"Who knows how much longer it will be, but others have crossed over to the US, and have found a job, and have even sent for their families. I am not the only one crossing, I am number 57 out of 72, but we do not walk together, all 72—that would call too much attention to us. We walk at a good pace, each one with their thoughts, we walk from sun to sun without stopping almost; others have done it." (...) These are the words of renowned writer Elena Poniatowska on 72migrantes.com, a virtual altar honoring the 72 migrants massacred in a ranch in San Fernando, a municipality in the border state of Tamaulipas, Mexico, in August 2010. Attempting to recreate the thoughts of unidentified victim number 57 on his trek towards the... (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)

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)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

A major, but too-little-considered problem for Software Engineering is a lack of consensus concerning Computer Science and how this relates to developing unpredictable computing technology. We consider some implications for SE of computer systems differing scientific basis, exemplified with the International Standard Organisations Open Systems Interconnection layered architectural model. An architectural view allows comparison of computing technology components facilitating a view of computing as a continuum. For example, at one layer of computer architecture, components written in Turing-complete machine language can (...) be seen as deterministic and consistent with a theoretical paradigm of CS. At another layer, components closer to the human sphere have been seen as non-deterministic and inconsistent with theoretical CS. We compare unpredictable development of computing technology against the cyclic legacy of technological advance and scientific discovery, and suggest that SE indicates an enabling cycle, discernible in previous scientific revolution, is stalled or possibly hidden. The CS consequence of divorcing technological advance from scientific consensus is particularly concerning. For example human/computing events could be seen as unpredictable virtual phenomena that somehow extend the ontology of CS. Our approach challenges practical and philosophical boundaries by investigating if applying scientific method resolves any SE/Science dichotomy. (shrink)

Narrative inquiry in a nursing practicum One approach to creating research‐based nursing education is to think and write narratively about the daily life of a BScN program student and her teacher in diverse settings and over time. Gail, as a nurse‐teacher, and Faith, as a nursing student and now Public Health Nurse, reconstruct their teaching–learning experiences in an integrated practicum in maternal–child health services as a narrative inquiry. After presenting this reconstruction of experience at a conference on maternal scholarship, further (...) inquiry into their experiences shows how narrative inquiry matters to construction of nursing praxis and to life‐long learning as a nurse. Teaching–learning relationships are seen as a template for a student's connections to people experiencing nursing care and to other clinicians. Construction of stories to live by that take into account becoming a nurse, constructing knowledge and enacting caring–healing nursing practices is illuminated through narrative inquiry. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (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)

In 1984, eight-year-old Paula Logares was called into a judge’s chambers and was told the man and woman she lived with were not her parents. Her parents had been disappeared during the dirty war, and now, through her blood, scientists would be able to return her to her birth family. Paula, thus, became the first “stolen” child in Argentina to be identified via the incipient technology of DNA identification. With this forensic first, DNA identification has emerged as a central tool (...) of good governance the world round. From routine crime fighting to international criminal tribunals, DNA plays a crucial role in attempts to reckon with crimes of the body. As an alternative origin for forensic DNA, Argentina offers an early example of science emerging from social movements in the Global South. Drawing on twenty-seven months of fieldwork with family members, activists, and scientists, this article documents the ways in which DNA has emerged as a core site of subject formation for individuals and families affected by the terror of the dictatorship and for the Argentine nation-state, as it reckons with the legacies of repression. Through a feminist, postcolonial frame, I offer the concept of restitution as a way of attending to the forms of biocitizenship that emerge during times of humanitarian crisis and transitional justice. As a tool of reproductive governance, forensic DNA acts not only as a powerful disciplinary site of biocitizenship but also as a potential space to reimagine the social contract between the body, the public, and the state. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (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.

Context: Participatory arts-based methods such as photovoice, drama and music have increasingly been used to engage young people who are exposed to psychosocial risks. These methods have the potential to empower youth and provide them with an accessible and welcoming environment to express and manage difficult feelings and experiences. These effects are, however, dependent on the way these methods are implemented and how potential ethical concerns are handled. Objective: Using the current literature on arts-based health research as a foundation, this (...) paper examines ethical issues emerging from participatory arts methods with young people with traumatic experiences. Results: We present a typology covering relevant issues such as power, accessibility, communication, trust and ownership, across the domains of partnership working, project entry, participation and dissemination. Drawing on our extensive clinical and research experiences, existing research and novel in-practice examples, we offer guidance for ethical dilemmas that might arise at different phases of research. Conclusion: Adequate anticipation and consideration of ethical issues, together with the involvement of young people, will help ensure that arts methods are implemented in research and practice with young people in a fair, meaningful and empowering way. Patient or Public Contribution: The issues reviewed are largely based on the authors' experience conducting participatory research. Each of the projects referenced has its own systems for PPI including, variously, consultations with advisory groups, coproduction, youth ambassadors and mentor schemes. One of the coauthors, Josita Kavitha Thirumalai, is a young person trained in peer support and has provided extensive input across all stages. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

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.

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

The patient, an 89-year-old man—let’s call him Mr. Smith—had no known relatives, friends, or advance directives. He was a bright man and served as a scientist in the Reagan administration.

Populated by lesbian, gay, bisexual, trans*, queer (LGBTQ) and allied youth, school-based gay straight alliances (GSAs) offer a unique opportunity to re-imagine or redefine youth subjectivity, especially with regards to the intersections of sexual orientation, gender identity, and civic rights. Tracing the evolution of youth subjectivity from the emergence of Canadian schooling in the 1860s, I turn to Ontario’s Bill 13 as a recent example of how GSAs are subverting, or resisting these norms, and in so doing, operate as a (...) kind of counter-public. Drawing from Jenks’ (2005) archetypes of the Dionysian and Apollonian child, I assert that GSAs can embody a third type of child subjectivity, the Athenian child (Smith, 2011; 2014) and, in so doing, provide theoretical space to reconstitute subjectivity for all youth. (shrink)

A Review of Lindsay Judson and Vassilis Karasmanis , Remembering Socrates: Philosophical Essays, Clarendon Press, Oxford, 2006.

One of Hume's most well-known works and a masterpiece of philosophy, A Treatise of Human Nature is indubitably worth taking the time to read.

Unpopular in its day, David Hume's sprawling, three-volume 'A Treatise of Human Nature' (1739-40) has withstood the test of time and had enormous impact on subsequent philosophical thought. Hume's comprehensive effort to form an observationally grounded study of human nature employs John Locke's empiric principles to construct a theory of knowledge from which to evaluate metaphysical ideas. A key to modern studies of eighteenth-century Western philosophy, the Treatise considers numerous classic philosophical issues, including causation, existence, freedom and necessity, and morality. (...) Unabridged republication of the edition originally published by Oxford at the Clarendon Press, London, 1888. (shrink)

Antimicrobial resistance (AMR) is one of the defining global health threats of our time, but no international legal instrument currently offers the framework and mechanisms needed to address it. Fortunately, the actions needed to address AMR have considerable overlap with the actions needed to confront other pandemic threats.

The AMA Council on Ethical and Judicial Affairs (CEJA) has written a position paper on how social medical use challenges medical professionalism. The report offers persuasive ethical and practical guidelines for nonclinical internet use, specifically for social networking.This commentary provides a framework from which to apply these guidelines, but adds that there may be important situations in which physicians are not able to act in accordance. The guidelines call for professional reporting of questionable online portrayals or behaviors, but this commentary (...) argues that this may be not only cumbersome to implement, but may violate aspects of constitutional rights. While online social networking may in many ways be a new application of old challenges, there may be other aspects that require novel approaches to medical professionalism. (shrink)

In this paper, we present the results of two surveys that investigate subjects’ judgments about what can be known or justifiably believed about lottery outcomes on the basis of statistical evidence, testimonial evidence, and “mixed” evidence, while considering possible anchoring and priming effects. We discuss these results in light of seven distinct hypotheses that capture various claims made by philosophers about lay people’s lottery judgments. We conclude by summarizing the main findings, pointing to future research, and comparing our findings to (...) recent studies by Turri and Friedman. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

Originally published in 1945, this book presents the content of the Girton College Founders' Memorial Lecture for that year, which was delivered by A. D. Lindsay. This book will be of value to anyone with an interest in philosophy and the relationship between intelligence and morality.

The notion of risk plays a central role in economics, finance, health, psychology, law and elsewhere, and is prevalent in managing challenges and resources in day-to-day life. In recent work, Duncan Pritchard (2015, 2016) has argued against the orthodox probabilistic conception of risk on which the risk of a hypothetical scenario is determined by how probable it is, and in favour of a modal conception on which the risk of a hypothetical scenario is determined by how modally close it is. (...) In this article, we use Pritchard’s discussion as a springboard for a more wide-ranging discussion of the notion of risk. We introduce three different conceptions of risk: the standard probabilistic conception, Pritchard’s modal conception, and a normalcy conception that is new (though it has some precursors in the psychological literature on risk perception). Ultimately, we argue that the modal conception is ill-suited to the roles that a notion of risk is required to play and explore the prospects for a form of pluralism about risk, embracing both the probabilistic and the normalcy conceptions. (shrink)

THE GOOD 8 THE CLEVER say, those charming verses of Miss Wordsworth's, the first Principal of Lady Margaret Hall. A text, however familiar, is read at the beginning of the discourse, so I shall begin by reading the verses: I WISH to take,  ...