Mechanical Artifacts in Optical Projection Tomography: Classification and Automatic Calibration

Optical projection tomography (OPT) is a powerful tool for biomedical studies. It achieves 3D visualization of mesoscopic biological samples with high spatial resolution using conventional tomographic-reconstruction algorithms. However, various artifacts degrade the quality of the reconstructed images due to experimental imperfections in the OPT instruments. While many efforts have been made to characterize and correct for these artifacts, they focus on one specific type of artifacts, whereas a comprehensive catalog of all sorts of mechanical artifacts does not currently exist. In this work, we systematically document many mechanical artifacts. We rely on a 3D description of the imaging system that uses a set of angular and translational parameters. We provide a catalog of artifacts. It lists their cause, resulting effects, and existing correction methods. Then, we introduce an automatic calibration algorithm that is able to recover the unknown system parameters fed into the final 3D iterative reconstruction algorithm for a distortion-free volumetric image. Simulations with beads data and experimental results on a fluorescent textile fiber confirm that our algorithm successfully removes miscalibration artifacts in the reconstruction

Long-term monitoring of tropical moist forest extent (from 1990 to 2019): Description of the dataset

The need for accurate information on the state and evolution of tropical forest types at regional and continental scales is widely recognized, particularly to analyze the forest diversity and dynamics, to assess degradation and deforestation processes and to better manage these natural resources. Here we document the approach that was developed by JRC to map and monitor the extent of moist tropical forests and their changes (degradation, deforestation and regrowth) over the last three decades (1990-2020) at fine spatial resolution (30 m × 30 m). The approach is based on the analysis of each valid observation from the Landsat archive and allows to capture disturbances with a short-duration appearance on satellite imagery such as selective logging, fires, and severe weather events (hurricanes, dryness). This new approach allows characterizing the sequential dynamics of forest cover changes by providing transition stages from the initial observation period to the most recent year (2019 for this report). For the first time at the pantropical scale the occurrence and extent of forest degradation can be documented on an annual basis in addition to the monitoring of deforestation. After a short introduction (chapter 1), this technical report describes the study area (chapter 2), the input data (chapter 3), the method that has been developed (chapter 4), and the outcomes of this study (chapter 5). A discussion is also provided regarding the specificities and added value of the outcomes (chapter 6), and the known limitations and future expected improvements (chapter 7). This new pan-tropical scale deforestation and forest degradation monitoring system will contribute to the EU Observatory on deforestation, forest degradation, changes in the world’s forest cover, and associated drivers, which is an action being implemented in the framework of the Communication from the Commission to step up EU action to protect and restore the World’s forests (COM(2019) 352).JRC.D.1-Bio-econom

AP4 deficiency: A novel form of neurodegeneration with brain iron accumulation?

OBJECTIVE: To describe the clinico-radiological phenotype of 3 patients harboring a homozygous novel AP4M1 pathogenic mutation. METHODS: The 3 patients from an inbred family who exhibited early-onset developmental delay, tetraparesis, juvenile motor function deterioration, and intellectual deficiency were investigated by magnetic brain imaging using T1-weighted, T2-weighted, T2*-weighted, fluid-attenuated inversion recovery, susceptibility weighted imaging (SWI) sequences. Whole-exome sequencing was performed on the 3 patients. RESULTS: In the 3 patients, brain imaging identified the same pattern of bilateral SWI hyposignal of the globus pallidus, concordant with iron accumulation. A novel homozygous nonsense mutation was identified in AP4M1, segregating with the disease and leading to truncation of half of the adap domain of the protein. CONCLUSIONS: Our results suggest that AP4M1 represents a new candidate gene that should be considered in the neurodegeneration with brain iron accumulation (NBIA) spectrum of disorders and highlight the intersections between hereditary spastic paraplegia and NBIA clinical presentations

The Athena X-ray Integral Field Unit: a consolidated design for the system requirement review of the preliminary definition phase

The Athena X-ray Integral Unit (X-IFU) is the high resolution X-ray spectrometer, studied since 2015 for flying in the mid-30s on the Athena space X-ray Observatory, a versatile observatory designed to address the Hot and Energetic Universe science theme, selected in November 2013 by the Survey Science Committee. Based on a large format array of Transition Edge Sensors (TES), it aims to provide spatially resolved X-ray spectroscopy, with a spectral resolution of 2.5 eV (up to 7 keV) over an hexagonal field of view of 5 arc minutes (equivalent diameter). The X-IFU entered its System Requirement Review (SRR) in June 2022, at about the same time when ESA called for an overall X-IFU redesign (including the X-IFU cryostat and the cooling chain), due to an unanticipated cost overrun of Athena. In this paper, after illustrating the breakthrough capabilities of the X-IFU, we describe the instrument as presented at its SRR, browsing through all the subsystems and associated requirements. We then show the instrument budgets, with a particular emphasis on the anticipated budgets of some of its key performance parameters. Finally we briefly discuss on the ongoing key technology demonstration activities, the calibration and the activities foreseen in the X-IFU Instrument Science Center, and touch on communication and outreach activities, the consortium organisation, and finally on the life cycle assessment of X-IFU aiming at minimising the environmental footprint, associated with the development of the instrument. Thanks to the studies conducted so far on X-IFU, it is expected that along the design-to-cost exercise requested by ESA, the X-IFU will maintain flagship capabilities in spatially resolved high resolution X-ray spectroscopy, enabling most of the original X-IFU related scientific objectives of the Athena mission to be retained. (abridged).Comment: 48 pages, 29 figures, Accepted for publication in Experimental Astronomy with minor editin

Implementation d'un algorithme de reduction de taille des reseaux de neurones

This document describes the implementation of a neuron pruning method with pyTorch, and analyzes the results obtained by applying this method on convolutional and residual networks. The performance of the algorithm is measured in different test cases and with varying parameters

An End-to-End Networks to Synthetize Intonation using a Generalized Command Response Model

The generalized command response (GCR) model represents intonation as a superposition of muscle responses to spike command signals. We have previously shown that the spikes can be predicted by a two-stage system, consisting of a recurrent neural network and a post-processing procedure, but the responses themselves were fixed dictionary atoms. We propose an end-to-end neural architecture that replaces the dictionary atoms with trainable second-order recurrent elements analogous to recursive filters. We demonstrate gradient stability under modest conditions, and show that the system can be trained by imposing temporal sparsity constraints. Subjective listening tests demonstrate that the system can synthesize intonation with high naturalness, comparable to state-of-the-art acoustic models, and retains the physiological plausibility of the GCR model

APP Mutations in Cerebral Amyloid Angiopathy with or without Cortical Calcifications: Report of Three Families and a Literature Review

International audienceBACKGROUND: Specific APP mutations cause cerebral amyloid angiopathy (CAA) with or without Alzheimer's disease (AD). OBJECTIVE: We aimed at reporting APP mutations associated with CAA, describe the clinical, cerebrospinal fluid AD biomarkers, and neuroimaging features, and compare them with the data from the literature. METHODS: We performed a retrospective study in two French genetics laboratories by gathering all clinical and neuroimaging data from patients referred for a genetic diagnosis of CAA with an age of onset before 66 years and fulfilling the other Boston revised criteria. We studied the segregation of mutations in families and performed a comprehensive literature review of all cases reported with the same APP mutation. RESULTS: We screened APP in 61 unrelated French patients. Three mutations, located in the Aβ coding region, were detected in five patients from three families: p.Ala692Gly (Flemish), p.Glu693Lys (Italian), and p.Asp694Asn (Iowa). Patients exhibited CAA and progressive cognitive impairment associated with cortical calcifications in the Iowa and Italian mutation carriers, but not the patient carrying the Flemish mutation. CONCLUSIONS: This is the first evidence of cortical calcification in patients with an APP mutation other than the Iowa mutation. We discuss the radiological, cerebrospinal fluid, and clinical phenotype of patients carrying these mutations in the literature

Speech Biomarkers in Rapid Eye Movement Sleep Behavior Disorder and Parkinson Disease.

International audienceObjective: This multilanguage study used simple speech recording and high-end pattern analysis to provide sensitive and reliable noninvasive biomarkers of prodromal versus manifest α-synucleinopathy in patients with idiopathic rapid eye movement sleep behavior disorder (iRBD) and early-stage Parkinson disease (PD).Methods: We performed a multicenter study across the Czech, English, German, French, and Italian languages at 7 centers in Europe and North America. A total of 448 participants (337 males), including 150 with iRBD (mean duration of iRBD across language groups 0.5-3.4 years), 149 with PD (mean duration of disease across language groups 1.7-2.5 years), and 149 healthy controls were recorded; 350 of the participants completed the 12-month follow-up. We developed a fully automated acoustic quantitative assessment approach for the 7 distinctive patterns of hypokinetic dysarthria.Results: No differences in language that impacted clinical parkinsonian phenotypes were found. Compared with the controls, we found significant abnormalities of an overall acoustic speech severity measure via composite dysarthria index for both iRBD (p = 0.002) and PD (p < 0.001). However, only PD (p < 0.001) was perceptually distinct in a blinded subjective analysis. We found significant group differences between PD and controls for monopitch (p < 0.001), prolonged pauses (p < 0.001), and imprecise consonants (p = 0.03); only monopitch was able to differentiate iRBD patients from controls (p = 0.004). At the 12-month follow-up, a slight progression of overall acoustic speech impairment was noted for the iRBD (p = 0.04) and PD (p = 0.03) groups.Interpretation: Automated speech analysis might provide a useful additional biomarker of parkinsonism for the assessment of disease progression and therapeutic interventions. ANN NEUROL 2021;90:62-75