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)

The idea of arousal as a non-specific state of activation has been implicated as an explanatory factor for many aspects of human behavior, ranging from emotional experiences to learning and memory. Critiques of this concept have highlighted that arousal is ambiguous and evidence for its role in emotion is mixed. However, contemporary emotion theories and empirical research continue to incorporate the concept of arousal in ways that fail to address its problems. Here, we review the origins of the term arousal (...) in physiology and trace how it has been translated and applied to psychology (particularly as it relates to emotion). We consider whether the construct of arousal is currently (a) consistent and (b) useful in understanding human behavior. (shrink)

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)

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.

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 review of Elizabeth Anderson’s Hijacked: How Neoliberalism Turned the Work Ethic against Workers and How Workers Can Take It Back (Cambridge University Press, 2023), sets out Anderson’s main claim, that the original Protestant work ethic split into two different work ethics, the conservative (anti-worker) and the progressive (pro-worker) work ethics, and that the conservative work ethic “hijacked” the work ethic, turning it into a tool for the rich to dominate and harm workers and the poor. Conservative thinkers have, Anderson (...) argues, managed to discredit, erase, or deceptively coöpt proponents of the progressive work ethic; her book accordingly aims to re-introduce readers to the suppressed, centuries-long progressive work ethic tradition, and to offer it as a tool for critiquing and counteracting the most recent incarnation of the conservative work ethic, neoliberalism. In the course of doing so, Anderson also re-categorizes a number of supposed heroes of the conservative work ethic, such as John Locke and Adam Smith, as in fact proponents of the progressive work ethic. The review gives attention to each chapter of Anderson’s book. (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)

Despite concerns of consumer protection andenvironmental groups that the use of geneticallyproduced growth hormone in milk-producing cows mayadversely impact the safety of the milk supply,scientific evidence and governmental findings from theUSA appear to indicate that milk fromtreated cows is identical in quality, taste, andnutritional value to milk from untreated cows. Limitedexperience to date in the USA demonstrateslittle consumer resistance to milk from cows that havereceived the growth hormone, which can lead to a 15%increase in milk production. In fact, if there (...) is noperceived differentiation between the two forms ofmilk, the issue offers little choice to consumers atlarge, and may result in economic benefit only toselected dairy farmers, as well as the producers ofthe genetically produced growth hormone. Thissituation in the USA may be an example ofdysfunctional technology transfer, with desirablebenefits to a few, and as yet unknown benefits to thesociety. The USA has taken a bold move inapproving the use of bovine growth hormone in milk-producing cows, while the European Union has takena divergent approach by enacting lengthy moratoriumsagainst its use. The basic lesson to be learned fromthe bST case is that lack of awareness amonggovernment officials and the public at large serves asa significant impediment to the adoption of newtechnologies. Accordingly, delays may occur indelivery of significant social benefits to thepopulation as a whole. Obviously, the issue extendsbeyond bST. (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.

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.

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)

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)

Understanding how people comprehend visual narratives (including picture stories, comics, and film) requires the combination of traditionally separate theories that span the initial sensory and perceptual processing of complex visual scenes, the perception of events over time, and comprehension of narratives. Existing piecemeal approaches fail to capture the interplay between these levels of processing. Here, we propose the Scene Perception & Event Comprehension Theory (SPECT), as applied to visual narratives, which distinguishes between front-end and back-end cognitive processes. Front-end processes occur (...) during single eye fixations and are comprised of attentional selection and information extraction. Back-end processes occur across multiple fixations and support the construction of event models, which reflect understanding of what is happening now in a narrative (stored in working memory) and over the course of the entire narrative (stored in long-term episodic memory). We describe relationships between front- and back-end processes, and medium-specific differences that likely produce variation in front-end and back-end processes across media (e.g., picture stories vs. film). We describe several novel research questions derived from SPECT that we have explored. By addressing these questions, we provide greater insight into how attention, information extraction, and event model processes are dynamically coordinated to perceive and understand complex naturalistic visual events in narratives and the real world. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Modern Biblical Criticism as a Tool of Statecraft (1700–1900) by Scott W. Hahn and Jeffrey L. MorrowSteven C. SmithModern Biblical Criticism as a Tool of Statecraft (1700–1900) by Scott W. Hahn and Jeffrey L. Morrow (Steubenville, OH: Emmaus Academic, 2020), 312 pp.Almost anyone who has suffered through a course in biblical studies at a secular (or, increasingly so, Christian) university, read a book, or heard a lecture from (...) one of its scholarly progenies is acquainted with the litany of hermeneutical absolutes. Among the factum historicum are the following certainties: the Enlightenment rescued the Bible from the Dark Ages; the Old Testament was shaped out of the mythical clay of Hellenism; Israel's priesthood was a lamentable development that hijacked an earlier, socially oriented love-of-neighbor religion, replacing it with its bloodthirsty, sacrificial cult; the Documentary Hypothesis is not merely a theory, but the scientific truth of how the Pentateuch emerged; one must separate the Jesus of history from the Christ of faith; Peter and Paul clashed over their dueling Christianities; and above all, historical criticism is the only reliable lens by which the Bible is to be studied.In Modern Biblical Criticism as a Tool of Statecraft (1700–1900), Hahn and Morrow expose such positivisms as the outflow of Europe's secularized universities over these centuries. Not only did politically motivated institutions seek to diminish the theological truths of Scripture (and sadly, were often successful at it), but they eventually repurposed the Bible as "a work of historical fiction," such that the Sacred Page was "to be studied like other ancient myths and fairy tales; it is one fairy tale among many" (24). The authors present a thoroughly researched and meticulously detailed study of the period, and throughout the book amply demonstrate that the aforementioned tropes (and numerous others), no matter how often or how confidently recited, are merely one slant on "the story of biblical criticism" in the modern age.Taking their lead from the lead of Pope Benedict XVI, Hahn and Morrow provide a much-needed critique of historical biblical exegesis and its "appearance of quasi-scientific certainty."1 These salient words of the biblical-theologian Pope, articulated in a variety of contexts (e.g., Verbum Domini), provide the jumping-off point for this robust three-hundred-page voyage. And it is a journey through a divided and secularized Europe, with notable stops in England, France, and above all, Germany. This "divided" Europe, the authors explain, was not a result of the Protestant [End Page 985] Reformation, nor of the so-called "war of religions" that sprang from it—no. The divisions run much deeper still. Drawing upon Andrew Jones's important Before Church and State, Hahn and Morrow rightly lament the societal competition that developed within late medieval Christendom between church and state.2Building upon Jones's work, the authors rightly stress that there indeed existed "a unified medieval worldview wherein what we might think of as temporal authorities and spiritual authorities were united in a single purpose—the extension of the kingdom of God—and this was the background that unified Christendom" (3). As Jones point out, this earlier period of European history "was a world not of the religious and the secular, but of the New Testament and the Old, of virtue and vice, grace and law.... It was an integral vision which included all of societal reality."3 Sadly, the reality of "sacramental kingdoms," in which there lived a reciprocal respect and vision of unity between throne and alter, was torn asunder long before the 1700s, the time at which the present volume commences. Over time, this formerly unified European world gave way to the very complicated, deeply skeptical, and highly politicized world of nation-states. And biblical criticism (along with many other worthy and creative endeavors), became deeply mired in "statecraft."Here, it is worth mentioning that the book should be approached as the rightful heir to an earlier volume (which involved one of its authors, Hahn), Politicizing the Bible.4 While Modern Biblical Criticism may be intelligently read upon its own merits, the reader would do well to pick up the earlier... (shrink)