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2010
Friedrich, Nikolas, Joana M. Santos, Yan Liu, Angelina S. Palma, Ester Leon, Savvas Saouros, Makoto Kiso, Michael J. Blackman, Stephen Matthews, Ten Feizi, and Dominique Soldati-Favre. "Members of a Novel Protein Family Containing Microneme Adhesive Repeat Domains Act as Sialic Acid-binding Lectins during Host Cell Invasion by Apicomplexan Parasites." Journal of Biological Chemistry. 285 (2010): 2064-2076. Abstract
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Ferreira, AJ, C. Cruz, M. H. Godinho, PS Kulkarni, CAM Afonso, and Paulo Ivo Cortez Teixeira. "Shear-induced lamellar ionic liquid-crystal foam." Liquid Crystals. 37.4 (2010): 377-382. Abstract
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Paulino, Hervé, João André Martins, João Louren{\c c}o, and Nuno Duro. "SmART: An Application Reconfiguration Framework." Complex Systems Design & Management. Eds. Marc Aiguier, Francis Bretaudeau, and Daniel Krob. Springer Berlin Heidelberg, 2010. 73-84. Abstract
SmART (Smart Application Reconfiguration Tool) is a framework for the automatic configuration of systems and applications. The tool implements an application configuration workflow that resorts to the similarities between configuration files (i.e., patterns such as parameters, comments and blocks) to allow a syntax independent manipulation and transformation of system and application configuration files.Without compromising its generality, SmART targets virtualized IT infrastructures, configuring virtual appliances and its applications. SmART reduces the time required to (re)configure a set of applications by automating time-consuming steps of the process, independently of the nature of the application to be configured. Industrial experimentation and utilization of SmART show that the framework is able to correctly transform a large amount of configuration files into a generic syntax and back to their original syntax. They also show that the elapsed time in that process is adequate to what would be expected of an interactive tool. SmART is currently being integrated into the VIRTU bundle, whose trial version is available for download from the project’s web page.
Nunes, Isabel L., and Jurek Kirakowski Usabilidade de interfaces – versão Portuguesa do Software Usability Measurement Inventory (SUMI) [Interfaces Usability – Portuguese version of the Software Usability Measurement Inventory (SUMI)]. Eds. P. Arezes, J. S. Baptista, M. P. Barroso, P. Carneiro, P. Cordeiro, N. Costa, R. Melo, A. S. Miguel, and G. P. Perestrelo. Occupational Safety and Hygiene (SHO10). Guimarães - Portugal: SPOSHO, 2010. Abstract
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Barquinha, Pedro, Luis Pereira, Gonçalo Gonçalves, Danjela Kuscer, Marija Kosec, Anna Vilà, Antonis Olziersky, Juan Ramon Morante, Rodrigo Martins, and Elvira Fortunato. "{Low-temperature sputtered mixtures of high-$ąppa$ and high bandgap dielectrics for GIZO TFTs}." Journal of the Society for Information Display. 18 (2010): 762. AbstractWebsite
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2009
Karlovich, Alexei Yu., and Ilya M. Spitkovsky. "Connectedness of spectra of Toeplitz operators on Hardy spaces with Muckenhoupt weights over Carleson curves." Integral Equations and Operator Theory. 65.1 (2009): 83-114. AbstractWebsite

Harold Widom proved in 1966 that the spectrum of a Toeplitz operator \(T(a)\) acting on the Hardy space \(H^p(\mathbb{T})\) over the unit circle \(\mathbb{T}\) is a connected subset of the complex plane for every bounded measurable symbol \(a\) and \(1 < p < \infty\). In 1972, Ronald Douglas established the connectedness of the essential spectrum of \(T(a)\) on \(H^2(\mathbb{T})\). We show that, as was suspected, these results remain valid in the setting of Hardy spaces \(H^p(\Gamma,w)\), \( 1 < p < \infty \), with general Muckenhoupt weights \(w\) over arbitrary Carleson curves \(\Gamma\).

Eberth, David A., Yoshitsugu Kobayashi, Yuong-Nam Lee, Octávio Mateus, François Therrien, Darla K. Zelenitsky, and Mark A. Norell. "Assignment of Yamaceratops dorngobiensis and associated redbeds at Shine Us Khudag (eastern Gobi, Dorngobi Province, Mongolia) to the redescribed Javkhlant Formation (Upper Cretaceous)." Journal of Vertebrate Paleontology. 29 (2009): 295-302. AbstractWebsite
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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, J. J. Moura, M. Tegoni, and A. Desmyter. "Camelid nanobodies raised against an integral membrane enzyme, nitric oxide reductase." Protein Sci. 18 (2009): 619-28. 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). 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.

Moura, J., L. Krippahl, S. Pauleta, R. Almeida, and S. Del Acqua. "Molecular interactions/electron transfer protein complexes using Docking algorithms, spectroscopy (NMR) and site direct mutagenesis." Febs Journal. 276 (2009): 11. AbstractWebsite
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Almeida, PL; Kundu, S.; Borges, JP; Godinho, and MH; Figueirinhas. "Electro-optical light scattering shutter using electrospun cellulose-based nano- and microfibers." 95 (2009): –-. Abstract
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Barquinha, P., L. Pereira, G. GONCALVES, R. Martins, D. Kuscer, M. Kosec, and E. Fortunato. "Performance and Stability of Low Temperature Transparent Thin-Film Transistors Using Amorphous Multicomponent Dielectrics." Journal of the Electrochemical Society. 156 (2009): H824-H831. AbstractWebsite
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Karlovich, Alexei Yu. "Asymptotics of Toeplitz matrices with symbols in some generalized Krein algebras." Modern Analysis and Applications: Mark Krein Centenary Conference, Vol. 1. Operator Theory Advances and Applications, 190. Eds. V. Adamyan, Y. Berezansky, I. Gohberg, M. Gorbachuk, V. Gorbachuk, A. Kochubei, H. Langer, and G. Popov. Basel: Birkhäuser, 2009. 341-359. Abstract

Let \(\alpha,\beta\in(0,1)\) and
\[
K^{\alpha,\beta}:=\left\{a\in L^\infty(\mathbb{T}):\
\sum_{k=1}^\infty |\widehat{a}(-k)|^2 k^{2\alpha}<\infty,\
\sum_{k=1}^\infty |\widehat{a}(k)|^2 k^{2\beta}<\infty
\right\}.
\]
Mark Krein proved in 1966 that \(K^{1/2,1/2}\) forms a Banach algebra. He also observed that this algebra is important in the asymptotic theory of finite Toeplitz matrices. Ten years later, Harold Widom extended
earlier results of Gabor Szegö for scalar symbols and established the asymptotic trace formula
\[
\operatorname{trace}f(T_n(a))=(n+1)G_f(a)+E_f(a)+o(1)
\quad\text{as}\ n\to\infty
\]
for finite Toeplitz matrices \(T_n(a)\) with matrix symbols \(a\in K^{1/2,1/2}_{N\times N}\). We show that if \(\alpha+\beta\ge 1\) and \(a\in K^{\alpha,\beta}_{N\times N}\), then the Szegö-Widom asymptotic trace formula holds with \(o(1)\) replaced by \(o(n^{1-\alpha-\beta})\).

Schoch, CL, PW Crous, JZ Groenewald, EWA Boehm, TI Burgess, J. de Gruyter, GS de Hoog, LJ Dixon, M. Grube, C. Gueidan, Y. Harada, S. Hatakeyama, K. Hirayama, T. Hosoya, SM Huhndorf, KD Hyde, EBG Jones, J. Kohlmeyer, A. Kruys, YM Li, R. Lucking, HT Lumbsch, L. Marvanova, JS Mbatchou, AH Mcvay, AN Miller, GK Mugambi, L. Muggia, MP Nelsen, P. Nelson, CA Owensby, AJL Phillips, S. Phongpaichit, SB Pointing, V. Pujade-Renaud, HA Raja, ER Plata, B. Robbertse, C. Ruibal, J. Sakayaroj, T. Sano, L. Selbmann, CA Shearer, T. Shirouzu, B. Slippers, S. Suetrong, K. Tanaka, B. Volkmann-Kohlmeyer, MJ WINGFIELD, AR Wood, JHC Woudenberg, H. Yonezawa, Y. Zhang, and JW Spatafora. "A class-wide phylogenetic assessment of Dothideomycetes." Studies in Mycology. 64 (2009): 1-15. Abstract

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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
Karlovich, Alexei Yu. "Remark on the boundedness of the Cauchy singular integral operator on variable Lebesgue spaces with radial oscillating weights." Journal of Function Spaces and Applications. 7 (2009): 301-311. AbstractWebsite

Recently V. Kokilashvili, N. Samko, and S. Samko have proved a sufficient condition for the boundedness of the Cauchy singular integral operator on variable Lebesgue spaces with radial oscillating weights over Carleson curves. This condition is formulated in terms of Matuszewska-Orlicz indices of weights. We prove a partial converse of their result.

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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Almeida, PL, S. Kundu, D. Beja, J. Fonseca, J. L. Figueirinhas, and M. H. Godinho. "Deformation of isotropic and anisotropic liquid droplets dispersed in a cellulose liquid crystalline derivative." Cellulose. 16.3 (2009): 427-434. Abstract
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Almeida, PL, S. Kundu, J. P. Borges, M. H. Godinho, and J. L. Figueirinhas. "Electro-optical light scattering shutter using electrospun cellulose-based nano-and microfibers." Applied Physics Letters. 95.4 (2009): 043501. Abstract
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Araújo, João, and Janusz Konieczny. "General theorems on automorphisms of semigroups and their applications." J. Aust. Math. Soc.. 87 (2009): 1-17. AbstractWebsite
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Rivas, M. G., M. S. P. Carepo, C. S. Mota, M. Korbas, M. C. Durand, A. T. Lopes, CD Brondino, AS Pereira, GN George, A. Dolla, JJG Moura, and I. Moura. "Molybdenum Induces the Expression of a Protein Containing a New Heterometallic Mo-Fe Cluster in Desulfovibrio alaskensis." Biochemistry. 48 (2009): 873-882. AbstractWebsite

The characterization of a novel Mo-Fe protein (MorP) associated with a system that responds to Mo in Desulfovibrio alaskensis is reported. Biochemical characterization shows that MorP is a periplasmic homomultimer of high molecular weight (260 +/- 13 kDa) consisting of 16-18 monomers of 15321.1 +/- 0.5 Da. The UV/visible absorption spectrum of the as-isolated protein shows absorption peaks around 280, 320, and 570 nm with extinction coefficients of 18700, 12800, and 5000 M(-1) cm(-1), respectively. Metal content, EXAFS data and DFT calculations support the presence of a Mo-2S-[2Fe-2S]-2S-Mo cluster never reported before. Analysis of the available genomes from Desulfovibrio species shows that the MorP encoding gene is located downstream of a sensor and a regulator gene. This type of gene arrangement, called two component system, is used by the cell to regulate diverse physiological processes in response to changes in environmemtal conditions. Increase of both gene expression and protein production was observed when cells were cultured in the presence of 45 mu M molybdenum. Involvement of this system in Mo tolerance of sulfate reducing bacteria is proposed.

Childs, Robert A., Angelina S. Palma, Steve Wharton, Tatyana Matrosovich, Yan Liu, Wengang Chai, Maria A. Campanero-Rhodes, Yibing Zhang, Markus Eickmann, Makoto Kiso, Alan Hay, Mikhail Matrosovich, and Ten Feizi. "Receptor-binding specificity of pandemic influenza A (H1N1) 2009 virus determined by carbohydrate microarray." Nature Biotechnology. 27 (2009): 797-799. Abstract
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Valtchev, Stanimir, Beatriz Borges, Kostadin Brandisky, and Ben J. Klaassens. "Resonant Contactless Energy Transfer With Improved Efficiency." IEEE Transactions on Power Electronics. 24 (2009): 685-699. AbstractWebsite
This paper describes the theoretical and experimental results achieved in optimizing the application of the series loaded series resonant converter for contactless energy transfer. The main goal of this work is to define the power stage operation mode that guarantees the highest possible efficiency. The results suggest a method to select the physical parameters (operation frequency, characteristic impedance, transformer ratio, etc.) to achieve that efficiency improvement. The research clarifies also the effects of the physical separation between both halves of the ferromagnetic core on the characteristics of the transformer. It is shown that for practical values of the separation distance, the leakage inductance, being part of the resonant inductor, remains almost unchanged. Nevertheless, the current distribution between the primary and the secondary windings changes significantly due to the large variation of the magnetizing inductance. An approximation in the circuit analysis permits to obtain more rapidly the changing values of the converter parameters. The analysis results in a set of equations which solutions are presented graphically. The graphics show a shift of the best efficiency operation zone, compared to the converter with an ideally coupled transformer. Experimental results are presented confirming that expected tendency.
Valtchev, S., B. Borges, K. Brandisky, and JB Klaassens. "Resonant contactless energy transfer with improved efficiency." IEEE Transactions on Power Electronics. 24 (2009): 685-699. Abstract
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