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) 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)

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)

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)

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)

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) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

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)

This study examines whether character strengths predict resilience (operationalized as stable or higher mental health and subjective well-being despite an adverse event) over a period of approximately one month during the COVID-19 pandemic lockdown in Spain. Using a longitudinal design, participants (N = 348 adults) completed online measures of sociodemographic data, information regarding their situation in relation to the COVID-19, character strengths, general mental health, life satisfaction, positive affect and negative affect. All variables were measured at Time 1 and Time (...) 2, except for sociodemographic and most COVID-related information (Time 1 only). Time 1 data collection was conducted between March 21, 2020 and April 2, 2020, i.e., approximately the second week of lockdown in Spain. Time 2 data collection was conducted between April 24, 2020 and May 18, 2020, after the Spanish government announced ita intention to progressively release the lockdown. A principal component analysis of character strengths was conducted. Five character strength factors were extracted: fortitude, goodness, intellectual, interpersonal, and restraint. Factor structures at Times 1 and 2 were highly consistent. All character strength factors at Time 1 correlated positively with life satisfaction and positive affect, and negatively with negative affect and mental health at T2 (higher scores in the mental health measure indicate poorer mental health). Fortitude strengths showed the highest correlations. We conducted a series of regression analyses with strength factors at Time 1 as predictors, and mental health, life satisfaction, and positive and negative affect as dependent variables, controlling for their baseline levels. To test the directionality of the relationship between strengths and the dependent variables, all analyses were reversed. All character strength factors predicted an increase in mental health. They also predicted positive affect, with the exception of strengths of restraint. Fortitude, intellectual and interpersonal strengths predicted an increase in life satisfaction. Finally, fortitude strengths, interpersonal strengths, and strengths of restraint, predicted a decrease in negative affect. None of the reversed analyses yielded significant effects. Limitations, implications, and possible character strengths-based interventions aimed at promoting mental health in the COVID-19 pandemic are discussed. (shrink)

Night: The presence of the absence, the dissolution of the person in the night, the horror of being, the reality of the unreal, it takes us more to the absence of God than to God, to the absence of every entity. Dawn: Not being conscious of the existence of that unchangeable supposed centre of the person within time does not mean that we cannot be able to explain the not static changeable and relational personal identity in other ways. Day: It (...) is me who flows, but I am not in the flow like a support from where life flows, I am flowing in my own reality. This is not similar to an egology, it does not mean that everything exists and is loved to me, but it does mean that everything is seen and loved for me. (shrink)

This volume explores the Pre-Columbian Andean concepts of time, space, and the human body through objects, skeletal remains, and language. This interdisciplinary approach to conceptualizing what the Andean concepts of being may have been brings contemporary approaches to past notions of the sacred, with each discipline adding its own unique perspective to the Andean ontology. A particular strength of this volume is that most of the contributors are South American researchers, offering North American scholars entry into scholarship that has been (...) confined to Spanish language publications. (shrink)

Wolfgang Pauli referred to him as 'my discovery,' Robert Oppenheimer described him as 'one of the most gifted theorists' and Niels Bohr found him enormously stimulating. Who was the man in question, Gunnar Källén (1926-1968)? His appearance in the physics sky was like a shooting star. His contributions to the scientific debate caused excitement among young and old. Similar to his friend and mentor, Wolfgang Pauli, he demanded honesty and rigor in physics - a distinct dividing line between fact and (...) speculation. In his obituary, Arthur S. Wightman would write: 'Gunnar Källén was a proud continuer of the tradition in quantum field theory established by Wolfgang Pauli. His papers on quantum electrodynamics in the period 1950-1954 carried the non-perturbative approach to quantum electrodynamics forward to a point beyond which very little essential progress has been made up to the present day. At the time I was trying to puzzle out the grammar of the language of quantum field theory, and here was Källén already writing poetry in the language!'. In addition to being a remarkable scientist, Källén had a very interesting personality, well worth exploring. In her book, physicist Cecilia Jarlskog traces both the personal and scientific trajectory of this unsung hero of the early days of high-energy physics and quantum field theory. A number of invited contributions by members of the Källén family and distinguished researchers from the field, all of them personally acquainted with Källén, combine to form an authentic portrait of the researcher and the man. Last but not least, the reader will become acquainted with some aspects of the history of particle physics in those days, as related by Källén and those who corresponded with him. A commented selection of his most important and not easily accessible papers is included as an added bonus for specialists. (shrink)

It seems trivial to identify sound sequences as music or speech, particularly when the sequences come from different sound sources, such as an orchestra and a human voice. Can we also easily distinguish these categories when the sequence comes from the same sound source? On the basis of which acoustic features? We investigated these questions by examining listeners’ classification of sound sequences performed by an instrument intertwining both speech and music: the dùndún talking drum. The dùndún is commonly used in (...) south-west Nigeria as a musical instrument but is also perfectly fit for linguistic usage in what has been described as speech surrogates in Africa. One hundred seven participants from diverse geographical locations (15 different mother tongues represented) took part in an online experiment. Fifty-one participants reported being familiar with the dùndún talking drum, 55% of those being speakers of Yorùbá. During the experiment, participants listened to 30 dùndún samples of about 7s long, performed either as music or Yorùbá speech surrogate (n= 15 each) by a professional musician, and were asked to classify each sample as music or speech-like. The classification task revealed the ability of the listeners to identify the samples as intended by the performer, particularly when they were familiar with the dùndún, though even unfamiliar participants performed above chance. A logistic regression predicting participants’ classification of the samples from several acoustic features confirmed the perceptual relevance of intensity, pitch, timbre, and timing measures and their interaction with listener familiarity. In all, this study provides empirical evidence supporting the discriminating role of acoustic features and the modulatory role of familiarity in teasing apart speech and music. (shrink)

La argumentación: ¿construcción cultural o desarrollo cognitivo? es una publicación que toma parte en el debate de fondo que han mantenido las ciencias cognitivas en los últimos tiempos acerca de la relación lenguaje/pensamientos. El texto constituye un análisis de la ontogénesis del habla, afrontado desde la psicolingüística, con un respaldo en la teoría cognitiva de Piaget, la teoría socio contextual de Vygotsky y con actualizados aportes de la teoría socio-cultural, conformando una totalidad orientada a caracterizar el desarrollo de la argumentación (...) en edades tempranas. La publicación que ahora presentamos se constituye en un valioso pretexto académico para ahondar en un tema tan poco estudiado como lo es la conformación de pensamiento y discurso argumentativos. Precio: 16.000 pesos. (shrink)

Contra la opinión generalizada de que la "mímesis" deja de ser un paradigma del arte a partir del siglo XVIII, este artículo, inspirado en una idea general de Gadamer, intenta mostrar su vigencia apoyándose para ello en una revisión de los textos griegos fundadores de la teoría y en otras fuentes que dan fe de la evolución del concepto en la estética occidental. Muy lejos de la desfiguración moderna, que lo redujo a la simple copia de apariencias sensibles, el concepto (...) original de "mímesis" alude a un hacer paralelo con la naturaleza: se fundamenta, por un lado, en la noción pitagórica del orden universal presente en el movimiento de los cuerpos celestes, así como en el alma humana y en la belleza de las obras de arte, y, por otro, en la noción aristotélica de "reconocimiento" como un volver a conocer que deja de lado todo lo inesencial. (shrink)

In this paper we continue the study of the variety \ of monadic Gödel algebras. These algebras are the equivalent algebraic semantics of the S5-modal expansion of Gödel logic, which is equivalent to the one-variable monadic fragment of first-order Gödel logic. We show three families of locally finite subvarieties of \ and give their equational bases. We also introduce a topological duality for monadic Gödel algebras and, as an application of this representation theorem, we characterize congruences and give characterizations of (...) the locally finite subvarieties mentioned above by means of their dual spaces. Finally, we study some further properties of the subvariety generated by monadic Gödel chains: we present a characteristic chain for this variety, we prove that a Glivenko-type theorem holds for these algebras and we characterize free algebras over n generators. (shrink)

This empirical investigation showed that contrary to the popular notion that apologies signify weakness, the victims of mistakes made by leaders consistently perceived leaders who apologized as more transformational than those who did not apologize. In a field experiment (Study 1), male referees who were perceived as having apologized for mistakes made officiating hockey games were rated by male coaches (n = 93) as more transformational than when no apology was made. Studies 2 (n = 50) and 3 (n = (...) 224) replicated this effect in two vignette studies to enhance internal and ecological validity. Contrary to expectations in Study 3, there were no apology×leader gender interactions. Theoretical and practical implications are discussed. (shrink)

Current empirical work suggests that early social experiences could have a substantial impact on the areas of the brain responsible for representation of the body. In this context, one aspect of functioning that may be particularly susceptible to social experiences is interoception. Interoceptive functioning has been linked to several areas of the brain which show protracted post-natal development, thus leaving a substantial window of opportunity for environmental input to impact the development of the interoceptive network. We first introduce a biopsychosocial (...) model of interoceptive development. In our proposed model of interoceptive development, attachment related processes are purported to affect the development of interoception by influencing the growth of neural architecture and by modifying functioning of the HPA axis. Further, the idea that patterns of caretaking affect children’s development of interoception is presented. This model explains both normatively developing interoception and accounts for instances in which dysfunctional attachment related processes can lead to either a hypersensitivity or a blunted awareness of bodily cues. Second, we report findings from two existing datasets showing significant relationships between attachment related processes and interoception. In the first study, looking at a sample of healthy young adults (n = 132, 66 males), we assessed self-reported interoceptive awareness and attachment style. We found relationships between aspects of interoception and attachment style such that avoidant individuals reported lower interoceptive functioning across several dimensions (r’s (130) = -.20 to -.26, p’s<.05). More anxious individuals, on the other hand, reported heightened interoceptive across several dimensions (r’s(130)=.18 to.43, p’s <.05). In the second study, we examined the congruence between a person’s self-reported negative emotion and a measure of sympathetic nervous system arousal (SCL). The congruence score was positively associated with parental rejection of negative emotion. These results suggest that parenting style, as reported by the mother, are associated with a child’s ability to coordinate their self-reported emotional and physiological responding across a series of independent assessments, r(108)= -.24, p<.05. In other words, the more maternal reported parental rejection of child negative emotions, the less congruent a child’s self and physiological reports of distress. (shrink)

Is human nature something that the natural and social sciences aim to describe, or is it a pernicious fiction? What role, if any, does ”human nature’ play in directing and informing scientific work? Can we talk about human nature without invoking---either implicitly or explicitly---a contrast with human culture? It might be tempting to think that the respectability of ”human nature’ is an issue that divides natural and social scientists along disciplinary boundaries, but the truth is more complex. The contributors to (...) this collection take very different stances with regard to the idea of human nature. They come from the fields of psychology, the philosophy of science, social and biological anthropology, evolutionary theory, and the study of animal cognition. Some of them are ”human nature’ enthusiasts, some are sceptics, and some say that human nature is a concept with many faces, each of which plays a role in its own investigative niche. Some want to eliminate the notion altogether, some think it unproblematic, others want to retain it with reforming modifications. Some say that human nature is a target for investigation that the human sciences cannot do without, others argue that the term does far more harm than good. The diverse perspectives articulated in this book help to explain why we disagree about human nature, and what, if anything, might resolve that disagreement. Introduction Tim Lewens 1 Doubling Down on the Nomological Notion of Human Nature Edouard Machery 2 Trait Bin and Trait Cluster Accounts of Human Nature Grant Ramsey 3 A Developmental Systems Account of Human Nature Karola Stotz and Paul Griffiths 4 Human Nature, Natural Pedagogy, and Evolutionary Causal Essentialism Cecilia Heyes 5 Human Nature John Dupré 6 Sceptical Reflections on Human Nature Kim Sterelny 7 The Social Construction of Human Nature Kevin N. Laland and Gillian R. Brown 8 The Use and Non-Use of the Human Nature Concept by Evolutionary Biologists Peter J. Richerson 9 Human Ontogenies as Historical Processes Christina Toren 10 Divide and Conquer Maria Kronfeldner. (shrink)

Skeptical theists are seeking for some reasonable solutions to the evidential problem of evil. One of the most fundamental responses of skeptical theism is that the concept of “gratuitous evil”, which cannot be a proof of the absence of God. Therefore, it is not the existence of God that skeptical theism suspects. Instead, skeptical theism contemplates whether the evil in the world really has a “gratuitous” basis. This paper focuses on Peter van Inwagen's “no-minimum claim”. No-minimum claim” stands in opposition (...) to the views that assume that God minimizes the evils that exist in the world in order to achieve justice. “No-minimum claim” acknowledges that these evils still have enormous amounts to people. Thus “no-minimum claim” suggests that the evils experienced in the world are incompatible with the “best of all possible worlds” views or the other explanations of classical theodicy. According to the “no minimum claim”, the reason why the amount of evil in the world still seems so high may be God’s deliberate calculations in effecting the distribution of these evils. In order to reach these calculations, it is not necessary for the amount of evil that God allowed to reflect on the world to be perfectly manifested at the minimum level. The purpose of this paper is to consider the skeptical theism approach within the framework of Peter van Inwagen's “no-minimum claim” and to limit his arguments to an alternative approach to skeptic theism. Our claim is that such view coincides with skeptical theism, but the “no- minimum claim” still has some ambiguities at the point of the limits of evil. From this, we can conclude that the “no minimum claim” has received many objections in the skeptical theism literature and these objections are justified at certain points. (shrink)

This Teacher Education Project is an intervention research aimed at creating new school roles for educating students as readers and writers as well as citizens. The methodological framework was based on Vygotsky’s discussions of method as praxis, as well as on both the Marxist practical–materialistic–revolutionary activity and Engeström’s extensions of Cultural Historical Activity Theory. The work at school was motivated by students’ limited awareness of reading and writing. The goal was to involve the school as a community in understanding and (...) transforming the ways in which reading and writing were addressed in classrooms. The methodology used for organizing and carrying out the project was devised so as to allow for three activity systems that partially interact with their objects – that is, reading and writing as tools for teaching-learning in different areas in order to constitute students as citizens. However, for this paper, we will focus solely on the Teacher Education Activity System, which we termed Teacher Support Team. Three episodes are discussed in this paper: Two video sessions with the Teacher Support Team, the first of which took place in 2010, and the second in 2011; and a classroom reading class session that was videotaped in 2011 as part of the Teacher Support Team work. The theoretical and practical work developed was targeted at creating a mutual Zone of Proximal Development that supported teachers, coordinators, and the principal, through the appropriation of reading and writing as processes. The results show that the organization of the project as interrelated activity systems enhanced the entire school’s prospects of appropriating the reading and writing teaching-learning processes, by focusing on the same object, in the diverse systems that framed the project. (shrink)