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2013
Pimenta, J, Viegas A, Sardinha J, Martins IC, Cabrita EJ, Fontes CMGA, Prates JAM, Pereira RMLN.  2013.  NMR Solution Structure and SRP54M predicted interaction of the N-Terminal sequence (1-30) of the ovine Doppel protein. Peptides. 49:32-40. AbstractWebsite

Prion protein (PrPC) biosynthesis involves a multi-step process that includes translation and post-translational modifications. While PrP has been widely investigated, for the homolog Doppel (Dpl), limited knowledge is available. In this study, we focused on a vital step of eukaryotic protein biosynthesis: targeting by the signal recognition particle (SRP). Taking the ovine Dpl (OvDpl(1-30)) peptide as a template, we studied its behavior in two different hydrophobic environments using CD and NMR spectroscopy. In both trifluoroethanol (TFE) and dihexanoyl-sn-glycero-3-phosphatidylcholine (DHPC), the OvDpl(1-30) peptide revealed to fold in an alpha-helical conformation with a well-defined central region extending from residue Cys8 until Ser22. The NMR structure was subsequently included in a computational docking complex with the conserved M-domain of SRP54 protein (SRP54M), and further compared with the N-terminal structures of mouse Dpl and bovine PrPC proteins. This allowed the determination of (i) common predicted N-terminal/SRP54M polar contacts (Asp331, Gln335, Glu365 and Lys432) and (ii) different N–C orientations between prion and Dpl peptides at the SRP54M hydrophobic groove, that are in agreement with each peptide electrostatic potential. Together, these findings provide new insights into the biosynthesis of prion-like proteins. Besides they also show the role of protein conformational switches in signalization toward the endoplasmic membrane, a key event of major significance in the cell cycle. They are thus of general applicability to the study of the biological function of prion-like as well as other proteins.

Vale, TM, Dias RJ, Lourenço JM.  2013.  On the Relevance of Total-Order Broadcast Implementations in Replicated Software Transactional Memories. Multicore Software Engineering, Performance, and Tools. 8063(João M. Lourenço, Farchi, Eitan, Eds.).:49–60.: Springer Berlin Heidelberg Abstract2013-musepat.pdf

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Dias, RJ, Pessanha V, Lourenço JM.  2013.  Precise Detection of Atomicity Violations. Hardware and Software: Verification and Testing. 7857(Biere, Armin, Nahir, Amir, Vos, Tanja, Eds.).:8-23.: Springer Berlin / Heidelberg Abstract2012-hvc.pdf

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Silva, JA, Vale TM, Lourenço JM, Paulino H.  2013.  Replicação Parcial com Memória Transacional Distribuída. Proceedings of INForum Simpósio de Informática. :310–321., Lisbon, Portugal: Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa Abstract2013-inforum-js.pdf

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Araújo, A, Barros R, Mateus T, Gaspar D, Neves N, Vicente A, Filonovich SA, Barquinha P, Fortunato E, Ferraria AM, do Rego ABM, Bicho A, Águas H, Martins R.  2013.  Role of a disperse carbon interlayer on the performances of tandem a-Si solar cells. Science and Technology of Advanced Materials. 14(4)
dos Santos, R, Rocha A, Matias A, Duarte C, de Sá-Nogueira I, Lourenco N, Borges JP, Vidinha P.  2013.  Development of antimicrobial Ion Jelly fibers. RSC Adv.. 3:24400-24405.: The Royal Society of Chemistry Abstract

We report a method to obtain electrospun fibers based on ionic liquids and gelatin, exhibiting antimicrobial properties.

Pedrosa, P, Veigas B, Machado D, Perdigão J, Portugal I, Couto I, Viveiros M, Baptista {PV}.  2013.  Detec{\c c}ão de MDRTB por gold-nanoprobes – uma nova abordagem tecnológica desenvolvida em Portugal. Abstract
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Gawande, MB, Guo H, Rathi AK, Branco PS, Chen Y, Varma RS, Peng D-L.  2013.  First application of core-shell Ag@Ni magnetic nanocatalyst for transfer hydrogenation reactions of aromatic nitro and carbonyl compounds. RSC ADVANCES. 3:1050-1054., Number 4 Abstract
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Gawande, MB, Bonifacio VDB, Varma RS, Nogueira ID, Bundaleski N, Ghumman ACA, Teodoro OMND, Branco PS.  2013.  Magnetically recyclable magnetite-ceria (Nanocat-Fe-Ce) nanocatalyst - applications in multicomponent reactions under benign conditions. GREEN CHEMISTRY. 15:1226-1231., Number 5 Abstract
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Gawande, MB, Rathi AK, Branco PS, Potewar TM, Velhinho A, Nogueira ID, Tolstogouzov A, Ghumman ACA, Teodoro OMND.  2013.  Nano-MgO-ZrO2 mixed metal oxides: characterization by SIMS and application in the reduction of carbonyl compounds and in multicomponent reactions. RSC ADVANCES. 3:3611-3617., Number 11 Abstract
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Montagner, C, Sanches D, Pedroso J, Melo MJ, Vilarigues M.  2013.  Ochres and earths: Matrix and chromophores characterization of 19th and 20th century artist materials. Spectrochimica Acta Part a-Molecular and Biomolecular Spectroscopy. 103:409-416. AbstractWebsite
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Verma, AK, Goyal A, Freire F, Bule P, Venditto I, Bras JLA, Santos H, Cardoso V, Bonifacio C, Thompson A, Romao MJ, Prates JAM, Ferreira LMA, Fontes CMGA, Najmudin S.  2013.  Overexpression, crystallization and preliminary X-ray crystallographic analysis of glucuronoxylan xylanohydrolase (Xyn30A) from Clostridium thermocellum. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 69:1440-1442. AbstractWebsite
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Velasco, LF, Maurino V, Laurenti E, Fonseca IM, Lima JC, Ania CO.  2013.  Photoinduced reactions occurring on activated carbons. A combined photooxidation and ESR study. Applied Catalysis a-General. 452:1-8. Abstract
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Viegas, A, Sardinha J, Freire F, Duarte DF, Carvalho AL, Fontes CMGA, Romao MJ, Macedo AL, Cabrita EJ.  2013.  Solution structure, dynamics and binding studies of a family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11). Biochemical Journal. 451:289-300. AbstractWebsite
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Viegas, A, Sardinha J, Duarte DF, Carvalho AL, Fontes CMGA, Romao MJ, Macedo AL, Cabrita EJ.  2013.  Solution Structure, Dynamics and Binding Studies of a Family 11 Carbohydrate-Binding Module from Clostridium thermocellum (CtCBM11). Biochemical Journal. 451:289-300. AbstractWebsite

Non-catalytic cellulosomal carbohydrate-binding modules (CBMs) are responsible for increasing the catalytic efficiency of cellulosic enzymes by selectively putting the substrate (a wide range of poly- and oligosaccharides) and enzyme into close contact. In the present work we carried out an atomistic rationalization of the molecular determinants of ligand specificity of a family 11 CBM from thermophilic C. thermocellum (CtCBM11), based on a NMR and molecular modeling approach. We have determined the NMR solution structure of CtCBM11 at 25 and 50 ºC and derived information on the residues of the protein involved in ligand recognition and on the influence of the length of the saccharide chain on binding. We obtained models of the CtCBM11/cellohexaose and CtCBM11/cellotetraose complexes by docking in accordance with the NMR experimental data. Specific ligand/protein CH-π and Van der Waals interactions were found to be determinant for the stability of the complexes and for defining specificity. Using the order parameters derived from backbone dynamics analysis in the presence and absence of ligand and at 25 and 50 ºC, we determined that the protein’s backbone conformational entropy is slightly positive. This data in combination with the negative binding entropy calculated from ITC studies supports a selection mechanism where a rigid protein selects a defined oligosaccharide conformation.

Ruivo, A, Ventura MG, Gomes da Silva MDR, Laia CAT.  2013.  Synthesis of gold nanoparticles in sol-gel glass porogens containing bmim BF4 ionic liquid. Journal of Sol-Gel Science and Technology. 68:234-244., Number 2 AbstractWebsite
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2012
Simão, J, Veiga L{\'ıs.  2012.  QoE-JVM: An Adaptive and Resource-Aware Java Runtime for Cloud Computing, sep. 2nd International Symposium on Secure Virtual Infrastructures (DOA-SVI 2012), OTM Conferences 2012. : Springer, LNCS Abstract2012-doa-simao.pdf

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Rameshan, N, Veiga L.  2012.  RATS - Resource Aware Thread Scheduling for JVM-level Clustering, sep. INFORUM 2012 - Simpósio de Informática. Abstractinforum-2012-navaneeth.pdf

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Silva, JPM, Veiga L{\'ıs.  2012.  Reprodução Probabilística de Execuções na JVM em Multi-processadores, sep. INFORUM 2012 - Simpósio de Informática. Abstractinforum-2012-jpsilva-replay.pdf

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Vale, TM, Dias RJ, Lourenço JM.  2012.  Uma Infraestrutura para Suporte de Memória Transacional Distribuída, sep. Proceedings of INForum Simpósio de Informática. :177–189., Lisbon, Portugal: Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa Abstract2012-inforum-tv.pdf

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Gawande, MB, Rathi AK, Branco PS, Nogueira ID, Velhinho A, Shrikhande JJ, Indulkar UU, Jayaram RV, Ghumman ACA, Bundaleski N, Teodoro OMND.  2012.  Regio- and Chemoselective Reduction of Nitroarenes and Carbonyl Compounds over Recyclable Magnetic Ferrite-Nickel Nanoparticles (Fe3O4-Ni) by Using Glycerol as a Hydrogen Source, OCT. CHEMISTRY-A EUROPEAN JOURNAL. 18:12628-12632., Number 40 Abstract
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Velloso, GT.  2012.  {Brain-Computer Interface (BCI): a methodological proposal to assess the impacts of medical applications in 2022}, November. Enterprise and Work Innovation Studies. 8:57-81., Number 8 AbstractWebsite

Technology assessment is essentially an approach, a collective of the systematic methods used to scientifically investigate the conditions for and the consequences of technology and technicising and to denote their societal evaluation. It is an investigation about the technological developments as well as an evaluation of its potential impacts on society. The assessment of emerging technologies, however, requires special attention. Brain-Computer Interface (BCI) is an emerging 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 software without intermediates. To address these kinds of technologies at early stages of development, Constructive Technology Assessment (CTA), a member of Technology Assessment approaches, has been considered as one of the most fitting approaches. 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 many challenges are yet to be overcome. Therefore, the objective of this article is to discuss and present a methodological approach to assess brain-computer interface technology considering constructive technology assessment and future oriented technology analysis as the main processes to undertake the assessment. The assessment will focus only on the non-invasive type of BCI and for medical applications in three defined areas: Communication & Control, Motor Substitution and Motor Recovery for a time horizon of 10 years, 2022. These areas were chosen based on the capability of BCI to serve as a replacement of normal neuromuscular pathways. That makes it one of the best technologies to help people in activating and controlling assistive technologies which enable communication and control of the environment. However, the real impacts o

Veigas, {BMR}, Jacob {JAM}, Costa {MN }, de Santos {DPS}, Bettencourt {MV}, Inácio J, de Martins {RFP}, Barquinha {PMC}, Fortunato {EMC}, Baptista {PMRV}.  2012.  Gold on paper-paper platform for Au-nanoprobe TB detection, nov. Lab On A Chip. 12:4802–8., Number 22: RSC - Royal Society of Chemistry Abstract

Tuberculosis (TB) remains one of the most serious infectious diseases in the world and the rate of new cases continues to increase. The development of cheap and simple methodologies capable of identifying TB causing agents belonging to the Mycobacterium tuberculosis Complex (MTBC), at point-of-need, in particular in resource-poor countries where the main TB epidemics are observed, is of paramount relevance for the timely and effective diagnosis and management of patients. TB molecular diagnostics, aimed at reducing the time of laboratory diagnostics from weeks to days, still require specialised technical personnel and labour intensive methods. Recent nanotechnology-based systems have been proposed to circumvent these limitations. Here, we report on a paper-based platform capable of integrating a previously developed Au-nanoprobe based MTBC detection assay-we call it {"}Gold on Paper{"}. The Au-nanoprobe assay is processed and developed on a wax-printed microplate paper platform, allowing unequivocal identification of MTBC members and can be performed without specialised laboratory equipment. Upon integration of this Au-nanoprobe colorimetric assay onto the 384-microplate, differential colour scrutiny may be captured and analysed with a generic {"}smartphone{"} device. This strategy uses the mobile device to digitalise the intensity of the colour associated with each colorimetric assay, perform a Red Green Blue (RGB) analysis and transfer relevant information to an off-site lab, thus allowing for efficient diagnostics. Integration of the GPS location metadata of every test image may add a new dimension of information, allowing for real-time epidemiologic data on MTBC identification.

Baptista, P, Veigas {BMR}, Portugal I, Couto I, Viveiros M.  2012.  Using Au-nanoprobes por point-of-need diagnostics of TB., jan. Magazine da Sociedade Portuguesa de Microbiologia. 2012, Number 1 Abstract

Tuberculosis remains one of the most serious infectious diseases worldwide requiring new tools to circumvent current molecular diagnostics limitations. Nanodiagnostics, i.e. nanotechnology based diagnostics, may do just that by decreasing the time needed for the molecular characterisation of the infecting agent, and allowing for miniaturisation and portability for point-of-need adapted to remote regions without suitable lab equipment.