Inverse-problem approach for particle digital holography: accurate location based on local optimization

We propose a microparticle localization scheme in digital holography. Most conventional digital holography methods are based on Fresnel transform and present several problems such as twin-image noise, border effects, and other effects. To avoid these difficulties, we propose an inverse-problem approach, which yields the optimal particle set that best models the observed hologram image. We resolve this global optimization problem by conventional particle detection followed by a local refinement for each particle. Results for both simulated and real digital holograms show strong improvement in the localization of the particles, particularly along the depth dimension. In our simulations, the position precision is > or =1 microm rms. Our results also show that the localization precision does not deteriorate for particles near the edge of the field of view.     

Promoting energy-saving behaviour: formal social groups as promising middle actors for municipal interventions

City governments worldwide are trying to motivate their citizens to reduce their energy use—a particular challenge as they try to reach individual households. A promising strategy to engage the public broadly entails collaborating with middle actors to multiply the effects of municipal interventions. Some of these middle actors are formal social groups (e.g. sports clubs and neighbourhood associations). We conducted an online experiment (N = 136) to determine whether such interventions were more effective when they are communicated through formal social groups than when communicated through city governments. Participants received letters containing advice for saving energy in the household. Willingness to participate was higher when the letters came from formal social groups than when they came from a city agency. Furthermore, actual members of formal social groups generally were more willing to participate. Our evidence suggests that formal social groups are promising middle actors for energy conservation campaigns and that city governments should engage more often with these groups to communicate with residents.     

The Study of a 231 French Patient Cohort Significantly Extends the Mutational Spectrum of the Two Major Usher Genes MYO7A and USH2A

Usher syndrome is an autosomal recessive disorder characterized by congenital hearing loss combined with retinitis pigmentosa, and in some cases, vestibular areflexia. Three clinical subtypes are distinguished, and MYO7A and USH2A represent the two major causal genes involved in Usher type I, the most severe form, and type II, the most frequent form, respectively. Massively parallel sequencing was performed on a cohort of patients in the context of a molecular diagnosis to confirm clinical suspicion of Usher syndrome. We report here 231 pathogenic MYO7A and USH2A genotypes identified in 73 Usher type I and 158 Usher type II patients. Furthermore, we present the ACMG classification of the variants, which comprise all types. Among them, 68 have not been previously reported in the literature, including 12 missense and 16 splice variants. We also report a new deep intronic variant in USH2A. Despite the important number of molecular studies published on these two genes, we show that during the course of routine genetic diagnosis, undescribed variants continue to be identified at a high rate. This is particularly pertinent in the current era, where therapeutic strategies based on DNA or RNA technologies are being developed.     

Cigarette Smoke Condensate Exposure Induces Receptor for Advanced Glycation End-Products (RAGE)-Dependent Sterile Inflammation in Amniotic Epithelial Cells

Maternal smoking is a risk factor of preterm prelabor rupture of the fetal membranes (pPROM), which is responsible for 30% of preterm births worldwide. Cigarettes induce oxidative stress and inflammation, mechanisms both implicated in fetal membranes (FM) weakening. We hypothesized that the receptor for advanced glycation end-products (RAGE) and its ligands can result in cigarette-dependent inflammation. FM explants and amniotic epithelial cells (AECs) were treated with cigarette smoke condensate (CSC), combined or not with RAGE antagonist peptide (RAP), an inhibitor of RAGE. Cell suffering was evaluated by measuring lactate dehydrogenase (LDH) medium-release. Extracellular HMGB1 (a RAGE ligand) release by amnion and choriodecidua explants were checked by western blot. NF-κB pathway induction was determined by a luciferase gene reporter assay, and inflammation was evaluated by cytokine RT-qPCR and protein quantification. Gelatinase activity was assessed using a specific assay. CSC induced cell suffering and HMGB1 secretion only in the amnion, which is directly associated with a RAGE-dependent response. CSC also affected AECs by inducing inflammation (cytokine release and NFκB activation) and gelatinase activity through RAGE engagement, which was linked to an increase in extracellular matrix degradation. This RAGE dependent CSC-induced inflammation associated with an increase of gelatinase activity could explain a pathological FM weakening directly linked to pPROM.     

Direct extraction of the mean particle size from a digital hologram

Digital holography, which consists of both acquiring the hologram image in a digital camera and numerically reconstructing the information, offers new and faster ways to make the most of a hologram. We describe a new method to determine the rough size of particles in an in-line hologram. This method relies on a property that is specific to interference patterns in Fresnel holograms: Self-correlation of a hologram provides access to size information. The proposed method is both simple and fast and gives results with acceptable precision. It suppresses all the problems related to the numerical depth of focus when large depth volumes are analyzed.     

A terrestrial biotic ligand model. 1. Development and application to Cu and Ni toxicities to barley root elongation in soils

A Terrestrial Biotic Ligand Model (TBLM) was developed using noncalcareous soils from Europe based on Cu and Ni speciation and barley (Hordeum vulgare cv. Regina) root elongation bioassays. Free metal ion (M2+) activity was computed by the WHAM VI model using inputs of soil metal, soil organic matter, and alkali and alkaline earth metals concentrations, and pH in soil solution. The TBLM assumes that metal in soil and in the solution are in equilibrium. Metal ions react with the biotic ligand, the receptor site, and inhibit root elongation. Other ions, principally H+, Ca2+ and Mg2+, compete with M2+ and, therefore, affect its toxicity. Toxicity is correlated only to the fraction of the total biotic ligand sites occupied by M2+. Compared to other models using either the soil metal concentration or M2+ activity as the toxic dose, the TBLM provides a more consistent method to normalize and compare Cu and Ni toxicities to root elongation among different soils. The TBLM was able to predictthe EC50 soil Cu and Ni concentrations generally within a factor of 2 of the observed values, a level of precision similar to that for the aquatic Biotic Ligand Model, indicating its potential utility in metals risk assessment in soils.     

Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins

Family GH13, also known as the alpha-amylase family, is the largest sequence-based family of glycoside hydrolases and groups together a number of different enzyme activities and substrate specificities acting on alpha-glycosidic bonds. This polyspecificity results in the fact that the simple membership of this family cannot be used for the prediction of gene function based on sequence alone. In order to establish robust groups that show an improved correlation between sequence and enzymatic specificity, we have performed a large-scale analysis of 1691 family GH13 sequences by combining clustering, similarity search and phylogenetic methods. About 80% of the sequences could be reliably classified into 35 subfamilies. Most subfamilies appear monofunctional (i.e. contain enzymes with the same substrate and the same product). The close examination of the other, apparently polyspecific, subfamilies revealed that they actually group together enzymes with strongly related (or even sometimes virtually identical) activities. Overall our subfamily assignment allows to set the limits for genomic function prediction on this large family of biologically and industrially important enzymes.     

Probing cellular traction forces with magnetic nanowires and microfabricated force sensor arrays

In this paper, the use of magnetic nanowires for the study of cellular response to force is demonstrated. High-aspect ratio Ni rods with diameter 300?nm and lengths up to 20?μm were bound to or internalized by pulmonary artery smooth muscle cells (SMCs) cultured on arrays of flexible micropost force sensors. Forces and torques were applied to the cells by driving the nanowires with AC magnetic fields in the frequency range 0.1-10?Hz, and the changes in cellular contractile forces were recorded with the microposts. These local stimulations yield global force reinforcement of the cells' traction forces, but this contractile reinforcement can be effectively suppressed upon addition of a calcium channel blocker, ruthenium red, suggesting the role of calcium channels in the mechanical response. The responsiveness of the SMCs to actuation depends on the frequency of the applied stimulation. These results show that the combination of magnetic nanoparticles and micropatterned, flexible substrates can provide new approaches to the study of cellular mechanotransduction.     

Sputtered tungsten-based ternary and quaternary layers for nanocrystalline diamond deposition

Many of today's demanding applications require thin-film coatings with high hardness, toughness, and thermal stability. In many cases, coating thickness in the range 2-20 microm and low surface roughness are required. Diamond films meet many of the stated requirements, but their crystalline nature leads to a high surface roughness. Nanocrystalline diamond offers a smoother surface, but significant surface modification of the substrate is necessary for successful nanocrystalline diamond deposition and adhesion. A hybrid hard and tough material may be required for either the desired applications, or as a basis for nanocrystalline diamond film growth. One possibility is a composite system based on carbides or nitrides. Many binary carbides and nitrides offer one or more mentioned properties. By combining these binary compounds in a ternary or quaternary nanocrystalline system, we can tailor the material for a desired combination of properties. Here, we describe the results on the structural and mechanical properties of the coating systems composed of tungsten-chromium-carbide and/or nitride. These WC-Cr-(N) coatings are deposited using magnetron sputtering. The growth of adherent nanocrystalline diamond films by microwave plasma chemical vapor deposition has been demonstrated on these coatings. The WC-Cr-(N) and WC-Cr-(N)-NCD coatings are characterized with atomic force microscopy and SEM, X-ray diffraction, X-ray photoelectron spectroscopy, Raman spectroscopy, and nanoindentation.     

Variational algorithms to remove stationary noise: applications to microscopy imaging

A framework and an algorithm are presented in order to remove stationary noise from images. This algorithm is called 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. For example, structured patterns such as stripes appear in the images. The model described here addresses these cases. Applications are presented with images acquired using different modalities: scanning electron microscope, FIB-nanotomography, and an emerging fluorescence microscopy technique called selective plane illumination microscopy.