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 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)

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) 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)

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)

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)

Peter Abelard (1079–1142 ce) was the most wide‐ranging philosopher of the twelfth century. He quickly established himself as a leading teacher of logic in and near Paris shortly after 1100. After his affair with Heloise, and his subsequent castration, Abelard became a monk, but he returned to teaching in the Paris schools until 1140, when his work was condemned by a Church Council at Sens. His logical writings were based around discussion of the “Old Logic”: Porphyry's Isagoge, aristotle'S Categories and (...) On Interpretation and boethius'S textbook on topical inference. They comprise a freestanding Dialectica (“Logic”; probably c.1116), a set of commentaries (known as the Logica [Ingredientibus], c. 1119) and a later (c. 1125) commentary on the Isagoge (Logica Nostrorum Petititoni Sociorum or Glossulae). In a work Abelard called his Theologia, issued in three main versions (between 1120 and c.1134), he attempted a logical analysis of trinitarian relations and explored the philosophical problems surrounding God's claims to omnipotence and omniscience. The Collationes (“Debates,” also known as “Dialogue between a Christian, a Philosopher and a Jew”; probably c.1130) present a rational investigation into the nature of the highest good, in which the Christian and the Philosopher (who seems to be modeled on a philosopher of pagan antiquity) are remarkably in agreement. The unfinished Scito teipsum (“Know thyself,” also known as the “Ethics”; c.1138) analyses moral action. (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)

Perhaps the best way to understand Harold Bloom's enigmatic theory of "poetic misprision" is to avoid the immanent critique altogether. It is best described, rather , as a synthesis. Bloom seems to have taken Aristotle's mimesis and linked it to Freud's concept of sublimation,1 with particular emphasis on the role that sublimation plays in "the family romance." Even if one were to hedge a bit and take into account the fact that neo-Freudian re-evaluations of orthodox psychoanalysis have succeeded in extracting (...) the purely sexual component out of the psychodynamics of sublimation, one is still left with the notion of sublimation as anxiety producing. Thus it is that, according to Bloom, the modern poet, in particular, sublimates his imitation of a strong precursor poet. Since the emphasis today is on desexualizing libido, Freud's original sexual vocabulary seems to have survived for its metaphorical value alone; the "unconscious fear of castration," for example, is simply a metaphor for "the poet's fear of ceasing to be a poet," a man's fear of ceasing to be a man. No matter how much we "modernize" Freud, the fact will always remain that the psychoanalytic context is the context of psychopathology: "a variety of the uncanny." · 1. See Sigmund Freud, Three Contributions to the Theory of Sex, in The Basic Writings of Sigmund Freud, ed. and trans. A. A. Brill , pp. 625-26. David D. Cooper is an associate in the department of English at the University of California, Santa Barbara. Using the critical paradigm developed in the present essay, he has written a book on Thomas Merton's poetry. See also: "Poetry, Revisionism, Repression" by Harold Boom in Vol. 2, No. 2; "Formalism, Savagery, and Care; or, The Function of Criticism Once Again" by Jerome J. McGann in Vol. 2, No. 3. (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)

D E Cooper; Is Language Learned?1, Journal of Philosophy of Education, Volume 9, Issue 1, 30 May 2006, Pages 93–104, https://doi.org/10.1111/j.1467-9752.1975.tb.

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)

From March 1841 until the end of 1845, W. R. Grove held the post of Professor of Experimental Philosophy at the London Institution. No previous study of the Institution has dealt in detail with the period of Grove's tenure of this, the first professorship. Here, by reference to the various manuscripts and publications of the Institution, and to Grove's papers and correspondence, it is possible to describe the background to Grove's appointment and the achievements of his term of office.

David KC Cooper,1 David Ayares21Thomas E Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; 2Revivicor, Blacksburg, VA, USA: The transplantation of organs and cells from pigs into humans could overcome the critical and continuing problem of the lack of availability of deceased human organs and cells for clinical transplantation. Developments in the genetic engineering of pigs have enabled considerable progress to be made in the experimental laboratory in overcoming the immune barriers to successful xenotransplantation. With regard (...) to pig organ xenotransplantation, antibody- and cell-mediated rejection have largely been overcome, and the current major barrier is the development of coagulation dysregulation. This is believed to be due to a combination of immune activation of the vascular endothelial cells of the graft and molecular incompatibilities between the pig and primate coagulation–anticoagulation systems. Pigs with new genetic modifications specifically directed to this problem are now becoming available. With regard to less complex tissues, such as islets, neuronal cells, and corneas, the remaining barriers are less problematic, and graft survival in nonhuman primate models extends for >1 year in all three cases. In planning the initial clinical trials, consideration will be concentrated on the risk–benefit ratio, based to a large extent on the results of preclinical studies in nonhuman primates. If the benefit to the patient is anticipated to be high, eg, insulin-independent control of glycemia, and the potential risks low, eg, minimal risk of transfer of a porcine infectious agent, then a clinical trial would be justified.Keywords: infection, pigs, genetically-engineered, xenotransplantation, islets, xenotransplantation, organs. (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)

For the past two decades, the humanistic disciplines have been dominated by poststructuralist theories and, more recently, a not unrelated curricular philosophy best defined as hardline multiculturalism, much discussed and often misunderstood. When linked together, they form an internal contradiction that is the moral challenge of liberal education today. Traditional political alignments cannot explain current divisions among the humanities professoriate. Ideological quarrels only obscure a deeper moral debate between an ascendant poststructuralism and a resurgent liberal humanism. It is important to (...) reappropriate liberal humanism in an effort to revitalize humanistic inquiry and renew its place in creative public discourse, and check a danger posed by poststructuralism's fascination with power and epistemological relativism which threaten to erase the ethical border between education and indoctrination. (shrink)

No writer or public intellectual of our era has been as sensitive to the role of faith in the lives of ordinary Americans as Robert Coles. Though not religious in the conventional sense, Coles is unparalleled in his astute understanding and respect for the relationship between secular life and sacredness, which cuts across his large body of work. Drawing inspiration from figures like Dietrich Bonhoeffer, Dorothy Day, and Simone Weil, Coles’s extensive writings explore the tug of war between faith and (...) doubt. As Coles himself admits, the “back-and-forthness between faith and doubt is the story of my life.” These thirty-one thought-provoking essays are drawn from Coles’s weekly column in the Catholic publication _America_. In them, he turns his inquisitive lens on a range of subjects and issues, from writers and painters to his recent reading and film viewing, contemporary events and lingering controversies, recollections of past and present mentors, events of his own daily life, and ordinary encounters with students, patients, neighbors, and friends. Addressing moral questions openly and honestly with a rare combination of rectitude and authorial modesty, these essays position Coles as a preeminent, durable, and trusted voice in the continuing national conversation over religion, civic life, and moral purpose. (shrink)

Preface -- Introduction : after the cave -- Part I. The life of philosophy and the life of Rousseau; The reveries of the solitary walker : an introduction -- Part II. "What am I?" : first walk; "A faithful record" : second walk; Becoming a philosopher : third walk; Being a philosopher : fourth, fifth, and sixth walks; Becoming a more perfect philosopher : seventh, eighth, and ninth walks; Coda : the love of wisdom and the wisdom of love : (...) tenth walk. . (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)

Old Havana: Spirit of the Living City artistically captures the architecture, people, and daily life of La Habana Vieja through the lenses of two visionary photographers and colleagues, one American and the other Cuban. Chip Cooper and Néstor Martí began collaborating in 2008, documenting the picturesque features of the oldest and most historically rich quarter in Cuba's capital city at the behest of Eusebio Leal Spengler, the historian of the city of Havana and the director of the Habana Vieja (...) restoration project. Cooper's and Martí's images highlight the spirit of change and renewal underlying the restoration of this international treasure and its revival as a vibrant business and residential area. Inspired by the work of twentieth century American photographer Walker Evans, Cooper and Martí, through perspectives both unique and deeply entwined, capture the humanity of the city, in a language at once universal and transcendent. (shrink)

" In this book, Laurence Cooper focuses his attention on three giants of the philosophic tradition for whom this inner force was a major preoccupation and something separate from and greater than the desire for self-preservation.

Traditionally, philosophical writings on personal identity have taken the form of attempts to discover the dominant criterion for deciding when a person at one time is identical with a person at some other time. Among the candidates for the role of dominant criterion have been bodily continuity and memory . In the normal case, where a person P is identical with a person P′ at an earlier time, it is true that P and P′ share a continuous body, that P (...) can remember experiences of P′, and that many other relationships hold between P and P′. Consequently, the debate as to which of the normal criteria is the dominant one has usually taken the form of imagining strange cases in which one or more of the normal criteria are lacking, and attempting to say, in such cases, who is identical with who. The scene was set, at least for modern times, by Locke's prince/pauper example, in which, according to Locke, the ability to remember experiences of a person having a different body guarantees, nevertheless, that one is that person—and hence that the memory criterion is dominant over the bodily identity one. (shrink)