Taxonomic revision of doubtful Brazilian freshwater shrimp species of genus Macrobrachium (Decapoda, Palaemonidae)

The freshwater prawns of the genus Macrobrachium Spence Bate, 1868 are widely distributed in rivers of tropical and subtropical regions and represent an interesting group with controversial taxonomy. The morphological characters traditionally used to separate species have shown a high intraspecific variation. Doubts about the status of M. birai Lobao, Melo & Fernandes, 1986, M. holthuisi Genofre & Lobao, 1978 and M. petronioi Melo, Lobao & Fernandes, 1986 have been arisen due to the high resemblance of the former two species with M. olfersi (Wiegmann, 1836), and the latter one with M. potiuna (Muller, 1880). Therefore, we performed a detailed morphological analysis of these species, including new characters not usually used in the species recognition. The present results here with molecular data lead us to conclude that M. birai and M. holthuisi are junior synonyms of M. olfersi, and M. petronioi is a junior synonym of M. potiuna. Considering these synonymies, 17 valid species are now reported for the Brazilian territory.

The incorporeal order in Plato's Philebus

In this paper, I intend to analyze how Plato's Philebus takes up some specific topics of Platonic dialectic and employs them to understand how the cognitive soul can be affected by false pleasures, false opinions, and false images. This study aims to criticize certain modern readings of Platonism, chiefly esoteric theory based on Plato's unwritten doctrine, which stipulate a revision of the Platonic theory of forms and defend the emergence of a new ontology explained by two principles, the One and the unlimited Dyad of great and small, conceived both as formal principle and material principle.

A revision of species diversity in the Neotropical genus Oreobates (Anura: Strabomantidae), with the description of three new species from the Amazonian slopes of the Andes

We revisit species diversity within Oreobates (Anura: Strabomantidae) by combining molecular phylogenetic analyses of the 16S rRNA amphibian barcode fragment with the study of the external morphology of living and preserved specimens. Molecular and morphological evidence support the existence of 23 species within Oreobates, and three additional candidate species (Oreobates sp. [Ca JF809995], Oreobates sp. [Ca EU368903], Oreobates cruralis [Ca EU192295]). We describe and name three new species from the Andean humid montane forests of Departamento Cusco, southern Peru: O. amarakaeri New Species from Rio Nusinuscato and Rio Mabe, at elevations ranging from 670 to 1000 m in the Andean foothills; O. machiguenga, new species, from Rio Kimbiri (1350 m), a small tributary of the Apurimac River, in the western versant of Cordillera Vilcabamba; and O. gemcare, new species, from the Kosnipata Valley at elevations ranging from 2400 to 2800 m. The three new species are readily distinguished from all other Oreobates by at least one qualitative morphological character. Three species are transferred to Oreobates from three genera of Strabomantidae: Hypodactylus lundbergi, Pristimantis crepitans, and Phrynopus ayacucho (for which the advertisement call, coloration in life, and male characteristics are described for first time). Oreobates simmonsi is transferred to the genus Lynchius. Hylodes verrucosus is considered a junior synonym of Hylodes philippi. In addition, H. philippi is removed from the synonymy of O. quixensis and considered a nomem dubium within Hypodactylus. The inclusion of Phrynopus ayacucho in Oreobates extends the ecological range of the genus to the cold Andean puna. Oreobates is thus distributed from the Amazonian lowlands in southern Colombia to northern Argentina, reaching the Brazilian Atlantic dry forests in eastern Brazil, across an altitudinal range from ca. 100 to 3850 m.

The revision of the Brazilian Forest Act: increased deforestation or a historic step towards balancing agricultural development and nature conservation?

Almost two-thirds of the Brazilian territory still has prevalence of natural vegetation. Although not all pristine, much of these areas have high conservation value. 170 million hectare (Mha) of the natural vegetation is located within Federal and State protected areas. Most of the remaining 367 Mha is on private agriculture lands, where the Forest Act is the most important legal framework for conservation. In July 2010, the Brazilian parliament began the analysis of a substitutive legislation for the Forest Act. The main motivations for the revision is that, on the one hand, it has been found ineffective in protecting natural vegetation, and on the other hand, it is perceived as a barrier against development in the agriculture sector. The substitutive Forest Act, as it presently stands, does not represent a balance between existing standpoints and objectives; it may drive development towards either more private protection through market-driven compensation actions, or increased deforestation and less nature protection/restoration. This article uses outcomes from modeling analyses to discuss weaknesses of the substitutive Forest Act and to suggest possible improvements. (C) 2011 Elsevier Ltd. All rights reserved.

Revision of Singlet Quantum Yields in the Catalyzed Decomposition of Cyclic Peroxides

The chemiluminescence of cyclic peroxides activated by oxidizable fluorescent dyes is an example of chemically initiated electron exchange luminescence (CIEEL), which has been used also to explain the efficient bioluminescence of fireflies. Diphenoyl peroxide and dimethyl-1,2-dioxetanone were used as model compounds for the development of this CIEEL mechanism. However, the chemiexcitation efficiency of diphenoyl peroxide was found to be much lower than originally described. In this work, we redetermine the chemiexcitation quantum efficiency of dimethyl-1,2-dioxetanone, a more adequate model for firefly bioluminescence, and found a singlet quantum yield (Phi(s)) of 0.1%, a value at least 2 orders of magnitude lower than previously reported. Furthermore, we synthesized two other 1,2-dioxetanone derivatives and confirm the low chemiexcitation efficiency (Phi(s) < 0.1%) of the intermolecular CIEEL-activated decomposition of this class of cyclic. peroxides. These results are compared with other chemiluminescent reactions, supporting the general trend that intermolecular CIEEL systems are much less efficient in generating singlet excited states than analogous intramolecular processes (Phi(s) approximate to 50%), with the notable exception of the peroxyoxalate reaction (Phi(s) approximate to 60%).

A hymenopterists' guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions

Hymenoptera exhibit an incredible diversity of phenotypes, the result of similar to 240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These resources are designed to facilitate accessible and extensible research on hymenopteran phenotypes. Outreach with the hymenopterist community is of utmost importance to the HAO project, and this paper is a direct response to questions that arose from project workshops. In a concerted attempt to surmount barriers of understanding, especially regarding the format, utility, and development of the HAO, we discuss the roles of homology, "preferred terms", and "structural equivalency". We also outline the use of Universal Resource Identifiers (URIs) and posit that they are a key element necessary for increasing the objectivity and repeatability of science that references hymenopteran anatomy. Pragmatically, we detail a mechanism (the "URI table") by which authors can use URIs to link their published text to the HAO, and we describe an associated tool (the "Analyzer") to derive these tables. These tools, and others, are available through the HAO Portal website (http://portal.hymao.org). We conclude by discussing the future of the HAO with respect to digital publication, cross-taxon ontology alignment, the advent of semantic phenotypes, and community-based curation.

Revision and cladistic analysis of Neotropical genus Psilochlorops Duda (Diptera: Chloropidae)

Five new species are described herein for the Neotropical genus Psilochlorops, up to now known only from the type-species, P. clavitibia Duda-P. brunneus sp. n., P. elongatum sp. n., P. flavisoma sp. n., P. nigrifemur sp. n. and P. paganelliae sp. n. All new species are described in detail and illustrated. A key to the species of the genus is provided. The diagnosis of Psilochlorops, after the addition of these species, is emended. A cladistic analysis of the genus indicates that Psilochlorops is monophyletic and show the affinities between the species.

Revision of Nanophareus, a mysterious harvestman genus from Chile, with descriptions of three new species (Opiliones: Laniatores: Gonyleptidae)

The Chilean genus Nanophareus Roewer, 1929 is revised and three new species are described: N. araucanus sp. nov. (type locality: Parque Nacional La Campana, Valparaiso, Chile); N. bipartitus sp. nov. (type locality: Parque Nacional La Campana, Valparaiso, Chile); N. bosqenublado sp. nov. (type locality: Parque Nacional Fray Jorge, Coquimbo, Chile). The type species, N. palpalis Roewer, 1929, is redescribed and a lectotype is designated. A cladistic analysis was performed using these three new species plus N. palpalis and 14 more laniatorid species, and a data matrix of 72 characters: Seven from the ocularium, 22 from the dorsal scutum, one from the venter, one from the chelicera, eight from the pedipalp, 24 from male legs, and nine from male genitalia. Two equally most parsimonious trees were found (L = 210; C.I. = 0.41; R.I. = 0.51). Nanophareus was recovered as nested within a paraphyletic subfamily Pachylinae. The genus Nanophareus was found to be monophyletic based on the following exclusive synapomorphies: An external row of enlarged tubercles inserted among small ones on lateral margin of the dorsal scutum (innapplicable in N. bosqenublado); the ventro-basal margin of pedipalpal tibia curved 90 degrees in lateral view; and retrolateral seta of the pedipalpal tibia with a socket apically bifid (socket and seta longer than pedipalpal tibia length).

Revision of the genera Interrhodeus, Pennarhodeus and Poropodalius (Acari: Rhodacaridae)

The genera Interrhodeus Karg, Pennarhodeus Karg and Poropodalius Karg are redescribed on the basis of one species of Interrhodeus, four species of Pennarhodeus and five species of Poropodalius, including the type species of each genus. All species are redescribed on the basis of the type specimens, and keys for the separation of the species of the latter two genera are provided. Re-examination of these species shows that these three genera are correctly placed in the family Rhodacaridae.

A Revision of Hortia (Rutaceae)

A taxonomic revision of the genus Hortia (Rutaceae) is presented. Hortia is a Neotropical genus with most of the species occurring in the Amazonian region. The species are woody, nearly all trees, with simple leaves crowded near the apices of the branches, showy broad corymbose terminal inflorescences, reddish to pink flowers, and berries with abundant oil glands. Ten species are recognized here, most of them occurring in Brazil. A key to the species, descriptions, synonyms, illustrations, as (yell as comments on the geographic distribution, ecology, and economic uses of each species are presented.

Neotropical termites: revision of Armitermes Wasmann (Isoptera, Termitidae, Syntermitinae) and phylogeny of the Syntermitinae

We present a comprehensive phylogenetic analysis of Syntermitinae, including representatives of all genera of the subfamily, along with all 12 species assigned formerly to the genus Armitermes Wasmann (Termitidae, Syntermitinae), and 4 new species described herein. Syntermitinae was recovered as a natural group and the hypothesis that the frontal tube indicates convergence between Syntermitinae and Nasutitermitinae was corroborated. Also, several diagnostic characters proposed in the original description of Syntermitinae are discussed. Alongside the phylogenetic study, a taxonomic revision of the Neotropical genus Armitermes was carried out, resulting in division of the genus into four genera. Taxonomic novelties are: Armitermes now includes A. armiger (Motschulsky), A. bidentatus Rocha & Cancello sp.n. and A. spininotus Rocha & Cancello sp.n.; Silvestritermes Rocha & Cancello gen.n. includes S. euamignathus (Silvestri) comb.n., S. lanei (Canter) comb.n., S. gnomus (Constantino) comb.n., S. duende Rocha & Cancello sp.n., S. minutus (Emerson) comb.n., S. almirsateri Rocha & Cancello sp.n. and S. holmgreni (Snyder) comb.n.; Uncitermes Rocha & Cancello gen.n. includes U. teevani (Emerson) comb.n.; Mapinguaritermes Rocha & Cancello gen.n. includes M. peruanus (Holmgren) comb.n. and M. grandidens (Emerson) comb.n. A new synonymy is proposed for A. cerradoensis Mathews under S. euamignathus. All soldiers are described and illustrated, as are the mandibles and digestive tract of the worker and the imago caste, when available. We provide a dichotomous key, based on soldiers, for all genera of Syntermitinae, and distribution maps and dichotomous keys, based on soldiers, for the species of Armitermes and all the new genera described herein.

A UML profile for the OBO relation ontology

Background: Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain. Results: We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO). Conclusions: The use of an established and well-known graphical language in the development of biomedical ontologies provides a more intuitive form of capturing and representing knowledge than using only text-based notations. The use of the profile requires the domain expert to reason about the underlying semantics of the concepts and relationships being modeled, which helps preventing the introduction of inconsistencies in an ontology under development and facilitates the identification and correction of errors in an already defined ontology.

BayGO: Bayesian analysis of ontology term enrichment in microarray data

Abstract Background The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. Results BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. Conclusion The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

Los manglares de la costa brasileña: revision preliminar de la literatura

Los manglares ocurren intermitentemente a lo largo del litoral brasileño desde Cabo Orange (4°21'N) en Amapá hasta la ciudad de Laguna (28°30'S). En este trabajo se sugiere la división del litoral en 7 trechos que comparten características geomorfológicas y rangos de condiciones meteorológicas similares. Estes trechos son: Litoral Guianense, Golfão Amazónico, Litoral de Ponta Coruçá a Ponta Mangues Secos, Litoral de Ponta Mangues Secos al Cabo Calcanhar, Litoral del Cabo Calcanhar al Recôncavo Baiano, Litoral Oriental y Costa Cristalina. El mayor desarrollo del manglar ocurre en los trechos Guianense y del Gofão Amazónico. Los manglares se desarrollhan por todo el litoral aún en los sectores donde la precipitación es en el orden de 500 mm/año. En las costas expuestas se desarrolla en las áreas anegadas detrás de medanos, canales, lagunas y márgenes de los estuarios, penetrando en ocasiones 30-40 km. Coloniza además las márgenes de las grandes bahías hasta los 28°30'S donde la temperatura anual es de 19.6°C y la temperatura media del mes más frío es de 15.7°C. En el trecho del Litoral Cristalino, el manglar alcanza su límite latitudinal en el estado de Santa Catarina. Rhizophora alcanza 27°53'S mientras que Avicennia continúa hasta los 28°30'S en Laguna. En la isla de Santa Catarina se encuentran manglares bien desarrollados dominados por Avicennia. Estos manglares alcanzan un porte promedio de 7.0 ± 0.4 m, tienen un DAP de 17.9 cm, densidades totales (≥ 2.5 cm) de 431 ± 93 árboles/ha y áreas basimétricas (≥ 2.5 cm) de 7.42 ± 0.80 m2/ha. Las áreas basimétricas bajas se deben al dominio de los rodales por pocos ejemplares de diámetros moderados. Debido a estas bajas densidades, la copa es rala y los bosques son extremadamente abiertos

A Fuzzy Ontology-Driven Approach to Semantic Interoperability in e-Government Big Data

With the increasing production of information from e-government initiatives, there is also the need to transform a large volume of unstructured data into useful information for society. All this information should be easily accessible and made available in a meaningful and effective way in order to achieve semantic interoperability in electronic government services, which is a challenge to be pursued by governments round the world. Our aim is to discuss the context of e-Government Big Data and to present a framework to promote semantic interoperability through automatic generation of ontologies from unstructured information found in the Internet. We propose the use of fuzzy mechanisms to deal with natural language terms and present some related works found in this area. The results achieved in this study are based on the architectural definition and major components and requirements in order to compose the proposed framework. With this, it is possible to take advantage of the large volume of information generated from e-Government initiatives and use it to benefit society.