Building and Refining Abstract Planning Cases by Change of Representation Language

ion is one of the most promising approaches to improve the performance of problem solvers. In several domains abstraction by dropping sentences of a domain description -- as used in most hierarchical planners -- has proven useful. In this paper we present examples which illustrate significant drawbacks of abstraction by dropping sentences. To overcome these drawbacks, we propose a more general view of abstraction involving the change of representation language. We have developed a new abstraction methodology and a related sound and complete learning algorithm that allows the complete change of representation language of planning cases from concrete to abstract. However, to achieve a powerful change of the representation language, the abstract language itself as well as rules which describe admissible ways of abstracting states must be provided in the domain model. This new abstraction approach is the core of Paris (Plan Abstraction and Refinement in an Integrated System), a system in which abstract planning cases are automatically learned from given concrete cases. An empirical study in the domain of process planning in mechanical engineering shows significant advantages of the proposed reasoning from abstract cases over classical hierarchical planning.Comment: See http://www.jair.org/ for an online appendix and other files accompanying this articl

Analytical methods for bacterial kinetics studies

Methods utilize mathematical equations and models and specialized computer techniques. Techniques apply to food production, complex chemicals production, and polluted water purification

Low-Level HIV-I Replication and the Dynamics of the Resting CD4(+) T Cell Reservoir for HIV-I in the Setting of HAART

In the setting of highly active antiretroviral therapy (HAART), plasma levels of human immunodeficiency type-I (HIV-I) rapidly decay to below the limit of detection of standard clinical assays. However, reactivation of remaining latently infected memory CD4(+) T cells is a source of continued virus production, forcing patients to remain on HAART despite clinically undetectable viral loads. Unfortunately, the latent reservoir decays slowly, with a half-life of up to 44 months, making it the major known obstacle to the eradication of HIV-I infection. However, the mechanism underlying the long half-life of the latent reservoir is unknown. The most likely potential mechanisms are low-level viral replication and the intrinsic stability of latently infected cells. Methods: Here we use a mathematical model of T cell dynamics in the setting of HIV-I infection to probe the decay characteristics of the latent reservoir upon initiation of HAART. We compare the behavior of this model to patient derived data in order to gain insight into the role of low-level viral replication in the setting of HAART. Results: By comparing the behavior of our model to patient derived data, we find that the viral dynamics observed in patients on HAART could be consistent with low-level viral replication but that this replication would not significantly affect the decay rate of the latent reservoir. Rather than low-level replication, the intrinsic stability of latently infected cells and the rate at which they are reactivated primarily determine the observed reservoir decay rate according to the predictions of our model. Conclusion: The intrinsic stability of the latent reservoir has important implications for efforts to eradicate HIV-I infection and suggests that intensified HAART would not accelerate the decay of the latent reservoir.NIH AI 065960, AI 143222, AI 51178Doris Duke Charitable FoundationThe Howard Hughes Medical InstituteIntegrative Biolog

IMPOSTER PHENOMENON: DISTINCT CONSTRUCT OR ACHIEVEMENT-RELATED AFFECTIVE EXPERIENCE?

Imposter Phenomenon (IP), also known as Imposter Syndrome, is an internal experience that has been observed to occur in high achieving individuals. These individuals do not believe their achievements are due to their own abilities or hard-work: They credit external sources such as luck, errors in admissions or grading, or fooling others as the reason for any successes. IP has been observed in many populations including college professors, medical, dental, nursing and pharmacy students, librarians with graduate degrees, and other successful professionals. Previous research has found that individuals who experience IP may also experience fear of failure, fear of negative evaluation, and perfectionism. However, the literature does not appear to completely agree on whether IP is a distinct psychological phenomenon, an affective state, or a compilation of other constructs that is poorly labeled. The present study examined whether IP, fear of failure, fear of negative evaluation, and perfectionism are highly correlated with and predictive of one another, in high achieving individuals. Results indicate that high scores on measures of imposter phenomenon are associated with high scores on measures of fear of failure, fear of negative evaluation, and perfectionism; however, the relationship between variables is not significantly moderated by achievement

Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes

Functional residues in proteins tend to be highly conserved over evolutionary time. However, to what extent functional sites impose evolutionary constraints on nearby or even more distant residues is not known. Here, we report pervasive conservation gradients toward catalytic residues in a dataset of 524 distinct enzymes: evolutionary conservation decreases approximately linearly with increasing distance to the nearest catalytic residue in the protein structure. This trend encompasses, on average, 80% of the residues in any enzyme, and it is independent of known structural constraints on protein evolution such as residue packing or solvent accessibility. Further, the trend exists in both monomeric and multimeric enzymes and irrespective of enzyme size and/or location of the active site in the enzyme structure. By contrast, sites in protein–protein interfaces, unlike catalytic residues, are only weakly conserved and induce only minor rate gradients. In aggregate, these observations show that functional sites, and in particular catalytic residues, induce long-range evolutionary constraints in enzymes.Fil: Jack, Benjamin R.. University of Texas at Austin; Estados UnidosFil: Meyer, Austin G.. University of Texas at Austin; Estados UnidosFil: Echave, Julián. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Wilke, Claus O.. University of Texas at Austin; Estados Unido

RnaseIII and T4 Polynucleotide Kinase Sequence Biases and Solutions During RNA-Seq Library Construction

Background: RNA-seq is a next generation sequencing method with a wide range of applications including single nucleotide polymorphism (SNP) detection, splice junction identification, and gene expression level measurement. However, the RNA-seq sequence data can be biased during library constructions resulting in incorrect data for SNP, splice junction, and gene expression studies. Here, we developed new library preparation methods to limit such biases. Results: A whole transcriptome library prepared for the SOLiD system displayed numerous read duplications (pile-ups) and gaps in known exons. The pile-ups and gaps of the whole transcriptome library caused a loss of SNP and splice junction information and reduced the quality of gene expression results. Further, we found clear sequence biases for both 5' and 3' end reads in the whole transcriptome library. To remove this bias, RNaseIII fragmentation was replaced with heat fragmentation. For adaptor ligation, T4 Polynucleotide Kinase (T4PNK) was used following heat fragmentation. However, its kinase and phosphatase activities introduced additional sequence biases. To minimize them, we used OptiKinase before T4PNK. Our study further revealed the specific target sequences of RNaseIII and T4PNK. Conclusions: Our results suggest that the heat fragmentation removed the RNaseIII sequence bias and significantly reduced the pile-ups and gaps. OptiKinase minimized the T4PNK sequence biases and removed most of the remaining pile-ups and gaps, thus maximizing the quality of RNA-seq data.National Institute on Alcohol Abuse and Alcoholism (NIAAA) AA12404, AA019382, AA020926, AA016648National Institutes of Health (NIH) R01 GM088344Waggoner Center for Alcohol and Addiction Researc