CONTROLLED ADSORPTION OF CYTOCHROME C TO NANOSTRUCTURED GOLD SURFACES - Inês Gomes; Maria J. Feio; Nuno C. Santos; Peter Eaton; Ana Paula Serro; Benilde Saramago; Eulália Pereira; Ricardo Franco (J. Nanopart. Res., 2012)

Cross-section and staining-based techniques for investigating organic materials in painted and polychrome works of art: a review - I.C.A. Sandu, S. Schäfer, D. Magrini, S. Bracci & C. A. Roque (Microscopy and Microanalysis, 2012)

Cross-Section and Staining-Based Techniques for Investigating Organic Materials in Painted and Polychrome Works of Art: A Review. - Irina C A Sandu; Stephan Schäfer; Magrini, Donata; Bracci, Susanna; Roque, Ana C A (Microscopy and Microanalysis, 2012)
The article presents a review of the use of cross-section and staining techniques for investigating natural organic materials (mainly proteinaceous and oil-based binders/varnishes) in painted and polychrome artworks, considering the requirements of conservation practice and routine diagnostics. The reviewed literature calls attention to the importance of using cross sections to prepare samples for optical microscopy and to different properties of embedding resins; the most appropriate instrumental conditions for optical microscopy; and the advantages and disadvantages of the most common staining techniques. A few case studies were selected to illustrate the use of autofluorescence (intrinsic fluorescence) and induced fluorescence (using specific staining tests and fluorophore-labeled antibodies) for mapping and identifying organic paint materials in cross sections. New directions of research in cross-section analyses and fluorescence-based techniques for the identification and mapping of artistic materials are presented. The complementary use of different stains on the same cross section, further exploration of intrinsic and induced fluorescence of aged versus fresh materials, and applicability of cross-section observation and staining as complementary methods for assessing the effectiveness of restoration treatments, such as cleaning and consolidation, are discussed in the last section of the article.

The Development and Use of Industrial Robots – the Educational/Work Science Perspective (part 1) - Fischer, Martin (2012)

The development and use of industrial robots – the educational/work science perspective – part 2 - Zimpelmann, Eike (2012)

Dextran-Coated Magnetic Supports Modified with a Biomimetic Ligand for IgG Purification - Sara D F Santana; Vijaykumar L Dhadge; Roque, Ana C A (ACS Applied Materials and Interfaces, 2012)
extran-coated iron oxide magnetic particles modified with ligand 22/8, a protein A mimetic ligand, were prepared and assessed for IgG purification. Dextran was chosen as the agent to modify the surface of magnetic particles by presenting a negligible level of nonspecific adsorption. For the functionalization of the particles with the affinity ligand toward antibodies, three methods have been explored. The optimum coupling method yielded a theoretical maximum capacity for human IgG calculated as 568 ± 33 mg/g and a binding affinity constant of 7.7 × 104 M–1. Regeneration, recycle and reuse of particles was also highly successful for five cycles with minor loss of capacity. Moreover, this support presented specificity and effectiveness for IgG adsorption and elution at pH 11 directly from crude extracts with a final purity of 95% in the eluted fraction.

Ditto – Deterministic Execution Replay for the Java Virtual Machine on Multi-processors - Silva, João (Instituto Superior Técnico, 2012)
In this work, we propose RATS, a middleware to enhance and extend the Terracotta framework for Java with the ability to transparently execute multi-threaded Java applications to provide a single-system image. It supports efficient scheduling of threads, according to available resources, across several nodes in a Terracotta cluster, taking advantage of the extra computational and memory resources available. It also supports profiling to gather application characteristics such as dispersion of thread workload, thread inter-arrival time and resource usage of the application. Profiling and clustering capabilities are inserted with the help of byte code instrumentations. We developed a range of alternative scheduling heuristics and classify them based on the application and cluster behavior. The middleware is tested with different applications with varying thread characteristics to assess and classify the scheduling heuristics with respect to application speed-ups. Results indicate that, for a CPU intensive application, it is possible to classify the scheduling heuristic based on application and cluster properties and also achieve linear speed ups. Furthermore, we show that a memory intensive application is able to scale its memory usage considerably when compared to running the application on a single JVM.
(Supervised by Luís Veiga)

Doxorubicin vs. ladirubicin: methods for improving osteosarcoma treatment - Paula I P Soares; Dias, Sérgio; Novo, Carlos; Ferreira, Isabel; Borges, João Paulo (Mini reviews in medicinal chemistry, 2012)
Osteosarcoma is the most common primary bone tumor in children and adolescents, with a 5-year disease free survival rate of 70%. Current chemotherapy regimens comprise a group of chemotherapeutic agents in which doxorubicin is included. However, tumor resistance to anthracyclines and cardiotoxicity are limiting factors for its usage. Liposomal formulations of doxorubicin improve its anti-cancer effects but are still insufficient. The research in this area has lead to the production of anthracyclines analogues, such as ladirubicin, the leading compound of alkylcyclines. This new anticancer agent has shown promising results in vivo and in vitro, being effective against osteosarcoma cell lines, including those with a multidrug resistant phenotype. In phase I clinical trials, this molecule caused mild side effects and did not induce significant cardiotoxicity at doses ranging from 1 to 16 mg/m2, resulting in a peak plasma concentration (Cmax) ranging from 0.5 to 1.5 μM. The recommended doses for phase II studies were 12 and 14 mg/m2 in heavily and minimally pretreated/non-pretreated patients, respectively. Phase II clinical trials in ovary, breast, colorectal cancer, NSCLC and malignant melanoma are underway. Given the improved molecular targeting efficacy of these new compounds, ongoing approaches have sought to improve drug delivery systems, to improve treatment efficacy while reducing systemic toxicity. The combination of these two approaches may be a good start for the discovery of new treatment for osteosarcoma.

Dynamic transitions in RNA polymerase II density profiles during transcription termination - Ana Rita Grosso; De Almeida, Sérgio Fernandes; Braga, José; Carmo-fonseca, Maria; de Almeida, Sérgio Fernandes; Braga, José; Almeida, Fernandes De; Carmo-fonseca, Maria; Res, Genome; Almeida, Fernandes De; Ana Rita Grosso; Carmo-fonseca, Maria (Genome research, 2012)
Eukaryotic protein-coding genes are transcribed by RNA polymerase II (RNAPII) through a cycle composed of three main phases: initiation, elongation, and termination. Recent studies using chromatin immunoprecipitation coupled to high-throughput sequencing suggest that the density of RNAPII molecules is higher at the 3'-end relative to the gene body. Here we show that this view is biased due to averaging density profiles for "metagene" analysis. Indeed, the majority of genes exhibit little, if any, detectable accumulation of polymerases during transcription termination. Compared with genes with no enrichment, genes that accumulate RNAPII at the 3'-end are shorter, more frequently contain the canonical polyadenylation [poly(A)] signal AATAAA and G-rich motifs in the downstream sequence element, and have higher levels of expression. In 1% to 4% of actively transcribing genes, the RNAPII enriched at the 3'-end is phosphorylated on Ser5, and we provide evidence suggesting that these genes have their promoter and terminator regions juxtaposed. We also found a striking correlation between RNAPII accumulation and nucleosome organization, suggesting that the presence of nucleosomes after the poly(A) site induces pausing of polymerases, leading to their accumulation. Yet we further observe that nucleosome occupancy at the 3'-end of genes is dynamic and correlates with RNAPII density. Taken together, our results provide novel insight to transcription termination, a fundamental process that remains one of the least understood stages of the transcription cycle.

ECO - Evaluation and Certification System - GEOTPU (FCT-UNL, 2012)

The Effect of Anthropomorphic Movements of Assembly Robots on Human Prediction - Kuz, S.; Heinicke, A.; Schwichtenhövel, D.; Mayer, Marcel Ph.; Schlick, C. (Advances in Ergonomics in Manufacturing, 2012)
From a user centered point of view an important basic requirement to enable human-robot cooperation is to achieve conformity with operator's expectations of robot behavior. Therefore, this study focuses on the question, whether anthropomorphic robot movement trajectories can lead to an improved anticipation of the robot's behavior. Based on a virtual simulation environment a robotized assembly cell consisting of the assembly robot and the actual workplace was considered. In order to be able to simulate anthropomorphic movements, the human wrist trajectories of defined pick and place movements were obtained using an infrared motion capture system. The captured data were used to navigate the virtual assembly robot. Within the experiment anthropomorphic and robotic trajectories were distinguished. During the experiment, the main task of the participants was to predict the movement's destination as quickly as possible. Thus, the corresponding reaction value was analyzed to investigate the influence of anthropomorphic robot movements on human prediction in industrial environments.

Effect of substrate temperature on the properties of pyrolytically deposited nitrogen-doped zinc oxide thin films - Golshahi, S.,; Rozati, S.M.,; Botelho do Rego, A.M.,; Wang, J.,; Elangovan, E.,; Martins; E. Fortunato (Materials Science and Engineering: B, 2012)

Efficient Support for In-Place Metadata in Transactional Memory - Ricardo J. Dias; Vale, Tiago M.; João M. Lourenço (Euro-Par 2012 Parallel Processing, 2012)
Implementations of Software Transactional Memory (STM) algorithms associate metadata with the memory locations accessed during a transaction’s lifetime. This metadata may be stored either in-place, by wrapping every memory cell in a container that includes the memory cell itself and the corresponding metadata; or out-place (also called external), by resorting to a mapping function that associates the memory cell address with an external table entry containing the corresponding metadata. The implementation techniques for these two approaches are very different and each STM framework is usually biased towards one of them, only allowing the efficient implementation of STM algorithms following that approach, hence inhibiting the fair comparison with STM algorithms falling into the other. In this paper we introduce a technique to implement in-place metadata that does not wrap memory cells, thus overcoming the bias by allowing STM algorithms to directly access the transactional metadata. The proposed technique is available as an extension to the DeuceSTM framework, and enables the efficient implementation of a wide range of STM algorithms and their fair (unbiased) comparison in a common STM infrastructure. We illustrate the benefits of our approach by analyzing its impact in two popular TM algorithms with two different transactional workloads, TL2 and multi-versioning, with bias to out-place and in-place respectively.
Distinguished Paper Award

Efficient Thread Scheduling for Distributed Java VM - Rameshan, Navaneeth (Instituto Superior Técnico, 2012)
In this work, we propose RATS, a middleware to enhance and extend the Terracotta framework for Java with the ability to transparently execute multi-threaded Java applications to provide a single-system image. It supports efficient scheduling of threads, according to available resources, across several nodes in a Terracotta cluster, taking advantage of the extra computational and memory resources available. It also supports profiling to gather application characteristics such as dispersion of thread workload, thread inter-arrival time and resource usage of the application. Profiling and clustering capabilities are inserted with the help of byte code instrumentations. We developed a range of alternative scheduling heuristics and classify them based on the application and cluster behavior. The middleware is tested with different applications with varying thread characteristics to assess and classify the scheduling heuristics with respect to application speed-ups. Results indicate that, for a CPU intensive application, it is possible to classify the scheduling heuristic based on application and cluster properties and also achieve linear speed ups. Furthermore, we show that a memory intensive application is able to scale its memory usage considerably when compared to running the application on a single JVM.
(Supervised by Luís Veiga)

Efficient Thread Scheduling for Distributed Java VM - Rameshan, Navaneeth (Instituto Superior Técnico, 2012)
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The electronic transport mechanism in indium molybdenum oxide thin films RF sputtered at room temperature - E. Elamurugu; P. Shanmugam; G. Goncalves; N. Franco; E. Alves; R. Martins; E. Fortunato (Epl, 2012)

Electrospinning of Ion Jelly fibers - Pimenta, Andreia F. R.; Baptista, Ana Catarina; Carvalho, Tânia; Brogueira, Pedro; Nuno Lourenço; Afonso, Carlos; Barreiros, Susana; Vidinha, Pedro; Borges, João Paulo (Materials Letters, 2012)
Ion Jelly materials combine the chemical versatility and conductivity of an ionic liquid (IL) with the morphological versatility of a biopolymer (gelatin). They exhibit very interesting properties, such as conductivities up to 10− 4 S cm− 1, and high thermostability up to 180 °C, and have been used successfully to design electrochromic windows. In this work we report on the preparation of Ion Jelly fibers through electrospinning in order to obtain high surface area conductive materials. We have used the IL 1-(2-hydroxyethyl)-3-methyl-imidazolium tetrafluoroborate ([C2OHmim]BF4), which exhibits conveniently high ionic conductivity (over 10− 3 S cm− 1) and electrochemical stability (electrochemical window over 6.0 V). The morphology of the obtained fibers was quantified using Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). We found that on average the effect of the IL on fiber diameter differs for lower and higher IL concentrations and that this effect was correlated with the initial conductivity and viscosity of Ion Jelly electrospinning solution. Moreover we also found that conductivities of Ion Jelly fibers are of the same order of magnitude as the conductivities of Ion Jelly dense films (~ 10− 4 S cm− 1). To the best of our knowledge, this is the first report on the incorporation of an IL into gelatin fibers using electrospinning. This opens up new opportunities for the application of gelatin fibers in electrochemical and biomedical devices.

Electrospun hydroxyapatite fibers from a simple sol–gel system - Franco, Patrícia Q; João, Carlos; Silva, Jorge Carvalho; Borges, João Paulo (Materials Letters, 2012)
This work reports the production of hydroxyapatite (HA) sub-micron fibers by combining electrospinning and a non-alkoxide sol–gel system, using cheap precursors. Phosphorus pentoxide (P2O5) and calcium nitrate tetrahydrate (Ca(NO3)2.4H2O) were used as precursors of phosphorus and calcium, respectively. The fibers were electrospun from a mixture of the gel formed from the system Ca(NO3)2.4H2O/P2O5 with polymeric solutions of polyvinylpyrrolidone (PVP) in water and ethanol/water mixtures. The fibers were analyzed for their morphology (Scanning Electron Microscopy, SEM), chemical composition (Fourier Transform Infrared Spectroscopy, FTIR) and structure (X-ray diffraction, XRD). The fibers obtained were composed mainly of type B carbonated HA with traces of β-tricalcium phosphate (β-TCP). SEM analysis revealed that increasing the concentration of water in the solvent system, used in the preparation of electrospinning solutions, led to fibers with smaller diameters and narrower diameter distribution.

Enigmatic reticulated filaments in subsurface granite - Miller, A. Z.,; Hernández-Mariné, M.,; Jurado, V.,; Dionísio, A.,; Barquinha; Fortunato; Afonso, M. J.,; Chaminé, H. I.,; Saiz-Jimenez, C. (Environmental Microbiology Reports, 2012)

Exploring Human-Robot Cooperation Possibilities for Semiconductor Manufacturing - Weiss, Astrid (2012)

Fine Tuning of Redox Networks on Multiheme Cytochromes from Geobacter sulfurreducens Drives Physiological Electron/Proton Energy Transduction - Leonor Morgado; Joana M Dantas; Bruix, Marta; Londer, Yuri Y.; Salgueiro, , Carlos A. (Bioinorganic Chemistry and Applications, 2012)
The bacterium Geobacter sulfurreducens (Gs) can grow in the presence of extracellular terminal acceptors, a property that is currently explored to harvest electricity from aquatic sediments and waste organic matter into microbial fuel cells. A family composed of five triheme cytochromes (PpcA-E) was identified in Gs. These cytochromes play a crucial role by bridging the electron transfer from oxidation of cytoplasmic donors to the cell exterior and assisting the reduction of extracellular terminal acceptors. The detailed thermodynamic characterization of such proteins showed that PpcA and PpcD have an important redox-Bohr effect that might implicate these proteins in the e−/H+ coupling mechanisms to sustain cellular growth. The physiological relevance of the redox-Bohr effect in these proteins was studied by determining the fractional contribution of each individual redox-microstate at different pH values. For both proteins, oxidation progresses from a particular protonated microstate to a particular deprotonated one, over specific pH ranges. The preferred e−/H+ transfer pathway established by the selected microstates indicates that both proteins are functionally designed to couple e−/H+ transfer at the physiological pH range for cellular growth.

Fishing human monoclonal antibodies from a CHO cell supernatant with boronic acid magnetic particles - L. Borlido; A. M. Azevedo; A. G. Sousa; P. H. Oliveira; Roque, A. C. A.; M. R. Aires-Barros (Journal of Chromatography B, 2012)
In this work we have evaluated the potential of boronic acid functionalized magnetic particles for the one-step capture of a human monoclonal antibody (mAb) from a Chinese hamster ovary (CHO) cell culture supernatant. For comparison, Protein A coated magnetic particles were also used. The most important factor influencing the overall process yield and product purity in boronic acid particles was found to be the binding pH. Basic pH values promoted higher purities while resulting in decreased yields due to the competing effects of molecules such as glucose and lactate present in the cell culture supernatant. After optimization, the particles were successfully used in a multi-cycle purification process of the mAb from the CHO feedstock. Boronic acid particles were able to achieve an average overall yield of 86% with 88% removal of CHO host cell proteins (HCP) when the binding was performed at pH 7.4, while at pH 8.5 these values were 58% and 97%, respectively. In both cases, genomic DNA removal was in excess of 97%. Comparatively, Protein A particles recorded an average overall yield of 80% and an HCP removal greater than 99%. The adsorption of the mAb to the boronic acid particles was shown to be mediated by strong affinity interactions. Overall, boronic acid based purification processes can offer a cost-effective alternative to Protein A as the direct capturing step from the mammalian cell culture.

Fluorescence recognition of proteinaceous binders in works of art by a novel integrated system of investigation - Irina C A Sandu; Roque, Ana C A; Paolo Matteini; Stephan Schäfer; Giovanni Agati; Catarina R Correia; Joana F F P Viana (Microscopy Research and Technique, 2012)
Fluorescence microscopy and microspectrofluorometry are important tools in the characterization and identification of proteins, offering a great range of applications in conservation science. Because of their high selectivity and sensitivity, the combination of these techniques can be exploited for improved recognition and quantification of proteinaceous binders in paintings and polychromed works of art. The present article explores an analytical protocol integrating fluorescence microscopy and fluorometry for both identification and mapping of proteinaceous binders (in particular egg and glues) in paint samples. The study has been carried out on historically accurate reconstructions simulating the structure and composition of tempera and oil paints containing these binders. To assess the spatial distribution of specific proteins within the paint layers, cross-sections from the reconstructions were analyzed by fluorescence imaging after staining with an exogenous fluorophore. Reference fluorescence spectra for each layer were acquired by a multichannel spectral analyzer and compared after Gaussian deconvolution. The results obtained demonstrated the effectiveness of the integrated protocol, highlighting the potential for the use of fluorescent staining coupled with microspectrofluorometry as a routine diagnostic tool in conservation science. The current work creates a set of fully characterized reference samples for further comparison with those from actual works of art.

Gold nanoparticles in the clinical laboratory: principles of preparation and applications - Hassan M. E. Azzazy; Mai M. H. Mansour; Tamer M. Samir; Ricardo Franco (Clinical Chemistry and Laboratory Medicine, 2012)

GOLD NANOPARTICLES-BASED FLUORESCENCE IMMUNOASSAY FOR MALARIA ANTIGEN DETECTION - Bassem S. S. Guirgis; Cláudia Sá e Cunha; Inês Gomes; Miguel Cavadas; Isabel Silva; Gonçalo Doria; Gregory L. Blatch; Pedro V. Baptista; Eulália Pereira; Hassan M. E. Azzazy; Maria M. Mota; Miguel Prudêncio; et al. (Anal. Bioanal. Chem., 2012)

Gold on paper-paper platform for Au-nanoprobe TB detection - Veigas, Bruno,; Jacob, Jorge M.,; Costa; Santos, GMC,; Viveiros, Miguel,; Inacio, Joao,; Martins; Barquinha; Fortunato; Pedro Viana Baptista (Lab on a Chip, 2012)

High mobility and visible-near infrared transparent titanium doped indium oxide thin films produced by spray pyrolysis - Parthiban, S.,; Gokulakrishnan, V.,; Elangovan, E.,; Gonçalves, G.,; Ramamurthi, K.,; Fortunato; R. Martins (Thin Solid Films, 2012)

High resolution melting: improvements in the genetic diagnosis of hypertrophic cardiomyopathy in a Portuguese cohort - Santos, S.; Marques, V.; Pires, M.; Silveira, L.; Oliveira, H.; Lanca, V.; Brito, D.; Madeira, H.; Esteves, J. F.; Freitas, A.; Carreira, I. M.; Gaspar, I. M.; et al. (BMC Med Genet, 2012)

Human-Robot-Interaction in manufacturing - a historical retrospective - Zschieschang, Eva (ITAS-KIT, 2012)

Human Robot Interaction - Integration of the Employee to increase Flexibility - Thomas, Carsten (2012)

Hydrogen plasma treatment of very thin p-type nanocrystalline Si films grown by RF-PECVD in the presence of B(CH3)(3) - Filonovich, Sergej Alexandrovich,; Águas, Hugo,; Busani, Tito,; Vicente, António,; Araújo, Andreia,; Gaspar, Diana,; Vilarigues, Marcia,; Leitão, Joaquim,; Fortunato; Martins, Rodrigo. (Science and Technology of Advanced Materials, 2012)

In-Place Metainfo Support in DeuceSTM - Ricardo J. Dias; Vale, Tiago M.; João M. Lourenço (Talk presented at the 2nd Euro-TM Workshop on Transactional Memory, 2012)
Several Software Transactional Memory (STM) algorithms have been developed in the last few years. These algorithms differ in many different properties, such as progress and safety guarantees, contention management, etc. Some STM frameworks (DSTM2, DeuceSTM) were developed to allow the implementation and comparison of many different algorithms using the same transactional interface. The information required by an STM algorithm is either associated with the execution of a transaction (frequently referred as transaction descriptor), or associated with each memory location (or object reference) accessed within the transaction. The transaction descriptor is typically stored in a thread-local memory space and maintains the information necessary to validate and commit a memory transaction. The information associated with each memory location depends on the nature of the STM algorithm, which we will henceforth refer to as metadata, and may be composed by e.g. locks, timestamps or version lists. Since metadata is associated with each memory location, there are two main strategies regarding the location for storing such metadata: The metadata is stored either near each memory location (in-place strategy); or in a mapping table that associates the metadata with the corresponding memory location (out- place strategy). DeuceSTM is one of the most efficient STM frameworks available for the Java programming language and provides a well defined interface that allows to implement several STM algorithms using an out-place strategy. This work describes the adaptation and extension of DeuceSTM to support the in-place metadata strategy. Our approach complies to the following properties: Efficiency –- The STM implementation does not rely on an auxiliary mapping table, thus providing faster direct access to the transactional metadata; Non-transactional code is oblivious to the presence of metadata in objects, hence there is no performance overhead whatsoever for non-transactional code; Transactional code avoids the extra memory dereference imposed by the decorator pattern; Primitive types are fully supported, even in transactional code; And we provide a solution for fully supporting transactional N-dimensional arrays, which again impose no overhead on non-transactional code. Transparency –- The STM implementation automatically identifies, creates and initializes the necessary additional metadata fields in the objects; Non-transactional code is oblivious to the presence of metadata in objects, hence no code changes are required; The new transactional array types (supporting metadata for individual cells) are compatible with the standard arrays, hence not requiring any pre-/post- processing of the arrays when invoking standard or third-party non-transactional libraries. Performance benchmarking has confirmed that our approach for supporting in-place metadata in DeuceSTM, alongside with the existing out-place strategy, is a valid functional complement, widening the range of algorithms that can be efficiently implemented in DeuceSTM, enabling their fair comparison in a common infrastructure.
Workshop talk

Incorporation of silver nanoparticles on textile materials - Inês Osório; Rui Igreja; Ricardo Franco; João Cortez (Materials Lett., 2012)

Innovation assessment in a local branch of a rail transport industry: Case study - Nuno Boavida; Susana Martins Moretto (Tecnología Base de la Innovación?, 2012)

Investigation of O7+ swift heavy ion irradiation on molybdenum doped indium oxide thin films - Gokulakrishnan, V.,; Parthiban, S.,; Elangovan, E.,; Jeganathan, K.,; Kanjilal, D.,; Asokan, K.,; Martins; Fortunato; K. Ramamurthi (Radiation Physics and Chemistry, 2012)

Joint Cognitive Systems: How to design the human place in HRI? - Mayer, Marcel Ph. (2012)

KIT-Focus: Anthropomatics and Robotics - Asfour, Tamim (2012)

Konsoliderad rapport angående användning av VR och fjärrexperiment i utbildning - SCUTARU, G.; SANDU, F.; COCORADA, E.; PAVALACHE, M.; Gomes, L.; Coito, F.; MÖRSKY-LINDQUIST, A.K.; TALABA, D.; NEUNDORF, V.; FEDAK, V.; Others (2012)
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Localized electroencephalography sensor and detection of evoked potentials - T. Araújo; N. Nunes; C. Quintão; Gamboa, H. (Proc INSTICC 2nd International Workshop on Computing Paradigms for Mental Health - MindCare 2012 (MINDCARE 2012), 2012)

Long-term biosignals visualization and processing - Gomes, R; N. Neuza; J. Sousa; Gamboa, H. (Proceedings of Biosignals - 5th International Conference on Bio-Inspired and Signal Processing (BIOSIGNALS 2012), 2012)

Microstructure control of dual-phase inkjet-printed a-WO3/TiO2/WOX films for high-performance electrochromic applications - P. J. Wojcik; A. S. Cruz; L. Santos; L. Pereira; R. Martins; E. Fortunato (J. Mater. Chem., 2012)

Miniaturized wireless controlled electroestimulator - T. Araújo; N. Nunes; Gamboa, H. (Proceedings of Biodevices - 5th International Conference on Bio-Inspired and Signal Processing (BIODEVICES 2012), 2012)

MODELING AND HYBRID CONTROL OF A NONLINEAR DC SERVOMOTOR - Palma, L. B.; Coito, F. V. (2012)
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Models for Identification of Erroneous Atom-to-Atom Mapping of Reactions Performed by Automated Algorithms - C. Muller; G. Marcou; D. Horvath; J. Aires-de-Sousa; A. Varnek (J. Chem. Inf. Model, 2012)

A Modular Distributed Transactional Memory Framework - Vale, Tiago M. (Universidade Nova de Lisboa, 2012)
The traditional lock-based concurrency control is complex and error-prone due to its low-level nature and composability challenges. Software transactional memory (STM), inherited from the database world, has risen as an exciting alternative, sparing the programmer from dealing explicitly with such low-level mechanisms. In real world scenarios, software is often faced with requirements such as high availability and scalability, and the solution usually consists on building a distributed system. Given the benefits of STM over traditional concurrency controls, Distributed Software Transactional Memory (DSTM) is now being investigated as an attractive alternative for distributed concurrency control. Our long-term objective is to transparently enable multithreaded applications to execute over a DSTM setting. In this work we intend to pave the way by defining a modular DSTM framework for the Java programming language. We extend an existing, efficient, STM framework with a new software layer to create a DSTM framework. This new layer interacts with the local STM using well-defined interfaces, and allows the implementation of different distributed memory models while providing a non-intrusive, familiar, programming model to applications, unlike any other DSTM framework. Using the proposed DSTM framework we have successfully, and easily, implemented a replicated STM which uses a Certification protocol to commit transactions. An evaluation using common STM benchmarks showcases the efficiency of the replicated STM, and its modularity enables us to provide insight on the relevance of different implementations of the Group Communication System required by the Certification scheme, with respect to performance under different workloads.
(Supervised by João M. Lourenço)
Keywords: Concurrency Control; Distributed Systems; Replication; Transactional Memory

Multicomponent dielectrics for oxide TFT - Pereira; Barquinha; Gonçalves, G.,; Fortunato; Rodrigo Martins (Proceedings, 2012)

Multifrequency EPR Study of Fe(3+) and Co(2+) in the Active Site of Desulforedoxin - Mathies, G.; Almeida, R. M.; Gast, P.; Moura, J. J.; Groenen, E. J. (J Phys Chem B, 2012)

Multifunctional zinc oxide nanostructures for a new generation of devices - V. Musat; E. Fortunato; M. Purica; M. Mazilu; A. M. B. do Rego; B. Diaconu; T. Busani (Mater. Chem. Phys., 2012)

Multipliers with transparent a-GIZO TFTs using a neural model - Bahubalindruni, Ganga,; Duarte, Candido,; Tavares, Vitor Grade,; Barquinha; Martins; Fortunato; de Oliveira, Pedro Guedes (20th Telecommunications Forum (TELFOR), 2012)

N-Type Oxide Semiconductor Thin-Film Transistors - Barquinha P.,; Martins R.; Fortunato E., (GaN and ZnO-based Materials and Devices, 2012)

Natural hydraulic lime based grouts- the selection of grout injection parameters for masonry consolidation - Ana Brás; Fernando M.A. Henriques (Construction & Building Materials, 2012)

The new mobility paradigm: Transformation of value chain and business models - Fournier, Guy; Hinderer, Henning; Schmid, Daniel; Seign, René; Baumann, Manuel (Enterprise and Work Innovation Studies, 2012)
Four categories of innovations have been identified by Freeman and Perez: incremental innovations, radical innovations, new technological systems (systemic innovations), and technological revolutions or new techno-economic paradigms. New techno-economic paradigms represent changes in technological systems that are so far-reaching in their effects that they have a major influence on the behaviour of the entire economy. Scarcity of oil and external costs like global warming are the key arguments and the main drivers of the change of the current paradigm. They will affect especially the mobility of individuals and the interlinked business models. Novel business models within newly created markets will raise e.g. extended mobility services, activities aiming at the infrastructure, new opportunities in the field of energy transmission and supply and even new strategies of recycling, reusing or reducing the use of resources in order to address global scarcity issues. Especially for the established players of the automotive industry like original equipment manufacturers (OEMs) or 1st and 2nd tier suppliers this implicates opportunities and risks at the same time. But also new players will get the chance to create and enter new markets with new or extended products or services and lead the new value chain. This paper compiles and evaluates current approaches and business models of selected OEMs together with upcoming players. Additionally their positions within the existing value chain are being analyzed and classified. Bringing together the identified drivers of changes with current trends within the automotive industry the authors also show new concepts of extended business models, e.g. the idea of an ecosystem, that have the potential to cause an additional shift of power within the global mobility value chain.

New Polymer Networks for PDLC Films Application - A. I. Mouquinho; K. Petrova; M. T. Barros; J. Sotomayor (New Polymers for Special Applications, 2012)

On the road to improve the bioremediation and electricity-harvesting skills of Geobacter sulfurreducens: functional and structural characterization of multihaem cytochromes - Leonor Morgado; Fernandes, Ana P.; Joana M Dantas; Silva, , Marta A.; Salgueiro, , Carlos A. (Biochemical Society transactions, 2012)
Extracellular electron transfer is one of the physiological hallmarks of Geobacter sulfurreducens, allowing these bacteria to reduce toxic and/or radioactive metals and grow on electrode surfaces. Aiming to functionally optimize the respiratory electron-transfer chains, such properties can be explored through genetically engineered strains. Geobacter species comprise a large number of different multihaem c-type cytochromes involved in the extracellular electron-transfer pathways. The functional characterization of multihaem proteins is particularly complex because of the coexistence of several microstates in solution, connecting the fully reduced and oxidized states. NMR spectroscopy has been used to monitor the stepwise oxidation of each individual haem and thus to obtain information on each microstate. For the structural study of these proteins, a cost-effective isotopic labelling of the protein polypeptide chains was combined with the comparative analysis of 1H-13C HSQC (heteronuclear single-quantum correlation) NMR spectra obtained for labelled and unlabelled samples. These new methodological approaches allowed us to study G. sulfurreducens haem proteins functionally and structurally, revealing functional mechanisms and key residues involved in their electron-transfer capabilities. Such advances can now be applied to the design of engineered haem proteins to improve the bioremediation and electricity-harvesting skills of G. sulfurreducens.

Open Innovation and Social Network Analysis - Cândido, Ana C. (Enterprise and Work Innovation Studies, 2012)
In this work we propose the use of Social Network Analysis to understand the positioning of the concept of Open Innovation in the literature, offering thereby a complementary approach to existing literature review up to now. The main motivation of this network analysis is to contribute to the understanding of the concept of Open Innovation, with its spread to different areas of knowledge over the years and its relationship with other concepts in the literature. Some 403 articles published in the database of the Science Direct during the years 2003 to 2011 were analyzed. The data was collected separately by year, considering the following information: journals in which the articles were published; countries of origin of the articles’ authors, keywords of these articles and year of publication. The results reveal the intense growth of the use of the words "Open Innovation" in articles from different areas of knowledge, as well as its increasing interconnection with other concepts, allowing the understanding of its diffusion in the literature.
The present article is based on the report for the Doctoral Conference of the PhD programme in Technology Assessment, held at FCT-UNL Campus, Monte de Caparica, July 9th, 2012. The PhD thesis has the supervision of Prof. Cristina Sousa (ISCTE-IUL), and co-supervision of Prof. José Cardoso e Cunha (FCT-UNL).

Optical Imaging Applications for the Study of Cultural Heritage Artifacts - Sandu I.C.A, Joosten I., Leal N. (Optical imaging: Technology, Methods and Applications, 2012)

Optimisation of flow behaviour and stability of superplasticized fresh hydraulic lime grouts through design of experiments - Luis G. Baltazar; Fernando M.A. Henriques; Fernando Jorne (Construction & Building Materials, 2012)

Oxide Semiconductor Thin-Film Transistors: A Review of Recent Advances - E. Fortunato; P. Barquinha; R. Martins (Adv. Mater., 2012)

p-Type CuxO Films Deposited at Room Temperature for Thin-Film Transistors - V. Figueiredo; E. Elangovan; R. Barros; J. V. Pinto; T. Busani; R. Martins; E. Fortunato (, J. Disp. Technol., 2012)

P-type oxide based thin film transistors produced at low temperatures - Martins; Figueiredo, V.,; Barros, R.,; Barquinha; Gonçalves, G.,; Pereira; Ferreira; E. Fortunato (SPIE, 2012)

Parcel-Based Connectivity Analysis of fMRI Data for the Study of Epileptic Seizure Propagation - Tana, M; Bianchi, A; Sclocco, R; Franchin, T; Cerutti, S; Leal, A (Brain Topography (DOI:10.1007/s10548-012-0225-2), 2012)

Pivotal role of the strictly conserved aromatic residue F15 in the cytochrome c7 family - Joana M Dantas; Leonor Morgado; Londer, Yuri Y.; Fernandes, Ana P.; Ricardo O. Louro; Pokkuluri, P.R.; Schiffer, Marianne; Salgueiro, , Carlos A. (Journal of Biological Inorganic Chemistry, 2012)
Cytochromes c7 are periplasmic triheme proteins that have been reported exclusively in δ-proteobacteria. The structures of five triheme cytochromes identified in Geobacter sulfurreducens and one in Desulfuromonas acetoxidans have been determined. In addition to the hemes and axial histidines, a single aromatic residue is conserved in all these proteins - phenylalanine 15 (F15). PpcA is a member of the G. sulfurreducens cytochrome c7 family that performs electron/proton energy transduction in addition to electron transfer that leads to the reduction of extracellular electron acceptors. For the first time we probed the role of the F15 residue in the PpcA functional mechanism, by replacing this residue with the aliphatic leucine by site-directed mutagenesis. The analysis of NMR spectra of both oxidized and reduced forms showed that the heme core and the overall fold of the mutated protein were not affected. However, the analysis of 1H-15N heteronuclear single quantum coherence NMR spectra evidenced local rearrangements in the α-helix placed between hemes I and III that lead to structural readjustments in the orientation of heme axial ligands. The detailed thermodynamic characterization of F15L mutant revealed that the reduction potentials are more negative and the redox-Bohr effect is decreased. The redox potential of heme III is most affected. It is of interest that the mutation in F15, located between hemes I and III in PpcA, changes the characteristics of the two hemes differently. Altogether, these modifications disrupt the balance of the global network of cooperativities, preventing the F15L mutant protein from performing a concerted electron/proton transfer.

Platforms for enrichment of phosphorylated proteins and peptides in proteomics - Batalha, Iris L; Lowe, Christopher R.; Roque, Ana C A (Trends in Biotechnology, 2012)
Protein phosphorylation is a complex and highly dynamic process involved in numerous biological events. Abnormal phosphorylation is one of the underlying mechanisms for the development of cancer and metabolic disorders. The identification and absolute quantification of specific phospho-signatures can help elucidate protein functions in signaling pathways and facilitate the development of new and personalized diagnostic and therapeutic tools. This review presents a variety of strategies currently utilized for the enrichment of phosphorylated proteins and peptides before mass spectrometry analysis during proteomic studies. The investigation of specific affinity reagents, allied to the integration of different enrichment processes, is triggering the development of more selective, rapid and cost-effective high-throughput automated platforms.

Poly (epsilon-caprolactone)/siloxane biohybrids with application in "smart windows" - Rodrigues L.C.; Silva M.M.; Smith M.J.,; Gonçalves A.,; Fortunato E., (Synthetic Metals, 2012)

Preparation and Characterization of Polymeric Nanoparticles Composed of Poly(DL-lactide-co-glycolide) and Poly(DL-lactide-co-glycolide)-co-poly(ethylene glycol) 10%Triblock end-capped with a galactose moiety - I. N. Peça; K. T. Petrova; M. M. Cardoso; M. T. Barros (React. Funct. Polym., 2012)

Probing radiation damage by alternated current conductivity as a method to characterize electron hopping conduction in DNA molecules - P.J. Gomes; M. Coelho; M. Dionísio; P.A. Ribeiro; M. Raposo (Applied Physics Letters, 2012)

Projections of energy services demand for residential buildings: Insights from a bottom-up methodology - Gouveia, João Pedro; Patrícia Fortes; Júlia Seixas (Energy, 2012)
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Keywords: energy services demand; residential buildings

Protein Folding Modulates the Swapped Dimerization Mechanism of Methyl-Accepting Chemotaxis Heme Sensors - Silva, , Marta A.; Lucas, , Tânia G.; Salgueiro, , Carlos A.; Gomes, , Cláudio M. (PLoS ONE, 2012)
The periplasmic sensor domains GSU0582 and GSU0935 are part of methyl accepting chemotaxis proteins in the bacterium Geobacter sulfurreducens. Both contain one c-type heme group and their crystal structures revealed that these domains form swapped dimers with a PAS fold formed from the two protein chains. The swapped dimerization of these sensors is related to the mechanism of signal transduction and the formation of the swapped dimer involves significant folding changes and conformational rearrangements within each monomeric component. However, the structural changes occurring during this process are poorly understood and lack a mechanistic framework. To address this issue, we have studied the folding and stability properties of two distinct heme-sensor PAS domains, using biophysical spectroscopies. We observed substantial differences in the thermodynamic stability (ΔG = 14.6 kJ.mol−1 for GSU0935 and ΔG = 26.3 kJ.mol−1 for GSU0582), and demonstrated that the heme moiety undergoes conformational changes that match those occurring at the global protein structure. This indicates that sensing by the heme cofactor induces conformational changes that rapidly propagate to the protein structure, an effect which is directly linked to the signal transduction mechanism. Interestingly, the two analyzed proteins have distinct levels of intrinsic disorder (25% for GSU0935 and 13% for GSU0582), which correlate with conformational stability differences. This provides evidence that the sensing threshold and intensity of the propagated allosteric effect is linked to the stability of the PAS-fold, as this property modulates domain swapping and dimerization. Analysis of the PAS-domain shows that disorder segments are found either at the hinge region that controls helix motions or in connecting segments of the β-sheet interface. The latter is known to be widely involved in both intra- and intermolecular interactions, supporting the view that it's folding and stability are at the basis of the specificity and regulation of many types of PAS-containing signaling proteins.

Protein identification and localization using mass spectrometry and staining tests in cross-sections of polychrome samples - S. Kuckova; et al (Journal of Cultural Heritage, 2012)
The identification and localization of the proteinaceous binders are essential issues in studies of painting materials and techniques, for further proposing valid restoration and conservation treatments of the painted or polychrome works of art. The challenge for analytical chemists and conservation scientists is the availability of methods able to simultaneously identify and map the presence of the binders in the multilayered structure of a sample and the possibility to use a very low amount of sample from the studied art object (considering also the criteria of minimum sampling). These methods should be fast, reproducible in different artefacts and in case of mixture of protein-based binders with other non-proteinaceous constituents (oils, resins, waxes, gums etc.) and also economical (both in terms of materials and time consume). In this context, the present paper proposes an innovative protocol of investigation using two complementary techniques – Matrix-Assisted Laser Desorption/Ionisation – Time of Flight Mass Spectrometry (MALDI-TOF MS) and staining tests (one visible and one fluorescent stain) assisted by Optical Microscopy (OM) on cross-section of samples – for the simultaneous identification and mapping of protein – and oil-based binders in paint materials. The novelty is based on the use of MALDI-TOF MS on cross-sections of paints together with a fluorescent stain for protein identification and mapping (mainly used in the area of proteomics) complementing the use of a traditional visible stain for oil-based material identification. The protocol was successfully applied on several samples taken from a Czech medieval polychrome sculpture, entitled “The Mourning of Jesus Christ” (16th century) belonging to the Moravian Gallery (Brno).

QoE-JVM: An Adaptive and Resource-Aware Java Runtime for Cloud Computing - Simão, J.; Veiga, L. (On the Move to Meaningful Internet Systems: OTM 2012, 2012)
Cloud computing has been dominated by system-level virtual machines to enable the management of resources using a coarse grained approach, largely in a manner independent from the applications running on these infrastructures. However, in such environments, although different types of applications can be running, the resources are often delivered in a equal manner to each one, missing the opportunity to manage the available resources in a more efficient and application aware or driven way. Our proposal is QoE-JVM supporting Java applications with a global and elastic distributed image of a high-level virtual machine (HLLVM), where total resource consumption and allocation (within and across applications in the infrastructure) are driven by incremental gains in quality-of-execution (QoE), which relates the resources allocated to an application and the performance the application can extract from having those resources. In this paper, we discuss how critical resources (memory and CPU) can be allocated among HLL-VMs, so that Cloud providers can exchange resource slices among virtual machines, continually adaptdressing where those resources are required, while being able to determine where the reduction will be more economically effective, i.e., will contribute in lesser extent to performance degradation.
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Recent advances into vanadyl, vanadate and decavanadate interactions with actin - Ramos, S.; Moura, J. J. G.; Aureliano, M. (Metallomics, 2012)

RELAZIONE SUGLI ASPETTI FORMATIVI - SCUTARU, G.; SANDU, F.; COCORADA, E.; PAVALACHE, M.; KRISTALY, D.; Gomes, L.; Coito, F.; MÖRSKY-LINDQUIST, A.K.; CSEREY, S.; DASCĂLU, M.; Others (2012)
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Revealing the structural origin of the redox-Bohr effect: the first solution structure of a cytochrome from Geobacter sulfurreducens - Leonor Morgado; Paixão, Vítor B.; Schiffer, Marianne; Pokkuluri, P.R.; Bruix, Marta; Salgueiro, , Carlos A. (Biochemical Journal, 2012)
Gs (Geobacter sulfurreducens) can transfer electrons to the exterior of its cells, a property that makes it a preferential candidate for the development of biotechnological applications. Its genome encodes over 100 cytochromes and, despite their abundance and key functional roles, to date there is no structural information for these proteins in solution. The trihaem cytochrome PpcA might have a crucial role in the conversion of electronic energy into protonmotive force, a fundamental step for ATP synthesis in the presence of extracellular electron acceptors. In the present study, 15N-labelled PpcA was produced and NMR spectroscopy was used to determine its solution structure in the fully reduced state, its backbone dynamics and the pH-dependent conformational changes. The structure obtained is well defined, with an average pairwise rmsd (root mean square deviation) of 0.25 Å (1 Å=0.1 nm) for the backbone atoms and 0.99 Å for all heavy atoms, and constitutes the first solution structure of a Gs cytochrome. The redox-Bohr centre responsible for controlling the electron/proton transfer was identified, as well as the putative interacting regions between PpcA and its redox partners. The solution structure of PpcA will constitute the foundation for studies aimed at mapping out in detail these interacting regions.

The role of intramolecular interactions in the functional control of multiheme cytochromes c - Fonseca, B.M.; Paquete, C.M.; Salgueiro, C.A.; Louro, R.O. (FEBS Lett, 2012)
Detailed thermodynamic and structural data measured in soluble monomeric multiheme cytochromes c provided the basis to investigate the functional significance of interactions between redox co-factors. The steep decay of intramolecular interactions with distance means that close proximity of the redox centers is necessary to modulate the intrinsic reduction potentials in a significant way. This ensures selection of specific populations during redox activity in addition to maintaining fast intramolecular electron transfer. Therefore, intramolecular interactions between redox co-factors play an important role in establishing the biological function of the protein by controlling how electrons flow through and are distributed among the co-factors.

Sintering Behavior of Nano- and Micro-Sized ZnO Powder Targets for rf Magnetron Sputtering Applications - N. Neves; R. Barros; E. Antunes; Ferreira, I.; J. Calado; E. Fortunato; R. Martins (J. Am. Ceram. Soc., 2012)

Solar Architecture Conference - Amado, Miguel; São José Sousa (2012)

Strongly Photosensitive and Fluorescent F8T2 Electrospun Fibers - Ferreira; Baptista, Ana Catarina,; Leitão, Joaquim,; Soares, Jorge,; Fortunato; Martins; Borges, João Paulo (Macromol. Mater. Eng., 2012)

Substrate-dependent modulation of the enzymatic catalytic activity: Reduction of nitrate, chlorate and perchlorate by respiratory nitrate reductase from Marinobacter hydrocarbonoclasticus 617 - Marangon, J.; de Sousa, P. M. Paes; Moura, I.; Brondino, C. D.; Moura, J. J.; P.J. González (Biochim Biophys Acta, 2012)

Synthesis of [MoS4]2 – M (M = Cu and Cd) clusters: Potential NMR structural probes for orange protein - B.K. Maiti; T. Avilés; Matzapetakis, M.; Moura, I.; Pauleta, S. R.; Moura, J. J. G. (Eur J Inorg Chem, 2012)

Textural Evolution Evaluated by EBSD and XRD after Thermal Treatment in Ni-Ti Shape Memory Alloy - "S.B. Ribeiro", "T.G. Andrade", "A.S. Paula", "J.F.C. Lins", "K.K. Mahesh", "F.M. Braz Fernandes" (Materials Science Forum, 2012)

TIMES_PT: Integrated Energy System Modeling - Gouveia, João Pedro; Dias, Luis; Patrícia Fortes; Júlia Seixas (1st Int'l Workshop on Information Technology for Energy Applications (IT4ENERGY'2012), 2012)

Transparent Oxide Electronics: From Materials to Devices - Barquinha; Martins; Pereira; E. Fortunato (John Wiley & Sons, Ltd, 2012)

TribuSTM Instrumentation Rules - Tiago Vale; Ricardo Jorge Dias (Departamento de Informática FCT/UNL, 2012)

Uma Infraestrutura para Suporte de Memória Transacional Distribuída - Vale, Tiago M.; Ricardo J. Dias; João M. Lourenço (Proceedings of INForum Simpósio de Informática, 2012)
As técnicas e algoritmos desenvolvidos sobre diferentes infraestruturas específicas dificilmente podem ser comparados entre si. Este princípio também se aplica às infraestruturas para execução de Memória Transacional Distribuída (MTD), pois não só são muito escassas aquelas que permitem o desenvolvimento, teste e comparação de vários algoritmos e técnicas de implementação, como fornecem uma interface intrusiva para o programador. Sem uma comparação justa, não é possível aferir quais as técnicas e algoritmos mais apropriados em cada contexto de utilização (workload). Neste artigo propomos uma infraestrutura generalista, muito flexível, que possibilita a experimentação de várias estratégias de MTD, permitindo o desenvolvimento de uma grande variedade de algoritmos e de técnicas de implementação eficientes e otimizadas. Através da sua utilização, é agora possível a comparação de técnicas e algoritmos em diferentes contextos de utilização (workloads), recorrendo a uma única infraestrutura e com implicações mínimas no código da aplicação.
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Keywords: Arquitetura de software; Concorrência; Java; Memória transacional distribuída; Replicação

Understanding the Ion Jelly Conductivity Mechanism - T. Carvalho; V. Augusto; A. R. Brás; N. M. T. Lourenço; C. A. M. Afonso; S. Barreiros; N. T. Correia; P. Vidinha; E. J. Cabrita; C. J. Dias; M. Dionísio; B. Roling (The Journal of Physical Chemistry B, 2012)

Understanding the molecular recognition between antibody fragments and protein A biomimetic ligand - Ricardo J F Branco; Ana M G C Dias; Roque, Ana C A (Journal of Chromatography A, 2012)
Afﬁnity chromatography with protein A from Staphylococcus aureus (SpA) is the most widespread and accepted methodology for antibody capture during the downstream process of antibody manufacturing. A triazine based ligand (ligand 22/8) was previously developed as an inexpensive and robust alternative to SpA chromatography (Li et al. [12] and Teng et al. [11]). Despite the experimental success, there is no structural information on the binding modes of ligand 22/8 to antibodies, namely to Immunoglobulin G (IgG) molecules and fragments. In this work, we addressed this issue by a molecular docking approach allied to molecular dynamics simulations. Theoretical results conﬁrmed the preference of the synthetic ligand to bind IgG through the binding site found in the crystallographic structure of the natural complex between SpA and the Fc fragment of IgG. Our studies also suggested other unknown “hot-spots” for speciﬁc binding of the afﬁnity ligand at the hinge between VH and CH1 domains of Fab fragment. The best docking poses were further analysed by molecular dynamics studies at three different protonation states (pH 3, 7 and 11). The main interactions between ligand 22/8 and the IgG fragments found at pH 7 were weaker at pH 3 and pH 11 and in these conditions the ligand start losing tight contact with the binding site, corroborating the experimental evidence for protein elution from the chromatographic adsorbents at these pH conditions.

Using Program Closures to Make an Application Programming Interface (Api) Implementation Thread Safe - Farchi, Eitan; Segall, Itai; João M. Lourenço; Sousa, Diogo G. (Proceedings of the 2012 Workshop on Parallel and Distributed Systems: Testing, Analysis, and Debugging, 2012)
Consider a set of methods implementing an Application Programming Interface (API) of a given library or program module that is to be used in a multithreaded setting. If those methods were not originally designed to be thread safe, races and deadlocks are expected to happen. This work introduces the novel concept of program closure and describes how it can be applied in a methodology used to make the library or module implementation thread safe, by identifying the high level data races introduced by interleaving the parallel execution of methods from the API. High-level data races result from the misspecification of the scope of an atomic block, by wrongly splitting it into two or more atomic blocks sharing a data dependency. Roughly speaking, the closure of a program P, clos(P), is obtained by incrementally adding new threads to P in such a way that enables the identification of the potential high level data races that may result from running P in parallel with other programs. Our model considers the methods implementing the API of a library of program module as concurrent programs and computes and analyses their closure in order to identify high level data races. These high level data races are inspected and removed to make the interface thread safe. We illustrate the application of this methodology with a simple use case.
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Keywords: concurrency; software transactional memory; static analysis; testing; verification

Verification of Snapshot Isolation in Transactional Memory Java Programs - Ricardo J. Dias; Dino Distefano; João Costa Seco; João M. Lourenço (ECOOP 2012 – Object-Oriented Programming, 2012)
This paper presents an automatic verification technique for transactional memory Java programs executing under snapshot isolation level. We certify which transactions in a program are safe to execute under snapshot isolation without triggering the write-skew anomaly, opening the way to run-time optimizations that may lead to considerable performance enhancements. Our work builds on a novel deep-heap analysis technique based on separation logic to statically approximate the read- and write-sets of a transactional memory Java program. We implement our technique and apply our tool to a set of micro benchmarks and also to one benchmark of the STAMP package. We corroborate known results, certifying some of the examples for safe execution under snapshot isolation by proving the absence of write-skew anomalies. In other cases our analysis has identified transactions that potentially trigger previously unknown write-skew anomalies.
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VM Economics for Java Cloud Computing - An Adaptive and Resource-Aware Java Runtime with Quality-of-Execution - José Simão; Luís Veiga (The 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2012), 2012)
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Where has the debates on social involvement on HRI gone? - Moniz, António B. (ITAS-KIT, 2012)

Write-Write Conflict Detection for Distributed TM Systems - Ricardo J. Dias; Vale, Tiago M.; João M. Lourenço (Talk presented at the 1st Euro-TM Workshop on Distributed Transactional Memory (WDTM'12), 2012)
Typical Distributed Transactional Memory (DTM) systems provide serializability by detecting read-write conflicts between accesses to shared data objects. Detecting read-write conflicts requires the bookkeeping of all the read and write accesses to the shared objects made inside the transaction, and the validation of all these accesses in the end of a transaction. For most DTM algorithms, the validation of a transaction requires the broadcast of its read-set to all the nodes of the distributed system during the commit phase. Since applications tend to read more than write, the overhead associated with the bookkeeping of read accesses, and the amount of network traffic generated during the commit, is a main performance problem in DTM systems. Database systems frequently rely on weaker isolation models to improve performance. In particular, Snapshot Isolation (SI) is widely used in industry. An interesting aspect of SI is that only write-write conflicts are checked at commit time and considered for detecting conflicting transactions. As main result, a DTM using this isolation model does not need to keep track of the read accesses, considerably reducing the bookkeeping overhead, and also eliminates the need of broadcasting the read-set at transaction commit time, thus reducing the network traffic and considerably increase the scalability of the whole system. By only detecting write-write conflicts, this isolation model allows a much higher commit rate, which comes at the expense of allowing some real conflicting transactions to commit. Thus, relaxing the isolation of a transactional program may lead previously correct programs to misbehave due to the anomalies resulting from malign data-races that are now allowed by the relaxed transactional run-time. These anomalies can be precisely characterized, and are often called in the literature as write-skew anomalies. Write-skew anomalies can be avoided dynamically with the introduction of algorithms that verify the serializability of running transactions, which may result in a non-negligible overhead. Our approach is to avoid the run-time overhead by statically asserting that a DTM program will execute without generating write-skew anomalies at runtime, while only verifying write-write conflicts. Conflicting transactions can be made “safe” by code rewriting using well known techniques. Our verification technique uses separation logic, a logic for verifying intensive heap manipulation programs, which was extended to construct abstract read- and write-sets for each transaction in the DTM program. This verification technique is implemented in the StarTM tool, which analyzes transactional Java bytecode programs. The transactions that cannot be verified by our tool are executed under serializable isolation (detecting read-write conflicts), while for the “safe” transactions we only detect write-write conflicts. The results of our experiments when verifying micro-benchmarks, such as linked lists and binary trees, and partially verifying some macro-benchmarks, such as the STAMP benchmark, strongly encourage the ongoing work for the application of this technique to DTM.
Workshop talk

{Análise de um processo decisório controverso: a co-incineração em Souselas [Analysis of a controversial decision process: the co-incineration at Souselas]} - Maia, Maria João; Ana Isabel Moiteiro; Lanka Horstink; Mário Farelo; Rosa Antunes (Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology, 2012)
The scientific controversy generated around the destiny given to the fraction of hazardous industrial waste produced in Portugal and how the country dealt with this situation was the stand out point in Souselas case. Here, the dominant aspect of the analysis focused on the implementation of a solution for the treatment of hazardous industrial waste. These wastes result from industrial processes contain or are contaminated, by substances that, at certain concentrations, represent a risk to human health or to the environment. Their treatment can be done using co-incineration in existing cement factories. Having in mind the environment analysis of a controversial process, through the statements made by the different actors involved, the case of Souselas was our object of study. Initially, the actors involved in the process were identified and characterized, in terms of position, interests and / or concerns. This analysis has strengthened with the gathering of documentary elements of analysis. In a second phase the historical process was prepared. Only then, the conditions to make an interpretation of what really happened in the process were gathered, then , it was possible to identify which parts were successful and unsuccessful, and to interpret “why” these successes and failures occurred. Thus, after the identification of key variables and leverage points, a causal diagram and a schematic simulation of the behaviour of reference in case Souselas was designed. We conclude that the process of Souselas was a significant milestone with regard to social organization and spontaneous local actors in situations of opposition to central government decisions with local impact. It was also a turning point in governance according to the model of representative democracy, whose technocratic and elitist character is called into question. The Souselas case emphasized itself as a microcosm on the conflict of interests that we find at a global level heightened since the 90s and that
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Keywords: Co-incineration; Hazardous indu; leverage points; Participatory Decision Process; Portugal; Souselas

3D Au-Ag heterometallic supramolecular cage: Triplet capture by heavy atom effect - Rodriguez, Laura; Lima, Joao C.; Ferrer, Montserrat; Rossell, Oriol; Engeser, Marianne (Inorganica Chimica Acta, 2012)
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Antifungals on paper conservation: An overview - S{\'ılvia Sequeira; Cabrita, Eurico J.; Filomena M. Macedo (International Biodeterioration & Biodegradation, 2012)
Since its invention, paper has become one of the main carriers of our cultural, scientific, political, economic and historical information. Given the importance of this material, its preservation is a matter of great interest. Paper can be deteriorated due to physical, chemical and biological agents. Within microorganisms, fungi are the major paper biodeteriogens. Throughout history, several methods have been used to prevent and stop fungal deterioration on paper based materials. In this work we present a review of the main chemical and physical methods used to avoid fungal paper biodeterioration until nowadays and also of some new approaches tested recently. The advantages and disadvantages of these methods are discussed as well as their health effects. Studies regarding antifungal compositions, methods of application, performance and effects on the treated materials are also presented with the aim of providing a clear set of conclusions on the topic. (C) 2012 Elsevier Ltd. All rights reserved.
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Blue emission of carbamic acid oligooxazoline biotags - Bonifacio, Vasco D. B.; Correia, Vanessa G.; Pinho, Mariana G.; Lima, Joao C.; Aguiar-Ricardo, Ana (Materials Letters, 2012)
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Chemistry and applications of flavylium compounds: a handful of colours - Pina, Fernando; Melo, Maria J.; Laia, Cesar A. T.; A. Jorge Parola; Lima, Joao C. (Chemical Society Reviews, 2012)
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Chrome yellow in nineteenth century art: historic reconstructions of an artists' pigment - Otero, Vanessa; Carlyle, Leslie; Vilarigues, Marcia; Melo, Maria J. (Rsc Advances, 2012)
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Times Cited: 1 Melo, Maria Joao/C-8594-2011; Carlyle, Leslie/D-7173-2013; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, LAQV/N-9835-2013 Melo, Maria Joao/0000-0001-7393-6801; 1

Combining infrared spectroscopy with chemometric analysis for the characterization of proteinaceous binders in medieval paints - Miguel, Catarina; Lopes, Joao A.; Clarke, Mark; Melo, Maria Joao (Chemometrics and Intelligent Laboratory Systems, 2012)
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Times Cited: 1 Melo, Maria Joao/C-8594-2011; Lopes, Joao/H-1733-2011; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, ANALYSIS/M-4644-2013; REQUIMTE, LAQV/N-9835-2013 Melo, Maria Joao/0000-0001-7393-6801; Lopes, Joao/0000-0002-1657-344X; 1

Complete resolution of the reaction Rates of flavylium Networks. The role played by 2-phenyl-2H-chromen-4-ol and the hydroxyl attack to the quinoidal Base - Vesselin Petrov; Pina, Fernando (Journal of Mathematical Chemistry, 2012)
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Times Cited: 0 Pina, Fernando/C-8161-2011; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, LAQV/N-9835-2013 Pina, Fernando/0000-0001-8529-6848; 0

Correlation between Photophysical Parameters and Gold-Gold Distances in Gold(I) (4-Pyridyl)ethynyl Complexes - Rodriguez, Laura; Ferrer, Montserrat; Crehuet, Ramon; Anglada, Josep; Lima, Joao Carlos (Inorganic Chemistry, 2012)
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Designer-oligosaccharide microarrays to decipher ligands in mammalian and prokaryotic glucan-recognition systems - Palma, Angelina S.; Liu, Yan; Zhang, Yibing; Zhang, Hongtao; Luis, Ana S.; Carvalho, Ana Luisa; Gilbert, Harry J.; Boraston, Alisdair; Fontes, Carlos M. G. A.; Chai, Wengang; Ten, Feizi (Glycobiology, 2012)
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Times Cited: 0 Palma, Angelina/D-2052-2013; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; Carvalho, Ana Luisa/G-5638-2011; REQUIMTE, SMB/M-5694-2013; REQUIMTE, UCIBIO/N-9846-2013 Carvalho, Ana Luisa/0000-0002-3824-0240; Joint Meeting of the Society-for-Glycobiology and American-Society-for-Matrix-Biology Nov 11-14, 2012 San Diego, CA Soc Glycobiol; Amer Soc Matrix Biol 0

Desulfovibrio vulgaris bacterioferritin uses H2O2 as a co-substrate for iron oxidation and reveals DPS-like DNA protection and binding activities - Timoteo, Cristina G.; Guilherme, Marcia; Penas, Daniela; Folgosa, Filipe; Tavares, Pedro; Pereira, Alice S. (BIOCHEMICAL JOURNAL, 2012)
A gene encoding Bfr (bacterioferritin) was identified and isolated from the genome of Desulfovibrio vulgaris cells, and overexpressed in Escherichia coli. In vitro, H2O2 oxidizes Fe2+ ions at much higher reaction rates than O-2. The H2O2 oxidation of two Fe2+ ions was proven by Mossbauer spectroscopy of rapid freeze-quenched samples. On the basis of the Mossbauer parameters of the intermediate species we propose that D. vulgaris Bfr follows a mineralization mechanism similar to the one reported for vertebrate H-type ferritins subunits, in which a diferrous centre at the ferroxidase site is oxidized to diferric intermediate species, that are subsequently translocated into the inner nanocavity. D. vulgaris recombinant Bfr oxidizes and stores up to 600 iron atoms per protein. This Bfr is able to bind DNA and protect it against hydroxyl radical and DNase deleterious effects. The use of H2O2 as an oxidant, combined with the DNA binding and protection activities, seems to indicate a DPS (DNA-binding protein from starved cells)-like role for D. vulgaris Bfr.
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Development of novel ionic liquids based on ampicillin - Ferraz, Ricardo; Branco, Luis C.; Marrucho, Isabel M.; Araujo, Joao M. M.; Rebelo, Luis Paulo N.; da Ponte, Manuel Nunes; Prudencio, Cristina; Noronha, Joao Paulo; Petrovski, Zeljko (Medchemcomm, 2012)
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Times Cited: 8 da Ponte, Manuel/B-3620-2010; Rebelo, Luis Paulo/B-5285-2008; Branco, Luis/C-6426-2013; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Araujo, Joao /J-2585-2013; Chaves, Pedro/K-1288-2013; Prudencio, Cristina/L-8398-2013; Noronha, Joao Paulo/C-6423-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, CENG/M-4555-2013; REQUIMTE, ANALYSIS/M-4644-2013; REQUIMTE, LAQV/N-9835-2013 da Ponte, Manuel/0000-0003-4499-4521; Branco, Luis/0000-0003-2520-1151; Prudencio, Cristina/0000-0002-9920-936X; Noronha, Joao Paulo/0000-0002-1515-4518; 8

Electrochromic Properties of Inkjet Printed Vanadium Oxide Gel on Flexible Polyethylene Terephthalate/Indium Tin Oxide Electrodes - Costa, Claudia; Pinheiro, Carlos; Henriques, Ines; Laia, Cesar A. T. (Acs Applied Materials & Interfaces, 2012)
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Times Cited: 2 Laia, Cesar/C-8651-2011; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, LAQV/N-9835-2013 Laia, Cesar/0000-0001-6410-6072; 2

Electroosmotic flow modulation in capillary electrophoresis by organic cations from ionic liquids - Mendes, Acacio; Branco, Luis C.; Morais, Cristiana; Simplicio, Ana Luisa (Electrophoresis, 2012)
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Times Cited: 5 Simplicio, Ana/B-9047-2011; Branco, Luis/C-6426-2013; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, LAQV/N-9835-2013 Branco, Luis/0000-0003-2520-1151; 5

Enhancement of antibiotic effect via gold: silver-alloy nanoparticles - Santos, Maria Margarida Moreira dos; Queiroz, Margarida João; Baptista, Pedro Miguel Ribeiro Viana (Journal Of Nanoparticle Research, 2012)
A strategy for the development of novel antimicrobials is to combine the stability and pleiotropic effects of inorganic compounds with the specificity and efficiency of organic compounds, such as antibiotics. Here we report on the use of gold:silver-alloy (Au:Ag-alloy) nanoparticles, obtained via a single-step citrate co-reduction method, combined to conventional antibiotics to enhance their antimicrobial effect on bacteria. Addition of the alloy nanoparticles considerably decreased the dose of antibiotic necessary to show antimicrobial effect, both for bacterial cells growing in rich medium in suspension and for bacterial cells resting in a physiological buffer on a humid cellulose surface. The observed effect was more pronounced than the sum of the individual effects of the nanoparticles and antibiotic. We demonstrate the enhancement effect of Au:Ag-alloy nanoparticles with a size distribution of 32.5±7.5nm mean diameter on the antimicrobial effect of (i) kanamycin onEscherichia coli(Gram-negative bacterium), and (ii) a β-lactam antibiotic on both a sensitive and resistant strain ofStaphylococcus aureus(Gram-positive bacterium). Together, these results may pave the way for the combined use of nanoparticle–antibiotic conjugates towards decreasing antibiotic resistance currently observed for certain bacteria and conventional antibiotics.
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Keywords: Antibiotic; Antimicrobial; E. coli; Gold:silver-alloy nanoparticles; Gram-negative bacteria; S. aureus

ESCHERICHIA COLI EXPRESSION, PURIFICATION, CRYSTALLIZATION, AND STRUCTURE DETERMINATION OF BACTERIAL COHESIN-DOCKERIN COMPLEXES - Bras, Joana L. A.; Carvalho, Ana Luisa; Viegas, Aldino; Najmudin, Shabir; Alves, Victor D.; Prates, Jose A. M.; Ferreira, Luis M. A.; Romao, Maria J.; Gilbert, Harry J.; Fontes, Carlos M. G. A. (Cellulases, 2012)
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Times Cited: 2 Romao, Maria/A-4115-2013; Viegas, Aldino/A-1889-2011; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; Prates, Jose/K-9934-2013; Carvalho, Ana Luisa/G-5638-2011; REQUIMTE, SMB/M-5694-2013; REQUIMTE, UCIBIO/N-9846-2013 Romao, Maria/0000-0002-3004-0543; Viegas, Aldino/0000-0003-1733-136X; Prates, Jose/0000-0003-1032-5987; Carvalho, Ana Luisa/0000-0002-3824-0240; 2

A facile synthesis of cysteine-ferrite magnetic nanoparticles for application in multicomponent reactions-a sustainable protocol - Gawande, Manoj B; Velhinho, Alexandre; Nogueira, Isabel D.; Ghumman, C. A. A.; Teodoro, O. M. N. D.; Branco, Paula S. (RSC ADVANCES, 2012)
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The First Mammalian Aldehyde Oxidase Crystal Structure INSIGHTS INTO SUBSTRATE SPECIFICITY - Coelho, Catarina; Mahro, Martin; Trincao, Jose; Carvalho, Alexandra T. P.; Ramos, Maria Joao; Terao, Mineko; Garattini, Enrico; Leimkuehler, Silke; Romao, Maria Joao (Journal of Biological Chemistry, 2012)
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Times Cited: 9 Romao, Maria/A-4115-2013; Coelho, Catarina /D-2073-2013; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, SMB/M-5694-2013; REQUIMTE, UCIBIO/N-9846-2013 Romao, Maria/0000-0002-3004-0543; Coelho, Catarina /0000-0003-1852-5406; 9

Gold-nanobeacons for real-time monitoring of RNA synthesis - Rosa, Joao; Conde, Joao; Jesus M. de la Fuente; Lima, Joao C.; Pedro V. Baptista (Biosensors & Bioelectronics, 2012)
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Hofmeister effects of ionic liquids in protein crystallization: Direct and water-mediated interactions - Kowacz, M.; Mukhopadhyay, A.; Carvalho, A. L.; Esperanca, Jmss; Romao, M. J.; Rebelo, L. P. N. (Crystengcomm, 2012)
We have performed experiments on the crystallization of two low molecular weight, positively charged proteins, lysozyme and ribonuclease A, using ionic liquids as either crystallization additives or, in particular cases, as precipitating agents. The ionic liquids (ILs) have been ordered according to their salting-in/out ability and the relative position of these ionic liquids in this ranking has been rationalized by considering their hydration properties (positive-negative, hydrophobic-hydrophilic). The ability to screen the effective charge of cationic proteins and aid protein nucleation (salting-out) has been shown to be superior for large polarizable anions with low charge density, negatively hydrated-Cl-, Br-, [SCN](-), methane-[C1SO3](-) and ethanesulfonates [C2SO3](-), than for anions with a relatively stable hydration shell, positively hydrated-lactate [Lac](-), butylsulfonate [C4SO3](-) and acetate [Ac](-). Upon increasing the background salt concentration, where electrostatic interactions are already effectively screened, the ability of the IL ions to stabilize proteins in solution (salting-in) has been shown to increase as the ions are likely to migrate to the non-polar protein surface and lower protein-water interfacial tension. This tendency is enhanced as the focus moves from those ions with positively hydrated hydrophilic compartments (e. g. [Ac](-)) to those with negatively hydrated groups (e. g. [C1SO3](-)) and the prevailing hydrophobic hydration (e. g. [C4SO3](-)). The observed inversion in the relative effect of ILs on protein crystallization with increasing ionic strength of the aqueous media has been interpreted as the differing effects of ion adsorption: charge screening and interfacial tension modification. Moreover, this work can further help in our understanding of the influence of ionic liquids on conformational changes of biomacromolecules in solution. Identification of the specific incorporation sites for choline and acetate ions, localized in two lysozyme crystals grown in pure IL solutions without any buffer or inorganic precipitant, can give us some insight into the role of the ionic liquid ions in protein structure development.
ISI Document Delivery No.: 968QN Times Cited: 14 Cited Reference Count: 69 Kowacz, Magdalena Mukhopadhyay, Abhik Carvalho, Ana Luisa Esperanca, Jose M. S. S. Romao, Maria J. Rebelo, Luis Paulo N. Rebelo, Luis Paulo/B-5285-2008; Romao, Maria/A-4115-2013; Mukhopadhyay, Abhik/D-2119-2013; Kowacz, Magdalena/D-2386-2013; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Esperanca, Jose/B-5116-2008; Chaves, Pedro/K-1288-2013; Carvalho, Ana Luisa/G-5638-2011; REQUIMTE, SMB/M-5694-2013; REQUIMTE, UCIBIO/N-9846-2013 Mukhopadhyay, Abhik/0000-0002-9808-7620; Rebelo, Luis Paulo/0000-0002-5247-2443; Romao, Maria/0000-0002-3004-0543; Mukhopadhyay, Abhik/0000-0002-7755-0401; Kowacz, Magdalena/0000-0001-5729-6816; Esperanca, Jose/0000-0001-9615-8678; Carvalho, Ana Luisa/0000-0002-3824-0240; Fundacao para a Ciencia e a Tecnologia, Portugal [PEst-C/EQB/LA0006/2011, PEst-OE/EQB/LA0004/2011, SFRH/BPD/30142/2006, SFRH/BPD/63554/2009]; Research Executive Agency [PERG05-GA-2009-249182] The authors acknowledge financial support from Fundacao para a Ciencia e a Tecnologia, Portugal, through grants PEst-C/EQB/LA0006/2011 to the Associate Lab REQUIMTE and PEst-OE/EQB/LA0004/2011 to the ITQB and through post-doctoral grants SFRH/BPD/30142/2006 and SFRH/BPD/63554/2009. The authors thank the Research Executive Agency for Marie Curie Reintegration grant PERG05-GA-2009-249182. The authors also acknowledge the SOLEIL synchrotron facility (Paris, France) for access and technical support during data collection. 14 9 60 Royal soc chemistry Cambridge
Keywords: surface-tension measurements molecular-dynamics simulations aqueous-solutions cytochrome-c salting-out functional conversion hydration lysozyme stability extraction Chemistry Crystallography

Improving Operator Performance through the Use of a Multivariable Human-Machine Control Strategy - Antunes, R.; Coito, F.; Duarte-Ramos, H. (Technological Innovation for Value Creation, 2012)
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Indole based cyclooxygenase inhibitors: synthesis, biological evaluation, docking and NMR screening - Mónica S. Estevão; Lu{\'ısa C. R. Carvalho; Marisa Freitas; Ana Gomes; Viegas, Aldino; João Manso; Stefan Erhadrt; Cabrita, Eurico J.; Marques, Maria Manuel B. (European Journal of Medicinal Chemistry, 2012)
The close structural similarity between the two cyclooxygenase (COXs) isoforms and the absence of selective inhibitors without side effects continues to stimulate the development of novel approaches towards selective anti-inflammatory drugs. In the present study a small library of new indolic compounds involving two different substitutions patterns at the indole scaffold was synthesized. In order to establish a relation between the spatial distribution of known functional groups related with inhibitory activity, two substitution patterns were explored: one with substituents at N-1, C-3, C-5 positions and another at C-2, C-3 and C5 positions. Accordingly, indole positions C-5, C-3 and N-1 were substituted with: sulfonamide or methylsulfone at C-5, p-halo-benzyl group at C-3, and an alkyl chain with a trifluoromethyl group at N-1. Alternatively, a p-halo-benzyl group was introduced at C-2, leaving the indolic nitrogen free. Inhibitory studies were performed and the activity results obtained against both COXs isoforms were rationalized based on docking and NMR studies. Docking studies show that dialkyation at C-2 and C-3 favors a binding with an orientation similar to that of the known selective inhibitor SC-558. From the tested compounds, this substitution pattern is correlated with the highest inhibitory activity and selectivity: 70% COX-2 inhibition at 50 M, and low COX-1 inhibition (18±9%). Additionally, Saturation Transfer Difference NMR experiments reveal different interaction patterns with both COXs isoforms that may be related with different orientations of the sulfonamide group in the binding pocket. Despite the moderated inhibitory activities found, this study represents an innovative approach towards COXs inhibitory activity rationalization and to the design of anti-inflammatory drugs.
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Inkjet Printing of Sol-Gel Synthesized Hydrated Tungsten Oxide Nanoparticles for Flexible Electrochromic Devices - Costa, Claudia; Pinheiro, Carlos; Henriques, Ines; Laia, Cesar A. T. (Acs Applied Materials & Interfaces, 2012)
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Times Cited: 8 Laia, Cesar/C-8651-2011; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, LAQV/N-9835-2013 Laia, Cesar/0000-0001-6410-6072; 9

Kinetics of Zn2+ complexation by a ditopic phenanthroline-azamacrocyclic scorpiand-like receptor - Gonzalez, Jorge; Gavara, Raquel; Gadea, Oscar; Blasco, Salvador; Garcia-Espana, Enrique; Pina, Fernando (Chemical Communications, 2012)
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Times Cited: 3 Pina, Fernando/C-8161-2011; Gavara, Raquel/C-6669-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, LAQV/N-9835-2013 Pina, Fernando/0000-0001-8529-6848; Gavara, Raquel/0000-0002-7198-9392; 3

Micro-Raman study of Medieval Cistercian 12-13th century manuscripts: Santa Maria de Alcobaca, Portugal - Muralha, Vania S. F.; Miguel, Catarina; Melo, Maria Joao (Journal of Raman Spectroscopy, 2012)
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Times Cited: 3 Melo, Maria Joao/C-8594-2011; Muralha, Vania/C-7018-2013; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, LAQV/N-9835-2013 Melo, Maria Joao/0000-0001-7393-6801; Muralha, Vania/0000-0001-5488-9069; Si 3

Nanophotonics for Molecular Diagnostics and Therapy Applications - Conde, Joao; Rosa, Joao; Lima, Joao C.; Pedro V. Baptista (International Journal of Photoenergy, 2012)
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Nanophotonics for molecular diagnostics and therapy applications - João Conde; João Rosa; Lima, João C.; Baptista, Pedro V (International Journal Of Photoenergy, 2012)
Light has always fascinated mankind and since the beginning of recorded history it has been both a subject of research and a tool for investigation of other phenomena. Today, with the advent of nanotechnology, the use of light has reached its own dimension where light-matter interactions take place at wavelength and subwavelength scales and where the physical/chemical nature of nanostructures controls the interactions. This is the field of nanophotonics which allows for the exploration and manipulation of light in and around nanostructures, single molecules, and molecular complexes. What is more is the use of nanophotonics in biomolecular interactionsnanobiophotonicshas prompt for a plethora of molecular diagnostics and therapeutics making use of the remarkable nanoscale properties. In this paper, we shall focus on the uses of nanobiophotonics for molecular diagnostics involving specific sequence characterization of nucleic acids and for gene delivery systems of relevance for therapy strategies. The use of nanobiophotonics for the combined diagnostics/therapeutics (theranostics) will also be addressed, with particular focus on those systems enabling the development of safer, more efficient, and specific platforms. Finally, the translation of nanophotonics for theranostics into the clinical setting will be discussed.
The authors acknowledge FCT/MCTES-CIGMH(Portugal) for financial support.
Keywords: DNA; Metal Nanoparticles; Spherical nucleic

New insights into the chemistry of fac- Ru(CO)(3) (2+) fragments in biologically relevant conditions: The CO releasing activity of Ru(CO)(3)Cl-2(1,3-thiazole) , and the X-ray crystal structure of its adduct with lysozyme - Santos, M. F. A.; Seixas, J. D.; Coelho, A. C.; Mukhopadhyay, A.; Reis, P. M.; Romao, M. J.; Romao, C. C.; Santos-Silva, T. (Journal of Inorganic Biochemistry, 2012)
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Times Cited: 3 Romao, Carlos /D-1162-2010; Romao, Maria/A-4115-2013; Mukhopadhyay, Abhik/D-2119-2013; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Reis, Patricia/I-7422-2013; Coelho, Ana Catarina/J-3331-2013; Chaves, Pedro/K-1288-2013; Santos-Silva, Teresa/D-2050-2013; REQUIMTE, SMB/M-5694-2013; REQUIMTE, UCIBIO/N-9846-2013; PTMS, RNEM/C-1589-2014 Romao, Carlos /0000-0001-5061-3743; Romao, Maria/0000-0002-3004-0543; Mukhopadhyay, Abhik/0000-0002-7755-0401; Reis, Patricia/0000-0001-6320-7496; 3

Noble metal nanoparticles applications in cancer - João Conde; Gonçalo Doria; Baptista, Pedro Viana (Journal of drug delivery, 2012)
Nanotechnology has prompted new and improved materials for biomedical applications with particular emphasis in therapy and diagnostics. Special interest has been directed at providing enhanced molecular therapeutics for cancer, where conventional approaches do not effectively differentiate between cancerous and normal cells; that is, they lack specificity. This normally causes systemic toxicity and severe and adverse side effects with concomitant loss of quality of life. Because of their small size, nanoparticles can readily interact with biomolecules both at surface and inside cells, yielding better signals and target specificity for diagnostics and therapeutics. This way, a variety of nanoparticles with the possibility of diversified modification with biomolecules have been investigated for biomedical applications including their use in highly sensitive imaging assays, thermal ablation, and radiotherapy enhancement as well as drug and gene delivery and silencing. Here, we review the available noble metal nanoparticles for cancer therapy, with particular focus on those already being translated into clinical settings.
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Notes on a testing web framework for BST - Ferreira, Paulo (CITI / DI-FCT-UNL, 2012)
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Novel Clostridium thermocellum Type I Cohesin-Dockerin Complexes Reveal a Single Binding Mode - Bras, Joana L. A.; Alves, Victor D.; Carvalho, Ana Luia; Najmudin, Shabir; Prates, Jose A. M.; Ferreira, Luis M. A.; Bolam, David N.; Romao, Maria Joao; Gilbert, Harry J.; Fontes, Carlos M. G. A. (Journal of Biological Chemistry, 2012)
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Times Cited: 1 Romao, Maria/A-4115-2013; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; Prates, Jose/K-9934-2013; Carvalho, Ana Luisa/G-5638-2011; REQUIMTE, SMB/M-5694-2013; REQUIMTE, UCIBIO/N-9846-2013 Romao, Maria/0000-0002-3004-0543; Prates, Jose/0000-0003-1032-5987; Carvalho, Ana Luisa/0000-0002-3824-0240; 2

A novel dinuclear MoVI complex with tris(3,5-dimethyl-1H-pyrazol-1-yl)methane - Gago, Sandra; Gomes, Ana C.; Cunha-Silva, Luis; Pillinger, Martyn; Goncalves, Isabel S.; Almeida Paz, Filipe A. (Acta Crystallographica Section C-Crystal Structure Communications, 2012)
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Times Cited: 0 Gago, Sandra/H-5413-2012; Cunha-Silva, Luis/A-8765-2012; Pillinger, Martyn/H-2639-2013; Goncalves, Isabel/H-3742-2013; Gomes, Ana/G-2636-2010; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, MAT/M-4540-2013; REQUIMTE, NSF/N-1636-2013; Almeida Paz, Filipe/F-3430-2010; REQUIMTE, LAQV/N-9835-2013 Gago, Sandra/0000-0003-0221-8508; Cunha-Silva, Luis/0000-0001-9229-1412; Pillinger, Martyn/0000-0002-6243-7692; Goncalves, Isabel/0000-0002-2836-7715; Gomes, Ana/0000-0001-9598-1275; Almeida Paz, Filipe/0000-0003-2051-5645; 3 0

Novel emissive bio-inspired non-proteinogenic coumarin-alanine amino acid: fluorescent probe for polyfunctional systems - Oliveira, Elisabete; Luis Capelo, Jose; Lima, Joao Carlos; Lodeiro, Carlos (Amino Acids, 2012)
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On the analysis of compensation correctness - Cátia Vaz; Carla Ferreira (J. Log. Algebr. Program., 2012)
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On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP - Roldao, Antonio; Mellado, Maria Candida M.; J. C. Lima; Carrondo, Manuel J. T.; Alves, Paula M.; Oliveira, R. (Plos Computational Biology, 2012)
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Optimization-Based Design of Nano-CMOS LC-VCOs - P Pereira; Fino, H.; Coito, F.; Ventim-Neves, M. (Technological Innovation for Value Creation, 2012)
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Photochemical behaviour of activated carbons under UV irradiation - Velasco, Leticia F.; Fonseca, Isabel M.; Parra, Jose B.; Lima, Joao C.; Ania, Conchi O. (Carbon, 2012)
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Photochemistry of 2-(4-hydroxystyryl)-1-naphthopyrylium - Gavara, Raquel; Leydet, Yoann; Vesselin Petrov; Pina, Fernando (Photochemical & Photobiological Sciences, 2012)
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Times Cited: 3 Gavara, Raquel/C-6669-2013; Pina, Fernando/C-8161-2011; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, LAQV/N-9835-2013 Gavara, Raquel/0000-0002-7198-9392; Pina, Fernando/0000-0001-8529-6848; 3

Photochromism of flavylium systems. An overview of a versatile multistate system - Pina, Fernando; Vesselin Petrov; Laia, Cesar A. T. (Dyes and Pigments, 2012)
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Times Cited: 15 Pina, Fernando/C-8161-2011; Laia, Cesar/C-8651-2011; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, LAQV/N-9835-2013 Pina, Fernando/0000-0001-8529-6848; Laia, Cesar/0000-0001-6410-6072; Si 15

Platinated DNA Affects Zinc Finger Conformation. The Interaction of a Platinated Single-Stranded Oligonucleotide and the C-terminal Zinc Finger of the Nucleocapsid Protein HIVNCp7 - Susana Maria Quintal; Viegas, Aldino; Stefan Erhardt; Cabrita, Eurico J.; Nicholas P. Farrell (Biochemistry, 2012)
This paper describes for the first time the intimate molecular details of the association between a platinated oligonucleotide and a zinc-finger peptide. Site-specific platination of the guanine in a ss hexanucleotide gave {[Pt(dien)d(5’-TACGCC-3’)], Pt(dien)(6-mer)}, II, characterized by mass spectrometry and 1H-NMR spectroscopy. The work extends the study of platinum-nucleobase complex-zinc finger interactions using small molecules such as [Pt(dien)(9-EtGua)]2+, I . The structure of the (34-52) C-terminal finger of the HIV nucleocapsid protein HIVNCp7 (ZF1) was characterized by 1H-NMR spectroscopy and compared with that of the N-terminal single finger and the 2-finger “intact” NCp7. Interaction of II with ZF1 results in significant changes in comparison to the “free” uncomplexed hexanucleotide – the major shifts occur for Trp37 resonances are broadened and shifted upfield and other major shifts are for Gln45 (H21, H3, Q), Met46 (NH, H2), Lys47 (NH, Q) and Glu50 (H2, H3). The Zn-Cys/His chemical shifts show only marginal deviations. The solution structure of ZF1, the 6-mer/ZF1 and II/ZF1 adducts were calculated from the NOESY-derived distance constraints. The DNA position in II/ZF1 is completely different than in the absence of platinum. Major differences are the appearance of new Met46-Cyt6H5 and Trp37-Cyt5H5 contacts but severe weakening of the Trp37-Gua4 contact, attributed to the steric effects caused by Gua4 platination, accompanied by a change in the position of the aromatic ring. The results demonstrate the feasibility of targetting specific ZF motifs with DNA-tethered coordination compounds, such as Pt compounds and Co-macrocycles – with implications for drug targetting and indeed the intimate mechansims of DNA repair of platinated DNA.
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The Prion-like Protein Doppel Enhances Ovine Spermatozoa Fertilizing Ability - J. Pimenta; Dias, F. M. V.; C. C. Marques; M. C. Baptista; M. I. Vasques; A. E. M. Horta; J. P. Barbas; R. Soares; P. Mesquita; E. Cabrita; Fontes, Cmga; J. A. Prates; et al. (Reproduction in Domestic Animals, 2012)
The function of prion-like protein Doppel was suggested to be related to male fertility. In this study, the importance of ovine Doppel polypeptide on spermatozoa capacitation and fertilization was evaluated. After refolding, recombinant Doppel (rDpl) was supplemented with different concentrations (40, 80 or 190 ng/ml) to ovine spermatozoa during the capacitation process. In experiment 1, post-thawed ovine spermatozoa were incubated with different concentrations of rDpl during 1 h for swim-up, and changes in sperm motility, concentration, vigour, viability and capacitation were monitored (10 replicates). In experiment 2, the fertilization ability of post-swim-up spermatozoa incubated as above was tested through heterologous fertilization of bovine in vitro matured oocytes (n = 423, three replicates). Regardless of dosage, rDpl improved (p = 0.03) spermatozoa viability. Sperm individual motility and vigour were the highest (p = 0.04) for the group receiving 190 ng/ml rDpl. Sperm supplemented with the highest doses of rDpl achieved higher (p = 0.02) fertilization rates (56.0 +/- 3.0%) than control (39.1 +/- 2.2%) and 40 ng/ml rDpl (39.8 +/- 2.7%). Preliminary data suggest that Doppel protein may enhance in vitro spermatozoa fertilizing ability.
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PSO-Based Design of RF Integrated Inductor - P Pereira; Coito, F.; Fino, H. (Technological Innovation for Value Creation, 2012)
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Spectroscopic Evidence for and Characterization of a Trinuclear Ferroxidase Center in Bacterial Ferritin from Desulfovibrio vulgaris Hildenborough - Pereira, Alice S.; Timoteo, Cristina G.; Guilherme, Marcia; Folgosa, Filipe; Naik, Sunil G.; Duarte, Americo G.; Huynh, Boi Hanh; Tavares, Pedro (Journal Of The American Chemical Society, 2012)
Ferritins are ubiquitous and can be found in practically all organisms that utilize Fe. They are composed of 24 subunits forming a hollow sphere with an inner cavity of similar to 80 angstrom in diameter. The main function of ferritin is to oxidize the cytotoxic Fe2+ ions and store the oxidized Fe in the inner cavity. It has been established that the initial step of rapid oxidation of Fe2+ (ferroxidation) by H-type ferritins, found in vertebrates, occurs at a diiron binding center, termed the ferroxidase center. In bacterial ferritins, however, X-ray crystallographic evidence and amino acid sequence analysis revealed a trinuclear Fe binding center comprising a binuclear Fe binding center (sites A and B), homologous to the ferroxidase center of H-type ferritin, and an adjacent mononuclear Fe binding site (site C). In an effort to obtain further evidence supporting the presence of a trinuclear Fe binding center in bacterial ferritins and to gain information on the states of the iron bound to the trinuclear center, bacterial ferritin from Desulfovibrio vulgaris (DvFtn) and its E130A variant was loaded with substoichiometric amounts of Fe2+, and the products were characterized by Mossbauer and EPR spectroscopy. Four distinct Fe species were identified: a paramagnetic diferrous species, a diamagnetic diferrous species, a mixed valence Fe2+Fe3+ species, and a mononuclear Fe2+ species. The latter three species were detected in the wild-type DvFtn, while the paramagnetic diferrous species was detected in the E130A variant. These observations can be rationally explained by the presence of a trinuclear Fe binding center, and the four Fe species can be properly assigned to the three Fe binding sites. Further, our spectroscopic data suggest that (1) the fully occupied trinuclear center supports an all ferrous state, (2) sites B and C are bridged by a mu-OH group forming a diiron subcenter within the trinuclear center, and (3) this subcenter can afford both a mixed valence Fe2+Fe3+ state and a diferrous state. Mechanistic insights provided by these new findings are discussed and a minimal mechanistic scheme involving O-O bond cleavage is proposed.
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Structural studies of the p22HBP/SOUL family of heme-binding proteins - Aveiro, S. S.; Freire, F.; Clayton, J.; Cameloc, M.; Carvalho, A. L.; Ferreira, G. C.; Romao, M. J.; Macedo, A. L.; Goodfellow, B. J. (Febs Journal, 2012)
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Times Cited: 0 Freire, Filipe/F-6505-2010; Romao, Maria/A-4115-2013; Macedo, Anjos/D-7216-2013; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; Carvalho, Ana Luisa/G-5638-2011; REQUIMTE, SMB/M-5694-2013; REQUIMTE, UCIBIO/N-9846-2013 Freire, Filipe/0000-0002-5310-0668; Romao, Maria/0000-0002-3004-0543; Macedo, Anjos/0000-0002-2613-4838; Carvalho, Ana Luisa/0000-0002-3824-0240; Si 1 22nd IUBMB Congress/37th FEBS Congress Sep 04-09, 2012 Seville, SPAIN Iubmb; febs 0

Structural, Physical, and Chemical Modifications Induced by Microwave Heating on Native Agar-like Galactans - Ana M. M. Sousa; Simone Morais; Maria H. Abreu; Rui Pereira; Isabel Sousa-Pinto; Cabrita, Eurico J.; Cristina Delerue-Matos; Maria Pilar Gonca̧lves (Jornal of Agricultural and Food Chemistry, 2012)
Native agars from Gracilaria vermiculophylla produced in sustainable aquaculture systems (IMTA) were extracted under conventional (TWE) and microwave (MAE) heating. The optimal extracts from both processes were compared in terms of their properties. The agars’ structure was further investigated through Fourier transform infrared and NMR spectroscopy. Both samples showed a regular structure with an identical backbone, β-D-galactose (G) and 3,6-anhydro-α-L-galactose (LA) units; a considerable degree of methylation was found at C6 of the G units and, to a lesser extent, at C2 of the LA residues. The methylation degree in the G units was lower for MAEopt agar; the sulfate content was also reduced. MAE led to higher agar recoveries with drastic extraction time and solvent volume reductions. Two times lower values of [η] and Mv obtained for the MAEopt sample indicate substantial depolymerization of the polysaccharide backbone; this was reflected in its gelling properties; yet it was clearly appropriate for commercial application in soft-texture food products.
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Supercritical CO2-assisted preparation of a \{PMMA\} composite membrane for bisphenol A recognition in aqueous environment - Mara Soares da Silva; Raquel Viveiros; Mónica B. Coelho; Aguiar-Ricardo, Ana; Casimiro, Teresa (Chemical Engineering Science, 2012)
This work reports a novel strategy to prepare affinity composite membranes using supercritical fluid technology. By blending molecularly imprinted polymeric particles with PMMA, a porous hybrid structure with affinity to the template molecule, bisphenol A, was prepared using a supercritical carbon dioxide (scCO2)-assisted method. Membranes were characterized in terms of morphology, mechanical performance and transport properties. The ability of the polymers and hybrid membranes to adsorb bisphenol A was tested in aqueous solutions and fitted to a linearized Langmuir equation, showing that adsorption takes place at homogeneous affinity binding sites within the imprinted surface. Filtration experiments showed that the imprinted hybrid membrane was able to adsorb higher amounts of template even in non-equilibrium dynamic binding conditions. The hybridization of the \{PMMA\} membrane herein reported conveys two important improvements over neat \{PMMA\} membrane: it introduced molecular affinity towards the template molecule and significantly increased the permeability of the porous structures, which are key parameters in processes that involve membranes. This technique could expand the applications of polymeric beads powders and enhance the efficiency of the membrane's transport properties. Our work presents a new method to confer affinity to a porous structure by immobilization of imprinted polymers, combining polymer synthesis and membrane formation using supercritical fluid technology.
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Keywords: Adsorption

Supercritical fluid technology as a new strategy for the development of semi-covalent molecularly imprinted materials - Mara Soares da Silva; Raquel Viveiros; Aguiar-Ricardo, Ana; Bonifacio, Vasco D. B.; Casimiro, Teresa (RSC Adv., 2012)
Molecularly imprinted polymeric particles with molecular recognition towards Bisphenol A (BPA) were synthesized for the first time using the semi-covalent imprinting approach in supercritical carbon dioxide (scCO2). The material{'}s affinity to BPA was achieved by co-polymerizing ethylene glycol dimethacrylate (EGDMA) with a template-containing monomer{,} Bisphenol A dimethacrylate (BPADM) in scCO2. Bisphenol A is then cleaved from the polymeric matrix by hydrolysis with tetrabutylammonium hydroxide (n-Bu4OH) also in a supercritical environment{,} taking advantage of the high diffusivity of scCO2. The selectivity of the molecular imprinted polymer (MIP) was assessed by evaluating its capability to bind BPA in comparison with progesterone and [small alpha]-ethinylestradiol. In addition{,} the cross-linked particles were used to prepare a PMMA-based hybrid imprinted membrane by a scCO2-assisted phase inversion method. Results show that the incorporation of MIP particles was able to confer molecular affinity to BPA to the membrane and that at dynamic conditions of filtration{,} this imprinted porous structure was able to adsorb a higher amount of BPA than the corresponding non-imprinted hybrid membrane. Our work represents a valuable greener alternative to conventional methods{,} for the synthesis of affinity materials which are able to maintain molecular recognition properties in water.
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Synthesis and properties of reversible ionic liquids using CO2, mono- to multiple functionalization - Carrera, Goncalo V. S. M.; da Ponte, Manuel Nunes; Branco, Luis C. (Tetrahedron, 2012)
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Times Cited: 3 da Ponte, Manuel/B-3620-2010; Branco, Luis/C-6426-2013; Carrrera, Goncalo/C-7536-2013; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, CENG/M-4555-2013; REQUIMTE, LAQV/N-9835-2013 da Ponte, Manuel/0000-0003-4499-4521; Branco, Luis/0000-0003-2520-1151; 3

A Technology-Aware Optimization of RF Integrated Inductors - P Pereira; Sallem, A.; Fakhfakh, M.; Fino, M.H.; Coito, F. (Nova Science Publishers, Inc., 2012)
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Thermodynamic and fluorescence emission properties of the Zn(II), Cd(II) and Pb(II) complexes with a fluorescent chelator bearing phenanthroline and naphthalene subunits - Bazzicalupi, Carla; Biagini, Silvia; Bianchi, Antonio; Faggi, Enrico; Giorgi, Claudia; Gratteri, Paola; Pina, Fernando; Valtancoli, Barbara (Inorganica Chimica Acta, 2012)
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Times Cited: 1 Pina, Fernando/C-8161-2011; Caparica, cqfb_staff/H-2611-2013; REQUIMTE, AL/H-9106-2013; Chaves, Pedro/K-1288-2013; REQUIMTE, PHOTO/M-4229-2013; REQUIMTE, LAQV/N-9835-2013 Pina, Fernando/0000-0001-8529-6848; 1

Thymus mastichina: Chemical Constituents and their Anti-cancer Activity - Gordo, Joana; Patr{\'ıcia Máximo; Eurico Cabrita; Ana Lourenço; Abel Oliva; Joana Almeida; Mariana Filipe; Pedro Cruz; Rita Barcia; Miguel Santos; Helder Cruz (Natural Product Communications, 2012)
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The Type Discipline of Behavioral Separation (Long version with proofs) - Luís Caires; João Costa Seco (CITI / DI-FCT-UNL, 2012)
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A Type System for Flexible Role Assignment in Multiparty Communicating Systems - Pedro Baltazar; Luís Caires; Vasco T. Vasconcelos; Hugo T. Vieira (Proceedings of the 7th International Symposium on Trustworthy Global Computing (TGC), 2012)
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Type-based Protocol Conformance and Aliasing Control in Concurrent Java Programs - Sérgio Silva (DI-FCT-UNL, 2012)
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Understanding the Ion Jelly Conductivity Mechanism - T. Carvalho; V. Augusto; A. R. Brás; N. M. T. Lourenço; C. A. M. Afonso; S. Barreiros; N. T. Correia; P. Vidinha; E. J. Cabrita; M. Dion{\'ısio; B. Roling (Journal of Physical Chemistry B, 2012)
The properties of the light flexible device, ion jelly, which combines gelatin with an ionic liquid (IL) were recently reported being promising to develop safe and highly conductive electrolytes. This article aims for the understanding of the ion jelly conductive mechanism using dielectric relaxation spectroscopy (DRS) in the frequency range 10-1-106 Hz; the study was complemented with differential scanning calorimetry (DSC) and pulse field gradient nuclear magnetic resonance (PFG NMR) spectroscopy. The room temperature ionic liquid 1-butyl-3-methylimmidazolium dicyanamide (BMIMDCA) used as received (1.9% w/w water content) and with 6.6% (w/w) of water content and two ion jellies with two different ratios BMIMDCA/gelatin/water % (w/w), IJ1 (41.1/46.7/12.2) and IJ3 (67.8/25.6/6.6), have been characterized. A glass transition was detected by DSC for all materials allowing for classifying them as glass formers. For the ionic liquid, it was observed that the glass transition temperature decreases with the increase of water content. While in subsequent calorimetric runs crystallization was observed for BMIMDCA with negligible water content, no crystallization was detected for any of the ion jelly materials upon themal cycling. To the dielectric spectra of all tested materials, both dipolar relaxation and conductivity contribute; at the lowest frequencies, electrode and interfacial polarization highly dominate. Conductivity, which manifests much more intensity relative to dipolar reorientations, strongly evidences subdiffusive ion dynamics at high frequencies. From dielectric measures, transport properties as mobility and diffusion coefficients were extracted. Data treatment was carried out in order to deconvolute the average diffusion coefficients estimated from dielectric data in its individual contributions of cations (D+) and anions (D-). The D+ values thus obtained for IJ3, the ion jelly with the highest IL/gelatin ratio, cover a large temperature range up to room temperature and revealed excellent agreement with direct measurements from PFG NMR, obeying to the same VFT equation. For BMIMDCA6.6%water, which has the same water amount as IJ3, the diffusion coefficients were only estimated from DRS measurements over a limited temperature range; however, a single VFT equation describes both DRS and PFG NMR data. Moreover, it was found that the diffusion coefficients and mobility are similar for the ionic liquid and IJ3, which points to a role of both water and gelatin weakening the contact ion pair, facilitating the translational motion of ions and promoting its dissociation; nevertheless, it is conceivable that a critical composition of gelatin that leads to those properties. The VFT temperature dependence observed for the conductivity was found to be determined by a similar dependence of the mobility. Both conductivity and segmental motion revealed to be correlated as inferred by the relatively low values of the decoupling indexes. The obtained results show that ion jelly could be in fact a very promising material to design novel electrolytes for different electrochemical devices, having a performance close to the IL but presenting an additional stability regarding electrical measurements and resistance against crystallization relative to the bulk ionic liquid.
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Working note on a type-checking algorithm for BST - Luís Caires; João Costa Seco (CITI / DI-FCT-UNL, 2012)
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{Bridging Present and Future of Brain-Computer Interfaces: An Assessment of Impacts} - Velloso, Gabriel T. (Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology, 2012)
Technology assessment is essentially a systematic method used to investigate technology developments and assess their potential impacts on society. The assessment of emerging technologies, however, requires special attention. To address technologies at early stages of development, Constructive Technology Assessment (CTA) is considered to be one of the best options to bypass the Collingridge dilemma - which fundamentally states that controlling the direction of a technology’s development is very hard. Technologies at early stages of development might appear to be unorganized, chaotic and with high level of uncertainty on future paths to take. Future Oriented Technology Analysis (FTA) represents any systematic process to produce judgments about the characteristics of emerging technologies, its development pathways, and potential future impacts. Technology Assessment is considered to be one of three subjects which form the umbrella concept of FTA. The technology assessed on this project, Brain-Computer Interface (BCI) or Brain-Machine Interface (BMI) is an emerging technology. BCIs can be defined as a technology which allows for the direct communication between the brain and an external device. It is a truly direct connection, with no use of the normal output pathways of peripheral nerves and muscles, allowing for the brain to have control over objects and softwares without intermediates. As an emerging technology, BCI is at its early stages of research and thus many challenges are still ahead. Mainstream adoption is not expected in least 10 years. There are still many problems and challenges to be overcome. The real impacts of BCI will depend directly on the development of competing technologies. If there is improvement in BCI research, then the potential applications and end users could grow dramatically. The findings of this project will be of relevant importance to researchers of the technology (especially on what concerns their interactions with other stakeholders
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Keywords: Brain-Computer Int; Constructive Technology Assessment; Emerging Technologies; Technology Assessment

{Esforços para a construção da visão prospectiva no Brasil: evidências e lições que podem ser retiradas do estudo cooperativo entre Japão e Finlândia [Efforts to build a foresight vision in Brazil: evi} - Ana Clara Cândido (Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology, 2012)
In the last decades, with the consequent strong competitiveness of an increasingly globalized world, the foresight studies have gained importance in the business environment and also became important tool for formulation of public policy. This work examines the recent foresight studies from Brazil, Finland and Japan, to understand the main goals, motivations and methodologies used. And finally drawing lessons from international cooperation in foresight studies that might be interesting for the Brazilian case. It can be concluded it is extremely useful to look at the studies conducted by countries with more experience in the foresight as a way to deepen and develop methods analysis. The work conducted by Japan and Finland showed that is possible succeed through studies in cooperation, even with the different features of the national reality.
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Keywords: Brazil; Foresight exercises; International Cooperation; NISTEP/ Tekes

{Microstructure control of dual-phase inkjet-printed a-WO3/TiO2/WOX films for high-performance electrochromic applications} - Pawel Jerzy Wojcik; Cruz, Ana Sofia; Santos, L\'ıdia; Pereira, Lu\'ıs; Rodrigo Martins; Elvira Fortunato (Journal of Materials Chemistry, 2012)
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{Políticas de Financiamento de I&D em Portugal [R&D financing policies in Portugal]} - Ana Clara Cândido; Isabel Marques Rosa (Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology, 2012)
This paper aims to present the main events over the years on public policies for financing R & D in Portugal, with special focus on the QREN (National Strategic Reference Framework). Between 2007 and 2013, is the QREN which provides the framework to be applied to economic policy in Portugal. The Incentives System for Companies Investment is one of the key instruments of economic promotion policies, particularly in terms of promoting innovation and regional development. The review made shows us that there is not still a systemic and integrated policy innovation in Portugal, but there is a set of instruments that can play a role in this policy and also has missed coherence and coordination between them.
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Keywords: Funding of R&D incentives; Portugal; Public Policy; QREN

{Processo de desenvolvimento e difusão de cloud computing: estudo sobre as redes de colaboração no Brasil [Development and diffusion process of cloud computing: Study on collaboration networks in Brazi} - Ana Clara Cândido (Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology, 2012)
This report is the result of the presentation of the Thesis Plan, performed on December 13, 2011, during the activities of the Winter School of Doctoral Program in Technology Assessment. It is intended to describe the main information about the Thesis Plan and also the definition of the main concepts involved. Can also view the presentation file that is available on the page of the student's PhD thesis Ana Cândido in Moodle (http://moodle.fct.unl.pt/mod/resource/view.php?inpopup=true&id=157805). The following step in this report will be the development of the discipline of “Project IV” and so also the preparation for Doctoral Conference will take place in June 2012.
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Keywords: Cloud Computing; Disruptive Innovation; Open Innovation; Technological Development and Diffusion

{The use of indicators and evidence in governance and policy development of Science, Technology and Innovation} - Manuel Laranja; Nuno Boavida (Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology, 2012)
In this paper we reflect upon how policy-makers look for, interpret and use evidence for reflection and policy development. We propose an exploratory framework that sets out two of the elements necessary to a conceptualization of what may explain the way in which evidence and indicators are used in STI policy development: the type of evaluative approach and the styles of governance.
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Keywords: evidence based policy; Indicators; innovation policy

Transparent Oxide Electronics - Pedro Baquinha; Rodrigo Martins; Pereira, Luis; Elvira Fortunato (Wiley, 2012)
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Detection of Snapshot Isolation Anomalies in Software Transactional Memory: A Static Analysis Approach - Ricardo J. Dias; João Costa Seco; João M. Lourenço (Universidade Nova de Lisboa, 2011)

New spectroscopic and electrochemical insights on a class I superoxide reductase: evidence for an intramolecular electron-transfer pathway - Folgosa, F.; Cordas, C. M.; Santos, J. A.; Pereira, A. S.; Moura, J. J.; Tavares, P; Moura, I. (Biochem J, 2011)
SORs (superoxide reductases) are enzymes involved in bacterial resistance to reactive oxygen species, catalysing the reduction of superoxide anions to hydrogen peroxide. So far three structural classes have been identified. Class I enzymes have two iron-centre-containing domains. Most studies have focused on the catalytic iron site (centre II), yet the role of centre I is poorly understood. The possible roles of this iron site were approached by an integrated study using both classical and fast kinetic measurements, as well as direct electrochemistry. A new heterometallic form of the protein with a zinc-substituted centre I, maintaining the iron active-site centre II, was obtained, resulting in a stable derivative useful for comparison with the native all-iron from. Second-order rate constants for the electron transfer between reduced rubredoxin and the different SOR forms were determined to be 2.8 x 10 M(1) . s(1) and 1.3 x 10 M(1) . s(1) for SORFe(IIII)-Fe(II) and for SORFe(IIII)-Fe(III) forms respectively, and 3.2 x 10 M(1) . s(1) for the SORZn(II)-Fe(III) form. The results obtained seem to indicate that centre I transfers electrons from the putative physiological donor rubredoxin to the catalytic active iron site (intramolecular process). In addition, electrochemical results show that conformational changes are associated with the redox state of centre I, which may enable a faster catalytic response towards superoxide anion. The apparent rate constants calculated for the SOR-mediated electron transfer also support this observation.
1470-8728 (Electronic)0264-6021 (Linking)Journal ArticleResearch Support, Non-U.S. Gov't
Keywords: Desulfovibrio vulgaris/enzymology/metabolism; Electrochemistry; Electron Transport; Iron/chemistry/metabolism; Kinetics; Oxidation-Reduction; Oxidoreductases/*chemistry/metabolism; Reactive Oxygen Species; Rubredoxins/chemistry/metabolism; Superoxide Dismutase/chemistry/metabolism; Superoxides/chemistry/metabolism

Sistema de deteccion y cuantificacion de material biologico constituido por uno o mas sensores opticos y una o mas fuentes de luz, proceso asociado y aplicaciones relacionadas. - Martins, Rodrigo Ferrao De Paiva; Baptista, Pedro Miguel Ribeiro Viana; Fortunato, Elvira Maria Correia (2011)
Sistema para detección, identificación y cuantificación en material biológico, compuesto por una o más fuentes de luz (1) combinado con uno o más fotosensores ópticos (6 y 7) y diversos componentes electrónicos (4), necesarios para obtener/procesar la señal emitida caracterizado por: a) La fuente de luz (1), pulsada (2) o no, compuesta de láseres de estado sólido de baja energía o diodos emisores de luz, cuyo rango de longitud de onda está localizado entre 400 y 800 nm con una intensidad de luminosidad controlable que varía entre los valores de 0.01 mW/cm 2 y 100 mW/cm 2 ; b) El fotosensor, sencillo (6 y 7a) y (6 y 7b) o integrado (6, 4 y 7) compuesto de películas delgadas de silicio amorfo o nanocristalino o microcristalino y/o por semiconductores de cerámica tales como IGZO, IAgZO, SnZIO, GZIO, CuOIZ, GITO, entre otros, y basado en estructuras tipo pi'ii'n o MIS, que funciona en un rango de longitudes de onda desde el infrarrojo hasta el ultravioleta, y prové una información cualitativa y cuantitativa basada en la hibridización especifica y selectiva de sondas funcionalizadas con nanopartículas de metal; c) Siendo provista la eliminación del sistema a través de una fuente de energía convencional o a través de baterías fotovoltaicas, que dan portabilidad al sistema, siendo focalizada la luz emitida sobre la muestra, preferiblemente utilizando microlentes, siendo la muestra o muestras no fijadas físicamente al sensor o sensores, colocando la muestra biológica referida (5) sobre el lado opuesto (6) del sustrato donde se deposita el fotosensor (6 y 7).
ES2365079T; G01N33/543

Editorial Note - António Moniz; José Miquel Cabeças (Enterprise and Work Innovation Studies, 2011)
No abstract is available for this item.
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{Decision making processes based on innovation indicators: which implications for technology assessment?} - Nuno Boavida (Enterprise and Work Innovation Studies, 2011)
The present work deals with the use of innovation indicators in the decision-making process. It intends to contribute to the discussion on the construction, use and analysis of indicator systems and also to evaluate its weight on decision-making in innovation. The goal is to help understand how innovation indicators can influence technology policy and through it, society at large. This work will start by analysing the use of indicators (their problems and consistency) and other sources of information that contribute to build the opinions of innovation decision makers. This will be followed by a survey and interviews with main innovation actors. The results will shed light on the impact of the use of indicators by the innovation community – both in terms of technology policy and in the social sphere. Proposals and implications for the future will be advanced, hopefully adding new contributions to the governance of the science, technology and innovation field.
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Keywords: decision; innovation indicators; technology policy

{Decision-making process in radiology: the magnetic resonance example in the TA context} - Maia, Maria João (Enterprise and Work Innovation Studies, 2011)
In order to understand the decision-making process in a Radiology Department, taking the Magnetic Resonance Equipment as an example, this paper reports a project to be followed. It is a guideline for future work development regarding Technology Assessment in Radiology. The Theoretical Framework is divided is three big issues. The first is “Technology Assessment”. Starting with the definition of some important concepts, the history and development of Technology Assessment will be addressed. The aim of this issue is to give a general main idea concerning TA contextualization. Doing a transposition of this subject to health area, it is also important to understand the particularities of Health Technology Assessment, second issue. Portugal framework on this subject will also be addressed. As so, the Portuguese National Health System is characterized and the decision-making stakeholders identified, has well as the competences for the decision-making process in general. The third issue is Decision-Making and its aim is to give a general elucidation on decision-making matters. To accomplish this, a research methodology was outlined, so that six research questions could be answered and five hypotheses could be accepted or refuted, in the future. With this research methodology, the Portuguese state of the art Magnetic Resonance equipment existence will be studied, using a survey as a resource. In the future, a mapping stakeholder technique will be used to identify the decision making key stakeholders and a survey will be applied to map theirs skills and competences in the process, where a pre-test was already applied. The results of this pre-test are presented.
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Keywords: decision-making; Health technology assessment; Magnetic resonance imaging; Radiology; stakeholders

Editorial Note - António Moniz; José Miquel Cabeças (Enterprise and Work Innovation Studies, 2011)
No abstract is available for this item.
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{Societal embedding in high-speed train technology development: dominant perspective from a case study} - Susana Martins Moretto (Enterprise and Work Innovation Studies, 2011)
The present article posits constructive technology assessment as the dominant perspective of societal embedding practices in the technical development process by the high-speed train manufacturing industry, resulting from a research study conducted in 2011 (Moretto 2011). The article covers the main elements of the study, being the high-speed train manufacturing industry’s strategic intelligence, technology pattern, knowledge exchange, technology trajectories; and finally presents the arguments justifying constructive technology assessment as the dominant approach.
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Keywords: Constructive Technology Assessment; high-speed train manufacturing industry; strategic intelligence

Gd(III) chelates as NMR probes of protein-protein interactions. Case study: rubredoxin and cytochrome c3 - Almeida, R. M.; Geraldes, C. F.; Pauleta, S. R.; Moura, J. J. (Inorg Chem, 2011)
Two cyclen-derived Gd probes, [Gd-DOTAM](3+) and [Gd-DOTP](5-) (DOTAM = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetamide; DOTP = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methylenephosphonate)), were assessed as paramagnetic relaxation enhancement (PRE)-inducing probes for characterization of protein-protein interactions. Two proteins, Desulfovibrio gigas rubredoxin and Desulfovibrio gigas cytochrome c(3), were used as model partners. In a (1)H NMR titration it was shown that [Gd-DOTP](5-) binds to cytochrome c(3) near heme IV, causing pronounced PREs, characterized by line width broadenings of the heme methyl resonances at ratios as low as 0.08. A K(d) of 23 +/- 1 muM was calculated based on chemical shift perturbation of selected heme methyl resonances belonging to three different heme groups, caused by allosteric effects upon [Gd-DOTP](5-) binding to cytochrome c(3) at a molar ratio of 2. The other probe, [Gd-DOTAM](3+), caused PREs on a well-defined patch near the metal center of rubredoxin (especially the patch constituted by residues D19-G23 and W37-S45, which broaden beyond detection). This effect was partially reversed for some resonances (C6-Y11, in particular) when cytochrome c(3) was added to this system. Both probes were successful in causing reversible PREs at the partner binding site, thus showing to be good probes to identify partners' binding sites and since the interaction is reversible to structurally characterize protein complexes by better defining the complex interface.
1520-510X (Electronic)0020-1669 (Linking)Journal ArticleResearch Support, Non-U.S. Gov't

Real-time monitoring of PCR amplification of proto-oncogene c-MYC using a Ta₂O₅ electrolyte-insulator-semiconductor sensor - Rita Branquinho; Bruno Veigas; Vaz Pinto, Joana; Martins, Rodrigo Ferrão de Paiva; Fortunato, Elvira Maria Correia; Baptista, Pedro Miguel Ribeiro Viana (Biosensors & Bioelectronics, 2011)
We present a new approach for real-time monitoring of PCR amplification of a specific sequence from the human c-MYC proto-oncogene using a Ta(2)O(5) electrolyte-insulator-semiconductor (EIS) sensor. The response of the fabricated EIS sensor to cycle DNA amplification was evaluated and compared to standard SYBR-green fluorescence incorporation, showing it was possible to detect DNA concentration variations with 30 mV/μM sensitivity. The sensor's response was then optimized to follow in real-time the PCR amplification of c-MYC sequence from a genomic DNA sample attaining an amplification profile comparable to that of a standard real-time PCR. Owing to the small size, ease of fabrication and low-cost, the developed Ta(2)O(5) sensor may be incorporated onto a microfluidic device and then used for real-time PCR. Our approach may circumvent the practical and economical obstacles posed by current platforms that require an external fluorescence detector difficult to miniaturize and incorporate into a lab-on-chip system.
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Keywords: Cancer; DNA quantification; EIS; Field effect based sensors; Real-time PCR; Sensors/Biosensors; Tantalum pentoxide

Low-spin heme b(3) in the catalytic center of nitric oxide reductase from Pseudomonas nautica - Timoteo, C. G.; Pereira, A. S.; Martins, C. E.; Naik, S. G.; Duarte, A. G.; Moura, J. J.; Tavares, P; Huynh, B. H.; Moura, I. (Biochemistry, 2011)
Respiratory nitric oxide reductase (NOR) was purified from membrane extract of Pseudomonas (Ps.) nautica cells to homogeneity as judged by polyacrylamide gel electrophoresis. The purified protein is a heterodimer with subunits of molecular masses of 54 and 18 kDa. The gene encoding both subunits was cloned and sequenced. The amino acid sequence shows strong homology with enzymes of the cNOR class. Iron/heme determinations show that one heme c is present in the small subunit (NORC) and that approximately two heme b and one non-heme iron are associated with the large subunit (NORB), in agreement with the available data for enzymes of the cNOR class. Mossbauer characterization of the as-purified, ascorbate-reduced, and dithionite-reduced enzyme confirms the presence of three heme groups (the catalytic heme b(3) and the electron transfer heme b and heme c) and one redox-active non-heme Fe (Fe(B)). Consistent with results obtained for other cNORs, heme c and heme b in Ps. nautica cNOR were found to be low-spin while Fe(B) was found to be high-spin. Unexpectedly, as opposed to the presumed high-spin state for heme b(3), the Mossbauer data demonstrate unambiguously that heme b(3) is, in fact, low-spin in both ferric and ferrous states, suggesting that heme b(3) is six-coordinated regardless of its oxidation state. EPR spectroscopic measurements of the as-purified enzyme show resonances at the g approximately 6 and g approximately 2-3 regions very similar to those reported previously for other cNORs. The signals at g = 3.60, 2.99, 2.26, and 1.43 are attributed to the two charge-transfer low-spin ferric heme c and heme b. Previously, resonances at the g approximately 6 region were assigned to a small quantity of uncoupled high-spin Fe(III) heme b(3). This assignment is now questionable because heme b(3) is low-spin. On the basis of our spectroscopic data, we argue that the g = 6.34 signal is likely arising from a spin-spin coupled binuclear center comprising the low-spin Fe(III) heme b(3) and the high-spin Fe(B)(III). Activity assays performed under various reducing conditions indicate that heme b(3) has to be reduced for the enzyme to be active. But, from an energetic point of view, the formation of a ferrous heme-NO as an initial reaction intermediate for NO reduction is disfavored because heme [FeNO](7) is a stable product. We suspect that the presence of a sixth ligand in the Fe(II)-heme b(3) may weaken its affinity for NO and thus promotes, in the first catalytic step, binding of NO at the Fe(B)(II) site. The function of heme b(3) would then be to orient the Fe(B)-bound NO molecules for the formation of the N-N bond and to provide reducing equivalents for NO reduction.
1520-4995 (Electronic)0006-2960 (Linking)Journal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov't
Keywords: *Catalytic Domain; Absorption; Amino Acid Sequence; Electron Spin Resonance Spectroscopy; Heme/*chemistry/metabolism; Molecular Sequence Data; Optical Processes; Oxidation-Reduction; Oxidoreductases/*chemistry/*metabolism; Pseudomonas/*enzymology; Spectrophotometry, Ultraviolet; Spectroscopy, Mossbauer

The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states - Coelho, C.; Gonzalez, P. J.; Moura, J. G.; Moura, I.; Trincao, J.; Joao Romao, M. (J Mol Biol, 2011)
The periplasmic nitrate reductase (NapAB) from Cupriavidus necator is a heterodimeric protein that belongs to the dimethyl sulfoxide reductase family of mononuclear Mo-containing enzymes and catalyzes the reduction of nitrate to nitrite. The protein comprises a large catalytic subunit (NapA, 91 kDa) containing the molybdenum active site plus one [4Fe-4S] cluster, as well as a small subunit (NapB, 17 kDa), which is a diheme c-type cytochrome involved in electron transfer. Crystals of the oxidized form of the enzyme diffracted beyond 1.5 A at the European Synchrotron Radiation Facility. This is the highest resolution reported to date for a nitrate reductase, providing true atomic details of the protein active center, and this showed further evidence on the molybdenum coordination sphere, corroborating previous data on the related Desulfovibrio desulfuricans NapA. The molybdenum atom is bound to a total of six sulfur atoms, with no oxygen ligands or water molecules in the vicinity. In the present work, we were also able to prepare partially reduced crystals that revealed two alternate conformations of the Mo-coordinating cysteine. This crystal form was obtained by soaking dithionite into crystals grown in the presence of the ionic liquid [C(4)mim]Cl(-). In addition, UV-Vis and EPR spectroscopy studies showed that the periplasmic nitrate reductase from C. necator might work at unexpectedly high redox potentials when compared to all periplasmic nitrate reductases studied to date.
1089-8638 (Electronic)0022-2836 (Linking)Journal ArticleResearch Support, Non-U.S. Gov't
Keywords: Amino Acid Sequence; Catalytic Domain; Crystallography, X-Ray; Cupriavidus necator/*enzymology; Cysteine/chemistry; Dithionite/chemistry; Electron Spin Resonance Spectroscopy; Ionic Liquids/chemistry; Molecular Sequence Data; Molybdenum/chemistry; Nitrate Reductase/*chemistry; Periplasm/enzymology; Protein Conformation

Continuous-wave EPR at 275GHz: application to high-spin Fe(3+) systems - Mathies, G.; Blok, H.; Disselhorst, J. A.; Gast, P.; van der Meer, H.; Miedema, D. M.; Almeida, R. M.; Moura, J. J.; Hagen, W. R.; Groenen, E. J. (J Magn Reson, 2011)
The 275GHz electron-paramagnetic-resonance spectrometer we reported on in 2004 has been equipped with a new probe head, which contains a cavity especially designed for operation in continuous-wave mode. The sensitivity and signal stability that is achieved with this new probe head is illustrated with 275GHz continuous-wave spectra of a 1mM frozen solution of the complex Fe(III)-ethylenediamine tetra-acetic acid and of 10mM frozen solutions of the protein rubredoxin, which contains Fe(3+) in its active site, from three different organisms. The high quality of the spectra of the rubredoxins allows the determination of the zero-field-splitting parameters with an accuracy of 0.5GHz. The success of our approach results partially from the enhanced absolute sensitivity, which can be reached using a single-mode cavity. At least as important is the signal stability that we were able to achieve with the new probe head.
1096-0856 (Electronic)1090-7807 (Linking)Journal ArticleResearch Support, Non-U.S. Gov't
Keywords: Anisotropy; Edetic Acid/chemistry; Electron Spin Resonance Spectroscopy/instrumentation/*methods; Equipment Design; Ferrous Compounds/*chemistry; Rubredoxins/*chemistry; Sensitivity and Specificity; Solutions/chemistry; Spin Labels

Efficient and Correct Transactional Memory Programs Combining Snapshot Isolation and Static Analysis - Ricardo J. Dias; João M. Lourenço; Preguiça, Nuno (Proceedings of the 3rd USENIX Conference on Hot Topics in Parallelism (HotPar'11), 2011)
Concurrent programs may suffer from concurrency anomalies that may lead to erroneous and unpredictable program behaviors. To ensure program correctness, these anomalies must be diagnosed and corrected. This paper addresses the detection of both low- and high-level anomalies in the Transactional Memory setting. We propose a static analysis procedure and a framework to address Transactional Memory anomalies. We start by dealing with the classic case of low-level dataraces, identifying concurrent accesses to shared memory cells that are not protected within the scope of a memory transaction. Then, we address the case of high-level dataraces, bringing the programmer's attention to pairs of memory transactions that were misspecified and should have been combined into a single transaction. Our framework was applied to a set of programs, collected form different sources, containing well known low- and high-level anomalies. The framework demonstrated to be accurate, confirming the effectiveness of using static analysis techniques to precisely identify concurrency anomalies in Transactional Memory programs.
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Nitrite reduction by xanthine oxidase family enzymes: a new class of nitrite reductases - Maia, L. B.; Moura, J. J. (J Biol Inorg Chem, 2011)
Mammalian xanthine oxidase (XO) and Desulfovibrio gigas aldehyde oxidoreductase (AOR) are members of the XO family of mononuclear molybdoenzymes that catalyse the oxidative hydroxylation of a wide range of aldehydes and heterocyclic compounds. Much less known is the XO ability to catalyse the nitrite reduction to nitric oxide radical (NO). To assess the competence of other XO family enzymes to catalyse the nitrite reduction and to shed some light onto the molecular mechanism of this reaction, we characterised the anaerobic XO- and AOR-catalysed nitrite reduction. The identification of NO as the reaction product was done with a NO-selective electrode and by electron paramagnetic resonance (EPR) spectroscopy. The steady-state kinetic characterisation corroborated the XO-catalysed nitrite reduction and demonstrated, for the first time, that the prokaryotic AOR does catalyse the nitrite reduction to NO, in the presence of any electron donor to the enzyme, substrate (aldehyde) or not (dithionite). Nitrite binding and reduction was shown by EPR spectroscopy to occur on a reduced molybdenum centre. A molecular mechanism of AOR- and XO-catalysed nitrite reduction is discussed, in which the higher oxidation states of molybdenum seem to be involved in oxygen-atom insertion, whereas the lower oxidation states would favour oxygen-atom abstraction. Our results define a new catalytic performance for AOR-the nitrite reduction-and propose a new class of molybdenum-containing nitrite reductases.
1432-1327 (Electronic)0949-8257 (Linking)Journal ArticleResearch Support, Non-U.S. Gov't
Keywords: Aldehyde Oxidoreductases/metabolism; Electron Spin Resonance Spectroscopy; Models, Biological; Nitrite Reductases/*metabolism; Nitrites/*metabolism; Oxidation-Reduction; Xanthine Oxidase/*metabolism

Synthesis of a new pyranoanthocyanin dimer linked through a methyl-methine bridge - Oliveira, Joana; Mateus, Nuno; Rodriguez-borges, Jose E.; Cabrita, Eurico J.; Silva, Artur M. S.; de Freitas, Victor (Tetrahedron Letters, 2011)
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Analysis of nucleotides binding to chromatography supports provided by nuclear magnetic resonance spectroscopy - Cruz, Carla; Cabrita, Eurico J.; Queiroz, Joao A. (Journal of Chromatography a, 2011)
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Effects of molybdate and tungstate on expression levels and biochemical characteristics of formate dehydrogenases produced by Desulfovibrio alaskensis NCIMB 13491 - Mota, C. S.; Valette, O.; Gonzalez, P. J.; Brondino, C. D.; Moura, J. J.; Moura, I.; Dolla, A.; Rivas, M. G. (J Bacteriol, 2011)
Formate dehydrogenases (FDHs) are enzymes that catalyze the formate oxidation to carbon dioxide and that contain either Mo or W in a mononuclear form in the active site. In the present work, the influence of Mo and W salts on the production of FDH by Desulfovibrio alaskensis NCIMB 13491 was studied. Two different FDHs, one containing W (W-FDH) and a second incorporating either Mo or W (Mo/W-FDH), were purified. Both enzymes were isolated from cells grown in a medium supplemented with 1 muM molybdate, whereas only the W-FDH was purified from cells cultured in medium supplemented with 10 muM tungstate. We demonstrated that the genes encoding the Mo/W-FDH are strongly downregulated by W and slightly upregulated by Mo. Metal effects on the expression level of the genes encoding the W-FDH were less significant. Furthermore, the expression levels of the genes encoding proteins involved in molybdate and tungstate transport are downregulated under the experimental conditions evaluated in this work. The molecular and biochemical properties of these enzymes and the selective incorporation of either Mo or W are discussed.
1098-5530 (Electronic)0021-9193 (Linking)Journal ArticleResearch Support, Non-U.S. Gov't
Keywords: Desulfovibrio/*enzymology/metabolism; Formate Dehydrogenases/genetics/*metabolism; Gene Expression Regulation, Bacterial/*drug effects; Gene Expression Regulation, Enzymologic/*drug effects; Molybdenum/*pharmacology; Tungsten/*pharmacology

{A selecção de indicadores no estudo prospectivo “Forecasting the carbon footprint to road freight transport in 2020” [Indicator selection in the foresight study “Forecasting the carbon footprint to ro} - Nuno Boavida (Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology, 2011)
This work examines a recent study that used various forecasting methods and in particular the Delphi method, to understand how the indicators were selected during the development of the prospective study. It can be concluded that the indicators in the study were selected through discussion on existing knowledge (formal and informal) and the broad consensus of the respective community, which established and confirmed the choice of indicators as the most relevant to prospectively examine the matter concerned. The technical support provided to choose certain forecasting methods as well as to choose the methods that could not be used throughout the development of the work, contributed to the strength of the list of indicators.
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Keywords: carbon footprint; CO2 emissions; Delphi method; forecasting; Indicators; road freight transport

Practical verification of high-level dataraces in transactional memory programs - Pessanha, Vasco; Ricardo J. Dias; João M. Lourenço; Farchi, Eitan; Sousa, Diogo (Proceedings of 9th the Workshop on Parallel and Distributed Systems: Testing, Analysis, and Debugging, 2011)
In this paper we present MoTh, a tool that uses static analysis to enable the automatic verification of concurrency anomalies in Transactional Memory Java programs. Currently MoTh detects high-level dataraces and stale-value errors, but it is extendable by plugging-in sensors, each sensor implementing an anomaly detecting algorithm. We validate and benchmark MoTh by applying it to a set of well known concurrent buggy programs and by close comparison of the results with other similar tools. The results achieved so far are very promising, yielding good accuracy while triggering only a very limited number of false warnings.
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Keywords: concurrency; software transactional memory; static analysis; testing; verification

Saturation-Transfer Difference (STD) NMR: A Simple and Fast Method for Ligand Screening and Characterization of Protein Binding - Viegas, Aldino; Manso, Joao; Franklin L. Nobrega; Cabrita, Eurico J. (Journal of Chemical Education, 2011)
Saturation transfer difference (STD) NMR has emerged as one of the most popular ligand-based NMR techniques for the study of protein-ligand interactions. The success of this technique is a consequence of its robustness and the fact that it is focused on the signals of the ligand, without any need of processing NMR information about the receptor and only using small quantities of nonlabeled macromolecule. Moreover, the attractiveness of this experiment is also extendable to the classroom. In the context of a practical NMR class, this experiment is ideal to illustrate some fundamental NMR concepts, such as the nuclear Overhauser effect and relaxation in a multidisciplinary context, bridging chemistry and biochemistry with a taste of medicinal chemistry. We use the readily available human serum albumin (HSA), 6-d,l-methyl-tryptophan (6-CH3-Trp), and 7- d,l-methyl-tryptophan (7-CH3-Trp) to introduce the STD-NMR experiment and to illustrate its applicability for ligand screening, mapping of binding moieties, and determination of the dissociation constant, in a context that can be explored or adapted to the student’s course level and topic (chemistry or biochemistry). We also cover the most important theoretical aspects of the STD experiment, calling attention to some of its limitations and drawbacks without a complex theoretical approach.
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The Anaerobe-Specific Orange Protein Complex of Desulfovibrio vulgaris Hildenborough Is Encoded by Two Divergent Operons Coregulated by sigma(54) and a Cognate Transcriptional Regulator - Fievet, Anouchka; My, Laetitia; Cascales, Eric; Ansaldi, Mireille; Pauleta, Sofia R.; Moura, Isabel; Dermoun, Zorah; Bernard, Christophe S.; Dolla, Alain; Aubert, Corinne (Journal of Bacteriology, 2011)
Analysis of sequenced bacterial genomes revealed that the genomes encode more than 30% hypothetical and conserved hypothetical proteins of unknown function. Among proteins of unknown function that are conserved in anaerobes, some might be determinants of the anaerobic way of life. This study focuses on two divergent clusters specifically found in anaerobic microorganisms and mainly composed of genes encoding conserved hypothetical proteins. We show that the two gene clusters DVU2103-DVU2104-DVU2105 (orp2) and DVU2107-DVU2108-DVU2109 (orp1) form two divergent operons transcribed by the sigma(54)-RNA polymerase. We further demonstrate that the sigma(54)-dependent transcriptional regulator DVU2106, located between orp1 and orp2, collaborates with sigma(54)-RNA polymerase to orchestrate the simultaneous expression of the divergent orp operons. DVU2106, whose structural gene is transcribed by the sigma(70)-RNA polymerase, negatively retrocontrols its own expression. By using an endogenous pulldown strategy, we identify a physiological complex composed of DVU2103, DVU2104, DVU2105, DVU2108, and DVU2109. Interestingly, inactivation of DVU2106, which is required for orp operon transcription, induces morphological defects that are likely linked to the absence of the ORP complex. A putative role of the ORP proteins in positioning the septum during cell division is discussed.
Times Cited: 0

Coupling single base extension to a spectral codification tool for increased throughput screening - Letícia Giestas; Lima, João Carlos; Baptista, Pedro V (Journal of Biotechnology, 2011)
We report a new strategy that combines a Forster Resonance Energy Transfer (FRET) based spectral codification tool with a single base extension (SBE) reaction for rapid and medium-throughput analysis of single nucleotide polymorphisms (SNPs). This strategy is based on the spectral codification - a donor (fluorophore labeled probe complementary to the region adjacent to an SNP) is used to induce specific FRET signatures from an acceptor fluorophore revealing the SNP variant. Using an SBE reaction and differently labeled ddNTPs, we can directly question each donor probe and retrieve information about which allele variant is present at that locus. The potential of the method is demonstrated by application to simultaneous questioning of two loci in the same reaction tube. Following calibration with all possible combinations of FRET pairs, an evaluation algorithm was calibrated so as to optimize base calling and allow unequivocal allele scoring with more than 80% confidence (for two simultaneous loci being questioned, one homo-and one heterozygous). In conclusion, this spectral codification approach may constitute a solution towards increasing throughput capability of single base extension based assays.
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Keywords: FRET; Single base extension; SNP genotyping; Spectral codification

Analysis of the antioxidant activity of an indole library: cyclic voltammetry versus ROS scavenging activity - Estevao, Monica S.; Carvalho, Luisa C.; Ferreira, Luisa M.; Fernandes, Eduarda; Marques, M. Manuel B. (TETRAHEDRON LETTERS, 2011)
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Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria - Mukhopadhyay, A.; Kladova, A. V.; Bursakov, S. A.; Gavel, O. Y.; Calvete, J. J.; Shnyrov, V. L.; Moura, I.; Moura, J. J.; Romao, M. J.; Trincao, J. (J Biol Inorg Chem, 2011)
Adenylate kinases (AK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, three metal ions, zinc, cobalt, and iron, have been found in AK from Gram-negative bacteria. Crystal structures of substrate-free AK from Desulfovibrio gigas with three different metal ions (Zn(2+), Zn-AK; Co(2+), Co-AK; and Fe(2+), Fe-AK) bound in its LID domain have been determined by X-ray crystallography to resolutions 1.8, 2.0, and 3.0 A, respectively. The zinc and iron forms of the enzyme were crystallized in space group I222, whereas the cobalt-form crystals were C2. The presence of the metals was confirmed by calculation of anomalous difference maps and by X-ray fluorescence scans. The work presented here is the first report of a structure of a metal-containing AK from a Gram-negative bacterium. The native enzyme was crystallized, and only zinc was detected in the LID domain. Co-AK and Fe-AK were obtained by overexpressing the protein in Escherichia coli. Zn-AK and Fe-AK crystallized as monomers in the asymmetric unit, whereas Co-AK crystallized as a dimer. Nevertheless, all three crystal structures are very similar to each other, with the same LID domain topology, the only change being the presence of the different metal atoms. In the absence of any substrate, the LID domain of all holoforms of AK was present in a fully open conformational state. Normal mode analysis was performed to predict fluctuations of the LID domain along the catalytic pathway.
1432-1327 (Electronic)0949-8257 (Linking)Journal ArticleResearch Support, Non-U.S. Gov't
Keywords: Adenylate Kinase/*chemistry/metabolism; Amino Acid Sequence; Biocatalysis; Cobalt/*chemistry/metabolism; Crystallography, X-Ray; Desulfovibrio gigas/*enzymology; Humans; Iron/*chemistry/metabolism; Models, Molecular; Molecular Sequence Data; Molecular Structure; Organometallic Compounds/*chemistry/metabolism; Sequence Alignment; Zinc/*chemistry/metabolism

From the Lisbon strategy to EU2020: illusion or progress for european economies? - António Brandão Moniz (Universidade Nova de Lisboa, IET-Research on Enterprise and Work Innovation, Faculty of Science and Technology, 2011)
The majority of papers published in the last decades on European Union policy strongly stress the importance of the so-called Lisbon Strategy approved in the year 2000. The same applies to studies and reports on the shift of the European countries towards modernisation and restructuring policy in recent years. This EU development strategy defines a new direction for the coordination of national policies. But why has it become so important? One of the reasons is the fact that many of the papers are based on the concept of “knowledge society” as the key driver for an increased competitiveness of all political and economic regions of Europe. In this context, the term “knowledge” means the inter-linkage of education (including training, qualification, skills) and innovation (including research, information and communication). The use of the concept represents an important shift in the European strategy: further development would not only be based on investment in material infrastructures, but also more on the immaterial ground. However, this Lisbon Strategy was criticised by many politicians and opinion-makers in the first years of this century because the European structures were not prepared for such a quick change. At the same time, the focus for investment moved away from the traditional support of industrial sectors (manufacturing, agriculture and fisheries, construction) towards the “new economy” sectors. The vision of a knowledge society remained appealing also in a changing international context: the Middle East wars (Afghanistan, Iraq and Israel-Palestine) and the fast growth of the Chinese economy. However, the shadows of new recessions have strongly questioned the options made by the European Council. New challenges have emerged with the need to redefine collective strategies in terms of European development as set by the Lisbon strategy. “Europe 2020” is one more attempt to define a new strategy. But at present no clear path has been identifi
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Keywords: European Union; innovation; knowledge society; Lisbon Strategy

Gold and silver nanoparticles for clinical diagnostics - From genomics to proteomics. - Baptista, Pedro Miguel Ribeiro Viana (Journal of Proteomics, 2011)
Nanotechnology has prompted researchers to develop new and improved materials aimed at biomedical applications with particular emphasis in diagnostics and therapy. Special interest has been directed at providing enhanced biomolecular diagnostics, including SNP detection gene expression profiles and biomarker characterisation. These strategies have focused on the development of nanoscale devices and platforms that can be used for single molecule characterisation of nucleic acid, DNA or RNA, and protein at an increased rate when compared to traditional techniques. Also, several advances have been reported on DNA analysis in real time, at both high resolution and very high throughputs, suitable for biomedical diagnostics. Here, we shall provide a review of available nanotechnology-based platforms for biomolecular recognition, and their application to molecular diagnostics and genome analysis, with emphasis on the use of noble metal nanoparticles for simple and specific analysis systems. Particular focus will be put on those already being translated into clinical settings. This article is part of a Special Issue entitled: Clinical Proteomics.
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Keywords: Genome screening; Gold nanoparticles; Protein biomarkers; silver nanoparticles; SNPs; Translation into clinics

Portable optoelectronic biosensing platform for identification of mycobacteria from the Mycobacterium tuberculosis complex - Silva, Leonardo Bione; Bruno Veigas; Gonçalo Doria; Pedro Costa; João Inácio; Rodrigo Martins; Elvira Fortunato; Baptista, Pedro Viana (Biosensors & Bioelectronics, 2011)
In this paper we report on the fabrication and performance of a portable and low cost optoelectronic platform integrating a double color tuned light emitting diode as light source, an amorphous/nanocrystalline silicon photodetector with a flat spectral response in the wavelength range from 520. nm to 630. nm and integrated electronic for signal acquisition and conditioning constituted by current to voltage converter, a filter and an amplification stage, followed by an analog to digital converter, with appropriate software for full automation to minimize human error. Incorporation of the double color tuned light emitting diode provides for a simple yet innovative solution to signal acquisition independently from the light intensity and/or solution concentration, while considerably decreasing production costs. Detection based on Au-nanoprobes constitutes the biorecognition step and allowed identification of specific sequences of Mycobacterium tuberculosis complex, namely Mycobacterium bovis and M. tuberculosis in biological samples.
This work was partially supported by the Portuguese Science Foundation (FCT-MCTES) for CENIMAT/I3N, CIGMH; Projects PTDC/SAU-BEB/66511/2006, PTDC/EEA-ELC/74236/2006 and PTDC/FIS/74274/2006. SFRH/BD/24665/2005 for L.B.Silva, SFRH/BD/64136/2009 for P. Costa and SFRH/BDE/15544/2005 & STAB Vida, Lda for G. Doria.
Keywords: Amorphous thin film silicon color sensor; DNA; Gold-nanoparticles; Mycobacterium tuberculosis; Optoelectronic platform; Tuberculosis

{From the Lisbon strategy to EU2020: illusion or progress for european economies?} - António Brandão Moniz (Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology, 2011)
The majority of papers published in the last decades on European Union policy strongly stress the importance of the so-called Lisbon Strategy approved in the year 2000. The same applies to studies and reports on the shift of the European countries towards modernisation and restructuring policy in recent years. This EU development strategy defines a new direction for the coordination of national policies. But why has it become so important? One of the reasons is the fact that many of the papers are based on the concept of “knowledge society” as the key driver for an increased competitiveness of all political and economic regions of Europe. In this context, the term “knowledge” means the inter-linkage of education (including training, qualification, skills) and innovation (including research, information and communication). The use of the concept represents an important shift in the European strategy: further development would not only be based on investment in material infrastructures, but also more on the immaterial ground. However, this Lisbon Strategy was criticised by many politicians and opinion-makers in the first years of this century because the European structures were not prepared for such a quick change. At the same time, the focus for investment moved away from the traditional support of industrial sectors (manufacturing, agriculture and fisheries, construction) towards the “new economy” sectors. The vision of a knowledge society remained appealing also in a changing international context: the Middle East wars (Afghanistan, Iraq and Israel-Palestine) and the fast growth of the Chinese economy. However, the shadows of new recessions have strongly questioned the options made by the European Council. New challenges have emerged with the need to redefine collective strategies in terms of European development as set by the Lisbon strategy. “Europe 2020” is one more attempt to define a new strategy. But at present no clear path has been identified. Whether the
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Keywords: European Union; innovation; knowledge society; Lisbon Strategy

NMR Insight into the Supramolecular Structure of Daunorubicin Loaded Polymer Nanoparticles - Ivanova, Galya; Simeonova, Margarita; Cabrita, Eurico J.; Rangel, Maria (Journal of Physical Chemistry B, 2011)
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New chiral imidazolium ionic liquids from isomannide - Gomes da Silva, M. D. R.; Pereira, M Manuela A (CARBOHYDRATE RESEARCH, 2011)
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Artefacts induced on c-type haem proteins by electrode surfaces - Paes de Sousa, P. M.; Pauleta, S. R.; Simoes Goncalves, M. L.; Pettigrew, G. W.; Moura, I.; Moura, J. J.; Correia dos Santos, M. M. (J Biol Inorg Chem, 2011)
In this work it is demonstrated that the characterization of c-type haem containing proteins by electrochemical techniques needs to be cautiously performed when using pyrolytic graphite electrodes. An altered form of the cytochromes, which has a redox potential 300 mV lower than that of the native state and displays peroxidatic activity, can be induced by interaction with the pyrolytic graphite electrode. Proper control experiments need to be performed, as altered conformations of the enzymes containing c-type haems can show activity towards the enzyme substrate. The work was focused on the study of the activation mechanism and catalytic activity of cytochrome c peroxidase from Paracoccus pantotrophus. The results could only be interpreted with the assignment of the observed non-turnover and catalytic signals to a non-native conformation state of the electron-transferring haem. The same phenomenon was detected for Met-His monohaem cytochromes (mitochondrial cytochrome c and Desulfovibrio vulgaris cytochrome c-553), as well as for the bis-His multihaem cytochrome c(3) from Desulfovibrio gigas, showing that this effect is independent of the axial coordination of the c-type haem protein. Thus, the interpretation of electrochemical signals of c-type (multi)haem proteins at pyrolytic graphite electrodes must be carefully performed, to avoid misassignment of the signals and incorrect interpretation of catalytic intermediates.
1432-1327 (Electronic)0949-8257 (Linking)Journal Article
Keywords: *Electrodes; Carbon/*chemistry; Cytochrome-c Peroxidase/chemistry; Electrochemistry/*methods; Hemeproteins/*chemistry; Paracoccus pantotrophus/enzymology; Protein Structure, Secondary

Competências para a Tomada de Decisão na Radiologia: Uma abordagem de Avaliação de Tecnologia [Competences for decision taking in Radiology: A Technology Assessment approach] - Maia, Maria João; António Brandão Moniz (Universidade Nova de Lisboa, IET-Research on Enterprise and Work Innovation, Faculty of Science and Technology, 2011)
We are facing an era, where pressures on health costs are extremely high, and the reforms in health system are almost constant. But over time, one factor remains unchanged – Technology continues being the sustenance of health care. Manufacturers, clinicians, patients, diagnostic and therapeutic technicians, hospital managers, government leaders, among others, either in public or private sector, are increasingly demanding in the sustained seek for information that support its decisions. Those decisions are about different types of issues: if, or how the technology can be developed, whether a technology should or should not enter the market, whether to acquire and use certain technology, and so forth. Such demand is well implied in the growth and development of Health Technology Assessment (HTA). This specialised field is commonly understood according to the International Network of Agencies for Health Technology Assessment (INAHTA, 2003) as an multidisciplinary analysis and decisional field, which studies the implications of clinical, social, ethical and economic development, dissemination and use of health technologies, without neglecting its political analysis (Goodman, 2004). The political decisions made based on HTA reports should be based on scientific evidence, linking efforts between the technical, economic and political dimensions, resourcing to a participatory vision, so that we can translate the best possible decision (Novaes 2006). On the other hand, the success of these decisions depends critically on the skills of the researcher to convey wisdom and confidence in applying rules of argumentation (Grunwald, 2007). In this paper we analyse the technical and methodological aspects of HTA, seen as a tool for evaluating health procedures and techniques. And we analyse the needs for skills and qualifications development of the actors involved in this process.
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Keywords: competences; decision-making; Magnetic Resonance; Radiology; stakeholders; Technology Assessment

The tetranuclear copper active site of nitrous oxide reductase: the CuZ center - Dell'Acqua, S.; Pauleta, S. R.; Moura, I.; Moura, J. J. (J Biol Inorg Chem, 2011)
This review focuses on the novel CuZ center of nitrous oxide reductase, an important enzyme owing to the environmental significance of the reaction it catalyzes, reduction of nitrous oxide, and the unusual nature of its catalytic center, named CuZ. The structure of the CuZ center, the unique tetranuclear copper center found in this enzyme, opened a novel area of research in metallobiochemistry. In the last decade, there has been progress in defining the structure of the CuZ center, characterizing the mechanism of nitrous oxide reduction, and identifying intermediates of this reaction. In addition, the determination of the structure of the CuZ center allowed a structural interpretation of the spectroscopic data, which was supported by theoretical calculations. The current knowledge of the structure, function, and spectroscopic characterization of the CuZ center is described here. We would like to stress that although many questions have been answered, the CuZ center remains a scientific challenge, with many hypotheses still being formed.
1432-1327 (Electronic)0949-8257 (Linking)Journal ArticleResearch Support, Non-U.S. Gov'tReview
Keywords: Catalytic Domain; Copper/*metabolism; Crystallography, X-Ray; Oxidoreductases/*chemistry/*metabolism; Protein Structure, Secondary

{Competências para a Tomada de Decisão na Radiologia: Uma abordagem de Avaliação de Tecnologia [Competences for decision taking in Radiology: A Technology Assessment approach]} - Maia, Maria João; António Brandão Moniz (Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology, 2011)
We are facing an era, where pressures on health costs are extremely high, and the reforms in health system are almost constant. But over time, one factor remains unchanged – Technology continues being the sustenance of health care. Manufacturers, clinicians, patients, diagnostic and therapeutic technicians, hospital managers, government leaders, among others, either in public or private sector, are increasingly demanding in the sustained seek for information that support its decisions. Those decisions are about different types of issues: if, or how the technology can be developed, whether a technology should or should not enter the market, whether to acquire and use certain technology, and so forth. Such demand is well implied in the growth and development of Health Technology Assessment (HTA). This specialised field is commonly understood according to the International Network of Agencies for Health Technology Assessment (INAHTA, 2003) as an multidisciplinary analysis and decisional field, which studies the implications of clinical, social, ethical and economic development, dissemination and use of health technologies, without neglecting its political analysis (Goodman, 2004). The political decisions made based on HTA reports should be based on scientific evidence, linking efforts between the technical, economic and political dimensions, resourcing to a participatory vision, so that we can translate the best possible decision (Novaes 2006). On the other hand, the success of these decisions depends critically on the skills of the researcher to convey wisdom and confidence in applying rules of argumentation (Grunwald, 2007). In this paper we analyse the technical and methodological aspects of HTA, seen as a tool for evaluating health procedures and techniques. And we analyse the needs for skills and qualifications development of the actors involved in this process.
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Keywords: competences; decision-making; Magnetic Resonance; Radiology; stakeholders; Technology Assessment

{How composite indicators of innovation can influence technology policy decision?} - Nuno Boavida (Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology, 2011)
This working paper is based on the development of the Thesis Plan presented for the Units Project II and Project III at the 1st Winter School of PhD programme on Technology Assessment at FCT/UNL. It focuses the methodology analysis and includes empirical information elements, in order to understand how composite indicators of innovation can influence technology policy decisions. In order to test the hypotheses raised in the Thesis Plan, two separate phases were designed. On the first part, the work tests hypotheses 1 and partially 2, identifying the quality, depth and limitations of three famous complex indicator-based systems, namely the Science, Technology and Industry Scoreboard, the European Innovation Scoreboard 2008 and Innovation Union Scoreboard 2010. On the second phase, the remaining hypotheses are tested adding media databases analysis, which will provide complementary information to a set of interviews to policy makers, in order to understand the role of the composite indicators on technology decisions.
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Keywords: composite indicators; European Innovation Scoreboard; Innov; innovation; technology policy decisions

Comparative electrochemical study of superoxide reductases - Cordas, Cristina M.; Raleiras, Patricia; Auchère, Françoise; Moura, Isabel; Moura, Jose J. G. (Eur. Biophys. J., 2011)
... CM Cordas (&) Á P . Raleiras Á F . Auche`re Á I. Moura Á JJG Moura ... de Quımica, Universidade Nova de Lisboa, 2859-516 Caparica, Portugal e-mail: cristina. cordas @dq.fct ... Present Address: P . Raleiras Department of Photochemistry and Molecular Science, PO Box 523, 75120 ...
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Actin as a potential target for decavanadate - Ramos, S.; Moura, J. J.; Aureliano, M. (J Inorg Biochem, 2011)
ATP prevents G-actin cysteine oxidation and vanadyl formation specifically induced by decavanadate, suggesting that the oxometalate-protein interaction is affected by the nucleotide. The ATP exchange rate is increased by 2-fold due to the presence of decavanadate when compared with control actin (3.1x10(-3) s(-1)), and an apparent dissociation constant (k(dapp)) of 227.4+/-25.7 muM and 112.3+/-8.7 muM was obtained in absence or presence of 20 muM V(10), respectively. Moreover, concentrations as low as 50 muM of decameric vanadate species (V(10)) increases the relative G-actin intrinsic fluorescence intensity by approximately 80% whereas for a 10-fold concentration of monomeric vanadate (V(1)) no effects were observed. Upon decavanadate titration, it was observed a linear increase in G-actin hydrophobic surface (2.6-fold), while no changes were detected for V(1) (0-200 muM). Taken together, three major ideas arise: i) ATP prevents decavanadate-induced G-actin cysteine oxidation and vanadate reduction; ii) decavanadate promotes actin conformational changes resulting on its inactivation, iii) decavanadate has an effect on actin ATP binding site. Once it is demonstrated that actin is a new potential target for decavanadate, being the ATP binding site a suitable site for decavanadate binding, it is proposed that some of the biological effects of vanadate can be, at least in part, explained by decavanadate interactions with actin.
1873-3344 (Electronic)0162-0134 (Linking)Journal ArticleResearch Support, Non-U.S. Gov't
Keywords: Actins/*chemistry; Adenosine Triphosphate/chemistry; Animals; Electron Spin Resonance Spectroscopy; Rabbits; Vanadates/*chemistry

The electron transfer complex between nitrous oxide reductase and its electron donors - Dell'Acqua, S.; Moura, I.; Moura, J. J.; Pauleta, S. R. (J Biol Inorg Chem, 2011)
Identifying redox partners and the interaction surfaces is crucial for fully understanding electron flow in a respiratory chain. In this study, we focused on the interaction of nitrous oxide reductase (N(2)OR), which catalyzes the final step in bacterial denitrification, with its physiological electron donor, either a c-type cytochrome or a type 1 copper protein. The comparison between the interaction of N(2)OR from three different microorganisms, Pseudomonas nautica, Paracoccus denitrificans, and Achromobacter cycloclastes, with their physiological electron donors was performed through the analysis of the primary sequence alignment, electrostatic surface, and molecular docking simulations, using the bimolecular complex generation with global evaluation and ranking algorithm. The docking results were analyzed taking into account the experimental data, since the interaction is suggested to have either a hydrophobic nature, in the case of P. nautica N(2)OR, or an electrostatic nature, in the case of P. denitrificans N(2)OR and A. cycloclastes N(2)OR. A set of well-conserved residues on the N(2)OR surface were identified as being part of the electron transfer pathway from the redox partner to N(2)OR (Ala495, Asp519, Val524, His566 and Leu568 numbered according to the P. nautica N(2)OR sequence). Moreover, we built a model for Wolinella succinogenes N(2)OR, an enzyme that has an additional c-type-heme-containing domain. The structures of the N(2)OR domain and the c-type-heme-containing domain were modeled and the full-length structure was obtained by molecular docking simulation of these two domains. The orientation of the c-type-heme-containing domain relative to the N(2)OR domain is similar to that found in the other electron transfer complexes.
1432-1327 (Electronic)0949-8257 (Linking)Journal ArticleResearch Support, Non-U.S. Gov't

The mechanism of formate oxidation by metal-dependent formate dehydrogenases - Mota, C. S.; Rivas, M. G.; Brondino, C. D.; Moura, I.; Moura, J. J.; Gonzalez, P. J.; Cerqueira, N. M. (J Biol Inorg Chem, 2011)
Metal-dependent formate dehydrogenases (Fdh) from prokaryotic organisms are members of the dimethyl sulfoxide reductase family of mononuclear molybdenum-containing and tungsten-containing enzymes. Fdhs catalyze the oxidation of the formate anion to carbon dioxide in a redox reaction that involves the transfer of two electrons from the substrate to the active site. The active site in the oxidized state comprises a hexacoordinated molybdenum or tungsten ion in a distorted trigonal prismatic geometry. Using this structural model, we calculated the catalytic mechanism of Fdh through density functional theory tools. The simulated mechanism was correlated with the experimental kinetic properties of three different Fdhs isolated from three different Desulfovibrio species. Our studies indicate that the C-H bond break is an event involved in the rate-limiting step of the catalytic cycle. The role in catalysis of conserved amino acid residues involved in metal coordination and near the metal active site is discussed on the basis of experimental and theoretical results.
1432-1327 (Electronic)0949-8257 (Linking)Journal ArticleResearch Support, Non-U.S. Gov't

P-glycoprotein activity assessment in rat brain endothelial cells-A search for new rifampicin-derived p-glycoprotein inducers - Vilas-Boas, V.; Silva, R.; Vieira, C.; Martins, I.; L. Ferreira; Branco, P.; Remiao, F (TOXICOLOGY LETTERS, 2011)
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47th Congress of the European-Societies-of-Toxicology, Paris, FRANCE, AUG 28-31, 2011

Pro-oxidant effects of ``ecstasy{''} and its metabolites in mouse brain synaptosomes - Barbosa, D. J.; Capela, JP; Oliveira, J. M. A.; L. Ferreira; Branco, P.; Fernandes, E; Bastos, ML; F. Carvalho (TOXICOLOGY LETTERS, 2011)
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47th Congress of the European-Societies-of-Toxicology, Paris, FRANCE, AUG 28-31, 2011

Development of molecularly imprinted co-polymeric devices for controlled delivery of flufenamic acid using supercritical fluid technology - Mara Soares da Silva; Franklin L. Nobrega; Aguiar-Ricardo, Ana; Cabrita, Eurico J.; Casimiro, Teresa (Journal of Supercritical Fluids, 2011)
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Screening nucleotide binding to amino acid-coated supports by surface plasmon resonance and nuclear magnetic resonance - Cruz, Carla; Cabrita, Eurico J.; Queiroz, Joao A. (Analytical and Bioanalytical Chemistry, 2011)
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Analysis of the activation mechanism of Pseudomonas stutzeri cytochrome c peroxidase through an electron transfer chain - Paes de Sousa, P. M.; Rodrigues, D.; Timoteo, C. G.; Simoes Goncalves, M. L.; Pettigrew, G. W.; Moura, I.; Moura, J. J.; Correia dos Santos, M. M. (J Biol Inorg Chem, 2011)
The activation mechanism of Pseudomonas stutzeri cytochrome c peroxidase (CCP) was probed through the mediated electrochemical catalysis by its physiological electron donor, P. stutzeri cytochrome c-551. A comparative study was carried out, by performing assays with the enzyme in the resting oxidized state as well as in the mixed-valence activated form, using cyclic voltammetry and a pyrolytic graphite membrane electrode. In the presence of both the enzyme and hydrogen peroxide, the peak-like signal of cytochrome c-551 is converted into a sigmoidal wave form characteristic of an E(r)C'(i) catalytic mechanism. An intermolecular electron transfer rate constant of (4 +/- 1) x 10(5) M(-1) s(-1) was estimated for both forms of the enzyme, as well as a similar Michaelis-Menten constant. These results show that neither the intermolecular electron transfer nor the catalytic activity is kinetically controlled by the activation mechanism of CCP in the case of the P. stutzeri enzyme. Direct enzyme catalysis using protein film voltammetry was unsuccessful for the analysis of the activation mechanism, since P. stutzeri CCP undergoes an undesirable interaction with the pyrolytic graphite surface. This interaction, previously reported for the Paracoccus pantotrophus CCP, induces the formation of a non-native conformation state of the electron-transferring haem, which has a redox potential 200 mV lower than that of the native state and maintains peroxidatic activity.
1432-1327 (Electronic)0949-8257 (Linking)Journal ArticleResearch Support, Non-U.S. Gov't
Keywords: *Enzyme Activation; Bacterial Proteins/chemistry/*metabolism; Catalysis; Cytochrome-c Peroxidase/chemistry/*metabolism; Electrochemistry; Electron Transport/*physiology; Oxidation-Reduction; Paracoccus pantotrophus/enzymology; Pseudomonas stutzeri/*enzymology

Electrochemical behaviour of Dps-a mini-ferritin - Cordas, Cristina M.; Wilton, Joana; Cardoso, Tania; Folgosa, Filipe; Pereira, Alice S.; Tavares, Pedro (EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2011)
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8th EBSA European Biophysics Congress, Budapest, HUNGARY, AUG 23-27, 2011