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2011
Sampaio, P, Ferreira P, Veiga L.  2011.  Transparent scalability with clustering for Java e-science applications. Proceedings of the 11th IFIP WG 6.1 international conference on Distributed applications and interoperable systems. :270–277., Berlin, Heidelberg: Springer-Verlag Abstract2011-dais-sampaio.pdf

The two-decade long history of events relating object-oriented programming, the development of persistence and transactional support, and the aggregation of multiple nodes in a single-system image cluster, appears to convey the following conclusion: programmers ideally would develop and deploy applications against a single shared global memory space (heap of objects) of mostly unbounded capacity, with implicit support for persistence and concurrency, transparently backed by a possibly large number of clustered physical machines.

In this paper, we propose a new approach to the design of OODB systems for Java applications: (O3)2 (pronounced ozone squared). It aims at providing to developers a single-system image of virtually unbounded object space/heap with support for object persistence, object querying, transactions and concurrency enforcement, backed by a cluster of multi-core machines with Java VMs that is kept transparent to the user/developer. It is based on an existing persistence framework (ozone-db) and the feasibility and performance of our approach has been validated resorting to the OO7 benchmark.

Palma, LB, Coito FV.  2011.  Tuning PCA controllers based on manual control data. Emerging Technologies & Factory Automation (ETFA), 2011 IEEE 16th Conference on. :1–4.: IEEE. Abstract

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Nunes, N, Araújo T, Gamboa H.  2011.  Two-Modes Cyclic Biosignal Clustering based on Time Series Analysis. Proceedings of Biosignals - International Conference on Bio-inspired Systems and Signal Processing (BIOSTEC 2011). , Rome, Italy
Luís, JE.  2011.  TxBtrfs — A Transactional Snapshot-based File System. FCT - Universidade Nova de Lisboa. (João M. Lourenço, Ed.).: Universidade Nova de Lisboa Abstract2011-joao_luis.pdf

Several decades ago, the file system was the container of choice for large bulks of related information, kept in hundreds of files, and relying on applications specifically created to handle them. These configurations weren't scalable and could easily become difficult to maintain, leading to the development and adoption of Database Management Systems (DBMS). These systems, capable of efficiently handling vast amounts of data, allowed heavy concurrency without requiring the programmer to deal with concurrency-control mechanisms, by encapsulating operations within transactions.
The properties of Transactions rapidly became an object of desire by many, and efforts to bring them to general-purpose programming environments began. In recent years there have been breakthroughs in bringing the transactional semantics to memory, using Software Transactional Memory (STM), providing abstractions to concurrency-control on the application-level. However, STM failed to meet some expectations, specially regarding I/O operations, forcing the abstraction to go deeper in the system: directly to the file system.
In this document we shall discuss file systems in general, their properties and common structure, although focusing in those with transactional or versioning capabilities. Later on, we will present our proposed enhancement of an existing Linux file system (Btrfs), in order to offer transactional semantics to applications, while detecting potential conflicts between concurrent flows of execution and reconciling their changes whenever possible.

Coito, F, Palma LB.  2011.  Unfalsification based Fault Tolerant Controller. Emerging Technologies & Factory Automation (ETFA), 2011 IEEE 16th Conference on. :1–4.: IEEE. Abstract

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Atilano, ML, Yates J, Glittenberg M, Filipe* SR, Ligoxygakis* P.  2011.  Wall teichoic acids of Staphylococcus aureus limit recognition by the Drosophila Peptidoglycan Recognition Protein-SA to promote pathogenicity. PLoS Pathogens. 7:e1002421.
Fortunato, E, Martins R.  2011.  Where science fiction meets reality? With oxide semiconductors! Phys. Status Solidi-Rapid Res. Lett. . 5:336-339.
Godinho, LM, de Sá-Nogueira I.  2011.  Characterization and regulation of a bacterial sugar phosphatase of the haloalkanoate dehalogenase superfamily, AraL, from Bacillus subtilis. FEBS Journal. 278:2511–2524., Number 14 Abstract

AraL from Bacillus subtilis is a member of the ubiquitous haloalkanoate dehalogenase superfamily. The araL gene has been cloned, over-expressed in Escherichia coli and its product purified to homogeneity. The enzyme displays phosphatase activity, which is optimal at neutral pH (7.0) and 65 °C. Substrate screening and kinetic analysis showed AraL to have low specificity and catalytic activity towards several sugar phosphates, which are metabolic intermediates of the glycolytic and pentose phosphate pathways. On the basis of substrate specificity and gene context within the arabinose metabolic operon, a putative physiological role of AraL in the detoxification of accidental accumulation of phosphorylated metabolites has been proposed. The ability of AraL to catabolize several related secondary metabolites requires regulation at the genetic level. In the present study, using site-directed mutagenesis, we show that the production of AraL is regulated by a structure in the translation initiation region of the mRNA, which most probably blocks access to the ribosome-binding site, preventing protein synthesis. Members of haloalkanoate dehalogenase subfamily IIA and IIB are characterized by a broad-range and overlapping specificity anticipating the need for regulation at the genetic level. We provide evidence for the existence of a genetic regulatory mechanism controlling the production of AraL.

de Sa, MH, Ferreira JL, Melo MJ, Ramos AM.  2011.  An AFM contribution to the understanding of surface effects caused by ageing and cleaning on acrylic glass. The Shadows by Lourdes Castro, a case study. Surface and Interface Analysis. 43:1165-1170., Number 8 AbstractWebsite
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de Sa, MH, Eaton P, Ferreira JL, Melo MJ, Ramos AM.  2011.  Ageing of vinyl emulsion paints - an atomic force microscopy study. Surface and Interface Analysis. 43:1160-1164., Number 8 AbstractWebsite
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Baptista, {PV}, c}alo Doria G{\c, Conde J.  2011.  Alloy metal nanoparticles for multicolor cancer diagnostics. Colloidal Quantum Dots/Nanocrystals for Biomedical Applications VI. : SPIE-International Society for Optical Engineering Abstract

Cancer is a multigenic complex disease where multiple gene loci contribute to the phenotype. The ability to simultaneously monitor differential expression originating from each locus results in a more accurate indicator of degree of cancerous activity than either locus alone. Metal nanoparticles have been thoroughly used as labels for in vitro identification and quantification of target sequences. We have synthesized nanoparticles with assorted noble metal compositions in an alloy format and functionalized them with thiol-modified ssDNA (nanoprobes). These nanoprobes were then used for the simultaneous specific identification of several mRNA targets involved in cancer development - one pot multicolor detection of cancer expression. The different metal composition in the alloy yield different {"}colors{"} that can be used as tags for identification of a given target. Following a non-cross-linking hybridization procedure previously developed in our group for gold nanoprobes, these multicolor nanoprobes were used for the molecular recognition of several different targets including differently spliced variants of relevant genes (e.g. gene products involved in chronic myeloid leukemia BCR, ABL, BCR-ABL fusion product). Based on the spectral signature of mixtures, before and after induced aggregation of metal nanoparticles, the correct identification could be made. Further application to differentially quantify expression of each locus in relation to another will be presented. The differences in nanoparticle stability and labeling efficiency for each metal combination composing the colloids, as well as detection capability for each nanoprobe will be discussed. Additional studies will be conducted towards allele specific expression studies.

Lima, JC, Rodriguez L.  2011.  Applications of gold(I) alkynyl systems: a growing field to explore. Chemical Society Reviews. 40:5442-5456., Number 11 Abstract
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Costa, JC, Ortigueira MD, Batista AG.  2011.  ARMA Modelling of Sleep Spindles. Second IFIP WG 5.5/SOCOLNET Doctoral Conference on Computing, Electrical and Industrial Systems. : Doceis Abstract
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Viegas, A, Manso J, Corvo MC, Marques MMB, Cabrita EJ.  2011.  Binding of ibuprofen, ketorolac and diclofenac to COX-1 and COX-2 studied by saturation transfer difference NMR. Journal of Medicinal Chemistry. 54:8555-8562. AbstractWebsite

Saturation Transfer Difference-NMR (STD-NMR) spectroscopy has emerged as a powerful screening tool and a straightforward way to study the binding epitopes of active compounds in early stage lead discovery in pharmaceutical research. Here we report the application of STD NMR to characterize the binding of the anti-inflammatory drugs ibuprofen, diclofenac and ketorolac to COX-1 and COX-2. Using well-studied COX inhibitors and by comparing STD signals with crystallographic structures we show that there is a relation between the orientations of ibuprofen and diclofenac in the COX-2 active site and the relative STD responses detected in the NMR experiments. Based on this analysis we propose that ketorolac should bind to the COX-2 active site in similar orientation as that of diclofenac. We also show that the combination of STD NMR with competition experiments constitutes a valuable tool to address the recently proposed behavior of COX-2 as functional heterodimers and complement enzyme activity studies in the effort to rationalize COX inhibition mechanisms.

Viegas, A, Manso J, Corvo M, Marques MM, Cabrita EJ.  2011.  Binding of ibuprofen, ketorolac, and diclofenac to COX-1 and COX-2 studied by saturation transfer difference NMR. J Med Chem. 54:8555-62., Number 24 AbstractWebsite

Saturation transfer difference NMR (STD-NMR) spectroscopy has emerged as a powerful screening tool and a straightforward way to study the binding epitopes of active compounds in early stage lead discovery in pharmaceutical research. Here we report the application of STD-NMR to characterize the binding of the anti-inflammatory drugs ibuprofen, diclofenac, and ketorolac to COX-1 and COX-2. Using well-studied COX inhibitors and by comparing STD signals with crystallographic structures, we show that there is a relation between the orientations of ibuprofen and diclofenac in the COX-2 active site and the relative STD responses detected in the NMR experiments. On the basis of this analysis, we propose that ketorolac should bind to the COX-2 active site in an orientation similar to that of diclofenac. We also show that the combination of STD-NMR with competition experiments constitutes a valuable tool to address the recently proposed behavior of COX-2 as functional heterodimers and complements enzyme activity studies in the effort to rationalize COX inhibition mechanisms.

Viegas, A, Manso J, Corvo MC, Marques MMB, Cabrita EJ.  2011.  Binding of ibuprofen, ketorolac, and diclofenac to COX-1 and COX-2 studied by saturation transfer difference NMR. Journal of medicinal chemistry. 54:8555–8562., Number 24: ACS Publications Abstract
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Dias, AMGC, Hussain A, Marcos AS, Roque ACA.  2011.  A biotechnological perspective on the application of iron oxide magnetic colloids modified with polysaccharides. Biotechnology Advances. 29:142–155., Number 1 AbstractWebsite

Iron oxide magnetic nanoparticles {(MNPs)} alone are suitable for a broad spectrum of applications, but the low stability and heterogeneous size distribution in aqueous medium represent major setbacks. These setbacks can however be reduced or diminished through the coating of {MNPs} with various polymers, especially biopolymers such as polysaccharides. Polysaccharides are biocompatible, non-toxic and renewable; in addition, they possess chemical groups that permit further functionalization of the {MNPs.} Multifunctional entities can be created through decoration with specific molecules e.g. proteins, peptides, drugs, antibodies, biomimetic ligands, transfection agents, cells, and other ligands. This development opens a whole range of applications for iron oxide nanoparticles. In this review the properties of magnetic structures composed of {MNPs} and several polysaccharides {(Agarose}, Alginate, Carrageenan, Chitosan, Dextran, Heparin, Gum Arabic, Pullulan and Starch) will be discussed, in view of their recent and future biomedical and biotechnological applications.

Mahro, M, Coelho C, Trincao J, Rodrigues D, Terao M, Garattini E, Saggu M, Lendzian F, Hildebrandt P, Romao MJ, Leimkuehler S.  2011.  Characterization and Crystallization of Mouse Aldehyde Oxidase 3: From Mouse Liver to Escherichia coli Heterologous Protein Expression. Drug Metabolism and Disposition. 39:1939-1945., Number 10 AbstractWebsite
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Seixas de Melo, SJ, Cabral C, Lima JC, Macanita AL.  2011.  Characterization of the Singlet and Triplet Excited States of 3-Chloro-4-methylumbelliferone. Journal of Physical Chemistry a. 115:8392-8398., Number 30 Abstract
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Oliveira, J, Petrov V, Parola JA, Pina F, Azevedo J, Teixeira N, Bras NF, Fernandes PA, Mateus N, Ramos MJ, de Freitas V.  2011.  Chemical Behavior of Methylpyranomalvidin-3-O-glucoside in Aqueous Solution Studied by NMR and UV-Visible Spectroscopy. Journal of Physical Chemistry B. 115:1538-1545., Number 6 AbstractWebsite
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Branco, LC, Serbanovic A, da Ponte MN, Afonso CAM.  2011.  Chiral Guanidinium Ionic Liquids for Asymmetric Dihydroxylation of Olefins with Recycling of the Catalytic System by Supercritical CO2. Acs Catalysis. 1:1408-1413., Number 10 AbstractWebsite
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Ortigueira, MD, Rodríguez-Germá L, Trujillo JJ.  2011.  Complex Grünwald?Letnikov, Liouville, Riemann?Liouville, and Caputo derivatives for analytic functions Communications in Nonlinear Science and Numerical Simulation. AbstractWebsite

The well-known Liouville, Riemann?Liouville and Caputo derivatives are extended to the complex functions space, in a natural way, and it is established interesting connections between them and the Grünwald?Letnikov derivative. Particularly, starting from a complex formulation of the Grünwald?Letnikov derivative we establishes a bridge with existing integral formulations and obtained regularised integrals for Liouville, Riemann?Liouville, and Caputo derivatives. Moreover, it is shown that we can combine the procedures followed in the computation of Riemann?Liouville and Caputo derivatives with the Grünwald?Letnikov to obtain a new way of computing them. The theory we present here will surely open a new way into the fractional derivatives computation.

Gordo, J, Avo J, Parola JA, Lima JC, Pereira A, Branco PS.  2011.  Convenient Synthesis of 3-Vinyl and 3-Styryl Coumarins. Organic Letters. 13:5112-5115., Number 19 Abstract
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Serra, AS, Jorge SR, Silveira CM, Moura JJG, Jubete E, Ochoteco E, Cabañero G, Grande H, Almeida MG.  2011.  Cooperative use of cytochrome cd1 nitrite reductase and its redox partner cytochrome c552 to improve the selectivity of nitrite biosensing. Analytica Chimica Acta. 693:41-46., Number 1–2 AbstractWebsite
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Santos-Silva, T, Mukhopadhyay A, Seixas JD, Bernardes GJL, Romao CC, Romao MJ.  2011.  CORM-3 Reactivity toward Proteins: The Crystal Structure of a Ru(II) Dicarbonyl-Lysozyme Complex. Journal of the American Chemical Society. 133:1192-1195., Number 5 AbstractWebsite
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