Reconstruction of randomly and partially sampled STEM spectrum-images

Scanning transmission electron microscopy (STEM) offers the ability to acquire several single- and multi-channels signals generated simultaneously for each probe position: cathodoluminescence (CL), electron energy loss spectroscopy (EELS) and high-angle annular dark-field imaging (HAADF). However, in some cases, sensitive samples (e.g., biological samples or molecular structures) may suffer from irradiation damages during acquisition. As a consequence, it is often necessary to reduce probe current or dwell time, which could significantly lower the signal-to-noise ratio. Another approach consists in acquiring only a subset of pixels randomly chosen in a given region of interest. This particular experimental set-up has been implemented on the STEM VG HB501 (LPS, Orsay, France), with the beam following a predetermined random path. The reconstruction of HAADF images is then straightforward with well known algorithms. However, when reconstructing the associated spectrum image, the high number of energy bands makes the problem computationally expensive

Dopamine and Serotonin Are Both Required for Mate-Copying in Drosophila melanogaster

Mate-copying is a form of social learning in which the mate-choice decision of an individual (often a female) is influenced by the mate-choice of conspecifics. Drosophila melanogaster females are known to perform such social learning, and in particular, to mate-copy after a single observation of one conspecific female mating with a male of one phenotype, while the other male phenotype is rejected. Here, we show that this form of social learning is dependent on serotonin and dopamine. Using a pharmacological approach, we reduced dopamine or serotonin synthesis in adult virgin females with 3-iodotyrosine (3-IY) and DL-para-chlorophenylalanine (PCPA), respectively, and then tested their mate-copying performance. We found that, while control females without drug treatment copied the choice of the demonstrator, drug-treated females with reduced dopamine or serotonin chose randomly. To ensure the specificity of the drugs, the direct precursors of the neurotransmitters, either the dopamine precursor L-3,4-dihydroxyphenylalanine (L-DOPA) or the serotonin precursor 5-L-hydroxytryptophan (5-HTP) were given together with the drug, (respectively 3-IY and PCPA) resulting in a full rescue of the mate-copying defects. This indicates that dopamine and serotonin are both required for mate-copying. These results give a first insight into the mechanistic pathway underlying this form of social learning in D. melanogaster

Fast reconstruction of atomic-scale STEM-EELS images from sparse sampling

This paper discusses the reconstruction of partially sampled spectrum-images to accelerate the acquisition in scanning transmission electron microscopy (STEM). The problem of image reconstruction has been widely considered in the literature for many imaging modalities, but only a few attempts handled 3D data such as spectral images acquired by STEM electron energy loss spectroscopy (EELS). Besides, among the methods proposed in the microscopy literature, some are fast but inaccurate while others provide accurate reconstruction but at the price of a high computation burden. Thus none of the proposed reconstruction methods fulfills our expectations in terms of accuracy and computation complexity. In this paper, we propose a fast and accurate reconstruction method suited for atomic-scale EELS. This method is compared to popular solutions such as beta process factor analysis (BPFA) which is used for the first time on STEM-EELS images. Experiments based on real as synthetic data will be conducted

Cultural flies:Conformist social learning in fruitflies predicts long-lasting mate-choice traditions

Despite theoretical justification for the evolution of animal culture, empirical evidence for it beyond mammals and birds remains scant, and we still know little about the process of cultural inheritance. In this study, we propose a mechanism-driven definition of animal culture and test it in the fruitfly. We found that fruitflies have five cognitive capacities that enable them to transmit mating preferences culturally across generations, potentially fostering persistent traditions (the main marker of culture) in mating preference. A transmission chain experiment validates a model of the emergence of local traditions, indicating that such social transmission may lead initially neutral traits to become adaptive, hence strongly selecting for copying and conformity. Although this situation was suggested decades ago, it previously had little empirical support.</p

Copernicus Marine Service Ocean State Report

This is the final version. Available from Taylor & Francis via the DOI in this record

Effect of alirocumab on mortality after acute coronary syndromes. An analysis of the ODYSSEY OUTCOMES randomized clinical trial

Background: Previous trials of PCSK9 (proprotein convertase subtilisin-kexin type 9) inhibitors demonstrated reductions in major adverse cardiovascular events, but not death. We assessed the effects of alirocumab on death after index acute coronary syndrome. Methods: ODYSSEY OUTCOMES (Evaluation of Cardiovascular Outcomes After an Acute Coronary Syndrome During Treatment With Alirocumab) was a double-blind, randomized comparison of alirocumab or placebo in 18 924 patients who had an ACS 1 to 12 months previously and elevated atherogenic lipoproteins despite intensive statin therapy. Alirocumab dose was blindly titrated to target achieved low-density lipoprotein cholesterol (LDL-C) between 25 and 50 mg/dL. We examined the effects of treatment on all-cause death and its components, cardiovascular and noncardiovascular death, with log-rank testing. Joint semiparametric models tested associations between nonfatal cardiovascular events and cardiovascular or noncardiovascular death. Results: Median follow-up was 2.8 years. Death occurred in 334 (3.5%) and 392 (4.1%) patients, respectively, in the alirocumab and placebo groups (hazard ratio [HR], 0.85; 95% CI, 0.73 to 0.98; P=0.03, nominal P value). This resulted from nonsignificantly fewer cardiovascular (240 [2.5%] vs 271 [2.9%]; HR, 0.88; 95% CI, 0.74 to 1.05; P=0.15) and noncardiovascular (94 [1.0%] vs 121 [1.3%]; HR, 0.77; 95% CI, 0.59 to 1.01; P=0.06) deaths with alirocumab. In a prespecified analysis of 8242 patients eligible for ≥3 years follow-up, alirocumab reduced death (HR, 0.78; 95% CI, 0.65 to 0.94; P=0.01). Patients with nonfatal cardiovascular events were at increased risk for cardiovascular and noncardiovascular deaths (P<0.0001 for the associations). Alirocumab reduced total nonfatal cardiovascular events (P<0.001) and thereby may have attenuated the number of cardiovascular and noncardiovascular deaths. A post hoc analysis found that, compared to patients with lower LDL-C, patients with baseline LDL-C ≥100 mg/dL (2.59 mmol/L) had a greater absolute risk of death and a larger mortality benefit from alirocumab (HR, 0.71; 95% CI, 0.56 to 0.90; Pinteraction=0.007). In the alirocumab group, all-cause death declined wit h achieved LDL-C at 4 months of treatment, to a level of approximately 30 mg/dL (adjusted P=0.017 for linear trend). Conclusions: Alirocumab added to intensive statin therapy has the potential to reduce death after acute coronary syndrome, particularly if treatment is maintained for ≥3 years, if baseline LDL-C is ≥100 mg/dL, or if achieved LDL-C is low. Clinical Trial Registration: URL: https://www.clinicaltrials.gov. Unique identifier: NCT01663402

Reconstruction rapide d'images multi-bandes partiellement échantillonnées en spectromicroscopie EELS

In electron energy loss spectroscopy (EELS), the sample to be analyzed is exposed to an electron beam, and the measure of the energy loss after passing through the material informs about the chemical composition. For samples particularly sensitive to electronic irradiation damages, such as organic materials, the experimenter is constrained to reduce the total electron dose received by the sample while obtaining a satisfying signal-to-noise ratio. With the recent development of sampling modules adapted to scanning transmission electron microscopes (STEM), the initial raster acquisition (i.e., line-by-line) has become highly configurable. Henceforth, it is now possible to visit any set of spatial positions during the acquisition. Based on these technical advances, a lot of works proposed optimized acquisition schemes for preserving sensitive samples. For a global electron dose equivalent to standard sampling, these strategies consist in visiting less spatial positions, i.e., to perform partial sampling. As a consequence, a higher electron dose per spatial position is allowed, which permits to increase the signal-to-noise ratio for each sampled spectrum. Yet, a post-processing step is required to infer the missing spectra. Among the reconstruction techniques used in the literature, the interpolation methods are fast but rather inaccurate ; they are particularly efficient for displaying the full image along the acquisition process. On the contrary, the dictionary learning-based methods are very performant, but are memory and computation demanding. They are chosen in priority to refine the reconstructed image after experimenting. Finally, only a few works attempt to fill this gap. The main objective of this Ph.D. thesis is to propose fast and accurate reconstruction algorithms for STEM-EELS imaging. Similarly to the interpolation methods, they should be fast enough to visualize the reconstructed image along the acquisition. Meanwhile, they should also achieve better reconstruction performances than those reached by interpolation, close to those of dictionary learning-based methods. To that end, regularized least square methods are proposed in the context of spatially smooth samples or of periodic crystalline samples. The proposed algorithms are then tested based on synthetic as well as real data experiments. The interest of partial-sampling based methods and the performances with respect to other reconstruction methods are evaluated.En spectroscopie de perte d’énergie des électrons (EELS), l’échantillon à analyser est soumis à un faisceau d’électron et une détection de l’énergie perdue au cours de la traversée du matériau renseigne sur la composition chimique du composé. Pour des échantillons particulièrement sensibles aux dégâts d'irradiation électronique, comme par exemple des matériaux organiques, on cherche à limiter la dose totale d'électrons reçue par l'échantillon tout en obtenant un rapport signal-sur-bruit satisfaisant. Avec le développement récent de modules d’échantillonnage adaptés aux microscopes en transmission à balayage (STEM), l’acquisition initialement réalisée ligne par ligne est devenue hautement paramétrable. Ainsi, il est désormais possible de visiter un ensemble de positions spatiales quelconques au cours de l’acquisition. De nombreux travaux ont proposé de s’appuyer sur ces avancées techniques pour permettre une acquisition optimisée pour des échantillons sensibles. Pour une dose d’électron globale équivalente à un échantillonnage standard, ces stratégies consistent à visiter moins de positions spatiales, et donc à procéder à un échantillonnage partiel. Par conséquent, une dose d’électron par position spatiale plus élevée est autorisée, ce qui permet d’augmenter le rapport signal-sur-bruit de chaque spectre mesuré. En contrepartie, une étape de post-traitement est nécessaire pour reconstruire l’ensemble de l’image, en particulier les spectres associés aux positions spatiales non visitées au cours de l’acquisition. Parmi les techniques de reconstruction utilisées dans la littérature, les méthodes d’interpolation sont rapides mais peu précises ; elles sont d’un intérêt tout particulier pour visualiser l’image complète au cours de l’acquisition. Au contraire, les techniques par apprentissage de dictionnaire sont très performantes, mais coûteuses tant en mémoire qu’en temps de calcul, et sont donc privilégiées pour raffiner l’image reconstruite après l’expérimentation. En définitive, peu de travaux ont cherché à combler ce fossé. L’objectif principal de cette thèse est de proposer des algorithmes de reconstruction rapides et performants en imagerie EELS. Ils devront, comme pour les méthodes d’interpolation, être suffisamment rapides pour visualiser l’image reconstruite au cours de l’acquisition. D’autre part, ces méthodes devront également afficher de meilleures performances que celles données par l’interpolation, voire proches de celles des techniques par apprentissage de dictionnaire. Pour cela, des méthodes par moindres carrés régularisés sont envisagées dans le cas d’échantillons spatialement lisses et d’échantillons cristallins périodiques. Les algorithmes proposés sont ensuite testés en s’appuyant sur des données synthétiques et réelles. L’intérêt de l’approche par acquisition partielle et les performances par rapport à d’autres méthodes de reconstruction sont étudiés