Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal (...) rigor of ontologies to better support computation. 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 computation and for cross-species data integration. Results: To enhance the CL's utility for computational analyses, 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. We avoid multiple uses of is_a by linking DC-CL terms to terms in other ontologies via additional, formally defined relations such as has_function. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. Accordingly, we propose our method as a general strategy for the ontological representation of cells. DC-CL is available from http://www.obofoundry.org. (shrink)

The Protein Ontology (PRO) 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)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (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)

La città vivente sotto le ombre e le macerie dell'estraneazione.

On an evidentialist position, it is epistemically rational for us to believe propositions that are (stably) supported by our total evidence. We are epistemically permitted to believe such propositions or even ought to do so. Epistemic rationality is normative. One popular way to explain the normativity appeals to epistemic teleology. The primary aim of this paper is to argue that appeals to epistemic teleology do not support that we ought to believe what is rational to believe, only that we are (...) permitted to do so. In arguing for that, I defend an epistemic teleological position that is radical in nature. It involves no commitment to aiming at the truth. I conclude by dispelling some worries that have been raised about my position. (shrink)

Enjoying great popularity in decision theory, epistemology, and philosophy of science, Bayesianism as understood here is fundamentally concerned with epistemically ideal rationality. It assumes a tight connection between evidential probability and ideally rational credence, and usually interprets evidential probability in terms of such credence. Timothy Williamson challenges Bayesianism by arguing that evidential probabilities cannot be adequately interpreted as the credences of an ideal agent. From this and his assumption that evidential probabilities cannot be interpreted as the actual credences of human (...) agents either, he concludes that no interpretation of evidential probabilities in terms of credence is adequate. I argue to the contrary. My overarching aim is to show on behalf of Bayesians how one can still interpret evidential probabilities in terms of ideally rational credence and how one can maintain a tight connection between evidential probabilities and ideally rational credence even if the former cannot be interpreted in terms of the latter. By achieving this aim I illuminate the limits and prospects of Bayesianism. (shrink)

The development of explicit theories of dynamic context change has led to a fundamentally new perspective on the interpretation of discourse. In this paper I show that this development also opens up the possibility of approaching subclausal composition along similar lines. More specifically, I argue that a dynamic theory where type-driven rules apply directly to overt surface structures and fill in missing information by building anaphoric bridges is more faithful to natural language semantics than the classical Montagovian approach.

As one tries to grasp love and its images within José Leonilson's production, a multiplicity of aspects and meanings are seen that also relate to Louise Bourgeois's oeuvre in regard to the interest in human relations. Through a comparative approach to both artists' poetics, an understanding is created that love is not a simplistic action and all the words read in or applied to their visual discourse must be considered within a wide range of love in visual and literary images. (...) Keywords: literature and visual arts / love / creativity / Bourgeois, Louise / Leonilson, José / word and image. (shrink)

In everyday life and in science we acquire evidence of evidence and based on this new evidence we often change our epistemic states. An assumption underlying such practice is that the following EEE Slogan is correct: 'evidence of evidence is evidence' (Feldman 2007, p. 208). We suggest that evidence of evidence is best understood as higher-order evidence about the epistemic state of agents. In order to model evidence of evidence we introduce a new powerful framework for modelling epistemic states, Dyadic (...) Bayesianism. Based on this framework, we then discuss characterizations of evidence of evidence and argue for one of them. Finally, we show that whether the EEE Slogan holds, depends on the specific kind of evidence of evidence. (shrink)

How should an agent revise her epistemic state in the light of doxastic disagreement? The problems associated with answering this question arise under the assumption that an agent’s epistemic state is best represented by her degree of belief function alone. We argue that for modeling cases of doxastic disagreement an agent’s epistemic state is best represented by her confirmation commitments and the evidence available to her. Finally, we argue that given this position it is possible to provide an adequate answer (...) to the question of how to rationally revise one’s epistemic state in the light of disagreement. (shrink)

Escribir hoy en día un libro sobre hermenéutica, que tal hermenéutica se refiera a la desarrollada por G. Gadamer en su conocido Verdad y método y que se pretenda añadir algo nuevo a lo mucho escrito sobre el tema parecería, a primera vista, empresa irrealizable. Que ambas pretensiones inspiren la sólida monografía de María G. Navarro —titulada Interpretar y argumentar— constituye empresa audaz y arriesgada, plena de coraje innovador, que provoca admiración, curiosidad e interés. Contra lo que pudiera parecer a (...) primera vista, el libro contiene un alto componente de originalidad y creatividad, debido a la estratagema metodoló-gica de que se sirve la autora. A saber, una hermenéutica in obliquo, estrategia consistente en interpretar a la hermenéutica gadameriana a través del prisma de la lógica de la argumentación. (shrink)

The project “A Plurality of Lives” was funded and hosted by the Pufendorf Institute for Advanced Studies at Lund University, Sweden. The aim of the project was to better understand how a second origin of life, either in the form of a discovery of extraterrestrial life, life developed in a laboratory, or machines equipped with abilities previously only ascribed to living beings, will change how we understand and relate to life. Because of the inherently interdisciplinary nature of the project aim, (...) the project took an interdisciplinary approach with a research group made up of 12 senior researchers representing 12 different disciplines. The project resulted in a joint volume, an international symposium, several new projects, and a network of researchers in the field, all continuing to communicate about and advance the aim of the project. (shrink)

In recent years, a central debate in the philosophy of mind and cognitive science concerns the role of the body in perception and cognition. For many contemporary philosophers, not only cognition but also perception is connected mainly with the brain, where the processing of input from the senses takes place; whereas for the proponents of ‘embodied cognition’ other aspects of the body beyond the brain, including the environment, play a constitutive role in cognitive processes. In terms of perception, a new (...) theory has emerged which stresses perception’s active character and claims that the embodied subject and the environment, with which it interacts, form a dynamic system. Supporters of ‘enactive perception’ such as Susan Hurley and Alva Noë maintain that the physical substrate or the supervenience basis of perceptual experience and phenomenal consciousness may include besides the brain and the nervous system other bodily and environmental features. Yet, it will be argued in this paper that the interaction between the subject and the environment forms a system of causal relations, so we can theoretically interfere in the causal chains and create hallucinations, which cannot be distinguished from veridical perception, or a virtual reality as in the film Matrix (1999). This kind of argument and its related thought experiments aim to stress the primacy of the brain in determining phenomenal states, and show that the body and certain interactions with the environment have a causal, but not a constitutive or essential role, in forming phenomenal consciousness. (shrink)

This book constitutes refereed proceedings of the COST 2102 International Training School on Cognitive Behavioural Systems held in Dresden, Germany, in February 2011. The 39 revised full papers presented were carefully reviewed and selected from various submissions. The volume presents new and original research results in the field of human-machine interaction inspired by cognitive behavioural human-human interaction features. The themes covered are on cognitive and computational social information processing, emotional and social believable Human-Computer Interaction (HCI) systems, behavioural and contextual analysis (...) of interaction, embodiment, perception, linguistics, semantics and sentiment analysis in dialogues and interactions, algorithmic and computational issues for the automatic recognition and synthesis of emotional states. (shrink)

CUPRINS CONTUR Re-Introducere sau: Dincolo de „teoria şi practica” informării şi documentării – Spre o hermeneutică posibilă şi necesară ......................................................... 11 Desfăşurătorul întâlnirilor Atelierului Hermeneutica Bibliohtecaria (Philobiblon) .................................................................................................... ......... 21 FOCUS Noul Program al revistei şi Politica ei Editorială: PHILOBIBLON – Transylvanian Journal of Multidisciplinary Research in Humanities .............. 29 Raluca TRIFU, István KIRÁLY V., Consideraţii filosofice, epistemologice şi scientometrice legate de sensurile ştiinţei şi profesiei bibliotecare – Pentru situarea proiectului unei cercetări ............................................................ 31 Valeria SALÁNKI, Cultura organizaţională şi comunicarea în (...) bibliotecă - Studiu asupra culturii organizaţionale în Biblioteca Centrală Universitară „Lucian Blaga” din Cluj ........................................................................................ 44 Raluca TRIFU, István KIRÁLY V., Globalizare şi Individualizare, sau: Marketingul ca metaforă pentru reasumarea şi reconturarea sensurilor serviciilor de bibliotecă – O iniţiativă şi o experienţă românească .................114 Claudiu GAIU, Gabriel Naudé (1600-1653 ) – în slujba Puterii şi a Cărţii ..... 128 Alin Mihai GHERMAN, Timpul scrierii – Manuscrisele .................................... 140 Dana Maria MĂRCUŞ, Sărbătoarea cărţii. Percepţia societăţii româneşti interbelice asupra cărţii şi lecturii ...................................................................... 148 Orsolya ANTAL,Taine în jurul unei satire în spirit voltairian în limbă maghiară de la sfârşitul secolului al XVIII-lea .................................................................... 197 Kinga PAPP, Colligatul Ms 354 şi dramele pierdute ale lui József Mártonfi ....213 Gabriela RUS, Roxana BĂLĂUCĂ, Venceslav Melka în colecţia Bibliotecii Centrale Universitare „Lucian Blaga” Cluj-Napoca ........................................ 222 5 Hermeneutica Bibliothecaria – Antologie Philobiblon - Volumul V Nicolina HALGAŞ, Dimensiunea educativă a bibliotecii publice prin servicii de animaţie pentru copii ....................................................................................... 249 Tünde JANKÓ, Alina NEALCOŞ, Maria CRIŞAN, Mariana GROS, Carmen GOGA, Biblioteca Filială de Ştiinţe Economice - Tradiţional versus modern ................271 Adriana MAN SZÉKELY, Emil SALAMON, Colaborarea Bibliotecii Centrale Universitare „Lucian Blaga” din Cluj-Napoca cu Banca Mondială ............. 290 ORIZONTURI Aurel Teodor CODOBAN, Mass-media şi filosofia – Filosoful ca jurnalist, sau sinteza unei ideologii ostensive ............................................................................. 301 Marian PETCU, Şcoala de ziaristică de la Bucureşti (1951-1989) – Istorii recente .................................................................................................... .. 314 Marcel BODEA S., Timpul matematic în mecanica clasică – o perspectivă epistemologică...................................................................................... ................... 332 Florina ILIS, Fenomenul science fiction şi feţele timpului ................................ 354 Rodica FRENŢIU, Yasunari Kawabata şi nostalgia timpului fără timp ......... 373 Rodica TRANDAFIR, Timpul şi muzica .............................................................. 390 István KIRÁLY V., Întemeierea filosofiei şi ateismul la tânărul Heidegger - Prolegomene la o perspectivă existenţial-ontologică ......................................423 Elena CHIABURU, Consideraţii privitoare la vînzarea la Cochii Vechi şi mezat .................................................................................................... ............... 437 Vlad POPOVICI, Istoriografia medicală românească (1813-2008) .................463 Gheorghe VAIS, Remodelări urbane în Clujul perioadei dualiste (1867-1918)..... 481 Cristina VIDRUŢIU, Ciuma – profilul unei recurenţe istorice supusă unui transplant artistic .................................................................................................. 497 Anna Emese VINCZE, Iluziile pozitive din perspectiva psihologiei evoluţioniste .................................................................................................... 506 6 Hermeneutica Bibliothecaria – Antologie Philobiblon - Volumul V REFLEXII Florentina RĂCĂTĂIANU, Irina Petraş, Literatura română contemporană - O panoramă - Recenzie ...................................................................................... 527 Raluca TRIFU, Filosofia informaţiei si cibernetica – Recenzie ......................... 530 Iulia GRAD, Tematizări în eticile aplicate – perspective feministe (Mihaela Frunză) - Recenzie ................................................................................534 Adrian GRĂNESCU, Biblioteca lui Hitler, cărţile care i-au format personalitatea, de Timothy W. Ryback – Recenzie ............................................. 537 În colecţia BIBLIOTHECA BIBLIOLOGICA au apărut ..............................551 Revista PHILOBIBLON – Volumele apărute ......................................... 556. (shrink)

¿Qué es razonar?, ¿qué es interpretar?, ¿cómo podemos estar seguros de que determinadas interpretaciones, en ciertos contextos políticos, sociales, culturales, etc., son más razonables que otras? Estas preguntas se encuentran en el origen de dos tradiciones de pensamiento: la hermenéutica y la analítica.

Epileptogenesis involves an increase in excitatory synaptic strength in the brain in a manner similar to synaptic potentiation. In the present study we investigated the mechanisms of short-term synaptic potentiation in patients with focal epilepsy by using 5 Hz repetitive transcranial magnetic stimulation (rTMS), a non invasive neurophysiological technique able to investigate the mechanisms of synaptic plasticity in humans. Ten patients with focal idiopathic cortical epilepsy were studied. 5 Hz-rTMS (10 stimuli-trains, 120% of motor threshold, RMT) was delivered over the (...) first dorsal interosseus (FDI) motor area of both (affected and unaffected) hemispheres. Changes in the motor evoked potential (MEP) size in the FDI muscle during the trains and the RMT were measured and compared between the hemispheres. 5 Hz-rTMS was also delivered in a group of healthy subjects over both hemispheres. 5 Hz-rTMS in patients elicited a reduced MEP facilitation compared to normal subjects. The reduced MEP amplitude was more evident in the affected hemisphere than in the unaffected hemisphere. RMT in the affected hemisphere was higher than in the unaffected hemisphere and in healthy subjects. Our findings showing a decreased response to 5 Hz-rTMS over the affected hemisphere, differently from the expected results suggest a reduced cortical excitability in epileptic patients. We hypothesize an altered balance between excitatory and inhibitory circuits in epileptic patients under chronic therapy. (shrink)

This book is in honour of Professor Anna-Sofia Maurin on her 50th birthday. It consists of eighteen essays on metaphysical issues written by Swedish and international scholars.

The Anna Karenina Theory says: all conscious states are alike; each unconscious state is unconscious in its own way. This note argues that many components have to function properly to produce consciousness, but failure in any one of many different ones can yield an unconscious state in different ways. In that sense the Anna Karenina theory is true. But in another respect it is false: kinds of unconsciousness depend on kinds of consciousness.

A number of recent writers have expressed scepticism about the viability of a specifically moral concept of obligation, and some of the considerations offered have been interesting and persuasive. This is a scepticism that has its roots in Nietzsche, even if he is mentioned only rather rarely in the debate. More proximately, the scepticism in question receives seminal expression in Elizabeth Anscombe's 1958 essay, ‘Modern Moral Philosophy’, a piece that is often paid lip-service to, but—like Nietzsche's work—has only rarely been (...) taken seriously by those wishing to defend the conception of obligation under attack. This is regrettable. Anscombe's essay is powerful and direct, and it makes a forthright case for the claim that, in the absence of a divine law conception of ethics, any specifically moral concept of obligation must be redundant, and that the best that can be hoped for in a secular age is some sort of neo-Aristotelianism. Anscombe is right about this, we think. And, among those who disagree, one of the very few to have taken her on at all explicitly is Christine Korsgaard, whose Kantianism of course commits her to the view that the concept of moral obligation is central, with or without God. Here, we try to show that Korsgaard loses the argument. (shrink)

In this paper we investigate composition models of incarnation, according to which Christ is a compound of qualitatively and numerically different constituents. We focus on three-part models, according to which Christ is composed of a divine mind, a human mind, and a human body. We consider four possible relational structures that the three components could form. We argue that a ‘hierarchy of natures’ model, in which the human mind and body are united to each other in the normal way, and (...) in which they are jointly related to the divine mind by the relation of co-action, is the most metaphysically plausible model. Finally, we consider the problem of how Christ can be a single person even when his components may be considered persons. We argue that an Aristotelian metaphysics, according to which identity is a matter of function, offers a plausible solution: Christ's components may acquire a radically new identity through being parts of the whole, which enables them to be reidentified as parts, not persons. (shrink)

Book review of Maria Lugones's Pilgramages/peregrinajes: Theorizing coalition against multiple oppressions (Rowman & Littlefield 2003).

A review of Maria Luisa Ardizzone's Reading as the Angels Read: Speculation and Politics in Dante’s Banquet. Toronto: University of Toronto Press, 2016. xii 1 454 pp. $95.

El libro de María González Navarro se presenta a sí mismo como una “nueva hermenéutica” (23). La novedad involucra dos aspectos: uno que llamaremos metateórico y otro hermenéutico en propiedad. Hablando metateóricamente, el libro presenta una hermenéutica gadameriana vigorizada y robustecida por las teorías pragma-dialécticas de la argumentación. Desde el punto de vista hermenéutico propiamente dicho, la novedad reposa en que se considera que la interpretación correcta está indesligablemente vinculada a la argumentación abductiva.

Review of Maria Kronfeldner, Darwinian Creativity and Memetics, Acumen, 2011.

An introduction to our edited volume, The Metaphysics of Relations, covering a range of issues including the problem of order, the ontological status of relations, reasons for ancient scepticism about relational properties, and two ways of drawing the distinction between internal and external relations.

The Metaphysics of Relations is an anthology of thirteen original papers plus an introduction, addressing the philosophical issue of relations from a contemporary and historical perspective. The result is a remarkably coherent whole, where the different papers shed light on each other even though very few of them explicitly address interconnections. As a consequence, the book works really well as an introduction to the philosophical issue on relations, while the individual papers represent cutting edge research on the particular issues that (...) they focus on. The mix of contemporary and historical perspectives means you get a snapshot view of the contemporary issues, as well as insights into their historical development. (shrink)

A relatively unknown woman named Maria Theresa Short opened a popular observatory in 1835 in Ed inburgh - a time and place where men of science and property had long failed to make a viable space for astronomy. She exhibited scientific instruments to a general public, along with a great telescope and a walk-in camera obscura that projected live views of the city and continues to delight audiences to this day. To better understand Short's accomplishments, achieved as scientific and (...) public life became increasingly closed to women, this study explores her largely untold story, and maps some of the places of science around it. Finding local contingencies, multiple sites and practices by diverse groups, it proposes that tensions within the connections between science and spectacle and the use of popularization to promote its professionalization produced gaps that even a marginal figure like Maria Short could inhabit and exploit. (shrink)

Mit dem Werk des österreichischen Dichters kam Witold Hulewicz ziemlich früh in Berührung. Fasziniert von dessen Dichtkunst, nahm er mit Rilke Briefkontakte auf. Die Korrespondenz belebte sich wesentlich, als Hulewicz an den ersten Üb ertragungen ins Polnische arbeitete. Im vorliegenden Artikel bemüht sich die Autorin nicht nur die freundschaftlichen Kontakte darzustellen, sondern auf die Rolle Hulewiczs als Übersetzer und Verbreiter des Rilkschen Werkes in Polen hinzu weisen.