The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.

Little is known about the mechanisms by which psychology graduate programs transmit responsible conduct of research (RCR) values. A national sample of 968 current students and recent graduates of mission-diverse doctoral psychology programs completed a Web-based survey on their research ethics challenges, perceptions of RCR mentoring and department climate, whether they were prepared to conduct research responsibly, and whether they believed psychology as a discipline promotes scientific integrity. Research experience, mentor RCR instruction and modeling, and department RCR policies predicted student (...) RCR preparedness. Mentor RCR instruction, department RCR policies, and faculty modeling of RCR behaviors predicted confidence in the RCR integrity of the discipline. Implications for training are discussed. (shrink)

Caesar left off writing de Bello Gallico at the end of the Alesia campaign in 51 B.C., and his account of the civil war begins in January 49. There was therefore a gap ofa year and more between the narratives in the two collections of Caesar's own Commentaries. Some time soon after Caesar's death, his officer A. Hirtius decided toknit together these unlinked narratives, supplying a preface to account for hisprocedure. It is usually assumed, and it is assumed here, that (...) this Preface, whichappears at the start of B.G. 8 in the MSS, should be taken to mean that its author wasthe author too of the book immediately following, which connects de Bello Gallico with de Bello Civili by narrating, essentially, the transactions of the year 50. (shrink)

Since the Persian Wars, the Areopagus had allegedly usurped certain ‘additional functions’. By removing them, and assigning them instead to the Council, the assembled People, and the jury-courts, Ephialtes undid the last institutional bastion of aristocratic political authority, and set the copestones on Athens' democratic order.

Since the Persian Wars, the Areopagus had allegedly usurped certain ‘additional functions’. By removing them, and assigning them instead to the Council, the assembled People, and the jury-courts, Ephialtes undid the last institutional bastion of aristocratic political authority, and set the copestones on Athens' democratic order.

Economic inequality has become a focus of prime interest for economic analysts and policy makers. This book provides an integrated approach to the topics of inequality and personal income distribution. It covers the practical and theoretical bases for inequality analysis, applications to real world problems and the foundations of theoretical approaches to income distribution. It also analyses models of the distribution of labour earnings and of income from wealth. The long-run development of income - and wealth - distribution over many (...) generations is also examined. Special attention is given to an assessment of the merits and weaknesses of standard economic models, to illustrating the implications of distributional mechanisms using real data and illustrative examples, and to providing graphical interpretation of formal arguments. Examples are drawn from US, UK and international sources. (shrink)

This article examines the Roman tradition that Numa once negotiated with Jupiter about human sacrifice. Complete versions of the myth survive in Ovid, Plutarch and Arnobius. Previous studies of this tradition have proposed four main interpretations of it, which have done important service in modern reconstructions of the character of Roman religion. These scholarly treatments raise several questions. First, are they actually supported by, or the most convincing way of reading, the surviving ancient sources? If so, have they been correctly (...) attributed? Why might a specific ancient author present the myth of Numa and Jupiter in a manner which suggests one interpretation rather than another? What ideological and theological work does the story do for Ovid, for Plutarch and for Arnobius? Finally, can this myth, in whatever version, support the weight of the implications put on it for the character of Roman religion? This article seeks to enhance our understanding of this myth in its surviving versions, not just by analysing the evidence for each of the modern interpretations, but also by considering why ancient authors tell the myth of Numa and Jupiter the way they do. It is argued that their choices illustrate best not one meaning of the myth nor one Roman way of piety but the richness and diversity of religious reflection in antiquity. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

Since 2000, research within positive psychology has exploded, as reflected in dozens of meta-analyses of different interventions and targeted processes, including strength spotting, positive affect, meaning in life, mindfulness, gratitude, hope, and passion. Frequently, researchers treat positive psychology processes of change as distinct from each other and unrelated to processes in clinical psychology. This paper presents a comprehensive framework for positive psychology processes that crosses theoretical orientation, links coherently to clinical psychology and its more dominantly “negative” processes, and supports practitioners (...) in their efforts to personalize positive psychological interventions. We argue that a multi-dimensional and multi-level extended evolutionary approach can organize effective processes of change in psychosocial interventions, by focusing interventions on context-appropriate variation, selection, and retention of processes, arranged in terms of key biopsychosocial dimensions across psychological, biophysiological, and sociocultural levels of analysis. We review widely studied positive psychology constructs and programs and show how this evolutionary approach can readily accommodate them and provide a common language and framework for improving human and community flourishing. We conclude that Interventions should start with the person, not the protocol. (shrink)

In this review of the central tenets of hope theory, we examine the meta-theoretical, theoretical, and methodological foundations of the literature base. Our analysis moves from a broad examination of the research landscape in hope theory across disciplines, to a deeper investigation of the empirical literature in university students. This review highlights the significant impact of this body of research in advancing our understanding of aspects of thriving characterized by hope. However, we also evidence several limitations that may impede the (...) advancement of the next wave of growth in this field. To address these limitations, we argue for an interdisciplinary approach to expanding the meta-theoretical, theoretical, and methodological horizons, enabling a more dynamic systems approach to the study of hope. Drawing on the intersection of positive psychology with systems thinking, we describe a methodological approach that enables a deeper examination of the processes and interactions through which hope emerges, using an analysis of the lived experience of young people. It is proposed that this research agenda will bring to life an alternate story about the resourcefulness of our youth through their own voice, enabling us to leverage this in the design of more effective strategies to facilitate hope in the future. This research agenda provides a roadmap that will provide alternative methodologies that address the current limitations in the field of hope research and, importantly, can provide fuel to spur on the acceleration of the next wave of research and practice in the field of positive psychology more broadly. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...) along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

How did the events of the early modern period affect the way gender and the self were represented? This collection of essays attempts to respond to this question by analysing a wide spectrum of cultural concerns - humanism, technology, science, law, anatomy, literacy, domesticity, colonialism, erotic practices, and the theatre - in order to delineate the history of subjectivity and its relationship with the postmodern fragmented subject. The scope of this analysis expands the terrain explored by feminist theory, while its (...) feminist focus reveals that the subject is always gendered - although the terms in which gender is conceived and represented change across history. Feminist Readings of Early Modern Culture not only explores the representation of gendered subjects, but in its commitment to balancing the productive tensions of methodological diversity, also speaks to contemporary challenges facing feminism. (shrink)

This paper outlines the academic architecture of CityLab as graduate program course initiative and Principles of Responsible Management Education capstone exemplar. When the United Nations launched the Millennium Goals in 2000 to focus global development on humanity rather than GDP, the Global Compact was launched as a collateral effort, challenging business, government, and social sector leaders to transform the global economic system. In 2007, the Six PRME focused on business schools, challenging them to reorient their curricula towards preparing students to (...) lead the world in building “an inclusive and sustainable economy.” CityLab is an example of innovating the learning experience and challenging learners to take leadership roles in efforts to enhance the value of livable cities as the foundation of an inclusive and sustainable global economy for the Urban Century. (shrink)

Though emotional faces preferentially reach awareness, the present study utilised both objective and subjective indices of awareness to determine whether they enhance subjective awareness and “blindsight”. Under continuous flash suppression, participants localised a disgusted, fearful or neutral face (objective index), and rated their confidence (subjective index). Psychopathic traits were also measured to investigate their influence on emotion perception. As predicted, fear increased localisation accuracy, subjective awareness and “blindsight” of upright faces. Coldhearted traits were inversely related to subjective awareness, but not (...) “blindsight”, of upright fearful faces. In a follow-up experiment using inverted faces, increased localisation accuracy and awareness, but not “blindsight”, were observed for fear. Surprisingly, awareness of inverted fearful faces was positively correlated with coldheartedness. These results suggest that emotion enhances both pre-conscious processing and the qualitative experience of awareness, but that pre-conscious and conscious processing of emotional faces rely on at least partially dissociable cognitive mechanisms. (shrink)

E4BP4, a mammalian basic leucine zipper (bZIP) transcription factor, was first identified through its ability to bind and repress viral promoter sequences. Subsequently, E4BP4 and homologues in other species have been implicated in a diverse range of processes including commitment to cell survival versus apoptosis, the anti‐inflammatory response and, most recently, in the mammalian circadian oscillatory mechanism. In some of these cases at least, E4BP4 appears to act antagonistically with members of the related PAR family of transcription factors with which (...) it shares DNA‐binding specificity. This diversity of function is mirrored by the regulatory pathways impinging on E4BP4, which include regulation by ras via the lymphokine IL‐3 in murine B‐cells, by thyroid hormone during Xenopus tail resorption, by glucocorticoids in murine fibroblasts and by calcium in rat smooth muscle cells. This article will cover the unfolding role/s of and regulation of E4BP4, E4BP4‐like proteins and PAR factors in species as diverse as mouse and C. elegans. BioEssays 24:1023–1029, 2002. © 2002 Wiley‐Periodicals, Inc. (shrink)

The chromodomain is a highly conserved sequence motif that has been identified in a variety of animal and plant species. In mammals, chromodomain proteins appear to be either structural components of large macromolecular chromatin complexes or proteins involved in remodelling chromatin structure. Recent work has suggested that apart from a role in regulating gene activity, chromodomain proteins may also play roles in genome organisation. This article reviews progress made in characterising mammalian chromodomain proteins and emphasises their emerging role in the (...) regulation of gene expression and genome organisation. BioEssays 22:124–137, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

Individuals with anxiety disorders show deficits in the discrimination between a cue that predicts an aversive outcome and a safe stimulus that predicts the absence of that outcome. This impairment has been linked to increased spontaneous recovery of fear following extinction, however it is unknown if there is a link between discrimination and return of fear in a novel context. It is also unknown if impaired discrimination mediates the relationship between trait anxiety and either spontaneous recovery or context renewal. The (...) present study used a differential fear conditioning paradigm to examine the relationships between trait anxiety, discrimination learning, spontaneous recovery and context renewal in healthy volunteers. Fear learning was assessed using continuous ratings of US expectancy and subjective ratings of fear. Discrimination mediated the relationships between trait anxiety and both spontaneous recovery and context renewal such that elevated trait anxiety was associated with poorer discrimination, which in turn was associated with increased fear at test phases. Results are discussed in terms of the genesis and maintenance of anxiety disorders. (shrink)

The relatively new field of evolutionary developmental biology continues to attract considerable attention from biologists, philosophers, and historians, in part, because work in this field demonstrates that important changes are underway within biology. Though studies of development and evolution were closely connected during the 19th century, continued work in genetics fostered a general split between the two during the first decades of the twentieth century (e.g., Allen 1978; Gilbert 1978; Mayr and Provine 1980; Gilbert, Opitz and..

There is mounting evidence that language comprehension involves the activation of mental imagery of the content of utterances (Barsalou, 1999;Bergen, Chang, & Narayan, 2004;Bergen, Narayan, & Feldman, 2003;Narayan, Bergen, & Weinberg, 2004;Richardson, Spivey, McRae, & Barsalou, 2003;Stanfield & Zwaan, 2001;Zwaan, Stanfield, & Yaxley, 2002). This imagery can have motor or perceptual content. Three main questions about the process remain under‐explored, however. First, are lexical associations with perception or motion sufficient to yield mental simulation, or is the integration of lexical semantics (...) into larger structures, like sentences, necessary? Second, what linguistic elements (e.g., verbs, nouns, etc.) trigger mental simulations? Third, how detailed are the visual simulations that are performed? A series of behavioral experiments address these questions, using a visual object categorization task to investigate whether up‐ or down‐related language selectively interferes with visual processing in the same part of the visual field (followingRichardson et al., 2003). The results demonstrate that either subject nouns or main verbs can trigger visual imagery, but only when used in literal sentences about real space—metaphorical language does not yield significant effects—which implies that it is the comprehension of the sentence as a whole and not simply lexical associations that yields imagery effects. These studies also show that the evoked imagery contains detail as to the part of the visual field where the described scene would take place. (shrink)

The abbreviation-symbols of the Romans, found in ancient uncial MSS., may be roughly divided into three classes: Those peculiar to juristic writing, e.g. R.P. ‘res priuata’ , Q.D.R.A. ‘qua de re agitur.’ They are properly called ‘notae iuris.’ They abound in the famous Verona MS. of Gaius. A few used in histories, etc., e.g. R.P. 'respublica' , Q. ‘Quintus’ . Valerius Probus, who compiled a manual of ancient Notae, calls this class ‘notae publicae’. They appear in such MSS. as the (...) codex Puteanus of Livy ; and since they have been transferred into modern editions of the Latin historians, etc., no one is at a loss to interpret them nowadays, although they puzzled mediaeval scribes. Symbols of ordinary words of frequent occurrence in any type of literature, e.g. Q. ‘que.’ It is this class which is the subject of this article. (shrink)

Mrs. Dall, in her article A Seventh-Century English Edition of Virgil , shows that Virgil glosses taken from marginalia in the same MS. of the poems often preserve something of their original coherence in the two kindred glossaries, Affatim and the Second Amplonian, in spite of all the reshuffling of these two collections. Thus a small group of Virgil items appears in Affatim on p. 491 of Goetz's apograph : Carecta, Crateras, etc. The second last of this ‘Virgil cluster’ is (...) Cada: vasa vinaria. It appears also in Ampl. II. Ca[t]da: vas vinaria, and in Ampl. I. Cada: vasa vinaria, and is apparently taken , ultimately or immediately, from a marginal annotation on Aen. 1, 195 ‘uina bonus quae deinde cadis onerarat Acestes’ for in the Virgil Glossary printed by Goetz in C.G.L. IV. 427–470 we find Cadis: vasis vinariis. (shrink)