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.

Introduction: the age of Paine -- Portrait of a failure -- The great American cause -- The peculiar honor of France -- The Age of Reason -- An honest and useful life.

Introduction Watching the Doctor In some cultures, it is said, villagers cluster around a healer and a patient, eagerly listening to their conversation and ...

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)

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)

In lieu of an abstract, here is a brief excerpt of the content:Reply to Russell's letter of 16 May 1960 by Albert Shalom EDITORIAL NOTE To illustrate a list ofrecent acquisitions in Russell (Summer 1981), we printed in facsimile Russell's letter of 16 May 1960 to Professor Albert Shalom concerning the interpretation of Wittgenstein's Tractatus LogicoPhilosophicus. The correspondence between Russell and Shalom began when Shalom wrote on I May 1960 asking whether Russell had the time and inclination to read a (...) translation of a lecture which Shalom had given the previous December in Paris. The paper was entitled "The Metaphysical Thinking Underlying Wittgenstein's Tractatus". Shalom had received "different and even contradictory appraisals" of his paper, and he very much wanted to have Russell's opinion of it. Close to the age ofninety, Russell was entering a hectic period in his life in which he worked assiduouslyfor the Campaign for Nuclear Disarmament. He had published three books in 1959 and had produced prefaces and introductions for other people. As usual, he was besieged with mail including numerous requests to read unsolicited manuscripts sent to him quite regularly. Yet he had managed to answer correspondence in a very personal way. In November 1959, he had been involved in a controversy regarding the refusal ofthe editor of Mind to review Ernest Gellner's Words and Things, a book which attacked the then prevalent philosophy of linguistic analysis and for which Russell had written the introduction. In the early months of1960, he took time out from his usual writing on the nuclear threat to reply to several articles devoted to his theory of descriptions and his ethical theory in the journal Philosophy. Russell's reply (4 May 1960) to Shalom's first letter states: "Thank you for your letter ofMay I. I shall be interested to see your paper on Wittgenstein's Tractatus, but, as I am very busy, it may be some time before I can read it carefully." On 8 May Shalom wrote back in appreciation enclosing his paper and an offprint of an article, "Qu'est-ce qu'un concept?", Revue internationale dephilosophie, 50 (1959): I-IS. The main objection raised against his paper, Shalom admitted, was that Wittgenstein was not concerned with problems of epistemology at the time of his writing the Tractatus. Nonetheless, Shalom felt that the "picture theory" of reality implies an epistemology, and he was unable to see a fallacy in his paper: "Perhaps the fact that I'm not a logician has something to do with the matter. Ifyou could enlighten me on this point I should be most grateful to you." 45 28th April 1982. 46 Russell winter 1982-83 Russell's letter of 16 May followed. On 25 May Shalom challenged Russell's interpretation. Far /rom underestimating the notion of structure, Shalom claimed that he had emphasized the notion as the key to understanding the Tractatus. "In fact, my main point is that Wittgenstein's analyses of various concepts are unintelligible unless understood as arguments in terms of the dominating idea ofstructure or form. And that is what I understand as a metaphysical argument." Shalom went on to say that his interest in any philosopher was to try to discover the chief concepts employed in the philosopher's analysis and to examine the manner in which the analysis was performed. For this reason, the later Wittgenstein was not devoid ofinterest. In a postscript, he asked Russell whether he would be in London in July ofthat year, and ifso, whether a meeting was possible. Russell replied on 18June as follows: "Thank you for your letter ofMay 25. I am sorry that at present my time and thought are so occupied with matters very remote from those with whichyour letter deals that I cannot offeryou a reasoned reply. Unfortunately, I do not expect to be in London in July so that I am afraid a meeting will hardly be possible." On 14 Shalom requested the return of his paper, and Russell complied on 19 July. Shalom is now Professor ofPhilosophy at McMaster. We invited him to comment on his exchange with Russell, particularly Russell's letter of16 May 1960. His comments take the form ofa further (and no doubtfinal) letter in the exchange.-Carl... (shrink)

Blending social analysis and philosophy, Albert Borgmann maintains that technology creates a controlling pattern in our lives.

Relativity is the most important scientific idea of the twentieth century. Albert Einstein is the unquestioned founder of modern physics. His Special and General theories of Relativity introduced the idea to the world. In this classic short book he explains clearly, using the minimum amount of mathematical terms, the basic ideas and principles of his theory of Relativity. Unsurpassed by any subsequent books on Relativity, this remains the most popular and useful exposition of Einstein's immense contribution to human knowledge.

Time magazine's "Man of the Century", Albert Einstein is the founder of modern physics and his theory of relativity is the most important scientific idea of the modern era. In this short book, Einstein explains, using the minimum of mathematical terms, the basic ideas and principles of the theory that has shaped the world we live in today. Unsurpassed by any subsequent books on relativity, this remains the most popular and useful exposition of Einstein's immense contribution to human knowledge. With (...) a new foreword by Derek Raine. (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 ...

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.

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)

_Time_'s 'Man of the Century', Albert Einstein is the unquestioned founder of modern physics. His theory of relativity is the most important scientific idea of the modern era. In this short book Einstein explains, using the minimum of mathematical terms, the basic ideas and principles of the theory which has shaped the world we live in today. Unsurpassed by any subsequent books on relativity, this remains the most popular and useful exposition of Einstein's immense contribution to human knowledge.

_Time_'s 'Man of the Century', Albert Einstein is the unquestioned founder of modern physics. His theory of relativity is the most important scientific idea of the modern era. In this short book Einstein explains, using the minimum of mathematical terms, the basic ideas and principles of the theory which has shaped the world we live in today. Unsurpassed by any subsequent books on relativity, this remains the most popular and useful exposition of Einstein's immense contribution to human knowledge.

Relativity is the most important scientific idea of the twentieth century. Albert Einstein is the unquestioned founder of modern physics. His Special and General theories of Relativity introduced the idea to the world. In this classic short book he explains clearly, using the minimum amount of mathematical terms, the basic ideas and principles of his theory of Relativity. Unsurpassed by any subsequent books on Relativity, this remains the most popular and useful exposition of Einstein's immense contribution to human knowledge.

America is a wonderful and magnificent country that affords its citizens the broadest freedoms and the greatest prosperity in the world. But it also has its share of warts. It is embroiled in a war that many of its citizens consider unjust and even illegal. It continues to ravage the natural environment and ignore poverty both at home and abroad, and its culture is increasingly driven by materialism and consumerism. But America, for better or for worse, is still a nation (...) that we have built. So why then, asks Albert Borgmann in this most timely and urgent work, are we failing to take responsibility for it? In Real American Ethics , Borgmann asks us to reevaluate our role in the making of American values. Taking his cue from Winston Churchill—who once observed that we shape our buildings, and then our buildings shape us—Borgmann considers the power of our most enduring institutions and the condition of our present moral makeup to propose inspired new ways in which we, as ordinary citizens, can act to improve our country. This, he shows, includes everything from where we choose to live and what we spend our money on to daunting tasks like the reshaping of our cities—habits and actions that can guide us to more accomplished and virtuous lives. Using prose that is easy and direct throughout, Borgmann’s position is grounded neither by conservative nor liberal ideology, but in his understanding that he is a devoted citizen among many. In an age in which the blame game is the only game in town, this patriotic book is an eloquent reminder of the political strength we all wield when we work together. (shrink)

Focusing democratic theory on the pressing issue of punishment, Punishment, Participatory Democracy, and the Jury argues for participatory institutional designs as antidotes to the American penal state. Citizen action in institutions like the jury and restorative justice programs can foster the attunement, reflectiveness, and full-bodied communication needed as foundations for widespread civic responsibility for criminal justice.

Bringing expert knowledge to bear in an open and deliberative way to help solve pressing social problems is a major concern today, when technocratic and bureaucratic decision making often occurs with little or no input from the general public. 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 with and deliberation about major (...) social issues. Sparking a critical and constructive dialogue among social theories of the professions, professional ethics, and political theories of deliberative democracy, Dzur reveals interests, motivations, strengths, and vulnerabilities in conventional professional roles that provide guideposts for this new approach. He then applies it in examining three practical arenas in which experiments in collaboration and power-sharing between professionals and citizens have been undertaken: public journalism, restorative justice, and the bioethics movement. Finally, he draws lessons from these cases to refine this innovative theory and identify the kinds of challenges practitioners face in being both democratic and professional. (shrink)