Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Abstractabstract:Vaccine hesitancy continues to pose a formidable obstacle to increasing national COVID-19 vaccination rates in the US, but this is not the first time that American vaccination efforts have confronted resistance and apathy. This study examines the history of US vaccination efforts against smallpox, polio, and measles, highlighting persistent drivers of vaccine hesitancy as well as factors that helped overcome it. The research reveals that logistical barriers, negative portrayals in the media, and fears about safety stymied inoculation efforts as early (...) as the 18th century and continue to do so. However, vaccine hesitancy has been markedly diminished when trusted community leaders have guided efforts, when ordinary citizens have felt personally invested in the success of the vaccine, and when vaccination efforts have been tied to broader projects to improve public health and social cohesion. Deliberately cultivating such factors could be an effective strategy for lessening opposition today, when COVID-19's distinctive characteristics make addressing vaccine hesitancy more urgent than it has ever been. (shrink)

ABSTRACT Real-time graphical interval logic is a modal logic for reasoning about time in which the basic modality is the interval. The logic differs from other logics in that it has a natural intuitive graphical representation that resembles the timing diagrams drawn by system designers. We have developed an automted deduction system for the logic, which includes a theorem prover and a user interface. The theorem prover checks the validity of proofs in the logic and produces counterexamples to invalid proofs. (...) The user interface includes a graphical editor that enables the user to create graphical formulas on a workstation display, and a database and proof manager that tracks proof dependencies and allows graphical formulas to be stored and retrieved. In this paper we describe the logic, the automated deduction system, and an application to robotics. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

_From Knowledge to Beatitude _is a collection of original essays on the intersection between Christian theology and spiritual life primarily in the twelfth and thirteenth centuries, especially in the Parisian School of St. Victor, which honors the influential work of Grover A. Zinn, Jr. Written by distinguished scholars from various fields of medieval studies, these essays range from the study of the exegetical school of twelfth-century St. Victor and medieval glossed Bibles to the medieval cultural reception of women visionaries, preachers, (...) and crusaders. Although focused on St. Victor, they provide analyses of Christian themes up to the modern period. A common thread is Zinn’s careful attention to the connections between medieval spirituality and biblical studies, the origin of these ideas, and their lasting influence in Christian culture. The essays take us from Hugh of St. Victor’s foundation—material culture—to the “beatitude” of a wider understanding of Victorine culture and its lasting legacy. This volume is a fitting tribute to a generous scholar, teacher, and mentor. It will appeal to historians, scholars of religion and theology, and art historians. "_From Knowledge to Beatitude_ serves a need and fills an important gap in the Victorine tradition, the history of medieval exegesis, and medieval studies. The volume also honors the contributions of Grover Zinn, an important medieval scholar and teacher. It serves as a model for doing research and generalizing in the field of medieval studies and demonstrates how the last generation and the current generation of medieval scholars have plowed through difficult primary and secondary sources to make the medieval traditions clear." —_Philip Krey, Lutheran Theological Seminary at Philadelphia_. (shrink)

This volume collects contributions from leading scholars of early modern philosophy from a wide variety of philosophical and geographic backgrounds. The distinguished contributors offer very different, competing approaches to the history of philosophy.Many chapters articulate new, detailed methods of doing history of philosophy. These present conflicting visions of the history of philosophy as an autonomous sub-discipline of professional philosophy. Several other chapters offer new approaches to integrating history into one's philosophy by re-telling the history of recent philosophy. A number of (...) chapters explore the relationship between history of philosophy and history of science.Among the topics discussed and debated in the volume are: the status of the principle of charity; the nature of reading texts; the role of historiography within the history of philosophy; the nature of establishing proper context. (shrink)

The issue of the theory-ladenness of observation has long troubled philosophers of science, largely because it seems to threaten the objectivity of science. However, the way in which prior beliefs influence the perception of data is in part an empirical issue that can be investigated by cognitive psychology. This point is illustrated through an experimental analogue of scientific data-interpretation tasks in which subjects judging the covariation between personality variables based their judgments on pure data, their theoretical intuitions about the variables, (...) or both data and prior theoretical beliefs. Results showed that the perceived magnitude of correlations was greatest when subjects relied solely on theoretical intuitions; that data-based judgments were drawn in the direction of those prior beliefs; but that exposure to data nonetheless moderated the strength of the prior theories. In addition, prior beliefs were found to influence judgments only after a brief priming interval, suggesting that subjects needed time to retrieve their theoretical intuitions from memory. These results suggest ways to investigate the processes mediating theory-laden observation, and, contrary to the fears of positivist philosophers, imply that the theory-ladenness of observation does not entail that theoretical beliefs are immune to data. (shrink)

Background: The factors influencing parents’ willingness to enroll their children in biobanks are poorly understood. This study sought to assess parents’ willingness to enroll their children, and their perceived benefits, concerns, and information needs under different consent and data-sharing scenarios, and to identify factors associated with willingness. Methods: This large, experimental survey of patients at the 11 eMERGE Network sites used a disproportionate stratified sampling scheme to enrich the sample with historically underrepresented groups. Participants were randomized to receive one of (...) three consent and data-sharing scenarios. Results: In total, 90,000 surveys were mailed and 13,000 individuals responded (15.8% response rate). 5737 respondents were parents of minor children. Overall, 55% (95% confidence interval 50–59%) of parents were willing to enroll their youngest minor child in a hypothetical biobank; willingness did not differ between consent and data-sharing scenarios. Lower educational attainment, higher religiosity, lower trust, worries about privacy, and attitudes about benefits, concerns, and information needs were independently associated with less willingness to allow their child to participate. Of parents who were willing to participate themselves, 25% were not willing to allow their child to participate. Being willing to participate but not willing to allow one’s child to participate was independently associated with multiple factors, including race, lower educational attainment, lower annual household income, public health care insurance, and higher religiosity. Conclusions: Fifty-five percent of parents were willing to allow their youngest minor child to participate in a hypothetical biobank. Building trust, protecting privacy, and addressing attitudes may increase enrollment and diversity in pediatric biobanks. (shrink)

(No abstract is available for this citation).

What the nineteenth century knew of attamen or at tamen it did not learn from dictionaries. The two last revisions of Forcellini, Corradini's and De-Vit's, provided eight examples between them, of which three were false. Klotz added one, Georges two, Smith two: one of these five was false, and two more lie under much suspicion. Freund gave no instance whatsoever. In preparing his first volume, which appeared in 1834, he turned, like a good compiler, to the first volume of (...) Hand's Tursellinus, published in 1829. What he found there, on p. 450, was ‘de at tamen uide in tamen’; so he sat down quickly and wrote ‘attamen adv., s. tamen’. But Hand's Tursellinus, which never reached tamen, had proceeded no further than multum when Freund in 1840 produced the last volume of his dictionary; so he did not redeem his promise, and when you got there the cupboard was bare. This perfidy was faithfully imitated by the English and American dictionaries of Andrews, White and Riddle, Lewis and Short. To all intents and purposes one was left to depend on one's own reading and on the observations of Madvig at Cic. de fin. pp. 286 and 425 and opusc. I p. 491. (shrink)

Hastings Center Report, Volume 52, Issue S1, Page S3-S11, March‐April 2022.

This paper proposes a generalization of the Kripke semantics of intuitionistic logic IL appropriate for intuitionistic Łukasiewicz logic IŁL — a logic in the intersection between IL and (classical) Łukasiewicz logic. This generalised Kripke semantics is based on the poset sum construction, used in Bova and Montagna (Theoret Comput Sci 410(12):1143–1158, 2009) to show the decidability (and PSPACE completeness) of the quasiequational theory of commutative, integral and bounded GBL algebras. The main idea is that w \Vdash \sigma—which for IL is (...) a relation between worlds w and formulas \sigma, and can be seen as a function taking values in the booleans w \Vdash \sigma \in {B}—becomes a function taking values in the unit interval w \Vdash \sigma \in [0,1]. An appropriate monotonicity restriction (which we call sloping functions) needs to be put on such functions in order to ensure soundness and completeness of the semantics. (shrink)

A Fellow of the Royal Society rebuffs orthodox scientific conclusions.

BackgroundPeople with upper extremity amputations report receiving insufficient information about treatment options. Furthermore, patients commonly report not knowing what questions to ask providers. A question prompt sheet, or list of questions, can support patient-centered care by empowering patients to ask questions important to them, promoting patient-provider communication, and increasing patient knowledge. This study assessed information needs among people with UE amputations about UE vascularized composite allotransplantation and developed a UE VCA-QPS.MethodsThis multi-site, cross-sectional, mixed-methods study involved in-depth and semi-structured interviews with (...) people with UE amputations to assess information needs and develop a UE VCA-QPS. Qualitative data were analyzed by thematic analysis; quantitative data were analyzed by descriptive statistics. The initial UE VCA-QPS included 130 items across 18 topics.ResultsEighty-nine people with UE amputations participated. Most were male, had a mean age of 46 years, and had a unilateral and below-elbow amputation. Participants desired information about UE VCA eligibility, evaluation process, surgery, risks, rehabilitation, and functional outcomes. After refinement, the final UE VCA-QPS included 35 items, across 9 topics. All items were written at a ≤ 6th grade reading level. Most semi-structured interview participants reported being ‘completely’ or ‘very’ likely to use a UE VCA-QPS.ConclusionPeople with UE amputations have extensive information needs about UE VCA. The UE VCA-QPS aims to address patients’ information needs and foster patient-centered care. Future research should assess whether the UE VCA-QPS facilitates patient-provider discussion and informed decision-making for UE VCA. (shrink)

The concept of wilderness, as denned in the U.S.A. Wilderness Act of 1964, is analyzed and found to be ambiguous. This is an administrative advantage. The concept of underground wilderness is then introduced and found to be applicable under the terms of the Act. It is argued that the longest cave in the world, the Flint Ridge Cave System in Mammoth Cave National Park, Kentucky, can and should be officially declared as wilderness by Congress even though the surface above it (...) is now developed. (shrink)

There was a strong consensus in the commentaries that animals' performances in metacognition paradigms indicate high-level decisional processes that cannot be explained associatively. Our response summarizes this consensus and the support for the idea that these performances demonstrate animal metacognition. We amplify the idea that there is an adaptive advantage favoring animals who can – in an immediate moment of difficulty or uncertainty – construct a decisional assemblage that lets them find an appropriate behavioral solution. A working consciousness would serve (...) this function well. This explains why animals may have the functional equivalent of human declarative consciousness. However, like other commentators who were friendly to this equivalence, we approach carefully the stronger claims that animals' metacognitive performances imply full-blown self-awareness or phenomenal consciousness. We discuss the commentators' interesting ideas for future research, as well as their intriguing ideas about the evolution and development of metacognition and its relation to theory of mind. We also discuss residual confusions about existing research and remaining methodological issues. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls. Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents. Probands were more likely to carry an additional large copy-number variant when compared to matched controls. The clinical (...) features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease. © 2010 Nature America, Inc. All rights reserved. (shrink)