Showing papers by "Instituto Superior Técnico published in 2009"

Sparse Reconstruction by Separable Approximation

Abstract: Finding sparse approximate solutions to large underdetermined linear systems of equations is a common problem in signal/image processing and statistics. Basis pursuit, the least absolute shrinkage and selection operator (LASSO), wavelet-based deconvolution and reconstruction, and compressed sensing (CS) are a few well-known areas in which problems of this type appear. One standard approach is to minimize an objective function that includes a quadratic (lscr 2) error term added to a sparsity-inducing (usually lscr1) regularizater. We present an algorithmic framework for the more general problem of minimizing the sum of a smooth convex function and a nonsmooth, possibly nonconvex regularizer. We propose iterative methods in which each step is obtained by solving an optimization subproblem involving a quadratic term with diagonal Hessian (i.e., separable in the unknowns) plus the original sparsity-inducing regularizer; our approach is suitable for cases in which this subproblem can be solved much more rapidly than the original problem. Under mild conditions (namely convexity of the regularizer), we prove convergence of the proposed iterative algorithm to a minimum of the objective function. In addition to solving the standard lscr2-lscr1 case, our framework yields efficient solution techniques for other regularizers, such as an lscrinfin norm and group-separable regularizers. It also generalizes immediately to the case in which the data is complex rather than real. Experiments with CS problems show that our approach is competitive with the fastest known methods for the standard lscr2-lscr1 problem, as well as being efficient on problems with other separable regularization terms.

Quasinormal modes of black holes and black branes

Abstract: Quasinormal modes are eigenmodes of dissipative systems. Perturbations of classical gravitational backgrounds involving black holes or branes naturally lead to quasinormal modes. The analysis and classification of the quasinormal spectra require solving non-Hermitian eigenvalue problems for the associated linear differential equations. Within the recently developed gauge-gravity duality, these modes serve as an important tool for determining the near-equilibrium properties of strongly coupled quantum field theories, in particular their transport coefficients, such as viscosity, conductivity and diffusion constants. In astrophysics, the detection of quasinormal modes in gravitational wave experiments would allow precise measurements of the mass and spin of black holes as well as new tests of general relativity. This review is meant as an introduction to the subject, with a focus on the recent developments in the field.

Synthesis and applications of Rhodamine derivatives as fluorescent probes

Abstract: Rhodamine dyes are widely used as fluorescent probes owing to their high absorption coefficient and broad fluorescence in the visible region of electromagnetic spectrum, high fluorescence quantum yield and photostability. A great interest in the development of new synthetic procedures for preparation of Rhodamine derivatives has arisen in recent years because for most applications the probe must be covalently linked to another (bio)molecule or surface. In this critical review the strategies for modification of Rhodamine dyes and a discussion on the variety of applications of these new derivatives as fluorescent probes are given (108 references).

Geodesic stability, Lyapunov exponents, and quasinormal modes

Abstract: Geodesic motion determines important features of spacetimes. Null unstable geodesics are closely related to the appearance of compact objects to external observers and have been associated with the characteristic modes of black holes. By computing the Lyapunov exponent, which is the inverse of the instability time scale associated with this geodesic motion, we show that, in the eikonal limit, quasinormal modes of black holes in any dimensions are determined by the parameters of the circular null geodesics. This result is independent of the field equations and only assumes a stationary, spherically symmetric and asymptotically flat line element, but it does not seem to be easily extendable to anti-de Sitter spacetimes. We further show that (i) in spacetime dimensions greater than four, equatorial circular timelike geodesics in a Myers-Perry black-hole background are unstable, and (ii) the instability time scale of equatorial null geodesics in Myers-Perry spacetimes has a local minimum for spacetimes of dimension d ≥ 6.

Prevention of zeolite deactivation by coking

Abstract: The deactivation of acid zeolite catalysts is essentially due to the formation and trapping of heavy secondary products (coke) within the pores (channels and cages). As in these nanosized pores the growth of these products is sterically limited, the coke composition, i.e., the quantitative distribution in nature and size of the components, can be determined and the scheme and mechanisms of coke formation established. Moreover, coupling activity, acidity and adsorption data with coke composition leads to information on the location and deactivating effect of coke molecules. Based on the influence on coking and deactivation rates of the features of reactions and zeolite catalysts, general rules are proposed for limiting the rate of formation of coke molecules and minimising their deactivating effect.

Injection and Trapping of Tunnel Ionized Electrons into Laser Produced Wakes

Abstract: A method, which utilizes the large difference in ionization potentials between successive ionization states of trace atoms, for injecting electrons into a laser-driven wakefield is presented. Here a mixture of helium and trace amounts of nitrogen gas was used. Electrons from the K shell of nitrogen were tunnel ionized near the peak of the laser pulse and were injected into and trapped by the wake created by electrons from majority helium atoms and the L shell of nitrogen. The spectrum of the accelerated electrons, the threshold intensity at which trapping occurs, the forward transmitted laser spectrum, and the beam divergence are all consistent with this injection process. The experimental measurements are supported by theory and 3D OSIRIS simulations.

The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients

Abstract: Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications in the treatment of this common genetic disease. Burkholderia cenocepacia infection is particularly problematic since this organism has high levels of antibiotic resistance, making it difficult to eradicate; the resulting chronic infections are associated with severe declines in lung function and increased mortality rates. B. cenocepacia strain J2315 was isolated from a CF patient and is a member of the epidemic ET12 lineage that originated in Canada or the United Kingdom and spread to Europe. The 8.06-Mb genome of this highly transmissible pathogen comprises three circular chromosomes and a plasmid and encodes a broad array of functions typical of this metabolically versatile genus, as well as numerous virulence and drug resistance functions. Although B. cenocepacia strains can be isolated from soil and can be pathogenic to both plants and man, J2315 is representative of a lineage of B. cenocepacia rarely isolated from the environment and which spreads between CF patients. Comparative analysis revealed that ca. 21% of the genome is unique in comparison to other strains of B. cenocepacia, highlighting the genomic plasticity of this species. Pseudogenes in virulence determinants suggest that the pathogenic response of J2315 may have been recently selected to promote persistence in the CF lung. The J2315 genome contains evidence that its unique and highly adapted genetic content has played a significant role in its success as an epidemic CF pathogen.

More sustainable approaches for the synthesis of N-based heterocycles.

Abstract: Centro de Quı́mica-Fı́sica Molecular (CQFM) and Institute of Nanosciences and Nanotechnology (IN), Departamento de Engenharia Quı́mica e Biológica, Instituto Superior Técnico, 1049-001 Lisboa, Portugal, REQUIMTE, Departamento de Quı́mica, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal, and iMed.UL, Faculdade de Farmácia da Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal

Physics at a future Neutrino Factory and super-beam facility

Abstract: The conclusions of the Physics Working Group of the International Scoping Study of a future Neutrino Factory and super-beam facility (the ISS) are presented. The ISS was carried out by the international community between NuFact05, (the 7th International Workshop on Neutrino Factories and Super-beams, Laboratori Nazionali di Frascati, Rome, 21–26 June 2005) and NuFact06 (Ivine, CA, 24–30 August 2006). The physics case for an extensive experimental programme to understand the properties of the neutrino is presented and the role of high-precision measurements of neutrino oscillations within this programme is discussed in detail. The performance of second-generation super-beam experiments, beta-beam facilities and the Neutrino Factory are evaluated and a quantitative comparison of the discovery potential of the three classes of facility is presented. High-precision studies of the properties of the muon are complementary to the study of neutrino oscillations. The Neutrino Factory has the potential to provide extremely intense muon beams and the physics potential of such beams is discussed in the final section of the report.

Ex vivo expansion of human mesenchymal stem cells: A more effective cell proliferation kinetics and metabolism under hypoxia

Abstract: The low bone marrow (BM) MSC titers demand a fast ex vivo expansion process to meet the clinically relevant cell dosage. Attending to the low oxygen tension of BM in vivo, we studied the influence of hypoxia on human BM MSC proliferation kinetics and metabolism. Human BM MSC cultured under 2% (hypoxia) and 20% O(2) (normoxia) were characterized in terms of proliferation, cell division kinetics and metabolic patterns. BM MSC cultures under hypoxia displayed an early start of the exponential growth phase, and cell numbers obtained at each time point throughout culture were consistently higher under low O(2), resulting in a higher fold increase after 12 days under hypoxia (40 +/- 10 vs. 30 +/- 6). Cell labeling with PKH26 allowed us to determine that after 2 days of culture, a significant higher cell number was already actively dividing under 2% compared to 20% O(2) and BM MSC expanded under low oxygen tension displayed consistently higher percentages of cells in the latest generations (generations 4-6) until the 5th day of culture. Cells under low O(2) presented higher specific consumption of nutrients, especially early in culture, but with lower specific production of inhibitory metabolites. Moreover, 2% O(2) favored CFU-F expansion, while maintaining BM MSC characteristic immunophenotype and differentiative potential. Our results demonstrated a more efficient BM MSC expansion at 2% O(2), compared to normoxic conditions, associated to an earlier start of cellular division and supported by an increase in cellular metabolism efficiency towards the maximization of cell yield for application in clinical settings.

Quasinormal modes of black holes and black branes

Abstract: Quasinormal modes are eigenmodes of dissipative systems. Perturbations of classical gravitational backgrounds involving black holes or branes naturally lead to quasinormal modes. The analysis and classification of the quasinormal spectra requires solving non-Hermitian eigenvalue problems for the associated linear differential equations. Within the recently developed gauge-gravity duality, these modes serve as an important tool for determining the near-equilibrium properties of strongly coupled quantum field theories, in particular their transport coefficients, such as viscosity, conductivity and diffusion constants. In astrophysics, the detection of quasinormal modes in gravitational wave experiments would allow precise measurements of the mass and spin of black holes as well as new tests of general relativity. This review is meant as an introduction to the subject, with a focus on the recent developments in the field.

A Bayesian exploration-exploitation approach for optimal online sensing and planning with a visually guided mobile robot

Abstract: We address the problem of online path planning for optimal sensing with a mobile robot. The objective of the robot is to learn the most about its pose and the environment given time constraints. We use a POMDP with a utility function that depends on the belief state to model the finite horizon planning problem. We replan as the robot progresses throughout the environment. The POMDP is high-dimensional, continuous, non-differentiable, nonlinear, non-Gaussian and must be solved in real-time. Most existing techniques for stochastic planning and reinforcement learning are therefore inapplicable. To solve this extremely complex problem, we propose a Bayesian optimization method that dynamically trades off exploration (minimizing uncertainty in unknown parts of the policy space) and exploitation (capitalizing on the current best solution). We demonstrate our approach with a visually-guide mobile robot. The solution proposed here is also applicable to other closely-related domains, including active vision, sequential experimental design, dynamic sensing and calibration with mobile sensors.

The Next-to-Minimal Supersymmetric Standard Model

Abstract: We review the theoretical and phenomenological aspects of the Next-to-Minimal Supersymmetric Standard Model: the Higgs sector including radiative corrections and the 2-loop beta-functions for all parameters of the general NMSSM; the tadpole and domain wall problems, baryogenesis; NMSSM phenomenology at colliders, B physics and dark matter; specific scenarios as the constrained NMSSM, Gauge Mediated Supersymmetry Breaking, U(1)'-extensions, CP and R-parity violation.

Boom-and-Bust Development Patterns Across the Amazon Deforestation Frontier

Abstract: The Brazilian Amazon is globally important for biodiversity, climate, and geochemical cycles, but is also among the least developed regions in Brazil. Economic development is often pursued through forest conversion for cattle ranching and agriculture, mediated by logging. However, on the basis of an assessment of 286 municipalities in different stages of deforestation, we found a boom-and-bust pattern in levels of human development across the deforestation frontier. Relative standards of living, literacy, and life expectancy increase as deforestation begins but then decline as the frontier evolves, so that pre- and postfrontier levels of human development are similarly low. New financial incentives and policies are creating opportunities for a more sustained development trajectory that is not based on the depletion of nature and ecosystem services.

Globalization and human cooperation

Abstract: Globalization magnifies the problems that affect all people and that require large-scale human cooperation, for example, the overharvesting of natural resources and human-induced global warming. However, what does globalization imply for the cooperation needed to address such global social dilemmas? Two competing hypotheses are offered. One hypothesis is that globalization prompts reactionary movements that reinforce parochial distinctions among people. Large-scale cooperation then focuses on favoring one's own ethnic, racial, or language group. The alternative hypothesis suggests that globalization strengthens cosmopolitan attitudes by weakening the relevance of ethnicity, locality, or nationhood as sources of identification. In essence, globalization, the increasing interconnectedness of people worldwide, broadens the group boundaries within which individuals perceive they belong. We test these hypotheses by measuring globalization at both the country and individual levels and analyzing the relationship between globalization and individual cooperation with distal others in multilevel sequential cooperation experiments in which players can contribute to individual, local, and/or global accounts. Our samples were drawn from the general populations of the United States, Italy, Russia, Argentina, South Africa, and Iran. We find that as country and individual levels of globalization increase, so too does individual cooperation at the global level vis-a-vis the local level. In essence, “globalized” individuals draw broader group boundaries than others, eschewing parochial motivations in favor of cosmopolitan ones. Globalization may thus be fundamental in shaping contemporary large-scale cooperation and may be a positive force toward the provision of global public goods.

Biodiversity of cyanobacteria and green algae on monuments in the Mediterranean Basin: an overview

Abstract: The presence and deteriorating action of micro-organisms on monuments and stone works of art have received considerable attention in the last few years. Knowledge of the microbial populations living on stone materials is the starting point for successful conservation treatment and control. This paper reviews the literature on cyanobacteria and chlorophyta that cause deterioration of stone cultural heritage (outdoor monuments and stone works of art) in European countries of the Mediterranean Basin. Some 45 case studies from 32 scientific papers published between 1976 and 2009 were analysed. Six lithotypes were considered: marble, limestone, travertine, dolomite, sandstone and granite. A wide range of stone monuments in the Mediterranean Basin support considerable colonization of cyanobacteria and chlorophyta, showing notable biodiversity. About 172 taxa have been described by different authors, including 37 genera of cyanobacteria and 48 genera of chlorophyta. The most widespread and commonly reported taxa on the stone cultural heritage in the Mediterranean Basin are, among cyanobacteria, Gloeocapsa, Phormidium and Chroococcus and, among chlorophyta, Chlorella, Stichococcus and Chlorococcum. The results suggest that cyanobacteria and chlorophyta colonize a wide variety of substrata and that this is related primarily to the physical characteristics of the stone surface, microclimate and environmental conditions and secondarily to the lithotype.

Genome-Wide Identification of Saccharomyces cerevisiae Genes Required for Maximal Tolerance to Ethanol

Abstract: The understanding of the molecular basis of yeast resistance to ethanol may guide the design of rational strategies to increase process performance in industrial alcoholic fermentations. In this study, the yeast disruptome was screened for mutants with differential susceptibility to stress induced by high ethanol concentrations in minimal growth medium. Over 250 determinants of resistance to ethanol were identified. The most significant gene ontology terms enriched in this data set are those associated with intracellular organization, biogenesis, and transport, in particular, regarding the vacuole, the peroxisome, the endosome, and the cytoskeleton, and those associated with the transcriptional machinery. Clustering the proteins encoded by the identified determinants of ethanol resistance by their known physical and genetic interactions highlighted the importance of the vacuolar protein sorting machinery, the vacuolar H+-ATPase complex, and the peroxisome protein import machinery. Evidence showing that vacuolar acidification and increased resistance to the cell wall lytic enzyme β-glucanase occur in response to ethanol-induced stress was obtained. Based on the genome-wide results, the particular role of the FPS1 gene, encoding a plasma membrane aquaglyceroporin which mediates controlled glycerol efflux, in ethanol stress resistance was further investigated. FPS1 expression contributes to decreased [3H]ethanol accumulation in yeast cells, suggesting that Fps1p may also play a role in maintaining the intracellular ethanol level during active fermentation. The increased expression of FPS1 confirmed the important role of this gene in alcoholic fermentation, leading to increased final ethanol concentration under conditions that lead to high ethanol production.

Signal restoration with overcomplete wavelet transforms: comparison of analysis and synthesis priors

Abstract: The variational approach to signal restoration calls for the minimization of a cost function that is the sum of a data fidelity term and a regularization term, the latter term constituting a 'prior'. A synthesis prior represents the sought signal as a weighted sum of 'atoms'. On the other hand, an analysis prior models the coefficients obtained by applying the forward transform to the signal. For orthonormal transforms, the synthesis prior and analysis prior are equivalent; however, for overcomplete transforms the two formulations are different. We compare analysis and synthesis e1-norm regularization with overcomplete transforms for denoising and deconvolution.

SN 2008S: An electron-capture SN from a super-AGB progenitor?

Abstract: We present comprehensive photometric and spectroscopic observations of the faint transient SN 2008S discovered in the nearby galaxy NGC 6946. SN 2008S exhibited slow photometric evolution and almost no spectral variability during the first nine months, implying a long photon diffusion time and a high-density circumstellar medium. Its bolometric luminosity (≃10^(41) erg s^(−)1 at peak) is low with respect to most core-collapse supernovae but is comparable to the faintest Type II-P events. Our quasi-bolometric light curve extends to 300 d and shows a tail phase decay rate consistent with that of ^(56)Co. We propose that this is evidence for an explosion and formation of ^(56)Ni (0.0014 ± 0.0003 M_⊙). Spectra of SN 2008S show intense emission lines of Hα, [Ca ii] doublet and Ca ii near-infrared (NIR) triplet, all without obvious P-Cygni absorption troughs. The large mid-infrared (MIR) flux detected shortly after explosion can be explained by a light echo from pre-existing dust. The late NIR flux excess is plausibly due to a combination of warm newly formed ejecta dust together with shock-heated dust in the circumstellar environment. We reassess the progenitor object detected previously in Spitzer archive images, supplementing this discussion with a model of the MIR spectral energy distribution. This supports the idea of a dusty, optically thick shell around SN 2008S with an inner radius of nearly 90 au and outer radius of 450 au, and an inferred heating source of 3000 K. The luminosity of the central star is L ≃ 10^(4.6) L_⊙ . All the nearby progenitor dust was likely evaporated in the explosion leaving only the much older dust lying further out in the circumstellar environment. The combination of our long-term multiwavelength monitoring data and the evidence from the progenitor analysis leads us to support the scenario of a weak electron-capture supernova explosion in a super-asymptotic giant branch progenitor star (of initial mass 6–8 M_⊙ ) embedded within a thick circumstellar gaseous envelope. We suggest that all of main properties of the electron-capture SN phenomenon are observed in SN 2008S and future observations may allow a definitive answer.

Nonlinear QCD meets data: A global analysis of lepton-proton scattering with running coupling Balitsky-Kovchegov evolution

Abstract: We perform a global fit to the structure function F{sub 2} measured in lepton-proton experiments at small values of Bjorken-x, x{<=}0.01, for all experimentally available values of Q{sup 2}, 0.045 GeV{sup 2}{<=}Q{sup 2}{<=}800 GeV{sup 2}. We show that the recent improvements resulting from the inclusion of running coupling corrections allow for a description of data in terms of nonlinear QCD evolution equations. In this approach F{sub 2} is calculated within the dipole model with all Bjorken-x dependence described by the running coupling Balitsky-Kovchegov equation. Two different initial conditions for the evolution are used, both yielding good fits to data with {chi}{sup 2}/d.o.f.<1.1. The proton longitudinal structure function F{sub L}, not included in the fits, is also well described. Our analysis allows to perform a first principle extrapolation of the proton-dipole scattering amplitude once the initial condition has been fitted to presently available data. We provide predictions for F{sub 2} and F{sub L} in the kinematical regions of interest for future colliders and ultra-high energy cosmic rays. A numerical implementation of our results down to x=10{sup -12} is released as a computer code for public use.

Homogenization of Climate Data: Review and New Perspectives Using Geostatistics

Abstract: The homogenization of climate data is of major importance because non-climatic factors make data unrepresentative of the actual climate variation, and thus the conclusions of climatic and hydrological studies are potentially biased. A great deal of effort has been made in the last two decades to develop procedures to identify and remove non-climatic inhomogeneities. This paper reviews the characteristics of several widely used procedures and discusses the potential advantages of geostatistical techniques. In a case study, the geostatistical simulation approach is applied to precipitation data from 66 monitoring stations located in the southern region of Portugal (1980–2001). The results from this procedure are then compared with those from three well established statistical tests: the Standard normal homogeneity test (SNHT) for a single break, the Buishand range test, and the Pettit test. Promising results from the case study open new research perspectives on the homogenization of climate time series.