Integration of a 3D hydrogel matrix within a hollow core photonic crystal fibre for DNA probe immobilization

In this paper, we demonstrate the integration of a 3D hydrogel matrix within a hollow core photonic crystal fibre (HC-PCF). In addition, we also show the fluorescence of Cy5-labelled DNA molecules immobilized within the hydrogel formed in two different types of HC-PCF. The 3D hydrogel matrix is designed to bind with the amino groups of biomolecules using an appropriate cross-linker, providing higher sensitivity and selectivity than the standard 2D coverage, enabling a greater number of probe molecules to be available per unit area. The HC-PCFs, on the other hand, can be designed to maximize the capture of fluorescence to improve sensitivity and provide longer interaction lengths. This could enable the development of fibre-based point-of-care and remote systems, where the enhanced sensitivity would relax the constraints placed on sources and detectors. In this paper, we will discuss the formation of such polyethylene glycol diacrylate (PEGDA) hydrogels within a HC-PCF, including their optical properties such as light propagation and auto-fluorescence.

Simulation Environment for Multi-Robot Cooperative 3D Target Perception

4th International Conference, SIMPAR 2014, Bergamo, Italy, October 20-23, 2014

3D GIS modelling using ESRI's CityEngine: a case study from the University Jaume I in Castellon de la Plana Spain

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Amorphous silicon e 3D sensors applied to object detection

Nowadays, existing 3D scanning cameras and microscopes in the market use digital or discrete sensors, such as CCDs or CMOS for object detection applications. However, these combined systems are not fast enough for some application scenarios since they require large data processing resources and can be cumbersome. Thereby, there is a clear interest in exploring the possibilities and performances of analogue sensors such as arrays of position sensitive detectors with the final goal of integrating them in 3D scanning cameras or microscopes for object detection purposes. The work performed in this thesis deals with the implementation of prototype systems in order to explore the application of object detection using amorphous silicon position sensors of 32 and 128 lines which were produced in the clean room at CENIMAT-CEMOP. During the first phase of this work, the fabrication and the study of the static and dynamic specifications of the sensors as well as their conditioning in relation to the existing scientific and technological knowledge became a starting point. Subsequently, relevant data acquisition and suitable signal processing electronics were assembled. Various prototypes were developed for the 32 and 128 array PSD sensors. Appropriate optical solutions were integrated to work together with the constructed prototypes, allowing the required experiments to be carried out and allowing the achievement of the results presented in this thesis. All control, data acquisition and 3D rendering platform software was implemented for the existing systems. All these components were combined together to form several integrated systems for the 32 and 128 line PSD 3D sensors. The performance of the 32 PSD array sensor and system was evaluated for machine vision applications such as for example 3D object rendering as well as for microscopy applications such as for example micro object movement detection. Trials were also performed involving the 128 array PSD sensor systems. Sensor channel non-linearities of approximately 4 to 7% were obtained. Overall results obtained show the possibility of using a linear array of 32/128 1D line sensors based on the amorphous silicon technology to render 3D profiles of objects. The system and setup presented allows 3D rendering at high speeds and at high frame rates. The minimum detail or gap that can be detected by the sensor system is approximately 350 μm when using this current setup. It is also possible to render an object in 3D within a scanning angle range of 15º to 85º and identify its real height as a function of the scanning angle and the image displacement distance on the sensor. Simple and not so simple objects, such as a rubber and a plastic fork, can be rendered in 3D properly and accurately also at high resolution, using this sensor and system platform. The nip structure sensor system can detect primary and even derived colors of objects by a proper adjustment of the integration time of the system and by combining white, red, green and blue (RGB) light sources. A mean colorimetric error of 25.7 was obtained. It is also possible to detect the movement of micrometer objects using the 32 PSD sensor system. This kind of setup offers the possibility to detect if a micro object is moving, what are its dimensions and what is its position in two dimensions, even at high speeds. Results show a non-linearity of about 3% and a spatial resolution of < 2µm.

Biomimetic superhydrophobic surfaces patterned with wettable spots as implantable chips for in vivo high-content 3D biomaterials response assessment

"Tissue engineering: part A", vol. 21, suppl. 1 (2015)

Two different 3D biogeochemical models for the NW mediterranean sea: validation with Meris data and intercomparison

Report for the scientific sojourn carried out at the University of New South Wales from February to June the 2007. Two different biogeochemical models are coupled to a three dimensional configuration of the Princeton Ocean Model (POM) for the Northwestern Mediterranean Sea (Ahumada and Cruzado, 2007). The first biogeochemical model (BLANES) is the three-dimensional version of the model described by Bahamon and Cruzado (2003) and computes the nitrogen fluxes through six compartments using semi-empirical descriptions of biological processes. The second biogeochemical model (BIOMEC) is the biomechanical NPZD model described in Baird et al. (2004), which uses a combination of physiological and physical descriptions to quantify the rates of planktonic interactions. Physical descriptions include, for example, the diffusion of nutrients to phytoplankton cells and the encounter rate of predators and prey. The link between physical and biogeochemical processes in both models is expressed by the advection-diffusion of the non-conservative tracers. The similarities in the mathematical formulation of the biogeochemical processes in the two models are exploited to determine the parameter set for the biomechanical model that best fits the parameter set used in the first model. Three years of integration have been carried out for each model to reach the so called perpetual year run for biogeochemical conditions. Outputs from both models are averaged monthly and then compared to remote sensing images obtained from sensor MERIS for chlorophyll.

3D gait assessment in young and elderly subjects using foot-worn inertial sensors.

This study describes the validation of a new wearable system for assessment of 3D spatial parameters of gait. The new method is based on the detection of temporal parameters, coupled to optimized fusion and de-drifted integration of inertial signals. Composed of two wirelesses inertial modules attached on feet, the system provides stride length, stride velocity, foot clearance, and turning angle parameters at each gait cycle, based on the computation of 3D foot kinematics. Accuracy and precision of the proposed system were compared to an optical motion capture system as reference. Its repeatability across measurements (test-retest reliability) was also evaluated. Measurements were performed in 10 young (mean age 26.1±2.8 years) and 10 elderly volunteers (mean age 71.6±4.6 years) who were asked to perform U-shaped and 8-shaped walking trials, and then a 6-min walking test (6MWT). A total of 974 gait cycles were used to compare gait parameters with the reference system. Mean accuracy±precision was 1.5±6.8cm for stride length, 1.4±5.6cm/s for stride velocity, 1.9±2.0cm for foot clearance, and 1.6±6.1° for turning angle. Difference in gait performance was observed between young and elderly volunteers during the 6MWT particularly in foot clearance. The proposed method allows to analyze various aspects of gait, including turns, gait initiation and termination, or inter-cycle variability. The system is lightweight, easy to wear and use, and suitable for clinical application requiring objective evaluation of gait outside of the lab environment.

Cell Adhesion Peptide RGDSP and Laminin Support Proliferation and Migration of Postnatal Retinal Stem Cells in a 3D Hydrogel Culture System

Purpose: Retinal stem cells (RSCs) can be isolated from radial glia population of the newborn mouse retina (Angénieux et al., 2006). These RSCs have great capacity to renew and generate neurons including cells differentiated towards the photoreceptor lineage (Mehri-Soussi et al., 2006). However, our published results showed poor integration and survival rate after cell grafting into the retina. The uncontrollable environment of retina seems to be the problem. To bypass this, we are trying to generate hemi-retinal tissue in vitro that can be used for transplantation. Methods: Expanded RSCs were seeded in a mixture of poly-ethylene-glycol (PEG)-polymer-based hydrogels crosslinked by peptides that also serve as substrates for matrix metalloproteinases. Different doses of crosslinker peptides were tested. Several growth factors were studied to stimulate cell proliferation and differentiation. Results: Cells were trapped in hydrogels and cultured in the presence of FGF2 and EGF. Spherical cell clusters indicating proliferation appeared within several days, but there was no cell migration within the gel. We then added cell adhesion molecules integrin ligand RGDSP, or laminin, or a combination of both, into the gel. Cells grown with laminin showed the best proliferation. Cells grown with RGDSP proliferated a few times and then started to spread out. Cells grown with the combination of RGDSP and laminin showed better proliferation than with RGDSP alone and larger spread-outs than with laminin alone. After stimulations with first FGF2 and EGF, and then only FGF2, some cells showed neuronal morphology after 2 weeks. The neuronal population was assessed by the presence of neuronal marker b-tubulin-III. Glial cells were also present. Further characterizations are undergoing. Conclusions: RSC can grow and migrate in 3D hydrogel with the addition of FGF2, EGF, RGDSP and laminin. Further developments are necessary to form a homogenous tissue containing retinal cells.

A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis.

BACKGROUND: The yeast Schizosaccharomyces pombe is frequently used as a model for studying the cell cycle. The cells are rod-shaped and divide by medial fission. The process of cell division, or cytokinesis, is controlled by a network of signaling proteins called the Septation Initiation Network (SIN); SIN proteins associate with the SPBs during nuclear division (mitosis). Some SIN proteins associate with both SPBs early in mitosis, and then display strongly asymmetric signal intensity at the SPBs in late mitosis, just before cytokinesis. This asymmetry is thought to be important for correct regulation of SIN signaling, and coordination of cytokinesis and mitosis. In order to study the dynamics of organelles or large protein complexes such as the spindle pole body (SPB), which have been labeled with a fluorescent protein tag in living cells, a number of the image analysis problems must be solved; the cell outline must be detected automatically, and the position and signal intensity associated with the structures of interest within the cell must be determined. RESULTS: We present a new 2D and 3D image analysis system that permits versatile and robust analysis of motile, fluorescently labeled structures in rod-shaped cells. We have designed an image analysis system that we have implemented as a user-friendly software package allowing the fast and robust image-analysis of large numbers of rod-shaped cells. We have developed new robust algorithms, which we combined with existing methodologies to facilitate fast and accurate analysis. Our software permits the detection and segmentation of rod-shaped cells in either static or dynamic (i.e. time lapse) multi-channel images. It enables tracking of two structures (for example SPBs) in two different image channels. For 2D or 3D static images, the locations of the structures are identified, and then intensity values are extracted together with several quantitative parameters, such as length, width, cell orientation, background fluorescence and the distance between the structures of interest. Furthermore, two kinds of kymographs of the tracked structures can be established, one representing the migration with respect to their relative position, the other representing their individual trajectories inside the cell. This software package, called "RodCellJ", allowed us to analyze a large number of S. pombe cells to understand the rules that govern SIN protein asymmetry. CONCLUSIONS: "RodCell" is freely available to the community as a package of several ImageJ plugins to simultaneously analyze the behavior of a large number of rod-shaped cells in an extensive manner. The integration of different image-processing techniques in a single package, as well as the development of novel algorithms does not only allow to speed up the analysis with respect to the usage of existing tools, but also accounts for higher accuracy. Its utility was demonstrated on both 2D and 3D static and dynamic images to study the septation initiation network of the yeast Schizosaccharomyces pombe. More generally, it can be used in any kind of biological context where fluorescent-protein labeled structures need to be analyzed in rod-shaped cells. AVAILABILITY: RodCellJ is freely available under http://bigwww.epfl.ch/algorithms.html, (after acceptance of the publication).

Temporal diffeomorphic free-form deformation: application to motion and strain estimation from 3D echocardiography

This paper presents a new registration algorithm, called Temporal Di eomorphic Free Form Deformation (TDFFD), and its application to motion and strain quanti cation from a sequence of 3D ultrasound (US) images. The originality of our approach resides in enforcing time consistency by representing the 4D velocity eld as the sum of continuous spatiotemporal B-Spline kernels. The spatiotemporal displacement eld is then recovered through forward Eulerian integration of the non-stationary velocity eld. The strain tensor iscomputed locally using the spatial derivatives of the reconstructed displacement eld. The energy functional considered in this paper weighs two terms: the image similarity and a regularization term. The image similarity metric is the sum of squared di erences between the intensities of each frame and a reference one. Any frame in the sequence can be chosen as reference. The regularization term is based on theincompressibility of myocardial tissue. TDFFD was compared to pairwise 3D FFD and 3D+t FFD, bothon displacement and velocity elds, on a set of synthetic 3D US images with di erent noise levels. TDFFDshowed increased robustness to noise compared to these two state-of-the-art algorithms. TDFFD also proved to be more resistant to a reduced temporal resolution when decimating this synthetic sequence. Finally, this synthetic dataset was used to determine optimal settings of the TDFFD algorithm. Subsequently, TDFFDwas applied to a database of cardiac 3D US images of the left ventricle acquired from 9 healthy volunteers and 13 patients treated by Cardiac Resynchronization Therapy (CRT). On healthy cases, uniform strain patterns were observed over all myocardial segments, as physiologically expected. On all CRT patients, theimprovement in synchrony of regional longitudinal strain correlated with CRT clinical outcome as quanti ed by the reduction of end-systolic left ventricular volume at follow-up (6 and 12 months), showing the potential of the proposed algorithm for the assessment of CRT.

3D seismic facies characterization and geological patterns recognition (Australian North West Shelf)

EXECUTIVE SUMMARY This PhD research, funded by the Swiss Sciences Foundation, is principally devoted to enhance the recognition, the visualisation and the characterization of geobodies through innovative 3D seismic approaches. A series of case studies from the Australian North West Shelf ensures the development of reproducible integrated 3D workflows and gives new insight into local and regional stratigraphic as well as structural issues. This project was initiated in year 2000 at the Geology and Palaeontology Institute of the University of Lausanne (Switzerland). Several collaborations ensured the improvement of technical approaches as well as the assessment of geological models. - Investigations into the Timor Sea structural style were carried out at the Tectonics Special Research Centre of the University of Western Australia and in collaboration with Woodside Energy in Perth. - Seismic analysis and attributes classification approach were initiated with Schlumberger Oilfield Australia in Perth; assessments and enhancements of the integrated seismic approaches benefited from collaborations with scientists from Schlumberger Stavanger Research (Norway). Adapting and refining from "linear" exploration techniques, a conceptual "helical" 3D seismic approach has been developed. In order to investigate specific geological issues this approach, integrating seismic attributes and visualisation tools, has been refined and adjusted leading to the development of two specific workflows: - A stratigraphic workflow focused on the recognition of geobodies and the characterization of depositional systems. Additionally, it can support the modelling of the subsidence and incidentally the constraint of the hydrocarbon maturity of a given area. - A structural workflow used to quickly and accurately define major and secondary fault systems. The integration of the 3D structural interpretation results ensures the analysis of the fault networks kinematics which can affect hydrocarbon trapping mechanisms. The application of these integrated workflows brings new insight into two complex settings on the Australian North West Shelf and ensures the definition of astonishing stratigraphic and structural outcomes. The stratigraphic workflow ensures the 3D characterization of the Late Palaeozoic glacial depositional system on the Mermaid Nose (Dampier Subbasin, Northern Carnarvon Basin) that presents similarities with the glacial facies along the Neotethys margin up to Oman (chapter 3.1). A subsidence model reveals the Phanerozoic geodynamic evolution of this area (chapter 3.2) and emphasizes two distinct mode of regional extension for the Palaeozoic (Neotethys opening) and Mesozoic (abyssal plains opening). The structural workflow is used for the definition of the structural evolution of the Laminaria High area (Bonaparte Basin). Following a regional structural characterization of the Timor Sea (chapter 4.1), a thorough analysis of the Mesozoic fault architecture reveals a local rotation of the stress field and the development of reverse structures (flower structures) in extensional setting, that form potential hydrocarbon traps (chapter 4.2). The definition of the complex Neogene structural architecture associated with the fault kinematic analysis and a plate flexure model (chapter 4.3) suggest that the Miocene to Pleistocene reactivation phases recorded at the Laminaria High most probably result from the oblique normal reactivation of the underlying Mesozoic fault planes. This episode is associated with the deformation of the subducting Australian plate. Based on these results three papers were published in international journals and two additional publications will be submitted. Additionally this research led to several communications in international conferences. Although the different workflows presented in this research have been primarily developed and used for the analysis of specific stratigraphic and structural geobodies on the Australian North West Shelf, similar integrated 3D seismic approaches will have applications to hydrocarbon exploration and production phases; for instance increasing the recognition of potential source rocks, secondary migration pathways, additional traps or reservoir breaching mechanisms. The new elements brought by this research further highlight that 3D seismic data contains a tremendous amount of hidden geological information waiting to be revealed and that will undoubtedly bring new insight into depositional systems, structural evolution and geohistory of the areas reputed being explored and constrained and other yet to be constrained. The further development of 3D texture attributes highlighting specific features of the seismic signal, the integration of quantitative analysis for stratigraphic and structural processes, the automation of the interpretation workflow as well as the formal definition of "seismo-morphologic" characteristics of a wide range of geobodies from various environments would represent challenging examples of continuation of this present research. The 21st century will most probably represent a transition period between fossil and other alternative energies. The next generation of seismic interpreters prospecting for hydrocarbon will undoubtedly face new challenges mostly due to the shortage of obvious and easy targets. They will probably have to keep on integrating techniques and geological processes in order to further capitalise the seismic data for new potentials definition. Imagination and creativity will most certainly be among the most important quality required from such geoscientists.

3D culture of postnatal retinal stem cells using self assembling polymers

PURPOSE We have previously shown that retinal stem cells (RSCs) can be isolated from the radial glia population of the newborn mouse retina (Angénieux et al., 2006). These RSCs have a great capacity to renew and to generate a large number of neurons including cells differentiated towards the photoreceptor lineage (Mehri-Soussi et al., 2006). However, recent published results from our lab revealed that such cells have a poor integration and survival rate after grafting. The uncontrolled environment of a retina seems to prevent good integration and survival after grafting in vivo. To bypass this problem, we are evaluating the possibility of generating in vitro a hemi-retinal tissue before transplantation. METHODS RSC were expanded and cells passaged <10 were seeded in a solution containing poly-ethylene-glycol (PEG) polymer based hydrogels crosslinked with peptides that are chosen to be substrates for matrix metalloproteinases. Various doses of cross linkers peptides allowing connections between PEG polymers were tested. Different growth factors were studied to stimulate cell proliferation and differentiation. RESULTS Cells survived only in the presence of EGF and FGF-2 and generated colonies with a sphere shape. No cells migrated within the gel. To improve the migration and the repartition of the cells in the gels, the integrin ligand RGDSP was added into the gel. In the presence of FGF-2 and EGF, newly formed cell clusters appeared by cell proliferation within several days, but again no outspreading of cells was observed. No difference was even seen when the stiffness of the hydrogels or the concentration of the integrin ligand RGDSP were changed. However, our preliminary results show that RSCs still form spheres when laminin is entrapped in the gel, but they started to spread out having a neuronal morphology after around 2 weeks. The neuronal population was assessed by the presence of the neuronal marker b-tubulin-III. This differentiation was achieved after successive steps of stimulations including FGF-2 and EGF, and then only FGF-2. Glial cells were also present. Further characterizations are under process. CONCLUSIONS RSC can be grown in 3D. Preliminary results show that neuronal cell phenotype acquisition can be instructed by exogenous stimulations and factors linked to the gel. Further developments are necessary to form a homogenous tissue containing retinal cells.

Modelling syntectonic sedimentation: combining a discrete element model of tectonic. Deformation and process-based sedimentary Model in 3D.

This paper presents a new numerical program able to model syntectonic sedimentation. The new model combines a discrete element model of the tectonic deformation of a sedimentary cover and a process-based model of sedimentation in a single framework. The integration of these two methods allows us to include the simulation of both sedimentation and deformation processes in a single and more effective model. The paper describes briefly the antecedents of the program, Simsafadim-Clastic and a discrete element model, in order to introduce the methodology used to merge both programs to create the new code. To illustrate the operation and application of the program, analysis of the evolution of syntectonic geometries in an extensional environment and also associated with thrust fault propagation is undertaken. Using the new code, much more complex and realistic depositional structures can be simulated together with a more complex analysis of the evolution of the deformation within the sedimentary cover, which is seen to be affected by the presence of the new syntectonic sediments.

Pipework data in design system integration

This thesis work describes the creation of a pipework data structure for design system integration. Work is completed in pulp and paper plant delivery company with global engineering network operations in mind. User case of process design to 3D pipework design is introduced with influence of subcontracting engineering offices. Company data element list is gathered by using key person interviews and results are processed into a pipework data element list. Inter-company co-operation is completed in standardization association and common standard for pipework data elements is found. As result inter-company created pipework data element list is introduced. Further list usage, development and relations to design software vendors are evaluated.

Capaware: plataforma de desarrollo de software libre para aplicacines geográficas 3D multicapa

En este trabajo se presenta Capaware, una plataforma de software libre para el desarrollo de aplicaciones geográficas 3D multicapa, que surge a partir de la iniciativa del Instituto Tecnológico de Canarias en colaboración con la Universidad de Las Palmas de Gran Canaria. Este entorno simplifica la creación de aplicaciones 3D sobre territorios geográficos extensos, disponiendo de una herramienta muy visual que aporta un nuevo punto de vista muy importante para una toma de decisiones eficaz. Capaware proporciona una interfaz fácil de usar y muy flexible que simplifica el desarrollo de nuevas aplicaciones, permitiéndonos crear rápidamente entornos virtuales con múltiples capas de información sobre el terreno. Con las capacidades clásicas de un Sistema de Información Geográfica (SIG), Capaware permite actualmente la carga de capas WMS sobre entornos 3D, añadir objetos 3D sobre el terreno, y visualizar elementos dinámicos, ofreciendo una nueva perspectiva de la información analizada. Así mismo, podemos administrar las capas de recursos y elementos que se pueden representar sobre la zona geográfica en cuestión. (...)