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)

Mutual funds are common investments because they provide a cost-effective and effective means to vary your investments (or possess an assortment of securities -- stocks, bonds, etc.) without having to make a huge starting investment.

Positivist medical historians, guided by the savoir of modern western biomedicine, have long depicted medieval medicine as an aberration along the continuum of scientific and medical progress. Historical epistemology, founded in the ideas of Cavailles, Foucault, Davidson, and Hacking, however, allows the historian to disrupt this false continuum and to unchain medieval medicine from modern medicine. Postmodernist approaches, such as those sourced in Lyotard, Barthes, and Derrida, allow the historian to further deconstruct medieval and modern medical discourse, revealing a multitude (...) of narrative lenses spinning around biomedical and biocultural strands. In liberating these two medical systems and setting them within the distinct historical and epistemological contexts that both shaped and were shaped by them, the historian can revision the theories, practices, and culture of medieval medicine without having to anachronistically justify them according to modern medical discourse. (shrink)

The issue of musical identity—of what defines works of music, gives each its unique character and distinguishes them from one another—is one of the central issues in the philosophy of music. Too often in the philosophical literature it is approached as a purely theoretical question, one that can be answered adequately through careful intellectual consideration of scores and performances. The typical philosophical approach to the performance of Western art music, particularly that composed between the Baroque and Romantic eras, is to (...) offer descriptions of how musical works come into being, what their origins may be, which of their structural and aesthetic elements must be observed and conserved in their representations, and so on. It takes the written notation of a musical work, the score, to be a kind of blueprint created by a composer, defining and describing an autonomous musical entity, the musical work, such that another person might perform it. The work is recognized paradoxically as something existing independently of, yet deriving its identity from, its origins with the composer. (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)

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)

In this open peer commentary, we categorize the possible “neuroscience in national security” definitions of misuse of science and identify which, if any, are uniquely presented by advances in neuroscience. To define misuse, we first define what we would consider appropriate use: the application of reasonably safe and effective technology, based on valid and reliable scientific research, to serve a legitimate end. This definition presents distinct opportunities for assessing misuse: misuse is the application of invalid or unreliable science, or is (...) the use of reliable scientific methods to serve illegitimate ends. Ultimately, we conclude that while national security is often a politicized issue, assessing the state of scientific progress should not be. (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)

To succeed, every organization including theatre necessarily requires human and material resources. The material resources cannot on their own function. It is the human capital within the organization that utilizes and drives the materials in a certain direction in order to achieve predetermined objectives. This places the human capital in a pivotal role and justifies the attention often paid to personnel matters in organizations. Personnel themselves have to be managed. One potent avenue for adequately managing human resources towards the realization (...) of predetermined goals and objectives is good and effective communication. This paper examines the options open to the Theatre Administrator (the head of theatre organizations)) in order to foster coherence and adequately harmonize theatre personnel towards achieving the goals of guaranteeing satisfaction, having a full house and maximizing profits. (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)

KEY POINTS In Canada, commercial data brokers collect deidentified patient data from pharmacies, private drug insurers, the federal government and medical clinics without patient consent. Although pharmaceutical companies are the data brokers’ primary customers, academics and nonprofit and public entities also use commercial data sets, given the absence of a coordinated public approach to collecting these data across Canada. Risks of commercialized patient data include loss of anonymity, surveillance and marketing, discrimination and violation of Indigenous data sovereignty. Coordinated infrastructure for (...) the collection and coordination of health data across Canada and updated privacy legislation would protect individuals and communities and enable appropriate data uses. (shrink)

People seem more divided than ever before over social and political issues, entrenched in their existing beliefs and unwilling to change them. Empirical research on mechanisms driving this resistance to belief change has focused on a limited set of well-known, charged, contentious issues and has not accounted for deliberation over reasons and arguments in belief formation prior to experimental sessions. With a large, heterogeneous sample (N = 3,001), we attempt to overcome these existing problems, and we investigate the causes and (...) consequences of resistance to belief change for five diverse and less contentious socio-political issues. After participants chose initially to support or oppose a given socio-political position, they were provided with reasons favoring their chosen position (affirming reasons), reasons favoring the other, unchosen position (conflicting reasons), or all reasons for both positions (reasons for both sides). Our results indicate that participants are more likely to stick with their initial decisions than to change them no matter which reasons are considered, and that this resistance to belief change is likely due to a motivated, biased evaluation of the reasons to support their initial beliefs (prior-belief bias). More specifically, they rated affirming reasons more favorably than conflicting reasons—even after accounting for reported prior knowledge about the issue, the novelty of the reasons presented, and the reported strategy used to make the initial decision. In many cases, participants who did not change their positions tended to become more confident in the superiority of their positions after considering many reasons for both sides. (shrink)

The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, (...) effectiveness, and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready data sets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defi ning the next generation of pharmacometric informatics. (shrink)

In the prehistoric time, there was an inclination of human beings to protect their existence by living in societies. They confine themselves in the society because of having their qualities of mutual love and amity. The general tendencies of human beings are to develop bonds. These bonds happen in various ways. Society cannot survive without bonds. Bonds have significance in philosophical discussion. In the history of contemporary philosophy, applied philosophy is one of the several other aspects. Applied philosophy deals with (...) Human rights, Euthanasia, Feminism, Abortion, Animal rights, Bonds etc. Brenda Almond, a leading figure in applied philosophy, has offered arguments in favor of her viewpoint regarding the importance of human bonds. In this paper, Almond‟s view on the nature and significance of bond has been analyzed. However, bond has also been studied from ethical perspective in this paper. And finally, it is claimed that marriage and cosmopolitanism make bonds stronger. Philosophy and Progress, Vol#61-62; No#1-2; Jan-Dec 2017 P 147-164. (shrink)

Following Freud’s analysis of the fragile line between the uncanny double and its comic redoubling, I identify the doubling of the double found in critical moments of Hegelian dialectic as producing a kind of comic effect. It almost goes without saying that two provides greater pleasure than one, the loneliest number. Many also find two to be preferable to three, the tired trope of dialectic as a teleological waltz. Two seems to offer lightness, relieving one from her loneliness and lacking (...) the complications of a third who comes in between. And yet, we learn through Marx and Freud that the double (even the double of tragedy and farce) borders on something closer to horror than comedy. -/- In the following, I would like to explore why four is funnier than two in my staging of dialectic as the doubling of the double or, to borrow a movie title from Laurel and Hardy, “Twice Two” (Roach et al. 1933a). I will begin by exploring the formulations of the double in the form of a pair of opposites and in the form of a pair of twins. The literary tropes of the double as the odd couple, on one side, and the twins, on the other, appear to serve very different narrative functions, which incite different kinds of affective responses from the audience. However, the form of the opposed double sometimes conceals the realization that the empty or fragmented content of the first is only reduplicated in the second. The “straight man” of the odd couple cannot see himself in his counterpart “the comic.” The redoubling of the double, however, forces not only the audience, but the original double on stage to confront what was already present, but unrealized, from the beginning. To illustrate this redoubling of the double within the opening of Hegel’s Science of Logic, I consider two short films by Laurel and Hardy in which the comic duo redoubles itself. The formula (2 x 2) produces a comic excess through the dialectical redoubling of there uncanny double. (shrink)

A collection of articles on the the principles of social justice from an Australian Catholic perspective. Contents: Forward (Archbishop Philip Wilson), Introduction (James Franklin), The right to life (James Franklin), The right to serve and worship God in public and private (John Sharpe), The right to religious formation (Richard Rymarz), The right to personal liberty under just law (Michael Casey), The right to equal protection of just law regardless of sex, nationality, colour or creed (Sam Gregg), The right to freedom (...) of expression (Damian Grace), The right to choose and freely maintain a state of life, married or single, lay or religious (Marita Winters), The right to education (Anthony Cleary), The right to petition government for the redress of grievances (Paul Russell), The right to a nationality (Andrew Hamilton), The right to have access to the means of livelihood, by migration when necessary (Brenda Hubber), The right of association and peaceful assembly (Michael Hogan), The right to work and choose one's occupation (Ian Blandthorn), The right to personal ownership, use and disposal of property subject to the right of others (Brian Coman), The right to a living wage (Garrick Small), The right to collective bargaining (Keith Harvey), The right to associate by industries and professions to obtain economic justice (Henrik Jurisevic), The right to assistance from society, if necessary from the State, in distress of persons and family (Catherine Althaus), Afterword (James Franklin). (shrink)

Henry Molaison, aged eighty-two, died at the end of 2008, and just after noon on exactly the first anniversary of his death, December 2, 2009, scientists began slicing his brain into 2,500 tissue samples. Known primarily in his lifetime as only H.M., he left his brain to science so that it could be dissected and digitally mapped – a gift much beloved by many scientists. An amnesiac in life, H.M. first rose to prominence in 1962 when Dr. Brenda Milner, (...) a pioneer in the field of neuropsychology, demonstrated that though H.M. was severely amnesic and could not remember past activities, he could nevertheless learn certain habits. The experiment involved the now famous mirror drawing. This article, written by a philosopher/artist and a neuroscientist/neuroaesthetician, argues that artists are unable to verbally articulate thoughts about their own art practice for reasons similar to why H.M. could not. All memories are not stored in the same part of the brain. Different categories of memories i.e., semantic memory or procedural memory, are stored in different parts of the brain. We argue that the procedural memory is not readily accessible to semantic memory. (shrink)