PASSATA - Object oriented numerical simulation software for adaptive optics

We present the last version of the PyrAmid Simulator Software for Adaptive opTics Arcetri (PASSATA), an IDL and CUDA based object oriented software developed in the Adaptive Optics group of the Arcetri observatory for Monte-Carlo end-to-end adaptive optics simulations. The original aim of this software was to evaluate the performance of a single conjugate adaptive optics system for ground based telescope with a pyramid wavefront sensor. After some years of development, the current version of PASSATA is able to simulate several adaptive optics systems: single conjugate, multi conjugate and ground layer, with Shack Hartmann and Pyramid wavefront sensors. It can simulate from 8m to 40m class telescopes, with diffraction limited and resolved sources at finite or infinite distance from the pupil. The main advantages of this software are the versatility given by the object oriented approach and the speed given by the CUDA implementation of the most computational demanding routines. We describe the software with its last developments and present some examples of application.Comment: 9 pages, 2 figures, 3 tables. SPIE conference Astronomical Telescopes and Instrumentation, 26 June - 01 July 2016, Edinburgh, Scotland, United Kingdo

Infinite impulse response modal filtering in visible adaptive optics

Diffraction limited resolution adaptive optics (AO) correction in visible wavelengths requires a high performance control. In this paper we investigate infinite impulse response filters that optimize the wavefront correction: we tested these algorithms through full numerical simulations of a single-conjugate AO system comprising an adaptive secondary mirror with 1127 actuators and a pyramid wavefront sensor (WFS). The actual practicability of the algorithms depends on both robustness and knowledge of the real system: errors in the system model may even worsen the performance. In particular we checked the robustness of the algorithms in different conditions, proving that the proposed method can reject both disturbance and calibration errors

Microwave Measurements of the Tropolone-Formic Acid Doubly Hydrogen Bonded Dimer

The microwave spectrum was measured for the doubly hydrogen bonded dimer formed between tropolone and formic acid. The predicted symmetry of this dimer was C2v(M), and it was expected that the concerted proton tunneling motion would be observed. After measuring 25 a- and b-type rotational transitions, no splittings which could be associated with a concerted double proton tunneling motion were observed. The calculated barrier to the proton tunneling motion is near 15 000 cm-1, which would likely make the tunneling frequencies too small to observe in the microwave spectra. The rotational and centrifugal distortion constants determined from the measured transitions were A = 2180.7186(98) MHz, B = 470.873 90(25) MHz, C = 387.689 84(22) MHz, DJ = 0.0100(14) kHz, DJK = 0.102(28) kHz, and DK = 13.2(81) kHz. The B3LYP/aug-cc-pVTZ calculated rotational constants were within 1% of the experimentally determined values

Aviram-Ratner rectifying mechanism for DNA base pair sequencing through graphene nanogaps

We demonstrate that biological molecules such as Watson-Crick DNA base pairs can behave as biological Aviram-Ratner electrical rectifiers because of the spatial separation and weak hydrogen bonding between the nucleobases. We have performed a parallel computational implementation of the ab-initio non-equilibrium Green's function (NEGF) theory to determine the electrical response of graphene---base-pair---graphene junctions. The results show an asymmetric (rectifying) current-voltage response for the Cytosine-Guanine base pair adsorbed on a graphene nanogap. In sharp contrast we find a symmetric response for the Thymine-Adenine case. We propose applying the asymmetry of the current-voltage response as a sensing criterion to the technological challenge of rapid DNA sequencing via graphene nanogaps

Automated computation of materials properties

Materials informatics offers a promising pathway towards rational materials design, replacing the current trial-and-error approach and accelerating the development of new functional materials. Through the use of sophisticated data analysis techniques, underlying property trends can be identified, facilitating the formulation of new design rules. Such methods require large sets of consistently generated, programmatically accessible materials data. Computational materials design frameworks using standardized parameter sets are the ideal tools for producing such data. This work reviews the state-of-the-art in computational materials design, with a focus on these automated $\textit{ab-initio}$ frameworks. Features such as structural prototyping and automated error correction that enable rapid generation of large datasets are discussed, and the way in which integrated workflows can simplify the calculation of complex properties, such as thermal conductivity and mechanical stability, is demonstrated. The organization of large datasets composed of $\textit{ab-initio}$ calculations, and the tools that render them programmatically accessible for use in statistical learning applications, are also described. Finally, recent advances in leveraging existing data to predict novel functional materials, such as entropy stabilized ceramics, bulk metallic glasses, thermoelectrics, superalloys, and magnets, are surveyed.Comment: 25 pages, 7 figures, chapter in a boo

The AFLOW Fleet for Materials Discovery

The traditional paradigm for materials discovery has been recently expanded to incorporate substantial data driven research. With the intent to accelerate the development and the deployment of new technologies, the AFLOW Fleet for computational materials design automates high-throughput first principles calculations, and provides tools for data verification and dissemination for a broad community of users. AFLOW incorporates different computational modules to robustly determine thermodynamic stability, electronic band structures, vibrational dispersions, thermo-mechanical properties and more. The AFLOW data repository is publicly accessible online at aflow.org, with more than 1.7 million materials entries and a panoply of queryable computed properties. Tools to programmatically search and process the data, as well as to perform online machine learning predictions, are also available.Comment: 14 pages, 8 figure

{SelfPose}: {3D} Egocentric Pose Estimation from a Headset Mounted Camera

We present a solution to egocentric 3D body pose estimation from monocular images captured from downward looking fish-eye cameras installed on the rim of a head mounted VR device. This unusual viewpoint leads to images with unique visual appearance, with severe self-occlusions and perspective distortions that result in drastic differences in resolution between lower and upper body. We propose an encoder-decoder architecture with a novel multi-branch decoder designed to account for the varying uncertainty in 2D predictions. The quantitative evaluation, on synthetic and real-world datasets, shows that our strategy leads to substantial improvements in accuracy over state of the art egocentric approaches. To tackle the lack of labelled data we also introduced a large photo-realistic synthetic dataset. xR-EgoPose offers high quality renderings of people with diverse skintones, body shapes and clothing, performing a range of actions. Our experiments show that the high variability in our new synthetic training corpus leads to good generalization to real world footage and to state of theart results on real world datasets with ground truth. Moreover, an evaluation on the Human3.6M benchmark shows that the performance of our method is on par with top performing approaches on the more classic problem of 3D human pose from a third person viewpoint.Comment: 14 pages. arXiv admin note: substantial text overlap with arXiv:1907.1004

OSAnalyzer: A Bioinformatics Tool for the Analysis of Gene Polymorphisms Enriched with Clinical Outcomes

Background: The identification of biomarkers for the estimation of cancer patients\u2019 survival is a crucial problem in modern oncology. Recently, the Affymetrix DMET (Drug Metabolizing Enzymes and Transporters) microarray platform has offered the possibility to determine the ADME (absorption, distribution, metabolism, and excretion) gene variants of a patient and to correlate them with drug-dependent adverse events. Therefore, the analysis of survival distribution of patients starting from their profile obtained using DMET data may reveal important information to clinicians about possible correlations among drug response, survival rate, and gene variants. Methods: In order to provide support to this analysis we developed OSAnalyzer, a software tool able to compute the overall survival (OS) and progression-free survival (PFS) of cancer patients and evaluate their association with ADME gene variants. Results: The tool is able to perform an automatic analysis of DMET data enriched with survival events. Moreover, results are ranked according to statistical significance obtained by comparing the area under the curves that is computed by using the log-rank test, allowing a quick and easy analysis and visualization of high-throughput data. Conclusions: Finally, we present a case study to highlight the usefulness of OSAnalyzer when analyzing a large cohort of patient

Multivalve Endocarditis With Multiple Peripheral and Pulmonary Embolisms: A Case Report

A síndrome febril indeterminada no idoso coloca sempre alguma dificuldade diagnóstica. A endocardite infecciosa, pela relativa raridade e pela atipia das suas manifestações é muitas vezes esquecida neste grupo etário, onde outras causas, nomeadamente neoplásicas, são primeiramente consideradas. Os autores apresentam um caso clínico de uma doente idosa com endocardite infecciosa subaguda mitral e tricuspide, cujo diagnóstico foi estabelecido apenas após embolização periférica. Para além de fenómenos embólicos múltiplos, esta doente teve ainda como complicação um aneurisma micótico da artéria femural esquerda a que foi operada