Physicists regularly invoke universal laws, such as those of motion and electromagnetism, to explain events. Biological and medical scientists have no such laws. How then do they acquire a reliable body of knowledge about biological organisms and human disease? One way is by repeatedly returning to, manipulating, observing, interpreting, and reinterpreting certain subjects—such as flies, mice, worms, or microbes—or, as they are known in biology, “model systems.” Across the natural and social sciences, other disciplinary fields have developed canonical examples that (...) have played a role comparable to that of biology’s model systems, serving not only as points of reference and illustrations of general principles or values but also as sites of continued investigation and reinterpretation. The essays in this collection assess the scope and function of model objects in domains as diverse as biology, geology, and history, attending to differences between fields as well as to epistemological commonalities. Contributors examine the role of the fruit fly Drosophila and nematode worms in biology, troops of baboons in primatology, box and digital simulations of the movement of the earth’s crust in geology, and meteorological models in climatology. They analyze the intensive study of the prisoner’s dilemma in game theory, ritual in anthropology, the individual case in psychoanalytic research, and Athenian democracy in political theory. The contributors illuminate the processes through which particular organisms, cases, materials, or narratives become foundational to their fields, and they examine how these foundational exemplars—from the fruit fly to Freud’s Dora—shape the knowledge produced within their disciplines. Contributors Rachel A. Ankeny Angela N. H. Creager Amy Dahan Dalmedico John Forrester Clifford Geertz Carlo Ginzburg E. Jane Albert Hubbard Elizabeth Lunbeck Mary S. Morgan Josiah Ober Naomi Oreskes Susan Sperling Marcel Weber M. Norton Wise. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

In their paper, “Conversational Artificial Intelligence in Psychotherapy: A New Therapeutic Tool or Agent?” Sedlakova and Trachsel (2023) claim that therapeutic insights and therapeutic changes are...

© 2015, Springer-Verlag Berlin Heidelberg.Genetic studies have identified single nucleotide polymorphisms associated with the risk of prostate cancer. It remains unclear whether such genetic variants are associated with disease aggressiveness. The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which at the time had been validated to be associated with PC risk from 25,674 cases with PC. Cases were grouped according to race, Gleason score and aggressiveness. Statistical analyses were used to compare the frequency (...) of the SNPs between different disease cohorts. After adjusting for multiple testing, only PC-risk SNP rs2735839 was significantly and inversely associated with aggressive and high-grade disease in European men. Similar associations with aggressive and high-grade disease were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels in both European and African-American men. Our results provide further support that a PC-risk SNP rs2735839 near the KLK3 gene on chromosome 19q13 may be associated with aggressive and high-grade PC. Future prospectively designed, case-case GWAS are needed to identify additional SNPs associated with PC aggressiveness. (shrink)

Rapid advancements in artificial intelligence and machine learning (AI/ML) in healthcare raise pressing questions about how much users should trust AI/ML systems, particularly for high stakes clinical decision-making. Ensuring that user trust is properly calibrated to a tool’s computational capacities and limitations has both practical and ethical implications, given that overtrust or undertrust can influence over-reliance or under-reliance on algorithmic tools, with significant implications for patient safety and health outcomes. It is, thus, important to better understand how variability in trust (...) criteria across stakeholders, settings, tools and use cases may influence approaches to using AI/ML tools in real settings. As part of a 5-year, multi-institutional Agency for Health Care Research and Quality-funded study, we identify trust criteria for a survival prediction algorithm intended to support clinical decision-making for left ventricular assist device therapy, using semistructured interviews (n=40) with patients and physicians, analysed via thematic analysis. Findings suggest that physicians and patients share similar empirical considerations for trust, which were primarilyepistemicin nature, focused on accuracy and validity of AI/ML estimates. Trust evaluations considered the nature, integrity and relevance of training data rather than the computational nature of algorithms themselves, suggesting a need to distinguish ‘source’ from ‘functional’ explainability. To a lesser extent, trust criteria were also relational (endorsement from others) and sometimes based on personal beliefs and experience. We discuss implications for promoting appropriate and responsible trust calibration for clinical decision-making use AI/ML. (shrink)

In “What are Humans Doing in the Loop?” Salloch and Eriksen (2024) argue for a collaborative decision-making approach to using machine learning-based AI decisional support systems in medicine, rece...

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

We report specific heat and μSR measurements on Th and/or B substituted UBe13. The specific heat data show that either Th or B substitution reduces the Kondo temperature TK and increases the entropy at the superconducting transition by almost 20%, indicating an enhanced density of states. However, whereas μSR shows clear evidence for magnetic correlations for Th substitutions, no magnetism is observed for B substitutions. The enhanced specific heat jump in the B-substituted material is associated with a change in the (...) superconducting properties as TK is reduced. (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)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

BackgroundIn the Canadian Alliance for Healthy Hearts and Minds (CAHHM) cohort, participants underwent magnetic resonance imaging (MRI) of the brain, heart, and abdomen, that generated incidental findings (IFs). The approach to managing these unexpected results remain a complex issue. Our objectives were to describe the CAHHM policy for the management of IFs, to understand the impact of disclosing IFs to healthy research participants, and to reflect on the ethical obligations of researchers in future MRI studies.MethodsBetween 2013 and 2019, 8252 participants (...) (mean age 58 ± 9 years, 54% women) were recruited with a follow-up questionnaire administered to 909 participants (40% response rate) at 1-year. The CAHHM policy followed a restricted approach, whereby routine feedback on IFs was not provided. Only IFs of severe structural abnormalities were reported.ResultsSevere structural abnormalities occurred in 8.3% (95% confidence interval 7.7–8.9%) of participants, with the highest proportions found in the brain (4.2%) and abdomen (3.1%). The majority of participants (97%) informed of an IF reported no change in quality of life, with 3% of participants reporting that the knowledge of an IF negatively impacted their quality of life. Furthermore, 50% reported increased stress in learning about an IF, and in 95%, the discovery of an IF did not adversely impact his/her life insurance policy. Most participants (90%) would enrol in the study again and perceived the MRI scan to be beneficial, regardless of whether they were informed of IFs. While the implications of a restricted approach to IF management was perceived to be mostly positive, a degree of diagnostic misconception was present amongst participants, indicating the importance of a more thorough consent process to support participant autonomy.ConclusionThe management of IFs from research MRI scans remain a challenging issue, as participants may experience stress and a reduced quality of life when IFs are disclosed. The restricted approach to IF management in CAHHM demonstrated a fair fulfillment of the overarching ethical principles of respect for autonomy, concern for wellbeing, and justice. The approach outlined in the CAHHM policy may serve as a framework for future research studies.Clinical trial registrationhttps://clinicaltrials.gov/ct2/show/nct02220582. (shrink)

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)

Given the need for enforceable guardrails for artificial intelligence (AI) that protect the public and allow for innovation, the U.S. Government recently issued a Blueprint for an AI Bill of Rights which outlines five principles of safe AI design, use, and implementation. One in particular, the right to notice and explanation, requires accurately informing the public about the use of AI that impacts them in ways that are easy to understand. Yet, in the healthcare setting, it is unclear what goal (...) the right to notice and explanation serves, and the moral importance of patient-level disclosure. We propose three normative functions of this right: (1) to notify patients about their care, (2) to educate patients and promote trust, and (3) to meet standards for informed consent. Additional clarity is needed to guide practices that respect the right to notice and explanation of AI in healthcare while providing meaningful benefits to patients. (shrink)

In “Revive and Refuse: Capacity, Autonomy, and Refusal of Care After Opioid Overdose”, Marshall, Derse, Weiner, and Joseph contend that patients who may appear to satisfy the standard criteria for...

Previous research has yielded inconsistent findings concerning the relationship between envy and schadenfreude. Three studies examined whether the distinction between benign and malicious envy can resolve this inconsistency. We found that malicious envy is related to schadenfreude, while benign envy is not. This result held both in the Netherlands where benign and malicious envy are indicated by separate words (Study 1: Sample A, N = 139; Sample B, N = 150), and in the USA where a single word is used (...) to denote both types (Study 2, N = 180; Study 3, N = 349). Moreover, the effect of malicious envy on schadenfreude was independent of other antecedents of schadenfreude (such as feelings of inferiority, disliking the target person, anger, and perceived deservedness). These findings improve our understanding of the antecedents of schadenfreude and help reconcile seemingly contradictory findings on the relationship between envy and schadenfreude. (shrink)

MEDIEVAL LOGICS LAMBERT MARIE DE RIJK (ed.), Die mittelalterlichen Traktate De mod0 opponendiet respondendi, Einleitung und Ausgabe der einschlagigen Texte. (Beitrage zur Geschichte der Philosophie und Theologie des Mittelalters, Neue Folge Band 17.) Miinster: Aschendorff, 1980. 379 pp. No price stated. THE SEVENTEENTH CENTURY MARTA FATTORI, Lessico del Novum Organum di Francesco Bacone. Rome: Edizioni dell'Ateneo 1980. Two volumes, il + 543, 520 pp. Lire 65.000. VIVIAN SALMON, The study of language in 17th century England. (Amsterdam Studies in the Theory (...) and History of Linguistic Science, Series 111: Studies in theHistory of Linguistics, Volume 17.) Amsterdam: John Benjamins B.V., 1979.x + 218 pp. Dfl. 65. Theoria cum Praxi. Zum Verhaltnis von Theorie und Praxis im 17. und 18. Jahrhundert. (Akten des 111. Internationalen Leibnizkongress, Hannover, 12. bis 17.November 1977, Band 111: Logik, Erkenntnistheorie, Wissenschaftstheorie, Metaphysik, Theologie.) Wiesbaden: Franz Steiner Verlag, 1980. vii + 269 pp. DM 48. CLASSICAL AND NON-CLASSICAL LOGICS MICHAEL CLARK, The place of syllogistic in logical theory. Nottingham: University of Nottingham Press, 1980. ix + 151 pp. £3.00. A.F. PARKER-RHODES, The theory of indistinguishables. Dordrecht, Boston and London: D. Reidel Publishing Company, 1981. xvii + 216 pp. Dfl.90.00/$39.50. NICHOLAS RESCHER and ROBERT BRANDOM, The logic of inconsistency. Oxford:Basil Blackwell, 1980. x + 174 pp. f 11.50. MISCELLANEOUS J. ZELENY, The logic of Marx. Translated from the German by T. Carver. Oxford: Basil Blackwell, 1980. xcii + 247 pp. £12.50. FELIX KAUFMANN, The infinite in mathematics. Edited by Brian McGuinness. Introduction by E. Nagel. Translation from the German by Paul Foulkes. Dordrecht: Reidel, 1978. xvii + 235 pp. Dfl 85/$39.50 (cloth); Dfl 45/$19.95 (paper). PAMELA MCCORDUCK, Machines who think. San Francisco: W.H. Freeman and Company, 1979. xiv + 275 pp. $14.95. J. MITTELSTRASS (ed.), Enzyklopadie Philosophie und Wissenschaftstheorie Bd. 1 : A-G. Mannheim, Wien, Ziirich: Bibliographisches Institut, 1980. 835 pp. DM 128. (shrink)

Background Advance Care Planning via Group Visits (ACP-GV) is a patient-centered intervention facilitated by a clinician using a group modality to promote healthcare decision-making among veterans. Participants in the group document a “Next Step” to use in planning for their future care needs. The next step may include documentation of preferences in an advance directive, discussing plans with family, or anything else to fulfill their ACP needs. This evaluation seeks to determine whether there are identifiable subgroups of group participants with (...) differing needs prior to delivery of the ACP-GV program and, if so, to use information about the subgroups to enhance the program offered to veterans in United States Department of Veterans Affairs (VA) healthcare settings. Methods We conducted a secondary analysis of national data from a quality improvement evaluation. Patient- and provider-level data from administrative healthcare records for VA users in all 50 states, territories, and the District of Columbia provides data on veterans attending ACP-GV during federal fiscal years 2018–2022 (N = 26,857). Latent class analysis seeks to identify the various subgroups of veterans based on their level of ACP self-efficacy before attending ACP-GV and any demographic differences across the resulting subgroups of veterans attending ACP-GV. ACP self-efficacy is derived from seven items obtained from a participant worksheet used during the group. Results Analysis revealed two distinct groups of veterans, distinguishable by their pre-ACP-GV levels of one aspect of ACP self-efficacy: prior knowledge of ACP. Veterans with higher prior knowledge of ACP are associated with an identified next step focused on checking their current AD status and updating it, and veterans with lower ACP prior knowledge are associated with identifying a next step to discuss ACP more fully with family. Differences in age, sex, race, ethnicity, and marital status exist across subgroups of veterans. Conclusion Greater attention must be paid to ACP and veterans’ prior knowledge of ACP to consistently encourage annual review and status updates. (shrink)

Book Information Strong Hermeneutics: Contingency and Moral Identity. By Nicholas H. Smith. Routledge. London. 1997. Pp. x + 197. Paperback, £14.99.

Qualitative and quantitative methods were used to investigate how shopping behaviors and environment influence dietary intake and weight status among homeless Minnesotans living in food deserts. Seven focus groups (n = 53) and a quantitative survey (n = 255), using the social cognitive theory as the theoretical framework, were conducted at two homeless shelters (S1 and S2) in the Twin Cities area. Heights, weights, and 24-h dietary recalls were also collected. Food stores within a five-block radius of the shelters were (...) evaluated for the price and availability of foods and compared to the Thrifty Food Plan’s market basket prices (MBP). Results showed that almost 80% of the sample was overweight or obese, with women consuming less than the recommended level for the fruits, vegetables, and milk food groups and excess for the fats/oils/sweets food group. Focus groups and participant surveys indicated that the shelter infrastructure and surrounding community influenced the types of foods available, food store access, and the foods purchased and consumed. Participants relied on food assistance programs, including food stamps, to supplement their food supply; however, some felt the high food prices at neighboring stores limited food choice and that food stamps did not adequately cover food costs. Results from the food store survey found the majority of food prices exceeded Midwest or national MBP. To promote healthier dietary intake and weight status, community-based interventions and city planners should aim to increase access to food through improved food availability and food access within the shelter environment and surrounding community. (shrink)

The historical crisis, by J. T. Marcus.--History and the search for identity, by P. Smith.--The role of history, by J. H. Plumb.--History as progress, by E. H. Carr.--On optimism, by P. Gay.--The purpose of history, by G. R. Elton.--The uses of history, by D. H. Fischer.--The dangers of history, by H. Butterfield.--Unity of history, by P. Smith.--History as private enterprise, by H. Zinn.--The historian and his day, by J. H. Hexter.--Present interest, by S. Kracauer.--On becoming an historian, by (...) M. Duberman.--Vietnam analogy: Greece, not Munich, by A. J. Mayer.--Analogies, by D. H. Fischer.--The tragic element in modern international conflict, by H. Butterfield. (shrink)

This note is prompted by a re-reading of the late Professor J. L. Austin's British Academy Lecture of 1956 “Ifs and Cans” and Professor P. H. Nowell-Smith's rejoinder to it. Austin states his topic at the beginning, and though he re-formulates it more precisely later on, it will suffice for my purposes to quote the opening short paragraph. He asks: “Are cans constitutionally iffy? Whenever, that is, we say that we can do something, or could do something, or could (...) have done something, is there an if in the offing—suppressed, it may be, but due nevertheless to appear when we set out our sentence in full or when we give an explanation of its meaning?”. Towards the end of his lecture he states his conclusion concerning the issue, viz. determinism, which is usually prominent at least implicitly in our discussion of such questions, in the following terms: “Determinism, whatever it may be, may yet be the case, but at least it appears not consistent with what we ordinarily say and presumably think.”. (shrink)

Contributed articles on Buddhist doctrines and philosophy; festschrift in honor of Narayan Hemandas Samtani, Buddhist scholar.

In lieu of an abstract, here is a brief excerpt of the content:Book Reviews Die Megariker: Kommentierte Sammlung der Testimonien. By Klaus D~ring. (Amsterdam : Verlag B. R. Griiner N.V., 1972. Pp. xii q- 185) D~Sring has assembled the first complete collection of textual fragments concerning the Megarian philosophers of the fourth and third centuries B.c., together with a commentary. The fragments are divided by the author into four groups, each centered around one of the better-known figures of the school: (...) Euclid, Eubulides, Diodorus Cronus, Stilpo. Evidences concerning lesser-known personalities are included under the figure to whose "circle" they belonged. A fifth group of texts appears in an Anhang devoted to the sophist Bryson (often mistakenly associated with the Megarians) and his student Polyxenus. Divisions in the commentary parallel those in the text. The author also adds a stemma summarizing his conclusions about teacher-pupil relationships within the school, and there is a selective bibliography and a SteUenregister. An index, which in view of the work's organization would be helpful, is not included. Simply as a collection of texts, this is a major addition to the scholarship in its field; with the author's commentary, it is the most important work on the Megarians since Kurt von Fritz's Real-Encyclopiidie article.1 D~Sringpresents convincing evidence that some widely disseminated opinions about the school have little or no foundation. Some of his alternative views have important consequences, and not only for the history of the Megarians. DSring rejects the dates customarily assigned to the school's founder Euclid (ca. 450ca. 380), pointing out that there is actually no good evidence for them (pp. 73-74). His own figures (ca. 435-ca. 365) rely on the evidence of Plato's Theaetetus to give the year 369 as a terminus post quem for Euclid's death. The first consequence of this chronology is that the story of Euclid stealing into Athens disguised as a woman in order to avoid the anti-Megarian decree of 432 must be rejected; Dfiring feels that it is probably one of a family of tales elaborated by later writers "urn die Macht der Philosophie zu demonstrieren " (p. 74). A more important consequence is in store when this chronology is combined with a reassessment of the evidence relating to Euclid's philosophical position. D6ring rejects the traditional description of Euclid as a "neo-Eleatic" who attempted to combine a strict Parmenidean monism with Socrates' ethical views by identifying the "One" with the "Good." Following yon Fritz, he sees this as "eine ziemlich gewaltsame antike Doxographenkonstruktion" (p. 83). His own view reverses the importance of Socratic and Eleatic elements in Euclid's thought, making him "[ein] Sokratiker, der die dem Sokratischen Denken inh~ente eleatische Komponente weiterentwickelt hat" (p. 87). Together with the revision of Euclid's dates, this would appear to eliminate decisively Kr~imer's thesis that Euclid originated the "Gleichsetzung ontologischer und axiologischer Momente''e fundamental to Platonic metaphysics. First, Euclid was only a few years older than Plato (not "at least two decades," as KrOner requires); second, there is no evidence whatever that he had studied the Eleatic doctrines before meeting Socrates; and finally, the purported "Gleichsetzung" appears to be rather the work of doxographers (pp. 87-89). When we add DSring's skeptical assessment of the story of Plato's Megarian period (p. 76), there remains little evidence to support the theory that Euclid was the ultimate source of Plato'S metaphysics. The most famous achievements of the M~garians were in the sphere of logic. Here, x Suppl. V (1931), s. v. "Megariker." H. J. Kr~mer, Arete bei Platon und Aristoteles (Heidelberg, 1959), p. 506. [52H 522 HISTORY OF PHILOSOPHY Dtring's work should provide the impetus for further research; his collection of texts is much more comprehensive than anything previously available, and his commentary, although deliberately limited to an overview, at least provides a good account of the status quaestionis. The material on the paradoxes attributed to the Megarians (pp. 106-114) is particularly valuable; he gives a good conspectus of the extensive literature on the "Liar" and "sorites," and his remarks on the lesser-known paradoxes (the "Man Who Escapes Notice," the "Electra," the "Hooded... (shrink)