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  • 1.
    Eriksson, Roger
    et al.
    Högskolan i Skövde, Institutionen för kommunikation och information.
    Olsson, Björn
    Högskolan i Skövde, Institutionen för kommunikation och information.
    Adapting Genetic Regulatory Models by Genetic Programming2004Inngår i: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 76, nr 1-3, s. 217-227Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this paper, we focus on the task of adapting genetic regulatory models based on gene expression data from microarrays. Our approach aims at automatic revision of qualitative regulatory models to improve their fit to expression data. We describe a type of regulatory model designed for this purpose, a method for predicting the quality of such models, and a method for adapting the models by means of genetic programming. We also report experimental results highlighting the ability of the methods to infer models on a number of artificial data sets. In closing, we contrast our results with those of alternative methods, after which we give some suggestions for future work.

  • 2.
    Fagerlind, Magnus
    et al.
    Högskolan i Skövde, Institutionen för vård och natur.
    Nilsson, Patric
    Högskolan i Skövde, Institutionen för vård och natur.
    Harlén, Mikael
    Högskolan i Skövde, Institutionen för vård och natur.
    Karlsson, Sandra
    Högskolan i Skövde, Institutionen för vård och natur.
    Rice, Scott A.
    Sch. of Biotech. and Biomol. Sci., University of New South Wales, Sydney, NSW 2052, Australia / Ctr. Mar. Biofouling and Bio-Innov., University of New South Wales, Sydney, NSW 2052, Australia.
    Kjelleberg, Staffan
    Sch. of Biotech. and Biomol. Sci., University of New South Wales, Sydney, NSW 2052, Australia / Ctr. Mar. Biofouling and Bio-Innov., University of New South Wales, Sydney, NSW 2052, Australia.
    Modeling the effect of acylated homoserine lactone antagonists in Pseudomonas aeruginosa2005Inngår i: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 80, nr 2, s. 201-213Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Pseudomonas aeruginosa is a gram-negative bacterium that causes serious illnesses, particularly in immunocompromised individuals, often with a fatal outcome. The finding that the acylated homoserine lactone quorum sensing (QS) system controls the production of virulence factors in P. aeruginosa makes this system a possible target for antimicrobial therapy. It has been suggested that an N-(3-oxododecanoyl)-homoserine lactone (3O-C12-HSL) antagonist, a QS blocker (QSB), would interfere efficiently with the quorum sensing system in P. aeruginosa and thus reduce the virulence of this pathogen. In this work, a mathematical model of the QS system in P. aeruginosa has been developed. The model was used to virtually add 3O-C12-HSL antagonists that differed in their affinity for the receptor protein and for their ability to mediate degradation of the receptor. The model suggests that very small differences in these parameters for different 3O-C12-HSL antagonists can greatly affect the success of QSB based inhibition of the QS system in P. aeruginosa. Most importantly, it is proposed that the ability of the 3O-C12-HSL antagonist to mediate degradation of LasR is the core parameter for successful QSB based inhibition of the QS system in P. aeruginosa. Finally, this study demonstrates that QSBs can shift the system to a low steady state, corresponding to an uninduced state and thus, suggests that the use of 3O-C12-HSL antagonists may constitute a promising therapeutic approach against P. aeruginosa involved infections.

  • 3.
    Karlsson, Diana
    et al.
    Högskolan i Skövde, Institutionen för vård och natur.
    Karlsson, Stefan
    Högskolan i Skövde, Institutionen för vård och natur.
    Gustafsson, Erik
    Högskolan i Skövde, Institutionen för vård och natur.
    Henriques Normark, Birgitta
    Swedish Institute for Infectious Disease Control, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
    Nilsson, Patric
    Högskolan i Skövde, Institutionen för vård och natur.
    Modeling the regulation of the competence-evoking quorum sensing network in Streptococcus pneumoniae2007Inngår i: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 90, nr 1, s. 211-223Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Competence for genetic transformation seems to play a fundamental role in the biology of Streptococcus pneumoniae and is believed to account for serotype switching, evolution of virulence factors, and rapid emergence of antibiotic resistance. The initiation of competence is regulated by the quorum sensing system referred as the ComABCDE pathway. Experimental studies reveal that competence is down-regulated a short time after its induction and several hypotheses about the mechanism(s) responsible for this shut-down have been presented. Possibly, a ComX-dependent gene product, such as a repressor or a phosphatase, is involved. To better understand the down-regulation of the competence-evoking system in S. pneumoniae, a mathematical model was set up. By analyzing the model, we suggest that shut-down of competence possibly occurs at the transcriptional level on the comCDE operon. As a result of introducing a putative comX-dependent repressor, which inhibits expression of comCDE and comX, in the mathematical model, competence is demonstrated to appear in waves. This is supported by experimental studies showing the appearance of successive competence cycles in pneumococcal batch cultures.

  • 4.
    Lindlöf, Angelica
    et al.
    Högskolan i Skövde, Institutionen för datavetenskap.
    Olsson, Björn
    Högskolan i Skövde, Institutionen för datavetenskap.
    Genetic network inference: the effects of preprocessing2003Inngår i: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 72, nr 3, s. 229-239Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Clustering of gene expression data and gene network inference from such data has been a major research topic in recent years. In clustering, pairwise measurements are performed when calculating the distance matrix upon which the clustering is based. Pairwise measurements can also be used for gene network inference, by deriving potential interactions above a certain correlation or distance threshold. Our experiments show how interaction networks derived by this simple approach exhibit low—but significant—sensitivity and specificity. We also explore the effects that normalization and prefiltering have on the results of methods for identifying interactions from expression data. Before derivation of interactions or clustering, preprocessing is often performed by applying normalization to rescale the expression profiles and prefiltering where genes that do not appear to contribute to regulation are removed. In this paper, different ways of normalizing in combination with different distance measurements are tested on both unfiltered and prefiltered data, different prefiltering criteria are considered.

  • 5.
    Windridge, David
    et al.
    Middlesex University, London, UK / University of Surrey, Guildford, UK.
    Thill, Serge
    Högskolan i Skövde, Institutionen för informationsteknologi. Högskolan i Skövde, Forskningscentrum för Informationsteknologi. University of Plymouth, UK.
    Representational fluidity in embodied (artificial) cognition2018Inngår i: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 172, s. 9-17Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Theories of embodied cognition agree that the body plays some role in human cognition, but disagree on the precise nature of this role. While it is (together with the environment) fundamentally engrained in the so-called 4E (or multi-E) cognition stance, there also exists interpretations wherein the body is merely an input/output interface for cognitive processes that are entirely computational.

    In the present paper, we show that even if one takes such a strong computationalist position, the role of the body must be more than an interface to the world. To achieve human cognition, the computational mechanisms of a cognitive agent must be capable not only of appropriate reasoning over a given set of symbolic representations; they must in addition be capable of updating the representational framework itself (leading to the titular representational fluidity). We demonstrate this by considering the necessary properties that an artificial agent with these abilities need to possess.

    The core of the argument is that these updates must be falsifiable in the Popperian sense while simultaneously directing representational shifts in a direction that benefits the agent. We show that this is achieved by the progressive, bottom-up symbolic abstraction of low-level sensorimotor connections followed by top-down instantiation of testable perception-action hypotheses.

    We then discuss the fundamental limits of this representational updating capacity, concluding that only fully embodied learners exhibiting such a priori perception-action linkages are able to sufficiently ground spontaneously-generated symbolic representations and exhibit the full range of human cognitive capabilities. The present paper therefore has consequences both for the theoretical understanding of human cognition, and for the design of autonomous artificial agents.

  • 6.
    Ziemke, Tom
    Högskolan i Skövde, Institutionen för kommunikation och information. Högskolan i Skövde, Forskningscentrum för Informationsteknologi.
    On the role of emotion in biological and robotic autonomy2008Inngår i: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 91, nr 2, s. 401-408Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper reviews some of the differences between notions of biological and robotic autonomy, and how these differences have been reflected in discussions of embodiment, grounding and other concepts in AI and autonomous robotics. Furthermore, the relations between homeostasis, emotion and embodied cognition are discussed as well as recent proposals to model their interplay in robots, which reflects a commitment to a multi-tiered affectively/emotionally embodied view of mind that takes organismic embodiment more serious than usually done in biologically inspired robotics.

  • 7.
    Ziemke, Tom
    Högskolan i Skövde, Institutionen för informationsteknologi. Högskolan i Skövde, Forskningscentrum för Informationsteknologi. Cognition & Interaction Lab, Human-Centered Systems Division, Department of Computer & Information Science, Linköping University, Linköping, Sweden.
    The body of knowledge: On the role of the living body in grounding embodied cognition2016Inngår i: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 148, s. 4-11Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Embodied cognition is a hot topic in both cognitive science and Al, despite the fact that there still is relatively little consensus regarding what exactly constitutes 'embodiment'. While most embodied Al and cognitive robotics research views the body as the physical/sensorimotor interface that allows to ground computational cognitive processes in sensorimotor interactions with the environment, more biologically based notions of embodied cognition emphasize the fundamental role that the living body - and more specifically its homeostatic/allostatic self-regulation - plays in grounding both sensorimotor interactions and embodied cognitive processes. Adopting the latter position - a multi-tiered affectively embodied view of cognition in living systems - it is further argued that modeling organisms as layered networks of bodily self-regulation mechanisms can make significant contributions to our scientific understanding of embodied cognition. 

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