Ontology-based knowledge representation of experiment metadata in biological data mining

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes

A short survey of discourse representation models

With the advancement of technology and the wide adoption of ontologies as knowledge representation formats, in the last decade, a handful of models were proposed for the externalization of the rhetoric and argumentation captured within scientific publications. Conceptually, most of these models share a similar representation form of the scientific publication, i.e. as a series of interconnected elementary knowledge items. The main differences are given by the terminology used, the types of rhetorical and/or argumentation relations connecting the knowledge items and the foundational theories supporting these relations. This paper analyzes the state of the art and provides a concise comparative overview of the five most prominent discourse representation models, with the goal of sketching an unified model for discourse representation

Optimization of DNA extraction from human urinary samples for mycobiome community profiling.

IntroductionRecent data suggest the urinary tract hosts a microbial community of varying composition, even in the absence of infection. Culture-independent methodologies, such as next-generation sequencing of conserved ribosomal DNA sequences, provide an expansive look at these communities, identifying both common commensals and fastidious organisms. A fundamental challenge has been the isolation of DNA representative of the entire resident microbial community, including fungi.Materials and methodsWe evaluated multiple modifications of commonly-used DNA extraction procedures using standardized male and female urine samples, comparing resulting overall, fungal and bacterial DNA yields by quantitative PCR. After identifying protocol modifications that increased DNA yields (lyticase/lysozyme digestion, bead beating, boil/freeze cycles, proteinase K treatment, and carrier DNA use), all modifications were combined for systematic confirmation of optimal protocol conditions. This optimized protocol was tested against commercially available methodologies to compare overall and microbial DNA yields, community representation and diversity by next-generation sequencing (NGS).ResultsOverall and fungal-specific DNA yields from standardized urine samples demonstrated that microbial abundances differed significantly among the eight methods used. Methodologies that included multiple disruption steps, including enzymatic, mechanical, and thermal disruption and proteinase digestion, particularly in combination with small volume processing and pooling steps, provided more comprehensive representation of the range of bacterial and fungal species. Concentration of larger volume urine specimens at low speed centrifugation proved highly effective, increasing resulting DNA levels and providing greater microbial representation and diversity.ConclusionsAlterations in the methodology of urine storage, preparation, and DNA processing improve microbial community profiling using culture-independent sequencing methods. Our optimized protocol for DNA extraction from urine samples provided improved fungal community representation. Use of this technique resulted in equivalent representation of the bacterial populations as well, making this a useful technique for the concurrent evaluation of bacterial and fungal populations by NGS

Planning Curricular Proposals on Sound and Music with Prospective Secondary-School Teachers

Sound is a preferred context to build foundations on wave phenomena, one of the most important disciplinary referents in physics. It is also one of the best-set frameworks to achieve transversality, overcoming scholastic level and activating emotional aspects which are naturally connected with every day life, as well as with music and perception. Looking at sound and music by a transversal perspective - a border-line approach between science and art, is the adopted statement for a teaching proposal using meta-cognition as a strategy in scientific education. This work analyzes curricular proposals on musical acoustics, planned by prospective secondary-school teachers in the framework of a Formative Intervention Module answering the expectation of making more effective teaching scientific subjects by improving creative capabilities, as well as leading to build logical and scientific categorizations able to consciously discipline artistic activity in music students. With this aim, a particular emphasis is given to those concepts - like sound parameters and structural elements of a musical piece, which are best fitted to be addressed on a transversal perspective, involving simultaneously physics, psychophysics and music.Comment: 12 pages with 5 figures. Submitted for publication in Physics Curriculum Design, Development and Validation - GIREP 2008 book of selected papers, 200

An Investigation of Student Engagement in a Global Warming Debate

NOTE: This is a large file, 77 mb in size! This article describes an investigation into how using debate as a pedagogical tool for addressing earth system science concepts can promote active student learning, present a realistic and dynamic view of science, and provide a mechanism for integrating the scientific, political and social dimensions of global environmental change. Using global warming as an example of earth system science, the authors consider how participation in debate provides an avenue for engaging students in science. The investigation draws from studies of school science that focus on the use of argument as a pedagogical tool and examines how students make use of observationally-based climatic data sets when debating the cause of global warming. Educational levels: Graduate or professional