Guy Davenport - Academia.edu (original) (raw)
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Papers by Guy Davenport
The Plant Journal, Jun 1, 1995
Tobacco plants transformed with the RNA polymerase (RdRp) gene of potato virus X (PVX) that are e... more Tobacco plants transformed with the RNA polymerase (RdRp) gene of potato virus X (PVX) that are extremely resistant to infection by potato virus X have previously been described. The PVX-resistant plants accumulated the RdRp protein at a lower level than fully susceptible ...
This paper describes JAMES, a modern object-oriented Java framework for discrete optimization usi... more This paper describes JAMES, a modern object-oriented Java framework for discrete optimization using local search algorithms that exploits the generality of such metaheuristics by clearly separating search implementation and application from problem specification. A wide range of generic local searches are provided, including (stochastic) hill climbing, tabu search, variable neighbourhood search and parallel tempering. These can be applied easily to any user-defined problem by plugging in a custom neighbourhood for the corresponding solution type. The performance of several different search algorithms can be assessed and compared in order to select an appropriate optimization strategy. Also, the influence of parameter values can be studied. Implementations of specific components are included for subset selection, such as a predefined solution type, a generic problem definition and several subset neighbourhoods used to modify the set of selected items. Additional components for other ...
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The Central Repository provides the GCP with a central facility where digital resources can be st... more The Central Repository provides the GCP with a central facility where digital resources can be stored and shared with the entire GCP community (and beyond). The Central Repository provides a secure environment in which these resources are managed. Storage at the Central Repository provides the originator of such material the added-security of having an off-site duplicate of the resource. Conventional upload via FTP/HTTP Any type of resource can be uploaded using FTP/HTTP! The registration web page (HTTP) allows the upload of the resource file and the recording of the registration data. For very big files or when slow connections are used, as an intermediate step, the files can be uploaded to an FTP-site before they are registered. Resources that have been converted to XML (e.g. data templates) have a well-defined structure and structured queries could be performed on them. Upload of distributed resources The automated data capture maintains a list of data providers, which type resou...
This paper describes JAMES, a modern object-oriented Java framework for discrete optimization usi... more This paper describes JAMES, a modern object-oriented Java framework for discrete optimization using local search algorithms that exploits the generality of such metaheuristics by clearly separating search implementation and application from problem specification. A wide range of generic local searches are provided, including (stochastic) hill climbing, tabu search, variable neighbourhood search and parallel tempering. These can be applied easily to any user-defined problem by plugging in a custom neighbourhood for the corresponding solution type. The performance of several different search algorithms can be assessed and compared in order to select an appropriate optimization strategy. Also, the influence of parameter values can be studied. Implementations of specific components are included for subset selection, such as a predefined solution type, a generic problem definition and several subset neighbourhoods used to modify the set of selected items. Additional components for other ...
The Journal of general virology, 1997
The RNA-dependent RNA polymerase (RdRp) of potato virus X (PVX) contains a glycine-lysine-serine ... more The RNA-dependent RNA polymerase (RdRp) of potato virus X (PVX) contains a glycine-lysine-serine (GKS) motif. This motif is present in the replication enzyme of many RNA viruses and is thought to be required for nucleoside triphosphate-binding. Three single amino acid changes, glycine to alanine (AKS), lysine to asparagine (GNS) and lysine to glutamate (GES) within the GKS motif of the PVX RdRp were tested for their effect on PVX accumulation. The GNS and GES mutations rendered the virus unable to accumulate in either tobacco plants or protoplasts, whereas substitution of glycine with alanine had only a minor effect on accumulation of PVX. The glycine to alanine mutation reverted to wild-type after passage on Nicotiana clevelandii plants. These findings suggest that the GKS motif is required for PVX replication and that strong selection pressures are active to maintain necessary sequences of the viral RdRp.
The Plant Journal, Jun 1, 1995
Tobacco plants transformed with the RNA polymerase (RdRp) gene of potato virus X (PVX) that are e... more Tobacco plants transformed with the RNA polymerase (RdRp) gene of potato virus X (PVX) that are extremely resistant to infection by potato virus X have previously been described. The PVX-resistant plants accumulated the RdRp protein at a lower level than fully susceptible ...
This paper describes JAMES, a modern object-oriented Java framework for discrete optimization usi... more This paper describes JAMES, a modern object-oriented Java framework for discrete optimization using local search algorithms that exploits the generality of such metaheuristics by clearly separating search implementation and application from problem specification. A wide range of generic local searches are provided, including (stochastic) hill climbing, tabu search, variable neighbourhood search and parallel tempering. These can be applied easily to any user-defined problem by plugging in a custom neighbourhood for the corresponding solution type. The performance of several different search algorithms can be assessed and compared in order to select an appropriate optimization strategy. Also, the influence of parameter values can be studied. Implementations of specific components are included for subset selection, such as a predefined solution type, a generic problem definition and several subset neighbourhoods used to modify the set of selected items. Additional components for other ...
The Central Repository provides the GCP with a central facility where digital resources can be st... more The Central Repository provides the GCP with a central facility where digital resources can be stored and shared with the entire GCP community (and beyond). The Central Repository provides a secure environment in which these resources are managed. Storage at the Central Repository provides the originator of such material the added-security of having an off-site duplicate of the resource. Conventional upload via FTP/HTTP Any type of resource can be uploaded using FTP/HTTP! The registration web page (HTTP) allows the upload of the resource file and the recording of the registration data. For very big files or when slow connections are used, as an intermediate step, the files can be uploaded to an FTP-site before they are registered. Resources that have been converted to XML (e.g. data templates) have a well-defined structure and structured queries could be performed on them. Upload of distributed resources The automated data capture maintains a list of data providers, which type resou...
This paper describes JAMES, a modern object-oriented Java framework for discrete optimization usi... more This paper describes JAMES, a modern object-oriented Java framework for discrete optimization using local search algorithms that exploits the generality of such metaheuristics by clearly separating search implementation and application from problem specification. A wide range of generic local searches are provided, including (stochastic) hill climbing, tabu search, variable neighbourhood search and parallel tempering. These can be applied easily to any user-defined problem by plugging in a custom neighbourhood for the corresponding solution type. The performance of several different search algorithms can be assessed and compared in order to select an appropriate optimization strategy. Also, the influence of parameter values can be studied. Implementations of specific components are included for subset selection, such as a predefined solution type, a generic problem definition and several subset neighbourhoods used to modify the set of selected items. Additional components for other ...
The Journal of general virology, 1997
The RNA-dependent RNA polymerase (RdRp) of potato virus X (PVX) contains a glycine-lysine-serine ... more The RNA-dependent RNA polymerase (RdRp) of potato virus X (PVX) contains a glycine-lysine-serine (GKS) motif. This motif is present in the replication enzyme of many RNA viruses and is thought to be required for nucleoside triphosphate-binding. Three single amino acid changes, glycine to alanine (AKS), lysine to asparagine (GNS) and lysine to glutamate (GES) within the GKS motif of the PVX RdRp were tested for their effect on PVX accumulation. The GNS and GES mutations rendered the virus unable to accumulate in either tobacco plants or protoplasts, whereas substitution of glycine with alanine had only a minor effect on accumulation of PVX. The glycine to alanine mutation reverted to wild-type after passage on Nicotiana clevelandii plants. These findings suggest that the GKS motif is required for PVX replication and that strong selection pressures are active to maintain necessary sequences of the viral RdRp.