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Structural genomics seeks to expand rapidly the number of protein structures in order to extract the maximum amount of information from genomic sequence databases. The advent of several large-scale projects worldwide leads to many new challenges in the field of crystallographic macromolecular structure determination. A novel software package called PHENIX(More)
Emotions are an important aspect of human intelligence and have been shown to play a significant role in the human decision-making process. Researchers in areas such as cognitive science, philosophy, and artificial intelligence have proposed a variety of models of emotions. Most of the previous models focus on an agent's reactive behavior, for which they(More)
Tuberculosis poses a global health emergency, which has been compounded by the emergence of drug-resistant Mycobacterium tuberculosis (Mtb) strains. We used whole-genome sequencing to compare the accumulation of mutations in Mtb isolated from cynomolgus macaques with active, latent or reactivated disease. We sequenced 33 Mtb isolates from nine macaques with(More)
The circadian clock found in Synechococcus elongatus, the most ancient circadian clock, is regulated by the interaction of three proteins, KaiA, KaiB, and KaiC. While the precise function of these proteins remains unclear, KaiA has been shown to be a positive regulator of the expression of KaiB and KaiC. The 2.0-A structure of KaiA of S. elongatus reported(More)
The pathways that comprise cellular metabolism are highly interconnected, and alterations in individual enzymes can have far-reaching effects. As a result, global profiling methods that measure gene expression are of limited value in predicting how the loss of an individual function will affect the cell. In this work, we employed a new method of global(More)
Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX(More)
Over 30% of the world's population is infected with Mycobacterium tuberculosis (Mtb), yet only ∼5-10% will develop clinical disease. Despite considerable effort, researchers understand little about what distinguishes individuals whose infection progresses to active tuberculosis (TB) from those whose infection remains latent for decades. The variable course(More)
Psychological studies on teamwork have shown that an effective team often can anticipate information needs of teammates based on a shared mental model. Existing multi-agent models for teamwork are limited in their ability to support proactive information exchange among teammates. To address this issue, we have developed and implemented a multi-agent(More)
A new software system called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is being developed for the automation of crystallographic structure solution. This will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model, and facilitate structure solution for both the novice and expert(More)
Learning users' interest categories is challenging in a dynamic environment like the Web because they change over time. This paper describes a novel scheme to represent a user's interest categories, and an adaptive algorithm to learn the dynamics of the user's interests through positive and negative relevance feedback. We propose a three-descriptor model to(More)