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2014
Guimarães, D., J. P. Santos, M. L. Carvalho, M. S. Diniz, B. House, and V. M. Miller. "Analytical evidence of heterogeneous lead accumulation in the hypothalamic defence area and nucleus tractus solitarius." NeuroToxicology. 44 (2014): 91-97. AbstractWebsite

Lead is a potent toxicant associated with adverse cardiovascular effects and hypertension in children. Yet, few studies have determined if autonomic dysfunction associated with lead exposure involves brain regions which regulate autonomic responses. Central autonomic nuclei such as the nucleus tractus solitarius (NTS) and hypothalamic defence area (HDA) may be particularly sensitive to lead infiltration because they are adjacent to ventricles and areas with semi-permeable blood-brain-barriers. To understand if autonomic nuclei are sensitive to lead accumulation Wistar rats were exposed to lead from the gestational period and lead levels were quantified in brain regions that regulate arterial pressure: the NTS and the HDA. Energy dispersive X-ray fluorescence (EDXRF) was used to quantify total brain lead levels and revealed no differences between exposed and control tissues; measured values were close to the detection limit (2μg/g). Electrothermal atomic absorption spectrometry (ETAAS) was also used, which has a greater sensitivity, to quantify lead. There was ∼2.1μg/g lead in the NTS and ∼3.1μg/g lead in the HDA of exposed rats, and no lead in the control rats. There were greater lead levels in the HDA (∼50%) as compared with the NTS. Pathology studies revealed more prominent lead granules in the HDA as compared with the NTS. Increased microglia and astrocyte activation was also noted in the NTS of lead exposed rats as compared with the HDA. Regional differences in neuro-inflammatory responses likely contribute to heterogeneous lead accumulation, with enhanced clearance of lead in the NTS. Future studies will resolve the mechanisms underpinning tissue-specific lead accumulation.

Guimarães, D., J. P. Santos, M. L. Carvalho, M. S. Diniz, B. House, and V. M. Miller. "Analytical evidence of heterogeneous lead accumulation in the hypothalamic defence area and nucleus tractus solitarius." NeuroToxicology. 44 (2014): 91-97. AbstractWebsite

Lead is a potent toxicant associated with adverse cardiovascular effects and hypertension in children. Yet, few studies have determined if autonomic dysfunction associated with lead exposure involves brain regions which regulate autonomic responses. Central autonomic nuclei such as the nucleus tractus solitarius (NTS) and hypothalamic defence area (HDA) may be particularly sensitive to lead infiltration because they are adjacent to ventricles and areas with semi-permeable blood-brain-barriers. To understand if autonomic nuclei are sensitive to lead accumulation Wistar rats were exposed to lead from the gestational period and lead levels were quantified in brain regions that regulate arterial pressure: the NTS and the HDA. Energy dispersive X-ray fluorescence (EDXRF) was used to quantify total brain lead levels and revealed no differences between exposed and control tissues; measured values were close to the detection limit (2μg/g). Electrothermal atomic absorption spectrometry (ETAAS) was also used, which has a greater sensitivity, to quantify lead. There was ∼2.1μg/g lead in the NTS and ∼3.1μg/g lead in the HDA of exposed rats, and no lead in the control rats. There were greater lead levels in the HDA (∼50%) as compared with the NTS. Pathology studies revealed more prominent lead granules in the HDA as compared with the NTS. Increased microglia and astrocyte activation was also noted in the NTS of lead exposed rats as compared with the HDA. Regional differences in neuro-inflammatory responses likely contribute to heterogeneous lead accumulation, with enhanced clearance of lead in the NTS. Future studies will resolve the mechanisms underpinning tissue-specific lead accumulation.

Silva, João A., João M. Lourenço, and Hervé Paulino. "Um Mecanismo de Caching para o Protocolo {SCORe}." Proceedings of INForum Simpósio de Informática. INForum 2014. Porto, Portugal: FEUP Edições, 2014. 260-275. Abstractinforum14-jsilva.pdf

Os protocolos de replicação parcial de dados apresentam um grande potencial de escalabilidade. O SCORe é um protocolo para replicação parcial proposto recentemente que faz uso de controlo de concorrência multi-versão. Neste artigo abordamos um dos problemas principais que afeta o desempenho deste tipo de protocolos: a localidade dos dados, i.e., pode-se dar o caso do nó local não ter uma cópia dos dados a que pretende aceder, e nesse caso é necessário realizar uma ou mais operações de leitura remota. Assim, a não ser que se empreguem técnicas para melhorar a localidade no acesso aos dados, o número de operações de leitura remota aumenta com o tamanho do sistema, acabando por afetar o desempenho do mesmo. Nesse sentido, introduzimos um mecanismo de caching que permite replicar cópias de dados remotos de maneira a que seja poss{\'ı}vel servir localmente dados remotos enquanto que se mantém a consistência dos mesmos e a escalabilidade oferecida pelo protocolo. Avaliamos o mecanismo de caching com um benchmark conhecido da literatura e os resultados experimentais mostram resultados animadores com algum aumento no desempenho do sistema e uma redução considerável da quantidade de operações de leitura remota.

Saponaro, A., S. R. Pauleta, F. Cantini, M. Matzapetakis, C. Hammann, C. Donadoni, L. Hu, G. Thiel, L. Banci, B. Santoro, and A. Moroni. "Structural basis for the mutual antagonism of cAMP and TRIP8b in regulating HCN channel function." Proc Natl Acad Sci U S A. 111 (2014): 14577-82. AbstractWebsite

cAMP signaling in the brain mediates several higher order neural processes. Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels directly bind cAMP through their cytoplasmic cyclic nucleotide binding domain (CNBD), thus playing a unique role in brain function. Neuronal HCN channels are also regulated by tetratricopeptide repeat-containing Rab8b interacting protein (TRIP8b), an auxiliary subunit that antagonizes the effects of cAMP by interacting with the channel CNBD. To unravel the molecular mechanisms underlying the dual regulation of HCN channel activity by cAMP/TRIP8b, we determined the NMR solution structure of the HCN2 channel CNBD in the cAMP-free form and mapped on it the TRIP8b interaction site. We reconstruct here the full conformational changes induced by cAMP binding to the HCN channel CNBD. Our results show that TRIP8b does not compete with cAMP for the same binding region; rather, it exerts its inhibitory action through an allosteric mechanism, preventing the cAMP-induced conformational changes in the HCN channel CNBD.

Branquinho, Rita, Daniela Salgueiro, Lídia Santos, Pedro Barquinha, Luis Pereira, Rodrigo Ferrão De Paiva Martins, and Elvira Fortunato. "{Aqueous Combustion Synthesis of Aluminum Oxide Thin Films and Application as Gate Dielectric in GZTO Solution-based TFTs.}." ACS applied materials {&} interfaces. 6 (2014): 195592-9. AbstractWebsite

Solution processing has been recently considered as an option when trying to reduce the costs associated to deposition under vacuum. In this context most of the research efforts have been centered in the development of the semiconductors processes nevertheless the development of the most suitable dielectrics for oxide based transistors is as relevant as the semiconductor layer itself. In this work we explore the solution combustion synthesis and report on a completely new and green route for the preparation of amorphous aluminum oxide thin films; introducing water as solvent. Optimized dielectric layers were obtained for a water based precursor solution with 0.1 M concentration and demonstrated high capacitance, 625 nF cm-2 at 10 kHz, and a permittivity of 7.1. These thin films were successfully applied as gate dielectric in solution processed gallium-zinc-tin oxide (GZTO) thin film transistors (TFTs) yielding good electrical performance such as subthreshold slope of about 0.3 V dec-1 and mobility above 1.3 cm2 V-1 s-1.

Branquinho, Rita, Daniela Salgueiro, Lidia Santos, Pedro Barquinha, Luis Pereira, Rodrigo Martins, and Elvira Fortunato. "Aqueous Combustion Synthesis of Aluminum Oxide Thin Films and Application as Gate Dielectric in GZTO Solution-Based TFTs." Acs Applied Materials & Interfaces. 6 (2014): 19592-19599. AbstractWebsite
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Katriel, Jacob, J. P. Marques, P. Indelicato, A. M. Costa, M. C. Martins, J. P. Santos, and F. Parente. "Approach towards the critical charge of some excited states of the Be isoelectronic series." Physical Review A. 90 (2014): 052519-5. AbstractWebsite
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Branquinho, Rita, Daniela Salgueiro, L??dia Lídia Santos, Pedro Barquinha, Luís Lu??s Pereira, Rodrigo Martins, and Elvira Fortunato. "{Aqueous combustion synthesis of aluminum oxide thin films and application as gate dielectric in GZTO solution-based TFTs}." ACS Applied Materials and Interfaces. 6 (2014): 19592-19599. AbstractWebsite

Solution processing has been recently considered as an option when trying to reduce the costs associated with deposition under vacuum. In this context, most of the research efforts have been centered in the development of the semiconductors processes nevertheless the development of the most suitable dielectrics for oxide based transistors is as relevant as the semiconductor layer itself. In this work we explore the solution combustion synthesis and report on a completely new and green route for the preparation of amorphous aluminum oxide thin films; introducing water as solvent. Optimized dielectric layers were obtained for a water based precursor solution with 0.1 M concentration and demonstrated high capacitance, 625 nF cm(-2) at 10 kHz, and a permittivity of 7.1. These thin films were successfully applied as gate dielectric in solution processed gallium-zinc-tin oxide (GZTO) thin film transistors (TFTs) yielding good electrical performance such as subthreshold slope of about 0.3 V dec(-1) and mobility above 1.3 cm(2) V(-1) s(-1).

Santos, I., M. S. Diniz, M. L. Carvalho, and J. P. Santos. "Assessment of Essential Elements and Heavy Metals Content on Mytilus galloprovincialis from River Tagus Estuary." Biological Trace Element Research (2014). AbstractWebsite

Trace elemental content was analysed in edible tissues of Mytilus galloprovincialis collected in five different sampling areas near the mouth of river Tagus estuary in Lisbon. The concentrations of essential elements (S, K, Ca, Fe, Cu, Zn, As, Br and Sr) were determined by energy-dispersive X-ray fluorescence (EDXRF) spectrometry, while toxic elements (Cr, Cd, Hg, Se and Pb) were measured by inductively coupled plasma-atomic emission spectrometry (ICP-AES). The results show that the essential elements K and S are present at the highest concentrations in all the studied samples reaching 2,920 and 4,520 μg g(-1) (fresh weight), respectively. The highest levels of heavy metals found were in two areas close to the city for Pb and Cd, but below the maximum allowed values.

Rahangdale, H. V., M. Guerra, P. K. Das, S. De, J. P. Santos, D. Mitra, and S. Saha. "Determination of subshell-resolved <span class="aps-inline-formula"><math><mi>L</mi></math></span>-shell-ionization cross sections of gold induced by 15–40-keV electrons." Physical Review A. 89 (2014): 052708. AbstractWebsite
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Amaro, P., C. I. Szabo, S. Schlesser, A. Gumberidze, E. G. Kessler, A. Henins, E. O. Le Bigot, M. Trassinelli, J. M. Isac, P. Travers, M. Guerra, J. P. Santos, and P. Indelicato. "A vacuum double-crystal spectrometer for reference-free X-ray spectroscopy of highly charged ions." Radiation Physics and Chemistry. 98 (2014): 132-149. AbstractWebsite

Radiation Physics and Chemistry, 98 + (2014) 132-149. doi:10.1016/j.radphyschem.2014.01.015

Rahangdale, H. V., M. Guerra, P. K. Das, S. De, J. P. Santos, D. Mitra, and S. Saha. "Determination of subshell-resolved <span class="aps-inline-formula"><math><mi>L</mi></math></span>-shell-ionization cross sections of gold induced by 15–40-keV electrons." Physical Review A. 89 (2014): 052708. AbstractWebsite
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Amaro, P., C. I. Szabo, S. Schlesser, A. Gumberidze, E. G. Kessler, A. Henins, E. O. Le Bigot, M. Trassinelli, J. M. Isac, P. Travers, M. Guerra, J. P. Santos, and P. Indelicato. "A vacuum double-crystal spectrometer for reference-free X-ray spectroscopy of highly charged ions." Radiation Physics and Chemistry. 98 (2014): 132-149. AbstractWebsite

Radiation Physics and Chemistry, 98 + (2014) 132-149. doi:10.1016/j.radphyschem.2014.01.015

Altstadt, S. G., et al. "{$^{13,14}$B(n, $\gamma$) via Coulomb Dissociation for Nucleosynthesis towards the r-Process}." Nuclear Data Sheets. 120 (2014): 197-200. AbstractWebsite
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Cunha, Jácome, João Paulo Fernandes, Jorge Mendes, Rui Pereira, and João Saraiva. "Design and Implementation of Queries for Model-Driven Spreadsheets." Central European Functional Programming School - 5th Summer School, CEFP 2013, Revised Selected Papers. Eds. Viktória Zsók, and et al. Lecture Notes in Computer Science. Heidelberg: Springer, 2014. Abstractdsl13_query.pdf

This paper presents a domain-specific querying language for model-driven spreadsheets. We briefly show the design of the language and present in detail its implementation, from the denormalization of data and translation of our user-friendly query language to a more efficient query, to the execution of the query using Google. To validate our work, we executed an empirical study, comparing QuerySheet with an alternative spreadsheet querying tool, which produced positive results.

Cunha, Jácome, João Paulo Fernandes, and João Saraiva. "Spreadsheet Engineering." Central European Functional Programming School - 5th Summer School, CEFP 2013, Revised Selected Papers. Eds. Viktória Zsók, and et al. Lecture Notes in Computer Science. Springer, Heidelberg 2014. Abstractdsl13_notes.pdf

These tutorial notes present a methodology for spreadsheet engineering. First, we present data mining and database techniques to reason about spreadsheet data. These techniques are used to compute relationships between spreadsheet elements (cells/columns/rows). These relations are then used to infer a model defining the business logic of the spreadsheet. Such a model of a spreadsheet data is a visual domain specific language that we embed in a well-known spreadsheet system. The embedded model is the building block to define techniques for model-driven spreadsheet development, where advanced techniques are used to guarantee the model-instance synchronization. In this model-driven environment, any user data update as to follow the the model-instance conformance relation, thus, guiding spreadsheet users to introduce correct data. Data refinement techniques are used to synchronize models and instances after users update/evolve the model. These notes briefly describe our model-driven spreadsheet environment, the MDSheet environment, that implements the presented methodology. To evaluate both proposed techniques and the MDSheet tool, we have conducted, in laboratory sessions, an empirical study with the summer school participants. The results of this study are presented in these notes.

Safari, L., P. Amaro, J. P. Santos, and F. Fratini. "Angular and polarization analysis for two-photon decay of <span class="aps-inline-formula"><math xmlns="http://www.w3.org/1998/Math/MathML"><mrow><mn>2</mn><mi>s</mi></mrow></math>&." Physical Review A. 90 (2014): 014502. AbstractWebsite

The amplitude of two-photon transitions between hyperfine states in hydrogenlike ions is derived based on the relativistic Dirac equation and second-order perturbation theory. We study angular and linear polarization properties of the photon pair emitted in the decay of $2s$ states, where spin-flip and non-spin-flip transitions are highlighted. We pay particular attention to hydrogenlike uranium, since it is an ideal candidate for investigating relativistic and high-multipole effects, such as spin-flip transitions. Two types of emission patterns are identified: (i) non-spin-flip transitions are found to be characterized by an angular distribution of the type $W($\theta${})$\sim${}1+{cos}^{2}$\theta${}$ while the polarizations of the emitted photons are parallel; and (ii) spin-flip transitions have somewhat smaller decay rates and are found to be characterized by an angular distribution of the type $W($\theta${})$\sim${}1$-${}1/3{cos}^{2}$\theta${}$ while the polarizations of the emitted photons are orthogonal, where $$\theta${}$ is the angle between photons directions. Deviations due to nondipole and relativistic contributions are evaluated for both types of transitions. This work is the first step toward exploring the effect of the nucleus over the angular and polarization properties of the photon pairs emitted by two-photon transitions.

Safari, L., P. Amaro, J. P. Santos, and F. Fratini. "Angular and polarization analysis for two-photon decay of <span class="aps-inline-formula"><math xmlns="http://www.w3.org/1998/Math/MathML"><mrow><mn>2</mn><mi>s</mi></mrow></math>&." Physical Review A. 90 (2014): 014502. AbstractWebsite

The amplitude of two-photon transitions between hyperfine states in hydrogenlike ions is derived based on the relativistic Dirac equation and second-order perturbation theory. We study angular and linear polarization properties of the photon pair emitted in the decay of $2s$ states, where spin-flip and non-spin-flip transitions are highlighted. We pay particular attention to hydrogenlike uranium, since it is an ideal candidate for investigating relativistic and high-multipole effects, such as spin-flip transitions. Two types of emission patterns are identified: (i) non-spin-flip transitions are found to be characterized by an angular distribution of the type $W($\theta${})$\sim${}1+{cos}^{2}$\theta${}$ while the polarizations of the emitted photons are parallel; and (ii) spin-flip transitions have somewhat smaller decay rates and are found to be characterized by an angular distribution of the type $W($\theta${})$\sim${}1$-${}1/3{cos}^{2}$\theta${}$ while the polarizations of the emitted photons are orthogonal, where $$\theta${}$ is the angle between photons directions. Deviations due to nondipole and relativistic contributions are evaluated for both types of transitions. This work is the first step toward exploring the effect of the nucleus over the angular and polarization properties of the photon pairs emitted by two-photon transitions.

Fratini, F., L. Safari, A. G. Hayrapetyan, K. Jankala, P. Amaro, and J. P. Santos. "Quantized form factor shift in the presence of free electron laser radiation." EPL (Europhysics Letters). 107 (2014): 13002. AbstractWebsite

In electron scattering, the target form factors contribute significantly to the diffraction pattern and carry information on the target electromagnetic charge distribution. Here we show that the presence of electromagnetic radiation, as intense as currently available in free electron lasers, shifts the dependence of the target form factors by a quantity that depends on the number of photons absorbed or emitted by the electron as well as on the parameters of the electromagnetic radiation. As example, we show the impact of intense ultraviolet and soft X-ray radiation on elastic electron scattering by the Ne-like argon ion and by the xenon atom. We find that the shift brought by the radiation to the form factor is of the order of some percent. Our results may open up a new avenue to explore matter with the assistance of laser.

Fratini, F., L. Safari, A. G. Hayrapetyan, K. Jankala, P. Amaro, and J. P. Santos. "Quantized form factor shift in the presence of free electron laser radiation." EPL (Europhysics Letters). 107 (2014): 13002. AbstractWebsite

In electron scattering, the target form factors contribute significantly to the diffraction pattern and carry information on the target electromagnetic charge distribution. Here we show that the presence of electromagnetic radiation, as intense as currently available in free electron lasers, shifts the dependence of the target form factors by a quantity that depends on the number of photons absorbed or emitted by the electron as well as on the parameters of the electromagnetic radiation. As example, we show the impact of intense ultraviolet and soft X-ray radiation on elastic electron scattering by the Ne-like argon ion and by the xenon atom. We find that the shift brought by the radiation to the form factor is of the order of some percent. Our results may open up a new avenue to explore matter with the assistance of laser.

Saponaro, A. C., M. Matzapetakis, B. Santoro, S. R. Pauleta, and A. Moroni. "The Auxiliary Subunit TRIP8B Inhibits the Binding of CAMP to HCN2 Channels Through an Allosteric Mechanism." Biophysical Journal. Vol. 106. Biophys J, 106. 2014. 758a. Abstract
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Johnston, E. M., S. Dell'acqua, S. Ramos, S. R. Pauleta, I. Moura, and E. I. Solomon. "Determination of the active form of the tetranuclear copper sulfur cluster in nitrous oxide reductase." J Am Chem Soc. 136 (2014): 614-7. AbstractWebsite

N2OR has been found to have two structural forms of its tetranuclear copper active site, the 4CuS Cu(Z)* form and the 4Cu2S Cu(Z) form. EPR, resonance Raman, and MCD spectroscopies have been used to determine the redox states of these sites under different reductant conditions, showing that the Cu(Z)* site accesses the 1-hole and fully reduced redox states, while the Cu(Z) site accesses the 2-hole and 1-hole redox states. Single-turnover reactions of N2OR for Cu(Z) and Cu(Z)* poised in these redox states and steady-state turnover assays with different proportions of Cu(Z) and Cu(Z)* show that only fully reduced Cu(Z)* is catalytically competent in rapid turnover with N2O.

JP, Borges, Canejo JP, Fernandes SN, Brogueira P, and GODINHO MH. "Cellulose‐Based Liquid Crystalline Composite Systems." Nanocellulose Polymer Nanocomposites: Fundamentals and Applications. Ed. Vijay Kumar Thakur. Scrivener Publishing - Wiley. Scrivener Publishing - Wiley, 2014. 215-235. Abstract
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Azevedo, S. G., S., Carvalho, H., H., Cruz-Machado, and V. "A cross case analysis of RFID deployment Fast Fashion Supply Chain." Advances in Intelligent Systems and Computing. 2014. 45-57. Abstract
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Sá, Sofia, Manoj B. Gawande, Alexandre Velhinho, João Pedro Veiga, Nenad Bundaleski, João Trigueiro, Alexander Tolstogouzov, Orlando M. N. D. Teodoro, Radek Zboril, Rajender S. Varma, and Paula S. Branco. "Magnetically recyclable magnetite-palladium (Nanocat-Fe-Pd) nanocatalyst for the Buchwald-Hartwig reaction." 16 (2014): 3494-3500. Abstract

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