Abstract: Method of determining the compositional evolution of fluids present in a porous medium as a result of biodegradation. A biodegradation compositional scheme is defined from twelve chemical classes allowing the hydrocarbons and the gases resulting from biodegradation to be described. The initial amount of each one of these chemical classes contained in the fluids before biodegradation is determined. A reaction scheme is then defined for biodegradation, wherein the chemical classes react with electron acceptors according to parallel reactions having different velocities, and each class reacts with these acceptors according to sequential reactions. The biodegradation reaction velocities are determined for each class. The composition of the fluids is then deduced by assessing the amount of each chemical class by applying the reaction scheme. The composition of the biodegraded hydrocarbons, as well as the amount of acid gas and of methane produced, are notably deduced.

Abstract: Method of conducting chromatography comprising controlling a retention time of one or more chemical species in a mixture by determining at least one conceptual segment of: a) the one or more chemical species, b) a mobile phase component, and c) a stationary phase component. The method further includes defining an identity and an equivalent number of each of the at least one conceptual segment.

Abstract: The present disclosure relates to methods and systems that may be used for detection of one or more pathogens and determining one or more agents in response to pathogen detection.

Abstract: A method of optimizing a chemical reaction in a plate-type open reactor, the method consisting in: establishing a dynamic model of the reactor for a given reaction on the basis of a model of the reactor and its heat exchanges; applying an integration software tool to the dynamic model in order to solve the above-mentioned equations; determining and optimizing a set of dimension and/or operation parameters of the reactor on the basis of evaluating targets to be achieved, constraints to be complied with, and variable data for the reactor and/or the reaction; building a plate reactor of the said type accordingly to the set of optimized parameters; and doing measurements of physical parameters during the execution of said reaction in the built reactor, for validating its operation.

Abstract: A method provides an index that is indicative of the state of a subject, as to a biological condition, based on a sample from the subject. An embodiment of this method includes: deriving from the sample a profile data set, the profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables evaluation of the biological condition; and in deriving the profile data set, achieving such measure for each constituent under measurement conditions that are substantially repeatable; and applying values from the profile data set to an index function that provides a mapping from an instance of a profile data set into a single-valued measure of biological condition, so as to produce an index pertinent to the biological condition of the subject.

Abstract: The present invention relates to drug discovery methods, particularly methods for assaying compounds for activity as Aurora kinase inhibitors. This invention also relates to a pharmacophore describing compounds that are able to promote a conformational change in the protein AuroraB and whose binding constant for the two-step process is given as Ki*. Finally, this invention also relates to compounds having the features of the pharmacophore.

Abstract: Methods of conducting industrial manufacture, research or development. The method comprise computer-implemented steps of modeling at least one physical property of a mixture of at least two chemical species by determining at least one conceptual segment for each of the chemical species. The steps of determining at least one conceptual segment for each of the chemical species include defining an identity and an equivalent number of each conceptual segment.

Abstract: Computing units are determined for performing molecular docking calculations in parallel with the number of computing units and the width of the data paths allocated by relative complexity of operations. Data can be expected to arrive at downstream computing units as it is needed, leading to higher utilization of computing units. Computing units are hardware components that are specific to a calculation performed. For molecular docking calculations, functions of molecular subsets or of combinations of molecular subsets are calculated. Determinations include fit between molecular subsets, affinity or energy of “fit” between molecular subsets, etc. Affinity might include inter-atomic energy, bond energy, energy of atoms immersed in a field, etc. The calculations could be used to simulate and/or estimate likelihoods of molecular interactions.

Abstract: A system for conducting performing real-time harmonics analysis of an electrical power distribution and transmission system is disclosed. The system includes a data acquisition component, a power analytics server and a client terminal. The data acquisition component is communicatively connected to a sensor configured to acquire real-time data output from the electrical system. The power analytics server is communicatively connected to the data acquisition component and is comprised of a virtual system modeling engine, an analytics engine and a machine learning engine. The machine learning engine is configured to store and process patterns observed from the real-time data output and the predicted data output, forecasting harmonic distortions in the electrical system subjected to a simulated contingency event.

Abstract: A method for predicting the formation of silicon nanocrystals in an oxide matrix is disclosed. Initially, fundamental data for a set of microscopic processes that can occur during one or more material processing operations are obtained. Kinetic models are then built by utilizing the fundamental data for a set of reactions that can contribute substantially to the formation of silicon nanocrystals in a silicon oxide matrix. Finally, the kinetic models are applied to predict shape, size distribution, spatial arrangements of silicon nanocrystals.

Abstract: Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or comparative genome hybridization microarray, comprising selecting a plurality of potential target sequences, generating a plurality of candidate probes from the target sequences, filtering the plurality of candidate probes by analyzing candidate probes for selected probe properties in silico. Microarrays comprising probes selected by the methods of the invention are particularly useful for comparative genome hybridization and location analysis.

Abstract: Apparatus, methods, media, signals and data structures for protein sequence analysis are disclosed. A method includes identifying, from among a first group of aligned protein sequences having at least a threshold degree of alignment with a first protein sequence, a second group of at least one of the aligned sequences having at least one insertion or deletion (“indel”) relative to the first protein sequence satisfying a predefined condition. The apparatus may include a processor circuit configured to carry out the method.

Abstract: A computer-readable storage medium encoded with computer-readable program code for causing a computer to perform a molecular dynamics simulation for determining the solvent accessible surface area of a molecule (M) with respect to atomic coordinates, wherein the molecule (M) comprises a plurality of atoms, a sphere (Bi) is assigned to each atom, and each sphere (Bi) comprises a radius (?i) and a center position (ri).

Abstract: The invention is directed to accurate calculation of a birefringence of a polymer stretched and oriented. Disclosed is a method for calculating a birefringence of a polymer in an information processing apparatus, having an amorphous state generating step including accepting input of a parameter, generating a model of the polymer on the basis of the parameter, and bringing the model into an amorphous state; a stretching step including stretching the model brought into the amorphous state; a birefringence calculating step including calculating a birefringence of the stretched model; and an outputting step including outputting the birefringence thus calculated.

Abstract: A field-based similarity search system and method includes a database for storing at least one candidate molecule, an input device for inputting a query molecule, and a processor for identifying a candidate molecule which is similar to the query molecule based on a similarity of fragment pair features.

Abstract: A multivariate diagnostic method based on optimizing diagnostic likelihood ratios through the effective use of multiple diagnostic tests is disclosed. The Neyman-Pearson Lemma provides a mathematical basis to produce optimal diagnostic results.

Abstract: A method for determining absorbent molecules that are effective for the property of acid gas removal from feedstreams comprising a) determining a set of known molecules that are effective for acid gas removal, b) defining descriptive parameters (descriptors) that correlate with the structure of molecules with known acid gas removal, c) assigning a value to each descriptor for each of the known molecules and developing a quantitative structure and property relationship (QSPR), and d) generating molecular structures that will be effective for acid gas removal from the structure and property relationship.

Abstract: Methods for analyzing circuit distortion based on contributions from separate circuit elements are presented. Local approximations that do not require high-order derivatives of device models are developed near an operating point for calculating distortion summaries including compression summaries and second-order intermodulation (IM2) distortion summaries.

Abstract: The invention relates to a method for the quality assessment of nucleic acid amplification reactions which is based on a mathematical approach for the quality assessment of complete nucleic acid amplification reactions and comprises the following steps: a) Carrying out an amplification reaction for at least one nucleic acid target molecule, b)Collecting time-related data reflecting the course of the amplification reaction, c) Fitting these time-related data with a growth model equation comprising at least one parameter, d) Obtaining, from said fitting process, at least one value for the at least one parameter.

Abstract: Character string divider divides a targeted character string into a plurality of groups at each bonding sites on a main chain. In the character string dividing process, the character string divider adds starting/ending symbols to the targeted character string, inserts a delimiter between adjacent characters, changes a notation related to oxo acids, reconstructs an atomic symbol consisting of two characters, changes a notation regarding a subscript or superscript, links hydrogen to another element, reconstructs a set of side chains, reconstructs a character string consisting of one group, reconstructs a back-end group, reconstructs a double bond in a group, and removes the starting/ending symbols. Character string reverser reverses the alignment of the groups.

Abstract: The invention relates to a crystal of the CC2-LZ domain of the NEMO protein, in which the three-dimensional structure has been determined by X-ray diffraction at a resolution of about 3.25 A. The invention also relates to methods for the crystallisation of the CC2-LZ domain. The CC2-LZ crystals and the information derived from the crystalline structures thereof are used for identifying and designing compounds interacting with CC2-LZ.

Abstract: The present invention relates generally to polyolefin production and to reducing volatile organic content (VOC) associated with the polyolefin. Techniques include the construction and implementation of a purge column model to calculate or estimate the VOC content in the polyolefin exiting the purge column. The techniques facilitate the design and operation of the polyolefin manufacturing process.

Abstract: The invention provides the structure of a human ?2-adrenergic receptor, a cholesterol consensus motif, and methods of identifying modulators of G-protein coupled receptors (GPCRs). Methods of using the modulators of the receptor, GPCRs, and the cholesterol consensus motif are also provided.

Abstract: The present disclosure describes methods, systems and techniques for determining a localized dielectric property of a molecule. A molecular model of at least a portion of the molecule is obtained. The molecular model is partitioned into cavities, and for each of the cavities, the permittivity within the cavity is iteratively determined based on permittivity outside of the cavity and electronic and nuclear polarizability within the cavity. Beneficially, this allows for different permittivities to be determined for different portions of the molecule, and is advantageous over simply assigning a single permittivity to the entire molecule.

Abstract: Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal or transverse direction at the tip, a polymer sequence is passed through the tip, and a change in an electrical current signal is measured as each polymer component passes through the tip. Each measured change in electrical current signals is compared with a database of reference signals, with each reference signal identified with a polymer component, to identify the unknown polymer component. The tip preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

Abstract: A processor based method for measuring dimensional properties of a photoresist profile by determining a number acid generators and quenchers within a photoresist volume, determining a number of photons absorbed by the photoresist volume, determining a number of the acid generators converted to acid, determining a number of acid and quencher reactions within the photoresist volume, calculating a development of the photoresist volume, producing with the processor a three-dimensional simulated scanning electron microscope image of the photoresist profile created by the development of the photoresist volume, and measuring the dimensional properties of the photoresist profile.

Abstract: A system is described that treats a solver as an ordered sequence of steps involving the different objects that have to be simulated and relationships between them. Tasks and the order of the tasks are obtained from each object and relationship. The tasks are merged into a sorted list. The solver traverses the list and passing each task to a corresponding object and relationship where the objects are interleaved during processing. The object or relationship then executes the task.

Abstract: The present invention provides methods for the assessment of diseases that result from the combined or interactive effects of two or more genetic variants, and in particular for diagnosing risk of developing such diseases in subjects using an analysis of genetic polymorphisms. Methods for the derivation of a net score indicative of a subject's risk of developing a disease are provided.

Abstract: Diagnostic method, based on the amounts of biogenic amines that are contained in a body fluid or other sample. A number of measured parameters related to the desired diagnostic information are derived from the amounts. For each diagnostic information desired, an input consisting of the identification of the diagnostic information is provided. The input is compared to the measured parameters and a diagnostic response is derived from the comparison. The measured parameters may be derived from the amounts of the biogenic amines according to a program stored in a memory. The detection of the less volatile amines and their separation from the more volatile ones may advantageously be enhanced by successively adding a base and an acid, in either possible succession, to the sample and analyzing the vapors emitted by the sample under heating.

Abstract: Detailed information of each analysis subject partial network is displayed on a left pane of a screen. The detailed information includes the number of nodes, the number of edges, and accumulative coverage of the analysis subject partial network for each disease. Based on the detailed information, a user can designate the analysis subject partial network of a disease the user wishes to analyze. When the user has designated the disease, a network diagram indicating a partial network related to the designated disease is displayed on a right pane.

Abstract: The examples described herein relate to methods and apparatus for cleanup prediction and monitoring. A disclosed method of predicting cleanup of a sample fluid obtained by a downhole tool includes drawing the sample fluid into the downhole tool via a probe assembly; measuring optical densities of the sample fluid at a plurality of different respective times; selecting at least some of the measured optical densities as fitting points; identifying one or more inversion parameters; and performing, via a processor, an inversion using the fitting points, the inversion parameters and simulation data to generate data associated with a predicted cleanup of the sample fluid.

Abstract: The present invention provides systems and methods that utilize an information architecture for disambiguating scientific names and other classification labels and the entities to which those names are applied, as well as a means of accessing data on those entities in a networked environment using persistent, unique identifiers.

Abstract: The invention is a method of optimizing the injection of a fluid into a porous medium, using modelling the migration of the fluid within the medium having application for oil reservoir development. A reservoir model is constructed. In each cell of this the model, a PNM model representative of the pore network in the cell is constructed. The concentration of the fluid is then determined in each cell by solving the cell-scale reactive transport equation. Fluid concentration modifications at the level of the fluid/rock interface, at the pore scale, are therefore taken into account by means of the PNM models. Corrective coefficients for the reactive transport equation and a law between the permeability of the porous medium and the porosity of the porous medium are thus calculated. Finally, fluid injection is optimized as a function of the concentrations in each cell.

Abstract: A ripple and foam creation apparatus and method using water particle data is provided to create ripples and foam, and detect positions of the created ripples and foam for a water simulation used to create visual special effects in animations or movies. The apparatus includes a water particle grouping module checking grouping types of water particles from received water particle data to selects small water masses, a ripple creation module determining a position for ripple creation by using the checked grouping types, a foam creation module detecting flow of the water particles and calculating a position for foam creation, and a ripple-foam moving/removing module detecting changes of the created foam and ripples over time and removing the created foam and ripples.

Abstract: A method and a system are provided for enhancing structure diagram generation (“SDG”). In SDG, aesthetic two-dimensional (“2-D”) coordinates for use in a diagrammatic representation (“diagram”) of a molecule are derived from a connection table for the molecule. SDG may also improve the aesthetic qualities of a chemical structure diagram having existing coordinates, if available. SDG is enhanced by expressing the symmetry present in the molecule, by making use of symmetry in the 2-D dynamics used to lay out rings and chains, by construction of bridges using an open polygon method together with a potential function, and by an elegant approach to the relative positioning of molecules (“free rectangle method”).

Abstract: A method is provided for obtaining a model of data describing a physical structure. The method comprises obtaining a set of time instance objects from a domain object. The method also comprises obtaining data describing a physical structure and time interval data related to the physical structure from each member of the set of time instance objects. The method additionally comprises creating a model of the data describing the physical structure in conjunction with the time interval data.

Abstract: A method for identifying a chemical substance from a set of output states provided by a chemical sensor array being exposed to the chemical substance, the method including: selecting, with an evaluation circuit, from a set of class descriptions for different chemical substances a first class description and one or more further class descriptions, wherein the first class description is related to a first chemical substance and a further class description is related to a further chemical substance; and estimating, with one or more estimating units, a first likelihood value and one or more further likelihood values, wherein the first likelihood value represents a probability that the set of output states corresponds to the first class description, and a respective further likelihood value represents a probability that the set of output states corresponds to a respective further class description.

Abstract: The present invention provides methods for analyzing a combination of biomarkers to individualize tyrosine kinase inhibitor therapy in patients who have been diagnosed with cancer. In particular, the assay methods of the present invention are useful for predicting, identifying, or monitoring the response of a tumor, tumor cell, or patient to treatment with a tyrosine kinase inhibitor using an algorithm based upon biomarker profiling. The assay methods of the present invention are also useful for predicting whether a patient has a risk of developing toxicity or resistance to treatment with a tyrosine kinase inhibitor. In addition, the assay methods of the present invention are useful for monitoring tyrosine kinase inhibitor therapy in a patient receiving the drug to evaluate whether the patient will develop resistance to the drug.

Abstract: The present invention relates to co-crystals of Liver X receptor beta ligand binding domain (LXR?-LBD) with agonists and to the three-dimensional X-ray crystal structures derived thereof.

Abstract: A method for generating information of a 3-dimensional molecular structure of a molecule, said method being executable by a computer under the control of a program stored in the computer, said method comprising the steps of: (a) receiving a 3-dimensional representation of the molecular structure of said molecule, comprising a first set of residue portions and a template; (b) repeating an optimization cycle, wherein a set of (b1) modifying the molecular structure of one or more of the first set of residue portions, (b2) relaxing said modified structure, and (b3) calculating an energy value of the structure and comparing said calculated value with a prestored base value or with a value calculated in a previously performed step (b3), is repeated; (c) until a predetermined criterion is fulfilled; and (d) outputting a data structure comprising information extracted from any of these steps to a storage medium or to a consecutive method.

Abstract: The present invention provides for the first time a quantum mechanics-based method for scoring protein-ligand interactions and binding affinity predictions, using quantum mechanical Hamiltonians and/or a combined quantum mechanical/molecular mechanical approach, and Poisson-Boltzmann (PB)-based solvation methods. Also provided is a method for using quantum mechanics to describe the enthalpic and solvation effects of binding. The method comprises comparing the calculated binding affinities to experimental values in order to measure the success of the method. The methods disclosed herein may further be used to score protein and drug or protein and inhibitor interactions. The present method can predict the free energy of binding of protein-ligand complexes with high accuracy so as to enable lead optimization, thus serving as a powerful tool in computational drug design.

Abstract: Creating genetic devices for use in micro-organisms or other biological systems is described. In an embodiment a computer system receives at a program editor, input specifying a plurality of part designs, at least some of which comprise part properties expressed as logical variables; and the input also specifies constraints on the logical variables. For example, the input is a computer program which specifies constraints on the logical variables which, for example, relate to properties of the DNA sequences such as reactions and biological behaviors. In an example, a compiler resolves the constraints using a database of genetic parts in order to generate candidate parts for the proposed genetic device. In examples the sequences of genetic parts are translated into reactions and simulated using an automated simulator and/or implemented in a living cell or other biological system. In embodiments the compiler also uses a database of reactions.

Abstract: The present embodiments relate to a system and method of measuring the methylation level of DNA. Some embodiments relate to a system and method of measuring methylation level of DNA with a gene array.

Abstract: A robust classification method for cancer detection from mass spectrometry data includes inputting the mass spectrometry data, preprocessing the spectrometry data, conducting robust feature selection, generating predictions for the test data sets using multiple data classifiers, the multiple data classifiers including artificial neural networks, support vector machines, weighted voting on data patterns, classification and regression trees, k-nearest neighbor classification, and logistic regression, and constructing and validating a meta-classifier by combining individual predictions of the multiple data classifiers to generate a robust prediction of a phenotype. The test data sets are used exclusively for validation of the meta-classifier.

Abstract: A process is provided for disposing a sensor in an environment for optimally obtaining characteristic measurements. The process includes modeling covariant sets of environment elements that correspond to conditions of the environment and of sensor elements that correspond to characteristic functionalities of the sensor. The process further includes covariantly coupling the environmental elements with the sensor elements to produce a third set of configuration elements; and combining the configuration elements to obtain a fitness function parameter. The process may additionally include adjusting the environment elements and the sensor elements; repeating operations for covariantly coupling and combining until obtaining the fitness function parameter over a defined region of the environment within a set of fitness function parameters.

Abstract: A method and apparatus for analysis of molecular combinations featuring two or more molecular subsets is described. The method computes the shape complementarity of the system utilizing a basis expansion representing molecular shapes of the first and second molecular subsets in a coordinate system. The precomputed sets of translated expansion coefficients for the first molecular subset are first constructed via application of a translation operator to a reference set of expansion coefficients and then stored on a computer recordable medium for later retrieval. Then, a shape complementarity score, representing a correlation of the first and second molecular subsets, is computed via suitable application of rotation operators to both the stored translated expansion coefficients of the first molecular subset and the reference expansion coefficients for the second molecular subset over the sequence of different sampled configurations for the molecular combination.

Abstract: A method for executing calculation of the Hartree-Fock method in a molecular orbital method by a distributed memory parallel computing system includes the steps of: using a computer cluster made up of a plurality of computers; dividing a density matrix into multiple density submatrixes and distributing them to the individual computers and storing therein; and executing calculation processes such as two-electron integration or the like relating to density submatrixes in each computer while sequentially transferring the multiple density submatrixes between the multiple computers.

Abstract: A method and systems for locating a source of particles, molecules, or fragments of molecules using particle, molecule, or fragment of molecule reception rate is disclosed. According to the invention, the particle, molecule, or fragment of molecules diffusion parameters in the search space are determined and a lattice is designed on the search space. After having determined whether or not at least one particle, molecule, or fragment of molecule is detected by a sensor, a probability is computed for each node of said search space lattice. The probability associated to each node of the search space lattice corresponds to the probability that the particle, molecule, or fragment of molecule source is located on the node. Then, the move of the sensor is evaluated according to the entropy of the computed probabilities.

Abstract: Some embodiments provide a system for accurately and efficiently modeling chemically amplified resist. During operation, the system can determine a quenched acid profile from an initial acid profile by applying multiple quenching models which are associated with different acid concentration ranges to the initial acid profile. One quenching model may be expressed as H=H0?B0, where H is an acid profile after quenching, H0 is an acid profile before quenching, and B0 is an initial base quencher profile. Another quenching model may be expressed as H=k·H0, where k is a constant. Next, the system can apply a smoothing kernel to the quenched acid profile to obtain a quenched-and-diffused acid profile. The smoothing kernel can generally be any weighted averaging function. The quenched-and-diffused acid profile can then be used to predict shapes that are expected to print on the wafer and to perform resolution enhancement techniques on a layout.

Abstract: A profiler which spatially profiles a hydrophobicity distribution for the transmembrane protein based on a scaled hydrophobicity value, includes an identifier for identifying a residue external to a membrane and removing the residue to obtain a truncated structure comprising plural residue side-chains, and a calculator which calculates plural residue centroids for the plural residue side-chains, calculates a distribution of the plural residue centroids, and obtains a geometric center for the distribution.