation, with examples of fifteen-velocity and nineteen-velocity models in three dimensions. Simulation of a diagonally lid-driven cavity flow in three dimensions at Re=500 and 2000 is performed. The results clearly demonstrate the superior numerical stability of the multiple-relaxation-time lattice Boltzmann equation over the popular lattice Bhatnagar-Gross-Krook equation.

  10. 3-D model of ICME in the interplanetary medium

    NASA Astrophysics Data System (ADS)

    Borgazzi, A.; Lara, A.; Niembro, T.

    2011-12-01

    We developed a method that describes with simply geometry the coordinates of intersection between the leading edge of an ICME and the position of an arbitrary satellite. When a fast CME is ejected from the Sun to the interplanetary space in most of the cases drives a shock. As the CME moves in the corona and later in the interplanetary space more material is stacking in the front and edges of the ejecta. In a first approximation, it is possible to assume the shape of these structures, the CME and the stacked material as a cone of revolution, (the ice-cream model [Schwenn et al., (2005)]). The interface may change due to the interaction of the structure and the non-shocked material in front of the ICME but the original shape of a cone of revolution is preserved. We assume, in a three dimensional geometry, an ice-cream cone shape for the ICME and apply an analytical model for its transport in the interplanetary medium. The goal of the present method is to give the time and the intersection coordinates between the leading edge of the ICME and any satellite that may be in the path of the ICME. With this information we can modelate the travel of the ICME in the interplanetary space using STEREO data.

  11. The Martian Water Cycle Based on 3-D Modeling

    NASA Technical Reports Server (NTRS)

    Houben, H.; Haberle, R. M.; Joshi, M. M.

    1999-01-01

    Understanding the distribution of Martian water is a major goal of the Mars Surveyor program. However, until the bulk of the data from the nominal missions of TES, PMIRR, GRS, MVACS, and the DS2 probes are available, we are bound to be in a state where much of our knowledge of the seasonal behavior of water is based on theoretical modeling. We therefore summarize the results of this modeling at the present time. The most complete calculations come from a somewhat simplified treatment of the Martian climate system which is capable of simulating many decades of weather. More elaborate meteorological models are now being applied to study of the problem. The results show a high degree of consistency with observations of aspects of the Martian water cycle made by Viking MAWD, a large number of ground-based measurements of atmospheric column water vapor, studies of Martian frosts, and the widespread occurrence of water ice clouds. Additional information is contained in the original extended abstract.

  12. 3D MHD modeling of twisted coronal loops

    NASA Astrophysics Data System (ADS)

    Reale, F.; Orlando, S.; Guarrasi, M.; Mignone, A.; Peres, G.; Hood, A. W.; Priest, E. R.

    2016-10-01

    We perform MHD modeling of a single bright coronal loop to include the interaction with a non-uniform magnetic field. The field is stressed by random footpoint rotation in the central region and its energy is dissipated into heating by growing currents through anomalous magnetic diffusivity that switches on in the corona above a current density threshold. We model an entire single magnetic flux tube in the solar atmosphere extending from the high-β chromosphere to the low-β corona through the steep transition region. The magnetic field expands from the chromosphere to the corona. The maximum resolution is ∼30 km. We obtain an overall evolution typical of loop models and realistic loop emission in the EUV and X-ray bands. The plasma confined in the flux tube is heated to active region temperatures (∼3 MK) after ∼2/3 hr. Upflows from the chromosphere up to ∼100 km s‑1 fill the core of the flux tube to densities above 109 cm‑3. More heating is released in the low corona than the high corona and is finely structured both in space and time.

  13. Elastic properties of model 3-D porous ceramics and foams

    NASA Astrophysics Data System (ADS)

    Roberts, Anthony; Garboczi, Edward

    2000-03-01

    The novel properties of many new porous materials are related to their interesting internal microstructure. Apart from simple cases, there exist no theoretical means of predicting the bulk properties of these materials. This limits our ability to guide microstructure optimization for a particular purpose. We use a large scale finite element method to demonstrate the complex relationship between microstructure and the effective properties of realistic three-dimensional model porous ceramics and foams. We find that pore-shape and interconnectivity strongly influence the properties of sintered ceramics. For porous foams we have studied the role of coordination number, random disorder, and strut shape on the Young's modulus and Poisson's ratio. We find that that Voronoi tesselations, commonly used to model solid foams, show unphysical behavior, in particular they are incompressible (rubber-like) at low densities. Deletion of just 10% of the bonds in the model reduces the bulk modulus by 75%, more in line with experimental evidence. The FEM results are generally in good agreement with experimental data for ceramics and foams, and can be used as both a predictive and interpretative tool by experimentalists.

  14. Introducing a New 3D Dynamical Model for Barred Galaxies

    NASA Astrophysics Data System (ADS)

    Jung, Christof; Zotos, Euaggelos E.

    2015-11-01

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

  15. Possibility of reconstruction of dental plaster cast from 3D digital study models

    PubMed Central

    2013-01-01

    Objectives To compare traditional plaster casts, digital models and 3D printed copies of dental plaster casts based on various criteria. To determine whether 3D printed copies obtained using open source system RepRap can replace traditional plaster casts in dental practice. To compare and contrast the qualities of two possible 3D printing options – open source system RepRap and commercially available 3D printing. Design and settings A method comparison study on 10 dental plaster casts from the Orthodontic department, Department of Stomatology, 2nd medical Faulty, Charles University Prague, Czech Republic. Material and methods Each of 10 plaster casts were scanned by inEos Blue scanner and the printed on 3D printer RepRap [10 models] and ProJet HD3000 3D printer [1 model]. Linear measurements between selected points on the dental arches of upper and lower jaws on plaster casts and its 3D copy were recorded and statistically analyzed. Results 3D printed copies have many advantages over traditional plaster casts. The precision and accuracy of the RepRap 3D printed copies of plaster casts were confirmed based on the statistical analysis. Although the commercially available 3D printing enables to print more details than the RepRap system, it is expensive and for the purpose of clinical use can be replaced by the cheaper prints obtained from RepRap printed copies. Conclusions Scanning of the traditional plaster casts to obtain a digital model offers a pragmatic approach. The scans can subsequently be used as a template to print the plaster casts as required. Using 3D printers can replace traditional plaster casts primarily due to their accuracy and price. PMID:23721330

  16. Impact of the 3-D model strategy on science learning of the solar system

    NASA Astrophysics Data System (ADS)

    Alharbi, Mohammed

    The purpose of this mixed method study, quantitative and descriptive, was to determine whether the first-middle grade (seventh grade) students at Saudi schools are able to learn and use the Autodesk Maya software to interact and create their own 3-D models and animations and whether their use of the software influences their study habits and their understanding of the school subject matter. The study revealed that there is value to the science students regarding the use of 3-D software to create 3-D models to complete science assignments. Also, this study aimed to address the middle-school students' ability to learn 3-D software in art class, and then ultimately use it in their science class. The success of this study may open the way to consider the impact of 3-D modeling on other school subjects, such as mathematics, art, and geography. When the students start using graphic design, including 3-D software, at a young age, they tend to develop personal creativity and skills. The success of this study, if applied in schools, will provide the community with skillful young designers and increase awareness of graphic design and the new 3-D technology. Experimental method was used to answer the quantitative research question, are there significant differences applying the learning method using 3-D models (no 3-D, premade 3-D, and create 3-D) in a science class being taught about the solar system and its impact on the students' science achievement scores? Descriptive method was used to answer the qualitative research questions that are about the difficulty of learning and using Autodesk Maya software, time that students take to use the basic levels of Polygon and Animation parts of the Autodesk Maya software, and level of students' work quality.

  17. Blind watermark algorithm on 3D motion model based on wavelet transform

    NASA Astrophysics Data System (ADS)

    Qi, Hu; Zhai, Lang

    2013-12-01

    With the continuous development of 3D vision technology, digital watermark technology, as the best choice for copyright protection, has fused with it gradually. This paper proposed a blind watermark plan of 3D motion model based on wavelet transform, and made it loaded into the Vega real-time visual simulation system. Firstly, put 3D model into affine transform, and take the distance from the center of gravity to the vertex of 3D object in order to generate a one-dimensional discrete signal; then make this signal into wavelet transform to change its frequency coefficients and embed watermark, finally generate 3D motion model with watermarking. In fixed affine space, achieve the robustness in translation, revolving and proportion transforms. The results show that this approach has better performances not only in robustness, but also in watermark- invisibility.

  18. A 3D interactive model and atlas of the jaw musculature of Alligator mississippiensis.

    PubMed

    Holliday, Casey M; Tsai, Henry P; Skiljan, Rebecca J; George, Ian D; Pathan, Sami

    2013-01-01

    Modern imaging and dissemination methods enable morphologists to share complex, three-dimensional (3D) data in ways not previously possible. Here we present a 3D interactive model of the jaw musculature of the American Alligator (Alligator mississippiensis). Alligator and crocodylian jaw musculature is notoriously challenging to inspect and interpret because of the derived nature of the feeding apparatus. Using Iodine-contrast enhanced microCT imaging, a segmented model of jaw muscles, trigeminal nerve, brain and skull are presented as a cross-sectional atlas and 3D, interactive pdf of the rendered model. Modern 3D dissemination methods like this 3D Alligator hold great potential for morphologists to share anatomical information to scientists, educators, and the public in an easily downloadable format. PMID:23762228

  19. Modeling the diffusion of phosphorus in silicon in 3-D

    SciTech Connect

    Baker, K.R.

    1994-12-31

    The use of matrix preconditioning in semiconductor process simulation is examined. The simplified nonlinear single-species model for the diffusion of phosphorus into silicon is considered. The experimental three-dimensional simulator, PEPPER3, which uses finite differences and the numerical method of lines to implement the reaction-diffusion equation is modified to allow NSPCG to be called to solve the linear system in the inner Newton loop. Use of NSPCG allowed various accelerators such as Generalized Minimal Residual (GMRES) and Conjugate Gradient (CG) to be used in conjunction with preconditioners such as Richardson, Jacobi, and Incomplete Cholesky.

  20. 3D Monte Carlo radiation transfer modelling of photodynamic therapy

    NASA Astrophysics Data System (ADS)

    Campbell, C. Louise; Christison, Craig; Brown, C. Tom A.; Wood, Kenneth; Valentine, Ronan M.; Moseley, Harry

    2015-06-01

    The effects of ageing and skin type on Photodynamic Therapy (PDT) for different treatment methods have been theoretically investigated. A multilayered Monte Carlo Radiation Transfer model is presented where both daylight activated PDT and conventional PDT are compared. It was found that light penetrates deeper through older skin with a lighter complexion, which translates into a deeper effective treatment depth. The effect of ageing was found to be larger for darker skin types. The investigation further strengthens the usage of daylight as a potential light source for PDT where effective treatment depths of about 2 mm can be achieved.

  1. Modeling of 3-D Woven Ceramic Matrix Composites

    NASA Technical Reports Server (NTRS)

    Murthy, Pappu L. N.; Sullivan, Roy M.; Mital, Subodh K.

    2003-01-01

    Three different approaches are being pursued at the NASA Glenn Research Center to predict the nanostructural behavior of three-dimensional woven ceramic matrix composites. These are: a micromechanics-based approach using W-CEMCAN (Woven Ceramic Matrix Composite Analyzer), a laminate analogy method and a structural frame approach (based on the finite element method). All three techniques are applied to predict the thermomechanical properties of a three-dimensional woven angle interlock C/SiC composite. The properties are predicted for room temperature and 1100 C and the predicted properties are compared to measurements. General observations regarding the three approaches for three-dimensional composite modeling are discussed.

  2. RETRAN-3D MOD003 Peach Bottom Turbine Trip 2 Multidimensional Kinetics Analysis Models and Results

    SciTech Connect

    Mori, Michitsugu; Ogura, Katsunori; Gose, Garry C.; Wu, J.-Y

    2003-04-15

    An analysis of the Peach Bottom Unit 2 Turbine Trip Test 2 (PB2/TT2) has been performed using RETRAN-3D MOD003. The purpose of the analysis was to investigate the PB2/TT2 overpressurization transient using the RETRAN-3D multidimensional kinetics model.

  3. Evolution of 3-D geologic framework modeling and its application to groundwater flow studies

    USGS Publications Warehouse

    Blome, Charles D.; Smith, David V.

    2012-01-01

    In this Fact Sheet, the authors discuss the evolution of project 3-D subsurface framework modeling, research in hydrostratigraphy and airborne geophysics, and methodologies used to link geologic and groundwater flow models.

  4. Evaluation of field development plans using 3-D reservoir modelling

    SciTech Connect

    Seifert, D.; Lewis, J.J.M.; Newbery, J.D.H.

    1997-08-01

    Three-dimensional reservoir modelling has become an accepted tool in reservoir description and is used for various purposes, such as reservoir performance prediction or integration and visualisation of data. In this case study, a small Northern North Sea turbiditic reservoir was to be developed with a line drive strategy utilising a series of horizontal producer and injector pairs, oriented north-south. This development plan was to be evaluated and the expected outcome of the wells was to be assessed and risked. Detailed analyses of core, well log and analogue data has led to the development of two geological {open_quotes}end member{close_quotes} scenarios. Both scenarios have been stochastically modelled using the Sequential Indicator Simulation method. The resulting equiprobable realisations have been subjected to detailed statistical well placement optimisation techniques. Based upon bivariate statistical evaluation of more than 1000 numerical well trajectories for each of the two scenarios, it was found that the wells inclinations and lengths had a great impact on the wells success, whereas the azimuth was found to have only a minor impact. After integration of the above results, the actual well paths were redesigned to meet external drilling constraints, resulting in substantial reductions in drilling time and costs.

  5. Lightning Modelling: From 3D to Circuit Approach

    NASA Astrophysics Data System (ADS)

    Moussa, H.; Abdi, M.; Issac, F.; Prost, D.

    2012-05-01

    The topic of this study is electromagnetic environment and electromagnetic interferences (EMI) effects, specifically the modelling of lightning indirect effects [1] on aircraft electrical systems present on deported and highly exposed equipments, such as nose landing gear (NLG) and nacelle, through a circuit approach. The main goal of the presented work, funded by a French national project: PREFACE, is to propose a simple equivalent electrical circuit to represent a geometrical structure, taking into account mutual, self inductances, and resistances, which play a fundamental role in the lightning current distribution. Then this model is intended to be coupled to a functional one, describing a power train chain composed of: a converter, a shielded power harness and a motor or a set of resistors used as a load for the converter. The novelty here, is to provide a pre-sizing qualitative approach allowing playing on integration in pre-design phases. This tool intends to offer a user-friendly way for replying rapidly to calls for tender, taking into account the lightning constraints. Two cases are analysed: first, a NLG that is composed of tubular pieces that can be easily approximated by equivalent cylindrical straight conductors. Therefore, passive R, L, M elements of the structure can be extracted through analytical engineer formulas such as those implemented in the partial element equivalent circuit (PEEC) [2] technique. Second, the same approach is intended to be applied on an electrical de-icing nacelle sub-system.

  6. 3D modeling and optimization of the ITER ICRH antenna

    NASA Astrophysics Data System (ADS)

    Louche, F.; Dumortier, P.; Durodié, F.; Messiaen, A.; Maggiora, R.; Milanesio, D.

    2011-12-01

    The prediction of the coupling properties of the ITER ICRH antenna necessitates the accurate evaluation of the resistance and reactance matrices. The latter are mostly dependent on the geometry of the array and therefore a model as accurate as possible is needed to precisely compute these matrices. Furthermore simulations have so far neglected the poloidal and toroidal profile of the plasma, and it is expected that the loading by individual straps will vary significantly due to varying strap-plasma distance. To take this curvature into account, some modifications of the alignment of the straps with respect to the toroidal direction are proposed. It is shown with CST Microwave Studio® [1] that considering two segments in the toroidal direction, i.e. a "V-shaped" toroidal antenna, is sufficient. A new CATIA model including this segmentation has been drawn and imported into both MWS and TOPICA [2] codes. Simulations show a good agreement of the impedance matrices in vacuum. Various modifications of the geometry are proposed in order to further optimize the coupling. In particular we study the effect of the strap box parameters and the recess of the vertical septa.

  7. A 3-D Model of Hot-Spot Formation in Inertial Confinement Fusion Implosions

    NASA Astrophysics Data System (ADS)

    Gong, X.; Goncharov, V. N.; Igumenshchev, I. V.

    2015-11-01

    A 3-D model describing the formation of a hot-spot in inertial confinement fusion (ICF) implosions is presented. The model includes thermal conduction and mass ablation effects in a 3-D distorted hot spot using an approach developed by Sanz. Evolution of the nonuniformity growth is calculated based on a sharp boundary model. The results of the model will be compared against 2-D DRACO and 3-D hydrodynamic code calculations. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

  8. 3D Modeling of Branching Structures for Anatomical Instruction

    PubMed Central

    Mattingly, William A.; Chariker, Julia H.; Paris, Richard; Chang, Dar-jen; Pani, John R.

    2015-01-01

    Branching tubular structures are prevalent in many different organic and synthetic settings. From trees and vegetation in nature, to vascular structures throughout human and animal biology, these structures are always candidates for new methods of graphical and visual expression. We present a modeling tool for the creation and interactive modification of these structures. Parameters such as thickness and position of branching structures can be modified, while geometric constraints ensure that the resulting mesh will have an accurate anatomical structure by not having inconsistent geometry. We apply this method to the creation of accurate representations of the different types of retinal cells in the human eye. This method allows a user to quickly produce anatomically accurate structures with low polygon counts that are suitable for rendering at interactive rates on commodity computers and mobile devices. PMID:27087764

  9. Modeling of Localized Neutral Particle Sources in 3D Edge Plasmas

    SciTech Connect

    Umansky, M V; Rognlien, T D; Fenstermacher, M E; Borchardt, M; Mutzke, A; Riemann, J; Schneider, R; Owen, L W

    2002-05-23

    A new edge plasma code BoRiS [1] has a fully 3D fluid plasma model. We supplement BoRiS with a 3D fluid neutral model including equations for parallel momentum and collisional perpendicular diffusion. This makes BoRiS an integrated plasma-neutral model suitable for a variety of applications. We present modeling results for a localized gas source in the geometry of the NCSX stellarator.

  10. Testing the hybrid-3D Hillslope Hydrological Model in a Real-World Controlled Environment

    NASA Astrophysics Data System (ADS)

    Hazenberg, P.; Broxton, P. D.; Gochis, D. J.; Niu, G. Y.; Pelletier, J. D.; Troch, P. A. A.; Zeng, X.

    2015-12-01

    Hillslopes play an important role for converting rainfall into runoff, and as such, influence theterrestrial dynamics of the Earth's climate system. Recently, we have developed a hybrid-3D (h3D) hillslope hydrological model that couples a 1D vertical soil column model with a lateral pseudo-2D saturated zone and overland flow model. The h3D model gives similar results as the CATchment HYdrological model (CATHY), which simulates the subsurface movement of water with the 3D Richards equation, though the runtime efficiency of the h3D model is about 2-3 orders of magnitude faster. In the current work, the ability of the h3D model to predict real-world hydrological dynamics is assessed using a number of recharge-drainage experiments within the Landscape Evolution Observatory (LEO) at the Biosphere 2 near Tucson, Arizona, USA. LEO offers accurate and high-resolution (both temporally and spatially) observations of the inputs, outputs and storage dynamics of several hillslopes. The level of detail of these observations is generally not possible with real-world hillslope studies. Therefore, LEO offers an optimal environment to test the h3D model. The h3D model captures the observed storage, baseflow, and overland flow dynamics of both a larger and a smaller hillslope. Furthermore, it simulates overland flow better than CATHY. The h3D model has difficulties correctly representing the height of the saturated zone close to the seepage face of the smaller hillslope, though. There is a gravel layer near this seepage face, and the numerical boundary condition of the h3D model is insufficient to capture the hydrological dynamics within this region. In addition, the h3D model is used to test the hypothesis that model parameters change through time due to the migration of soil particles during the recharge-drainage experiments. An in depth calibration of the h3D model parameters reveals that the best results are obtained by applying an event-based optimization procedure as compared

  11. A seismic modelling environment as a research and teaching tool for 3-D subsurface modelling

    NASA Astrophysics Data System (ADS)

    Burford, Dennis J.; Ger, Larry; Blake, Edwin H.; de Wit, Maarten J.; Doucouré, C. Moctar; Hart, Roger J.

    Early geological modelling and visualisation techniques were limited to manual cross-sections or isometric perspectives. Computer modelling has automated this task to a certain degree, but traditional approaches do not allow iterative validation during the modelling process. When the structure is complex and data sparse, as is often the case in geology, interactive 3-D modelling techniques should be employed that can interrogate new and existing data, guided by the geological experience of the modeller. Using the Vredefort dome in South Africa as a case study, we describe a Seismic Modelling Environment (SME) to demonstrate the potential of this type of computer-based modelling and geological visualisation. SME offers a novel approach to interactive 3-D modelling of complex geological structures using an extension of sweep representations and user-controlled forward modelling with seismic analysis for validation. Incorporation of validation techniques allows early confirmation or rejection of models. Tested by a group of third-year geology students, SME's iterative construction and exploration of a 3-D model clearly provided users with a superior understanding through visualisation. SME has, therefore, potential both as an educational as well as a research tool.

  12. On Fundamental Evaluation Using Uav Imagery and 3d Modeling Software

    NASA Astrophysics Data System (ADS)

    Nakano, K.; Suzuki, H.; Tamino, T.; Chikatsu, H.

    2016-06-01

    Unmanned aerial vehicles (UAVs), which have been widely used in recent years, can acquire high-resolution images with resolutions in millimeters; such images cannot be acquired with manned aircrafts. Moreover, it has become possible to obtain a surface reconstruction of a realistic 3D model using high-overlap images and 3D modeling software such as Context capture, Pix4Dmapper, Photoscan based on computer vision technology such as structure from motion and multi-view stereo. 3D modeling software has many applications. However, most of them seem to not have obtained appropriate accuracy control in accordance with the knowledge of photogrammetry and/or computer vision. Therefore, we performed flight tests in a test field using an UAV equipped with a gimbal stabilizer and consumer grade digital camera. Our UAV is a hexacopter and can fly according to the waypoints for autonomous flight and can record flight logs. We acquired images from different altitudes such as 10 m, 20 m, and 30 m. We obtained 3D reconstruction results of orthoimages, point clouds, and textured TIN models for accuracy evaluation in some cases with different image scale conditions using 3D modeling software. Moreover, the accuracy aspect was evaluated for different units of input image—course unit and flight unit. This paper describes the fundamental accuracy evaluation for 3D modeling using UAV imagery and 3D modeling software from the viewpoint of close-range photogrammetry.

  13. Development of 3D electromagnetic modeling tools for airborne vehicles

    NASA Technical Reports Server (NTRS)

    Volakis, John L.

    1992-01-01

    The main goal of this project is to develop methodologies for scattering by airborne composite vehicles. Although our primary focus continues to be the development of a general purpose code for analyzing the entire structure as a single unit, a number of other tasks are also pursued in parallel with this effort. These tasks are important in testing the overall approach and in developing suitable models for materials coatings, junctions and, more generally, in assessing the effectiveness of the various parts comprising the final code. Here, we briefly discuss our progress on the five different tasks which were pursued during this period. Our progress on each of these tasks is described in the detailed reports (listed at the end of this report) and the memoranda included. The first task described below is, of course, the core of this project and deals with the development of the overall code. Undoubtedly, it is the outcome of the research which was funded by NASA-Ames and the Navy over the past three years. During this year we developed the first finite element code for scattering by structures of arbitrary shape and composition. The code employs a new absorbing boundary condition which allows termination of the finite element mesh only 0.3 lambda from the outer surface of the target. This leads to a remarkable reduction of the mesh size and is a unique feature of the code. Other unique features of this code include capabilities to model resistive sheets, impedance sheets and anisotropic materials. This last capability is the latest feature of the code and is still under development. The code has been extensively validated for a number of composite geometries and some examples are given. The validation of the code is still in progress for anisotropic and larger non-metallic geometries and cavities. The developed finite element code is based on a Galerkin's formulation and employs edge-based tetrahedral elements for discretizing the dielectric sections and the region

  14. Treating benign optic nerve tumors with a 3-D conformal plan

    SciTech Connect

    Millunchick, Cheryl Hope

    2013-07-01

    A 68 year old male patient presented for radiation therapy for treatment of a benign tumor, a glioma of his left optic nerve. The radiation oncologist intended to prescribe 52.2 Gy to the planning target volume, while maintaining a maximum of 54 Gy to the optic nerves and the optic chiasm and a maximum of 40–45 Gy to the globes in order to minimize the possibility of damaging the optic system, which is especially important as this is a benign tumor. The dosimetrist devised a conformal non-coplanar three-dimensional plan with a slightly weighted forward planning component. This plan was created in approximately 15 minutes after the critical organs and the targets were delineated and resulted in an extremely conformal and homogenous plan, treating the target while sparing the nearby critical structures. This approach can also be extended to other tumors in the brain - benign or malignant.

  15. 3D tissue engineered micro-tumors for optical-based therapeutic screening platform

    NASA Astrophysics Data System (ADS)

    Spano, Joseph L.; Schmitt, Trevor J.; Bailey, Ryan C.; Hannon, Timothy S.; Elmajdob, Mohamed; Mason, Eric M.; Ye, Guochang; Das, Soumen; Seal, Sudipta; Fenn, Michael B.

    2016-03-01

    Melanoma is an underserved area of cancer research, with little focus on studying the effects of tumor extracellular matrix (ECM) properties on melanoma tumor progression, metastasis, and treatment efficacy. We've developed a Raman spectral mapping-based in-vitro screening platform that allows for nondestructive in-situ, multi-time point assessment of a novel potential nanotherapeutic adjuvant, nanoceria (cerium oxide nanoparticles), for treating melanoma. We've focused primarily on understanding melanoma tumor ECM composition and how it influences cell morphology and ICC markers. Furthermore, we aim to correlate this with studies on nanotherapeutic efficacy to coincide with the goal of predicting and preventing metastasis based on ECM composition. We've compiled a Raman spectral database for substrates containing varying compositions of fibronectin, elastin, laminin, and collagens type I and IV. Furthermore, we've developed a machine learning-based semi-quantitative analysis platform utilizing dimensionality reduction with subsequent pixel classification and semi-quantitation of ECM composition using Direct Classical Least Squares for classification and estimation of the reorganization of these components by taking 2D maps using Raman spectroscopy. Gaining an understanding of how tissue properties influence ECM organization has laid the foundation for future work utilizing Raman spectroscopy to assess therapeutic efficacy and matrix reorganization imparted by nanoceria. Specifically, this will allow us to better understand the role of HIF1a in matrix reorganization of the tumor microenvironment. By studying the relationship between substrate modulus and nanoceria's ability to inhibit an ECM that is conducive to tumor formation, we endeavor to show that nanoceria may prevent or even revert tumor conducive microenvironments.

  16. Calculation of the 3D density model of the Earth

    NASA Astrophysics Data System (ADS)

    Piskarev, A.; Butsenko, V.; Poselov, V.; Savin, V.

    2009-04-01

    The study of the Earth's crust is a part of investigation aimed at extension of the Russian Federation continental shelf in the Sea of Okhotsk Gathered data allow to consider the Sea of Okhotsk' area located outside the exclusive economic zone of the Russian Federation as the natural continuation of Russian territory. The Sea of Okhotsk is an Epi-Mesozoic platform with Pre-Cenozoic heterogeneous folded basement of polycyclic development and sediment cover mainly composed of Paleocene - Neocene - Quaternary deposits. Results of processing and complex interpretation of seismic, gravity, and aeromagnetic data along profile 2-DV-M, as well as analysis of available geological and geophysical information on the Sea of Okhotsk region, allowed to calculate of the Earth crust model. 4 layers stand out (bottom-up) in structure of the Earth crust: granulite-basic (density 2.90 g/cm3), granite-gneiss (limits of density 2.60-2.76 g/cm3), volcanogenic-sedimentary (2.45 g/cm3) and sedimentary (density 2.10 g/cm3). The last one is absent on the continent; it is observed only on the water area. Density of the upper mantle is taken as 3.30 g/cm3. The observed gravity anomalies are mostly related to the surface relief of the above mentioned layers or to the density variations of the granite-metamorphic basement. So outlining of the basement blocks of different constitution preceded to the modeling. This operation is executed after Double Fourier Spectrum analysis of the gravity and magnetic anomalies and following compilation of the synthetic anomaly maps, related to the basement density and magnetic heterogeneity. According to bathymetry data, the Sea of Okhotsk can be subdivided at three mega-blocks. Taking in consideration that central Sea of Okhotsk area is aseismatic, i.e. isostatic compensated, it is obvious that Earth crust structure of these three blocks is different. The South-Okhotsk depression is characteristics by 3200-3300 m of sea depths. Moho surface in this area is at

  17. 3d Modeling of cultural heritage objects with a structured light system.

    NASA Astrophysics Data System (ADS)

    Akca, Devrim

    3D modeling of cultural heritage objects is an expanding application area. The selection of the right technology is very important and strictly related to the project requirements, budget and user's experience. The triangulation based active sensors, e.g. structured light systems are used for many kinds of 3D object reconstruction tasks and in particular for 3D recording of cultural heritage objects. This study presents the experiences in the results of two such projects in which a close-range structured light system is used for the 3D digitization. The paper includes the essential steps of the 3D object modeling pipeline, i.e. digitization, registration, surface triangulation, editing, texture mapping and visualization. The capabilities of the used hardware and software are addressed. Particular emphasis is given to a coded structured light system as an option for data acquisition.

  18. Extraction of the 3D Free Space from Building Models for Indoor Navigation

    NASA Astrophysics Data System (ADS)

    Diakité, A. A.; Zlatanova, S.

    2016-10-01

    For several decades, indoor navigation has been exclusively investigated in a 2D perspective, based on floor plans, projection and other 2D representations of buildings. Nevertheless, 3D representations are closer to our reality and offer a more intuitive description of the space configuration. Thanks to recent advances in 3D modelling, 3D navigation is timidly but increasingly gaining in interest through the indoor applications. But, because the structure of indoor environment is often more complex than outdoor, very simplified models are used and obstacles are not considered for indoor navigation leading to limited possibilities in complex buildings. In this paper we consider the entire configuration of the indoor environment in 3D and introduce a method to extract from it the actual navigable space as a network of connected 3D spaces (volumes). We describe how to construct such 3D free spaces from semantically rich and furnished IFC models. The approach combines the geometric, the topological and the semantic information available in a 3D model to isolate the free space from the rest of the components. Furthermore, the extraction of such navigable spaces in building models lacking of semantic information is also considered. A data structure named combinatorial maps is used to support the operations required by the process while preserving the topological and semantic information of the input models.

  19. A spheroid-based 3-D culture model for pancreatic cancer drug testing, using the acid phosphatase assay.

    PubMed

    Wen, Z; Liao, Q; Hu, Y; You, L; Zhou, L; Zhao, Y

    2013-07-01

    Current therapy for pancreatic cancer is multimodal, involving surgery and chemotherapy. However, development of pancreatic cancer therapies requires a thorough evaluation of drug efficacy in vitro before animal testing and subsequent clinical trials. Compared to two-dimensional culture of cell monolayer, three-dimensional (3-D) models more closely mimic native tissues, since the tumor microenvironment established in 3-D models often plays a significant role in cancer progression and cellular responses to the drugs. Accumulating evidence has highlighted the benefits of 3-D in vitro models of various cancers. In the present study, we have developed a spheroid-based, 3-D culture of pancreatic cancer cell lines MIAPaCa-2 and PANC-1 for pancreatic drug testing, using the acid phosphatase assay. Drug efficacy testing showed that spheroids had much higher drug resistance than monolayers. This model, which is characteristically reproducible and easy and offers rapid handling, is the preferred choice for filling the gap between monolayer cell cultures and in vivo models in the process of drug development and testing for pancreatic cancer.

  20. A Shell/3D Modeling Technique for the Analysis of Delaminated Composite Laminates

    NASA Technical Reports Server (NTRS)

    Krueger, Ronald; OBrien, T. Kevin

    2000-01-01

    A shell/3D modeling technique was developed for which a local solid finite element model is used only in the immediate vicinity of the delamination front. The goal was to combine the accuracy of the full three-dimensional solution with the computational efficiency of a shell finite element model. Multi-point constraints provided a kinematically compatible interface between the local 3D model and the global structural model which has been meshed with shell finite elements. Double Cantilever Beam, End Notched Flexure, and Single Leg Bending specimens were analyzed first using full 3D finite element models to obtain reference solutions. Mixed mode strain energy release rate distributions were computed using the virtual crack closure technique. The analyses were repeated using the shell/3D technique to study the feasibility for pure mode I, mode II and mixed mode I/II cases. Specimens with a unidirectional layup and with a multidirectional layup were simulated. For a local 3D model, extending to a minimum of about three specimen thicknesses on either side of the delamination front, the results were in good agreement with mixed mode strain energy release rates obtained from computations where the entire specimen had been modeled with solid elements. For large built-up composite structures the shell/3D modeling technique offers a great potential for reducing the model size, since only a relatively small section in the vicinity of the delamination front needs to be modeled with solid elements.

  1. Mechanically assisted 3D ultrasound for pre-operative assessment and guiding percutaneous treatment of focal liver tumors

    NASA Astrophysics Data System (ADS)

    Sadeghi Neshat, Hamid; Bax, Jeffery; Barker, Kevin; Gardi, Lori; Chedalavada, Jason; Kakani, Nirmal; Fenster, Aaron

    2014-03-01

    Image-guided percutaneous ablation is the standard treatment for focal liver tumors deemed inoperable and is commonly used to maintain eligibility for patients on transplant waitlists. Radiofrequency (RFA), microwave (MWA) and cryoablation technologies are all delivered via one or a number of needle-shaped probes inserted directly into the tumor. Planning is mostly based on contrast CT/MRI. While intra-procedural CT is commonly used to confirm the intended probe placement, 2D ultrasound (US) remains the main, and in some centers the only imaging modality used for needle guidance. Corresponding intraoperative 2D US with planning and other intra-procedural imaging modalities is essential for accurate needle placement. However, identification of matching features of interest among these images is often challenging given the limited field-of-view (FOV) and low quality of 2D US images. We have developed a passive tracking arm with a motorized scan-head and software tools to improve guiding capabilities of conventional US by large FOV 3D US scans that provides more anatomical landmarks that can facilitate registration of US with both planning and intra-procedural images. The tracker arm is used to scan the whole liver with a high geometrical accuracy that facilitates multi-modality landmark based image registration. Software tools are provided to assist with the segmentation of the ablation probes and tumors, find the 2D view that best shows the probe(s) from a 3D US image, and to identify the corresponding image from planning CT scans. In this paper, evaluation results from laboratory testing and a phase 1 clinical trial for planning and guiding RFA and MWA procedures using the developed system will be presented. Early clinical results show a comparable performance to intra-procedural CT that suggests 3D US as a cost-effective alternative with no side-effects in centers where CT is not available.

  2. KENO3D Visualization Tool for KENO V.a and KENO-VI Geometry Models

    SciTech Connect

    Horwedel, J.E.; Bowman, S.M.

    2000-06-01

    Criticality safety analyses often require detailed modeling of complex geometries. Effective visualization tools can enhance checking the accuracy of these models. This report describes the KENO3D visualization tool developed at the Oak Ridge National Laboratory (ORNL) to provide visualization of KENO V.a and KENO-VI criticality safety models. The development of KENO3D is part of the current efforts to enhance the SCALE (Standardized Computer Analyses for Licensing Evaluations) computer software system.

  3. Obtaining valid geologic models from 3-D resistivity inversion of magnetotelluric data at Pahute Mesa, Nevada

    USGS Publications Warehouse

    Rodriguez, Brian D.; Sweetkind, Donald S.

    2015-01-01

    The 3-D inversion was generally able to reproduce the gross resistivity structure of the “known” model, but the simulated conductive volcanic composite unit horizons were often too shallow when compared to the “known” model. Additionally, the chosen computation parameters such as station spacing appear to have resulted in computational artifacts that are difficult to interpret but could potentially be removed with further refinements of the 3-D resistivity inversion modeling technique.

  4. 3D Viability Imaging of Tumor Phantoms Treated with Single Walled Carbon Nanohorns and Photothermal Therapy

    PubMed Central

    Whitney, Jon; Dewitt, Matthew; Whited, Bryce M.; Carswell, William; Simon, Alex; Rylander, Christopher G.; Rylander, Marissa Nichole

    2013-01-01

    Objective A new image analysis method called the Spatial Phantom Evaluation of Cellular Thermal Response in Layers (SPECTRL) is presented for assessing spatial viability response to nanoparticle enhanced photothermal therapy in tissue representative phantoms. Materials and Methods Sodium alginate phantoms seeded with MDA-MB-231 breast cancer cells and single walled nanohorns were laser irradiated with an ytterbium fiber laser at a wavelength of 1064 nm and irradiance of 3.8 watts/cm2 for 10–80 seconds. SPECTRL quantitatively assessed and correlated 3D viability with spatiotemporal temperature. Results and Conclusions Based on this analysis, kill and transition zones increased from 3.7 mm3 and 13 mm3 respectively to 44.5 mm3 and 44.3 mm3 as duration was increased from 10–80 seconds. SPECTRL provides a quantitative tool for measuring precise spatial treatment regions, providing information necessary to tailor therapy protocols. PMID:23780336

  5. Liver Tumor Segmentation from MR Images Using 3D Fast Marching Algorithm and Single Hidden Layer Feedforward Neural Network.

    PubMed

    Le, Trong-Ngoc; Bao, Pham The; Huynh, Hieu Trung

    2016-01-01

    Objective. Our objective is to develop a computerized scheme for liver tumor segmentation in MR images. Materials and Methods. Our proposed scheme consists of four main stages. Firstly, the region of interest (ROI) image which contains the liver tumor region in the T1-weighted MR image series was extracted by using seed points. The noise in this ROI image was reduced and the boundaries were enhanced. A 3D fast marching algorithm was applied to generate the initial labeled regions which are considered as teacher regions. A single hidden layer feedforward neural network (SLFN), which was trained by a noniterative algorithm, was employed to classify the unlabeled voxels. Finally, the postprocessing stage was applied to extract and refine the liver tumor boundaries. The liver tumors determined by our scheme were compared with those manually traced by a radiologist, used as the "ground truth." Results. The study was evaluated on two datasets of 25 tumors from 16 patients. The proposed scheme obtained the mean volumetric overlap error of 27.43% and the mean percentage volume error of 15.73%. The mean of the average surface distance, the root mean square surface distance, and the maximal surface distance were 0.58 mm, 1.20 mm, and 6.29 mm, respectively. PMID:27597960

  6. Liver Tumor Segmentation from MR Images Using 3D Fast Marching Algorithm and Single Hidden Layer Feedforward Neural Network

    PubMed Central

    2016-01-01

    Objective. Our objective is to develop a computerized scheme for liver tumor segmentation in MR images. Materials and Methods. Our proposed scheme consists of four main stages. Firstly, the region of interest (ROI) image which contains the liver tumor region in the T1-weighted MR image series was extracted by using seed points. The noise in this ROI image was reduced and the boundaries were enhanced. A 3D fast marching algorithm was applied to generate the initial labeled regions which are considered as teacher regions. A single hidden layer feedforward neural network (SLFN), which was trained by a noniterative algorithm, was employed to classify the unlabeled voxels. Finally, the postprocessing stage was applied to extract and refine the liver tumor boundaries. The liver tumors determined by our scheme were compared with those manually traced by a radiologist, used as the “ground truth.” Results. The study was evaluated on two datasets of 25 tumors from 16 patients. The proposed scheme obtained the mean volumetric overlap error of 27.43% and the mean percentage volume error of 15.73%. The mean of the average surface distance, the root mean square surface distance, and the maximal surface distance were 0.58 mm, 1.20 mm, and 6.29 mm, respectively. PMID:27597960

  7. Considerations on the Use of 3-D Geophysical Models to Predict Test Ban Monitoring Observables

    SciTech Connect

    Harris, D B; Zucca, J J; McCallen, D B; Pasyanos, M E; Flanagan, M P; Myers, S C; Walter, W R; Rodgers, A J; Harben, P E

    2007-07-09

    The use of 3-D geophysical models to predict nuclear test ban monitoring observables (phase travel times, amplitudes, dispersion, etc.) is widely anticipated to provide improvements in the basic seismic monitoring functions of detection, association, location, discrimination and yield estimation. A number of questions arise when contemplating a transition from 1-D, 2-D and 2.5-D models to constructing and using 3-D models, among them: (1) Can a 3-D geophysical model or a collection of 3-D models provide measurably improved predictions of seismic monitoring observables over existing 1-D models, or 2-D and 2 1/2-D models currently under development? (2) Is a single model that can predict all observables achievable, or must separate models be devised for each observable? How should joint inversion of disparate observable data be performed, if required? (3) What are the options for model representation? Are multi-resolution models essential? How does representation affect the accuracy and speed of observable predictions? (4) How should model uncertainty be estimated, represented and how should it be used? Are stochastic models desirable? (5) What data types should be used to construct the models? What quality control regime should be established? (6) How will 3-D models be used in operations? Will significant improvements in the basic monitoring functions result from the use of 3-D models? Will the calculation of observables through 3-D models be fast enough for real-time use or must a strategy of pre-computation be employed? (7) What are the theoretical limits to 3-D model development (resolution, uncertainty) and performance in predicting monitoring observables? How closely can those limits be approached with projected data availability, station distribution and inverse methods? (8) What priorities should be placed on the acquisition of event ground truth information, deployment of new stations, development of new inverse techniques, exploitation of large

  8. Optimisation of Ionic Models to Fit Tissue Action Potentials: Application to 3D Atrial Modelling

    PubMed Central

    Lovell, Nigel H.; Dokos, Socrates

    2013-01-01

    A 3D model of atrial electrical activity has been developed with spatially heterogeneous electrophysiological properties. The atrial geometry, reconstructed from the male Visible Human dataset, included gross anatomical features such as the central and peripheral sinoatrial node (SAN), intra-atrial connections, pulmonary veins, inferior and superior vena cava, and the coronary sinus. Membrane potentials of myocytes from spontaneously active or electrically paced in vitro rabbit cardiac tissue preparations were recorded using intracellular glass microelectrodes. Action potentials of central and peripheral SAN, right and left atrial, and pulmonary vein myocytes were each fitted using a generic ionic model having three phenomenological ionic current components: one time-dependent inward, one time-dependent outward, and one leakage current. To bridge the gap between the single-cell ionic models and the gross electrical behaviour of the 3D whole-atrial model, a simplified 2D tissue disc with heterogeneous regions was