Srql: Sorted relational query language

A relation is an unordered collection of records. Often, however, there is an underlying order (e.g., a sequence of stock prices), and users want to pose queries that reflect this order (e.g., find a weekly moving average). SQL provides no support for posing such queries. In this paper, we show how a rich class of queries reflecting sort order can be naturally expressed and efficiently executed with simple extensions to SQL. 1

Evolutionarily Conserved Linkage between Enzyme Fold, Flexibility, and Catalysis

Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 Å away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme–substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme–substrate interactions, thereby impacting the mechanism of catalyzed chemistry. These results have implications for understanding the mechanism of allostery, and for protein engineering and drug design

SRQL: Sorted Relational Query Language

A relation is an unordered collection of records. Often, however, there is an underlying order (e.g., a sequence of stock prices), and users want to pose queries that reflect this order (e.g., find a weekly moving average). SQL provides no support for posing such queries. In this paper, we show how a rich class of queries reflecting sort order can be naturally expressed and efficiently executed with simple extensions to SQL. 1. Introduction Ordered data, or sequences, can be found in a wide range of commercial, statistical, and scientific applications. These applications require DBMS support to store, manipulate, and query sequences efficiently, and such support is missing in RDBMSs since the relational model provides sets of tuples as its only data structure. SQL [2], the most widely used query language for relational systems is incapable of answering some common queries posed by commercial and scientific applications, such as moving aggregates. One approach that is being explored in..

SRQL: Sorted Relational Query Language

A relation is an unordered collection of records. Often, however, there is an underlying order (e.g., a sequence of stock prices), and users want to pose queries that reflect this order (e.g., find a weekly moving average). SQL provides no support for posing such queries. In this paper, we show how a rich class of queries reflecting sort order can be naturally expressed and efficiently executed with simple extensions to SQL. 1. Introduction Ordered data, or sequences, can be found in a wide range of commercial, statistical, and scientific applications. These applications require DBMS support to store, manipulate, and query sequences efficiently, and such support is missing in RDBMSs since the relational model provides sets of tuples as its only data structure. SQL [2], the most widely used query language for relational systems is incapable of answering some common queries posed by commercial and scientific applications, such as moving aggregates. One approach that is being explored in..

Managing Soil Science Experiments Using ZOO

Introduction Over the past three years, in collaboration with several domain scientists, we have studied the needs of a wide range of experimental disciplines, developed solutions to some of the basic problems in experiment management, and have made significant progress towards implementing a simple Desktop Experiment Management Environment (DEME) called Zoo. Our work has proceeded in a tight loop between developing generic experiment management technology that is implemented in a generic tool, Zoo, installing customized enhancements of the tool that constitute full systems (complete Customized Desktop Experiment ManagementSystems (CDEMSs)) in laboratories 1 of interest, and using the provided feedback to guide our research directions. The overall Zoo project has been described in the 1996 VLDB Conference [7]. Specific aspects of the project and some of the Zoo mo

A potential role for stress-induced microbial alterations in IgA-associated irritable bowel syndrome with diarrhea

Stress is a known trigger for flares of inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS); however, this process is not well understood. Here, we find that restraint stress in mice leads to signs of diarrhea, fecal dysbiosis, and a barrier defect via the opening of goblet-cell associated passages. Notably, stress increases host immunity to gut bacteria as assessed by immunoglobulin A (IgA)-bound gut bacteria. Stress-induced microbial changes are necessary and sufficient to elicit these effects. Moreover, similar to mice, many diarrhea-predominant IBS (IBS-D) patients from two cohorts display increased antibacterial immunity as assessed by IgA-bound fecal bacteria. This antibacterial IgA response in IBS-D correlates with somatic symptom severity and was distinct from healthy controls or IBD patients. These findings suggest that stress may play an important role in patients with IgA-associated IBS-D by disrupting the intestinal microbial community that alters gastrointestinal function and host immunity to commensal bacteria