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2012
L.C., R, M.M. S, Smith M.J., Gonçalves A., Fortunato E..  2012.  Poly (epsilon-caprolactone)/siloxane biohybrids with application in "smart windows". Synthetic Metals. 161:23-24.
Gomes, PJ, Coelho M, Dionísio M, Ribeiro PA, Raposo M.  2012.  Probing radiation damage by alternated current conductivity as a method to characterize electron hopping conduction in DNA molecules. Applied Physics Letters. 101(12):123702-1-4.Website
Gouveia, JP, Fortes P, Seixas J.  2012.  Projections of energy services demand for residential buildings: Insights from a bottom-up methodology. Energy. 47:430–442., Number 1: Elsevier Ltd AbstractWebsite

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Silva, MA, Lucas TG, Salgueiro CA, Gomes CM.  2012.  Protein Folding Modulates the Swapped Dimerization Mechanism of Methyl-Accepting Chemotaxis Heme Sensors. PLoS ONE. 7(9):e46328. AbstractWebsite

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.

Kuckova, S, et al.  2012.  Protein identification and localization using mass spectrometry and staining tests in cross-sections of polychrome samples. Journal of Cultural Heritage. AbstractWebsite

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).

Velasco, LF, Fonseca IM, Parra JB, Lima JC, Ania CO.  2012.  Photochemical behaviour of activated carbons under UV irradiation. Carbon. 50:249-258., Number 1 Abstract
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Gavara, R, Leydet Y, Petrov V, Pina F.  2012.  Photochemistry of 2-(4-hydroxystyryl)-1-naphthopyrylium. Photochemical & Photobiological Sciences. 11:1691-1699., Number 11 AbstractWebsite
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Pina, F, Petrov V, Laia CAT.  2012.  Photochromism of flavylium systems. An overview of a versatile multistate system. Dyes and Pigments. 92:877-889., Number 2 AbstractWebsite
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Quintal, SM, Viegas A, Erhardt S, Cabrita EJ, Farrell NP.  2012.  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. Biochemistry. 51:1752-1761. AbstractWebsite

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.

Pimenta, J, Dias FMV, Marques CC, Baptista MC, Vasques MI, Horta AEM, Barbas JP, Soares R, Mesquita P, Cabrita E, Fontes C, Prates JA, Pereira RM.  2012.  The Prion-like Protein Doppel Enhances Ovine Spermatozoa Fertilizing Ability. Reproduction in Domestic Animals. 47:196-202. Abstract

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.

Pereira, P, Coito F, Fino H.  2012.  PSO-Based Design of RF Integrated Inductor. Technological Innovation for Value Creation. :475–482.: Springer Boston Abstract

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2011
Pessanha, V, Dias RJ, Lourenço JM, Farchi E, Sousa D.  2011.  Practical verification of high-level dataraces in transactional memory programs, July. Proceedings of 9th the Workshop on Parallel and Distributed Systems: Testing, Analysis, and Debugging. :26–34., New York, NY, USA: ACM Abstract2011-padtad.pdf

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.

Silva, {LB}, Veigas B, c}alo Doria G{\c, Costa P, Inácio J, Martins R, Fortunato E, Baptista {PV}.  2011.  Portable optoelectronic biosensing platform for identification of mycobacteria from the Mycobacterium tuberculosis complex, jan. Biosensors & Bioelectronics. 26:2012–2017., Number 5: Elsevier Abstract

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.

Vilas-Boas, V, Silva R, Vieira C, Martins I, Ferreira L, Branco P, Remiao F.  2011.  P-glycoprotein activity assessment in rat brain endothelial cells-A search for new rifampicin-derived p-glycoprotein inducers, AUG 28. TOXICOLOGY LETTERS. 205:S94-S95., Number 1: European Soc Toxicol Abstract
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Barbosa, DJ, Capela JP, Oliveira JMA, Ferreira L, Branco P, Fernandes E, Bastos ML, Carvalho F.  2011.  Pro-oxidant effects of ``ecstasy{''} and its metabolites in mouse brain synaptosomes, AUG 28. TOXICOLOGY LETTERS. 205:S113., Number 1: European Soc Toxicol Abstract
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Avo, J, Parola AJ, Lima JC, Pina F, Cunha-Silva L.  2011.  Phase transition thermochromism based on C-H acidity of 4-alkylflavylium compounds in Pluronic F-127, 2011. Journal of Materials Chemistry. 21:16628-16637. AbstractWebsite

In moderately acidic water/ethanol solutions, 7-(naphthalen-2-ylmethyl)-5,6-dihydrobenzo[c]xanthen12-ium perchlorate shows C-H proton acidity giving rise to an ethylenic base species, instead of the hydration products of the typical flavylium network of chemical reactions, hemiketal, cis-chalcone and trans-chalcone. The kinetics of this acid-base process is much slower, k(obs)(s(-1)) = 3.5 x 10(-3) + 0.16[H(+)], than those commonly observed for O-H deprotonation. In the presence of the triblock copolymer Pluronic F-127, the ethylenic base is dramatically stabilized shifting the pK(a) from 1.35 (in ethanol : water (1 : 1) to -0.35. Taking profit from the well-described temperature dependence of this polymer, a phase transition thermochromic system was achieved. The system was cycled between 5 and 35 degrees C with negligible changes in absorbance after 20 cycles.

Leydet, Y, Gavara R, Cunha-Silva L, Parola AJ, Pina F.  2011.  Phase-Dependent Photochromism of a Lactone-Stabilized Chromene from a Flavylium Reaction Network, 2011. Chemistry-a European Journal. 17:3663-3671. AbstractWebsite

New trans-2-hydroxychalcones bearing a carboxylate group at position 2' (Ct(-)) were synthesized (compounds 2 and 3). These compounds lead to a network of chemical reactions depending on pH value, light, and solvent. In water, when the pH value is lowered, the ionized trans-chalcone is protonated and the flavylium cation AH(+) is formed at very acidic pH values through hemiketal B and cis-chalcone Cc, with global acidity constants of pK'(a) <= -1 and approximate to 0.1, respectively, for 2 and 3. The electron-acceptor character of the carboxylic substituent not only increases the observed acidity of the flavylium cation, but also decreases the rate of the ring-opening/closing from a subsecond timescale to hours relative to model compound 1 (without carboxylate). The photochemistry of the network was studied in detail by means of continuous irradiation, monitored by UV/Vis absorption and H-1 and C-13 NMR spectroscopic analysis. Although compound 3 is only slightly photoactive, compound 2 (Ct(-)) reacts in aqueous solutions (lambda(irr) = 313 nm) to form B- and Cc(-), with a global quantum yield of 0.15, and fully reverts back to Ct(-) with a rate constant of k = 6.7 x 10(-5) s(-1). The flavylium cation is no longer formed in methanol, and irradiation of Ct(-) leads to the formation of B- and the new lactone-trapped chromene species La. The formation of La takes place through a sequence of three photochemical steps: photoisomerization of Ct(-), photo-ring-closing reaction of Cc , and photolactonization of B-. Only the cis/trans isomerization and ring-closing reactions are thermally reversible on a timescale of seconds and hours, respectively. A photochromic system was achieved in rigid matrices of methanol (at 77 K) and 1-dodecanol (5 degrees C) by irradiating lactone La to give a red ortho-quinone allide through a photo-ring-opening reaction; the color disappears with a rate constant of k = 1.25 x 10(-2) s(-1) in 1-dodecanol at 5 degrees C.

Cavadas, M, González-Fernández Á, Franco R.  2011.  Pathogen mimetic stealth nanocarriers for drug delivery: a future possibility. Nanomedicine: Nanotechnology, Biology, and Medicine. 7(6):730-743.
Merino, EG, Rodrigues C, Viciosa TM, Melo C, Sotomayor J, Dionísio M, Correia NT.  2011.  Phase Transformations Undergone by Triton X-100 Probed by Differential Scanning Calorimetry and Dielectric Relaxation Spectroscopy. Physical Chemistry B. 12336(1):12336–12347. AbstractWebsite

The phase transformations of the surfactant Triton X-100 were investigated by differential scanning calorimetry (DSC), polarized optical microscopy (POM), and dielectric relaxation spectroscopy (DRS). In particular, crystallization was induced at different cooling rates comprised between 13 and 0.5 K min–1. Vitrification was detected by both DSC and DRS techniques with a glass transition temperature of 212 K (measured on heating by DSC) allowing classifying Triton X-100 as a glass former. A fully amorphous material was obtained by cooling at a rate ≥10 K min–1, while crystallization was observed for lower cooling rates. The temperature of the onset of melt-crystallization was found to be dependent on the cooling scan rate, being higher the lower was the scan rate. In subsequent heating scans, the material undergoes cold-crystallization except if cooled previously at a rate ≤1 K min–1. None of the different thermal histories led to a 100% crystalline material because always the jump typical of the glass transformation in both heat flux (DSC) and real permittivity (DRS) is observed. It was also observed that the extent/morphology of the crystalline phase depends on the degree of undercooling, with higher spherulites developing for lower undercooling degree (24 K ≤ Tm – Tcr ≤ 44 K) in melt-crystallization and a grain-like morphology emerging for Tm – Tcr ≈ 57 K either in melt- or cold-crystallization. The isothermal cold- and melt-crystallizations were monitored near above the calorimetric glass transition temperature by POM (221 K) and real-time DRS (Tcr = 219, 220, and 221 K) to evaluate the phase transformation from an amorphous to a semicrystalline material. By DRS, the α-relaxation associated with the dynamic glass transition was followed, with the observation that it depletes upon both type of crystallizations with no significant changes either in shape or in location. Kinetic parameters were obtained from the time evolution of the normalized permittivity according to a modified Avrami model taking in account the induction time. The reason the isothermal crystallization occurs to a great extent in the vicinity of the glass transition was rationalized as the simultaneous effect of (i) a high dynamic fragile behavior and (ii) the occurrence of catastrophic nucleation/crystal growth probably enabled by a preordering tendency of the surfactant molecules. This is compatible with the estimated low Avrami exponent (1.12 ≤ n ≤ 1.6), suggesting that relative short length scale motions govern the crystal growth in Triton X-100 coherent with the observation of a grainy crystallization by POM.

Gonçalves, N.  2011.  Planeamento Sustentável – Qual o modelo? Faculdade de Ciências e Tecnologia. (Amado, Miguel, Ed.)., Lisbon
Borlido, L, Azevedo AM, Roque ACA, Aires-Barros MR.  2011.  Potential of boronic acid functionalized magnetic particles in the adsorption of human antibodies under mammalian cell culture conditions. Journal of Chromatography A. 1218(43):7821-7827. AbstractWebsite

In this work, we systematically evaluated the potential of using boronic acid functionalized magnetic particles in the capturing of human immunoglobulin G under typical mammalian cell culture conditions. For comparison, Protein A coated magnetic particles were also used. The binding pH was found to significantly influence the adsorption isotherms of boronic acid particles with the higher capacities (0.216 g IgG/g support) being observed at pH 7.4. Comparatively, this value was 0.109 g IgG/g support, for Protein A particles under the same conditions. Both particles revealed very fast adsorption kinetics with more than 70% of the maximum binding capacity being achieved in a few seconds. The effect of glucose and lactate, which are known to interact with boronic acid, was evaluated. For glucose, the binding capacity was significantly influenced by the pH and decreased as pH increased. At pH 9.5, a 70% lower binding capacity was observed for glucose concentrations as low as 0.5 g/l. The effect of lactate was less pronounced and almost pH independent reaching at most 20% decrease in binding capacity. Nevertheless, the effect of both molecules was always lower at pH 7.4. The optimization of the elution conditions enabled complete recovery of bound IgG from boronic acid particles using 50mM Tris-HCl, 200 mM sorbitol, 200 mM NaCl at pH 8.5.

Pessanha, V.  2011.  Practical Verification of Anomalies in Transactional Memory Programs. FCT - Universidade Nova de Lisboa. (João M. Lourenço, Ed.).: Universidade Nova de Lisboa Abstract2011-vasco_pessanha.pdf

Transactional Memory (TM) is an approach to concurrency control in general pur- pose programming languages that inherits the concept of transaction from the database setting. Unlike other language constructs such as locks, TM has an optimistic approach to concurrency control by allowing more than one thread to access simultaneously the same critical section. A transaction always executes as if it is alone in the system, and in the end its effects are undone (rolled back) if it conflicts with another concurrent transac- tions. In spite of the potential for increasing scalability and performance, TM is a recent and developing programming model and still has a very limited impact in real-world applications.
Designing and developing concurrent software is difficult and error prone. Concur- rent programs exhibit concurrency anomalies that originate faults and failures. Despite some claims that TM programs are less error prone, they still exhibit concurrency anoma- lies such as high-level dataraces, i.e., wrong delimitations of transactions’ scope, and stale-value errors, that occur when the value of a shared variable jumps from an atomic block to another.
Programs with this kind of anomalies can exhibit unpredictable and wrong behaviour, not fulfilling the goals for which they were conceived.
This work aims the detection of anomalies through static analysis of transactional Java ByteCode programs that execute in strong atomicity. A extensible and flexible framework is proposed, which can be extended with plugins that detect specific types of anomalies. With this framework we expect to prove that high-level dataraces and stale-value errors can be detected with reasonable precision through static analysis.

Keywords: Atomicity Violation, High-Level Datarace, Static Analysis, Concurrency, Software Transactional Memory

Lima, JC, Rodriguez L.  2011.  Phosphine-Gold(I) Compounds as Anticancer Agents: General Description and Mechanisms of Action. Anti-Cancer Agents in Medicinal Chemistry. 11:921-928., Number 10 Abstract
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Gavara, R, Petrov V, Lopez V, Pina F.  2011.  Photochromism of naphthoflavylium. On the role of 4-OH hemiketal in flavylium network. Journal of Photochemistry and Photobiology a-Chemistry. 220:4-10., Number 1 AbstractWebsite
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