Simultaneous segmentation and grading of anatomical structures for patient's classification: application to Alzheimer's Disease

Data used in the preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database (www.loni.ucla.edu/ADNI).In this paper, we propose an innovative approach to robustly and accurately detect Alzheimer's disease (AD) based on the distinction of specific atrophic patterns of anatomical structures such as hippocampus (HC) and entorhinal cortex (EC). The proposed method simultaneously performs segmentation and grading of structures to efficiently capture the anatomical alterations caused by AD. Known as SNIPE (Scoring by Non-local Image Patch Estimator), the novel proposed grading measure is based on a nonlocal patch-based frame-work and estimates the similarity of the patch surrounding the voxel under study with all the patches present in different training populations. In this study, the training library was composed of two populations: 50 cognitively normal subjects (CN) and 50 patients with AD, randomly selected from the ADNI database. During our experiments, the classification accuracy of patients (CN vs. AD) using several biomarkers was compared: HC and EC volumes, the grade of these structures and finally the combination of their volume and their grade. Tests were completed in a leave-one-out framework using discriminant analysis. First, we showed that biomarkers based on HC provide better classification accuracy than biomarkers based on EC. Second, we demonstrated that structure grading is a more powerful measure than structure volume to distinguish both populations with a classification accuracy of 90%. Finally, by adding the ages of subjects in order to better separate age-related structural changes from disease-related anatomical alterations, SNIPE obtained a classification accuracy of 93%Data collection and sharing for this project were funded by the Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904). ADNI is funded by the National Insti- tute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: Abbott, AstraZeneca AB, Bayer Schering Pharma AG, Bristol-Myers Squibb, Eisai Global Clinical Development, Elan Corporation, Genentech, GE Healthcare, GlaxoSmithKline, Innogenetics, Johnson and Johnson, Eli Lilly and Co., Medpace, Inc., Merck and Co., Inc., Novartis AG, Pfizer Inc, F. Hoffman-La Roche, Schering-Plough, Synarc, Inc., as well as non-profit partners the Alzheimer's Association and Alzheimer's Drug Discovery Foundation, with participation from the U.S. Food and Drug Administration. Private sector contributions to ADNI are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimer's Disease Cooperative Study at the University of California, San Diego. ADNI data are disseminated by the Laboratory for Neuro Imaging at the University of California, Los Angeles. This research was also supported by NIH grants P30AG010129, K01 AG030514, and the Dana Foundation.Coupé, P.; Eskildsen, SF.; Manjón Herrera, JV.; Fonov, VS.; Collins, DL.; Alzheimer's Dis Neuroimaging (2012). Simultaneous segmentation and grading of anatomical structures for patient's classification: application to Alzheimer's Disease. NeuroImage. 59(4):3736-3747. https://doi.org/10.1016/j.neuroimage.2011.10.080S3736374759

Probing neutron-hidden neutron transitions with the MURMUR experiment

MURMUR is a new passing-through-walls neutron experiment designed to constrain neutron/hidden neutron transitions allowed in the context of braneworld scenarios or mirror matter models. A nuclear reactor can act as a hidden neutron source, such that neutrons travel through a hidden world or sector. Hidden neutrons can propagate out of the nuclear core and far beyond the biological shielding. However, hidden neutrons can weakly interact with usual matter, making possible for their detection in the context of low-noise measurements. In the present work, the novelty rests on a better background discrimination and the use of a mass of a material - here lead - able to enhance regeneration of hidden neutrons into visible ones to improve detection. The input of this new setup is studied using both modelizations and experiments, thanks to tests currently performed with the experiment at the BR2 research nuclear reactor (SCK$\cdot$CEN, Mol, Belgium). A new limit on the neutron swapping probability p has been derived thanks to the measurements taken during the BR2 Cycle 02/2019A: $p < 4.0 \ \times 10^{-10}$ at 95% CL. This constraint is better than the bound from the previous passing-through-wall neutron experiment made at ILL in 2015, despite BR2 is less efficient to generate hidden neutrons by a factor 7.4, thus raising the interest of such experiment using regenerating materials.Comment: 15 pages, 8 figures, final version, accepted for publication in European Physical Journal

X-ray He-like ions diagnostics: New Computations for Photoionized Plasmas: I. preliminary considerations

Using the new version of the photoionization code Titan designed for plane-parallel photoionized thick hot media, which is unprecedented from the point of view of line transfer, we have undertaken a study of the influence of different parameters on the He-like and H-like emission of a medium photoionized by an X-ray source. We explain why in modelling the emitting medium it is important to solve in a self-consistent way the thermal and ionization equilibria and to take into account the interconnection between the different ions. We give the equivalent widths of the sum of the He-like triplets and the triplet intensity ratios $G$ and $R$, for the most important He-like ions, for a range of density, column density, and ionization parameter, in the case of constant density media. We show that the line intensities from a given ion can be accounted for, either by small values of both the column density and of the ionization parameter, or by large values of both quantities, and it is necessary to take into account several ions to disentangle these possibilities. We show also that a "pure recombination spectrum" almost never exists in a photoionized medium: either it is thin, and resonance lines are formed by radiative excitation, or it is thick, and free-bound absorption destroys the resonance photons as they undergo resonant diffusion.Comment: 19 pages, 14 figures, accepted in A &

Carbon and greenhouse gas balances in an age sequence of temperate pine plantations

© Author(s) 2014. This study investigated differences in the magnitude and partitioning of the carbon (C) and greenhouse gas (GHG) balances in an age sequence of four white pine (Pinus strobus L.) afforestation stands (7, 20, 35 and 70 years old as of 2009) in southern Ontario, Canada. The 4-year (2004-2008) mean annual carbon dioxide (CO2) exchanges, based on biometric and eddy covariance data, were combined with the 2-year means of static chamber measurements of methane (CH4) and nitrous oxide (N2O) fluxes (2006-2007) and dissolved organic carbon (DOC) export below 1 m soil depth (2004-2005). The total ecosystem C pool increased with age from 46 to 197 t C ha-1 across the four stands. Rates of organic matter cycling (i.e. litterfall and decomposition) were similar among the three older stands. In contrast, considerable differences related to stand age and site quality were observed in the magnitude and partitioning of individual CO2 fluxes, showing a peak in production and respiration rates in the middle-age (20-year-old) stand growing on fertile post-agricultural soil. The DOC export accounted for 10% of net ecosystem production (NEP) at the 7-year-old stand but <2% at the three older stands. The GHG balance from the combined exchanges of CO2, CH4 and N2O was 2.6, 21.6, 13.5 and 4.8 t CO2 equivalent ha-1 yearg-1 for the 7-, 20-, 35- and 70-year-old stands, respectively. The maximum annual contribution from the combined exchanges of CH4 and N2O to the GHG balance was 13 and 8% in the 7- and 70-year-old stands, respectively, but <1% in the two highly productive middle-age (20- and 35-year-old) stands. Averaged over the entire age sequence, the CO2 exchange was the main driver of the GHG balance in these forests. The cumulative CO2 sequestration over the 70 years was estimated at 129 t C and 297 t C ha-1 yearg-1 for stands growing on low- and high-productivity sites, respectively. This study highlights the importance of accounting for age and site quality effects on forest C and GHG balances. It further demonstrates a large potential for net C sequestration and climate benefits gained through afforestation of marginal agricultural and fallow lands in temperate regions

Mixed-Model Noise Removal in 3D MRI via Rotation-and-Scale Invariant Non-Local Means

Mixed noise is a major issue influencing quantitative analysis in different forms of magnetic resonance image (MRI), such as T1 and diffusion image like DWI and DTI. Using different filters sequentially to remove mixed noise will severely deteriorate such medical images. We present a novel algorithm called rotation-and-scale invariant nonlocal means filter (RSNLM) to simultaneously remove mixed noise from different kinds of three-dimensional (3D) MRI images. First, we design a new similarity weights, including rank-ordered absolute difference (ROAD), coming from a trilateral filter (TriF) that is obtained to detect the mixed and high-level noise. Then, we present a shape view to consider the MRI data as a 3D operator, with which the similarity between the patches is calculated with the rigid transformation. The translation, rotation and scale have no influence on the similarity. Finally, the adaptive parameter estimation method of ROAD is illustrated, and the effective proof that validates the proposed algorithm is presented. Experiments using synthetic data with impulse noise, Rician noise, and the real MRI data confirm that the proposed method yields superior performance compared with current state-of-the-art methods

SoLid : Search for Oscillations with Lithium-6 Detector at the SCK-CEN BR2 reactor

Sterile neutrinos have been considered as a possible explanation for the recent reactor and Gallium anomalies arising from reanalysis of reactor flux and calibration data of previous neutrino experiments. A way to test this hypothesis is to look for distortions of the anti-neutrino energy caused by oscillation from active to sterile neutrino at close stand-off (similar to 6-8m) of a compact reactor core. Due to the low rate of anti-neutrino interactions the main challenge in such measurement is to control the high level of gamma rays and neutron background. The SoLid experiment is a proposal to search for active-to-sterile anti-neutrino oscillation at very short baseline of the SCK center dot CEN BR2 research reactor. This experiment uses a novel approach to detect anti-neutrino with a highly segmented detector based on Lithium-6. With the combination of high granularity, high neutron-gamma discrimination using 6LiF:ZnS(Ag) and precise localization of the Inverse Beta Decay products, a better experimental sensitivity can be achieved compared to other state-of-the-art technology. This compact system requires minimum passive shielding allowing for very close stand off to the reactor. The experimental set up of the SoLid experiment and the BR2 reactor will be presented. The new principle of neutrino detection and the detector design with expected performance will be described. The expected sensitivity to new oscillations of the SoLid detector as well as the first measurements made with the 8 kg prototype detector deployed at the BR2 reactor in 2013-2014 will be reported

Evolution of the X-ray spectrum in the flare model of Active Galactic Nuclei

Nayakshin & Kazanas (2002) have considered the time-dependent illumination of an accretion disc in Active Galactic Nuclei, in the lamppost model. We extend their study to the flare model, which postulates the release of a large X-ray flux above a small region of the accretion disc. A fundamental difference with the lamppost model is that the region of the disc below the flare is not illuminated before the onset of the flare. A few test models show that the spectrum which follows immediately the increase in continuum flux should display the characteristics of a highly illuminated but dense gas, i.e. very intense X-ray emission lines and ionization edges in the soft X-ray range. The behaviour of the iron line is different in the case of a "moderate" and a ``strong'' flare: for a moderate flare, the spectrum displays a neutral component of the Fe K$\alpha$ line at 6.4 keV, gradually leading to more highly ionized lines. For a strong flare, the lines are already emitted by FeXXV (around 6.7 keV) after the onset, and have an equivalent width of several hundreds of eV. We find that the observed correlations between $R$, $\Gamma$, and the X-ray flux, are well accounted by a combination of flares having not achieved pressure equilibrium, strongly suggesting that the observed spectrum is dominated by regions in non-pressure equilibrium, typical of the onset of the flares. Finally a flare being confined to a small region of the disc, the spectral lines should be narrow (except for a weak Compton broadening), Doppler shifted, and moving.Comment: 14 pages, 13 figures, accepted in A & A, english corrected versio

Image guidance in neurosurgical procedures, the "Visages" point of view.

This paper gives an overview of the evolution of clinical neuroinformatics in the domain of neurosurgery. It shows how image guided neurosurgery (IGNS) is evolving according to the integration of new imaging modalities before, during and after the surgical procedure and how this acts as the premise of the Operative Room of the future. These different issues, as addressed by the VisAGeS INRIA/INSERM U746 research team (http://www.irisa.fr/visages), are presented and discussed in order to exhibit the benefits of an integrated work between physicians (radiologists, neurologists and neurosurgeons) and computer scientists to give adequate answers toward a more effective use of images in IGNS