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.

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 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)

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)

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)

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)

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)

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)

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)

In this article, I argue that gender is a primary cultural frame for coordinating behavior and organizing social relations. I describe the implications for understanding how gender shapes social behavior and organizational structures. By my analysis, gender typically acts as a background identity that biases, in gendered directions, the performance of behaviors undertaken in the name of organizational roles and identities. I develop an account of how the background effects of the gender frame on behavior vary by the context that (...) different organizational and institutional structures set but can also infuse gendered meanings into organizational practices. Next, I apply this account to two empirical illustrations to demonstrate that we cannot understand the shape that the structure of gender inequality and gender difference takes in particular institutional or societal contexts without taking into account the background effects of the gender frame on behavior in these contexts. (shrink)

Si bien la cirugía es parte fundamental de la medicina y de gran relevancia en la sociedad actual, no ha sido tomada en cuenta por la filosofía de la medicina. Debido a la naturaleza eminentemente práctica de la cirugía, una indagación sistemática nos permitirá, entre otros aspectos, dilucidar rasgos generales de las prácticas científicas en las que el conocimiento tácito es esencial. Por lo que, con la finalidad de integrar a la cirugía dentro del marco general de la filosofía de (...) la medicina, se propone un primer corpus tentativo de problemas en los que puede centrarse la filosofía de la cirugía, que incluyen: cuestiones epistémicas acerca del aprendizaje de las habilidades quirúrgicas y su transformación; la evidencia utilizada en cirugía, así como la forma en la que los cirujanos validan sus intervenciones frente a otras especialidades médicas y si está justificada epistémicamente la falta de ensayos clínicos aleatorizados; finalmente se examina la forma de aprobación de los dispositivos médicos que son ampliamente utilizados en cirugía. Esto, mostrará que la filosofía de la cirugía tiene el potencial para establecerse como un área autónoma dentro de la filosofía de la medicina. (shrink)

René Descartes is often thought to have exerted a pernicious influence on our views concerning the relationship of humans to the environment. The view that because animals are machines, “thoughtless brutes,” they have no moral standing, and we thus have a right to use them to further our own interests, is attributed to him. A celebrated passage from the Discourse on Method adds fuel to the view that he subscribes to the “dominion” theory. I argue that this picture is misleading (...) and unfair. Descartes does not hold the dominion theory, and there is evidence that he accords animals (and plants) moral standing. Most importantly, Descartes holds that it is a human good to subordinate one’s interests to those of the larger universe. He can, in fact, be seen as a forerunner of modern ecocentrism. (shrink)

1. Properties of mirror neurons in monkeys. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (...) . . . 000 1.1. Action types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 000 1.2. Context effects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 000 2. Is there a human ‘mirror neuron system’? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 000 2.1. Monkeys versus humans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 000 2.2. Action understanding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 000 3. The development of mirroring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 000 3.1. Imitation in newborns? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 000 3.2. Effects of experience . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 000 3.3. Effects of sensorimotor experience . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. (shrink)

Background The ambulance service provides emergency care to meet the patient’s medical and nursing needs. Based on professional nursing values, this should be done within a caring relationship with a holistic approach as the opposite would risk suffering related to disengagement from the patient’s emotional and existential needs. However, knowledge is sparse on how ambulance personnel can meet caring needs and avoid suffering, particularly in conjunction with urgent and emergency situations. Aim The aim of the study was to explore ambulance (...) nurses’ experiences of relationships with patients in urgent and emergency situations. Methods Data collection was performed using individual open-ended interviews with six ambulance nurses. The data were analyzed using a thematic analysis. Results Relationships with patients during urgent and emergency assignments emerged as three themes: “ Ambiguous silence,” “ Professional competence” and “ Challenging inadequacy” comprising eight sub-themes in total. The result shows that the ambulance nurses found it difficult to prioritize between medical care and establishing a caring relationship with the patient. However, sometimes a wordless relationship was perceived sufficient and considered a first step towards a verbal relationship. Conclusions Ambulance nurses experience that a caring relationship cannot and does not need to be prioritized in the acute stage. This uncovers a dichotomy approach to medical care versus caring relationships that exclude a holistic approach. Thus, patients’ emotional, existential and physical needs are not considered as equally important. Clinical relevance: It is important to stimulate reflection on core ethical nursing values, in training and simulation exercises among clinically active ambulance nurses. (shrink)

Background: Previous studies have investigated the effects of dance interventions on Parkinson’s motor and non-motor symptoms in an effort to develop an integrated view of dance as a therapeutic intervention. This within-subject study questions whether dance can be simply considered a form of exercise by comparing a Dance for Parkinson’s class with a matched-intensity exercise session lacking dance elements like music, metaphorical language, and social reality of art-partaking.Methods: In this repeated-measure design, 7 adults with Parkinson’s were tested four times; before (...) and after a Dance for Parkinson’s class, as well as before and after a matched-intensity exercise session. Physiological measures included heart rate and electrodermal activity. Self-reported affect and body self-efficacy were collected. Gait symmetry and dual task cost were analyzed using the 6 min walking test and Timed-Up-and-Go test, respectively.Results: Average heart rate was the same for both conditions, while electrodermal activity was higher during Dance for Parkinson’s. Significant differences were found in body self-efficacy, beauty subscale, symmetry of gait, and dual task performance.Conclusion: Dance, compared to an exercise intervention of matched intensity, yields different outcomes through the means of intrinsic artistic elements, which may influence affective responses, the experience of beauty, self-efficacy, and gait performance. (shrink)