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2013
Maiti, Biplab K., Teresa Avilés, Marta S. P. Carepo, Isabel Moura, Sofia R. Pauleta, and José J. G. Moura. "Rearrangement of Mo-Cu-S Cluster Reflects the Structural Instability of Orange Protein Cofactor." Z. Anorg. Allg. Chem.. 639.8-9 (2013): 1361-1364.
M. Figueiredo, Evans G., and J. Goes. "A Reference-Free 7-bit 500 MS/s Pipeline ADC Using Current-Mode Reference Shifting and Built-in Threshold Quantizers." Analog Integrated Circuits and Signal Processing Journal (Springer). vol. 75.no. 1 (2013): pp. 53-65.
Veiga, João, Rui Micaelo, and Adelino Ferreira Rutting models for the use in pavement maintenance management. 9th International Conference on the Bearing Capacity of Roads, Railways and Airfields. Trondheim, Norway, 2013.
Ramos, Luís P., João T. Mexia, and Pedro P. Mota. "Sample partitioning estimation for ergodic diffusions." Communications in Statistics - Simulation and Computation (2013).Website
Tschopp, E., and O. Mateus. "The skull and neck of a new flagellicaudatan sauropod from the Morrison Formation and its implication for the evolution and ontogeny of diplodocid dinosaurs." Journal of Systematic Palaeontology. 11.7 (2013): 853-888. Abstracttschopp__mateus_2013_the_skull_and_neck_of_a_new_flagellicaudatan_sauropod_from_the_morrison.pdfWebsite

A new taxon of diplodocid sauropod, Kaatedocus siberi gen. et sp. nov., is recognized based on well-preserved cervical vertebrae and skull from the Morrison Formation (Kimmeridgian, Late Jurassic) of northern Wyoming, USA. A phylogenetic analysis places it inside Diplodocinae (Sauropoda: Flagellicaudata: Diplodocidae), as a sister taxon to a clade uniting Tornieria africana and the classical diplodocines Barosaurus lentus and Diplodocus. The taxon is diagnosed by a unique combination of plesiomorphic and derived traits, as well as the following unambiguous autapomorphies within Diplodocidae: frontals separated anteriorly by a U-shaped notch; squamosals restricted to the post-orbital region; presence of a postparietal foramen; a narrow, sharp and distinct sagittal nuchal crest; the paired basal tuber with a straight anterior edge in ventral view; anterior end of the prezygapophyses of mid- and posterior cervical vertebrae is often an anterior extension of the pre-epipophysis, which projects considerably anterior to the articular facet; anterodorsal corner of the lateral side of the posterior cervical vertebrae marked by a rugose tuberosity; posterior margin of the prezygapophyseal articular facet of posterior cervical vertebrae bordered posteriorly by conspicuous transverse sulcus; posterior cervical neural spines parallel to converging. The inclusion of K. siberi and several newly described characters into a previously published phylogenetic analysis recovers the new taxon as basal diplodocine, which concurs well with the low stratigraphical position of the holotype specimen. Dinheirosaurus and Supersaurus now represent the sister clade to Apatosaurus and Diplodocinae and therefore the most basal diplodocid genera. The geographical location in the less known northern parts of the Morrison Fm., where K. siberi was found, corroborates previous hypotheses on faunal provinces within the formation. The probable subadult ontogenetic stage of the holotype specimen allows analysis of ontogenetic changes and their influence on diplodocid phylogeny.

Moreira Felismina TC, Sharma Sanjiv, Dutra Rosa AF Noronha João PC Cass Anthony EG Sales Goreti M. F. "Smart Plastic Antibody Material (SPAM) tailored on disposable screen printed electrodes for protein recognition: application to Myoglobin detection." Biosensors and Bioelectronics. 42 (2013): 76.
Viegas, Aldino, João Sardinha, Daniel F. Duarte, Ana Luisa Carvalho, Carlos M. G. A. Fontes, Maria Joao Romao, Anjos L. Macedo, and Eurico J. Cabrita. "Solution Structure, Dynamics and Binding Studies of a Family 11 Carbohydrate-Binding Module from Clostridium thermocellum (CtCBM11)." Biochemical Journal. 451 (2013): 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.

Corvo, Marta C., João Sardinha, Sonia C. Menezes, Sandra Einloft, Marcus Seferin, Jairton Dupont, Teresa Casimiro, and Eurico J. Cabrita. "Solvation of CO2 in [C4mim][BF4] and [C4mim][PF6] ionic liquids revealed by High Pressure NMR." Angewandte Chemie International Edition. 49.52 (2013): 13024-13027.Website
Morgado, Carmen, and Fernanda Barbosa. "A Structured Approach to Problem Solving in CS1/2." International Journal of Advanced Computer Science. Vol. 3.(7) (2013): ISSN: 2251-6379.
Santos, Susana, Débora Azeitona, Nuno Lapa, João Morais, Helena Lopes, and Benilde Mendes Study on the effect of thermal pre-treatments in the thermophilic anaerobic digestion of a potato peel waste. Proceedings of the International Anaerobic Digestion Symposium within the BioGasWorld 2013. Berlin, Germany: German Society for Sustainable Biogas and Bioenergy Utilisation, 2013. Abstractbiogas_world_2013_santos_et_al_2013.pdf

This work aimed to study the effect of different pre-treatments applied to a potato peel residue, in a thermophilic Anaerobic Digestion (AD) process. All samples were subjected to a mechanical pre-treatment through milling to a particle size below 2 mm. The thermal pre-treatments applied consisted of autoclaving the residue at a gauge pressure of 1.2 bar, under a temperature of 122°C, and for 20, 35 and 55 minutes: assays E122.20, E122.35 and E122.55, respectively. The control assay was performed on a ground residue, which was not submitted to any thermal pre-treatment. All pre-treated residues were subjected to an AD process in a CSTR reactor at 49±1°C. The experimental data showed that the highest methane percentages were very similar (about 92% v/v) for all samples submitted to the thermal pre-treatments. For the control assay, the highest percentage of methane was 87.9% (v/v). The highest biogas yields were recorded in the trial E122.35 (646±50 cm3.g-1 CODremoved), against only 250±20 cm3.g-1 CODremoved for the control assay. The highest biogas yields for VSremoved were attained in the assays E122.55 and E122.35, with values of 646±48 cm3.g-1 VSremoved and 634±59 cm3.g-1 VSremoved, respectively. Globally, the yields registered for the assay E122.35 were similar to those determined in the assay E122.55. Due to the lower energy consumption during the pre-treatment performed in the assay E122.35, this was considered to be the most suitable pre-treatment for this type of residue.

Ferrão, Lúcio Emanuel Represas, Seco João Ricardo Viegas Da Costa, Caires Luis Manuel Marques Da Costa, Caleira Borrêga, Gonçalo Filipe Xavier, António Augusto Vieira Melo, and OutSystems-Software em Rede SA SYSTEMS, METHODS, AND APPARATUS FOR MODEL-BASED SECURITY CONTROL., 2013. Abstract

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Brusatte, S. L., R. J. Butler, O. Mateus, J. S. Steyer, and J. H. Whiteside Terrestrial vertebrates from the Late Triassic of Portugal: new records of temnospondyls and archosauriforms from a Pangaean rift sequence. 61st Symposium on Vertebrate Palaeontology and Comparative Anatomy. Edinburgh, 2013. Abstractbrusatte_et_al_2013_triassic_algarve_portugal_temnospondyls_svpca.org_years_2013_edinburgh_abstracts.pdf

The Late Triassic (ca. 237-201.5 million years ago) was a transitional interval in the evolution of terrestrial ecosystems, during which ‘modern’ clades such as archosaurs and mammals were radiating while ‘archaic’ groups such as temnospondyl amphibians and basal synapsids remained abundant. Little is known about the Triassic terrestrial (nonmarine) vertebrates of the Iberian Peninsula. The Algarve Basin of southern Portugal is an extensional rift basin formed during the breakup of Pangaea, which is filled with terrestrial, lacustrine, and marginal marine siliciclastics of the Grés de Silves Formation, interbedded with CAMP basalts that mark the end-Triassic extinction (radioisotopically dated to ~198-201.5 Ma). Since 2009, our field project in the Algarve has discovered numerous vertebrate specimens within the Grés de Silves, including a monodominant bonebed containing hundreds of specimens of metoposaurids, a peculiar group of temnospondyls that filled crocodile-like predatory niches in lacustrine and fluvial environments. These specimens appear to belong to a new species of Metoposaurus, similar to M. diagnosticus and M. krasiejowensis from central Europe but possessing several putative autapomorphies of the braincase and lower jaw. We also discovered a mandible of a phytosaur, the first specimen of these long-snouted, semi-aquatic archosauriforms from the Iberian Peninsula. These discoveries of characteristic Carnian Norian taxa indicate that the fossil-bearing portion of the Grés de Silves is Late Triassic in age, and provide further evidence that metoposaurids and phytosaurs commonly occurred together in low palaeolatitudes during this time.

Ribeiro, V., F. Holwerda, and O. Mateus. "Theropod egg sites from the Lourinhã Formation, Portugal." Journal of Vertebrate Paleontology, Program and Abstracts, 2013 (2013): 198.ribeiro_et_al_2013_theropod_egg_sites_lourinha_svp_meeting_abstracts_213.pdf
Veiga, C., J. McClelland, S. Moinuddin, K. Ricketts, M. Modat, S. Ourselin, D. D'Souza, and G. Royle. "Towards adaptive radiotherapy for head and neck patients: Validation of an in-house deformable registration algorithm." International Conference on the Use of Computers in Radiotherapy (ICCR). Melbourne 2013. Abstract

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Mota, Bruna, Maria Isabel Gomes, and Ana Paula Barbosa-póvoa. "Towards supply chain sustainability: balancing costs with environmental and social impacts." Computer Aided Process Engineering. Eds. Andrzej Kraslawski, and Ilkka Turunen. Elsevier, 2013. 895-900. Abstract2013_motagomesbpovoa_escape23.pdf

This work presents a multi-objective optimization methodology that accounts for economic, environmental and social concerns in a supply chain with reverse flows. Environmental impact assessment is considered through the use of Recipe 2008. A social benefit indicator is developed where the creation of employment in less developed regions is preferred. The multi-objective approach is used to reach a solution of compromise between the three sustainability pillars. The model is applied to a case study developed in collaboration with a Portuguese company, leader in battery production.

Micaelo, R., and A. Ferreira TRACC EXPERT – Ferramenta de apoio à seleção de técnicas adaptadas às mudanças climáticas. 7º Congresso Rodoviário Português. Lisboa, 2013.
Micaelo, Rui, Maria Colás Victoria, and Francisco Ochoa TRACC-EXPERT – Ferramenta de apoio à selecção de técnicas rodoviárias adaptadas às mudanças climáticas. 17.º Congreso Ibero-Latinoamericano del Asfalto. Antigua, Guatemala, 2013.
Schulp, AS, M. J. Polcyn, O. Mateus, and LL Jacobs. "Two rare mosasaurs from the Maastrichtian of Angola and the Netherlands." Netherlands Journal of Geosciences — Geologie en Mijnbouw. 92.1 (2013): 3-10. Abstractschulp_et_al_2013_two_rare_mosasaurs_from_the_maastrichtian_of_angola__njg-92-1-schulp.pdf

We report here the addition of two rare mosasaur taxa to the Maastrichtian marine amniote fauna of Angola. The new specimens include a dentary fragment referable to the large carnivore Prognathodon saturator and an isolated tooth of the small durophage Carinodens belgicus. Both were recovered from Maastrichtian outcrops in southern Angola in 2011. Additionally, a complete posterior mandibular unit of a large mosasaur from the type Maastrichtian of The Netherlands, collected some time prior to 1879 and previously identified as ‘Mosasaurus giganteus’, is described and reassigned here to Prognathodon saturator; historical issues surrounding the taxonomic attribution of this specimen are clarified. The new material extends the known geographic distribution of Prognathodon saturator and Carinodens belgicus.

Moreira, Ana, João Araújo, Awais Rashid, and Miguel Goulão. "Using Aspects to Model Volatile Concerns." Aspect-Oriented Requirements Engineering. Eds. Ana Moreira, Ruzanna Chitchyan, João Araújo, and Awais Rashid. Berlin Heidelberg: Springer, 2013. 183-205. Abstract

A rapidly changing market leads to software systems with highly volatile requirements. In many cases, new demands in software can often be met by extending the functionality of systems already in operation. By modularizing volatile requirements that can be altered at the client’s initiative or according to market demands, we can build a stepping-stone for management of requirements change. The volatility must be managed in a way that reduces the time and costs associated with updating a system to meet the new requirements. In this chapter, we present an approach for handling volatile concerns during early life cycle software modeling. The key insight is that techniques for aspect-oriented software development can be applied to modularize volatility and to weave volatile concerns into the base software artifacts.

Macedo, Patricia, Tiago Cardoso, and Luis M. Camarinha-Matos. "Value systems alignment in product servicing networks." Working Conference on Virtual Enterprises. Springer, Berlin, Heidelberg, 2013. 71-80. Abstract

The notion of service-enhanced product brings new perspectives for value creation and differentiation in manufacturing. The existence of complex and highly customized products, the inclusion of business services that add value to the product typically require the collaboration of multiple stakeholders. It is natural that each stakeholder has its own set of values and preferences and as a result, conflicts among them might emerge due to some values misalignment. Therefore, the Value System Alignment assessment should be included when selecting partner for the formation of long-term collaborative networks for the operation and management of the product life-cycle. This paper presents the implementation of a Value System alignment assessment model, as a component of the cloud-based collaborative environment designed to support a mix of collaborative enterprise networks involved in the solar energy sector.

Mendes, P., Rybarczyk Y., Rybarczyk P., and Vernay D. "A web-based platform for the therapeutic education of patients with physical disabilities." 6th International Conference of Education, Research and Innovation. Seville, Spain 2013. poster.pdf
Araújo, João, Miguel Goulão, Ana Moreira, Inês Simão, Vasco Amaral, and Elisa L. A. Baniassad. "Advanced modularity for building SPL feature models: a model-driven approach." SAC. 2013. 1246-1253. Abstract
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Matias Urbieta, Gustavo Rossi, Silvia E. Gordillo, Armanda Rodrigues, João Araújo, and Ana Moreira. "An Aspect-Oriented Approach for Spatial Concerns in Web Applications." J. UCS. 19 (2013): 110-131. Abstract
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Maurício, R., C. J. Dias, N. Jubilado, and F. Santana. "Biofilm thickness measurement using an ultrasound method in a liquid phase." Environmental Monitoring and Assessment. 185 (2013): 8125-8133. AbstractWebsite
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