Characterization of 10 new tetranucleotide microsatellite markers for the European eagle owl, Bubo bubo: Useful tools for conservation strategies

Bubo bubo is the largest owl in the world, showing a wide geographical distribution throughout the Palaearctic region. It underwent a demographic decline in many European countries during the last century and was considered “vulnerable” (Annex II of the CITES). Nowadays, it is classified as “Least Concern” according to IUCN. Despite its ecological importance and conservation status, few polymorphic molecular markers are available to study its diversity and population genetics. We report on the isolation and development of 10 new microsatellites for the Eagle owl, B. bubo. All loci (10 tetra-nucleotide) are characterized by high polymorphism levels. Number of alleles ranged from 5 to 13 and expected heterozygosity varied from 0.733 to 0.840. These microsatellites would be very useful to assess the genetic diversity, connectivity patterns and parentage of B. bubo. This information will allow to establish new conservation strategies and improve the management of the species.

Ontology forecasting in scientific literature:semantic concepts prediction based on innovation-adoption priors

The ontology engineering research community has focused for many years on supporting the creation, development and evolution of ontologies. Ontology forecasting, which aims at predicting semantic changes in an ontology, represents instead a new challenge. In this paper, we want to give a contribution to this novel endeavour by focusing on the task of forecasting semantic concepts in the research domain. Indeed, ontologies representing scientific disciplines contain only research topics that are already popular enough to be selected by human experts or automatic algorithms. They are thus unfit to support tasks which require the ability of describing and exploring the forefront of research, such as trend detection and horizon scanning. We address this issue by introducing the Semantic Innovation Forecast (SIF) model, which predicts new concepts of an ontology at time t + 1, using only data available at time t. Our approach relies on lexical innovation and adoption information extracted from historical data. We evaluated the SIF model on a very large dataset consisting of over one million scientific papers belonging to the Computer Science domain: the outcomes show that the proposed approach offers a competitive boost in mean average precision-at-ten compared to the baselines when forecasting over 5 years.

Integration of process planning and scheduling using mobile-agent based approach in a networked manufacturing environment

Effective and efficient implementation of intelligent and/or recently emerged networked manufacturing systems require an enterprise level integration. The networked manufacturing offers several advantages in the current competitive atmosphere by way to reduce, by shortening manufacturing cycle time and maintaining the production flexibility thereby achieving several feasible process plans. The first step in this direction is to integrate manufacturing functions such as process planning and scheduling for multi-jobs in a network based manufacturing system. It is difficult to determine a proper plan that meets conflicting objectives simultaneously. This paper describes a mobile-agent based negotiation approach to integrate manufacturing functions in a distributed manner; and its fundamental framework and functions are presented. Moreover, ontology has been constructed by using the Protégé software which possesses the flexibility to convert knowledge into Extensible Markup Language (XML) schema of Web Ontology Language (OWL) documents. The generated XML schemas have been used to transfer information throughout the manufacturing network for the intelligent interoperable integration of product data models and manufacturing resources. To validate the feasibility of the proposed approach, an illustrative example along with varied production environments that includes production demand fluctuations is presented and compared the proposed approach performance and its effectiveness with evolutionary algorithm based Hybrid Dynamic-DNA (HD-DNA) algorithm. The results show that the proposed scheme is very effective and reasonably acceptable for integration of manufacturing functions.

Forms, Foundations, and the Ethos of Foremost: Zen Practice, Epistemology, and Ontology in Reflective Knowledge Organization

In reflecting on the practice of knowledge organization, we tacitly or explicitly root our conceptions of work and its value in some epistemic and ontological foundation. Zen Buddhist philosophy offers a unique set of conceptions vis-à-vis organizing, indexing, and describing documents.When we engage in knowledge organization, we are setting our mind to work with an intention. We intend to make some sort of intervention. We then create a form a realization of an abstraction (like classes or terms) [1], we do this from a foundation of some set of beliefs (epistemology, ontology, and ethics), and because we have to make decisions about what to privilege, we need to decide what is foremost in our minds. We must ask what is the most important thing?Form, foundation, and the ethos of foremost require evoke in our reflection on work number of ethical, epistemic, and ontological concerns that ripple throughout our conceptions of space, “good work”, aesthetics, and moral mandate [2,3]. We reflect on this.

Criação de uma ontologia e respectiva povoação a partir do processamento de relatórios médicos

A evolução tecnológica tem provocado uma evolução na medicina, através de sistemas computacionais voltados para o armazenamento, captura e disponibilização de informações médicas. Os relatórios médicos são, na maior parte das vezes, guardados num texto livre não estruturado e escritos com vocabulário proprietário, podendo ocasionar falhas de interpretação. Através das linguagens da Web Semântica, é possível utilizar antologias como modo de estruturar e padronizar a informação dos relatórios médicos, adicionando¬ lhe anotações semânticas. A informação contida nos relatórios pode desta forma ser publicada na Web, permitindo às máquinas o processamento automático da informação. No entanto, o processo de criação de antologias é bastante complexo, pois existe o problema de criar uma ontologia que não cubra todo o domínio pretendido. Este trabalho incide na criação de uma ontologia e respectiva povoação, através de técnicas de PLN e Aprendizagem Automática que permitem extrair a informação dos relatórios médicos. Foi desenvolvida uma aplicação, que permite ao utilizador converter relatórios do formato digital para o formato OWL. ABSTRACT: Technological evolution has caused a medicine evolution through computer systems which allow storage, gathering and availability of medical information. Medical reports are, most of the times, stored in a non-structured free text and written in a personal way so that misunderstandings may occur. Through Semantic Web languages, it’s possible to use ontology as a way to structure and standardize medical reports information by adding semantic notes. The information in those reports can, by these means, be displayed on the web, allowing machines automatic information processing. However, the process of creating ontology is very complex, as there is a risk creating of an ontology that not covering the whole desired domain. This work is about creation of an ontology and its population through NLP and Machine Learning techniques to extract information from medical reports. An application was developed which allows the user to convert reports from digital for¬ mat to OWL format.

Barn owl feathers as biomonitors of mercury: sources of variation

Given their central role in mercury (Hg) excretion and suitability as reservoirs, bird feathers are useful Hg biomonitors. Nevertheless, the interpretation of Hg concentrations is still questioned as a result of a poor knowledge of feather physiology and mechanisms affecting Hg deposition. Given the constraints of feather availability to ecotoxicological studies, we tested the effect of intraindividual differences in Hg concentrations according to feather type (body vs. flight feathers), position in the wing and size (mass and length) in order to understand how these factors could affect Hg estimates. We measured Hg concentration of 154 feathers from 28 un-moulted barn owls (Tyto alba), collected dead on roadsides. Median Hg concentration was 0.45 (0.076–4.5) mg kg-1 in body feathers, 0.44 (0.040–4.9) mg kg-1 in primary and 0.60 (0.042–4.7) mg kg-1 in secondary feathers, and we found a poor effect of feather type on intra-individual Hg levels. We also found a negative effect of wing feather mass on Hg concentration but not of feather length and of its position in the wing. We hypothesize that differences in feather growth rate may be the main driver of between-feather differences in Hg concentrations, which can have implications in the interpretation of Hg concentrations in feathers. Finally, we recommend that, whenever possible, several feathers from the same individual should be analysed. The five innermost primaries have lowest mean deviations to both betweenfeather and intra-individual mean Hg concentration and thus should be selected under restrictive sampling scenarios.

Empirical ontology design patterns

Knowledge graphs (KGs) and ontologies have been widely adopted for modelling numerous domains. However, understanding the content of an ontology/KG is far from straightforward: existing methods partially address this issue. This thesis is based on the assumption that identifying the Ontology Design Patterns (ODPs) in an ontology or a KG contributes to address this problem. Most times, the reused ODPs are not explicitly annotated, or their reuse is unintentional. Therefore, there is a challenge to automatically identify ODPs in existing ontologies and KGs, which is the main focus of this research work. This thesis analyses the role of ODPs in ontology engineering, through experiences in actual ontology projects, placing this analysis in the context of existing ontology reuse approaches. Moreover, this thesis introduces a novel method for extracting empirical ODPs (EODPs) from ontologies, and a novel method for extracting EODPs from knowledge graphs, whose schemas are implicit. The first method groups the extracted EODPs in clusters: conceptual components. Each conceptual component represents a modelling problem, e.g. representing collections. As EODPs are fragments possibly extracted from different ontologies, some of them will fall in the same cluster, meaning that they are implemented solutions to the same modelling problem. EODPs and conceptual components enable the empirical observation and comparison of modelling solutions to common modelling problems in different ontologies. The second method extracts EODPs from a KG as sets of probabilistic axioms/constraints involving the ontological entities instantiated. These EODPs may support KG inspection and comparison, providing insights on how certain entities are described in a KG. An additional contribution of this thesis is an ontology for annotating ODPs in ontologies and KGs.

Supporting requirement elicitation and ontology testing in knowledge graph engineering

Knowledge graphs and ontologies are closely related concepts in the field of knowledge representation. In recent years, knowledge graphs have gained increasing popularity and are serving as essential components in many knowledge engineering projects that view them as crucial to their success. The conceptual foundation of the knowledge graph is provided by ontologies. Ontology modeling is an iterative engineering process that consists of steps such as the elicitation and formalization of requirements, the development, testing, refactoring, and release of the ontology. The testing of the ontology is a crucial and occasionally overlooked step of the process due to the lack of integrated tools to support it. As a result of this gap in the state-of-the-art, the testing of the ontology is completed manually, which requires a considerable amount of time and effort from the ontology engineers. The lack of tool support is noticed in the requirement elicitation process as well. In this aspect, the rise in the adoption and accessibility of knowledge graphs allows for the development and use of automated tools to assist with the elicitation of requirements from such a complementary source of data. Therefore, this doctoral research is focused on developing methods and tools that support the requirement elicitation and testing steps of an ontology engineering process. To support the testing of the ontology, we have developed XDTesting, a web application that is integrated with the GitHub platform that serves as an ontology testing manager. Concurrently, to support the elicitation and documentation of competency questions, we have defined and implemented RevOnt, a method to extract competency questions from knowledge graphs. Both methods are evaluated through their implementation and the results are promising.

Knowledge-based Chord Embeddings

This thesis develops AI methods as a contribution to computational musicology, an interdisciplinary field that studies music with computers. In systematic musicology a composition is defined as the combination of harmony, melody and rhythm. According to de La Borde, harmony alone "merits the name of composition". This thesis focuses on analysing the harmony from a computational perspective. We concentrate on symbolic music representation and address the problem of formally representing chord progressions in western music compositions. Informally, chords are sets of pitches played simultaneously, and chord progressions constitute the harmony of a composition. Our approach combines ML techniques with knowledge-based techniques. We design and implement the Modal Harmony ontology (MHO), using OWL. It formalises one of the most important theories in western music: the Modal Harmony Theory. We propose and experiment with different types of embedding methods to encode chords, inspired by NLP and adapted to the music domain, using both statistical (extensional) knowledge by relying on a huge dataset of chord annotations (ChoCo), intensional knowledge by relying on MHO and a combination of the two. The methods are evaluated on two musicologically relevant tasks: chord classification and music structure segmentation. The former is verified by comparing the results of the Odd One Out algorithm to the classification obtained with MHO. Good performances (accuracy: 0.86) are achieved. We feed a RNN for the latter, using our embeddings. Results show that the best performance (F1: 0.6) is achieved with embeddings that combine both approaches. Our method outpeforms the state of the art (F1 = 0.42) for symbolic music structure segmentation. It is worth noticing that embeddings based only on MHO almost equal the best performance (F1 = 0.58). We remark that those embeddings only require the ontology as an input as opposed to other approaches that rely on large datasets.

De Novo Assembly And Transcriptome Analysis Of The Rubber Tree (hevea Brasiliensis) And Snp Markers Development For Rubber Biosynthesis Pathways.

Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection.

Trabalho, tempo livre e emancipação humana : os determinantes ontologicos das politicas sociais de lazer

Universidade Estadual de Campinas . Faculdade de Educação Física

A selvagem dança do corpo

Universidade Estadual de Campinas . Faculdade de Educação Física

Fire management and the nesting of Athene cunicularia (Aves, Strigidae) in grasslands in central Cerrado, Brazil

Fire management is a common practice in several reserves in the Cerrado, but its influences on bird reproduction remain unknown. In addition, the nesting biology of the Burrowing Owl (Athene cunicularia) has been studied in numerous environments, but not in tropical grasslands managed by fire. This study examined the effects of fire management on the nesting biology of A. cunicularia in Emas National Park, State of Goias, central Brazilian Cerrado. We compared the number of breeding pairs and their burrows in October and November 2009 at 15 study sites in grasslands managed by fire (firebreaks) and unmanaged grasslands adjacent to and distant from firebreaks. We visited active burrows two-four times and described the burrow entrances and sentinel sites and counted and observed adults and young. A total of 19 burrows were found at firebreaks. One and two burrows were found in grasslands adjacent to and distant from firebreaks, respectively. For all burrows found, one to three young reached the adult size, being able to fly and/or run in early November. The 22 burrows found were in the ground, associated or not with termite and ant nests. Most (86.4%) burrows had only one entrance. Only three burrows had two or three entrances. Structures used as sentinel perches by adults were mounds in front of the burrow entrances, termite nests, shrubs and trees. Most of these sentinel sites were shorter than 2 m high and located less than 10 m from the burrow entrance. At Emas National Park, firebreaks appear to provide more attractive conditions to the nesting of A. cunicularia than unmanaged grasslands, likely because of the short herbaceous stratum due to frequent burning of firebreaks. This study suggests that fire management provides suitable conditions for the successful reproduction of A. cunicularia in firebreaks at Emas National Park.

AtPIN: Arabidopsis thaliana Protein Interaction Network

Background: Protein-protein interactions (PPIs) constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets. Description: All interactions were divided into experimentally demonstrated or predicted. The PPIs in the AtPIN database present a cellular compartment classification (C(3)) which divides the PPI into 4 classes according to its interaction evidence and subcellular localization. It has been shown in the literature that a pair of genuine interacting proteins are generally expected to have a common cellular role and proteins that have common interaction partners have a high chance of sharing a common function. In AtPIN, due to its integrative profile, the reliability index for a reported PPI can be postulated in terms of the proportion of interaction partners that two proteins have in common. For this, we implement the Functional Similarity Weight (FSW) calculation for all first level interactions present in AtPIN database. In order to identify target proteins of cytosolic glutamyl-tRNA synthetase (Cyt-gluRS) (AT5G26710) we combined two approaches, AtPIN search and yeast two-hybrid screening. Interestingly, the proteins glutamine synthetase (AT5G35630), a disease resistance protein (AT3G50950) and a zinc finger protein (AT5G24930), which has been predicted as target proteins for Cyt-gluRS by AtPIN, were also detected in the experimental screening. Conclusions: AtPIN is a friendly and easy-to-use tool that aggregates information on Arabidopsis thaliana PPIs, ontology, and sub-cellular localization, and might be a useful and reliable strategy to map protein-protein interactions in Arabidopsis. AtPIN can be accessed at http://bioinfo.esalq.usp.br/atpin.

Chicken skeletal muscle-associated macroarray for gene discovery

Macro- and microarrays are well-established technologies to determine gene functions through repeated measurements of transcript abundance. We constructed a chicken skeletal muscle-associated array based on a muscle-specific EST database, which was used to generate a tissue expression dataset of similar to 4500 chicken genes across 5 adult tissues (skeletal muscle, heart, liver, brain, and skin). Only a small number of ESTs were sufficiently well characterized by BLAST searches to determine their probable cellular functions. Evidence of a particular tissue-characteristic expression can be considered an indication that the transcript is likely to be functionally significant. The skeletal muscle macroarray platform was first used to search for evidence of tissue-specific expression, focusing on the biological function of genes/transcripts, since gene expression profiles generated across tissues were found to be reliable and consistent. Hierarchical clustering analysis revealed consistent clustering among genes assigned to 'developmental growth', such as the ontology genes and germ layers. Accuracy of the expression data was supported by comparing information from known transcripts and tissue from which the transcript was derived with macroarray data. Hybridization assays resulted in consistent tissue expression profile, which will be useful to dissect tissue-regulatory networks and to predict functions of novel genes identified after extensive sequencing of the genomes of model organisms. Screening our skeletal-muscle platform using 5 chicken adult tissues allowed us identifying 43 'tissue-specific' transcripts, and 112 co-expressed uncharacterized transcripts with 62 putative motifs. This platform also represents an important tool for functional investigation of novel genes; to determine expression pattern according to developmental stages; to evaluate differences in muscular growth potential between chicken lines, and to identify tissue-specific genes.