Electivities and resource use by an assemblage of lizards endemic to the dunes of the São Francisco River, northeastern Brazil

This study describes the pattern of resource use by one assemblage of lizards inhabiting a desert-like dune field in the Brazilian Caatinga. We evaluated food and microhabitat availability and phases of lizard activity, as well as use of, and electivities for, food and microhabitats. Six of the seven most abundant species are endemic to the dunes, and their diets under-represented arthropods possessing chemical defenses. The two fossorial gymnophthalmids were similar in presenting no electivities for microhabitat but differed in diet, electivities for food and phase of activity. The five species of epigeous lizards include one group presenting positive electivities for protected and shaded microhabitats (Procellosaurinus erythrocercus, Briba brasiliana, and Tropidurus psammonastes) and another presenting negative electivities for such microhabitats (Eurolophosaurus divaricatus and Cnemidophorus spec. nov.). The tropidurid T. psammonastes presented the earliest activity in the morning, the strongest positive electivities for protected and shaded areas and negative electivity for exposed areas, and was the only species to present high positive electivity for ants. The only other tropidurid in the area, E. divaricatus, also ate ants but presented positive electivity for flowers. The medium-sized teiid Cnemidophorus spec. nov. showed the highest negative electivity for shaded areas, high positive electivity for open areas, and high negative electivity for protected areas. This pattern leads to use of microhabitat that is similar to that of E. divaricatus, which has a very different diet, and different from that of T. psammonastes, whose diet is comparable in the consumption of insect larvae and large-sized items. We discuss the evolution of the detected patterns of resource electivities.Este estudo descreve o padrão de uso de recursos por uma assembléia de lagartos de um campo de dunas da Caatinga. Avaliamos a disponibilidade de recursos e as fases de atividade dos lagartos, bem como seu uso e suas eletividades por alimento e micro-hábitats. Seis das sete espécies mais abundantes são endêmicas das dunas, e suas dietas sub-representaram artrópodes com defesas químicas. Os dois gimnoftalmídeos fossórios mostraram-se semelhantes por não apresentar eletividades por micro-hábitats, mas diferiram quanto à dieta, às eletividades por alimentos e à fase de atividade. As cinco espécies de lagartos epígeos incluem um grupo com eletividade positiva por micro-hábitats protegidos e sombreados (Procellosaurinus erythrocercus, Briba brasiliana e Tropidurus psammonastes) e outro com eletividades negativas pelos mesmos (Eurolophosaurus divaricatus e Cnemidophorus spec. nov.). O tropidurídeo T. psammonastes apresentou atividade mais precocemente pela manhã, as eletividades positivas mais fortes por áreas protegidas e sombreadas e eletividades negativas por áreas expostas, sendo a única espécie com eletividade positiva alta por formigas. O outro tropidurídeo da área, E. divaricatus, também alimentou-se de formigas mas apresentou eletividade positiva por flores. O teiídeo de médio porte Cnemidophorus spec. nov. apresentou as maiores eletividades negativas por áreas sombreadas e a maior eletividade positiva por áreas abertas, bem como uma alta eletividade negativa por áreas protegidas. Assim, seu padrão de uso de micro-hábitat é similar ao de E. divaricatus, que possui uma dieta muito distinta, e diferente do padrão de T. psammonastes, cuja dieta é semelhante (larvas de insetos e itens de maior tamanho). Discutimos a evolução dos padrões detectados de eletevidades por recursos

Development of an information retrieval tool for biomedical patents

Supplementary material associated with this article can be found, in the online version, at doi: 10.1016/j.cmpb.2018.03.012 .Background and objective. The volume of biomedical literature has been increasing in the last years. Patent documents have also followed this trend, being important sources of biomedical knowledge, technical details and curated data, which are put together along the granting process. The field of Biomedical text mining (BioTM) has been creating solutions for the problems posed by the unstructured nature of natural language, which makes the search of information a challenging task. Several BioTM techniques can be applied to patents. From those, Information Retrieval (IR) includes processes where relevant data are obtained from collections of documents. In this work, the main goal was to build a patent pipeline addressing IR tasks over patent repositories to make these documents amenable to BioTM tasks. Methods. The pipeline was developed within @Note2, an open-source computational framework for BioTM, adding a number of modules to the core libraries, including patent metadata and full text retrieval, PDF to text conversion and optical character recognition. Also, user interfaces were developed for the main operations materialized in a new @Note2 plug-in. Results. The integration of these tools in @Note2 opens opportunities to run BioTM tools over patent texts, including tasks from Information Extraction, such as Named Entity Recognition or Relation Extraction. We demonstrated the pipelines main functions with a case study, using an available benchmark dataset from BioCreative challenges. Also, we show the use of the plug-in with a user query related to the production of vanillin. Conclusions. This work makes available all the relevant content from patents to the scientific community, decreasing drastically the time required for this task, and provides graphical interfaces to ease the use of these tools.This work is co-funded by the Programa Operacional Re- gional do Norte, under the “Portugal2020”, through the Euro- pean Regional Development Fund ( ERDF ), within project SISBI- Ref a NORTE-01-0247-FEDER-003381 . This study was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01- 0145-FEDER-00 6 684) and BioTecNorte operation (NORTE-01-0145- FEDER-0 0 0 0 04) funded by European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte.info:eu-repo/semantics/publishedVersio

Cancer evolution: mathematical models and computational inference.

Cancer is a somatic evolutionary process characterized by the accumulation of mutations, which contribute to tumor growth, clinical progression, immune escape, and drug resistance development. Evolutionary theory can be used to analyze the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular data. We review recent approaches to modeling the evolution of cancer, including population dynamics models of tumor initiation and progression, phylogenetic methods to model the evolutionary relationship between tumor subclones, and probabilistic graphical models to describe dependencies among mutations. Evolutionary modeling helps to understand how tumors arise and will also play an increasingly important prognostic role in predicting disease progression and the outcome of medical interventions, such as targeted therapy.FM would like to acknowledge the support of The University of Cambridge, Cancer Research UK and Hutchison Whampoa Limited.This is the final published version. It first appeared at http://sysbio.oxfordjournals.org/content/early/2014/10/07/sysbio.syu081.short?rss=1

Biomaterials as Tendon and Ligament Substitutes: Current Developments

Tendon and ligament have specialized dynamic microenvironment characterized by a complex hierarchical extracellular matrix essential for tissue functionality, and responsible to be an instructive niche for resident cells. Among musculoskeletal diseases, tendon/ligament injuries often result in pain, substantial tissue morbidity, and disability, affecting athletes, active working people and elder population. This represents not only a major healthcare problem but it implies considerable social and economic hurdles. Current treatments are based on the replacement and/or augmentation of the damaged tissue with severe associated limitations. Thus, it is evident the clinical challenge and emergent need to recreate native tissue features and regenerate damaged tissues. In this context, the design and development of anisotropic bioengineered systems with potential to recapitulate the hierarchical architecture and organization of tendons and ligaments from nano to macro scale will be discussed in this chapter. Special attention will be given to the state-of-the-art fabrication techniques, namely spinning and electrochemical alignment techniques to address the demanding requirements for tendon substitutes, particularly concerning the importance of biomechanical and structural cues of these tissues. Moreover, the poor innate regeneration ability related to the low cellularity and vascularization of tendons and ligaments also anticipates the importance of cell based strategies, particularly on the stem cells role for the success of tissue engineered therapies. In summary, this chapter provides a general overview on tendon and ligaments physiology and current conventional treatments for injuries caused by trauma and/or disease. Moreover, this chapter presents tissue engineering approaches as an alternative to overcome the limitations of current therapies, focusing on the discussion about scaffolds design for tissue substitutes to meet the regenerative medicine challenges towards the functional restoration of damaged or degenerated tendon and ligament tissues.Portuguese Foundation for Science and Technology for the post-doctoral grant (SFRH/BPD/111729/2015) and for the projects Recognize (UTAP-ICDT/CTM-BIO/0023/2014) and POC I-01-0145-FEDER-007

Nonlocalized modulation of periodic reaction diffusion waves: The Whitham equation

In a companion paper, we established nonlinear stability with detailed diffusive rates of decay of spectrally stable periodic traveling-wave solutions of reaction diffusion systems under small perturbations consisting of a nonlocalized modulation plus a localized perturbation. Here, we determine time-asymptotic behavior under such perturbations, showing that solutions consist to leading order of a modulation whose parameter evolution is governed by an associated Whitham averaged equation

Designing whey protein-based architectures under application of moderate electric fields

info:eu-repo/semantics/publishedVersio

Hereditary breast cancer and ancestry in the Madeira archipelago: An exploratory study

Access to genetic testing and counselling in remote areas such as the Madeira archipelago, in the Northern Atlantic Ocean, may be complex. Different counselling methods, including telegenetics, should be explored. In this study, we characterise the Hereditary Breast/Ovarian Cancer (HBOC) families with Madeira ancestry enrolled in our programme. Of a total of 3, 566 index patients tested between January 2000 and June 2018, 68 had Madeira ancestry and 22 were diagnosed with a pathogenic germline variant (PV). As in the whole group, BRCA2 PV were more frequent in Madeira patients (68.4%: c.9382C>T (26.3%), c.658_659del (21%), c.156_157insAlu (10.5%), c.793+1G>A (5.3%) and c.298A>T (5.3%). However, the most frequently diagnosed PV in Madeira patients was the BRCA1 c.3331_3334del (31.6%). BRCA1/2 detection rates were 27.9% and 10.5% for Madeira and the whole group, respectively. This study is the first characterisation of HBOC patients with Madeira ancestry. A distinct pattern of BRCA1/2 variants was observed, and the geographic clustering of BRCA1 c.3331_3334del variant may support the possibility of a founder mutation previously described in Northern Portugal. The high detection rate observed reinforces the need to reduce gaps in access to genetic testing in Madeira and other remote areas. According to current guidelines, timely identification of HBOC patients can contribute to their ongoing care and treatment

Influence of carbonation on the chloride ion diffusion coefficient in fly ash concrete

The incorporation of fly ash (FA) in cementitious matrices has been frequently used in order to make the matrix more resistant to the action of chlorides. On the other hand, it is known that Ca(OH)2 existing in the matrix is consumed by the pozzolanic reactions, which makes easier the carbonation front advance. Given that the chloride ingress and carbonation are the two main causes of degradation in reinforced concrete, we speculate about the behaviour of FA concrete when the structure is submitted simultaneously to chlorides and carbonation. This work studied the influence of carbonation on the chloride migration coefficient in FA concrete. For this, specimens with 0% and 40% replacement of cement CEM I 42.5R by FA were casted with water/binder 0.55 and 0.50 respectively. After 90 days of curing period, half of samples were subjected to accelerated carbonation (20ºC ,55%RH and 4%CO2) for 1, 2 and 3 months. The other half was protected with plastic film during the same period. Non-steady-state migration tests, according to LNEC E463 (Portuguese specification), were performed with specimens subjected to both experimental conditions. The results show that, for these conditions, the carbonation has a direct influence on chloride diffusion coefficient, increasing it. For FA concrete samples this effect is more evident. In these cases, the carbonated samples studied showed a diffusion coefficient up to two times higher than noncarbonated ones. The increase in large capillary pores, caused by carbonation, can be responsible for the increase of chloride penetration into concrete subjected to combined actio

NOTAS E RESENHAS

FOTOINTERPRETAÇÃO E QUNATIFICAÇÃO PARA AVALIAÇÃO DE TRNSFORMAÇÕES NO USO DA TERRA - Miguel C. SANCHEZ CARACTERIZAÇÃO DA MODERNIZAÇÃO DA AGRICULTURA E DO DESENVOLVIMENTO RURAL EM URBELANDIA - Miguel C. SANCHEZ EMPREGO DO SENSORIAMENTO REMOTO NOS ESTUDOS DOS EFEITOS DA EROSÃO EM PAREAS DE RESERVATÓRIO - Myrna T. VIANA RECUPERAÇÃO DE RECURSOS A PARTIR DO LIXO URBANO EM RIO CLARO - Geraldo RODRIGUE

Revisiting the vanishing refuge model of diversification

Much of the debate around speciation and historical biogeography has focused on the role of stabilizing selection on the physiological (abiotic) niche, emphasizing how isolation and vicariance, when associated with niche conservatism, may drive tropical speciation. Yet, recent re-emphasis on the ecological dimensions of speciation points to a more prominent role of divergent selection in driving genetic, phenotypic, and niche divergence. The vanishing refuge model (VRM), first described by Vanzolini and Williams (1981), describes a process of diversification through climate-driven habitat fragmentation and exposure to new environments, integrating both vicariance and divergent selection. This model suggests that dynamic climates and peripheral isolates can lead to genetic and functional (i.e., ecological and phenotypic) diversity, resulting in sister taxa that occupy contrasting habitats with abutting distributions. Here, we provide predictions for populations undergoing divergence according to the VRM that encompass habitat dynamics, phylogeography, and phenotypic differentiation across populations. Such integrative analyses can, in principle, differentiate the operation of the VRM from other speciation models. We applied these principles to a lizard species, Coleodactylus meridionalis, which was used to illustrate the model in the original paper. We incorporate data on inferred historic habitat dynamics, phylogeography and thermal physiology to test for divergence between coastal and inland populations in the Atlantic Forest of Brazil. Environmental and genetic analyses are concordant with divergence through the VRM, yet physiological data are not. We emphasize the importance of multidisciplinary approaches to test this and alternative speciation models while seeking to explain the extraordinarily high genetic and phenotypic diversity of tropical biomes