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)

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)

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)

Ethical or ‘socially sustainable’ sourcing mechanisms mandating labour standards among the suppliers and subcontractors that organisations source goods and services from are becoming more common. The issue of how labour activist groups such as trade unions can encourage organisations to adopt and strengthen these mechanisms within domestic production networks is largely unexplored. Using three cases of domestic sustainable sourcing campaigns developed by unions in Britain, the strategies used by labour activists, the characteristics of the organisations targeted and the motivations of (...) lead firms for improving sourcing practices are analysed. The article makes a significant contribution by demonstrating that organisational susceptibility to reputational risk is a key factor influencing the capacity of activist groups to convince and compel their targets to improve sourcing practices. It argues that different types of organisations are susceptible to reputational damage in different ways, that risk events provide opportunities for unions to strengthen their leverage against target organisations, and that the multidimensional nature of corporate reputation needs to be better considered for understanding how campaigns are framed and executed. (shrink)

Ethical guidance from the British Medical Association about treating doctor–patients is compared and contrasted with evidence from a qualitative study of general practitioners who have been patients. Semistructured interviews were conducted with 17 GPs who had experienced a significant illness. Their experiences were discussed and issues about both being and treating doctor–patients were revealed. Interpretative phenomenological analysis was used to evaluate the data. In this article data extracts are used to illustrate and discuss three key points that summarise the BMA (...) ethical guidance, in order to develop a picture of how far experiences map onto guidance. The data illustrate and extend the complexities of the issues outlined by the BMA document. In particular, differences between experienced GPs and those who have recently completed their training are identified. This analysis will be useful for medical professionals both when they themselves are unwell and when they treat doctor–patients. It will also inform recommendations for professionals who educate medical students or trainees. (shrink)

This book presents the foundations of a general theory of algebras. Often called “universal algebra”, this theory provides a common framework for all algebraic systems, including groups, rings, modules, fields, and lattices. Each chapter is replete with useful illustrations and exercises that solidify the reader's understanding. The book begins by developing the main concepts and working tools of algebras and lattices, and continues with examples of classical algebraic systems like groups, semigroups, monoids, and categories. The essence of the book lies (...) in Chapter 4, which provides not only basic concepts and results of general algebra, but also the perspectives and intuitions shared by practitioners of the field. The book finishes with a study of possible uniqueness of factorizations of an algebra into a direct product of directly indecomposable algebras. There is enough material in this text for a two semester course sequence, but a one semester course could also focus primarily on Chapter 4, with additional topics selected from throughout the text. (shrink)

Using Chicago as our case, this article puts forth a notion of black placemaking that privileges the creative, celebratory, playful, pleasurable, and poetic experiences of being black and being around other black people in the city. Black placemaking refers to the ways that urban black Americans create sites of endurance, belonging, and resistance through social interaction. Our framework offers a corrective to existing accounts that depict urban blacks as bounded, plagued by violence, victims and perpetrators, unproductive, and isolated from one (...) another and the city writ large. While ignoring neither the external assaults on black spaces nor the internal dangers that can make everyday life difficult, we highlight how black people make places in spite of those realities. Our four cases – the black digital commons, black public housing reunions, black lesbian and gay nightlife, and black Little League baseball – elucidate the matter of black lives across genders, sexualities, ages, classes, and politics. (shrink)

Transgender and gender expansive (TGE) youth often seek a variety of gender-affirming healthcare services, including pubertal suppression and hormone therapy requiring that TGE youth and their parents participate in informed consent and decision making. While youth must demonstrate the ability to understand and appreciate treatment options, risks, benefits, and alternatives as well as make and express a treatment choice, standardized approaches to assess the capacity of TGE youth to consent or assent in clinical practice are not routinely used. This scoping (...) review identified the currently available data regarding adolescent capacity to consent to gender-affirming medical treatments. Articles relevant to assessing adolescent capacity for clinical decision-making were identified using OVID Medline, Web of Science, and PubMed. Articles were reviewed and thematically analyzed. Eight relevant articles were identified using three tools for measuring adolescent clinical decision-making capacity: Measure of Understanding, Measure of Competence, and MacArthur Competence Assessment Tool (MacCAT). These studies explored hypothetical treatment decisions, mental health treatment decisions, HIV treatment decisions, genetic testing decisions, and gender-affirming medical decisions. Only one study specifically examines the capacity of TGE youth to consent to medical treatments. Age was correlated with capacity in most, but not all studies. Other studies found cognitive measures (IQ, literacy, numeracy) may impact important aspects of capacity (understanding and reasoning). For clinicians caring for TGE youth, tools such as the MacArthur Competence Assessment Tool for Treatment (MacCAT-T) may prove useful, in conjunction with consideration of youth developmental abilities and utilization of shared decision-making practices. A standardized, collaborative approach to assessing TGE youth capacity would benefit TGE youth and their parents, and allow clinicians to more easily resolve ethical concerns. (shrink)

Although the Ca2+‐dependent proteinase (calpain) system has been found in every vertebrate cell that has been examined for its presence and has been detected in Drosophila and parasites, the physiological function(s) of this system remains unclear. Calpain activity has been associated with cleavages that alter regulation of various enzyme activities, with remodeling or disassembly of the cell cytoskeleton, and with cleavages of hormone receptors. The mechanism regulating activity of the calpain system in vivo also is unknown. It has been proposed (...) that binding of the calpains to phospholipid in a cell membrane lowers the Ca2+ concentration, [Ca2+], required for the calpains to autolyze, and that autolysis converts an inactive proenzyme into an active protease. Recent studies, however, show that the calpains bind to specific proteins and not to phospholipids, and that binding to cell membranes does not affect the [Ca2+] required for autolysis. It seems likely that calpain activity is regulated by binding of Ca2+ to specific sites on the calpain molecule, with binding to each site eliciting a response (proteolytic activity, calpastatin binding, etc.) specific for that site. Regulation must also involve an, as yet, undiscovered mechanism that increases the affinity of the Ca2+‐binding sites for Ca2+. (shrink)

Collaboration on the First Edition of Spacetime Physics began in the mid-1960s when Edwin Taylor took a junior faculty sabbatical at Princeton University where John Wheeler was a professor. The resulting text emphasized the unity of spacetime and those quantities (such as proper time, proper distance, mass) that are invariant, the same for all observers, rather than those quantities (such as space and time separations) that are relative, different for different observers. The book has become a standard introduction to (...) relativity. The Second Edition of Spacetime Physics embodies what the authors have learned during an additional quarter century of teaching and research. They have updated the text to reflect the immense strides in physics during the same period and modernized and increased the number of exercises, for which the First Edition was famous. Enrichment boxes provide expanded coverage of intriguing topics. An enlarged final chapter on general relativity includes new material on gravity waves, black holes, and cosmology. The Second Edition of Spacetime Physics provides a new generation of readers with a deep and simple overview of the principles of relativity. (shrink)

The past 50 years have seen an accumulation of evidence suggesting that associative learning depends on high-level cognitive processes that give rise to propositional knowledge. Yet, many learning theorists maintain a belief in a learning mechanism in which links between mental representations are formed automatically. We characterize and highlight the differences between the propositional and link approaches, and review the relevant empirical evidence. We conclude that learning is the consequence of propositional reasoning processes that cooperate with the unconscious processes involved (...) in memory retrieval and perception. We argue that this new conceptual framework allows many of the important recent advances in associative learning research to be retained, but recast in a model that provides a firmer foundation for both immediate application and future research. (shrink)

Dr Taylor's book analyses the disease concept as it developed in medical history and seeks to clarify it with the help of concepts largely derived from logical class theories. A solution is proposed to the problem of how to distinguish between the class of 'patients' and the class of 'healthy persons' which corresponds to the actual diagnostic practices of doctors. The earliest theories of disease postulated concrete entities which exist independently of the body. The notion of disease entity has (...) lost its original ontological connotations and instead its important feature has become the possession of a unitary and self-contained character. Dr Taylor describes the modern theories as essentially 'reactive' in character, that is the symptoms of a disease are the bodily reactions to the 'noxae'. After seeing the subject in its historical content, Dr Taylor goes on to discuss in detail the notion of the classification of diseases, making extensive use of modern views on the logic of classes. (shrink)

BackgroundInaccurate, false or incomplete research publications may mislead readers including researchers and decision-makers. It is therefore important that such problems are identified and rectified promptly. This usually involves collaboration between the research institutions and academic journals involved, but these interactions can be problematic.MethodsThese recommendations were developed following discussions at World Conferences on Research Integrity in 2013 and 2017, and at a specially convened 3-day workshop in 2016 involving participants from 7 countries with expertise in publication ethics and research integrity. The (...) recommendations aim to address issues surrounding cooperation and liaison between institutions and journals about possible and actual problems with the integrity of reported research arising before and after publication.ResultsThe main recommendations are that research institutions should: develop mechanisms for assessing the integrity of reported research that are distinct from processes to determine whether individual researchers have committed misconduct;release relevant sections of reports of research integrity or misconduct investigations to all journals that have published research that was investigated;take responsibility for research performed under their auspices regardless of whether the researcher still works at that institution or how long ago the work was done;work with funders to ensure essential research data is retained for at least 10 years.Journals should: respond to institutions about research integrity cases in a timely manner;have criteria for determining whether, and what type of, information and evidence relating to the integrity of research reports should be passed on to institutions;pass on research integrity concerns to institutions, regardless of whether they intend to accept the work for publication;retain peer review records for at least 10 years to enable the investigation of peer review manipulation or other inappropriate behaviour by authors or reviewers.ConclusionsVarious difficulties can prevent effective cooperation between academic journals and research institutions about research integrity concerns and hinder the correction of the research record if problems are discovered. While the issues and their solutions may vary across different settings, we encourage research institutions, journals and funders to consider how they might improve future collaboration and cooperation on research integrity cases. (shrink)

Gilead et al. propose an ontology of abstract representations based on folk-psychological conceptions of cognitive architecture. There is, however, no evidence that the experience of cognition reveals the architecture of cognition. Scale-free architectural models propose that cognition has the same computational architecture from sub-cellular to whole-organism scales. This scale-free architecture supports representations with diverse functions and levels of abstraction.

Binz et al. propose a general framework for meta-learning and contrast it with built-by-hand Bayesian models. We comment on some architectural assumptions of the approach, its relation to the active inference framework, its potential applicability to living systems in general, and the advantages of the latter in addressing the explanation problem.

In this response, we provide further clarification of the propositional approach to human associative learning. We explain why the empirical evidence favors the propositional approach over a dual-system approach and how the propositional approach is compatible with evolution and neuroscience. Finally, we point out aspects of the propositional approach that need further development and challenge proponents of dual-system models to specify the systems more clearly so that these models can be tested.

The functions of the somatosensory system are multiple. We use tactile input to localize and experience the various qualities of touch, and proprioceptive information to determine the position of different parts of the body with respect to each other, which provides fundamental information for action. Further, tactile exploration of the characteristics of external objects can result in conscious perceptual experience and stimulus or object recognition. Neuroanatomical studies suggest parallel processing as well as serial processing within the cerebral somatosensory system that (...) reflect these separate functions, with one processing stream terminating in the posterior parietal cortex (PPC), and the other terminating in the insula. We suggest that, analogously to the organisation of the visual system, somatosensory processing for the guidance of action can be dissociated from the processing that leads to perception and memory. In addition, we find a second division between tactile information processing about external targets in service of object recognition and tactile information processing related to the body itself. We suggest the posterior parietal cortex subserves both perception and action, whereas the insula principally subserves perceptual recognition and learning. (shrink)

The hanging of the mobile aloft was annually performed with a solemnity and care suited to so important a matter. For each year, as it was resurrected from its storage place, it hung foolishly askew, demoralized by vicissitude, like a drunkard's hat crushed out of shape. Not that it had not still an equilibrium, a static balance, which it would assume and, if disturbed, would assume again, as if to declare idiocy alone immortal. It did not wait, in order to (...) have an equilibrium, for an artful hand to give it one. Such equilibrium as it had, from the accidental concert of its parts, it had with the indifferent equanimity of all things merely physical. Beauty was its accident, as idiocy also was its accident. It was as innocent of virtue as it was innocent of sin: it knew no propriety, therefore deserted none. I admired in it only what I demanded of it, a virtue of which it knew nothing. Yet, for my part, I permitted myself no such egotist reflection. I regarded it all as the contrivance of the hand which adjusted it. In my child's world, that was the secret of my mother's hand, which no other sought to compete with, much less to penetrate. She knew, at least her hand knew, that of all of the possible equilibria which were available equally for choice, there was one special equilibrium needed, only one which was alive, resonant, essential to the production of that effect to which it intricately ministered. That equilibrium was indispensable to the music which the mobile gave forth, its beginning and its end, the poise from which its movement issued, the cadence in which it came with perfect finality to rest. (shrink)

Historically Wales has been regarded as a country with relatively low levels of school exclusion, particularly in comparison with England. This has been used as an indicator of Wales’ commitment to the UN Convention on the Rights of the Child, which foregrounds a rights-based agenda that would argue school exclusion is a consequence of broader socio-economic structures than individual actions. However, simple analyses may mask a different picture of school exclusions in Wales. In this article, we study more detailed information (...) on formal school exclusions by looking at ‘instances’ of school exclusion, which considers the frequency and length of formal school exclusions in Wales, and alongside recorded school absence. The article also demonstrates that the pupils ‘at risk’ of formal school exclusion varies by when they experience school exclusion during their educational lifecourse. The article concludes by highlighting that patterns of school exclusion are complex, and that interpretation of these patterns depends on what kind of measure of school exclusion is used. By publishing these results, the article hopes to persuade policymakers and practitioners to re-examine their processes of exclusion to ensure they are commensurate with the law and to prevent unnecessary school exclusions. (shrink)