Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

Working within the sensing, intuition, feeling, thinking (SIFT) approach to biblical hermeneutics, the present study invited a hermeneutical community of 23 type-aware participants to explore the account of the Death of Lazarus as reported in John 11: 1–17 within type-alike groups differentiated according to the participants’ dominant function-orientation. Five groups were constituted differentiating: introverted sensing, introverted intuition, extraverted intuition, introverted and extraverted feeling and introverted and extraverted thinking. These five groups generated distinctive readings of the narrative that were characteristic of (...) the individual type preference. Contribution: The SIFT method, situated within the reader perspective approach to biblical hermeneutics, is concerned with attending to the influence exerted by the psychological type profile of the reader on interpreting the text. The present study goes beyond previous work by comparing the responses of five hermeneutical communities (each distinguished by a different dominant function-orientation) to the same passage of scripture. (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)

Philosophers and geographers have converged on the topic of public space, fascinated and in many ways alarmed by fundamental changes in the way post-industrial societies produce space for public use, and in the way citizens of these same societies perceive and constitute themselves as a public. This volume advances this inquiry, making extensive use of political and social theory, while drawing intimate connections between political principles, social processes, and the commonplaces of our everyday environments.

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)

John L. Austin believed that in the illocution he had discovered a fundamental element of our speech, the understanding of which would disclose the significance of all kinds of linguistic action: not only proposing marriage and finding guilt, but also stating, reporting, conjecturing, and all the rest of the things men can do linguistically. 2 We claim that the illocution, the full-fledged speech-act, is central to religious utterances as well, and that it provides a perspicuity in understanding them not elsewhere (...) provided in the work of recent philosophy of religion. In particular we hold that understanding religious talk through the illocution shows the way in which the representative and affective elements are connected to one another and to the utterance as a whole. There may, further, be features in such an analysis which can be extended to other forms of discourse than religious. (shrink)

The importance of working memory in reading and mathematics performance has been widely studied, with recent research examining the components of WM and their roles in these educational outcomes. However, the differing relationships between these abilities and the foundational skills involved in the development of reading and mathematics have received less attention. Additionally, the separation of verbal, visual and spatial storage and processing and subsequent links with foundational skills and downstream reading and mathematics has not been widely examined. The current (...) study investigated the separate contributions of processing and storage from verbal, visual and spatial tasks to reading and mathematics, whilst considering influences on the underlying skills of verbal comprehension and counting, respectively. Ninety-two children aged 7- to 8-years were assessed. It was found that verbal comprehension was predicted by verbal storage and reading was predicted by verbal and spatial storage. Counting was predicted by visual processing and storage, whilst mathematics was related to verbal and spatial storage. We argue that resources for tasks relying on external representations of stimuli related mainly to storage, and were largely verbal and spatial in nature. When a task required internal representation, there was a draw on visual processing and storage abilities. Findings suggest a possible meaningful separability of types of processing. Further investigation of this could lead to the development of an enhanced WM model, which might better inform interventions and reasonable adjustments for children who struggle with reading and mathematics due to WM deficits. (shrink)

Working memory deficits are pervasive co-morbidities of epilepsy. Although the pathophysiological mechanisms underpinning these impairments remain elusive, it is thought that WM depends on oscillatory interactions within and between nodes of large-scale functional networks. These include the hippocampus and default mode network as well as the prefrontal cortex and frontoparietal central executive network. Here, we review the functional roles of neural oscillations in subserving WM and the putative mechanisms by which epilepsy disrupts normative activity, leading to aberrant oscillatory signatures. We (...) highlight the particular role of interictal epileptic activity, including interictal epileptiform discharges and high frequency oscillations in WM deficits. We also discuss the translational opportunities presented by greater understanding of the oscillatory basis of WM function and dysfunction in epilepsy, including potential targets for neuromodulation. (shrink)

Applying ideas drawn from contemporary critical theory, this book historicizes psychoanalysis through a new and significant theorization of the Gothic. The central premise is that the nineteenth-century Gothic produced a radical critique of accounts of sublimity and Freudian psychoanalysis. This book makes a major contribution to an understanding of both the nineteenth century and the Gothic discourse which challenged the dominant ideas of that period. Writers explored include Mary Shelley, Edgar Allan Poe, Robert Louis Stevenson, and Bram Stoker.

Contemporary literature on consciousness, with some exceptions, rarely considers the olfactory system. In this article the characteristics of olfactory consciousness, viewed from the standpoint of the phenomenal /access distinction, are examined relative to the major senses. The review details several qualitative differences in both olfactory P consciousness and A consciousness . The basis for these differences is argued to arise from the functions that the olfactory system performs and from the unique neural architecture needed to instantiate them. These data suggest, (...) at a minimum, that P and A consciousness are uniquely configured in olfaction and an argument can be made that the P and A distinction may not hold for this sensory system. (shrink)

How (Not) to Be Secular is what Jamie Smith calls "your hitchhiker's guide to the present" -- it is both a reading guide to Charles Taylor's monumental work A Secular Age and philosophical guidance on how we might learn to live in our times. Taylor's landmark book A Secular Age (2007) provides a monumental, incisive analysis of what it means to live in the post-Christian present -- a pluralist world of competing beliefs and growing unbelief. Jamie Smith's book (...) is a compact field guide to Taylor's insightful study of the secular, making that very significant but daunting work accessible to a wide array of readers. Even more, though, Smith's How (Not) to Be Secular is a practical philosophical guidebook, a kind of how-to manual on how to live in our secular age. It ultimately offers us an adventure in self-understanding and maps out a way to get our bearings in today's secular culture, no matter who "we" are -- whether believers or skeptics, devout or doubting, self-assured or puzzled and confused. This is a book for any thinking person to chew on. (shrink)

Prologue, invitation to thinking about God In the Hebrew Bible? -- Part I, questions about God? -- Why does God in the Bible have a body? -- What do God's body parts in the Bible mean? -- Why is God angry in the Bible? -- Does God in the Bible have gender or sexuality? -- Part II, questions about God in the world? -- What can creation tell us about God? -- Who-or what-is the Satan? -- Why do people suffer (...) according to the Hebrew Bible? -- Epilogue, God in the Bible and beyond. (shrink)

The Descartes Dictionary is an accessible guide to the world of the seventeenth-century philosopher René Descartes. Meticulously researched and extensively cross-referenced, this unique book covers all his major works, ideas and influences, and provides a firm grounding in the central themes of Descartes' thought. The introduction provides a biographical sketch, a brief account of Descartes' philosophical works, and a summary of the current state of Cartesian studies, discussing trends in research over the past four decades. The A-Z entries include clear (...) definitions of the key terms used in Descartes' writings and detailed synopses of his works. Also included are entries noting philosophical influences, of both figures that influenced Descartes and those that he in turn influenced. For anyone reading or studying Descartes, rationalism, or modern philosophy more generally, this original resource provides a wealth of useful information, analysis, and criticism. Including clear explanations of often complex terminology, The Descartes Dictionary covers everything that is essential to a sound understanding of Descartes' philosophy. (shrink)

Introduction: Christian moral action -- Stanley Hauerwas -- Reinhard Hütter -- Common threads -- Thomas Aquinas -- Toward an ecumenical ethic of grace -- Conclusion: A community-centered ecumenical ethic of grace.

This article suggests evidence for and reasons why prior acquisition may either facilitate or inhibit acquisition of a new construction. It investigates acquisition of the German passive and future constructions which contain a lexical verb with either the auxiliary sein “to be” or werden “to become”, and are related through these to potential supporting constructions. We predicted that a supported construction should be acquired earlier, faster, and unusually rapidly. An inhibited construction should show an extended depressed usage. We analyzed a (...) dense corpus of a German boy between 2;0 and 5;0. He acquired the sein- before the werden-passive. The former was supported by his prior acquisition of the sein copula, whereas the werden-passive itself supported one werden copula construction. He acquired the werden-future extremely slowly due to the hindrance of a semantically identical construction. These results fit with an emergentist approach in which apparently “sudden” acquisition is still due to gradual learning mechanisms. (shrink)

Narrative theology views the truths of scripture through an iconographic lens to indicate God's intimate involvement in human life. However, when narrative theology becomes "narrative theological ethics," the transformative power of narrative about God receives more emphasis than the power of God itself. Narrative theology quickly moves toward linguistic idolatry when God's grace is valued merely as an important facet of a powerful narrative rather than as the foundation of Christian moral action.