A high-performance computing framework for Monte Carlo ocean color simulations

This paper presents a high-performance computing (HPC) framework for Monte Carlo (MC) simulations in the ocean color (OC) application domain. The objective is to optimize a parallel MC radiative transfer code named MOX, developed by the authors to create a virtual marine environment for investigating the quality of OC data products derived from in situ measurements of in-water radiometric quantities. A consolidated set of solutions for performance modeling, prediction, and optimization is implemented to enhance the efficiency of MC OC simulations on HPC run-time infrastructures. HPC, machine learning, and adaptive computing techniques are applied taking into account a clear separation and systematic treatment of accuracy and precision requirements for large-scale MC OC simulations. The added value of the work is the integration of computational methods and tools for MC OC simulations in the form of an HPC-oriented problem-solving environment specifically tailored to investigate data acquisition and reduction methods for OC field measurements. Study results highlight the benefit of close collaboration between HPC and application domain researchers to improve the efficiency and flexibility of computer simulations in the marine optics application domain. (C) 2016 The Authors. Concurrency and Computation: Practice and Experience Published by John Wiley & Sons Ltd.Portuguese Foundation for Science and Technology (FCT/MEC) [PEst-OE/EEI/UI0527/2011]; ESA [22576/09/I-OL, ARG/003-025/1406/CIMA]; NOVA LINCS [UID/CEC/04516/2013]info:eu-repo/semantics/publishedVersio

Effects of light polarization and waves slope statistics on the reflectance factor of the sea surface

Above-water radiometry depends on estimates of the reflectance factor rho of the sea surface to compute the in situ water-leaving radiance. The Monte Carlo code for ocean color simulations MOX is used in this study to analyze the effect of different environmental components on r values. A first aspect is examining the reflectance factor without and by accounting for the sky-radiance polarization. The influence of the sea-surface statistics at discrete grid points is then considered by presenting a new scheme to define the variance of the waves slope. Results at different sun elevations and sensor orientations indicate that the light polarization effect on r simulations reduces from similar to 17 to similar to 10% when the wind speed increases from 0 to 14ms(-1). An opposite tendency characterizes the modeling of the sea-surface slope variance, with r differences up to similar to 12% at a wind speed of 10ms(-1). The joint effect of polarization and the the sea-surface statistics displays a less systematic dependence on the wind speed, with differences in the range similar to 13 to similar to 18%. The r changes due to the light polarization and the variance of the waves slope become more relevant at sky-viewing geometries respectively lower and higher than 40 degrees with respect to the zenith. An overall compensation of positive and negative offsets due to light polarization is finally documented when considering different sun elevations. These results address additional investigations which, by combining the modeling and experimental components of marine optics, better evaluate specific measurement protocols for collecting above-water radiometric data in the field. (C) 2016 Optical Society of Americ

Entropic repulsion and scaling limit for a finite number of non-intersecting subcritical FK interfaces

This article is devoted to the study of a finite system of long clusters of subcritical 2-dimensional FK-percolation with q $\geq$ 1, conditioned on mutual avoidance. We show that the diffusive scaling limit of such a system is given by a system of Brownian bridges conditioned not to intersect: the so-called Brownian watermelon. Moreover, we give an estimate of the probability that two sets of $r$ points at distance $n$ of each other are connected by distinct clusters. As a byproduct, we obtain the asymptotics of the probability of the occurrence of a large finite cluster in a supercritical random-cluster model.Comment: 60 pages, 6 figures. Second version (minor modifications

An experimental evaluation of a loop versus a reference design for two-channel microarrays

Motivation: Despite theoretical arguments that socalled "loop designs" of two-channel DNA microarray experiments are more efficient, biologists keep on using "reference designs". We describe two sets of microarray experiments with RNA from two different biological systems (TPA-stimulated mammalian cells and Streptomyces coelicor). In each case, both a loop and a reference design were performed using the same RNA preparations with the aim to study their relative efficiency. Results: The results of these experiments show that (1) the loop design attains a much higher precision than the reference design, (2) multiplicative spot effects are a large source of variability, and if they are not accounted for in the mathematical model, for example by taking log-ratios or including spot-effects, then the model will perform poorly. The first result is reinforced by a simulation study. Practical recommendations are given on how simple loop designs can be extended to more realistic experimental designs and how standard statistical methods allow the experimentalist to use and interpret the results from loop designs in practice

Le Elezioni Politiche 2013

Le elezioni politiche del 24 e 25 febbraio 2013 hanno sancito un forte cambiamento della struttura del sistema partitico italiano. In un contesto di altissima volatilità elettorale e di accelerato declino della partecipazione al voto, il sistema è divenuto sostanzialmente tripolare, dopo vent’anni di strutturazione e tenuta del bipolarismo. A questo esito hanno concorso da un lato l’erosione dei principali schieramenti politici che a partire dal novembre 2011 avevano sostenuto l’esperienza del governo Monti (nonché la deludente prova elettorale dello stesso Presidente del Consiglio uscente), e dall’altro lo straordinario successo del Movimento 5 stelle. Quest’ultimo, al primo test elettorale di livello nazionale, ha raccolto un risultato sorprendente, giungendo ad oltre un quarto dei voti validi. Siamo di fronte ad una parentesi momentanea dovuta all’effetto combinato di crisi economica e crisi politica, oppure le contraddizioni interne alla Seconda Repubblica l’hanno condotta effettivamente al suo crepuscolo? Come uscirà il sistema partitico italiano da questa nuova fase di destabilizzazione? Questo quarto Dossier CISE, che raccoglie contributi apparsi sul sito web del Cise prima e dopo le elezioni, fornisce una prima analisi del voto, presentando elaborazioni su dati aggregati, stime dei flussi elettorali, alcune prime analisi su dati di sondaggio, nonché una panoramica dei nuovi eletti e un’appendice ricca di tabelle e mappe riassuntive del risultato elettorale. Come i precedenti Dossier, si tratta di uno strumento prodotto rapidamente all’indomani del voto, con l’intento di suggerire primi spunti di interpretazione da approfondire in seguito, cercando di contribuire alla lettura di un risultato elettorale cruciale, in una delicata fase di cambiamento del sistema partitico italiano

Advanced Radiative Transfer Models for the simulation of In situ and Satellite Ocean Color data (ARTEMIS-OC): the Novel Adjacency Perturbation Simulator for Coastal Areas (NAUSICAA) code

oai:publications.jrc.ec.europa.eu:JRC141105This report, the second in a series, leverages JRC extensive experience in developing and applying highly accurate radiative transfer models to simulate in situ and satellite aquatic data, which are integrated into the JRC’s Advanced Radiative Transfer Models for In situ and Satellite Ocean Color data (ARTEMIS-OC) software suite. ARTEMIS-OC includes i) the FEM code for simulating unpolarised solar radiation in open-ocean environments, ii) the PERSEA code to ensure a flexible and comprehensive modelling of the optical properties of realistic atmosphere and water environments, iii) the SkyFEM, FEMrad-OC, and AquaFEM codes, which are tailored FEM-PERSEA configurations to reproduce the radiance detected by sky-looking, satellite and in-water sensors, respectively; and iv) the NAUSICAA code to simulate unpolarised solar radiation in coastal and inland water regions, i.e., in the presence of nearby land perturbations. All algorithms account for multiple scattering and allow varying illumination and observation geometries. The present report focuses on the NAUSICAA code and its applications in investigating and reducing uncertainties in OC data products. The ultimate goal of this report series is to provide a comprehensive description of the ARTEMIS-OC simulation tools in support of the Copernicus Programme launched in 2014 to establish a European capacity for Earth Observation.JRC.D.2 - Ocean and Wate

The information and decision support needs of older women (>75 yrs) facing treatment choices for breast cancer : a qualitative study

Objective Primary Endocrine Therapy (PET) is a good alternative to surgery for breast cancer in older frailer women. Overall survival rates are equivalent although rates of local control are inferior. There is little research regarding the decision support needs of older patients faced with this choice. This qualitative study aimed to explore these among older breast cancer patients offered a choice of treatment, as the basis to develop an appropriate decision support tool. Methods Semi-structured interviews were undertaken with older women (>75 years) with breast cancer who had been offered a choice of PET or surgery at diagnosis. Women's involvement in their treatment decision and support for the process were explored and analysed using framework analysis. Results Thirty-three interviews were undertaken (median age 82, range 75–95 years, 22 PET, 11 surgery). Most women, regardless of treatment choice, wanted tailored information about the different treatment options, their impact on independence, the practicalities of treatment and the risk of recurrence and spread. Surgery was the treatment of choice in women wanting optimal disease control; those choosing PET felt that they were ‘too old’ for surgery and wanted minimal disruption. Conclusions Older women described making active treatment decisions. However, some knowledge was inaccurate. Women wanted information and decision support from their clinicians along with a specific tailored information booklet to support this proces

Validation of standard and alternative satellite ocean-color chlorophyll products off Western Iberia

Chlorophyll a concentration (Chl) product validation off theWestern Iberian coast is here undertaken by directly comparing remote sensing data with in situ surface reference values. Both standard and recently developed alternative algorithms are considered for match-up data analysis. The investigated standard products are those produced by the MERIS (algal 1 and algal 2) and MODIS (OC3M) algorithms. The alternative data products include those generatedwithin the CoastColour Project and Ocean Color Climate Change Initiative (OC-CCI) funded by ESA, as well as a neural net model trained with field measurements collected in the Atlantic off Portugal (MLPATLP). Statistical analyses showed that satellite Chl estimates tend to be larger than in situ reference values. The study also revealed that a non-uniform Chl distribution in the water column can be a concurring factor to the documented overestimation tendency when considering larger optical depth match-up stations. Among standard remote sensing products, MODIS OC3M and MERIS algal 2 yield the best agreement with in situ data. The performance of MLPATLP highlights the capability of regional solutions to further improve Chl retrieval by accounting for environmental specificities. Results also demonstrate the relevance of oceanographic regions such as the Nazaré area to evaluate how complex hydrodynamic conditions can influence the quality of Chl products.This studywas performed in the framework of HabSpot FCT Project, PTDC/MAR/100348/2008 and European Space Agency projects DUE CoastColour (ESRIN/AO/1-6141/09/l-EC) and Climate Change Iniciative — Ocean Color (AO-1/6207/09/I-LG). The work has been also partially supported by the European Space Agency within the framework of the MERIS Validation Activities under contract n. 12595/09/I-OL, and sampling activities benefited from European projects HERMES (GOCE-CT-2005-511234) and Hermione (EC contract 226354) support. We would like to thank NASA OBPG for the MODIS data and ESA Project AOPT-2423 for providing MERIS full resolution images. Ana C. Brito was funded by a Portuguese Post-doc grant from FCT (BPD/63017/2009) and by the Investigador FCT Program (IF/00331/2013). Davide D'Alimonte was funded by Investigador FCT Program (IF/00541/2013).info:eu-repo/semantics/publishedVersio

In-water lidar simulations: the ALADIN ADM-Aeolus backscattered signal at 355 nm

The Lidar Ocean Color (LiOC) Monte Carlo code has been developed to simulate the in-water propagation of the lidar beam emitted by the ALADIN ADM-Aeolus instrument in the ultraviolet (UV) spectral region (∼ 355 nm). To this end, LiOC accounts for reflection/transmission processes at the sea surface, absorption and multiple scattering in the water volume, and reflection from the sea bottom. The water volume components included in the model are pure seawater, Chlorophyll-a concentration (Chl-a), Colored Dissolved Organic Matter (CDOM), and/or a generic absorbing species. By considering the transmission/reception measurement geometry of ALADIN ADM-Aeolus, the study documents the variability of the normalized backscattered signal in different bio-optical conditions. The potential for data product retrieval based on information at 355 nm is considered by developing a demonstrative lookup table to estimate the absorption budget exceeding that explained by Chl-a. Results acknowledge the interest of space programs in exploiting UV bands for ocean color remote sensing, as, for instance, addressed by the PACE mission of NASA