Sawtooth period changes with mode conversion current drive on Alcator C-Mod

DEFC0299ER54512. Reproduction,  translation,  publication,  use and disposal,  in whole or in part,  by or for the United States government is permitted. Submitted for publication to Plasma Physics and Controlled Fusion. Sawtooth period changes with mode conversion current drive on Alcator C-Mo

OntoGene in BioCreative II

BACKGROUND: Research scientists and companies working in the domains of biomedicine and genomics are increasingly faced with the problem of efficiently locating, within the vast body of published scientific findings, the critical pieces of information that are needed to direct current and future research investment. RESULTS: In this report we describe approaches taken within the scope of the second BioCreative competition in order to solve two aspects of this problem: detection of novel protein interactions reported in scientific articles, and detection of the experimental method that was used to confirm the interaction. Our approach to the former problem is based on a high-recall protein annotation step, followed by two strict disambiguation steps. The remaining proteins are then combined according to a number of lexico-syntactic filters, which deliver high-precision results while maintaining reasonable recall. The detection of the experimental methods is tackled by a pattern matching approach, which has delivered the best results in the official BioCreative evaluation. CONCLUSION: Although the results of BioCreative clearly show that no tool is sufficiently reliable for fully automated annotations, a few of the proposed approaches (including our own) already perform at a competitive level. This makes them interesting either as standalone tools for preliminary document inspection, or as modules within an environment aimed at supporting the process of curation of biomedical literature

SPHERE: the exoplanet imager for the Very Large Telescope

Observations of circumstellar environments to look for the direct signal of exoplanets and the scattered light from disks has significant instrumental implications. In the past 15 years, major developments in adaptive optics, coronagraphy, optical manufacturing, wavefront sensing and data processing, together with a consistent global system analysis have enabled a new generation of high-contrast imagers and spectrographs on large ground-based telescopes with much better performance. One of the most productive is the Spectro-Polarimetic High contrast imager for Exoplanets REsearch (SPHERE) designed and built for the ESO Very Large Telescope (VLT) in Chile. SPHERE includes an extreme adaptive optics system, a highly stable common path interface, several types of coronagraphs and three science instruments. Two of them, the Integral Field Spectrograph (IFS) and the Infra-Red Dual-band Imager and Spectrograph (IRDIS), are designed to efficiently cover the near-infrared (NIR) range in a single observation for efficient young planet search. The third one, ZIMPOL, is designed for visible (VIR) polarimetric observation to look for the reflected light of exoplanets and the light scattered by debris disks. This suite of three science instruments enables to study circumstellar environments at unprecedented angular resolution both in the visible and the near-infrared. In this work, we present the complete instrument and its on-sky performance after 4 years of operations at the VLT.Comment: Final version accepted for publication in A&

Interpretation of Brain Morphology in Association to Alzheimer's Disease Dementia Classification Using Graph Convolutional Networks on Triangulated Meshes

We propose a mesh-based technique to aid in the classification of Alzheimer's disease dementia (ADD) using mesh representations of the cortex and subcortical structures. Deep learning methods for classification tasks that utilize structural neuroimaging often require extensive learning parameters to optimize. Frequently, these approaches for automated medical diagnosis also lack visual interpretability for areas in the brain involved in making a diagnosis. This work: (a) analyzes brain shape using surface information of the cortex and subcortical structures, (b) proposes a residual learning framework for state-of-the-art graph convolutional networks which offer a significant reduction in learnable parameters, and (c) offers visual interpretability of the network via class-specific gradient information that localizes important regions of interest in our inputs. With our proposed method leveraging the use of cortical and subcortical surface information, we outperform other machine learning methods with a 96.35% testing accuracy for the ADD vs. healthy control problem. We confirm the validity of our model by observing its performance in a 25-trial Monte Carlo cross-validation. The generated visualization maps in our study show correspondences with current knowledge regarding the structural localization of pathological changes in the brain associated to dementia of the Alzheimer's type.Comment: Accepted for the Shape in Medical Imaging (ShapeMI) workshop at MICCAI International Conference 202

Features of the normal choriocapillaris with OCT-angiography: Density estimation and textural properties

The main objective of our work is to perform an in depth analysis of the structural features of normal choriocapillaris imaged with OCT Angiography. Specifically, we provide an optimal radius for a circular Region of Interest (ROI) to obtain a stable estimate of the subfoveal choriocapillaris density and characterize its textural properties using Markov Random Fields. On each binarized image of the choriocapillaris OCT Angiography we performed simulated measurements of the subfoveal choriocapillaris densities with circular Regions of Interest (ROIs) of different radii and with small random displacements from the center of the Foveal Avascular Zone (FAZ). We then calculated the variability of the density measure with different ROI radii. We then characterized the textural features of choriocapillaris binary images by estimating the parameters of an Ising model. For each image we calculated the Optimal Radius (OR) as the minimum ROI radius required to obtain a standard deviation in the simulation below 0.01. The density measured with the individual OR was 0.52 ± 0.07 (mean ± STD). Similar density values (0.51 ± 0.07) were obtained using a fixed ROI radius of 450 μm. The Ising model yielded two parameter estimates (β = 0.34 ± 0.03; γ = 0.003 ± 0.012; mean ± STD), characterizing pixel clustering and white pixel density respectively. Using the estimated parameters to synthetize new random textures via simulation we obtained a good reproduction of the original choriocapillaris structural features and density. In conclusion, we developed an extensive characterization of the normal subfoveal choriocapillaris that might be used for flow analysis and applied to the investigation pathological alterations

Prediction of Thrombectomy Functional Outcomes using Multimodal Data

Recent randomised clinical trials have shown that patients with ischaemic stroke {due to occlusion of a large intracranial blood vessel} benefit from endovascular thrombectomy. However, predicting outcome of treatment in an individual patient remains a challenge. We propose a novel deep learning approach to directly exploit multimodal data (clinical metadata information, imaging data, and imaging biomarkers extracted from images) to estimate the success of endovascular treatment. We incorporate an attention mechanism in our architecture to model global feature inter-dependencies, both channel-wise and spatially. We perform comparative experiments using unimodal and multimodal data, to predict functional outcome (modified Rankin Scale score, mRS) and achieve 0.75 AUC for dichotomised mRS scores and 0.35 classification accuracy for individual mRS scores.Comment: Accepted at Medical Image Understanding and Analysis (MIUA) 202

Evolution and environment of the eastern linear pottery culture: A case study in the site of Polgár-Piócási-Dűlő

A salvage excavation preceding a major investment project was conducted in 2006–2007, during which associated settlement features of a Middle Neolithic, Eastern Linear Pottery Culture (Alföld Linearbandkeramik – ALBK) were uncovered in an area called Piócási-dűlő on the eastern outskirts of Polgár. The features of the ALBK settlement date from two periods. The cluster of multi-functional pits yielding a rich assortment of finds, the handful of post-holes and an unusual ritual well found in the southern part of the investigated area formed one unit from the earliest phase of the Middle Neolithic (ALBK I). The settlement’s other occupation can be assigned to the late phase of the Middle Neolithic (ALBK IV). Five houseplans representing the remains of timber-framed buildings outlined a distinct area with three multi-functional pits. Associated with the above features were 8 burials. The preliminary archaeobotanical results from Polgár–Piócási-dűlő are based on the plant material found within the sediments of 11 archaeological structures, which mainly represent pits and a welI. It can be stated that the natural environment offered habitats in which oak trees dominated in the local vegetation, forming floodplain forests and wooded steppes. They also provided food in the form of fruits and formed an optimal habitat for domestic animals. Arable fields were probably also established in the vicinity of the settlements, suggested by findings of macroscopic plant remains that represented cultivated species. In both settlement phases lithic production activities are manifested both by the local on-site lithic production and – most importantly – by the presence of imported, mainly mesolocal, raw materials that point to contacts with deposit areas, or off-site preliminary working of obsidian and limnoquartzites. The kit of harvesting tools and a large number of grinding stones – especially in the younger phase – for the preparation of plant food suggest a major role of plant cultivation

A Spatial Distribution Study of Faunal Remains from Two Lower Magdalenian Occupation Levels in El Mirón Cave, Cantabria, Spain

Abstract: Human behaviour can be reconstructed by analysing specific activities and campsite organization using spatial analysis. The dense occupation layers of the Lower Cantabrian Magdalenian in the Northern Spain reveal varied aspects of Upper Palaeolithic lifeways, including evidence of specific localized activities. The outer vestibule of El Mirón cave has a particularly rich and intact Lower Magdalenian occupation horizon, Levels 15–17. The excavations in the outer vestibule “Cabin” area of the site revealed excellent bone preservation. Artefacts and faunal remains were individually recorded and sediments water-screened to yield a large sample of archaeological finds and spatial data. Zooarchaeological analysis provided the taxonomic, anatomic and taphonomic determination of the faunal individual finds. Smaller animal remains were categorized and counted; special attention was given to the identification of anthropogenic modifications such as burnt bones or bone flakes. These small refuse items are considered to be useful, in situ indicators of localized activities. The spatial distribution analysis of this dense and complex palimpsest of El Mirón Lower Cantabrian Magdalenian layers required GIS based methods including density analysis, heatmaps and cluster analysis. Based on the spatial distribution of Level 15 and 16 faunal remains, different activity areas were identified comprising hearth, working and dropping zones. These results imply the deliberately segregated use of space within the Lower Cantabrian Magdalenian site area, in which bone-processing activities played a central rol