Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Scalability, efficiency, and security had been a persistent problem over the years in data mining, several techniques had been proposed and implemented but none had been able to solve the problem of scalability, efficiency and security from cloud computing. In this research, we solve the problem scalability, efficiency and security in data mining over cloud computing by using a restful web services and combination of different technologies and tools, our model was trained by using different machine learning algorithm, and finally (...) using different validation and cross-validation methods to compare and validate our results. We build, train, test and deploy our model by restful API services which can be called through an endpoint, and with very high accuracy and huge success. (shrink)

Revonsuo’s influential Threat Simulation Theory predicts that people exposed to survival threats will have more threat dreams, and evince enhanced responses to dream threats, compared to those living in relatively safe conditions. Participants in a high crime area differed significantly from participants in a low crime area in having greater recent exposure to a life-threatening event . Contrary to TST’s predictions, the SA participants reported significantly fewer threat dreams , and did not differ from the Welsh participants in responses to (...) dream threats . Overall, the incidence of threat in dreams was extremely low—less than 20% of dreams featured realistic survival threats. Escape from dream threats occurred in less than 2% of dreams. We conclude that this evidence contradicts key aspects of TST. (shrink)

Malcolm-Smith, Solms, Turnbull and Tredoux [Malcolm-Smith, S., Solms, M., Turnbull, O., & Tredoux, C. . Threat in dreams: An adaptation? Consciousness and Cognition, 17, 1281–1291.] conducted a rigorous study that sampled two populations differentially exposed to threat in real life, and found that critical predictions from the Threat Simulation Theory of dreams [Revonsuo, A. . The reinterpretation of dreams: An evolutionary hypothesis of the function of dreaming. Behavioral and Brain Sciences, 23, 877-901.; Revonsuo, A. . Did ancestral humans (...) dream for their lives? Behavioral and Brain Sciences, 23, 1063–1082.] were not supported. Specifically, we found no evidence of increased realistic threats to physical survival or enhanced threat avoidance in the dreams of those from the exposed population. Revonsuo and Valli’s [Revonsuo, A., & Valli, K. . How to test the threat simulation theory. Consciousness and Cognition, 17, 1292-1296.] commentary on our study argues that the methods we used are so flawed as to render the results meaningless. In this response article, we address the criticisms raised in their commentary. (shrink)

While he is widely acknowledged as the most important Russian thinker of the nineteenth century, Vladimir Soloviev's place in the landscape of world philosophy nevertheless remains uncertain. Approaching him through a single synoptic lens, this book foregrounds his unique envisioning of the interaction between humanity and the material world. By investigating the development of a single theme in his work--his idea of the "spiritualization of matter", the "task" of humanity--Smith constructs a rounded picture of Soloviev's overall importance to an (...) understanding. If nineteenth-century thought, as well as to modern theology and philosophy. The picture that emerges is of a writer whose contribution to a Christian philosophy of matter resonates with many of the religious debates of modernity. (shrink)

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)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple (...) clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

1 Evidence-based policy requires researchers to provide the answers to ecological questions that are of interest to policy makers. To find out what those questions are in the UK, representatives from 28 organizations involved in policy, together with scientists from 10 academic institutions, were asked to generate a list of questions from their organizations. 2 During a 2-day workshop the initial list of 1003 questions generated from consulting at least 654 policy makers and academics was used as a basis for (...) generating a short list of 100 questions of significant policy relevance. Short-listing was decided on the basis of the preferences of the representatives from the policy-led organizations. 3 The areas covered included most major issues of environmental concern in the UK, including agriculture, marine fisheries, climate change, ecosystem function and land management. 4 The most striking outcome was the preference for general questions rather than narrow ones. The reason is that policy is driven by broad issues rather than specific ones. In contrast, scientists are frequently best equipped to answer specific questions. This means that it may be necessary to extract the underpinning specific question before researchers can proceed. 5 Synthesis and applications. Greater communication between policy makers and scientists is required in order to ensure that applied ecologists are dealing with issues in a way that can feed into policy. It is particularly important that applied ecologists emphasize the generic value of their work wherever possible. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:247 TWO PUZZLES IN MOSSNER'S LIFE OF DAVID HUME It is a tribute to the rare quality of Mossner's great Life of David Hume that in those few instances where he seems to have got something wrong, one feels an irresistible urge to put the record straight. The two puzzles that have perplexed me are: (1) Why was Adam Smith adamant in his refusal to take the responsibility (...) for publishing the Dialogues after Hume's death? ; and (2) why, despite his long-standing resolution not to answer his opponents directly, did Hume in October 1775 take the step of drawing up the short Advertisement, disavowing his Treatise of Human Nature, which was to be prefixed to the second volume of all future editions of Essays and Treatises? The clue to the first puzzle is to be found in Boswell 's Life of Johnson: On the 6th of March [1754] came out Lord Bolingbroke's works, published by Mr David Mallet. The wild and pernicious ravings, under the name of "Philosophy," which were thus ushered into the world, gave great offence to all well-principled men. Johnson, hearing of their tendency, which nobody disputed, was roused with a just indignation, and pronounced this memorable sentence upon the noble author and his editor. "Sir, he was a scoundrel and a coward; a scoundrel, for charging a blunderbuss against religion and morality; a coward, because he had not resolution to fire it off himself, but left half a crown to a beggarly Scotchman, to draw the trigger after his death!" The editors of the 1934 Oxford Edition note: "Adam Smith, perhaps had this saying in mind when, in 1776, he refused the request of the dying Hume to edit 248 after his death his Dialogues on Natural Religion. Hume wrote back:? think... your scruples groundless. Was Mallet any wise hurt by his publication of Lord Bolingbroke? He received an office afterwards from the present King and Lord Bute, the most prudish men in the world... '."4 I don't think that this letter of Hume's was an answer to a letter from Smith (who was a notoriously bad correspondent, see below). I think that, on his way back from London to his mother at Kirkcaldy, Smith had made up his mind to tell his beloved friend, to his face, that he was determined not to undertake this task. One must put oneself in Smith's position in 1776. He had (it is true) an annuity of £300 from the Bucci euch estates, and he had just spent ten years writing The Wealth of Nations. But he did not think this annuity sufficient for him to be justified in devoting the rest of his life to literary pursuits, despite the wealth of material which was already more or less complete, and has been posthumously published. He knew his masterpiece was not going to make him much money (single books did not do so in those days), but he hoped that it might put him in the way of a job or a royal pension -- as Beattie's Truth had secured a pension for him, three years earlier. Moreover, Smith had just spent three years in London, where Boswell had engineered that he be elected to the celebrated dining Club presided over by Johnson and Burke (where Smith was none too popular), and he knew well that if he were to bring out the Dialogues after Hume's death, the members of the Club would say (and feel) the same sort of things about Hume and him, as Johnson had said (and felt) about 249 Bolingbroke and Mallet. London society was a small world, and this sort of gossip would not advance his (Smith's) chance of getting a job, nor would it enhance Hume's reputation. He decided to dig in his toes, and was perfectly justified in doing so. So, of course, the modern editors of Boswell 's Johnson are right in their conjecture. But Mossner says that Smith was suffering under a bad conscience about this refusal, when he came to write his marvellous letter (which caused him so much trouble), and which was appended to the posthumous publication... (shrink)

Although Peano arithmetic is necessarily incomplete, Isaacson argued that it is in a sense conceptually complete: proving a statement of the language of PA that is independent of PA will require conceptual resources beyond those needed to understand PA. This paper gives a test of Isaacon’s thesis. Understanding PA requires understanding the functions of addition and multiplication. It is argued that grasping these primitive recursive functions involves grasping the double ancestral, a generalized version of the ancestral operator. Thus, we can (...) test Isaacon’s thesis by seeing whether when we phrase arithmetic in a context with the double ancestral operator, the result is conservative over PA. This is a stronger version of the test given by Smith, who argued that understanding the predicate “natural number” requires understanding the ancestral operator, but did not investigate what is required to understand the arithmetic functions. (shrink)

Book reviewed:Prakash Sethi and Oliver Williams, Economic Imperatives and Ethical Values in Global Business.

Part of the baths regulations preserved on a bronze plaque, engraved more or less identically on each side, from the copper mine at Vipasca, Lusitania. The manager is to wash, clean and grease the waterheating vats once a month. Such vats, as mentioned by Vitruvius in his discussion of public baths , were three in number: aena supra hypocausim tria sunt componenda. They were sizeable articles: Propertius seems to see himself tortured in one: Veneris torrebar aeno. The greasing was to (...) keep aerugo, copper rust, at bay; for this purpose Cato in general recommends amurca, lees of olive oil: ahena omnia amurca unguito…et aerugo non erit molesta; and also for greasing axles amurca axem unguito. For bronze tablets exposed to the weather such as the numerous public records on temple walls and the like Pliny recommends olive oil: aera…robiginem celerius trahunt…nisi oleo perunguantur. The phrase e recenti which occurs in both versions of the text is unexampled, and the CIL editors suggest that it means ex integro, afresh. However I am inclined to think that the engraver had a faulty copy in front of him and we should read adipe recenti. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Poems Ancient and Contemporary HELAINE L. SMITH On the cover of Like: Poems by A. E. Stallings is a double photograph of a double image: two ancient carved heads, in profile and facing each other, of the pole horses of a quadriga, a four-horse chariot, dated about 570 BC, and currently in the collection of The Acropolis Museum. The marble horse in profile on the right side of (...) the cover, looking to the left, has a longer neck and face, and is undamaged except for a hairline crack at the neck. Its counterpart has a broader cheek, with light chipping above the nostril and an ear broken off. But they so mirror each other, they are so “like,” that at first glance one might suppose the photographs to be the right and left sides of the same horse. The bottom half of the cover of Like is an exact replica of the top, but the tinting is different, the heads in the top band cream-colored, in the arion 27.1 spring/summer 2019 Like: Poems by A. E. Stallings was published in 2018 by Farrar, Straus and Giroux, New York. Stallings’s earlier books of poetry include Archaic Smile (1999), Hapax (2006), Olives (2012), and a verse translation of Lucretius’ The Nature of Things (2007). bottom a delicate ochre or sand. There is, then, on the very cover of Like a promise of complex correspondence and subtle variation within the volume itself. Stallings’s title suggests poetry as the art of locating and articulating likeness or as the act of finding one thing in another. And in Stallings’s delicate, robust, witty, and humane use of the past, “like” also and most significantly means that they—the figures of ancient myth—and we are alike in our shared experience and shared humanity. Stallings sometimes presents classical and mythological references glancingly, and that is part of the delight—catching the joke in Hermes’ epithet, “lord of florists,”1 finding in “The Rosehead Nail” that the local blacksmith in Monteagle, Tennessee, “was a god / Before... the tasks / That had been craft were jobbed out to machine.” Likeness is, of course, the mode of Homeric simile, and in “Selvage” Stallings turns the simile of Odyssey 22.468–73, in which Homer compares the hanged maids to thrushes caught in a net, into a different but contextually relevant parallel: “they hang... From the warp like a dozen ancient loom weights,” a likeness that evolves from Stallings’s double entendre in line seven describing the maids as “spinsters of their own doom,” an allusion both to the task, properly theirs, of weaving and to their disclosure to their lovers of Penelope’s secret unravelling. Stallings can expand as well as adapt Homeric similes. At Iliad 2.87–2.90 Homer likens the Achaians’ assembly at Agamemnon’s command to arm and attack Troy to bees leaving the hive: Like the swarm of clustering bees that issue forever in fresh bursts from the hollow in the stone, and hang like bunched grapes as they hover beneath the flowers in springtime fluttering in swarms together this way and that way so the many nations of men from the ships and the shelters along the front of the deep sea beach marched in order by companies to the assembly2 178 poems ancient and contemporary Homer finds likeness in the orderly setting forth—of bees, of men—to do what is required. This, on the other hand, is what Stallings does: Colony Collapse Disorder (Iliad, 2.87–2.90) Just as a swarm pours from a hollow rock In one long beeline for the wild thyme, Alighting in clusters on this purple and that, But is stricken with a mass amnesia That disorients the compass of the sun, And they forget the steps to traditional dances, And each helicopters into a different dimness Taking their saddlebags of sweetness with them, And the hive goes dark, the queen is left to starve, And the drones humbug the whimper of the world, And the palace falls to ruins, broken into By vandals who would loot the golden stores Left in the brittle wax hexameters, Just so... And “so” her... (shrink)

To find more information about Rowman and Littlefield titles, please visit www.rowmanlittlefield.com.

This paper sets James K. A. Smith’s Awaiting the King against the background of the previous volumes in Smith’s Cultural Liturgies trilogy, and outlines this book’s argument for readers not familiar with it, bringing out the influence of St Augustine and Oliver O’Donovan. It draws attention to Smith’s responses within the book to earlier critics and, in turn, points towards two lines of critique of it.

In this paper I argue against Michael Morris’ claim, that the Tractatus view involves holding that the possibility of truth-functional combination is prior to the possibility for sentential constituents to combine with one another. I provide an alternative interpretation in which I deny the presence of any distinction in the Tractatus between these two possibilities. I then turn to Adrian Moore’s ‘disjunctivist’ account of sentencehood, itself inspired by the Tractatus view. I argue that Moore’s account need not involve a commitment (...) to the kind of priority Morris describes, and that it need not involve a commitment to transcendental idealism. (shrink)

A systematic treatment of Hume's conception of imagination in all the main topics of his philosophy.

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...) have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)

Substantivalists believe that spacetime and its parts are fundamental constituents of reality. Relationalists deny this, claiming that spacetime enjoys only a derivative existence. I begin by describing how the Galilean symmetries of Newtonian physics tell against both Newton's brand of substantivalism and the most obvious relationalist alternative. I then review the obvious substantivalist response to the problem, which is to ditch substantival space for substantival spacetime. The resulting position has many affinities with what are arguably the most natural interpretations of (...) special and general relativity. I move on to consider and reject two recent antisubstantivalist lines of thought. The interim conclusion is that the best argument for relationalism is an appeal to Ockham's razor. However, for this to be successful there must be genuine relationalist theories that share the theoretical virtues of their substantivalist rivals but without the additional ontological commitment. The bulk of the paper is therefore an investigation of various concrete relationalist proposals. I distinguish three options for the relationalist in the face of the success of Galilean invariant physics and trace how these generalise to relativistic physics. One of the options is particularly promising but, since its basic objects end up being spacetime points, this does not help the prospects of relationalism as traditionally conceived. I end with some reflections on the fate of substantivalism in the aftermath of the Hole Argument, concluding that we have as yet to be given good reasons to abandon the natural, substantivalist interpretation of current physics. (shrink)

Explainable artificial intelligence (XAI) seeks to produce explanations for those machine learning methods which are deemed opaque. However, there is considerable disagreement about what this means and how to achieve it. Authors disagree on what should be explained (topic), to whom something should be explained (stakeholder), how something should be explained (instrument), and why something should be explained (goal). In this paper, I employ insights from means-end epistemology to structure the field. According to means-end epistemology, different means ought to be (...) rationally adopted to achieve different epistemic ends. Applied to XAI, different topics, stakeholders, and goals thus require different instruments. I call this the means-end account of XAI. The means-end account has a descriptive and a normative component: on the one hand, I show how the specific means-end relations give rise to a taxonomy of existing contributions to the field of XAI; on the other hand, I argue that the suitability of XAI methods can be assessed by analyzing whether they are prescribed by a given topic, stakeholder, and goal. (shrink)

What is morality? How many moral values are there? And what are they? According to the theory of morality-as-cooperation, morality is a collection of biological and cultural solutions to the problems of cooperation recurrent in human social life. This theory predicts that there will be as many different types of morality as there are different types of cooperation. Previous research, drawing on evolutionary game theory, has identified at least seven different types of cooperation, and used them to explain seven different (...) types of morality: family values, group loyalty, reciprocity, heroism, deference, fairness and property rights. Here we explore the conjecture that these simple moral ‘elements’ combine to form a much larger number of more complex moral ‘molecules’, and that as such morality is a combinatorial system. For each combination of two elements, we hypothesise a candidate moral molecule, and successfully locate an example of it in the professional and popular literature. These molecules include: fraternity, blood revenge, family pride, filial piety, gavelkind, primogeniture, friendship, patriotism, tribute, diplomacy, common ownership, honour, confession, turn taking, restitution, modesty, mercy, munificence, arbitration, mendicancy, and queuing. These findings indicate that morality – like many other physical, biological, psychological and cultural systems – is indeed a combinatorial system. Thus morality-as-cooperation provides a principled and powerful theory, that explains why there are many moral values, and successfully predicts what they will be; and it generates a systematic framework that has the potential to explain all moral ideas, possible and actual. Pursuing the many implications of this theory will help to place the study of morality on a more secure scientific footing. (shrink)

Immanuel Kant is often considered to be the source of the contemporary idea of human dignity, but his conception of human dignity and its relation to human value and to the requirement to respect others have not been widely understood. Kant on Human Dignity offers the first in-depth study in English of this subject. Based on a comprehensive analysis of all the passages in which Kant uses the term ;dignity, as well as an analysis of the most prominent arguments for (...) a value of human beings in the Kant literature, the book carefully examines different ways of construing the relationship between dignity, value and respect for others. It takes seriously Kant s Copernican Revolution in moral philosophy: Kant argues that moral imperatives cannot be based on any values without yielding heteronomy. Instead it is imperatives of reason that determine what is valuable. The requirement to respect all human beings is one such imperative. Respect for human beings does not follow from human dignity for this would violate autonomy but is an unconditional command of reason. Following this train of thought yields a unified account of Kant s moral philosophy. (shrink)

This paper reviews the hole argument as an argument against spacetime substantivalism. After a careful presentation of the argument itself, I critically review possible responses.

WE must first state the subject of our inquiry and the faculty to which it belongs: its subject is demonstration and the faculty that carries it out demonstrative science.

ABSTRACT The use of broad consent for genomics research raises important ethical questions for the conduct of genomics research, including relating to its acceptability to research participants and comprehension of difficult scientific concepts. To explore these and other challenges, we conducted a study using qualitative methods with participants enrolled in an H3Africa Rheumatic Heart Disease genomics study (the RHDGen network) in Zambia to explore their views on broad consent, sample and data sharing and secondary use. In-depth interviews were conducted with (...) RHDGen participants (n = 18), study staff (n = 5) and with individuals who refused to participate (n = 3). In general, broad consent was seen to be reasonable if reasons for storing the samples for future research use were disclosed. Some felt that broad consent should be restricted by specifying planned future studies and that secondary research should ideally relate to original disease for which samples were collected. A few participants felt that broad consent would delay the return of research results to participants. This study echoes findings in other similar studies in other parts of the continent that suggested that broad consent could be an acceptable consent model in Africa if careful thought is given to restrictions on re-use. (shrink)

In his paper ``What is Structural Realism?'' James Ladyman drew a distinction between epistemological structural realism and metaphysical (or ontic) structural realism. He also drew a suggestive analogy between the perennial debate between substantivalist and relationalist interpretations of spacetime on the one hand, and the debate about whether quantum mechanics treats identical particles as individuals or as `non-individuals' on the other. In both cases, Ladyman's suggestion is that an ontic structural realist interpretation of the physics might be just what is (...) needed to overcome the stalemate. The main thesis of this paper is that, whatever the interpretative difficulties of generally covariant spacetime physics are, they do not support or suggest structural realism. In particular, I hope to show that there is in fact no analogy that supports a similar interpretation of the metaphysics of spacetime points and of quantum particles. (shrink)

In this article, I offer a detailed examination of Margaret Macdonald's response to the Cartesian sceptical argument from dreaming. I show that Macdonald's views were not well understood by her contemporaries, and I suggest that this misunderstanding has led to her omission from subsequent discussions of this subject. I end with a brief demonstration of the fact that Macdonald's central claims have re-emerged in contemporary epistemology.