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2009
Oliveira, F., A. J. Soares, and G. Kremer. "H-theorem and trend to equilibrium of chemically reacting mixtures of gases." Kinetic and Related Models. 2 (2009): 333-343.Website
Lourenço, João M., Nuno Preguiça, Ricardo J. Dias, João Nuno Silva, João Garcia, and Luís Veiga NGenVM: New Generation Execution Environments. EuroSys. Nuremberg, Germany, 2009. Abstractngenvm-poster.pdf

This document describes a work-in-progress development of NGen-VM, a distributed infrastructure that manages execution environments with run-time and programming language support targeting applications developed in the Java programming language, deployed over clusters of many-core computers. For each running application or suite of related applications, a dedicated single-system image will be provided, regardless of the concurrent threads running on a single machine (on several cores) or scattered on different computers. Such system images rely on a single model for concurrency management (Transactional Shared Memory Model), in order fill the gap between the hardware infrastructure of clusters of many-core nodes and the application runtime that is independent from that hardware infrastructure. Interactions between threads in the same tasks will be supported by a Transactional Memory framework that provides the programming language with Atomic and Isolated code regions. Interactions between thread on different machines will also use the Transactional Memory model, but now resorting to a Distributed Shared Memory abstraction.

Amado, Miguel P., J. Pinto, C. V. Santos, E. B. Moura, and V. G. Silva. "Public Participation in Sustainable Urban Planning." Journal of World Academy of Science, Enginnering and Techonology.Vol. 53 (2009): pp.597-603.
Santos Oliveira, J. F., B. Mendes, and N. Lapa Resíduos: Gestão, Tratamento e sua Problemática em Portugal. Lisboa: Lidel, 2009.Website
Ramos, Luís, Manuel L. Esquível, João T. Mexia, and João L. Silva. "Some Asymptotic Expansions and Distribution Approximations outside a CLT Context." Proceedings of 6th St. Petersburg Workshop on Simulation. 1. 2009. 444-448. Abstract
Some asymptotic expansions non necessarily related to the central limit theorem are discussed. After observing that the smoothing inequality of Esseen implies the proximity, in the Kolmogorov distance sense, of the distributions of the random variables of two random sequences satisfying a sort of general asymptotic relation, two instances of this observation are presented. A first example, partially motivated by the the statistical theory of high precision measurements, is given by a uniform asymptotic approximation to $(g(X+ μ_n))_{n ın \mathbbm{N}}$, where $g$ is some smooth function, $X$ is a random variable having a moment and a bounded density and $(μ_{n})_{n ın \mathbbm{N}}$ is a sequence going to infinity; the multivariate case as well as the proofs and a complete set of references will be published elsewhere. We next present a second class of examples given by a randomization of the interesting parameter in some classical asymptotic formulas, namely, a generic Laplace's type integral, by the sequence $(μ_n X)_{n ın \mathbbm{N}}$, $X$ being a Gamma distributed random variable. Finally, a simulation study of this last example is presented in order to stress the quality of asymptotic approximations proposed.
Salema, Maria Isabel Gomes, Ana Paula Barbosa Póvoa, and Augusto Q. Novais. "A strategic and tactical model for closed-loop supply chains." OR Spectrum. 31 (2009): 573-599. AbstractWebsite

In this paper, a strategic location-allocation model is developed for the simultaneous design of forward and reverse supply chains. Strategic decisions such as network design are accounted for together with tactical decisions, namely, production, storage and distribution planning. The integration between strategic and tactical decisions is achieved by considering two interconnected time scales: a macro and a micro time. At macro level, the supply chain is designed in order to account for the existing demands and returns, whose satisfaction is planned simultaneously at the micro level where tactical decisions are taken. A Mixed Integer Linear Programming formulation is obtained which is solved to optimality using standard Branch & Bound techniques. Finally, the model accuracy and applicability is illustrated through the resolution of a case study.

Figueiredo, Ondina M., Teresa Pereira Silva, and João Pedro Veiga. "Ancient glazed ceramic tiles: a long-term, study from the remediation of environmental impacts to the non-destructive characterization of materials." Proceedings of the International Seminar on Conservation of Glazed Ceramic Tiles: Research and Practice. 2009. Abstract
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Silva, Tiago A. N., C. R. Leal, A. Rodrigues, M. F. Bento, and João M. C. Travassos Anisotropic Solutions Applied to a Smart Damper. IV ECCOMAS Thematic Conference on Smart Structures and Materials (SMART'09)., 2009. Abstract
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Neves, ER, S. Schafer, A. Phillips, J. Canejo, and MF Macedo. "Antifungal effect of different methyl and propyl paraben mixtures on the treatment of paper biodeterioration." International Biodeterioration & Biodegradation. 63 (2009): 267-272. Abstract
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Roque, A. A., Tiago A. N. Silva, J. M. F. Calado, and J. C. Q. Dias An Approach to Fault Diagnosis of Rolling Bearings. Vol. 4. WSEAS TRANSACTIONS on SYSTEMS and CONTROL, 4.4. World Scientific and Engineering Academy and Society (WSEAS), 2009. Abstract
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Abdollahzadeh, J., EM Goltapeh, A. Javadi, M. Shams-Bakhsh, R. Zare, and AJL Phillips. "Barriopsis iraniana and Phaeobotryon cupressi: two new species of the Botryosphaeriaceae from trees in Iran." Persoonia. 23 (2009): 1-8. Abstract
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Figueiredo, Ondina M., Teresa Pereira Silva, João Pedro Veiga, Isabel M. Prudêncio, Isabel M. Dias, Maria Antónia Matos, and Alexandre Manuel Pais. "Blue pigments in XVI-XVII century glazes: a comparative study between portuguese faiences and contemporary chinese porcelains manufactured for portuguese market." 18th International Materials Research Congress & 2nd Latin-American Symposium Physics & Chemistry Methods in Archeology, Art and Cultural Heritage Conservation, LASMAC-IMRS2009, August 16-20, 2009. 2009. Abstract
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Conrath, K., AS Pereira, C. E. Martins, C. G. Timoteo, P. Tavares, S. Spinelli, J. Kinne, C. Flaudrops, C. Cambillau, S. Muyldermans, I. Moura, JJG Moura, M. Tegoni, and A. Desmyter. "Camelid nanobodies raised against an integral membrane enzyme, nitric oxide reductase." Protein Science. 18 (2009): 619-628. AbstractWebsite

Nitric Oxide Reductase (NOR) is an integral membrane protein performing the reduction of NO to N(2)O. NOR is composed of two subunits: the large one (NorB) is a bundle of 12 transmembrane helices (TMH). It contains a b type heme and a binuclear iron site, which is believed to be the catalytic site, comprising a heme b and a non-hemic iron. The small subunit (NorC) harbors a cytochrome c and is attached to the membrane through a unique TMH. With the aim to perform structural and functional studies of NOR, we have immunized dromedaries with NOR and produced several antibody fragments of the heavy chain (VHHs, also known as nanobodies (TM)). These fragments have been used to develop a faster NOR purification procedure, to proceed to crystallization assays and to analyze the electron transfer of electron donors. BIAcore experiments have revealed that up to three VHHs can bind concomitantly to NOR with affinities in the nanomolar range. This is the first example of the use of VHHs with an integral membrane protein. Our results indicate that VHHs are able to recognize with high affinity distinct epitopes on this class of proteins, and can be used as versatile and valuable tool for purification, functional study and crystallization of integral membrane proteins.

Meil, Pamela, Maria Stratigaki, Petros Linardos, Per Tengblad, Peter Docherty, Duco Bannink, Antonio Moniz, Margarida Paulos, Bettina Krings, and Linda Nierling Challenges for Europe under value chain restructuring: Contributions to policy debates., 2009. Abstract

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Jacobs, LL, O. Mateus, M. J. Polcyn, AS Schulp, CR Scotese, A. Goswami, KM Ferguson, JA Robbins, DP Vineyard, and AB Neto. "Cretaceous paleogeography, paleoclimatology, and amniote biogeography of the low and mid-latitude South Atlantic Ocean." Bulletin de la Societe Geologique de France. 180 (2009): 333-341. Abstract
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Jacobs, L., M. Polcyn, O. Mateus, Schulp, and A. Neto. "The Cretaceous Skeleton Coast of Angola." Journal of Vertebrate Paleontology. 29 (2009): 121. Abstract
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Jacobs, LL, M. J. Polcyn, O. Mateus, AS Schulp, and A. Neto. "The Cretaceous Skeleton Coast of Angola." Journal of Vertebrate Paleontology. 29 (2009): 121. Abstract
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Guerra, M., F. Parente, and J. P. Santos. "Electron impact ionization of atomic target inner-shells." Journal of Physics: Conference Series. 194 (2009): 042047. AbstractWebsite
There is a need for reliable theoretical methods to calculate electron-impact total ionization cross sections for the large number of neutral atoms and ions with open shell structures. These cross sections are used in a wide range of scientific and industrial applications, such as astrophysical plasmas, atmospheric science, X-ray lasers, magnetic fusion, radiation physics, semiconductor fabrication, accelerator physics and tumor therapy physics. The binary-encounter-Bethe (BEB) model [1], using an analytic formula that requires only two atomic constants, the binding energy and kinetic energy of the electrons, generates direct ionization cross sections for any neutral atom (or molecule), which are reliable in intensity (15%) and shape from the ionization threshold to a few keV in the incident energy [3], or to thousands keV if we consider its relativistic version(RBEB) [2]. In this work we present K- and L-shell ionization cross sections calculations for heavy atoms.
Guerra, M., F. Parente, and J. P. Santos. "Electron impact ionization of atomic target inner-shells." Journal of Physics: Conference Series. 194 (2009): 042047. AbstractWebsite

There is a need for reliable theoretical methods to calculate electron-impact total ionization cross sections for the large number of neutral atoms and ions with open shell structures. These cross sections are used in a wide range of scientific and industrial applications, such as astrophysical plasmas, atmospheric science, X-ray lasers, magnetic fusion, radiation physics, semiconductor fabrication, accelerator physics and tumor therapy physics. The binary-encounter-Bethe (BEB) model [1], using an analytic formula that requires only two atomic constants, the binding energy and kinetic energy of the electrons, generates direct ionization cross sections for any neutral atom (or molecule), which are reliable in intensity (15%) and shape from the ionization threshold to a few keV in the incident energy [3], or to thousands keV if we consider its relativistic version(RBEB) [2]. In this work we present K- and L-shell ionization cross sections calculations for heavy atoms.

Filonovich, SA, H. Aguas, I. Bernacka-Wojcik, C. Gaspar, M. Vilarigues, LB Silva, E. Fortunato, and R. Martins. "Highly conductive p-type nanocrystalline silicon films deposited by RF-PECVD using silane and trimethylboron mixtures at high pressure." Vacuum. 83.10 (2009): 1253-1256. Abstract
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Filonovich, SA, H. Aguas, I. Bernacka-Wojcik, C. Gaspar, M. Vilarigues, LB Silva, E. Fortunato, and R. Martins. "Highly conductive p-type nanocrystalline silicon films deposited by RF-PECVD using silane and trimethylboron mixtures at high pressure." Vacuum. 83 (2009): 1253-1256. Abstract
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Santos-Silva, T., F. Ferroni, A. Thapper, J. Marangon, P. J. González, A. C. Rizzi, I. Moura, JJG Moura, MJ Romão, and CD Brondino. "Kinetic, structural, and EPR studies reveal that aldehyde oxidoreductase from Desulfovibrio gigas does not need a sulfido ligand for catalysis and give evidence for a direct Mo-C interaction in a biological system." Journal of the American Chemical Society. 131 (2009): 7990-7998. Abstract
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Silva, V., J. Fernandes, L. B. Oliveira, M. Véstias, and H. Neto. "Magnetic RAM Reconfigurable Array." (2009). Abstract
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Silva, M., H. Machado, and AJL Phillips. "Mycosphaerella species occurring on Eucalyptus globulus in Portugal." European Journal of Plant Pathology. 125 (2009): 425-433. Abstract
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Martins, R., Leandro Raniero, Luis Pereira, Daniel Costa†, Hugo Aguas, Sonia Pereira, Leonardo Silva, A. Gonçalves, I. Ferreira, and E. Fortunato. "Nanostructured silicon and its application to solar cells, position sensors and thin film transistors." Philosophical Magazine. 89.28-30 (2009): 2699-2721. Abstract
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