Sharing of experimental clinical research data usually happens between individuals or research groups rather than via public repositories, in part due to the need to protect research participant privacy. This approach to data sharing makes it difficult to connect journal articles with their underlying datasets and is often insufficient for ensuring access to data in the long term. Voluntary data sharing services such as the Yale Open Data Access (YODA) and Clinical Study Data Request (CSDR) projects have increased accessibility to (...) clinical datasets for secondary uses while protecting patient privacy and the legitimacy of secondary analyses but these resources are generally disconnected from journal articles—where researchers typically search for reliable information to inform future research. New scholarly journal and article types dedicated to increasing accessibility of research data have emerged in recent years and, in general, journals are developing stronger links with data repositories. There is a need for increased collaboration between journals, data repositories, researchers, funders, and voluntary data sharing services to increase the visibility and reliability of clinical research. Using the journal Scientific Data as a case study, we propose and show examples of changes to the format and peer-review process for journal articles to more robustly link them to data that are only available on request. We also propose additional features for data repositories to better accommodate non-public clinical datasets, including Data Use Agreements (DUAs). (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

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)

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)

When developing the Ontology of Biomedical Investigations (OBI), the process of adding classes with similar patterns of logical definition is time consuming, error prone, and requires an editor to...

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

In part one I present a positive argument for the claim that philosophical argument can rationally overturn common sense. It is widely agreed that science can overturn common sense. But every scientific argument, I argue, relies on philosophical assumptions. If the scientific argument succeeds, then its philosophical assumptions must be more worthy of belief than the common sense proposition under attack. But this means there could be a philosophical argument against common sense, each of whose premises is just as worthy (...) of belief as the scientist’s philosophical assumptions. If so, then the purely philosophical argument will also succeed. In part two I consider three motivations, each of which comprises a distinct philosophical methodology, for the opposing view: the Moorean idea that common sense enjoys greater plausibility than philosophy; case judgments should trump general principles; reflective equilibrium and conservatism. I argue that all three motivations fail. (shrink)

The rapidly growing research on hybrid organizations in recent years suggests that these organizations may have particular abilities to facilitate institutional change. This article contributes to our understanding of change and, in particular, sustainable transformation in society by highlighting the importance of organizational forms. Looking more closely at the role of hybrid organizations in processes of path generation, we analyze the conditions under which hybrid organizations may enable path generation. A retrospective exploratory case study of the Swedish hybrid organization The (...) Natural Step confirms how hybrids can take part in- and may facilitate the early phases of path generation: assimilation and coalescence. The conclusion drawn is that hybrids have multivocal abilities that enable them to earn trust and authority to open up “neutral” spaces for orientation and connection between actors in separated sub-paths, and that this in turn may ease tensions and trigger dialogue and exchange, also between former opponents. Yet, as also seen in the case, this enabling position of the hybrid may be both fragile and temporary. (shrink)

Perception is our key to the world. It plays at least three different roles in our lives. It justifies beliefs and provides us with knowledge of our environment. It brings about conscious mental states. It converts informational input, such as light and sound waves, into representations of invariant features in our environment. Corresponding to these three roles, there are at least three fundamental questions that have motivated the study of perception. How does perception justify beliefs and yield knowledge of our (...) environment? How does perception bring about conscious mental states? How does a perceptual system accomplish the feat of converting varying informational input into mental representations of invariant features in our environment? -/- This book presents a unified account of the phenomenological and epistemological role of perception that is informed by empirical research. So it develops an account of perception that provides an answer to the first two questions, while being sensitive to scientific accounts that address the third question. The key idea is that perception is constituted by employing perceptual capacities - for example the capacity to discriminate instances of red from instances of blue. Perceptual content, consciousness, and evidence are each analyzed in terms of this basic property of perception. Employing perceptual capacities constitutes phenomenal character as well as perceptual content. The primacy of employing perceptual capacities in perception over their derivative employment in hallucination and illusion grounds the epistemic force of perceptual experience. In this way, the book provides a unified account of perceptual content, consciousness, and evidence. (shrink)

I argue that there are phenomenological constraints on what it is to see an object, and that these are overlooked by some theories that offer allegedly sufficient causal and counterfactual conditions on object-seeing.

Those who model doxastic states with a set of probability functions, rather than a single function, face a pressing challenge: can they provide a plausible decision theory compatible with their view? Adam Elga and others claim that they cannot, and that the set of functions model should be rejected for this reason. This paper aims to answer this challenge. The key insight is that the set of functions model can be seen as an instance of the supervaluationist approach to vagueness (...) more generally. We can then generate our decision theory by applying the general supervaluationist semantics to decision-theoretic claims. The result: if an action is permissible according to all functions in the set, it’s determinately permissible; if impermissible according to all, determinately impermissible; and – crucially – if permissible according to some, but not all, it’s indeterminate whether it’s permissible. This proposal handles with ease some difficult cases ) on which alternative decision theories falter. One reason this view has been overlooked in the literature thus far is that all parties to the debate presuppose that an acceptable decision theory must classify each action as either permissible or impermissible. But I will argue that this thought is misguided. Seeing the set of functions model as an instance of supervaluationism provides a compelling motivation for the claim that there can be indeterminacy in the rationality of some actions. (shrink)

This book breaks new ground in our understanding of how we perceive and represent the space around us - one of the central topics in cognitive psychology. It presents a new view of development and spatial cognition by reversing the usual focus on vision and examining the evidence on representation in the total absence of vision without specific brain damage. Findings from the author's work with congenitally totally blind and with sighted children, together with studies from a wide variety of (...) other areas, are set in the context of intersensory and spatial development. Touch and movement are considered as converging sources of reference information with and without vision. The findings have important implications for future work in many fields, particularly developmental pscychology; cognition, cognitive neuroscience and visual handicap, and make this new work essential reading for students and researchers in these fields. (shrink)

Objectives: This study was designed to explore the prevalence and types of stipulations required of investigators by the institutional review board of one institution over a five year period.Design: Stipulations to research proposals were documented from the minutes of the IRB meetings.Setting: Community hospital.Participants: IRB submissions.Main measurements: Number and type of IRB stipulations.Results: Nineteen research submissions were approved without any stipulations. For the remainder, the majority of stipulations related to consent forms .Conclusions: Consent forms appear to be at highest risk (...) for IRB stipulations. Being aware of high risk areas before submission of research proposals may reduce the frequency of stipulations required of investigators. (shrink)

In response to Mnesilochus′ disparaging comments regarding Agathon's unusual dress, the tragic poet replies:.

Notes on the text and interpretation of passages in Plutarch's Life of Alexander.

It seems obvious that Nietzsche has influenced the Dialectic of Enlightenment (1947). The extent to which Adorno and Horkheimer base their argument on Nietzsche, however, remains controversial. By analyzing an early draft of the first excursion of the Dialectic of Enlightenment from 1943, this article demonstrates that Nietzsche was more important for the development of its main concepts than has been assumed, in particular his analysis of myth and enlightenment. In the earlier version of the Ulysses-chapter Nietzsche, together with Rudolf (...) Borchardt, is a pivotal point of reference. Indeed, it is the Nietzschean reflection on Homer and on the pre-Homerian epic—and Borchardt’s interpretation of these themes—that Adorno views as the first original form of the dialectics of enlightenment. (shrink)

In discussions of perception and its relation to knowledge, it is common to distinguish what one comes to believe on the basis of perception from the distinctively perceptual basis of one's belief. The distinction can be drawn in terms of propositional contents: there are the contents that a perceiver comes to believe on the basis of her perception, on the one hand; and there are the contents properly attributed to perception itself, on the other. Consider the content.

In this paper, I argue that certain perceptual relations are represented in visual experience.

Increasing public knowledge of science is a widely recognized goal, but what that knowledge might consist of is rarely unpacked. Existing measures of science literacy tend to focus on textbook knowledge of science. Yet constructing a meaningful list of facts, even facts in application, is not only difficult but less than satisfying as an indicator of what people actually know—or need to know—as citizens. Revisiting this concept from a more sociological perspective yields a rather different concept that is here termed (...) “critical science literacy.” The implications of this reconsideration for thinking about citizen perspectives, for the work of science journalists and other professional interpreters, and for the design and evaluation of new approaches to science communication are explored. (shrink)

Reply to John Campbell's contribution to a symposium on *The Contents of Visual Experience*.

In this paper I argue that it's possible that the contents of some visual experiences are influenced by the subject's prior beliefs, hopes, suspicions, desires, fears or other mental states, and that this possibility places constraints on the theory of perceptual justification that 'dogmatism' or 'phenomenal conservativism' cannot respect.

The first full philological edition in English of the Roman philosopher Seneca's De Clementia. It includes the Latin text with apparatus criticus, a new English translation, a substantial introduction, and a commentary on matters of textual and literary criticism and issues of socio-political, historical, cultural, and philosophical significance.

Noting the pervasiveness of the adoption of "responsibility" as a core ideal of neoliberal governance, the contributors to Competing Responsibilities challenge contemporary understandings and critiques of that concept in political, social, and ethical life. They reveal that neoliberalism's reification of the responsible subject masks the myriad forms of individual and collective responsibility that people engage with in their everyday lives, from accountability, self-sufficiency, and prudence to care, obligation, and culpability. The essays—which combine social theory with ethnographic research from Europe, North (...) America, Africa, and New Zealand—address a wide range of topics, including critiques of corporate social responsibility practices; the relationships between public and private responsibilities in the context of state violence; the tension between calls on individuals and imperatives to groups to prevent the transmission of HIV; audit culture; and how health is cast as a citizenship issue. Competing Responsibilities allows for the examination of modes of responsibility that extend, challenge, or coexist with the neoliberal focus on the individual cultivation of the self. Contributors Barry D. Adam, Elizabeth Anne Davis, Filippa Lentzos, Jessica Robbins-Ruszkowski, Nikolas Rose, Rosalind Shaw, Cris Shore, Jessica M. Smith, Susanna Trnka, Catherine Trundle, Jarrett Zigon. (shrink)

Recently, the thesis that experience is fundamentally a matter of representing the world as being a certain way has been questioned by austere relationalists. I defend this thesis by developing a view of perceptual content that avoids their objections. I will argue that on a relational understanding of perceptual content, the fundamental insights of austere relationalism do not compete with perceptual experience being representational. As it will show that most objections to the thesis that experience has content apply only to (...) accounts of perceptual content on which perceptual relations to the world play no explanatory role. With austere relationalists, I will argue that perceptual experience is fundamentally relational. But against austere relationalists, I will argue that it is fundamentally both relational and representational. (shrink)

The introduction of social distancing, as part of efforts to try and curb the spread of the COVID-19 pandemic, has brought about drastic disruption to the world of the performing arts. In the UK the majority of professional orchestral musicians are freelance and therefore self-employed. These players, previously engaged in enjoyable, busy, successful, portfolio careers, are currently unable to earn a living carrying out their everyday work of performing music, and their future working lives are surrounded by great uncertainty. The (...) aim of the present study was to examine how established professional musicians are experiencing this period, and to look for similarities and differences between the experiences of musicians in the middle of their performing careers, with those of older players. Single semi-structured interviews were carried out over Zoom with 24 freelance, self-employed orchestral musicians; 12 mid-career musicians aged 35–45, and 12 seasoned musicians aged 53 and over. Thematic analysis identified themes common to both groups: the loss of a much-loved performing career, missing music making and colleagues, and anxiety about the future of the music profession. It also identified differences between the two groups: challenges to their identity as a musician, the extent of their anxiety about finances, the extent of their emotional distress, attitudes toward practicing and engaging in collaborative music making, and confusion over future career plans. Findings are discussed with reference to lifespan models of musicians' career development, the PERMA model of wellbeing, and the concept of resilience. (shrink)

In recent years, digital tools, such as WhatsApp, have been increasingly deployed to support group interaction and collaboration in higher education contexts. To understand contemporary, digitally-mediated collaborative dynamics – including the role played by tutors and the situated nature of group development – robust and innovative methodologies are needed. In this paper, we illustrate how integrating qualitative methods with quantitative tools used in qualitative ways makes it possible to trace how tutors adapt their style to support group development, which in (...) turn triggers student development in a circular and responsive process. To make visible this contemporary phenomenon, we combine thematic content analysis – a qualitative tool – with a quantitative method: Social Network Analysis. Drawing on data generated by two WhatsApp learning groups in research exploring the collaborative construction of boundary objects in a master’s level “E-learning Psychology” course, we suggest that our methodological approach has the potential to support interrogation of complex and dynamic digitally-mediated group interactions. Our results show the situational nature of an effective tutorship style through its complex adaptation to learners’ maturity, digital tools, and learning goals. (shrink)

L’enjeu de ce recueil est de contribuer à repenser la notion de limite, en l’envisageant sous les différentes figures, philosophiques, écologiques, politiques, que lui confère notre présent. Comme le montrent, sous des modalités diverses, les contributions de ce collectif, la limite peut et doit être conçue en dehors des valeurs négatives – borne, restriction ou frontière –, qui en affaiblissent la portée. Elle peut alors être pensée sur le fond de cet illimité où s’ouvre la question même du dehors. Si (...) la finitude demeure la condition de l’existence, de l’art et de la pensée, assumer notre condition finie ne consiste donc pas à se murer dans le connu, mais bien à en transgresser les bornes, et ce faisant, à s’illimiter. Au plus loin de la fermeture des frontières que prônent certaines politiques, ou de la certitude dogmatique dans laquelle certains cherchent à réassurer leur pensée, la limite ne vit que de son rapport fécond à l’illimité. Interrogeant l’existence, la politique, l’art – autant dire, la pensée même –, les textes de ce recueil mettent au jour un certain don de l’illimité. (shrink)

Peirce considera a matemática uma ciência informativa realmente capaz de aumentar nosso conhecimento. Isso significa que a matemática não é limitada à análise conceitual, mas possui um objeto real de investigação. O coração da visão peirciana da matemática é que o raciocínio matemático não é desenvolvido somente por meio de conceitos gerais, mas lida com um inevitável elemento de individualidade. A conclusão de uma inferência indutiva pode conter informação que não está absolutamente presente nas suas premissas, podendo vir a ser (...) somente por meio de trabalho concreto por parte do matemático. Peirce descreve esse trabalho como observação e experimentação sobre diagramas individuais. Enquanto a idéia de um elemento individual na matemática já está presente em Kant (e pode também ser traçada até Aristóteles), a sua base está na diferença entre Kant e Peirce acerca da análise categorial. A abordagem semiótica peirciana da matemática implica uma mudança, do plano do objeto denotado para o do próprio signo. Isso vale tanto para as inferências geométricas como para as inferências algébricas, que Peirce pode igualar nesse aspecto. Em ambos os casos, o elemento individual da matemática deve ser encontrado dentro do próprio diagrama, sem referência ao objeto denotado. Enquanto o diagrama é em todo caso um token, isso não pode explicar sua individualidade essencial, para cujo fim a justaposição indicial de suas partes deve ser examinada. (shrink)

This interdisciplinary essay looks at the use of popular history for the critical understanding of the reconstruction of crime and patriarchal hierarchy. By way of reviewing the recent movie The Limehouse Golem, it illustrates the significance of theoretically engaging with a period crime fiction movie. It is argued that this assessment is less relevant in terms of producing historical understanding. Rather historical fiction reveals instead our own contemporary cultural fixations.

This is a review of the book Archiving Sovereignty by Stewart Motha. Typical of critical legal writing, the monograph challenges our conditioned perception about the sovereign State. As such, it provides us with access to an archive of sovereign violence created by the law. It is argued that judicial decisions sustain and recreate sovereign power by way of destruction of facts. The focus here is on states with imperial histories, taking as case studies several islands in the Indian ocean region.

I offer an explanation of how subjects are able to perceive the intrinsic spatial properties of objects, given that subjects always perceive from a particular location. The argument proceeds in two steps. First, I argue that a conception of space is necessary to perceive the intrinsic spatial properties of objects. This conception of space is spelled out by showing that perceiving intrinsic properties requires perceiving objects as the kind of things that are perceivable from other locations. Second, I show that (...) having such a conception of space presupposes that a subject represent her location in relation to perceived objects. More precisely the thesis is that a subject represents her location as the location from which she both perceives objects and would act in relation to objects were she to act. So I argue that perception depends on the capacity to know what it would be to act in relation to objects. (shrink)

In this paper I argue that causal relations between objects are represented in visual experience, and contrast my argument and its conclusion with Michotte's results from the 1960's.