Endoscopic low coherence interferometry applied to tri-dimensional contouring of upper airways

This thesis presents a novel approach for optical tri-dimensional contouring, requiring only one acquisition to extract a contour depth. It is based on an interferometric setup, using a reduced coherence light source, and is fully adaptable to endoscopic procedure commonly in used in ear-nose-throat (ENT) medicine. It has been demonstrated that the method can be successfully applied to imaging of porcine upper airways. Although this method uses interferometry to obtain depth range measurement, the phase signal is not directly evaluated, rather the location of the coherent superposition of two waves is extracted, and thus provides a robust technique even in harsh environment. The key feature is to extract the coherent area on the image by locating intentionally induced fringes created by off-axis superposition of a smooth reference wave and an object wave coming from a rough or diffusing sample through an optical system with limited aperture. A model for the propagation of the light through the optical system has been developed. It takes into account the broadened emission spectrum of the light source, as well as the statistical speckle effect induced by the illumination of a rough surface with partially coherent light. Simulated results have been carefully compared with measurements, both in the spatial domain and in the Fourier domain (spatial frequencies response), which has permitted to better understand the processes involved in the creation of the interference fringes, and improve the design of the device. Different filters have been investigated in order to extract the depth information from acquired interferograms. By using Gabor filterbanks, which do not need any a priori knowledge of the signal, selectivity of the extracted signal has been enhanced by a factor of 1.3 compared to a simple local Fourier spectrum evaluation, and time of the extraction procedure divided by 6, even when compared to fast iterative calculation in the Fourier spectrum. Moreover, by imposing the frequency and/or orientation of the signal to detect, which can be known by a simple calibration procedure, it has been proved that the selectivity can be further enhanced by a factor of 2.5, keeping the calculation time as short or even shorter. A compact prototype has been designed and built, with a specific multiple fibers arrangement for illumination. The system is separated in two parts: the first one is directly attached to the rigid endoscope, and contains imaging as well as recombining object/reference wave optics, and the detector. It fits into a box with overall dimensions of 115 × 83 × 94 mm. The second part contains the laser source, the scanning arm and the injection optics for the fibered system. It is designed to be left on a small cart. This device can potentially be brought to the bedside, and used during routine endoscopic check-up. Associated with the device, a complete framework has been elaborated in order to simplify the acquisition procedure as well as the signal processing. This results in a fully automated environment taking in charge hardware control, data storage and signal processing, up to the tri-dimensional scene rendering

Scalable Control Strategies and a Customizable Swarm Robotic Platform for Boundary Coverage and Collective Transport Tasks

abstract: Swarms of low-cost, autonomous robots can potentially be used to collectively perform tasks over large domains and long time scales. The design of decentralized, scalable swarm control strategies will enable the development of robotic systems that can execute such tasks with a high degree of parallelism and redundancy, enabling effective operation even in the presence of unknown environmental factors and individual robot failures. Social insect colonies provide a rich source of inspiration for these types of control approaches, since they can perform complex collective tasks under a range of conditions. To validate swarm robotic control strategies, experimental testbeds with large numbers of robots are required; however, existing low-cost robots are specialized and can lack the necessary sensing, navigation, control, and manipulation capabilities. To address these challenges, this thesis presents a formal approach to designing biologically-inspired swarm control strategies for spatially-confined coverage and payload transport tasks, as well as a novel low-cost, customizable robotic platform for testing swarm control approaches. Stochastic control strategies are developed that provably allocate a swarm of robots around the boundaries of multiple regions of interest or payloads to be transported. These strategies account for spatially-dependent effects on the robots' physical distribution and are largely robust to environmental variations. In addition, a control approach based on reinforcement learning is presented for collective payload towing that accommodates robots with heterogeneous maximum speeds. For both types of collective transport tasks, rigorous approaches are developed to identify and translate observed group retrieval behaviors in Novomessor cockerelli ants to swarm robotic control strategies. These strategies can replicate features of ant transport and inherit its properties of robustness to different environments and to varying team compositions. The approaches incorporate dynamical models of the swarm that are amenable to analysis and control techniques, and therefore provide theoretical guarantees on the system's performance. Implementation of these strategies on robotic swarms offers a way for biologists to test hypotheses about the individual-level mechanisms that drive collective behaviors. Finally, this thesis describes Pheeno, a new swarm robotic platform with a three degree-of-freedom manipulator arm, and describes its use in validating a variety of swarm control strategies.Dissertation/ThesisDoctoral Dissertation Mechanical Engineering 201

Inflammatory cardiomyopathy - diagnosis and risk stratification in myocarditis

Background: Acute myocarditis remains a challenging clinical diagnosis with limited epidemiological data and poorly defined markers of adverse risk. We sought to build a better understanding of myocarditis epidemiology and to integrate clinical, genetic and advanced imaging data to generate new insights into myocarditis pathobiology. Methods and Results: (1) Evaluation of population-level hospital admission data from NHS England from 1998-2017 revealed a rising incidence of myocarditis, at least two-fold greater than that reported from pathological registries, most commonly amongst men with median age 36 years and women aged 46 years, with distinct peaks over Winter and the greatest burden in London. (2) Cardiovascular magnetic resonance (CMR) phenotype study of a 114 prospectively recruited patients with acute myocarditis demonstrated the natural history of changes in left ventricular parameters over 12 months and revealed a correlation between change in myocardial mechanics, specifically circumferential strain, and extent of myocardial oedema by T2 mapping (R=-0.70, p=0.01). (3) Genetic sequencing of 231 unrelated patients recruited with acute myocarditis revealed the presence of truncating variants in key cardiomyopathy genes in 4.8% of the cohort, particularly linked to arrhythmogenic ventricular cardiomyopathy (AVC) with significant enrichment compared with 1054 healthy volunteers indicating a potential overlap between myocarditis and AVC (odds ratio 8.2; 95% CI 2.4-28.3; p=0.001). (4) Retrospective long-term clinical outcome study of 401 patients with mid-wall/subepicardial late gadolinium enhancement (LGE) but otherwise normal LV volumes and function suggestive of healed myocarditis demonstrated a low risk of actual or aborted sudden cardiac death over a median follow-up of 4.3 years (incidence rate per 100 patient-years of 0.05%). (5) Psychological study of post-traumatic stress disorder amongst 231 patients with acute myocarditis compared with 44 patients with acute myocardial infarction highlighted the profound and long-lasting psychological morbidity associated uniquely with myocarditis. Conclusion: Myocarditis is a heterogeneous disease that remains vastly underestimated in prevalence. Integration of advanced CMR techniques with genomic data may provide incremental value in early diagnosis, non-invasive surveillance and identification of high-risk individuals who may benefit from a more personalised approach with close monitoring and targeted therapy.Open Acces

Space and Earth Sciences, Computer Systems, and Scientific Data Analysis Support, Volume 1

This Final Progress Report covers the specific technical activities of Hughes STX Corporation for the last contract triannual period of 1 June through 30 Sep. 1993, in support of assigned task activities at Goddard Space Flight Center (GSFC). It also provides a brief summary of work throughout the contract period of performance on each active task. Technical activity is presented in Volume 1, while financial and level-of-effort data is presented in Volume 2. Technical support was provided to all Division and Laboratories of Goddard's Space Sciences and Earth Sciences Directorates. Types of support include: scientific programming, systems programming, computer management, mission planning, scientific investigation, data analysis, data processing, data base creation and maintenance, instrumentation development, and management services. Mission and instruments supported include: ROSAT, Astro-D, BBXRT, XTE, AXAF, GRO, COBE, WIND, UIT, SMM, STIS, HEIDI, DE, URAP, CRRES, Voyagers, ISEE, San Marco, LAGEOS, TOPEX/Poseidon, Pioneer-Venus, Galileo, Cassini, Nimbus-7/TOMS, Meteor-3/TOMS, FIFE, BOREAS, TRMM, AVHRR, and Landsat. Accomplishments include: development of computing programs for mission science and data analysis, supercomputer applications support, computer network support, computational upgrades for data archival and analysis centers, end-to-end management for mission data flow, scientific modeling and results in the fields of space and Earth physics, planning and design of GSFC VO DAAC and VO IMS, fabrication, assembly, and testing of mission instrumentation, and design of mission operations center

Diversity, drivers and dispersal of East Antarctic soil microbiota

Microbes are the life support system of the biosphere. Their metabolic activities have been tightly linked to establishing and maintaining core ecosystem processes around the globe, including the polar deserts of terrestrial Antarctica. Shaped by the continent’s extreme abiotic constraints and physical isolation, core ecosystem processes such as primary production and geochemical cycling often involve unique taxa with novel functional traits thus emphasizing the high conservational value of endemic microbiota. Up till now, microorganisms were rarely considered in Antarctic conservation frameworks despite growing concerns about complex environmental change and our anthropogenic footprint. Major gaps in biodiversity surveys and a general lack of understanding in the basic ecological concepts (niche and neutral) underlying the assemblage of Antarctic soil microbial communities has led to their poor protection status and regional sampling bias. Systematic retrieval of baseline data across the continent is therefore much needed, especially in Eastern Antarctica. In support of bridging this gap, we combined a comprehensive amplicon survey (>700 soil samples) with multivariate analyses and high-end modelling approaches to discern biogeographic patterns of polar soil bacteria, micro-eukarya and archaea throughout two coastal regions in Eastern Antarctica – the Windmill Islands and hyperarid Vestfold Hills. This thesis entails three simple but important mission statements: (1) to unveil the diversity of East Antarctic soil microbiota using a multi-domain approach; (2) to identify key edaphic drivers and threshold tipping points by advancing methods for quantifying multispecies responses to change along environmental gradients; and (3) to explore the influence of wind-driven dispersal as a new initiative for monitoring ecosystem change using a combination of dust samples and particulate trajectory modelling with historical climate data. Soil biodiversity profiles and co-occurrence networks found bacteria, micro-eukarya and archaea likely to be jointly responsible for molding the microbial backbone of Antarctic polar desert ecosystems. Species co-existence is proposed to be linked to tradeoffs between niche (environmental filtering and competition) and neutral (dispersal, speciation and drift) processes. However, the scales weighing these processes are heavily tipped in favor of strong niche-partitioning, which is expected given the harsh abiotic constraints. Bacteria (average Chao1 = 1427.57), the most strongly niche-driven (wPLN = 1.000, wNB = <0.001), were found to be inherently more diverse than micro-eukarya (average Chao1 = 92.93) and archaea (average Chao1 = 45.60) in the same environments where they co-occurred. In comparison, neutrality played a larger role in the assemblage of micro-eukaryotic (wPLN = <0.001, wNB = 1.000) and archaeal (wPLN = 0.960, wNB = 0.040) communities – especially at the Vestfold Hills, which were identified as a potentially sensitive sink location for local windblown particles travelling westward from the Windmill Islands. Employment of a modified Gradient Forest model enabled us to explore non-linear relationships between biodiversity (>17, 000 sequence variants) and the environment (79 physiochemical variables), for the first time, on the hyperarid Vestfold Hills soil microbiome. Moisture availability was primarily responsible for shaping the regional microbiome. Highest rates of compositional turnover were observed for rarer lineages of bacteria and micro-eukarya within the 10 – 12 % moisture range. Often the most responsive were taxa with phototrophic or nutrient-cycling capacities such as Cyanobacteria, Chlorophyta and Ochrophyta, which were detected in relatively high amounts within soil at Old Wallow (OW) and Rookery Lake (RL). High dispersal propensity of Chlorophyta (>75 %), based on dust biodiversity profiles (n = 25), generated some insight on the potential implications of wind-driven dispersal upon current ecosystem dynamics as Antarctica warms up. In theory, habitat expansion for micro-algal blooms via aeolian processes may lead to increased phototrophic capacity thereby resulting in potential competition for dominance between primary production strategies across Eastern Antarctica. Cascading events from this hypothetical scenario would be especially pertinent if aeolian deposition occurred within the vicinity of bird and seal colonies, like those found at OW and RL in the Vestfold Hills. When also taking into account the distinctive soil micro-eukaryotic and bacterial components at these two East Antarctic sites, OW and RL were recommended as conservation targets for further sampling and protection. Escalation of consequences from climate change and human activities are major threats to Antarctica’s unique biodiversity. In the coming century, strengthening of links between science and governance will be key towards forming a solid basis for future conservation planning and management across Antarctica. Integration of microbial data has been identified as crucial to this action. This thesis tackles one part of the equation by bringing attention to the vastly understudied coastal regions of Eastern Antarctica. More baseline surveys and research, however, are needed to capture the full scope of biodiversity offered by the Antarctic soil microbiome. This enormous effort would require sustained funding, increased international cooperation and greater year-round access to all regions

Structural Proteomics of the Fungal Cell Wall

Fungi are surrounded by a thick layer of carbohydrates and proteins, which is essential for the cell’s viability – the fungal cell wall. Proteins are incorporated into this organelle in different ways: some are covalently linked to the carbohydrate moiety of the cell wall via Glycosylphosphatidylinositol (GPI)-anchors or alkali-sensitive linkages, others are indirectly attached to the cell wall via disulfide bonds. Cell wall proteins are involved in various cellular functions, such as cell wall biosynthesis, adhesion to external surfaces, or sensing. The GPI-anchored cell wall proteome of the thermophilic model organism Chaetomium thermophilum was identified in the first part of this thesis. First, a prediction of GPI-proteins, anchored to the cell wall and the plasma membrane was done. The prediction was then complemented by mass-spectrometric identification of GPI-anchored cell wall proteins in isolated cell walls. The detected proteins were then analyzed concerning their functions and putative roles and interesting targets for pharmaceutical applications and fundamental research were established, including Gel1/2, Kre9/Knh1, and Ecm33. In addition, the ultrastructure of the C. thermophilum cell wall was analyzed via transmission electron microscopy, revealing short microfibrils in its outer layer and its similarity to the cell wall of S. cerevisiae. The thesis then advances to the analysis of the A-domains of the Candida glabrata adhesins Awp1 and Awp3, which are members of adhesin cluster VI. Although the fungal pathogen lacks certain virulence factors – such as hyphae formation – C. glabrata infections are commonly observed; its large repertoire of adhesins is believed to be the reason therefore. Awp1A and Awp3A both consist of a β helix domain and an α crystallin domain. They are structurally similar to carbohydrate binding proteins, e. g. polysaccharide lyases, but carbohydrate binding could not be observed. A sequence similarity network (SSN) elucidates their high similarity to cluster V adhesins Awp2 and Awp4 and thereby reinforces previous classifications. The structures of Awp1 and Awp3 provide first insights into new types of adhesins in C. glabrata that include the adhesin clusters V and VI. Furthermore, the G-protein coupled receptor Pth11 from C. thermophilum was analyzed. It contains an N-terminal CFEM domain – a domain exclusively found in fungal cell wall and plasma membrane proteins – that is predicted to be the ligand binding site. The CtPth11 CFEM domain consists of five α helices and reveals two potential binding sites, divided by F48. Distinct conformers of F48 allow formation of a tunnel through the domain. A model of the CtPth11 CFEM domain and transmembrane region – based on prediction of neighboring residues via sequence covariation analysis – shows that both potential binding sites are accessible. In a fragment screen, four fragments were bound in the same cavity; three of them could be fitted into their respective electron densities. These hydrophobic fragments are placed in the hydrophobic cavity, with only few additional interactions, which is in accordance with the proposal that Pth11 senses hydrophobic cues on the plant surface

Conference on Intelligent Robotics in Field, Factory, Service, and Space (CIRFFSS 1994), volume 1

The AIAA/NASA Conference on Intelligent Robotics in Field, Factory, Service, and Space (CIRFFSS '94) was originally proposed because of the strong belief that America's problems of global economic competitiveness and job creation and preservation can partly be solved by the use of intelligent robotics, which are also required for human space exploration missions. Individual sessions addressed nuclear industry, agile manufacturing, security/building monitoring, on-orbit applications, vision and sensing technologies, situated control and low-level control, robotic systems architecture, environmental restoration and waste management, robotic remanufacturing, and healthcare applications