The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

From its inception, the focus of ontological engineering has been to support the reusability and shareability of ontologies, as well as interoperability of ontology-based software systems. Among th...

The book moves from descriptive through to more interpretative phenomenological methods to enable the reader to learn to use the main approaches to ...

This article provides information about Berne's financial situation at the time the Economic Society was founded. The canton was in an exceptionally fortunate position, having accumulated a sizeable cash reserve that was in part used for loans and investments on the London capital market. Throughout the century, the Bernese government followed a very cautious investment strategy. The main reason for purchasing overseas securities was that they helped the patricians to become independent from tax-paying subjects. Economic imperatives ruled out increases of (...) the cash reserve or further involvement in the overcrowded domestic capital market. However, by investing abroad Berne became increasingly dependent on the goodwill of its debtors, for which it was criticised by the Economic Patriots amongst others. (shrink)

In this title the author explores the time-tested practice and philosophy using modern examples from more than a decade of experience with this ancient practice. He brings the principles of yoga into focus and makes them user-friendly for yogis living in the post modern era.

Analytic skill can contribute to a theology of the Bible and a theological hermeneutic in two ways, by refining the formulation of a doctrine of Scripture and a correlative hermeneutic, and by illuminating how problematic hermeneutical presuppositions have in some cases become part of exegetical practice. The contribution that the analytic style of reflection can make to the theological enterprise need not be vitiated by a common criticism of analytic modes of engaging with texts, namely, that they tend toward being (...) ahistorical, though the objection deserves to be considered carefully. (shrink)

The doctrine of the communication of natures has played a primarily descriptive role in the history of Christology, and so it is perhaps unsurprising that it has largely gone missing from contemporary theology. This is a serious oversight. But Karl Barth is a noteworthy exception to the reductionist trend, and he provides the Reformed tradition's most complete and substantive engagement with the communication of natures and its implications for dogmatic theology. Through a close reading of volume IV/2 of the Church (...) Dogmatics , this essay considers Karl Barth's vital emphasis upon the communicatio naturarum and the role it plays in his actualist Christology. Barth demonstrates that the traditional threefold communication (of attributes, graces, and operations) has material as well as formal importance. According to Barth, we see in Christ not the mere coincidence of two natures, nor an interpenetration, nor the transformation of one into the other – but mutual operation and interpretation, where divinity and humanity each acquires and has its determination in the other. (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)

An objection to shifty epistemologies such as subject-sensitive invariantism is that it predicts that agents are susceptible to guaranteed losses. Bob Beddor (Analysis, 81, 193–198, 2021) argues that these guaranteed losses are not a symptom of irrationality, on the grounds that forgetful agents are susceptible to guaranteed losses without being irrational. I agree that forgetful agents are susceptible to guaranteed losses without being irrational– but when we investigate why, the analogy with shifty epistemology breaks down. I argue that agents with (...) shifty epistemologies are susceptible to guaranteed losses in a way which is a symptom of irrationality. Along the way I make a suggestion about what it takes for an agent to be coherent over time. I close by offering a taxonomy of shifty epistemologies. (shrink)

This study aims to highlight how an existential-humanistic perspective can inform athlete support and in doing so, emphasize the importance of explicating the philosophical underpinnings of athlete lifestyle support. Drawing on applied experience with elite youth cricketers over a 12-month period, ethnographic data were collected through the observation, maintenance of case notes, and a practitioner reflective diary. Based on thematic analysis, we created three nonfictional vignettes that we use to illustrate how existential-humanistic theorizing can inform lifestyle support. We discuss the (...) implications of this professional philosophy in terms of considerations for performance and talent development programs, and how holistic support for athletes is positioned. We also discuss implications for athlete lifestyle and performance psychology practitioners, with regard to training, underpinning theoretical grounding of support and the strategic positioning of their practitioner roles. (shrink)

J. Baird Callicott defends a communitarian environmental ethic that grounds moral standing in shared kinship and community. This normative theory is unacceptable because it is out of synch with our considered moral judgments as environmental philosophers. Ecological communitarianism excludes in advance entities that would obviously qualify for moral standing, and scuttles itself in the process.

An eighty‐six–year‐old woman has had lifelong obsessive‐compulsive disorder. At times, it has been so severe that she has lost touch with reality and been psychotic. She is actively followed by a community mental health nurse. Since she is physically frail, the nurse visits her at home and liaises with the attending psychiatrist, who adjusts medications as needed. Currently, the patient is stable, and there is no evidence of psychosis.The patient's home deteriorates, and several repairs are needed. The nurse questions the (...) patient about this, and the patient agrees to have her nephew arrange for the repairs and pay for them out of her bank account. The nurse asks how the nephew has access to the account. The patient mentions that he has power of attorney, but when asked to supply the document giving him this authority, she becomes confused and supplies a number of bank statements instead. The nurse is surprised to see several withdrawals for over ten thousand dollars each. When she questions the patient about these, the patient simply suggests that her nephew must have “needed the money” for something. The nurse questions her repeatedly about this matter, but she refuses to give further details. The patient becomes quite upset whenever the nurse brings it up and states, “This is my money, and he wouldn't take it unless he needed it to help me.”Should the nurse challenge the patient's right to make her own financial decisions in order to avoid a risk of exploitation by her family members? Does the patient have the right to refuse a capacity assessment, which could determine her decision‐making abilities in this area? (shrink)

This commentary examines several key points in David Horan’s paper “The Argu­mentative Unity of Plato’s Parmenides.” First, I discuss the general view of the paper, which engages with the first two hypotheses and in particular, the thought experiment passage in hypothesis 2 that is seen as a key to resolving the dilemma of participation. I consider the proposed view that hypothesis 1 takes up from its premise a strictly unitary, or non-multiple “one,” and hypothesis 2 takes up from its premise (...) a one that admits of multiplicity, not a non-multiple “one.” I argue for an alternative reading whereby the premise of hypothesis 1 is not “if one is one” and hypothesis 2 is “if one is not one,” but rather that both hypotheses fall under the premise “if one is.”. (shrink)

The orientation of public space is either logocentric or eclectic. The surface of a Philippine jeepney is an example of a successful inversion of American militaristic individualism into a place for the celebration of idiosyncrasies. Using Walter Benjamin’s differentiation between allegory and symbolism – and photographs of Philippine jeepney art – this essay problematizes the collapse of contemporary spirituality into a political demographic.

In the following article, I situate Daniel Bensaïd’s ‘Strategy and Politics’ within the different phases of his thinking about strategy as well as his own general theoretical background that informs parts of the text.

Introduction -- Direct algorithms of decompositions of matrices by non-orthogonal transformations -- Direct algorithms of decompositions of matrices by orthogonal transformations -- Direct algorithms of solution of linear equations -- Iterative algorithms of solution of linear equations -- Direct algorithms of solution of eigenvalue problem -- Iterative algorithms of solution of eigenvalue problem -- Algorithms of solution of singular value decomposition.

Narrative construction is a discursive practice: storytellers draw on the language, signs and symbols of their culture to provide meaning through stories. Stories that reflect the values, ideals an...

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

By questions of “canon,” we mean questions of what is fictionally true of some character, story, or world. What is canon is treated as authoritative or official, usually by creators and fans alike. But disputes about canon have arisen as storytellers and publishers have sought to capitalize on the popularity of their characters, churning out more and more stories to meet public demand, and at the same time engaging with growing fan bases. As audiences have become more involved, and as (...) fictional worlds have become messier, the authoritative nature of canon—and who authorizes it—has begun to erode. In this paper, we characterize canon as an article in the evolving relation between authors and audiences. More specifically, we characterize canon as an intangible good, subject to a form of cultural negotiation, resting on a power relation between producers and consumers of fictions. In Part I, we consider the author’s evolving role, and the rights of the creator to a story, character, or world. In Part II, we discuss the emerging activities of fans, particularly as they weigh on issues of canon. In Part III, we discuss canon as being subject to cultural negotiation, highlighting the importance of power dynamics in this negotiation. (shrink)

The parallel drawn by Norman between the dorsal and ventral systems and direct and indirect approaches is based on two misrepresentations of the direct approach – that it is concerned only with the unconscious control of action, and that it cannot explain learning. We propose a way of understanding the visual system differences from within the direct approach.

If humans subject animals to painful, damaging, or frightening procedures to achieve scientific progress, then the very least that humankind can do is to insist that regulations be put in place to protect animals and that they be properly implemented and enforced. However, recent practice in the United Kingdom suggests that this is not the case. Europe’s new regime on the protection of animals used for scientific purposes—Directive 2010/63—must act as a catalyst for significant change and is a significant recognition (...) of the intrinsic value of animals. Before this Directive, the cost/benefit analysis undertaken in the United Kingdom allowed for a large margin of error so that animal welfare was an aggregated concept, and any aggregated finding of “adequate” animal welfare was not militated by individual cases of exacerbated animal detriment. The recognition that each animal has value as an individual means that the levels of animal welfare or protection expected of scientific establishments can no longer simply be those that are, in generic terms, appropriate for the aggregated mass of animals. Instead, the welfare standards applied are appropriate and rendered effectual for all individual animals. (shrink)

Nurses practising in mental health are faced with challenging decisions concerning confidentiality if a patient is deemed a potential risk to self or others, because releasing pertinent information pertaining to the patient may be necessary to circumvent harm. However, decisions to withhold or disclose confidential information that are inappropriately made may lead to adverse outcomes for stakeholders, including nurses and their patients. Nonetheless, there is a dearth of contemporary research literature to advise nurses in these circumstances. Cognitive Continuum Theory presents (...) a single‐system intuitive‐analytical approach to examining and understanding nurse cognition, analogous to the recommended single‐system approach to decision‐making in mental health known as structured clinical judgement. Both approaches incorporate cognitive poles of wholly intuition and analysis and a dynamic continuum characterised by a ‘common sense’ blending of intuitive and analytical cognition, whereby cues presented to a decision‐maker for judgement tasks are weighed and assessed for relevance. Furthermore, Cognitive Continuum Theory promotes the importance of determining pattern recognition and functional relations strategies, which can be used to understand the operationalisation of nurse cognition. (shrink)

The best way to divide control over children’s education between private and state authorities is unclear. This task has ethical implications that this thesis explores—in the context of a pluralist liberal democracy. In cases where authority over children’s education is granted to private groups, like ethnic or religious minorities, rights are often part of the default vocabulary adopted by politically liberal commentaries. These rights are often viewed as a shield that offers the group immunity from state interference. Some illiberal minority (...) groups argue that they need to be shielded from state interference because the persistence of their cultural or religious identity depends on it. For example, the Amish community in Wisconsin argued in Wisconsin v. Yoder that the future of their community would be jeopardized if they were forced to send their children to school beyond the age of fourteen. While a rights-based approach does explain many of the variables connected with cases like these, the explanation is incomplete. I will offer two clarifications to the rights-based view. First, in the event that a minority group is shielded from state interference, it is not clear that it would be morally legitimate for the group to take over the authority of the state. I will, then, offer a plausible theory that could justify the self-governing authority of minority groups in these situations. My second clarification is that the concept of individual autonomy, often the central liberal value protected by rights, is too broad to support a zero-tolerance approach toward illiberal groups. This indicates that illiberal minority groups might still have a claim to self-governing authority even though they arguably interfere with the autonomy of their children. Some interference with minor elements of individual autonomy should arguably be tolerated in cases where the ruination or assimilation of the group’s unique culture or religion is at stake. (shrink)

I argue that Diogenes and early Cynicism can be understood in an explicitly social and political context, where Cynic praxis, performative public action, can be seen to make visible oppositions inherent to the polity. In doing so, Diogenes’ praxis should be understood as a form of immanent critique, one that demonstrates, for example, that nature and custom are interrelated oppositions in the polis. Cynicism here is understood as a form of immanent critique because Diogenes challenges the social norms of the (...) polis without endorsing external universal standards or predetermined models, but from illuminating dynamics from within the polis and polity. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Hoping is an integral part of what it is to be human, and its significance for education has been widely noted. Hope is, however, a contested category of human experience and getting to grips with its characteristics and dynamics is a difficult task. The paper argues that hope is not a singular undifferentiated experience and is best understood as a socially mediated human capacity with varying affective, cognitive and behavioural dimensions. Drawing on the philosophy, theology and psychology of hope, five (...) modes of hoping are outlined: patient, critical, sound, resolute and transformative. The key aim of the paper is to illustrate how different modes of hoping are associated with different pedagogical strategies. Phrased differently, the paper seeks to delineate a range of pedagogies of hope. The phrase ‘pedagogy of hope’ is very much associated with critical theory—one thinks instantly of, for example, Paulo Freire, Henry Giroux or bell hooks. There are many pedagogies of hope, however, and an explicitly conservative text such as William Bennett’s Book of Virtues has as strong a claim to the title as Freire’s radical and utopian ideas. A broader argument, therefore, is that there is nothing inherently radical or subversive about a pedagogy of hope. Pedagogies of hope can serve to reproduce social relations as well as to transform them. (shrink)

In this paper, I argue that the notion of ‘reasonableness’ that is, for many, at the heart of the Philosophy for Children approach particularly and education for democratic citizenship more broadly, is constituted within the epistemology of ‘white ignorance’ and operates in such a way that it is unlikely to transgress the boundaries of white ignorance so as to view it from without. Drawing on scholarship in critical legal studies and social epistemology, I highlight how notions of reasonableness often include (...) consensus, ‘racialised common sense’ and the ‘typical’ view. In addition the promotion of particular dispositions on the grounds of ‘reasonableness’ both promotes stability and limits how one may think otherwise. Thus, P4C practices that fail to historicise, examine and challenge prevailing notions of reasonableness establish an epistemically ‘gated’ community of inquiry. (shrink)

The increasing use of pharmacotherapy raises specific ethical concerns for psychologists working with vulnerable populations. Due to a shortage of trained specialists, professionals without training in mental health, such as primary care providers, are increasingly prescribing and monitoring psychotropic medications. Vulnerable populations face additional barriers to mental health treatment and are at heightened risk when these factors intersect. Hence, these patients experience unique barriers to receiving optimal psychopharmacological care and are differentially vulnerable to deleterious outcomes associated with misdiagnosis and overmedication. (...) Taken together, these factors fuel inequities in the access, quality, and utilization of mental health care. Psychologists working with these patients are ethically mandated to protect patients from harm and ensure equitable care across patient populations. Specifically, psychologists must respond to the dilemma of how to effectively treat patients within these vulnerable populations who have been misdiagnosed or poorly medicated while remaining within the bounds of their competence. This article recommends pathways to address these dilemmas through education, training, research, and advocacy. (shrink)

Although Burt clearly explains how modern genomic techniques work, and describes their limitations, her conclusion that they are therefore not valuable additions to understanding social outcomes is unwarranted. Understanding the causes of complex social outcomes depends on understanding how social, individual, and genetic factors complexly interact with each other. None can be understood without reference to the others.

Background: Humor, both producing and appreciating, underpins positive social interactions acting as a facilitator of communication. There are clear links to wellbeing that go along with this form of social engagement. However, humor appears to be a seldom studied, cross-disciplinary area of investigation when applied to people with an intellectual disability, this review collates the current state of knowledge regarding the role of humor behavior in the social interactions of people with intellectual disabilities and their carers. Method: A systematic review (...) utilizing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was completed which aimed to explore the current state of knowledge and quality of empirical evidence relating to humor in people with intellectual disabilities. Following this, articles were grouped thematically and summarized. A comprehensive search of four electronic databases (1954–2017) and additional search strategies yielded 32 articles which met the final inclusion criteria. Results: Humor played a significant positive and negative role in the social interactions of people with intellectual disabilities. Research had investigated humor in the classroom and humor expression in different groups including those with autism, Down syndrome, Angelman syndrome, Williams syndrome and Rett syndrome. Few investigations directly studied humor appreciation and comprehension hence themes did not focus solely on humor production/appreciation. Humor comprehension was reportedly supported by gestures. Some groups with intellectual disabilities found non-literal humor (e.g. sarcasm, irony) more difficult to understand which may affect social relationships. Various types of humor were found to be appreciated. The role of humor in relationship development, social facilitation, creativity and stigma had all received some limited attention. Humor also played a role for carer groups in coping with and enjoying the caring role. Research varied in quality with few experimental studies and mainly quasi-experimental and well-conducted qualitative studies. Conclusions: This review revealed the importance of humor behavior in many aspects of the social lives of people with intellectual disabilities. Limited disparate research exists pertaining to humor in this group, suggesting the need for further robust research in this area, including more high quality primary research in the areas of humor production, appreciation, comprehension and stigma. (shrink)