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 Nurses’ 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 nurses’ 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 (RIA’s), 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 communautés du coralligène dominées par des gorgonaires ont été sévèrement affectées par des évènements de mortalités massives liés au réchauffement de la Méditerranée. Pour évaluer la contribution des bactéries associées à l’holobionte Paramuricea clavata à son fonctionnement et sa santé, il est apparu primordial de caractériser le compartiment microbien naturel de ce gorgonaire tempéré.Dans ce contexte, l’objectif général de cette thèse était de décrire les interactions existant entre la gorgone rouge P. clavata et ses bactéries associées en Méditerranée nord-occidentale. Les analyses entreprises par des techniques culture-indépendantes basées sur l’analyse des ADN ribosomiques 16S bactériens ont inclus (i) la caractérisation de la variation spatio-temporelle des communautés bactériennes, (ii) la localisation des bactéries dans les tissus de l’hôte, (iii) l’évaluation de la stabilité des associations gorgones-bactéries en conditions de stress et (iv) la détermination de la spécificité d’hôte des bactéries dominantes entre différentes espèces de gorgonaires sympatriques (Eunicella singularis, Eunicella cavolini et Corallium rubrum). Les résultats obtenus ont établi que P. clavata et son microbiote forment un holobionte au sein duquel hôte et bactéries vivent en étroite association, stable dans le temps et l’espace ou en conditions de stress. Les communautés bactériennes associées sont principalement endosymbiotiques et dominées par un ribotype bactérien appartenant à un genre nouveau de la famille des Hahellaceae qui semble présenter une forte spécificité d’hôte. Ces résultats suggèrent un rôle particulier de ce genre bactérien chez les holobiontes gorgonaires. Ces travaux ont permis d’initier la connaissance du compartiment bactérien des quatre espèces de gorgonaires les plus abondantes dans les habitats côtiers. Les éléments acquis et les différents outils mis au point pourront être intégrés à de nouvelles recherches sur le rôle des associations symbiotiques dans la santé et le devenir des populations de gorgonaires face aux changements environnementaux en cours

Prediction of Cellular Identities from Trajectory and Cell Fate Information

Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative approach to cell identification during early $\textit{C. elegans}$ embryogenesis using machine learning. Cell identification during $\textit{C. elegans}$ embryogenesis would provide insights into neural development with implications for higher organisms including humans. We employed random forest, MLP, and LSTM models, and tested cell classification accuracy on 3D time-lapse confocal datasets spanning the first 4 hours of embryogenesis. By leveraging a small number of spatial-temporal features of individual cells, including cell trajectory and cell fate information, our models achieve an accuracy of over 91%, even with limited data. We also determine the most important feature contributions and can interpret these features in the context of biological knowledge. Our research demonstrates the success of predicting cell identities in time-lapse imaging sequences directly from simple spatio-temporal features

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 metric—the solid-angle uncertainty—to compare the ability of multiview microscopes to estimate the orientation of single dipoles. Next, we compare a broad class of microscopes using this metric—single- 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. </jats:p