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)

This article attempts to answer a question that many dancers and non-dancers may have. What is dance according to the media? Furthermore, how does the written word portray dance in the media? To answer these ques-tions, this research focuses on the role that the discourse of dance in media plays in the public sphere’s knowledge construction of dance. This is impor-tant to study because the public sphere’s meaning of dance will determine whether dance education is promoted or banned in schools (...) and in society. The aim of this paper is to contribute to the existing literature of dance in the media. One limitation of this contribution is that the research uses only newspaper articles as a source of analysis. Future research should include an analysis of visual and audio clips of dance as portrayed in the media. (shrink)

Without extensive argument or elaboration of implications, the author presents Smith's views on ethical matters peculiarly important to our own era. Having previously assumed that Smith's statement alone is sufficient, the author permits him to speak extensively.--C. E. B.

Without extensive argument or elaboration of implications, the author presents Smith's views on ethical matters peculiarly important to our own era. Having previously assumed that Smith's statement alone is sufficient, the author permits him to speak extensively.--C. E. B.

Between 1905 and 1913, French physicist Jean Perrin's experiments on Brownian motion ostensibly put a definitive end to the long debate regarding the real existence of molecules, proving the atomic theory of matter. While Perrin's results had a significant impact at the time, later examination of his experiments questioned whether he really gained experimental access to the molecular realm. The experiments were successful in determining the mean kinetic energy of the granules of Brownian motion; however, the values for molecular magnitudes (...) Perrin inferred from them simply presupposed that the granule mean kinetic energy was the same as the mean molecular kinetic energy in the fluid in which the granules move. This stipulation became increasingly questionable in the years between 1908 and 1913, as significantly lower values for these magnitudes were obtained from other experimental results like alpha-particle emissions, ionization, and Planck's blackbody radiation equation. In this case study in the history and philosophy of science, George E. Smith and Raghav Seth here argue that despite doubts, Perrin's measurements were nevertheless exemplars of theory-mediated measurement-the practice of obtaining values for an inaccessible quantity by inferring them from an accessible proxy via theoretical relationships between them. They argue that it was actually Perrin more than any of his contemporaries who championed this approach during the years in question. The practice of theory-mediated measurement in physics had a long history before 1900, but the concerted efforts of Perrin, Rutherford, Millikan, Planck, and their colleagues led to the central role this form of evidence has had in microphysical research ever since. Seth and Smith's study thus replaces an untenable legend with an account that is not only tenable, but more instructive about what the evidence did and did not show. (shrink)

This paper presents a version of neurophenomenology based on generative modelling techniques developed in computational neuroscience and biology. Our approach can be described as _computational phenomenology_ because it applies methods originally developed in computational modelling to provide a formal model of the descriptions of lived experience in the phenomenological tradition of philosophy (e.g., the work of Edmund Husserl, Maurice Merleau-Ponty, etc.). The first section presents a brief review of the overall project to naturalize phenomenology. The second section presents and evaluates (...) philosophical objections to that project and situates our version of computational phenomenology with respect to these projects. The third section reviews the generative modelling framework. The final section presents our approach in detail. We conclude by discussing how our approach differs from previous attempts to use generative modelling to help understand consciousness. In summary, we describe a version of computational phenomenology which uses generative modelling to construct a computational model of the inferential or interpretive processes that best explain this or that kind of lived experience. (shrink)

Precision targeting of specific white matter bundles that traverse the subcallosal cingulate has been linked to efficacy of deep brain stimulation for treatment resistant depression. Methods to confirm optimal target engagement in this heterogenous region are now critical to establish an objective treatment protocol. As yet unexamined are the time-frequency features of the SCC evoked potential, including spectral power and phase-clustering. We examined these spectral features—evoked power and phase clustering—in a sample of TRD patients with implanted SCC stimulators. Electroencephalogram was (...) recorded during wakeful rest. Location of electrical stimulation in the SCC target region was the experimental manipulation. EEG was analyzed at the surface level with an average reference for a cluster of frontal sensors and at a time window identified by prior study. Morlet wavelets generated indices of evoked power and inter-trial phase clustering. Enhanced phase clustering at theta frequency was observed in every subject and was significantly correlated with SCC-EP magnitude, but only during left SCC stimulation. Stimulation to dorsal SCC evinced stronger phase clustering than ventral SCC. There was a weak correlation between phase clustering and white matter density. An increase in evoked delta power was also coincident with SCC-EP, but was less consistent across participants. DBS evoked time-frequency features index mm-scale changes to the location of stimulation in the SCC target region and correlate with structural characteristics implicated in treatment optimization. Results also imply a shared generative mechanism between evoked potentials evinced by electrical stimulation and evoked potentials evinced by auditory/visual stimuli and behavioral tasks. Understanding how current injection impacts downstream cortical activity is essential to building new technologies that adapt treatment parameters to individual differences in neurophysiology. (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.

Socrates is one of the most important yet enigmatic philosophers of all time; his fame has endured for centuries despite the fact that he never actually wrote anything. In 399 B.C.E., he was tried on the charge of impiety by the citizens of Athens, convicted by a jury, and sentenced to death (ordered to drink poison derived from hemlock). About these facts there is no disagreement. However, as the sources collected in this book and the scholarly essays that follow them (...) show, several of even the most basic facts about these events were controversial in antiquity, and the questions persist today: How and why was Socrates brought to trial? Why did the jurors, members of the world's first democracy, find him guilty? When he was given an opportunity to escape execution, why did he refuse to do so and instead accept the punishment that he and his friends agreed was unjustly assigned to him? How exactly did Socrates die? Differences of opinion on these and other issues continue to arouse our curiosity and to challenge new generations of students and scholars. The Trial and Execution of Socrates: Sources and Controversies is the first work to collect in one place all of the major ancient sources on Socrates' death--those of both his critics and his defenders--as well as recent scholarly views. Part I includes new translations of Plato's Euthyphro, Apology, Crito, and the death scene from Phaedo, as well as other ancient sources that shed light on Socrates' trial and execution. Part II features some of the most influential recent scholarship on this historically momentous event with work by M. F. Burnyeat, Robert Parker, Mark L. McPherran, Thomas C. Brickhouse and Nicholas D. Smith, Richard Kraut, Christopher Gill, and Enid Bloch (whose essay is published here for the first time). Ideal for undergraduate surveys of ancient Greek philosophy and upper-level courses on Socrates and Socratic philosophy, this unique collection provides an unprecedented look into the many perplexing questions surrounding the trial and execution of this remarkable man. (shrink)

Pancreatitis is a complex, progressively destructive inflammatory disorder. Alcohol was long thought to be the primary causative agent, but genetic contributions have been of interest since the discovery that rare PRSS1, CFTR and SPINK1 variants were associated with pancreatitis risk. We now report two associations at genome-wide significance identified and replicated at PRSS1-PRSS2 and X-linked CLDN2 through a two-stage genome-wide study. The PRSS1 variant likely affects disease susceptibility by altering expression of the primary trypsinogen gene. The CLDN2 risk allele is (...) associated with atypical localization of claudin-2 in pancreatic acinar cells. The homozygous CLDN2 genotype confers the greatest risk, and its alleles interact with alcohol consumption to amplify risk. These results could partially explain the high frequency of alcohol-related pancreatitis in men. © 2012 Nature America, Inc. All rights reserved. (shrink)

When the COVID-19 surge hit New York City hospitals, the Division of Medical Ethics at Weill Cornell Medical College, and our affiliated ethics consultation services, faced waves of ethical issues sweeping forward with intensity and urgency. In this article, we describe our experience over an eight-week period (16 March through 10 May 2020), and describe three types of services: clinical ethics consultation (CEC); service practice communications/interventions (SPCI); and organizational ethics advisement (OEA). We tell this narrative through the prism of time, (...) describing the evolution of ethical issues and trends as the pandemic unfolded. We delineate three phases: anticipation and preparation, crisis management, and reflection and adjustment. The first phase focused predominantly on ways to address impending resource shortages and to plan for remote ethics consultation, and CECs focused on code status discussions with surrogates. The second phase was characterized by the dramatic convergence of a rapid increase in the number of critically ill patients, a growing scarcity of resources, and the reassignment/ redeployment of staff outside their specialty areas. The third phase was characterized by the recognition that while the worst of the crisis was waning, its medium- and long-term consequences continued to pose immense challenges. We note that there were times during the crisis that serving in the role of clinical ethics consultant created a sense of dis-ease as novel as the coronavirus itself. In retrospect we learned that our activities far exceeded the familiar terrain of clinical ethics consultation and extended into other spheres of organizational life in novel ways that were unanticipated before this pandemic. To that end, we defined and categorized a middle level of ethics consultation, which we have termed service practice communication intervention (SPCI). This is an underappreciated dimension of the work that ethics consult services are capable of in times of crisis. We believe that the pandemic has revealed the many enduring ways that ethics consultation services can more robustly contribute to the ethical life of their institutions moving forward. (shrink)

The fusion of law and equity in common law systems was a crucial moment in the development of the modern law. In this volume leading scholars assess the significance of the fusion of law and equity from comparative, doctrinal, historical and theoretical perspectives.

Socrates is one of the most important yet enigmatic philosophers of all time; his fame has endured for centuries despite the fact that he never actually wrote anything. In 399 B.C.E., he was tried on the charge of impiety by the citizens of Athens, convicted by a jury, and sentenced to death. About these facts there is no disagreement. However, as the sources collected in this book and the scholarly essays that follow them show, several of even the most basic (...) facts about these events were controversial in antiquity, and the questions persist today: How and why was Socrates brought to trial? Why did the jurors, members of the world's first democracy, find him guilty? When he was given an opportunity to escape execution, why did he refuse to do so and instead accept the punishment that he and his friends agreed was unjustly assigned to him? How exactly did Socrates die? Differences of opinion on these and other issues continue to arouse our curiosity and to challenge new generations of students and scholars. The Trial and Execution of Socrates: Sources and Controversies is the first work to collect in one place all of the major ancient sources on Socrates' death--those of both his critics and his defenders--as well as recent scholarly views. Part I includes new translations of Plato's Euthyphro, Apology, Crito, and the death scene from Phaedo, as well as other ancient sources that shed light on Socrates' trial and execution. Part II features some of the most influential recent scholarship on this historically momentous event with work by M. F. Burnyeat, Robert Parker, Mark L. McPherran, Thomas C. Brickhouse and Nicholas D. Smith, Richard Kraut, Christopher Gill, and Enid Bloch. Ideal for undergraduate surveys of ancient Greek philosophy and upper-level courses on Socrates and Socratic philosophy, this unique collection provides an unprecedented look into the many perplexing questions surrounding the trial and execution of this remarkable man. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)