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)

One important problem in cognitive science is to understand the development of cognitive processes in children and to devise computer models to explore the mechanisms that underlie these changes. Our research addresses these general goals. In particular, we are concerned with developmental changes in cognitive strategies in typical children and in children with mild mental retardation.

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

In this article I want to clarify the text of one of the short maxims assigned to Pythagoras in the ancient tradition, which are known as symbola or acusmata. Before I turn to the acusma in question, it is important to understand the context in which it appears. It occurs in Chapter 17 of Book 4 of Aelian's Historical Miscellany. Aelian's work was written in the early third century a.d. in Rome, and is a ‘miscellaneous collection of anecdotes and historical (...) material’. It consists of short chapters, usually a page or less long, that are for the most part independent of one another. Chapter 17 of Book 4 is about a page long and is devoted to the sayings and doings of Pythagoras. There is no particular connection between it and the surrounding chapters, and it is clearly meant to stand on its own. The preceding chapter tells us that if we went to Callias for guidance he would turn us into drinkers, … if to Alcibiades, arrogant cheats, if to Demosthenes, orators, … if to Aristides, just men, … if to Socrates, wise men. The following chapter recounts an anecdote about Plato's arrival in Sicily and his reception by the tyrant Dionysius the Younger. The chapter that I am concerned with, Chapter 17, begins by asserting that Pythagoras taught that his ‘lineage was superior to that of ordinary mortals’. This is followed by a list of superhuman acts and traits of Pythagoras, for example his ability to be in Metapontum and Croton at the same time and his golden thigh. The second two-thirds of the chapter are then devoted to the miscellaneous teachings of Pythagoras. Most of these take the form of the brief taboos and maxims known elsewhere as symbola or acusmata, among which is the text on which I want to focus here. (shrink)

The uncertainty on measurements, given by the Heisenberg principle, is a quantum concept usually not taken into account in General Relativity. From a cosmological point of view, several authors wonder how such a principle can be reconciled with the Big Bang singularity, but, generally, not whether it may affect the reliability of cosmological measurements. In this letter, we express the Compton mass as a function of the cosmological redshift. The cosmological application of the indetermination principle unveils the differences of the (...) Hubble-Lemaître constant value, $$H_0$$, as measured from the Cepheids estimates and from the Cosmic Microwave Background radiation constraints. In conclusion, the $$H_0$$ tension could be related to the effect of indetermination derived in comparing a kinematic with a dynamic measurement. (shrink)

When classes of structures are not first-order definable, we might still try to find a nice description. There are two common ways for doing this. One is to expand the language, leading to notions of pseudo-elementary classes, and the other is to allow infinite conjuncts and disjuncts. In this paper we examine the intersection. Namely, we address the question: Which classes of structures are both pseudo-elementary and ${\mathcal {L}}_{\omega _1, \omega }$ -elementary? We find that these are exactly the classes (...) that can be defined by an infinitary formula that has no infinitary disjunctions. (shrink)

Supercommentary on Siddhāntabindu of Madhusūdana Sarasvatī, exegesis of Daśaślokī, treatise of the Advaita school in Indic philosophy, by Śaṅkarācārya.

Revisiting African philosophy’s classic questions, D. A. Masolo advances understandings of what it means to be human—whether of African or other origin. Masolo reframes indigenous knowledge as diversity: How are we to understand the place and structure of consciousness? How does the everyday color the world we know? Where are the boundaries between self and other, universal and particular, and individual and community? From here, he takes a dramatic turn toward Africa’s current political situation and considers why individual rights and (...) freedoms have not been recognized, respected, demanded, or enforced. Masolo offers solutions for containing socially destructive conduct and antisocial tendencies by engaging community. His unique thinking about community and the role of the individual extends African philosophy in new, global directions. (shrink)

Lexical Semantics is about the meaning of words. Although obviously a central concern of linguistics, the semantic behaviour of words has been unduly neglected in the current literature, which has tended to emphasize sentential semantics and its relation to formal systems of logic. In this textbook D. A. Cruse establishes in a principled and disciplined way the descriptive and generalizable facts about lexical relations that any formal theory of semantics will have to encompass. Among the topics covered in depth are (...) idiomaticity, lexical ambiguity, synonymy, hierarchical relations such as hyponymy and meronymy, and various types of oppositeness. Syntagmatic relations are also treated in some detail. The discussions are richly illustrated by examples drawn almost entirely from English. Although a familiarity with traditional grammar is assumed, readers with no technical linguistic background will find the exposition always accessible. All readers with an interest in semantics will find in this original text not only essential background but a stimulating new perspective on the field. (shrink)

Justice will once take the place which the Magians are keeping now, for it is they who lord it over the world.

In debates about criteria for human death, several camps have emerged, the main two focusing on either loss of the "organism as a whole" (the mainstream view) or loss of consciousness or "personhood." Controversies also rage over the proper definition of "irreversible" in criteria for death. The situation is reminiscent of the proverbial blind men palpating an elephant; each describes the creature according to the part he can touch. Similarly, each camp grasps some aspect of the complex reality of death. (...) The personhood camp, in contrast to the mainstream "organism" camp, recognizes that a human organism can still be a biological living whole even without brain function. The mainstream camp, in contrast to the personhood camp, recognizes that a person can be permanently, even irreversibly unconscious, and still be a living person so long as his/her body is alive. The author proposes that hylomorphic dualism incorporates both these key insights. But to complete the picture of the entire "death elephant," a fundamental paradigm shift is needed to make sense of other seemingly conflicting insights. The author proposes a "semantic bisection" of the concept of death, analogous to the traditional distinction at the beginning of life between "conception" and "birth." To avoid the semantic baggage associated with the term "death," the two new death-related concepts are referred to as "passing away" (or "deceased") and "deanimation," corresponding, respectively, to sociolegal ceasing-to-be (mirror image of birth) and ontological/theological ceasing-to-be of the bodily organism (mirror image of conception). Regarding criteria, the distinguishing feature is whether the cessation of function is permanent (passing away) or irreversible (deanimation). If the "dead donor rule" were renamed the "deceased donor rule" (both acronyms felicitously being "DDR"), the ethics of organ transplantation from non–heart-beating donors could, in principle, be validly governed by the DDR, even though the donors are not yet ontologically "deanimated." Thus, the paradigm shift satisfies both those who insist on maintaining the DDR and those who claim that it has all along been receiving only lip service and should be explicitly loosened to include those who are "as good as dead." Even so, a number of practical caveats remain to be worked out for non–heart-beating protocols. (shrink)

Signals to the brain from the flows of energy around the body, varied primarily by declining amounts of food energy in the stomach, can explain the pattern of meals in the laboratory rat, the differences between dark and light phases, and the development of obesity ion the rat wioth VMH lesions but normal sating.

This paper presents a new formal model for D–N explanation that gives intuitive criteria of acceptability, avoids the known trivializations, and links explanation with confirmation theory. Although set in the twenty-five year tradition of attempts to formalize D–N explanation, it proposes a new direction for the model that is to be distinguished from the syntactical and informational approaches by its introduction of restrictions which derive from the use which the D–N model can have in hypothesis testing. This model, illustrating the (...) verificational approach, revises the classic H–O requirements and amends the notion of partial self-explanation to meet a criticism to which the H–O notion is vulnerable. (shrink)

This article is written from within the Catholic, and more particularly the Augustinian/Thomist tradition of moral theology. It analyses the response of the Catholic Magisterium to the prospect of germline-genetic engineering (GGE). This is a very new issue and the Church has little definitive teaching on it. The statements of Popes and Vatican congregations or commissions have not settled the key questions. An analysis of theological themes drawn from secular writers points beyond pragmatic safety considerations toward intrinsic ethical limits to (...) GGE. Given the impossibility of identifying would-have-been-created persons who would be “treated” by this intervention, altering the human genome for the sake of future generations cannot be regarded as “therapy.” Further theological considerations suggest that GGE may not be morally permissible, even in the case of identifiable genetic diseases. This is an area where more theological reflection is needed. (shrink)

A comprehensive introduction to the ways in which meaning is conveyed in language. Alan Cruse covers semantic matters, but also deals with topics that are usually considered to fall under pragmatics. A major aim is to highlight the richness and subtlety of meaning phenomena, rather than to expound any particular theory. Rich in examples and exercises, Meaning in Language provides an invaluable descriptive approach to this area of linguistics for undergraduates and postgraduates alike.

A three-valued propositional logic is presented, within which the three values are read as ?true?, ?false? and ?nonsense?. A three-valued extended functional calculus, unrestricted by the theory of types, is then developed. Within the latter system, Bochvar analyzes the Russell paradox and the Grelling-Weyl paradox, formally demonstrating the meaninglessness of both.

The International Federation of Gynecology and Obstetrics (FIGO) Committee for the Ethical Aspects of Human Reproduction and Women9s Health advises against tubal occlusion (TO) performed at the time of caesarean section (CS/TO) or following a vaginal delivery (VD/TO) if this sterilisation has not been discussed with the woman in an earlier phase of her pregnancy. This advice is neither in accordance with existing medical custom nor evidence based. Particularly in less-resourced locations, adherence to it would deny much wanted one-off sterilisation (...) opportunities to hundreds of thousands of women, many of whom have no reliable contraceptive alternative. To be sure, a well-timed discussion in pregnancy about a potential peripartum TO is preferable and, if conducted as a matter of course (as the Committee appears to promote), would represent an enormous improvement on current practice. Earlier counselling has the advantage that it results in fewer women who regret having rejected the CS/TO or VD/TO option. However, there is no evidence that earlier counselling leads to a smaller proportion of regretted sterilisations. Consequently, where early TO counselling has been impossible, forgotten or deliberately omitted on pronatalist, traditional, financial, cultural or religious grounds, offering a perinatal sterilisation belatedly and in an unbiased, culturally sensitive manner is often verifiably better than not presenting that option at all, notably where high parity and uterine scars are particularly dangerous. Belated counselling, as will be demonstrated in this paper, saves many lives. The Committee9s blanket rejection of belated counselling on perinatal sterilisation is therefore unjustified. (shrink)

Upshot: According to its introduction, the aim of Enaction is to “present the paradigm of enaction as a framework for a far-reaching renewal of cognitive science as a whole.” While many of the chapters make progress towards this aim, the book as a whole does not present enactivism as a coherent framework, and it could be argued that enactivism’s embrace of phenomenology means it is no longer a theory of cognition.