Provenance-based Validation of E-Science Experiments

E-Science experiments typically involve many distributed services maintained by different organisations. After an experiment has been executed, it is useful for a scientist to verify that the execution was performed correctly or is compatible with some existing experimental criteria or standards, not necessarily anticipated prior to execution. Scientists may also want to review and verify experiments performed by their colleagues. There are no existing frameworks for validating such experiments in today's e-Science systems. Users therefore have to rely on error checking performed by the services, or adopt other ad hoc methods. This paper introduces a platform-independent framework for validating workflow executions. The validation relies on reasoning over the documented provenance of experiment results and semantic descriptions of services advertised in a registry. This validation process ensures experiments are performed correctly, and thus results generated are meaningful. The framework is tested in a bioinformatics application that performs protein compressibility analysis.

Provenance: The Bridge Between Experiments and Data

Current scientific applications are often structured as workflows and rely on workflow systems to compile abstract experiment designs into enactable workflows that utilise the best available resources. The automation of this step and of the workflow enactment, hides the details of how results have been produced. Knowing how compilation and enactment occurred allows results to be reconnected with the experiment design. We investigate how provenance helps scientists to connect their results with the actual execution that took place, their original experiment and its inputs and parameters.

An Injection-locked Diode Laser for Cold Rydberg Atom Experiments

A free-running, temperature stabilized diode laser has been injection-locked to an external cavity diode laser for use in cold Rydberg atom experiments. Cold rubidium atoms in a magneto-optical trap (MOT) are excited to Rydberg states using a 10 ns laser pulse. The Rydberg atoms spontaneously ionize due to dipole forces, and the collisional ionization dynamics are observed as a function of atom density and principal quantum number of the Rydberg state, n. The injection-locked diode laser will be used as a repumper in conjunction with a dark spontaneous-force optical trap (SPOT) to increase the Rydberg state density. We report on the design of the injection-locked laser system.

Exogenous shocks and misattribution of responsibility for economic performance: results from survey experiments

Recent models of economic voting assume that citizens can discount exogenous factors when assessing government's economic performance. Yet there is evidence that Latin American voters do not behave in such way, and attribute to presidents outcomes that are beyond their control. This paper presents three survey experiments designed to explore mechanisms that could potentially correct such misattribution, and therefore contribute to debiasing individual behavior towards government evaluation. Our results provide individual-level evidence of the misattribution found in aggregate studies of electorate behavior, and reinforce psychologist's skepticism towards prospects of mental decontamination, as we found very scant evidence that providing information, raising awareness, or increasing motivation to correct biases infuenced individual's evaluation of president's performance.

An essay on impression management: three randomized experiments with financial analysts

This thesis aims to explore the concept of impression management from the financial analysts’ point of view. Impression management is the definition of the act of an agent manipulating an impression that another person have of this agent, in the context of this thesis it happens when a company make graphics to disclosure financial-accounting information in order to manipulate the market’s perception of their performance. Three types of impression management were analyzed: presentation enhancement (color manipulation), measurement distortion (scale manipulation) and selectivity (the disclosure of positive information only). While presentation enhancement improved only the most impulsive financial analysts’ perception of firm’s performance, the measurement distortion improved the perception of performance for both groups of financial analysts (impulsive and reflective). Finally, selectivity improved the financial analysts’ perception of firm’s performance for both groups (impulsive and reflective), although impulsive financial analysts assigned lower ratings when compared to their reflective peers, on average, to a hypothetical company.

Respirometric techniques for assessment of biological kinetics in constructed wetland

The aim of this research was the development of a procedure to measure biological kinetics of organic matter oxidation and nitrification in constructed wetland, by using respirometric techniques. Columns simulating cores of vertical subsurface flow systems were investigated. The oxygen uptake rate (OUR) of the columns was calculated on the basis of the difference of DO concentrations measured continuously at the top and at the bottom of the column. From the respirogram, the following kinetic parameters have been evaluated: maximum rate of oxidation of readily biodegradable COD, maximum rate of nitrification, endogenous respiration of the biomass grown inside the bed. In order to improve the interpretation of the respirograms, additional respirometric tests were carried out on the wetland columns by using pure substrates, such as acetate (carbon source) and ammonium (substrate for nitrification). The kinetic parameters obtained from respirograms can be useful for control and design of constructed wetlands or for improving nutrient and carbon mass balances.

Some experiments with high order compact methods using a computer algebra software - Part I

We consider a procedure for obtaining a compact fourth order method to the steady 2D Navier-Stokes equations in the streamfunction formulation using the computer algebra system Maple. The resulting code is short and from it we obtain the Fortran program for the method. To test the procedure we have solved many cavity-type problems which include one with an analytical solution and the results are compared with results obtained by second order central differences to moderate Reynolds numbers. (c) 2005 Elsevier B.V. All rights reserved.

Some experiments with high order compact methods using a computer algebra software - Part II (non-uniform grid)

We generalize a procedure proposed by Mancera and Hunt [P.F.A. Mancera, R. Hunt, Some experiments with high order compact methods using a computer algebra software-Part 1, Appl. Math. Comput., in press, doi: 10.1016/j.amc.2005.05.015] for obtaining a compact fourth-order method to the steady 2D Navier-Stokes equations in the streamfunction formulation-vorticity using the computer algebra system Maple, which includes conformal mappings and non-uniform grids. To analyse the procedure we have solved a constricted stepped channel problem, where a fine grid is placed near the re-entrant corner by transformation of the independent variables. (c) 2006 Elsevier B.V. All rights reserved.

Stochastic dynamics in exotic and native blowflies: an analysis combining laboratory experiments and a two-patch metapopulation model

In this study we explored the stochastic population dynamics of three exotic blowfly species, Chrysomya albiceps, Chrysomya megacephala and Chrysomya putoria, and two native species, Cochliomyia macellaria and Lucilia eximia, by combining a density-dependent growth model with a two-patch metapopulation model. Stochastic fecundity, survival and migration were investigated by permitting random variations between predetermined demographic boundary values based on experimental data. Lucilia eximia and Chrysomya albiceps were the species most susceptible to the risk of local extinction. Cochliomyia macellaria, C. megacephala and C. putoria exhibited lower risks of extinction when compared to the other species. The simultaneous analysis of stochastic fecundity and survival revealed an increase in the extinction risk for all species. When stochastic fecundity, survival and migration were simulated together, the coupled populations were synchronized in the five species. These results are discussed, emphasizing biological invasion and interspecific interaction dynamics.

Electrolytic treatment applied to the industrial effluent containing persistent wastes monitored by Bartha respirometric assays

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Aerobic biodegradation of butanol and gasoline blends

This work aimed to assess the aerobic biodegradation of butanol/gasoline, blends (5; 10; 15 and 20% v/v), being the latter compared to the ethanol/gasoline blend (20% v/v). Two experimental techniques were employed, namely the respirometric method and the redox indicator DCPIP test. in the former, experiments simulating the contamination of natural environments (addition of 50 mL of fuel kg(-1) of soil from a non-contaminated site and 20 mL of fuel L(-1) of water from a river) were carried out in biometer flasks (250 mL), used to measure the microbial CO(2) production. The DCPIP test assessed the capability of four inocula to biodegrade the blends of 20%. The addition of butanol at different concentrations enhanced the biodegradation of gasoline in soil. However, no practical gains were observed for concentrations of butanol above 10%. Ethanol showed to have a much faster biodegradation rate than butanol, particularly in water, and the following order of biodegradability was found: ethanol > butanol > gasoline. The addition of the alcohols to the gasoline resulted in positive synergic effects on the biodegradation of the fuels in soil and water matrices. Furthermore, results suggest that, in soil, butanol better enhanced the biodegradation of gasoline than ethanol. (C) 2009 Elsevier Ltd. All rights reserved

Complementarity of eastern and western hemisphere long-baseline neutrino oscillation experiments

We present a general formalism for extracting information on the fundamental parameters associated with neutrino masses and mixings from two or more long baseline neutrino oscillation experiments. This formalism is then applied to the current most likely experiments using neutrino beams from the Japan Hadron Facility (JHF) and Fermilab's NuMI beamline. Different combinations of muon neutrino or muon anti-neutrino running are considered. The type of neutrino mass hierarchy is extracted using the effects of matter on neutrino propogation. Contrary to naive expectation, we find that both beams using neutrinos is more suitable for determining the hierarchy provided that the neutrino energy divided by baseline (E/L) for NuMI is smaller than or equal to that of JHF, whereas to determine the small mixing angle, theta(13), and the CP or T violating phase delta, one neutrino and the other anti-neutrino are most suitable. We make extensive use of bi-probability diagrams for both understanding and extracting the physics involved in such comparisons.

Method for determination of vertical bar U(e)3 vertical bar in neutrino oscillation appearance experiments

We point out that determination of the MNS matrix element \U-e3\ = s(13) in long-baseline nu(mu) --> nu(e) neutrino oscillation experiments suffers from large intrinsic uncertainty due to the unknown CP violating phase delta and sign of Deltam(13)(2). We propose a new strategy for accurate determination of theta(13); tune the beam energy at the oscillation maximum and do the measurement both in neutrino and antineutrino channels. We show that it automatically resolves the problem of parameter ambiguities which involves delta, theta(13), and the sign of Deltam(13)(2). (C) 2002 Elsevier B.V. B.V. All rights reserved.

Laboratory study on the bioremediation of diesel oil contaminated soil from a petrol station

O objetivo do presente estudo foi investigar possíveis métodos para aumentar a taxa de biodegradação aeróbia de hidrocarbonetos (tratamentos ex-situ). Neste trabalho, processos de biorremediação foram aplicados a um solo arenoso com alto nível de contaminação ocasionada por um vazamento de um tanque de armazenamento de óleo diesel subterrâneo em um posto de combustíveis. Experimentos em escala laboratorial (respirômetros de Bartha) foram utilizados para avaliar a biodegradação do óleo diesel. Estímulo da biodegradação foi realizado utilizando-se as técnicas de bioestímulo (adição de soluções de nitrogênio e fósforo ou surfactante Tween 80) e de bioaumento (consórcio bacteriano isolado de um sistema de landfarming). Para investigar as interações entre os fatores otimizadores, e encontrar a melhor combinação entre esses agentes, o estudo foi baseado em um delineamento experimental fatorial completo. A eficiência de biodegradação foi simultaneamente medida com dois métodos: respirométrico (produção de CO2 microbiano) e cromatografia gasosa. Testes de toxicidade aguda com Daphnia similis foram aplicados para examinar a eficiência dos processos em termos de geração de produtos menos tóxicos. Resultados mostraram que todas as estratégias de biorremediação aceleraram a biorremediação natural do solo contaminado e os melhores resultados foram obtidos quando os tratamentos tinham adição de nutrientes. Dados respirométricos indicaram uma máxima mineralização de hidrocarbonetos de 19,8%, obtida com a combinação dos três agentes, com uma remoção de hidrocarbonetos totais de petróleo (TPH) de 45,5% em 55 dias de tratamento. No final dos experimentos, duas espécies predominantes de bactéria foram isoladas e identificadas como Staphylococcus hominis e Kocuria palustris.

Oxidative dissolution of bornite by Acidithiobacillus ferrooxidans

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)