This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

This article examines the distinction between active matter and active materials, and it offers foundational remarks toward a system of classification for active materials. Active matter is typically identified as matter that exhibits two characteristic features: self-propelling parts, and coherent dynamical activity among the parts. These features are exhibited across a wide range of organic and inorganic materials, and they are jointly sufficient for classifying matter as active. Recently, the term “active materials” has entered scientific use as a complement, supplement, (...) and extension of “active matter.” At the same time, new work in the philosophy of science has considered the problem of how to classify the products of synthetic and laboratory processes, and the extent to which the aims of classifying natural kinds compare and contrasts with the aims of classifying these synthetic kinds. In this article, I apply those considerations to the problems of classifying and characterizing active materials. In doing so, I also argue for a conception of active materials’ coherent dynamical activity as multiscale, rather than emergent, and I discuss how the special non-equilibrium status of active materials factors in to classificatory concerns. (shrink)

Vocal fry is a phonation, or voicing, in which an individual drops their voice below its natural register and consequently emits a low, growly, creaky tone of voice. Media outlets have widely acknowledged it as a generational vocal style characteristic of millennial women. Critics of vocal fry often claim that it is an exclusively female vocal pattern, and some say that the voicing is so distracting that they cannot understand what is being said under the phonation. Claiming that a phonation (...) is so distracting as to prevent uptake of the semantic content of an utterance associated with it is an extreme reaction, especially when accompanied by demands for women to change their phonation. We argue that this reaction limits women's communicative autonomy. We analyze the extreme reaction to female vocal fry, which we characterize as a non-content-based response, from the perspectives of philosophy of language, feminist epistemology, and linguistics. We argue that when fry is heard as annoying and distracting, it is because the hearer interprets the speaker as echoing an utterance from a position of authority to which she is not entitled. We show that this reaction encodes conscious or unconscious sexist attitudes toward women's voices. (shrink)

This interview, conducted over the span of several months, tracks the respective journeys of Constantin V. Boundas and Daniel W. Smith with the philosophy of Gilles Deleuze. Rather than “becoming Deleuzian,” which is neither desirable nor possible, these exchanges reflect an array of encounters with Deleuze. These include the initial discoveries of Deleuze’s writings by Boundas and Smith, in-person meetings between Boundas and Deleuze, and the wide-ranging and influential philosophical work on Deleuze’s concepts produced by both Boundas and (...) Smith. At stake in this discussion are key contributions by Deleuze to continental philosophy, including the distinction between the virtual and the actual and the very nature of a “concept.” Also at stake is the formative or pedagogical impact of a philosopher, like Deleuze, on those who find and fully engage with his texts, concepts, and project. Cette interview, menée sur plusieurs mois, suit les parcours respectifs de Constantin V. Boundas et Daniel W. Smith avec la philosophie de Gilles Deleuze. Au lieu de « devenir Deleuzien, » ce qui n’est ni souhaitable ni possible, ces échanges reflètent un éventail de rencontres avec Deleuze. Il s’agit notamment des premières découvertes des écrits de Deleuze par Boundas et Smith, des rencontres en personne entre Boundas et Deleuze, et du travail philosophique vaste et in????luent sur les concepts de Deleuze produit par Boundas et Smith. L’enjeu ici étant les contributions clés de Deleuze à la philosophie continentale, y compris la distinction entre le virtuel et l’actuel, et la nature même d’un « concept. » Mais il y a aussi l’impact formateur ou pédagogique d’un philosophe, comme Deleuze, sur ceux qui trouvent et s’engagent pleinement dans ses textes, ses concepts et ses projets. (shrink)

The concept of sustainable development considers environmental, social and economic issues in general. And the goals of resource conservation and socio-economic development do not contradict each other, but contribute to mutual reinforcement. The purpose of this study is to build and test an economic and mathematical model for the formation of strategies for the behavior of an economic entity with an increase in the impact of negative environmental factors. The proposed strategies and their models are based on the income-expenditure balance (...) equation, which takes into account both quantitative and qualitative characteristics. The constructed models are considered in the state space. The research methodology is based on building models in the form of linear combinations of functions of a homogeneous external impact and various spatial combinations of economic sources (sinks). The study makes it possible to assess the dependence of the amount of resources used for life support on the chosen adaptive strategy. Within the framework of the proposed model, it was found that the criterion for the effectiveness of the applied strategy can be an indicator of satisfaction with the state, the preservation of which, simultaneously with the preservation of the size of resources used, corresponds to the direction of optimization. This approach is consistent with the concept of sustainable development. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

This reply to an ongoing debate between conspiracy theory researchers from different disciplines exposes the conceptual confusions that underlie some of the disagreements in conspiracy theory research. Reconciling these conceptual confusions is important because conspiracy theories are a multidisciplinary topic and a profound understanding of them requires integrative insights from different fields. Specifically, we distinguish research focussing on conspiracy *theories* (and theorizing) from research of conspiracy *belief* (and mindset, theorists) and explain how particularism with regards to conspiracy theories does not (...) mean we cannot define a problematic subclass of conspiracy beliefs, while avoiding the problems of generalism. We hope this reply helps conspiracy theory researchers recognize the differences between studying conspiracy theories and conspiracy beliefs and appreciate the possibilities for fruitful, integrative, and interdisciplinary research. (shrink)

Epistemic permissivism is the view that it is possible for two people to rationally hold incompatible attitudes toward some proposition on the basis of one body of evidence. In this paper, I defend a particular version of permissivism – unacknowledged permissivism (UP) – which says that permissivism is true, but that no one can ever rationally believe that she is in a permissive case. I show that counter to what virtually all authors who have discussed UP claim, UP is an (...) attractive view: it is compatible with the intuitive motivations for permissivism and avoids a significant challenge to permissivism: the arbitrariness objection. (shrink)

In the literature on philosophical progress it is often assumed that agreement is a necessary condition for progress. This assumption is sensible only if agreement is a reliable sign of the truth, since agreement on false answers to philosophical questions would not constitute progress. This paper asks whether agreement among philosophers is (or would be) likely to be a reliable sign of truth. Insights from social choice theory are used to identify the conditions under which agreement among philosophers would be (...) a reliable indicator of the truth, and it is argued that we lack good reason to think that philosophical inquiry meets these conditions. The upshot is that philosophical agreement is epistemically uninformative: agreement on the answer to a philosophical question does not supply even a prima facie reason to think that the agreed-upon view is true. However, the epistemic uninformativeness of philosophical agreement is not an indictment of philosophy's progress, because philosophy is valuable independent of its ability to generate agreement on the correct answers to philosophical questions. (shrink)

We argue that the evolutionary function of reasoning is to allow us to secure more accurate beliefs and more effective intentions through collective deliberation. This sets our view apart both from traditional intellectualist accounts, which take the evolutionary function to be individual deliberation, and from interactionist accounts such as the one proposed by Mercier and Sperber, which agrees that the function of reasoning is collective but holds that it aims to disseminate, rather than come up with, accurate beliefs. We argue (...) that our collectivized intellectualism offers the best explanation of the range of biases that human reasoning is prone to, and that it does better than interactionism at offering a function of reasoning that would have been adaptive for our distant ancestors who first evolved this capacity. (shrink)

This entry provides an overview of the current state of the debate between epistemic permissivists and impermissivists. Three important choice points for the permissivist are identified, and implications are discussed for plausibility of the resulting versions of permissivism.

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

This chapter explores the opportunities and limitations of the ideal of transparency in responsible innovation, by consulting the virtual case of "The Circle", a company which appears in Dave Eggers' novel The Circle. The Circle is a high-tech company with the main purpose of being responsive to societal needs. They want to eradicate unethical behaviour in society, enhance public health and make a positive impact on the environment. The ultimate goal of The Circle is to reach 100% full transparency in (...) the world, which is impossible without any societal desirability. In first instance, it is free choice of people to accept and embrace the products and services of The Circle, who invest resources in keeping customers happy and in raising awareness about the dangers of privacy. The chapter concludes that The Circle meets the requirements regarding the outcomes of responsible innovation, at least to a certain extent, while at the same time, one feels unease about certain activities they undertake. (shrink)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)

The aim of this paper is to provide a conceptual framework that will help in understanding and evaluating, along social and ethical lines, the issue of killing day-old male chicks and two alternative directions of responsible innovations to solve this issue. The following research questions are addressed: Why is the killing of day-old chicks morally problematic? Are the proposed alternatives morally sound? To what extent do the alternatives lead to responsible innovation? The conceptual framework demonstrates clearly that there is a (...) moral “lock-in”, and why the killing of day-old chicks is indeed an issue. Furthermore, it is shown that both alternative directions address some important objections with regard to the killing of day-old chicks, but that they also raise new dilemmas. It also becomes clear that the framework enables and secures anticipation, reflection, deliberation with and responsiveness to stakeholders, the four dimensions of responsible innovation, in a structured way. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...) fusion framework. The first is the challenge involved in handling multiple complex terminologies, which is addressed by drawing on a set of Space Domain Ontologies. Another challenge is the complex combinatorics involved when considering all possible feature combinations. This can be mitigated by using integer linear programming optimization that is outlined by the Complex Conceptual Spaces Single Observation mathematical model framework. A third challenge is the complicated physics that is involved in a spacecraft collision that must be addressed to obtain a better understanding of threat assessment. Overcoming these various challenges allows for a quantitative ranking for the potential of a kinetic kill collision across multiple spacecraft pairs. In addition to overcoming these challenges this paper will break down threat assessment into four domains and identify a ranking of threat both for each individual domain and for the four domains combined. Simulation results are shown to verify the developed concepts. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

Previous work has shown that the Complex Conceptual Spaces − Single Observation Mathematical framework is a useful tool for event characterization. This mathematical framework is developed on the basis of Conceptual Spaces and uses integer linear programming to find the needed similarity values. The work of this paper is focused primarily on space event characterization. In particular, the focus is on the ranking of threats for malicious space events such as a kinetic kill. To make the Conceptual Spaces framework work, (...) the similarity values between the contents of observations on the one hand and the properties of the entities observed on the other needs to be found. This paper shows how to exploit Dempster-Shafer theory to implement a statistical approach for finding these similarities values. This approach will allow a user to identify the uncertainty involved in similarity value data, which can later be propagated through the developed mathematical model in order for the user to know the overall uncertainty in the observation-to-concept mappings needed for space event characterization. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Volume 19, Issue 9, September 2019, Page 64-66.

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...) or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

Because corporate social responsibility can be beneficial to both companies and its stakeholders, interest in factors that support CSR performance has grown in recent years. A thorough integration of CSR in core business processes is particularly important for achieving effective long-term CSR practices. Here, we explored the individual CSR-related competencies that support CSR implementation in a corporate context. First, a systematic literature review was performed in which relevant scientific articles were identified and analyzed. Next, 28 CSR directors and managers were (...) interviewed. The literature review complemented with interview data resulted in the following eight distinct CSR-related competencies: Anticipating CSR challenges; Understanding CSR-relevant systems and subsystems; Understanding CSR-relevant standards; CSR management competencies, including Leading CSR programs, Managing CSR programs, and Identifying and realizing CSR-related business opportunities; Realizing CSR-supportive interpersonal processes; Employing CSR-supportive personal characteristics and attitudes; Personal value-driven competencies, including Ethical normative competencies, Balancing personal ethical values and business objectives, and Realizing self-regulated CSR-related behaviors and active involvement; and Reflecting on personal CSR views and experiences. Based on these results, implications for further research on this topic, as well as implications for practitioners, are discussed. (shrink)

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)

In 2035 global egg demand will have risen 50% from 1985. Because we are not able to tell in the egg whether it will become a male or female chick, billons of one day-old male chicks will be killed. International research initiatives are underway in this area, and governments encourage the development of an alternative with the goal of eliminating the culling of day-old male chicks. The Netherlands holds an exceptional position in the European egg trade, but is also the (...) only country in the European Union where the downside of the egg sector, the practice of killing day-old male chicks, is a recurrent subject of societal debate. ‘Preventing the killing of young animals’ and ‘in ovo sex determination’ are the two alternative approaches available to solve this problem. It is clear that both approaches solve the problem of killing day-old male chicks, either by keeping them alive or by preventing them from living, but they also raise a lot of new animal welfare-related dilemmas. A thorough analysis was undertaken of these dilemmas and the results are presented in this article. The analysis resulted in an ethical framework based on the two main approaches in bioethics: a consequentialist approach and a deontological approach. This ethical framework was used to develop an online survey administered to ascertain Dutch public opinion about these alternative approaches. The results show that neither alternative will be fully accepted, or accepted by more than half of Dutch society. However, the survey does provide an insight into the motives that are important for people’s choice: food safety and a good treatment of animals. Irrespective of the approach chosen, these values should be safeguarded and communicated clearly. (shrink)

Graduates' employability indicates the excellent education and relevant preparation they obtained from their respective degrees. Tracer studies have enabled higher education institutions to profile their graduates while also reflecting on the quality of education they provide. With the foregoing, a tracer study determined the demographic and academic profile of teacher education graduates from 2017 to 2020 in a state university in the West Philippines. It also ascertained the advanced studies they attended after college, their employment data, the relevance of college (...) preparation with their current employment, difficulties they encountered while securing employment and in their present job, and recommendations to strengthen the teacher education program. The study utilized a descriptive survey research design with 80 non-random samples chosen based on availability. The survey was based on the Philippine Commission on Higher Education with modifications elucidated from previous studies. Results showed that graduates took the teacher education program with a strong passion for the teaching profession. More graduates received honors and awards, passed the licensure examinations for teachers, attended advanced studies for professional development, and are employable. Besides, the graduates’ college preparation is relevant to their current employment. Further, difficulties and problems encountered and recommendations to strengthen the teacher education program were noted. These findings may serve as a baseline for curriculum review and give suggestions for future tracer studies. (shrink)

Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifiziert werden können. Dafür wiederum bedarf es robuster Theorien von Grundbegriffen wie Art, Spezies, Teil, Ganzes, Funktion, Prozess, Fragment, Sequenz, Expression, Grenze, Locus, Umwelt, System usw. (...) Solche Begriffe gehören zum impliziten Wissen jedes Biologen. Sie spiegeln einerseits eine Dimension der biologischen Wirklichkeit wider, die auch vor dem Hintergrund der biologischen Evolution unverändert bleibt. Andererseits verlangt deren theoretische Behandlung nach zeitgemäßen Analoga der in der traditionellen aristotelischen Metaphysik entwickelten Methoden. Zugleich können so die explizit formulierten Theorien und Definitionen bereitgestellt werden, die für computergestützte Informationssysteme unabdingbar sind. Das Entwickeln derartiger Theorien und Definitionen ist eine Aufgabe der Philosophie, die in diesem Sinne herausgefordert ist, zwischen Biologie und Informatik zu vermitteln. (shrink)

COVID-19 began in China in December 2019. As of January 2021, over a hundred million instances had been reported worldwide, leaving a deep socio-economic impact globally. Current investigation studies determined that artificial intelligence (AI) can play a key role in reducing the effect of the virus spread. The prediction of COVID-19 incidence in different countries and territories is important because it serves as a guide for governments, healthcare providers, and the general public in developing management strategies to battle the disease. (...) The prediction proved beneficial in the early months of 2020 to alert nations and territories in danger of an outbreak, allowing them to take preventative measures. Despite the fact that the COVID-19 outbreak has expanded to practically every location on the planet, the prediction has value in terms of monitoring the intensity of the spread and recovery, as well as determining the likelihood of a sequel or tertiary epidemic. COVID-19, like influenza, could become a seasonal or recurring epidemic in the future. COVID-19 activity must so be predicted and monitored now and in the future. (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)

The embedding and promotion of social change is faced with aparadoxical challenge. In order to mainstream an approach to socialchange such as responsible research and innovation and makeit into a practical reality rather than an abstract ideal, we need tohave conceptual clarity and empirical evidence. But, in order to beable to gather empirical evidence, we have to presuppose that theapproach already exists in practice. This paper proposes a social labmethodology that is suited to deal with this circularity. Themethodology combines the (...) defining features of social labs emergingfrom the literature such as agility and real-world focus withestablished theories and approaches such as action research andexperiential learning. Thereby it enables the parallel investigationand propagation of RRI. The framework thus constructed provides atheoretical embedding of sociallabs and overcomes some of theknown limitations of the constitutive approaches. (shrink)

R&D collaborations between industry, government, civil society, and research ) have recently gained attention from R&D theorists and practitioners. In aiming to come to grips with their complexity, past models have generally taken a stakeholder-analytical approach based on stakeholder types. Yet stakeholder types are difficult to operationalise. We therefore argue that a processual model is more suited for studying the interaction in QHCs because it eschews matters of titles and identities. We develop such a model in which the QHC is (...) represented as a process of generating four types of value: research value, market value, political value, and societal value. We then apply this processual model in analysing real-life cases of friction in QHCs. Friction is seen, not as an interpersonal clash, but as a discrepancy between two or more value-creation processes that compete for limited resources. (shrink)

The comprehensive nature of information and insight available in the Upanishads, the Indian philosophical systems like the Advaita Philosophy, Sabdabrahma Siddhanta, Sphota Vaada and the Shaddarsanas, in relation to the idea of human consciousness, mind and its functions, cognitive science and scheme of human cognition and communication are presented. All this is highlighted with vivid classification of conscious-, cognitive-, functional- states of mind; by differentiating cognition as a combination of cognitive agent, cognizing element, cognized element; formation; form and structure of (...) cognition, instruments and means of cognition, validity of cognition and the nature of energy/matter which facilitates and also is the medium of cognition- cognizing process; and also as the container and content of cognition. The human communication process which is just the reverse of cognizing process is also presented with necessary description and detail. The sameness of cognitive / communicative process during language acquisition and communication processes and the modes of language acquisition and communication are also given. The hardware and software of human cognition, language acquisition and communication as envisaged in Indian spiritual and philosophical expressions are given. In the light of the information and insight obtained as above, the axioms for human cognition / communication are formed, framed and presented. A brain-wave frequency modulation / demodulation model of human cognition, communication and language acquisition and communication process based on Upanishadic expressions, Shaddarsanas and Sabdabrahma Siddhhanta is defined and discussed here. The use of these theories and models and axioms in mind-machine modelling and natural language comprehension branch of artificial intelligence will be put forward and highlighted. (shrink)

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

The nature of time is perceived by intellectuals variedly. An attempt is made in this paper to reconcile such varied views in the light of the Upanishads and related Indian spiritual and philosophical texts. The complex analysis of modern mathematics is used to represent the nature and presentation physical and psychological times so differentiated. Also the relation between time and energy is probed using uncertainty relations, forms of energy and phases of matter.

Moral judgments about an action are influenced by the action’s intentionality. The reverse is also true: judgments of intentionality can be influenced by an action’s moral valence. For example, respondents judge a harmful side-effect of an intended outcome to be more intentional than a helpful side-effect. Debate continues regarding the mechanisms underlying this “side-effect effect” and the conditions under which it will persist. The research behind this chapter tested whether the side-effect effect is intact in adolescents with psychopathic traits, who (...) are characterized by persistent immoral behavior, deficient moral emotions, and impairments in some forms of moral judgment. Results showed no differences between healthy adolescents and those with psychopathic traits: both groups judged harmful side-effects to be more intentional than helpful side-effects by an approximately 2:1 ratio. The chapter discusses these results in light of hypothesized mechanisms underlying the side-effect effect, and in light of our current understanding of moral reasoning deficits in psychopathy. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

Letters commenting on Hardwig, J "Is There a Duty to Die?" with a reply to those letters by the author.

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

In real-time, Twitter strongly imprints world events, popular culture, and the day-to-day; Twitter records an ever growing compendium of language use and change; and Twitter has been shown to enable certain kinds of prediction. Vitally, and absent from many standard corpora such as books and news archives, Twitter also encodes popularity and spreading through retweets. Here, we describe Storywrangler, an ongoing, day-scale curation of over 100 billion tweets containing around 1 trillion 1-grams from 2008 to 2020. For each day, we (...) break tweets into 1-, 2-, and 3-grams across 150+ languages, record usage frequencies, and generate Zipf distributions. We make the data set available through an interactive time series viewer, and as downloadable time series and daily distributions. We showcase a few examples of the many possible avenues of study we aim to enable including how social amplification can be visualized through ‘contagiograms’. (shrink)

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

That uses of language not only can, but even normally do, have the character of actions was a fact largely unrealised by those engaged in the study of language before the present century, at least in the sense that there was lacking any attempt to come to terms systematically with the action-theoretic peculiarities of language use. Where the action-character of linguistic phenomena was acknowledged, it was normally regarded as a peripheral matter, relating to derivative or nonstandard aspects of language which (...) could afford to be ignored. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

Purpose Prescription stimulant use as “cognitive enhancers” has been described among undergraduate college students. However, the use of prescription stimulants among future health care professionals is not well characterized. This study was designed to determine the prevalence of prescription stimulant misuse among students at an academic health sciences center. -/- Method Electronic surveys were e-mailed to 621 medical, pharmacy, and respiratory therapy students at East Tennessee State University for four consecutive weeks in fall 2011. Completing the survey was voluntary and (...) anonymous. Surveys asked about reasons for, frequency of, and side effects of nonprescription misuse of prescription stimulants. Given the sensitive material, an opportunity to win one of ten $50 gift cards was used as an incentive. -/- Results Three hundred seventy-two (59.9%) students completed the survey from three disciplines (47.6% medical, 70.5% pharmacy, and 57.6% respiratory therapy). Overall, 11.3% of responders admitted to misusing prescription stimulants. There was more misuse by respiratory therapy students, although this was not statistically significant (10.9% medicine, 9.7% pharmacy, 26.3% respiratory therapy; P = .087). Reasons for prescription stimulant misuse included to enhance alertness/ energy (65.9%), to improve academic performance (56.7%), to experiment (18.2%), and to use recreationally/get high (4.5%). -/- Conclusions Prescription stimulant misuse was prevalent among participating students, but further research is needed to describe prevalence among future health care workers more generally. The implications and consequences of such misuse require further study across professions with emphasis on investigating issues of academic dishonesty (e.g., “cognitive enhancement”), educational quality, and patient safety or health care quality. (shrink)

This introduction to the Journal of Business Research special issue on anti-consumption briefly defines and highlights the importance of anticonsumption research, provides an overview of the latest studies in the area, and suggests an agenda for future research on anti-consumption.