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)

The Human Eros is an outstanding accomplishment, a work of genuine wisdom. It combines meticulous scholarship with an enviable mastery of cultural and philosophical history to address pressing concerns of human beings, nature, and philosophy itself. While comprised of essays spanning over two decades, the book presents a powerfully coherent philosophical vision which Alexander names, alternately, “eco-ontology,” “humanistic naturalism,” and “ecological humanism.” Whatever the name, the approach is humane and intellectually compelling, offering insight and direction to pragmatism, aesthetics, existentialism, (...) environmental philosophy, and anyone in search of wisdom. It is an immensely readable book, too. (shrink)

A curious and comparatively neglected element of death penalty jurisprudence in America is my target in this paper. That element concerns the circumstances under which severely mentally disabled persons, incarcerated on death row, may have their sentences carried out. Those circumstances are expressed in a part of the law which turns out to be indefensible. This legal doctrine—competence-for-execution —holds that a condemned, death-row inmate may not be killed if, at the time of his scheduled execution, he lacks an awareness of (...) his impending death or the reasons for it. I argue that the law of CFE should be abandoned, along with the notion that it is permissible to kill the deeply disturbed just so long as they meet some narrow test of readiness to die. By adopting CFE, the courts have been forced to give independent conceptual and moral significance to a standard for competence that simply cannot bear the weight placed upon it. To be executable, CFE requires that a condemned prisoner meet a standard demonstrating an awareness of certain facts about his death. Yet this standard both leads to confusing and counter-intuitive results and is unsupported either by the reasons advanced by the courts on its behalf or by any of the standard theoretical justifications of criminal punishment. If executing the profoundly psychotic or delusional is wrong the law needs a better account of the wrong done when prisoners like Ford are killed. I suggest wherein that wrong might be located. (shrink)

The paper considers contemporary models of presumption in terms of their ability to contribute to a working theory of presumption for argumentation. Beginning with the Whatelian model, we consider its contemporary developments and alternatives, as proposed by Sidgwick, Kauffeld, Cronkhite, Rescher, Walton, Freeman, Ullmann-Margalit, and Hansen. Based on these accounts, we present a picture of presumptions characterized by their nature, function, foundation and force. On our account, presumption is a modal status that is attached to a claim and has the (...) effect of shifting, in a dialogue, a burden of proof set at a local level. Presumptions can be analysed and evaluated inferentially as components of rule-based structures. Presumptions are defeasible, and the force of a presumption is a function of its normative foundation. This picture seeks to provide a framework to guide the development of specific theories of presumption. (shrink)

Environmental health research produces scientific knowledge about environmental hazards crucial for public health and environmental justice movements that seek to prevent or reduce exposure to these hazards. The environment in environmental health research is conceptualized as the range of possible social, biological, chemical, and/or physical hazards or risks to human health, some of which merit study due to factors such as their probability and severity, the feasibility of their remediation, and injustice in their distribution. This paper explores the ethics of (...) identifying the relevant environment for environmental health research, as judgments involved in defining an environmental hazard or risk, judgments of that hazard or risk's probability, severity, and/ or injustice, as well as the feasibility of its remediation, all ought to appeal to non-epistemic as well as epistemic values. I illustrate by discussing the case of environmental lead, a housing-related hazard that remains unjustly distributed by race and class and is particularly dangerous to children. Examining a controversy in environmental health research ethics where researchers tested multiple levels of lead abatement in lead-contaminated households, I argue that the broader perspective on the ethics of environmental health research provided in the first part of this paper may have helped prevent this controversy. (shrink)

This paper discusses ethical issues surrounding Integrated Assessment Models (IAMs) of the economic effects of climate change, and how climate economists acting as policy advisors ought to represent the uncertain possibility of catastrophe. Some climate economists, especially Martin Weitzman, have argued for a precautionary approach where avoiding catastrophe should structure climate economists’ welfare analysis. This paper details ethical arguments that justify this approach, showing how Weitzman’s “fat tail” probabilities of climate catastrophe pose ethical problems for widely used IAMs. The main (...) claim is that economists who ignore or downplay catastrophic risks in their representations of uncertainty likely fall afoul of ethical constraints on scientists acting as policy advisors. Such scientists have duties to honestly articulate uncertainties and manage (some) inductive risks, or the risks of being wrong in different ways. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

I suggest that the social justice issues raised by Internet regulation can be exposed and examined by using a methodology adapted from that described by John Rawls in 'A Theory of Justice'. Rawls' theory uses the hypothetical scenario of people deliberating about the justice of social institutions from the 'original position' as a method of removing bias in decision-making about justice. The original position imposes a 'veil of ignorance' that hides the particular circumstances of individuals from them so that they (...) will not be influenced by self-interest. I adapt Rawls' methodology by introducing an abstract description of information technology to those deliberating about justice from within the original position. This abstract description focuses on computing devices that users can use to access information and information networks that information devices use to communicate. The abstractness of this description prevents the particular characteristics of the Internet and the computing devices in use from influencing the decisions about the just use and regulation of information technology and networks. From this abstract position, the principles of justice that the participants accept for the rest of society will also apply to the computing devices people use to communicate, and to Internet regulation. (shrink)

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological (...) traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

The shape of the Earth's surface, its topography, is a fundamental dimension of the environment, shaping or mediating many other environmental flows or functions. But there is a major divergence in the way that topography is conceptualized in different domains. Topographic cartographers, information scientists, geomorphologists and environmental modelers typically conceptualize topographic variability as a continuous field of elevations or as some discrete approximation to such a field. Pilots, explorers, anthropologists, ecologists, hikers, and archeologists, on the other hand, typically conceptualize this (...) same variability in terms of hills and valleys, mountains and plains, barrows and trenches, that is, as (special sorts of) objects, with locations, shapes, and often names of their own. In this chapter, we sketch an approach to bridging this fundamental gap in geographic information infrastructure. (shrink)

Information may be defined as the conceptual or communicable part of the content of mental acts. The content of mental acts includes sensory data as well as concepts, particular as well as general information. An information system is an external (non-mental) system designed to store such content. Information systems afford indirect transmission of content between people, some of whom may put information into the system and others who are among those who use the system. In order for communication to happen, (...) the conceptual systems of the originators and users of the information must be sufficiently similar. A formal conceptual framework that can provide the basis for exchange of information is termed an ontology. In its most fundamental form, ontology studies the most basic constituents of reality. Traditionally, ontology seeks to reflects structures that are independent of thought and cognition. The term ontology is used more broadly in artificial intelligence and software engineering, to refer to the conceptual basis for an information system. (shrink)

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological (...) traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

Matters of Certainty and Conviction. In the section on certainty, Shaw puts forth a proof of the external world, and considers topics such as change, difference, time, consciousness, substance and quality.

This paper argues that epistemic errors rooted in group- or identity- based biases, especially those pertaining to disability, are undertheorized in the literature on medical error. After sketching dominant taxonomies of medical error, we turn to the field of social epistemology to understand the role that epistemic schemas play in contributing to medical errors that disproportionately affect patients from marginalized social groups. We examine the effects of this unequal distribution through a detailed case study of ableism. There are four primary (...) mechanisms through which the epistemic schema of ableism distorts communication between nondisabled physicians and disabled patients: testimonial injustice, epistemic overconfidence, epistemic erasure, and epistemic derailing. Measures against epistemic injustices in general and against schema-based medical errors in particular are ultimately issues of justice that must be better addressed at all levels of health care practice. (shrink)

Since it is only five years since the publication of our paper, "Geographical categories: An ontological investigation" (Smith and Mark 2001), it seems somewhat strange to be making retrospective comments on the piece. Nevertheless, the field is moving quickly, and much has happened since the article appeared. A large number of papers have already cited the work, which suggests that there is a seam here that people find worthy of being mined. In this short essay, we first review the paper (...) and attempt to assess its significance from the perspective of our current work. We then put the paper in the context of our individual and joint works, which led up to it, and summarize our research trajectories since the paper appeared, pointing out what some of this reveals about spatial ontology in general. We conclude with some remarks on the future of ontological research in geographical information science. (shrink)

This paper addresses the problem: Can a synergy be derived from Keiji Nishitani’s conceptualization of Śūnyatā and Paul Tillich’s concept of Being Itself, as philosophies about Ultimate Reality, with the application of Wesley Wildman’s procedures based on the methodology of the Comparative Religious Ideas Project? The paper defines philosophy of religion and argues that it is justified as an academic discipline. A review of the literature demonstrates that both Nishitani and Tillich share common philosophical ground in phenomenological existentialism and nihilism. (...) The paper proceeds to discuss the biographies and religious philosophies of both Keiji Nishitani and Paul Tillich. Subsequently, the paper details the Comparative Religious Ideas Project (CRIP) methodology and then applies Wildman’s procedures to these two philosophers. The thesis concludes that a synergy exists about Ultimate Reality between the contemporary religious philosophies of Nishitani’s description of Buddhism and Tillich’s explanation of Christianity. (shrink)

Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological theorizing in abstract (...) fashion about the world was supplemented by the study, based on the use of logical methods, of the ontological commitments or presuppositions embodied in scientific theories. In recent years both types of ontological study have found application in the world of information systems, for example in the construction of frameworks for knowledge representation and in database design and translation. As ontology is in this way drawn closer to the domain of real-world applications, the question arises as to whether it is possible to use empirical methods in studying ontological theories. More specifically: can we use empirical methods to test the ontological theories embodied in human cognition? We set forth the outlines of a framework for the formulation and testing of such theories as they relate to the specific domain of geographic objects and categories. (shrink)

In December 2013, the Nonhuman Rights Project (NhRP) filed a petition for a common law writ of habeas corpus in the New York State Supreme Court on behalf of Tommy, a chimpanzee living alone in a cage in a shed in rural New York (Barlow, 2017). Under animal welfare laws, Tommy’s owners, the Laverys, were doing nothing illegal by keeping him in those conditions. Nonetheless, the NhRP argued that given the cognitive, social, and emotional capacities of chimpanzees, Tommy’s confinement constituted (...) a profound wrong that demanded remedy by the courts. Soon thereafter, the NhRP filed habeas corpus petitions on behalf of Kiko, another chimpanzee housed alone in Niagara Falls, and Hercules and Leo, two chimpanzees held in research facilities at Stony Brook University. Thus began the legal struggle to move these chimpanzees from captivity to a sanctuary, an effort that has led the NhRP to argue in multiple courts before multiple judges. The central point of contention has been whether Tommy, Kiko, Hercules, and Leo have legal rights. To date, no judge has been willing to issue a writ of habeas corpus on their behalf. Such a ruling would mean that these chimpanzees have rights that confinement might violate. Instead, the judges have argued that chimpanzees cannot be bearers of legal rights because they are not, and cannot be persons. In this book we argue that chimpanzees are persons because they are autonomous. (shrink)

John Searle’s The Construction of Social Reality and Hernando de Soto’s The Mystery of Capital shifted the focus of current thought on capital and economic development to the cultural and conceptual ideas that underpin market economies and that are taken for granted in developed nations. This collection of essays assembles 21 philosophers, economists, and political scientists to help readers understand these exciting new theories.

This is an excerpt of a report that highlights and explores five questions which arose from The Unity of Consciousness and Sensory Integration conference at Brown University in November of 2011. This portion of the report explores the question: Is the mechanism of sensory integration spatio-temporal?

Families play an essential role in deceased organ procurement. As the person cannot directly communicate his or her wishes regarding donation, the family is often the only source of information regarding consent or refusal. We provide a systematic description and analysis of the different roles the family can play, and actions the family can take, in the organ procurement process across different jurisdictions and consent systems. First, families can inform or update healthcare professionals about a person’s donation wishes. Second, families (...) can authorize organ procurement in the absence of deceased’s preferences and the default is not to remove organs, and oppose donation where there is no evidence of preference but the default is to presume consent; in both cases, the decision could be based on their own wishes or what they think the deceased would have wanted. Finally, families can overrule the known wishes of the deceased, which can mean preventing donation, or permitting donation when the deceased refused it. We propose a schema of 4 levels on which to map these possible family roles: no role, witness, surrogate, and full decisional authority. We conclude by mapping different jurisdictions onto this schema to provide a more comprehensive understanding of the consent system for organ donation and some important nuances about the role of families. This classificatory model aims to account for the majority of the world’s consent systems. It provides conceptual and methodological guidance that can be useful to researchers, professionals, and policymakers involved in organ procurement. (shrink)

Is the societal-level of analysis sufficient today to understand the values of those in the global workforce? Or are individual-level analyses more appropriate for assessing the influence of values on ethical behaviors across country workforces? Using multi-level analyses for a 48-society sample, we test the utility of both the societal-level and individual-level dimensions of collectivism and individualism values for predicting ethical behaviors of business professionals. Our values-based behavioral analysis indicates that values at the individual-level make a more significant contribution to (...) explaining variance in ethical behaviors than do values at the societal-level. Implicitly, our findings question the soundness of using societal-level values measures. Implications for international business research are discussed. (shrink)

A letter to The Times of London, May 9, 1992 protesting the Cambridge University proposal to award an honorary degree to M. Jacques Derrida.

This project continues our interdisciplinary research into computational and cognitive aspects of narrative comprehension. Our ultimate goal is the development of a computational theory of how humans understand narrative texts. The theory will be informed by joint research from the viewpoints of linguistics, cognitive psychology, the study of language acquisition, literary theory, geography, philosophy, and artificial intelligence. The linguists, literary theorists, and geographers in our group are developing theories of narrative language and spatial understanding that are being tested by the (...) cognitive psychologists and language researchers in our group, and a computational model of a reader of narrative text is being developed by the AI researchers, based in part on these theories and results and in part on research on knowledge representation and reasoning. This proposal describes the knowledge-representation and natural-language-processing issues involved in the computational implementation of the theory; discusses a contrast between communicative and narrative uses of language and of the relation of the narrative text to the story world it describes; investigates linguistic, literary, and hermeneutic dimensions of our research; presents a computational investigation of subjective sentences and reference in narrative; studies children’s acquisition of the ability to take third-person perspective in their own storytelling; describes the psychological validation of various linguistic devices; and examines how readers develop an understanding of the geographical space of a story. This report is a longer version of a project description submitted to NSF. This document, produced in May 2007, is a L ATEX version of Technical Report 89-07 (Buffalo: SUNY Buffalo Department of Computer Science, August 1989), with slightly.. (shrink)

This is an excerpt of a report that highlights and explores five questions which arose from The Unity of Consciousness and Sensory Integration conference at Brown University in November of 2011. This portion of the report explores the question: How should we study experience, given unity relations?

This is an excerpt from a report that highlights and explores five questions which arose from the workshop on perceptual learning and perceptual recognition at the University of Toronto, Mississauga on May 10th and 11th, 2012. This excerpt explores the question: How can philosophers and psychologists most fruitfully collaborate?

This report highlights and explores five questions which arose from The Unity of Consciousness and Sensory Integration conference at Brown University in November of 2011: 1. What is the relationship between the unity of consciousness and sensory integration? 2. Are some of the basic units of consciousness multimodal? 3. How should we model the unity of consciousness? 4. Is the mechanism of sensory integration spatio-temporal? 5. How Should We Study Experience, Given Unity Relations?

This is an excerpt of a report that highlights and explores five questions which arose from The Unity of Consciousness and Sensory Integration conference at Brown University in November of 2011. This portion of the report explores the question: Are some of the basic units of consciousness multimodal?

Inspired by recent progress in multi-agent Reinforcement Learning (RL), in this work we examine the collective intelligent behaviour of theoretical universal agents by introducing a weighted mixture operation. Given a weighted set of agents, their weighted mixture is a new agent whose expected total reward in any environment is the corresponding weighted average of the original agents' expected total rewards in that environment. Thus, if RL agent intelligence is quantified in terms of performance across environments, the weighted mixture's intelligence is (...) the weighted average of the original agents' intelligences. This operation enables various interesting new theorems that shed light on the geometry of RL agent intelligence, namely: results about symmetries, convex agent-sets, and local extrema. We also show that any RL agent intelligence measure based on average performance across environments, subject to certain weak technical conditions, is identical (up to a constant factor) to performance within a single environment dependent on said intelligence measure. (shrink)

We submit this brief in support of the Nonhuman Rights Project’s efforts to secure habeas corpus relief for the elephant named Happy. The Supreme Court, Bronx County, declined to grant habeas corpus relief and order Happy’s transfer to an elephant sanctuary, relying, in part, on previous decisions that denied habeas relief for the NhRP’s chimpanzee clients, Kiko and Tommy. Those decisions use incompatible conceptions of ‘person’ which, when properly understood, are either philosophically inadequate or, in fact, compatible with Happy’s personhood.

This is an excerpt of a report that highlights and explores five questions which arose from The Unity of Consciousness and Sensory Integration conference at Brown University in November of 2011. This portion of the report explores the question: How should we model the unity of consciousness?

This is an excerpt from a report that highlights and explores five questions which arose from the workshop on perceptual learning and perceptual recognition at the University of Toronto, Mississauga on May 10th and 11th, 2012. This excerpt explores the question: How do we recognize distinct types of emotion in music?

This report highlights and explores five questions which arose from the workshop on perceptual learning and perceptual recognition at the University of Toronto, Mississauga on May 10th and 11th, 2012: 1. How should we demarcate perceptual learning from perceptual development? 2. What are the origins of multimodal associations? 3. Does our representation of time provide an amodal framework for multi-sensory integration? 4. What counts as cognitive penetration? 5. How can philosophers and psychologists most fruitfully collaborate?

This is an excerpt from a report that highlights and explores five questions which arose from the workshop on perceptual learning and perceptual recognition at the University of Toronto, Mississauga on May 10th and 11th, 2012. This excerpt explores the question: What counts as cognitive penetration?

This is an excerpt from a report that highlights and explores five questions which arose from the workshop on perceptual learning and perceptual recognition at the University of Toronto, Mississauga on May 10th and 11th, 2012. This excerpt explores the question: How should we demarcate perceptual learning from perceptual development?

This is an excerpt from a report that highlights and explores five questions which arose from the workshop on perceptual learning and perceptual recognition at the University of Toronto, Mississauga on May 10th and 11th, 2012. This excerpt explores the question: Does our representation of time provide and amodal framework for multi-sensory integration?

This is an excerpt from a report that highlights and explores five questions which arose from the workshop on perceptual learning and perceptual recognition at the University of Toronto, Mississauga on May 10th and 11th, 2012. This excerpt explores the question: What are the origins of multimodal associations?

The latest edition of the Diagnostic and Statistical Manual of Mental Disorders included the Social Communication Disorder as a new mental disorder characterized by deficits in pragmatic abilities. Although the introduction of SPCD in the psychiatry nosography depended on a variety of reasons—including bridging a nosological gap in the macro-category of Communication Disorders—in the last few years researchers have identified major issues in such revision. For instance, the symptomatology of SPCD is notably close to that of Autism Spectrum Disorder. This (...) opens up the possibility that individuals with very similar symptoms can be diagnosed differently and receive different clinical treatments and social support. The aim of this paper is to review recent debates on SPCD, particularly as regards its independence from ASD. In the first part, we outline the major aspects of the DSM-5 nosological revision involving ASD and SPCD. In the second part, we focus on the validity and reliability of SPCD. First, we analyze literature on three potential validators of SPCD, i.e., etiology, response to treatment, and measurability. Then, we turn to reliability issues connected with the introduction of the grandfather clause and the use of the concepts of spectrum and threshold in the definition of ASD. In the conclusion, we evaluate whether SPCD could play any role in contemporary psychiatry other than that of an independent mental disorder and discuss the role that non-epistemic factors could play in the delineation of the future psychiatry nosography. (shrink)

This paper argues that higher-order doubt generates an epistemic dilemma. One has a higher-order doubt with regards to P insofar as one justifiably withholds belief as to what attitude towards P is justified. That is, one justifiably withholds belief as to whether one is justified in believing, disbelieving, or withholding belief in P. Using the resources provided by Richard Feldman’s recent discussion of how to respect one’s evidence, I argue that if one has a higher-order doubt with regards to P, (...) then one is not justified in having any attitude towards P. Otherwise put: No attitude towards the doubted proposition respects one’s higher-order doubt. I argue that the most promising response to this problem is to hold that when one has a higher-order doubt about P, the best one can do to respect such a doubt is to simply have no attitude towards P. Higher-order doubt is thus much more rationally corrosive than non-higher-order doubt, as it undermines the possibility of justifiably having any attitude towards the doubted proposition. (shrink)

Peter van Inwagen's Direct Argument (DA) purports to establish the incompatibility of determinism and moral responsibility, without appealing to the notion of avoidability, a notion on whose analysis compatibilists and incompatibilists disagree. Van Inwagen intended DA to refute compatibilism, or at least to shift the burden of proof onto the compatibilist. In this paper, we offer a critical assessment of DA. We examine a variety of objections to DA due to John Fischer and Mark Ravizza, Ishtiyaque Haji, Seth Shabo, Michael (...) McKenna, and David Widerker. We divide these objections into those based on dialectical considerations (section 1), and objections in the form of counterexamples to a central principle which the Direct Argument employs (sec 2). The conclusion we reach is that the proponent of DA can deal plausibly with these objections, thus establishing DA as a powerful argument in favor of incompatibilism. (shrink)

Machine learning algorithms may radically improve our ability to diagnose and treat disease. For moral, legal, and scientific reasons, it is essential that doctors and patients be able to understand and explain the predictions of these models. Scalable, customisable, and ethical solutions can be achieved by working together with relevant stakeholders, including patients, data scientists, and policy makers.

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

Despite the frequency of stillbirths, the subsequent implications are overlooked and underappreciated. We present findings from comprehensive, systematic literature reviews, and new analyses of published and unpublished data, to establish the effect of stillbirth on parents, families, health-care providers, and societies worldwide. Data for direct costs of this event are sparse but suggest that a stillbirth needs more resources than a livebirth, both in the perinatal period and in additional surveillance during subsequent pregnancies. Indirect and intangible costs of stillbirth are (...) extensive and are usually met by families alone. This issue is particularly onerous for those with few resources. Negative effects, particularly on parental mental health, might be moderated by empathic attitudes of care providers and tailored interventions. The value of the baby, as well as the associated costs for parents, families, care providers, communities, and society, should be considered to prevent stillbirths and reduce associated morbidity. (shrink)