The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

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. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Starting from the premise that firms are distinct in terms of their capacity to create innovations, this article explores the rationale for R&D cooperation and the choice between alliances that involve information sharing, cost sharing or both. Defining innovative capability as the probability of creating an innovation, it examines firm strategy in a duopoly market, where firms have to decide whether or not to cooperate to acquire a fixed cost R&D infrastructure that would endow each firm with a firm-specific innovative (...) capability. Furthermore, since emerging industries are often characterized by high technological uncertainty and diverse firm focus that makes the exploitation of spillovers difficult, this article focuses on a zero spillover context. It demonstrates that asymmetry has an impact on alliance choice and social welfare, as a function of ex-post market competition and fixed costs of R&D. With significant asymmetry no alliance may be formed, while with similar firms the cost sharing alliance is dominant. Finally, it ascertains the settings under which the equilibrium outcome is distinct from that maximizing social welfare, thereby highlighting some conditions under which public investment in a technology park can be justified. (shrink)

We propose a naturalistic version of the “guesser–knower” paradigm in which the experimental subject has an opportunity to choose which individual to follow to a hidden food source. This design allows nonhumans to display the attribution of knowledge to another conspecific, rather than a human, in a naturalistic context (finding food), and it is readily adapted to different species.

SummaryAs part of a prospective controlled study of the psychosomatic effects of elective tubal sterilization, 138 women were questioned about their menstrual functioning before sterilization, and again 6 months and 12 months post-operatively, using standardized interviewing procedures. Adverse changes, including increased menstrual loss, shorter menstrual cycles and greater use of pads or tampons were reported by sterilized subjects at both of the post-operative interviews. Control subjects reported several comparable effects, although adverse changes overall were reported more commonly by sterilized women (...) than by control subjects. However, many of the reported changes appeared to be related to pre-operative contraceptive methods, although consistent increases in use of pads or tampons were found in women who had pre-operatively used neither the pill nor the IUD. (shrink)

The game theoretical approach to R&D cooperation does not investigate the role of trust in the initiation and success of R&D cooperation: it either assumes that firms are non-opportunists or that the R&D cooperation is supported by an incentive mechanism that eliminates opportunism. In contrast, the present paper focuses on these issues by introducing incomplete information and two types of firms: opportunist and non-opportunist. Defining trust as the belief of each firm that its potential collaborator will respect the contract, it (...) identifies the trust conditions under which firms initiate R&D alliances and contribute to their success. The higher the spillovers, the higher the level of trust required to initiate R&D cooperation for non-opportunists, while the inverse holds for opportunists. (shrink)

Mary P. Nichols, Socrates on Friendship and Community: Reflections on Plato’s Symposium, Phaedrus, and Lysis. Cambridge: Cambridge University Press, 2008. Pp. viii + 229. ISBN 978-0-521-89973-4. Laurence D. Cooper, Eros in Plato, Rousseau, and Nietzsche: The Politics of Infinity. University Park: The Pennsylvania State University Press, 2008. Pp. xii + 357. ISBN 978-0-271-03330-3.

With rapid changes in technology, knowledge innovation has become more and more complex. Complex partners facilitate knowledge creation and innovation in complex problem-solving. Relying on R&D cooperation with forerunners, latecomers can acquire new knowledge factors and new ideas and use them to create new knowledge. This study demonstrated the knowledge innovation mechanism based on linkages between periphery knowledge and core knowledge with knowledge map theory and set methodology. A case of R&D cooperation between latecomers and forerunners was introduced to verify (...) this mechanism. The results show that latecomers could share forerunners’ periphery knowledge in R&D cooperation through formal and informal interaction and acquire the core knowledge factors in periphery knowledge based on the linkages between them. With these core knowledge factors, latecomers integrate them into their internal knowledge system and create new knowledge. By analyzing the linkages between periphery and core knowledge factors, this study creatively demonstrates the knowledge innovation mechanism in knowledge linkage perspective. It deepens the understanding of R&D cooperation between latecomers and forerunners and expands the focus of knowledge innovation theory. This study provides a new insight into latecomers effectively activating internal and external knowledge resources through R&D cooperation. (shrink)

In the report, the author raises the problem of personal freedom, referring to the concept of metanoia by R. Laing and D. Cooper. On the basis of Laing's ideas, the understanding of freedom is conceptualized as the acquisition of a true "I" through the experience of mental illness, which was introduced into the field of philosophical comprehension. Using the example of Cooper's metanoia scheme, the transition from the state of alienation and adaptation to free self-realization as from unreasonableness (...) to sanity is considered. The author raises the question about the criteria of norm and pathology in the course of realization of personal freedom. The urgency of the further development of Laing's and Cooper's ideas in the aspect of the possibility of implementing existential metanoia in the modern socio-cultural context is substantiated. (shrink)

An ongoing study examining the discursive negotiation of ethnic and gendered embodied identities of adolescent girls in Japan with Japanese and `white' mixed-parentage is extended to also investigate and compare boys. This study draws on Feminist Poststructuralist Discourse Analysis which views women and girls as `simultaneously positioned as relatively powerless within a range of dominant discourses on gender, but as relatively powerful within alternative and competing social discourses'. Here, this is taken further by also giving voice to boys. Furthermore, ethnic (...) discourses are examined alongside of gender discourses. Not only girls constructed the `idealized Other', within discourses of femininity, but boys similarly viewed their bodies against a model of idealized masculinity within discourses of masculinities. The boys revealed a feminized, narcissistic body consciousness where they struggled to resist a `discourse of foreign grotesqueness' and instead worked to embody themselves within a positive `discourse of foreign attractiveness', as did the girls. (shrink)

ABSTRACTAlthough social anxiety symptoms are robustly linked to biased self-evaluations across time, the mechanisms of this relation remain unclear. The present study tested three maladaptive emotion regulation strategies – state post-event processing, state experiential avoidance, and state expressive suppression – as potential mediators of this relation. Undergraduate participants rated their social skill in an impromptu conversation task and then returned to the laboratory approximately two days later to evaluate their social skill in the conversation again. Consistent with expectations, state post-event (...) processing and state experiential avoidance mediated the relation between social anxiety symptoms and worsening self-evaluations of social skill, particularly for positive qualities. State expressive suppression did not mediate the relation between social anxiety symptoms and cha... (shrink)

By constructing a maximal incomplete d.r.e. degree, the nondensity of the partial order of the d.r.e. degrees is established. An easy modification yields the nondensity of the n-r.e. degrees and of the ω-r.e. degrees.

Philosophers constantly discuss Responsibility. Yet in every discussion of which I am aware, a rather obvious point is ignored. The obvious point is that responsibility is ascribed to collectives, as well as to individual persons. Blaming attitudes are held towards collectives as well as towards individuals. Responsibility is often ascribed to nations, towns, clubs, groups, teams, and married couples. ‘Germany was responsible for the Second World War’; ‘The club as a whole is to blame for being relegated’. Such statements are (...) not rare. (shrink)

Burning fossil fuel in the North American continent contributes more to the CO2 global warming problem than in any other continent. The resulting climate changes are expected to alter food production. The overall changes in temperature, moisture, carbon dioxide, insect pests, plant pathogens, and weeds associated with global warming are projected to reduce food production in North America. However, in Africa, the projected slight rise in rainfall is encouraging, especially since Africa already suffers from severe shortages of rainfall. For all (...) regions, a reduction in fossil fuel burning is vital. Adoption of sound ecological resource management, especially soil and water conservation and the prevention of deforestation, is important. Together, these steps will benefit agriculture, the environment, farmers, and society as a whole. (shrink)

Live donor kidney transplantation is the best treatment option for most patients with late-stage chronic kidney disease; however, the rate of living kidney donation has declined in the United States. A consensus conference was held June 5-6, 2014 to identify best practices and knowledge gaps pertaining to live donor kidney transplantation and living kidney donation. Transplant professionals, patients, and other key stakeholders discussed processes for educating transplant candidates and potential living donors about living kidney donation; efficiencies in the living donor (...) evaluation process; disparities in living donation; and financial and systemic barriers to living donation. We summarize the consensus recommendations for best practices in these educational and clinical domains, future research priorities, and possible public policy initiatives to remove barriers to living kidney donation. (shrink)

Can civic engagement rescue the humanities from a prolonged identity crisis? How can the practices and methods, the conventions and innovations of humanities teaching and scholarship yield knowledge that contributes to the public good? These are just two of the vexing questions David D. Cooper tackles in his essays on the humanities, literacy, and public life. As insightful as they are provocative, these essays address important issues head-on and raise questions about the relevance and roles of humanities teaching and (...) scholarship, the moral footings and public purposes of the humanities, engaged teaching practices, institutional and disciplinary reform, academic professionalism, and public scholarship in a democracy. Destined to stir discussion about the purposes of the humanities and the problems we face during an era of declining institutional support, public alienation and misunderstanding, student ambivalence, and diminishing resources, the questions Cooper raises in this book are uncomfortable and, in his view, necessary for reflection, renewal, and reform. With frank, deft assessments, Cooper reports on active learning initiatives that reenergized his own teaching life while reshaping the teaching mission of the humanities, including service learning, collaborative learning, the learning community movement, and student-centered and deliberative pedagogy. (shrink)