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2012
Carlucci, A., M. Raimondo, J. Santos, and AJL Phillips. "Species of Plectosphaerella causing root and collar rot of cucurbits and other hosts in Southern Italy." Persoonia. 28 (2012): 34-48.
Guimarães, D., M. L. Carvalho, V. Geraldes, I. Rocha, and J. P. Santos. "Study of lead accumulation in bones of Wistar rats by X-ray fluorescence analysis: aging effect." Metallomics. 4 (2012): 66. AbstractWebsite

The accumulation of lead in several bones of Wistar rats with time was determined and compared Q3 for the different types of bones. Two groups were studied: a control group (n = 20), not exposed to lead and a contaminated group (n = 30), exposed to lead from birth, first indirectly through
mother’s milk, and then directly through a diet containing lead acetate in drinking water (0.2%). Rats age ranged from 1 to 11 months, with approximately 1 month intervals and each of the collections had 3 contaminated rats and 2 control rats. Iliac, femur, tibia–fibula and skull have been analysed by energy dispersive X-ray fluorescence technique (EDXRF). Samples of formaldehyde used to preserve the bone tissues were also analysed by Electrothermal Atomic Absorption (ETAAS), showing that there was no significant loss of lead from the tissue to the preservative. The bones mean lead concentration of exposed rats range from 100 to 300 mg g 1 while control rats never exceeded 10 mg g 1. Mean bone lead concentrations were compared and
the concentrations were higher in iliac, femur and tibia–fibula and after that skull. However, of all the concentrations in the different collections, only those in the skull were statistically Q4 significantly different (p o 0.05) from the other types of bones. Analysis of a radar chart also allowed us to say that these differences tend to diminish with age. The Spearman correlation test applied to mean lead concentrations showed strong and very strong positive correlations between
all different types of bones. This test also showed that mean lead concentrations in bones are negatively correlated with the age of the animals. This correlation is strong in iliac and femur and very strong in tibia–fibula and skull. It was also shown that the decrease of lead accumulation with age is made by three plateaus of accumulation,

Cunha, Jácome, João P. Fernandes, Hugo Ribeiro, and João Saraiva. "Towards a Catalog of Spreadsheet Smells." Proceedings of the 12th International Conference on Computational Science and Its Applications - Volume Part IV. ICCSA'12. Berlin, Heidelberg: Springer-Verlag, 2012. 202-216. Abstracticcsa-sq12.pdf

Spreadsheets are considered to be the most widely used programming language in the world, and reports have shown that 90% of real-world spreadsheets contain errors. In this work, we try to identify spreadsheet smells, a concept adapted from software, which consists of a surface indication that usually corresponds to a deeper problem. Our smells have been integrated in a tool, and were computed for a large spreadsheet repository. Finally, the analysis of the results we obtained led to the refinement of our initial catalog.

Carvalho, T., V. Augusto, A. R. Brás, N. M. T. Lourenço, CAM Afonso, S. Barreiros, N. T. Correia, P. Vidinha, E. J. Cabrita, M. Dionísio, and B. Roling. "Understanding the Ion Jelly Conductivity Mechanism." Journal of Physical Chemistry B. 116 (2012): 2664-2676. Abstract

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.

Brás, C. P., M. Fukushima, J. J. Júdice, and S. S. Rosa. "Variational Inequality Formulation of the Asymmetric Eigenvalue Complementarity Problem and Its Solution by Means of Gap Functions." Pacific Journal of Optimization. 8.(2) (2012): 197-215. AbstractWebsite

In this paper, the solution of the asymmetric eigenvalue complementarity problem (EiCP) is investigated by means of a variational inequality formulation. This problem is then solved by finding a stationary point of the gap function and the regularized gap function. A nonlinear programming formulation of the EiCP results from the gap function. A hybrid algorithm combining a projection technique and a modified Josephy-Newton method is proposed to solve the EiCP by finding a stationary point of the regularized gap function. Numerical results show that the proposed method can in general solve EiCPs efficiently.

Romain, Charles, Vitor Rosa, Christophe Fliedel, Frederic Bier, Frederic Hild, Richard Welter, Samuel Dagorne, and Teresa Aviles. "{Highly active zinc alkyl cations for the controlled and immortal ring-opening polymerization of epsilon-caprolactone}." {DALTON TRANSACTIONS}. {41} (2012): {3377-3379}. Abstract

{Zinc alkyl cations supported by N,N-BIAN-type bidentate ligands were found to be highly active in the immortal ROP of epsilon-caprolactone to yield narrowly disperse and chain length-controlled poly(epsilon-caprolactone), whether in solution or bulk polymerization conditions.}

R. Santos-Tavares, N. Paulino, Goes J. “Time-Domain Optimization of Amplifiers Based on Distributed Genetic Algorithms”. Lambert Academic Publishing (ISBN 978-3-8473-2925-1), 2012.
Silva, Teresa Pereira, Daniel PS Oliveira, João Pedro Veiga, Diogo Rosa, and Ondina M. Figueiredo. "An approach to the binding state of indium in natural chalcogenides through the analysis of In L3 edge XANES spectra." 1º Encontro Nacional dos Utilizadores da Radiação de Sincrotrão= 1st Meeting of Synchrotron Radiation Users from Portugal. 2012. Abstract
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Graham, Lisa M., Vandana Gupta, Georgia Schafer, Delyth M. Reid, Matti Kimberg, Kevin M. Dennehy, William G. Hornsell, Reto Guler, Maria A. Campanero-Rhodes, Angelina S. Palma, Ten Feizi, Stella K. Kim, Peter Sobieszczuk, Janet A. Willment, and Gordon D. Brown. "The C-type Lectin Receptor CLECSF8 (CLEC4D) Is Expressed by Myeloid Cells and Triggers Cellular Activation through Syk Kinase." Journal of Biological Chemistry. 287 (2012): 25964-25974. Abstract
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Cardoso, Alberto, M. T. Restivo, P. Cioga, M. Delgado, J. N. Monsanto, J. Bicker, E. Nunes, and P. Gil. "Demonstration of Online Educational Modules with Online Experiments." REV2012 - Remote Engineering & Virtual Instrumentation. n/a 2012. Abstract
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Kowacz, Magdalena, Abhik Mukhopadhyay, Ana Luisa Carvalho, Jose M. S. S. Esperanca, Maria J. Romao, and Luis Paulo N. Rebelo. "Hofmeister effects of ionic liquids in protein crystallization: Direct and water-mediated interactions." Crystengcomm. 14 (2012): 4912-4921. AbstractWebsite
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Guimarães, D., M. L. Carvalho, M. Becker, A. von Bohlen, V. Geraldes, I. Rocha, and J. P. Santos. "Lead concentration in feces and urine of exposed rats by x-ray fluorescence and electrothermal atomic absorption spectrometry." X-Ray Spectrometry. 41 (2012): 80. AbstractWebsite

Measurements made in feces and urine of Wistar rats exposed to lead acetate (n = 20) in drinking water since the fetal period were compared with those obtained from a control group (n = 20) in order to assess the age influence on Pb excretion. The measurements were made in different collections of rats aging between 1 and 11 months. To determine the Pb content of the samples, total reflection X-ray fluorescence (TXRF) and electrothermal atomic absorption spectrometry (ETAAS) were used for the urine samples and energy dispersive X-ray fluorescence (EDXRF) was used for the feces.The results show high concentrations of Pb being eliminated from the organism by urine and feces in contaminated rats. Values vary from (600`140)mgl1 to (5 460`115)mgl1 in urine and from (4 500`300)mgg1 to (11 400`3 300)mgg1 in dry feces. The control rats show, in general, low lead concentrations or below detection limits. The fecal/urinary ratio was studied. It was shown to be about three to four orders of magnitude and positively correlated with time. It was verified in feces and urine that excretion decreases with the animal age and that this decrease is made by different levels of excretion. The excretions of Pb in urine and in feces are positively correlated.A good agreement was found between the results obtained with TXRF and ETAAS for urine samples. This work also stresses the suitability of these techniques in the study of Pb intoxication.

Ribeiro, AR, I. Martinho, JB Tillak, I. Bernacka-Wojcik, D. Barata, PAS Jorge, H. Águas, and AG Oliva. "Microfluidic chip for spectroscopic and refractometric analysis." OFS2012 22nd International Conference on Optical Fiber Sensor. International Society for Optics and Photonics, 2012. 84211Y. Abstract
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Pereira, Luis, Pedro Barquinha, Goncalo Goncalves, Elvira Fortunato, and Rodrigo Martins. "Multicomponent dielectrics for oxide TFT." Oxide-Based Materials and Devices Iii. Eds. F. H. Teherani, D. C. Look, and D. J. Rogers. Vol. 8263. Proceedings of SPIE, 8263. 2012. Abstract
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Santos, M. F. A., J. D. Seixas, A. C. Coelho, A. Mukhopadhyay, P. M. Reis, MJ Romão, C. C. Romão, and T. Santos-Silva. "New insights into the chemistry of fac-[Ru(CO)3]2 + fragments in biologically relevant conditions: The CO releasing activity of [Ru(CO)3Cl2(1,3-thiazole)], and the X-ray crystal structure of its adduct with lysozyme." Journal of Inorganic Biochemistry. 117 (2012): 285-291. Abstract
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Bras, Joana L. A., Victor D. Alves, Ana Luisa Carvalho, Shabir Najmudin, Jose A. M. Prates, Luis M. A. Ferreira, David N. Bolam, Maria Joao Romao, Harry J. Gilbert, and Carlos M. G. A. Fontes. "Novel Clostridium thermocellum Type I Cohesin-Dockerin Complexes Reveal a Single Binding Mode." The Journal of biological chemistry. 287 (2012): 44394-405.Website
Rosa, R., M. S. Pimentel, J. Boavida-Portugal, T. Teixeira, K. Trübenbach, and M. Diniz. "Ocean warming enhances malformations, premature hatching, metabolic suppression and oxidative stress in the early life stages of a keystone squid." PLoS ONE. 7 (2012). AbstractWebsite
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Martins, R., V. Figueiredo, R. Barros, P. Barquinha, G. GONCALVES, L. Pereira, I. Ferreira, and E. Fortunato. "P-type oxide based thin film transistors produced at low temperatures." Oxide-Based Materials and Devices Iii. Eds. F. H. Teherani, D. C. Look, and D. J. Rogers. Vol. 8263. Proceedings of SPIE, 8263. 2012. Abstract
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Guimarães, D., M. L. Carvalho, V. Geraldes, I. Rocha, and J. P. Santos. "Study of lead accumulation in bones of Wistar rats by X-ray fluorescence analysis: aging effect." Metallomics. 4 (2012): 66. AbstractWebsite

The accumulation of lead in several bones of Wistar rats with time was determined and compared Q3 for the different types of bones. Two groups were studied: a control group (n = 20), not exposed to lead and a contaminated group (n = 30), exposed to lead from birth, first indirectly throughmother’s milk, and then directly through a diet containing lead acetate in drinking water (0.2%). Rats age ranged from 1 to 11 months, with approximately 1 month intervals and each of the collections had 3 contaminated rats and 2 control rats. Iliac, femur, tibia–fibula and skull have been analysed by energy dispersive X-ray fluorescence technique (EDXRF). Samples of formaldehyde used to preserve the bone tissues were also analysed by Electrothermal Atomic Absorption (ETAAS), showing that there was no significant loss of lead from the tissue to the preservative. The bones mean lead concentration of exposed rats range from 100 to 300 mg g 1 while control rats never exceeded 10 mg g 1. Mean bone lead concentrations were compared andthe concentrations were higher in iliac, femur and tibia–fibula and after that skull. However, of all the concentrations in the different collections, only those in the skull were statistically Q4 significantly different (p o 0.05) from the other types of bones. Analysis of a radar chart also allowed us to say that these differences tend to diminish with age. The Spearman correlation test applied to mean lead concentrations showed strong and very strong positive correlations betweenall different types of bones. This test also showed that mean lead concentrations in bones are negatively correlated with the age of the animals. This correlation is strong in iliac and femur and very strong in tibia–fibula and skull. It was also shown that the decrease of lead accumulation with age is made by three plateaus of accumulation,

Carvalho, T., V. Augusto, A. R. Bras, N. M. T. Lourenco, CAM Afonso, S. Barreiros, N. T. Correia, P. Vidinha, E. J. Cabrita, C. J. Dias, M. Dionisio, and B. Roling. "Understanding the Ion Jelly Conductivity Mechanism." Journal of Physical Chemistry B. 116 (2012): 2664-2676. Abstract
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Inês, Cunha, Marques João Paulo, Gil Luís, Neagu E. R., Dias C. J., Marat-Mendes J. N., and Lança M. C. "Water Content Control to Improve Space Charge Storage in a Cork Derivative." Materiais2011. Materials Science Forum. 2012. Abstract
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Gawande, Manoj B., Anuj Rathi, Isabel D. Nogueira, C. a. a. Ghumman, N. Bundaleski, O. M. N. D. Teodoro, and Paula S. Branco. "{A Recyclable Ferrite-Co Magnetic Nanocatalyst for the Oxidation of Alcohols to Carbonyl Compounds}." ChemPlusChem. 77 (2012): 865-871. AbstractWebsite

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Correia, C., A. L. Pereira, A. R. C. Duarte, A. M. Frias, A. J. Pedro, J. T. Oliveira, R. A. Sousa, and R. L. Reis. "{Dynamic culturing of cartilage tissue: The significance of hydrostatic pressure}." Tissue Engineering - Part A. 18 (2012). Abstract

Human articular cartilage functions under a wide range of mechanical loads in synovial joints, where hydrostatic pressure (HP) is the prevalent actuating force. We hypothesized that the formation of engineered cartilage can be augmented by applying such physiologic stimuli to chondrogenic cells or stem cells, cultured in hydrogels, using custom-designed HP bioreactors. To test this hypothesis, we investigated the effects of distinct HP regimens on cartilage formation in vitro by either human nasal chondrocytes (HNCs) or human adipose stem cells (hASCs) encapsulated in gellan gum (GG) hydrogels. To this end, we varied the frequency of low HP, by applying pulsatile hydrostatic pressure or a steady hydrostatic pressure load to HNC-GG constructs over a period of 3 weeks, and evaluated their effects on cartilage tissue-engineering outcomes. HNCs (10×10 6 cells/mL) were encapsulated in GG hydrogels (1.5{%}) and cultured in a chondrogenic medium under three regimens for 3 weeks: (1) 0.4 MPa Pulsatile HP; (2) 0.4 MPa Steady HP; and (3) Static. Subsequently, we applied the pulsatile regimen to hASC-GG constructs and varied the amplitude of loading, by generating both low (0.4 MPa) and physiologic (5 MPa) HP levels. hASCs (10×10 6 cells/mL) were encapsulated in GG hydrogels (1.5{%}) and cultured in a chondrogenic medium under three regimens for 4 weeks: (1) 0.4 MPa Pulsatile HP; (2) 5 MPa Pulsatile HP; and (3) Static. In the HNC study, the best tissue development was achieved by the pulsatile HP regimen, whereas in the hASC study, greater chondrogenic differentiation and matrix deposition were obtained for physiologic loading, as evidenced by gene expression of aggrecan, collagen type II, and sox-9; metachromatic staining of cartilage extracellular matrix; and immunolocalization of collagens. We thus propose that both HNCs and hASCs detect and respond to physical forces, thus resembling joint loading, by enhancing cartilage tissue development in a frequency- and amplitude-dependant manner. © Copyright 2012, Mary Ann Liebert, Inc.

Santo, V. E., A. R. C. Duarte, E. G. Popa, M. E. Gomes, J. F. Mano, and R. L. Reis. "{Enhancement of osteogenic differentiation of human adipose derived stem cells by the controlled release of platelet lysates from hybrid scaffolds produced by supercritical fluid foaming}." Journal of Controlled Release. 162 (2012). Abstract

A new generation of scaffolds capable of acting not only as support for cells but also as a source of biological cues to promote tissue regeneration is currently a hot topic of in bone Tissue Engineering (TE) research. The inclusion of growth factor (GF) controlled release functionalities in the scaffolds is a possible strategy to achieve such goal. Platelet Lysate (PL) is an autologous source of GFs, providing several bioactive agents known to act on bone regeneration. In this study, chitosan-chondroitin sulfate nanoparticles loaded with PL were included in a poly(d,l-lactic acid) foam produced by supercritical fluid foaming. The tridimensional (3D) structures were then seeded with human adipose-derived stem cells (hASCs) and cultured in vitro under osteogenic stimulus. The osteogenic differentiation of the seeded hASCs was observed earlier for the PL-loaded constructs, as shown by the earlier alkaline phosphatase peak and calcium detection and stronger Runx2 expression at day 7 of culture, in comparison with the control scaffolds. Osteocalcin gene expression was upregulated in presence of PL during all culture period, which indicates an enhanced osteogenic induction. These results suggest the synergistic effect of PL and hASCs in combinatory TE strategies and support the potential of PL to increase the multifunctionality of the 3D hybrid construct for bone TE applications. © 2012 Elsevier B.V. All rights reserved.

Duarte, A. R. C., S. S. Silva, J. F. Mano, and R. L. Reis. "{Ionic liquids as foaming agents of semi-crystalline natural-based polymers}." Green Chemistry. 14 (2012). Abstract

In this work, the ability to foam semi-crystalline natural-based polymers by supercritical fluid technology is evaluated. The application of this technique to natural polymers has been limited due to the fact that they are normally semi-crystalline polymers, which do not plasticize in the presence of carbon dioxide. This can be overcome by the use of plasticizers, such as glycerol, which is a commonly used plasticizer, or ionic liquids, which have recently been proposed as plasticizing agents for different polymers. Following the green chemistry principles, the main aim is, hereafter, the design and development of new 3D architectures of natural-based polymers, combining ionic liquids (IL) and supercritical fluid (SCF) technology. A polymeric blend of starch, one of the most abundantly occurring natural polymers, and poly-$ε$-caprolactone, a synthetic polymer, which is a biodegradable aliphatic polyester commonly used in an array of biomedical applications (SPCL), was processed by supercritical fluid foaming, at different operating conditions, namely pressure (10.0 up to 20.0 MPa), temperature (35 up to 60 °C) and soaking time (30 min up to 3 h). The ionic liquid tested in this work was 1-butyl-3-methylimidazolium acetate ([bmim]Ac). The interactions between SPCL and [bmim] Ac or glycerol were analysed by Fourier transform infrared spectroscopy, differential scanning calorimetry and by mechanical tests, using both tensile and compressive modes. Morphological analysis, porosity, interconnectivity and pore size distribution of the matrixes were evaluated and the morphology was analyzed by scanning electron microscopy and by micro-computed tomography. To our knowledge the use of ionic liquids as foaming agents is reported here for the first time. The results obtained suggest that this approach can further promote the development of composite polymer-IL materials, particularly for catalysis, chromatography, extraction and separation purposes. © The Royal Society of Chemistry 2012.