Relationships and events: towards a general theory of reification and truthmaking.

We propose a novel ontological analysis of relations and relationships based on a re-visitation of a classic problem in the practice of knowledge repre- sentation and conceptual modeling, namely relationship reification. Our idea is that a relation holds in virtue of a relationship's existence. Relationships are therefore truthmakers of relations. In this paper we present a general theory or reification and truthmaking, and discuss the interplay between events and rela- tionships, suggesting that relationships are the focus of events, which emerge from the context (the scene) they occur in

Joint Contour Net Analysis for Feature Detection in Lattice Quantum Chromodynamics Data

In this paper we demonstrate the use of multivariate topological algorithms to analyse and interpret Lattice Quantum Chromodynamics (QCD) data. Lattice QCD is a long established field of theoretical physics research in the pursuit of understanding the strong nuclear force. Complex computer simulations model interactions between quarks and gluons to test theories regarding the behaviour of matter in a range of extreme environments. Data sets are typically generated using Monte Carlo methods, providing an ensemble of configurations, from which observable averages must be computed. This presents issues with regard to visualisation and analysis of the data as a typical ensemble study can generate hundreds or thousands of unique configurations. We show how multivariate topological methods, such as the Joint Contour Net, can assist physicists in the detection and tracking of important features within their data in a temporal setting. This enables them to focus upon the structure and distribution of the core observables by identifying them within the surrounding data. These techniques also demonstrate how quantitative approaches can help understand the lifetime of objects in a dynamic system.Comment: 30 pages, 19 figures, 4 table

Avaliação da qualidade físico-química e microbiológica de sete marcas de leite padronizados produzidas nos Estados de Goiás e Minas Gerais e comercializadas no Distrito Federal.

Resumo: O leite é um produto rico em proteínas, carboidratos e vitaminas, sendo um alimento de alto valor nutricional. Pela sua composição físico-química, é um meio propício ao desenvolvimento de micro-organismos. A obtenção, o beneficiamento e o armazenamento devem ser feitos de maneira higiênica para garantir a qualidade final do produto. Os objetivos deste trabalho foram avaliar a qualidade físico-química e microbiológica de sete marcas de leites padronizados comercializadas no Distrito Federal. As amostras foram oriundas de sete laticínios, cinco do Estado de Goiás, e duas de Minas Gerais. As análises foram realizadas no Laboratório de Análise de Alimentos da Universidade de Brasília seguindo normas do Instituto Adolfo Lutz. Os resultados foram comparados aos limites estabelecidos pela Instrução Normativa n°51 e revelam qualidade satisfatória para os parâmetros físico-químicos para as setes marcas. Entretanto, as análises qualitativas de eficiência da pasteurização e microbiológica indicam leites impróprios para o consumo humano. Não foi detectada presença de antibióticos nas marcas. [Evaluation of physico-chemical and microbiological of seven brands of standardized milk produced in the states of Goiás and Minas Gerais and marketed in the Federal District]. Abstract: Milk is a product rich in protein, carbohydrates and vitamins being a food of high nutritional value. By its physico-chemical composition is a propitious means to the development of microorganisms. Obtaining, processing and storage shall be made in a hygienic manner to ensure the quality of the final product. The aims of this study were to evaluate the physico-chemical and microbiological characteristics of the seven brands of standardized milks marketed in the Federal District. The samples were from seven dairy, five State of Goiás and two of Minas Gerais. The analyzes were performed at the Laboratory of Food Analysis, University of Brasilia, following rules of the Institute Adolfo Lutz. The results were compared to the limits established by Normative Instruction No. 51 and show satisfactory quality for physico-chemical parameters for the seven brands. However, qualitative analysis of efficiency of pasteurization and microbiological indicate milks unfit for human consumption. Antibiotics were not detected in all marks

Avaliação qualitativa e quantitativa de leite Tipo A comercializados no Distrito Federal.

Resumo: O leite tipo A é processado em granjas leiteiras. Possui maior valor agregado e menor carga microbiológica. O objetivo desse trabalho foi avaliar a qualidade do produto comercializado no Distrito Federal. Foram avaliadas duas marcas durante quatro meses. As amostras foram avaliadas em testes de fraude e foram feitas análise físico-química. Ambas as marcas apresentaram índice crioscópico em desacordo com a legislação vigente e presença de sacarose. Esse resultado evidencia a fraude para aumentar o rendimento do produto. Além disso, a marca B apresentou bicarbonato em sua composição e teste de peroxidase negativa em 14,3% das amostras. Esses resultados mostram que a marca B fraudou o leite na tentativa de reduzir a carga microbiana. [Qualitative and Quantitative Evaluation of type A milk marketed in the Federal District]. Abstract: The type A milk is processed into dairy farms. Has a higher value and lower microbiological load. The aim of this study was to evaluate the quality of the product marketed in the Federal District. We evaluated two brands during four months. The samples were evaluated in tests of fraud and physicochemical analysis. Both brands had cryoscopic index in disagreement with current legislation and presence of sucrose. This result evidences the fraud to increase product yield. In addition, the type B showed bicarbonate in their composition and peroxidase negative test in 14,3% of samples. These results show that type B defrauded milk in attempt to reduce the microbial load

Reification and Truthmaking Patterns

Reification is a standard technique in conceptual modeling, which consists of including in the domain of discourse entities that may otherwise be hidden or implicit. However, deciding what should be rei- fied is not always easy. Recent work on formal ontology offers us a simple answer: put in the domain of discourse those entities that are responsible for the (alleged) truth of our propositions. These are called truthmakers. Re-visiting previous work, we propose in this paper a systematic analysis of truthmaking patterns for properties and relations based on the ontolog- ical nature of their truthmakers. Truthmaking patterns will be presented as generalization of reification patterns, accounting for the fact that, in some cases, we do not reify a property or a relationship directly, but we rather reify its truthmakers

Towards an Ontological Modelling of Preference Relations

Preference relations are intensively studied in Economics, but they are also approached in AI, Knowledge Representation, and Conceptual Modelling, as they provide a key concept in a variety of domains of application. In this paper, we propose an ontological foundation of preference relations to formalise their essential aspects across domains. Firstly, we shall discuss what is the ontological status of the relata of a preference relation. Secondly, we investigate the place of preference relations within a rich taxonomy of relations (e.g. we ask whether they are internal or external, essential or contingent, descriptive or nondescriptive relations). Finally, we provide an ontological modelling of preference relation as a module of a foundational (or upper) ontology (viz. OntoUML). The aim of this paper is to provide a sharable foundational theory of preference relation that foster interoperability across the heterogeneous domains of application of preference relations

Avaliação da presença de metais pesados em nove méis produzidos e comercializados no Distrito Federal.

Resumo: O mel brasileiro é produzido principalmente por abelhas africanizadas a partir do néctar ou da secreção das plantas e, devido às suas características genéticas dessas espécies de abelhas, dispensa o uso de antibióticos e pesticidas, como acaricidas e fungicidas. A composição das amostras de méis está intimamente relacionada com o tipo de florada utilizada por estas abelhas para a elaboração do produto final. Um dos componentes de grande importância são os minerais presentes no mel que representam de 0,02% a 1%. Dentre estes minerais observamos os chamados metais pesados, que podem indicar tanto a origem geográfica do mel quanto o nível de poluição ambiental por estes metais. Logo, faz-se necessário a pesquisa da presença ou não de metais pesados nas amostras comercializadas. Por isso, o objetivo deste trabalho foi analisar nove amostras provenientes de nove apiários localizados na região do Distrito Federal, quanto à presença de metais de Cádmio, Chumbo, Cobre, Cromo, Níquel e Zinco. As determinações foram realizadas por espectrometria de emissão atômica com plasma acoplado e os resultados demonstraram que as concentrações de Cádmio e Zinco estão em conformidade com a legislação vigente. As concentrações dos demais metais (Chumbo, Cobre, Cromo e Níquel) estão abaixo do limite de detecção. [Evaluation of the presence of heavy metals in nine honeys produced and marketed in the Federal District]. Abstract: The Brazilian honey is mainly produced by Africanized bees that due to their genetic characteristics dispense the use of antibiotics and pesticides, acaricides and fungicides. However, it is necessary to investigate the presence or absence of heavy metals in marketed samples. Therefore, the aim of this study was to analyze nine samples from nine apiaries located in the Federal District, as the presence of metals Cadmium, Lead, Copper, Chromium, Nickel and Zinc. The determinations were performed by atomic emission spectrometry with inductively coupled plasma and the results showed that the concentrations of Cadmium and Zinc are in accordance with current legislation. The concentrations of other metals (Lead, Copper, Chromium and Nickel) are below the detection limit

Grapevine yellows: Comparison of different procedures for DNA extraction and amplification with PCR for routine diagnosis of phytoplasmas in grapevine

In order to devise a procedure to be used as reference for detection of grapevine phytoplasmas and monitoring of Flavescence dorée, 12 combinations comprising three methods of plant DNA extraction and 4 procedures for amplification in polymerase chain reaction of phytoplasma DNA were examined in parallel using the same plant tissues infected with phytoplasmas. In a first series tissues of periwinkles (Catharanthus roseus) infected with phytoplasma isolates of the Elm yellows group (16SrV) and maintained in the greenhouse, were used. In a second series tissues of grapevines (Vitis vinifera) naturally infected with Flavescence dorée or Palatinate grapevine yellows phytoplasma were used. The DNA preparations obtained with each of the three extraction procedures were used undiluted or serially diluted, as target DNA in the 4 nested-polymerase chain reactions. The results showed differences in the efficiency among different methods of extraction as well as in the sensitivity among the DNA amplification procedures, which improved when DNA extracted from field grapevines was diluted. After additional comparative validation on numerous field-collected samples of GY-affected grapevines, the quickest extraction procedure was selected for use in routine diagnosis, with nested-PCR amplification either of ribosomal DNA or of the FD9 DNA fragment specific for Flavescence dorée and other 16SrV group phytoplasmas

Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)

The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org

Identifying the coiled-coil triple helix structure of β-peptide nanofibers at atomic resolution

Peptide self-assembly represents a powerful bottom-up approach to the fabrication of new nanomaterials. β3-peptides are non-natural peptides composed entirely of β-amino acids, which have an extra methylene in the backbone and we reported the first fibers derived from the self-assembly of β3-peptides that adopt unique 14-helical structures. β3-peptide assemblies represent a class of stable nanomaterials that can be used to generate bio- and magneto-responsive materials with proteolytic stability. However, the three-dimensional structure of many of these materials remains unknown. In order to develop structure-based criteria for the design of new β3-peptide-based biomaterials with tailored function, we investigated the structure of a tri-β3-peptide nanoassembly by molecular dynamics simulations and X-ray fiber diffraction analysis. Diffraction data was collected from aligned fibrils formed by Ac-β3[LIA] in water and used to inform and validate the model structure. Models with threefold radial symmetry resulted in stable fibers with a triple-helical coiled-coil motif and measurable helical pitch and periodicity. The fiber models revealed a hydrophobic core and twist along the fiber axis arising from a maximization of contacts between hydrophobic groups of adjacent tripeptides on the solvent-exposed fiber surface. These atomic structures of macro-scale fibers derived from β3-peptide-based materials provide valuable insight into the effects of the geometric placement of the side-chains and the influence of solvent on the core fiber structure which is perpetuated in the superstructure morphology