Abstract: The present invention relates to a computationally efficient method of finding patterns in any data that can be expressed in the form of arrays of binary features or arrays of categorical features. This includes data represented by continuous-valued attributes that can be transformed to a categorical representation, such as the discovery of patterns of genetic variability that may be causally related to diseases or traits, as well as the discovery of patterns of protein biomarkers that may be used for medical diagnostics, prognostics, and therapeutics. The invention further relates to a program storage device having instructions for controlling a computer system to perform the methods, and to a program storage device containing data structures used in the practice of the methods.

Abstract: The present invention is an improved method of resequencing DNA using microarrays to rapidly map and identify SNPs, deletions and amplification events present in the genome of an organism. The method is performed by hybridizing a reference and a test genome to two separate arrays with each array exhibiting a specific intensity pattern. The intensity differences between the reference and the test genome arrays are used to produce a mutation map. The mapped differences are resequenced on a set of resequencing arrays to identify specific genetic mutations.

Abstract: Gene expression profiling in multiple myeloma patients identifies genes that distinguish between patients with subsequent early death or long survival after treatment. Poor survival is linked to over-expression of genes such as ASPM, OPN3 and CKS1B which are located in chromosome 1q. Given the frequent amplification of 1q in many cancers, it is possible that these genes can be used as powerful prognostic markers and therapeutic targets for multiple myeloma and other cancer.

Abstract: Machine executable method of analyzing growth curve data to identify the transition from a baseline phase into a growth phase. Applications of the method include analysis of results from time-dependent monitoring of amplicon synthesis in a nucleic acid amplification reaction to quantify a starting amount of a nucleic acid template in a test sample. The method advantageously simplifies the quantitation by circumventing the need to establish thresholds used for calculating initiation of the growth phase, to calculate derivatives, or to perform linear regression analysis.

Abstract: Method for sequencing nucleic acids in which the values of the CID spectrum calculated for an assumed sequence are compared with the measured spectrum of the nucleic acid and the degree of correspondence is calculated, at least one position of the assumed sequence is modified and the degree of correspondence with the measured spectrum is recalculated.

Abstract: A semiconductor wafer is radiated with an electron beam so that the inelastic scattering takes place in the narrow region, and current flows out from the narrow region; the amount of current is dependent on the substance or substances in the narrow region so that the analyst evaluates the degree of contamination on the basis of the substance or substances specified in the narrow region.

Abstract: The invention discloses a Non-Equilibrium Capillary Electrophoresis of Equilibrium Mixtures (NECEEM) method and NECEEM-based practical applications. The NECEEM method is a homogeneous technique, which, in contrast to heterogeneous methods, does not require affixing molecules to a solid substrate. The method of the invention facilitates 3 practical applications. In the first application, the method allows the finding of kinetic and thermodynamic parameters of complex formation. It advantageously allows for revealing two parameters, the equilibrium dissociation constant, Kd, and the monomolecular rate constant of complex decay, koff, in a single experiment. In the second practical application, the method of this invention provides an approach for quantitative affinity analysis of target molecules. It advantageously allows for the use of affinity probes with relatively high values of koff.

Abstract: The virtual screening of a database of molecules is based on explicit three-dimensional molecular superpositions. The torsional flexibility of the database molecules is taken fully into account, and an arbitrary number of conformation-dependent molecular features may be considered. A fragmentation-reassembly approach is utilized, which allows for an efficient sampling of the conformational space. A fast clique-based pattern-matching algorithm generates alignments of pairs of adjacent molecular fragments on the (rigid) query molecule that are subsequently reassembled to complete database molecules. Using conventional molecular features (hydrogen bond donors and acceptors, charges, and hydrophobic groups), it is possible to rapidly produce accurate alignments of medium-sized drug-like molecules. Examples with a test database containing a diverse set of 1780 drug-like molecules (including all conformers) show that average query processing times of the order of 0.

Abstract: A method for designing a metal ion for use in a molecular dynamics simulation can include the steps of building a metal ion molecule having a center atom and a dummy atom, assigning a van der Waals radius to the center atom, and assigning a charge to the dummy atom. A metal ion molecule may have the center atom covalently linked to one or more dummy atoms resulting in the metal ion molecule having a polyhedron geometry. New force field parameters may be used in methods for designing metal ions for use in molecular dynamics simulations.

Abstract: A PNA zip-code chip in which PNA zip-code probes are immobilized on a substrate at high density using an epoxy compound as a linker, and method for fabricating such PNA chip. The use of PNA provides the chip with superior properties to DNA chips, allowing precise diagnosis of congenital diseases or base mutations with much higher sensitivity than is achievable with a DNA chip. The use of the PNA zip-code chip enables diagnosis of gene mutations in a simple manner, using only hybridization reaction, without the difficulties associated with processes in which probes must be immobilized directly on a substrate every time the target gene changes.

Abstract: Subterranean treatment formation using a model which takes into account the pore level physics by coupling the local pore scale phenomena to the macroscopic variables (Darcy velocity, pressure and reactant cup-mixing concentration) through the structure-property relationships (permeability-porosity, average pore size-porosity and interfacial area-porosity) and the dependence of the fluid-solid mass transfer coefficient and fluid phase dispersion coefficient on the evolving pore scale variables (average pore size, local Reynolds and Schmidt numbers).

Abstract: Biomarkers that are diagnostic of type 1 diabetes, type 2 diabetes and/or diabetic disorder are identified. Detection of different biomarkers of the invention are also diagnostic of the degree of severity of type 1 diabetes, type 2 diabetes and/or diabetic disorder. An analysis includes the parameters of matching for BMI and Tanner stage. Receiver-operator characteristic (ROC) curves were established to assess association of the biomarkers with a disease.

Abstract: A family of minimally cross-hybridizing nucleotide sequences, methods of use, etc. A specific family of 1168 24mers is described.

Abstract: A method and computer program product for simulating a pan coating process estimates at least one of tablet coating uniformity or coated tablet weight uniformity for tablets within a tablet bed of a pan. The simulation includes obtaining a plurality of parameters associated with the pan coating process, selecting tablet paths for each cycle of a simulation tablet in the tablet bed, determining a coating amounts for the tablet based on selected tablet paths, determining cycle times for the tablet, and summing the determined coating amounts and cycle times for the tablet. The simulation is repeated for each of a defined number of simulation tablets representing the tablets within the tablet bed to determine tablet coating uniformity and/or coated tablet weight uniformity for the tablets. Tablet paths and/or cycle times are determined randomly, e.g., in accordance with a Monte Carlo method.

Abstract: Disclosed are methods for reliably detecting the presence of proteins, including proteins with various post-translational modifications (phosphorylation, glycosylation, methylation, acetylation, etc.) in a sample by the use of one or more capture agents that recognize and interact with recognition sequences uniquely characteristic of a protein or a set of proteins (Proteome Epitope Tags, or PETs) in the sample. Arrays comprising these capture agents or PETs are also provided.

Abstract: A method of assisting individuals in making food choices by providing two nutritional indices. One is a numerical expression of a food's overall nutrient density and the other is a separate numerical expression that relates to a food's caloric density that is a prediction of the satiating effect of a food. A visual aid in the form of a graph or chart is provided so individuals using the indices can refer to the chart to determine food selections in accordance with the individual's dietary goals.

Abstract: The present invention is directed to a sequence dependent polynucleotide nanomechanical device based on a nucleic acid paranemic crossover (PX) molecule which is a four-stranded structure related to parallel double crossover molecules, except that every possible crossover takes place. Eliminating two crossovers leads to a topoisomer, termed JX2, in which one pair of ends are switched (rotated 180°) while the other pair of ends remain the same. The device can be cycled between the two states, PX and JX2, by replacing single strands that set the state to be PX or JX2.

Abstract: Pieces of software and databases are used to facilitate the design and synthesis of genes. The synthesis techniques allow identification, quantification, transcription, translation, and manipulation of portions of the gene sequence represented as 0's and 1's in a computing system. These pieces of software and databases compile constraint information provided by a user to create synthetic genes to express proteins lacking disordered or variable regions and containing surface mutations that promote solubility and/or crystallization. Regions of the gene sequence that do not form stable structures can be removed and replaced by a short biological linker to improve crystallization of proteins.

Abstract: A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

Abstract: Dynamic inference is leveraged to provide online sequence data labeling. This provides real-time alternatives to current methods of inference for sequence data. Instances estimate an amount of uncertainty in a prediction of labels of sequence data and then dynamically predict a label when an uncertainty in the prediction is deemed acceptable. The techniques utilized to determine when the label can be generated are tunable and can be personalized for a given user and/or a system. Employed decoding techniques can be dynamically adjusted to tradeoff system resources for accuracy. This allows for fine tuning of a system based on available system resources. Instances also allow for online inference because the inference does not require knowledge of a complete set of sequence data.