The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

ブッダとは誰か?仏教とは何か?3・11の震災後の言葉を探して仏教に問いかける―仏教と真剣に向き合う僧侶、研究者との対話を通して、仏教の「新しいいま」が見えてくる。.

Emotions change over time. A comprehensive understanding of emotions will require that their temporal nature be observed and analysed. By observing emotion over time, one can disentangle and simultaneously analyse temporal variability within individuals and between-individual variability using a two-step process approach. First, within-person temporal patterns (e.g., covariation, lead–lag relation, periodicity, etc.) are assessed for each subject. Second, between-person analyses are conducted on the within-person patterns. These two steps can be done simultaneously with hierarchical linear models (HLM) or in two (...) actual steps with the process approach. HLM is limited to the intra-individual analysis of linear patterns (e.g., slope, intercept), whereas the process approach can be used to examine non-linear aspects of intra-individual change, such as multivariate patterns, within-subject skew, or phase relations between oscillating processes. In this paper we provide a description of the process approach and present several examples of, as well as suggestions for, intra-individual analysis applied to emotion and individual differences. (shrink)

The purpose of this study was to determine if there is a relationship between the ethical climate of the organization and the development of person-organization fit. The relationship between an individual's stage of moral development and his/her perceived ethical work environment was examined using a sample of 86 working students. Results indicate that a match between individual preferences and present position proved most satisfying. Subjects expressing a match between their preferences for an ethical work climate and their present ethical work (...) climate indicated that they were less likely to leave their positions. (shrink)

We have been asked to consider how a "Constitution of Civic Virtue" might contribute to a "good society." To answer this question, we need to have some idea of what a good society might be, and we need to be able to articulate that idea. Certainly, we think we know a good movie when we see it, a good book when we read it, a good argument when we hear it, and a good idea when we have one, but we (...) are not sure we have a handle on what a good society is. Even what we think we know about good books, movies, arguments, and ideas gives us pause. For we are not sure we can always explain why we think a particular movie is good or a book is bad. And even when we can explain it, we find that many people disagree with us about such matters. Indeed, we, at times, even disagree with each other. By this we do not mean to suggest any skepticism about there being such a thing as a good book, a good film, a good wine, a good car, or even a good person. If there is one thing we think we know in this world, it is that there are good persons-quite amazingly good actually. Nor do we mean to deny that there may be such a thing as a good society, though we are not so confident about this. A lot depends on what is meant by those words. Having said this, we will set our skepticism aside and now offer a conception of a good society; but we no more expect everyone to agree with this conception then we expect them to agree with one of us that "The Tao of Steve" was a really good movie. (shrink)

In their important work on locus equations, Sussman and his colleagues have helped to simplify the theoretical problem of how human listeners identify place of articulation contrasts among consonants, but much work remains before this problem is solved.

This paper examines the collective fraudulent behaviors taking place during the residential real estate bubble in the United States from 2002 to 2006 and the influence of others’ choices on decision making leading to a herd mentality. The antecedents of collective fraud are discussed in terms of the sociological theory behind human herding and the fraudulent behaviors during the real estate bubble are examined. Using archival witness testimony as a primary basis for analysis, this paper argues that without widespread collective (...) fraud, the bubble may not have developed and the herd mentality may have dissipated without the consequences of financial disaster. The aim of an analysis of this nature is to offer a plausible explanation of some of the preconditions to the event under study. (shrink)

The most recent work toward compiling a comprehensive database of adenosine‐to‐inosine RNA editing events suggests that the potential for RNA editing is much more pervasive than previously thought; indeed, it is manifest in more than 100 million potential editing events located primarily within Alu repeat elements of the human transcriptome. Pairs of inverted Alu repeats are found in a substantial number of human genes, and when transcribed, they form long double‐stranded RNA structures that serve as optimal substrates for RNA editing (...) enzymes. A small subset of edited Alu elements has been shown to exhibit diverse functional roles in the regulation of alternative splicing, miRNA repression, and cis‐regulation of distant RNA editing sites. The low level of editing for the remaining majority may be non‐functional, yet their persistence in the primate genome provides enhanced genomic flexibility that may be required for adaptive evolution. (shrink)

I. Introduction Two kinds of remedies have traditionally been employed for breach of contract: legal relief and equitable relief. Legal relief normally takes the form of money damages. Equitable relief normally consists either of specific performance or an injunction – that is, the party in breach may be ordered to perform an act or to refrain from performing an act. In this article I will use a “consent theory of contract” to assess the choice between money damages and specific performance. (...) According to such a theory, contractual obligation is dependent on more fundamental entitlements of the parties and arises as a result of the parties' consent to transfer alienable rights. My thesis will be that the normal rule favoring money damages should be replaced with one that presumptively favors specific performance unless the parties have consented to money damages instead. The principal obstacle to such an approach is the reluctance of courts to specifically enforce contracts for personal services. The philosophical distinction between alienable and inalienable rights bolsters this historical reticence, since a right to personal services may be seen as inalienable. I will then explain why, if the subject matter of a contract for personal services is properly confined to an alienable right to money damages for failure to perform, specific enforcement of such contracts is no longer problematic. Finally, I shall consider whether the subject matter of contracts for corporate services is properly confined to money damages like contracts for personal services, or whether performance of corporate services can be made the subject of a valid rights transfer and judicially compelled in the same manner as contracts for external resources. (shrink)

BackgroundThis paper discusses the contentious issue of reuse of stored biological samples and data obtained from research participants in past clinical research to answer future ethical and scientifically valid research questions. Many countries have regulations and guidelines that guide the use and exportation of stored biological samples and data. However, there are variations in regulations and guidelines governing the reuse of stored biological samples and data in Sub-Saharan Africa including Malawi.DiscussionThe current research ethics regulations and guidelines in Malawi do not (...) allow indefinite storage and reuse of biological samples and data for future unspecified research. This comes even though the country has managed to answer pertinent research questions using stored biological samples and data. We acknowledge the limited technical expertise and equipment unavailable in Malawi that necessitates exportation of biological samples and data and the genuine concern raised by the regulatory authorities about the possible exploitation of biological samples and data by researchers. We also acknowledge that Malawi does not have bio-banks for storing biological samples and data for future research purposes. This creates room for possible exploitation of biological samples and data collected from research participants in primary research projects in Malawi. However, research ethics committees require completion and approval of material transfer agreements and data transfer agreements for biological samples and data collected for research purposes respectively and this requirement may partly address the concern raised by the regulatory authorities. Our concern though is that there is no such requirement for biological samples and data collected from patients for clinical or diagnostic purposes.SummaryIn conclusion, we propose developing a medical data and material transfer agreement for biological samples and data collected from patients for clinical or diagnostic purposes in both public and private health facilities that may end up in research centers outside Malawi. We also propose revision of the current research ethics regulations and guidelines in Malawi in order to allow secondary use of biological samples and data collected from primary research projects as a way of maximizing the use of collected samples and data. Finally, we call for consultation of all stakeholders within the Malawi research community when regulatory authorities are developing policies that govern research in Malawi. (shrink)

The most important contemporary development in rhetoric for the theory of argumentation is Jeanne Fahnestock's program of figural logic, the ruling insight of which is that figures epitomize arguments. Working primarily with the antimetabolic formula at the heart of Gregor Mendel's paper “Experiments in Plant Hybridization,” I investigate the figural bases of the logic anchoring this foundational essay in genetics. In addition to antimetabole, the formula also depends crucially on ploche, polyptoton, onomatopoeia, antithesis, synecdoche, reification, and metaphor.

Psychological adaptation underlies all human behavior. Thus, rape could either arise from a rape-specific psychological adaptation or it could be a side-effect of a more general psychological adaptation not directly related to rape. The rape-specific hypothesis and the incidental effect hypothesis are explained. Determining the specific environmental cues that men’s sexual psyche has been designed by selection to process will allow us to decide which of these two hypotheses is true. I focus on rape, and briefly look at other types (...) of sexual coercion, such as sexual harassment and incest. (shrink)

This study examines the influence of ethical fit on employee attitudes and intentions to turnover. The results of this investigation provides support for the conjecture that ethical work climate is an important variable in the study of person-organization fit. Ethical fit was found to be significantly related to turnover intentions, continuance commitment, and affective commitment, but not to job satisfaction. Results are discussed in regard to some of the affective and cognitive distinctions among satisfaction, commitment, and behavioral intentions.

In lieu of an abstract, here is a brief excerpt of the content:Philosophy and Literature 29.2 (2005) 379-393 [Access article in PDF] Love, Self-Deception, and the Moral "Must" Randy Ramal Claremont Graduate University I One significant impact that conceptual relativism has had on current discussions in moral philosophy is the denial of intelligibility to discourses that affirm moral absolutism. The denial is typically based on two allied arguments. The first argument entails that the justification of absolute moral laws and values (...) presupposes the existence of an Archimedean standpoint, but since such viewpoint is unintelligible, a "view from nowhere" as it has been called, then affirming moral absolutism could only be the result of a confused temptation for metaphysical universality and objectivity. The second argument states that since all moral values and concepts are the products of particular cultural-linguistic contexts, it would not make sense to speak of absolute values that have application in other cultural-linguistic contexts.I sympathize with the critical spirit in which this dual argument is made. The unintelligibility of a neutral standpoint and the obvious contextuality of all moral discourses render meaningless any attempt to affirm metaphysically-based moral absolutes. But what this argument fails to acknowledge is that the ordinary language of moral absoluteness is not only infinitely distant from the metaphysical claims to Olympian grounds but also internally related to the absolute moral judgments and principles it invokes. Furthermore, it is doubtful that one could speak at all of moral discourse as needing metaphysical justification. It would not make sense to speak of moral discourse as either needing or not needing metaphysical backing because both notions ignore the ordinary contexts of moral discourse, where the issue of philosophical justification does not arise. The point here is not simply to reject the [End Page 379] metaphysical need for justifying moral discourse but to question the intelligibility of the attempt itself.1In what follows I argue that the ordinary claims to moral absoluteness, be it to give moral advice, to justify personal beliefs and actions, or to judge and criticize the conduct of other people, are perfectly intelligible practices that embody ordinary moral judgments and values. I elucidate the intelligibility of these moral claims by discussing Leo Tolstoy's "The Death of Ivan Ilych," Proust's Remembrance of Things Past, and Ann Beattie's "Learning to Fall." These works, I argue, portray an ethical notion of "need" that expresses natural, and intelligible, affirmations of moral necessity. The context of this affirmation concerns the ethical call to end all self-deception about one's love life.Traditionally, the relationship between love and self-deception has been interpreted to suggest that people often deceive themselves about love in order to fulfill a deep need in them to give meaning to their lives. This interpretation is often invoked to explain, on the one hand, why people who are in love might claim otherwise and, on the other hand, why those who are not in love at all convince themselves of the opposite. Although this interpretation is not philosophical in nature and does not necessarily entail the denial of all discourses of moral necessity, the idea that self-deception fulfils a deep need in people is often invoked as a philosophical explanation of the notion of "need." One example of such philosophical explanation is Martha Nussbaum's Love's Knowledge, where she endorses the traditional interpretation of the relation between love and self-deception through a discussion, among other works, of the above mentioned works by Proust and Beattie.There is no doubt that self-deception, whether in regards to one's love life or other aspects of it, could sometimes arise as a result of a need in people to give their existence some meaningful stability. But this interpretation cannot apply to all cases of love and self deception because the radical plurality of our notions of love prevents such explanatory reductionism. The insistence on this type of reductionism, it seems to me, rests on a common tendency among moral philosophers, Nussbaum included, to read into literature personal ethical views that are not intended by it. The task of the moral philosopher... (shrink)

A caged animal in the heart of the city, thousands of miles from its natural habitat, neurotically pacing in its confinement . . . Zoos offer a convenient way to indulge a cultural appetite for novelty and diversion, and to teach us, albeit superficially, about animals. Yet what, conversely, do they tell us about the people who create, maintain, and patronize them, and about animal captivity in general? Rather than foster an appreciation for the lives and attributes of animals, zoos, (...) in Randy Malamud's view, reinforce the idea that we are, by nature, an imperial species: that our power and ingenuity entitles us to violate the natural order by tearing animals from the fabric of their ecosystems and displaying them in an "order" of our own making. In so doing, he argues, zoos not only contribute to the rapid disintegration of our ecosystems, but also deaden our very sensibilities to constraint, spatial disruption, and physical pain. Invoking an array of literary depictions of animals, from Albee's Zoo Story and Virginia Woolf's diaries to the films of Harold Pinter and the poetry of Marianne Moore, Reading Zoos links culture, literature, and nature in an engaging and accessible introduction to environmental ethics, animal rights, cultural critique, and literary representation. (shrink)

Unchangeable. Unwavering. Let God's Truth Anchor You. The world is a sea of clashing beliefs and thoughts. Your own feelings and circumstances change from one day to the next. Your heart longs for something to hold on to...something to steer you in the right direction and give you peace. Only God's truth can satisfy that longing. Bestselling author Randy Alcorn shares daily meditations, Scripture readings, and inspirational quotes to help you grasp the wisdom and love found in the eternal Word (...) of God. When you know the truth, you'll be better prepared to... recognize your place in God's plan detect the deceit you encounter in the world point others to Jesus, who is Truth personified God's truth is real, alive, and able to transform you into the person you long to be. This is your invitation to refresh your heart and find lasting security. (shrink)

It is hypothesized that human faces judged to be attractive by people possess two features—averageness and symmetry—that promoted adaptive mate selection in human evolutionary history by way of production of offspring with parasite resistance. Facial composites made by combining individual faces are judged to be attractive, and more attractive than the majority of individual faces. The composites possess both symmetry and averageness of features. Facial averageness may reflect high individual protein heterozygosity and thus an array of proteins to which parasites (...) must adapt. Heterozygosity may be an important defense of long-lived hosts against parasites when it occurs in portions of the genome that do not code for the essential features of complex adaptations. In this case heterozygosity can create a hostile microenvironment for parasites without disrupting adaptation. Facial bilateral symmetry is hypothesized to affect positive beauty judgments because symmetry is a certification of overall phenotypic quality and developmental health, which may be importantly influenced by parasites. Certain secondary sexual traits are influenced by testosterone, a hormone that reduces immunocompetence. Symmetry and size of the secondary sexual traits of the face (e.g., cheek bones) are expected to correlate positively and advertise immunocompetence honestly and therefore to affect positive beauty judgments. Facial attractiveness is predicted to correlate with attractive, nonfacial secondary sexual traits; other predictions from the view that parasite-driven selection led to the evolution of psychological adaptations of human beauty perception are discussed. The view that human physical attractiveness and judgments about human physical attractiveness evolved in the context of parasite-driven selection leads to the hypothesis that both adults and children have a species-typical adaptation to the problem of identifying and favoring healthy individuals and avoiding parasite-susceptible individuals. It is proposed that this adaptation guides human decisions about nepotism and reciprocity in relation to physical attractiveness. (shrink)

This provocative book outlines a powerful and original theory of liberty structured by the liberal conception of justice and the rule of law. Drawing on insights from philosophy, political theory, economics, and law, he shows how this new conception of liberty can confront, and solve, the central societal problems of knowledge, interest, and power.

Suppose you are on a commercial airplane that is flying at 35,000 feet. Next to you sits a man who appears to be sleeping. In fact, this man has been drugged and put upon the plane without his knowledge or consent. He has never flown on a plane before and, indeed, has no idea what an airplane is. Suddenly the man awakes and looks around him. Terrified by the alien environment in which he finds himself, he searches for a door (...) or window from which to make an escape. As luck would have it, he is seated right next to a window exit and he begins to pull the handle that will open the window. You are aware that opening the window exit at this altitude will cause the cabin to quickly depressurize and that this man, you, and probably several other passengers will be sucked out the window to your deaths. You desperately want to stop him from opening the window. Now assume that for some reason it is impossible to prevent him physically from performing the deadly act. Your only option is to rationally persuade him to leave the window exit alone. You cry out to him and, with both hands on the handles, he turns to face you and waits to hear what you have to say. What sort of argument would you make? (shrink)

The increasing corporatization of education has served to expose the university as a business—and one with a highly stratified division of labor. In _Chalk Lines_ editor Randy Martin presents twelve essays that confront current challenges facing the academic workforce in U.S. colleges and universities and demonstrate how, like chalk lines, divisions between employees may be creatively redrawn. While tracing the socioeconomic conditions that have led to the present labor situation on campuses, the contributors consider such topics as the political implications (...) of managerialism and the conceptual status of academic labor. They examine the trend toward restructuring and downsizing, the particular plight of the adjunct professor, the growing emphasis on vocational training in the classroom, and union organizing among university faculty, staff, and graduate students. Placing such issues within the context of the history of labor movements as well as governmental initiatives to train a workforce capable of competing in the global economy, _Chalk Lines_ explores how universities have attempted to remake themselves in the image of the corporate sector. Originally published as an issue of _Social Text_, this expanded volume, which includes four new essays, offers a broad view of academic labor in the United States. With its important, timely contribution to debates concerning the future of higher education, _Chalk Lines_ will interest a wide array of academics, administrators, policymakers, and others invested in the state—and fate—of academia. _ Contributors._ Stanley Aronowitz, Jan Currie, Zelda F. Gamson, Emily Hacker, Stefano Harney, Randy Martin, Bart Meyers, David Montgomery, Frederick Moten, Christopher Newfield, Gary Rhoades, Sheila Slaughter, Jeremy Smith, Vincent Tirelli, William Vaughn, Lesley Vidovich, Ira Yankwitt. (shrink)

The legal risks associated with health research involving human subjects have been highlighted recently by a number of lawsuits launched against those involved in conducting and evaluating the research. Some of these cases have been fully addressed by the legal system, resulting in judgments that provide some guidance. The vast majority of cases have either settled before going to trial, or have not yet been addressed by the courts, leaving us to wonder what might have been and what guidance future (...) cases may bring. What is striking about the lawsuits that have been commenced is the broad range of individuals/institutions that are named as defendants and the broad range of allegations that are made. The research community should take this early experience as a warning and should reflect carefully on practices where research involving human subjects is concerned. (shrink)