Implications of Bohmian quantum ontology for psychopathology

This article discusses the prospects of quantum psychiatry from a Bohmian point of view, which provides an ontological interpretation of quantum theory, and extends such ontology to include mind. At first, we discuss the more general relevance of quantum theory to psychopathology. The basic idea is that because quantum theory emphasizes the role of wholeness, it might be relevant to psychopathology, where breakdown of unity in the mental domain is a key feature. We then discuss the role of information in psychopathology, and consider the connections with quantum theory in this area. In particular, we discuss David Bohm’s notion of active information, which arises in the ontological interpretation of quantum theory, and is suggested to play a fundamental role as the bridge between mind and matter. Some such bridge is needed if we are to understand how subtle mental properties are able to influence more manifest physical properties in the brain (all the way to the molecular and possibly microtubular level), and how changes in those possibly quantum‐level physical processes are able to influence higher cognitive functions. We also consider the implications of the notion of active information for psychopathology. The prospects of implementing the Bohmian scheme in neuroquantal terms are then briefly considered. Finally, we discuss some possible therapeutic implications of Bohm’s approach to information and the relation of mind and matter.

Implications of Bohmian quantum ontology for psychopathology

This article discusses the prospects of quantum psychiatry from a Bohmian point of view, which provides an ontological interpretation of quantum theory, and extends such ontology to include mind. At first, we discuss the more general relevance of quantum theory to psychopathology. The basic idea is that because quantum theory emphasizes the role of wholeness, it might be relevant to psychopathology, where breakdown of unity in the mental domain is a key feature. We then discuss the role of information in psychopathology, and consider the connections with quantum theory in this area. In particular, we discuss David Bohm’s notion of active information, which arises in the ontological interpretation of quantum theory, and is suggested to play a fundamental role as the bridge between mind and matter. Some such bridge is needed if we are to understand how subtle mental properties are able to influence more manifest physical properties in the brain (all the way to the molecular and possibly microtubular level), and how changes in those possibly quantum‐level physical processes are able to influence higher cognitive functions. We also consider the implications of the notion of active information for psychopathology. The prospects of implementing the Bohmian scheme in neuroquantal terms are then briefly considered. Finally, we discuss some possible therapeutic implications of Bohm’s approach to information and the relation of mind and matter.

A Hub System for Cloud-Computing Based Business-Collaboration: Automating Ontology-Enabled Electronic Business-Service Discovery

The management and coordination of business-process collaboration experiences changes because of globalization, specialization, and innovation. Service-oriented computing (SOC) is a means towards businessprocess automation and recently, many industry standards emerged to become part of the service-oriented architecture (SOA) stack. In a globalized world, organizations face new challenges for setting up and carrying out collaborations in semi-automating ecosystems for business services. For being efficient and effective, many companies express their services electronically in what we term business-process as a service (BPaaS). Companies then source BPaaS on the fly from third parties if they are not able to create all service-value inhouse because of reasons such as lack of reasoures, lack of know-how, cost- and time-reduction needs. Thus, a need emerges for BPaaS-HUBs that not only store service offers and requests together with information about their issuing organizations and assigned owners, but that also allow an evaluation of trust and reputation in an anonymized electronic service marketplace. In this paper, we analyze the requirements, design architecture and system behavior of such a BPaaS-HUB to enable a fast setup and enactment of business-process collaboration. Moving into a cloud-computing setting, the results of this paper allow system designers to quickly evaluate which services they need for instantiationg the BPaaS-HUB architecture. Furthermore, the results also show what the protocol of a backbone service bus is that allows a communication between services that implement the BPaaS-HUB. Finally, the paper analyzes where an instantiation must assign additional computing resources vor the avoidance of performance bottlenecks.

Unified Taxonomy for Reference Ontology of Shape Features in Product Model

This paper presents a unified taxonomy of shape features. Such taxonomy is required to construct ontologies to address heterogeneity in product/shape models. Literature provides separate classifications for volumetric, deformation and free-form surface features. The unified taxonomy proposed allows classification, representation and extraction of shape features in a product model. The novelty of the taxonomy is that the classification is based purely on shape entities and therefore it is possible to automatically extract the features from any shape model. This enables the use of this taxonomy to build reference ontology.

Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions

Background: The number of genome-wide association studies (GWAS) has increased rapidly in the past couple of years, resulting in the identification of genes associated with different diseases. The next step in translating these findings into biomedically useful information is to find out the mechanism of the action of these genes. However, GWAS studies often implicate genes whose functions are currently unknown; for example, MYEOV, ANKLE1, TMEM45B and ORAOV1 are found to be associated with breast cancer, but their molecular function is unknown. Results: We carried out Bayesian inference of Gene Ontology (GO) term annotations of genes by employing the directed acyclic graph structure of GO and the network of protein-protein interactions (PPIs). The approach is designed based on the fact that two proteins that interact biophysically would be in physical proximity of each other, would possess complementary molecular function, and play role in related biological processes. Predicted GO terms were ranked according to their relative association scores and the approach was evaluated quantitatively by plotting the precision versus recall values and F-scores (the harmonic mean of precision and recall) versus varying thresholds. Precisions of similar to 58% and similar to 40% for localization and functions respectively of proteins were determined at a threshold of similar to 30 (top 30 GO terms in the ranked list). Comparison with function prediction based on semantic similarity among nodes in an ontology and incorporation of those similarities in a k nearest neighbor classifier confirmed that our results compared favorably. Conclusions: This approach was applied to predict the cellular component and molecular function GO terms of all human proteins that have interacting partners possessing at least one known GO annotation. The list of predictions is available at http://severus.dbmi.pitt.edu/engo/GOPRED.html. We present the algorithm, evaluations and the results of the computational predictions, especially for genes identified in GWAS studies to be associated with diseases, which are of translational interest.

Ontology analysis of global gene expression differences of human bone marrow stromal cells cultured on 3D scaffolds or 2D films

Differences in gene expression of human bone marrow stromal cells (hBMSCs) during culture in three-dimensional (3D) nanofiber scaffolds or on two-dimensional (2D) films were investigated via pathway analysis of microarray mRNA expression profiles. Previous work has shown that hBMSC culture in nanofiber scaffolds can induce osteogenic differentiation in the absence of osteogenic supplements (OS). Analysis using ontology databases revealed that nanofibers and OS regulated similar pathways and that both were enriched for TGF-beta and cell-adhesion/ECM-receptor pathways. The most notable difference between the two was that nanofibers had stronger enrichment for cell-adhesion/ECM-receptor pathways. Comparison of nanofibers scaffolds with flat films yielded stronger differences in gene expression than comparison of nanofibers made from different polymers, suggesting that substrate structure had stronger effects on cell function than substrate polymer composition. These results demonstrate that physical (nanofibers) and biochemical (OS) signals regulate similar ontological pathways, suggesting that these cues use similar molecular mechanisms to control hBMSC differentiation. Published by Elsevier Ltd.

MAS Ontology: uma ontologia de métodos orientados a agentes

A modelagem orientada a agentes surge como paradigma no desenvolvimento de software, haja vista a quantidade de iniciativas e estudos que remetem à utilização de agentes de software como solução para tratar de problemas mais complexos. Apesar da popularidade de utilização de agentes, especialistas esbarram na falta de universalidade de uma metodologia para construção dos Sistemas Multiagentes (MAS), pois estas acabam pecando pelo excesso ou falta de soluções para modelar o problema. Esta dissertação propõe o uso de uma Ontologia sobre Metodologias Multiagentes, seguindo os princípios da Engenharia de Métodos Situacionais que se propõe a usar fragmentos de métodos para construção de metodologias baseados na especificidade do projeto em desenvolvimento. O objetivo do estudo é sedimentar o conhecimento na área de Metodologias Multiagentes, auxiliando o engenheiro de software a escolher a melhor metodologia ou o melhor fragmento de metodologia capaz de modelar um Sistema Multiagentes.

FBS Linkage ontology and technique to support engineering change management

© 2014, Springer-Verlag London. Engineering changes are essential for any product development, and their management has become a crucial discipline. Research in engineering change management has brought about some methods and tools to support dealing with changes. This work extends the change prediction method through incorporation of a function–behaviour–structure (FBS) scheme. These additional levels of detail provide the rationales for change propagation and allow a more proactive management of changes. First, we develop the ontology of this method based on a comprehensive comparison of three seminal functional reasoning schemes. Then, we demonstrate the FBS Linkage technique by applying it to a diesel engine. Finally, we evaluate the method.

semantic oriented ontology cohesion metrics for ontology-based systems

Ontologies play a core role to provide shared knowledge models to semantic-driven applications targeted by Semantic Web. Ontology metrics become an important area because they can help ontology engineers to assess ontology and better control project management and development of ontology based systems, and therefore reduce the risk of project failures. In this paper, we propose a set of ontology cohesion metrics which focuses on measuring (possibly inconsistent) ontologies in the context of dynamic and changing Web. They are: Number of Ontology Partitions (NOP), Number of Minimally Inconsistent Subsets (NMIS) and Average Value of Axiom Inconsistencies (AVAI). These ontology metrics are used to measure ontological semantics rather than ontological structure. They are theoretically validated for ensuring their theoretical soundness, and further empirically validated by a standard test set of debugging ontologies. The related algorithms to compute these ontology metrics also are discussed. These metrics proposed in this paper can be used as a very useful complementarity of existing ontology cohesion metrics.