Abstract: Data in a database describe an application domain such as a satisfiability problem. The data are represented in a manner that expresses the structure inherent in the data and one such representation uses group theory and represents the data as one or more “augmented clauses,” where each clause has a pair (c, G) including a database element c and a group G of group elements g acting on it. A query is encoded in a group theory representation and is executed on the group theory representation of the data to identify database elements and associated group elements satisfying the query. If desired, the satisfying database elements are converted from the group theory representation to the native representation of the data.

Abstract: This disclosure provides methods for detecting and localizing DNA mutations by DNA microarray. In various embodiments, the described methods include use of restriction endonuclease(s) and/or mismatch-recognition nuclease(s) to detect and/or localize mutations. In one representative method, reference and target DNA are digested using one or more restriction endonucleases, resultant DNA strands are labeled (e.g., using a DNA polymerase), and the labeled mixture of DNAs is hybridized to a microarray. In another representative method, reference and target DNA are denatured and annealed to form a mixture containing heteroduplex DNA, one or more mismatch-recognition nuclease(s) are used to nick or cleave at least a portion of the heteroduplex DNA, resultant DNA strands are labeled (e.g., using a DNA polymerase) and the labeled mixture of DNAs is hybridized to a microarray.

Abstract: A method for forming arrays of metal, alloy, semiconductor or magnetic clusters is described. The method comprises placing a scaffold on a substrate, the scaffold comprising molecules selected from the group consisting of polynucleotides, polypeptides, and perhaps combinations thereof. Polypeptides capable of forming ? helices are currently preferred for forming scaffolds. Arrays are then formed by contacting the scaffold with plural, monodispersed ligand-stabilized clusters. Each cluster, prior to contacting the scaffold, includes plural exchangeable ligands bonded thereto. If the clusters are metal clusters, then the metal preferably is selected from the group consisting of Ag, Au, Pt, Pd and mixtures thereof. A currently preferred metal is gold, and a currently preferred metal cluster is Au55 having a radius of from about 0.7 to about 1 nm. Compositions also are described, one use for which is in the formation of cluster arrays.

Abstract: The disclosure provides proteins that can be used to determine the redox status of an environment (such as the environment within a cell or subcellular compartment). These proteins are green fluorescent protein (GFP) variants (also referred to as redox sensitive GFP (rosGFP) mutants), which have been engineered to have two cysteine amino acids near the chromophore and within disulfide bonding distance of each other. Also provided are nucleic acid molecules that encode rosGFPs, vectors containing such encoding molecules, and cells transformed therewith. The disclosure further provides methods of using the rosGFPs (and encoding molecules) to analyze the redox status of an environment, such as a cell, or a subcellular compartment within a cell. In certain embodiments, both redox status and pH are analyzed concurrently.

Abstract: This disclosure provides methods for detecting and localizing DNA mutations by DNA microarray. In various embodiments, the described methods include use of restriction endonuclease(s) and/or mismatch-recognition nuclease(s) to detect and/or localize mutations. In one representative method, reference and target DNA are digested using one or more restriction endonucleases, resultant DNA strands are labeled (e.g., using a DNA polymerase), and the labeled mixture of DNAs is hybridized to a microarry. In another representative method, reference and target DNA are denatured and annealed to form a mixture containing heteroduplex DNA, one or more mismatch-recognition nuclease(s) are used to nick or cleave at least a portion of the heteroduplex DNA, resultant DNA strands are labeled (e.g., using a DNA polymerase) and the labeled mixture of DNAs is hybridized to a microarray.

Abstract: Nucleic acid molecules that encode plant proteins involved in photoperiodism and circadian rhythms are disclosed. These molecules may be introduced into plants in order to alter the photoperiodic and/or circadian clock-based gene expression of the plants.

Abstract: The disclosure provides proteins that can be used to determine the redox status of an environment (such as the environment within a cell or subcellular compartment). These proteins are green fluorescent protein (GFP) variants (also referred to as redox sensitive GFP (rosGFP) mutants), which have been engineered to have two cysteine amino acids near the chromophore and within disulfide bonding distance of each other. Also provided are nucleic acid molecules that encode rosGFPs, vectors containing such encoding molecules, and cells transformed therewith. The disclosure further provides methods of using the rosGFPs (and encoding molecules) to analyze the redox status of an environment, such as a cell, or a subcellular compartment within a cell. In certain embodiments, both redox status and pH are analyzed concurrently.

Abstract: Nucleic acid molecules that encode plant proteins involved in photoperiodism and circadian rhythms are disclosed. These molecules may be introduced into plants in order to alter the photoperiodic and/or circadian clock-based gene expression of the plants.

Abstract: A method for forming arrays of metal, alloy, semiconductor or magnetic clusters is described. The method comprises placing a scaffold on a substrate, the scaffold comprising, for example, polynucleotides and/or polypeptides, and coupling the clusters to the scaffold. Methods of producing arrays in predetermined patterns and electronic devices that incorporate such patterned arrays are also described.

Abstract: Engineered fluorescent proteins, nucleic acids encoding them and methods of use are provided.

Abstract: A method for forming arrays of metal, alloy, semiconductor or magnetic clusters is described. The method comprises placing a scaffold on a substrate, the scaffold comprising, for example, polynucleotides and/or polypeptides, and coupling the clusters to the scaffold. Methods of producing arrays in predetermined patterns and electronic devices that incorporate such patterned arrays are also described.

Abstract: The nucleic acid that encodes the Arabidopsis ELF3 protein, which is involved in photoperiodism and circadian rhythms, is disclosed. This nucleic acid may be introduced into plants in order to alter the photoperiodic and/or circadian clock-based gene expression of the plants.

Abstract: Engineered fluorescent proteins, nucleic acids encoding them and methods of use.

Abstract: Subsearch, where a satisfiability algorithm searches through the original theory for ground clauses that satisfy some numeric property, is represented in terms of S(C,P,u,s), the set of ground instances of C that have u literals unvalued by P and s literals satisfied by the assignments in P. This representation allows an intelligent search to be performed to answer subsearch problems posed in terms of S(C,P,u,s). Intelligent Subsearch uses truth value assignments to atoms to eliminate sets of bindings to universally quantified variables within a quantified clausal constraint; the bindings being eliminated because the bindings cannot satisfy a specific statement. Intelligent subsearch backtracks away from poor choices in the search for bindings to variables within the quantified clauses. In typical uses, intelligent subsearch can reduce the time of the checking problem from O(DU) to O(D&agr;U) for some &agr;<1.

Abstract: Microelectronic devices have a semiconductor/conducting polymer interface are disclosed. The conducting polymer may be electrically contacted in a manner to assure that it remains exposed to the environment. If the environment is an inert electrolyte to which additional electrodes are contacted, the conducting polymer can be electrochemically oxidized or reduced to control its electrochemical potential and a tunable (variable barrier) diode results. This tunable diode is a device that rectifies current like a traditional diode, but unlike traditional diodes, the effective barrier height of the tunable diode can be actively controlled. This control can be an element of an active device or a means for fabricating fixed barrier diodes with controlled barrier heights. Alternatively, the environment can contain an analyte to be sensed, either directly or through a mediating layer. The electrical characteristics (e.g.

Abstract: Nucleic acid molecules that encode a plant promoter involved in photoperiodism and circadian rhythms are disclosed. These molecules may be introduced into plants in order to alter the photoperiodic and/or circadian clock-based gene expression of the plants.

Abstract: A system for determining schedules and processing other optimization problems includes a local optimization engine and a global optimization engine. The local optimization engine operates based on heuristics, and includes a prioritizer, a constructor, and an analyzer to make large “coherent” moves in the search space, thus helping to avoid local optima without relying entirely on random moves. The global optimization engine takes the individual schedules produced by the local optimization engine and optimizes them using Linear Programming/Integer Programming techniques.

Abstract: Assignment of attributes to elements subject to constraints is achieved using a system that has a systematic engine and a nonsystematic engine. The systematic engine includes a schedule developer for producing partial proposed assignments, a pruning processor for determining violations of discrepancy limits by a partial proposed assignment, and a bound selector for relaxing discrepancy limits as needed. The non-systematic engine includes a schedule packer for modifying assignments proposed by the systematic engine and an evaluator for comparing the modified assignments with the constraints.

Abstract: A method and apparatus for laser frequency stabilization and precise laser frequency tuning comprises splitting a laser beam into two beam portions and recombining the two portions after they traverse differing optical distances. The thus-processed combined beam exhibits a time variation in intensity, the time variation being a function of the time rate of change of the laser beam. A signal proportional to the laser frequency's time rate of change is derived from the time variation of the processed beam's intensity and used to generate a control signal to provide feedback to control the laser frequency, thereby providing for laser frequency stabilization. Precise laser frequency tuning may be achieved by introducing a controlled variation in the derived signal, such as by adjusting a frequency differential introduced between the beam portions, or by otherwise introducing a controlled variation in the signal derived from the processed beam.

Abstract: Thermodynamically metastable skutterudite crystalline-structured compounds are disclosed having preselected stoichiometric compositions and superior and optimizable thermoelectric properties. The compounds are formed at low nucleation temperatures and satisfy the formula:M.sub.1-x M'.sub.4-y Co.sub.y M".sub.12wherein:M=any metal, metalloid, or mixture thereof, except for La, Ce, Pr, Nd, and Eu when x=0, and M'=Fe, Ru, or Os, and M"=Sb, P, or As;M'=Fe, Ru, Os, Rh, or mixture thereof;M"Sb, As, P, Bi, Ge.sub.0.5-w Se.sub.0.5+w, wherein w=0 to 0.5 or mixture thereof;x=0 to 1;y=0 to 4; andwherein M' and/or M" are doped or undoped. These compounds generally have the crystalline structure of a skutterudite, wherein the crystalline structure is cubic with 34 atoms in the unit-cell in the space group Im3. The M".sub.12 atoms occupy unit-cell sites 24(g), the M'.sub.4-y atoms form a cubic sublattice occupying unit-cell sites 8(c), and the M.sub.