Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

As so often with his published texts, the experience of reading Nietzsche’s notebooks is at once mesmerising and infuriating. One is in the presence of a thinker who, on the one hand, meditates deeply on fundamental issues in philosophy and psychology but who, on the other, refuses to be pinned down. The fact that Nietzsche’s style is so elusive can account for the enormously disparate interpretations of his work and it is no surprise that his notebooks have been read in (...) the most extreme fashion. The notebooks have a chequered history having been variously touted as the crowning achievement of his philosophy, and as not repaying the effort of reading. (shrink)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical power and (...) great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic (...) similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Sorensen (1992) has provided two modal-logical schemas to reconstruct the logical structure of two types of destructive thought experiments: the Necessity Refuter and the Possibility Refuter. The schemas consist of five propositions which Sorensen claims but does not prove to be inconsistent.We show that the five propositions, as presented by Sorensen, are not inconsistent, but by adding a premise (and a logical truth), we prove that the resulting sextet of premises is inconsistent. Häggqvist (2009) has provided a different modal-logical schema (...) (Counterfactual Refuter), which is equivalent to four premises, again claimed to be inconsistent. We show that this schema also is not inconsistent, for similar reasons. Again, we add another premise to achieve inconsistency. The conclusion is that all three modal-logical reconstructions of the arguments that accompany thought experiments, two by Sorensen and one by Häggqvist, have now been made rigorously correct. This may inaugurate new avenues to respond to destructive thought experiments. (shrink)

[For an updated version of this thesis, see Frederik A. Bakker, Epicurean Meteorology: Sources, Method, Scope and Organization, Leiden/Boston: Brill, 2016] This dissertation consists of three studies dealing with various aspects of Epicurean cosmology. The first study discusses the Epicurean practice of explaining astronomical and meteorological phenomena by multiple alternative theories. The second study compares the meteorological accounts of Epicurus and Lucretius with other ancient meteorologies as regards the scope and order of their subject matter. The third one examines the (...) claim that Epicurus and Lucretius held the earth to be flat. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

This is a contribution to a Book symposium on The Limits of Free Will: Selected Essays by Paul Russell. Russell provides replies to three critics of The Limits of Free Will. The first reply is to Robert Wallace and focuses on the question of whether there is a conflict between the core compatibilist and pessimist components of the "critical compatibilist" position that Russell has advanced. The second reply is to Angela Smith's discussion of the "narrow" interpretation of moral responsibility (...) responsibility (as defended by R. Jay Wallace) and how best to respond to it. The third and last reply is concerned with Christopher Bennett's criticism of Russell's views concerning "motivational scepticism" and the possibility of pure practical reasons. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

This article examines the ways in which Adam Smith and G. W. F Hegel conceptualize the identity of workers in a market economy. Although both see human beings as shaped in and through social rela- tionships, the relation between the worker and his work is seen in different ways. For Smith, workers “have” human capital, while for Hegel workers “are” brewers, butchers or bakers;; their profession is part of their identity. This conceptual difference, which is reflected in different (...) “varieties of capitalism” today, shows that not only degrees, but also kinds of embeddedness need to be taken into account in discussions of the relation between individual and society. (shrink)

I examine the history of the concept of spontaneity in philosophy and the social sciences, particularly as it relates to monetary phenomena. I then offer an argument for the general significance of spontaneity. The essay concludes that scholars across the humanities and social sciences, whatever their (disciplinary, political, ideological, etc.) persuasion, would be well-served to further develop the theory of spontaneity and its social effects.

This abstract is a synopsis of the paper "An Expert System for Diagnosing Whooping Cough Using CLIPS." The bacterium Bordetella pertussis causes whooping cough, a highly infectious respiratory ailment with several phases of symptoms. An accurate and timely diagnosis is critical for effective treatment and the avoidance of future transmission. The construction of an expert system for detecting whooping cough using the CLIPS (C Language Integrated Production System) architecture is highlighted in this abstract. The expert system provides standardized and systematic (...) evaluation, which reduces the chance of misdiagnosis and improves patient outcomes. Maintenance and upgrades are required to keep the system current with growing medical knowledge. More study in this area has the potential to advance expert systems in identifying and managing a variety of medical disorders. (shrink)

Sumário. Apresentação. PARTE I. 1. O legado filosófico de P. F. Strawson, Itamar Luís Gelain e Jaimir Conte; 2 . Strawson e o caso dos metafísicos descritivos, Itamar Luís Gelain; 3. Metafísica e linguagem comum: sobre uma conturbada herança wittgensteiniana de Strawson, Jônadas Techio; 4. Strawson e Descartes, Albertinho Luiz Gallina; 5. Strawson: sobre Kant e Berkeley, Robert Calabria; 6. O empirismo pós-kantiano de Strawson, Wenceslao J. González; 7. Reabilitando Strawson, Marco Antonio Franciotti; 8. Strawson e o ceticismo em Individuals, (...) Plínio Junqueira Smith; 9. Strawson e a causação visível, João Paulo Monteiro; 10. A verdade dos fatos, Susana Badiola; 11. Estabelecer limites: implicações epistemológicas da lógica, Roberta Corvi; 12. Referência e termos singulares, Carlos E. Caorsi; 13. Strawson: da experiência possível para a ação possível, Márlon Henrique Teixeira; 14. Atitudes reativas e responsabilidade moral, Cristina de Moraes Nunes; 15. Strawson e Hume: uma comparação a propósito de “Moralidade social e ideal individual”, Amán Rosales Rodríguez; PARTE II. 16. Liberdade e ressentimento, P. F. Strawson. Tradução: Jaimir Conte; 17. Moralidade social e ideal individual, P. F. Strawson, Tradução: Jaimir Conte. Seleção bibliográfica. (shrink)

Background: Obstetrics and gynaecology are many and common, where a woman suffers from problems related to pregnancy or her reproductive organs. Any part of her body may be affected due to some symptoms that are completely related to the reproductive organs when she is in a critical period for her, whether in her menstrual cycle, pregnancy, or disease conditions. The bulk of cases of diseases related to women and childbirth are dealt with great care and special care, as all diseases (...) related to women are considered very sensitive diseases due to the presence of the disease in sensitive and not simple places. A gynaecologist is a specialist in all diseases and problems related to the female sexual organs. They perform regular preventive medical exams, such as cervical smear tests and breast exams. It also provides consultations for women of all ages about the problems of contraception, infertility and menopause. Objectives: The objective of this expert system is to help and facilitate women in diagnosing diseases related to their obstetrics and gynaecology, a simple expert system has been designed consisting of ten various common diseases that affect women whether During or without pregnancy, Methods: In this system, the system consists of a list of some common symptoms, the correct diagnosis adopted for these diseases, and how to treat diseases in the correct way with the help of a consultant obstetrician and gynaecologist, Dr. Fathi Muhammad Al-Habibi, and these diseases are: uterine cancer, cervical cancer, Infertility, double uterus, ectopic pregnancy, endometrial cancer, female sexual dysfunction, endometriosis, faecal incontinence, female infertility, CLIPS Expert System language was used to design and implement the proposed expert system. Results: The proposed ten obstetrics and gynaecology diagnostic expert system was evaluated by medical students and they were satisfied with its performance. Conclusions: The proposed expert system is very useful for obstetricians and gynaecologists, patients with reproductive system problems, and recent graduates. (shrink)

The Industrial Ontologies Foundry (IOF) was formed to create a suite of interoperable ontologies. Ontologies that would serve as a foundation for data and information interoperability in all areas of manufacturing. To ensure that each ontology is developed in a structured and mutually coherent manner, the IOF has committed to the tiered architecture of ontology building based on the Basic Formal Ontology (BFO) as top level. One of the critical elements of a successful tiered architecture build is the domain mid-level (...) ontologies. However, thus far there has been no mid-level manufacturing ontology that is based on BFO. The IOF has recently released the IOF Core version 1 beta to fill this gap. This paper documents the development process and gives an overview of the current content of the IOF Core. Finally, the paper describes how the IOF Core can be used as the basis for a more domain-specific Supply Chain Ontology. (shrink)

This essay expands on Barry Smith’s paper “Against Fantology” of 2005, which defends the view that analytic philosophy has throughout its history been marked by a tendency to conceive the syntax of first-order predicate logic as a key to ontology. I present fantology (or "F(a)ntology") in the light of a more general and in itself ontologically neutral operation that I call a default ontologization of a language. I then discuss Quine’s views, since he is the most outspoken fantologist in (...) the second half of the twentieth century. As Smith points out, “fantology sometimes takes the form of a thesis according to which the language of standard predicate logic can serve the formulation of the truths of natural science in a uniquely illuminating way”. Hence Quine’s doctrine according to which the ontological commitments of a theory become evident only when the theory has been regimented in fantological clothing. (shrink)

Objective: A deep understanding of the relationship between a scarce drug's dose and clinical response is necessary to appropriately distribute a supply-constrained drug along these lines. Summary of key data: The vast majority of drug development and repurposing during the COVID-19 pandemic – an event that has made clear the ever-present scarcity in healthcare systems –has been ignorant of scarcity and dose optimisation's ability to help address it. Conclusions: Future pandemic clinical trials systems should obtain dose optimisation data, as these (...) appear necessary to enable appropriate scarce resource allocation according to societal values. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

PREMISSA No século XIX, ocorreram transformações impulsionadas pela emergência de novas fontes energéticas (água e petróleo), por novos ramos industriais e pela alteração profunda nos processos produtivos, com a introdução de novas máquinas e equipamentos. Depois de 300 anos de exploração por parte das nações europeias, iniciou -se, principalmente nas colônias latino-americanas, um processo intenso de lutas pela independência. É no século XIX, já com a consolidação do sistema capitalista na Europa, que se encontra a herança intelectual mais próxima da (...) qual surgirá a Sociologia como ciência particular. No início desse século, as ideias do Conde de Saint-Simon (1760-1825), de Georg Wilhelm Friedrich Hegel (1770-1831), de David Ricardo (1772-1823) e de Charles Darwin (1809-1882), entre outros, foram o elo para que Alexis de Tocqueville (1805-1859), Auguste Comte (1798-1857), Karl Marx (1818 -1883) e Herbert Spencer (1820-1903), entre outros, desenvolvessem reflexões sobre a sociedade de seu tempo. Auguste Comte e Karl Marx foram os pensadores que lançaram as bases do pensamento sociológico e de duas grandes tradições – a positivista e a socialista – que muito influenciaram o desenvolvimento da Sociologia no Brasil. 1 AUGUSTE COMTE E A TRADIÇÃO POSITIVISTA Isidore Auguste Marie François Xavier Comte nasceu em Montpellier, na França, em 19 de janeiro de 1798. Com 16 anos de idade, ingressou na Escola Politécnica de Paris, fato que teria significativa influência na orientação posterior de seu pensamento. De 1817 a 1824, foi secretário do Conde de Saint-Simon. Comte declarou que, com Saint -Simon, aprendeu muitas coisas que jamais encontraria nos livros e que, no pouco tempo em que conviveu com o conde, fez mais progressos do que faria em muitos anos, se estivesse sozinho. Toda a obra de Comte está permeada pelos acontecimentos que ocorreram após a Revolução Francesa de 1789. Ele defendeu parte dos princípios revolucionários e criticou a restauração da monarquia, preocupando-se fundamentalmente em reorganizar a sociedade, que, no seu entender, estava em ebulição e mergulhada no caos. Para Comte, a desordem e a anarquia imperavam em virtude da confusão de princípios (metafísicos e teológicos), que não se adequavam à sociedade industrial em expansão. Era, portanto, necessário superar esse estado de coisas, usando a razão como fundamento da nova sociedade. Propôs, então, a mudança da sociedade por meio da reforma intelectual plena das pessoas. De acordo com o pensador, com a modificação do pensamento humano, por meio do método científico, que ele chamava de “filosofia positiva”, haveria uma reforma das instituições. Com a proposta do estudo da sociedade por meio da análise de seus processos e estruturas, e da reforma prática das instituições, Comte criou uma nova ciência, à qual deu o nome de “física social”, passando a chamá-la posteriormente de Sociologia. A Sociologia representava, para Comte, o coroamento da evolução do conhecimento, mediante o emprego de métodos utilizados por outras ciências, que buscavam conhecer os fenômenos constantes e repetitivos da natureza: a observação, a experimentação, a comparação e a classificação. De acordo com esse pensador, a Sociologia, como as ciências naturais, deve sempre procurar a reconciliação entre os aspectos estáticos e os dinâmicos do mundo natural ou, no caso da sociedade humana, entre a ordem e o progresso. O lema da “filosofia positiva” proposta por Comte era “conhecer para prever, prever para prover”, ou seja, o conhecimento é necessário para fazer previsões e também para solucionar possíveis problemas. A influência de Comte no desenvolvimento da Sociologia foi marcante, sobretudo, na escola francesa, evidenciando-se em Émile Durkheim e seus contemporâneos e seguidores. Seu pensamento esteve presente em muitas das tentativas de criar tipologias para explicar a sociedade. Suas principais obras são: Curso de filosofia positiva (1830-1842), Discurso sobre o espírito positivo (1848), Catecismo positivista (1852) e Sistema de política positiva (1854). Para concluirmos, Comte explanava que para a superação da anarquia reinante na nova sociedade industrial, a filosofia positivista defendia a subordinação do progresso à ordem. O mesmo era contra o retorno de Luís XVIII ao trono: em sua concepção, a sociedade industrial que emergia requeria um governo fundado na razão. 2 A TRADIÇÃO SOCIALISTA: KARL MARX E FRIEDRICH ENGELS Karl Heinrich Marx nasceu em Tréveris, na antiga Prússia, hoje Alemanha, em 1818 e, em 1830, ingressou no Liceu Friedrich Wilhelm, nessa mesma cidade. Anos depois, foi cursar Direito na Universidade de Bonn, transferindo-se para Berlim em seguida. Pouco a pouco, entretanto, seus interesses migraram para a Filosofia, área na qual defendeu, em 1841, a tese de doutorado A diferença da filosofia da natureza em Demócrito e Epicuro. Sua vida universitária foi marcada pelo debate político e intelectual influenciado pelo pensamento de Ludwig Feuerbach (1804-1872) e, principalmente, pelo de Georg Wilhelm Friedrich Hegel (1770- 1831). Friedrich Engels (1820-1895) nasceu em Barmen (Renânia), na antiga Prússia, hoje Alemanha, filho mais velho de um rico industrial do ramo têxtil. Terminou sua formação secundária em 1837 e a partir de então sua formação intelectual foi por conta própria (autodidata), com alguns cursos universitários esparsos e de curta duração. Desde cedo começou a trabalhar nas empresas de seu pai e foi nessa condição que se deslocou para Bremen por três anos e depois foi enviado pelos pais a Manchester, na Inglaterra, onde trabalhou nas fábricas da família. Engels ficou impressionado com a miséria na qual viviam os trabalhadores das fábricas inglesas. Os dois, Marx e Engels, se encontraram em 1842, quando Marx passou a escrever para A Gazeta Renana, jornal da província de Colônia, do qual Engels era colaborador e mais tarde editor-chefe. O jornal, que criticava o poder prussiano, foi fechado em 1843, e Marx se viu desempregado. Ao perder o emprego, mudou-se para Paris, na França. Ali escreveu, em 1844, os Manuscritos econômico-filosóficos (só publicados em 1932) e, junto com F. Engels, o livro A sagrada família. Por sua vez, F. Engels, em 1844, decidiu voltar para a Alemanha, onde publicou, em 1845, A situação da classe trabalhadora na Inglaterra. Entre 1845 e 1847, Marx exilou-se em Bruxelas, na Bélgica, onde escreveu A ideologia alemã (em parceria com Friedrich Engels) e Miséria da filosofia (1847), obra na qual criticou o filósofo Pierre-Joseph Proudhon (1809-1865). Em 1848, ainda na Bélgica, a parceria com Engels se solidificou ao escreverem juntos o livreto O Manifesto Comunista. Em 1848, Marx foi expulso da Bélgica e retornou a Colônia, na Alemanha (Prússia), sempre pensando na possibilidade de uma mudança estrutural em sua terra natal. Isso, entretanto, não aconteceu e Marx foi expulso da Alemanha em 1849, ano em que migrou para Londres, na Inglaterra, onde permaneceu até o fim da vida. Lá escreveu O 18 Brumário de Luís Bonaparte (1852), sua mais importante obra de reflexão sobre a vida política europeia do século XIX, desenvolveu pesquisas e concluiu seu maior trabalho: O capital: crítica da economia política. O primeiro volume dessa obra foi publicado em 1867; os outros três, em 1885, 1894 e 1905, após a morte de Marx, revisados por F. Engels. 2.1 O contexto histórico e a obra de Marx e Engels Para situar a obra de Marx e Engels, é necessário conhecer um pouco do que acontecia em meados do século XIX. Com as transformações que ocorriam no mundo ocidental, principalmente na esfera da produção industrial, houve um crescimento expressivo no número de trabalhadores industriais urbanos, com uma consequência evidente: precariedade da vida dos operários nas cidades. As condições de trabalho no interior das fábricas eram péssimas. Os empregados eram superexplorados, alimentavam-se mal e trabalhavam em ambientes insalubres. Para enfrentar essa situação e tentar modificá-la, os trabalhadores passaram a se organizar em associações e sindicatos e a promover movimentos de reivindicação. Desenvolveu-se, então, uma discussão das condições sociais, políticas e econômicas para se definirem as possibilidades de intervenção nessa realidade. Desde o início do século XIX, muitos pensadores discutiram essas questões, nas perspectivas socialista e anarquista. Na Inglaterra podem ser citados, entre outros: William Godwin (1756-1836), Thomas Spence (1750-1814), Thomas Paine (1737-1809), Robert Owen (1771-1858) e Thomas Hodgkin (1787-1866). Na França, destacaram-se Étienne Cabet (1788- 1856), Flora Tristan (1803-1844), Charles Fourier (1772-1837) e Pierre-Joseph Proudhon (1809-1865). Marx e Engels levaram em conta esses pensadores, debatendo com alguns contemporâneos e criticando-os. Além disso, incorporaram a tradição da economia clássica inglesa, presente principalmente nas obras de Adam Smith e de David Ricardo. Pode-se dizer, portanto, que Marx e Engels desenvolveram seu trabalho com base na análise crítica da economia política inglesa, do socialismo utópico francês e da filosofia alemã. Esses dois autores não buscavam definir uma ciência específica para estudar a sociedade (como a Sociologia, para Auguste Comte) ou situar seu trabalho em um campo científico particular. Em alguns escritos, Marx afirmou que a História seria a ciência que mais se aproximava de suas preocupações, por abarcar as múltiplas dimensões da sociedade, a qual deveria ser analisada na totalidade, não havendo uma separação rígida entre os aspectos sociais, econômicos, políticos, ideológicos, religiosos, culturais etc. O objetivo de Marx e Engels era estudar criticamente a sociedade capitalista com base em seus princípios constitutivos e em seu desenvolvimento, visando dotar a classe trabalhadora de uma análise política da sociedade de seu tempo. Assim, a tradição socialista nascida da luta dos trabalhadores, muitos anos antes e em situações diferentes, tem como expressão intelectual o pensamento de Karl Marx e Friedrich Engels. Para entender as concepções fundamentais de Marx e Engels é necessário fazer a conexão entre as lutas da classe trabalhadora, suas aspirações e as ideias revolucionárias que estavam presentes no século XIX na Europa. Para eles, o conhecimento científico da realidade só tem sentido quando visa à transformação dessa mesma realidade. A separação entre teoria e prática não é discutida, pois a “verdade histórica” não é algo abstrato e que se define teoricamente; sua verificação está na prática. Apesar de haver algumas diferenças em seus escritos, os elementos essenciais do pensamento de Marx e Engels podem ser assim sintetizados: • historicidade das ações humanas – crítica ao idealismo alemão; • divisão social do trabalho e o surgimento das classes sociais – a luta de classes; • o fetichismo da mercadoria e o processo de alienação; • crítica à economia política e ao capitalismo; • transformação social e revolução; • utopia – sociedade comunista. A obra desses dois autores é muito vasta e não ficou vinculada estritamente aos movimentos sociais dos trabalhadores. Pouco a pouco foi introduzida nas universidades como parte do estudo em diferentes áreas do conhecimento. Estudiosos de Filosofia, Sociologia, Ciência Política, Economia, História e Geografia, entre outras áreas, foram influenciados por ela. Na Sociologia, como afirma Irving M. Zeitlin, no livro Ideología y teoría sociológica, tanto Max Weber quanto Émile Durkheim fizeram, em suas obras, um debate com as ideias de Karl Marx. Pelas análises da sociedade capitalista de seu tempo e a repercussão que tiveram em todo o mundo, principalmente no século XX, nos movimentos sociais e nas universidades, Marx e Engels são considerados autores clássicos da Sociologia. No campo dessa disciplina, porém, o pensamento deles ficou um pouco restrito, pois perdeu aquela relação entre teoria e prática (práxis), ou seja, entre a análise crítica e a prática revolucionária. Essa relação esteve presente, por exemplo, na vida e na obra dos russos Vladimir Ilitch Ulianov, conhecido como Lênin (1870-1924), e Leon D. Bronstein, conhecido como Trotsky (1879-1940), da alemã Rosa Luxemburgo (1871-1919) e do italiano Antonio Gramsci (1891- 1937), que tiveram significativa influência no movimento operário do século XX. Com base no trabalho de Marx e Engels, muitos autores desenvolveram estudos acadêmicos em vários campos do conhecimento. Podemos citar, por exemplo, Georg Lukács (1885-1971), Theodor Adorno (1903-1969), Walter Benjamin (1892-1940), Henri Lefebvre (1901-1991), Lucien Goldmanm (1913 -1970), Louis Althusser (1918 -1990), Nikos Poulantzas (1936-1979), Edward P. Thompson (1924-1993) e Eric Hobsbawm (1917 -2012). O pensamento de Marx e Engels continua, assim, presente em todo o mundo, com múltiplas tendências e variações, sempre gerando controvérsias. REFERENCIAL TEÓRICO GEMKOW, H.; PSUA, I. M. L. Marx e Engels: Vida e Obra. São Paulo: Alfa e Ômega, 1984. 232 pp. GIANOTTI, J. A. Comte. São Paulo: Abril Cultural, 1978. 318 pp. (Col. Os Pensadores) KONDER, L. Marx: vida e obra. 7ª ed. São Paulo: Paz e Terra, 2007. 154 pp. (Col. Vida e Obra). (shrink)

La filosofía de la ciencia se desarrolló durante la primera mitad del siglo xx bajo el supuesto de que la ciencia podía caracterizarse por la estructura lógica tanto del conocimiento articulado en las teorías más exitosas como de sus explicaciones. En la segunda mitad del siglo xx se cuestiona fuertemente esa idea, pero se sigue asumiendo que la filosofía de la ciencia debe hacerse siguiendo los cánones de una epistemología fundamentalista que considera que el avance de la ciencia pasa por (...) una ontología cada vez mas austera guiada por la idea de "mientras menos mejor". Desde esta perspectiva fundamentalista, el que las diferentes ciencias hablen de diferentes tipos de cosas es un obstáculo al entendimiento, producto de la imperfección del conocimiento actual. Este ideal nos invita a pensar que la epistemología debe hacerse reflexionando sobre el conocimiento articulado en nuestras teorías más austeras y nos compromete con propuestas reduccionistas problemáticas que no permiten explicar la diversidad de recursos epistémicos que de hecho utilizan los científicos. En este libro promovemos una epistemología que no sigue el lema de "mientras menos mejor", sino el de "organizar nuestros recursos epistémicos de manera que se genere entendimiento". Así, la misma estructura de las explicaciones y las prácticas (que incluye métodos y normas respecto de lo que se considera plausible y valioso) es lo que nos da la pauta para responder a la pregunta de qué es lo que hay. Esta estrategia epistémica nos obliga a hacer una filosofía de la ciencia muy cercana a la ciencia, reconociendo la pluralidad de sus métodos, objetivos y prácticas, sin reducir la filosofía de la ciencia a la sociología o a cualquier otra ciencia en particular. (shrink)

Background: There is no doubt that strawberry diseases are one of the most important reasons that led to the destruction of strawberry plants and their crops. This leads to obvious damage to these plants and they become inedible. Discovering these diseases after a good step for proper and correct treatment. Determining the treatment with high accuracy depends on the method used in the diagnosis. Correctly, expert systems can greatly help in avoiding damage to these plants. The expert system correctly diagnoses (...) strawberry disease to make it easier for farmers to find the right treatment based on the appropriate diagnosis. Objectives: The main goal of this expert system is to get the appropriate diagnosis of disease and the correct treatment. Methods: In this paper the design of the proposed Expert System which was produced to help Farmers and students interested in agriculture strawberry in diagnosing many of the strawberry diseases such as: Leaf Spots, Grey Mold, Red Stele/Red Core, Wilt, Powdery Mildew, Alternaria Spot, Black Root Rot, Anthracnose (black spot), and Angular Leaf Spot. The proposed expert system presents an overview about strawberry diseases are given, the cause of diseases are outlined and the treatment of disease whenever possible is given out. CLIPS language was used for designing and implementing the proposed expert system. Results: The proposed strawberry diseases diagnosis expert system was evaluated by Farmers and they were satisfied with its performance. Conclusions: The Proposed expert system is very useful for Farmers with strawberry problem and students interested in agriculture strawberry. (shrink)

Information communications and Technology were introduced into secondary schools with the goal of giving teachers access to information while encouraging their distinctive and innovative techniques for teaching and learning. Teachers become enthusiastic and committed to their work when given demanding tasks that result in positive educational outcomes. However, it is clear that instructors in Kenya continue to fall behind in this area. Without a grasp of leadership behaviors, ICT integration in Kenya remains a phantom. The study aims to evaluate the (...) principal's intellectual stimulation techniques and the empowering use of ICT in teaching and learning in Kenyan public secondary schools. The study used a sequential explanatory mixed method design and focused on 62 school principals chosen through census, 186 teachers, and 372 students selected using a simple random sample process. Data was collected using MLQ-structured questionnaire interviews, document analysis, and checklists. Descriptive analysis was used to explain the patterns in the data and the status of variables, while inferential analysis was used to evaluate the relationship between the variables using regression analysis. The study found a moderately substantial positive correlation between ICT use in school and intellectual stimulation r (108) = 0.534, p < 0.001). It was discovered that principals' actions were a significant predictor of ICT adoption in secondary schools; therefore, principals were recommended to foster a culture of trust among teachers by establishing a welcoming workplace atmosphere. This would encourage instructors to overcome challenges using creative and new approaches, ultimately boosting the usage of ICT in the classroom. (shrink)

The study’s main thesis is that respect for some moral values is a condition for methodologically rational decisions, namely, decisions which do not satisfy the condition are either not methodologically rational at all, or not fully rational. The paper shows supporting arguments for the thesis in terms of the philosophical theories by Aristotle, Immanuel Kant, Tadeusz Kotarbiński, Max Weber, Jean-Paul Sartre and some other thinkers. Their presentation undergoes phenomenological analysis of the phenomenon of decision making.

One of the more obscure arguments for Rawls’ difference principle dubbed ‘the Pareto argument for inequality’ has been criticised by G. A. Cohen (1995, 2008) as being inconsistent. In this paper, we examine and clarify the Pareto argument in detail and argue (1) that justification for the Pareto principles derives from rational selfinterest and thus the Pareto principles ought to be understood as conditions of individual rationality, (2) that the Pareto argument is not inconsistent, contra Cohen, and (3) that the (...) kind of bargaining model required to arrive at the particular unequal distribution that the difference principle picks out is a model that is not based on bargaining according to one’s threat advantage. (shrink)

IPCC SPECIAL REPORT ON CLIMATE CHANGE AND LAND (SRCCL) -/- Chapter 3: Climate Change and Land: An IPCC special report on climate change, desertification, land degradation, sustainable land management, food security, and greenhouse gas fluxes in terrestrial ecosystems.

Influential interpretations of Heidegger’s Origin of the Work of Art focus on the view that great art is massive and communal—typically structures like temples and cathedrals. This approach, however, faces two interpretive problems. First, what are we to do with artworks in the essay that clearly are not monumental or communal, such as van Gogh’s Shoes? Second, how should we understand our experience of works such as the Greek temple, which once were but are no longer central in this way? (...) Heidegger himself says that great art of the past becomes either a relic of the past or a mere object of aesthetic experience, but his description of his own experience with a Greek temple seems to contradict this. To understand Heidegger’s views on art—including his explicit claims about the limited vitality of great art of the past and his unintentional case for the continued power of great art of the past—it is crucial to distinguish, first, between Heidegger’s notions of world and worldhood, and, second, between two senses of what makes art great—world disclosure and world gathering. Doing so allows us to make better sense both of the essay as a whole and the potential continued vitality of great art of the past. (shrink)

The search for understanding is a major aim of science. Traditionally, understanding has been undervalued in the philosophy of science because of its psychological underpinnings; nowadays, however, it is widely recognized that epistemology cannot be divorced from psychology as sharp as traditional epistemology required. This eliminates the main obstacle to give scientific understanding due attention in philosophy of science. My aim in this paper is to describe an account of scientific understanding as an emergent feature of our mastering of different (...) (causal) explanatory frameworks that takes place through the mastering of scientific practices. Different practices lead to different kinds of representations. Such representations are often heterogeneous. The integration of such representations constitute understanding. (shrink)

Voltaire has presented in his Letters on the English different themes, from religious ethics, literacy, politics, to dramas and science. The letters present us a comparison between England and France. In this parallel we shall present how Voltaire was concerned in evaluate a high standard of taste and refinements. This paper will review some of the last letters of those, which testify about this criterion of taste as a modern point of view. We shall present in Voltaire the eminence of (...) modernity in taste, refinements and on liberty of enjoying the ecstasies of a cosmopolitan life fulfilled with entertainments and luxury. We shall present how Voltaire fought against barbarism in benefit of civilization and some how against religiosity in benefit of an ethic hedonism. (shrink)

Abstract: Artificial Intelligence (AI) is revolutionizing the agricultural sector by enhancing productivity and sustainability. This paper explores the transformative impact of AI technologies on agriculture, focusing on their applications in precision farming, predictive analytics, and automation. AI-driven tools enable more efficient management of crops and resources, leading to improved yields and reduced environmental impact. The paper examines key AI technologies, including machine learning algorithms for crop monitoring, robotics for automated planting and harvesting, and data analytics for optimizing resource use. Additionally, (...) it addresses challenges such as data privacy, technology adoption barriers, and the ethical implications of AI in farming. By integrating AI into agricultural practices, the industry can achieve greater efficiency and sustainability, paving the way for future advancements. (shrink)

Jus post Bellum is, like Jus ad Bellum and Jus in Bello, a part of just war theory. Jus post Bellum is distinguished from the other parts of just war theory by being primarily concerned with the principles necessary for securing a just and lasting peace after the end of a war. Traditionally, jus post bellum has focused primarily on three goals: [1] compensating those who have been the victims of unjust aggression, while respecting the rights of the aggressors, [2] (...) punishing and rehabilitating those guilty of war crimes and other violations of the principles of Jus ad Bellum and Jus in Bello and [3] developing measures that will prevent future war and violence (Orend 2000 and May 2012). In this chapter, I outline an account of political forgiveness and explain the role that political forgiveness can have in promoting the goals of jus post bellum. My conception of political forgiveness requires some unpacking. Let me begin with individual forgiveness, which I understand along familiar Butlerian lines as the renunciation of resentment (Butler, Sermon IX in McNaughton 2017: 75-83), though with a bit of a twist. More exactly, ● An individual, I, forgives J for doing F if and only if I renounces all her own warrant for resenting J for doing F. Resentment is a judgment-sensitive attitude, and, therefore, it tends to track judgments concerning its warrant (Scanlon 1998: 20 and Smith 2015). In cases of perfect forgiveness, I’s renunciation causes her to cease feeling resentment toward J for doing F, though, of course, less perfect cases are possible. I reject the idea that there is a sharp discontinuity between individual and political forgiveness, a position argued for by, e.g., Peter Digeser (1998 and 2001). By contrast, I understand political forgiveness as the renunciation of resentment by the relevant political body in question. With greater precision, ● A sovereign political body, P, forgives J for doing F if and only if P renounces all warrant that its citizens have for resenting, as part of their public lives, J for doing F. A little more explanation is in order. Sovereign political bodies, such as national governments, claim degrees of control over the lives of their citizens, in both their public and their private aspects, though the claims with respect to the former tend to be considerably more expansive than the claims with respect to the latter. I assume here that, at least in the case of legitimate governments, these claims of control are often valid. Such governments may reasonably renounce certain grounds for motivating action in the public sphere. For example, governments may renounce all warrant that its citizens have, as part of their public lives, for hating members of marginalized groups. In practice, this means that, while citizens might continue to act in their private lives out of hatred for members of these groups, their appeal to this hatred is seen by the state as irrelevant to matters of law and public policy as well as being wholly out-of-place in public discourse. Political forgiveness toward J for doing F, as I understand it, involves an analogous rejection of resentment, on the part of citizens in their public lives, toward J for doing F. I turn now to the matter of how political forgiveness supports securing a just and lasting peace between former belligerents. With respect to the first goal of jus post bellum, political forgiveness helps to balance compensation for victims and respect for the rights of defeated aggressors by countering the all-too-human tendency to overvalue harms done to oneself and to members of one’s group. As regards the second goal, political forgiveness plays a similar role but also provides a model for rehabilitation by exemplifying among the victorious the behavior to be emulated by the vanquished. Finally, political forgiveness promotes the third goal of jus post bellum by providing a space for nations to meet as moral equals rather than allowing one nation to have the moral high ground over the other. None of this, of course, means that political forgiveness should be unearned or that it should be confused with condonation (Kolnai 1973 and Pettigrove 2004). However, the question of what is required to put oneself in a position to be forgiven as part of jus post bellum is a matter that goes beyond the scope of this chapter. (shrink)

Background: -/- One influential view is that vulnerability to major depressive disorder (MDD) is associated with a proneness to experience negative emotions in general. In contrast, blame attribution theories emphasise the importance of blaming oneself rather than others for negative events. Our previous exploratory study provided support for the attributional hypothesis that patients with remitted MDD show no overall bias towards negative emotions, but a selective bias towards emotions entailing self-blame relative to emotions that entail blaming others. More specifically, we (...) found a decreased proneness for contempt/disgust towards others relative to oneself (i.e. self-contempt bias). Here, we report a definitive test of the competing general negative versus specific attributional bias theories of MDD. Methods: -/- We compared a medication-free remitted MDD (n = 101) and a control group (n = 70) with no family or personal history of MDD on a previously validated experimental test of moral emotions. The task measures proneness to specific emotions associated with different types of self-blame (guilt, shame, self-contempt/disgust, self-indignation/anger) and blame of others (other-indignation/anger, other-contempt/disgust) whilst controlling for the intensity of unpleasantness. Results: -/- We confirmed the hypothesis that patients with MDD exhibit an increased self-contempt bias with a reduction in contempt/disgust towards others. Furthermore, they also showed a decreased proneness for indignation/anger towards others. Conclusions: -/- This corroborates the prediction that vulnerability to MDD is associated with an imbalance of specific self- and other-blaming emotions rather than a general increase in negative emotions. This has important implications for neurocognitive models and calls for novel focussed interventions to rebalance blame in MDD. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Importance: Patients with remitted major depressive disorder (MDD) were previously found to display abnormal functional magnetic resonance imaging connectivity (fMRI) between the right superior anterior temporal lobe (RSATL) and the subgenual cingulate cortex and adjacent septal region (SCSR) when experiencing self-blaming emotions relative to emotions related to blaming others (eg, "indignation or anger toward others"). This finding provided the first neural signature of biases toward overgeneralized self-blaming emotions (eg, "feeling guilty for everything"), known to have a key role in cognitive (...) vulnerability to MDD. It is unknown whether this neural signature predicts risk of recurrence, a crucial step in establishing its potential as a prognostic biomarker, which is urgently needed for stratification into pathophysiologically more homogeneous subgroups and for novel treatments. -/- Objective: To use fMRI in remitted MDD at baseline to test the hypothesis that RSATL-SCSR connectivity for self-blaming relative to other-blaming emotions predicts subsequent recurrence of depressive episodes. -/- Design, setting, and participants: A prospective cohort study from June 16, 2011, to October 10, 2014, in a clinical research facility completed by 75 psychotropic medication-free patients with remitted MDD and no relevant comorbidity. In total, 31 remained in stable remission, and 25 developed a recurring episode over the 14 months of clinical follow-up and were included in the primary analysis. Thirty-nine control participants with no personal or family history of MDD were recruited for further comparison. -/- Main outcomes and measures: Between-group difference (recurring vs stable MDD) in RSATL connectivity, with an a priori SCSR region of interest for self-blaming vs other-blaming emotions. -/- Results: We corroborated our hypothesis that during the experience of self-blaming vs other-blaming emotions, RSATL-SCSR connectivity predicted risk of subsequent recurrence. The recurring MDD group showed higher connectivity than the stable MDD group (familywise error-corrected P < .05 over the a priori SCSR region of interest) and the control group. In addition, the recurring MDD group also exhibited RSATL hyperconnectivity with the right ventral putamen and claustrum and the temporoparietal junction. Together, these regions predicted recurrence with 75% accuracy. -/- Conclusions and relevance: To our knowledge, this study is the first to provide a robust demonstration of an fMRI signature of recurrence risk in remitted MDD. Additional studies are needed for its further optimization and validation as a prognostic biomarker. (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)