Critical Thinking Activities and the Enhancement of Ethical Awareness: An application of a ‘Rhetoric of Disruption’ to the undergraduate general education classroom

This article explores how critical thinking activities and assignments can function to enhance students’ ethical awareness and sense of civic responsibility. Employing Levinas’s Othercentered theory of ethics, Burke’s notion of ‘the paradox of substance’, and Murray’s concept of ‘a rhetoric of disruption’, this article explores the nature of critical thinking activities designed to have students question their (often taken-for-granted) moral assumptions and interrogate their (often unexamined) moral identities. This article argues that such critical thinking activities can trigger a metacognitive destabilization of subjectivity, understood as a dialectical prerequisite (along with exposure to otherness) for increased ethical awareness. This theoretical model is illustrated through a discussion of three sample classroom activities designed to destabilize moral assumptions and identity, thereby clearing the way for a heightened acknowledgment of otherness. In so doing, this article provides an alternative (and dialectically inverted) strategy for addressing one of the central goals of many General Education curricula: the development of ethical awareness and civic responsibility. Rather than introducing students to alternative perspectives and divergent cultures with the expectation that heightened moral awareness will follow, this article suggests classroom activities and course assignments aimed at disrupting moral subjectivity and creating an opening in which otherness can be more fully acknowledged and the diversity of our world more fully appreciated

The roles of the DAZ family in spermatogenesis: More than just translation?

The DAZ family of genes are important fertility factors in animals, including humans. The family consists of Y-linked DAZ, and autosomal homologs Boule and Dazl. All three genes encode RNA-binding proteins that are nearly exclusively expressed in germ cells. The DAZ family is highly conserved, with ancestral Boule present in sea anemones through humans, Dazl conserved among vertebrates, and DAZ present only in higher primates. Here we review studies on DAZ family genes from multiple organisms, and summarize the common features of each DAZ gene and their roles during spermatogenesis in animals. DAZ family proteins are thought to activate the translation of RNA targets, but recent work has uncovered additional functions. Boule, Dazl, and DAZ likely function through similar mechanisms, and we present known functions of the DAZ family in spermatogenesis, and discuss possible mechanisms in addition to translation activation

OntoFox: web-based support for ontology reuse

<p>Abstract</p> <p>Background</p> <p>Ontology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, the OBO Foundry principles require that these ontologies be open and non-redundant, avoiding duplication of terms through the re-use of existing resources. As current options to do so present various difficulties, a new approach, MIREOT, allows specifying import of single terms. Initial implementations allow for controlled import of selected annotations and certain classes of related terms.</p> <p>Findings</p> <p>OntoFox <url>http://ontofox.hegroup.org/</url> is a web-based system that allows users to input terms, fetch selected properties, annotations, and certain classes of related terms from the source ontologies and save the results using the RDF/XML serialization of the Web Ontology Language (OWL). Compared to an initial implementation of MIREOT, OntoFox allows additional and more easily configurable options for selecting and rewriting annotation properties, and for inclusion of all or a computed subset of terms between low and top level terms. Additional methods for including related classes include a SPARQL-based ontology term retrieval algorithm that extracts terms related to a given set of signature terms and an option to extract the hierarchy rooted at a specified ontology term. OntoFox's output can be directly imported into a developer's ontology. OntoFox currently supports term retrieval from a selection of 15 ontologies accessible via SPARQL endpoints and allows users to extend this by specifying additional endpoints. An OntoFox application in the development of the Vaccine Ontology (VO) is demonstrated.</p> <p>Conclusions</p> <p>OntoFox provides a timely publicly available service, providing different options for users to collect terms from external ontologies, making them available for reuse by import into client OWL ontologies.</p

Ontology of core data mining entities

In this article, we present OntoDM-core, an ontology of core data mining entities. OntoDM-core defines themost essential datamining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. The ontology has been thoroughly assessed following the practices in ontology engineering, is fully interoperable with many domain resources and is easy to extend

VO: Vaccine Ontology

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented

Developing Nondestructive Techniques for Managing Conflicts Between Fisheries and Double-Crested Cormorant Colonies

Double-crested cormorants (Phalacrocorax auritus) have been identified as the source of significant mortality to juvenile salmonids (Oncorhynchus spp.) in the Columbia River Basin. Management plans for reducing the size of a large colony on East Sand Island (OR, USA) in the Columbia River estuary are currently being developed. We evaluated habitat enhancement and social attraction as nondestructive techniques for managing cormorant nesting colonies during 2004–2007. We tested these techniques on unoccupied plots adjacent to the East Sand Island cormorant colony. Cormorants quickly colonized these plots and successfully raised young. Cormorants also were attracted to nest and raised young on similar plots at 2 islands approximately 25 km from East Sand Island; 1 island had a history of successful cormorant nesting whereas the other was a site where cormorants had previously nested unsuccessfully. On a third island with no history of cormorant nesting or nesting attempts, these techniques were unsuccessful at attracting cormorants to nest. Our results suggest that some important factors influencing attraction of nesting cormorants using these techniques include history of cormorant nesting, disturbance, and presence of breeding cormorants nearby. These techniques may be effective in redistributing nesting cormorants away from areas where fish stocks of conservation concern are susceptible to predation, especially if sites with a recent history of cormorant nesting are available within their foraging or dispersal range.Keywords: salmonids, social attraction, Phalacrocorax auritus, predation, habitat enhancement, cormoran

EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources

Processing and Characterization of Precision Microparts from Nickel-based Materials

The objective of this research was to study the influence of electroplating parameters on electrodeposit characteristics for the production of nickel (Ni) and nickel-iron (Ni-Fe) microparts by photoelectroforming. The research focused on the most relevant parameter for industry, which is the current density, because it determines the process time and the consumed energy. The results of the Ni and Ni-Fe characterisations can be divided into two aspects closely linked with each other ; the morphology and the hardness

Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility

The Visual Orbit of the 1.1-day Spectroscopic Binary \sigma^2 Coronae Borealis from Interferometry at the CHARA Array

We present an updated spectroscopic orbit and a new visual orbit for the double-lined spectroscopic binary \sigma^2 Coronae Borealis based on radial velocity measurements at the Oak Ridge Observatory in Harvard, Massachusetts and interferometric visibility measurements at the CHARA Array on Mount Wilson. \sigma^2 CrB is composed of two Sun-like stars of roughly equal mass in a circularized orbit with a period of 1.14 days. The long baselines of the CHARA Array have allowed us to resolve the visual orbit for this pair, the shortest period binary yet resolved interferometrically, enabling us to determine component masses of 1.137 \pm 0.037 M_sun and 1.090 \pm 0.036 M_sun. We have also estimated absolute V-band magnitudes of MV (primary) = 4.35 \pm 0.02 and MV(secondary) = 4.74 \pm 0.02. A comparison with stellar evolution models indicates a relatively young age of 1-3 Gyr, consistent with the high Li abundance measured previously. This pair is the central component of a quintuple system, along with another similar-mass star, \sigma^1 CrB, in a ~ 730-year visual orbit, and a distant M-dwarf binary, \sigma CrB C, at a projected separation of ~ 10 arcmin. We also present differential proper motion evidence to show that components C & D (ADS 9979C & D) listed for this system in the Washington Double Star Catalog are optical alignments that are not gravitationally bound to the \sigma CrB system.Comment: 40 pages, 14 figures. Accepted by Ap