Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

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)

Ran is one of the most abundant and best conserved of the small GTP binding and hydrolyzing proteins of eukaryotes. It is located predominantly in cell nuclei. Ran is a member of the Ras family of GTPases, which includes the Ras and Ras‐like proteins that regulate cell growth and division, the Rho and Rac proteins that regulate cytoskeletal organization and the Rab proteins that regulate vesicular sorting. Ran differs most obviously from other members of the Ras family in both its (...) nuclear localization, and its lack of sites required for post‐translational lipid modification. Ran is, however, similar to other Ras family members in requiring a specific guanine nucleotide exchange factor (GEF) and a specific GTPase activating protein (GAP) as stimulators of overall GTPase activity. In this review, the multiple cellular functions of Ran are evaluated with respect to its known biochemistry and molecular interactions. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

We address concerns raised by Maul (2012) regarding the validity of the Mayer-Salovey-Caruso Emotional Intelligence Test (MSCEIT). We respond to requests for clarifications of our model, and explain why the MSCEIT’s scoring methods stand up to scrutiny and why many reported reliabilities of the MSCEIT may be underestimates, using reanalyses of the test’s standardization sample of N = 5,000 to illustrate our point. We also organize findings from four recent articles that provide evidence for the MSCEIT’s validity based on its (...) relations with other tests. (shrink)

Building on an illustrative case of a systemic environmental threat and its multi‐stakeholder response, this paper draws attention to the changing political impacts of corporations in the digital age. Political Corporate Social Responsibility (PCSR) theory suggests an expanded sense of politics and corporations, including impacts that may range from voluntary initiatives to overcome governance gaps, to avoiding state regulation via corporate political activity. Considering digitalization as a stimulus, we explore potential responsibilities of corporations toward public goods in contexts with functioning (...) governments. We show that digitalization—in the form of transparency, surveillance, and data‐sharing—offers corporations’ scope for deliberative public participation. The starry sky beetle infestation endangering public and private goods is thereby used to illustrate the possibility of expanding the political role of corporations in the digital sphere. We offer a contribution by conceptualizing data‐deliberation as a Habermasian variation of PCSR, defined as the (a) voluntary disclosure of corporate data and its transparent, open sharing with the public sector (b) along with the cooperation with governmental institutions on data analytics methods for examining large‐scale datasets (c) thereby complying with existing national and international regulations on data protection, in particular with respect to privacy and personal data. (shrink)

Scientific realists claim we can justifiably believe that science is getting at the truth. But they have long faced historical challenges: various episodes across history appear to demonstrate that even strongly supported scientific theories can be overturned and left behind. In response, realists have developed new positions and arguments. As a result of specific challenges from the history of science, and realist responses, we find ourselves with an ever increasing data-set bearing on the (possible) relationship between science and truth. The (...) present volume introduces new historical cases impacting the debate, and advances the discussion of cases that have only very recently been introduced. At the same time, shifts in philosophical positions affect the very kind of case study that is relevant. Thus the historical work must proceed hand in hand with philosophical analysis of the different positions and arguments in play. It is with this in mind that the volume is divided into two sections, entitled “Historical cases for the debate,” and “Contemporary scientific realism”. All sides agree that historical cases are informative with regard to how, or whether, science connects with truth. Defying proclamations as early as the 1980s announcing the death knell of the scientific realism debate, here is that rare thing: a philosophical debate making steady and definite progress. Moreover, the progress it is making concerns one of humanity’s most profound and important questions: the relationship between science and truth, or, put more boldly, the epistemic relation between humankind and the reality in which we find ourselves. (shrink)

COVID-19 has revealed that science needs to learn how to better deal with the irreducible uncertainty that comes with global systemic risks as well as with the social responsibility of science towards the public good. Further developing the epistemological principles of new theories and experimental practices, alternative investigative pathways and communication, and diverse voices can be an important contribution of history and philosophy of science and of science studies to ongoing transformations of the scientific enterprise.

We present here an approach to the fine structure of L based solely on elementary model theoretic ideas, and illustrate its use in a proof of Global Square in L. We thereby avoid the Lévy hierarchy of formulas and the subtleties of master codes and projecta, introduced by Jensen [3] in the original form of the theory. Our theory could appropriately be called ”Hyperfine Structure Theory”, as we make use of a hierarchy of structures and hull operations which refines the (...) traditional Lα -or Jα-sequences with their Σn-hull operations.§1. Introduction. In 1938, K. Gödel defined the model L of set theory to show the relative consistency of Cantor's Continuum Hypothesis. L is defined as a unionof initial segments which satisfy: L0 = ∅, Lλ = ∪α<λLα for limit ordinals λ, and, crucially, Lα + 1 = the collection of 1st order definable subsets of Lα. Since every transitive model of set theory must be closed under 1st order definability, L turns out to be the smallest inner model of set theory. Thus it occupies the central place in the set theoretic spectrum of models.The proof of the continuum hypothesis in L is based on the very uniform hierarchical definition of the L-hierarchy. The Condensation Lemma states that if π : M → Lα is an elementary embedding, M transitive, then some ; the lemma can be proved by induction on α. If a real, i.e., a subset of ω, is definable over some Lα,then by a Löwenheim-Skolem argument it is definable over some countable M as above, and hence over some, < ω1. This allows one to list the reals in L in length ω1 and therefore proves the Continuum Hypothesis in L. (shrink)

Infinitism is an ancient view in epistemology about the structure of knowledge and epistemic justification, according to which there are no foundational reasons for belief. The view has never been popular, and is often associated with skepticism, but after languishing for centuries it has recently begun a resurgence. Ad Infinitum presents new work on the topic by leading epistemologists. They shed new light on infinitism's distinctive strengths and weaknesses, and address questions, new and old, about its account of justification, reasoning, (...) epistemic responsibility, disagreement, and trust, among other important issues. The volume clarifies the relationship between infinitism and other epistemological views, such as skepticism, coherentism, foundationalism and contextualism, and it offers novel perspectives on the metaphysics, epistemology, and ethics of regresses and reasons. (shrink)

Motile bacteria respond to environmental cues to move to more favorable locations. The components of the chemotaxis signal transduction systems that mediate these responses are highly conserved among prokaryotes including both eubacterial and archael species. The best‐studied system is that found in Escherichia coli. Attractant and repellant chemicals are sensed through their interactions with transmembrane chemoreceptor proteins that are localized in multimeric assemblies at one or both cell poles together with a histidine protein kinase, CheA, an SH3‐like adaptor protein, CheW, (...) and a phosphoprotein phosphatase, CheZ. These multimeric protein assemblies act to control the level of phosphorylation of a response regulator, CheY, which dictates flagellar motion. Bacterial chemotaxis is one of the most‐understood signal transduction systems, and many biochemical and structural details of this system have been elucidated. This is an exciting field of study because the depth of knowledge now allows the detailed molecular mechanisms of transmembrane signaling and signal processing to be investigated. BioEssays 28:9–22, 2006. © 2005 Wiley Periodicals, Inc. (shrink)

We present here an approach to the fine structure of L based solely on elementary model theoretic ideas, and illustrate its use in a proof of Global Square in L. We thereby avoid the Lévy hierarchy of formulas and the subtleties of master codes and projecta, introduced by Jensen [3] in the original form of the theory. Our theory could appropriately be called ”Hyperfine Structure Theory”, as we make use of a hierarchy of structures and hull operations which refines the (...) traditional Lα -or Jα-sequences with their Σn-hull operations.§1. Introduction. In 1938, K. Gödel defined the model L of set theory to show the relative consistency of Cantor's Continuum Hypothesis. L is defined as a unionof initial segments which satisfy: L0 = ∅, Lλ = ∪α<λLα for limit ordinals λ, and, crucially, Lα + 1 = the collection of 1st order definable subsets of Lα. Since every transitive model of set theory must be closed under 1st order definability, L turns out to be the smallest inner model of set theory. Thus it occupies the central place in the set theoretic spectrum of models.The proof of the continuum hypothesis in L is based on the very uniform hierarchical definition of the L-hierarchy. The Condensation Lemma states that if π : M → Lα is an elementary embedding, M transitive, then some ; the lemma can be proved by induction on α. If a real, i.e., a subset of ω, is definable over some Lα,then by a Löwenheim-Skolem argument it is definable over some countable M as above, and hence over some, < ω1. This allows one to list the reals in L in length ω1 and therefore proves the Continuum Hypothesis in L. (shrink)

In this paper, we suggest some of the dimensions of the problematic concept of Alzheimer Disease as a natural disease discerned by increasingly sophisticated medical scientific progress. Taking a page from Max Weber concerning unique events, we show some of the conceptual building blocks and social processes that have coalesced into the perception of certain phenomena as abnormalities that are seen as implicated in the development of a degenerative disease distinct from the process of normal, but variable, brain aging. We (...) note some of the decisions and social forces pushing for particular conceptualizations, interpretations, and reifications of brain alterations. In so doing, we suggest that the mystery of the "there" may not be much different from, and probably is, the mystery of the "everywhere". (shrink)

A decade ago, we reviewed the field of clinical ethics; assessed its progress in research, education, and ethics committees and consultation; and made predictions about the future of the field. In this article, we revisit clinical ethics to examine our earlier observations, highlight key developments, and discuss remaining challenges for clinical ethics, including the need to develop a global perspective on clinical ethics problems.

Mit der Digitalisierung geht ein fundamentaler, herausfordernder Wandel einher. Durch eine Begriffsbestimmung und Operationalisierung wird in diesem Beitrag der digitale Wandel aus wirtschaftsphilosophischer Sicht vorgestellt. Zunächst werden wirtschaftsphilosophische Grundlagen der Digitalisierung wie die Informationsethik erläutert, gefolgt von einer Diskussion der digitalen Wertschöpfung, die auf Überwachung aufbaut und von einer Überwachungskultur gespeist wird. Schließlich werden Zukunftsperspektiven zum Internet der Dinge, Pricing, Privatheit und der Digitalen Demokratie skizziert.

Recent developments in global business gave rise to innovative forms of digital-exchange, facilitated by a new big data-based infrastructure – the sharing economy platform. SEPs are rapidly expanding, challenging the political-economic order and the classical division of work in society. Against the background of the current sustainability crisis, we discuss the increasingly momentous role of SEPs as a potential driver toward a more sustainable economy and society. Drawing on the theoretical lens of political CSR theory, we first outline how SEPs (...) are applying institutional strategies to gain a competitive advantage, thereby shaping contexts in their favor and triggering an erosion of foundations of social sustainability. However, SEPs also strive for legitimacy by taking over novel social responsibilities via profound digital capacities. Thus SEPs carry the potential to contribute to a more sustainable future economy. Our chapter considers future pathways of platform CSR regimes and a democratization of SEPs building on political CSR theory. (shrink)

Practical medical decisions are closely integrated with ethical and religious beliefs in the Philippines. This is shown in a survey of Filipino physicians' attitudes towards severely compromised neonates. This is also the reason why the ethical analysis of critical care practices must be situated within the context of local culture. Kagandahang loob and kusang loob are indigenous Filipino ethical concepts that provide a framework for the analysis of several critical care practices. The practice of taking-from-the-rich-to-give-to-the-poor in public hospitals is not (...) compatible with these concepts. The legislated definition of death and other aspects of the Philippine Law on Organ Transplants also fail to be compatible with these concepts. Many ethical issues that arise in a critical care setting have their roots outside the seemingly isolated clinical setting. Critical care need not apply only to individuals in a serious clinical condition. Vulnerable populations require critical attention because potent threats to their lives exist in the water that they drink and the air that they breathe. We cannot ignore these threa ts even as we move inevitably towards a technologically dependent, highly commercialized approach to health management. (shrink)

We present here an approach to the fine structure of L based solely on elementary model theoretic ideas, and illustrate its use in a proof of Global Square in L. We thereby avoid the Lévy hierarchy of formulas and the subtleties of master codes and projecta, introduced by Jensen [3] in the original form of the theory. Our theory could appropriately be called ”Hyperfine Structure Theory”, as we make use of a hierarchy of structures and hull operations which refines the (...) traditional Lα -or Jα-sequences with their Σn-hull operations.§1. Introduction. In 1938, K. Gödel defined the model L of set theory to show the relative consistency of Cantor's Continuum Hypothesis. L is defined as a unionof initial segments which satisfy: L0 = ∅, Lλ = ∪α<λLα for limit ordinals λ, and, crucially, Lα + 1 = the collection of 1st order definable subsets of Lα. Since every transitive model of set theory must be closed under 1st order definability, L turns out to be the smallest inner model of set theory. Thus it occupies the central place in the set theoretic spectrum of models.The proof of the continuum hypothesis in L is based on the very uniform hierarchical definition of the L-hierarchy. The Condensation Lemma states that if π : M → Lα is an elementary embedding, M transitive, then some ; the lemma can be proved by induction on α. If a real, i.e., a subset of ω, is definable over some Lα,then by a Löwenheim-Skolem argument it is definable over some countable M as above, and hence over some, < ω1. This allows one to list the reals in L in length ω1 and therefore proves the Continuum Hypothesis in L. (shrink)

The article develops and extends the theory of Glenn Kessler (Frege, Mill and the foundations of arithmetic, Journal of Philosophy 77, 1980) that a (cardinal) number is a relation between a heap and a unit-making property that structures the heap. For example, the relation between some swan body mass and "being a swan on the lake" could be 4.

These new studies of Wittgenstein's Tractatus represent a significant step beyond recent polemical debate.

In recent years, scholars have begun to lay the groundwork to justify a distinct application of ethics to the field of public health. They have highlighted important features that differentiate public health ethics from bioethics, especially public health’s emphasis on population health rather than issues of individual health. Articulations of public health ethics also tend to emphasize the role of social justice compared to the predominance of autonomy in the bioethical literature. Now that the field of public health ethics is (...) developing a unique focus and a language of its own, including a code of ethics disseminated by the American Public Health Association, the future of public health ethics may well be global health ethics, focusing on issues of global justice. As public health ethics evolves from its nascent stage of reflection to a place of action and application in the national and global arenas, two interrelated developments will need to occur: public health professionals, including practitioners, policymakers, and scholars, will need a richer understanding of the ethical challenges practitioners face on a daily basis and scholars will need to develop useful tools that practitioners may employ for identifying and tackling these ethical challenges. (shrink)

Ethical challenges in public health can have a significant impact on the health of communities if they impede efficiencies and best practices. Competing needs for resources and a plurality of values can challenge public health policymakers and practitioners to make fair and effective decisions for their communities. In this paper, the authors offer an analytic framework designed to assist policymakers and practitioners in managing the ethical tensions they face in daily practice. Their framework is built upon the following set of (...) six considerations: determining population-level utility of the proposed action; demonstrating evidence of need and effectiveness of actions; establishing fairness of goals and proposed implementation strategies; ensuring accountability; and, assessing expected efficiencies and costs associated with the proposed action. Together, these considerations create a structured guide to assist decision-makers in identifying potential ethical challenges and in assessing the moral considerations that underlie public health practice - and possibly even, if the conditions are met, reduce the creation of ethical tension. Although the authors’empirical experiences provide the basis for the framework advanced here, their approach remains to be tested and evaluated by public health practitioners. (shrink)

Sister (Sr.) Marie Simone Roach, of the Sisters of St. Martha of Antigonish, Nova Scotia, died at the Motherhouse on 2 July 2016 at the age of 93, leaving behind a rich legacy of theoretical and practical work in the areas of care, caring and nursing ethics. She was a humble soul whose deep and scholarly thinking thrust her onto the global nursing stage where she will forever be tied to a central concept in nursing, caring, through her Six Cs (...) of Caring model. In Canada, she was the lead architect of the Canadian Nurses Association's first code of ethics, and her influence on revisions to it is still profound more than 35 years later. In this paper, four global scholars in nursing and ethics are invited to reflect on Sr. Simone's contribution to nursing and health‐care, and we link her work to nursing and health‐care going forward. (shrink)

Uses Buddhist philosophy to discuss diversity as a value, one that can contribute to equity in a globalizing world.