| 1. |
- del Peso-Santos, Teresa, et al.
(författare)
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Coregulation by phenylacetyl-coenzyme A-responsive PaaX integrates control of the upper and lower pathways for catabolism of styrene by Pseudomonas sp. strain Y2.
- 2006
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Ingår i: J Bacteriol. - 0021-9193. ; 188:13, s. 4812-21
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Tidskriftsartikel (refereegranskat)abstract
- The P(styA) promoter of Pseudomonas sp. strain Y2 controls expression of the styABCD genes, which are required for the conversion of styrene to phenylacetate, which is further catabolized by the products of two paa gene clusters. Two PaaX repressor proteins (PaaX1 and PaaX2) regulate transcription of the paa gene clusters of this strain. In silico analysis of the P(styA) promoter region revealed a sequence located just within styA that is similar to the reported PaaX binding sites of Escherichia coli and the proposed PaaX binding sites of the paa genes of Pseudomonas species. Here we show that protein extracts from some Pseudomonas strains that have paaX genes, but not from a paaX mutant strain, can bind and retard the migration of a P(styA) specific probe. Purified maltose-binding protein (MBP)-PaaX1 fusion protein specifically binds the P(styA) promoter proximal PaaX site, and this binding is eliminated by the addition of phenylacetyl-coenzyme A. The sequence protected by MBP-PaaX1 binding was defined by DNase I footprinting. Moreover, MBP-PaaX1 represses transcription from the P(styA) promoter in a phenylacetyl-coenzyme A-dependent manner in vitro. Finally, the inactivation of both paaX gene copies of Pseudomonas sp. strain Y2 leads to a higher level of transcription from the P(styA) promoter, while heterologous expression of the PaaX1 in E. coli greatly decreases transcription from the P(styA) promoter. These findings reveal a control mechanism that integrates regulation of styrene catabolism by coordinating the expression of the styrene upper catabolic operon to that of the paa-encoded central pathway and support a role for PaaX as a major regulatory protein in the phenylacetyl-coenzyme A catabolon through its response to the levels of this central metabolite.
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| 2. |
- Krunic, Verica, et al.
(författare)
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Affordance based word-to-meaning association
- 2009
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Ingår i: ICRA. - : VDE Verlag GmbH. - 9781424427888 ; , s. 4138-4143
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Konferensbidrag (refereegranskat)abstract
- This paper presents a method to associate meanings to words in manipulation tasks. We base our model on an affordance network, i.e., a mapping between robot actions, robot perceptions and the perceived effects of these actions upon objects. We extend the affordance model to incorporate words. Using verbal descriptions of a task, the model uses temporal co-occurrence to create links between speech utterances and the involved objects, actions and effects. We show that the robot is able form useful word-to-meaning associations, even without considering grammatical structure in the learning process and in the presence of recognition errors. These word-to-meaning associations are embedded in the robot's own understanding of its actions. Thus they can be directly used to instruct the robot to perform tasks and also allow to incorporate context in the speech recognition task.
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| 3. |
- Krunic, Verica, et al.
(författare)
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Associating word descriptions to learned manipulation task models
- 2008
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Ingår i: IEEE/RSJ International Conference on Intelligent RObots and Systems (IROS). - Nice, France.
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Konferensbidrag (refereegranskat)abstract
- This paper presents a method to associate meanings to words in manipulation tasks. We base our model on an affordance network, i.e., a mapping between robot actions, robot perceptions and the perceived effects of these actions upon objects. This knowledge is acquired by the robot in an unsupervised way by self-interaction with the environment. When a human user is involved in the process and describes a particular task, the robot can form associations between the (co-occurrence of) speech utterances and the involved objects, actions and effects. We extend the affordance model to incorporate a simple description of speech as a set of words. We show that, across many experiences, the robot is able form useful word-to-meaning associations, even without considering grammatical structure in the learning process and in the presence of recognition errors. Word-to-meaning associations are then used to instruct the robot to perform tasks and also allow to incorporate context in the speech recognition task.
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| 4. |
- Morrison, John C., et al.
(författare)
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Numerical methods for solving the Hartree-Fock equations of diatomic molecules I.
- 2009
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Ingår i: Communications in Computational Physics. - 1815-2406 .- 1991-7120. ; 5:5, s. 959-985
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Tidskriftsartikel (refereegranskat)abstract
- The theory of domain decomposition is described and used to divide the variable domain of a diatomic molecule into separate regions which are solved independently. This approach makes it possible to use fast Krylov methods in the broad interior of the region while using explicit methods such as Gaussian elimination on the boundaries. As is demonstrated by solving a number of model problems, these methods enable one to obtain solutions of the relevant partial differential equations and eigenvalue equations accurate to six significant figures with a small amount of computational time. Since the numerical approach described in this article decomposes the variable space into separate regions where the equations are solved independently, our approach is very well-suited to parallel computing and offers the long term possibility of studying complex molecules by dividing them into smaller fragments that are calculated separately.
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