Browsing by Issue Date, starting with "2016-05"
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- Computational complexity of solving polynomial differential equations over unbounded domainsPublication . Pouly, Amaury; Graça, DanielIn this paper we investigate the computational complexity of solving ordinary differential equations (ODES) y' = p(y) over unbounded time domains, where p is a vector of polynomials. Contrarily to the bounded (compact) time case, this problem has not been well-studied, apparently due to the "intuition" that it can always be reduced to the bounded case by using rescaling techniques. However, as we show in this paper, rescaling techniques do not seem to provide meaningful insights on the complexity of this problem, since the use of such techniques introduces a dependence on parameters which are hard to compute.We present algorithms which numerically solve these ODES over unbounded time domains. These algorithms have guaranteed accuracy, i.e. given some arbitrarily large time t and error bound 8 as input, they will output a value (y) over tilde which satisfies parallel to y(t)-(y) over tilde parallel to <= epsilon. We analyze the complexity of these algorithms and show that they compute y in time polynomial in several quantities including the time t, the accuracy of the output 8 and the length of the curve y from 0 to t, assuming it exists until time t. We consider both algebraic complexity and bit complexity. (C) 2016 Elsevier B.V. All rights reserved.
- Increased diversification rates follow shifts to bisexuality in liverwortsPublication . Laenen, Benjamin; Machac, Antonin; Gradstein, S. Robbert; Shaw, Blanka; Patino, Jairo; Desamore, Aurelie; Goffinet, B.; Cox, C. J.; Shaw, A. Jonathan; Vanderpoorten, AlainShifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts. We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests. We find that the transitions in sexual systems are significantly biased toward unisexuality, even though bisexuality is coupled with increased diversification. Sexual systems are strongly conserved deep within the liverwort tree but become much more labile toward the present. Bisexuality appears to be a key innovation in liverworts. Its effects on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have the opposite effect when compared to angiosperms, leading to contrasting diversification patterns between the two groups. The high prevalence of unisexuality among liverworts suggests, however, a strong selection for sexual dimorphism.
- The IMBPC HVAC system: a complete MBPC solution for existing HVAC systemsPublication . Ruano, Antonio; Pesteh, Shabnam; Silva, Sergio; Duarte, Helder; Mestre, Gonçalo; Ferreira, Pedro M.; Khosravani, Hamid Reza; Horta, RicardoThis paper introduces the Intelligent MBPC (IMBPC) HVAC system, a complete solution to enable Model Based Predictive Control (MBPC) of existing HVAC installations in a building. The IMPBC HVAC minimizes the economic cost needed to maintain controlled rooms in thermal comfort during the periods of occupation. The hardware and software components of the IMBPC system are described, with a focus on the MBPC algorithm employed.The installation of IMBPC HVAC solution in a University building is described, and the results obtained in terms of economical savings and thermal comfort obtained are compared with standard, temperature regulated control. (C) 2016 Elsevier B.V. All rights reserved.
- Molecular detection of tick-borne bacteria and protozoa in cervids and wild boars from PortugalPublication . Pereira, André; Parreira, Ricardo; Nunes, Monica; Casadinho, Afonso; Vieira, Maria Luisa; Campino, Lenea; Maia, CarlaBackground: Wildlife can act as reservoir of different tick-borne pathogens, such as bacteria, parasites and viruses. The aim of the present study was to assess the presence of tick-borne bacteria and protozoa with veterinary and zoonotic importance in cervids and wild boars from the Centre and South of Portugal.Methods: One hundred and forty one blood samples from free-ranging ungulates including 73 red deer (Cervus elaphus), 65 wild boars (Sus scrofa) and three fallow deer (Dama dama) were tested for the presence of Anaplasma marginale/A. ovis, A. phagocytophilum, Anaplasma/Ehrlichia spp., Babesia/Theileria spp., Borrelia burgdorferi (sensu lato) (s.l.), and Rickettsia spp. DNA by PCR.Results: Anaplasma spp. DNA was detected in 33 (43.4 %) cervids (31 red deer and two fallow deer) and in two (3.1 %) wild boars while Theileria spp. were found in 34 (44.7 %) cervids (32 red deer and two fallow deer) and in three (4.6 %) wild boar blood samples. Sequence analysis of msp4 sequences identified A. marginale, A. ovis, while the analysis of rDNA sequence data disclosed the presence of A. platys and A. phagocytophilum and T. capreoli and Theileria sp. OT3. Anaplasma spp./Theileria spp. mixed infections were found in 17 cervids (22.4 %) and in two wild boars (3.1 %). All samples were negative for Babesia sp., B. burgdorferi (s.l.), Ehrlichia sp. or Rickettsia sp.Conclusions: This is the first detection of Anaplasma marginale, A. ovis, A. phagocytophilum, A. platys, Theileria capreoli and Theileria sp. OT3 in cervids and wild boars from Portugal. Further studies concerning the potential pathogenicity of the different species of Anaplasma and Theileria infecting wild ungulates, the identification of their vector range, and their putative infectivity to domestic livestock and humans should be undertaken.
- Are personality traits consistent in fish? The influence of social contextPublication . Castanheira, Maria Filipa; Cerqueira, Marco; Millot, Sandie; Gonçalves, Rui A.; Oliveira, Catarina C. V.; Conceição, Luis E. C.; Martins, Catarina I. M.Individual differences in behavioural and physiological responses to challenges are progressively accepted as adaptive variation and reveal a strong degree of evolutionary conservation throughout the vertebrate taxa. Previous studies in gilthead seabream (Sparus aurata) suggested that individual differences in behaviour reflect distinct coping styles or personality, contrasting consistent traits associations. One of the traits that have been shown to be consistent over time and across context is the escape response under a restraining test. Using this trait as a proxy of personality in seabream the influence of social context in the consistency of escape behaviour was investigated. Individually tagged juvenile seabream (n = 360; 70.18 +/- 11.44 g; mean +/- SD) were subjected to a restraining test that consisted of keeping each fish in an emerged net for one minute. Behaviours measured in the net (latency to escape; number of escape attempts and total time spent on escaping) were collapsed into first principal component scores using Principal Components Analysis (PCA). Using the PCA scores the individuals were distributed into homogeneous groups (n = 30 each group) of proactive, reactive and intermediate. Control groups consisted of mixed groups with 1/3 of each coping style. After one month the same individuals were exposed to the same test (restraining test) to assess consistency of behavioural responses. Results indicate that homogenous groups of proactive (p = 0.086) and reactive (p = 0.159) individuals did not exhibit consistent behavioural responses as opposed to the intermediate (p = 0.028) and control groups (p < 0.001). This study thus confirms that the social context in which fish are kept significantly influence personality traits. (C) 2016 Elsevier B.V. All rights reserved.
- Insights on the association between somatic aneuploidy and ostreid herpesvirus 1 detection in the oysters Crassostrea gigas, C. angulata and their F1 hybridsPublication . Batista, Frederico; Lopez-Sanmartin, Monserrat; Boudry, Pierre; Navas, Jose I.; Ruano, Francisco; Renault, Tristan; Fonseca, Vera G.; Leitao, AlexandraCytogenetic abnormalities associated with viral infections, including from viruses of the Herpesvirales order, have been reported in vertebrate species. Ostreid herpesvirus 1 (OsHV-1) has been detected worldwide during mortality outbreaks of the Pacific oyster Crassostrea gigas. On the other hand, a high proportion of aneuploid cells in somatic tissues have been observed in C. gigas. In this study, we analysed the putative association between aneuploidy levels and the detection of OsHV-1 in gills of C. gigas, the Portuguese oyster C. angulata and their F1 hybrids cultured in Ria Formosa (Portugal). OsHV-1 was detected by PCR in 5.4% of the total of oysters analysed (n = 111) namely in 11.1%, 8.0% and 1.7% of C. gigas, C. angulata and F1 hybrid respectively. Sequencing analysis of a viral fragment amplified with the C2/C6 primer pair revealed a high similarity with the OsHV-1 reference type. Moreover, in situ hybridization confirmed the presence of OsHV-1 in gill tissue. Oysters where OsHV-1 was detected had a significantly higher mean percentage of aneuploid cells (25%) than the ones where the virus was not detected (18%). However, the overall low percentage of positive samples contrasted with the high mean percentage of aneuploidy observed, with 50% of the oysters analysed showing a percentage of aneuploid cells between 20% and 30%. We hypothesize that somatic aneuploidy may adversely affect oysters making them more prone to OsHV-1 infection, but the virus is unlikely to be the cause of somatic aneuploidy.
- Classification of landforms in Southern Portugal (Ria Formosa Basin)Publication . Granja-Martins, Fernando M.; Fernandez, Helena; MGP Isidoro, Jorge; Jordan, Antonio; Zavala, LorenaA Geographic Information Systems-based tool is used for macro-landform classification following the Hammond procedure, based upon a Digital Terrain Model (DTM) created from ordinary Kriging. Gentle slopes, surface curvature, highlands and lowlands areas are derived from the DTM. Combining this information allows the classification of terrain units (landforms). The procedure is applied to the Ria Formosa basin (Southern Portugal), with five different terrain types classified (plains, tablelands, plains with hills, open hills and hills).
- Isolation Driven Divergence in Osmoregulation in Galaxias maculatus (Jenyns, 1848) (Actinopterygii: Osmeriformes)Publication . Ruiz-Jarabo, Ignacio; Gonzalez-Wevar, Claudio A.; Oyarzun, Ricardo; Fuentes, Juan; Poulin, Elie; Bertran, Carlos; Vargas-Chacoff, LuisBackgroundMarine species have colonized extreme environments during evolution such as freshwater habitats. The amphidromous teleost fish, Galaxias maculatus is found mainly migrating between estuaries and rivers, but some landlocked populations have been described in lakes formed during the last deglaciation process in the Andes. In the present study we use mtDNA sequences to reconstruct the historical scenario of colonization of such a lake and evaluated the osmoregulatory shift associated to changes in habitat and life cycle between amphidromous and landlocked populations.ResultsStandard diversity indices including the average number of nucleotide differences (Pi) and the haplotype diversity index (H) indicated that both populations were, as expected, genetically distinctive, being the landlocked population less diverse than the diadromous one. Similarly, pairwise G(ST) and N-ST comparison detected statistically significant differences between both populations, while genealogy of haplotypes evidenced a recent founder effect from the diadromous stock, followed by an expansion process in the lake. To test for physiological differences, individuals of both populations were challenged with a range of salinities from 0 to 30 ppt for 8 days following a period of progressive acclimation. The results showed that the landlocked population had a surprisingly wider tolerance to salinity, as landlocked fish survival was 100% from 0 to 20 ppt, whereas diadromous fish survival was 100% only from 10 to 15 ppt. The activity of ATPase enzymes, including Na+/K+-ATPase (NKA), and H+-ATPase (HA) was measured in gills and intestine. Activity differences were detected between the populations at the lowest salinities, including differences in ATPases other than NKA and HA. Population differences in mortality are not reflected in enzyme activity differences, suggesting divergence in other processes.ConclusionsThese results clearly demonstrate the striking adaptive changes of G. maculatus osmoregulatory system, especially at hyposmotic environments, associated to a drastic shift in habitat and life cycle at a scale of a few thousand years.
- The medicinal potential of plants from the genus Plantago (Plantaginaceae)Publication . Gonçalves, Sandra; Romano, AnabelaPlantago is a genus comprising more than 200 plant species used extensively all over the world as functional foods and remedies for a wide range of diseases. This review summarizes the traditional uses, bioactive compounds and pharmacological activities of this genus. The medicinal value of Plantago species in part reflects the gel nature of the polysaccharides extracted from their seeds, which are not only therapeutic, but can also be used for drug delivery and toxin removal. Phytochemical studies have shown that Plantago species also produce other important bioactive compounds such as phenylpropanoid glycosides, iridoids, triterpenes, flavonoids and phenolic acids. Bioactive extracts and isolated compounds can therefore be developed as therapeutic formulations. Some traditional uses of these plants have been pharmacologically validated by identifying specific bioactive molecules, although the mechanisms of action remain unclear. The Plantago genus is also a promising source of novel bioactive molecules and multifunctional polysaccharides because only a few species have been investigated comprehensively thus far. (c) 2016 Published by Elsevier B.V.
- Detection of Bonamia exitiosa in the European flat oyster Ostrea edulis in southern PortugalPublication . Batista, Frederico; Lopez-Sanmartin, M.; Grade, A.; Navas, J. I.; Ruano, F.Bonamiosis is a disease caused by protozoan parasites of the genus Bonamia (phylum Haplosporidia) that has been responsible for mass mortalities in different oyster species worldwide (for review see Bower 2011; Engelsma et al. 2014). Within the genus Bonamia, there are four known species, namely B. ostreae (Pichot et al. 1980), B. rougheyi (Farley, Wolff & Elston 1988), B. exitiosa (Hine, Cochennec-Laureau & Berthe 2001) and B. perspora (Carnegie et al. 2006). B. exitiosa was originally described in Ostrea chilensis in New Zealand (Hine et al. 2001), and since then, it has been observed in several other countries. In Europe, B. exitiosa was detected for the first time in 2007 in the Atlantic coast of Spain (Abollo et al. 2008).