Parallel 3D Simulation of a Fault Gouge using the Lattice Solid Model

Despite the insight gained from 2-D particle models, and given that the dynamics of crustal faults occur in 3-D space, the question remains, how do the 3-D fault gouge dynamics differ from those in 2-D? Traditionally, 2-D modeling has been preferred over 3-D simulations because of the computational cost of solving 3-D problems. However, modern high performance computing architectures, combined with a parallel implementation of the Lattice Solid Model (LSM), provide the opportunity to explore 3-D fault micro-mechanics and to advance understanding of effective constitutive relations of fault gouge layers. In this paper, macroscopic friction values from 2-D and 3-D LSM simulations, performed on an SGI Altix 3700 super-cluster, are compared. Two rectangular elastic blocks of bonded particles, with a rough fault plane and separated by a region of randomly sized non-bonded gouge particles, are sheared in opposite directions by normally-loaded driving plates. The results demonstrate that the gouge particles in the 3-D models undergo significant out-of-plane motion during shear. The 3-D models also exhibit a higher mean macroscopic friction than the 2-D models for varying values of interparticle friction. 2-D LSM gouge models have previously been shown to exhibit accelerating energy release in simulated earthquake cycles, supporting the Critical Point hypothesis. The 3-D models are shown to also display accelerating energy release, and good fits of power law time-to-failure functions to the cumulative energy release are obtained.

3D statistical shape models to embed spatial relationship information

This paper presents the creation of 3D statistical shape models of the knee bones and their use to embed information into a segmentation system for MRIs of the knee. We propose utilising the strong spatial relationship between the cartilages and the bones in the knee by embedding this information into the created models. This information can then be used to automate the initialisation of segmentation algorithms for the cartilages. The approach used to automatically generate the 3D statistical shape models of the bones is based on the point distribution model optimisation framework of Davies. Our implementation of this scheme uses a parameterized surface extraction algorithm, which is used as the basis for the optimisation scheme that automatically creates the 3D statistical shape models. The current approach is illustrated by generating 3D statistical shape models of the patella, tibia and femoral bones from a segmented database of the knee. The use of these models to embed spatial relationship information to aid in the automation of segmentation algorithms for the cartilages is then illustrated.

Automatic segmentation of the knee bones using 3D active shape models

This paper presents an automated segmentation approach for MR images of the knee bones. The bones are the first stage of a segmentation system for the knee, primarily aimed at the automated segmentation of the cartilages. The segmentation is performed using 3D active shape models (ASM), which are initialized using an affine registration to an atlas. The 3D ASMs of the bones are created automatically using a point distribution model optimization scheme. The accuracy and robustness of the segmentation approach was experimentally validated using an MR database of fat suppressed spoiled gradient recall images.

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.

The Cloud Computing and Computer Virology

Евгений Николов, Димитрина Полимирова - Докладът представя текущото състояние на “облачните изчисления” и “облачните информационни атаки” в светлината на компютърната вирусология и информационната сигурност. Обсъдени са категориите “облачни възможни информационни атаки” и “облачни успешни информационни атаки”. Коментирана е архитектурата на “облачните изчисления” и основните компоненти, които изграждат тяхната инфраструктура, съответно “клиенти” (“clients”), „центрове за съхранение на данни“ (“datacenters”) и „разпределени сървъри“ (“dirstributed servers”). Коментирани са и услугите, които се предлагат от “облачните изчисления” – SaaS, HaaS и PaaS. Посочени са предимствата и недостатъците на компонентите и услугите по отношение на “облачните информационни атаки”. Направен е анализ на текущото състояние на “облачните информационни атаки” на територията на България, Балканския полуостров и Югоизточна Европа по отношение на компонентите и на услугите. Резултатите са представени под формата на 3D графични обекти. На края са направени съответните изводи и препоръки под формата на заключение.

A framework for automatic feature extraction from airborne light detection and ranging data

Recent advances in airborne Light Detection and Ranging (LIDAR) technology allow rapid and inexpensive measurements of topography over large areas. Airborne LIDAR systems usually return a 3-dimensional cloud of point measurements from reflective objects scanned by the laser beneath the flight path. This technology is becoming a primary method for extracting information of different kinds of geometrical objects, such as high-resolution digital terrain models (DTMs), buildings and trees, etc. In the past decade, LIDAR gets more and more interest from researchers in the field of remote sensing and GIS. Compared to the traditional data sources, such as aerial photography and satellite images, LIDAR measurements are not influenced by sun shadow and relief displacement. However, voluminous data pose a new challenge for automated extraction the geometrical information from LIDAR measurements because many raster image processing techniques cannot be directly applied to irregularly spaced LIDAR points. ^ In this dissertation, a framework is proposed to filter out information about different kinds of geometrical objects, such as terrain and buildings from LIDAR automatically. They are essential to numerous applications such as flood modeling, landslide prediction and hurricane animation. The framework consists of several intuitive algorithms. Firstly, a progressive morphological filter was developed to detect non-ground LIDAR measurements. By gradually increasing the window size and elevation difference threshold of the filter, the measurements of vehicles, vegetation, and buildings are removed, while ground data are preserved. Then, building measurements are identified from no-ground measurements using a region growing algorithm based on the plane-fitting technique. Raw footprints for segmented building measurements are derived by connecting boundary points and are further simplified and adjusted by several proposed operations to remove noise, which is caused by irregularly spaced LIDAR measurements. To reconstruct 3D building models, the raw 2D topology of each building is first extracted and then further adjusted. Since the adjusting operations for simple building models do not work well on 2D topology, 2D snake algorithm is proposed to adjust 2D topology. The 2D snake algorithm consists of newly defined energy functions for topology adjusting and a linear algorithm to find the minimal energy value of 2D snake problems. Data sets from urbanized areas including large institutional, commercial, and small residential buildings were employed to test the proposed framework. The results demonstrated that the proposed framework achieves a very good performance. ^

Rigid and non-rigid point-based medical image registration

The primary goal of this dissertation is to develop point-based rigid and non-rigid image registration methods that have better accuracy than existing methods. We first present point-based PoIRe, which provides the framework for point-based global rigid registrations. It allows a choice of different search strategies including (a) branch-and-bound, (b) probabilistic hill-climbing, and (c) a novel hybrid method that takes advantage of the best characteristics of the other two methods. We use a robust similarity measure that is insensitive to noise, which is often introduced during feature extraction. We show the robustness of PoIRe using it to register images obtained with an electronic portal imaging device (EPID), which have large amounts of scatter and low contrast. To evaluate PoIRe we used (a) simulated images and (b) images with fiducial markers; PoIRe was extensively tested with 2D EPID images and images generated by 3D Computer Tomography (CT) and Magnetic Resonance (MR) images. PoIRe was also evaluated using benchmark data sets from the blind retrospective evaluation project (RIRE). We show that PoIRe is better than existing methods such as Iterative Closest Point (ICP) and methods based on mutual information. We also present a novel point-based local non-rigid shape registration algorithm. We extend the robust similarity measure used in PoIRe to non-rigid registrations adapting it to a free form deformation (FFD) model and making it robust to local minima, which is a drawback common to existing non-rigid point-based methods. For non-rigid registrations we show that it performs better than existing methods and that is less sensitive to starting conditions. We test our non-rigid registration method using available benchmark data sets for shape registration. Finally, we also explore the extraction of features invariant to changes in perspective and illumination, and explore how they can help improve the accuracy of multi-modal registration. For multimodal registration of EPID-DRR images we present a method based on a local descriptor defined by a vector of complex responses to a circular Gabor filter.

Rigid and Non-rigid Point-based Medical Image Registration

The primary goal of this dissertation is to develop point-based rigid and non-rigid image registration methods that have better accuracy than existing methods. We first present point-based PoIRe, which provides the framework for point-based global rigid registrations. It allows a choice of different search strategies including (a) branch-and-bound, (b) probabilistic hill-climbing, and (c) a novel hybrid method that takes advantage of the best characteristics of the other two methods. We use a robust similarity measure that is insensitive to noise, which is often introduced during feature extraction. We show the robustness of PoIRe using it to register images obtained with an electronic portal imaging device (EPID), which have large amounts of scatter and low contrast. To evaluate PoIRe we used (a) simulated images and (b) images with fiducial markers; PoIRe was extensively tested with 2D EPID images and images generated by 3D Computer Tomography (CT) and Magnetic Resonance (MR) images. PoIRe was also evaluated using benchmark data sets from the blind retrospective evaluation project (RIRE). We show that PoIRe is better than existing methods such as Iterative Closest Point (ICP) and methods based on mutual information. We also present a novel point-based local non-rigid shape registration algorithm. We extend the robust similarity measure used in PoIRe to non-rigid registrations adapting it to a free form deformation (FFD) model and making it robust to local minima, which is a drawback common to existing non-rigid point-based methods. For non-rigid registrations we show that it performs better than existing methods and that is less sensitive to starting conditions. We test our non-rigid registration method using available benchmark data sets for shape registration. Finally, we also explore the extraction of features invariant to changes in perspective and illumination, and explore how they can help improve the accuracy of multi-modal registration. For multimodal registration of EPID-DRR images we present a method based on a local descriptor defined by a vector of complex responses to a circular Gabor filter.

AdaptMCloud: uma estratégia para adaptação dinâmica de aplicações Multi-Cloud

Multi-Cloud Applications are composed of services offered by multiple cloud platforms where the user/developer has full knowledge of the use of such platforms. The use of multiple cloud platforms avoids the following problems: (i) vendor lock-in, which is dependency on the application of a certain cloud platform, which is prejudicial in the case of degradation or failure of platform services, or even price increasing on service usage; (ii) degradation or failure of the application due to fluctuations in quality of service (QoS) provided by some cloud platform, or even due to a failure of any service. In multi-cloud scenario is possible to change a service in failure or with QoS problems for an equivalent of another cloud platform. So that an application can adopt the perspective multi-cloud is necessary to create mechanisms that are able to select which cloud services/platforms should be used in accordance with the requirements determined by the programmer/user. In this context, the major challenges in terms of development of such applications include questions such as: (i) the choice of which underlying services and cloud computing platforms should be used based on the defined user requirements in terms of functionality and quality (ii) the need to continually monitor the dynamic information (such as response time, availability, price, availability), related to cloud services, in addition to the wide variety of services, and (iii) the need to adapt the application if QoS violations affect user defined requirements. This PhD thesis proposes an approach for dynamic adaptation of multi-cloud applications to be applied when a service is unavailable or when the requirements set by the user/developer point out that other available multi-cloud configuration meets more efficiently. Thus, this work proposes a strategy composed of two phases. The first phase consists of the application modeling, exploring the similarities representation capacity and variability proposals in the context of the paradigm of Software Product Lines (SPL). In this phase it is used an extended feature model to specify the cloud service configuration to be used by the application (similarities) and the different possible providers for each service (variability). Furthermore, the non-functional requirements associated with cloud services are specified by properties in this model by describing dynamic information about these services. The second phase consists of an autonomic process based on MAPE-K control loop, which is responsible for selecting, optimally, a multicloud configuration that meets the established requirements, and perform the adaptation. The adaptation strategy proposed is independent of the used programming technique for performing the adaptation. In this work we implement the adaptation strategy using various programming techniques such as aspect-oriented programming, context-oriented programming and components and services oriented programming. Based on the proposed steps, we tried to assess the following: (i) the process of modeling and the specification of non-functional requirements can ensure effective monitoring of user satisfaction; (ii) if the optimal selection process presents significant gains compared to sequential approach; and (iii) which techniques have the best trade-off when compared efforts to development/modularity and performance.

The application of 3D printing to study microfluidic architecture for 'on-chip' mixing systems for SRCD and UV spectroscopy

This paper details methodologies that have been explored for the fast proofing of on-chip architectures for Circular Dichroism techniques. Flow-cell devices fabricated from UV transparent Quartz are used for these experiments. The complexity of flow-cell production typically results in lead times of six months from order to delivery. Only at that point can the on-chip architecture be tested empirically and any required modifications determined ready for the next six month iteration phase. By using the proposed 3D printing and PDMS moulding techniques for fast proofing on-chip architectures the optimum design can be determined within a matter of hours prior to commitment to quartz chip production.

Advanced Applications of 3D Dosimetry and 3D Printing in Radiation Therapy

As complex radiotherapy techniques become more readily-practiced, comprehensive 3D dosimetry is a growing necessity for advanced quality assurance. However, clinical implementation has been impeded by a wide variety of factors, including the expense of dedicated optical dosimeter readout tools, high operational costs, and the overall difficulty of use. To address these issues, a novel dry-tank optical CT scanner was designed for PRESAGE 3D dosimeter readout, relying on 3D printed components and omitting costly parts from preceding optical scanners. This work details the design, prototyping, and basic commissioning of the Duke Integrated-lens Optical Scanner (DIOS).

The convex scanning geometry was designed in ScanSim, an in-house Monte Carlo optical ray-tracing simulation. ScanSim parameters were used to build a 3D rendering of a convex ‘solid tank’ for optical-CT, which is capable of collimating a point light source into telecentric geometry without significant quantities of refractive-index matched fluid. The model was 3D printed, processed, and converted into a negative mold via rubber casting to produce a transparent polyurethane scanning tank. The DIOS was assembled with the solid tank, a 3W red LED light source, a computer-controlled rotation stage, and a 12-bit CCD camera. Initial optical phantom studies show negligible spatial inaccuracies in 2D projection images and 3D tomographic reconstructions. A PRESAGE 3D dose measurement for a 4-field box treatment plan from Eclipse shows 95% of voxels passing gamma analysis at 3%/3mm criteria. Gamma analysis between tomographic images of the same dosimeter in the DIOS and DLOS systems show 93.1% agreement at 5%/1mm criteria. From this initial study, the DIOS has demonstrated promise as an economically-viable optical-CT scanner. However, further improvements will be necessary to fully develop this system into an accurate and reliable tool for advanced QA.

Pre-clinical animal studies are used as a conventional means of translational research, as a midpoint between in-vitro cell studies and clinical implementation. However, modern small animal radiotherapy platforms are primitive in comparison with conventional linear accelerators. This work also investigates a series of 3D printed tools to expand the treatment capabilities of the X-RAD 225Cx orthovoltage irradiator, and applies them to a feasibility study of hippocampal avoidance in rodent whole-brain radiotherapy.

As an alternative material to lead, a novel 3D-printable tungsten-composite ABS plastic, GMASS, was tested to create precisely-shaped blocks. Film studies show virtually all primary radiation at 225 kVp can be attenuated by GMASS blocks of 0.5cm thickness. A state-of-the-art software, BlockGen, was used to create custom hippocampus-shaped blocks from medical image data, for any possible axial treatment field arrangement. A custom 3D printed bite block was developed to immobilize and position a supine rat for optimal hippocampal conformity. An immobilized rat CT with digitally-inserted blocks was imported into the SmART-Plan Monte-Carlo simulation software to determine the optimal beam arrangement. Protocols with 4 and 7 equally-spaced fields were considered as viable treatment options, featuring improved hippocampal conformity and whole-brain coverage when compared to prior lateral-opposed protocols. Custom rodent-morphic PRESAGE dosimeters were developed to accurately reflect these treatment scenarios, and a 3D dosimetry study was performed to confirm the SmART-Plan simulations. Measured doses indicate significant hippocampal sparing and moderate whole-brain coverage.

A cloud-based system for measuring radiation treatment plan similarity

PURPOSE: Radiation therapy is used to treat cancer using carefully designed plans that maximize the radiation dose delivered to the target and minimize damage to healthy tissue, with the dose administered over multiple occasions. Creating treatment plans is a laborious process and presents an obstacle to more frequent replanning, which remains an unsolved problem. However, in between new plans being created, the patient's anatomy can change due to multiple factors including reduction in tumor size and loss of weight, which results in poorer patient outcomes. Cloud computing is a newer technology that is slowly being used for medical applications with promising results. The objective of this work was to design and build a system that could analyze a database of previously created treatment plans, which are stored with their associated anatomical information in studies, to find the one with the most similar anatomy to a new patient. The analyses would be performed in parallel on the cloud to decrease the computation time of finding this plan. METHODS: The system used SlicerRT, a radiation therapy toolkit for the open-source platform 3D Slicer, for its tools to perform the similarity analysis algorithm. Amazon Web Services was used for the cloud instances on which the analyses were performed, as well as for storage of the radiation therapy studies and messaging between the instances and a master local computer. A module was built in SlicerRT to provide the user with an interface to direct the system on the cloud, as well as to perform other related tasks. RESULTS: The cloud-based system out-performed previous methods of conducting the similarity analyses in terms of time, as it analyzed 100 studies in approximately 13 minutes, and produced the same similarity values as those methods. It also scaled up to larger numbers of studies to analyze in the database with a small increase in computation time of just over 2 minutes. CONCLUSION: This system successfully analyzes a large database of radiation therapy studies and finds the one that is most similar to a new patient, which represents a potential step forward in achieving feasible adaptive radiation therapy replanning.

A Provenance-Aware Policy Language (cProvl) and a Data Traceability Model (cProv) for the Cloud

Provenance plays a pivotal in tracing the origin of something and determining how and why something had occurred. With the emergence of the cloud and the benefits it encompasses, there has been a rapid proliferation of services being adopted by commercial and government sectors. However, trust and security concerns for such services are on an unprecedented scale. Currently, these services expose very little internal working to their customers; this can cause accountability and compliance issues especially in the event of a fault or error, customers and providers are left to point finger at each other. Provenance-based traceability provides a mean to address part of this problem by being able to capture and query events occurred in the past to understand how and why it took place. However, due to the complexity of the cloud infrastructure, the current provenance models lack the expressibility required to describe the inner-working of a cloud service. For a complete solution, a provenance-aware policy language is also required for operators and users to define policies for compliance purpose. The current policy standards do not cater for such requirement. To address these issues, in this paper we propose a provenance (traceability) model cProv, and a provenance-aware policy language (cProvl) to capture traceability data, and express policies for validating against the model. For implementation, we have extended the XACML3.0 architecture to support provenance, and provided a translator that converts cProvl policy and request into XACML type.

Radio over fiber enabling PON fronthaul in a two-tiered cloud

Avec l’avènement des objets connectés, la bande passante nécessaire dépasse la capacité des interconnections électriques et interface sans fils dans les réseaux d’accès mais aussi dans les réseaux coeurs. Des systèmes photoniques haute capacité situés dans les réseaux d’accès utilisant la technologie radio sur fibre systèmes ont été proposés comme solution dans les réseaux sans fil de 5e générations. Afin de maximiser l’utilisation des ressources des serveurs et des ressources réseau, le cloud computing et des services de stockage sont en cours de déploiement. De cette manière, les ressources centralisées pourraient être diffusées de façon dynamique comme l’utilisateur final le souhaite. Chaque échange nécessitant une synchronisation entre le serveur et son infrastructure, une couche physique optique permet au cloud de supporter la virtualisation des réseaux et de les définir de façon logicielle. Les amplificateurs à semi-conducteurs réflectifs (RSOA) sont une technologie clé au niveau des ONU(unité de communications optiques) dans les réseaux d’accès passif (PON) à fibres. Nous examinons ici la possibilité d’utiliser un RSOA et la technologie radio sur fibre pour transporter des signaux sans fil ainsi qu’un signal numérique sur un PON. La radio sur fibres peut être facilement réalisée grâce à l’insensibilité a la longueur d’onde du RSOA. Le choix de la longueur d’onde pour la couche physique est cependant choisi dans les couches 2/3 du modèle OSI. Les interactions entre la couche physique et la commutation de réseaux peuvent être faites par l’ajout d’un contrôleur SDN pour inclure des gestionnaires de couches optiques. La virtualisation réseau pourrait ainsi bénéficier d’une couche optique flexible grâce des ressources réseau dynamique et adaptée. Dans ce mémoire, nous étudions un système disposant d’une couche physique optique basé sur un RSOA. Celle-ci nous permet de façon simultanée un envoi de signaux sans fil et le transport de signaux numérique au format modulation tout ou rien (OOK) dans un système WDM(multiplexage en longueur d’onde)-PON. Le RSOA a été caractérisé pour montrer sa capacité à gérer une plage dynamique élevée du signal sans fil analogique. Ensuite, les signaux RF et IF du système de fibres sont comparés avec ses avantages et ses inconvénients. Finalement, nous réalisons de façon expérimentale une liaison point à point WDM utilisant la transmission en duplex intégral d’un signal wifi analogique ainsi qu’un signal descendant au format OOK. En introduisant deux mélangeurs RF dans la liaison montante, nous avons résolu le problème d’incompatibilité avec le système sans fil basé sur le TDD (multiplexage en temps duplexé).

Ionisation and discharge in cloud-forming atmospheres of brown dwarfs and extrasolar planets

Brown dwarfs and giant gas extrasolar planets have cold atmospheres with rich chemical compositions from which mineral cloud particles form. Their properties, like particle sizes and material composition, vary with height, and the mineral cloud particles are charged due to triboelectric processes in such dynamic atmospheres. The dynamics of the atmospheric gas is driven by the irradiating host star and/or by the rotation of the objects that changes during its lifetime. Thermal gas ionisation in these ultra-cool but dense atmospheres allows electrostatic interactions and magnetic coupling of a substantial atmosphere volume. Combined with a strong magnetic field , a chromosphere and aurorae might form as suggested by radio and x-ray observations of brown dwarfs. Non-equilibrium processes like cosmic ray ionisation and discharge processes in clouds will increase the local pool of free electrons in the gas. Cosmic rays and lighting discharges also alter the composition of the local atmospheric gas such that tracer molecules might be identified. Cosmic rays affect the atmosphere through air showers in a certain volume which was modelled with a 3D Monte Carlo radiative transfer code to be able to visualise their spacial extent. Given a certain degree of thermal ionisation of the atmospheric gas, we suggest that electron attachment to charge mineral cloud particles is too inefficient to cause an electrostatic disruption of the cloud particles. Cloud particles will therefore not be destroyed by Coulomb explosion for the local temperature in the collisional dominated brown dwarf and giant gas planet atmospheres. However, the cloud particles are destroyed electrostatically in regions with strong gas ionisation. The potential size of such cloud holes would, however, be too small and might occur too far inside the cloud to mimic the effect of, e.g. magnetic field induced star spots.