Improving minimum rate predictors algorithm for compression of volumetric medical images

Medical imaging technologies are experiencing a growth in terms of usage and image resolution, namely in diagnostics systems that require a large set of images, like CT or MRI. Furthermore, legal restrictions impose that these scans must be archived for several years. These facts led to the increase of storage costs in medical image databases and institutions. Thus, a demand for more efficient compression tools, used for archiving and communication, is arising. Currently, the DICOM standard, that makes recommendations for medical communications and imaging compression, recommends lossless encoders such as JPEG, RLE, JPEG-LS and JPEG2000. However, none of these encoders include inter-slice prediction in their algorithms. This dissertation presents the research work on medical image compression, using the MRP encoder. MRP is one of the most efficient lossless image compression algorithm. Several processing techniques are proposed to adapt the input medical images to the encoder characteristics. Two of these techniques, namely changing the alignment of slices for compression and a pixel-wise difference predictor, increased the compression efficiency of MRP, by up to 27.9%. Inter-slice prediction support was also added to MRP, using uni and bi-directional techniques. Also, the pixel-wise difference predictor was added to the algorithm. Overall, the compression efficiency of MRP was improved by 46.1%. Thus, these techniques allow for compression ratio savings of 57.1%, compared to DICOM encoders, and 33.2%, compared to HEVC RExt Random Access. This makes MRP the most efficient of the encoders under study.

Contributions to HEVC Prediction for Medical Image Compression

Medical imaging technology and applications are continuously evolving, dealing with images of increasing spatial and temporal resolutions, which allow easier and more accurate medical diagnosis. However, this increase in resolution demands a growing amount of data to be stored and transmitted. Despite the high coding efficiency achieved by the most recent image and video coding standards in lossy compression, they are not well suited for quality-critical medical image compression where either near-lossless or lossless coding is required. In this dissertation, two different approaches to improve lossless coding of volumetric medical images, such as Magnetic Resonance and Computed Tomography, were studied and implemented using the latest standard High Efficiency Video Encoder (HEVC). In a first approach, the use of geometric transformations to perform inter-slice prediction was investigated. For the second approach, a pixel-wise prediction technique, based on Least-Squares prediction, that exploits inter-slice redundancy was proposed to extend the current HEVC lossless tools. Experimental results show a bitrate reduction between 45% and 49%, when compared with DICOM recommended encoders, and 13.7% when compared with standard HEVC.

Enhanced spectral compression in nonlinear optical fibres

We propose two new approaches to enhance the spectral compression process arising from nonlinear pulse propagation in an optical fibre. We numerically show that an additional sinusoidal temporal phase modulation of the pulse enables efficient reduction of the intensity level of side lobes in the spectrum. Another strategy is to select a regime of propagation in which normal group-velocity dispersion reshapes the initial stretched pulse to a near-Fourier-transform-limited rectangular waveform.

Enhanced nonlinear spectral compression in fiber by external sinusoidal phase modulation

We propose a new, simple approach to enhance the spectral compression process arising from nonlinear pulse propagation in an optical fiber. We numerically show that an additional sinusoidal temporal phase modulation of the pulse enables efficient reduction of the intensity level of the side lobes in the spectrum that are produced by the mismatch between the initial linear negative chirp of the pulse and the self-phase modulation-induced nonlinear positive chirp. Remarkable increase of both the extent of spectrum narrowing and the quality of the compressed spectrum is afforded by the proposed approach across a wide range of experimentally accessible parameters.

Enhanced nonlinear spectral compression in fibre by sinusoidal phase modulation

We propose a simple approach to enhance the spectral compression arising from nonlinear pulse propagation in a Kerr medium. We numerically show that an additional sinusoidal temporal phase modulation enables efficient reduction of the intensity level of spectral side lobes.

Chitosan gel film bandages: correlating structure, composition, and antimicrobial properties

Chitosan gel films were successfully obtained by evaporation cast from chitosan solutions in aqueous acidic solutions of organic acids (lactic and acetic acid) as gel film bandages, with a range of additives that directly influence film morphology and porosity. We show that the structure and composition of a wide range of 128 thin gel films, is correlated to the antimicrobial properties, their biocompatibility and resistance to biodegradation. Infrared spectroscopy and solid-state 13C nuclear magnetic resonance spectroscopy was used to correlate film molecular structure and composition to good antimicrobial properties against 10 of the most prevalent Gram positive and Gram negative bacteria. Chitosan gel films reduce the number of colonies after 24 h of incubation by factors of ∼105–107 CFU/mL, compared with controls. For each of these films, the structure and preparation condition has a direct relationship to antimicrobial activity and effectiveness. These gel film bandages also show excellent stability against biodegradation with lysozyme under physiological conditions (5% weight loss over a period of 1 month, 2% in the first week), allowing use during the entire healing process. These chitosan thin films and subsequent derivatives hold potential as low-cost, dissolvable bandages, or second skin, with antimicrobial properties that prohibit the most relevant intrahospital bacteria that infest burn injuries.

Content-aware compression for big textual data analysis

A substantial amount of information on the Internet is present in the form of text. The value of this semi-structured and unstructured data has been widely acknowledged, with consequent scientific and commercial exploitation. The ever-increasing data production, however, pushes data analytic platforms to their limit. This thesis proposes techniques for more efficient textual big data analysis suitable for the Hadoop analytic platform. This research explores the direct processing of compressed textual data. The focus is on developing novel compression methods with a number of desirable properties to support text-based big data analysis in distributed environments. The novel contributions of this work include the following. Firstly, a Content-aware Partial Compression (CaPC) scheme is developed. CaPC makes a distinction between informational and functional content in which only the informational content is compressed. Thus, the compressed data is made transparent to existing software libraries which often rely on functional content to work. Secondly, a context-free bit-oriented compression scheme (Approximated Huffman Compression) based on the Huffman algorithm is developed. This uses a hybrid data structure that allows pattern searching in compressed data in linear time. Thirdly, several modern compression schemes have been extended so that the compressed data can be safely split with respect to logical data records in distributed file systems. Furthermore, an innovative two layer compression architecture is used, in which each compression layer is appropriate for the corresponding stage of data processing. Peripheral libraries are developed that seamlessly link the proposed compression schemes to existing analytic platforms and computational frameworks, and also make the use of the compressed data transparent to developers. The compression schemes have been evaluated for a number of standard MapReduce analysis tasks using a collection of real-world datasets. In comparison with existing solutions, they have shown substantial improvement in performance and significant reduction in system resource requirements.

Behavior of Granular Materials Under Triaxial Compression with Pulsating Deviator Stress, HR-131, Special Report

Behavior of granular material subjected to repeated load triaxial compression tests is characterized by a model based on rate process theory. Starting with the Arrhenius equation from chemical kinetics, the relationship of temperature, shear stress, normal stress and volume change to deformation rate is developed. The proposed model equation includes these factors as a product of exponential terms. An empirical relationship between deformation and the cube root of the number of stress applications at constant temperature and normal stress is combined with the rate equation to yield an integrated relationship of temperature, deviator stress, confining pressure and number of deviator stress applications to axial strain. The experimental program consists of 64 repeated load triaxial compression tests, 52 on untreated crushed stone and 12 on the same crushed stone material treated with 4% asphalt cement. Results were analyzed with multiple linear regression techniques and show substantial agreement with the model equations. Experimental results fit the rate equation somewhat better than the integrated equation when all variable quantities are considered. The coefficient of shear temperature gives the activation enthalpy, which is about 4.7 kilocalories/mole for untreated material and 39.4 kilocalories/mole for asphalt-treated material. This indicates the activation enthalpy is about that of the pore fluid. The proportionality coefficient of deviator stress may be used to measure flow unit volume. The volumes thus determined for untreated and asphalt-treated material are not substantially different. This may be coincidental since comparison with flow unit volumes reported by others indicates flow unit volume is related to gradation of untreated material. The flow unit volume of asphalt-treated material may relate to asphalt cement content. The proposed model equations provide a more rational basis for further studies of factors affecting deformation of granular materials under stress similar to that in pavement subjected to transient traffic loads.

Proprioception in ankle sprain from exercises and bandages

Ankle sprains are the most common injuries in sports, usually causing damage to the lateral ligaments. Recurrence has as usual result permanent instability, and thus loss of proprioception. This fact, together with residual symptoms, is what is known as chronic ankle instability, CAI, or FAI, if it is functional. This problem tries to be solved by improving musculoskeletal stability and proprioception by the application of bandages and performing exercises. The aim of this study has been to review articles (meta-analisis, systematic reviews and revisions) published in 2009-2015 in PubMed, Medline, ENFISPO and BUCea, using keywords such as “sprain instability”, “sprain proprioception”, “chronic ankle instability”. Evidence affirms that there does exist decreased proprioception in patients who suffer from CAI. Rehabilitation exercise regimen is indicated as a treatment because it generates a subjective improvement reported by the patient, and the application of bandages works like a sprain prevention method limiting the range of motion, reducing joint instability and increasing confidence during exercise. As podiatrists we should recommend proprioception exercises to all athletes in a preventive way, and those with CAI or FAI, as a rehabilitation programme, together with the application of bandages. However, further studies should be generated focusing on ways of improving proprioception, and on the exercise patterns that provide the maximum benefit.

Characterization of the glial scar tissue in a murine model of spinal cord compression, with focus on hyaluronan

Spinal cord injury (SCI) is a devastating neurological disorder that affects thousands of people each year. Although in recent decades significant progress has been made in relation to understanding the molecular and cellular events underlying the nervous damage, spinal cord injury is still a highly disabling condition for which there is no curative therapy. People affected by spinal cord injuries manifested dysfunction or loss, temporary or permanent, of motor, sensory and / or autonomic functions depending on the spinal lesion damaged. Currently, the incidence rate of this type of injury is approximately 15-40 cases per million people worldwide. At the origin of these lesions are: road accidents, falls, interpersonal violence and the practice of sports. In this work we placed the hypothesis that HA is one of the component of the scar tissue formed after a compressive SCI, that it is likely synthetised by the perilesional glial cells and that it might support the permeation of the glial scar during the late phase of SCI. Nowadays, much focus is drawn on the recovery of CNS function, made impossible after SCI due to the high content of sulfated proteoglycans in the extracellular matrix. Counterbalancing the ratio between these proteoglycans and hyaluronic acid could be one of the experimental therapy to re-permeate the glial scar tissue formed after SCI, making possible axonal regrowth and functional recovery. Therefore, we established a model of spinal cord compression in mice and studied the glial scar tissue, particularly through the characterization of the expression of enzymes related to the metabolism of HA and the subsequent concentration thereof at different distances of the lesion epicenter. Our results show that the lesion induced in mice shows results similar to those produced in human lesions, in terms of histologic similarities and behavioral results. but these animals demonstrate an impressive spontaneous reorganization mechanism of the spinal cord tissue that occurs after injury and allows for partial recovery of the functions of the CNS. As regards the study of the glial scar, changes were recorded at the level of mRNA expression of enzymes metabolizing HA i.e., after injury there was a decreased expression of HA synthases 1-2 (HAS 1-2) and an increase of the expression HAS3 synthase mRNA, as well as the enzymes responsible for the HA catabolism, HYAL 1-2. But the amount of HA measured through the ELISA test was found unchanged after injury, it is not possible to explain this fact only with the change of expression of enzymes. At two weeks and in response to SCI, we found synthesized HA by reactive astrocytes and probably by others like microglial cells as it was advanced by the HA/GFAP+ and HA/IBA1+ cells co-location.

Modélisation et analyse d'une machine à absorption/compression hybride fonctionnant à partir de rejets thermiques basse température

Les applications de réfrigération sont aujourd’hui majoritairement réalisées par des machines à compression alimentées en électricité. Animées à partir d’une source chaude, l’utilisation de machines à absorption permet d’utiliser très peu d’électricité comparée à une machine à compression et d’utiliser des réfrigérants écologiques. Le faible coefficient de performance et le coût élevé de ces machines est compensé par l’utilisation de rejets thermiques industriels destinés à être rejeté dans l’environnement et donc considérés comme gratuits. Le but de cette étude est de modéliser une machine à absorption hybride, utilisant le couple de fluide eau et ammoniac, en y ajoutant un compresseur ou booster dans la zone haute pression du circuit et d’évaluer ses performances. Cette modification crée une pression intermédiaire au désorbeur permettant de diminuer la température des rejets thermiques exploitables. Une température de rejets réutilisable de 50°C, contre 80°C actuellement, ouvrirait alors la voie à de nouvelles sources communes d’énergie. Le logiciel ASPEN Plus de simulation des procédés a été choisi afin de modéliser en régime permanent le système. Le modèle est en partie validé par l’étude expérimentale d’une machine à absorption commerciale de 10kW pour des applications de climatisation. Cette machine est située au Laboratoire des Technologies de l’Énergie d’Hydro-Québec. Ensuite, une étude de design permet de montrer, à puissance de réfrigération constante, les impacts bénéfiques de la technologie hybride sur le rendement exergétique, mais également sur la taille globale des échangeurs nécessaires. La technologie hybride est alors analysée économiquement face à une machine à absorption chauffée au gaz pour montrer sa rentabilité.