The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

Alongside concerns for animal welfare, concerns for land, water, and climate are undermining established food identities in many parts of the world. In Aotearoa New Zealand, agrifood relations are bound tightly into national identities and the materialities of export dependence on dairying and agriculture more widely. Dairy/ing identities have been central to national development projects and the politics that underpin them for much of New Zealand’s history. They are central to an intransigent agrifood political ontology. For the last decade, however, (...) they have been challenged by the identity politics of ethical food consumption. This paper explores the ensuing contests and asks how they are reshaping agrifood identities. We draw on interviews with 15 participants in Aotearoa New Zealand who have made dietary transitions that reduce or exclude dairy products. Our aim is not to identify a new post-dairying identity or claim a reconfigured national identity, but to examine the collision of production-consumption values in the context of a dominant place-based food identity. We ask how participants navigate contradictory commitments to becoming ‘good environmental citizens’ whilst remaining ‘good national citizens’. The paper offers insights for examining similar struggles elsewhere and the potential to shift agrifood relations and undermine entrenched political ontologies through ethical food consumption values. (shrink)

Neural substrates of fatigue in traumatic brain injury are not well understood despite the considerable burden of fatigue on return to productivity. Fatigue is associated with diminishing performance under conditions of high cognitive demand, sense of effort, or need for motivation, all of which are associated with cognitive control brain network integrity. We hypothesize that the pathophysiology of TBI results in damage to diffuse cognitive control networks, disrupting coordination of moment-to-moment monitoring, prediction, and regulation of behavior. We investigate the cingulo-opercular (...) and frontoparietal networks, which are engaged to sustain attention for task and maintain performance. A total of 61 individuals with mild TBI and 42 orthopedic control subjects participated in functional MRI during performance of a constant effort task requiring altering the amount of effort utilized to manually squeeze a pneumostatic bulb across six 30-s trials. Network-based statistics assessed within-network organization and fluctuation with task manipulations by group. Results demonstrate small group differences in network organization, but considerable group differences in the evolution of task-related modulation of connectivity. The mild TBI group demonstrated elevated CO connectivity throughout the task with little variation in effort level or time on task, while CO connectivity diminished over time in controls. Several interregional CO connections were predictive of fatigue in the TBI group. In contrast, FP connectivity fluctuated with task manipulations and predicted fatigue in the controls, but connectivity fluctuations were delayed in the mild traumatic brain injury group and did not relate to fatigue. Thus, the mTBI group’s hyper-connectivity of the CO irrespective of task demands, along with hypo-connectivity and delayed peak connectivity of the FP, may allow for attainment of task goals, but also contributes to fatigue. Findings are discussed in relation to performance monitoring of prediction error that relies on internal cues from sensorimotor feedback during task performance. Delay or inability to detect and respond to prediction errors in TBI, particularly evident in bilateral insula-temporal CO connectivity, corresponds to day-to-day fatigue and fatigue during task performance. (shrink)

This book is a collection of secondary essays on America's most important philosophic thinkers—statesmen, judges, writers, educators, and activists—from the colonial period to the present. Each essay is a comprehensive introduction to the thought of a noted American on the fundamental meaning of the American regime.

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)

This paper proposes a generalization of the Kripke semantics of intuitionistic logic IL appropriate for intuitionistic Łukasiewicz logic IŁL — a logic in the intersection between IL and (classical) Łukasiewicz logic. This generalised Kripke semantics is based on the poset sum construction, used in Bova and Montagna (Theoret Comput Sci 410(12):1143–1158, 2009) to show the decidability (and PSPACE completeness) of the quasiequational theory of commutative, integral and bounded GBL algebras. The main idea is that w \Vdash \sigma—which for IL is (...) a relation between worlds w and formulas \sigma, and can be seen as a function taking values in the booleans w \Vdash \sigma \in {B}—becomes a function taking values in the unit interval w \Vdash \sigma \in [0,1]. An appropriate monotonicity restriction (which we call sloping functions) needs to be put on such functions in order to ensure soundness and completeness of the semantics. (shrink)

Pancreatitis is a complex, progressively destructive inflammatory disorder. Alcohol was long thought to be the primary causative agent, but genetic contributions have been of interest since the discovery that rare PRSS1, CFTR and SPINK1 variants were associated with pancreatitis risk. We now report two associations at genome-wide significance identified and replicated at PRSS1-PRSS2 and X-linked CLDN2 through a two-stage genome-wide study. The PRSS1 variant likely affects disease susceptibility by altering expression of the primary trypsinogen gene. The CLDN2 risk allele is (...) associated with atypical localization of claudin-2 in pancreatic acinar cells. The homozygous CLDN2 genotype confers the greatest risk, and its alleles interact with alcohol consumption to amplify risk. These results could partially explain the high frequency of alcohol-related pancreatitis in men. © 2012 Nature America, Inc. All rights reserved. (shrink)

We say that A≤LRB if every B-random set is A-random with respect to Martin–Löf randomness. We study this relation and its interactions with Turing reducibility, classes, hyperimmunity and other recursion theoretic notions.

The editor's introduction discusses Clarence I. Lewis's conceptual pragmatism when compared with post-empiricist epistemology and argues that several Cartesian assumptions play a major role in the work, not unlike those of Logical Positivism. The suggestion is made that the Cartesian legacy still hidden in Logical Positivism turns out to be a rather heavy ballast for Lewis’s project of restructuring epistemology in a pragmatist key. More in detail, the sore point is the nature of inter-subjectivity. For Lewis, no (...) less than for the Logical Positivists at the time of the Protocols Controversy and Husserl in the Cartesian Meditations, this is a problem without a solution. The reason is that all these philosophers are apparently unable to realize that the existence of a plurality of knowing subjects cannot be treated at once both as a speculative problem and a methodological one. Lewis, thanks to his pragmatist approach both comes closer to the right answer and offers an even more naïve unsatisfactory solution to the pseudo-problem under discussion. The fact that he has clear in mind that inter-subjectivity means not only a plurality of linguistic utterances but also a co-existence of different kinds of practical behaviour. Eventually, the very idea of mind, the key-idea in the book, suffers from the above mentioned tension. In fact, if inter-subjective communication and action is considered at a methodological level, the very idea of mind would not need an analysis, and no kind of ‘reflexive’ analysis. Methodology might be limited to a ‘naïve’ level where the existence of the world and a plurality of subjects be taken as a bedrock of uncritically accepted evidence. Philosophical reflection on ultimate evidence, instead, would take a different approach, maybe the one Wittgenstein was putting into practice in the same years when Mind and the world order was written, namely it would be bound to question the very meaning of the idea of ‘mind’ as an undue fiction – the same carried out by Descartes – when he assumed the Cogito to be at once a body of self-evident truths and a thing or substance, the familiar Platonic idea of psyche or soul. (shrink)

The Search for the Legacy of the USPHS Syphilis Study at Tuskegee is a collection of essays from experts in a variety of fields seeking to redefine the legacy of the infamous Tuskegee Syphilis Study. The essayists place the legacy of the study within the evolution of racial and ethnic relations in the United States. Contributors include two leading historians on the study, two former United States Surgeons General, and other prominent scholars from a wide range of fields.

This volume includes a lucid discussion of recent developments by philosophers such as Block, Davidson, Fodor, Kim, Lewis, Mellor, Putnam, Schiffer, Shoemaker, ...

This is the twenty-sixth volume in the Library of Living Philosophers, a series founded by Paul A. Schilpp in 1939 and edited by him until 1981, when the editorship was taken over by Lewis E. Hahn. This volume follows the design of previous volumes. As Schilpp conceived this series, every volume would have the following elements: an intellectual autobiography of the philosopher, a series of expository and critical articles written by exponents and opponents of the philosopher's thought, replies to (...) these critics and commentators by the philosopher, and as nearly complete a bibliography of the published work of the philosopher as possible. (shrink)

Background: The factors influencing parents’ willingness to enroll their children in biobanks are poorly understood. This study sought to assess parents’ willingness to enroll their children, and their perceived benefits, concerns, and information needs under different consent and data-sharing scenarios, and to identify factors associated with willingness. Methods: This large, experimental survey of patients at the 11 eMERGE Network sites used a disproportionate stratified sampling scheme to enrich the sample with historically underrepresented groups. Participants were randomized to receive one of (...) three consent and data-sharing scenarios. Results: In total, 90,000 surveys were mailed and 13,000 individuals responded (15.8% response rate). 5737 respondents were parents of minor children. Overall, 55% (95% confidence interval 50–59%) of parents were willing to enroll their youngest minor child in a hypothetical biobank; willingness did not differ between consent and data-sharing scenarios. Lower educational attainment, higher religiosity, lower trust, worries about privacy, and attitudes about benefits, concerns, and information needs were independently associated with less willingness to allow their child to participate. Of parents who were willing to participate themselves, 25% were not willing to allow their child to participate. Being willing to participate but not willing to allow one’s child to participate was independently associated with multiple factors, including race, lower educational attainment, lower annual household income, public health care insurance, and higher religiosity. Conclusions: Fifty-five percent of parents were willing to allow their youngest minor child to participate in a hypothetical biobank. Building trust, protecting privacy, and addressing attitudes may increase enrollment and diversity in pediatric biobanks. (shrink)

Le systeme cartesien est enracine dans la metaphysique qui s'impose avant (non plus apres: meta) la physique. Pourtant, Descartes decouvre avec Beeckman la physico-mathematique, qui applique une methode mathematique a toute la nature. Optique, dioptrique et meteores occupent ses annees parisiennes. Aux Pays-Bas, il consacre neuf mois au commencement de la metaphysique, mais l'abandonne quand il apprend l'existence de faux soleils. Leur explication lui fait elargir la science a l'ensemble du Monde a partir de la lumiere. Il fera connaitre sa (...) methode dans le Discours, avec un resume de sa metaphysique. Comment Descartes avait-il ete incite a demontrer que l'existence de Dieu est plus certaine que les mathematiques? Quels furent les themes nouveaux des Meditations? Alors, l'arbre de la philosophie va deployer ses branches, jusqu'a ce dernier fruit, la generosite. Seule la mort interrompt La Recherche de la Verite, son principal bien en cette vie. (shrink)

Ways of World-making is a bold and imaginative combination of metaphysical speculation and logical analysis. Its author thinks of it "as belonging in that mainstream of modern philosophy that began when Kant exchanged the structure of the world for the structure of the mind, continued when C. I. Lewis exchanged the structure of the mind for the structure of concepts, and that now proceeds to exchange the structure of concepts for the structure of the several symbol systems of the (...) sciences, philosophy, the arts, perception, and everyday discourse". It moves from unique truth and a fixed and found world to a multiplicity of "right and even conflicting versions of worlds in the making.". (shrink)

Recent work in the history of philosophy of science details the Kantianism of philosophers often thought opposed to one another, e.g., Hans Reichenbach, C.I. Lewis, Rudolf Carnap, and Thomas Kuhn. Historians of philosophy of science in the last two decades have been particularly interested in the Kantianism of Reichenbach, Carnap, and Kuhn, and more recently, of Lewis. While recent historical work focuses on recovering the threatened-to-be-forgotten Kantian themes of early twentieth-century philosophy of science, we should not elide the (...) differences between the Kantian strands running throughout this work. In this paper, I disentangle a few of these strands in the work of Reichenbach and Lewis focusing especially on their theories of relativized, constitutive a priori principles in empirical knowledge. In particular, I highlight three related differences between Reichenbach and Lewis concerning their motivations in analyzing scientific knowledge and scientific practice, their differing conceptions of constitutivity, and their relativization of constitutive a priori principles. In light of these differences, I argue Lewis’s Kantianism is more similar to Kuhn’s Kantianism than Reichenbach’s, and so might be of more contemporary relevance to social and practice-based approaches to the philosophy of science. (shrink)

The Johns Hopkins-Fogarty African Bioethics Training Program (FABTP) has offered a fully-funded, one-year, non-degree training opportunity in research ethics to health professionals, ethics committee members, scholars, journalists and scientists from countries across sub-Saharan Africa. In the first 9 years of operation, 28 trainees from 13 African countries have trained with FABTP. Any capacity building investment requires periodic critical evaluation of the impact that training dollars produce. In this paper we describe and evaluate FABTP and the efforts of its trainees.Our data (...) show that since 2001, the 28 former FABTP trainees have authored or co-authored 105 new bioethics-related publications; were awarded 33 bioethics-related grants; played key roles on 78 bioethics-related research studies; and participated in 198 bioethics workshops or conferences. Over the past nine years, trainees have collectively taught 48 separate courses related to bioethics and have given 170 presentations on various topics in the field. Many former trainees have pursued and completed doctoral degrees in bioethics; some have become editorial board members for bioethics journals. Female trainees were, on average, less experienced at matriculation and produced fewer post-training outputs than their male counterparts. More comprehensive studies are needed to determine the relationships between age, sex, previous experience and training program outputs. (shrink)

The need today, according to Cohen, is not for more criticism of old theories of induction but for new theories to criticize. In his recent book, he presents a new theory of induction in which he attempts to develop Bacon's seminal ideas "in a way that is not vitiated by obsession with the mathematical calculus of probabilities." Consequently, "induction" in the title would seem to refer to Baconian Induction, i.e. induction by variation of circumstances as distinct from induction by enumeration. (...) The author offers his book as an analysis of the logical syntax of "support" for such induction. He prefers the metaphor of "support" to Carnap's metaphor of "confirmation" since the former is spatial and the latter is temporal and "... inductive support is timeless support for timeless propositions...." The first six chapters, the bulk of the book, are philosophical in character, while the last chapter contains a formalization of a system of inductive logic based on C. I. Lewis. In the philosophical sections, the author proposes that induction as used in various fields, e.g. by the scientist or lawyer, does not differ in method or logical syntax but in subject-matter. For this reason, he finds it necessary to present a logical system of induction as a conclusion to the book. Cohen invites criticism of his new theory of induction. The present reviewer feels that the author has misunderstood Aristotelian induction. Aristotelian induction means, primarily, being led from one truth to another and not the enumeration of instances. Rhetorical example has, for Aristotle, the nature of induction. Furthermore, the author himself seems to introduce time as a factor when he assesses inductive support in legal reasoning. This seems inconsistent with "timeless support for timeless propositions." Cohen's new theory is one that is worth a critical examination.--L. A. (shrink)

The Toronto experience suggests that there may be several general lessons for academic health sciences complexes to learn from the Olivieri/Apotex affair regarding the ethics, independence, and integrity of clinical research sponsored by for profit enterprises. From a local perspective, the OAA occurred when there already was a focus on the complex and changing relationships among the University of Toronto, its medical school, the fully affiliated teaching hospitals, and off campus faculty because of intertwined interests and responsibilities. The OAA became (...) a catalyst that accelerated various systemic reforms, particularly concerning academic/industry relations. In this article, the evolving governance framework for the Toronto academic health sciences complex is reviewed and these policy and process reforms discussed. These reforms have created collaborative activity among research ethics boards and contract research offices of the partner institutions, and allowed the joint university/hospital ethics centre to play a role in governance and policy, while respecting the missions and mandates of the involved institutions. Although few of the policies are dramatically innovative, what is arguably novel is the elaboration of an overarching governance framework that aims to move ethics to a central focus in the academic complex. Time alone will tell how sustainable and effective these changes are. (shrink)