Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

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

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...) along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.

Die MISCELLANEA MEDIAEVALIA präsentieren seit ihrer Gründung durch Paul Wilpert im Jahre 1962 Arbeiten des Thomas-Instituts der Universität zu Köln. Das Kernstück der Publikationsreihe bilden die Akten der im zweijährigen Rhythmus stattfindenden Kölner Mediaevistentagungen, die vor über 50 Jahren von Josef Koch, dem Gründungsdirektor des Instituts, ins Leben gerufen wurden. Der interdisziplinäre Charakter dieser Kongresse prägt auch die Tagungsakten: Die MISCELLANEA MEDIAEVALIA versammeln Beiträge aus allen mediävistischen Disziplinen - die mittelalterliche Geschichte, die Philosophie, die Theologie sowie die Kunst- und Literaturwissenschaften (...) sind Teile einer Gesamtbetrachtung des Mittelalters. (shrink)

This book is an attempt to get to the bottom of an acute and perennial tension between our best scientific pictures of the fundamental physical structure of the world and our everyday empirical experience of it. The trouble is about the direction of time. The situation (very briefly) is that it is a consequence of almost every one of those fundamental scientific pictures--and that it is at the same time radically at odds with our common sense--that whatever can happen can (...) just as naturally happen backwards. Albert provides an unprecedentedly clear, lively, and systematic new account--in the context of a Newtonian-Mechanical picture of the world--of the ultimate origins of the statistical regularities we see around us, of the temporal irreversibility of the Second Law of Thermodynamics, of the asymmetries in our epistemic access to the past and the future, and of our conviction that by acting now we can affect the future but not the past. Then, in the final section of the book, he generalizes the Newtonian picture to the quantum-mechanical case and (most interestingly) suggests a very deep potential connection between the problem of the direction of time and the quantum-mechanical measurement problem. The book aims to be both an original contribution to the present scientific and philosophical understanding of these matters at the most advanced level, and something in the nature of an elementary textbook on the subject accessible to interested high-school students. Table of Contents: Preface 1. Time-Reversal Invariance 2. Thermodynamics 3. Statistical Mechanics 4. The Reversibility Objections and the Past-Hypothesis 5. The Scope of Thermodynamics 6. The Asymmetries of Knowledge and Intervention 7. Quantum Mechanics Appendix: Gedankenexperiments with Heat Engines Index Reviews of this book: The foundations of statistical mechanisms are often presented in physics textbooks in a rather obscure and confused way. By challenging common ways of thinking about this subject, Time and Chance can do quite a lot to improve this situation. --Jean Bricmont, Science Albert is perfecting a style of foundational analysis that is uniquely his own...It has a surgical precision...and it is ruthless with pretensions. The foundations of thermodynamics is a topic that has accumulated a good deal of dead wood; this is a fire that will burn and burn. --Simon W. Saunders, Oxford University As usual with Albert's work, the exposition is brisk and to the point, and exceptionally clear...The book will be an extremely valuable contribution to the literature on the subject of philosophical issues in thermodynamics and statistical mechanics, a literature which has been thin on the ground but is now growing as it deserves to. --Lawrence Sklar, University of Michigan. (shrink)

Die MISCELLANEA MEDIAEVALIA präsentieren seit ihrer Gründung durch Paul Wilpert im Jahre 1962 Arbeiten des Thomas-Instituts der Universität zu Köln. Das Kernstück der Publikationsreihe bilden die Akten der im zweijährigen Rhythmus stattfindenden Kölner Mediaevistentagungen, die vor über 50 Jahren von Josef Koch, dem Gründungsdirektor des Instituts, ins Leben gerufen wurden. Der interdisziplinäre Charakter dieser Kongresse prägt auch die Tagungsakten: Die MISCELLANEA MEDIAEVALIA versammeln Beiträge aus allen mediävistischen Disziplinen - die mittelalterliche Geschichte, die Philosophie, die Theologie sowie die Kunst- und Literaturwissenschaften (...) sind Teile einer Gesamtbetrachtung des Mittelalters. (shrink)

From the author of Quantum Mechanics and Experience, a hugely influential book that challenged key assertions by Niels Bohr and other founders of quantum mechanics, A Guess at the Riddle provides a major metaphysical overhaul of one of physics' most intractable problems-the quest to bridge quantum and classical physics in order to understand the nature of reality.

L’Union Européenne vit sous un régime de démocratie représentative de type fédéral dont la particularité est d’être en vigueur dans un État qui n’est pas fédéral. Les critiques qui l’accablent aujourd’hui sont en grande partie liées aux ambiguïtés et aux impasses qu’engendre l’enchevêtrement, pas toujours très clair, des pouvoirs actuellement exercés par le Parlement, la Commission et le Conseil. Une autre partie de la critique est plus tranchante : elle récuse le principe même de la construction européenne en l’accusant d’instituer (...) un déni de démocratie. Trois arguments étayent ce réquisitoire : le premier pointe la perte de souveraineté nationale ; le second le manque de représentativité des élus ; le troisième le déficit de légitimité des autorités en place. Des révisions apportées à chacun de ces trois facteurs permettraient-elles de conforter la démocratie dans le cadre européen? (shrink)

Sartre importe à l'histoire vivante de la philosophie sous plusieurs angles. Héritier de Hegel qui le hante, il conteste celui-ci dans sa conviction « totaliste ». S'il reste fidèle au dynamisme hégélien, à l'interrogation constante du vécu, il les traduit pourtant par nos langages présents.

In this article, we analyze and reject two versions of the content‐argument against animal beliefs, namely, the ontological argument from Davidson and the epistemological argument from Stich. One of the main defects of the strongest version of the argument is that it over‐intellectualizes belief ascriptions in humans and thus sets the comparative bar for belief ascriptions in animals too high. In the second part of the article, we develop a gradualist notion of belief which captures basic beliefs as well as (...) Davidsonian linguistic beliefs, and we specify the conditions under which belief ascriptions to nonlinguistic animals are justified. (shrink)

We develop a version of a direct perception account of emotion recognition on the basis of a metaphysical claim that emotions are individuated as patterns of characteristic features. On our account, emotion recognition relies on the same type of pattern recognition as is described for object recognition. The analogy allows us to distinguish two forms of directly perceiving emotions, namely perceiving an emotion in the absence of any top-down processes, and perceiving an emotion in a way that significantly involves some (...) top-down processes ; and, in addition, an inference-based evaluation of an emotion. Our model clarifies the epistemology of emotion recognition. (shrink)

In this eloquent guide to the meanings of the postmodern era, Albert Borgmann charts the options before us as we seek alternatives to the joyless and artificial culture of consumption. Borgmann connects the fundamental ideas driving his understanding of society's ills to every sphere of contemporary social life, and goes beyond the language of postmodern discourse to offer a powerfully articulated vision of what this new era, at its best, has in store. "[This] thoughtful book is the first remotely (...) realistic map out of the post modern labyrinth."—Joseph Coates, _The Chicago Tribune_ "Rather astoundingly large-minded vision of the nature of humanity, civilization and science."—_Kirkus Reviews_. (shrink)

In this paper, I critically assess different interpretations of Bohmian mechanics that are not committed to an ontology based on the wave function being an actual physical object that inhabits configuration space. More specifically, my aim is to explore the connection between the denial of configuration space realism and another interpretive debate that is specific to Bohmian mechanics: the quantum potential versus guidance approaches. Whereas defenders of the quantum potential approach to the theory claim that Bohmian mechanics is better formulated (...) as quasi-Newtonian, via the postulation of forces proportional to acceleration; advocates of the guidance approach defend the notion that the theory is essentially first-order and incorporates some concepts akin to those of Aristotelian physics. Here I analyze whether the desideratum of an interpretation of Bohmian mechanics that is both explanatorily adequate and not committed to configuration space realism favors one of these two approaches to the theory over the other. Contrary to some recent claims in the literature, I argue that the quasi-Newtonian approach based on the idea of a quantum potential does not come out the winner. (shrink)

In the recent literature on concepts, two extreme positions concerning animal minds are predominant: the one that animals possess neither concepts nor beliefs, and the one that some animals possess concepts as well as beliefs. A characteristic feature of this controversy is the lack of consensus on the criteria for possessing a concept or having a belief. Addressing this deficit, we propose a new theory of concepts which takes recent case studies of complex animal behavior into account. The main aim (...) of the paper is to present an epistemic theory of concepts and to defend a detailed theory of criteria for having concepts. The distinction between nonconceptual, conceptual, and propositional representations is inherent to this theory. Accordingly, it can be reasonably argued that some animals, e.g., grey parrots and apes, operate on conceptual representations. (shrink)

Albert Dzur proposes an approach he calls "democratic professionalism" to build bridges between specialists in domains like law, medicine, and journalism and the lay public in such a way as to enable and enhance broader public engagement ...

Holding On to Reality is a brilliant history of information, from its inception in the natural world to its role in the transformation of culture to the current Internet mania and is attendant assets and liabilities. Drawing on the history of ideas, the details of information technology, and the boundaries of the human condition, Borgmann illuminates the relationship between things and signs, between reality and information. "[Borgmann] has offered a stunningly clear definition of information in Holding On to Reality.... He (...) leaves room for little argument, unless one wants to pose the now vogue objection: I guess it depends on what you mean by nothing."—Paul Bennett, Wired "A superb anecdotal analysis of information for a hype-addled age."—New Scientist "This insightful and poetic reflection on the changing nature of information is a wonderful antidote to much of the current hype about the 'information revolution.' Borgmann reminds us that whatever the reality of our time, we need 'a balance of signs and things' in our lives."—Margaret Wertheim, LA Weekly. (shrink)

Die MISCELLANEA MEDIAEVALIA präsentieren seit ihrer Gründung durch Paul Wilpert im Jahre 1962 Arbeiten des Thomas-Instituts der Universität zu Köln. Das Kernstück der Publikationsreihe bilden die Akten der im zweijährigen Rhythmus stattfindenden Kölner Mediaevistentagungen, die vor über 50 Jahren von Josef Koch, dem Gründungsdirektor des Instituts, ins Leben gerufen wurden. Der interdisziplinäre Charakter dieser Kongresse prägt auch die Tagungsakten: Die MISCELLANEA MEDIAEVALIA versammeln Beiträge aus allen mediävistischen Disziplinen - die mittelalterliche Geschichte, die Philosophie, die Theologie sowie die Kunst- und Literaturwissenschaften (...) sind Teile einer Gesamtbetrachtung des Mittelalters. (shrink)