Abstract: A method of biological assay comprises the steps of providing an enzyme substrate comprising two fluorescence dye groups bound to a flexible peptide, the dye groups being of proximity sufficiently close so as to allow free energy attractions to draw the dyes together to essentially self-quench fluorescence of the dye groups, wherein self quenching of fluorescence of the dye groups is effected by dye dimerization or stacking, and enzymatically cleaving the peptide to release the fluorescence dye groups from dye dimerization or stacking, thereby producing an increase in fluorescence intensity. A protease substrate for use in the method of the invention is also disclosed. This invention finds use in detection and identification of microorganisms, sterilization assurance, pharmaceutical discovery, enzyme assays, immunoassays, and other biological assays.

Abstract: The invention is directed to a method of multigenerational analysis of plants modified by insertional mutagenesis, and a method for associating plant mutant trait and genotype information. The invention is further directed to a method for managing data pertaining to plant mutant trait and genotype information in a database. The invention is further directed to a system for managing plant mutant trait and genotype information in a database, a system for allowing users to associate plant trait and genotype information, a system for facilitating business transactions with a user regarding plant materials or a gene sequence of interest to user and a computer-readable medium embodying a program of instructions for execution by a computer for implementing a system for allowing users to associate plant trait and genotype information.

Abstract: Background noise from relevant data sets, including for example over-the-counter sales data, absenteeism data, etc., is subtracted using a background estimation algorithm that outputs residual data. The effects of hypothetical anomalous events, such as a bio-terrorist attack, on the relevant data sets are modeled to create replica data. The replica data may be based on input from epidemiologists and various scenario templates including information on disease manifestation and other intelligence. The residual data and the replica data are then matched using a detector. Types of detectors include for example adaptive matched-filter detectors, change detectors and Bayesian Inference Networks. An alarm is triggered if a real anomalous event similar to a hypothetical anomalous event is detected. A Geographical Information System (GIS) may be used to display data from individual zip codes.

Abstract: Methods and apparatus for classifying or predicting the classes for samples based on gene expression are described. Also described are methods and apparatus for ascertaining or discovering new, previously unknown classes based on gene expression.

Abstract: Methodology for the automated design of proteins is disclosed. Various methods executed by a computer for generating probability matrices, protein sequences, combinatorial libraries of proteins, and optimization of various parameters related to protein design are disclosed. Methodology is applicable to the design and analysis of protein structures and protein sequences.

Abstract: The present invention relates to compositions and methods for cancer diagnostics, including but not limited to, cancer markers. In particular, the present invention provides gene expression profiles associated with prostate cancers. Genes identified as cancer markers using the methods of the present invention find use in the diagnosis and characterization of prostate cancer. In addition, the genes provide targets for cancer drug screens and therapeutic applications.

Abstract: The present invention provides a detection article including at least one fluid control film layer having at least one microstructured major surface with a plurality of microchannels therein. The microchannels are configured for uninterrupted fluid flow of a fluid sample throughout the article. The film layer includes an acquisition zone for drawing the fluid sample into the plurality of microchannels at least by spontaneous fluid transport. The film layer also includes a detection zone having at least one detection element that facilitates detection of a characteristic of the fluid sample within at least one microchannel of the detection zone.

Abstract: Freestanding particles comprising a plurality of segments, wherein the particle length is from 20 nm to 50 ?m and the particle width is form 5 nm to 50 ?m.

Abstract: The present invention provides a method for determining concentration of blood glucose by using the change in the rising time. The chemical reaction between the blood glucose and enzyme within the test strip to generate the analog source that used to determine the concentration of the blood glucose in the measuring meter. Thus, the rising curve can be obtained after the analog source is treated, such that the concentration of the blood glucose can be determined.

Abstract: A novel extension of the vector space model for computing chemical similarity is described. In one embodiment, a method calculates similarity between molecules and molecular descriptors using the singular value composition (SVD) of a molecule/descriptor matrix and, for example, an identity matrix, to create a low dimensional representation of the original descriptor space. Probe or query molecules then can be projected into the low dimensional representation and compared to the molecules from the original matrix.

Abstract: A method of pipelining a disease specific diagnostic algorithm on an n-bit data word stored in a memory whereby the n-bit data word is divided into clinical tests describing ranges of normal values. Then, each of the clinical tests of the n-bit data word is read out from memory. Upon receiving a first of the results of the clinical tests, the result is compared with the normal value and the detection algorithm is computed based on the first result. This results in continuation with the next test if positive or terminate if negative. The above-steps are repeated recursively until all of the required test in the diagnostic algorithm are computed to provide the complete diagnosis of a disease.

Abstract: The present invention facilitates in silico evaluation of molecules for biological activity by providing a computer-based method to predict whether oligonucleotides may possess biological activity and the efficacy of the biological activity based on the three-dimensional structure and charge characteristics of the oligonucleotides. Biological activities include, but are not limited to, cellular proliferation, induction of cell cycle arrest and apoptosis.

Abstract: The invention includes the fitted quaternary structure of insulin receptor. It also includes methods of identifying compounds that modulate insulin receptor activity by producing a compound that interacts with all or part of the fitted quaternary structure of insulin receptor or a fragment or derivative thereof and which thereby modulates insulin receptor activity.

Abstract: Methods and systems are provided for detecting the accidental use of short and long samples in the clinical analysis of a sample, specimen, or assay. The systems can include a clinical analyzer for determining one or more values for one or more measurable characteristics of a sample. These values are used in combination with reference data stored in a data module to generate a probability that the sample tested is a short sample, a long sample, or an acceptable sample. This probability and/or the status of the sample as a short sample, a long sample, or an acceptable sample are output to a user.

Abstract: Digital computational circuit comprising a network made of a plurality of identical repetitive DNA-based conductive elements. The DNA-based elements used for the purposes of the invention employ a P-bridge as a tunnel junction for a net charge. The DNA-based element of which the circuit is made may be a DNA SET transistor. The circuit may comprise a DNA resistor built from a plurality of SET transistor elements a series, with a constant over-threshold gate voltage. The circuit may further comprise NOT and NOR gates. The NOT gate can be made of a DNA-based transistor and a resistor, and the resistor can be made by using a DNA SET transistor with a constant over-threshold gate voltage, and by placing a plurality of such DNA SET transistors in series until the resistivity reaches the desired value. The NOR gate, on the other hand, can be built from two NOT elements wherein the output of the first NOT element is connected to the resistor of the second NOT element as it voltage supply.

Abstract: A method for preparing probes, as well as several probes for use in qualitative or quantitative hybridization assays are disclosed. The method comprises constructing an oligonucleotide that is sufficiently complementary to hybridize to a region of rRNA selected to be unique to a non-viral organism or group of non-viral organisms sought to be detected, said region of rRNA being selected by comparing one or more variable region rRNA sequences of said non-viral organism or group of non-viral organisms with one or more variable region rRNA sequences from one or more non-viral organisms sought to be distinguished. Hybridization assay probes for Mycobacterium avium, Mycobacterium intracellulare, the Mycobacterium tuberculosis-complex bacteria, Mycoplasma pneumoniae, Legionella, Salmonella, Chlamydia trachomatis, Campylobacter, Proteus mirabilis, Enterococcus, Enterobacter cloacae, E. coli, Pseudomonas group I, Neisseria gonorrhoeae, bacteria, and fungi also are disclosed.

Abstract: Methods for identifying a member of a mass-coded molecular library, which is a ligand for a biomolecule and binds to the biomolecule at the binding site of a known second ligand for the biomolecule are described. The methods includes contacting a mass-coded molecular library with a biomolecule; separating the biomolecule-ligand complexes from the unbound members of the mass-coded molecular library; contacting the biomolecule-ligand complexes with a second ligand to dissociate biomolecule-ligand complexes in which the ligand binds to the biomolecule at the binding site of the second ligand, thereby forming biomolecule-second ligand complexes and dissociated ligands; separating the dissociated ligands and biomolecule-second ligand complexes; and determining the molecular mass of each dissociated ligand.

Abstract: The present invention provides a fast and efficient method for determining the three-dimensional conformation of a protein. The steps of the method of the invention include: 1) formation of physical distance constraints, e.g., forming intramolecular chemical crosslinks of known size between residues of a protein; 2) enriching the number of the molecules that have intramolecular chemical crosslinks in the reaction pool, e.g., using size separation to remove proteins with intermolecular bonds; 3) exposing the enriched reaction pool to a protease that cuts the protein at specific sites to produce peptide fragments; 4) measuring the size of the peptide fragments to determine linkage sites with a certain spatial relationship in the protein; and 5)interpreting the data produced to determine spatial geometry and protein structure based on the deduced spatial relationship of the linkage sites.

Abstract: Methods of using NMR spectroscopy for identifying ligands that bind to structurally uncharacterized proteins, and improving the binding affinity of ligands for biological targets are disclosed. One aspect of the method includes preparing first NMR spectra of a first complex comprising the biological target and a paramagnetically labeled derivative of a first ligand, preparing a second NMR spectra of a second complex comprising the biological target and a second ligand, and analyzing the spectra to determine whether the second ligand binds to the biological target within the paramagnetic zone of the paramagnetically labeled derivative. The first and second steps may be performed simultaneously, consecutively, or in any order.

Abstract: A method predicts at least one property of a candidate molecule. A set of reference molecules is classified as either possessing or not possessing at least one property. A subset of the molecules is selected from which a plurality of marker molecules is chosen. The marker molecules are used to predict whether the candidate molecule possesses at least one property.