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)
The leader integrity literature has described how professional behavior influences perceptions of integrity, yet behavior in leaders’ personal lives potentially affects those perceptions. The present paper examined how personal life behavior affects leaders. We assessed high profile political sex scandals to explore the research questions of how indiscretions in personal life affect leaders and how leaders recover from public revelations of sexual indiscretions. The results revealed that whether politicians survived the scandal depended on the degree to which the indiscretion deviated (...) from accepted norms, the degree to which the behavior departed from the politician’s expressed values, the leader’s political power, and whether the leader fully engaged in atonement under conditions when denying the allegations is not possible. These components were inter-related such that atonement was possible if the behavior was neither too extreme nor out of character and the leader had sufficient political power. The model was then tested with a sample of business executives engaged in sex scandals, finding support for its elements. (shrink)
Recently, the gender asterisk has become more widespread in grammatical gender languages in order to represent all genders. Such gender-fair language is intended to help better address women and other genders and make their interests and achievements more visible. Critics often argue this would make the language less comprehensible and less aesthetically appealing. Two experiments examined the effects of the gender asterisk on text comprehensibility, aesthetic perception, and interest. N = 159 and N = 127 participants were randomly provided with (...) a text in either masculine-only form or alternatively in gender-fair language with the gender asterisk. The results of the first experiment showed no impairment of comprehensibility and aesthetic evaluation of the texts by the gender asterisk and no effect on interest in the game, while the second experiment showed significant impairments of comprehensibility, aesthetic evaluation, and interest in the game by the gender asterisk. The proportion of singular forms is discussed as a possible explanation for the different results. Experiment 1 predominantly used plural forms like die Spieler*innen and did not include forms such as der*die Spieler*in, whereas Experiment 2 included many such more complex singular forms. We argue that this issue might be crucial, and that it deserves full attention in future studies. (shrink)
Published in 1891, Edmund Husserl’s first book, Philosophie der Arithmetik, aimed to “prepare the scientific foundations for a future construction of that discipline.” His goals should seem reasonable to contemporary philosophers of mathematics: . . . through patient investigation of details, to seek foundations, and to test noteworthy theories through painstaking criticism, separating the correct from the erroneous, in order, thus informed, to set in their place new ones which are, if possible, more adequately secured. [7, p. 5]2 But the (...) ensuing strategy for grounding mathematical knowledge sounds strange to the modern ear. For Husserl cast his work as a sequence of “psychological and logical investigations,” providing a psychological analysis.. (shrink)
Scientific inquiry possibly shares with people's ordinary understanding the same evolutionary determinants, and affect-laden intuitions that shape moral judgments also play a decisive role in decision-making, planning, and scientific reasoning. Therefore, if ordinary understanding does differ from scientific inquiry, the reason does not reside in the fact that the former (but not the latter) is endowed with moral considerations.
Rogers & McClelland's (R&M's) précis represents an important effort to address key issues in concepts and categorization, but few of the simulations deliver what is promised. We argue that the models are seriously underconstrained, importantly incomplete, and psychologically implausible; more broadly, R&M dwell too heavily on the apparent successes without comparable concern for limitations already noted in the literature.
An attention shift from a stationary to a changing object has to occur in feature space, in order to bind these stimuli into a unitary percept. This time-consuming shift leads to the perception of a changing stimulus further ahead along its trajectory. This attentional framework is able to accommodate the flash-lag effect in its multiple empirical manifestations.
The Hilbert space formalism is a powerful language to express many cognitive phenomena. Here, relevant concepts from signal detection theory are recast in that language, allowing an empirically testable extension of the quantum probability formalism to psychophysical measures, such as detectability and discriminability.
I. From Psychoanalysis to Political Christology In the wake of critical theory, Herbert Marcuse interprets the dialectic of enlightenment not only from a Marxist perspective, as the co-optation of the movements toward freedom by the capitalist regime. With Sigmund Freud, he also recognizes the cyclic logic of the civilizing process, which appears in the oedipal dramaturgy. Until now, the father's removal by the son has always been followed by a restoration of the ruling principle through the son, Marcuse writes in (...) Eros and Civilization.1 For Marcuse, enlightenment thus becomes transparent in its oedipal myth. The psychoanalytical insight…. (shrink)
Though we agree with their argument that language is shaped by domain-general learning processes, Christiansen & Chater (C&C) neglect to detail how the development of these processes shapes language change. We discuss a number of examples that show how developmental processes at multiple levels and timescales are critical to understanding the origin of domain-general mechanisms that shape language evolution.
Precision cell signaling activities of reactive electrophilic species (RES) are arguably among the most poorly‐understood means to transmit biological messages. Latest research implicates native RES to be a chemically‐distinct subset of endogenous redox signals that influence cell decision making through non‐enzyme‐assisted modifications of specific proteins. Yet, fundamental questions remain regarding the role of RES as bona fide second messengers. Here, we lay out three sets of criteria we feel need to be met for RES to be considered as true cellular (...) signals that directly mediate information transfer by modifying “first‐responding” sensor proteins. We critically assess the available evidence and define the extent to which each criterion has been fulfilled. Finally, we offer some ideas on the future trajectories of the electrophile signaling field taking inspiration from work that has been done to understand canonical signaling mediators. (shrink)
Most models of generational succession in sexually reproducing populations necessarily move back and forth between genic and genotypic spaces. We show that transitions between and within these spaces are usually hidden by unstated assumptions about processes in these spaces. We also examine a widely endorsed claim regarding the mathematical equivalence of kin-, group-, individual-, and allelic-selection models made by Lee Dugatkin and Kern Reeve. We show that the claimed mathematical equivalence of the models does not hold. *Received January 2007; revised (...) April 2008. †To contact the authors, please write to: Elisabeth Lloyd, Department of History and Philosophy of Science, 130 Goodbody Hall, Indiana University, Bloomington, IN 47405; e-mail: [email protected]; Richard Lewontin, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138; Marcus Feldman, Department of Biological Sciences, Stanford University, Stanford, CA 94305; e-mail: [email protected] (shrink)
The proteasome family of proteases comprises oligomeric assemblies of very different symmetry. In different sizes, it features ring‐like oligomers with dihedral symmetry that allow the stacking of further rings of regulatory subunits as observed in the modular proteasome system, but also less symmetric helical assemblies. Comprehensive sequence and structural analyses of proteasome homologs reveal a parsimonious scenario of how symmetry may have emerged from a monomeric ancestral precursor and how it may have evolved throughout the proteasome family. The four characterized (...) representatives—ancestral β subunit (Anbu), HslV, betaproteobacterial proteasome homolog (BPH), and the 20S proteasome—are outlasting cornerstones in the family's evolutionary history, each marking a transition in symmetry. This article contextualizes the evolutionary and functional key aspects of these symmetry transitions, explaining how they facilitated the diversification and concurrent evolution of independent proteolytic systems side by side, each with its customized network of auxiliary interactors. -/- . (shrink)
