Variational algorithms to remove stationary noise. Application to microscopy imaging.

International audienceA framework and an algorithm are presented in order to remove stationary noise from images. This algorithm is called VSNR (Variational Stationary Noise Remover). It can be interpreted both as a restoration method in a Bayesian framework and as a cartoon+texture decomposition method. In numerous denoising applications the white noise assumption fails: structured patterns (e.g. stripes) appear in the images. The model described here addresses these cases. Applications are presented with images acquired using different modalities: scan- ning electron microscope, FIB-nanotomography, and an emerging fluorescence microscopy technique called SPIM (Selective Plane Illumination Microscope)

High-resolution in-depth imaging of optically cleared thick samples using an adaptive SPIM

Today, Light Sheet Fluorescence Microscopy (LSFM) makes it possible to image fluorescent samples through depths of several hundreds of microns. However, LSFM also suffers from scattering, absorption and optical aberrations. Spatial variations in the refractive index inside the samples cause major changes to the light path resulting in loss of signal and contrast in the deepest regions, thus impairing in-depth imaging capability. These effects are particularly marked when inhomogeneous, complex biological samples are under study. Recently, chemical treatments have been developed to render a sample transparent by homogenizing its refractive index (RI), consequently enabling a reduction of scattering phenomena and a simplification of optical aberration patterns. One drawback of these methods is that the resulting RI of cleared samples does not match the working RI medium generally used for LSFM lenses. This RI mismatch leads to the presence of low-order aberrations and therefore to a significant degradation of image quality. In this paper, we introduce an original optical-chemical combined method based on an adaptive SPIM and a water-based clearing protocol enabling compensation for aberrations arising from RI mismatches induced by optical clearing methods and acquisition of high-resolution in-depth images of optically cleared complex thick samples such as Multi-Cellular Tumour Spheroids

Deep and Clear Optical Imaging of Thick Inhomogeneous Samples

Inhomogeneity in thick biological specimens results in poor imaging by light microscopy, which deteriorates as the focal plane moves deeper into the specimen. Here, we have combined selective plane illumination microscopy (SPIM) with wavefront sensor adaptive optics (wao). Our waoSPIM is based on a direct wavefront measure using a Hartmann-Shack wavefront sensor and fluorescent beads as point source emitters. We demonstrate the use of this waoSPIM method to correct distortions in three-dimensional biological imaging and to improve the quality of images from deep within thick inhomogeneous samples

Live cell division dynamics monitoring in 3D large spheroid tumor models using light sheet microscopy

<p>Abstract</p> <p>Background</p> <p>Multicellular tumor spheroids are models of increasing interest for cancer and cell biology studies. They allow considering cellular interactions in exploring cell cycle and cell division mechanisms. However, 3D imaging of cell division in living spheroids is technically challenging and has never been reported.</p> <p>Results</p> <p>Here, we report a major breakthrough based on the engineering of multicellular tumor spheroids expressing an histone H2B fluorescent nuclear reporter protein, and specifically designed sample holders to monitor live cell division dynamics in 3D large spheroids using an home-made selective-plane illumination microscope.</p> <p>Conclusions</p> <p>As illustrated using the antimitotic drug, paclitaxel, this technological advance paves the way for studies of the dynamics of cell divion processes in 3D and more generally for the investigation of tumor cell population biology in integrated system as the spheroid model.</p

Valorization of wine industry by-products: Characterization of phenolic profile and investigation of potential healthy properties

In the last years, the importance of food waste management and recovery is emphasized by the international guidelines to promote a circular economy approach. Wine industry is one of the sectors with the highest waste production, with a potential negative environmental impact. Winemaking by-products are mainly used to produce distillates, fertilizers and livestock feed, but alternative approaches for their management could be the formulation of healthy products. The aim of this study was the application of in vitro methods for a preliminary evaluation of the phenolic pattern and the associated biological properties of winemaking by-products from different red grape varieties. The methods were: 1) Folin-Cocalteau's assay for the assessment of total polyphenol content; 2) the vanillin assay for the quantification of total procyanidin content; 3) the pH differential method for the determination of total anthocyanin content; 4) DPPH and FRAP assays for the measurement of total antioxidant activity; 4) High Performance Thin Layer Chromatography for separation of phenolic substances and assessment of their antioxidant capacity; 5) dipeptidyl peptidase (DPPIV) inhibition assay to evaluate possible effects on glucose homeostasis. The results showed that grape pomace, particularly when including seeds, was a valuable source of polyphenols with significant antioxidant potential and promising activity on DPPIV, supporting its use in formulating healthy foods/food supplements

The 20 years of PROSITE

PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. In this article, we describe the implementation of a new method to assign a status to pattern matches, the new PROSITE web page and a new approach to improve the specificity and sensitivity of PROSITE methods. The latest version of PROSITE (release 20.19 of 11 September 2007) contains 1319 patterns, 745 profiles and 764 ProRules. Over the past 2 years, about 200 domains have been added, and now 53% of UniProtKB/Swiss-Prot entries (release 54.2 of 11 September 2007) have a PROSITE match. PROSITE is available on the web at: http://www.expasy.org/prosit

The 20 years of PROSITE

PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. In this article, we describe the implementation of a new method to assign a status to pattern matches, the new PROSITE web page and a new approach to improve the specificity and sensitivity of PROSITE methods. The latest version of PROSITE (release 20.19 of 11 September 2007) contains 1319 patterns, 745 profiles and 764 ProRules. Over the past 2 years, about 200 domains have been added, and now 53% of UniProtKB/Swiss-Prot entries (release 54.2 of 11 September 2007) have a PROSITE match. PROSITE is available on the web at: http://www.expasy.org/prosite/

Neurodegeneration-associated proteins in human olfactory neurons collected by nasal brushing

The olfactory neuroepithelium is located in the upper vault of the nasal cavity, lying on the olfactory cleft and projecting into the dorsal portion of the superior and middle turbinates beyond the mid-portion of the nasal septum. It is composed of a variety of cell types including olfactory sensory neurons, supporting glial-like cells, microvillar cells, and basal stem cells. The cells of the neuroepithelium are often intermingled with respiratory and metaplastic epithelial cells. Olfactory neurons undergo a constant self-renewal in the timespan of 2\u20133 months; they are directly exposed to the external environment, and thus they are vulnerable to physical and chemical injuries. The latter might induce metabolic perturbations and ultimately be the cause of cell death. However, the lifespan of olfactory neurons is biologically programmed, and for this reason, these cells have an accelerated metabolic cycle leading to an irreversible apoptosis. These characteristics make these cells suitable for research related to nerve cell degeneration and aging. Recent studies have shown that a non-invasive and painless olfactory brushing procedure allows an efficient sampling from the olfactory neuroepithelium. This approach allows to detect the pathologic prion protein in patients with sporadic Creutzfeldt\u2013Jakob disease, using the real-time quaking-induced conversion assay. Investigating the expression of all the proteins associated to neurodegeneration in the cells of the olfactory mucosa is a novel approach toward understanding the pathogenesis of human neurodegenerative diseases. Our aim was to investigate the expression of \u3b1-synuclein, \u3b2-amyloid, tau, and TDP-43 in the olfactory neurons of normal subjects. We showed that these proteins that are involved in neurodegenerative diseases are expressed in olfactory neurons. These findings raise the question on whether a relationship exists between the mechanisms of protein aggregation that occur in the olfactory bulb during the early stage of the neurodegenerative process and the protein misfolding occurring in the olfactory neuroepithelium

Spatial extent and ecotoxicological risk assessment of a micropollutant-contaminated wastewater plume in Lake Geneva

In this study, the spatial extent of a wastewater-influenced water mass (plume) originating from a wastewater treatment plant outlet in Vidy Bay (Lake Geneva) was monitored by two manned submersibles from June to August 2011. The main goal was to assess whether micropollutants in the wastewater mass cause an ecotoxicological risk to the aquatic environment, and to determine how far the zone of risk extends beyond the wastewater outlet. Real-time measurements of elevated electrical conductivity were used as a proxy to indicate the presence of wastewater-influenced water. Conductivity was highest in immediate proximity to the wastewater outlet, though if all measurements obtained over the duration of the sampling campaign were integrated, elevated conductivity extended over an area of at least 1km2 surrounding the outlet. Additionally, water samples were collected within and outside Vidy Bay, and were analyzed for 39 micropollutants (pharmaceuticals, pesticides, and corrosion inhibitors). Micropollutant concentrations were generally in the low ng/L range, though for some substances >100ng/L was measured. The concentrations of most pharmaceuticals, which are primarily wastewater-derived, decreased with decreasing conductivity and with increasing distance from the wastewater outlet. Pesticide concentrations, in contrast, were homogeneous throughout Vidy Bay and the lake. An ecotoxicological risk assessment based on the cumulative risk exerted by all measured substances indicated that the wastewater caused a zone of potential ecotoxicological risk that extended well into the deep lake and in the direction of a downstream drinking water intake

Simulation of an SEIR infectious disease model on the dynamic contact network of conference attendees

The spread of infectious diseases crucially depends on the pattern of contacts among individuals. Knowledge of these patterns is thus essential to inform models and computational efforts. Few empirical studies are however available that provide estimates of the number and duration of contacts among social groups. Moreover, their space and time resolution are limited, so that data is not explicit at the person-to-person level, and the dynamical aspect of the contacts is disregarded. Here, we want to assess the role of data-driven dynamic contact patterns among individuals, and in particular of their temporal aspects, in shaping the spread of a simulated epidemic in the population. We consider high resolution data of face-to-face interactions between the attendees of a conference, obtained from the deployment of an infrastructure based on Radio Frequency Identification (RFID) devices that assess mutual face-to-face proximity. The spread of epidemics along these interactions is simulated through an SEIR model, using both the dynamical network of contacts defined by the collected data, and two aggregated versions of such network, in order to assess the role of the data temporal aspects. We show that, on the timescales considered, an aggregated network taking into account the daily duration of contacts is a good approximation to the full resolution network, whereas a homogeneous representation which retains only the topology of the contact network fails in reproducing the size of the epidemic. These results have important implications in understanding the level of detail needed to correctly inform computational models for the study and management of real epidemics