Context-based interaction design for smart homes

This paper presents the notion of Context-based Activity Design (CoBAD) that represents context with its dynamic changes and normative activities in an interactive system design. The development of CoBAD requires an appropriate context ontology model and inference mechanisms. The incorporation of norms and information field theory into Context State Transition Model, and the implementation of new conflict resolution strategies based on the specific situation are discussed. A demonstration of CoBAD using a human agent scenario in a smart home is also presented. Finally, a method of treating conflicting norms in multiple information fields is proposed.

Conflict resolution in overlapping information fields for context-based activity design

Norms are a set of rules that govern the behaviour of human agent, and how human agent behaves in response to the given certain conditions. This paper investigates the overlapping of information fields (set of shared norms) in the Context State Transition Model, and how these overlapping fields may affect the choices and actions of human agent. This paper also includes discussion on the implementation of new conflict resolution strategies based on the situation specification. The reasoning about conflicting norms in multiple information fields is discussed in detail.)

Modeling requirement driven architecture of adaptive healthcare system based on semiotics

In order to improve the quality of healthcare services, the integrated large-scale medical information system is needed to adapt to the changing medical environment. In this paper, we propose a requirement driven architecture of healthcare information system with hierarchical architecture. The system operates through the mapping mechanism between these layers and thus can organize functions dynamically adapting to user’s requirement. Furthermore, we introduce the organizational semiotics methods to capture and analyze user’s requirement through ontology chart and norms. Based on these results, the structure of user’s requirement pattern (URP) is established as the driven factor of our system. Our research makes a contribution to design architecture of healthcare system which can adapt to the changing medical environment.

Multi-agent based modeling and simulation of complex system in hospital

This study puts forward a method to model and simulate the complex system of hospital on the basis of multi-agent technology. The formation of the agents of hospitals with intelligent and coordinative characteristics was designed, the message object was defined, and the model operating mechanism of autonomous activities and coordination mechanism was also designed. In addition, the Ontology library and Norm library etc. were introduced using semiotic method and theory, to enlarge the method of system modelling. Swarm was used to develop the multi-agent based simulation system, which is favorable for making guidelines for hospital's improving it's organization and management, optimizing the working procedure, improving the quality of medical care as well as reducing medical charge costs.

Normative modeling for personalized clinical pathway using organizational semiotics methods

Clinical pathways are widely adopted by many large hospitals around the world in order to provide high-quality patient treatment and reduce the length and cost of hospital stay. However, nowadays most of them are static and nonpersonalized. Our objective is to capture and represent clinical pathway using organizational semiotics method including Semantic Analysis which determines semantic units in clinical pathway, their relationship and their patterns of behavior, and Norm Analysis which extracts and specifies the norms that establish how and when these medical behaviors will occur. Finally, we propose a method to develop clinical pathway ontology based on the results of Semantic Analysis and Norm analysis. This approach will give a contribution to design personalized clinical pathway by defining a set of possible patterns of behavior and theClinical pathways are widely adopted by many large hospitals around the world in order to provide high-quality patient treatment and reduce the length and cost of hospital stay. However, nowadays most of them are static and nonpersonalized. Our objective is to capture and represent clinical pathway using organizational semiotics method including Semantic Analysis which determines semantic units in clinical pathway, their relationship and their patterns of behavior, and Norm Analysis which extracts and specifies the norms that establish how and when these medical behaviors will occur. Finally, we propose a method to develop clinical pathway ontology based on the results of Semantic Analysis and Norm analysis. This approach will give a contribution to design personalized clinical pathway by defining a set of possible patterns of behavior and the norms that govern the behavior based on patient’s condition.

Fractal spatialities

This paper argues for the use of ‘fractals’ in theorising sociospatial relations. From a realist position, a nonmathematical but nonmetaphoric and descriptive view of ‘fractals’ is advanced. Insights from the natural sciences are combined with insights on the position of the observer from Luhmann and notions of assemblages and repetitions from Deleuze. It is argued that the notion of ‘fractals’ can augment current understanding of sociospatialities in three ways. First, it can pose questions about the scalar position of the observer or the grain of observation; second, as a signifier of particular attributes, it prompts observation and description of particular structuring processes; and third, the epistemic access afforded by the concept can open up possibilities for transformative interventions and thereby inform the same. The theoretical usefulness of the concept is demonstrated by discussing the territory, place, scale, and networks (TPSN) model for theorising sociospatial relations advanced by B Jessop, N Brenner, and M Jones in their 2008 paper “Theorizing sociospatial relations”, published in this journal (volume 26, pages 389–401). It is suggested that a heuristic arising from a ‘fractal’ ontology can contribute to a polymorphous, as opposed to polyvalent, understanding of sociospatial relations.

Artefact-oriented business process modelling: an ontological dependency approach

Business process modelling can help an organisation better understand and improve its business processes. Most business process modelling methods adopt a task- or activity-based approach to identifying business processes. Within our work, we use activity theory to categorise elements within organisations as being either human beings, activities or artefacts. Due to the direct relationship between these three elements, an artefact-oriented approach to organisation analysis emerges. Organisational semiotics highlights the ontological dependency between affordances within an organisation. We analyse the ontological dependency between organisational elements, and therefore produce the ontology chart for artefact-oriented business process modelling in order to clarify the relationship between the elements of an organisation. Furthermore, we adopt the techniques from semantic analysis and norm analysis, of organisational semiotics, to develop the artefact-oriented method for business process modelling. The proposed method provides a novel perspective for identifying and analysing business processes, as well as agents and artefacts, as the artefact-oriented perspective demonstrates the fundamental flow of an organisation. The modelling results enable an organisation to understand and model its processes from an artefact perspective, viewing an organisation as a network of artefacts. The information and practice captured and stored in artefact can also be shared and reused between organisations that produce similar artefacts.

Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces

Background: Early microbial colonization of the gut reduces the incidence of infectious, inflammatory and autoimmune diseases. Recent population studies reveal that childhood hygiene is a significant risk factor for development of inflammatory bowel disease, thereby reinforcing the hygiene hypothesis and the potential importance of microbial colonization during early life. The extent to which early-life environment impacts on microbial diversity of the adult gut and subsequent immune processes has not been comprehensively investigated thus far. We addressed this important question using the pig as a model to evaluate the impact of early-life environment on microbe/host gut interactions during development. Results: Genetically-related piglets were housed in either indoor or outdoor environments or in experimental isolators. Analysis of over 3,000 16S rRNA sequences revealed major differences in mucosa-adherent microbial diversity in the ileum of adult pigs attributable to differences in earlylife environment. Pigs housed in a natural outdoor environment showed a dominance of Firmicutes, in particular Lactobacillus, whereas animals housed in a hygienic indoor environment had reduced Lactobacillus and higher numbers of potentially pathogenic phylotypes. Our analysis revealed a strong negative correlation between the abundance of Firmicutes and pathogenic bacterial populations in the gut. These differences were exaggerated in animals housed in experimental isolators. Affymetrix microarray technology and Real-time Polymerase Chain Reaction revealed significant gut-specific gene responses also related to early-life environment. Significantly, indoorhoused pigs displayed increased expression of Type 1 interferon genes, Major Histocompatibility Complex class I and several chemokines. Gene Ontology and pathway analysis further confirmed these results.

Comparative genomics suggests that an ancestral polyploidy event leads to enhanced root nodule symbiosis in the Papilionoideae

Root nodule symbiosis (RNS) is one of the most efficient biological systems for nitrogen fixation and it occurs in 90% of genera in the Papilionoideae, the largest subfamily of legumes. Most papilionoid species show evidence of a polyploidy event occurred approximately 58 million years ago. Although polyploidy is considered to be an important evolutionary force in plants, the role of this papilionoid polyploidy event, especially its association with RNS, is not understood. In this study, we explored this role using an integrated comparative genomic approach and conducted gene expression comparisons and gene ontology enrichment analyses. The results show the following: (1) approximately a quarter of the papilionoid-polyploidy-derived duplicate genes are retained; (2) there is a striking divergence in the level of expression of gene duplicate pairs derived from the polyploidy event; and (3) the retained duplicates are frequently involved in the processes crucial for RNS establishment, such as symbiotic signalling, nodule organogenesis, rhizobial infection and nutrient exchange and transport. Thus, we conclude that the papilionoid polyploidy event might have further refined RNS and induced a more robust and enhanced symbiotic system. This conclusion partly explains the widespread occurrence of the Papilionoideae.

Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa

Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast-and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement.

Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array

The increasing amount of available expressed gene sequence data makes whole-transcriptome analysis of certain crop species possible. Potato currently has the second largest number of publicly available expressed sequence tag (EST) sequences among the Solanaceae. Most of these ESTs, plus other proprietary sequences, were combined and used to generate a unigene assembly. The set of 246,182 sequences produced 46,345 unigenes, which were used to design a 44K 60-mer oligo array (Potato Oligo Chip Initiative: POCI). In this study, we attempt to identify genes controlling and driving the process of tuber initiation and growth by implementing large-scale transcriptional changes using the newly developed POCI array. Major gene expression profiles could be identified exhibiting differential expression at key developmental stages. These profiles were associated with functional roles in cell division and growth. A subset of genes involved in the regulation of the cell cycle, based on their Gene Ontology classification, exhibit a clear transient upregulation at tuber onset indicating increased cell division during these stages. The POCI array allows the study of potato gene expression on a much broader level than previously possible and will greatly enhance analysis of transcriptional control mechanisms in a wide range of potato research areas. POCI sequence and annotation data are publicly available through the POCI database (http://pgrc.ipk-gatersleben.de/poci).

Theoretical perspectives of enterprise architecture

The number of published Enterprise Architecture (EA) research has increased during the last few years. As a discipline, EA is still young and lacking theoretical foundation. Lately some research trying to ground EA to theory has been published, including linkage to systems theory. Enterprise Architecture can be defined as; (i) a formal description of the current and future state(s) of an organisation, and (ii) a managed change between these states to meet organisation’s stakeholders’ goals and to create value to the organisation. Based on this definition, this conceptual paper tries to shed light to theoretical underpinnings of EA from three theoretical perspectives; EA as a communication media, EA as an activity, and EA as an information technology system. Our conclusions are that; (i) EA can be categorised as a communication media and theoretically underpinned by ontology and semiotics, (ii) EA can be explained and theoretically underpinned by Activity Theory, and (iii) EA can be categorised as an information technology system and theoretically underpinned by General Systems Theory and Technology Acceptance Theory.

Metaproteomics analysis reveals the adaptation process for the chicken gut microbiota

The animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identified Clostridiales, Bacteroidaceae, and Lactobacillaceae species as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged to Lactobacillus spp., 155 belonged to Clostridium spp., and 66 belonged to Streptococcus spp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.

A model intervenes: the many faces of moral hazard

This article builds on advances in social ontology to develop a new understanding of how mainstream economic modelling affects reality. We propose a new framework for analysing and describing how models intervene in the social sphere. This framework allows us to identify and articulate three key epistemic features of models as interventions: specificity, portability and formal precision. The second part of the article uses our framework to demonstrate how specificity, portability and formal precision explain the use of moral hazard models in a variety of different policy contexts, including worker compensation schemes, bank regulation and the euro-sovereign debt crisis.