The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

How many words—and which ones—are sufficient to define all other words? When dictionaries are analyzed as directed graphs with links from defining words to defined words, they reveal a latent structure. Recursively removing all words that are reachable by definition but that do not define any further words reduces the dictionary to a Kernel of about 10% of its size. This is still not the smallest number of words that can define all the rest. About 75% of the Kernel turns (...) out to be its Core, a “Strongly Connected Subset” of words with a definitional path to and from any pair of its words and no word's definition depending on a word outside the set. But the Core cannot define all the rest of the dictionary. The 25% of the Kernel surrounding the Core consists of small strongly connected subsets of words: the Satellites. The size of the smallest set of words that can define all the rest—the graph's “minimum feedback vertex set” or MinSet—is about 1% of the dictionary, about 15% of the Kernel, and part-Core/part-Satellite. But every dictionary has a huge number of MinSets. The Core words are learned earlier, more frequent, and less concrete than the Satellites, which are in turn learned earlier, more frequent, but more concrete than the rest of the Dictionary. In principle, only one MinSet's words would need to be grounded through the sensorimotor capacity to recognize and categorize their referents. In a dual-code sensorimotor/symbolic model of the mental lexicon, the symbolic code could do all the rest through recombinatory definition. (shrink)

What enables individually simple insects like ants to act with such precision and purpose as a group? How do trillions of individual neurons produce something as extraordinarily complex as consciousness? What is it that guides self-organizing structures like the immune system, the World Wide Web, the global economy, and the human genome? These are just a few of the fascinating and elusive questions that the science of complexity seeks to answer. In this remarkably accessible and companionable book, leading complex systems (...) scientist Melanie Mitchell provides an intimate, detailed tour of the sciences of complexity, a broad set of efforts that seek to explain how large-scale complex, organized, and adaptive behavior can emerge from simple interactions among myriad individuals. Comprehending such systems requires a wholly new approach, one that goes beyond traditional scientific reductionism and that re-maps long-standing disciplinary boundaries. Based on her work at the Santa Fe Institute and drawing on its interdisciplinary strategies, Mitchell brings clarity to the workings of complexity across a broad range of biological, technological, and social phenomena, seeking out the general principles or laws that apply to all of them. She explores as well the relationship between complexity and evolution, artificial intelligence, computation, genetics, information processing, and many other fields. Richly illustrated and vividly written, Complexity : A Guided Tour offers a comprehensive and eminently comprehensible overview of the ideas underlying complex systems science, the current research at the forefront of this field, and the prospects for the field's contribution to solving some of the most important scientific questions of our time. (shrink)

The stories from the Clergy Health Initiative and Word Made Flesh missionary organization exhibit transformations that ushered Christian leaders into deeper love of God, neighbor, and themselves.

Integrative and naturalistic philosophy of mind can both learn from and contribute to the contemporary cognitive sciences of dreaming. Two related phenomena concerning self-representation in dreams demonstrate the need to bring disparate fields together. In most dreams, the protagonist or dream self who experiences and actively participates in dream events is or represents the dreamer: but in an intriguing minority of cases, self-representation in dreams is displaced, disrupted, or even absent. Working from dream reports in established databanks, we examine two (...) key forms of polymorphism of self-representation: dreams in which I take an external visuospatial perspective on myself, and those in which I take someone else's perspective on events. In remembering my past experiences or imagining future or possible experiences when awake, I sometimes see myself from an external or 'observer' perspective. By relating the issue of perspective in dreams to established research traditions in the study of memory and imagery, and noting the flexibility of perspective in dreams, we identify new lines of enquiry. In other dreams, the dreamer does not appear to figure at all, and the first person perspective on dream events is occupied by someone else, some other person or character. We call these puzzling cases 'vicarious dreams' and assess some potential ways to make sense of them. Questions about self-representation and perspectives in dreams are intriguing in their own right and pose empirical and conceptual problems about the nature of self-representation with implications beyond the case of dreaming. (shrink)

How does the body influence the way we see the world? _Imagination, Illness and Injury_ examines the psychological factors behind perceptual limitations and distortions and links a broad range of somatic manifestations with their resolution. Melanie Starr Costello applies Jungian theory to a variety of cases, attributing psychosomatic phenomena to cognitive processes that are common to us all. She analyses the role of illness in several life narratives, and interprets the appearance of somatic phenomena during important phases of analytic treatment. (...) Together these case narratives present a significant challenge to established views of psychosomatics. Subjects covered include: archetypal constrictions of identity somatic elements of perception the psyche-soma split. _Imagination, Illness and Injury _brings a fresh perspective to the understanding and treatment of the psychotherapy client as a psycho-somatic unity. Jungian analysts, psychoanalysts, and psychotherapists will greatly benefit from the clinical applications of archetypal theory presented here. (shrink)

Background: Few robust autism-specific outcome assessments have been developed specifically for use by teachers in special schools. The Assessment of Barriers to Learning in Education – Autism is a newly developed teacher assessment to identify and show progress in barriers to learning for pupils on the autism spectrum with coexisting intellectual disabilities. Aims: This study aimed to conduct a preliminary validity and reliability evaluation of the ABLE-Autism. Methods and procedures: Forty-eight autistic pupils attending special schools were assessed using the ABLE-Autism. (...) Multi-level modelling was used to evaluate test-retest reliability, internal consistency and convergent validity with the Teacher Autism Progress Scale. Outcomes and results: Results showed excellent test-retest reliability and internal consistency. A large effect size suggested that the ABLE-Autism is strongly correlated with the Teacher Autism Progress Scale. Teacher feedback was positive and suggested that the ABLE-Autism is easily understood by teachers, relevant to autistic pupils in special schools, and adequately covers the skills and behaviours that teachers believe are important to assess for these pupils. Conclusions and implications: Although further validation is recommended, the preliminary evaluation of the ABLE-Autism suggests that it is a useful and has the potential to be an effective outcome assessment for autistic pupils in special schools. (shrink)

The underdevelopment of a pedagogical culture for research methods education and the lack of a body of knowledge with the potential to influence practice have been highlighted by previous studies. This systematic review explores the pedagogic approaches and strategies evident in recent literature (2014–2020) on teaching social science research methods in higher education. It synthesises 55 papers offering a detailed rationale for the approach and strategies employed in doctoral/post-doctoral education. While dispersed across journals, there is a plethora of case studies (...) and reflective accounts about teaching approach, strategy, tactics and tasks in research methods education. Most studies reviewed report on teaching qualitative methods and represent authors’ own teaching practices. Consistent with previous studies, experiential, active learning and student-centred approaches are predominantly discussed, often overlapping or combined with other approaches. This paper illustrates a growing pedagogic culture, represented by an increased volume of papers and theoretical discussion of practices, rationale and reflection on how research methods are taught and learnt. It is concluded that clear intention to engage in dialogue and contribute to evidence-based practice and knowledge in research methods education is evident, and that the ‘how to’ element is richly articulated and justified. (shrink)

Accompanying _The_ _Routledge Doctoral Student’s Companion_ this book examines what it means to be a doctoral student in education and the social sciences, providing a guide for those supervising students. Exploring the key role and pedagogical challenges that face supervisors in students’ personal development, the contributors outline the research capabilities which are essential for confidence, quality and success in doctorate level research. Providing guidance about helpful resources and methodological support, the chapters: frame important questions within the history of debates act (...) as a road map through international literatures make suggestions for good practice raise important questions and provide answers to key pedagogical issues provide advice on enabling students’ scholarly careers and identities. While there is no one solution to ideal supervision, this wide-ranging text offers resources that will help supervisors develop their own personal approach to supervision. Ideal for all supervisors whether assisting part-time of full-time students, it is also highly suitable for helping academics to support international students who confront Western doctoral traditions and academic cultures, helping both supervisor and student to understand why things are as they are. (shrink)

Matrix models are widely used in biology to predict the temporal evolution of stage-structured populations. One issue related to matrix models that is often disregarded is the sampling variability. As the sample used to estimate the vital rates of the models are of finite size, a sampling error is attached to parameter estimation, which has in turn repercussions on all the predictions of the model. In this study, we address the question of building confidence bounds around the predictions of matrix (...) models due to sampling variability. We focus on a density-dependent Usher model, the maximum likelihood estimator of parameters, and the predicted stationary stage vector. The asymptotic distribution of the stationary stage vector is specified, assuming that the parameters of the model remain in a set of the parameter space where the model admits one unique equilibrium point. Tests for density-dependence are also incidentally provided. The model is applied to a tropical rain forest in French Guiana. (shrink)

This paper examines six cross-sector partnerships in South Africa and Zambia. These partnerships were part of a research study undertaken between 2003 and 2005 and were selected because of their potential to contribute to poverty reduction in their respective countries. This paper examines the context in which the partnerships were established, their governance and accountability mechanisms and the engagement and participation of the partners and the intended beneficiaries in the partnerships. We argue that a partnership approach which has proven successful (...) in one context can be used as a valuable learning resource. However, a partnership's work, which includes all aspects of the partnership and its activities, cannot necessarily be transferred directly to another partnership without a thorough and locally informed analysis of the context in which it is implemented. In addition, we suggest that it is difficult to assess whether the good intentions behind partnerships were translated into real benefits for target groups as effective monitoring and evaluation procedures were not in place in the partnerships studied. Similarly, the absence of regularised governance and accountability systems in partnerships made it difficult to support partner and beneficiary participation and engagement. We conclude that there is a need to move beyond a 'one-size-fits-all' approach to partnerships and that partnership replication should focus more strongly on the transfer of learning about partnership processes instead of simply copying partnership activities. Moreover, the development of stronger mechanisms for assessing and ensuring accountability towards both partners and intended beneficiaries is required if partnerships are to meet their intended objectives. (shrink)

The cinematographic successes of Craig Brewer’s Black Snake Moan and Lars Von Trier's Manderlay are contingent upon the palpability of tension and attraction created by their respective, many racial and sexual relations, thus both films aggressively bring them to the fore by excessively rehearsing old stereotypes and taboos, and inverting the expected agents therein, to reveal their persistent, still-relevant power. Both films similarly test our convictions and squeamishness, but do so from entirely different moral stances. Brewer explores how an act (...) of charity and humanitarian openness can save lives, literally and spiritually. Von Trier explores how similar acts of openness can smother appreciation of the other and reenact the worst oppression. The former tells a persuasive story with wide appeal, while the latter tells a story that will make even the most desensitized viewers cringe. Using these pictures as paradigms, is either approach better for bringing prejudice into the light for thought and film? (shrink)

When engaging in community-based research, it is important to consider ethical research practices throughout the project. While current research practices require many investigators to obtain approval from an ethics review board before starting a project, more is required to ensure that ethical principles are applied once the investigations begin and after the investigations are complete. In response to this concern, as expressed by workers at a feminist non-profit during a community placement, we developed a tool to foster both greater ethical (...) and feminist research practice in community-based research. Using feminist theories, methodologies, and concepts such as epistemic justice, epistemic trust, and coauthorship, a tool was developed to support researchers and other collaborators in building relationships of reciprocity. This tool, called the Research Responsibility Agreement (RRA) invites all members of a research project to explicitly reflect on their role in the research, their relationships with other collaborators, their responsibility to contributing meaningfully in the project, and their plans to remain accountable to one another. In doing so, the RRA adds to existing tools that support ethical research by sharing explicit reflections from all collaborators on how to prevent harm and by asking them to reflect on ethical practices beyond the initial stages of the project. The RRA also encourages greater engagement from researchers and collaborators toward building meaningful relationships with each other, and with participants, to work together in advancing social change. As a practical tool that promotes reflection, that builds relationships, and that holds all parties accountable to ethical and feminist research practices, the RRA has the potential to generate impactful change in community-based research projects and beyond. While the RRA is tailored to community-based research, it can be applied widely to any research project and has the potential to revolutionize how research relationships are built across disciplines. (shrink)

Beim eingeschränkten Fokus auf (historische) Wahrheit und dem Hervorbringen von „Beweisen“ im Kontext der türkischen Leugnung des Genozids an den ArmenierInnen wurde einem wesentlichen ethischen Problem bisher keine sonderliche Beachtung geschenkt: Dass innerhalb dieser sozial situierten Praxis der Etablierung von Wissen über die historischen Tatsachen – also darüber, was passiert ist und wie diese Geschehnisse zu interpretieren sind – Ungerechtigkeiten im Hinblick darauf entstehen können, wen man als glaubwürdige epistemische Akteure anerkennt. Gemäss dieser Überlegung soll der vorliegende Beitrag zeigen, inwiefern (...) Nachfahren von Genozidopfern durch institutionalisierte Genozidleugnung einer spezifischen Art erneuter Dehumanisierung zum Opfer fallen, nämlich der epistemischen Ungerechtigkeit. Diese besagt, dass den Nachfahren der Opfergruppe die Glaubwürdigkeit und damit epistemische Autorität auf der Grundlage ihrer sozialen Zugehörigkeit abgesprochen wird. In diesem Sinne kann die Genozidleugnung als eine fortgesetzte Delegitimierung der Opfergruppe und Herabwürdigung ihrer Mitglieder verstanden werden, diesmal im Gewand einer Aberkennung ihrer essentiellen menschlichen Fähigkeit, Wissen zu generieren und weiterzugeben. (shrink)

Hegel qualifiait la pièce Antigone de Sophocle de tragédie la plus parfaite. Peut-on, encore aujourd’hui, malgré les critiques ultérieures, soutenir cette idée et la fonder? Si la perfection de cette tragédie tient dans le tissage de conflits que Sophocle construit, nous devrons d’abord effiler chaque conflit, pour ensuite affilier chaque position à ce qui la fonde, et suivre enfin le déroulé tragique du fil d’Antigone.

To what extent do I have a sense of agency over my thoughts while I dream? The sense of agency in dreams can alter in a variety of interesting ways distinct from normal, waking experience. In fact, dreams show many similarities to the experiences of individuals with schizophrenia. In this paper I analyze these alterations with a focus on distinguishing between reduced sense of agency and other cognitive features such as metacognition, confabulation and attention. I argue that some dream reports (...) demonstrate two interesting commonalities with schizophrenia: thought insertion (TI) and auditory hallucination (AH). This line of research has the potential to further our understanding of TI and AH in schizophrenia through the analysis of similar experience in a different conscious state. Through the analysis of dream reports, I found that although TI and AH both occur in dreams, TI is very rare. This is an interesting result since TI is common in patients with schizophrenia. I propose two speculative lines of explanation for the rarity of TI in dreams: first, the cognitive differences between the symptoms of schizophrenia and dreams, and second, the problem of dream reporting conditions. Dream reporting conditions are particularly important, as without controls, reports can be vague. Analysis of dream reports reveals that it is often unclear whether 'hearing voices' indicates sound phenomenology or thought phenomenology. I propose that dream reports could be disambiguated given the right experimental conditions and I suggest how this could be achieved in future experimental research. (shrink)

Given the profound influence of social media and emerging evidence of its effects on human behavior and health, bioethicists have an important role to play in the development of professional standards of conduct for health professionals using social media and in the design of online systems themselves. In short, social media is a bioethics issue that has serious implications for medical practice, research, and public health. Here, we inventory several ethical issues across four areas at the intersection of social media (...) and health: the impact of social networking sites on the doctor‐patient relationship, the development of e‐health platforms to deliver care, the use of online data and algorithms to inform health research, and the broader public health consequences of widespread social media use. In doing so, we review discussions of these topics and emphasize the need for bioethics to focus more deeply on the ways online technology platforms are designed and implemented. We argue that bioethicists should turn their attention to the ways in which consumer engagement, bias, and profit maximization shape online content and, consequently, human behavior and health. We also offer a set of recommendations and suggest future directions for addressing ethical challenges in these domains. (shrink)

While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. Current editing tools present challenges for working with large ontologies an...

This article is a response to an essay written by an academic in English Literature, Professor John Sutherland. Through close textual analysis,Sutherland purports to resolve a well-known literary question: whether the sexual encounter outlined in the Victorian novel Tess of the d'Urbervilles should be classified as rape or seduction. The present article rejects his conclusion on the matter. An(equally) close analysis of the fictional text in question and of Sutherland's gloss, demonstrates the partiality of his critique, both in literary-critical and (...) critical-legal terms. In addition, examination of the conceptual and historico-legal context regarding the notions of rape and seduction on both sides of the Atlantic highlights parallels between Sutherland's own partiality and that of the law. In short, the apparent objectivity of the textual analysis and subsequent critique undertaken by Sutherland is revealed as a continuation of legal and patriarchal prejudices defining rape and seduction. The use of close textual analysis as the key critical device promotes the apparent probity of his findings. Locating them in an essay collection designed for mass lay public consumption completes the circle – from partisan scholarship to `informed' popular prejudice. (shrink)

The Dreaming Mind provides an insightful, interdisciplinary approach to the study of dreaming, exploring its nature and examining some of the implications of dream states for theories of consciousness, cognition and the self. Offering an integrative approach into our understanding of dreams and the mind, it is essential reading for students and researchers of consciousness, dreams, philosophy and cognitive sciences, as well as anyone who is curious about dreaming.

Support to professional development and even to professionalization of workers, such as teachers, trainers, nurses, social workers, leaders, etc., is currently raising researcher’s interest especially in Education Sciences. Nevertheless, little research has been conducted on non-graduates young people’s accompaniment while many programs have been developed, especially in France, to support their professional integration. The purpose of this paper is to examine the links between trainers’ accompanying logic and the conscious awareness of competencies of young people without qualifications. This study highlights (...) how support practices are organized by trainers to help young people in precarious situations to become aware of their competencies by encouraging their reflexivity, their autonomy and their interactions with the others. (shrink)

This article offers an argument of genocide denial as an injustice perpetrated not only against direct victims and survivors of genocide, but also against future members of the victim group. In particular, I argue that in cases of persistent and systematic denial, i.e. denialism, it perpetrates an epistemic injustice against them: testimonial oppression. First, I offer an account of testimonial oppression and introduce Kristie Dotson’s notion of testimonial smothering as one form of testimonial oppression, a mechanism of coerced silencing particularly (...) pertinent to genocide denialism. Secondly, I turn to the epistemology of genocide denialism and, using the example of Turkey’s denialism of the Armenian genocide, show how it presents what Linda Martín Alcoff calls a substantive practice of ignorance. Thirdly, I apply these considerations to individual practices of genocide denial and analyse the particular characteristics of testimony on genocide, the speaker vulnerabilities involved and the conditions under which hearers will reliably fail to meet the dependencies of a speaker testifying to genocide. Finally, I explore the harms that testimonial oppression perpetrates on members of the victim group, insofar as it systematically deprives them of epistemic recognition. (shrink)

This article introduces the symposium “Toward a Philosophy of Blockchain,” which provides a philosophical contemplation of blockchain technology, the digital ledger software underlying cryptocurrencies such as bitcoin, for the secure transfer of money, assets, and information via the Internet without needing a third-party intermediary. The symposium offers philosophical scholarship on a new topic, blockchain technology, from a variety of perspectives. The philosophical themes discussed include mathematical models of reality, signification, and the sociopolitical institutions that structure human life and interaction. The (...) symposium also investigates the metaphilosophical theme of how to create a philosophy of anything, specifically a new topic such as blockchain technology. Repeated themes are identified, in all areas of philosophical inquiry, and conceptual resources are elaborated to contribute to a philosophical understanding of blockchain technology. Thus, philosophy as a metaphilosophical approach is shown to be able to provide an understanding of the conceptual, theoretical, and foundational dimensions of novelty and emergence in the world, with a particular focus on blockchain technology. (shrink)

In this article I am concerned with how relatively privileged people who wish to act in anti-oppressive ways respond to their own ignorance in ways that fall short of what is necessary for building coalitions against oppression. I consider María Lugones's sense of “world”-travel and José Medina's notion of epistemic friction-seeking as strategies for combating privileged ignorance, and assess how well they fare when put into practice by those suffering from privileged ignorance. Drawing on the resources of tourism studies, I (...) critique the political and material context that can turn these attempts to “world”-travel or seek epistemic friction into a morally and epistemically problematic epistemic tourism. Centrally, I argue that trying to learn what it's like to experience oppression is not an effective method of counteracting privileged ignorance, since the epistemic vices and cognitive distortions that created the ignorance in the first place continue to influence knowledge-creation even after they are acknowledged. Rather than attempting to understand “what it's like” to experience oppression, privileged progressives should undertake to learn about the provenance and purpose of their ignorance and the structures of oppression that facilitate and are facilitated by that ignorance. (shrink)