IVUS-based histology of atherosclerotic plaques: improving longitudinal resolution

Although Virtual Histology (VH) is the in-vivo gold standard for atherosclerosis plaque characterization in IVUS images, it suffers from a poor longitudinal resolution due to ECG-gating. In this paper, we propose an image- based approach to overcome this limitation. Since each tissue have different echogenic characteristics, they show in IVUS images different local frequency components. By using Redundant Wavelet Packet Transform (RWPT), IVUS images are decomposed in multiple sub-band images. To encode the textural statistics of each resulting image, run-length features are extracted from the neighborhood centered on each pixel. To provide the best discrimination power according to these features, relevant sub-bands are selected by using Local Discriminant Bases (LDB) algorithm in combination with Fisher’s criterion. A structure of weighted multi-class SVM permits the classification of the extracted feature vectors into three tissue classes, namely fibro-fatty, necrotic core and dense calcified tissues. Results shows the superiority of our approach with an overall accuracy of 72% in comparison to methods based on Local Binary Pattern and Co-occurrence, which respectively give accuracy rates of 70% and 71%

On theta functions of order four

We prove that the fourth powers of theta functions with even characteristics form a basis of the space of even theta functions of order four on a principally polarized Abelian variety without vanishing theta-null.Comment: 6 pages, minor changes, references adde

3D Anisotropic Hybrid Network: Transferring Convolutional Features from 2D Images to 3D Anisotropic Volumes

While deep convolutional neural networks (CNN) have been successfully applied for 2D image analysis, it is still challenging to apply them to 3D anisotropic volumes, especially when the within-slice resolution is much higher than the between-slice resolution and when the amount of 3D volumes is relatively small. On one hand, direct learning of CNN with 3D convolution kernels suffers from the lack of data and likely ends up with poor generalization; insufficient GPU memory limits the model size or representational power. On the other hand, applying 2D CNN with generalizable features to 2D slices ignores between-slice information. Coupling 2D network with LSTM to further handle the between-slice information is not optimal due to the difficulty in LSTM learning. To overcome the above challenges, we propose a 3D Anisotropic Hybrid Network (AH-Net) that transfers convolutional features learned from 2D images to 3D anisotropic volumes. Such a transfer inherits the desired strong generalization capability for within-slice information while naturally exploiting between-slice information for more effective modelling. The focal loss is further utilized for more effective end-to-end learning. We experiment with the proposed 3D AH-Net on two different medical image analysis tasks, namely lesion detection from a Digital Breast Tomosynthesis volume, and liver and liver tumor segmentation from a Computed Tomography volume and obtain the state-of-the-art results

Standardized spectral and radiometric calibration of consumer cameras

Consumer cameras, particularly onboard smartphones and UAVs, are now commonly used as scientific instruments. However, their data processing pipelines are not optimized for quantitative radiometry and their calibration is more complex than that of scientific cameras. The lack of a standardized calibration methodology limits the interoperability between devices and, in the ever-changing market, ultimately the lifespan of projects using them. We present a standardized methodology and database (SPECTACLE) for spectral and radiometric calibrations of consumer cameras, including linearity, bias variations, read-out noise, dark current, ISO speed and gain, flat-field, and RGB spectral response. This includes golden standard ground-truth methods and do-it-yourself methods suitable for non-experts. Applying this methodology to seven popular cameras, we found high linearity in RAW but not JPEG data, inter-pixel gain variations >400% correlated with large-scale bias and read-out noise patterns, non-trivial ISO speed normalization functions, flat-field correction factors varying by up to 2.79 over the field of view, and both similarities and differences in spectral response. Moreover, these results differed wildly between camera models, highlighting the importance of standardization and a centralized database

Quantitative nanoscale imaging using transmission He ion channelling contrast: Proof-of-concept and application to study isolated crystalline defects

A newly developed microscope prototype, namely npSCOPE, consisting of a Gas Field Ion Source (GFIS) column and a position sensitive Delay-line Detector (DLD) was used to perform Scanning Transmission Ion Microscopy (STIM) using keV He+ ions. One experiment used 25 keV ions and a second experiment used 30 keV ions. STIM imaging of a 50 nm thick free-standing gold membrane exhibited excellent contrast due to ion channelling and revealed rich microstructural features including isolated nanoscale twin bands which matched well with the contrast in the conventional ion-induced Secondary Electron (SE) imaging mode. Transmission Kikuchi Diffraction (TKD) and Backscattered Electron (BSE) imaging were performed on the same areas to correlate and confirm the microstructural features observed in STIM. Monte Carlo simulations of the ion and electron trajectories were performed with parameters similar to the experimental conditions to derive insights related to beam broadening and its effect in the degradation of transmission image resolution. For the experimental conditions used, STIM imaging showed a lateral resolution close to30 nm. Dark twin bands in bright grains as well as bright twin bands in dark grains were observed in STIM. Some of the twin bands were invisible in STIM. For the specific experimental conditions used, the ion transmission efficiency across a particular twin band was found to decrease by a factor of 2.8. Surprisingly, some grains showed contrast reversal when the Field of View (FOV) was changed indicating the sensitivity of the channelling contrast to even small changes in illumination conditions. These observations are discussed using ion channelling conditions and crystallographic orientations of the grains and twin bands. This study demonstrates for the first time the potential of STIM imaging using keV He+ ions to quantitatively investigate channelling in nanoscale structures including isolated crystalline defects

Miscellanea Herpetologica Gabonica XVI

peer reviewe

La vie entre quatre murs : travail et sociabilité en temps de confinement

Jusqu’à quel point le Covid-19 perturbe-t-il notre vie de tous les jours ? Comment la population française vit-elle le confinement ? Dans quelles mesures les inégalités sociales sont-elles exacerbées et la cohésion sociale menacée ? Le projet CoCo apporte des éléments de réponse à ces questions d’actualité en compa­rant les conditions de vie en France avant et après le blocage. Il s’agit du troisième rapport préliminaire de la série que nous publierons dans les prochaines semaines. Nous analysons ici la façon dont la société française a fait face aux 6 premières semaines de confinement, notamment en ce qui concerne les changements de conditions de travail et de vie sociale. Nous continuons à surveiller les éléments de santé et de bien-être autodéclarés comme dans les 2 précédents numéros

Randomizing genome-scale metabolic networks

Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the network is not statistically different from expected in a motivated ensemble. However, when dealing with metabolic networks, the randomization of the network using edge exchange generates fictitious reactions that are biochemically meaningless. Here we provide several natural ensembles of randomized metabolic networks. A first constraint is to use valid biochemical reactions. Further constraints correspond to imposing appropriate functional constraints. We explain how to perform these randomizations with the help of Markov Chain Monte Carlo (MCMC) and show that they allow one to approach the properties of biological metabolic networks. The implication of the present work is that the observed global structural properties of real metabolic networks are likely to be the consequence of simple biochemical and functional constraints.Comment: 30 Pages, 6 Main Figures, 6 Supplementary Figures, 1 Supplementary Tabl

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements