593 research outputs found
Joint Reconstruction of Multi-channel, Spectral CT Data via Constrained Total Nuclear Variation Minimization
We explore the use of the recently proposed "total nuclear variation" (TNV)
as a regularizer for reconstructing multi-channel, spectral CT images. This
convex penalty is a natural extension of the total variation (TV) to
vector-valued images and has the advantage of encouraging common edge locations
and a shared gradient direction among image channels. We show how it can be
incorporated into a general, data-constrained reconstruction framework and
derive update equations based on the first-order, primal-dual algorithm of
Chambolle and Pock. Early simulation studies based on the numerical XCAT
phantom indicate that the inter-channel coupling introduced by the TNV leads to
better preservation of image features at high levels of regularization,
compared to independent, channel-by-channel TV reconstructions.Comment: Submitted to Physics in Medicine and Biolog
Examination of Nursesâ Perceptions, Beliefs, and Conceptions Related to Rapid Bedside Implementation of Prone Therapy During the COVID-19 Pandemic
The COVID-19 pandemic of the SARS-CoV-2 virus created significant challenges for healthcare agencies and front-line healthcare workers. The SARS-CoV-2 virus has demonstrated a unique propensity to induce severe lung injury in the form of acute respiratory distress syndrome (ARDS). High rates of COVID-19 illness in the initial months of the pandemic in the United States led to a rapid influx of patients admitted to critical care units (CCUs) for ARDS. Prone positioning therapy (PPT) has shown substantial promise in treating refractory hypoxemia in people with severe ARDS but historically received poor acceptance as a first-line therapy. With the onset of the pandemic, hospitals became overwhelmed with critically ill COVID-19 patients experiencing severe ARDS, and utilization rates of PPT increased dramatically. This project evaluates the process by which one CCU in a metropolitan hospital rapidly implemented a PPT protocol for ARDS management during the COVID-19 pandemic. Interviews were conducted with five (n = 5) CCU RNs using semi-structured techniques. De-identified data from interview transcripts were analyzed using the interpretive phenomenological analysis (IPA) framework to produce a narrative account of nursesâ lived experiences during the rapid implementation of a PPT during the COVID-19 pandemic
Can WFS-T replace SQL ?
Background With the advent of rich internet applications (RIAâs), part of processing has been transferred from the server to the client. However, many geo-spatial applications still require serverside access to a geodatabase to select and manipulate data using SQL. It would be profitable if these actions could be handled by an out of the box serverside component, thus eliminating the need for the development of a custom serverside component. Can OGC standards like WMS and WFS play a role here? Since WFS-T provides select, insert, delete and update methods much like SQL, it was decided to investigate whether the WFS-T implementation specification could replace SQL when developing complex geo-spatial applications. Or is SQL still needed? Method To answer this research question, this approach was tested during the development of several tailor made internet GIS applications: - a wheater and crop growth monitoring system; - a discussion support system for the water domain; - a national cultural heritage portal. Results Filtering and manipulating serverside data by WFS-T using the OpenGIS Filter Encoding Standard (FES) fullfills the needs to a large extent. Almost all of the desired functionality is there. There is one major limitation: FES lacks the ability to define a filter expression based on a joined table. Dependant on the implementation a work around may be available. Xml-schemas support 1-to-many relationships. They can be implemented as a joined table, which as a result can be queried. For larger datasets - a couple of ten thousand records or more - WFS-T tends to end up with a bad performance. Larger datasets should be processed serverside. Downloading large amounts of data and processing them clientside is too time-consuming. Compared to SQL WFS-T has less possibilities to influence the serverside performance. So for performance reasons SQL stays inevitable to handle larger datasets
Les communautés bactériennes d'un holobionte méditerranéen, la gorgone rouge Paramuricea clavata : diversité, stabilité et spécificité
Coralligenous communities dominated by gorgonian species have been severely affected by diseases and mass mortality events linked to the current warming trends reported for the Mediterranean Sea. The characterization of the natural microbial compartment of this temperate gorgonian species becomes a crucial step in the evaluation of the bacterial contribution to health and functioning of the Paramuricea clavata holobiont.Under these circumstances, the global aim of this PhD work was to describe the interactions existing between the red gorgonian P. clavata and its associated bacteria in the Northwestern Mediterranean basin. The culture-independent analyses based on the bacterial 16S ribosomal DNA included (i) the characterization of spatiotemporal variation of the bacterial communities, (ii) the localization of the bacteria within host tissues, (iii) the evaluation of the stability of gorgonian-bacterial associations under stress conditions and (iv) the determination of the host-specificity of dominant bacteria in different sympatric gorgonian species (Eunicella singularis, Eunicella cavolini and Corallium rubrum).The results of this study highlighted that P. clavata and its microbiota form a holobiont in which host and bacteria live in close association. This association is spatiotemporally stable and maintained under stress conditions. Associated bacterial communities are mostly endosymbiotic and dominated by a bacterial ribotype belonging to a new genus within the Hahellaceae family that seems to be host-specific. These results suggest a particular role of this bacterial genus in the gorgonian holobionts. The present work enabled to initiate the understanding of the bacterial compartment in the 4 most abundant gorgonian species dwelling in the Mediterranean coastal habitats. This knowledge and the different tools that have been developed can be incorporated to new researches on the role of symbiotic associations in health and future trajectories of gorgonian populations in the current climate change context.Les communautĂ©s du coralligĂšne dominĂ©es par des gorgonaires ont Ă©tĂ© sĂ©vĂšrement affectĂ©es par des Ă©vĂšnements de mortalitĂ©s massives liĂ©s au rĂ©chauffement de la MĂ©diterranĂ©e. Pour Ă©valuer la contribution des bactĂ©ries associĂ©es Ă lâholobionte Paramuricea clavata Ă son fonctionnement et sa santĂ©, il est apparu primordial de caractĂ©riser le compartiment microbien naturel de ce gorgonaire tempĂ©rĂ©.Dans ce contexte, lâobjectif gĂ©nĂ©ral de cette thĂšse Ă©tait de dĂ©crire les interactions existant entre la gorgone rouge P. clavata et ses bactĂ©ries associĂ©es en MĂ©diterranĂ©e nord-occidentale. Les analyses entreprises par des techniques culture-indĂ©pendantes basĂ©es sur lâanalyse des ADN ribosomiques 16S bactĂ©riens ont inclus (i) la caractĂ©risation de la variation spatio-temporelle des communautĂ©s bactĂ©riennes, (ii) la localisation des bactĂ©ries dans les tissus de lâhĂŽte, (iii) lâĂ©valuation de la stabilitĂ© des associations gorgones-bactĂ©ries en conditions de stress et (iv) la dĂ©termination de la spĂ©cificitĂ© dâhĂŽte des bactĂ©ries dominantes entre diffĂ©rentes espĂšces de gorgonaires sympatriques (Eunicella singularis, Eunicella cavolini et Corallium rubrum). Les rĂ©sultats obtenus ont Ă©tabli que P. clavata et son microbiote forment un holobionte au sein duquel hĂŽte et bactĂ©ries vivent en Ă©troite association, stable dans le temps et lâespace ou en conditions de stress. Les communautĂ©s bactĂ©riennes associĂ©es sont principalement endosymbiotiques et dominĂ©es par un ribotype bactĂ©rien appartenant Ă un genre nouveau de la famille des Hahellaceae qui semble prĂ©senter une forte spĂ©cificitĂ© dâhĂŽte. Ces rĂ©sultats suggĂšrent un rĂŽle particulier de ce genre bactĂ©rien chez les holobiontes gorgonaires. Ces travaux ont permis dâinitier la connaissance du compartiment bactĂ©rien des quatre espĂšces de gorgonaires les plus abondantes dans les habitats cĂŽtiers. Les Ă©lĂ©ments acquis et les diffĂ©rents outils mis au point pourront ĂȘtre intĂ©grĂ©s Ă de nouvelles recherches sur le rĂŽle des associations symbiotiques dans la santĂ© et le devenir des populations de gorgonaires face aux changements environnementaux en cours
Phase Diverse Phase Retrieval for Microscopy: Comparison of Gaussian and Poisson Approaches
Phase diversity is a widefield aberration correction method that uses
multiple images to estimate the phase aberration at the pupil plane of an
imaging system by solving an optimization problem. This estimated aberration
can then be used to deconvolve the aberrated image or to reacquire it with
aberration corrections applied to a deformable mirror. The optimization problem
for aberration estimation has been formulated for both Gaussian and Poisson
noise models but the Poisson model has never been studied in microscopy nor
compared with the Gaussian model. Here, the Gaussian- and Poisson-based
estimation algorithms are implemented and compared for widefield microscopy in
simulation. The Poisson algorithm is found to match or outperform the Gaussian
algorithm in a variety of situations, and converges in a similar or decreased
amount of time. The Gaussian algorithm does perform better in low-light regimes
when image noise is dominated by additive Gaussian noise. The Poisson algorithm
is also found to be more robust to the effects of spatially variant aberration
and phase noise. Finally, the relative advantages of re-acquisition with
aberration correction and deconvolution with aberrated point spread functions
are compared.Comment: 13 pages, 9 figure
Single-fluorophore orientation determination with multiview polarized illumination : modeling and microscope design
Author Posting. © Optical Society of America, 2017. This article is posted here by permission of Optical Society of America for personal use, not for redistribution. The definitive version was published in Optics Express 25 (2017): 31309-31325, doi:10.1364/OE.25.031309.We investigate the use of polarized illumination in multiview microscopes for determining the orientation of single-molecule fluorescence transition dipoles. First, we relate the orientation of single dipoles to measurable intensities in multiview microscopes and develop an information-theoretic metricâthe solid-angle uncertaintyâto compare the ability of multiview microscopes to estimate the orientation of single dipoles. Next, we compare a broad class of microscopes using this metricâsingle- and dual-view microscopes with varying illumination polarization, illumination numerical aperture (NA), detection NA, obliquity, asymmetry, and exposure. We find that multi-view microscopes can measure all dipole orientations, while the orientations measurable with single-view microscopes is halved because of symmetries in the detection process. We also find that choosing a small illumination NA and a large detection NA are good design choices, that multiview microscopes can benefit from oblique illumination and detection, and that asymmetric NA microscopes can benefit from exposure asymmetry.National Institute of Health (NIH) (R01GM114274, R01EB017293)
An early chondrichthyan and the evolutionary assembly of a shark body plan
Although relationships among the major groups of living gnathostomes are well established, the relatedness of early jawed vertebrates to modern clades is intensely debated. Here, we provide a new description of
Gladbachus
, a Middle Devonian (Givetian approx. 385-million-year-old) stem chondrichthyan from Germany, and one of the very few early chondrichthyans in which substantial portions of the endoskeleton are preserved. Tomographic and histological techniques reveal new details of the gill skeleton, hyoid arch and jaws, neurocranium, cartilage, scales and teeth. Despite many features resembling placoderm or osteichthyan conditions, phylogenetic analysis confirms
Gladbachus
as a stem chondrichthyan and corroborates hypotheses that all acanthodians are stem chondrichthyans. The unfamiliar character combination displayed by
Gladbachus
, alongside conditions observed in acanthodians, implies that pre-Devonian stem chondrichthyans are severely under-sampled and strongly supports indications from isolated scales that the gnathostome crown group originated at the latest by the early Silurian (approx. 440 Ma). Moreover, phylogenetic results highlight the likely convergent evolution of conventional chondrichthyan conditions among earliest members of this primary gnathostome division, while skeletal morphology points towards the likely suspension feeding habits of
Gladbachus
, suggesting a functional origin of the gill slit condition characteristic of the vast majority of living and fossil chondrichthyans.
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Dissection of Molecular Assembly Dynamics by Tracking Orientation and Position of Single Molecules in Live Cells
Regulation of order, such as orientation and conformation, drives the function of most molecular assemblies in living cells but remains difficult to measure accurately through space and time. We built an instantaneous fluorescence polarization microscope, which simultaneously images position and orientation of fluorophores in living cells with single-molecule sensitivity and a time resolution of 100 ms. We developed image acquisition and analysis methods to track single particles that interact with higher-order assemblies of molecules. We tracked the fluctuations in position and orientation of molecules from the level of an ensemble of fluorophores down to single fluorophores. We tested our system in vitro using fluorescently labeled DNA and F-actin, in which the ensemble orientation of polarized fluorescence is known. We then tracked the orientation of sparsely labeled F-actin network at the leading edge of migrating human keratinocytes, revealing the anisotropic distribution of actin filaments relative to the local retrograde flow of the F-actin network. Additionally, we analyzed the position and orientation of septin-GFP molecules incorporated in septin bundles in growing hyphae of a filamentous fungus. Our data indicate that septin-GFP molecules undergo positional fluctuations within âŒ350 nm of the binding site and angular fluctuations within âŒ30° of the central orientation of the bundle. By reporting position and orientation of molecules while they form dynamic higher-order structures, our approach can provide insights into how micrometer-scale ordered assemblies emerge from nanoscale molecules in living cells
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