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Sample records for 3d tissue structures

  1. 3D topography of biologic tissue by multiview imaging and structured light illumination

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Zhang, Shiwu; Xu, Ronald

    2014-02-01

    Obtaining three-dimensional (3D) information of biologic tissue is important in many medical applications. This paper presents two methods for reconstructing 3D topography of biologic tissue: multiview imaging and structured light illumination. For each method, the working principle is introduced, followed by experimental validation on a diabetic foot model. To compare the performance characteristics of these two imaging methods, a coordinate measuring machine (CMM) is used as a standard control. The wound surface topography of the diabetic foot model is measured by multiview imaging and structured light illumination methods respectively and compared with the CMM measurements. The comparison results show that the structured light illumination method is a promising technique for 3D topographic imaging of biologic tissue.

  2. 3D multi-layered fibrous cellulose structure using an electrohydrodynamic process for tissue engineering.

    PubMed

    Kim, Minseong; Kim, GeunHyung

    2015-11-01

    Micro/nanofibrous structures have been applied widely in various tissue-engineering applications because the topological structures are similar to the extracellular matrix (ECM), which encourages a high degree of cell adhesion and growth. However, it has been difficult to produce a three-dimensional (3D) fibrous structure using controllable macro-pores. Recently, cellulose has been considered a high-potential natural-origin biomaterial, but its use in 3D biomedical structures has been limited due to its narrow processing window. Here, we suggest a new 3D cellulose scaffold consisting of multi-layered struts made of submicron-sized entangled fibers that were fabricated using an electrohydrodynamic direct jet (EHDJ) process that is spin-printing. By optimizing processing conditions (electric field strength, cellulose feeding rate, and distance between nozzle and target), we can achieve a multi-layered cellulose structure consisting of the cylindrically entangled cellulose fibers. To compare the properties of the fabricated 3D cellulose structure, we used a PCL fibrous scaffold, which has a similar fibrous morphology and pore geometry, as a control. The physical and in vitro biocompatibilities of both fibrous scaffolds were assessed using human dermal fibroblasts, and the cellulose structure showed higher cell adhesion and metabolic activities compared with the control. These results suggest the EHDJ process to be an effective fabricating tool for tissue engineering and the cellulose scaffold has high potential as a tissue regenerative material.

  3. Creation of a long-lifespan ciliated epithelial tissue structure using a 3D collagen scaffold

    PubMed Central

    Wang, Yuchi; Wong, Lid B.; Mao, Hua

    2009-01-01

    We describe a method of using a 3D collagen gel scaffold applied at the air-liquid interface to culture dissociated primary tracheal-bronchial ciliated cells into a ciliated epithelial tissue structure (CETS). This 3D collagen gel culture system enables the induction of ciliogenesis and continuously provides support, maintenance, development, differentiation and propagation for the growth of cilia into the CETS. The CETS developed by this system resembles the ciliary metachronal motility and morphological, histological and physiopharmacological characteristics of cells found in native and in vivo ciliated epithelia. The CETS can be sustained for months with a straightforward and simple maintenance protocol. The integrity of the functional ciliary activity of this CETS enables the evaluation of long-term effects of many pulmonary drug candidates without using animals. PMID:19836831

  4. A 3D bioprinting system to produce human-scale tissue constructs with structural integrity.

    PubMed

    Kang, Hyun-Wook; Lee, Sang Jin; Ko, In Kap; Kengla, Carlos; Yoo, James J; Atala, Anthony

    2016-03-01

    A challenge for tissue engineering is producing three-dimensional (3D), vascularized cellular constructs of clinically relevant size, shape and structural integrity. We present an integrated tissue-organ printer (ITOP) that can fabricate stable, human-scale tissue constructs of any shape. Mechanical stability is achieved by printing cell-laden hydrogels together with biodegradable polymers in integrated patterns and anchored on sacrificial hydrogels. The correct shape of the tissue construct is achieved by representing clinical imaging data as a computer model of the anatomical defect and translating the model into a program that controls the motions of the printer nozzles, which dispense cells to discrete locations. The incorporation of microchannels into the tissue constructs facilitates diffusion of nutrients to printed cells, thereby overcoming the diffusion limit of 100-200 μm for cell survival in engineered tissues. We demonstrate capabilities of the ITOP by fabricating mandible and calvarial bone, cartilage and skeletal muscle. Future development of the ITOP is being directed to the production of tissues for human applications and to the building of more complex tissues and solid organs. PMID:26878319

  5. A 3D bioprinting system to produce human-scale tissue constructs with structural integrity.

    PubMed

    Kang, Hyun-Wook; Lee, Sang Jin; Ko, In Kap; Kengla, Carlos; Yoo, James J; Atala, Anthony

    2016-03-01

    A challenge for tissue engineering is producing three-dimensional (3D), vascularized cellular constructs of clinically relevant size, shape and structural integrity. We present an integrated tissue-organ printer (ITOP) that can fabricate stable, human-scale tissue constructs of any shape. Mechanical stability is achieved by printing cell-laden hydrogels together with biodegradable polymers in integrated patterns and anchored on sacrificial hydrogels. The correct shape of the tissue construct is achieved by representing clinical imaging data as a computer model of the anatomical defect and translating the model into a program that controls the motions of the printer nozzles, which dispense cells to discrete locations. The incorporation of microchannels into the tissue constructs facilitates diffusion of nutrients to printed cells, thereby overcoming the diffusion limit of 100-200 μm for cell survival in engineered tissues. We demonstrate capabilities of the ITOP by fabricating mandible and calvarial bone, cartilage and skeletal muscle. Future development of the ITOP is being directed to the production of tissues for human applications and to the building of more complex tissues and solid organs.

  6. 3D Printing for Tissue Engineering

    PubMed Central

    Jia, Jia; Yao, Hai; Mei, Ying

    2016-01-01

    Tissue engineering aims to fabricate functional tissue for applications in regenerative medicine and drug testing. More recently, 3D printing has shown great promise in tissue fabrication with a structural control from micro- to macro-scale by using a layer-by-layer approach. Whether through scaffold-based or scaffold-free approaches, the standard for 3D printed tissue engineering constructs is to provide a biomimetic structural environment that facilitates tissue formation and promotes host tissue integration (e.g., cellular infiltration, vascularization, and active remodeling). This review will cover several approaches that have advanced the field of 3D printing through novel fabrication methods of tissue engineering constructs. It will also discuss the applications of synthetic and natural materials for 3D printing facilitated tissue fabrication. PMID:26869728

  7. Fabrication of scalable and structured tissue engineering scaffolds using water dissolvable sacrificial 3D printed moulds.

    PubMed

    Mohanty, Soumyaranjan; Larsen, Layla Bashir; Trifol, Jon; Szabo, Peter; Burri, Harsha Vardhan Reddy; Canali, Chiara; Dufva, Marin; Emnéus, Jenny; Wolff, Anders

    2015-10-01

    One of the major challenges in producing large scale engineered tissue is the lack of ability to create large highly perfused scaffolds in which cells can grow at a high cell density and viability. Here, we explore 3D printed polyvinyl alcohol (PVA) as a sacrificial mould in a polymer casting process. The PVA mould network defines the channels and is dissolved after curing the polymer casted around it. The printing parameters determined the PVA filament density in the sacrificial structure and this density resulted in different stiffness of the corresponding elastomer replica. It was possible to achieve 80% porosity corresponding to about 150 cm(2)/cm(3) surface to volume ratio. The process is easily scalable as demonstrated by fabricating a 75 cm(3) scaffold with about 16,000 interconnected channels (about 1m(2) surface area) and with a channel to channel distance of only 78 μm. To our knowledge this is the largest scaffold ever to be produced with such small feature sizes and with so many structured channels. The fabricated scaffolds were applied for in-vitro culturing of hepatocytes over a 12-day culture period. Smaller scaffolds (6×4 mm) were tested for cell culturing and could support homogeneous cell growth throughout the scaffold. Presumably, the diffusion of oxygen and nutrient throughout the channel network is rapid enough to support cell growth. In conclusion, the described process is scalable, compatible with cell culture, rapid, and inexpensive. PMID:26117791

  8. 3D bioprinting of tissues and organs.

    PubMed

    Murphy, Sean V; Atala, Anthony

    2014-08-01

    Additive manufacturing, otherwise known as three-dimensional (3D) printing, is driving major innovations in many areas, such as engineering, manufacturing, art, education and medicine. Recent advances have enabled 3D printing of biocompatible materials, cells and supporting components into complex 3D functional living tissues. 3D bioprinting is being applied to regenerative medicine to address the need for tissues and organs suitable for transplantation. Compared with non-biological printing, 3D bioprinting involves additional complexities, such as the choice of materials, cell types, growth and differentiation factors, and technical challenges related to the sensitivities of living cells and the construction of tissues. Addressing these complexities requires the integration of technologies from the fields of engineering, biomaterials science, cell biology, physics and medicine. 3D bioprinting has already been used for the generation and transplantation of several tissues, including multilayered skin, bone, vascular grafts, tracheal splints, heart tissue and cartilaginous structures. Other applications include developing high-throughput 3D-bioprinted tissue models for research, drug discovery and toxicology. PMID:25093879

  9. [Construction of 3D tissue-like structure using functional magnetite nanoparticles].

    PubMed

    Ito, Akira; Honda, Hiroyuki; Kamihira, Masamichi

    2008-01-01

    Magnetic nanoparticles for medical applications have been developed by many researchers. Since these nanoparticles have unique magnetic features not present in other materials, they can be applied to special medical techniques. Magnetite cationic liposomes (MCLs), one group of the cationic magnetic particles, can be used as carriers to introduce magnetite nanoparticles into target cells since their positively charged surface interacts with the negatively charged cell surface. Magnetite nanoparticles conjugated with antibodies (antibody-conjugated magnetoliposomes, AMLs) are applicable to introduce magnetite nanoparticles specifically into target cells, even when target cells coexist with other kinds of cells. Since the cells labeled with magnetite nanoparticles could be manipulated using magnets, we applied this technique to tissue engineering and termed it ;magnetic force-based tissue engineering (Mag-TE)'. Both magnetic force and functionalized magnetite nanoparticles were used in a process of tissue engineering: construction of multilayered cell sheet-like structures and tubular structures. Thus, the applications of these functionalized magnetite nanoparticles with their unique features will further improve tissue engineering techniques.

  10. Current progress in 3D printing for cardiovascular tissue engineering.

    PubMed

    Mosadegh, Bobak; Xiong, Guanglei; Dunham, Simon; Min, James K

    2015-03-16

    3D printing is a technology that allows the fabrication of structures with arbitrary geometries and heterogeneous material properties. The application of this technology to biological structures that match the complexity of native tissue is of great interest to researchers. This mini-review highlights the current progress of 3D printing for fabricating artificial tissues of the cardiovascular system, specifically the myocardium, heart valves, and coronary arteries. In addition, how 3D printed sensors and actuators can play a role in tissue engineering is discussed. To date, all the work with building 3D cardiac tissues have been proof-of-principle demonstrations, and in most cases, yielded products less effective than other traditional tissue engineering strategies. However, this technology is in its infancy and therefore there is much promise that through collaboration between biologists, engineers and material scientists, 3D bioprinting can make a significant impact on the field of cardiovascular tissue engineering.

  11. 3D bioprinting for engineering complex tissues.

    PubMed

    Mandrycky, Christian; Wang, Zongjie; Kim, Keekyoung; Kim, Deok-Ho

    2016-01-01

    Bioprinting is a 3D fabrication technology used to precisely dispense cell-laden biomaterials for the construction of complex 3D functional living tissues or artificial organs. While still in its early stages, bioprinting strategies have demonstrated their potential use in regenerative medicine to generate a variety of transplantable tissues, including skin, cartilage, and bone. However, current bioprinting approaches still have technical challenges in terms of high-resolution cell deposition, controlled cell distributions, vascularization, and innervation within complex 3D tissues. While no one-size-fits-all approach to bioprinting has emerged, it remains an on-demand, versatile fabrication technique that may address the growing organ shortage as well as provide a high-throughput method for cell patterning at the micrometer scale for broad biomedical engineering applications. In this review, we introduce the basic principles, materials, integration strategies and applications of bioprinting. We also discuss the recent developments, current challenges and future prospects of 3D bioprinting for engineering complex tissues. Combined with recent advances in human pluripotent stem cell technologies, 3D-bioprinted tissue models could serve as an enabling platform for high-throughput predictive drug screening and more effective regenerative therapies.

  12. 3D bioprinting for engineering complex tissues.

    PubMed

    Mandrycky, Christian; Wang, Zongjie; Kim, Keekyoung; Kim, Deok-Ho

    2016-01-01

    Bioprinting is a 3D fabrication technology used to precisely dispense cell-laden biomaterials for the construction of complex 3D functional living tissues or artificial organs. While still in its early stages, bioprinting strategies have demonstrated their potential use in regenerative medicine to generate a variety of transplantable tissues, including skin, cartilage, and bone. However, current bioprinting approaches still have technical challenges in terms of high-resolution cell deposition, controlled cell distributions, vascularization, and innervation within complex 3D tissues. While no one-size-fits-all approach to bioprinting has emerged, it remains an on-demand, versatile fabrication technique that may address the growing organ shortage as well as provide a high-throughput method for cell patterning at the micrometer scale for broad biomedical engineering applications. In this review, we introduce the basic principles, materials, integration strategies and applications of bioprinting. We also discuss the recent developments, current challenges and future prospects of 3D bioprinting for engineering complex tissues. Combined with recent advances in human pluripotent stem cell technologies, 3D-bioprinted tissue models could serve as an enabling platform for high-throughput predictive drug screening and more effective regenerative therapies. PMID:26724184

  13. Force-driven evolution of mesoscale structure in engineered 3D microtissues and the modulation of tissue stiffening

    PubMed Central

    Zhao, Ruogang; Chen, Christopher S.; Reich, Daniel H.

    2014-01-01

    The complex structures of tissues determine their mechanical strength. In engineered tissues formed through self-assembly in a mold, artificially imposed boundary constraints have been found to induce anisotropic clustering of the cells and the extracellular matrix in local regions. To understand how such tissue remodeling at the intermediate length-scale (mesoscale) affects tissue stiffening, we used a novel microtissue mechanical testing system to manipulate the remodeling of the tissue structures and to measure the subsequent changes in tissue stiffness. Microtissues were formed through cell driven self-assembly of collagen matrix in arrays of micro-patterned wells, each containing two flexible micropillars that measured the microtissues’ contractile forces and also their elastic moduli via magnetic actuation. We manipulated tissue remodeling by inducing myofibroblast differentiation with TGF-β1, by varying the micropillar spring constants or by blocking cell contractility with blebbistatin and collagen cross-linking with BAPN. We showed that increased anisotropic compaction of the collagen matrix, caused by increased micropillar spring constant or elevated cell contraction force, contributed to tissue stiffening. Conversely, collagen matrix and tissue stiffness were not affected by inhibition of cell-generated contraction forces.. Together, these measurements showed that mesoscale tissue remodeling is an important middle step linking tissue compaction forces and tissue stiffening. PMID:24630092

  14. Microfluidic Techniques for Development of 3D Vascularized Tissue

    PubMed Central

    Hasan, Anwarul; Paul, Arghya; Vrana, Nihal Engin; Zhao, Xin; Memic, Adnan; Hwang, Yu-Shik; Dokmeci, Mehmet R.; Khademhosseini, Ali

    2014-01-01

    Development of a vascularized tissue is one of the key challenges for the successful clinical application of tissue engineered constructs. Despite the significant efforts over the last few decades, establishing a gold standard to develop three dimensional (3D) vascularized tissues has still remained far from reality. Recent advances in the application of microfluidic platforms to the field of tissue engineering have greatly accelerated the progress toward the development of viable vascularized tissue constructs. Numerous techniques have emerged to induce the formation of vascular structure within tissues which can be broadly classified into two distinct categories, namely (1) prevascularization-based techniques and (2) vasculogenesis and angiogenesis-based techniques. This review presents an overview of the recent advancements in the vascularization techniques using both approaches for generating 3D vascular structure on microfluidic platforms. PMID:24906345

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

    PubMed

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

    2015-10-01

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

  16. Electrohydrodynamic jet process for pore-structure-controlled 3D fibrous architecture as a tissue regenerative material: fabrication and cellular activities.

    PubMed

    Kim, Min Seong; Kim, GeunHyung

    2014-07-22

    In this study, we propose a new scaffold fabrication method, "direct electro-hydrodynamic jet process," using the initial jet of an electrospinning process and ethanol media as a target. The fabricated three-dimensional (3D) fibrous structure was configured with multilayered microsized struts consisting of randomly entangled micro/nanofibrous architecture, similar to that of native extracellular matrixes. The fabrication of the structure was highly dependent on various processing parameters, such as the surface tension of the target media, and the flow rate and weight fraction of the polymer solution. As a tissue regenerative material, the 3D fibrous scaffold was cultured with preosteoblasts to observe the initial cellular activities in comparison with a solid-freeform fabricated 3D scaffold sharing a similar structural geometry. The cell-culture results showed that the newly developed scaffold provided outstanding microcellular environmental conditions to the seeded cells (about 3.5-fold better initial cell attachment and 2.1-fold better cell proliferation).

  17. Bioengineered silk scaffolds in 3D tissue modeling with focus on mammary tissues.

    PubMed

    Maghdouri-White, Yas; Bowlin, Gary L; Lemmon, Christopher A; Dréau, Didier

    2016-02-01

    In vitro generation of three-dimensional (3D) biological tissues and organ-like structures is a promising strategy to study and closely model complex aspects of the molecular, cellular, and physiological interactions of tissue. In particular, in vitro 3D tissue modeling holds promises to further our understanding of breast development. Indeed, biologically relevant 3D structures that combine mammary cells and engineered matrices have improved our knowledge of mammary tissue growth, organization, and differentiation. Several polymeric biomaterials have been used as scaffolds to engineer 3D mammary tissues. Among those, silk fibroin-based biomaterials have many biologically relevant properties and have been successfully used in multiple medical applications. Here, we review the recent advances in engineered scaffolds with an emphasis on breast-like tissue generation and the benefits of modified silk-based scaffolds.

  18. 3D Extracellular Matrix from Sectioned Human Tissues

    PubMed Central

    Campbell, Catherine B; Cukierman, Edna; Artym, Vira V

    2014-01-01

    Three-dimensional (3D) matrices have significant advantages compared to conventional two-dimensional (2D) matrices for studying cell adhesion, migration, and tissue organization. Cellular behavior is dependent on the surrounding matrix environment for signaling and induction of biological responses (Carletti, et al., 2011; Pampaloni, et al., 2007; Vlodavsky, 1999). 2D cultures induce an artificial polarity in cultured cells between upper and lower surfaces not present normally in the in vivo environment. No longer nonpolar, many aspects of cellular behavior are altered (Beacham, et al., 2007; Grinnell and Petroll, 2010; Yamada and Cukierman, 2007). In addition, 2D models lack the physical properties of 3D matrix, such as topography, stiffness, and dimensionality. To begin to mimic the 3D environment of in vivo connective tissue extracellular matrix (ECM), collagen gels have been used widely (see Unit 10.3). Culture of cells in collagen gels results in a bipolar fibroblast morphology that resembles the in vivo phenotype (Friedl and Brocker, 2000; Even-Ram and Yamada, 2005; Grinnell and Petroll, 2010). Although more physiological, 3D collagen gels lack the complex biochemical and physical microenvironment present in an in vivo ECM that regulates cellular physiological properties (Beacham, et al., 2007). A variety of methods to create a more in vivo-like ECM have been published (Yamada and Cukierman, 2007). Adding critical ECM components to 3D collagen matrices, including fibronectin, hyaluronan, link protein and glycosaminoglycans, can more accurately mimic the structural microenvironment of the native ECM (Friedl and Brocker, 2000). Other ECM models use cultured cell lines, such as fibroblasts, to derive an ECM lattice through secretion of an organized ECM (Beacham, et al., 2007). Different cell lines have been chosen to generate a specific microenvironment for study of particularly types of cellular behavior (Kutys and Yamada, 2013). For example, cultured bovine

  19. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  20. 3D Printing of Personalized Organs and Tissues

    NASA Astrophysics Data System (ADS)

    Ye, Kaiming

    2015-03-01

    Authors: Kaiming Ye and Sha Jin, Department of Biomedical Engineering, Watson School of Engineering and Applied Science, Binghamton University, State University of New York, Binghamton, NY 13902-6000 Abstract: Creation of highly organized multicellular constructs, including tissues and organs or organoids, will revolutionize tissue engineering and regenerative medicine. The development of these technologies will enable the production of individualized organs or tissues for patient-tailored organ transplantation or cell-based therapy. For instance, a patient with damaged myocardial tissues due to an ischemic event can receive a myocardial transplant generated using the patient's own induced pluripotent stem cells (iPSCs). Likewise, a type-1 diabetic patient can be treated with lab-generated islets to restore his or her physiological insulin secretion capability. These lab-produced, high order tissues or organs can also serve as disease models for pathophysiological study and drug screening. The remarkable advances in stem cell biology, tissue engineering, microfabrication, and materials science in the last decade suggest the feasibility of generating these tissues and organoids in the laboratory. Nevertheless, major challenges still exist. One of the critical challenges that we still face today is the difficulty in constructing or fabricating multicellular assemblies that recapitulate in vivo microenvironments essential for controlling cell proliferation, migration, differentiation, maturation and assembly into a biologically functional tissue or organoid structure. These challenges can be addressed through developing 3D organ and tissue printing which enables organizing and assembling cells into desired tissue and organ structures. We have shown that human pluripotent stem cells differentiated in 3D environments are mature and possess high degree of biological function necessary for them to function in vivo.

  1. Osteogenic potential of human adipose-tissue-derived mesenchymal stromal cells cultured on 3D-printed porous structured titanium.

    PubMed

    Lewallen, Eric A; Jones, Dakota L; Dudakovic, Amel; Thaler, Roman; Paradise, Christopher R; Kremers, Hilal M; Abdel, Matthew P; Kakar, Sanjeev; Dietz, Allan B; Cohen, Robert C; Lewallen, David G; van Wijnen, Andre J

    2016-05-01

    Integration of porous metal prosthetics, which restore form and function of irreversibly damaged joints, into remaining healthy bone is critical for implant success. We investigated the biological properties of adipose-tissue-derived mesenchymal stromal/stem cells (AMSCs) and addressed their potential to alter the in vitro microenvironment of implants. We employed human AMSCs as a practical source for musculoskeletal applications because these cells can be obtained in large quantities, are multipotent, and have trophic paracrine functions. AMSCs were cultured on surgical-grade porous titanium disks as a model for orthopedic implants. We monitored cell/substrate attachment, cell proliferation, multipotency, and differentiation phenotypes of AMSCs upon osteogenic induction. High-resolution scanning electron microscopy and histology revealed that AMSCs adhere to the porous metallic surface. Compared to standard tissue culture plastic, AMSCs grown in the porous titanium microenvironment showed differences in temporal expression for genes involved in cell cycle progression (CCNB2, HIST2H4), extracellular matrix production (COL1A1, COL3A1), mesenchymal lineage identity (ACTA2, CD248, CD44), osteoblastic transcription factors (DLX3, DLX5, ID3), and epigenetic regulators (EZH1, EZH2). We conclude that metal orthopedic implants can be effectively seeded with clinical-grade stem/stromal cells to create a pre-conditioned implant. PMID:26774799

  2. Osteogenic potential of human adipose-tissue-derived mesenchymal stromal cells cultured on 3D-printed porous structured titanium.

    PubMed

    Lewallen, Eric A; Jones, Dakota L; Dudakovic, Amel; Thaler, Roman; Paradise, Christopher R; Kremers, Hilal M; Abdel, Matthew P; Kakar, Sanjeev; Dietz, Allan B; Cohen, Robert C; Lewallen, David G; van Wijnen, Andre J

    2016-05-01

    Integration of porous metal prosthetics, which restore form and function of irreversibly damaged joints, into remaining healthy bone is critical for implant success. We investigated the biological properties of adipose-tissue-derived mesenchymal stromal/stem cells (AMSCs) and addressed their potential to alter the in vitro microenvironment of implants. We employed human AMSCs as a practical source for musculoskeletal applications because these cells can be obtained in large quantities, are multipotent, and have trophic paracrine functions. AMSCs were cultured on surgical-grade porous titanium disks as a model for orthopedic implants. We monitored cell/substrate attachment, cell proliferation, multipotency, and differentiation phenotypes of AMSCs upon osteogenic induction. High-resolution scanning electron microscopy and histology revealed that AMSCs adhere to the porous metallic surface. Compared to standard tissue culture plastic, AMSCs grown in the porous titanium microenvironment showed differences in temporal expression for genes involved in cell cycle progression (CCNB2, HIST2H4), extracellular matrix production (COL1A1, COL3A1), mesenchymal lineage identity (ACTA2, CD248, CD44), osteoblastic transcription factors (DLX3, DLX5, ID3), and epigenetic regulators (EZH1, EZH2). We conclude that metal orthopedic implants can be effectively seeded with clinical-grade stem/stromal cells to create a pre-conditioned implant.

  3. Biomimetic 3D tissue printing for soft tissue regeneration.

    PubMed

    Pati, Falguni; Ha, Dong-Heon; Jang, Jinah; Han, Hyun Ho; Rhie, Jong-Won; Cho, Dong-Woo

    2015-09-01

    Engineered adipose tissue constructs that are capable of reconstructing soft tissue with adequate volume would be worthwhile in plastic and reconstructive surgery. Tissue printing offers the possibility of fabricating anatomically relevant tissue constructs by delivering suitable matrix materials and living cells. Here, we devise a biomimetic approach for printing adipose tissue constructs employing decellularized adipose tissue (DAT) matrix bioink encapsulating human adipose tissue-derived mesenchymal stem cells (hASCs). We designed and printed precisely-defined and flexible dome-shaped structures with engineered porosity using DAT bioink that facilitated high cell viability over 2 weeks and induced expression of standard adipogenic genes without any supplemented adipogenic factors. The printed DAT constructs expressed adipogenic genes more intensely than did non-printed DAT gel. To evaluate the efficacy of our printed tissue constructs for adipose tissue regeneration, we implanted them subcutaneously in mice. The constructs did not induce chronic inflammation or cytotoxicity postimplantation, but supported positive tissue infiltration, constructive tissue remodeling, and adipose tissue formation. This study demonstrates that direct printing of spatially on-demand customized tissue analogs is a promising approach to soft tissue regeneration.

  4. 3D Printing and Biofabrication for Load Bearing Tissue Engineering.

    PubMed

    Jeong, Claire G; Atala, Anthony

    2015-01-01

    Cell-based direct biofabrication and 3D bioprinting is becoming a dominant technological platform and is suggested as a new paradigm for twenty-first century tissue engineering. These techniques may be our next step in surpassing the hurdles and limitations of conventional scaffold-based tissue engineering, and may offer the industrial potential of tissue engineered products especially for load bearing tissues. Here we present a topically focused review regarding the fundamental concepts, state of the art, and perspectives of this new technology and field of biofabrication and 3D bioprinting, specifically focused on tissue engineering of load bearing tissues such as bone, cartilage, osteochondral and dental tissue engineering.

  5. 3D Printing and Biofabrication for Load Bearing Tissue Engineering.

    PubMed

    Jeong, Claire G; Atala, Anthony

    2015-01-01

    Cell-based direct biofabrication and 3D bioprinting is becoming a dominant technological platform and is suggested as a new paradigm for twenty-first century tissue engineering. These techniques may be our next step in surpassing the hurdles and limitations of conventional scaffold-based tissue engineering, and may offer the industrial potential of tissue engineered products especially for load bearing tissues. Here we present a topically focused review regarding the fundamental concepts, state of the art, and perspectives of this new technology and field of biofabrication and 3D bioprinting, specifically focused on tissue engineering of load bearing tissues such as bone, cartilage, osteochondral and dental tissue engineering. PMID:26545741

  6. Powder-based 3D printing for bone tissue engineering.

    PubMed

    Brunello, G; Sivolella, S; Meneghello, R; Ferroni, L; Gardin, C; Piattelli, A; Zavan, B; Bressan, E

    2016-01-01

    Bone tissue engineered 3-D constructs customized to patient-specific needs are emerging as attractive biomimetic scaffolds to enhance bone cell and tissue growth and differentiation. The article outlines the features of the most common additive manufacturing technologies (3D printing, stereolithography, fused deposition modeling, and selective laser sintering) used to fabricate bone tissue engineering scaffolds. It concentrates, in particular, on the current state of knowledge concerning powder-based 3D printing, including a description of the properties of powders and binder solutions, the critical phases of scaffold manufacturing, and its applications in bone tissue engineering. Clinical aspects and future applications are also discussed.

  7. Powder-based 3D printing for bone tissue engineering.

    PubMed

    Brunello, G; Sivolella, S; Meneghello, R; Ferroni, L; Gardin, C; Piattelli, A; Zavan, B; Bressan, E

    2016-01-01

    Bone tissue engineered 3-D constructs customized to patient-specific needs are emerging as attractive biomimetic scaffolds to enhance bone cell and tissue growth and differentiation. The article outlines the features of the most common additive manufacturing technologies (3D printing, stereolithography, fused deposition modeling, and selective laser sintering) used to fabricate bone tissue engineering scaffolds. It concentrates, in particular, on the current state of knowledge concerning powder-based 3D printing, including a description of the properties of powders and binder solutions, the critical phases of scaffold manufacturing, and its applications in bone tissue engineering. Clinical aspects and future applications are also discussed. PMID:27086202

  8. Self assembled structures for 3D integration

    NASA Astrophysics Data System (ADS)

    Rao, Madhav

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

  9. Programmed synthesis of 3D tissues

    PubMed Central

    Todhunter, Michael E; Jee, Noel Y; Hughes, Alex J; Coyle, Maxwell C; Cerchiari, Alec; Farlow, Justin; Garbe, James C; LaBarge, Mark A; Desai, Tejal A; Gartner, Zev J

    2015-01-01

    Reconstituting tissues from their cellular building blocks facilitates the modeling of morphogenesis, homeostasis, and disease in vitro. Here, we describe DNA Programmed Assembly of Cells (DPAC) to reconstitute the multicellular organization of tissues having programmed size, shape, composition, and spatial heterogeneity. DPAC uses dissociated cells that are chemically functionalized with degradable oligonucleotide “velcro,” allowing rapid, specific, and reversible cell adhesion to other surfaces coated with complementary DNA sequences. DNA-patterned substrates function as removable and adhesive templates, and layer-by-layer DNA-programmed assembly builds arrays of tissues into the third dimension above the template. DNase releases completed arrays of microtissues from the template concomitant with full embedding in a variety of extracellular matrix (ECM) gels. DPAC positions subpopulations of cells with single-cell spatial resolution and generates cultures several centimeters long. We used DPAC to explore the impact of ECM composition, heterotypic cell-cell interactions, and patterns of signaling heterogeneity on collective cell behaviors. PMID:26322836

  10. Alginate/nanohydroxyapatite scaffolds with designed core/shell structures fabricated by 3D plotting and in situ mineralization for bone tissue engineering.

    PubMed

    Luo, Yongxiang; Lode, Anja; Wu, Chengtie; Chang, Jiang; Gelinsky, Michael

    2015-04-01

    Composite scaffolds, especially polymer/hydroxyapatite (HAP) composite scaffolds with predesigned structures, are promising materials for bone tissue engineering. Various methods including direct mixing of HAP powder with polymers or incubating polymer scaffolds in simulated body fluid for preparing polymer/HAP composite scaffolds are either uncontrolled or require long times of incubation. In this work, alginate/nano-HAP composite scaffolds with designed pore parameters and core/shell structures were fabricated using 3D plotting technique and in situ mineralization under mild conditions (at room temperature and without the use of any organic solvents). Light microscopy, scanning electron microscopy, microcomputer tomography, X-ray diffraction, and Fourier transform infrared spectroscopy were applied to characterize the fabricated scaffolds. Mechanical properties and protein delivery of the scaffolds were evaluated, as well as the cell response to the scaffolds by culturing human bone-marrow-derived mesenchymal stem cells (hBMSC). The obtained data indicate that this method is suitable to fabricate alginate/nano-HAP composite scaffolds with a layer of nano-HAP, coating the surface of the alginate strands homogeneously and completely. The surface mineralization enhanced the mechanical properties and improved the cell attachment and spreading, as well as supported sustaining protein release, compared to pure alginate scaffolds without nano-HAP shell layer. The results demonstrated that the method provides an interesting option for bone tissue engineering application.

  11. 3D printing of functional biomaterials for tissue engineering.

    PubMed

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

    2016-08-01

    3D printing is emerging as a powerful tool for tissue engineering by enabling 3D cell culture within complex 3D biomimetic architectures. This review discusses the prevailing 3D printing techniques and their most recent applications in building tissue constructs. The work associated with relatively well-known inkjet and extrusion-based bioprinting is presented with the latest advances in the fields. Emphasis is put on introducing two relatively new light-assisted bioprinting techniques, including digital light processing (DLP)-based bioprinting and laser based two photon polymerization (TPP) bioprinting. 3D bioprinting of vasculature network is particularly discussed for its foremost significance in maintaining tissue viability and promoting functional maturation. Limitations to current bioprinting approaches, as well as future directions of bioprinting functional tissues are also discussed. PMID:27043763

  12. Structured light field 3D imaging.

    PubMed

    Cai, Zewei; Liu, Xiaoli; Peng, Xiang; Yin, Yongkai; Li, Ameng; Wu, Jiachen; Gao, Bruce Z

    2016-09-01

    In this paper, we propose a method by means of light field imaging under structured illumination to deal with high dynamic range 3D imaging. Fringe patterns are projected onto a scene and modulated by the scene depth then a structured light field is detected using light field recording devices. The structured light field contains information about ray direction and phase-encoded depth, via which the scene depth can be estimated from different directions. The multidirectional depth estimation can achieve high dynamic 3D imaging effectively. We analyzed and derived the phase-depth mapping in the structured light field and then proposed a flexible ray-based calibration approach to determine the independent mapping coefficients for each ray. Experimental results demonstrated the validity of the proposed method to perform high-quality 3D imaging for highly and lowly reflective surfaces. PMID:27607639

  13. Generation of 3D synthetic breast tissue

    NASA Astrophysics Data System (ADS)

    Elangovan, Premkumar; Dance, David R.; Young, Kenneth C.; Wells, Kevin

    2016-03-01

    Virtual clinical trials are an emergent approach for the rapid evaluation and comparison of various breast imaging technologies and techniques using computer-based modeling tools. A fundamental requirement of this approach for mammography is the use of realistic looking breast anatomy in the studies to produce clinically relevant results. In this work, a biologically inspired approach has been used to simulate realistic synthetic breast phantom blocks for use in virtual clinical trials. A variety of high and low frequency features (including Cooper's ligaments, blood vessels and glandular tissue) have been extracted from clinical digital breast tomosynthesis images and used to simulate synthetic breast blocks. The appearance of the phantom blocks was validated by presenting a selection of simulated 2D and DBT images interleaved with real images to a team of experienced readers for rating using an ROC paradigm. The average areas under the curve for 2D and DBT images were 0.53+/-.04 and 0.55+/-.07 respectively; errors are the standard errors of the mean. The values indicate that the observers had difficulty in differentiating the real images from simulated images. The statistical properties of simulated images of the phantom blocks were evaluated by means of power spectrum analysis. The power spectrum curves for real and simulated images closely match and overlap indicating good agreement.

  14. 3D printing facilitated scaffold-free tissue unit fabrication.

    PubMed

    Tan, Yu; Richards, Dylan J; Trusk, Thomas C; Visconti, Richard P; Yost, Michael J; Kindy, Mark S; Drake, Christopher J; Argraves, William Scott; Markwald, Roger R; Mei, Ying

    2014-06-01

    Tissue spheroids hold great potential in tissue engineering as building blocks to assemble into functional tissues. To date, agarose molds have been extensively used to facilitate fusion process of tissue spheroids. As a molding material, agarose typically requires low temperature plates for gelation and/or heated dispenser units. Here, we proposed and developed an alginate-based, direct 3D mold-printing technology: 3D printing microdroplets of alginate solution into biocompatible, bio-inert alginate hydrogel molds for the fabrication of scaffold-free tissue engineering constructs. Specifically, we developed a 3D printing technology to deposit microdroplets of alginate solution on calcium containing substrates in a layer-by-layer fashion to prepare ring-shaped 3D hydrogel molds. Tissue spheroids composed of 50% endothelial cells and 50% smooth muscle cells were robotically placed into the 3D printed alginate molds using a 3D printer, and were found to rapidly fuse into toroid-shaped tissue units. Histological and immunofluorescence analysis indicated that the cells secreted collagen type I playing a critical role in promoting cell-cell adhesion, tissue formation and maturation.

  15. 3D Printing Facilitated Scaffold-free Tissue Unit Fabrication

    PubMed Central

    Tan, Yu; Richards, Dylan J.; Trusk, Thomas C.; Visconti, Richard P.; Yost, Michael J.; Kindy, Mark S.; Drake, Christopher J.; Argraves, William Scott; Markwald, Roger R.; Mei, Ying

    2014-01-01

    Tissue spheroids hold great potential in tissue engineering as building blocks to assemble into functional tissues. To date, agarose molds have been extensively used to facilitate fusion process of tissue spheroids. As a molding material, agarose typically requires low temperature plates for gelation and/or heated dispenser units. Here, we proposed and developed an alginate-based, direct 3D mold-printing technology: 3D printing micro-droplets of alginate solution into biocompatible, bio-inert alginate hydrogel molds for the fabrication of scaffold-free tissue engineering constructs. Specifically, we developed a 3D printing technology to deposit micro-droplets of alginate solution on calcium containing substrates in a layer-by-layer fashion to prepare ring-shaped 3D hydrogel molds. Tissue spheroids composed of 50% endothelial cells and 50% smooth muscle cells were robotically placed into the 3D printed alginate molds using a 3D printer, and were found to rapidly fuse into toroid-shaped tissue units. Histological and immunofluorescence analysis indicated that the cells secreted collagen type I playing a critical role in promoting cell-cell adhesion, tissue formation and maturation. PMID:24717646

  16. 3D conductive nanocomposite scaffold for bone tissue engineering

    PubMed Central

    Shahini, Aref; Yazdimamaghani, Mostafa; Walker, Kenneth J; Eastman, Margaret A; Hatami-Marbini, Hamed; Smith, Brenda J; Ricci, John L; Madihally, Sundar V; Vashaee, Daryoosh; Tayebi, Lobat

    2014-01-01

    Bone healing can be significantly expedited by applying electrical stimuli in the injured region. Therefore, a three-dimensional (3D) ceramic conductive tissue engineering scaffold for large bone defects that can locally deliver the electrical stimuli is highly desired. In the present study, 3D conductive scaffolds were prepared by employing a biocompatible conductive polymer, ie, poly(3,4-ethylenedioxythiophene) poly(4-styrene sulfonate) (PEDOT:PSS), in the optimized nanocomposite of gelatin and bioactive glass. For in vitro analysis, adult human mesenchymal stem cells were seeded in the scaffolds. Material characterizations using hydrogen-1 nuclear magnetic resonance, in vitro degradation, as well as thermal and mechanical analysis showed that incorporation of PEDOT:PSS increased the physiochemical stability of the composite, resulting in improved mechanical properties and biodegradation resistance. The outcomes indicate that PEDOT:PSS and polypeptide chains have close interaction, most likely by forming salt bridges between arginine side chains and sulfonate groups. The morphology of the scaffolds and cultured human mesenchymal stem cells were observed and analyzed via scanning electron microscope, micro-computed tomography, and confocal fluorescent microscope. Increasing the concentration of the conductive polymer in the scaffold enhanced the cell viability, indicating the improved microstructure of the scaffolds or boosted electrical signaling among cells. These results show that these conductive scaffolds are not only structurally more favorable for bone tissue engineering, but also can be a step forward in combining the tissue engineering techniques with the method of enhancing the bone healing by electrical stimuli. PMID:24399874

  17. 3D Printing of Scaffolds for Tissue Regeneration Applications

    PubMed Central

    Do, Anh-Vu; Khorsand, Behnoush; Geary, Sean M.; Salem, Aliasger K.

    2015-01-01

    The current need for organ and tissue replacement, repair and regeneration for patients is continually growing such that supply is not meeting the high demand primarily due to a paucity of donors as well as biocompatibility issues that lead to immune rejection of the transplant. In an effort to overcome these drawbacks, scientists working in the field of tissue engineering and regenerative medicine have investigated the use of scaffolds as an alternative to transplantation. These scaffolds are designed to mimic the extracellular matrix (ECM) by providing structural support as well as promoting attachment, proliferation, and differentiation with the ultimate goal of yielding functional tissues or organs. Initial attempts at developing scaffolds were problematic and subsequently inspired a growing interest in 3D printing as a mode for generating scaffolds. Utilizing three-dimensional printing (3DP) technologies, ECM-like scaffolds can be produced with a high degree of complexity and precision, where fine details can be included at a micron level. In this review, we discuss the criteria for printing viable and functional scaffolds, scaffolding materials, and 3DP technologies used to print scaffolds for tissue engineering. A hybrid approach, employing both natural and synthetic materials, as well as multiple printing processes may be the key to yielding an ECM-like scaffold with high mechanical strength, porosity, interconnectivity, biocompatibility, biodegradability, and high processability. Creating such biofunctional scaffolds could potentially help to meet the demand by patients for tissues and organs without having to wait or rely on donors for transplantation. PMID:26097108

  18. Long-Term Cultures of Human Cornea Limbal Explants Form 3D Structures Ex Vivo - Implications for Tissue Engineering and Clinical Applications.

    PubMed

    Szabó, Dóra Júlia; Noer, Agate; Nagymihály, Richárd; Josifovska, Natasha; Andjelic, Sofija; Veréb, Zoltán; Facskó, Andrea; Moe, Morten C; Petrovski, Goran

    2015-01-01

    Long-term cultures of cornea limbal epithelial stem cells (LESCs) were developed and characterized for future tissue engineering and clinical applications. The limbal tissue explants were cultivated and expanded for more than 3 months in medium containing serum as the only growth supplement and without use of scaffolds. Viable 3D cell outgrowth from the explants was observed within 4 weeks of cultivation. The outgrowing cells were examined by immunofluorescent staining for putative markers of stemness (ABCG2, CK15, CK19 and Vimentin), proliferation (p63α, Ki-67), limbal basal epithelial cells (CK8/18) and differentiated cornea epithelial cells (CK3 and CK12). Morphological and immunostaining analyses revealed that long-term culturing can form stratified 3D tissue layers with a clear extracellular matrix deposition and organization (collagen I, IV and V). The LESCs showed robust expression of p63α, ABCG2, and their surface marker fingerprint (CD117/c-kit, CXCR4, CD146/MCAM, CD166/ALCAM) changed over time compared to short-term LESC cultures. Overall, we provide a model for generating stem cell-rich, long-standing 3D cultures from LESCs which can be used for further research purposes and clinical transplantation.

  19. Long-Term Cultures of Human Cornea Limbal Explants Form 3D Structures Ex Vivo – Implications for Tissue Engineering and Clinical Applications

    PubMed Central

    Nagymihály, Richárd; Josifovska, Natasha; Andjelic, Sofija; Veréb, Zoltán; Facskó, Andrea; Moe, Morten C.; Petrovski, Goran

    2015-01-01

    Long-term cultures of cornea limbal epithelial stem cells (LESCs) were developed and characterized for future tissue engineering and clinical applications. The limbal tissue explants were cultivated and expanded for more than 3 months in medium containing serum as the only growth supplement and without use of scaffolds. Viable 3D cell outgrowth from the explants was observed within 4 weeks of cultivation. The outgrowing cells were examined by immunofluorescent staining for putative markers of stemness (ABCG2, CK15, CK19 and Vimentin), proliferation (p63α, Ki-67), limbal basal epithelial cells (CK8/18) and differentiated cornea epithelial cells (CK3 and CK12). Morphological and immunostaining analyses revealed that long-term culturing can form stratified 3D tissue layers with a clear extracellular matrix deposition and organization (collagen I, IV and V). The LESCs showed robust expression of p63α, ABCG2, and their surface marker fingerprint (CD117/c-kit, CXCR4, CD146/MCAM, CD166/ALCAM) changed over time compared to short-term LESC cultures. Overall, we provide a model for generating stem cell-rich, long-standing 3D cultures from LESCs which can be used for further research purposes and clinical transplantation. PMID:26580800

  20. Long-Term Cultures of Human Cornea Limbal Explants Form 3D Structures Ex Vivo - Implications for Tissue Engineering and Clinical Applications.

    PubMed

    Szabó, Dóra Júlia; Noer, Agate; Nagymihály, Richárd; Josifovska, Natasha; Andjelic, Sofija; Veréb, Zoltán; Facskó, Andrea; Moe, Morten C; Petrovski, Goran

    2015-01-01

    Long-term cultures of cornea limbal epithelial stem cells (LESCs) were developed and characterized for future tissue engineering and clinical applications. The limbal tissue explants were cultivated and expanded for more than 3 months in medium containing serum as the only growth supplement and without use of scaffolds. Viable 3D cell outgrowth from the explants was observed within 4 weeks of cultivation. The outgrowing cells were examined by immunofluorescent staining for putative markers of stemness (ABCG2, CK15, CK19 and Vimentin), proliferation (p63α, Ki-67), limbal basal epithelial cells (CK8/18) and differentiated cornea epithelial cells (CK3 and CK12). Morphological and immunostaining analyses revealed that long-term culturing can form stratified 3D tissue layers with a clear extracellular matrix deposition and organization (collagen I, IV and V). The LESCs showed robust expression of p63α, ABCG2, and their surface marker fingerprint (CD117/c-kit, CXCR4, CD146/MCAM, CD166/ALCAM) changed over time compared to short-term LESC cultures. Overall, we provide a model for generating stem cell-rich, long-standing 3D cultures from LESCs which can be used for further research purposes and clinical transplantation. PMID:26580800

  1. 3D Printing of Scaffolds for Tissue Regeneration Applications.

    PubMed

    Do, Anh-Vu; Khorsand, Behnoush; Geary, Sean M; Salem, Aliasger K

    2015-08-26

    The current need for organ and tissue replacement, repair, and regeneration for patients is continually growing such that supply is not meeting demand primarily due to a paucity of donors as well as biocompatibility issues leading to immune rejection of the transplant. In order to overcome these drawbacks, scientists have investigated the use of scaffolds as an alternative to transplantation. These scaffolds are designed to mimic the extracellular matrix (ECM) by providing structural support as well as promoting attachment, proliferation, and differentiation with the ultimate goal of yielding functional tissues or organs. Initial attempts at developing scaffolds were problematic and subsequently inspired an interest in 3D printing as a mode for generating scaffolds. Utilizing three-dimensional printing (3DP) technologies, ECM-like scaffolds can be produced with a high degree of complexity, where fine details can be included at a micrometer level. In this Review, the criteria for printing viable and functional scaffolds, scaffolding materials, and 3DP technologies used to print scaffolds for tissue engineering are discussed. Creating biofunctional scaffolds could potentially help to meet the demand by patients for tissues and organs without having to wait or rely on donors for transplantation. PMID:26097108

  2. 3D Printing of Scaffolds for Tissue Regeneration Applications.

    PubMed

    Do, Anh-Vu; Khorsand, Behnoush; Geary, Sean M; Salem, Aliasger K

    2015-08-26

    The current need for organ and tissue replacement, repair, and regeneration for patients is continually growing such that supply is not meeting demand primarily due to a paucity of donors as well as biocompatibility issues leading to immune rejection of the transplant. In order to overcome these drawbacks, scientists have investigated the use of scaffolds as an alternative to transplantation. These scaffolds are designed to mimic the extracellular matrix (ECM) by providing structural support as well as promoting attachment, proliferation, and differentiation with the ultimate goal of yielding functional tissues or organs. Initial attempts at developing scaffolds were problematic and subsequently inspired an interest in 3D printing as a mode for generating scaffolds. Utilizing three-dimensional printing (3DP) technologies, ECM-like scaffolds can be produced with a high degree of complexity, where fine details can be included at a micrometer level. In this Review, the criteria for printing viable and functional scaffolds, scaffolding materials, and 3DP technologies used to print scaffolds for tissue engineering are discussed. Creating biofunctional scaffolds could potentially help to meet the demand by patients for tissues and organs without having to wait or rely on donors for transplantation.

  3. 3D structure and nuclear targets

    NASA Astrophysics Data System (ADS)

    Dupré, Raphaël; Scopetta, Sergio

    2016-06-01

    Recent experimental and theoretical ideas are laying the ground for a new era in the knowledge of the parton structure of nuclei. We report on two promising directions beyond inclusive deep inelastic scattering experiments, aimed at, among other goals, unveiling the three-dimensional structure of the bound nucleon. The 3D structure in coordinate space can be accessed through deep exclusive processes, whose non-perturbative content is parametrized in terms of generalized parton distributions. In this way the distribution of partons in the transverse plane will be obtained, providing a pictorial view of the realization of the European Muon Collaboration effect. In particular, we show how, through the generalized parton distribution framework, non-nucleonic degrees of freedom in nuclei can be unveiled. Analogously, the momentum space 3D structure can be accessed by studying transverse-momentum-dependent parton distributions in semi-inclusive deep inelastic scattering processes. The status of measurements is also summarized, in particular novel coincidence measurements at high-luminosity facilities, such as Jefferson Laboratory. Finally the prospects for the next years at future facilities, such as the 12GeV Jefferson Laboratory and the Electron Ion Collider, are presented.

  4. Motif3D: Relating protein sequence motifs to 3D structure.

    PubMed

    Gaulton, Anna; Attwood, Teresa K

    2003-07-01

    Motif3D is a web-based protein structure viewer designed to allow sequence motifs, and in particular those contained in the fingerprints of the PRINTS database, to be visualised on three-dimensional (3D) structures. Additional functionality is provided for the rhodopsin-like G protein-coupled receptors, enabling fingerprint motifs of any of the receptors in this family to be mapped onto the single structure available, that of bovine rhodopsin. Motif3D can be used via the web interface available at: http://www.bioinf.man.ac.uk/dbbrowser/motif3d/motif3d.html.

  5. Discovering Structural Regularity in 3D Geometry

    PubMed Central

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

    2010-01-01

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

  6. 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.

  7. Perfused Multiwell Plate for 3D Liver Tissue Engineering

    PubMed Central

    Domansky, Karel; Inman, Walker; Serdy, James; Dash, Ajit; Lim, Matthew H. M.

    2014-01-01

    In vitro models that capture the complexity of in vivo tissue and organ behaviors in a scalable and easy-to-use format are desirable for drug discovery. To address this, we have developed a bioreactor that fosters maintenance of 3D tissue cultures under constant perfusion and we have integrated multiple bioreactors into an array in a multiwell plate format. All bioreactors are fluidically isolated from each other. Each bioreactor in the array contains a scaffold that supports formation of hundreds of 3D microscale tissue units. The tissue units are perfused with cell culture medium circulated within the bioreactor by integrated pneumatic diaphragm micropumps. Electronic controls for the pumps are kept outside the incubator and connected to the perfused multiwell by pneumatic lines. The docking design and open-well bioreactor layout make handling perfused multiwell plates similar to using standard multiwell tissue culture plates. A model of oxygen consumption and transport in the circulating culture medium was used to predict appropriate operating parameters for primary liver cultures. Oxygen concentrations at key locations in the system were then measured as a function of flow rate and time after initiation of culture to determine oxygen consumption rates. After seven days in culture, tissue formed from cells seeded in the perfused multiwell reactor remained functionally viable as assessed by immunostaining for hepatocyte and liver sinusoidal endothelial cell (LSEC) phenotypic markers. PMID:20024050

  8. 3D Bioprinting Human Chondrocytes with Nanocellulose-Alginate Bioink for Cartilage Tissue Engineering Applications.

    PubMed

    Markstedt, Kajsa; Mantas, Athanasios; Tournier, Ivan; Martínez Ávila, Héctor; Hägg, Daniel; Gatenholm, Paul

    2015-05-11

    The introduction of 3D bioprinting is expected to revolutionize the field of tissue engineering and regenerative medicine. The 3D bioprinter is able to dispense materials while moving in X, Y, and Z directions, which enables the engineering of complex structures from the bottom up. In this study, a bioink that combines the outstanding shear thinning properties of nanofibrillated cellulose (NFC) with the fast cross-linking ability of alginate was formulated for the 3D bioprinting of living soft tissue with cells. Printability was evaluated with concern to printer parameters and shape fidelity. The shear thinning behavior of the tested bioinks enabled printing of both 2D gridlike structures as well as 3D constructs. Furthermore, anatomically shaped cartilage structures, such as a human ear and sheep meniscus, were 3D printed using MRI and CT images as blueprints. Human chondrocytes bioprinted in the noncytotoxic, nanocellulose-based bioink exhibited a cell viability of 73% and 86% after 1 and 7 days of 3D culture, respectively. On the basis of these results, we can conclude that the nanocellulose-based bioink is a suitable hydrogel for 3D bioprinting with living cells. This study demonstrates the potential use of nanocellulose for 3D bioprinting of living tissues and organs. PMID:25806996

  9. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

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

    2015-07-15

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

  10. 3D printing of nano- and micro-structures

    NASA Astrophysics Data System (ADS)

    Ramasamy, Mouli; Varadan, Vijay K.

    2016-04-01

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

  11. 3D Structure of Tillage Soils

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  12. STAR3D: a stack-based RNA 3D structural alignment tool

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

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

    PubMed Central

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

    2015-01-01

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

  14. Dual multispectral and 3D structured light laparoscope

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  15. Synthesis of highly interconnected 3D scaffold from Arothron stellatus skin collagen for tissue engineering application.

    PubMed

    Ramanathan, Giriprasath; Singaravelu, Sivakumar; Raja, M D; Sivagnanam, Uma Tiruchirapalli

    2015-11-01

    The substrate which is avidly used for tissue engineering applications should have good mechanical and biocompatible properties, and all these parameters are often considered as essential for dermal reformation. Highly interconnected three dimensional (3D) wound dressing material with enhanced structural integrity was synthesized from Arothron stellatus fish skin (AsFS) collagen for tissue engineering applications. The synthesized 3D collagen sponge (COL-SPG) was further characterized by different physicochemical methods. The scanning electron microscopy analysis of the material demonstrated that well interconnected pores with homogeneous microstructure on the surface aids higher swelling index and that the material also possessed good mechanical properties with a Young's modulus of 0.89±0.2 MPa. Biocompatibility of the 3D COL-SPG showed 92% growth for both NIH 3T3 fibroblasts and keratinocytes. Overall, the study revealed that synthesized 3D COL-SPG from fish skin will act as a promising wound dressing in skin tissue engineering.

  16. 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/.

  17. 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

  18. Design of 3d Topological Data Structure for 3d Cadastre Objects

    NASA Astrophysics Data System (ADS)

    Zulkifli, N. A.; Rahman, A. Abdul; Hassan, M. I.

    2016-09-01

    This paper describes the design of 3D modelling and topological data structure for cadastre objects based on Land Administration Domain Model (LADM) specifications. Tetrahedral Network (TEN) is selected as a 3D topological data structure for this project. Data modelling is based on the LADM standard and it is used five classes (i.e. point, boundary face string, boundary face, tetrahedron and spatial unit). This research aims to enhance the current cadastral system by incorporating 3D topology model based on LADM standard.

  19. Electroactive 3D materials for cardiac tissue engineering

    NASA Astrophysics Data System (ADS)

    Gelmi, Amy; Zhang, Jiabin; Cieslar-Pobuda, Artur; Ljunngren, Monika K.; Los, Marek Jan; Rafat, Mehrdad; Jager, Edwin W. H.

    2015-04-01

    By-pass surgery and heart transplantation are traditionally used to restore the heart's functionality after a myocardial Infarction (MI or heart attack) that results in scar tissue formation and impaired cardiac function. However, both procedures are associated with serious post-surgical complications. Therefore, new strategies to help re-establish heart functionality are necessary. Tissue engineering and stem cell therapy are the promising approaches that are being explored for the treatment of MI. The stem cell niche is extremely important for the proliferation and differentiation of stem cells and tissue regeneration. For the introduction of stem cells into the host tissue an artificial carrier such as a scaffold is preferred as direct injection of stem cells has resulted in fast stem cell death. Such scaffold will provide the proper microenvironment that can be altered electronically to provide temporal stimulation to the cells. We have developed an electroactive polymer (EAP) scaffold for cardiac tissue engineering. The EAP scaffold mimics the extracellular matrix and provides a 3D microenvironment that can be easily tuned during fabrication, such as controllable fibre dimensions, alignment, and coating. In addition, the scaffold can provide electrical and electromechanical stimulation to the stem cells which are important external stimuli to stem cell differentiation. We tested the initial biocompatibility of these scaffolds using cardiac progenitor cells (CPCs), and continued onto more sensitive induced pluripotent stem cells (iPS). We present the fabrication and characterisation of these electroactive fibres as well as the response of increasingly sensitive cell types to the scaffolds.

  20. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

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

    2015-07-15

    X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations. PMID:26172844

  1. 3D bioprinting of vascularized, heterogeneous cell-laden tissue constructs.

    PubMed

    Kolesky, David B; Truby, Ryan L; Gladman, A Sydney; Busbee, Travis A; Homan, Kimberly A; Lewis, Jennifer A

    2014-05-21

    A new bioprinting method is reported for fabricating 3D tissue constructs replete with vasculature, multiple types of cells, and extracellular matrix. These intricate, heterogeneous structures are created by precisely co-printing multiple materials, known as bioinks, in three dimensions. These 3D micro-engineered environments open new -avenues for drug screening and fundamental studies of wound healing, angiogenesis, and stem-cell niches.

  2. AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures

    PubMed Central

    Zambrano, Rafael; Jamroz, Michal; Szczasiuk, Agata; Pujols, Jordi; Kmiecik, Sebastian; Ventura, Salvador

    2015-01-01

    Protein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series of predictive algorithms to identify aggregation-prone sites. A majority of these methods rely only on sequence. Therefore, they find difficulties to predict the aggregation properties of folded globular proteins, where aggregation-prone sites are often not contiguous in sequence or buried inside the native structure. The AGGRESCAN3D (A3D) server overcomes these limitations by taking into account the protein structure and the experimental aggregation propensity scale from the well-established AGGRESCAN method. Using the A3D server, the identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. Additionally, A3D server enables to take into account the dynamic fluctuations of protein structure in solution, which may influence aggregation propensity. This is possible in A3D Dynamic Mode that exploits the CABS-flex approach for the fast simulations of flexibility of globular proteins. The A3D server can be accessed at http://biocomp.chem.uw.edu.pl/A3D/. PMID:25883144

  3. 3D visualization of middle ear structures

    NASA Astrophysics Data System (ADS)

    Vogel, Uwe; Schmitt, Thomas

    1998-06-01

    The achievement of volume geometry data from middle ear structures and surrounding components performs a necessary supposition for the finite element simulation of the vibrational and transfer characteristics of the ossicular chain. So far those models base on generalized figures and size data from anatomy textbooks or particular manual and one- or two-dimensional distance measurements of single ossicles, mostly obtained by light microscopy, respectively. Therefore the goal of this study is to create a procedure for complete three-dimensional imaging of real middle ear structures (tympanic membrane, ossicles, ligaments) in vitro or even in vivo. The main problems are their microscopic size with relevant structures from 10 micrometer to 5 mm, representing various tissue properties (bone, soft tissue). Additionally, these structures are surrounded by the temporal bone, the most solid bone of the human body. Generally there exist several established diagnostic tools for medical imaging that could be used for geometry data acquisition, e.g., X-ray computed tomography and magnetic resonance imaging. Basically they image different tissue parameters, either bony structures (ossicles), or soft tissue (tympanic membrane, ligaments). But considering this application those standard techniques allow low spatial resolution only, usually in the 0.5 - 1mm range, at least in one spatial direction. Thus particular structures of the middle ear region could even be missed completely because of their spatial location. In vitro there is a way out by collecting three complete data sets, each distinguished by 90 degree rotation of a cube-shaped temporal bone specimen. That allows high-resolution imaging in three orthogonal planes, which essentially supports the three-dimensional interpolation of the unknown elements, starting from the regularly set elements of the cubic grid with an edge extension given by the original two-dimensional matrix. A different approach represents the

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  5. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

    PubMed Central

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

    2010-01-01

    Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913

  6. Development of a 3D cell printed construct considering angiogenesis for liver tissue engineering.

    PubMed

    Lee, Jin Woo; Choi, Yeong-Jin; Yong, Woon-Jae; Pati, Falguni; Shim, Jin-Hyung; Kang, Kyung Shin; Kang, In-Hye; Park, Jaesung; Cho, Dong-Woo

    2016-03-01

    Several studies have focused on the regeneration of liver tissue in a two-dimensional (2D) planar environment, whereas actual liver tissue is three-dimensional (3D). Cell printing technology has been successfully utilized for building 3D structures; however, the poor mechanical properties of cell-laden hydrogels are a major concern. Here, we demonstrate the printing of a 3D cell-laden construct and its application to liver tissue engineering using 3D cell printing technology through a multi-head tissue/organ building system. Polycaprolactone (PCL) was used as a framework material because of its excellent mechanical properties. Collagen bioink containing three different types of cells-hepatocytes (HCs), human umbilical vein endothelial cells , and human lung fibroblasts--was infused into the canals of a PCL framework to induce the formation of capillary--like networks and liver cell growth. A co-cultured 3D microenvironment of the three types of cells was successfully established and maintained. The vascular formation and functional abilities of HCs (i.e., albumin secretion and urea synthesis) demonstrated that the heterotypic interaction among HCs and nonparenchymal cells increased the survivability and functionality of HCs within the collagen gel. Therefore, our results demonstrate the prospect of using cell printing technology for the creation of heterotypic cellular interaction within a structure for liver tissue engineering.

  7. Superelastic, superabsorbent and 3D nanofiber-assembled scaffold for tissue engineering.

    PubMed

    Chen, Weiming; Ma, Jun; Zhu, Lei; Morsi, Yosry; Ei-Hamshary, Hany; Al-Deyab, Salem S; Mo, Xiumei

    2016-06-01

    Fabrication of 3D scaffold to mimic the nanofibrous structure of the nature extracellular matrix (ECM) with appropriate mechanical properties and excellent biocompatibility, remain an important technical challenge in tissue engineering. The present study reports the strategy to fabricate a 3D nanofibrous scaffold with similar structure to collagen in ECM by combining electrospinning and freeze-drying technique. With the technique reported here, a nanofibrous structure scaffold with hydrophilic and superabsorbent properties can be readily prepared by Gelatin and Polylactic acid (PLA). In wet state the scaffold also shows a super-elastic property, which could bear a compressive strain as high as 80% and recovers its original shape afterwards. Moreover, after 6 days of culture, L-929 cells grow, proliferate and infiltrated into the scaffold. The results suggest that this 3D nanofibrous scaffold would be promising for varied field of tissue engineering application.

  8. 3D imaging in CUBIC-cleared mouse heart tissue: going deeper

    PubMed Central

    Nehrhoff, Imke; Bocancea, Diana; Vaquero, Javier; Vaquero, Juan José; Ripoll, Jorge; Desco, Manuel; Gómez-Gaviro, María Victoria

    2016-01-01

    The ability to acquire high resolution 3D images of the heart enables to study heart diseases more in detail. In this work, the CUBIC (clear, unobstructed brain imaging cocktails and computational analysis) clearing protocol was optimized for thick mouse heart sections to enhance the penetration depth of the confocal microscope lasers into the tissue. In addition, the optimized CUBIC clearing of the heart enhances antibody penetration into the tissue by a factor of five. The present protocol enables deep 3D high-quality image acquisition in the heart allowing a much more accurate assessment of the cellular and structural changes that underlie heart diseases. PMID:27699132

  9. 3D imaging in CUBIC-cleared mouse heart tissue: going deeper

    PubMed Central

    Nehrhoff, Imke; Bocancea, Diana; Vaquero, Javier; Vaquero, Juan José; Ripoll, Jorge; Desco, Manuel; Gómez-Gaviro, María Victoria

    2016-01-01

    The ability to acquire high resolution 3D images of the heart enables to study heart diseases more in detail. In this work, the CUBIC (clear, unobstructed brain imaging cocktails and computational analysis) clearing protocol was optimized for thick mouse heart sections to enhance the penetration depth of the confocal microscope lasers into the tissue. In addition, the optimized CUBIC clearing of the heart enhances antibody penetration into the tissue by a factor of five. The present protocol enables deep 3D high-quality image acquisition in the heart allowing a much more accurate assessment of the cellular and structural changes that underlie heart diseases.

  10. Superabsorbent 3D Scaffold Based on Electrospun Nanofibers for Cartilage Tissue Engineering.

    PubMed

    Chen, Weiming; Chen, Shuai; Morsi, Yosry; El-Hamshary, Hany; El-Newhy, Mohamed; Fan, Cunyi; Mo, Xiumei

    2016-09-21

    Electrospun nanofibers have been used for various biomedical applications. However, electrospinning commonly produces two-dimensional (2D) membranes, which limits the application of nanofibers for the 3D tissue engineering scaffold. In the present study, a porous 3D scaffold (3DS-1) based on electrospun gelatin/PLA nanofibers has been prepared for cartilage tissue regeneration. To further improve the repairing effect of cartilage, a modified scaffold (3DS-2) cross-linked with hyaluronic acid (HA) was also successfully fabricated. The nanofibrous structure, water absorption, and compressive mechanical properties of 3D scaffold were studied. Chondrocytes were cultured on 3D scaffold, and their viability and morphology were examined. 3D scaffolds were also subjected to an in vivo cartilage regeneration study on rabbits using an articular cartilage injury model. The results indicated that 3DS-1 and 3DS-2 exhibited superabsorbent property and excellent cytocompatibility. Both these scaffolds present elastic property in the wet state. An in vivo study showed that 3DS-2 could enhance the repair of cartilage. The present 3D nanofibrous scaffold (3DS-2) would be promising for cartilage tissue engineering application. PMID:27559926

  11. Superabsorbent 3D Scaffold Based on Electrospun Nanofibers for Cartilage Tissue Engineering.

    PubMed

    Chen, Weiming; Chen, Shuai; Morsi, Yosry; El-Hamshary, Hany; El-Newhy, Mohamed; Fan, Cunyi; Mo, Xiumei

    2016-09-21

    Electrospun nanofibers have been used for various biomedical applications. However, electrospinning commonly produces two-dimensional (2D) membranes, which limits the application of nanofibers for the 3D tissue engineering scaffold. In the present study, a porous 3D scaffold (3DS-1) based on electrospun gelatin/PLA nanofibers has been prepared for cartilage tissue regeneration. To further improve the repairing effect of cartilage, a modified scaffold (3DS-2) cross-linked with hyaluronic acid (HA) was also successfully fabricated. The nanofibrous structure, water absorption, and compressive mechanical properties of 3D scaffold were studied. Chondrocytes were cultured on 3D scaffold, and their viability and morphology were examined. 3D scaffolds were also subjected to an in vivo cartilage regeneration study on rabbits using an articular cartilage injury model. The results indicated that 3DS-1 and 3DS-2 exhibited superabsorbent property and excellent cytocompatibility. Both these scaffolds present elastic property in the wet state. An in vivo study showed that 3DS-2 could enhance the repair of cartilage. The present 3D nanofibrous scaffold (3DS-2) would be promising for cartilage tissue engineering application.

  12. 3D-Printed ABS and PLA Scaffolds for Cartilage and Nucleus Pulposus Tissue Regeneration.

    PubMed

    Rosenzweig, Derek H; Carelli, Eric; Steffen, Thomas; Jarzem, Peter; Haglund, Lisbet

    2015-07-03

    Painful degeneration of soft tissues accounts for high socioeconomic costs. Tissue engineering aims to provide biomimetics recapitulating native tissues. Biocompatible thermoplastics for 3D printing can generate high-resolution structures resembling tissue extracellular matrix. Large-pore 3D-printed acrylonitrile butadiene styrene (ABS) and polylactic acid (PLA) scaffolds were compared for cell ingrowth, viability, and tissue generation. Primary articular chondrocytes and nucleus pulposus (NP) cells were cultured on ABS and PLA scaffolds for three weeks. Both cell types proliferated well, showed high viability, and produced ample amounts of proteoglycan and collagen type II on both scaffolds. NP generated more matrix than chondrocytes; however, no difference was observed between scaffold types. Mechanical testing revealed sustained scaffold stability. This study demonstrates that chondrocytes and NP cells can proliferate on both ABS and PLA scaffolds printed with a simplistic, inexpensive desktop 3D printer. Moreover, NP cells produced more proteoglycan than chondrocytes, irrespective of thermoplastic type, indicating that cells maintain individual phenotype over the three-week culture period. Future scaffold designs covering larger pore sizes and better mimicking native tissue structure combined with more flexible or resorbable materials may provide implantable constructs with the proper structure, function, and cellularity necessary for potential cartilage and disc tissue repair in vivo.

  13. 3D-Printed ABS and PLA Scaffolds for Cartilage and Nucleus Pulposus Tissue Regeneration

    PubMed Central

    Rosenzweig, Derek H.; Carelli, Eric; Steffen, Thomas; Jarzem, Peter; Haglund, Lisbet

    2015-01-01

    Painful degeneration of soft tissues accounts for high socioeconomic costs. Tissue engineering aims to provide biomimetics recapitulating native tissues. Biocompatible thermoplastics for 3D printing can generate high-resolution structures resembling tissue extracellular matrix. Large-pore 3D-printed acrylonitrile butadiene styrene (ABS) and polylactic acid (PLA) scaffolds were compared for cell ingrowth, viability, and tissue generation. Primary articular chondrocytes and nucleus pulposus (NP) cells were cultured on ABS and PLA scaffolds for three weeks. Both cell types proliferated well, showed high viability, and produced ample amounts of proteoglycan and collagen type II on both scaffolds. NP generated more matrix than chondrocytes; however, no difference was observed between scaffold types. Mechanical testing revealed sustained scaffold stability. This study demonstrates that chondrocytes and NP cells can proliferate on both ABS and PLA scaffolds printed with a simplistic, inexpensive desktop 3D printer. Moreover, NP cells produced more proteoglycan than chondrocytes, irrespective of thermoplastic type, indicating that cells maintain individual phenotype over the three-week culture period. Future scaffold designs covering larger pore sizes and better mimicking native tissue structure combined with more flexible or resorbable materials may provide implantable constructs with the proper structure, function, and cellularity necessary for potential cartilage and disc tissue repair in vivo. PMID:26151846

  14. 3D printing of tissue-simulating phantoms as a traceable standard for biomedical optical measurement

    NASA Astrophysics Data System (ADS)

    Dong, Erbao; Wang, Minjie; Shen, Shuwei; Han, Yilin; Wu, Qiang; Xu, Ronald

    2016-01-01

    Optical phantoms are commonly used to validate and calibrate biomedical optical devices in order to ensure accurate measurement of optical properties in biological tissue. However, commonly used optical phantoms are based on homogenous materials that reflect neither optical properties nor multi-layer heterogeneities of biological tissue. Using these phantoms for optical calibration may result in significant bias in biological measurement. We propose to characterize and fabricate tissue simulating phantoms that simulate not only the multi-layer heterogeneities but also optical properties of biological tissue. The tissue characterization module detects tissue structural and functional properties in vivo. The phantom printing module generates 3D tissue structures at different scales by layer-by-layer deposition of phantom materials with different optical properties. The ultimate goal is to fabricate multi-layer tissue simulating phantoms as a traceable standard for optimal calibration of biomedical optical spectral devices.

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

    PubMed

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

    2012-01-01

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

  16. Microfabrication of complex porous tissue engineering scaffolds using 3D projection stereolithography

    PubMed Central

    Gauvin, Robert; Chen, Ying-Chieh; Lee, Jin Woo; Soman, Pranav; Zorlutuna, Pinar; Nichol, Jason W.; Bae, Hojae; Chen, Shaochen; Khademhosseini, Ali

    2013-01-01

    The success of tissue engineering will rely on the ability to generate complex, cell seeded three-dimensional (3D) structures. Therefore, methods that can be used to precisely engineer the architecture and topography of scaffolding materials will represent a critical aspect of functional tissue engineering. Previous approaches for 3D scaffold fabrication based on top-down and process driven methods are often not adequate to produce complex structures due to the lack of control on scaffold architecture, porosity, and cellular interactions. The proposed projection stereolithography (PSL) platform can be used to design intricate 3D tissue scaffolds that can be engineered to mimic the microarchitecture of tissues, based on computer aided design (CAD). The PSL system was developed, programmed and optimized to fabricate 3D scaffolds using gelatin methacrylate (GelMA). Variation of the structure and prepolymer concentration enabled tailoring the mechanical properties of the scaffolds. A dynamic cell seeding method was utilized to improve the coverage of the scaffold throughout its thickness. The results demonstrated that the interconnectivity of pores allowed for uniform human umbilical vein endothelial cells (HUVECs) distribution and proliferation in the scaffolds, leading to high cell density and confluency at the end of the culture period. Moreover, immunohistochemistry results showed that cells seeded on the scaffold maintained their endothelial phenotype, demonstrating the biological functionality of the microfabricated GelMA scaffolds. PMID:22365811

  17. Microfabrication of complex porous tissue engineering scaffolds using 3D projection stereolithography.

    PubMed

    Gauvin, Robert; Chen, Ying-Chieh; Lee, Jin Woo; Soman, Pranav; Zorlutuna, Pinar; Nichol, Jason W; Bae, Hojae; Chen, Shaochen; Khademhosseini, Ali

    2012-05-01

    The success of tissue engineering will rely on the ability to generate complex, cell seeded three-dimensional (3D) structures. Therefore, methods that can be used to precisely engineer the architecture and topography of scaffolding materials will represent a critical aspect of functional tissue engineering. Previous approaches for 3D scaffold fabrication based on top-down and process driven methods are often not adequate to produce complex structures due to the lack of control on scaffold architecture, porosity, and cellular interactions. The proposed projection stereolithography (PSL) platform can be used to design intricate 3D tissue scaffolds that can be engineered to mimic the microarchitecture of tissues, based on computer aided design (CAD). The PSL system was developed, programmed and optimized to fabricate 3D scaffolds using gelatin methacrylate (GelMA). Variation of the structure and prepolymer concentration enabled tailoring the mechanical properties of the scaffolds. A dynamic cell seeding method was utilized to improve the coverage of the scaffold throughout its thickness. The results demonstrated that the interconnectivity of pores allowed for uniform human umbilical vein endothelial cells (HUVECs) distribution and proliferation in the scaffolds, leading to high cell density and confluency at the end of the culture period. Moreover, immunohistochemistry results showed that cells seeded on the scaffold maintained their endothelial phenotype, demonstrating the biological functionality of the microfabricated GelMA scaffolds.

  18. 3D printing method for freeform fabrication of optical phantoms simulating heterogeneous biological tissue

    NASA Astrophysics Data System (ADS)

    Wang, Minjie; Shen, Shuwei; Yang, Jie; Dong, Erbao; Xu, Ronald

    2014-03-01

    The performance of biomedical optical imaging devices heavily relies on appropriate calibration. However, many of existing calibration phantoms for biomedical optical devices are based on homogenous materials without considering the multi-layer heterogeneous structures observed in biological tissue. Using such a phantom for optical calibration may result in measurement bias. To overcome this problem, we propose a 3D printing method for freeform fabrication of tissue simulating phantoms with multilayer heterogeneous structure. The phantom simulates not only the morphologic characteristics of biological tissue but also absorption and scattering properties. The printing system is based on a 3D motion platform with coordinated control of the DC motors. A special jet nozzle is designed to mix base, scattering, and absorption materials at different ratios. 3D tissue structures are fabricated through layer-by-layer printing with selective deposition of phantom materials of different ingredients. Different mixed ratios of base, scattering and absorption materials have been tested in order to optimize the printing outcome. A spectrometer and a tissue spectrophotometer are used for characterizing phantom absorption and scattering properties. The goal of this project is to fabricate skin tissue simulating phantoms as a traceable standard for the calibration of biomedical optical spectral devices.

  19. Layer-by-layer assembly of 3D tissue constructs with functionalized graphene

    PubMed Central

    Shin, Su Ryon; Aghaei-Ghareh-Bolagh, Behnaz; Gao, Xiguang; Nikkhah, Mehdi; Jung, Sung Mi; Dolatshahi-Pirouz, Alireza; Kim, Sang Bok; Kim, Sun Min; Dokmeci, Mehmet R.; Tang, Xiaowu (Shirley); Khademhosseini, Ali

    2014-01-01

    Carbon-based nanomaterials have been considered as promising candidates to mimic certain structure and function of native extracellular matrix materials for tissue engineering. Significant progress has been made in fabricating carbon nanoparticle-incorporated cell culture substrates, but limited studies have been reported on the development of three-dimensional (3D) tissue constructs using these nanomaterials. Here, we present a novel approach to engineer 3D multi-layered constructs using layer-by-layer (LbL) assembly of cells separated with self-assembled graphene oxide (GO)-based thin films. The GO-based structures are shown to serve as cell adhesive sheets that effectively facilitate the formation of multi-layer cell constructs with interlayer connectivity. By controlling the amount of GO deposited in forming the thin films, the thickness of the multi-layer tissue constructs could be tuned with high cell viability. Specifically, this approach could be useful for creating dense and tightly connected cardiac tissues through the co-culture of cardiomyocytes and other cell types. In this work, we demonstrated the fabrication of stand-alone multi-layer cardiac tissues with strong spontaneous beating behavior and programmable pumping properties. Therefore, this LbL-based cell construct fabrication approach, utilizing GO thin films formed directly on cell surfaces, has great potential in engineering 3D tissue structures with improved organization, electrophysiological function, and mechanical integrity. PMID:25419209

  20. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

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

  1. Noninvasive metabolic imaging of engineered 3D human adipose tissue in a perfusion bioreactor.

    PubMed

    Ward, Andrew; Quinn, Kyle P; Bellas, Evangelia; Georgakoudi, Irene; Kaplan, David L

    2013-01-01

    The efficacy and economy of most in vitro human models used in research is limited by the lack of a physiologically-relevant three-dimensional perfused environment and the inability to noninvasively quantify the structural and biochemical characteristics of the tissue. The goal of this project was to develop a perfusion bioreactor system compatible with two-photon imaging to noninvasively assess tissue engineered human adipose tissue structure and function in vitro. Three-dimensional (3D) vascularized human adipose tissues were engineered in vitro, before being introduced to a perfusion environment and tracked over time by automated quantification of endogenous markers of metabolism using two-photon excited fluorescence (TPEF). Depth-resolved image stacks were analyzed for redox ratio metabolic profiling and compared to prior analyses performed on 3D engineered adipose tissue in static culture. Traditional assessments with H&E staining were used to qualitatively measure extracellular matrix generation and cell density with respect to location within the tissue. The distribution of cells within the tissue and average cellular redox ratios were different between static and perfusion cultures, while the trends of decreased redox ratio and increased cellular proliferation with time in both static and perfusion cultures were similar. These results establish a basis for noninvasive optical tracking of tissue structure and function in vitro, which can be applied to future studies to assess tissue development or drug toxicity screening and disease progression.

  2. Fabrication of a Layered Microstructured Polycaprolactone Construct for 3-D Tissue Engineering

    PubMed Central

    Sarkar, Sumona; Isenberg, Brett C.; Hodis, Eran; Leach, Jennie B.; Desai, Tejal A.; Wong, Joyce Y.

    2009-01-01

    Successful artificial tissue scaffolds support regeneration by promoting cellular organization as well as appropriate mechanical and biological functionality. We have previously shown in vitro that 2-D substrates with micron-scale grooves (5 μm deep, 18 μm wide, with 12 μm spacing) can induce cell orientation and ECM alignment. Here, we have transferred this microtopography onto biodegradable polycaprolactone (PCL) thin films. We further developed a technique to layer these cellularized microtextured scaffolds into a 3-D tissue construct. A surface modification technique was used to attach photoreactive acrylate groups on the PCL scaffold surface onto which polyethylene glycol (PEG-DA) -diacrylate gel could be photopolymerized. PEG-DA serves as an adhesive layer between PCL scaffolds, resulting in a VSMC-seeded layered 3-D composite structure that is highly organized and structurally stable. The PCL surface modification chemistry was confirmed via XPS, and the maintenance of cell number and orientation on the modified PCL scaffolds was demonstrated using colorometric and imaging techniques. Cell number and orientation were also investigated after cells were cultured in the layered 3-D configuration. Such 3-D tissue mimics fabricated with precise cellular organization will enable the systematic testing of the effects of cellular orientation on the functional and mechanical properties of tissue engineered blood vessels. PMID:18854127

  3. Soft Tissue Stability around Single Implants Inserted to Replace Maxillary Lateral Incisors: A 3D Evaluation

    PubMed Central

    Mangano, F. G.; Picciocchi, G.; Park, K. B.

    2016-01-01

    Purpose. To evaluate the soft tissue stability around single implants inserted to replace maxillary lateral incisors, using an innovative 3D method. Methods. We have used reverse-engineering software for the superimposition of 3D surface models of the dentogingival structures, obtained from intraoral scans of the same patients taken at the delivery of the final crown (S1) and 2 years later (S2). The assessment of soft tissues changes was performed via calculation of the Euclidean surface distances between the 3D models, after the superimposition of S2 on S1; colour maps were used for quantification of changes. Results. Twenty patients (8 males, 12 females) were selected, 10 with a failing/nonrestorable lateral incisor (test group: immediate placement in postextraction socket) and 10 with a missing lateral incisor (control group: conventional placement in healed ridge). Each patient received one immediately loaded implant (Anyridge®, Megagen, Gyeongbuk, South Korea). The superimposition of the 3D surface models taken at different times (S2 over S1) revealed a mean (±SD) reduction of 0.057 mm (±0.025) and 0.037 mm (±0.020) for test and control patients, respectively. This difference was not statistically significant (p = 0.069). Conclusions. The superimposition of the 3D surface models revealed an excellent peri-implant soft tissue stability in both groups of patients, with minimal changes registered along time. PMID:27298621

  4. Soft Tissue Stability around Single Implants Inserted to Replace Maxillary Lateral Incisors: A 3D Evaluation.

    PubMed

    Mangano, F G; Luongo, F; Picciocchi, G; Mortellaro, C; Park, K B; Mangano, C

    2016-01-01

    Purpose. To evaluate the soft tissue stability around single implants inserted to replace maxillary lateral incisors, using an innovative 3D method. Methods. We have used reverse-engineering software for the superimposition of 3D surface models of the dentogingival structures, obtained from intraoral scans of the same patients taken at the delivery of the final crown (S1) and 2 years later (S2). The assessment of soft tissues changes was performed via calculation of the Euclidean surface distances between the 3D models, after the superimposition of S2 on S1; colour maps were used for quantification of changes. Results. Twenty patients (8 males, 12 females) were selected, 10 with a failing/nonrestorable lateral incisor (test group: immediate placement in postextraction socket) and 10 with a missing lateral incisor (control group: conventional placement in healed ridge). Each patient received one immediately loaded implant (Anyridge®, Megagen, Gyeongbuk, South Korea). The superimposition of the 3D surface models taken at different times (S2 over S1) revealed a mean (±SD) reduction of 0.057 mm (±0.025) and 0.037 mm (±0.020) for test and control patients, respectively. This difference was not statistically significant (p = 0.069). Conclusions. The superimposition of the 3D surface models revealed an excellent peri-implant soft tissue stability in both groups of patients, with minimal changes registered along time. PMID:27298621

  5. [Tissue printing; the potential application of 3D printing in medicine].

    PubMed

    Visser, Jetze; Melchels, Ferry P W; Dhert, Wouter J A; Malda, Jos

    2013-01-01

    Complex structures based on a digital blueprint can be created using a 3D printer. As this blueprint can be created using patient imaging data, there are many potential patient-specific applications of 3D printing in medicine. Individually printed metal implants and synthetic devices are currently being used on a limited scale in clinical practice. Researchers in the field of regenerative medicine are now going a step further by printing a combination of cells, growth factors and biomaterials. This process is known as 'bioprinting'. It can be used to copy the complex organization of natural tissue required to repair or replace damaged tissues or organs. The technique needs to be optimized, however, and more knowledge is required regarding the development of printed living constructs into functional tissues before 'tissue from the printer' can be clinically applied. PMID:24382049

  6. Towards the design of 3D multiscale instructive tissue engineering constructs: Current approaches and trends.

    PubMed

    Oliveira, Sara M; Reis, Rui L; Mano, João F

    2015-11-01

    The design of 3D constructs with adequate properties to instruct and guide cells both in vitro and in vivo is one of the major focuses of tissue engineering. Successful tissue regeneration depends on the favorable crosstalk between the supporting structure, the cells and the host tissue so that a balanced matrix production and degradation are achieved. Herein, the major occurring events and players in normal and regenerative tissue are overviewed. These have been inspiring the selection or synthesis of instructive cues to include into the 3D constructs. We further highlight the importance of a multiscale perception of the range of features that can be included on the biomimetic structures. Lastly, we focus on the current and developing tissue-engineering approaches for the preparation of such 3D constructs: top-down, bottom-up and integrative. Bottom-up and integrative approaches present a higher potential for the design of tissue engineering devices with multiscale features and higher biochemical control than top-down strategies, and are the main focus of this review.

  7. Technique: imaging earliest tooth development in 3D using a silver-based tissue contrast agent.

    PubMed

    Raj, Muhammad T; Prusinkiewicz, Martin; Cooper, David M L; George, Belev; Webb, M Adam; Boughner, Julia C

    2014-02-01

    Looking in microscopic detail at the 3D organization of initiating teeth within the embryonic jaw has long-proved technologically challenging because of the radio-translucency of these tiny un-mineralized oral tissues. Yet 3D image data showing changes in the physical relationships among developing tooth and jaw tissues are vital to understand the coordinated morphogenesis of vertebrate teeth and jaws as an animal grows and as species evolve. Here, we present a new synchrotron-based scanning solution to image odontogenesis in 3D and in histological detail using a silver-based contrast agent. We stained fixed, intact wild-type mice aged embryonic (E) day 10 to birth with 1% Protargol-S at 37°C for 12-32 hr. Specimens were scanned at 4-10 µm pixel size at 28 keV, just above the silver K-edge, using micro-computed tomography (µCT) at the Canadian Light Source synchrotron. Synchrotron µCT scans of silver-stained embryos showed even the earliest visible stages of tooth initiation, as well as many other tissue types and structures, in histological detail. Silver stain penetration was optimal for imaging structures in intact embryos E15 and younger. This silver stain method offers a powerful yet straightforward approach to visualize at high-resolution and in 3D the earliest stages of odontogenesis in situ, and demonstrates the important of studying the tooth organ in all three planes of view.

  8. 3D scanning and printing skeletal tissues for anatomy education.

    PubMed

    Thomas, Daniel B; Hiscox, Jessica D; Dixon, Blair J; Potgieter, Johan

    2016-09-01

    Detailed anatomical models can be produced with consumer-level 3D scanning and printing systems. 3D replication techniques are significant advances for anatomical education as they allow practitioners to more easily introduce diverse or numerous specimens into classrooms. Here we present a methodology for producing anatomical models in-house, with the chondrocranium cartilage from a spiny dogfish (Squalus acanthias) and the skeleton of a cane toad (Rhinella marina) as case studies. 3D digital replicas were produced using two consumer-level scanners and specimens were 3D-printed with selective laser sintering. The fidelity of the two case study models was determined with respect to key anatomical features. Larger-scale features of the dogfish chondrocranium and frog skeleton were all well-resolved and distinct in the 3D digital models, and many finer-scale features were also well-resolved, but some more subtle features were absent from the digital models (e.g. endolymphatic foramina in chondrocranium). All characters identified in the digital chondrocranium could be identified in the subsequent 3D print; however, three characters in the 3D-printed frog skeleton could not be clearly delimited (palatines, parasphenoid and pubis). Characters that were absent in the digital models or 3D prints had low-relief in the original scanned specimen and represent a minor loss of fidelity. Our method description and case studies show that minimal equipment and training is needed to produce durable skeletal specimens. These technologies support the tailored production of models for specific classes or research aims. PMID:27146106

  9. 3D scanning and printing skeletal tissues for anatomy education.

    PubMed

    Thomas, Daniel B; Hiscox, Jessica D; Dixon, Blair J; Potgieter, Johan

    2016-09-01

    Detailed anatomical models can be produced with consumer-level 3D scanning and printing systems. 3D replication techniques are significant advances for anatomical education as they allow practitioners to more easily introduce diverse or numerous specimens into classrooms. Here we present a methodology for producing anatomical models in-house, with the chondrocranium cartilage from a spiny dogfish (Squalus acanthias) and the skeleton of a cane toad (Rhinella marina) as case studies. 3D digital replicas were produced using two consumer-level scanners and specimens were 3D-printed with selective laser sintering. The fidelity of the two case study models was determined with respect to key anatomical features. Larger-scale features of the dogfish chondrocranium and frog skeleton were all well-resolved and distinct in the 3D digital models, and many finer-scale features were also well-resolved, but some more subtle features were absent from the digital models (e.g. endolymphatic foramina in chondrocranium). All characters identified in the digital chondrocranium could be identified in the subsequent 3D print; however, three characters in the 3D-printed frog skeleton could not be clearly delimited (palatines, parasphenoid and pubis). Characters that were absent in the digital models or 3D prints had low-relief in the original scanned specimen and represent a minor loss of fidelity. Our method description and case studies show that minimal equipment and training is needed to produce durable skeletal specimens. These technologies support the tailored production of models for specific classes or research aims.

  10. Multiscale 3D bioimaging: from cell, tissue to whole organism

    NASA Astrophysics Data System (ADS)

    Lau, S. H.; Wang, Ge; Chandrasekeran, Margam; Fan, Victor; Nazrul, Mohd; Chang, Hauyee; Fong, Tiffany; Gelb, Jeff; Feser, Michael; Yun, Wenbing

    2009-05-01

    While electron microscopes and AFMs are capable of high resolution imaging to molecular levels, there is an ongoing problem in integrating these results into the larger scale structure and functions of tissue and organs within a complex organism. Imaging biological samples with optical microscopy is predominantly done with histology and immunohistochemistry, which can take up to a several weeks to prepare, are artifact prone and only available as individual 2D images. At the nano resolution scale, the higher resolution electron microscopy and AFM are used, but again these require destructive sample preparation and data are in 2D. To bridge this gap, we describe a rapid non invasive hierarchical bioimaging technique using a novel lab based x-ray computed tomography to characterize complex biological organism in multiscale- from whole organ (mesoscale) to calcified and soft tissue (microscale), to subcellular structures, nanomaterials and cellular-scaffold interaction (nanoscale). While MicroCT (micro x-ray computed tomography) is gaining in popularity for non invasive bones and tissue imaging, contrast and resolution are still vastly inadequate compared to histology. In this study we will present multiscale results from a novel microCT and nanoCT (nano x-ray tomography system). The novel MicroCT can image large specimen and tissue sample at histology resolution of submicron voxel resolution, often without contrast agents, while the nanoCT using x-ray optics similar to those used in synchrotron radiation facilities, has 20nm voxel resolution, suitable for studying cellular, subcellular morphology and nanomaterials. Multiscale examples involving both calcified and soft tissue will be illustrated, which include imaging a rat tibia to the individual channels of osteocyte canaliculli and lacunae and an unstained whole murine lung to its alveoli. The role of the novel CT will also be discussed as a possible means for rapid virtual histology using a biopsy of a human

  11. 3D Tissue Culturing: Tissue in Cube: In Vitro 3D Culturing Platform with Hybrid Gel Cubes for Multidirectional Observations (Adv. Healthcare Mater. 13/2016).

    PubMed

    Hagiwara, Masaya; Kawahara, Tomohiro; Nobata, Rina

    2016-07-01

    An in vitro 3D culturing platform enabling multidirectional observations of 3D biosamples is presented by M. Hagiwara and co-workers on page 1566. 3D recognition of a sample structure can be achieved by facilitating multi-directional views using a standard microscope without a laser system. The cubic platform has the potential to promote 3D culture studies, offering easy handling and compatibility with commercial culture plates at a low price tag. PMID:27384934

  12. 3D Tissue Culturing: Tissue in Cube: In Vitro 3D Culturing Platform with Hybrid Gel Cubes for Multidirectional Observations (Adv. Healthcare Mater. 13/2016).

    PubMed

    Hagiwara, Masaya; Kawahara, Tomohiro; Nobata, Rina

    2016-07-01

    An in vitro 3D culturing platform enabling multidirectional observations of 3D biosamples is presented by M. Hagiwara and co-workers on page 1566. 3D recognition of a sample structure can be achieved by facilitating multi-directional views using a standard microscope without a laser system. The cubic platform has the potential to promote 3D culture studies, offering easy handling and compatibility with commercial culture plates at a low price tag.

  13. A multi-scale controlled tissue engineering scaffold prepared by 3D printing and NFES technology

    NASA Astrophysics Data System (ADS)

    Yan, Feifei; Liu, Yuanyuan; Chen, Haiping; Zhang, Fuhua; Zheng, Lulu; Hu, Qingxi

    2014-03-01

    The current focus in the field of life science is the use of tissue engineering scaffolds to repair human organs, which has shown great potential in clinical applications. Extracellular matrix morphology and the performance and internal structure of natural organs are required to meet certain requirements. Therefore, integrating multiple processes can effectively overcome the limitations of the individual processes and can take into account the needs of scaffolds for the material, structure, mechanical properties and many other aspects. This study combined the biological 3D printing technology and the near-field electro-spinning (NFES) process to prepare a multi-scale controlled tissue engineering scaffold. While using 3D printing technology to directly prepare the macro-scaffold, the compositing NFES process to build tissue micro-morphology ultimately formed a tissue engineering scaffold which has the specific extracellular matrix structure. This scaffold not only takes into account the material, structure, performance and many other requirements, but also focuses on resolving the controllability problems in macro- and micro-forming which further aim to induce cell directed differentiation, reproduction and, ultimately, the formation of target tissue organs. It has in-depth immeasurable significance to build ideal scaffolds and further promote the application of tissue engineering.

  14. Control of vascular network location in millimeter-sized 3D-tissues by micrometer-sized collagen coated cells.

    PubMed

    Liu, Chun-Yen; Matsusaki, Michiya; Akashi, Mitsuru

    2016-03-25

    Engineering three-dimensional (3D) vascularized constructs remains a central challenge because capillary network structures are important for sufficient oxygen and nutrient exchange to sustain the viability of engineered constructs. However, construction of 3D-tissues at single cell level has yet to be reported. Previously, we established a collagen coating method for fabricating a micrometer-sized collagen matrix on cell surfaces to control cell distance or cell densities inside tissues. In this study, a simple fabrication method is presented for constructing vascular networks in 3D-tissues over micrometer-sized or even millimeter-sized with controlled cell densities. From the results, well vascularized 3D network structures can be observed with a fluorescence label method mixing collagen coated cells and endothelia cells, indicating that constructed ECM rich tissues have the potential for vascularization, which opens up the possibility for various applications in pharmaceutical or tissue engineering fields.

  15. Spread of excitation in 3-D models of the anisotropic cardiac tissue. III. Effects of ventricular geometry and fiber structure on the potential distribution.

    PubMed

    Colli Franzone, P; Guerri, L; Pennacchio, M; Taccardi, B

    1998-07-01

    In a previous paper we studied the spread of excitation in a simplified model of the left ventricle, affected by fiber structure and obliqueness, curvature of the wall and Purkinje network. In the present paper we investigate the extracellular potential distribution u in the same ventricular model. Given the transmembrane potential v, associated with the spreading excitation, the extracellular potential u is obtained as solution of a linear elliptic equation with the source term related to v. The potential distributions were computed for point stimulations at different intramural depths. The results of the simulations enabled us to identify a number of common features which appears in all the potential patterns irrespective of pacing site. In addition, by splitting the sources into an axial and conormal component, we were able to evaluate the contribution of the classical uniform dipole layer to the total potential field and the role of the superimposed axial component.

  16. Microdrop printing of hydrogel bioinks into 3D tissue-like geometries.

    PubMed

    Pataky, Kris; Braschler, Thomas; Negro, Andrea; Renaud, Philippe; Lutolf, Matthias P; Brugger, Juergen

    2012-01-17

    An optimized 3D inkjet printing process is demonstrated for structuring alginate into a tissue-like microvasculature capable of supporting physiological flow rates. Optimizing the reaction at the single-droplet level enables wet hydrogel droplets to be stacked, thus overcoming their natural tendancy to spread and coalesce. Live cells can be patterned using this process and it can be extended to a range of other hydrogels.

  17. 3D printing of composite tissue with complex shape applied to ear regeneration.

    PubMed

    Lee, Jung-Seob; Hong, Jung Min; Jung, Jin Woo; Shim, Jin-Hyung; Oh, Jeong-Hoon; Cho, Dong-Woo

    2014-06-01

    In the ear reconstruction field, tissue engineering enabling the regeneration of the ear's own tissue has been considered to be a promising technology. However, the ear is known to be difficult to regenerate using traditional methods due to its complex shape and composition. In this study, we used three-dimensional (3D) printing technology including a sacrificial layer process to regenerate both the auricular cartilage and fat tissue. The main part was printed with poly-caprolactone (PCL) and cell-laden hydrogel. At the same time, poly-ethylene-glycol (PEG) was also deposited as a sacrificial layer to support the main structure. After complete fabrication, PEG can be easily removed in aqueous solutions, and the procedure for removing PEG has no effect on the cell viability. For fabricating composite tissue, chondrocytes and adipocytes differentiated from adipose-derived stromal cells were encapsulated in hydrogel to dispense into the cartilage and fat regions, respectively, of ear-shaped structures. Finally, we fabricated the composite structure for feasibility testing, satisfying expectations for both the geometry and anatomy of the native ear. We also carried out in vitro assays for evaluating the chondrogenesis and adipogenesis of the cell-printed structure. As a result, the possibility of ear regeneration using 3D printing technology which allowed tissue formation from the separately printed chondrocytes and adipocytes was demonstrated.

  18. 3D-Fun: predicting enzyme function from structure.

    PubMed

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

    2008-07-01

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

  19. Micro-precise spatiotemporal delivery system embedded in 3D printing for complex tissue regeneration.

    PubMed

    Tarafder, Solaiman; Koch, Alia; Jun, Yena; Chou, Conrad; Awadallah, Mary R; Lee, Chang H

    2016-06-01

    Three dimensional (3D) printing has emerged as an efficient tool for tissue engineering and regenerative medicine, given its advantages for constructing custom-designed scaffolds with tunable microstructure/physical properties. Here we developed a micro-precise spatiotemporal delivery system embedded in 3D printed scaffolds. PLGA microspheres (μS) were encapsulated with growth factors (GFs) and then embedded inside PCL microfibers that constitute custom-designed 3D scaffolds. Given the substantial difference in the melting points between PLGA and PCL and their low heat conductivity, μS were able to maintain its original structure while protecting GF's bioactivities. Micro-precise spatial control of multiple GFs was achieved by interchanging dispensing cartridges during a single printing process. Spatially controlled delivery of GFs, with a prolonged release, guided formation of multi-tissue interfaces from bone marrow derived mesenchymal stem/progenitor cells (MSCs). To investigate efficacy of the micro-precise delivery system embedded in 3D printed scaffold, temporomandibular joint (TMJ) disc scaffolds were fabricated with micro-precise spatiotemporal delivery of CTGF and TGFβ3, mimicking native-like multiphase fibrocartilage. In vitro, TMJ disc scaffolds spatially embedded with CTGF/TGFβ3-μS resulted in formation of multiphase fibrocartilaginous tissues from MSCs. In vivo, TMJ disc perforation was performed in rabbits, followed by implantation of CTGF/TGFβ3-μS-embedded scaffolds. After 4 wks, CTGF/TGFβ3-μS embedded scaffolds significantly improved healing of the perforated TMJ disc as compared to the degenerated TMJ disc in the control group with scaffold embedded with empty μS. In addition, CTGF/TGFβ3-μS embedded scaffolds significantly prevented arthritic changes on TMJ condyles. In conclusion, our micro-precise spatiotemporal delivery system embedded in 3D printing may serve as an efficient tool to regenerate complex and inhomogeneous tissues. PMID

  20. Micro-precise spatiotemporal delivery system embedded in 3D printing for complex tissue regeneration.

    PubMed

    Tarafder, Solaiman; Koch, Alia; Jun, Yena; Chou, Conrad; Awadallah, Mary R; Lee, Chang H

    2016-04-25

    Three dimensional (3D) printing has emerged as an efficient tool for tissue engineering and regenerative medicine, given its advantages for constructing custom-designed scaffolds with tunable microstructure/physical properties. Here we developed a micro-precise spatiotemporal delivery system embedded in 3D printed scaffolds. PLGA microspheres (μS) were encapsulated with growth factors (GFs) and then embedded inside PCL microfibers that constitute custom-designed 3D scaffolds. Given the substantial difference in the melting points between PLGA and PCL and their low heat conductivity, μS were able to maintain its original structure while protecting GF's bioactivities. Micro-precise spatial control of multiple GFs was achieved by interchanging dispensing cartridges during a single printing process. Spatially controlled delivery of GFs, with a prolonged release, guided formation of multi-tissue interfaces from bone marrow derived mesenchymal stem/progenitor cells (MSCs). To investigate efficacy of the micro-precise delivery system embedded in 3D printed scaffold, temporomandibular joint (TMJ) disc scaffolds were fabricated with micro-precise spatiotemporal delivery of CTGF and TGFβ3, mimicking native-like multiphase fibrocartilage. In vitro, TMJ disc scaffolds spatially embedded with CTGF/TGFβ3-μS resulted in formation of multiphase fibrocartilaginous tissues from MSCs. In vivo, TMJ disc perforation was performed in rabbits, followed by implantation of CTGF/TGFβ3-μS-embedded scaffolds. After 4 wks, CTGF/TGFβ3-μS embedded scaffolds significantly improved healing of the perforated TMJ disc as compared to the degenerated TMJ disc in the control group with scaffold embedded with empty μS. In addition, CTGF/TGFβ3-μS embedded scaffolds significantly prevented arthritic changes on TMJ condyles. In conclusion, our micro-precise spatiotemporal delivery system embedded in 3D printing may serve as an efficient tool to regenerate complex and inhomogeneous tissues.

  1. Multifunctional 3D printing of heterogeneous hydrogel structures

    PubMed Central

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

    2016-01-01

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

  2. Multifunctional 3D printing of heterogeneous hydrogel structures

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  3. Multifunctional 3D printing of heterogeneous hydrogel structures.

    PubMed

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

    2016-01-01

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

  4. Multifunctional 3D printing of heterogeneous hydrogel structures.

    PubMed

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

    2016-09-15

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

  5. Automated RNA 3D Structure Prediction with RNAComposer.

    PubMed

    Biesiada, Marcin; Purzycka, Katarzyna J; Szachniuk, Marta; Blazewicz, Jacek; Adamiak, Ryszard W

    2016-01-01

    RNAs adopt specific structures to perform their activities and these are critical to virtually all RNA-mediated processes. Because of difficulties in experimentally assessing structures of large RNAs using NMR, X-ray crystallography, or cryo-microscopy, there is currently great demand for new high-resolution 3D structure prediction methods. Recently we reported on RNAComposer, a knowledge-based method for the fully automated RNA 3D structure prediction from a user-defined secondary structure. RNAComposer method is especially suited for structural biology users. Since our initial report in 2012, both servers, freely available at http://rnacomposer.ibch.poznan.pl and http://rnacomposer.cs.put.poznan.pl have been often visited. Therefore this chapter provides guidance for using RNAComposer and discusses points that should be considered when predicting 3D RNA structure. An application example presents current scope and limitations of RNAComposer. PMID:27665601

  6. 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.

  7. Bio-inspired mineralization of hydroxyapatite in 3D silk fibroin hydrogel for bone tissue engineering.

    PubMed

    Jin, Yashi; Kundu, Banani; Cai, Yurong; Kundu, Subhas C; Yao, Juming

    2015-10-01

    To fabricate hard tissue implants with bone-like structure using a biomimetic mineralization method is drawing much more attentions in bone tissue engineering. The present work focuses in designing 3D silk fibroin hydrogel to modulate the nucleation and growth of hydroxyapatite crystals via a simple ion diffusion method. The study indicates that Ca(2+) incorporation within the hydrogel provides the nucleation sites for hydroxyapatite crystals and subsequently regulates their oriented growth. The mineralization process is regulated in a Ca(2+) concentration- and minerlization time-dependent way. Further, the compressive strength of the mineralized hydrogels is directly proportional with the mineral content in hydrogel. The orchestrated organic/inorganic composite supports well the viability and proliferation of human osteoblast cells; improved cyto-compatibility with increased mineral content. Together, the present investigation reports a simple and biomimetic process to fabricate 3D bone-like biomaterial with desired efficacy to repair bone defects. PMID:26209967

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

    PubMed

    White, Diana; Coombe, Dennis; Rezania, Vahid; Tuszynski, Jack

    2016-01-01

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

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

    PubMed Central

    Rezania, Vahid; Tuszynski, Jack

    2016-01-01

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

  10. Establishing multi-modality datasets with the incorporation of 3D histopathology for soft tissue classification

    NASA Astrophysics Data System (ADS)

    de Ryk, Jessica; Thiesse, Jacqueline; Reinhardt, Joseph M.; Hoffman, Eric A.; McLennan, Geoffrey

    2006-03-01

    The development of multi-modality image analysis has gained increasing popularity over recent years. Multi-modality image databases are being developed to benefit patient clinical care, research and education. The incorporation of histopathology in these multi-modality datasets is complicated by the large differences in image quality, content and spatial association. We have developed a novel system, the large-scale image microtome array (LIMA), to bridge the gap between non-structurally destructive and destructive imaging such that reliable registration and incorporation of three-dimensional (3D) histopathology can be achieved. We have developed registration algorithms to align the micro-CT, LIMA and histopathology data to a common coordinate system. Using this multi-modality image dataset we have developed a classification algorithm to identify on a pixel basis, the tissue types present. The output from the classification processing is a 3D color coded map of tissue distributions. The resulting complete dataset provides an abundance of valuable information relating to the tissue sample including density, anatomical structure, color, texture and cellular information in three dimensions. In this study we have chosen to use normal and diseased lung tissue, however the flexibility of the image acquisition and subsequent processing algorithms makes it applicable to any soft organ tissue.

  11. 3D annotation and manipulation of medical anatomical structures

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  12. 3D Ultrasonic Wave Simulations for Structural Health Monitoring

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  13. Mesoscopic hydrogel molding to control the 3D geometry of bioartificial muscle tissues

    PubMed Central

    Bian, Weining; Liau, Brian; Badie, Nima

    2010-01-01

    This protocol describes a cell/hydrogel molding method for precise and reproducible biomimetic fabrication of three-dimensional (3D) muscle tissue architectures in vitro. Using a high aspect ratio soft lithography technique, we fabricate polydimethylsiloxane (PDMS) molds containing arrays of mesoscopic posts with defined size, elongation and spacing. On cell/hydrogel molding, these posts serve to enhance the diffusion of nutrients to cells by introducing elliptical pores in the cell-laden hydrogels and to guide local 3D cell alignment by governing the spatial pattern of mechanical tension. Instead of ultraviolet or chemical cross-linking, this method utilizes natural hydrogel polymerization and topographically constrained cell-mediated gel compaction to create the desired 3D tissue structures. We apply this method to fabricate several square centimeter large, few hundred micron-thick bioartificial muscle tissues composed of viable, dense, uniformly aligned and highly differentiated cardiac or skeletal muscle fibers. The protocol takes 4–5 d to fabricate PDMS molds followed by 2 weeks of cell culture. PMID:19798085

  14. Imaging of oxygenation in 3D tissue models with multi-modal phosphorescent probes

    NASA Astrophysics Data System (ADS)

    Papkovsky, Dmitri B.; Dmitriev, Ruslan I.; Borisov, Sergei

    2015-03-01

    Cell-penetrating phosphorescence based probes allow real-time, high-resolution imaging of O2 concentration in respiring cells and 3D tissue models. We have developed a panel of such probes, small molecule and nanoparticle structures, which have different spectral characteristics, cell penetrating and tissue staining behavior. The probes are compatible with conventional live cell imaging platforms and can be used in different detection modalities, including ratiometric intensity and PLIM (Phosphorescence Lifetime IMaging) under one- or two-photon excitation. Analytical performance of these probes and utility of the O2 imaging method have been demonstrated with different types of samples: 2D cell cultures, multi-cellular spheroids from cancer cell lines and primary neurons, excised slices from mouse brain, colon and bladder tissue, and live animals. They are particularly useful for hypoxia research, ex-vivo studies of tissue physiology, cell metabolism, cancer, inflammation, and multiplexing with many conventional fluorophors and markers of cellular function.

  15. Assembly of graphene sheets into 3D macroscopic structures.

    PubMed

    Yin, Shengyan; Niu, Zhiqiang; Chen, Xiaodong

    2012-08-20

    Integration of graphene sheets, 2D nanoscale building blocks, into 3D macroscopic assemblies and ultimately into a functional system is essential to explore the advanced properties of individual graphene sheets for macroscopic applications. This Concept paper summarizes different ways, such as flow-directed assembly, layer-by-layer deposition, template-directed method, and leavening strategy to assemble graphene sheets into the layered and porous 3D macroscopic structures. The obtained structures show unique properties, such as flexible network, high specific surface area, and outstanding electrical and mechanical properties. Furthermore, the functional systems based on such graphene 3D macroscopic structures have shown enhanced performance in the applications of energy storage, catalysis, environmental remediation, and sensing.

  16. Correlation-based discrimination between cardiac tissue and blood for segmentation of 3D echocardiographic images

    NASA Astrophysics Data System (ADS)

    Saris, Anne E. C. M.; Nillesen, Maartje M.; Lopata, Richard G. P.; de Korte, Chris L.

    2013-03-01

    Automated segmentation of 3D echocardiographic images in patients with congenital heart disease is challenging, because the boundary between blood and cardiac tissue is poorly defined in some regions. Cardiologists mentally incorporate movement of the heart, using temporal coherence of structures to resolve ambiguities. Therefore, we investigated the merit of temporal cross-correlation for automated segmentation over the entire cardiac cycle. Optimal settings for maximum cross-correlation (MCC) calculation, based on a 3D cross-correlation based displacement estimation algorithm, were determined to obtain the best contrast between blood and myocardial tissue over the entire cardiac cycle. Resulting envelope-based as well as RF-based MCC values were used as additional external force in a deformable model approach, to segment the left-ventricular cavity in entire systolic phase. MCC values were tested against, and combined with, adaptive filtered, demodulated RF-data. Segmentation results were compared with manually segmented volumes using a 3D Dice Similarity Index (3DSI). Results in 3D pediatric echocardiographic images sequences (n = 4) demonstrate that incorporation of temporal information improves segmentation. The use of MCC values, either alone or in combination with adaptive filtered, demodulated RF-data, resulted in an increase of the 3DSI in 75% of the cases (average 3DSI increase: 0.71 to 0.82). Results might be further improved by optimizing MCC-contrast locally, in regions with low blood-tissue contrast. Reducing underestimation of the endocardial volume due to MCC processing scheme (choice of window size) and consequential border-misalignment, could also lead to more accurate segmentations. Furthermore, increasing the frame rate will also increase MCC-contrast and thus improve segmentation.

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

    PubMed Central

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

    2013-01-01

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

  18. RNAComposer and RNA 3D structure prediction for nanotechnology.

    PubMed

    Biesiada, Marcin; Pachulska-Wieczorek, Katarzyna; Adamiak, Ryszard W; Purzycka, Katarzyna J

    2016-07-01

    RNAs adopt specific, stable tertiary architectures to perform their activities. Knowledge of RNA tertiary structure is fundamental to understand RNA functions beginning with transcription and ending with turnover. Contrary to advanced RNA secondary structure prediction algorithms, which allow good accuracy when experimental data are integrated into the prediction, tertiary structure prediction of large RNAs still remains a significant challenge. However, the field of RNA tertiary structure prediction is rapidly developing and new computational methods based on different strategies are emerging. RNAComposer is a user-friendly and freely available server for 3D structure prediction of RNA up to 500 nucleotide residues. RNAComposer employs fully automated fragment assembly based on RNA secondary structure specified by the user. Importantly, this method allows incorporation of distance restraints derived from the experimental data to strengthen the 3D predictions. The potential and limitations of RNAComposer are discussed and an application to RNA design for nanotechnology is presented.

  19. Injectable 3-D Fabrication of Medical Electronics at the Target Biological Tissues

    PubMed Central

    Jin, Chao; Zhang, Jie; Li, Xiaokang; Yang, Xueyao; Li, Jingjing; Liu, Jing

    2013-01-01

    Conventional transplantable biomedical devices generally request sophisticated surgery which however often causes big trauma and serious pain to the patients. Here, we show an alternative way of directly making three-dimensional (3-D) medical electronics inside the biological body through sequential injections of biocompatible packaging material and liquid metal ink. As the most typical electronics, a variety of medical electrodes with different embedded structures were demonstrated to be easily formed at the target tissues. Conceptual in vitro experiments provide strong evidences for the excellent performances of the injectable electrodes. Further in vivo animal experiments disclosed that the formed electrode could serve as both highly efficient ECG (Electrocardiograph) electrode and stimulator electrode. These findings clarified the unique features and practicability of the liquid metal based injectable 3-D fabrication of medical electronics. The present strategy opens the way for directly manufacturing electrophysiological sensors or therapeutic devices in situ via a truly minimally invasive approach. PMID:24309385

  20. Preparation and mechanical property of a novel 3D porous magnesium scaffold for bone tissue engineering.

    PubMed

    Zhang, Xue; Li, Xiao-Wu; Li, Ji-Guang; Sun, Xu-Dong

    2014-09-01

    Porous magnesium has been recently recognized as a biodegradable metal for bone substitute applications. A novel porous Mg scaffold with three-dimensional (3D) interconnected pores and with a porosity of 33-54% was produced by the fiber deposition hot pressing (FDHP) technology. The microstructure and morphologies of the porous Mg scaffold were characterized by scanning electron microscopy (SEM), and the effects of porosities on the microstructure and mechanical properties of the porous Mg were investigated. Experimental results indicate that the measured Young's modulus and compressive strength of the Mg scaffold are ranged in 0.10-0.37 GPa, and 11.1-30.3 MPa, respectively, which are fairly comparable to those of cancellous bone. Such a porous Mg scaffold having a 3D interconnected network structure has the potential to be used in bone tissue engineering.

  1. Injectable 3-D Fabrication of Medical Electronics at the Target Biological Tissues

    NASA Astrophysics Data System (ADS)

    Jin, Chao; Zhang, Jie; Li, Xiaokang; Yang, Xueyao; Li, Jingjing; Liu, Jing

    2013-12-01

    Conventional transplantable biomedical devices generally request sophisticated surgery which however often causes big trauma and serious pain to the patients. Here, we show an alternative way of directly making three-dimensional (3-D) medical electronics inside the biological body through sequential injections of biocompatible packaging material and liquid metal ink. As the most typical electronics, a variety of medical electrodes with different embedded structures were demonstrated to be easily formed at the target tissues. Conceptual in vitro experiments provide strong evidences for the excellent performances of the injectable electrodes. Further in vivo animal experiments disclosed that the formed electrode could serve as both highly efficient ECG (Electrocardiograph) electrode and stimulator electrode. These findings clarified the unique features and practicability of the liquid metal based injectable 3-D fabrication of medical electronics. The present strategy opens the way for directly manufacturing electrophysiological sensors or therapeutic devices in situ via a truly minimally invasive approach.

  2. Controlled implant/soft tissue interaction by nanoscale surface modifications of 3D porous titanium implants.

    PubMed

    Rieger, Elisabeth; Dupret-Bories, Agnès; Salou, Laetitia; Metz-Boutigue, Marie-Helene; Layrolle, Pierre; Debry, Christian; Lavalle, Philippe; Vrana, Nihal Engin

    2015-06-01

    Porous titanium implants are widely employed in the orthopaedics field to ensure good bone fixation. Recently, the use of porous titanium implants has also been investigated in artificial larynx development in a clinical setting. Such uses necessitate a better understanding of the interaction of soft tissues with porous titanium structures. Moreover, surface treatments of titanium have been generally evaluated in planar structures, while the porous titanium implants have complex 3 dimensional (3D) architectures. In this study, the determining factors for soft tissue integration of 3D porous titanium implants were investigated as a function of surface treatments via quantification of the interaction of serum proteins and cells with single titanium microbeads (300-500 μm in diameter). Samples were either acid etched or nanostructured by anodization. When the samples are used in 3D configuration (porous titanium discs of 2 mm thickness) in vivo (in subcutis of rats for 2 weeks), a better integration was observed for both anodized and acid etched samples compared to the non-treated implants. If the implants were also pre-treated with rat serum before implantation, the integration was further facilitated. In order to understand the underlying reasons for this effect, human fibroblast cell culture tests under several conditions (directly on beads, beads in suspension, beads encapsulated in gelatin hydrogels) were conducted to mimic the different interactions of cells with Ti implants in vivo. Physical characterization showed that surface treatments increased hydrophilicity, protein adsorption and roughness. Surface treatments also resulted in improved adsorption of serum albumin which in turn facilitated the adsorption of other proteins such as apolipoprotein as quantified by protein sequencing. The cellular response to the beads showed considerable difference with respect to the cell culture configuration. When the titanium microbeads were entrapped in cell

  3. Fabrication of low cost soft tissue prostheses with the desktop 3D printer

    PubMed Central

    He, Yong; Xue, Guang-huai; Fu, Jian-zhong

    2014-01-01

    Soft tissue prostheses such as artificial ear, eye and nose are widely used in the maxillofacial rehabilitation. In this report we demonstrate how to fabricate soft prostheses mold with a low cost desktop 3D printer. The fabrication method used is referred to as Scanning Printing Polishing Casting (SPPC). Firstly the anatomy is scanned with a 3D scanner, then a tissue casting mold is designed on computer and printed with a desktop 3D printer. Subsequently, a chemical polishing method is used to polish the casting mold by removing the staircase effect and acquiring a smooth surface. Finally, the last step is to cast medical grade silicone into the mold. After the silicone is cured, the fine soft prostheses can be removed from the mold. Utilizing the SPPC method, soft prostheses with smooth surface and complicated structure can be fabricated at a low cost. Accordingly, the total cost of fabricating ear prosthesis is about $30, which is much lower than the current soft prostheses fabrication methods. PMID:25427880

  4. Fabrication of low cost soft tissue prostheses with the desktop 3D printer

    NASA Astrophysics Data System (ADS)

    He, Yong; Xue, Guang-Huai; Fu, Jian-Zhong

    2014-11-01

    Soft tissue prostheses such as artificial ear, eye and nose are widely used in the maxillofacial rehabilitation. In this report we demonstrate how to fabricate soft prostheses mold with a low cost desktop 3D printer. The fabrication method used is referred to as Scanning Printing Polishing Casting (SPPC). Firstly the anatomy is scanned with a 3D scanner, then a tissue casting mold is designed on computer and printed with a desktop 3D printer. Subsequently, a chemical polishing method is used to polish the casting mold by removing the staircase effect and acquiring a smooth surface. Finally, the last step is to cast medical grade silicone into the mold. After the silicone is cured, the fine soft prostheses can be removed from the mold. Utilizing the SPPC method, soft prostheses with smooth surface and complicated structure can be fabricated at a low cost. Accordingly, the total cost of fabricating ear prosthesis is about $30, which is much lower than the current soft prostheses fabrication methods.

  5. Fabrication of low cost soft tissue prostheses with the desktop 3D printer.

    PubMed

    He, Yong; Xue, Guang-huai; Fu, Jian-zhong

    2014-01-01

    Soft tissue prostheses such as artificial ear, eye and nose are widely used in the maxillofacial rehabilitation. In this report we demonstrate how to fabricate soft prostheses mold with a low cost desktop 3D printer. The fabrication method used is referred to as Scanning Printing Polishing Casting (SPPC). Firstly the anatomy is scanned with a 3D scanner, then a tissue casting mold is designed on computer and printed with a desktop 3D printer. Subsequently, a chemical polishing method is used to polish the casting mold by removing the staircase effect and acquiring a smooth surface. Finally, the last step is to cast medical grade silicone into the mold. After the silicone is cured, the fine soft prostheses can be removed from the mold. Utilizing the SPPC method, soft prostheses with smooth surface and complicated structure can be fabricated at a low cost. Accordingly, the total cost of fabricating ear prosthesis is about $30, which is much lower than the current soft prostheses fabrication methods.

  6. Finite Element Analysis of Meniscal Anatomical 3D Scaffolds: Implications for Tissue Engineering

    PubMed Central

    Moroni, L; Lambers, F.M; Wilson, W; van Donkelaar, C.C; de Wijn, JR; Huiskesb, R; van Blitterswijk, C.A

    2007-01-01

    Solid Free-Form Fabrication (SFF) technologies allow the fabrication of anatomical 3D scaffolds from computer tomography (CT) or magnetic resonance imaging (MRI) patients’ dataset. These structures can be designed and fabricated with a variable, interconnected and accessible porous network, resulting in modulable mechanical properties, permeability, and architecture that can be tailored to mimic a specific tissue to replace or regenerate. In this study, we evaluated whether anatomical meniscal 3D scaffolds with matching mechanical properties and architecture are beneficial for meniscus replacement as compared to meniscectomy. After acquiring CT and MRI of porcine menisci, 3D fiber-deposited (3DF) scaffolds were fabricated with different architectures by varying the deposition pattern of the fibers comprising the final structure. The mechanical behaviour of 3DF scaffolds with different architectures and of porcine menisci was measured by static and dynamic mechanical analysis and the effect of these tissue engineering templates on articular cartilage was assessed by finite element analysis (FEA) and compared to healthy conditions or to meniscectomy. Results show that 3DF anatomical menisci scaffolds can be fabricated with pore different architectures and with mechanical properties matching those of natural menisci. FEA predicted a beneficial effect of meniscus replacement with 3D scaffolds in different mechanical loading conditions as compared to meniscectomy. No influence of the internal scaffold architecture was found on articular cartilage damage. Although FEA predictions should be further confirmed by in vitro and in vivo experiments, this study highlights meniscus replacement by SFF anatomical scaffolds as a potential alternative to meniscectomy. PMID:19662124

  7. 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.

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

    PubMed

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

    2016-08-01

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

  9. 3D Biofabrication Strategies for Tissue Engineering and Regenerative Medicine

    PubMed Central

    Bajaj, Piyush; Schweller, Ryan M.; Khademhosseini, Ali; West, Jennifer L.; Bashir, Rashid

    2014-01-01

    Over the past several decades, there has been an ever-increasing demand for organ transplants. However, there is a severe shortage of donor organs, and as a result of the increasing demand, the gap between supply and demand continues to widen. A potential solution to this problem is to grow or fabricate organs using biomaterial scaffolds and a person’s own cells. Although the realization of this solution has been limited, the development of new biofabrication approaches has made it more realistic. This review provides an overview of natural and synthetic biomaterials that have been used for organ/tissue development. It then discusses past and current biofabrication techniques, with a brief explanation of the state of the art. Finally, the review highlights the need for combining vascularization strategies with current biofabrication techniques. Given the multitude of applications of biofabrication technologies, from organ/tissue development to drug discovery/screening to development of complex in vitro models of human diseases, these manufacturing technologies can have a significant impact on the future of medicine and health care. PMID:24905875

  10. Tissue in Cube: In Vitro 3D Culturing Platform with Hybrid Gel Cubes for Multidirectional Observations.

    PubMed

    Hagiwara, Masaya; Kawahara, Tomohiro; Nobata, Rina

    2016-07-01

    An in vitro 3D culturing platform enabling multidirectional observations of 3D biosamples is presented. The 3D structure of biosamples can be recognized without fluorescence. The cubic platform employs two types of hydrogels that are compatible with conventional culture dishes or well plates, facilitating growth in culture, ease of handling, and viewing at multiple angles. PMID:27128576

  11. Tissue in Cube: In Vitro 3D Culturing Platform with Hybrid Gel Cubes for Multidirectional Observations.

    PubMed

    Hagiwara, Masaya; Kawahara, Tomohiro; Nobata, Rina

    2016-07-01

    An in vitro 3D culturing platform enabling multidirectional observations of 3D biosamples is presented. The 3D structure of biosamples can be recognized without fluorescence. The cubic platform employs two types of hydrogels that are compatible with conventional culture dishes or well plates, facilitating growth in culture, ease of handling, and viewing at multiple angles.

  12. Full 3-D transverse oscillations: a method for tissue motion estimation.

    PubMed

    Salles, Sebastien; Liebgott, Hervé; Garcia, Damien; Vray, Didier

    2015-08-01

    We present a new method to estimate 4-D (3-D + time) tissue motion. The method used combines 3-D phase based motion estimation with an unconventional beamforming strategy. The beamforming technique allows us to obtain full 3-D RF volumes with axial, lateral, and elevation modulations. Based on these images, we propose a method to estimate 3-D motion that uses phase images instead of amplitude images. First, volumes featuring 3-D oscillations are created using only a single apodization function, and the 3-D displacement between two consecutive volumes is estimated simultaneously by applying this 3-D estimation. The validity of the method is investigated by conducting simulations and phantom experiments. The results are compared with those obtained with two other conventional estimation methods: block matching and optical flow. The results show that the proposed method outperforms the conventional methods, especially in the transverse directions.

  13. Development of a 3D polymer reinforced calcium phosphate cement scaffold for cranial bone tissue engineering

    NASA Astrophysics Data System (ADS)

    Alge, Daniel L.

    The repair of critical-sized cranial bone defects represents an important clinical challenge. The limitations of autografts and alloplastic materials make a bone tissue engineering strategy desirable, but success depends on the development of an appropriate scaffold. Key scaffold properties include biocompatibility, osteoconductivity, sufficient strength to maintain its structure, and resorbability. Furthermore, amenability to rapid prototyping fabrication methods is desirable, as these approaches offer precise control over scaffold architecture and have the potential for customization. While calcium phosphate cements meet many of these criteria due to their composition and their injectability, which can be leveraged for scaffold fabrication via indirect casting, their mechanical properties are a major limitation. Thus, the overall goal of this work was to develop a 3D polymer reinforced calcium phosphate cement scaffold for use in cranial bone tissue engineering. Dicalcium phosphate dihydrate (DCPD) setting cements are of particular interest because of their excellent resorbability. We demonstrated for the first time that DCPD cement can be prepared from monocalcium phosphate monohydrate (MCPM)/hydroxyapatite (HA) mixtures. However, subsequent characterization revealed that MCPM/HA cements rapidly convert to HA during degradation, which is undesirable and led us to choose a more conventional formulation for scaffold fabrication. In addition, we developed a novel method for calcium phosphate cement reinforcement that is based on infiltrating a pre-set cement structure with a polymer, and then crosslinking the polymer in situ. Unlike prior methods of cement reinforcement, this method can be applied to the reinforcement of 3D scaffolds fabricated by indirect casting. Using our novel method, composites of poly(propylene fumarate) (PPF) reinforced DCPD were prepared and demonstrated as excellent candidate scaffold materials, as they had increased strength and ductility

  14. Chitosan-based hydrogel tissue scaffolds made by 3D plotting promotes osteoblast proliferation and mineralization.

    PubMed

    Liu, I-Hsin; Chang, Shih-Hsin; Lin, Hsin-Yi

    2015-05-13

    A 3D plotting system was used to make chitosan-based tissue scaffolds with interconnected pores using pure chitosan (C) and chitosan cross-linked with pectin (CP) and genipin (CG). A freeze-dried chitosan scaffold (CF/D) was made to compare with C, to observe the effects of structural differences. The fiber size, pore size, porosity, compression strength, swelling ratio, drug release efficacy, and cumulative weight loss of the scaffolds were measured. Osteoblasts were cultured on the scaffolds and their proliferation, type I collagen production, alkaline phosphatase activity, calcium deposition, and morphology were observed. C had a lower swelling ratio, degradation, porosity and drug release efficacy and a higher compressional stiffness and cell proliferation compared to CF/D (p < 0.05). Of the 3D-plotted samples, cells on CP exhibited the highest degree of mineralization after 21 d (p < 0.05). CP also had the highest swelling ratio and fastest drug release, followed by C and CG (p < 0.05). Both CP and CG were stiffer and degraded more slowly in saline solution than C (p < 0.05). In summary, 3D-plotted scaffolds were stronger, less likely to degrade and better promoted osteoblast cell proliferation in vitro compared to the freeze-dried scaffolds. C, CP and CG were structurally similar, and the different crosslinking caused significant changes in their physical and biological performances.

  15. Fabrication of 2D and 3D constructs from reconstituted decellularized tissue extracellular matrices.

    PubMed

    Takeda, Yuji S; Xu, Qiaobing

    2014-12-01

    We demonstrated a novel process to reconstitute a decellularized extracellular matrix (Recon-ECM) of heart and liver tissue using a combination of mechanical homogenization and enzymatic digestion. Such Recon-ECM was used as a biomaterial to produce flat or micro-patterned 2D films after crosslinking using replica molding. The mechanical properties of the resulting films were tuned by changing the type of crosslinking reagents. We also demonstrated the fabrication of mechanically robust 3D scaffolds by freeze-drying of the Recon-ECM solution. The porosity of the 3D scaffold was controlled by changing the concentration of the Recon-ECM. HepG2 cells were used to investigate the potential substrate of these engineered 2D patterned and 3D porous structures. The cell attachment, proliferation, and urea synthesis were evaluated, and the results indicate that the scaffold generated from Recon-ECM provides a biologically friendly environment for cells to grow. This method provides a new way to use decellularized ECM as a source of biomaterial to produce novel scaffolds with better controlled micro- and nano-scale structures, tunable physicochemical properties with desired biological functions.

  16. Chitosan-based hydrogel tissue scaffolds made by 3D plotting promotes osteoblast proliferation and mineralization.

    PubMed

    Liu, I-Hsin; Chang, Shih-Hsin; Lin, Hsin-Yi

    2015-06-01

    A 3D plotting system was used to make chitosan-based tissue scaffolds with interconnected pores using pure chitosan (C) and chitosan cross-linked with pectin (CP) and genipin (CG). A freeze-dried chitosan scaffold (CF/D) was made to compare with C, to observe the effects of structural differences. The fiber size, pore size, porosity, compression strength, swelling ratio, drug release efficacy, and cumulative weight loss of the scaffolds were measured. Osteoblasts were cultured on the scaffolds and their proliferation, type I collagen production, alkaline phosphatase activity, calcium deposition, and morphology were observed. C had a lower swelling ratio, degradation, porosity and drug release efficacy and a higher compressional stiffness and cell proliferation compared to CF/D (p < 0.05). Of the 3D-plotted samples, cells on CP exhibited the highest degree of mineralization after 21 d (p < 0.05). CP also had the highest swelling ratio and fastest drug release, followed by C and CG (p < 0.05). Both CP and CG were stiffer and degraded more slowly in saline solution than C (p < 0.05). In summary, 3D-plotted scaffolds were stronger, less likely to degrade and better promoted osteoblast cell proliferation in vitro compared to the freeze-dried scaffolds. C, CP and CG were structurally similar, and the different crosslinking caused significant changes in their physical and biological performances. PMID:25970802

  17. 3D Structure of the Dihydropyridine Receptor of Skeletal Muscle.

    PubMed

    Samsó, Montserrat

    2015-01-01

    Excitation contraction coupling, the rapid and massive Ca(2+) release under control of an action potential that triggers muscle contraction, takes places at specialized regions of the cell called triad junctions. There, a highly ordered supramolecular complex between the dihydropyridine receptor (DHPR) and the ryanodine receptor (RyR1) mediates the quasi-instantaneous conversion from T-tubule depolarization into Ca(2+) release from the sarcoplasmic reticulum (SR). The DHPR has several key modules required for EC coupling: the voltage sensors and II-III loop in the alpha1s subunit, and the beta subunit. To gain insight into their molecular organization, this review examines the most updated 3D structure of the DHPR as obtained by transmission electron microscopy and image reconstruction. Although structure determination of a heteromeric membrane protein such as the DHPR is challenging, novel technical advances in protein expression and 3D labeling facilitated this task. The 3D structure of the DHPR complex consists of a main body with five irregular corners around its perimeter encompassing the transmembrane alpha 1s subunit besides the intracellular beta subunit, an extended extracellular alpha 2 subunit, and a bulky intracellular II-III loop. The structural definition attained at 19 Å resolution enabled docking of the atomic coordinates of structural homologs of the alpha1s and beta subunits. These structural features, together with their relative location with respect to the RyR1, are discussed in the context of the functional data. PMID:26913147

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

    PubMed

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

    2015-07-29

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

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

    PubMed Central

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

    2015-01-01

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

  20. Formation of coherent structures in 3D laminar mixing flows

    NASA Astrophysics Data System (ADS)

    Speetjens, Michel; Clercx, Herman

    2009-11-01

    Mixing under laminar flow conditions is key to a wide variety of industrial systems of size extending from microns to meters. Examples range from the traditional (and still very relevant) mixing of viscous fluids via compact processing equipment down to emerging micro-fluidics applications. Profound insight into laminar mixing mechanisms is imperative for further advancement of mixing technology (particularly for complex micro-fluidics systems) yet remains limited to date. The present study concentrates on a fundamental transport phenomenon of potential relevance to laminar mixing: the formation of coherent structures in the web of 3D fluid trajectories due to fluid inertia. Such coherent structures geometrically determine the transport properties of the flow and better understanding of their formation and characteristics may offer ways to control and manipulate the mixing properties of laminar flows. The formation of coherent structures and its impact upon 3D transport properties is demonstrated by way of examples.

  1. Controlled implant/soft tissue interaction by nanoscale surface modifications of 3D porous titanium implants

    NASA Astrophysics Data System (ADS)

    Rieger, Elisabeth; Dupret-Bories, Agnès; Salou, Laetitia; Metz-Boutigue, Marie-Helene; Layrolle, Pierre; Debry, Christian; Lavalle, Philippe; Engin Vrana, Nihal

    2015-05-01

    Porous titanium implants are widely employed in the orthopaedics field to ensure good bone fixation. Recently, the use of porous titanium implants has also been investigated in artificial larynx development in a clinical setting. Such uses necessitate a better understanding of the interaction of soft tissues with porous titanium structures. Moreover, surface treatments of titanium have been generally evaluated in planar structures, while the porous titanium implants have complex 3 dimensional (3D) architectures. In this study, the determining factors for soft tissue integration of 3D porous titanium implants were investigated as a function of surface treatments via quantification of the interaction of serum proteins and cells with single titanium microbeads (300-500 μm in diameter). Samples were either acid etched or nanostructured by anodization. When the samples are used in 3D configuration (porous titanium discs of 2 mm thickness) in vivo (in subcutis of rats for 2 weeks), a better integration was observed for both anodized and acid etched samples compared to the non-treated implants. If the implants were also pre-treated with rat serum before implantation, the integration was further facilitated. In order to understand the underlying reasons for this effect, human fibroblast cell culture tests under several conditions (directly on beads, beads in suspension, beads encapsulated in gelatin hydrogels) were conducted to mimic the different interactions of cells with Ti implants in vivo. Physical characterization showed that surface treatments increased hydrophilicity, protein adsorption and roughness. Surface treatments also resulted in improved adsorption of serum albumin which in turn facilitated the adsorption of other proteins such as apolipoprotein as quantified by protein sequencing. The cellular response to the beads showed considerable difference with respect to the cell culture configuration. When the titanium microbeads were entrapped in cell

  2. Gene3D: comprehensive structural and functional annotation of genomes.

    PubMed

    Yeats, Corin; Lees, Jonathan; Reid, Adam; Kellam, Paul; Martin, Nigel; Liu, Xinhui; Orengo, Christine

    2008-01-01

    Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources. The main structural annotation is generated through scanning these sequences against the CATH structural domain database profile-HMM library. CATH is a database of manually derived PDB-based structural domains, placed within a hierarchy reflecting topology, homology and conservation and is able to infer more ancient and divergent homology relationships than sequence-based approaches. This data is supplemented with Pfam-A, other non-domain structural predictions (i.e. coiled coils) and experimental data from UniProt. In order to enhance the investigations possible with this data, we have also incorporated a variety of protein annotation resources, including protein-protein interaction data, GO functional assignments, KEGG pathways, FUNCAT functional descriptions and links to microarray expression data. All of this data can be accessed through a newly re-designed website that has a focus on flexibility and clarity, with searches that can be restricted to a single genome or across the entire sequence database. Currently Gene3D contains over 3.5 million domain assignments for nearly 5 million proteins including 527 completed genomes. This is available at: http://gene3d.biochem.ucl.ac.uk/ PMID:18032434

  3. 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.

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

    PubMed

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

    2016-04-08

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

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

    PubMed Central

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

    2016-01-01

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

  6. METHODS FOR USING 3-D ULTRASOUND SPECKLE TRACKING IN BIAXIAL MECHANICAL TESTING OF BIOLOGICAL TISSUE SAMPLES

    PubMed Central

    Yap, Choon Hwai; Park, Dae Woo; Dutta, Debaditya; Simon, Marc; Kim, Kang

    2014-01-01

    Being multilayered and anisotropic, biological tissues such as cardiac and arterial walls are structurally complex, making full assessment and understanding of their mechanical behavior challenging. Current standard mechanical testing uses surface markers to track tissue deformations and does not provide deformation data below the surface. In the study described here, we found that combining mechanical testing with 3-D ultrasound speckle tracking could overcome this limitation. Rat myocardium was tested with a biaxial tester and was concurrently scanned with high-frequency ultrasound in three dimensions. The strain energy function was computed from stresses and strains using an iterative non-linear curve-fitting algorithm. Because the strain energy function consists of terms for the base matrix and for embedded fibers, spatially varying fiber orientation was also computed by curve fitting. Using finite-element simulations, we first validated the accuracy of the non-linear curve-fitting algorithm. Next, we compared experimentally measured rat myocardium strain energy function values with those in the literature and found a matching order of magnitude. Finally, we retained samples after the experiments for fiber orientation quantification using histology and found that the results satisfactorily matched those computed in the experiments. We conclude that 3-D ultrasound speckle tracking can be a useful addition to traditional mechanical testing of biological tissues and may provide the benefit of enabling fiber orientation computation. PMID:25616585

  7. Evaluating 3D-printed biomaterials as scaffolds for vascularized bone tissue engineering.

    PubMed

    Wang, Martha O; Vorwald, Charlotte E; Dreher, Maureen L; Mott, Eric J; Cheng, Ming-Huei; Cinar, Ali; Mehdizadeh, Hamidreza; Somo, Sami; Dean, David; Brey, Eric M; Fisher, John P

    2015-01-01

    There is an unmet need for a consistent set of tools for the evaluation of 3D-printed constructs. A toolbox developed to design, characterize, and evaluate 3D-printed poly(propylene fumarate) scaffolds is proposed for vascularized engineered tissues. This toolbox combines modular design and non-destructive fabricated design evaluation, evaluates biocompatibility and mechanical properties, and models angiogenesis.

  8. 3D printed components with ultrasonically arranged microscale structure

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed

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

    2016-02-01

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

  10. 3D Printing technology over a drug delivery for tissue engineering.

    PubMed

    Lee, Jin Woo; Cho, Dong-Woo

    2015-01-01

    Many researchers have attempted to use computer-aided design (CAD) and computer-aided manufacturing (CAM) to realize a scaffold that provides a three-dimensional (3D) environment for regeneration of tissues and organs. As a result, several 3D printing technologies, including stereolithography, deposition modeling, inkjet-based printing and selective laser sintering have been developed. Because these 3D printing technologies use computers for design and fabrication, and they can fabricate 3D scaffolds as designed; as a consequence, they can be standardized. Growth of target tissues and organs requires the presence of appropriate growth factors, so fabrication of 3Dscaffold systems that release these biomolecules has been explored. A drug delivery system (DDS) that administrates a pharmaceutical compound to achieve a therapeutic effect in cells, animals and humans is a key technology that delivers biomolecules without side effects caused by excessive doses. 3D printing technologies and DDSs have been assembled successfully, so new possibilities for improved tissue regeneration have been suggested. If the interaction between cells and scaffold system with biomolecules can be understood and controlled, and if an optimal 3D tissue regenerating environment is realized, 3D printing technologies will become an important aspect of tissue engineering research in the near future.

  11. 3D Printing technology over a drug delivery for tissue engineering.

    PubMed

    Lee, Jin Woo; Cho, Dong-Woo

    2015-01-01

    Many researchers have attempted to use computer-aided design (CAD) and computer-aided manufacturing (CAM) to realize a scaffold that provides a three-dimensional (3D) environment for regeneration of tissues and organs. As a result, several 3D printing technologies, including stereolithography, deposition modeling, inkjet-based printing and selective laser sintering have been developed. Because these 3D printing technologies use computers for design and fabrication, and they can fabricate 3D scaffolds as designed; as a consequence, they can be standardized. Growth of target tissues and organs requires the presence of appropriate growth factors, so fabrication of 3Dscaffold systems that release these biomolecules has been explored. A drug delivery system (DDS) that administrates a pharmaceutical compound to achieve a therapeutic effect in cells, animals and humans is a key technology that delivers biomolecules without side effects caused by excessive doses. 3D printing technologies and DDSs have been assembled successfully, so new possibilities for improved tissue regeneration have been suggested. If the interaction between cells and scaffold system with biomolecules can be understood and controlled, and if an optimal 3D tissue regenerating environment is realized, 3D printing technologies will become an important aspect of tissue engineering research in the near future. PMID:25594413

  12. 3D structuring of biocompatible and biodegradable polymers via stereolithography.

    PubMed

    Gill, Andrew A; Claeyssens, Frederik

    2011-01-01

    The production of user-defined 3D microstructures from biocompatible and biodegradable materials via free-form fabrication is an important step to create off-the-shelf technologies to be used as tissue engineering scaffolds. One method of achieving this is the microstereolithography of block copolymers, allowing high resolution microstructuring of materials with tuneable physical properties. A versatile protocol for the production and photofunctionalisation of pre-polymers for microstereolithography is presented along with a discussion of the possible microstereolithography set-ups and previous work in the field.

  13. Nanostructured 3D Constructs Based on Chitosan and Chondroitin Sulphate Multilayers for Cartilage Tissue Engineering

    PubMed Central

    Silva, Joana M.; Georgi, Nicole; Costa, Rui; Sher, Praveen; Reis, Rui L.; Van Blitterswijk, Clemens A.; Karperien, Marcel; Mano, João F.

    2013-01-01

    Nanostructured three-dimensional constructs combining layer-by-layer technology (LbL) and template leaching were processed and evaluated as possible support structures for cartilage tissue engineering. Multilayered constructs were formed by depositing the polyelectrolytes chitosan (CHT) and chondroitin sulphate (CS) on either bidimensional glass surfaces or 3D packet of paraffin spheres. 2D CHT/CS multi-layered constructs proved to support the attachment and proliferation of bovine chondrocytes (BCH). The technology was transposed to 3D level and CHT/CS multi-layered hierarchical scaffolds were retrieved after paraffin leaching. The obtained nanostructured 3D constructs had a high porosity and water uptake capacity of about 300%. Dynamical mechanical analysis (DMA) showed the viscoelastic nature of the scaffolds. Cellular tests were performed with the culture of BCH and multipotent bone marrow derived stromal cells (hMSCs) up to 21 days in chondrogenic differentiation media. Together with scanning electronic microscopy analysis, viability tests and DNA quantification, our results clearly showed that cells attached, proliferated and were metabolically active over the entire scaffold. Cartilaginous extracellular matrix (ECM) formation was further assessed and results showed that GAG secretion occurred indicating the maintenance of the chondrogenic phenotype and the chondrogenic differentiation of hMSCs. PMID:23437056

  14. All dispenser printed flexible 3D structured thermoelectric generators

    NASA Astrophysics Data System (ADS)

    Cao, Z.; Shi, J. J.; Torah, R. N.; Tudor, M. J.; Beeby, S. P.

    2015-12-01

    This work presents a vertically fabricated 3D thermoelectric generator (TEG) by dispenser printing on flexible polyimide substrate. This direct-write technology only involves printing of electrodes, thermoelectric active materials and structure material, which needs no masks to transfer the patterns onto the substrate. The dimension for single thermoelectric element is 2 mm × 2 mm × 0.5 mm while the distance between adjacent cubes is 1.2 mm. The polymer structure layer was used to support the electrodes which are printed to connect the top ends of the thermoelectric material and ensure the flexibility as well. The advantages and the limitations of the dispenser printed 3D TEGs will also be evaluated in this paper. The proposed method is potential to be a low-cost and scalable fabrication solution for TEGs.

  15. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

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

    2013-06-23

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

  16. Cancer3D: understanding cancer mutations through protein structures

    PubMed Central

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

    2015-01-01

    The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14 700 proteins mapped to more than 24 300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution. PMID:25392415

  17. A Review of 3D Printing Techniques and the Future in Biofabrication of Bioprinted Tissue.

    PubMed

    Patra, Satyajit; Young, Vanesa

    2016-06-01

    3D printing has been around in the art, micro-engineering, and manufacturing worlds for decades. Similarly, research for traditionally engineered skin tissue has been in the works since the 1990s. As of recent years, the medical field also began to take advantage of the untapped potential of 3D printing for the biofabrication of tissue. To do so, researchers created a set of goals for fabricated tissues based on the characteristics of natural human tissues and organs. Fabricated tissue was then measured against this set of standards. Researchers were interested in not only creating tissue that functioned like natural tissues but in creating techniques for 3D printing that would print tissues quickly, efficiently, and ultimately result in the ability to mass produce fabricated tissues. Three promising methods of 3D printing emerged from their research: thermal inkjet printing with bioink, direct-write bioprinting, and organ printing using tissue spheroids. This review will discuss all three printing techniques, as well as their advantages, disadvantages, and the possibility of future advancements in the field of tissue fabrication.

  18. A Review of 3D Printing Techniques and the Future in Biofabrication of Bioprinted Tissue.

    PubMed

    Patra, Satyajit; Young, Vanesa

    2016-06-01

    3D printing has been around in the art, micro-engineering, and manufacturing worlds for decades. Similarly, research for traditionally engineered skin tissue has been in the works since the 1990s. As of recent years, the medical field also began to take advantage of the untapped potential of 3D printing for the biofabrication of tissue. To do so, researchers created a set of goals for fabricated tissues based on the characteristics of natural human tissues and organs. Fabricated tissue was then measured against this set of standards. Researchers were interested in not only creating tissue that functioned like natural tissues but in creating techniques for 3D printing that would print tissues quickly, efficiently, and ultimately result in the ability to mass produce fabricated tissues. Three promising methods of 3D printing emerged from their research: thermal inkjet printing with bioink, direct-write bioprinting, and organ printing using tissue spheroids. This review will discuss all three printing techniques, as well as their advantages, disadvantages, and the possibility of future advancements in the field of tissue fabrication. PMID:27193609

  19. Towards 3D in vitro models for the study of cardiovascular tissues and disease.

    PubMed

    Ryan, Alan J; Brougham, Claire M; Garciarena, Carolina D; Kerrigan, Steven W; O'Brien, Fergal J

    2016-09-01

    The field of tissue engineering is developing biomimetic biomaterial scaffolds that are showing increasing therapeutic potential for the repair of cardiovascular tissues. However, a major opportunity exists to use them as 3D in vitro models for the study of cardiovascular tissues and disease in addition to drug development and testing. These in vitro models can span the gap between 2D culture and in vivo testing, thus reducing the cost, time, and ethical burden of current approaches. Here, we outline the progress to date and the requirements for the development of ideal in vitro 3D models for blood vessels, heart valves, and myocardial tissue. PMID:27117348

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

    PubMed Central

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

    2008-01-01

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

  1. 3D Scaffolds with Different Stiffness but the Same Microstructure for Bone Tissue Engineering.

    PubMed

    Chen, Guobao; Dong, Chanjuan; Yang, Li; Lv, Yonggang

    2015-07-29

    A growing body of evidence has shown that extracellular matrix (ECM) stiffness can modulate stem cell adhesion, proliferation, migration, differentiation, and signaling. Stem cells can feel and respond sensitively to the mechanical microenvironment of the ECM. However, most studies have focused on classical two-dimensional (2D) or quasi-three-dimensional environments, which cannot represent the real situation in vivo. Furthermore, most of the current methods used to generate different mechanical properties invariably change the fundamental structural properties of the scaffolds (such as morphology, porosity, pore size, and pore interconnectivity). In this study, we have developed novel three-dimensional (3D) scaffolds with different degrees of stiffness but the same 3D microstructure that was maintained by using decellularized cancellous bone. Mixtures of collagen and hydroxyapatite [HA: Ca10(PO4)6(OH)2] with different proportions were coated on decellularized cancellous bone to vary the stiffness (local stiffness, 13.00 ± 5.55 kPa, 13.87 ± 1.51 kPa, and 37.7 ± 19.6 kPa; bulk stiffness, 6.74 ± 1.16 kPa, 8.82 ± 2.12 kPa, and 23.61 ± 8.06 kPa). Microcomputed tomography (μ-CT) assay proved that there was no statistically significant difference in the architecture of the scaffolds before or after coating. Cell viability, osteogenic differentiation, cell recruitment, and angiogenesis were determined to characterize the scaffolds and evaluate their biological responses in vitro and in vivo. The in vitro results indicate that the scaffolds developed in this study could sustain adhesion and growth of rat mesenchymal stem cells (MSCs) and promote their osteogenic differentiation. The in vivo results further demonstrated that these scaffolds could help to recruit MSCs from subcutaneous tissue, induce them to differentiate into osteoblasts, and provide the 3D environment for angiogenesis. These findings showed that the method we developed can build scaffolds with

  2. Fabrication of 3-D Submicron Glass Structures by FIB

    NASA Astrophysics Data System (ADS)

    Chao, C. H.; Shen, S. C.; Wu, J. R.

    2009-10-01

    The fabrication characteristic of focused ion beam (FIB) for Pyrex glass was investigated. FIB has several advantages such as high resolution, high material removal rates, low forward scattering, and direct fabrication in selective area without any etching mask. In this study, FIB-etched Pyrex glass was used for fast fabrication of 3-D submicron structures. A glass structure with 0.39 μm in width was fabricated. The experimental results in terms of limiting beam size, ion dose (ion/cm2), and beam current are discussed. The influence of XeF2 gas on FIB glass fabrication was investigated.

  3. Rapid casting of patterned vascular networks for perfusable engineered 3D tissues

    PubMed Central

    Miller, Jordan S.; Stevens, Kelly R.; Yang, Michael T.; Baker, Brendon M.; Nguyen, Duc-Huy T.; Cohen, Daniel M.; Toro, Esteban; Chen, Alice A.; Galie, Peter A.; Yu, Xiang; Chaturvedi, Ritika; Bhatia, Sangeeta N.; Chen, Christopher S.

    2012-01-01

    In the absence of perfusable vascular networks, three-dimensional (3D) engineered tissues densely populated with cells quickly develop a necrotic core [1]. Yet the lack of a general approach to rapidly construct such networks remains a major challenge for 3D tissue culture [2–4]. Here, we 3D printed rigid filament networks of carbohydrate glass, and used them as a cytocompatible sacrificial template in engineered tissues containing living cells to generate cylindrical networks which could be lined with endothelial cells and perfused with blood under high-pressure pulsatile flow. Because this simple vascular casting approach allows independent control of network geometry, endothelialization, and extravascular tissue, it is compatible with a wide variety of cell types, synthetic and natural extracellular matrices (ECMs), and crosslinking strategies. We also demonstrated that the perfused vascular channels sustained the metabolic function of primary rat hepatocytes in engineered tissue constructs that otherwise exhibited suppressed function in their core. PMID:22751181

  4. Controlled surface topography regulates collective 3D migration by epithelial-mesenchymal composite embryonic tissues.

    PubMed

    Song, Jiho; Shawky, Joseph H; Kim, YongTae; Hazar, Melis; LeDuc, Philip R; Sitti, Metin; Davidson, Lance A

    2015-07-01

    Cells in tissues encounter a range of physical cues as they migrate. Probing single cell and collective migratory responses to physically defined three-dimensional (3D) microenvironments and the factors that modulate those responses are critical to understanding how tissue migration is regulated during development, regeneration, and cancer. One key physical factor that regulates cell migration is topography. Most studies on surface topography and cell mechanics have been carried out with single migratory cells, yet little is known about the spreading and motility response of 3D complex multi-cellular tissues to topographical cues. Here, we examine the response to complex topographical cues of microsurgically isolated tissue explants composed of epithelial and mesenchymal cell layers from naturally 3D organized embryos of the aquatic frog Xenopus laevis. We control topography using fabricated micropost arrays (MPAs) and investigate the collective 3D migration of these multi-cellular systems in these MPAs. We find that the topography regulates both collective and individual cell migration and that dense MPAs reduce but do not eliminate tissue spreading. By modulating cell size through the cell cycle inhibitor Mitomycin C or the spacing of the MPAs we uncover how 3D topographical cues disrupt collective cell migration. We find surface topography can direct both single cell motility and tissue spreading, altering tissue-scale processes that enable efficient conversion of single cell motility into collective movement. PMID:25933063

  5. Controlled surface topography regulates collective 3D migration by epithelial-mesenchymal composite embryonic tissues.

    PubMed

    Song, Jiho; Shawky, Joseph H; Kim, YongTae; Hazar, Melis; LeDuc, Philip R; Sitti, Metin; Davidson, Lance A

    2015-07-01

    Cells in tissues encounter a range of physical cues as they migrate. Probing single cell and collective migratory responses to physically defined three-dimensional (3D) microenvironments and the factors that modulate those responses are critical to understanding how tissue migration is regulated during development, regeneration, and cancer. One key physical factor that regulates cell migration is topography. Most studies on surface topography and cell mechanics have been carried out with single migratory cells, yet little is known about the spreading and motility response of 3D complex multi-cellular tissues to topographical cues. Here, we examine the response to complex topographical cues of microsurgically isolated tissue explants composed of epithelial and mesenchymal cell layers from naturally 3D organized embryos of the aquatic frog Xenopus laevis. We control topography using fabricated micropost arrays (MPAs) and investigate the collective 3D migration of these multi-cellular systems in these MPAs. We find that the topography regulates both collective and individual cell migration and that dense MPAs reduce but do not eliminate tissue spreading. By modulating cell size through the cell cycle inhibitor Mitomycin C or the spacing of the MPAs we uncover how 3D topographical cues disrupt collective cell migration. We find surface topography can direct both single cell motility and tissue spreading, altering tissue-scale processes that enable efficient conversion of single cell motility into collective movement.

  6. Controlled Surface Topography regulates Collective 3D Migration by Epithelial-Mesenchymal Composite Embryonic Tissues

    PubMed Central

    Song, Jiho; Shawky, Joseph H.; Kim, YongTae; Hazar, Melis; LeDuc, Philip R.; Sitti, Metin; Davidson, Lance A.

    2015-01-01

    Cells in tissues encounter a range of physical cues as they migrate. Probing single cell and collective migratory responses to physically defined three-dimensional (3D) microenvironments and the factors that modulate those responses are critical to understanding how tissue migration is regulated during development, regeneration, and cancer. One key physical factor that regulates cell migration is topography. Most studies on surface topography and cell mechanics have been carried out with single migratory cells, yet little is known about the spreading and motility response of 3D complex multicellular tissues to topographical cues. Here, we examine the response to complex topographical cues of microsurgically isolated tissue explants composed of epithelial and mesenchymal cell layers from naturally 3D organized embryos of the aquatic frog Xenopus laevis. We control topography using fabricated micropost arrays (MPAs) and investigate the collective 3D migration of these multicellular systems in these MPAs. We find that the topography regulates both collective and individual cell migration and that dense MPAs reduce but do not eliminate tissue spreading. By modulating cell size through the cell cycle inhibitor Mitomycin C or the spacing of the MPAs we uncover how 3D topographical cues disrupt collective cell migration. We find surface topography can direct both single cell motility and tissue spreading, altering tissue-scale processes that enable efficient conversion of single cell motility into collective movement. PMID:25933063

  7. Cyclic Strain Anisotropy Regulates Valvular Interstitial Cell Phenotype and Tissue Remodeling in 3D Culture

    PubMed Central

    Gould, Russell A.; Chin, Karen; Santisakultarm, Thom P.; Dropkin, Amanda; Richards, Jennifer M.; Schaffer, Chris B.; Butcher, Jonathan T.

    2013-01-01

    Many planar connective tissues exhibit complex anisotropic matrix fiber arrangements that are critical to their biomechanical function. This organized structure is created and modified by resident fibroblasts in response to mechanical forces in their environment. The directionality of applied strain fields change dramatically during development, aging, and disease, but the specific effect of strain direction on matrix remodeling is less clear. Current mechanobiological inquiry of planar tissues is limited to equibiaxial or uniaxial stretch, which inadequately simulate many in vivo environments. In this study, we implement a novel bioreactor system to demonstrate the unique effect of controlled anisotropic strain on fibroblast behavior in 3D engineered tissue environments, using aortic valve interstitial fibroblast cells (VIC) as a model system. Cell seeded 3D collagen hydrogels were subjected to cyclic anisotropic strain profiles maintained at constant areal strain magnitude for up to 96 hours at 1Hz. Increasing anisotropy of biaxial strain resulted in increased cellular orientation and collagen fiber alignment along the principal directions of strain and cell orientation was found to precede fiber reorganization. Cellular proliferation and apoptosis were both significantly enhanced under increasing biaxial strain anisotropy (P < 0.05). While cyclic strain reduced both vimentin and alpha-smooth muscle actin compared to unstrained controls, vimentin and alpha-smooth muscle actin expression increased with strain anisotropy and correlated with direction (P < 0.05). Collectively, these results suggest that strain field anisotropy is an independent regulator of fibroblast cell phenotype, turnover, and matrix reorganization, which may inform normal and pathological remodeling in soft tissues. PMID:22281945

  8. Carbon nanotubes leading the way forward in new generation 3D tissue engineering.

    PubMed

    Hopley, Erin Leigh; Salmasi, Shima; Kalaskar, Deepak M; Seifalian, Alexander M

    2014-01-01

    Statistics from the NHS Blood and Transplant Annual Review show that total organ transplants have increased to 4213 in 2012, while the number of people waiting to receive an organ rose to 7613 that same year. Human donors as the origin of transplanted organs no longer meet the ever-increasing demand, and so interest has shifted to synthetic organ genesis as a form of supply. This focus has given rise to new generation tissue and organ engineering, in the hope of one day designing 3D organs in vitro. While research in this field has been conducted for several decades, leading to the first synthetic trachea transplant in 2011, scaffold design for optimising complex tissue growth is still underexplored and underdeveloped. This is mostly the result of the complexity required in scaffolds, as they need to mimic the cells' native extracellular matrix. This is an intricate nanostructured environment that provides cells with physical and chemical stimuli for optimum cell attachment, proliferation and differentiation. Carbon nanotubes are a popular addition to synthetic scaffolds and have already begun to revolutionise regenerative medicine. Discovered in 1991, these are traditionally used in various areas of engineering and technology; however, due to their excellent mechanical, chemical and electrical properties their potential is now being explored in areas of drug delivery, in vivo biosensor application and tissue engineering. The incorporation of CNTs into polymer scaffolds displays a variety of structural and chemical enhancements, some of which include: increased scaffold strength and flexibility, improved biocompatibility, reduction in cancerous cell division, induction of angiogenesis, reduced thrombosis, and manipulation of gene expression in developing cells. Moreover CNTs' tensile properties open doors for dynamic scaffold design, while their thermal and electrical properties provide opportunities for the development of neural, bone and cardiac tissue constructs

  9. Automatic structural matching of 3D image data

    NASA Astrophysics Data System (ADS)

    Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor

    2015-10-01

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

  10. Engineering multi-layered skeletal muscle tissue by using 3D microgrooved collagen scaffolds.

    PubMed

    Chen, Shangwu; Nakamoto, Tomoko; Kawazoe, Naoki; Chen, Guoping

    2015-12-01

    Preparation of three-dimensional (3D) micropatterned porous scaffolds remains a great challenge for engineering of highly organized tissues such as skeletal muscle tissue and cardiac tissue. Two-dimensional (2D) micropatterned surfaces with periodic features (several nanometers to less than 100 μm) are commonly used to guide the alignment of muscle myoblasts and myotubes and lead to formation of pre-patterned cell sheets. However, cell sheets from 2D patterned surfaces have limited thickness, and harvesting the cell sheets for implantation is inconvenient and can lead to less alignment of myotubes. 3D micropatterned scaffolds can promote cell alignment and muscle tissue formation. In this study, we developed a novel type of 3D porous collagen scaffolds with concave microgrooves that mimic muscle basement membrane to engineer skeletal muscle tissue. Highly aligned and multi-layered muscle bundle tissues were engineered by controlling the size of microgrooves and cell seeding concentration. Myoblasts in the engineered muscle tissue were well-aligned and had high expression of myosin heavy chain and synthesis of muscle extracellular matrix. The microgrooved collagen scaffolds could be used to engineer organized multi-layered muscle tissue for implantation to repair/restore the function of diseased tissues or be used to investigate the cell-cell interaction in 3D microscale topography.

  11. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

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

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

    PubMed

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

    2012-07-01

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

  13. 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.

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

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

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

  15. 3D geophysical investigations of shallow karstic structures

    NASA Astrophysics Data System (ADS)

    Rousset, D.; Genthon, P.; Perroud, H.; Sénéchal, G.

    2003-04-01

    The accurate determination of shallow kastified areas is of major importance for the quantitative modelling of fluid transfer as well as for geotechnical issues. Near surface geophysics offers a broad range of tools dedicated to the study of voids and other cavities filled with water or sediments. We present the results of various geophysical studies (seismics, GPR, 2-D and 3-D DC resitivity) in the Baget area, a hydrologically well monitored zone, in the vicinity of Moulis underground laboratory in the Central Pyrenees. The studied area is a 1Km long segment of a narrow EW valley, located on the boundary between limestones and shales, with emphasis on a 100m long anomalous zone. begin{itemize} Seismics doesn't allow to derive a focused image of the very shallow (< 2m) structure but amplitude anomalies suggest the presence of scattering structures in the valley. GPR data clearly show the sedimentary filling of the valley, overlying the generally transparent limestone basement. Two highly reflective zones evidence the presence of heterogeneities. 2-D DC resistivity exhibits very different results whether the lines are in the direction of the valley or perpendicular to it. Results suggest a strong influence of the topography leading to completely erroneous conclusions without complementary data. The presentation is focused on GPR and DC resitivity methods. The limitations of 3-D DC inversion is partly overcome by transforming the data from pole-pole pattern to dipole-dipole, allowing us to get more details on the shallow and short wavelenght structures with conventional software. Voids are indicated by the presence of a temporary river and speleological exploration but the results of the study show the absence of big cavities under the surface, within the first meters of limestone. GPR and DC resitivity studies reveal the presence of shallow metric heterogeneities which can be the water conduit system. 3-D investigation is necessary to get consistent results.

  16. Microscale technologies for imaging endogenous gene expression in individual cells within 3D tissues

    NASA Astrophysics Data System (ADS)

    Ye, Ting; Luo, Zhen; Ma, Yunzhe; Gill, Harvinder Singh; Nitin, N.

    2013-05-01

    The goal of this study was to develop an innovative approach to image gene expression in intact 3D tissues. Imaging gene expression of individual cells in 3D tissues is expected to have a significant impact on both clinical diagnostic applications and fundamental biological science and engineering applications in a laboratory setting. To achieve this goal, we have developed an integrated approach that combines: 1) microneedle-based minimally invasive intra-tissue delivery of oligonucleotide probes and Streptolysin O (SLO) or CPP; 2) SLO as a pore forming permeation enhancer to enable intracellular delivery of oligonucleotide probes and CPP peptides can also transport conjugated cargo in cells; and 3) fluorescence resonance energy transfer (FRET) pair of ON probes to improve specificity and sensitivity of RNA detection in tissue models. The results of this study demonstrate uniform coating and rapid release of ON probes from microneedles in a tissue environment. Microneedle assisted delivery of ON probes in 3D tissue does not result in cell damage and the ON probes are uniformly delivered in the tissue. The results also demonstrate the feasibility of FRET imaging of ON probes in 3D tissue and highlight the potential for imaging 28-s rRNA in individual living cells.

  17. Construction and Myogenic Differentiation of 3D Myoblast Tissues Fabricated by Fibronectin-Gelatin Nanofilm Coating

    PubMed Central

    Gribova, Varvara; Liu, Chen Yun; Nishiguchi, Akihiro; Matsusaki, Michiya; Boudou, Thomas; Picart, Catherine; Akashi, Mitsuru

    2016-01-01

    In this study, we used a recently developed approach of coating the cells with fibronectin-gelatin nanofilms to build 3D skeletal muscle tissue models. We constructed the microtissues from C2C12 myoblasts and subsequently differentiated them to form muscle-like tissue. The thickness of the constructs could be successfully controlled by altering the number of seeded cells. We were able to build up to ~ 76 µm thick 3D constructs that formed multinucleated myotubes. We also found that Rho-kinase inhibitor Y27632 improved myotube formation in thick constructs. Our approach makes it possible to rapidly form 3D muscle tissues and is promising for the in vitro construction of physiologically relevant human skeletal muscle tissue models. PMID:27125461

  18. Organ printing: computer-aided jet-based 3D tissue engineering.

    PubMed

    Mironov, Vladimir; Boland, Thomas; Trusk, Thomas; Forgacs, Gabor; Markwald, Roger R

    2003-04-01

    Tissue engineering technology promises to solve the organ transplantation crisis. However, assembly of vascularized 3D soft organs remains a big challenge. Organ printing, which we define as computer-aided, jet-based 3D tissue-engineering of living human organs, offers a possible solution. Organ printing involves three sequential steps: pre-processing or development of "blueprints" for organs; processing or actual organ printing; and postprocessing or organ conditioning and accelerated organ maturation. A cell printer that can print gels, single cells and cell aggregates has been developed. Layer-by-layer sequentially placed and solidified thin layers of a thermo-reversible gel could serve as "printing paper". Combination of an engineering approach with the developmental biology concept of embryonic tissue fluidity enables the creation of a new rapid prototyping 3D organ printing technology, which will dramatically accelerate and optimize tissue and organ assembly. PMID:12679063

  19. Evaluation of 3D nano-macro porous bioactive glass scaffold for hard tissue engineering.

    PubMed

    Wang, S; Falk, M M; Rashad, A; Saad, M M; Marques, A C; Almeida, R M; Marei, M K; Jain, H

    2011-05-01

    Recently, nano-macro dual-porous, three-dimensional (3D) glass structures were developed for use as bioscaffolds for hard tissue regeneration, but there have been concerns regarding the interconnectivity and homogeneity of nanopores in the scaffolds, as well as the cytotoxicity of the environment deep inside due to limited fluid access. Therefore, mercury porosimetry, nitrogen absorption, and TEM have been used to characterize nanopore network of the scaffolds. In parallel, viability of MG 63 human osteosarcoma cells seeded on scaffold surface was investigated by fluorescence, confocal and electron microscopy methods. The results show that cells attach, migrate and penetrate inside the glass scaffold with high proliferation and viability rate. Additionally, scaffolds were implanted under the skin of a male New Zealand rabbit for in vivo animal test. Initial observations show the formation of new tissue with blood vessels and collagen fibers deep inside the implanted scaffolds with no obvious inflammatory reaction. Thus, the new nano-macro dual-porous glass structure could be a promising bioscaffold for use in regenerative medicine and tissue engineering for bone regeneration. PMID:21445655

  20. Rapid prototyping for tissue-engineered bone scaffold by 3D printing and biocompatibility study

    PubMed Central

    He, Hui-Yu; Zhang, Jia-Yu; Mi, Xue; Hu, Yang; Gu, Xiao-Yu

    2015-01-01

    The prototyping of tissue-engineered bone scaffold (calcined goat spongy bone-biphasic ceramic composite/PVA gel) by 3D printing was performed, and the biocompatibility of the fabricated bone scaffold was studied. Pre-designed STL file was imported into the GXYZ303010-XYLE 3D printing system, and the tissue-engineered bone scaffold was fabricated by 3D printing using gel extrusion. Rabbit bone marrow stromal cells (BMSCs) were cultured in vitro and then inoculated to the sterilized bone scaffold obtained by 3D printing. The growth of rabbit BMSCs on the bone scaffold was observed under the scanning electron microscope (SEM). The effect of the tissue-engineered bone scaffold on the proliferation and differentiation of rabbit BMSCs using MTT assay. Universal testing machine was adopted to test the tensile strength of the bone scaffold. The leachate of the bone scaffold was prepared and injected into the New Zealand rabbits. Cytotoxicity test, acute toxicity test, pyrogenic test and intracutaneous stimulation test were performed to assess the biocompatibility of the bone scaffold. Bone scaffold manufactured by 3D printing had uniform pore size with the porosity of about 68.3%. The pores were well interconnected, and the bone scaffold showed excellent mechanical property. Rabbit BMSCs grew and proliferated on the surface of the bone scaffold after adherence. MTT assay indicated that the proliferation and differentiation of rabbit BMSCs on the bone scaffold did not differ significantly from that of the cells in the control. In vivo experiments proved that the bone scaffold fabricated by 3D printing had no acute toxicity, pyrogenic reaction or stimulation. Bone scaffold manufactured by 3D printing allows the rabbit BMSCs to adhere, grow and proliferate and exhibits excellent biomechanical property and high biocompatibility. 3D printing has a good application prospect in the prototyping of tissue-engineered bone scaffold. PMID:26380018

  1. Rapid prototyping for tissue-engineered bone scaffold by 3D printing and biocompatibility study.

    PubMed

    He, Hui-Yu; Zhang, Jia-Yu; Mi, Xue; Hu, Yang; Gu, Xiao-Yu

    2015-01-01

    The prototyping of tissue-engineered bone scaffold (calcined goat spongy bone-biphasic ceramic composite/PVA gel) by 3D printing was performed, and the biocompatibility of the fabricated bone scaffold was studied. Pre-designed STL file was imported into the GXYZ303010-XYLE 3D printing system, and the tissue-engineered bone scaffold was fabricated by 3D printing using gel extrusion. Rabbit bone marrow stromal cells (BMSCs) were cultured in vitro and then inoculated to the sterilized bone scaffold obtained by 3D printing. The growth of rabbit BMSCs on the bone scaffold was observed under the scanning electron microscope (SEM). The effect of the tissue-engineered bone scaffold on the proliferation and differentiation of rabbit BMSCs using MTT assay. Universal testing machine was adopted to test the tensile strength of the bone scaffold. The leachate of the bone scaffold was prepared and injected into the New Zealand rabbits. Cytotoxicity test, acute toxicity test, pyrogenic test and intracutaneous stimulation test were performed to assess the biocompatibility of the bone scaffold. Bone scaffold manufactured by 3D printing had uniform pore size with the porosity of about 68.3%. The pores were well interconnected, and the bone scaffold showed excellent mechanical property. Rabbit BMSCs grew and proliferated on the surface of the bone scaffold after adherence. MTT assay indicated that the proliferation and differentiation of rabbit BMSCs on the bone scaffold did not differ significantly from that of the cells in the control. In vivo experiments proved that the bone scaffold fabricated by 3D printing had no acute toxicity, pyrogenic reaction or stimulation. Bone scaffold manufactured by 3D printing allows the rabbit BMSCs to adhere, grow and proliferate and exhibits excellent biomechanical property and high biocompatibility. 3D printing has a good application prospect in the prototyping of tissue-engineered bone scaffold.

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

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

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

  3. Axonemal radial spokes: 3D structure, function and assembly.

    PubMed

    Pigino, Gaia; Ishikawa, Takashi

    2012-02-01

    The radial spoke (RS) is a complex of at least 23 proteins that works as a mechanochemical transducer between the central-pair apparatus and the peripheral microtubule doublets in eukaryotic flagella and motile cilia. The RS contributes to the regulation of the activity of dynein motors, and thus to flagellar motility. Despite numerous biochemical, physiological and structural studies, the mechanism of the function of the radial spoke remains unclear. Detailed knowledge of the 3D structure of the RS protein complex is needed in order to understand how RS regulates dynein activity. Here we review the most important findings on the structure of the RS, including results of our recent cryo-electron tomographic analysis of the RS protein complex. PMID:22754630

  4. YAP is essential for tissue tension to ensure vertebrate 3D body shape.

    PubMed

    Porazinski, Sean; Wang, Huijia; Asaoka, Yoichi; Behrndt, Martin; Miyamoto, Tatsuo; Morita, Hitoshi; Hata, Shoji; Sasaki, Takashi; Krens, S F Gabriel; Osada, Yumi; Asaka, Satoshi; Momoi, Akihiro; Linton, Sarah; Miesfeld, Joel B; Link, Brian A; Senga, Takeshi; Castillo-Morales, Atahualpa; Urrutia, Araxi O; Shimizu, Nobuyoshi; Nagase, Hideaki; Matsuura, Shinya; Bagby, Stefan; Kondoh, Hisato; Nishina, Hiroshi; Heisenberg, Carl-Philipp; Furutani-Seiki, Makoto

    2015-05-14

    Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues.

  5. 3D structure tensor analysis of light microscopy data for validating diffusion MRI

    PubMed Central

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A.; Kohama, Steven G.; Jespersen, Sune Nørhøj; Kroenke, Christopher D.

    2015-01-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image “stacks” acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations

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

    NASA Astrophysics Data System (ADS)

    Jaiswal, Neeru; Kishtawal, C. M.

    2016-05-01

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

  7. Evaluating 3D Printed Biomaterials as Scaffolds for Vascularized Bone Tissue Engineering

    PubMed Central

    Wang, Martha O.; Vorwald, Charlotte E.; Dreher, Maureen L.; Mott, Eric J.; Cheng, Ming-Huei; Cinar, Ali; Mehdizadeh, Hamidreza; Somo, Sami; Dean, David; Brey, Eric M.; Fisher, John P.

    2015-01-01

    The recent proliferation of three dimensional (3D) printing technologies has allowed the exploration of increasing complex designs, and, furthermore, the consideration of 3D printed constructs for biological applications. However, there is an unmet need for a consistent set of tools for the design and evaluation of these biological 3D printed constructs, particularly as they relate to engineered tissues. For example, identifying the most advantageous construct parameters for the rapid vascularization of an engineered tissue - a critical parameter in regenerative medicine - is difficult without a common group of measures. We demonstrate here a toolbox to design, characterize, and evaluate 3D printed scaffolds for vascularized tissue regenerative medicine. Our toolbox (1) identifies the range of design specifications using a modular design, (2) nondestructively compares the 3D printed scaffolds to the design, (3) evaluates biocompatibility and mechanical properties, and (4) predicts host vessel integration. As a case study, we designed, fabricated, and evaluated polymer scaffolds using a poly(propylene fumarate) based resin. Our work highlights the potential for these tools to be combined as a consistent methodology for the evaluation of porous 3D printed constructs for regenerative medicine. PMID:25387454

  8. Parametric estimation of 3D tubular structures for diffuse optical tomography

    PubMed Central

    Larusson, Fridrik; Anderson, Pamela G.; Rosenberg, Elizabeth; Kilmer, Misha E.; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L.

    2013-01-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction. PMID:23411913

  9. Laser 3D micro/nanofabrication of polymers for tissue engineering applications

    NASA Astrophysics Data System (ADS)

    Danilevičius, P.; Rekštytė, S.; Balčiūnas, E.; Kraniauskas, A.; Širmenis, R.; Baltriukienė, D.; Bukelskienė, V.; Gadonas, R.; Sirvydis, V.; Piskarskas, A.; Malinauskas, M.

    2013-02-01

    In this work, we applied a constructed multi-photon polymerization system based on diode-pumped solid state femtosecond Yb:KGW laser used as pulsed irradiation light source (300 fs, 1030 nm, 200 kHz) in combination with large area high sample translation velocity (up to 300 mm/s) linear motor-driven stages (100×100×50 mm3) designed for high resolution and throughput 3D micro/nanofabrication. It enables rapid prototyping out of most polymers up to cm in scale with sub-micrometer spatial resolution. This can be used for production of three-dimensional artificial polymeric scaffolds applied for cell growth and expansion experiments as well as tissue engineering. Biocompatibilities of different acrylate, hybrid organic-inorganic and biodegradable polymeric materials were evaluated experimentally in vitro. Various in size and form scaffolds of biocompatible photopolymers were successfully fabricated having intricate 3D geometry, thus demonstrating the potential of the applied method. Adult rabbit myogenic stem cell proliferation tests show artificial scaffolds to be applicable for biomedical practice. Additionally, a micromolding technique was used for a rapid multiplication of adequate laser manufactured structures.

  10. 3D structure tensor analysis of light microscopy data for validating diffusion MRI.

    PubMed

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A; Kohama, Steven G; Jespersen, Sune Nørhøj; Kroenke, Christopher D

    2015-05-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image "stacks" acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations that

  11. Subacute Tissue Response to 3D Graphene Oxide Scaffolds Implanted in the Injured Rat Spinal Cord.

    PubMed

    López-Dolado, Elisa; González-Mayorga, Ankor; Portolés, María Teresa; Feito, María José; Ferrer, María Luisa; Del Monte, Francisco; Gutiérrez, María Concepción; Serrano, María Concepción

    2015-08-26

    The increasing prevalence and high sanitary costs of lesions affecting the central nervous system (CNS) at the spinal cord are encouraging experts in different fields to explore new avenues for neural repair. In this context, graphene and its derivatives are attracting significant attention, although their toxicity and performance in the CNS in vivo remains unclear. Here, the subacute tissue response to 3D flexible and porous scaffolds composed of partially reduced graphene oxide is investigated when implanted in the injured rat spinal cord. The interest of these structures as potentially useful platforms for CNS regeneration mainly relies on their mechanical compliance with neural tissues, adequate biocompatibility with neural cells in vitro and versatility to carry topographical and biological guidance cues. Early tissue responses are thoroughly investigated locally (spinal cord at C6 level) and in the major organs (i.e., kidney, liver, lung, and spleen). The absence of local and systemic toxic responses, along with the positive signs found at the lesion site (e.g., filler effect, soft interface for no additional scaring, preservation of cell populations at the perilesional area, presence of M2 macrophages), encourages further investigation of these materials as promising components of more efficient material-based platforms for CNS repair.

  12. Characterisation of the surface structure of 3D printed scaffolds for cell infiltration and surgical suturing.

    PubMed

    Ruiz-Cantu, Laura; Gleadall, Andrew; Faris, Callum; Segal, Joel; Shakesheff, Kevin; Yang, Jing

    2016-03-01

    3D printing is of great interest for tissue engineering scaffolds due to the ability to form complex geometries and control internal structures, including porosity and pore size. The porous structure of scaffolds plays an important role in cell ingrowth and nutrition infusion. Although the internal porosity and pore size of 3D printed scaffolds have been frequently studied, the surface porosity and pore size, which are critical for cell infiltration and mass transport, have not been investigated. The surface geometry can differ considerably from the internal scaffold structure depending on the 3D printing process. It is vital to be able to control the surface geometry of scaffolds as well as the internal structure to fabricate optimal architectures. This work presents a method to control the surface porosity and pore size of 3D printed scaffolds. Six scaffold designs have been printed with surface porosities ranging from 3% to 21%. We have characterised the overall scaffold porosity and surface porosity using optical microscopy and microCT. It has been found that surface porosity has a significant impact on cell infiltration and proliferation. In addition, the porosity of the surface has been found to have an effect on mechanical properties and on the forces required to penetrate the scaffold with a surgical suturing needle. To the authors' knowledge, this study is the first to investigate the surface geometry of extrusion-based 3D printed scaffolds and demonstrates the importance of surface geometry in cell infiltration and clinical manipulation. PMID:26930179

  13. Characterisation of the surface structure of 3D printed scaffolds for cell infiltration and surgical suturing.

    PubMed

    Ruiz-Cantu, Laura; Gleadall, Andrew; Faris, Callum; Segal, Joel; Shakesheff, Kevin; Yang, Jing

    2016-03-01

    3D printing is of great interest for tissue engineering scaffolds due to the ability to form complex geometries and control internal structures, including porosity and pore size. The porous structure of scaffolds plays an important role in cell ingrowth and nutrition infusion. Although the internal porosity and pore size of 3D printed scaffolds have been frequently studied, the surface porosity and pore size, which are critical for cell infiltration and mass transport, have not been investigated. The surface geometry can differ considerably from the internal scaffold structure depending on the 3D printing process. It is vital to be able to control the surface geometry of scaffolds as well as the internal structure to fabricate optimal architectures. This work presents a method to control the surface porosity and pore size of 3D printed scaffolds. Six scaffold designs have been printed with surface porosities ranging from 3% to 21%. We have characterised the overall scaffold porosity and surface porosity using optical microscopy and microCT. It has been found that surface porosity has a significant impact on cell infiltration and proliferation. In addition, the porosity of the surface has been found to have an effect on mechanical properties and on the forces required to penetrate the scaffold with a surgical suturing needle. To the authors' knowledge, this study is the first to investigate the surface geometry of extrusion-based 3D printed scaffolds and demonstrates the importance of surface geometry in cell infiltration and clinical manipulation.

  14. 3D Printing of Human Tissue Mimics via Layer-by-Layer Assembly of Polymer/Hydrogel Biopapers

    NASA Astrophysics Data System (ADS)

    Ringeisen, Bradley

    2015-03-01

    The foundations of tissue engineering were built on two fundamental areas of research: cells and scaffolds. Multipotent cells and their derivatives are traditionally randomly seeded into sophisticated polymer or hydrogel scaffolds, ultimately with the goal of forming a tissue-like material through cell differentiation and cell-material interactions. One problem with this approach is that no matter how complex or biomimetic the scaffold is, the cells are still homogeneously distributed throughout this three dimensional (3D) material. Natural tissue is inherently heterogeneous on both a microscopic and macroscopic level. It also contains different types of cells in close proximity, extracellular matrix, voids, and a complex vascularized network. Recently developed 3D cell and organ printers may be able to enhance traditional tissue engineering experiments by building scaffolds layer-by-layer that are crafted to mimic the microscopic and macroscopic structure of natural tissue or organs. Over the past decade, my laboratory has developed a capillary-free, live cell printer termed biological laser printing, or BioLP. We find that printed cells do not express heat shock protein and retain >99% viability. Printed cells also incur no DNA strand fracture and preserve their ability to differentiate. Recent work has used a layer-by-layer approach, stacking sheets of hybrid polymer/hydrogel biopapers in conjunction with live cell printing to create 3D tissue structures. Our specific work is now focused on the blood-brain-barrier and air-lung interface and will be described during the presentation.

  15. Could 3D bioprinted tissues offer future hope for microtia treatment?

    PubMed

    Thomas, Daniel J

    2016-08-01

    Microtia is a congenital deformity where the pinna is underdeveloped. Contraindications to rib surgery for microtia reconstruction include high-risk surgical status and chest-wall deformities [1-2]. However does stem-cell-based 3D Bioprinting offer revolutionary therapeutic options for patients with such tissue abnormalities. As a technology, 3D-bioprinting is being developed to generate homogeneous tissues by depositing a low viscosity printable cellular-active gel which matures into a tissue [3]. Currently on-going research is developing the process towards producing cartilage tissues for use in reconstructive surgery. This process focuses on using the natural self-organising properties of cells in order to produce a functional tissue which has measurable: mechanical, metabolic and functional properties. PMID:27353851

  16. Could 3D bioprinted tissues offer future hope for microtia treatment?

    PubMed

    Thomas, Daniel J

    2016-08-01

    Microtia is a congenital deformity where the pinna is underdeveloped. Contraindications to rib surgery for microtia reconstruction include high-risk surgical status and chest-wall deformities [1-2]. However does stem-cell-based 3D Bioprinting offer revolutionary therapeutic options for patients with such tissue abnormalities. As a technology, 3D-bioprinting is being developed to generate homogeneous tissues by depositing a low viscosity printable cellular-active gel which matures into a tissue [3]. Currently on-going research is developing the process towards producing cartilage tissues for use in reconstructive surgery. This process focuses on using the natural self-organising properties of cells in order to produce a functional tissue which has measurable: mechanical, metabolic and functional properties.

  17. NFkB disrupts tissue polarity in 3D by preventing integration of microenvironmental signals.

    PubMed

    Becker-Weimann, Sabine; Xiong, Gaofeng; Furuta, Saori; Han, Ju; Kuhn, Irene; Akavia, Uri-David; Pe'er, Dana; Bissell, Mina J; Xu, Ren

    2013-11-01

    The microenvironment of cells controls their phenotype, and thereby the architecture of the emerging multicellular structure or tissue. We have reported more than a dozen microenvironmental factors whose signaling must be integrated in order to effect an organized, functional tissue morphology. However, the factors that prevent integration of signaling pathways that merge form and function are still largely unknown. We have identified nuclear factor kappa B (NFkB) as a transcriptional regulator that disrupts important microenvironmental cues necessary for tissue organization. We compared the gene expression of organized and disorganized epithelial cells of the HMT-3522 breast cancer progression series: the non-malignant S1 cells that form polarized spheres ('acini'), the malignant T4-2 cells that form large tumor-like clusters, and the 'phenotypically reverted' T4-2 cells that polarize as a result of correction of the microenvironmental signaling. We identified 180 genes that display an increased expression in disorganized compared to polarized structures. Network, GSEA and transcription factor binding site analyses suggested that NFkB is a common activator for the 180 genes. NFkB was found to be activated in disorganized breast cancer cells, and inhibition of microenvironmental signaling via EGFR, beta1 integrin, MMPs, or their downstream signals suppressed its activation. The postulated role of NFkB was experimentally verified: Blocking the NFkB pathway with a specific chemical inhibitor or shRNA induced polarization and inhibited invasion of breast cancer cells in 3D cultures. These results may explain why NFkB holds promise as a target for therapeutic intervention: Its inhibition can reverse the oncogenic signaling involved in breast cancer progression and integrate the essential microenvironmental control of tissue architecture.

  18. A survey of clearing techniques for 3D imaging of tissues with special reference to connective tissue.

    PubMed

    Azaripour, Adriano; Lagerweij, Tonny; Scharfbillig, Christina; Jadczak, Anna Elisabeth; Willershausen, Brita; Van Noorden, Cornelis J F

    2016-08-01

    For 3-dimensional (3D) imaging of a tissue, 3 methodological steps are essential and their successful application depends on specific characteristics of the type of tissue. The steps are 1° clearing of the opaque tissue to render it transparent for microscopy, 2° fluorescence labeling of the tissues and 3° 3D imaging. In the past decades, new methodologies were introduced for the clearing steps with their specific advantages and disadvantages. Most clearing techniques have been applied to the central nervous system and other organs that contain relatively low amounts of connective tissue including extracellular matrix. However, tissues that contain large amounts of extracellular matrix such as dermis in skin or gingiva are difficult to clear. The present survey lists methodologies that are available for clearing of tissues for 3D imaging. We report here that the BABB method using a mixture of benzyl alcohol and benzyl benzoate and iDISCO using dibenzylether (DBE) are the most successful methods for clearing connective tissue-rich gingiva and dermis of skin for 3D histochemistry and imaging of fluorescence using light-sheet microscopy.

  19. 3D Shape and Indirect Appearance by Structured Light Transport.

    PubMed

    OToole, Matthew; Mather, John; Kutulakos, Kiriakos N

    2016-07-01

    We consider the problem of deliberately manipulating the direct and indirect light flowing through a time-varying, general scene in order to simplify its visual analysis. Our approach rests on a crucial link between stereo geometry and light transport: while direct light always obeys the epipolar geometry of a projector-camera pair, indirect light overwhelmingly does not. We show that it is possible to turn this observation into an imaging method that analyzes light transport in real time in the optical domain, prior to acquisition. This yields three key abilities that we demonstrate in an experimental camera prototype: (1) producing a live indirect-only video stream for any scene, regardless of geometric or photometric complexity; (2) capturing images that make existing structured-light shape recovery algorithms robust to indirect transport; and (3) turning them into one-shot methods for dynamic 3D shape capture.

  20. Edge singularities and structure of the 3-D Williams expansion

    NASA Astrophysics Data System (ADS)

    Apel, Thomas; Leguillon, Dominique; Pester, Cornelia; Yosibash, Zohar

    2008-08-01

    The elastic solution in a vicinity of a re-entrant wedge can be described by a Williams like expansion in terms of powers of the distance to a point on the edge. This expansion has a particular structure due to the invariance of the problem by translation parallel to the edge. We show here that some terms, so-called primary solutions, derive directly from solutions to the 2-D corner problem posed in the orthogonal cross section of the domain. The others, baptized shadow functions, derive of the primary solutions by integration along the axis parallel to the edge. This 3-D Williams expansion is shown to be equivalent to the edge expansion proposed by Costabel et al. [M. Costabel, M. Dauge, Z. Yosibash, A quasidual function method for extracting edge stress intensity functions, SIAM J. Math. Anal. 35 (5) (2004) 1177-1202]. To cite this article: T. Apel et al., C. R. Mecanique 336 (2008).

  1. 3D bioprinting matrices with controlled pore structure and release function guide in vitro self-organization of sweat gland

    PubMed Central

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

    2016-01-01

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

  2. 3D complex: a structural classification of protein complexes.

    PubMed

    Levy, Emmanuel D; Pereira-Leal, Jose B; Chothia, Cyrus; Teichmann, Sarah A

    2006-11-17

    Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

  3. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

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

  4. 3D Wilson cycle: structural inheritance and subduction polarity reversals

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  5. 3D printing technology using high viscous materials - Synthesis of functional materials and fabrication of 3D metal structure

    NASA Astrophysics Data System (ADS)

    Hong, Seongik

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

  6. 3D Imaging with Structured Illumination for Advanced Security Applications

    SciTech Connect

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

    2015-09-01

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

  7. An Efficient 3D Imaging using Structured Light Systems

    NASA Astrophysics Data System (ADS)

    Lee, Deokwoo

    Structured light 3D surface imaging has been crucial in the fields of image processing and computer vision, particularly in reconstruction, recognition and others. In this dissertation, we propose the approaches to development of an efficient 3D surface imaging system using structured light patterns including reconstruction, recognition and sampling criterion. To achieve an efficient reconstruction system, we address the problem in its many dimensions. In the first, we extract geometric 3D coordinates of an object which is illuminated by a set of concentric circular patterns and reflected to a 2D image plane. The relationship between the original and the deformed shape of the light patterns due to a surface shape provides sufficient 3D coordinates information. In the second, we consider system efficiency. The efficiency, which can be quantified by the size of data, is improved by reducing the number of circular patterns to be projected onto an object of interest. Akin to the Shannon-Nyquist Sampling Theorem, we derive the minimum number of circular patterns which sufficiently represents the target object with no considerable information loss. Specific geometric information (e.g. the highest curvature) of an object is key to deriving the minimum sampling density. In the third, the object, represented using the minimum number of patterns, has incomplete color information (i.e. color information is given a priori along with the curves). An interpolation is carried out to complete the photometric reconstruction. The results can be approximately reconstructed because the minimum number of the patterns may not exactly reconstruct the original object. But the result does not show considerable information loss, and the performance of an approximate reconstruction is evaluated by performing recognition or classification. In an object recognition, we use facial curves which are deformed circular curves (patterns) on a target object. We simply carry out comparison between the

  8. In the beginning there were soft collagen-cell gels: towards better 3D connective tissue models?

    PubMed

    Brown, Robert A

    2013-10-01

    In the 40 years since Elsdale and Bard's analysis of fibroblast culture in collagen gels we have moved far beyond the concept that such 3D fibril network systems are better models than monolayer cultures. This review analyses key aspects of that progression of models, against a background of what exactly each model system tries to mimic. This story tracks our increasing understanding of fibroblast responses to soft collagen gels, in particularly their cytoskeletal contraction, migration and integrin attachment. The focus on fibroblast mechano-function has generated models designed to directly measure the overall force generated by fibroblast populations, their reaction to external loads and the role of the matrix structure. Key steps along this evolution of 3D collagen models have been designed to mimic normal skin, wound repair, tissue morphogenesis and remodelling, growth and contracture during scarring/fibrosis. As new models are developed to understand cell-mechanical function in connective tissues the collagen material has become progressively more important, now being engineered to mimic more complex aspects of native extracellular matrix structure. These have included collagen fibril density, alignment and hierarchical structure, controlling material stiffness and anisotropy. But of these, tissue-like collagen density is key in that it contributes to control of the others. It is concluded that across this 40 year window major progress has been made towards establishing a family of 3D experimental collagen tissue-models, suitable to investigate normal and pathological fibroblast mechano-functions.

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

    PubMed

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

    2014-07-01

    A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins. PMID:25069136

  10. The 3D structure of Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Patsourakos, Spiros

    2016-07-01

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

  11. Biodynamic Doppler imaging of subcellular motion inside 3D living tissue culture and biopsies (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Nolte, David D.

    2016-03-01

    Biodynamic imaging is an emerging 3D optical imaging technology that probes up to 1 mm deep inside three-dimensional living tissue using short-coherence dynamic light scattering to measure the intracellular motions of cells inside their natural microenvironments. Biodynamic imaging is label-free and non-invasive. The information content of biodynamic imaging is captured through tissue dynamics spectroscopy that displays the changes in the Doppler signatures from intracellular constituents in response to applied compounds. The affected dynamic intracellular mechanisms include organelle transport, membrane undulations, cytoskeletal restructuring, strain at cellular adhesions, cytokinesis, mitosis, exo- and endo-cytosis among others. The development of 3D high-content assays such as biodynamic profiling can become a critical new tool for assessing efficacy of drugs and the suitability of specific types of tissue growth for drug discovery and development. The use of biodynamic profiling to predict clinical outcome of living biopsies to cancer therapeutics can be developed into a phenotypic companion diagnostic, as well as a new tool for therapy selection in personalized medicine. This invited talk will present an overview of the optical, physical and physiological processes involved in biodynamic imaging. Several different biodynamic imaging modalities include motility contrast imaging (MCI), tissue-dynamics spectroscopy (TDS) and tissue-dynamics imaging (TDI). A wide range of potential applications will be described that include process monitoring for 3D tissue culture, drug discovery and development, cancer therapy selection, embryo assessment for in-vitro fertilization and artificial reproductive technologies, among others.

  12. Direct laser writing of 3D scaffolds for neural tissue engineering applications.

    PubMed

    Melissinaki, V; Gill, A A; Ortega, I; Vamvakaki, M; Ranella, A; Haycock, J W; Fotakis, C; Farsari, M; Claeyssens, F

    2011-12-01

    This study reports on the production of high-resolution 3D structures of polylactide-based materials via multi-photon polymerization and explores their use as neural tissue engineering scaffolds. To achieve this, a liquid polylactide resin was synthesized in house and rendered photocurable via attaching methacrylate groups to the hydroxyl end groups of the small molecular weight prepolymer. This resin cures easily under UV irradiation, using a mercury lamp, and under femtosecond IR irradiation. The results showed that the photocurable polylactide (PLA) resin can be readily structured via direct laser write (DLW) with a femtosecond Ti:sapphire laser and submicrometer structures can be produced. The maximum resolution achieved is 800 nm. Neuroblastoma cells were grown on thin films of the cured PLA material, and cell viability and proliferation assays revealed good biocompatibility of the material. Additionally, PC12 and NG108-15 neuroblastoma growth on bespoke scaffolds was studied in more detail to assess potential applications for neuronal implants of this material.

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

    PubMed Central

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

    2014-01-01

    Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function. PMID:24748753

  14. Bridging microscopes: 3D correlative light and scanning electron microscopy of complex biological structures.

    PubMed

    Lucas, Miriam S; Günthert, Maja; Gasser, Philippe; Lucas, Falk; Wepf, Roger

    2012-01-01

    The rationale of correlative light and electron microscopy (CLEM) is to collect data on different information levels--ideally from an identical area on the same sample--with the aim of combining datasets at different levels of resolution to achieve a more holistic view of the hierarchical structural organization of cells and tissues. Modern three-dimensional (3D) imaging techniques in light and electron microscopy opened up new possibilities to expand morphological studies into the third dimension at the nanometer scale and over various volume dimensions. Here, we present two alternative approaches to correlate 3D light microscopy (LM) data with scanning electron microscopy (SEM) volume data. An adapted sample preparation method based on high-pressure freezing for structure preservation, followed by freeze-substitution for multimodal en-bloc imaging or serial-section imaging is described. The advantages and potential applications are exemplarily shown on various biological samples, such as cells, individual organisms, human tissue, as well as plant tissue. The two CLEM approaches presented here are per se not mutually exclusive, but have their distinct advantages. Confocal laser scanning microscopy (CLSM) and focused ion beam-SEM (FIB-SEM) is most suitable for targeted 3D correlation of small volumes, whereas serial-section LM and SEM imaging has its strength in large-area or -volume screening and correlation. The second method can be combined with immunocytochemical methods. Both methods, however, have the potential to extract statistically relevant data of structural details for systems biology.

  15. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

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

    2012-01-01

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

  16. Multi-Scale Modeling of Tissues Using CompuCell3D

    PubMed Central

    Swat, Maciej H.; Thomas, Gilberto L.; Belmonte, Julio M.; Shirinifard, Abbas; Hmeljak, Dimitrij; Glazier, James A.

    2013-01-01

    The study of how cells interact to produce tissue development, homeostasis, or diseases was, until recently, almost purely experimental. Now, multi-cell computer simulation methods, ranging from relatively simple cellular automata to complex immersed-boundary and finite-element mechanistic models, allow in silico study of multi-cell phenomena at the tissue scale based on biologically observed cell behaviors and interactions such as movement, adhesion, growth, death, mitosis, secretion of chemicals, chemotaxis, etc. This tutorial introduces the lattice-based Glazier–Graner–Hogeweg (GGH) Monte Carlo multi-cell modeling and the open-source GGH-based CompuCell3D simulation environment that allows rapid and intuitive modeling and simulation of cellular and multi-cellular behaviors in the context of tissue formation and subsequent dynamics. We also present a walkthrough of four biological models and their associated simulations that demonstrate the capabilities of the GGH and CompuCell3D. PMID:22482955

  17. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases. PMID:26231917

  18. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases.

  19. Bone tissue phantoms for optical flowmeters at large interoptode spacing generated by 3D-stereolithography

    PubMed Central

    Binzoni, Tiziano; Torricelli, Alessandro; Giust, Remo; Sanguinetti, Bruno; Bernhard, Paul; Spinelli, Lorenzo

    2014-01-01

    A bone tissue phantom prototype allowing to test, in general, optical flowmeters at large interoptode spacings, such as laser-Doppler flowmetry or diffuse correlation spectroscopy, has been developed by 3D-stereolithography technique. It has been demonstrated that complex tissue vascular systems of any geometrical shape can be conceived. Absorption coefficient, reduced scattering coefficient and refractive index of the optical phantom have been measured to ensure that the optical parameters reasonably reproduce real human bone tissue in vivo. An experimental demonstration of a possible use of the optical phantom, utilizing a laser-Doppler flowmeter, is also presented. PMID:25136496

  20. Bone tissue phantoms for optical flowmeters at large interoptode spacing generated by 3D-stereolithography.

    PubMed

    Binzoni, Tiziano; Torricelli, Alessandro; Giust, Remo; Sanguinetti, Bruno; Bernhard, Paul; Spinelli, Lorenzo

    2014-08-01

    A bone tissue phantom prototype allowing to test, in general, optical flowmeters at large interoptode spacings, such as laser-Doppler flowmetry or diffuse correlation spectroscopy, has been developed by 3D-stereolithography technique. It has been demonstrated that complex tissue vascular systems of any geometrical shape can be conceived. Absorption coefficient, reduced scattering coefficient and refractive index of the optical phantom have been measured to ensure that the optical parameters reasonably reproduce real human bone tissue in vivo. An experimental demonstration of a possible use of the optical phantom, utilizing a laser-Doppler flowmeter, is also presented.

  1. Bone tissue phantoms for optical flowmeters at large interoptode spacing generated by 3D-stereolithography.

    PubMed

    Binzoni, Tiziano; Torricelli, Alessandro; Giust, Remo; Sanguinetti, Bruno; Bernhard, Paul; Spinelli, Lorenzo

    2014-08-01

    A bone tissue phantom prototype allowing to test, in general, optical flowmeters at large interoptode spacings, such as laser-Doppler flowmetry or diffuse correlation spectroscopy, has been developed by 3D-stereolithography technique. It has been demonstrated that complex tissue vascular systems of any geometrical shape can be conceived. Absorption coefficient, reduced scattering coefficient and refractive index of the optical phantom have been measured to ensure that the optical parameters reasonably reproduce real human bone tissue in vivo. An experimental demonstration of a possible use of the optical phantom, utilizing a laser-Doppler flowmeter, is also presented. PMID:25136496

  2. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  3. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells

    PubMed Central

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L.; Han, Jessica H.; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H.; Bussey, Kimberly J.; Meldrum, Deirdre R.

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an ‘epigenetic’ drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat’s differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  4. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-08-09

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action.

  5. 3D Vegetation Structure Extraction from Lidar Remote Sensing

    NASA Astrophysics Data System (ADS)

    Ni-Meister, W.

    2006-05-01

    Vegetation structure data are critical not only for biomass estimation and global carbon cycle studies, but also for ecosystem disturbance, species habitat and ecosystem biodiversity studies. However those data are rarely available at the global scale. Multispectral passive remote sensing has shown little success on this direction. The upcoming lidar remote sensing technology shows a great potential to measure vegetation vertical structure data globally. In this study, we present and test a Bayesian Stochastic Inversion (BSI) approach to invert a full canopy Geometric Optical and Radiative Transfer (GORT) model to retrieve 3-D vegetation structure parameters from large footprint (15m-25m diameter) vegetation lidar data. BSI approach allows us to take into account lidar-directly derived structure parameters, such as tree height and the upper and lower bounds of crown height and their uncertainties as the prior knowledge in the inversion. It provides not only the optimal estimates of model parameters, but also their uncertainties. We first assess the accuracy of vegetation structure parameter retrievals from vegetation lidar data through a comprehensive GORT input parameter sensitivity analysis. We calculated the singular value decomposition (SVD) of Jacobian matrix, which contains the partial derivatives of the combined model with respect to all relevant model input parameters and. Our analysis shows that with the prior knowledge of tree height, crown depth and crown shape, lidar waveforms is most sensitive to the tree density, then to the tree size and the least to the foliage area volume density. It indicates that tree density can be retrieved with the most accuracy and then the tree size, the least is the foliage area volume density. We also test the simplified BSI approach through a synthetic experiment. The synthetic lidar waveforms were generated based the vegetation structure data obtained from the Boreal Ecosystem Atmosphere Study (BOREAS). With the exact

  6. Optical 3D-coordinate measuring system using structured light

    NASA Astrophysics Data System (ADS)

    Schreiber, Wolfgang; Notni, Gunther; Kuehmstedt, Peter; Gerber, Joerg; Kowarschik, Richard M.

    1996-09-01

    The paper is aimed at the description of an optical shape measuring technique based on a consistent principle using fringe projection technique. We demonstrate a real 3D- coordinate measuring system where the sale of coordinates is given only by the illumination-structures. This method has the advantages that the aberration of the observing system and the depth-dependent imaging scale have no influence on the measuring accuracy and, moreover, the measurements are independent of the position of the camera with respect to the object under test. Furthermore, it is shown that the influence of specular effects of the surface on the measuring result can be eliminated. Moreover, we developed a very simple algorithm to calibrate the measuring system. The measuring examples show that a measuring accuracy of 10-4 (i.e. 10 micrometers ) within an object volume of 100 X 100 X 70 mm3 is achievable. Furthermore, it is demonstrated that the set of coordinate values can be processed in CNC- and CAD-systems.

  7. Slat Cove Unsteadiness Effect of 3D Flow Structures

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan M.; Khorrami, Mehdi R.

    2006-01-01

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

  8. 3D Soil Images Structure Quantification using Relative Entropy

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  9. Controlled Positioning of Cells in Biomaterials-Approaches Towards 3D Tissue Printing.

    PubMed

    Wüst, Silke; Müller, Ralph; Hofmann, Sandra

    2011-01-01

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

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

    PubMed Central

    Wüst, Silke; Müller, Ralph; Hofmann, Sandra

    2011-01-01

    Current tissue engineering techniques have various drawbacks: they often incorporate uncontrolled and imprecise scaffold geometries, whereas the current conventional cell seeding techniques result mostly in random cell placement rather than uniform cell distribution. For the successful reconstruction of deficient tissue, new material engineering approaches have to be considered to overcome current limitations. An emerging method to produce complex biological products including cells or extracellular matrices in a controlled manner is a process called bioprinting or biofabrication, which effectively uses principles of rapid prototyping combined with cell-loaded biomaterials, typically hydrogels. 3D tissue printing is an approach to manufacture functional tissue layer-by-layer that could be transplanted in vivo after production. This method is especially advantageous for stem cells since a controlled environment can be created to influence cell growth and differentiation. Using printed tissue for biotechnological and pharmacological needs like in vitro drug-testing may lead to a revolution in the pharmaceutical industry since animal models could be partially replaced by biofabricated tissues mimicking human physiology and pathology. This would not only be a major advancement concerning rising ethical issues but would also have a measureable impact on economical aspects in this industry of today, where animal studies are very labor-intensive and therefore costly. In this review, current controlled material and cell positioning techniques are introduced highlighting approaches towards 3D tissue printing. PMID:24956301

  11. 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 optimised to arrive at parameters for each cell type under electrotonic load. Parameters were then incorporated into the 3D atrial model, which as a result exhibited a spontaneously active SAN able to rhythmically excite the atria. The tissue-based optimisation of ionic models and the modelling process outlined are generic and applicable to image-based computer reconstruction and simulation of excitable tissue. PMID:23935704

  12. Phenotypic profiling of Raf inhibitors and mitochondrial toxicity in 3D tissue using biodynamic imaging.

    PubMed

    An, Ran; Merrill, Dan; Avramova, Larisa; Sturgis, Jennifer; Tsiper, Maria; Robinson, J Paul; Turek, John; Nolte, David D

    2014-04-01

    The existence of phenotypic differences in the drug responses of 3D tissue relative to 2D cell culture is a concern in high-content drug screening. Biodynamic imaging is an emerging technology that probes 3D tissue using short-coherence dynamic light scattering to measure the intracellular motions inside tissues in their natural microenvironments. The information content of biodynamic imaging is displayed through tissue dynamics spectroscopy (TDS) but has not previously been correlated against morphological image analysis of 2D cell culture. In this article, a set of mitochondria-affecting compounds (FCCP, valinomycin, nicardipine, ionomycin) and Raf kinase inhibitors (PLX4032, PLX4720, GDC, and sorafenib) are applied to multicellular tumor spheroids from two colon adenocarcinoma cell lines (HT-29 and DLD-1). These were screened by TDS and then compared against conventional image-based high-content analysis (HCA). The responses to the Raf inhibitors PLX4032 and PLX4720 are grouped separately by cell line, reflecting the Braf/Kras difference in these cell lines. There is a correlation between TDS and HCA phenotypic clustering for most cases, which demonstrates the ability of dynamic measurements to capture phenotypic responses to drugs. However, there are significant 2D versus 3D phenotypic differences exhibited by several of the drugs/cell lines.

  13. Phenotypic Profiling of Raf Inhibitors and Mitochondrial Toxicity in 3D Tissue Using Biodynamic Imaging

    PubMed Central

    An, Ran; Merrill, Dan; Avramova, Larisa; Sturgis, Jennifer; Tsiper, Maria; Robinson, J. Paul; Turek, John; Nolte, David D.

    2014-01-01

    The existence of phenotypic differences in the drug responses of 3D tissue relative to 2D cell culture is a concern in high-content drug screening. Biodynamic imaging is an emerging technology that probes 3D tissue using short-coherence dynamic light scattering to measure the intracellular motions inside tissues in their natural microenvironments. The information content of biodynamic imaging is displayed through tissue dynamics spectroscopy (TDS) but has not previously been correlated against morphological image analysis of 2D cell culture. In this article, a set of mitochondria-affecting compounds (FCCP, valinomycin, nicardipine, ionomycin) and Raf kinase inhibitors (PLX4032, PLX4720, GDC, and sorafenib) are applied to multicellular tumor spheroids from two colon adenocarcinoma cell lines (HT-29 and DLD-1). These were screened by TDS and then compared against conventional image-based high-content analysis (HCA). The responses to the Raf inhibitors PLX4032 and PLX4720 are grouped separately by cell line, reflecting the Braf/Kras difference in these cell lines. There is a correlation between TDS and HCA phenotypic clustering for most cases, which demonstrates the ability of dynamic measurements to capture phenotypic responses to drugs. However, there are significant 2D versus 3D phenotypic differences exhibited by several of the drugs/cell lines. PMID:24361645

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

    PubMed Central

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

    2015-01-01

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

  15. 3D bioprinting: A new insight into the therapeutic strategy of neural tissue regeneration.

    PubMed

    Hsieh, Fu-Yu; Hsu, Shan-hui

    2015-01-01

    Acute traumatic injuries and chronic degenerative diseases represent the world's largest unmet medical need. There are over 50 million people worldwide suffering from neurodegenerative diseases. However, there are only a few treatment options available for acute traumatic injuries and neurodegenerative diseases. Recently, 3D bioprinting is being applied to regenerative medicine to address the need for tissues and organs suitable for transplantation. In this commentary, the newly developed 3D bioprinting technique involving neural stem cells (NSCs) embedded in the thermoresponsive biodegradable polyurethane (PU) bioink is reviewed. The thermoresponsive and biodegradable PU dispersion can form gel near 37 °C without any crosslinker. NSCs embedded within the water-based PU hydrogel with appropriate stiffness showed comparable viability and differentiation after printing. Moreover, in the zebrafish embryo neural deficit model, injection of the NSC-laden PU hydrogels promoted the repair of damaged CNS. In addition, the function of adult zebrafish with traumatic brain injury was rescued after implantation of the 3D-printed NSC-laden constructs. Therefore, the newly developed 3D bioprinting technique may offer new possibilities for future therapeutic strategy of neural tissue regeneration.

  16. 3D bioprinting: A new insight into the therapeutic strategy of neural tissue regeneration

    PubMed Central

    Hsieh, Fu-Yu; Hsu, Shan-hui

    2015-01-01

    ABSTRACT Acute traumatic injuries and chronic degenerative diseases represent the world’s largest unmet medical need. There are over 50 million people worldwide suffering from neurodegenerative diseases. However, there are only a few treatment options available for acute traumatic injuries and neurodegenerative diseases. Recently, 3D bioprinting is being applied to regenerative medicine to address the need for tissues and organs suitable for transplantation. In this commentary, the newly developed 3D bioprinting technique involving neural stem cells (NSCs) embedded in the thermoresponsive biodegradable polyurethane (PU) bioink is reviewed. The thermoresponsive and biodegradable PU dispersion can form gel near 37°C without any crosslinker. NSCs embedded within the water-based PU hydrogel with appropriate stiffness showed comparable viability and differentiation after printing. Moreover, in the zebrafish embryo neural deficit model, injection of the NSC-laden PU hydrogels promoted the repair of damaged CNS. In addition, the function of adult zebrafish with traumatic brain injury was rescued after implantation of the 3D-printed NSC-laden constructs. Therefore, the newly developed 3D bioprinting technique may offer new possibilities for future therapeutic strategy of neural tissue regeneration. PMID:26709633

  17. Physicochemical properties of 3D collagen-CS scaffolds for potential use in neural tissue engineering.

    PubMed

    Pietrucha, Krystyna

    2015-09-01

    Collagen-based composite scaffolds have considerable potential due to their well-known ability to regenerate skin, bone and cartilage. However, the precise composition and structure of scaffolds that optimize their interaction with neural cells remains incompletely understood and yet to be explored. In the present study, a new family of bi-component 3D scaffolds consisting of collagen (Col) and chondroitin sulphate (CS) were synthesized using a two-stage process: multiple freeze-drying followed by carbodiimide modification. Col-CS matrices had an average pore diameter of 31 μm and a relatively high surface area to pore volume ratio. Importantly, the FTIR data indicated that the ratio between the intensity of amide III and 1452 cm(-1) for Col-CS scaffold was 0.87, which indicates that the Col triple helix was preserved during the formation of the bond between Col and CS. All experiments also clearly showed that the Col-CS matrices have a lower enzyme sensitivity and higher thermal resistance than Col alone. These differences are likely due to the relatively large amount of CS in the collagen sponges, which hinders access for attack at specific active sites of the Col triple helix. Improved binary composite scaffolds were designed for neural tissue engineering applications.

  18. Direct electrospinning of 3D auricle-shaped scaffolds for tissue engineering applications.

    PubMed

    Walser, Jochen; Stok, Kathryn S; Caversaccio, Marco D; Ferguson, Stephen J

    2016-05-12

    Thirty-two poly(ε)caprolactone (PCL) scaffolds have been produced by electrospinning directly into an auricle-shaped mould and seeded with articular chondrocytes harvested from bovine ankle joints. After seeding, the auricle shaped constructs were cultured in vitro and analysed at days 1, 7, 14 and 21 for regional differences in total DNA, glycosaminoglycan (GAG) and collagen (COL) content as well as the expression of aggrecan (AGG), collagen type I and type II (COL1/2) and matrix metalloproteinase 3 and 13 (MMP3/13). Stress-relaxation indentation testing was performed to investigate regional mechanical properties of the electrospun constructs. Electrospinning into a conductive mould yielded stable 3D constructs both initially and for the whole in vitro culture period, with an equilibrium modulus in the MPa range. Rapid cell proliferation and COL accumulation was observed until week 3. Quantitative real time PCR analysis showed an initial increase in AGG, no change in COL2, a persistent increase in COL1, and only a slight decrease initially for MMP3. Electrospinning of fibrous scaffolds directly into an auricle-shape represents a promising option for auricular tissue engineering, as it can reduce the steps needed to achieve an implantable structure.

  19. LATIS3D: The Gold Standard for Laser-Tissue-Interaction Modeling

    SciTech Connect

    London, R.A.; Makarewicz, A.M.; Kim, B.M.; Gentile, N.A.; Yang, Y.B.; Brlik, M.; Vincent, L.

    2000-02-29

    The goal of this LDRD project has been to create LATIS3D--the world's premier computer program for laser-tissue interaction modeling. The development was based on recent experience with the 2D LATIS code and the ASCI code, KULL. With LATIS3D, important applications in laser medical therapy were researched including dynamical calculations of tissue emulsification and ablation, photothermal therapy, and photon transport for photodynamic therapy. This project also enhanced LLNL's core competency in laser-matter interactions and high-energy-density physics by pushing simulation codes into new parameter regimes and by attracting external expertise. This will benefit both existing LLNL programs such as ICF and SBSS and emerging programs in medical technology and other laser applications.

  20. 3D Space Radiation Transport in a Shielded ICRU Tissue Sphere

    NASA Technical Reports Server (NTRS)

    Wilson, John W.; Slaba, Tony C.; Badavi, Francis F.; Reddell, Brandon D.; Bahadori, Amir A.

    2014-01-01

    A computationally efficient 3DHZETRN code capable of simulating High Charge (Z) and Energy (HZE) and light ions (including neutrons) under space-like boundary conditions with enhanced neutron and light ion propagation was recently developed for a simple homogeneous shield object. Monte Carlo benchmarks were used to verify the methodology in slab and spherical geometry, and the 3D corrections were shown to provide significant improvement over the straight-ahead approximation in some cases. In the present report, the new algorithms with well-defined convergence criteria are extended to inhomogeneous media within a shielded tissue slab and a shielded tissue sphere and tested against Monte Carlo simulation to verify the solution methods. The 3D corrections are again found to more accurately describe the neutron and light ion fluence spectra as compared to the straight-ahead approximation. These computationally efficient methods provide a basis for software capable of space shield analysis and optimization.

  1. 3D reconstructions with pixel-based images are made possible by digitally clearing plant and animal tissue

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Reconstruction of 3D images from a series of 2D images has been restricted by the limited capacity to decrease the opacity of surrounding tissue. Commercial software that allows color-keying and manipulation of 2D images in true 3D space allowed us to produce 3D reconstructions from pixel based imag...

  2. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications. PMID:25982877

  3. A lightweight tangible 3D interface for interactive visualization of thin fiber structures.

    PubMed

    Jackson, Bret; Lau, Tung Yuen; Schroeder, David; Toussaint, Kimani C; Keefe, Daniel F

    2013-12-01

    We present a prop-based, tangible interface for 3D interactive visualization of thin fiber structures. These data are commonly found in current bioimaging datasets, for example second-harmonic generation microscopy of collagen fibers in tissue. Our approach uses commodity visualization technologies such as a depth sensing camera and low-cost 3D display. Unlike most current uses of these emerging technologies in the games and graphics communities, we employ the depth sensing camera to create a fish-tank stereoscopic virtual reality system at the scientist's desk that supports tracking of small-scale gestures with objects already found in the work space. We apply the new interface to the problem of interactive exploratory visualization of three-dimensional thin fiber data. A critical task for the visual analysis of these data is understanding patterns in fiber orientation throughout a volume.The interface enables a new, fluid style of data exploration and fiber orientation analysis by using props to provide needed passive-haptic feedback, making 3D interactions with these fiber structures more controlled. We also contribute a low-level algorithm for extracting fiber centerlines from volumetric imaging. The system was designed and evaluated with two biophotonic experts who currently use it in their lab. As compared to typical practice within their field, the new visualization system provides a more effective way to examine and understand the 3D bioimaging datasets they collect.

  4. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications.

  5. Feedback Control for Steering Needles Through 3D Deformable Tissue Using Helical Paths

    PubMed Central

    Hauser, Kris; Alterovitz, Ron; Chentanez, Nuttapong; Okamura, Allison; Goldberg, Ken

    2010-01-01

    Bevel-tip steerable needles are a promising new technology for improving accuracy and accessibility in minimally invasive medical procedures. As yet, 3D needle steering has not been demonstrated in the presence of tissue deformation and uncertainty, despite the application of progressively more sophisticated planning algorithms. This paper presents a feedback controller that steers a needle along 3D helical paths, and varies the helix radius to correct for perturbations. It achieves high accuracy for targets sufficiently far from the needle insertion point; this is counterintuitive because the system is highly under-actuated and not locally controllable. The controller uses a model predictive control framework that chooses a needle twist rate such that the predicted helical trajectory minimizes the distance to the target. Fast branch and bound techniques enable execution at kilohertz rates on a 2GHz PC. We evaluate the controller under a variety of simulated perturbations, including imaging noise, needle deflections, and curvature estimation errors. We also test the controller in a 3D finite element simulator that incorporates deformation in the tissue as well as the needle. In deformable tissue examples, the controller reduced targeting error by up to 88% compared to open-loop execution. PMID:21179401

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

    PubMed

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

    2015-01-01

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

  7. 3D reconstruction of internal structure of animal body using near-infrared light

    NASA Astrophysics Data System (ADS)

    Tran, Trung Nghia; Yamamoto, Kohei; Namita, Takeshi; Kato, Yuji; Shimizu, Koichi

    2014-03-01

    To realize three-dimensional (3D) optical imaging of the internal structure of animal body, we have developed a new technique to reconstruct CT images from two-dimensional (2D) transillumination images. In transillumination imaging, the image is blurred due to the strong scattering in the tissue. We had developed a scattering suppression technique using the point spread function (PSF) for a fluorescent light source in the body. In this study, we have newly proposed a technique to apply this PSF for a light source to the image of unknown light-absorbing structure. The effectiveness of the proposed technique was examined in the experiments with a model phantom and a mouse. In the phantom experiment, the absorbers were placed in the tissue-equivalent medium to simulate the light-absorbing organs in mouse body. Near-infrared light was illuminated from one side of the phantom and the image was recorded with CMOS camera from another side. Using the proposed techniques, the scattering effect was efficiently suppressed and the absorbing structure can be visualized in the 2D transillumination image. Using the 2D images obtained in many different orientations, we could reconstruct the 3D image. In the mouse experiment, an anesthetized mouse was held in an acrylic cylindrical holder. We can visualize the internal organs such as kidneys through mouse's abdomen using the proposed technique. The 3D image of the kidneys and a part of the liver were reconstructed. Through these experimental studies, the feasibility of practical 3D imaging of the internal light-absorbing structure of a small animal was verified.

  8. Towards artificial tissue models: past, present, and future of 3D bioprinting.

    PubMed

    Arslan-Yildiz, Ahu; El Assal, Rami; Chen, Pu; Guven, Sinan; Inci, Fatih; Demirci, Utkan

    2016-03-01

    Regenerative medicine and tissue engineering have seen unprecedented growth in the past decade, driving the field of artificial tissue models towards a revolution in future medicine. Major progress has been achieved through the development of innovative biomanufacturing strategies to pattern and assemble cells and extracellular matrix (ECM) in three-dimensions (3D) to create functional tissue constructs. Bioprinting has emerged as a promising 3D biomanufacturing technology, enabling precise control over spatial and temporal distribution of cells and ECM. Bioprinting technology can be used to engineer artificial tissues and organs by producing scaffolds with controlled spatial heterogeneity of physical properties, cellular composition, and ECM organization. This innovative approach is increasingly utilized in biomedicine, and has potential to create artificial functional constructs for drug screening and toxicology research, as well as tissue and organ transplantation. Herein, we review the recent advances in bioprinting technologies and discuss current markets, approaches, and biomedical applications. We also present current challenges and provide future directions for bioprinting research.

  9. Towards artificial tissue models: past, present, and future of 3D bioprinting.

    PubMed

    Arslan-Yildiz, Ahu; El Assal, Rami; Chen, Pu; Guven, Sinan; Inci, Fatih; Demirci, Utkan

    2016-03-01

    Regenerative medicine and tissue engineering have seen unprecedented growth in the past decade, driving the field of artificial tissue models towards a revolution in future medicine. Major progress has been achieved through the development of innovative biomanufacturing strategies to pattern and assemble cells and extracellular matrix (ECM) in three-dimensions (3D) to create functional tissue constructs. Bioprinting has emerged as a promising 3D biomanufacturing technology, enabling precise control over spatial and temporal distribution of cells and ECM. Bioprinting technology can be used to engineer artificial tissues and organs by producing scaffolds with controlled spatial heterogeneity of physical properties, cellular composition, and ECM organization. This innovative approach is increasingly utilized in biomedicine, and has potential to create artificial functional constructs for drug screening and toxicology research, as well as tissue and organ transplantation. Herein, we review the recent advances in bioprinting technologies and discuss current markets, approaches, and biomedical applications. We also present current challenges and provide future directions for bioprinting research. PMID:26930133

  10. Toward high-speed 3D nonlinear soft tissue deformation simulations using Abaqus software.

    PubMed

    Idkaidek, Ashraf; Jasiuk, Iwona

    2015-12-01

    We aim to achieve a fast and accurate three-dimensional (3D) simulation of a porcine liver deformation under a surgical tool pressure using the commercial finite element software Abaqus. The liver geometry is obtained using magnetic resonance imaging, and a nonlinear constitutive law is employed to capture large deformations of the tissue. Effects of implicit versus explicit analysis schemes, element type, and mesh density on computation time are studied. We find that Abaqus explicit and implicit solvers are capable of simulating nonlinear soft tissue deformations accurately using first-order tetrahedral elements in a relatively short time by optimizing the element size. This study provides new insights and guidance on accurate and relatively fast nonlinear soft tissue simulations. Such simulations can provide force feedback during robotic surgery and allow visualization of tissue deformations for surgery planning and training of surgical residents. PMID:26530842

  11. Toward high-speed 3D nonlinear soft tissue deformation simulations using Abaqus software.

    PubMed

    Idkaidek, Ashraf; Jasiuk, Iwona

    2015-12-01

    We aim to achieve a fast and accurate three-dimensional (3D) simulation of a porcine liver deformation under a surgical tool pressure using the commercial finite element software Abaqus. The liver geometry is obtained using magnetic resonance imaging, and a nonlinear constitutive law is employed to capture large deformations of the tissue. Effects of implicit versus explicit analysis schemes, element type, and mesh density on computation time are studied. We find that Abaqus explicit and implicit solvers are capable of simulating nonlinear soft tissue deformations accurately using first-order tetrahedral elements in a relatively short time by optimizing the element size. This study provides new insights and guidance on accurate and relatively fast nonlinear soft tissue simulations. Such simulations can provide force feedback during robotic surgery and allow visualization of tissue deformations for surgery planning and training of surgical residents.

  12. Engineered 3D Silk-collagen-based Model of Polarized Neural Tissue

    PubMed Central

    Chwalek, Karolina; Sood, Disha; Cantley, William L.; White, James D.; Tang-Schomer, Min; Kaplan, David L.

    2015-01-01

    Despite huge efforts to decipher the anatomy, composition and function of the brain, it remains the least understood organ of the human body. To gain a deeper comprehension of the neural system scientists aim to simplistically reconstruct the tissue by assembling it in vitro from basic building blocks using a tissue engineering approach. Our group developed a tissue-engineered silk and collagen-based 3D brain-like model resembling the white and gray matter of the cortex. The model consists of silk porous sponge, which is pre-seeded with rat brain-derived neurons, immersed in soft collagen matrix. Polarized neuronal outgrowth and network formation is observed with separate axonal and cell body localization. This compartmental architecture allows for the unique development of niches mimicking native neural tissue, thus enabling research on neuronal network assembly, axonal guidance, cell-cell and cell-matrix interactions and electrical functions. PMID:26555926

  13. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    PubMed

    Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana

    2016-05-01

    Coupling the photoreduction of a metal precursor with 3D-printing technology is shown to allow the fabrication of conductive 3D hybrid structures consisting of metal nanoparticles and organic polymers shaped in complex multilayered architectures. 3D conductive structures are fabricated incorporating silver nitrate into a photocurable oligomer in the presence of suitable photoinitiators and exposing them to a digital light system.

  14. Postprocessing techniques for 3D non-linear structures

    NASA Technical Reports Server (NTRS)

    Gallagher, Richard S.

    1987-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-04-01

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

  16. A Novel Qualitative and Quantitative Biofilm Assay Based on 3D Soft Tissue.

    PubMed

    Hakonen, Bodil; Lönnberg, Linnea K; Larkö, Eva; Blom, Kristina

    2014-01-01

    The lack of predictable in vitro methods to analyze antimicrobial activity could play a role in the development of resistance to antibiotics. Current used methods analyze planktonic cells but for the method to be clinically relevant, biofilm in in vivo like conditions ought to be studied. Hence, our group has developed a qualitative and quantitative method with in vivo like 3D tissue for prediction of antimicrobial activity in reality. Devices (wound dressings) were applied on top of Pseudomonas aeruginosa inoculated Muller-Hinton (MH) agar or 3D synthetic soft tissues (SST) and incubated for 24 hours. The antibacterial activity was then analyzed visually and by viable counts. On MH agar two out of three silver containing devices showed zone of inhibitions (ZOI) and on SST, ZOI were detected for all three. Corroborating results were found upon evaluating the bacterial load in SST and shown to be silver concentration dependent. In conclusion, a novel method was developed combining visual rapid screening and quantitative evaluation of the antimicrobial activity in both tissue and devices. It uses tissue allowing biofilm formation thus mimicking reality closely. These conditions are essential in order to predict antimicrobial activity of medical devices in the task to prevent device related infections.

  17. Role of nanotopography in the development of tissue engineered 3D organs and tissues using mesenchymal stem cells.

    PubMed

    Salmasi, Shima; Kalaskar, Deepak M; Yoon, Wai-Weng; Blunn, Gordon W; Seifalian, Alexander M

    2015-03-26

    Recent regenerative medicine and tissue engineering strategies (using cells, scaffolds, medical devices and gene therapy) have led to fascinating progress of translation of basic research towards clinical applications. In the past decade, great deal of research has focused on developing various three dimensional (3D) organs, such as bone, skin, liver, kidney and ear, using such strategies in order to replace or regenerate damaged organs for the purpose of maintaining or restoring organs' functions that may have been lost due to aging, accident or disease. The surface properties of a material or a device are key aspects in determining the success of the implant in biomedicine, as the majority of biological reactions in human body occur on surfaces or interfaces. Furthermore, it has been established in the literature that cell adhesion and proliferation are, to a great extent, influenced by the micro- and nano-surface characteristics of biomaterials and devices. In addition, it has been shown that the functions of stem cells, mesenchymal stem cells in particular, could be regulated through physical interaction with specific nanotopographical cues. Therefore, guided stem cell proliferation, differentiation and function are of great importance in the regeneration of 3D tissues and organs using tissue engineering strategies. This review will provide an update on the impact of nanotopography on mesenchymal stem cells for the purpose of developing laboratory-based 3D organs and tissues, as well as the most recent research and case studies on this topic.

  18. Role of nanotopography in the development of tissue engineered 3D organs and tissues using mesenchymal stem cells

    PubMed Central

    Salmasi, Shima; Kalaskar, Deepak M; Yoon, Wai-Weng; Blunn, Gordon W; Seifalian, Alexander M

    2015-01-01

    Recent regenerative medicine and tissue engineering strategies (using cells, scaffolds, medical devices and gene therapy) have led to fascinating progress of translation of basic research towards clinical applications. In the past decade, great deal of research has focused on developing various three dimensional (3D) organs, such as bone, skin, liver, kidney and ear, using such strategies in order to replace or regenerate damaged organs for the purpose of maintaining or restoring organs’ functions that may have been lost due to aging, accident or disease. The surface properties of a material or a device are key aspects in determining the success of the implant in biomedicine, as the majority of biological reactions in human body occur on surfaces or interfaces. Furthermore, it has been established in the literature that cell adhesion and proliferation are, to a great extent, influenced by the micro- and nano-surface characteristics of biomaterials and devices. In addition, it has been shown that the functions of stem cells, mesenchymal stem cells in particular, could be regulated through physical interaction with specific nanotopographical cues. Therefore, guided stem cell proliferation, differentiation and function are of great importance in the regeneration of 3D tissues and organs using tissue engineering strategies. This review will provide an update on the impact of nanotopography on mesenchymal stem cells for the purpose of developing laboratory-based 3D organs and tissues, as well as the most recent research and case studies on this topic. PMID:25815114

  19. Chitosan-g-lactide copolymers for fabrication of 3D scaffolds for tissue engineering

    NASA Astrophysics Data System (ADS)

    Demina, T. S.; Zaytseva-Zotova, D. S.; Timashev, P. S.; Bagratashvili, V. N.; Bardakova, K. N.; Sevrin, Ch; Svidchenko, E. A.; Surin, N. M.; Markvicheva, E. A.; Grandfils, Ch; Akopova, T. A.

    2015-07-01

    Chitosan-g-oligo (L, D-lactide) copolymers were synthesized and assessed to fabricate a number of 3D scaffolds using a variety of technologies such as oil/water emulsion evaporation technique, freeze-drying and two-photon photopolymerization. Solid-state copolymerization method allowed us to graft up to 160 wt-% of oligolactide onto chitosan backbone via chitosan amino group acetylation with substitution degree reaching up to 0.41. Grafting of hydrophobic oligolactide side chains with polymerization degree up to 10 results in chitosan amphiphilic properties. The synthesized chitosan-g-lactide copolymers were used to design 3D scaffolds for tissue engineering such as spherical microparticles and macroporous hydrogels.

  20. 3D Imaging of Nanoparticle Distribution in Biological Tissue by Laser-Induced Breakdown Spectroscopy

    NASA Astrophysics Data System (ADS)

    Gimenez, Y.; Busser, B.; Trichard, F.; Kulesza, A.; Laurent, J. M.; Zaun, V.; Lux, F.; Benoit, J. M.; Panczer, G.; Dugourd, P.; Tillement, O.; Pelascini, F.; Sancey, L.; Motto-Ros, V.

    2016-07-01

    Nanomaterials represent a rapidly expanding area of research with huge potential for future medical applications. Nanotechnology indeed promises to revolutionize diagnostics, drug delivery, gene therapy, and many other areas of research. For any biological investigation involving nanomaterials, it is crucial to study the behavior of such nano-objects within tissues to evaluate both their efficacy and their toxicity. Here, we provide the first account of 3D label-free nanoparticle imaging at the entire-organ scale. The technology used is known as laser-induced breakdown spectroscopy (LIBS) and possesses several advantages such as speed of operation, ease of use and full compatibility with optical microscopy. We then used two different but complementary approaches to achieve 3D elemental imaging with LIBS: a volume reconstruction of a sliced organ and in-depth analysis. This proof-of-concept study demonstrates the quantitative imaging of both endogenous and exogenous elements within entire organs and paves the way for innumerable applications.

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

    NASA Astrophysics Data System (ADS)

    Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman

    2013-02-01

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

  2. Development of a Bioreactor to Culture Tissue Engineered Ureters Based on the Application of Tubular OPTIMAIX 3D Scaffolds.

    PubMed

    Seifarth, Volker; Gossmann, Matthias; Janke, Heinz Peter; Grosse, Joachim O; Becker, Christoph; Heschel, Ingo; Artmann, Gerhard M; Temiz Artmann, Aysegül

    2015-01-01

    Regenerative medicine, tissue engineering and biomedical research give hope to many patients who need bio-implants. Tissue engineering applications have already been developed based on bioreactors. Physiological ureter implants, however, do not still function sufficiently, as they represent tubular hollow structures with very specific cellular structures and alignments consisting of several cell types. The aim of this study was to a develop a new bioreactor system based on seamless, collagenous, tubular OPTIMAIX 3D prototype sponge as scaffold material for ex-vivo culturing of a tissue engineered ureter replacement for future urological applications. Particular emphasis was given to a great extent to mimic the physiological environment similar to the in vivo situation of a ureter. NIH-3T3 fibroblasts, C2C12, Urotsa and primary genitourinary tract cells were applied as co-cultures on the scaffold and the penetration of cells into the collagenous material was followed. By the end of this study, the bioreactor was functioning, physiological parameter as temperature and pH and the newly developed BIOREACTOR system is applicable to tubular scaffold materials with different lengths and diameters. The automatized incubation system worked reliably. The tubular OPTIMAIX 3D sponge was a suitable scaffold material for tissue engineering purposes and co-cultivation procedures.

  3. 3-D structure and dynamics of microtubule self-organization

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Ou-Yang, H. Daniel

    2008-03-01

    Laser scanning confocal microscopy was used to study the dynamics of 3D assemblies spontaneously formed in microtubule (MT) solutions. Microtubule solutions prepared by mixing and incubating tubulin in the presence of GTP and Oregon Green conjugated taxol in PM buffer were placed in long, sub-millimeter thin glass cells by the capillary action. Within 24 hours, starting with a uniform distribution, microtubules were found to be gradually separated into a few large ``buckled'' bundles along the long direction, and in the middle plane, of the sample cell. A well-defined wavelength of the buckling sinusoids was around 510 μm. The cross section of these round bundles was approximately 40 μm in diameter and the lengths were several centimeters. Detailed analysis of the 3-D image within the bundles revealed that each bundle seemed to consist of loosely packed MTs. It appeared that MTs were phase separated resulting from attractive interactions between charged MT fibers. The ``buckling'' behavior could be the result of geometrical constraints of the repulsive cell walls and the repulsive interaction between bundles. Detailed 3-D observations of the dynamic evolution of MT assembly could provide insight to the mechanisms of cellular MT organization and phase separation of charged colloidal rods.

  4. Fabrication and characterization of gels with integrated channels using 3D printing with microfluidic nozzle for tissue engineering applications.

    PubMed

    Attalla, R; Ling, C; Selvaganapathy, P

    2016-02-01

    The lack of a simple and effective method to integrate vascular network with engineered scaffolds and tissue constructs remains one of the biggest challenges in true 3D tissue engineering. Here, we detail the use of a commercially available, low-cost, open-source 3D printer modified with a microfluidic print-head in order to develop a method for the generation of instantly perfusable vascular network integrated with gel scaffolds seeded with cells. The print-head features an integrated coaxial nozzle that allows the fabrication of hollow, calcium-polymerized alginate tubes that can be easily patterned using 3D printing techniques. The diameter of the hollow channel can be precisely controlled and varied between 500 μm - 2 mm by changing applied flow rates or print-head speed. These channels are integrated into gel layers with a thickness of 800 μm - 2.5 mm. The structural rigidity of these constructs allows the fabrication of multi-layered structures without causing the collapse of hollow channels in lower layers. The 3D printing method was fully characterized at a range of operating speeds (0-40 m/min) and corresponding flow rates (1-30 mL/min) were identified to produce precise definition. This microfluidic design also allows the incorporation of a wide range of scaffold materials as well as biological constituents such as cells, growth factors, and ECM material. Media perfusion of the channels causes a significant viability increase in the bulk of cell-laden structures over the long-term. With this setup, gel constructs with embedded arrays of hollow channels can be created and used as a potential substitute for blood vessel networks. PMID:26842949

  5. Fabrication and characterization of gels with integrated channels using 3D printing with microfluidic nozzle for tissue engineering applications.

    PubMed

    Attalla, R; Ling, C; Selvaganapathy, P

    2016-02-01

    The lack of a simple and effective method to integrate vascular network with engineered scaffolds and tissue constructs remains one of the biggest challenges in true 3D tissue engineering. Here, we detail the use of a commercially available, low-cost, open-source 3D printer modified with a microfluidic print-head in order to develop a method for the generation of instantly perfusable vascular network integrated with gel scaffolds seeded with cells. The print-head features an integrated coaxial nozzle that allows the fabrication of hollow, calcium-polymerized alginate tubes that can be easily patterned using 3D printing techniques. The diameter of the hollow channel can be precisely controlled and varied between 500 μm - 2 mm by changing applied flow rates or print-head speed. These channels are integrated into gel layers with a thickness of 800 μm - 2.5 mm. The structural rigidity of these constructs allows the fabrication of multi-layered structures without causing the collapse of hollow channels in lower layers. The 3D printing method was fully characterized at a range of operating speeds (0-40 m/min) and corresponding flow rates (1-30 mL/min) were identified to produce precise definition. This microfluidic design also allows the incorporation of a wide range of scaffold materials as well as biological constituents such as cells, growth factors, and ECM material. Media perfusion of the channels causes a significant viability increase in the bulk of cell-laden structures over the long-term. With this setup, gel constructs with embedded arrays of hollow channels can be created and used as a potential substitute for blood vessel networks.

  6. Segmentation of bone structures in 3D CT images based on continuous max-flow optimization

    NASA Astrophysics Data System (ADS)

    Pérez-Carrasco, J. A.; Acha-Piñero, B.; Serrano, C.

    2015-03-01

    In this paper an algorithm to carry out the automatic segmentation of bone structures in 3D CT images has been implemented. Automatic segmentation of bone structures is of special interest for radiologists and surgeons to analyze bone diseases or to plan some surgical interventions. This task is very complicated as bones usually present intensities overlapping with those of surrounding tissues. This overlapping is mainly due to the composition of bones and to the presence of some diseases such as Osteoarthritis, Osteoporosis, etc. Moreover, segmentation of bone structures is a very time-consuming task due to the 3D essence of the bones. Usually, this segmentation is implemented manually or with algorithms using simple techniques such as thresholding and thus providing bad results. In this paper gray information and 3D statistical information have been combined to be used as input to a continuous max-flow algorithm. Twenty CT images have been tested and different coefficients have been computed to assess the performance of our implementation. Dice and Sensitivity values above 0.91 and 0.97 respectively were obtained. A comparison with Level Sets and thresholding techniques has been carried out and our results outperformed them in terms of accuracy.

  7. Point-, line-, and plane-shaped cellular constructs for 3D tissue assembly.

    PubMed

    Morimoto, Yuya; Hsiao, Amy Y; Takeuchi, Shoji

    2015-12-01

    Microsized cellular constructs such as cellular aggregates and cell-laden hydrogel blocks are attractive cellular building blocks to reconstruct 3D macroscopic tissues with spatially ordered cells in bottom-up tissue engineering. In this regard, microfluidic techniques are remarkable methods to form microsized cellular constructs with high production rate and control of their shapes such as point, line, and plane. The fundamental shapes of the cellular constructs allow for the fabrication of larger arbitrary-shaped tissues by assembling them. This review introduces microfluidic formation methods of microsized cellular constructs and manipulation techniques to assemble them with control of their arrangements. Additionally, we show applications of the cellular constructs to biological studies and clinical treatments and discuss future trends as their potential applications.

  8. PROMALS3D web server for accurate multiple protein sequence and structure alignments.

    PubMed

    Pei, Jimin; Tang, Ming; Grishin, Nick V

    2008-07-01

    Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087

  9. Optically clearing tissue as an initial step for 3D imaging of core biopsies to diagnose pancreatic cancer

    NASA Astrophysics Data System (ADS)

    Das, Ronnie; Agrawal, Aishwarya; Upton, Melissa P.; Seibel, Eric J.

    2014-02-01

    The pancreas is a deeply seated organ requiring endoscopically, or radiologically guided biopsies for tissue diagnosis. Current approaches include either fine needle aspiration biopsy (FNA) for cytologic evaluation, or core needle biopsies (CBs), which comprise of tissue cores (L = 1-2 cm, D = 0.4-2.0 mm) for examination by brightfield microscopy. Between procurement and visualization, biospecimens must be processed, sectioned and mounted on glass slides for 2D visualization. Optical information about the native tissue state can be lost with each procedural step and a pathologist cannot appreciate 3D organization from 2D observations of tissue sections 1-8 μm in thickness. Therefore, how might histological disease assessment improve if entire, intact CBs could be imaged in both brightfield and 3D? CBs are mechanically delicate; therefore, a simple device was made to cut intact, simulated CBs (L = 1-2 cm, D = 0.2-0.8 mm) from porcine pancreas. After CBs were laid flat in a chamber, z-stack images at 20x and 40x were acquired through the sample with and without the application of an optical clearing agent (FocusClear®). Intensity of transmitted light increased by 5-15x and islet structures unique to pancreas were clearly visualized 250-300 μm beneath the tissue surface. CBs were then placed in index matching square capillary tubes filled with FocusClear® and a standard optical clearing agent. Brightfield z-stack images were then acquired to present 3D visualization of the CB to the pathologist.

  10. Coupling 3D Monte Carlo light transport in optically heterogeneous tissues to photoacoustic signal generation

    PubMed Central

    Jacques, Steven L.

    2014-01-01

    The generation of photoacoustic signals for imaging objects embedded within tissues is dependent on how well light can penetrate to and deposit energy within an optically absorbing object, such as a blood vessel. This report couples a 3D Monte Carlo simulation of light transport to stress wave generation to predict the acoustic signals received by a detector at the tissue surface. The Monte Carlo simulation allows modeling of optically heterogeneous tissues, and a simple MATLAB™ acoustic algorithm predicts signals reaching a surface detector. An example simulation considers a skin with a pigmented epidermis, a dermis with a background blood perfusion, and a 500-μm-dia. blood vessel centered at a 1-mm depth in the skin. The simulation yields acoustic signals received by a surface detector, which are generated by a pulsed 532-nm laser exposure before and after inserting the blood vessel. A MATLAB™ version of the acoustic algorithm and a link to the 3D Monte Carlo website are provided. PMID:25426426

  11. Coupling 3D Monte Carlo light transport in optically heterogeneous tissues to photoacoustic signal generation.

    PubMed

    Jacques, Steven L

    2014-12-01

    The generation of photoacoustic signals for imaging objects embedded within tissues is dependent on how well light can penetrate to and deposit energy within an optically absorbing object, such as a blood vessel. This report couples a 3D Monte Carlo simulation of light transport to stress wave generation to predict the acoustic signals received by a detector at the tissue surface. The Monte Carlo simulation allows modeling of optically heterogeneous tissues, and a simple MATLAB™ acoustic algorithm predicts signals reaching a surface detector. An example simulation considers a skin with a pigmented epidermis, a dermis with a background blood perfusion, and a 500-μm-dia. blood vessel centered at a 1-mm depth in the skin. The simulation yields acoustic signals received by a surface detector, which are generated by a pulsed 532-nm laser exposure before and after inserting the blood vessel. A MATLAB™ version of the acoustic algorithm and a link to the 3D Monte Carlo website are provided.

  12. Site-specific 3D imaging of cells and tissues with a dual beam microscope

    PubMed Central

    Heymann, Jurgen A.W.; Hayles, Mike; Gestmann, Ingo; Giannuzzi, Lucille A.; Lich, Ben; Subramaniam, Sriram

    2006-01-01

    Current approaches to 3D imaging at subcellular resolution using confocal microscopy and electron tomography, while powerful, are limited to relatively thin and transparent specimens. Here we report on the use of a new generation of dual beam electron microscopes capable of site-specific imaging of the interior of cellular and tissue specimens at spatial resolutions about an order of magnitude better than those currently achieved with optical microscopy. The principle of imaging is based on using a focused ion beam to create a cut at a designated site in the specimen, followed by viewing the newly generated surface with a scanning electron beam. Iteration of these two steps several times thus results in the generation of a series of surface maps of the specimen at regularly spaced intervals, which can be converted into a three-dimensional map of the specimen. We have explored the potential of this sequential “slice-and-view” strategy for site-specific 3D imaging of frozen yeast cells and tumor tissue, and establish that this approach can identify the locations of intracellular features such as the 100 nm-wide yeast nuclear pore complex. We also show that 200 nm thick sections can be generated in situ by “milling” of resin-embedded specimens using the ion beam, providing a valuable alternative to manual sectioning of cells and tissues using an ultramicrotome. Our results demonstrate that dual beam imaging is a powerful new tool for cellular and subcellular imaging in 3D for both basic biomedical and clinical applications. PMID:16713294

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

    SciTech Connect

    Michael Cornforth

    2012-03-26

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

  14. 3D printing of porous hydroxyapatite scaffolds intended for use in bone tissue engineering applications.

    PubMed

    Cox, Sophie C; Thornby, John A; Gibbons, Gregory J; Williams, Mark A; Mallick, Kajal K

    2015-02-01

    A systematic characterisation of bone tissue scaffolds fabricated via 3D printing from hydroxyapatite (HA) and poly(vinyl)alcohol (PVOH) composite powders is presented. Flowability of HA:PVOH precursor materials was observed to affect mechanical stability, microstructure and porosity of 3D printed scaffolds. Anisotropic behaviour of constructs and part failure at the boundaries of interlayer bonds was highlighted by compressive strength testing. A trade-off between the ability to facilitate removal of PVOH thermal degradation products during sintering and the compressive strength of green parts was revealed. The ultimate compressive strength of 55% porous green scaffolds printed along the Y-axis and dried in a vacuum oven for 6h was 0.88 ± 0.02 MPa. Critically, the pores of 3D printed constructs could be user designed, ensuring bulk interconnectivity, and the imperfect packing of powder particles created an inherent surface roughness and non-designed porosity within the scaffold. These features are considered promising since they are known to facilitate osteoconduction and osteointegration in-vivo. Characterisation techniques utilised in this study include two funnel flow tests, scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), compressive strength testing and computed tomography (CT).

  15. 3D printing of porous hydroxyapatite scaffolds intended for use in bone tissue engineering applications.

    PubMed

    Cox, Sophie C; Thornby, John A; Gibbons, Gregory J; Williams, Mark A; Mallick, Kajal K

    2015-02-01

    A systematic characterisation of bone tissue scaffolds fabricated via 3D printing from hydroxyapatite (HA) and poly(vinyl)alcohol (PVOH) composite powders is presented. Flowability of HA:PVOH precursor materials was observed to affect mechanical stability, microstructure and porosity of 3D printed scaffolds. Anisotropic behaviour of constructs and part failure at the boundaries of interlayer bonds was highlighted by compressive strength testing. A trade-off between the ability to facilitate removal of PVOH thermal degradation products during sintering and the compressive strength of green parts was revealed. The ultimate compressive strength of 55% porous green scaffolds printed along the Y-axis and dried in a vacuum oven for 6h was 0.88 ± 0.02 MPa. Critically, the pores of 3D printed constructs could be user designed, ensuring bulk interconnectivity, and the imperfect packing of powder particles created an inherent surface roughness and non-designed porosity within the scaffold. These features are considered promising since they are known to facilitate osteoconduction and osteointegration in-vivo. Characterisation techniques utilised in this study include two funnel flow tests, scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), compressive strength testing and computed tomography (CT). PMID:25492194

  16. 3D reconstruction of prostate histology based on quantified tissue cutting and deformation parameters

    NASA Astrophysics Data System (ADS)

    Gibson, Eli; Gómez, José A.; Moussa, Madeleine; Crukley, Cathie; Bauman, Glenn; Fenster, Aaron; Ward, Aaron D.

    2012-03-01

    Methods for 3D histology reconstruction from sparse 2D digital histology images depend on knowledge about the positions, orientations, and deformations of tissue slices due to the histology process. This work quantitatively evaluates typical assumptions about the position and orientation of whole-mount prostate histology sections within coarsely sliced tissue blocks and about the deformation of tissue during histological processing and sectioning. 3-5 midgland tissue blocks from each of 7 radical prostatectomy specimens were imaged using magnetic resonance imaging before histology processing. After standard whole-mount paraffin processing and sectioning, the resulting sections were digitised. Homologous anatomic landmarks were identified on 22 midgland histology and MR images. Orientations and depths of sections relative to the front faces of the tissue blocks were measured based on the best-fit plane through the landmarks on the MR images. The mean+/-std section orientation was 1.7+/-1.1° and the mean+/-std depth of the sections was 1.0+/-0.5 mm. Deformation was assessed by using four transformation models (rigid, rigid+scale, affine and thin-plate-spline (TPS)) to align landmarks from histology and MR images, and evaluating each by measuring the target registration error (TRE) using a leave-one-out cross-validation. The rigid transformation model had higher mean TRE (p<0.001) than the other models, and the rigid+scale and affine models had higher mean TRE than the TPS model (p<0.001 and p<0.01 respectively). These results informed the design and development of a method for 3D prostate histology reconstruction based on extrinsic strand-shaped fiducial markers which yielded a 0.7+/-0.4 mm mean+/-std TRE.

  17. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    PubMed

    Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana

    2016-05-01

    On page 3712, E. Fantino, A. Chiappone, and co-workers fabricate conductive 3D hybrid structures by coupling the photo-reduction of metal precursors with 3D printing technology. The generated structures consist of metal nanoparticles embedded in a polymer matrix shaped into complex multilayered architectures. 3D conductive structures are fabricated with a digital light-processing printer incorporating silver salt into photocurable formulations. PMID:27167030

  18. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    PubMed

    Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana

    2016-05-01

    On page 3712, E. Fantino, A. Chiappone, and co-workers fabricate conductive 3D hybrid structures by coupling the photo-reduction of metal precursors with 3D printing technology. The generated structures consist of metal nanoparticles embedded in a polymer matrix shaped into complex multilayered architectures. 3D conductive structures are fabricated with a digital light-processing printer incorporating silver salt into photocurable formulations.

  19. 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.

  20. Bioprinted 3D Primary Liver Tissues Allow Assessment of Organ-Level Response to Clinical Drug Induced Toxicity In Vitro

    PubMed Central

    Funk, Juergen; Robbins, Justin B.; Crogan-Grundy, Candace; Presnell, Sharon C.; Singer, Thomas; Roth, Adrian B.

    2016-01-01

    Modeling clinically relevant tissue responses using cell models poses a significant challenge for drug development, in particular for drug induced liver injury (DILI). This is mainly because existing liver models lack longevity and tissue-level complexity which limits their utility in predictive toxicology. In this study, we established and characterized novel bioprinted human liver tissue mimetics comprised of patient-derived hepatocytes and non-parenchymal cells in a defined architecture. Scaffold-free assembly of different cell types in an in vivo-relevant architecture allowed for histologic analysis that revealed distinct intercellular hepatocyte junctions, CD31+ endothelial networks, and desmin positive, smooth muscle actin negative quiescent stellates. Unlike what was seen in 2D hepatocyte cultures, the tissues maintained levels of ATP, Albumin as well as expression and drug-induced enzyme activity of Cytochrome P450s over 4 weeks in culture. To assess the ability of the 3D liver cultures to model tissue-level DILI, dose responses of Trovafloxacin, a drug whose hepatotoxic potential could not be assessed by standard pre-clinical models, were compared to the structurally related non-toxic drug Levofloxacin. Trovafloxacin induced significant, dose-dependent toxicity at clinically relevant doses (≤ 4uM). Interestingly, Trovafloxacin toxicity was observed without lipopolysaccharide stimulation and in the absence of resident macrophages in contrast to earlier reports. Together, these results demonstrate that 3D bioprinted liver tissues can both effectively model DILI and distinguish between highly related compounds with differential profile. Thus, the combination of patient-derived primary cells with bioprinting technology here for the first time demonstrates superior performance in terms of mimicking human drug response in a known target organ at the tissue level. PMID:27387377

  1. A novel MR-guided interventional device for 3D circumferential access to breast tissue

    PubMed Central

    Smith, Matthew; Zhai, Xu; Harter, Ray; Sisney, Gale; Elezaby, Mai; Fain, Sean

    2008-01-01

    MRI is rapidly growing as a tool for image-guided procedures in the breast such as needle localizations, biopsy, and cryotherapy. The ability of MRI to resolve small (<1 cm) lesions allows earlier detection and diagnosis than with ultrasound. Most MR-guidance methods perform a two-dimensional compression of the breast that distorts tissue anatomy and limits medial access. This work presents a system for localizing breast lesions with 360° access to breast tissue. A novel system has been developed to perform breast lesion localization using MR guidance that uses a 3D radial coordinate system with four degrees of freedom. The device is combined with a novel breast RF coil for improved signal to noise and rotates 360° around the breast to allow medial, lateral, superior, and inferior access minimizing insertion depth to the target. Coil performance was evaluated using a human volunteer by comparing signal to noise from both the developed breast RF coil and a commercial seven-channel breast coil. The system was tested with a breast-shaped gel phantom containing randomly distributed MR-visible targets. MR-compatible localization needles were used to demonstrate the accuracy and feasibility of the concept for breast biopsy. Localization results were classified based on the relationship between the final needle tip position and the lesion. A 3D bladder concept was also tested using animal tissue to evaluate the device’s ability to immobilize deformable breast tissue during a needle insertion. The RF breast coil provided signal to noise values comparable to a seven-channel breast coil. The needle tip was in contact with the targeted lesion in 89% (25∕28) of all the trials and 100% (6∕6) of the trials with targeted lesions >6 mm. Target lesions were 3–4 mm in diameter for 47% (13∕28), 5–6 mm in diameter for 32% (9∕28), and over 6 mm in diameter for 21% (6∕28) of the trials, respectively. The 3D bladder concept was shown to immobilize a deformable animal

  2. Multiplexed 3D FRET imaging in deep tissue of live embryos

    PubMed Central

    Zhao, Ming; Wan, Xiaoyang; Li, Yu; Zhou, Weibin; Peng, Leilei

    2015-01-01

    Current deep tissue microscopy techniques are mostly restricted to intensity mapping of fluorophores, which significantly limit their applications in investigating biochemical processes in vivo. We present a deep tissue multiplexed functional imaging method that probes multiple Förster resonant energy transfer (FRET) sensors in live embryos with high spatial resolution. The method simultaneously images fluorescence lifetimes in 3D with multiple excitation lasers. Through quantitative analysis of triple-channel intensity and lifetime images, we demonstrated that Ca2+ and cAMP levels of live embryos expressing dual FRET sensors can be monitored simultaneously at microscopic resolution. The method is compatible with a broad range of FRET sensors currently available for probing various cellular biochemical functions. It opens the door to imaging complex cellular circuitries in whole live organisms. PMID:26387920

  3. 3D ultrasound to stereoscopic camera registration through an air-tissue boundary.

    PubMed

    Yip, Michael C; Adebar, Troy K; Rohling, Robert N; Salcudean, Septimiu E; Nguan, Christopher Y

    2010-01-01

    A novel registration method between 3D ultrasound and stereoscopic cameras is proposed based on tracking a registration tool featuring both ultrasound fiducials and optical markers. The registration tool is pressed against an air-tissue boundary where it can be seen both in ultrasound and in the camera view. By localizing the fiducials in the ultrasound volume, knowing the registration tool geometry, and tracking the tool with the cameras, a registration is found. This method eliminates the need for external tracking, requires minimal setup, and may be suitable for a range of minimally invasive surgeries. A study of the appearance of ultrasound fiducials on an air-tissue boundary is presented, and an initial assessment of the ability to localize the fiducials in ultrasound with sub-millimeter accuracy is provided. The overall accuracy of registration (1.69 +/- 0.60 mm) is a noticeable improvement over other reported methods and warrants patient studies.

  4. Directed assembly of cell-laden microgels for fabrication of 3D tissue constructs.

    PubMed

    Du, Yanan; Lo, Edward; Ali, Shamsher; Khademhosseini, Ali

    2008-07-15

    We present a bottom-up approach to direct the assembly of cell-laden microgels to generate tissue constructs with tunable microarchitecture and complexity. This assembly process is driven by the tendency of multiphase liquid-liquid systems to minimize the surface area and the resulting surface free energy between the phases. We demonstrate that shape-controlled microgels spontaneously assemble within multiphase reactor systems into predetermined geometric configurations. Furthermore, we characterize the parameters that influence the assembly process, such as external energy input, surface tension, and microgel dimensions. Finally, we show that multicomponent cell-laden constructs could be generated by assembling microgel building blocks and performing a secondary cross-linking reaction. This bottom-up approach for the directed assembly of cell-laden microgels provides a powerful and highly scalable approach to form biomimetic 3D tissue constructs and opens a paradigm for directing the assembly of mesoscale materials.

  5. 3-D ultrasound-guided robotic needle steering in biological tissue.

    PubMed

    Adebar, Troy K; Fletcher, Ashley E; Okamura, Allison M

    2014-12-01

    Robotic needle steering systems have the potential to greatly improve medical interventions, but they require new methods for medical image guidance. Three-dimensional (3-D) ultrasound is a widely available, low-cost imaging modality that may be used to provide real-time feedback to needle steering robots. Unfortunately, the poor visibility of steerable needles in standard grayscale ultrasound makes automatic segmentation of the needles impractical. A new imaging approach is proposed, in which high-frequency vibration of a steerable needle makes it visible in ultrasound Doppler images. Experiments demonstrate that segmentation from this Doppler data is accurate to within 1-2 mm. An image-guided control algorithm that incorporates the segmentation data as feedback is also described. In experimental tests in ex vivo bovine liver tissue, a robotic needle steering system implementing this control scheme was able to consistently steer a needle tip to a simulated target with an average error of 1.57 mm. Implementation of 3-D ultrasound-guided needle steering in biological tissue represents a significant step toward the clinical application of robotic needle steering.

  6. 3D printed miniaturized spectral system for tissue fluorescence lifetime measurements

    NASA Astrophysics Data System (ADS)

    Zou, Luwei; Mahmoud, Mohamad; Fahs, Mehdi; Liu, Rui; Lo, Joe F.

    2016-04-01

    Various types of collagens, e.g. type I and III, represent the main load-bearing components in biological tissues. Their composition changes during processes like wound healing and fibrosis. Collagens exhibit autofluorescence when excited by ultra-violet light, distinguishable by their unique fluorescent lifetimes across a range of emission wavelengths. Therefore, we designed a miniaturized spectral-lifetime detection system for collagens as a non-invasive probe for monitoring tissue in wound healing and scarring applications. A sine modulated LED illumination was applied to enable frequency domain (FD) fluorescence lifetime measurements under different wavelengths bands, separated via a series of longpass dichroics at 387nm, 409nm and 435nm. To achieve the minute scale of optomechanics, we employed a stereolithography based 3D printer with <50 μm resolution to create a custom designed optical mount in a hand-held form factor. We examined the characteristics of the 3D printed optical system with finite element modeling to simulate the effect of thermal (LED) and mechanical (handling) strain on the optical system. Using this device, the phase shift and demodulation of collagen types were measured, where the separate spectral bands enhanced the differentiation of their lifetimes.

  7. Ascorbate Enhances Elastin Synthesis in 3D Tissue-Engineered Pulmonary Fibroblasts Constructs

    PubMed Central

    Derricks, Kelsey E.; Rich, Celeste B.; Buczek-Thomas, Jo Ann; Nugent, Matthew A.

    2013-01-01

    Extracellular matrix remodeling is a continuous process that is critical to maintaining tissue homeostasis, and alterations in this process have been implicated in chronic diseases such as atherosclerosis, lung fibrosis, and emphysema. Collagen and elastin are subject to ascorbate-dependent hydroxylation. While this post-translational modification in collagen is critical for function, the role of hydroxylation of elastin is not well understood. A number of studies have indicated that ascorbate leads to reduced elastin synthesis. However, these studies were limited to analysis of cells grown under traditional 2D tissue culture conditions. To investigate this process we evaluated elastin and collagen synthesis in primary rat neonatal pulmonary fibroblasts in response to ascorbate treatment in traditional 2D culture and within 3D cross-linked gelatin matrices (Gelfoam). We observed little change in elastin or collagen biosynthesis in standard 2D cultures treated with ascorbate, yet observed a dramatic increase in elastin protein and mRNA levels in response to ascorbate in 3D cell-Gelfoam constructs. These data suggest that the cell-ECM architecture dictates pulmonary cell response to ascorbate, and that approaches aimed toward stimulating ECM repair or engineering functional cell-derived matrices should consider all aspects of the cellular environment. PMID:23648172

  8. Fabrication of scalable tissue engineering scaffolds with dual-pore microarchitecture by combining 3D printing and particle leaching.

    PubMed

    Mohanty, Soumyaranjan; Sanger, Kuldeep; Heiskanen, Arto; Trifol, Jon; Szabo, Peter; Dufva, Marin; Emnéus, Jenny; Wolff, Anders

    2016-04-01

    Limitations in controlling scaffold architecture using traditional fabrication techniques are a problem when constructing engineered tissues/organs. Recently, integration of two pore architectures to generate dual-pore scaffolds with tailored physical properties has attracted wide attention in tissue engineering community. Such scaffolds features primary structured pores which can efficiently enhance nutrient/oxygen supply to the surrounding, in combination with secondary random pores, which give high surface area for cell adhesion and proliferation. Here, we present a new technique to fabricate dual-pore scaffolds for various tissue engineering applications where 3D printing of poly(vinyl alcohol) (PVA) mould is combined with salt leaching process. In this technique the sacrificial PVA mould, determining the structured pore architecture, was filled with salt crystals to define the random pore regions of the scaffold. After crosslinking the casted polymer the combined PVA-salt mould was dissolved in water. The technique has advantages over previously reported ones, such as automated assembly of the sacrificial mould, and precise control over pore architecture/dimensions by 3D printing parameters. In this study, polydimethylsiloxane and biodegradable poly(ϵ-caprolactone) were used for fabrication. However, we show that this technique is also suitable for other biocompatible/biodegradable polymers. Various physical and mechanical properties of the dual-pore scaffolds were compared with control scaffolds with either only structured or only random pores, fabricated using previously reported methods. The fabricated dual-pore scaffolds supported high cell density, due to the random pores, in combination with uniform cell distribution throughout the scaffold, and higher cell proliferation and viability due to efficient nutrient/oxygen transport through the structured pores. In conclusion, the described fabrication technique is rapid, inexpensive, scalable, and compatible

  9. Fabrication of scalable tissue engineering scaffolds with dual-pore microarchitecture by combining 3D printing and particle leaching.

    PubMed

    Mohanty, Soumyaranjan; Sanger, Kuldeep; Heiskanen, Arto; Trifol, Jon; Szabo, Peter; Dufva, Marin; Emnéus, Jenny; Wolff, Anders

    2016-04-01

    Limitations in controlling scaffold architecture using traditional fabrication techniques are a problem when constructing engineered tissues/organs. Recently, integration of two pore architectures to generate dual-pore scaffolds with tailored physical properties has attracted wide attention in tissue engineering community. Such scaffolds features primary structured pores which can efficiently enhance nutrient/oxygen supply to the surrounding, in combination with secondary random pores, which give high surface area for cell adhesion and proliferation. Here, we present a new technique to fabricate dual-pore scaffolds for various tissue engineering applications where 3D printing of poly(vinyl alcohol) (PVA) mould is combined with salt leaching process. In this technique the sacrificial PVA mould, determining the structured pore architecture, was filled with salt crystals to define the random pore regions of the scaffold. After crosslinking the casted polymer the combined PVA-salt mould was dissolved in water. The technique has advantages over previously reported ones, such as automated assembly of the sacrificial mould, and precise control over pore architecture/dimensions by 3D printing parameters. In this study, polydimethylsiloxane and biodegradable poly(ϵ-caprolactone) were used for fabrication. However, we show that this technique is also suitable for other biocompatible/biodegradable polymers. Various physical and mechanical properties of the dual-pore scaffolds were compared with control scaffolds with either only structured or only random pores, fabricated using previously reported methods. The fabricated dual-pore scaffolds supported high cell density, due to the random pores, in combination with uniform cell distribution throughout the scaffold, and higher cell proliferation and viability due to efficient nutrient/oxygen transport through the structured pores. In conclusion, the described fabrication technique is rapid, inexpensive, scalable, and compatible

  10. The spatial accuracy of cellular dose estimates obtained from 3D reconstructed serial tissue autoradiographs.

    PubMed

    Humm, J L; Macklis, R M; Lu, X Q; Yang, Y; Bump, K; Beresford, B; Chin, L M

    1995-01-01

    In order to better predict and understand the effects of radiopharmaceuticals used for therapy, it is necessary to determine more accurately the radiation absorbed dose to cells in tissue. Using thin-section autoradiography, the spatial distribution of sources relative to the cells can be obtained from a single section with micrometre resolution. By collecting and analysing serial sections, the 3D microscopic distribution of radionuclide relative to the cellular histology, and therefore the dose rate distribution, can be established. In this paper, a method of 3D reconstruction of serial sections is proposed, and measurements are reported of (i) the accuracy and reproducibility of quantitative autoradiography and (ii) the spatial precision with which tissue features from one section can be related to adjacent sections. Uncertainties in the activity determination for the specimen result from activity losses during tissue processing (4-11%), and the variation of grain count per unit activity between batches of serial sections (6-25%). Correlation of the section activity to grain count densities showed deviations ranging from 6-34%. The spatial alignment uncertainties were assessed using nylon fibre fiduciary markers incorporated into the tissue block, and compared to those for alignment based on internal tissue landmarks. The standard deviation for the variation in nylon fibre fiduciary alignment was measured to be 41 microns cm-1, compared to 69 microns cm-1 when internal tissue histology landmarks were used. In addition, tissue shrinkage during histological processing of up to 10% was observed. The implications of these measured activity and spatial distribution uncertainties upon the estimate of cellular dose rate distribution depends upon the range of the radiation emissions. For long-range beta particles, uncertainties in both the activity and spatial distribution translate linearly to the uncertainty in dose rate of < 15%. For short-range emitters (< 100

  11. Effect of sterilization on structural and material properties of 3-D silk fibroin scaffolds.

    PubMed

    Hofmann, Sandra; Stok, Kathryn S; Kohler, Thomas; Meinel, Anne J; Müller, Ralph

    2014-01-01

    The development of porous scaffolds for tissue engineering applications requires the careful choice of properties, as these influence cell adhesion, proliferation and differentiation. Sterilization of scaffolds is a prerequisite for in vitro culture as well as for subsequent in vivo implantation. The variety of methods used to provide sterility is as diverse as the possible effects they can have on the structural and material properties of the three-dimensional (3-D) porous structure, especially in polymeric or proteinous scaffold materials. Silk fibroin (SF) has previously been demonstrated to offer exceptional benefits over conventional synthetic and natural biomaterials in generating scaffolds for tissue replacements. This study sought to determine the effect of sterilization methods, such as autoclaving, heat-, ethylene oxide-, ethanol- or antibiotic-antimycotic treatment, on porous 3-D SF scaffolds. In terms of scaffold morphology, topography, crystallinity and short-term cell viability, the different sterilization methods showed only few effects. Nevertheless, mechanical properties were significantly decreased by a factor of two by all methods except for dry autoclaving, which seemed not to affect mechanical properties compared to the native control group. These data suggest that SF scaffolds are in general highly resistant to various sterilization treatments. Nevertheless, care should be taken if initial mechanical properties are of interest.

  12. Multiple 3D RNA Structure Superposition Using Neighbor Joining.

    PubMed

    Hoksza, David; Svozil, Daniel

    2015-01-01

    Recent advances in RNA research and the steady growth of available RNA structures call for bioinformatics methods for handling and analyzing RNA structural data. Recently, we introduced SETTER-a fast and accurate method for RNA pairwise structure alignment. In this paper, we describe MultiSETTER, SETTER extension for multiple RNA structure alignment. MultiSETTER combines SETTER's decomposition of RNA structures into non-overlapping structural subunits with the multiple sequence alignment algorithm ClustalW adapted for the structure alignment. The accuracy of MultiSETTER was assessed by the automatic classification of RNA structures and its comparison to SCOR annotations. In addition, MultiSETTER classification was also compared to multiple sequence alignment-based and secondary structure alignment-based classifications provided by LocARNA and RNADistance tools, respectively. MultiSETTER precompiled Windows libraries, as well as the C++ source code, are freely available from http://siret.cz/multisetter.

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

    PubMed

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

    2010-03-01

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

  14. Optoacoustic 3D visualization of changes in physiological properties of mouse tissues from live to postmortem

    NASA Astrophysics Data System (ADS)

    Su, Richard; Ermiliov, Sergey A.; Liopo, Anton V.; Oraevsky, Alexander A.

    2012-02-01

    Using the method of 3D optoacoustic tomography, we studied changes in tissues of the whole body of nude mice as the changes manifested themselves from live to postmortem. The studies provided the necessary baseline for optoacoustic imaging of necrotizing tissue, acute and chronic hypoxia, and reperfusion. They also establish a new optoacoustic model of early postmortem conditions of the whole mouse body. Animals were scanned in a 37°C water bath using a three-dimensional optoacoustic tomography system previously shown to provide high contrast maps of vasculature and organs based on changes in the optical absorbance. The scans were performed right before, 5 minutes after, 2 hours and 1 day after a lethal injection of KCl. The near-infrared laser wavelength of 765 nm was used to evaluate physiological features of postmortem changes. Our data showed that optoacoustic imaging is well suited for visualization of both live and postmortem tissues. The images revealed changes of optical properties in mouse organs and tissues. Specifically, we observed improvements in contrast of the vascular network and organs after the death of the animal. We associated these with reduced optical scattering, loss of motion artifacts, and blood coagulation.

  15. A procedure to average 3D anatomical structures.

    PubMed

    Subramanya, K; Dean, D

    2000-12-01

    Creating a feature-preserving average of three dimensional anatomical surfaces extracted from volume image data is a complex task. Unlike individual images, averages present right-left symmetry and smooth surfaces which give insight into typical proportions. Averaging multiple biological surface images requires careful superimposition and sampling of homologous regions. Our approach to biological surface image averaging grows out of a wireframe surface tessellation approach by Cutting et al. (1993). The surface delineating wires represent high curvature crestlines. By adding tile boundaries in flatter areas the 3D image surface is parametrized into anatomically labeled (homology mapped) grids. We extend the Cutting et al. wireframe approach by encoding the entire surface as a series of B-spline space curves. The crestline averaging algorithm developed by Cutting et al. may then be used for the entire surface. Shape preserving averaging of multiple surfaces requires careful positioning of homologous surface regions such as these B-spline space curves. We test the precision of this new procedure and its ability to appropriately position groups of surfaces in order to produce a shape-preserving average. Our result provides an average that well represents the source images and may be useful clinically as a deformable model or for animation.

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

    PubMed

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

    2015-09-01

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

  17. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    PubMed

    Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana

    2016-05-01

    Coupling the photoreduction of a metal precursor with 3D-printing technology is shown to allow the fabrication of conductive 3D hybrid structures consisting of metal nanoparticles and organic polymers shaped in complex multilayered architectures. 3D conductive structures are fabricated incorporating silver nitrate into a photocurable oligomer in the presence of suitable photoinitiators and exposing them to a digital light system. PMID:26992060

  18. Modeling and Reconstruction of Micro-structured 3D Chitosan/Gelatin Porous Scaffolds Using Micro-CT

    NASA Astrophysics Data System (ADS)

    Gong, Haibo; Li, Dichen; He, Jiankang; Liu, Yaxiong; Lian, Qin; Zhao, Jinna

    2008-09-01

    Three dimensional (3D) channel networks are the key to promise the uniform distribution of nutrients inside 3D hepatic tissue engineering scaffolds and prompt elimination of metabolic products out of the scaffolds. 3D chitosan/gelatin porous scaffolds with predefined internal channels were fabricated and a combination of light microscope, laser confocal microscopy and micro-CT were employed to characterize the structure of porous scaffolds. In order to evaluate the flow field distribution inside the micro-structured 3D scaffolds, a computer reconstructing method based on Micro-CT was proposed. According to this evaluating method, a contrast between 3D porous scaffolds with and without predefined internal channels was also performed to assess scaffolds' fluid characters. Results showed that the internal channel of the 3D scaffolds formed the 3D fluid channel network; the uniformity of flow field distribution of the scaffolds fabricated in this paper was better than the simple porous scaffold without micro-fluid channels.

  19. 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

  20. The fabrication of double layer tubular vascular tissue engineering scaffold via coaxial electrospinning and its 3D cell coculture.

    PubMed

    Ye, Lin; Cao, Jie; Chen, Lamei; Geng, Xue; Zhang, Ai-Ying; Guo, Lian-Rui; Gu, Yong-Quan; Feng, Zeng-Guo

    2015-12-01

    A continuous electrospinning technique was applied to fabricate double layer tubular tissue engineering vascular graft (TEVG) scaffold. The luminal layer was made from poly(ɛ-caprolac-tone)(PCL) ultrafine fibers via common single axial electrospinning followed by the outer layer of core-shell structured nanofibers via coaxial electrospinning. For preparing the outer layernano-fibers, the PCL was electrospun into the shell and both bovine serum albumin (BSA) and tetrapeptide val-gal-pro-gly (VAPG) were encapsulated into the core. The core-shell structure in the outer layer fibers was observed by transmission electron microscope (TEM). The in vitro release tests exhibited the sustainable release behavior of BSA and VAPG so that they provided a better cell growth environment in the interior of tubular scaffold wall. The in vitro culture of smooth muscle cells (SMCs) demonstrated their potential to penetrate into the scaffold wall for the 3D cell culture. Subsequently, 3D cell coculture was conducted. First, SMCs were seeded on the luminal surface of the scaffold and cultured for 5 days, and then endothelial cells (ECs) were also seeded on the luminal surface and cocultured with SMCs for another 2 days. After stained with antibodies, 3D cell distribution on the scaffold was revealed by confocal laser scanning microscopy (CLSM) where ECs were mainly located on the luminal surface whereas SMCs penetrated into the surface and distributed inside the scaffold wall. This double layer tubular scaffold with 3D cell distribution showed the promise to develop it into a novel TEVG for clinical trials in the near future.

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

    PubMed

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

    2014-09-10

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

  2. Design, construction and mechanical testing of digital 3D anatomical data-based PCL-HA bone tissue engineering scaffold.

    PubMed

    Yao, Qingqiang; Wei, Bo; Guo, Yang; Jin, Chengzhe; Du, Xiaotao; Yan, Chao; Yan, Junwei; Hu, Wenhao; Xu, Yan; Zhou, Zhi; Wang, Yijin; Wang, Liming

    2015-01-01

    The study aims to investigate the techniques of design and construction of CT 3D reconstructional data-based polycaprolactone (PCL)-hydroxyapatite (HA) scaffold. Femoral and lumbar spinal specimens of eight male New Zealand white rabbits were performed CT and laser scanning data-based 3D printing scaffold processing using PCL-HA powder. Each group was performed eight scaffolds. The CAD-based 3D printed porous cylindrical stents were 16 piece × 3 groups, including the orthogonal scaffold, the Pozi-hole scaffold and the triangular hole scaffold. The gross forms, fiber scaffold diameters and porosities of the scaffolds were measured, and the mechanical testing was performed towards eight pieces of the three kinds of cylindrical scaffolds, respectively. The loading force, deformation, maximum-affordable pressure and deformation value were recorded. The pore-connection rate of each scaffold was 100 % within each group, there was no significant difference in the gross parameters and micro-structural parameters of each scaffold when compared with the design values (P > 0.05). There was no significant difference in the loading force, deformation and deformation value under the maximum-affordable pressure of the three different cylinder scaffolds when the load was above 320 N. The combination of CT and CAD reverse technology could accomplish the design and manufacturing of complex bone tissue engineering scaffolds, with no significant difference in the impacts of the microstructures towards the physical properties of different porous scaffolds under large load.

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

    PubMed

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

    2016-07-01

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

  4. 3D Imaging of Nanoparticle Distribution in Biological Tissue by Laser-Induced Breakdown Spectroscopy

    PubMed Central

    Gimenez, Y.; Busser, B.; Trichard, F.; Kulesza, A.; Laurent, J. M.; Zaun, V.; Lux, F.; Benoit, J. M.; Panczer, G.; Dugourd, P.; Tillement, O.; Pelascini, F.; Sancey, L.; Motto-Ros, V.

    2016-01-01

    Nanomaterials represent a rapidly expanding area of research with huge potential for future medical applications. Nanotechnology indeed promises to revolutionize diagnostics, drug delivery, gene therapy, and many other areas of research. For any biological investigation involving nanomaterials, it is crucial to study the behavior of such nano-objects within tissues to evaluate both their efficacy and their toxicity. Here, we provide the first account of 3D label-free nanoparticle imaging at the entire-organ scale. The technology used is known as laser-induced breakdown spectroscopy (LIBS) and possesses several advantages such as speed of operation, ease of use and full compatibility with optical microscopy. We then used two different but complementary approaches to achieve 3D elemental imaging with LIBS: a volume reconstruction of a sliced organ and in-depth analysis. This proof-of-concept study demonstrates the quantitative imaging of both endogenous and exogenous elements within entire organs and paves the way for innumerable applications. PMID:27435424

  5. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and 3-dimensional structural information

    PubMed Central

    Pei, Jimin; Grishin, Nick V.

    2015-01-01

    SUMMARY Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of 3-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  6. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  7. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D.

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  9. Determining 3-D motion and structure from image sequences

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

    A method of determining three-dimensional motion and structure from two image frames is presented. The method requires eight point correspondences between the two frames, from which motion and structure parameters are determined by solving a set of eight linear equations and a singular value decomposition of a 3x3 matrix. It is shown that the solution thus obtained is unique.

  10. The 3D Structure of the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Zoccali, Manuela; Valenti, Elena

    2016-06-01

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

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

    PubMed Central

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

    2002-01-01

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

  12. 3D force control for robotic-assisted beating heart surgery based on viscoelastic tissue model.

    PubMed

    Liu, Chao; Moreira, Pedro; Zemiti, Nabil; Poignet, Philippe

    2011-01-01

    Current cardiac surgery faces the challenging problem of heart beating motion even with the help of mechanical stabilizer which makes delicate operation on the heart surface difficult. Motion compensation methods for robotic-assisted beating heart surgery have been proposed recently in literature, but research on force control for such kind of surgery has hardly been reported. Moreover, the viscoelasticity property of the interaction between organ tissue and robotic instrument further complicates the force control design which is much easier in other applications by assuming the interaction model to be elastic (industry, stiff object manipulation, etc.). In this work, we present a three-dimensional force control method for robotic-assisted beating heart surgery taking into consideration of the viscoelastic interaction property. Performance studies based on our D2M2 robot and 3D heart beating motion information obtained through Da Vinci™ system are provided.

  13. Spheroid culture as a tool for creating 3D complex tissues.

    PubMed

    Fennema, Eelco; Rivron, Nicolas; Rouwkema, Jeroen; van Blitterswijk, Clemens; de Boer, Jan

    2013-02-01

    3D cell culture methods confer a high degree of clinical and biological relevance to in vitro models. This is specifically the case with the spheroid culture, where a small aggregate of cells grows free of foreign materials. In spheroid cultures, cells secrete the extracellular matrix (ECM) in which they reside, and they can interact with cells from their original microenvironment. The value of spheroid cultures is increasing quickly due to novel microfabricated platforms amenable to high-throughput screening (HTS) and advances in cell culture. Here, we review new possibilities that combine the strengths of spheroid culture with new microenvironment fabrication methods that allow for the creation of large numbers of highly reproducible, complex tissues.

  14. 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.

  15. Experimental Evaluation of Ultrasound-Guided 3D Needle Steering in Biological Tissue

    PubMed Central

    Abayazid, Momen; Vrooijink, Gustaaf J.; Patil, Sachin; Alterovitz, Ron; Misra, Sarthak

    2014-01-01

    Purpose In this paper, we present a system capable of automatically steering bevel-tip flexible needles under ultrasound guidance towards stationary and moving targets in gelatin phantoms and biological tissue while avoiding stationary and moving obstacles. We use three-dimensional (3D) ultrasound to track the needle tip during the procedure. Methods Our system uses a fast sampling-based path planner to compute and periodically update a feasible path to the target that avoids obstacles. We then use a novel control algorithm to steer the needle along the path in a manner that reduces the number of needle rotations, thus reducing tissue damage. We present experimental results for needle insertion procedures for both stationary and moving targets and obstacles for up to 90 mm of needle insertion. Results We obtained a mean targeting error of 0.32 ± 0.10 mm and 0.38 ± 0.19 mm in gelatin-based phantom and biological tissue, respectively. Conclusions The achieved submillimeter accuracy suggests that our approach is sufficient to target the smallest lesions (ϕ2 mm) that can be detected using state-of-the-art ultrasound imaging systems. PMID:24562744

  16. Improved MAGIC gel for higher sensitivity and elemental tissue equivalent 3D dosimetry

    SciTech Connect

    Zhu Xuping; Reese, Timothy G.; Crowley, Elizabeth M.; El Fakhri, Georges

    2010-01-15

    Purpose: Polymer-based gel dosimeter (MAGIC type) is a preferable phantom material for PET range verification of proton beam therapy. However, improvement in elemental tissue equivalency (specifically O/C ratio) is very desirable to ensure realistic time-activity measurements. Methods: Glucose and urea was added to the original MAGIC formulation to adjust the O/C ratio. The dose responses of the new formulations were tested with MRI transverse relaxation rate (R2) measurements. Results: The new ingredients improved not only the elemental composition but also the sensitivity of the MAGIC gel. The O/C ratios of our new gels agree with that of soft tissue within 1%. The slopes of dose response curves were 1.6-2.7 times larger with glucose. The melting point also increased by 5 deg. C. Further addition of urea resulted in a similar slope but with an increased intercept and a decreased melting point. Conclusions: Our improved MAGIC gel formulations have higher sensitivity and better elemental tissue equivalency for 3D dosimetry applications involving nuclear reactions.

  17. In vitro cartilage tissue engineering with 3D porous aqueous-derived silk scaffolds and mesenchymal stem cells.

    PubMed

    Wang, Yongzhong; Kim, Ung-Jin; Blasioli, Dominick J; Kim, Hyeon-Joo; Kaplan, David L

    2005-12-01

    Adult cartilage tissue has limited self-repair capacity, especially in the case of severe damages caused by developmental abnormalities, trauma, or aging-related degeneration like osteoarthritis. Adult mesenchymal stem cells (MSCs) have the potential to differentiate into cells of different lineages including bone, cartilage, and fat. In vitro cartilage tissue engineering using autologous MSCs and three-dimensional (3-D) porous scaffolds has the potential for the successful repair of severe cartilage damage. Ideally, scaffolds designed for cartilage tissue engineering should have optimal structural and mechanical properties, excellent biocompatibility, controlled degradation rate, and good handling characteristics. In the present work, a novel, highly porous silk scaffold was developed by an aqueous process according to these criteria and subsequently combined with MSCs for in vitro cartilage tissue engineering. Chondrogenesis of MSCs in the silk scaffold was evident by real-time RT-PCR analysis for cartilage-specific ECM gene markers, histological and immunohistochemical evaluations of cartilage-specific ECM components. Dexamethasone and TGF-beta3 were essential for the survival, proliferation and chondrogenesis of MSCs in the silk scaffolds. The attachment, proliferation, and differentiation of MSCs in the silk scaffold showed unique characteristics. After 3 weeks of cultivation, the spatial cell arrangement and the collagen type-II distribution in the MSCs-silk scaffold constructs resembles those in native articular cartilage tissue, suggesting promise for these novel 3-D degradable silk-based scaffolds in MSC-based cartilage repair. Further in vivo evaluation is necessary to fully recognize the clinical relevance of these observations.

  18. Confocal fluorometer for diffusion tracking in 3D engineered tissue constructs

    NASA Astrophysics Data System (ADS)

    Daly, D.; Zilioli, A.; Tan, N.; Buttenschoen, K.; Chikkanna, B.; Reynolds, J.; Marsden, B.; Hughes, C.

    2016-03-01

    We present results of the development of a non-contacting instrument, called fScan, based on scanning confocal fluorometry for assessing the diffusion of materials through a tissue matrix. There are many areas in healthcare diagnostics and screening where it is now widely accepted that the need for new quantitative monitoring technologies is a major pinch point in patient diagnostics and in vitro testing. With the increasing need to interpret 3D responses this commonly involves the need to track the diffusion of compounds, pharma-active species and cells through a 3D matrix of tissue. Methods are available but to support the advances that are currently only promised, this monitoring needs to be real-time, non-invasive, and economical. At the moment commercial meters tend to be invasive and usually require a sample of the medium to be removed and processed prior to testing. This methodology clearly has a number of significant disadvantages. fScan combines a fiber based optical arrangement with a compact, free space optical front end that has been integrated so that the sample's diffusion can be measured without interference. This architecture is particularly important due to the "wet" nature of the samples. fScan is designed to measure constructs located within standard well plates and a 2-D motion stage locates the required sample with respect to the measurement system. Results are presented that show how the meter has been used to evaluate movements of samples through collagen constructs in situ without disturbing their kinetic characteristics. These kinetics were little understood prior to these measurements.

  19. 3-D Structure of Molecules of Biological Significance

    ERIC Educational Resources Information Center

    Bennett, Alice S.; Schwenk, Karl

    1974-01-01

    Describes how to use the distinctive properties of osazone formation in conjunction with molecular model construction to demonstrate the relationship between the three-dimensional structures of simple sugars and the shapes of crystals they form. (BR)

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

    PubMed Central

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

    2010-01-01

    There have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse-grain model generation and evaluation at the Cα or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full-atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root-mean-square deviation of the best models from the native structures is 4.28 Å, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community-wide experiment for protein structure prediction CASP8. PMID:19927325

  1. 3D tissue-engineered construct analysis via conventional high-resolution microcomputed tomography without X-ray contrast.

    PubMed

    Voronov, Roman S; VanGordon, Samuel B; Shambaugh, Robert L; Papavassiliou, Dimitrios V; Sikavitsas, Vassilios I

    2013-05-01

    As the field of tissue engineering develops, researchers are faced with a large number of degrees of freedom regarding the choice of material, architecture, seeding, and culturing. To evaluate the effectiveness of a tissue-engineered strategy, histology is typically done by physically slicing and staining a construct (crude, time-consuming, and unreliable). However, due to recent advances in high-resolution biomedical imaging, microcomputed tomography (μCT) has arisen as a quick and effective way to evaluate samples, while preserving their structure in the original state. However, a major barrier for using μCT to do histology has been its inability to differentiate between materials with similar X-ray attenuation. Various contrasting strategies (hardware and chemical staining agents) have been proposed to address this problem, but at a cost of additional complexity and limited access. Instead, here we suggest a strategy for how virtual 3D histology in silico can be conducted using conventional μCT, and we provide an illustrative example from bone tissue engineering. The key to our methodology is an implementation of scaffold surface architecture that is ordered in relation to cells and tissue, in concert with straightforward image-processing techniques, to minimize the reliance on contrasting for material segmentation. In the case study reported, μCT was used to image and segment porous poly(lactic acid) nonwoven fiber mesh scaffolds that were seeded dynamically with mesenchymal stem cells and cultured to produce soft tissue and mineralized tissue in a flow perfusion bioreactor using an osteogenic medium. The methodology presented herein paves a new way for tissue engineers to identify and distinguish components of cell/tissue/scaffold constructs to easily and effectively evaluate the tissue-engineering strategies that generate them.

  2. Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs

    NASA Astrophysics Data System (ADS)

    Jung, Jin Woo; Lee, Jung-Seob; Cho, Dong-Woo

    2016-02-01

    Recently, much attention has focused on replacement or/and enhancement of biological tissues via the use of cell-laden hydrogel scaffolds with an architecture that mimics the tissue matrix, and with the desired three-dimensional (3D) external geometry. However, mimicking the heterogeneous tissues that most organs and tissues are formed of is challenging. Although multiple-head 3D printing systems have been proposed for fabricating heterogeneous cell-laden hydrogel scaffolds, to date only the simple exterior form has been realized. Here we describe a computer-aided design and manufacturing (CAD/CAM) system for this application. We aim to develop an algorithm to enable easy, intuitive design and fabrication of a heterogeneous cell-laden hydrogel scaffolds with a free-form 3D geometry. The printing paths of the scaffold are automatically generated from the 3D CAD model, and the scaffold is then printed by dispensing four materials; i.e., a frame, two kinds of cell-laden hydrogel and a support. We demonstrated printing of heterogeneous tissue models formed of hydrogel scaffolds using this approach, including the outer ear, kidney and tooth tissue. These results indicate that this approach is particularly promising for tissue engineering and 3D printing applications to regenerate heterogeneous organs and tissues with tailored geometries to treat specific defects or injuries.

  3. Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs.

    PubMed

    Jung, Jin Woo; Lee, Jung-Seob; Cho, Dong-Woo

    2016-01-01

    Recently, much attention has focused on replacement or/and enhancement of biological tissues via the use of cell-laden hydrogel scaffolds with an architecture that mimics the tissue matrix, and with the desired three-dimensional (3D) external geometry. However, mimicking the heterogeneous tissues that most organs and tissues are formed of is challenging. Although multiple-head 3D printing systems have been proposed for fabricating heterogeneous cell-laden hydrogel scaffolds, to date only the simple exterior form has been realized. Here we describe a computer-aided design and manufacturing (CAD/CAM) system for this application. We aim to develop an algorithm to enable easy, intuitive design and fabrication of a heterogeneous cell-laden hydrogel scaffolds with a free-form 3D geometry. The printing paths of the scaffold are automatically generated from the 3D CAD model, and the scaffold is then printed by dispensing four materials; i.e., a frame, two kinds of cell-laden hydrogel and a support. We demonstrated printing of heterogeneous tissue models formed of hydrogel scaffolds using this approach, including the outer ear, kidney and tooth tissue. These results indicate that this approach is particularly promising for tissue engineering and 3D printing applications to regenerate heterogeneous organs and tissues with tailored geometries to treat specific defects or injuries. PMID:26899876

  4. Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs

    PubMed Central

    Jung, Jin Woo; Lee, Jung-Seob; Cho, Dong-Woo

    2016-01-01

    Recently, much attention has focused on replacement or/and enhancement of biological tissues via the use of cell-laden hydrogel scaffolds with an architecture that mimics the tissue matrix, and with the desired three-dimensional (3D) external geometry. However, mimicking the heterogeneous tissues that most organs and tissues are formed of is challenging. Although multiple-head 3D printing systems have been proposed for fabricating heterogeneous cell-laden hydrogel scaffolds, to date only the simple exterior form has been realized. Here we describe a computer-aided design and manufacturing (CAD/CAM) system for this application. We aim to develop an algorithm to enable easy, intuitive design and fabrication of a heterogeneous cell-laden hydrogel scaffolds with a free-form 3D geometry. The printing paths of the scaffold are automatically generated from the 3D CAD model, and the scaffold is then printed by dispensing four materials; i.e., a frame, two kinds of cell-laden hydrogel and a support. We demonstrated printing of heterogeneous tissue models formed of hydrogel scaffolds using this approach, including the outer ear, kidney and tooth tissue. These results indicate that this approach is particularly promising for tissue engineering and 3D printing applications to regenerate heterogeneous organs and tissues with tailored geometries to treat specific defects or injuries. PMID:26899876

  5. Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs.

    PubMed

    Jung, Jin Woo; Lee, Jung-Seob; Cho, Dong-Woo

    2016-02-22

    Recently, much attention has focused on replacement or/and enhancement of biological tissues via the use of cell-laden hydrogel scaffolds with an architecture that mimics the tissue matrix, and with the desired three-dimensional (3D) external geometry. However, mimicking the heterogeneous tissues that most organs and tissues are formed of is challenging. Although multiple-head 3D printing systems have been proposed for fabricating heterogeneous cell-laden hydrogel scaffolds, to date only the simple exterior form has been realized. Here we describe a computer-aided design and manufacturing (CAD/CAM) system for this application. We aim to develop an algorithm to enable easy, intuitive design and fabrication of a heterogeneous cell-laden hydrogel scaffolds with a free-form 3D geometry. The printing paths of the scaffold are automatically generated from the 3D CAD model, and the scaffold is then printed by dispensing four materials; i.e., a frame, two kinds of cell-laden hydrogel and a support. We demonstrated printing of heterogeneous tissue models formed of hydrogel scaffolds using this approach, including the outer ear, kidney and tooth tissue. These results indicate that this approach is particularly promising for tissue engineering and 3D printing applications to regenerate heterogeneous organs and tissues with tailored geometries to treat specific defects or injuries.

  6. Cross modality registration of video and magnetic tracker data for 3D appearance and structure modeling

    NASA Astrophysics Data System (ADS)

    Sargent, Dusty; Chen, Chao-I.; Wang, Yuan-Fang

    2010-02-01

    The paper reports a fully-automated, cross-modality sensor data registration scheme between video and magnetic tracker data. This registration scheme is intended for use in computerized imaging systems to model the appearance, structure, and dimension of human anatomy in three dimensions (3D) from endoscopic videos, particularly colonoscopic videos, for cancer research and clinical practices. The proposed cross-modality calibration procedure operates this way: Before a colonoscopic procedure, the surgeon inserts a magnetic tracker into the working channel of the endoscope or otherwise fixes the tracker's position on the scope. The surgeon then maneuvers the scope-tracker assembly to view a checkerboard calibration pattern from a few different viewpoints for a few seconds. The calibration procedure is then completed, and the relative pose (translation and rotation) between the reference frames of the magnetic tracker and the scope is determined. During the colonoscopic procedure, the readings from the magnetic tracker are used to automatically deduce the pose (both position and orientation) of the scope's reference frame over time, without complicated image analysis. Knowing the scope movement over time then allows us to infer the 3D appearance and structure of the organs and tissues in the scene. While there are other well-established mechanisms for inferring the movement of the camera (scope) from images, they are often sensitive to mistakes in image analysis, error accumulation, and structure deformation. The proposed method using a magnetic tracker to establish the camera motion parameters thus provides a robust and efficient alternative for 3D model construction. Furthermore, the calibration procedure does not require special training nor use expensive calibration equipment (except for a camera calibration pattern-a checkerboard pattern-that can be printed on any laser or inkjet printer).

  7. Subtractive 3D printing of optically active diamond structures.

    PubMed

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

    2014-05-21

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

  8. Delineation of nuclear structures in 3D multicellular systems

    SciTech Connect

    2013-09-13

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

  9. Imaging solar coronal magnetic structures in 3D

    NASA Astrophysics Data System (ADS)

    Cartledge, N. P.

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

  10. Designing self-assembling 3D structures of microcapsules

    NASA Astrophysics Data System (ADS)

    Li, Like; Shum, Henry; Shklyaev, Oleg; Yashin, Victor; Balazs, Anna

    Self-assembly of complex, three-dimensional structures is commonly achieved by biological cells but difficult to realize in synthetic systems with micron-scale or larger components. Some previous modeling studies have considered only the planar self-assembly of microcapsules on a substrate. In this work, nanoparticles released from the capsules bind to the substrate and to the shells of nearby capsules. The non-uniform nanoparticle deposition on a capsule's surface leads to adhesion gradients, which drive the capsules to effectively ``climb'' on top of one another and self-organize in the vertical direction. We determine conditions that favor this structural organization. In particular, we study how the vertical structuring depends on the background fluid flow, the topography of the microcapsules and the underlying surface, the capsule-capsule interaction and that between the capsules and the substrate. The findings can provide design rules for the autonomous creation of novel nanocomposites, where the layers are formed from nanoparticle-containing and nanoparticle-decorated microcapsules.

  11. 3D Printing for Spacecraft Multi-Functional Structures

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    1999-11-22

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

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

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

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

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

    PubMed

    Wang, Jianwei; Zhang, Yong

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Wang, Jianwei; Zhang, Yong

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  17. Additively Manufactured Device for Dynamic Culture of Large Arrays of 3D Tissue Engineered Constructs.

    PubMed

    Costa, Pedro F; Hutmacher, Dietmar W; Theodoropoulos, Christina; Gomes, Manuela E; Reis, Rui L; Vaquette, Cédryck

    2015-04-22

    The ability to test large arrays of cell and biomaterial combinations in 3D environments is still rather limited in the context of tissue engineering and regenerative medicine. This limitation can be generally addressed by employing highly automated and reproducible methodologies. This study reports on the development of a highly versatile and upscalable method based on additive manufacturing for the fabrication of arrays of scaffolds, which are enclosed into individualized perfusion chambers. Devices containing eight scaffolds and their corresponding bioreactor chambers are simultaneously fabricated utilizing a dual extrusion additive manufacturing system. To demonstrate the versatility of the concept, the scaffolds, while enclosed into the device, are subsequently surface-coated with a biomimetic calcium phosphate layer by perfusion with simulated body fluid solution. 96 scaffolds are simultaneously seeded and cultured with human osteoblasts under highly controlled bidirectional perfusion dynamic conditions over 4 weeks. Both coated and noncoated resulting scaffolds show homogeneous cell distribution and high cell viability throughout the 4 weeks culture period and CaP-coated scaffolds result in a significantly increased cell number. The methodology developed in this work exemplifies the applicability of additive manufacturing as a tool for further automation of studies in the field of tissue engineering and regenerative medicine.

  18. 3D nano-structures for laser nano-manipulation.

    PubMed

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

    2013-01-01

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

  19. 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.

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

    PubMed

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

    2015-08-26

    3D printing of metallic microarchitectures with controlled internal structures is realized at room temperature in ambient air conditions by the manipulation of metal ion concentration and pulsed electric potentials in the electrolyte meniscus during the meniscus-guided electrodeposition. Precise control of the printing nozzle enables the drawing of complex 3D microarchitectures with well-defined geometries and positions. PMID:25917532

  1. Formation of 3D structures in a volumetric photocurable material via a holographic method

    NASA Astrophysics Data System (ADS)

    Vorzobova, N. D.; Bulgakova, V. G.; Veselov, V. O.

    2015-12-01

    The principle of forming 3D polymer structures is considered, based on the display of the 3D intensity distribution of radiation formed by a hologram in the bulk of a photocurable material. The conditions are determined for limiting the cure depth and reproducing the projected wavefront configuration.

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

    NASA Technical Reports Server (NTRS)

    Riggs, H. R.

    2000-01-01

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

  3. Fabrication of 3D tissue equivalent: an in vitro platform for understanding collagen evolution in healthy and diseased models

    NASA Astrophysics Data System (ADS)

    Urciuolo, F.; Imparato, G.; Casale, C.; Scamardella, S.; Netti, P.

    2013-04-01

    In this study we realized a three-dimensional human dermis equivalent (3D-HDE) and, by exploiting multi-photon microscopy (MPM) we validated its use as an in vitro model to study collagen network re-arrangement under simulated solar exposure. The realization of 3D-HDE has been pursed by means of a bottom-up tissue engineering strategy that comprises firstly the fabrication of micron sized tissue building blocks and then their assembly in a 3D tissue construct. The building blocks injected in a maturation chamber, and cultured under optimized culture condition, were able to fuse due to the establishment of cell-cell and cell-extra cellular matrix (ECM) interactions that induced a biological sintering process resulting in 3D-HDE production. The final 3D tissue was made-up by fibroblasts embedded in their own ECM rich in endogenous collagen type I, resembling the composition and the architecture of native human dermis. Second Harmonic Generation (SHG) and Two-Photon Excited Fluorescence (TPEF) imaging have been exploited to assess modification in collagen assembly before and after UV irradiation. Textural features and SHG to TPFE ratio of the endogenous ECM within 3D-HDE have been shown to vary after UVA irradiation, proving the hypothesis that the 3DHDE realized can be used as biological platform in vitro to study ECM modifications induced by photo-damage.

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

    NASA Astrophysics Data System (ADS)

    Allen, R.

    2003-04-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets. PMID:26824922

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed

    Gu, Qi; Tomaskovic-Crook, Eva; Lozano, Rodrigo; Chen, Yu; Kapsa, Robert M; Zhou, Qi; Wallace, Gordon G; Crook, Jeremy M

    2016-06-01

    Direct-write printing of stem cells within biomaterials presents an opportunity to engineer tissue for in vitro modeling and regenerative medicine. Here, a first example of constructing neural tissue by printing human neural stem cells that are differentiated in situ to functional neurons and supporting neuroglia is reported. The supporting biomaterial incorporates a novel clinically relevant polysaccharide-based bioink comprising alginate, carboxymethyl-chitosan, and agarose. The printed bioink rapidly gels by stable cross-linking to form a porous 3D scaffold encapsulating stem cells for in situ expansion and differentiation. Differentiated neurons form synaptic contacts, establish networks, are spontaneously active, show a bicuculline-induced increased calcium response, and are predominantly gamma-aminobutyric acid expressing. The 3D tissues will facilitate investigation of human neural development, function, and disease, and may be adaptable for engineering other 3D tissues from different stem cell types. PMID:27028356

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

    PubMed

    Gu, Qi; Tomaskovic-Crook, Eva; Lozano, Rodrigo; Chen, Yu; Kapsa, Robert M; Zhou, Qi; Wallace, Gordon G; Crook, Jeremy M

    2016-06-01

    Direct-write printing of stem cells within biomaterials presents an opportunity to engineer tissue for in vitro modeling and regenerative medicine. Here, a first example of constructing neural tissue by printing human neural stem cells that are differentiated in situ to functional neurons and supporting neuroglia is reported. The supporting biomaterial incorporates a novel clinically relevant polysaccharide-based bioink comprising alginate, carboxymethyl-chitosan, and agarose. The printed bioink rapidly gels by stable cross-linking to form a porous 3D scaffold encapsulating stem cells for in situ expansion and differentiation. Differentiated neurons form synaptic contacts, establish networks, are spontaneously active, show a bicuculline-induced increased calcium response, and are predominantly gamma-aminobutyric acid expressing. The 3D tissues will facilitate investigation of human neural development, function, and disease, and may be adaptable for engineering other 3D tissues from different stem cell types.

  11. Self-organization of polarized cerebellar tissue in 3D culture of human pluripotent stem cells.

    PubMed

    Muguruma, Keiko; Nishiyama, Ayaka; Kawakami, Hideshi; Hashimoto, Kouichi; Sasai, Yoshiki

    2015-02-01

    During cerebellar development, the main portion of the cerebellar plate neuroepithelium gives birth to Purkinje cells and interneurons, whereas the rhombic lip, the germinal zone at its dorsal edge, generates granule cells and cerebellar nuclei neurons. However, it remains elusive how these components cooperate to form the intricate cerebellar structure. Here, we found that a polarized cerebellar structure self-organizes in 3D human embryonic stem cell (ESC) culture. The self-organized neuroepithelium differentiates into electrophysiologically functional Purkinje cells. The addition of fibroblast growth factor 19 (FGF19) promotes spontaneous generation of dorsoventrally polarized neural-tube-like structures at the level of the cerebellum. Furthermore, addition of SDF1 and FGF19 promotes the generation of a continuous cerebellar plate neuroepithelium with rhombic-lip-like structure at one end and a three-layer cytoarchitecture similar to the embryonic cerebellum. Thus, human-ESC-derived cerebellar progenitors exhibit substantial self-organizing potential for generating a polarized structure reminiscent of the early human cerebellum at the first trimester. PMID:25640179

  12. High-Resolution 3-D Imaging and Tissue Differentiation with Transmission Tomography

    NASA Astrophysics Data System (ADS)

    Marmarelis, V. Z.; Jeong, J.; Shin, D. C.; Do, S.

    A three-dimensional High-resolution Ultrasonic Transmission Tomography (HUTT) system has been developed recently under the sponsorship of the Alfred Mann Institute at the University of Southern California that holds the promise of early detection of breast cancer (mm-size lesions) with greater sensitivity (true positives) and specificity (true negatives) than current x-ray mammograghy. In addition to sub-mm resolution in 3-D, the HUTT system has the unique capability of reliable tissue classification by means of the frequency-dependent attenuation characteristics of individual voxels that are extracted from the tomographic data through novel signal processing methods. These methods yield "multi-band signatures" of the various tissue types that are utilized to achieve reliable tissue differentiation via novel segmentation and classification algorithms. The unparalleled high-resolution and tissue differentiation capabilities of the HUTT system have been demonstrated so far with man-made and animal-tissue phantoms. Illustrative results are presented that corroborate these claims, although several challenges remain to make HUTT a clinically acceptable technology. The next critical step is to collect and analyze data from human subjects (female breasts) in order to demonstrate the key capability of the HUTT system to detect breast lesions early (at the mm-size stage) and to differentiate between malignant and benign lesions in a manner that is far superior (in terms of sensitivity and specificity) to the current x-ray mammography. The key initial application of the HUTT imaging technology is envisioned to be the early (at the mm-size) detection of breast cancer, which represents a major threat to the well-being of women around the world. The potential impact is estimated in hundreds of thousands lives saved, millions of unnecessary biopsies avoided, and billions of dollars saved in national health-care costs every year - to say nothing of the tens of thousands of

  13. Production of new 3D scaffolds for bone tissue regeneration by rapid prototyping.

    PubMed

    Fradique, R; Correia, T R; Miguel, S P; de Sá, K D; Figueira, D R; Mendonça, A G; Correia, I J

    2016-04-01

    The incidence of bone disorders, whether due to trauma or pathology, has been trending upward with the aging of the worldwide population. The currently available treatments for bone injuries are rather limited, involving mainly bone grafts and implants. A particularly promising approach for bone regeneration uses rapid prototyping (RP) technologies to produce 3D scaffolds with highly controlled structure and orientation, based on computer-aided design models or medical data. Herein, tricalcium phosphate (TCP)/alginate scaffolds were produced using RP and subsequently their physicochemical, mechanical and biological properties were characterized. The results showed that 60/40 of TCP and alginate formulation was able to match the compression and present a similar Young modulus to that of trabecular bone while presenting an adequate biocompatibility. Moreover, the biomineralization ability, roughness and macro and microporosity of scaffolds allowed cell anchoring and proliferation at their surface, as well as cell migration to its interior, processes that are fundamental for osteointegration and bone regeneration.

  14. Novel 3D scaffold with enhanced physical and cell response properties for bone tissue regeneration, fabricated by patterned electrospinning/electrospraying.

    PubMed

    Hejazi, Fatemeh; Mirzadeh, Hamid

    2016-09-01

    Developing three dimensional scaffolds mimicking the nanoscale structure of native extracellular matrix is a key parameter in tissue regeneration. In this study, we aimed to introduce a novel 3D structures composed of nanofibers (NF) and micro particles (MP) and compare their efficiency with 2D nanofibrous scaffold. The conventional nanofibrous PCL scaffolds are 2D mats fabricated by the electrospinning technique, whereas the NF/MP and patterned NF/MP PCL scaffolds are three dimensional structures fabricated by a modified electrospinning/electrospraying technique. The mentioned method was carried out by varying the electrospinning solution parameters and use of a metal mesh as the collector. Detailed fabrication process and morphological properties of the fabricated structures is discussed and porosity, pore size and PBS solution absorption value of the prepared structures are reported. Compared with the 2D structure, 3D scaffolds possessed enhanced porosity and pore size which led to the significant increase in their water uptake capacity. In vitro cell experiments were carried out on the prepared structures by the use of MG-63 osteosarcoma cell line. The fabricated 3D structures offered significantly increased cell attachment, spread and diffusion which were confirmed by SEM analysis. In vitro cytocompatibility assessed by MTT colorimetric assay indicated a continuous cell proliferation over 21 days on the innovative 3D structure, while on 2D mat cell proliferation stopped at early time points. Enhanced osteogenic differentiation of the seeded MG-63 cells on 3D scaffold was confirmed by the remarkable ALP activity together with increased and accelerated calcium deposition on this structure compared to 2D mat. Massive and well distributed bone minerals formed on patterned 3D structure were shown by EDX analysis. In comparison between NF/MP quasi-3D and Patterned NF/MP 3D scaffolds, patterned structures proceeded in all of the above properties. As such, the

  15. Novel 3D scaffold with enhanced physical and cell response properties for bone tissue regeneration, fabricated by patterned electrospinning/electrospraying.

    PubMed

    Hejazi, Fatemeh; Mirzadeh, Hamid

    2016-09-01

    Developing three dimensional scaffolds mimicking the nanoscale structure of native extracellular matrix is a key parameter in tissue regeneration. In this study, we aimed to introduce a novel 3D structures composed of nanofibers (NF) and micro particles (MP) and compare their efficiency with 2D nanofibrous scaffold. The conventional nanofibrous PCL scaffolds are 2D mats fabricated by the electrospinning technique, whereas the NF/MP and patterned NF/MP PCL scaffolds are three dimensional structures fabricated by a modified electrospinning/electrospraying technique. The mentioned method was carried out by varying the electrospinning solution parameters and use of a metal mesh as the collector. Detailed fabrication process and morphological properties of the fabricated structures is discussed and porosity, pore size and PBS solution absorption value of the prepared structures are reported. Compared with the 2D structure, 3D scaffolds possessed enhanced porosity and pore size which led to the significant increase in their water uptake capacity. In vitro cell experiments were carried out on the prepared structures by the use of MG-63 osteosarcoma cell line. The fabricated 3D structures offered significantly increased cell attachment, spread and diffusion which were confirmed by SEM analysis. In vitro cytocompatibility assessed by MTT colorimetric assay indicated a continuous cell proliferation over 21 days on the innovative 3D structure, while on 2D mat cell proliferation stopped at early time points. Enhanced osteogenic differentiation of the seeded MG-63 cells on 3D scaffold was confirmed by the remarkable ALP activity together with increased and accelerated calcium deposition on this structure compared to 2D mat. Massive and well distributed bone minerals formed on patterned 3D structure were shown by EDX analysis. In comparison between NF/MP quasi-3D and Patterned NF/MP 3D scaffolds, patterned structures proceeded in all of the above properties. As such, the

  16. 3D lidar imaging for detecting and understanding plant responses and canopy structure.

    PubMed

    Omasa, Kenji; Hosoi, Fumiki; Konishi, Atsumi

    2007-01-01

    Understanding and diagnosing plant responses to stress will benefit greatly from three-dimensional (3D) measurement and analysis of plant properties because plant responses are strongly related to their 3D structures. Light detection and ranging (lidar) has recently emerged as a powerful tool for direct 3D measurement of plant structure. Here the use of 3D lidar imaging to estimate plant properties such as canopy height, canopy structure, carbon stock, and species is demonstrated, and plant growth and shape responses are assessed by reviewing the development of lidar systems and their applications from the leaf level to canopy remote sensing. In addition, the recent creation of accurate 3D lidar images combined with natural colour, chlorophyll fluorescence, photochemical reflectance index, and leaf temperature images is demonstrated, thereby providing information on responses of pigments, photosynthesis, transpiration, stomatal opening, and shape to environmental stresses; these data can be integrated with 3D images of the plants using computer graphics techniques. Future lidar applications that provide more accurate dynamic estimation of various plant properties should improve our understanding of plant responses to stress and of interactions between plants and their environment. Moreover, combining 3D lidar with other passive and active imaging techniques will potentially improve the accuracy of airborne and satellite remote sensing, and make it possible to analyse 3D information on ecophysiological responses and levels of various substances in agricultural and ecological applications and in observations of the global biosphere. PMID:17030540

  17. Imaging and 3D Reconstruction of Cerebrovascular Structures in Embryonic Zebrafish

    PubMed Central

    Ethell, Douglas W.; Cameron, D. Joshua

    2014-01-01

    Zebrafish are a powerful tool to study developmental biology and pathology in vivo. The small size and relative transparency of zebrafish embryos make them particularly useful for the visual examination of processes such as heart and vascular development. In several recent studies transgenic zebrafish that express EGFP in vascular endothelial cells were used to image and analyze complex vascular networks in the brain and retina, using confocal microscopy. Descriptions are provided to prepare, treat and image zebrafish embryos that express enhanced green fluorescent protein (EGFP), and then generate comprehensive 3D renderings of the cerebrovascular system. Protocols include the treatment of embryos, confocal imaging, and fixation protocols that preserve EGFP fluorescence. Further, useful tips on obtaining high-quality images of cerebrovascular structures, such as removal the eye without damaging nearby neural tissue are provided. Potential pitfalls with confocal imaging are discussed, along with the steps necessary to generate 3D reconstructions from confocal image stacks using freely available open source software. PMID:24797110

  18. Fabrication and mechanical characterization of 3D electrospun scaffolds for tissue engineering.

    PubMed

    Wright, L D; Young, R T; Andric, T; Freeman, J W

    2010-10-01

    Electrospinning is a polymer processing technique that produces fibrous structures comparable to the extracellular matrix of many tissues. Electrospinning, however, has been severely limited in its tissue engineering capabilities because this technique has produced few three-dimensional structures. Sintering of electrospun materials provides a method to fabricate unique architectures and allow much larger structures to be made. Electrospun mats were sintered into strips and cylinders, and their tensile and compressive mechanical properties were measured. In addition, electrospun materials with salt pores (salt embedded within the material and then leached out) were fabricated to improve porosity of the electrospun materials for tissue engineering scaffolds. Sintered electrospun poly(D,L-lactide) and poly(L-lactide) (PDLA/PLLA) materials have higher tensile mechanical properties (modulus: 72.3 MPa, yield: 960 kPa) compared to unsintered PLLA (modulus: 40.36 MPa, yield: 675.5 kPa). Electrospun PDLA/PLLA cylinders with and without salt-leached pores had compressive moduli of 6.69 and 26.86 MPa, respectively, and compressive yields of 1.36 and 0.56 MPa, respectively. Sintering of electrospun materials is a novel technique that improves electrospinning application in tissue engineering by increasing the size and types of electrospun structures that can be fabricated.

  19. Confocal microscopy of thick tissue sections: 3D visualizaiton of rat kidney glomeruli

    EPA Science Inventory

    Confocal laser scanning microscopy (CLSM) as a technique capable of generating serial sections of whole-mount tissue and then reassembling the computer-acquired images as a virtual 3-dimentional structure. In many ways CLSM offers an alternative to traditional sectioning approac...

  20. Confocal Microscopy of thick tissue sections: 3D Visualization of rat kidney glomeruli

    EPA Science Inventory

    Confocal laser scanning microscopy (CLSM) as a technique capable of generating serial sections of whole-mount tissue and then reassembling the computer-acquired images as a virtual 3-dimentional structure. In many ways CLSM offers an alternative to traditional sectioning approac...

  1. 3D-printed haptic "reverse" models for preoperative planning in soft tissue reconstruction: a case report.

    PubMed

    Chae, Michael P; Lin, Frank; Spychal, Robert T; Hunter-Smith, David J; Rozen, Warren Matthew

    2015-02-01

    In reconstructive surgery, preoperative planning is essential for optimal functional and aesthetic outcome. Creating a three-dimensional (3D) model from two-dimensional (2D) imaging data by rapid prototyping has been used in industrial design for decades but has only recently been introduced for medical application. 3D printing is one such technique that is fast, convenient, and relatively affordable. In this report, we present a case in which a reproducible method for producing a 3D-printed "reverse model" representing a skin wound defect was used for flap design and harvesting. This comprised a 82-year-old man with an exposed ankle prosthesis after serial soft tissue debridements for wound infection. Soft tissue coverage and dead-space filling were planned with a composite radial forearm free flap (RFFF). Computed tomographic angiography (CTA) of the donor site (left forearm), recipient site (right ankle), and the left ankle was performed. 2D data from the CTA was 3D-reconstructed using computer software, with a 3D image of the left ankle used as a "control." A 3D model was created by superimposing the left and right ankle images, to create a "reverse image" of the defect, and printed using a 3D printer. The RFFF was thus planned and executed effectively, without complication. To our knowledge, this is the first report of a mechanism of calculating a soft tissue wound defect and producing a 3D model that may be useful for surgical planning. 3D printing and particularly "reverse" modeling may be versatile options in reconstructive planning, and have the potential for broad application.

  2. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  4. Sensitivity of an MT Array to 3D Structure Outside the Array Footprint

    NASA Astrophysics Data System (ADS)

    Booker, J. R.; Mackie, R. L.; Burd, A. I.; Pomposiello, M. C.; Favetto, A. B.

    2015-12-01

    Standard data collection strategy in magnetotellurics (MT) is to deploy a profile or array of sites that spans the target of interest. There is no expectation that structure can be imaged outside the area covered by sites. We have inverted two MT arrays for 3D structure under Argentina. The two arrays do not overlap, but serendipitously the 3D model for the northern array overlaps the position of a prominent 3D deep conductive structure seen in the inversion of the southern array. To our surprise this deep southern feature is also imaged by the northern array even though it is well outside the footprint of the northern array. It therefore appears that typical intuition about one's ability to image structure outside the span of the sites is not always true. We present model studies to demonstrate why this is so and under what conditions one can expect a 3D array to be capable of imaging structure outside the array.

  5. Two-photon polymerization microfabrication of hydrogels: an advanced 3D printing technology for tissue engineering and drug delivery.

    PubMed

    Xing, Jin-Feng; Zheng, Mei-Ling; Duan, Xuan-Ming

    2015-08-01

    3D printing technology has attracted much attention due to its high potential in scientific and industrial applications. As an outstanding 3D printing technology, two-photon polymerization (TPP) microfabrication has been applied in the fields of micro/nanophotonics, micro-electromechanical systems, microfluidics, biomedical implants and microdevices. In particular, TPP microfabrication is very useful in tissue engineering and drug delivery due to its powerful fabrication capability for precise microstructures with high spatial resolution on both the microscopic and the nanometric scale. The design and fabrication of 3D hydrogels widely used in tissue engineering and drug delivery has been an important research area of TPP microfabrication. The resolution is a key parameter for 3D hydrogels to simulate the native 3D environment in which the cells reside and the drug is controlled to release with optimal temporal and spatial distribution in vitro and in vivo. The resolution of 3D hydrogels largely depends on the efficiency of TPP initiators. In this paper, we will review the widely used photoresists, the development of TPP photoinitiators, the strategies for improving the resolution and the microfabrication of 3D hydrogels.

  6. 3D Normal Human Neural Progenitor Tissue-Like Assemblies: A Model of Persistent VZV Infection

    NASA Technical Reports Server (NTRS)

    Goodwin, Thomas J.

    2013-01-01

    Varicella-zoster virus (VZV) is a neurotropic human alphaherpesvirus that causes varicella upon primary infection, establishes latency in multiple ganglionic neurons, and can reactivate to cause zoster. Live attenuated VZV vaccines are available; however, they can also establish latent infections and reactivate. Studies of VZV latency have been limited to the analyses of human ganglia removed at autopsy, as the virus is strictly a human pathogen. Recently, terminally differentiated human neurons have received much attention as a means to study the interaction between VZV and human neurons; however, the short life-span of these cells in culture has limited their application. Herein, we describe the construction of a model of normal human neural progenitor cells (NHNP) in tissue-like assemblies (TLAs), which can be successfully maintained for at least 180 days in three-dimensional (3D) culture, and exhibit an expression profile similar to that of human trigeminal ganglia. Infection of NHNP TLAs with cell-free VZV resulted in a persistent infection that was maintained for three months, during which the virus genome remained stable. Immediate-early, early and late VZV genes were transcribed, and low-levels of infectious VZV were recurrently detected in the culture supernatant. Our data suggest that NHNP TLAs are an effective system to investigate long-term interactions of VZV with complex assemblies of human neuronal cells.

  7. Preparation and Evaluation of Gelatin-Chitosan-Nanobioglass 3D Porous Scaffold for Bone Tissue Engineering

    PubMed Central

    Maji, Kanchan; Dasgupta, Sudip; Pramanik, Krishna; Bissoyi, Akalabya

    2016-01-01

    The aim of the present study was to prepare and characterize bioglass-natural biopolymer based composite scaffold and evaluate its bone regeneration ability. Bioactive glass nanoparticles (58S) in the size range of 20–30 nm were synthesized using sol-gel method. Porous scaffolds with varying bioglass composition from 10 to 30 wt% in chitosan, gelatin matrix were fabricated using the method of freeze drying of its slurry at 40 wt% solids loading. Samples were cross-linked with glutaraldehyde to obtain interconnected porous 3D microstructure with improved mechanical strength. The prepared scaffolds exhibited >80% porosity with a mean pore size range between 100 and 300 microns. Scaffold containing 30 wt% bioglass (GCB 30) showed a maximum compressive strength of 2.2 ± 0.1 MPa. Swelling and degradation studies showed that the scaffold had excellent properties of hydrophilicity and biodegradability. GCB 30 scaffold was shown to be noncytotoxic and supported mesenchymal stem cell attachment, proliferation, and differentiation as indicated by MTT assay and RUNX-2 expression. Higher cellular activity was observed in GCB 30 scaffold as compared to GCB 0 scaffold suggesting the fact that 58S bioglass nanoparticles addition into the scaffold promoted better cell adhesion, proliferation, and differentiation. Thus, the study showed that the developed composite scaffolds are potential candidates for regenerating damaged bone tissue. PMID:26884764

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

    SciTech Connect

    Cornforth, Michael N.

    2013-05-03

    Combining contemporary cytogenetic methods with DNA CGH microarray technology and chromosome flow-sorting increases substantially the ability to resolve exchange breakpoints associated with interstitial deletions and translocations, allowing the consequences of radiation damage to be directly measured at low doses, while also providing valuable insights into molecular mechanisms of misrepair processes that, in turn, identify appropriate biophysical models of risk at low doses. The aims of this work apply to cells recovered from 3D tissue constructs of human skin and, for the purpose of comparison, the same cells irradiated in traditional 2D cultures. These aims are: to analyze by multi-flour fluorescence in situ hybridization (mFISH) the chromosomes in clonal descendents of individual human fibroblasts that were previously irradiated; to examine irradiated clones from Aim 1 for submicroscopic deletions by subjecting their DNA to comparative genomic hybridization (CGH) microarray analysis; and to flow-sort aberrant chromosomes from clones containing stable radiation-induced translocations and map the breakpoints to within an average resolution of 100 kb using the technique of 'array painting'.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  10. Mu-Synthesis robust control of 3D bar structure vibration using piezo-stack actuators

    NASA Astrophysics Data System (ADS)

    Mystkowski, Arkadiusz; Koszewnik, Andrzej Piotr

    2016-10-01

    This paper presents an idea for the Mu-Synthesis robust control of 3D bar structure vibration with using a piezo-stack actuators. A model of the 3D bar structure with uncertain parameters is presented as multi-input multi-output (MIMO) dynamics. Nominal stability and nominal performances of the open-loop 3D bar structure dynamic model is developed. The uncertain model-based robust controller is derived due to voltage control signal saturation and selected parameter perturbations. The robust control performances and robustness of the system due to uncertainties influence is evaluated by using singular values and a small gain theorem. Finally, simulation investigations and experimental results shown that system response of the 3D bar structure dynamic model with taken into account perturbed parameters met desired robust stability and system limits. The proposed robust controller ensures a good dynamics of the closed-loop system, robustness, and vibration attenuation.

  11. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

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

  12. Nanoparticle imaging. 3D structure of individual nanocrystals in solution by electron microscopy.

    PubMed

    Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A; Zettl, A; Alivisatos, A Paul

    2015-07-17

    Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale. PMID:26185247

  13. 3D structure of individual nanocrystals in solution by electron microscopy

    NASA Astrophysics Data System (ADS)

    Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T.; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A.; Zettl, A.; Alivisatos, A. Paul

    2015-07-01

    Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.

  14. Three‐dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues

    PubMed Central

    Baghabra, Jumana; Boges, Daniya J.; Holst, Glendon R.; Kreshuk, Anna; Hamprecht, Fred A.; Srinivasan, Madhusudhanan; Lehväslaiho, Heikki

    2016-01-01

    ABSTRACT Advances in the application of electron microscopy (EM) to serial imaging are opening doors to new ways of analyzing cellular structure. New and improved algorithms and workflows for manual and semiautomated segmentation allow us to observe the spatial arrangement of the smallest cellular features with unprecedented detail in full three‐dimensions. From larger samples, higher complexity models can be generated; however, they pose new challenges to data management and analysis. Here we review some currently available solutions and present our approach in detail. We use the fully immersive virtual reality (VR) environment CAVE (cave automatic virtual environment), a room in which we are able to project a cellular reconstruction and visualize in 3D, to step into a world created with Blender, a free, fully customizable 3D modeling software with NeuroMorph plug‐ins for visualization and analysis of EM preparations of brain tissue. Our workflow allows for full and fast reconstructions of volumes of brain neuropil using ilastik, a software tool for semiautomated segmentation of EM stacks. With this visualization environment, we can walk into the model containing neuronal and astrocytic processes to study the spatial distribution of glycogen granules, a major energy source that is selectively stored in astrocytes. The use of CAVE was key to the observation of a nonrandom distribution of glycogen, and led us to develop tools to quantitatively analyze glycogen clustering and proximity to other subcellular features. J. Comp. Neurol. 524:23–38, 2016. © 2015 Wiley Periodicals, Inc. PMID:26179415

  15. Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues.

    PubMed

    Calì, Corrado; Baghabra, Jumana; Boges, Daniya J; Holst, Glendon R; Kreshuk, Anna; Hamprecht, Fred A; Srinivasan, Madhusudhanan; Lehväslaiho, Heikki; Magistretti, Pierre J

    2016-01-01

    Advances in the application of electron microscopy (EM) to serial imaging are opening doors to new ways of analyzing cellular structure. New and improved algorithms and workflows for manual and semiautomated segmentation allow us to observe the spatial arrangement of the smallest cellular features with unprecedented detail in full three-dimensions. From larger samples, higher complexity models can be generated; however, they pose new challenges to data management and analysis. Here we review some currently available solutions and present our approach in detail. We use the fully immersive virtual reality (VR) environment CAVE (cave automatic virtual environment), a room in which we are able to project a cellular reconstruction and visualize in 3D, to step into a world created with Blender, a free, fully customizable 3D modeling software with NeuroMorph plug-ins for visualization and analysis of EM preparations of brain tissue. Our workflow allows for full and fast reconstructions of volumes of brain neuropil using ilastik, a software tool for semiautomated segmentation of EM stacks. With this visualization environment, we can walk into the model containing neuronal and astrocytic processes to study the spatial distribution of glycogen granules, a major energy source that is selectively stored in astrocytes. The use of CAVE was key to the observation of a nonrandom distribution of glycogen, and led us to develop tools to quantitatively analyze glycogen clustering and proximity to other subcellular features. PMID:26179415

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

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

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

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

    SciTech Connect

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

    2012-04-25

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

  18. Pulmonary CT image registration and warping for tracking tissue deformation during the respiratory cycle through 3D consistent image registration

    PubMed Central

    Li, Baojun; Christensen, Gary E.; Hoffman, Eric A.; McLennan, Geoffrey; Reinhardt, Joseph M.

    2008-01-01

    Tracking lung tissues during the respiratory cycle has been a challenging task for diagnostic CT and CT-guided radiotherapy. We propose an intensity- and landmark-based image registration algorithm to perform image registration and warping of 3D pulmonary CT image data sets, based on consistency constraints and matching corresponding airway branchpoints. In this paper, we demonstrate the effectivenss and accuracy of this algorithm in tracking lung tissues by both animal and human data sets. In the animal study, the result showed a tracking accuracy of 1.9 mm between 50% functional residual capacity (FRC) and 85% total lung capacity (TLC) for 12 metal seeds implanted in the lungs of a breathing sheep under precise volume control using a pulmonary ventilator. Visual inspection of the human subject results revealed the algorithm’s potential not only in matching the global shapes, but also in registering the internal structures (e.g., oblique lobe fissures, pulmonary artery branches, etc.). These results suggest that our algorithm has significant potential for warping and tracking lung tissue deformation with applications in diagnostic CT, CT-guided radiotherapy treatment planning, and therapeutic effect evaluation. PMID:19175115

  19. Integration of 3D Printed and Micropatterned Polycaprolactone Scaffolds for Guidance of Oriented Collagenous Tissue Formation In Vivo.

    PubMed

    Pilipchuk, Sophia P; Monje, Alberto; Jiao, Yizu; Hao, Jie; Kruger, Laura; Flanagan, Colleen L; Hollister, Scott J; Giannobile, William V

    2016-03-01

    Scaffold design incorporating multiscale cues for clinically relevant, aligned tissue regeneration has potential to improve structural and functional integrity of multitissue interfaces. The objective of this preclinical study is to develop poly(ε-caprolactone) (PCL) scaffolds with mesoscale and microscale architectural cues specific to human ligament progenitor cells and assess their ability to form aligned bone-ligament-cementum complexes in vivo. PCL scaffolds are designed to integrate a 3D printed bone region with a micropatterned PCL thin film consisting of grooved pillars. The patterned film region is seeded with human ligament cells, fibroblasts transduced with bone morphogenetic protein-7 genes seeded within the bone region, and a tooth dentin segment positioned on the ligament region prior to subcutaneous implantation into a murine model. Results indicate increased tissue alignment in vivo using micropatterned PCL films, compared to random-porous PCL. At week 6, 30 μm groove depth significantly enhances oriented collagen fiber thickness, overall cell alignment, and nuclear elongation relative to 10 μm groove depth. This study demonstrates for the first time that scaffolds with combined hierarchical mesoscale and microscale features can align cells in vivo for oral tissue repair with potential for improving the regenerative response of other bone-ligament complexes.

  20. Pulmonary CT image registration and warping for tracking tissue deformation during the respiratory cycle through 3D consistent image registration.

    PubMed

    Li, Baojun; Christensen, Gary E; Hoffman, Eric A; McLennan, Geoffrey; Reinhardt, Joseph M

    2008-12-01

    Tracking lung tissues during the respiratory cycle has been a challenging task for diagnostic CT and CT-guided radiotherapy. We propose an intensity- and landmark-based image registration algorithm to perform image registration and warping of 3D pulmonary CT image data sets, based on consistency constraints and matching corresponding airway branchpoints. In this paper, we demonstrate the effectivenss and accuracy of this algorithm in tracking lung tissues by both animal and human data sets. In the animal study, the result showed a tracking accuracy of 1.9 mm between 50% functional residual capacity (FRC) and 85% total lung capacity (TLC) for 12 metal seeds implanted in the lungs of a breathing sheep under precise volume control using a pulmonary ventilator. Visual inspection of the human subject results revealed the algorithm's potential not only in matching the global shapes, but also in registering the internal structures (e.g., oblique lobe fissures, pulmonary artery branches, etc.). These results suggest that our algorithm has significant potential for warping and tracking lung tissue deformation with applications in diagnostic CT, CT-guided radiotherapy treatment planning, and therapeutic effect evaluation.

  1. Prefabrication of 3D cartilage contructs: towards a tissue engineered auricle--a model tested in rabbits.

    PubMed

    von Bomhard, Achim; Veit, Johannes; Bermueller, Christian; Rotter, Nicole; Staudenmaier, Rainer; Storck, Katharina; The, Hoang Nguyen

    2013-01-01

    The reconstruction of an auricle for congenital deformity or following trauma remains one of the greatest challenges in reconstructive surgery. Tissue-engineered (TE) three-dimensional (3D) cartilage constructs have proven to be a promising option, but problems remain with regard to cell vitality in large cell constructs. The supply of nutrients and oxygen is limited because cultured cartilage is not vascular integrated due to missing perichondrium. The consequence is necrosis and thus a loss of form stability. The micro-surgical implantation of an arteriovenous loop represents a reliable technology for neovascularization, and thus vascular integration, of three-dimensional (3D) cultivated cell constructs. Auricular cartilage biopsies were obtained from 15 rabbits and seeded in 3D scaffolds made from polycaprolactone-based polyurethane in the shape and size of a human auricle. These cartilage cell constructs were implanted subcutaneously into a skin flap (15 × 8 cm) and neovascularized by means of vascular loops implanted micro-surgically. They were then totally enhanced as 3D tissue and freely re-implanted in-situ through microsurgery. Neovascularization in the prefabricated flap and cultured cartilage construct was analyzed by microangiography. After explantation, the specimens were examined by histological and immunohistochemical methods. Cultivated 3D cartilage cell constructs with implanted vascular pedicle promoted the formation of engineered cartilaginous tissue within the scaffold in vivo. The auricles contained cartilage-specific extracellular matrix (ECM) components, such as GAGs and collagen even in the center oft the constructs. In contrast, in cultivated 3D cartilage cell constructs without vascular pedicle, ECM distribution was only detectable on the surface compared to constructs with vascular pedicle. We demonstrated, that the 3D flaps could be freely transplanted. On a microangiographic level it was evident that all the skin flaps and the

  2. Prefabrication of 3D Cartilage Contructs: Towards a Tissue Engineered Auricle – A Model Tested in Rabbits

    PubMed Central

    von Bomhard, Achim; Veit, Johannes; Bermueller, Christian; Rotter, Nicole; Staudenmaier, Rainer; Storck, Katharina; The, Hoang Nguyen

    2013-01-01

    The reconstruction of an auricle for congenital deformity or following trauma remains one of the greatest challenges in reconstructive surgery. Tissue-engineered (TE) three-dimensional (3D) cartilage constructs have proven to be a promising option, but problems remain with regard to cell vitality in large cell constructs. The supply of nutrients and oxygen is limited because cultured cartilage is not vascular integrated due to missing perichondrium. The consequence is necrosis and thus a loss of form stability. The micro-surgical implantation of an arteriovenous loop represents a reliable technology for neovascularization, and thus vascular integration, of three-dimensional (3D) cultivated cell constructs. Auricular cartilage biopsies were obtained from 15 rabbits and seeded in 3D scaffolds made from polycaprolactone-based polyurethane in the shape and size of a human auricle. These cartilage cell constructs were implanted subcutaneously into a skin flap (15×8 cm) and neovascularized by means of vascular loops implanted micro-surgically. They were then totally enhanced as 3D tissue and freely re-implanted in-situ through microsurgery. Neovascularization in the prefabricated flap and cultured cartilage construct was analyzed by microangiography. After explantation, the specimens were examined by histological and immunohistochemical methods. Cultivated 3D cartilage cell constructs with implanted vascular pedicle promoted the formation of engineered cartilaginous tissue within the scaffold in vivo. The auricles contained cartilage-specific extracellular matrix (ECM) components, such as GAGs and collagen even in the center oft the constructs. In contrast, in cultivated 3D cartilage cell constructs without vascular pedicle, ECM distribution was only detectable on the surface compared to constructs with vascular pedicle. We demonstrated, that the 3D flaps could be freely transplanted. On a microangiographic level it was evident that all the skin flaps and the implanted

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

    SciTech Connect

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

    2004-04-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  5. In-body tissue-engineered aortic valve (Biovalve type VII) architecture based on 3D printer molding.

    PubMed

    Nakayama, Yasuhide; Takewa, Yoshiaki; Sumikura, Hirohito; Yamanami, Masashi; Matsui, Yuichi; Oie, Tomonori; Kishimoto, Yuichiro; Arakawa, Mamoru; Ohmuma, Kentaro; Tajikawa, Tsutomu; Kanda, Keiichi; Tatsumi, Eisuke

    2015-01-01

    In-body tissue architecture--a novel and practical regeneration medicine technology--can be used to prepare a completely autologous heart valve, based on the shape of a mold. In this study, a three-dimensional (3D) printer was used to produce the molds. A 3D printer can easily reproduce the 3D-shape and size of native heart valves within several processing hours. For a tri-leaflet, valved conduit with a sinus of Valsalva (Biovalve type VII), the mold was assembled using two conduit parts and three sinus parts produced by the 3D printer. Biovalves were generated from completely autologous connective tissue, containing collagen and fibroblasts, within 2 months following the subcutaneous embedding of the molds (success rate, 27/30). In vitro evaluation, using a pulsatile circulation circuit, showed excellent valvular function with a durability of at least 10 days. Interposed between two expanded polytetrafluoroethylene grafts, the Biovalves (N = 3) were implanted in goats through an apico-aortic bypass procedure. Postoperative echocardiography showed smooth movement of the leaflets with minimal regurgitation under systemic circulation. After 1 month of implantation, smooth white leaflets were observed with minimal thrombus formation. Functional, autologous, 3D-shaped heart valves with clinical application potential were formed following in-body embedding of specially designed molds that were created within several hours by 3D printer. PMID:24764308

  6. In-body tissue-engineered aortic valve (Biovalve type VII) architecture based on 3D printer molding.

    PubMed

    Nakayama, Yasuhide; Takewa, Yoshiaki; Sumikura, Hirohito; Yamanami, Masashi; Matsui, Yuichi; Oie, Tomonori; Kishimoto, Yuichiro; Arakawa, Mamoru; Ohmuma, Kentaro; Tajikawa, Tsutomu; Kanda, Keiichi; Tatsumi, Eisuke

    2015-01-01

    In-body tissue architecture--a novel and practical regeneration medicine technology--can be used to prepare a completely autologous heart valve, based on the shape of a mold. In this study, a three-dimensional (3D) printer was used to produce the molds. A 3D printer can easily reproduce the 3D-shape and size of native heart valves within several processing hours. For a tri-leaflet, valved conduit with a sinus of Valsalva (Biovalve type VII), the mold was assembled using two conduit parts and three sinus parts produced by the 3D printer. Biovalves were generated from completely autologous connective tissue, containing collagen and fibroblasts, within 2 months following the subcutaneous embedding of the molds (success rate, 27/30). In vitro evaluation, using a pulsatile circulation circuit, showed excellent valvular function with a durability of at least 10 days. Interposed between two expanded polytetrafluoroethylene grafts, the Biovalves (N = 3) were implanted in goats through an apico-aortic bypass procedure. Postoperative echocardiography showed smooth movement of the leaflets with minimal regurgitation under systemic circulation. After 1 month of implantation, smooth white leaflets were observed with minimal thrombus formation. Functional, autologous, 3D-shaped heart valves with clinical application potential were formed following in-body embedding of specially designed molds that were created within several hours by 3D printer.

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

    PubMed Central

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

    2016-01-01

    3D printing and ultrasound techniques are showing great promise in the evolution of human musculoskeletal tissue repair and regeneration medicine. The uniqueness of the present study was to combine low intensity pulsed ultrasound (LIPUS) and advanced 3D printing techniques to synergistically improve growth and osteogenic differentiation of human mesenchymal stem cells (MSC). Specifically, polyethylene glycol diacrylate bioinks containing cell adhesive Arginine-Glycine-Aspartic acid-Serene (RGDS) peptide and/or nanocrystalline hydroxyapatite (nHA) were used to fabricate 3D scaffolds with different geometric patterns via novel table-top stereolithography 3D printer. The resultant scaffolds provide a highly porous and interconnected 3D environment to support cell proliferation. Scaffolds with small square pores were determined to be the optimal geometric pattern for MSC attachment and growth. The optimal LIPUS working parameters were determined to be 1.5 MHz, 20% duty cycle with 150 mW/cm2 intensity. Results demonstrated that RGDS peptide and nHA containing 3D printed scaffolds under LIPUS treatment can greatly promote MSC proliferation, alkaline phosphatase activity, calcium deposition and total protein content. These results illustrate the effectiveness of the combination of LIPUS and biomimetic 3D printing scaffolds as a valuable combinatorial tool for improved MSC function, thus make them promising for future clinical and various regenerative medicine application. PMID:27597635

  8. Synthesis and 3D printing of biodegradable polyurethane elastomer by a water-based process for cartilage tissue engineering applications.

    PubMed

    Hung, Kun-Che; Tseng, Ching-Shiow; Hsu, Shan-Hui

    2014-10-01

    Biodegradable materials that can undergo degradation in vivo are commonly employed to manufacture tissue engineering scaffolds, by techniques including the customized 3D printing. Traditional 3D printing methods involve the use of heat, toxic organic solvents, or toxic photoinitiators for fabrication of synthetic scaffolds. So far, there is no investigation on water-based 3D printing for synthetic materials. In this study, the water dispersion of elastic and biodegradable polyurethane (PU) nanoparticles is synthesized, which is further employed to fabricate scaffolds by 3D printing using polyethylene oxide (PEO) as a viscosity enhancer. The surface morphology, degradation rate, and mechanical properties of the water-based 3D-printed PU scaffolds are evaluated and compared with those of polylactic-co-glycolic acid (PLGA) scaffolds made from the solution in organic solvent. These scaffolds are seeded with chondrocytes for evaluation of their potential as cartilage scaffolds. Chondrocytes in 3D-printed PU scaffolds have excellent seeding efficiency, proliferation, and matrix production. Since PU is a category of versatile materials, the aqueous 3D printing process developed in this study is a platform technology that can be used to fabricate devices for biomedical applications.

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

    PubMed

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

    2016-01-01

    3D printing and ultrasound techniques are showing great promise in the evolution of human musculoskeletal tissue repair and regeneration medicine. The uniqueness of the present study was to combine low intensity pulsed ultrasound (LIPUS) and advanced 3D printing techniques to synergistically improve growth and osteogenic differentiation of human mesenchymal stem cells (MSC). Specifically, polyethylene glycol diacrylate bioinks containing cell adhesive Arginine-Glycine-Aspartic acid-Serene (RGDS) peptide and/or nanocrystalline hydroxyapatite (nHA) were used to fabricate 3D scaffolds with different geometric patterns via novel table-top stereolithography 3D printer. The resultant scaffolds provide a highly porous and interconnected 3D environment to support cell proliferation. Scaffolds with small square pores were determined to be the optimal geometric pattern for MSC attachment and growth. The optimal LIPUS working parameters were determined to be 1.5 MHz, 20% duty cycle with 150 mW/cm(2) intensity. Results demonstrated that RGDS peptide and nHA containing 3D printed scaffolds under LIPUS treatment can greatly promote MSC proliferation, alkaline phosphatase activity, calcium deposition and total protein content. These results illustrate the effectiveness of the combination of LIPUS and biomimetic 3D printing scaffolds as a valuable combinatorial tool for improved MSC function, thus make them promising for future clinical and various regenerative medicine application. PMID:27597635

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

    PubMed

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

    2016-09-06

    3D printing and ultrasound techniques are showing great promise in the evolution of human musculoskeletal tissue repair and regeneration medicine. The uniqueness of the present study was to combine low intensity pulsed ultrasound (LIPUS) and advanced 3D printing techniques to synergistically improve growth and osteogenic differentiation of human mesenchymal stem cells (MSC). Specifically, polyethylene glycol diacrylate bioinks containing cell adhesive Arginine-Glycine-Aspartic acid-Serene (RGDS) peptide and/or nanocrystalline hydroxyapatite (nHA) were used to fabricate 3D scaffolds with different geometric patterns via novel table-top stereolithography 3D printer. The resultant scaffolds provide a highly porous and interconnected 3D environment to support cell proliferation. Scaffolds with small square pores were determined to be the optimal geometric pattern for MSC attachment and growth. The optimal LIPUS working parameters were determined to be 1.5 MHz, 20% duty cycle with 150 mW/cm(2) intensity. Results demonstrated that RGDS peptide and nHA containing 3D printed scaffolds under LIPUS treatment can greatly promote MSC proliferation, alkaline phosphatase activity, calcium deposition and total protein content. These results illustrate the effectiveness of the combination of LIPUS and biomimetic 3D printing scaffolds as a valuable combinatorial tool for improved MSC function, thus make them promising for future clinical and various regenerative medicine application.

  11. Self-Discovery of Structural Geology Concepts using Interactive 3D Visualization

    NASA Astrophysics Data System (ADS)

    Billen, M. I.; Saunders, J.

    2010-12-01

    Mastering structural geology concepts that depend on understanding three-dimensional (3D) geometries and imagining relationships among unseen subsurface structures are fundamental skills for geologists. Traditionally these skills are developed first, through use of 2D drawings of 3D structures that can be difficult to decipher or 3D physical block models that show only a limited set of relationships on the surfaces of the blocks, followed by application and testing of concepts in field settings. We hypothesize that this learning process can be improved by providing repeated opportunities to evaluate and explore synthetic 3D structures using interactive 3D visualization software. We present laboratory modules designed for undergraduate structural geology curriculum using a self-discovery approach to teach concepts such as: the Rule of V’s, structure separation versus fault slip, and the more general dependence of structural exposure on surface topography. The laboratory modules are structured to allow students to discover and articulate each concept from observations of synthetic data both on traditional maps and using the volume visualization software 3DVisualizer. Modules lead students through exploration of data (e.g., a dipping layered structure exposed in ridge-valley topography or obliquely offset across a fault) by allowing them to interactively view (rotate, pan, zoom) the exposure of structures on topographic surfaces and to toggle on/off the full 3D structure as a transparent colored volume. This tool allows student to easily visually understand the relationships between, for example a dipping structure and its exposure on valley walls, as well as how the structure extends beneath the surface. Using this method gives students more opportunities to build a mental library of previously-seen relationships from which to draw-on when applying concepts in the field setting. These laboratory modules, the data and software are freely available from KeckCAVES.

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

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  14. Bedside assistance in freehand ultrasonic diagnosis by real-time visual feedback of 3D scatter diagram of pulsatile tissue-motion

    NASA Astrophysics Data System (ADS)

    Fukuzawa, M.; Kawata, K.; Nakamori, N.; Kitsunezuka, Y.

    2011-03-01

    By real-time visual feedback of 3D scatter diagram of pulsatile tissue-motion, freehand ultrasonic diagnosis of neonatal ischemic diseases has been assisted at the bedside. The 2D ultrasonic movie was taken with a conventional ultrasonic apparatus (ATL HDI5000) and ultrasonic probes of 5-7 MHz with the compact tilt-sensor to measure the probe orientation. The real-time 3D visualization was realized by developing an extended version of the PC-based visualization system. The software was originally developed on the DirectX platform and optimized with the streaming SIMD extensions. The 3D scatter diagram of the latest pulsatile tissues has been continuously generated and visualized as projection image with the ultrasonic movie in the current section more than 15 fps. It revealed the 3D structure of pulsatile tissues such as middle and posterior cerebral arteries, Willis ring and cerebellar arteries, in which pediatricians have great interests in the blood flow because asphyxiated and/or low-birth-weight neonates have a high risk of ischemic diseases such as hypoxic-ischemic encephalopathy and periventricular leukomalacia. Since the pulsatile tissue-motion is due to local blood flow, it can be concluded that the system developed in this work is very useful to assist freehand ultrasonic diagnosis of ischemic diseases in the neonatal cranium.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-02-12

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

  17. 3D printing of high-resolution PLA-based structures by hybrid electrohydrodynamic and fused deposition modeling techniques

    NASA Astrophysics Data System (ADS)

    Zhang, Bin; Seong, Baekhoon; Nguyen, VuDat; Byun, Doyoung

    2016-02-01

    Recently, the three-dimensional (3D) printing technique has received much attention for shape forming and manufacturing. The fused deposition modeling (FDM) printer is one of the various 3D printers available and has become widely used due to its simplicity, low-cost, and easy operation. However, the FDM technique has a limitation whereby its patterning resolution is too low at around 200 μm. In this paper, we first present a hybrid mechanism of electrohydrodynamic jet printing with the FDM technique, which we name E-FDM. We then develop a novel high-resolution 3D printer based on the E-FDM process. To determine the optimal condition for structuring, we also investigated the effect of several printing parameters, such as temperature, applied voltage, working height, printing speed, flow-rate, and acceleration on the patterning results. This method was capable of fabricating both high resolution 2D and 3D structures with the use of polylactic acid (PLA). PLA has been used to fabricate scaffold structures for tissue engineering, which has different hierarchical structure sizes. The fabrication speed was up to 40 mm/s and the pattern resolution could be improved to 10 μm.

  18. Polyhedral 3D structure of human plasma very low density lipoproteins by individual particle cryo-electron tomography1[S

    PubMed Central

    Yu, Yadong; Kuang, Yu-Lin; Lei, Dongsheng; Zhai, Xiaobo; Zhang, Meng; Krauss, Ronald M.; Ren, Gang

    2016-01-01

    Human VLDLs assembled in the liver and secreted into the circulation supply energy to peripheral tissues. VLDL lipolysis yields atherogenic LDLs and VLDL remnants that strongly correlate with CVD. Although the composition of VLDL particles has been well-characterized, their 3D structure is elusive because of their variations in size, heterogeneity in composition, structural flexibility, and mobility in solution. Here, we employed cryo-electron microscopy and individual-particle electron tomography to study the 3D structure of individual VLDL particles (without averaging) at both below and above their lipid phase transition temperatures. The 3D reconstructions of VLDL and VLDL bound to antibodies revealed an unexpected polyhedral shape, in contrast to the generally accepted model of a spherical emulsion-like particle. The smaller curvature of surface lipids compared with HDL may also reduce surface hydrophobicity, resulting in lower binding affinity to the hydrophobic distal end of the N-terminal β-barrel domain of cholesteryl ester transfer protein (CETP) compared with HDL. The directional binding of CETP to HDL and VLDL may explain the function of CETP in transferring TGs and cholesteryl esters between these particles. This first visualization of the 3D structure of VLDL could improve our understanding of the role of VLDL in atherogenesis. PMID:27538822

  19. From pixel to voxel: a deeper view of biological tissue by 3D mass spectral imaging

    PubMed Central

    Ye, Hui; Greer, Tyler; Li, Lingjun

    2011-01-01

    Three dimensional mass spectral imaging (3D MSI) is an exciting field that grants the ability to study a broad mass range of molecular species ranging from small molecules to large proteins by creating lateral and vertical distribution maps of select compounds. Although the general premise behind 3D MSI is simple, factors such as choice of ionization method, sample handling, software considerations and many others must be taken into account for the successful design of a 3D MSI experiment. This review provides a brief overview of ionization methods, sample preparation, software types and technological advancements driving 3D MSI research of a wide range of low- to high-mass analytes. Future perspectives in this field are also provided to conclude that the positive and promises ever-growing applications in the biomedical field with continuous developments of this powerful analytical tool. PMID:21320052

  20. A 3D Toolbox to Enhance Physiological Relevance of Human Tissue Models.

    PubMed

    Picollet-D'hahan, Nathalie; Dolega, Monika E; Liguori, Lavinia; Marquette, Christophe; Le Gac, Séverine; Gidrol, Xavier; Martin, Donald K

    2016-09-01

    We discuss the current challenges and future prospects of flow-based organoid models and 3D self-assembling scaffolds. The existing paradigm of 3D culture suffers from a lack of control over organoid size and shape; can be an obstacle for cell harvesting and extended cellular and molecular analysis; and does not provide access to the function of exocrine glands. Moreover, existing organ-on-chip models are mostly composed of 2D extracellular matrix (ECM)-coated elastomeric membranes that do not mimic real organ architectures. A new comprehensive 3D toolbox for cell biology has emerged to address some of these issues. Advances in microfabrication and cell-culturing approaches enable the engineering of sophisticated models that mimic organ 3D architectures and physiological conditions, while supporting flow-based drug screening and secretomics-based diagnosis. PMID:27497676

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

    PubMed

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

    2010-09-27

    A novel method for fabrication of 2D and 3D metal nanoparticle structures and arrays is proposed. This technique is based on laser-induced transfer of molten metal nanodroplets from thin metal films. Metal nanoparticles are produced by solidification of these nanodroplets. The size of the transferred nanoparticles can be controllably changed in the range from 180 nm to 1500 nm. Several examples of complex 2D and 3D microstructures generated form gold nanoparticles are demonstrated. PMID:20941016

  2. Air-structured optical fibre drawn from a 3D-printed preform

    NASA Astrophysics Data System (ADS)

    Cook, Kevin; Leon-Saval, Sergio; Canning, John; Reid, Zane; Hossain, Md. Arafat; Peng, Gang-Ding

    2015-09-01

    We report the first optical fibre drawn from a 3D-printed preform. An air-structured polymer preform is printed using a modified butadiene plastic called Bendlay as opposed to the more-common Acrylonitrile Butadiene Styrene (ABS). The preform is subsequently drawn to fibre form at a relatively low temperature of 160 °C and maintains its air-structured cladding holes. Such ability to freely-design and 3D-print complex preform structures, such as photonic bandgap and photonic crystal structures, opens up an exciting new front in optical fibre fabrication.

  3. A review on powder-based additive manufacturing for tissue engineering: selective laser sintering and inkjet 3D printing

    NASA Astrophysics Data System (ADS)

    Farid Seyed Shirazi, Seyed; Gharehkhani, Samira; Mehrali, Mehdi; Yarmand, Hooman; Metselaar, Hendrik Simon Cornelis; Adib Kadri, Nahrizul; Azuan Abu Osman, Noor

    2015-06-01

    Since most starting materials for tissue engineering are in powder form, using powder-based additive manufacturing methods is attractive and practical. The principal point of employing additive manufacturing (AM) systems is to fabricate parts with arbitrary geometrical complexity with relatively minimal tooling cost and time. Selective laser sintering (SLS) and inkjet 3D printing (3DP) are two powerful and versatile AM techniques which are applicable to powder-based material systems. Hence, the latest state of knowledge available on the use of AM powder-based techniques in tissue engineering and their effect on mechanical and biological properties of fabricated tissues and scaffolds must be updated. Determining the effective setup of parameters, developing improved biocompatible/bioactive materials, and improving the mechanical/biological properties of laser sintered and 3D printed tissues are the three main concerns which have been investigated in this article.

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

    PubMed

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

    2012-04-20

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

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

    PubMed

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

    2013-11-01

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

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

    PubMed Central

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

    2015-01-01

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

  7. Fabrication and characterization of strontium incorporated 3-D bioactive glass scaffolds for bone tissue from biosilica.

    PubMed

    Özarslan, Ali Can; Yücel, Sevil

    2016-11-01

    Bioactive glass scaffolds that contain silica are high viable biomaterials as bone supporters for bone tissue engineering due to their bioactive behaviour in simulated body fluid (SBF). In the human body, these materials help inorganic bone structure formation due to a combination of the particular ratio of elements such as silicon (Si), calcium (Ca), sodium (Na) and phosphorus (P), and the doping of strontium (Sr) into the scaffold structure increases their bioactive behaviour. In this study, bioactive glass scaffolds were produced by using rice hull ash (RHA) silica and commercial silica based bioactive glasses. The structural properties of scaffolds such as pore size, porosity and also the bioactive behaviour were investigated. The results showed that undoped and Sr-doped RHA silica-based bioactive glass scaffolds have better bioactivity than that of commercial silica based bioactive glass scaffolds. Moreover, undoped and Sr-doped RHA silica-based bioactive glass scaffolds will be able to be used instead of undoped and Sr-doped commercial silica based bioactive glass scaffolds for bone regeneration applications. Scaffolds that are produced from undoped or Sr-doped RHA silica have high potential to form new bone for bone defects in tissue engineering.

  8. Fabrication and characterization of strontium incorporated 3-D bioactive glass scaffolds for bone tissue from biosilica.

    PubMed

    Özarslan, Ali Can; Yücel, Sevil

    2016-11-01

    Bioactive glass scaffolds that contain silica are high viable biomaterials as bone supporters for bone tissue engineering due to their bioactive behaviour in simulated body fluid (SBF). In the human body, these materials help inorganic bone structure formation due to a combination of the particular ratio of elements such as silicon (Si), calcium (Ca), sodium (Na) and phosphorus (P), and the doping of strontium (Sr) into the scaffold structure increases their bioactive behaviour. In this study, bioactive glass scaffolds were produced by using rice hull ash (RHA) silica and commercial silica based bioactive glasses. The structural properties of scaffolds such as pore size, porosity and also the bioactive behaviour were investigated. The results showed that undoped and Sr-doped RHA silica-based bioactive glass scaffolds have better bioactivity than that of commercial silica based bioactive glass scaffolds. Moreover, undoped and Sr-doped RHA silica-based bioactive glass scaffolds will be able to be used instead of undoped and Sr-doped commercial silica based bioactive glass scaffolds for bone regeneration applications. Scaffolds that are produced from undoped or Sr-doped RHA silica have high potential to form new bone for bone defects in tissue engineering. PMID:27524030

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

    PubMed Central

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

    2003-01-01

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

  10. 3D hydrogel environment rejuvenates aged pericytes for skeletal muscle tissue engineering

    PubMed Central

    Fuoco, Claudia; Sangalli, Elena; Vono, Rosa; Testa, Stefano; Sacchetti, Benedetto; Latronico, Michael V. G.; Bernardini, Sergio; Madeddu, Paolo; Cesareni, Gianni; Seliktar, Dror; Rizzi, Roberto; Bearzi, Claudia; Cannata, Stefano M.; Spinetti, Gaia; Gargioli, Cesare

    2014-01-01

    Skeletal muscle tissue engineering is a promising approach for the treatment of muscular disorders. However, the complex organization of muscle, combined with the difficulty in finding an appropriate source of regenerative cells and in providing an adequate blood supply to the engineered tissue, makes this a hard task to face. In the present work, we describe an innovative approach to rejuvenate adult skeletal muscle-derived pericytes (MP) based on the use of a PEG-based hydrogel scaffold. MP were isolated from young (piglet) and adult (boar) pigs to assess whether aging affects tissue regeneration efficiency. In vitro, MP from boars had similar morphology and colony forming capacity to piglet MP, but an impaired ability to form myotubes and capillary-like structures. However, the use of a PEG-based hydrogel to support adult MP significantly improved their myogenic differentiation and angiogenic potentials in vitro and in vivo. Thus, PEG-based hydrogel scaffolds may provide a progenitor cell “niche” that promotes skeletal muscle regeneration and blood vessel growth, and together with pericytes may be developed for use in regenerative applications. PMID:24910618

  11. 3D hydrogel environment rejuvenates aged pericytes for skeletal muscle tissue engineering.

    PubMed

    Fuoco, Claudia; Sangalli, Elena; Vono, Rosa; Testa, Stefano; Sacchetti, Benedetto; Latronico, Michael V G; Bernardini, Sergio; Madeddu, Paolo; Cesareni, Gianni; Seliktar, Dror; Rizzi, Roberto; Bearzi, Claudia; Cannata, Stefano M; Spinetti, Gaia; Gargioli, Cesare

    2014-01-01

    Skeletal muscle tissue engineering is a promising approach for the treatment of muscular disorders. However, the complex organization of muscle, combined with the difficulty in finding an appropriate source of regenerative cells and in providing an adequate blood supply to the engineered tissue, makes this a hard task to face. In the present work, we describe an innovative approach to rejuvenate adult skeletal muscle-derived pericytes (MP) based on the use of a PEG-based hydrogel scaffold. MP were isolated from young (piglet) and adult (boar) pigs to assess whether aging affects tissue regeneration efficiency. In vitro, MP from boars had similar morphology and colony forming capacity to piglet MP, but an impaired ability to form myotubes and capillary-like structures. However, the use of a PEG-based hydrogel to support adult MP significantly improved their myogenic differentiation and angiogenic potentials in vitro and in vivo. Thus, PEG-based hydrogel scaffolds may provide a progenitor cell "niche" that promotes skeletal muscle regeneration and blood vessel growth, and together with pericytes may be developed for use in regenerative applications.

  12. 3-D seismic velocity and attenuation structures in the geothermal field

    SciTech Connect

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

    2013-09-09

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

  13. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

    Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex. PMID:27493552

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  15. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

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

  16. Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins.

    PubMed

    Sillitoe, Ian; Lewis, Tony; Orengo, Christine

    2015-01-01

    The CATH database is a classification of protein structures found in the Protein Data Bank (PDB). Protein structures are chopped into individual units of structural domains, and these domains are grouped together into superfamilies if there is sufficient evidence that they have diverged from a common ancestor during the process of evolution. A sister resource, Gene3D, extends this information by scanning sequence profiles of these CATH domain superfamilies against many millions of known proteins to identify related sequences. Thus the combined CATH-Gene3D resource provides confident predictions of the likely structural fold, domain organisation, and evolutionary relatives of these proteins. In addition, this resource incorporates annotations from a large number of external databases such as known enzyme active sites, GO molecular functions, physical interactions, and mutations. This unit details how to access and understand the information contained within the CATH-Gene3D Web pages, the downloadable data files, and the remotely accessible Web services.

  17. Estimating the complexity of 3D structural models using machine learning methods

    NASA Astrophysics Data System (ADS)

    Mejía-Herrera, Pablo; Kakurina, Maria; Royer, Jean-Jacques

    2016-04-01

    Quantifying the complexity of 3D geological structural models can play a major role in natural resources exploration surveys, for predicting environmental hazards or for forecasting fossil resources. This paper proposes a structural complexity index which can be used to help in defining the degree of effort necessary to build a 3D model for a given degree of confidence, and also to identify locations where addition efforts are required to meet a given acceptable risk of uncertainty. In this work, it is considered that the structural complexity index can be estimated using machine learning methods on raw geo-data. More precisely, the metrics for measuring the complexity can be approximated as the difficulty degree associated to the prediction of the geological objects distribution calculated based on partial information on the actual structural distribution of materials. The proposed methodology is tested on a set of 3D synthetic structural models for which the degree of effort during their building is assessed using various parameters (such as number of faults, number of part in a surface object, number of borders, ...), the rank of geological elements contained in each model, and, finally, their level of deformation (folding and faulting). The results show how the estimated complexity in a 3D model can be approximated by the quantity of partial data necessaries to simulated at a given precision the actual 3D model without error using machine learning algorithms.

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

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

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

  19. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    NASA Astrophysics Data System (ADS)

    Beecroft, M.

    2016-07-01

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

  20. Quasi-3D Waveform Inversion for Velocity Structures and Source Process Analyses Using its Results

    NASA Astrophysics Data System (ADS)

    Hikima, K.; Koketsu, K.

    2007-12-01

    In this study, we propose an efficient waveform inversion method for 2-D velocity structures and 3-D velocity structures are constructed by interpolating the results of the 2-D inversions. We apply these methods to a source process study of the 2003 Miyagi-ken Hokubu earthquake. We will first construct a velocity model, then determine the source processes of this earthquake sequence using the Green's function calculated with the resultant 3-D velocity model. We formulate the inversion procedure in a 2-D cross section. In a 2-D problem, an earthquake is forced to be a line source. Therefore, we introduce approximate transformation from a line source to a point source (Vidale and Helmberger, 1987). We use the 2-D velocity-stress staggered-grid finite difference scheme, so that the source representation is somewhat different from the original 'source box method' and we apply additional corrections to calculated waveforms. The boundary shapes of layers are expressed by connected nodes and we invert observed waveforms for layer thicknesses at the nodes. We perform 2-D velocity inversions along cross sections which involve a medium-size earthquake and observation points. We assemble the results for many stations and interpolated them to construct the 3-D velocity model. Finally, we calculate waveforms from the target earthquake by the 3-D finite difference method with this velocity model to confirm the validity of the model. We next perform waveform inversions for source processes of the 2003 Miyagi-ken Hokubu earthquake sequence using the resultant 3-D velocity model. We divide the fault plane into northern and southern subplanes, so that the southern subplane includes the hypocenter of the mainshock and the largest foreshock. The strike directions of the northern and southern subplanes were N-S and NE-SW, respectively. The Green's functions for these source inversions are calculated using the reciprocal theorem. We determine the slip models using the 3- D structure and

  1. Acquisition of 3d Information for Vanished Structure by Using Only AN Ancient Picture

    NASA Astrophysics Data System (ADS)

    Kunii, Y.; Sakamoto, R.

    2016-06-01

    In order to acquire 3D information for reconstruction of vanished historical structure, grasp of 3D shape of such structure was attempted by using an ancient picture. Generally, 3D information of a structure is acquired by photogrammetric theory which requires two or more pictures. This paper clarifies that the geometrical information of the structure was obtained only from an ancient picture, and 3D information was acquired. This kind of method was applied for an ancient picture of the Old Imperial Theatre. The Old Imperial Theatre in the picture is constituted by two-point perspective. Therefore, estimated value of focal length of camera, length of camera to the Old Imperial Theatre and some parameters were calculated by estimation of field angle, using body height as an index of length and some geometrical information. Consequently, 3D coordinate of 120 measurement points on the surface of the Old Imperial Theatre were calculated respectively, and 3DCG modeling of the Old Imperial Theatre was realized.

  2. 3D OCT imaging in clinical settings: toward quantitative measurements of retinal structures

    NASA Astrophysics Data System (ADS)

    Zawadzki, Robert J.; Fuller, Alfred R.; Zhao, Mingtao; Wiley, David F.; Choi, Stacey S.; Bower, Bradley A.; Hamann, Bernd; Izatt, Joseph A.; Werner, John S.

    2006-02-01

    The acquisition speed of current FD-OCT (Fourier Domain - Optical Coherence Tomography) instruments allows rapid screening of three-dimensional (3D) volumes of human retinas in clinical settings. To take advantage of this ability requires software used by physicians to be capable of displaying and accessing volumetric data as well as supporting post processing in order to access important quantitative information such as thickness maps and segmented volumes. We describe our clinical FD-OCT system used to acquire 3D data from the human retina over the macula and optic nerve head. B-scans are registered to remove motion artifacts and post-processed with customized 3D visualization and analysis software. Our analysis software includes standard 3D visualization techniques along with a machine learning support vector machine (SVM) algorithm that allows a user to semi-automatically segment different retinal structures and layers. Our program makes possible measurements of the retinal layer thickness as well as volumes of structures of interest, despite the presence of noise and structural deformations associated with retinal pathology. Our software has been tested successfully in clinical settings for its efficacy in assessing 3D retinal structures in healthy as well as diseased cases. Our tool facilitates diagnosis and treatment monitoring of retinal diseases.

  3. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  4. The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture.

    PubMed

    Markaki, Yolanda; Smeets, Daniel; Fiedler, Susanne; Schmid, Volker J; Schermelleh, Lothar; Cremer, Thomas; Cremer, Marion

    2012-05-01

    Three-dimensional structured illumination microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization. PMID:22508100

  5. Structural response to 3D simulated earthquake motions in San Bernardino Valley

    USGS Publications Warehouse

    Safak, E.; Frankel, A.

    1994-01-01

    Structural repsonse to one- and three-dimensional (3D) simulated motions in San Bernardino Valley from a hypothetical earthquake along the San Andreas fault with moment magnitude 6.5 and rupture length of 30km is investigated. The results show that the ground motions and the structural response vary dramatically with the type of simulation and the location. -from Authors

  6. CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures.

    PubMed

    Vlahovicek, Kristian; Pintar, Alessandro; Parthasarathi, Laavanya; Carugo, Oliviero; Pongor, Sándor

    2005-07-01

    The WWW servers at http://www.icgeb.org/protein/ are dedicated to the analysis of protein 3D structures submitted by the users as the Protein Data Bank (PDB) files. CX computes an atomic protrusion index that makes it possible to highlight the protruding atoms within a protein 3D structure. DPX calculates a depth index for the buried atoms and makes it possible to analyze the distribution of buried residues. CX and DPX return PDB files containing the calculated indices that can then be visualized using standard programs, such as Swiss-PDBviewer and Rasmol. PRIDE compares 3D structures using a fast algorithm based on the distribution of inter-atomic distances. The options include pairwise as well as multiple comparisons, and fold recognition based on searching the CATH fold database. PMID:15980464

  7. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  8. Advanced methods for 3-D inelastic structural analysis for hot engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.

    1989-01-01

    Three-dimensional Inelastic Analysis Methods are described. These methods were incorporated into a series of new computer codes embodying a progression of mathematical models (mechanics of materials, specialty finite element, boundary element) for streamlined analysis of hot engine structures such as: (1) combustor liners, (2) turbine blades, and (3) turbine vanes. These models address the effects of high temperatures and thermal/mechanical loadings on the local (stress/strain) and global (displacements, frequencies, amplitudes, buckling) structural behavior of the three respective components. The methods and the three computer codes, referred to as MOMM (Mechanics Of Materials Model), MHOST (MARC-Hot Section Technology), and BEST3D (Boundary Element Stress Technology), have been developed and are briefly described.

  9. Proton HR-MAS spectroscopy and quantitative pathologic analysis of MRI/3D-MRSI-targeted postsurgical prostate tissues.

    PubMed

    Swanson, Mark G; Vigneron, Daniel B; Tabatabai, Z Laura; Males, Ryan G; Schmitt, Lars; Carroll, Peter R; James, Joyce K; Hurd, Ralph E; Kurhanewicz, John

    2003-11-01

    Proton high-resolution magic angle spinning ((1)H HR-MAS) NMR spectroscopy and quantitative histopathology were performed on the same 54 MRI/3D-MRSI-targeted postsurgical prostate tissue samples. Presurgical MRI/3D-MRSI targeted healthy and malignant prostate tissues with an accuracy of 81%. Even in the presence of substantial tissue heterogeneity, distinct (1)H HR-MAS spectral patterns were observed for different benign tissue types and prostate cancer. Specifically, healthy glandular tissue was discriminated from prostate cancer based on significantly higher levels of citrate (P = 0.04) and polyamines (P = 0.01), and lower (P = 0.02) levels of the choline-containing compounds choline, phosphocholine (PC), and glycerophosphocholine (GPC). Predominantly stromal tissue lacked both citrate and polyamines, but demonstrated significantly (P = 0.01) lower levels of choline compounds than cancer. In addition, taurine, myo-inositol, and scyllo-inositol were all higher in prostate cancer vs. healthy glandular and stromal tissues. Among cancer samples, larger increases in choline, and decreases in citrate and polyamines (P = 0.05) were observed with more aggressive cancers, and a MIB-1 labeling index correlated (r = 0.62, P = 0.01) with elevated choline. The elucidation of spectral patterns associated with mixtures of different prostate tissue types and cancer grades, and the inclusion of new metabolic markers for prostate cancer may significantly improve the clinical interpretation of in vivo prostate MRSI data.

  10. Fabrication of 3D porous SF/β-TCP hybrid scaffolds for bone tissue reconstruction.

    PubMed

    Park, Hyun Jung; Min, Kyung Dan; Lee, Min Chae; Kim, Soo Hyeon; Lee, Ok Joo; Ju, Hyung Woo; Moon, Bo Mi; Lee, Jung Min; Park, Ye Ri; Kim, Dong Wook; Jeong, Ju Yeon; Park, Chan Hum

    2016-07-01

    Bio-ceramic is a biomaterial actively studied in the field of bone tissue engineering. But, only certain ceramic materials can resolve the corrosion problem and possess the biological affinity of conventional metal biomaterials. Therefore, the recent development of composites of hybrid composites and polymers has been widely studied. In this study, we aimed to select the best scaffold of silk fibroin and β-TCP hybrid for bone tissue engineering. We fabricated three groups of scaffold such as SF (silk fibroin scaffold), GS (silk fibroin/small granule size of β-TCP scaffold) and GM (silk fibroin/medium granule size of β-TCP scaffold), and we compared the characteristics of each group. During characterization of the scaffold, we used scanning electron microscopy (SEM) and a Fourier transform infrared spectroscopy (FTIR) for structural analysis. We compared the physiological properties of the scaffold regarding the swelling ratio, water uptake and porosity. To evaluate the mechanical properties, we examined the compressive strength of the scaffold. During in vitro testing, we evaluated cell attachment and cell proliferation (CCK-8). Finally, we confirmed in vivo new bone regeneration from the implanted scaffolds using histological staining and micro-CT. From these evaluations, the fabricated scaffold demonstrated high porosity with good inter-pore connectivity, showed good biocompatibility and high compressive strength and modulus. In particular, the present study indicates that the GM scaffold using β-TCP accelerates new bone regeneration of implanted scaffolds. Accordingly, our scaffold is expected to act a useful application in the field of bone tissue engineering. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1779-1787, 2016. PMID:26999521

  11. Direct-growth carbon nanotubes on 3D structural microelectrodes for electrophysiological recording.

    PubMed

    Pan, Alice Ian; Lin, Min-Hsuan; Chung, Hui-Wen; Chen, Hsin; Yeh, Shih-Rung; Chuang, Yung-Jen; Chang, Yen-Chung; Yew, Tri-Rung

    2016-01-01

    A novel 3D carbon nanotube (CNT) microelectrode was developed through direct growth of CNTs on a gold pin-shaped 3D microelectrode at a low temperature (400 °C) for applications in neural and cardiac recording. With an electroplated Ni catalyst layer covering the entire surface of the pin-shaped structure, CNTs were synthesized on a 3D microelectrode by catalytic thermal chemical vapor deposition (CVD). According to the analyses by electrochemical impedance spectroscopy, the impedance of 3D microelectrodes after CNT growth and UV/O3 treatment decreased from 9.3 Ω mm(-2) to 1.2 Ω mm(-2) and the capacitance increased largely from 2.2 mF cm(-2) to 73.3 mF cm(-2). The existence of UVO3-treated CNT led to a large improvement of interfacial capacitance, contributing to the decrease of impedance. The electrophysiological detection capability of this 3D CNT microelectrode was demonstrated by the distinguished P waves, QRS complex and T waves in the electrocardiogram of the zebrafish heart and the action potential recorded from individual rat hippocampal neurons. The compatibility of integration with ICs, high resolution in space, electrophysiological signals, and non-invasive long-term recording suggest that the 3D CNT microelectrode exhibits promising potential for applications in electrophysiological research and clinical trials.

  12. Direct-growth carbon nanotubes on 3D structural microelectrodes for electrophysiological recording.

    PubMed

    Pan, Alice Ian; Lin, Min-Hsuan; Chung, Hui-Wen; Chen, Hsin; Yeh, Shih-Rung; Chuang, Yung-Jen; Chang, Yen-Chung; Yew, Tri-Rung

    2016-01-01

    A novel 3D carbon nanotube (CNT) microelectrode was developed through direct growth of CNTs on a gold pin-shaped 3D microelectrode at a low temperature (400 °C) for applications in neural and cardiac recording. With an electroplated Ni catalyst layer covering the entire surface of the pin-shaped structure, CNTs were synthesized on a 3D microelectrode by catalytic thermal chemical vapor deposition (CVD). According to the analyses by electrochemical impedance spectroscopy, the impedance of 3D microelectrodes after CNT growth and UV/O3 treatment decreased from 9.3 Ω mm(-2) to 1.2 Ω mm(-2) and the capacitance increased largely from 2.2 mF cm(-2) to 73.3 mF cm(-2). The existence of UVO3-treated CNT led to a large improvement of interfacial capacitance, contributing to the decrease of impedance. The electrophysiological detection capability of this 3D CNT microelectrode was demonstrated by the distinguished P waves, QRS complex and T waves in the electrocardiogram of the zebrafish heart and the action potential recorded from individual rat hippocampal neurons. The compatibility of integration with ICs, high resolution in space, electrophysiological signals, and non-invasive long-term recording suggest that the 3D CNT microelectrode exhibits promising potential for applications in electrophysiological research and clinical trials. PMID:26588673

  13. Fabrication and characterization of a 3-D non-homogeneous tissue-like mouse phantom for optical imaging

    NASA Astrophysics Data System (ADS)

    Avtzi, Stella; Zacharopoulos, Athanasios; Psycharakis, Stylianos; Zacharakis, Giannis

    2013-11-01

    In vivo optical imaging of biological tissue not only requires the development of new theoretical models and experimental procedures, but also the design and construction of realistic tissue-mimicking phantoms. However, most of the phantoms available currently in literature or the market, have either simple geometrical shapes (cubes, slabs, cylinders) or when realistic in shape they use homogeneous approximations of the tissue or animal under investigation. The goal of this study is to develop a non-homogeneous realistic phantom that matches the anatomical geometry and optical characteristics of the mouse head in the visible and near-infrared spectral range. The fabrication of the phantom consisted of three stages. Initially, anatomical information extracted from either mouse head atlases or structural imaging modalities (MRI, XCT) was used to design a digital phantom comprising of the three main layers of the mouse head; the brain, skull and skin. Based on that, initial prototypes were manufactured by using accurate 3D printing, allowing complex objects to be built layer by layer with sub-millimeter resolution. During the second stage the fabrication of individual molds was performed by embedding the prototypes into a rubber-like silicone mixture. In the final stage the detailed phantom was constructed by loading the molds with epoxy resin of controlled optical properties. The optical properties of the resin were regulated by using appropriate quantities of India ink and intralipid. The final phantom consisted of 3 layers, each one with different absorption and scattering coefficient (μa,μs) to simulate the region of the mouse brain, skull and skin.

  14. An approach in developing 3D fiber-deposited magnetic scaffolds for tissue engineering

    SciTech Connect

    De Santis, R.; Gloria, A.; D'Amora, U.; Zeppetelli, S.; Ambrosio, L.; Russo, T.

    2010-06-02

    Scaffolds should possess suitable properties to play their specific role. In this work, the potential of 3D fiber deposition technique to develop multifunctional and well-defined magnetic poly(epsilon-caprolactone)/iron oxide scaffolds has been highlighted, and the effect of iron oxide nanoparticles on the biological and mechanical performances has been assessed.

  15. Modeling 3D soil and sediment distributions for assessing catchment structure and hydrological feedbacks

    NASA Astrophysics Data System (ADS)

    Maurer, Thomas; Brück, Yasemine; Hinz, Christoph; Gerke, Horst H.

    2015-04-01

    Structural heterogeneity, namely the spatial distribution of soils and sediments (represented by mineral particles), characterizes catchment hydrological behavior. In natural catchments, local geology and the specific geomorphic processes determine the characteristics and spatial distribution of structures. In constructed catchments, structural features are determined primarily by the construction processes and the geological origin of the parent material. Objectives are scenarios of 3D catchment structures in form of complete 3D description of soil hydraulic properties generated from the knowledge of the formation processes. The constructed hydrological catchment 'Hühnerwasser' (Lower Lusatia, Brandenburg, Germany) was used for the calibration and validation of model results due to its well-known conditions. For the modelling of structural features, a structure generator was used to model i) quasi-deterministic sediment distributions using input data from a geological model of the parent material excavation site; ii) sediment distributions that are conditioned to measurement data from soil sampling; and iii) stochastic component sediment distributions. All three approaches allow a randomization within definable limits. Furthermore, the spoil cone / spoil ridge orientation, internal layering, surface compaction and internal spoil cone compaction were modified. These generated structural models were incorporated in a gridded 3D volume model constructed with the GOCAD software. For selected scenarios, the impact of structure variation was assessed by hydrological modelling with HYDRUS 2D/3D software. For that purpose, 3D distributions of soil hydraulic properties were estimated based on generated sediment properties using adapted pedotransfer functions. Results from the hydrological model were compared them to measured discharges from the catchment. The impact of structural feature variation on flow behaviour was analysed by comparing different simulation scenarios

  16. Structure light telecentric stereoscopic vision 3D measurement system based on Scheimpflug condition

    NASA Astrophysics Data System (ADS)

    Mei, Qing; Gao, Jian; Lin, Hui; Chen, Yun; Yunbo, He; Wang, Wei; Zhang, Guanjin; Chen, Xin

    2016-11-01

    We designed a new three-dimensional (3D) measurement system for micro components: a structure light telecentric stereoscopic vision 3D measurement system based on the Scheimpflug condition. This system creatively combines the telecentric imaging model and the Scheimpflug condition on the basis of structure light stereoscopic vision, having benefits of a wide measurement range, high accuracy, fast speed, and low price. The system measurement range is 20 mm×13 mm×6 mm, the lateral resolution is 20 μm, and the practical vertical resolution reaches 2.6 μm, which is close to the theoretical value of 2 μm and well satisfies the 3D measurement needs of micro components such as semiconductor devices, photoelectron elements, and micro-electromechanical systems. In this paper, we first introduce the principle and structure of the system and then present the system calibration and 3D reconstruction. We then present an experiment that was performed for the 3D reconstruction of the surface topography of a wafer, followed by a discussion. Finally, the conclusions are presented.

  17. Local-global alignment for finding 3D similarities in protein structures

    DOEpatents

    Zemla, Adam T.

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  18. Mixed-Mode Fracture and Fatigue Analysis of Cracked 3D Complex Structures using a 3D SGBEM-FEM Alternating Method

    NASA Astrophysics Data System (ADS)

    Bhavanam, Sharada

    The aim of this thesis is to numerically evaluate the mixed-mode Stress Intensity Factors (SIFs) of complex 3D structural geometries with arbitrary 3D cracks using the Symmetric Galerkin Boundary Element Method-Finite Element Method (SGBEM-FEM) Alternating Method. Various structural geometries with different loading scenarios and crack configurations were examined in this thesis to understand the behavior and trends of the mixed-mode SIFs as well as the fatigue life for these complex structural geometries. Although some 3D structures have empirical and numerical solutions that are readily available in the open literature, some do not; therefore this thesis presents the results of fracture and fatigue analyses of these 3D complex structures using the SGBEM-FEM Alternating Method to serve as reference for future studies. Furthermore, there are advantages of using the SGBEM-FEM Alternating Method compared to traditional FEM methods. For example, the fatigue-crack-growth and fatigue life can be better estimated for a structure because different fatigue models (i.e. Walker, Paris, and NASGRO) can be used within the same framework of the SGBEM-FEM Alternating Method. The FEM (un-cracked structure)/BEM(crack model) meshes are modeled independently, which speeds up the computation process and reduces the cost of human labor. A simple coarse mesh can be used for all fracture and fatigue analyses of complex structures. In this thesis, simple coarse meshes were used for 3D complex structures, which were below 5000 elements as compared to traditional FEM, which require meshes where the elements range on the order of ˜250,000 to ˜106 and sometimes even more than that.

  19. Multi-scale modelling of strongly heterogeneous 3D composite structures using spatial Voronoi tessellation

    NASA Astrophysics Data System (ADS)

    El Said, Bassam; Ivanov, Dmitry; Long, Andrew C.; Hallett, Stephen R.

    2016-03-01

    3D composite materials are characterized by complex internal yarn architectures, leading to complex deformation and failure development mechanisms. Net-shaped preforms, which are originally periodic in nature, lose their periodicity when the fabric is draped, deformed on a tool, and consolidated to create geometrically complex composite components. As a result, the internal yarn architecture, which dominates the mechanical behaviour, becomes dependent on the structural geometry. Hence, predicting the mechanical behaviour of 3D composites requires an accurate representation of the yarn architecture within structural scale models. When applied to 3D composites, conventional finite element modelling techniques are limited to either homogenised properties at the structural scale, or the unit cell scale for a more detailed material property definition. Consequently, these models fail to capture the complex phenomena occurring across multiple length scales and their effects on a 3D composite's mechanical response. Here a multi-scale modelling approach based on a 3D spatial Voronoi tessellation is proposed. The model creates an intermediate length scale suitable for homogenisation to deal with the non-periodic nature of the final material. Information is passed between the different length scales to allow for the effect of the structural geometry to be taken into account on the smaller scales. The stiffness and surface strain predictions from the proposed model have been found to be in good agreement with experimental results. The proposed modelling framework has been used to gain important insight into the behaviour of this category of materials. It has been observed that the strain and stress distributions are strongly dependent on the internal yarn architecture and consequently on the final component geometry. Even for simple coupon tests, the internal architecture and geometric effects dominate the mechanical response. Consequently, the behaviour of 3D woven

  20. Deposit3D: a tool for automating structure depositions to the Protein Data Bank

    SciTech Connect

    Badger, J. Hendle, J.; Burley, S. K.; Kissinger, C. R.

    2005-09-01

    This paper describes a Python script that may be used to gather all required structure-annotation information into an mmCIF file for upload through the RCSB PDB ADIT structure-deposition interface. Almost all successful protein structure-determination projects in the public sector culminate in a structure deposition to the Protein Data Bank (PDB). In order to expedite the deposition proces, Deposit3D has been developed. This command-line script calculates or gathers all the required structure-deposition information and outputs this data into a mmCIF file for subsequent upload through the RCSB PDB ADIT interface. Deposit3D might be particularly useful for structural genomics pipeline projects because it allows workers involved with various stages of a structure-determination project to pool their different categories of annotation information before starting a deposition session.

  1. Segmented images and 3D images for studying the anatomical structures in MRIs

    NASA Astrophysics Data System (ADS)

    Lee, Yong Sook; Chung, Min Suk; Cho, Jae Hyun

    2004-05-01

    For identifying the pathological findings in MRIs, the anatomical structures in MRIs should be identified in advance. For studying the anatomical structures in MRIs, an education al tool that includes the horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is necessary. Such an educational tool, however, is hard to obtain. Therefore, in this research, such an educational tool which helps medical students and doctors study the anatomical structures in MRIs was made as follows. A healthy, young Korean male adult with standard body shape was selected. Six hundred thirteen horizontal MRIs of the entire body were scanned and inputted to the personal computer. Sixty anatomical structures in the horizontal MRIs were segmented to make horizontal segmented images. Coronal, sagittal MRIs and coronal, sagittal segmented images were made. 3D images of anatomical structures in the segmented images were reconstructed by surface rendering method. Browsing software of the MRIs, segmented images, and 3D images was composed. This educational tool that includes horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is expected to help medical students and doctors study anatomical structures in MRIs.

  2. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints

    PubMed Central

    Magnus, Marcin; Boniecki, Michał J.; Dawson, Wayne; Bujnicki, Janusz M.

    2016-01-01

    RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb. PMID:27095203

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  4. Seismic source inversion using Green's reciprocity and a 3-D structural model for the Japanese Islands

    NASA Astrophysics Data System (ADS)

    Simutė, S.; Fichtner, A.

    2015-12-01

    We present a feasibility study for seismic source inversions using a 3-D velocity model for the Japanese Islands. The approach involves numerically calculating 3-D Green's tensors, which is made efficient by exploiting Green's reciprocity. The rationale for 3-D seismic source inversion has several aspects. For structurally complex regions, such as the Japan area, it is necessary to account for 3-D Earth heterogeneities to prevent unknown structure polluting source solutions. In addition, earthquake source characterisation can serve as a means to delineate existing faults. Source parameters obtained for more realistic Earth models can then facilitate improvements in seismic tomography and early warning systems, which are particularly important for seismically active areas, such as Japan. We have created a database of numerically computed 3-D Green's reciprocals for a 40°× 40°× 600 km size area around the Japanese Archipelago for >150 broadband stations. For this we used a regional 3-D velocity model, recently obtained from full waveform inversion. The model includes attenuation and radial anisotropy and explains seismic waveform data for periods between 10 - 80 s generally well. The aim is to perform source inversions using the database of 3-D Green's tensors. As preliminary steps, we present initial concepts to address issues that are at the basis of our approach. We first investigate to which extent Green's reciprocity works in a discrete domain. Considering substantial amounts of computed Green's tensors we address storage requirements and file formatting. We discuss the importance of the initial source model, as an intelligent choice can substantially reduce the search volume. Possibilities to perform a Bayesian inversion and ways to move to finite source inversion are also explored.

  5. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression.

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation.

  6. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression

    PubMed Central

    Jacob, J. Augustin; Kumar, N. Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  7. Advanced resin systems and 3D textile preforms for low cost composite structures

    NASA Technical Reports Server (NTRS)

    Shukla, J. G.; Bayha, T. D.

    1993-01-01

    Advanced resin systems and 3D textile preforms are being evaluated at Lockheed Aeronautical Systems Company (LASC) under NASA's Advanced Composites Technology (ACT) Program. This work is aimed towards the development of low-cost, damage-tolerant composite fuselage structures. Resin systems for resin transfer molding and powder epoxy towpreg materials are being evaluated for processability, performance and cost. Three developmental epoxy resin systems for resin transfer molding (RTM) and three resin systems for powder towpregging are being investigated. Various 3D textile preform architectures using advanced weaving and braiding processes are also being evaluated. Trials are being conducted with powdered towpreg, in 2D weaving and 3D braiding processes for their textile processability and their potential for fabrication in 'net shape' fuselage structures. The progress in advanced resin screening and textile preform development is reviewed here.

  8. Structure of complement receptor 2 in complex with its C3d ligand.

    PubMed

    Szakonyi, G; Guthridge, J M; Li, D; Young, K; Holers, V M; Chen, X S

    2001-06-01

    Complement receptor 2 (CR2/CD21) is an important receptor that amplifies B lymphocyte activation by bridging the innate and adaptive immune systems. CR2 ligands include complement C3d and Epstein-Barr virus glycoprotein 350/220. We describe the x-ray structure of this CR2 domain in complex with C3d at 2.0 angstroms. The structure reveals extensive main chain interactions between C3d and only one short consensus repeat (SCR) of CR2 and substantial SCR side-side packing. These results provide a detailed understanding of receptor-ligand interactions in this protein family and reveal potential target sites for molecular drug design. PMID:11387479

  9. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression.

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  10. The correlation of 3D DT-MRI fiber disruption with structural and mechanical degeneration in porcine myocardium.

    PubMed

    Zhang, Song; Crow, J Allen; Yang, Xiaoyong; Chen, Joseph; Borazjani, Ali; Mullins, Katie B; Chen, Wei; Cooper, Robert C; McLaughlin, Ronald M; Liao, Jun

    2010-10-01

    Evaluation of structural parameters following a myocardial infarction (MI) is important to assess left ventricular function and remodeling. In this study, we assessed the capability of 3D diffusion tensor magnetic resonance imaging (DT-MRI) to assess tissue degeneration shortly after an MI using a porcine model of infarction. Two days after an induced infarction, hearts were explanted and immediately scanned by a 3T MRI scanner with a diffusion tensor imaging protocol. 3D fiber tracks and clustering models were generated from the diffusion-weighted imaging data. We found in a normal explanted heart that DT-MRI fibers showed a multilayered helical structure, with fiber architecture and fiber density reflecting the integrity of muscle fibers. For infarcted heart explants, we observed either a lack of fibers or disruption of fibers in the infarcted regions. Contours of the disrupted DT-MRI fibers were found to be consistent with the infarcted regions. Both histological and mechanical analysis of the infarcted hearts suggested DT-MRI fiber disruption correlated with altered microstructure and tissue mechanics. The ability of 3D DT-MRI to accurately distinguish viable myocardium from dead myocardium only 2 days post infarct without the use of radioisotopes or ionotropic agents makes it a promising approach to evaluate cardiac damage early post-MI. PMID:20499182

  11. 3D Global Coronal Density Structure and Associated Magnetic Field near Solar Maximum

    NASA Astrophysics Data System (ADS)

    Kramar, Maxim; Airapetian, Vladimir; Lin, Haosheng

    2016-08-01

    Measurement of the coronal magnetic field is a crucial ingredient in understanding the nature of solar coronal dynamic phenomena at all scales. We employ STEREO/COR1 data obtained near maximum of solar activity in December 2012 (Carrington rotation, CR 2131) to retrieve and analyze the three-dimensional (3D) coronal electron density in the range of heights from 1.5 to 4 R_⊙ using a tomography method and qualitatively deduce structures of the coronal magnetic field. The 3D electron density analysis is complemented by the 3D STEREO/EUVI emissivity in 195 Å band obtained by tomography for the same CR period. We find that the magnetic field configuration during CR 2131 has a tendency to become radially open at heliocentric distances below ˜ 2.5 R_⊙. We compared the reconstructed 3D coronal structures over the CR near the solar maximum to the one at deep solar minimum. Results of our 3D density reconstruction will help to constrain solar coronal field models and test the accuracy of the magnetic field approximations for coronal modeling.

  12. 3D shape shearography with integrated structured light projection for strain inspection of curved objects

    NASA Astrophysics Data System (ADS)

    Anisimov, Andrei G.; Groves, Roger M.

    2015-05-01

    Shearography (speckle pattern shearing interferometry) is a non-destructive testing technique that provides full-field surface strain characterization. Although real-life objects especially in aerospace, transport or cultural heritage are not flat (e.g. aircraft leading edges or sculptures), their inspection with shearography is of interest for both hidden defect detection and material characterization. Accurate strain measuring of a highly curved or free form surface needs to be performed by combining inline object shape measuring and processing of shearography data in 3D. Previous research has not provided a general solution. This research is devoted to the practical questions of 3D shape shearography system development for surface strain characterization of curved objects. The complete procedure of calibration and data processing of a 3D shape shearography system with integrated structured light projector is presented. This includes an estimation of the actual shear distance and a sensitivity matrix correction within the system field of view. For the experimental part a 3D shape shearography system prototype was developed. It employs three spatially-distributed shearing cameras, with Michelson interferometers acting as the shearing devices, one illumination laser source and a structured light projector. The developed system performance was evaluated with a previously reported cylinder specimen (length 400 mm, external diameter 190 mmm) loaded by internal pressure. Further steps for the 3D shape shearography prototype and the technique development are also proposed.

  13. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

    Lo, Yu-Chen; Senese, Silvia; Damoiseaux, Robert; Torres, Jorge Z

    2016-08-19

    Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely used but are limited to structures sharing high chemical similarity. Here, we present a new computational approach called chemical similarity network analysis pull-down 3D (CSNAP3D) that combines 3D chemical similarity metrics and network algorithms for structure-based drug target profiling, ligand deorphanization, and automated identification of scaffold hopping compounds. In conjunction with 2D chemical similarity fingerprints, CSNAP3D achieved a >95% success rate in correctly predicting the drug targets of 206 known drugs. Significant improvement in target prediction was observed for HIV reverse transcriptase (HIVRT) compounds, which consist of diverse scaffold hopping compounds targeting the nucleotidyltransferase binding site. CSNAP3D was further applied to a set of antimitotic compounds identified in a cell-based chemical screen and identified novel small molecules that share a pharmacophore with Taxol and display a Taxol-like mechanism of action, which were validated experimentally using in vitro microtubule polymerization assays and cell-based assays.

  14. Impact of 3-D printed PLA- and chitosan-based scaffolds on human monocyte/macrophage responses: unraveling the effect of 3-D structures on inflammation.

    PubMed

    Almeida, Catarina R; Serra, Tiziano; Oliveira, Marta I; Planell, Josep A; Barbosa, Mário A; Navarro, Melba

    2014-02-01

    Recent studies have pointed towards a decisive role of inflammation in triggering tissue repair and regeneration, while at the same time it is accepted that an exacerbated inflammatory response may lead to rejection of an implant. Within this context, understanding and having the capacity to regulate the inflammatory response elicited by 3-D scaffolds aimed for tissue regeneration is crucial. This work reports on the analysis of the cytokine profile of human monocytes/macrophages in contact with biodegradable 3-D scaffolds with different surface properties, architecture and controlled pore geometry, fabricated by 3-D printing technology. Fabrication processes were optimized to create four different 3-D platforms based on polylactic acid (PLA), PLA/calcium phosphate glass or chitosan. Cytokine secretion and cell morphology of human peripheral blood monocytes allowed to differentiate on the different matrices were analyzed. While all scaffolds supported monocyte/macrophage adhesion and stimulated cytokine production, striking differences between PLA-based and chitosan scaffolds were found, with chitosan eliciting increased secretion of tumor necrosis factor (TNF)-α, while PLA-based scaffolds induced higher production of interleukin (IL)-6, IL-12/23 and IL-10. Even though the material itself induced the biggest differences, the scaffold geometry also impacted on TNF-α and IL-12/23 production, with chitosan scaffolds having larger pores and wider angles leading to a higher secretion of these pro-inflammatory cytokines. These findings strengthen the appropriateness of these 3-D platforms to study modulation of macrophage responses by specific parameters (chemistry, topography, scaffold architecture). PMID:24211731

  15. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGES

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

  16. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible dockin