Abstract: A sensor interface system and a sensor integration module support individual sensors and sensor arrays, with network connectivity and critical functions required for analog and digital sensors when deployed in field applications used for chemical, biological, radiation, nuclear and explosives (CBRNE) material identification. The sensor integration module enables efficient integration of a single sensor or for multiple sensors into an array using a modular sensor interface unit and provides individual TCP/IP addresses for each detector element, signal processing for the sensor data and communications capabilities establishing each detector and the sensor array as network elements on a distributed network.

Abstract: A multi-analyte diagnostic system for use with a computer. The diagnostic system includes a flow analyzer including a co-planar light source-optical detector array, the flow analyzer being communicatable with the computer. The diagnostic system also includes a memory medium readable by the computer and storing computer instructions. The instructions include the following steps. A biological sample is run through the flow analyzer. The identity and quantity of at least one analyte of interest in the biological fluid is determined substantially simultaneously to the sample-running step.

Abstract: A method and apparatus are disclosed which produce quantum entanglement and non-local effects of various substances on responsive targets such as biological and/or chemical systems through quantum entanglement. In one broad embodiment, the apparatus includes a quantum entanglement generating source, said source emitting a plurality of quantum-entangling members such as photons when said source operates; and a substance disposed adjacent to said source, said substance being responsive to said members; such that when said source emits said members which pass through said substance and a biological system, said members first quantum-entangle with quantum entities in said substance, then travel to said biological system such as a human body and subsequently entangle with quantum entities inside the biological system producing non-local effect of the substance on said biological system through quantum entanglement.

Abstract: An apparatus, system, and method for optimization. The apparatus, system, and method include a mechanism for ending an optimization when all models within one design tolerance of an optimum model have been simulated.

Abstract: A method for carrying out analyses of a gas comprising one or more species Si, Sj, . . . , Sn by using of ion mobility spectrometry includes in carrying out two subsequent analyses in different conditions and comparing the results of these two analyses. The different conditions in the two analyses are such as to modify either the residence time of the ions corresponding to the species in the reaction zone or in the drift zone of the ion mobility spectrometer, or, selectively, the concentration of at least one of these ions.

Abstract: A methodology for facilitating the identification, authentication or quality control of packaged products is described comprising a marking and an authentication phase. In the marking phase the method involves obtaining an analytical specification, and for example an analytical spectrum, of a reference chemical composition for the product; and recording the data on a machine readable data storage means provided in direct mechanical association with the packaging thereof, and for example being incorporated into or onto or as a part of such packaging. The authentication phase comprises applying a suitable data reader to the data storage means to read the recorded data and reconstruct the recorded analytical specification; chemically analysing a sample of the product to obtain a measured analytical specification; comparing the measured and recorded readings within predetermined tolerance limits. A system to perform the method and a product marked accordingly are also described.

Abstract: A novel human IL-18 native crystalline structure is identified.

Abstract: A method for interpreting data that is produced after a group of amino acids and acylcarnitines are derivatized from blood spots taken from newborn babies and scanned by a tandem mass spectrometer. Concentration levels of each metabolite, which are directly proportional to the butyl ester fragment after derivatization, are compared to threshold flags for determining a significance of any deviation of the metabolite relative to the flag threshold. The threshold flags are diagnostic limits to the data retrieved from each blood spot. The data includes metabolite concentrations and molar ratios of metabolites with other metabolites. Samples are labeled normal for a disease if the concentration of any of the metabolite concentrations or molar ratio concentration do not deviate from the flag threshold, but, in contrast, the sample must be further evaluated if a value is elevated or deficient to some degree.

Abstract: A method for interpreting data that is produced after a group of amino acids and acylcarnitines are derivatized from blood spots taken from newborn babies and scanned by a tandem mass spectrometer. Concentration levels of each metabolite, which are directly proportional to the butyl ester fragment after derivatization, are compared to threshold flags for determining a significance of any deviation of the metabolite relative to the flag threshold. The threshold flags are diagnostic limits to the data retrieved from each blood spot. The data includes metabolite concentrations and molar ratios of metabolites with other metabolites. Samples are labeled normal for a disease if the concentration of any of the metabolite concentrations or molar ratio concentration do not deviate from the flag threshold, but, in contrast, the sample must be further evaluated if a value is elevated or deficient to some degree.

Abstract: The present invention provides methods for determining the structure and/or function of one or more domains of a cation-dependent (and preferably calcium-dependent) polypeptide (particularly a calcium-dependent enzyme, which may be a protease such as calpain) in the presence of one or more cations. The invention further provides methods for identifying a ligand having the ability to bind to one or more ligand-binding domains (LBDs) of a cation-dependent (and preferably calcium-dependent) polypeptide, and ligands identified by these methods. The invention also provides methods of treating or preventing physical disorders in animals using these ligands.

Abstract: The present application provides a method for predicting the functional site of a protein using data of the entire proteins of an organism of which genome data or cDNA data is known. More specifically, the present application provides a method for predicting a protein functional site, comprising the steps of calculating the frequency of occurrence of an oligopeptide in the entire proteins, calculating the value of each amino-acid residue contributing to the frequency of occurrence as the representative value of the function, and predicting the protein functional site by using the representative value of function as an indicator. The present also provides a system for predicting a functional site for automatically performing said methods.

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: A method for interpreting data that is produced after a group of amino acids and acylcarnitines are derivatized from blood spots taken from newborn babies and scanned by a tandem mass spectrometer. Concentration levels of each metabolite, which are directly proportional to the butyl ester fragment after derivatization, are compared to threshold flags for determining a significance of any deviation of the metabolite relative to the flag threshold. The threshold flags are diagnostic limits to the data retrieved from each blood spot. The data includes metabolite concentrations and molar ratios of metabolites with other metabolites. Samples are labeled normal for a disease if the concentration of any of the metabolite concentrations or molar ratio concentration do not deviate from the flag threshold, but, in contrast, the sample must be further evaluated if a value is elevated or deficient to some degree.

Abstract: A programmed computer analyzes data from a mass spectrometer. A spectrum corresponding to an unknown sample is perturbed in various ways, and each perturbed spectrum is compared with the spectrum of a known or reference substance. The perturbed spectrum having the highest correlation with the known spectrum, and which is also physically plausible, is considered to be the best fit. The method indicates in what specific ways the unknown sample differs from, or is similar to, the known substance.

Abstract: The first crystal structure of the androgen receptor ligand binding domain has been determined to 2.0 angstrom resolution. Disclosed are the coordinates for the crystal structure, and methods for determining agonists, partial agonists, antagonists, partial antagonists and selective androgen receptors modulators (SARMs) of the androgen receptor.

Abstract: A method for interpreting data that is produced after a group of amino acids and acylcarnitines are derivatized from blood spots taken from newborn babies and scanned by a tandem mass spectrometer. Concentration levels of each metabolite, which are directly proportional to the butyl ester fragment after derivatization, are compared to threshold flags for determining a significance of any deviation of the metabolite relative to the flag threshold. The threshold flags are diagnostic limits to the data retrieved from each blood spot. The data includes metabolite concentrations and molar ratios of metabolites with other metabolites. Samples are labeled normal for a disease if the concentration of any of the metabolite concentrations or molar ratio concentration do not deviate from the flag threshold, but, in contrast, the sample must be further evaluated if a value is elevated or deficient to some degree.

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: Systems and methods are described for processing an emission signal, such as a fluorescent signal, to compensate for noise in an excitation beam, such as a laser beam. As one example, a scanning system is described that includes an excitation signal generator that provides an excitation signal having one or more representative excitation values representative of an excitation beam; an excitation reference provider that provides at least one excitation reference value; a normalization factor generator that compares the excitation reference value to at least one representative excitation value, thereby generating a normalization factor; and a comparison processor that adjusts at least one emission value corresponding to the at least one representative excitation value based, at least in part, on the normalization factor.

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: The x-ray crystal structure of BACE or BACE-like proteins is useful for solving the structure of other molecules or molecular complexes, and identifying and/or designing potential modifiers of BACE activity.

Abstract: The present invention relates to a data storage medium encoded with the corresponding structure coordinates of molecules and molecular complexes which comprise the active site binding pockets of IMPDH. Such data storage material is capable of displaying such molecules and molecular complexes, or their structural homologues, as a graphical three-dimensional representation on a computer screen. This invention also relates to methods of using the structure coordinates to solve the structure of homologous proteins or protein complexes. In addition, this invention relates to methods of using the structure coordinates to screen and design compounds, including inhibitory compounds, that bind to IMPDH or homologues thereof. This invention also relates to molecules and molecular complexes which comprise the active site binding pockets of IMPDH or close structural homologues of the active site binding pockets. This invention also relates to compounds and pharmaceutical compositions which are inhibitors of IMPDH.

Abstract: Steric features inherent in the three dimensional disposition of atoms in molecules can be represented as multiplets using a defined set of steric descriptors. The resulting multiplets can be encoded in a compressed form of bitstring known as a bitmap. Such bitmaps can be generated in compressed form and used to compare individual conformers or ensembles of conformers of molecules to each other without decompression. Such comparisons are useful in molecular similarity analysis, in molecular diversity analysis, in database searching, and in conformational analysis.

Abstract: A system and a method for screening of nucleation tendency of a molecule, such as a macromolecule, based on acoustic, electrostatic or hybrid acoustic/electrostatic levitation of a droplet for optimizing crystallization conditions for said molecule. This allows for a controlled approach to determination of supersaturation and allows for screening of crystal nucleation conditions within minutes and hours instead of months and years with a minute amount of starting material compared to conventional crystallization methods.

Abstract: Devices and techniques for estimating the concentration of one or more agents in a fluid environment employ a plurality of measurements of a sensor attribute that changes in response to an agent. Measurements taken before the agent/reagent combination reaches a steady-state may be used. The plurality of measurements are processed using a nonlinear, parametric model of the interaction between the sensor and the agent to determine the concentration of the agent. The model takes into account the finite capacity of a sensor reagent. The model characterizes the interaction of individual agent/reagent combinations with a set of parameters. These parameters require minimal testing to calculate. The invention enables the response of a sensor to an agent over the entire range of agent concentration levels to be efficiently and accurately characterized. The invention also enables the prediction of collective responses given parameters characterizing a plurality of agent/reagent combinations.

Abstract: Methods for inferentially determining various properties of a gas mixture, when the speed of sound in the gas is known at an arbitrary temperature and pressure. The method can be applied to natural gas mixtures, where the known parameters are the sound speed, temperature, pressure, and concentrations of any dilute components of the gas. The method uses a set of reference gases and their calculated density and speed of sound values to estimate the density of the subject gas. Additional calculations can be made to estimate the molecular weight of the subject gas, which can then be used as the basis for heating value calculations. The method may also be applied to inferentially determine density and molecular weight for gas mixtures other than natural gases.

Abstract: Methods for determining the chemical structures, substructures and/or ionic structural arrangements of unknown or partially structurally characterized compounds from mass spectrometric data are disclosed. The methods of the invention are directed to elucidating the molecular structures of compounds by identifying the structures of ions generated from those compounds through the use of tandem mass spectrometry and subsequently conducting a library search of structurally characterized tandem product spectra from known ions for specific matches. The collective structural information and/or alternative structural candidates are then constructed from the determined ion structures and other structural characteristics using a structure generator and/or a structure assembly and/or a structure reduction system. The structure or substructure determination process can be continuously improved by adding additional data, e.g., information obtained from molecules previously structurally characterized using this method.

Abstract: An automatic peak selection method for multidimensional data that selects peaks from very noisy data such as two-dimensional liquid chromatography-mass spectrometry (LC-MS) data is described. Such data are characterized by non-normally distributed noise that varies in different dimensions. The method computes local noise thresholds for each one-dimensional component of the data. Each point has a local noise threshold applied to it for each dimension of the data set, and a point is selected as a candidate peak only if its value exceeds all of the applied local noise thresholds. Contiguous candidate peaks are clustered into actual peaks. The method is preferably implemented as part of a high-throughput platform for analyzing complex biological mixtures.

Abstract: Embodiments of the invention provide methods for evaluating the accuracy of a molecular model properties model (or predictions generated using a molecular properties model). The accuracy of a molecular properties model may be evaluated using three general approaches, (i) by using the same data set to both train the model and to estimate the accuracy of the model, (ii) by using distinct data sets to train and subsequently test a model, and (iii) by using multiple models (or sets of predictions).

Abstract: A dynamic range relaxation algorithm is applied to simulate borehole failure under a variety of stress conditions. The borehole and its neighborhood are modeled by a number of regions by a plurality of interconnected nodes. The bonds between the nodes may be modeled as springs, rods, or beams. The strength of the bonds has a statistical variation to accurately simulate real world situations. The model may include, in addition to the borehole and the far earth formations, a liner, a casing, and/or a gravel pack. Simulation is carried out for different strength of the bonds.

Abstract: The use for biological screening purposes of a subset (library) of a large combinatorially accessible chemical universe increases the efficiency of the screening process only if the subset contains members representative of the total diversity of the universe. In order to insure inclusion in the subset of molecules representing the total diversity of the universe under consideration, valid molecular descriptors which quantitatively reflect the diversity of the molecules in the universe are required. A unique validation method is used to examine both a new three dimensional steric metric and some prior art metrics. With this method, the relative usefulness/validity of individual metrics can be ascertained from their application to randomly selected literature data sets.

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: A device for quantitatively determining an analyte is provided to conspicuously improve the performance of the quantitative determination. This device is equipped with a flow channel, an analyte detecting unit for capturing and detecting the analyte, and a quantitative measurement unit for quantitatively determining the analyte, wherein a signal generated when the analyte detecting unit has detected the analyte is divided into a plurality of parts in the direction of the flow in the flow channel at the quantitative measurement unit for processing. Also provided are technologies including one for controlling the density of molecules attached to the surface of a solid. In these technologies, when molecules are attached to a substrate, the density of attached molecules is controlled, by having an electrolyte also present in a solution containing the molecules to adjust the screening effect by the electrolyte, and by taking into consideration the effective size of a molecule.

Abstract: This invention is directed to the crystal structures of MK2, and to the use of these structures in rational drug design methods to identify agents that may interact with active sites of MK2 proteins. Such agents may be useful as therapeutic agents.

Abstract: Molecules are represented as one dimensional strings of atoms having a linear position and a width. One dimensional representations are compared to assess the likelihood of similarity in chemical behavior.

Abstract: The intensity of an odour can be quantified by determining what is the response of an odour sensing device to that odour, then transforming the response data to an odour intensity value based on transformation data relating to a set of selected reference odours. The transformation data includes organoleptic data indicating how odour intensity values assigned to the set of reference odours by a sensory panel depend upon the concentration of the reference compounds and includes data indicating how the response data of the odour sensing device when exposed to the set of reference odours depends upon the concentration of the reference compounds. The reference odours may be basic odours defining the dimensions of a multi-dimensional space in which odours can be defined.

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: A computer implemented method modifies an experimental electron density map. A set of selected known experimental and model electron density maps is provided and standard templates of electron density are created from the selected experimental and model electron density maps by clustering and averaging values of electron density in a spherical region about each point in a grid that defines each selected known experimental and model electron density maps. Histograms are also created from the selected experimental and model electron density maps that relate the value of electron density at the center of each of the spherical regions to a correlation coefficient of a density surrounding each corresponding grid point in each one of the standard templates. The standard templates and the histograms are applied to grid points on the experimental electron density map to form new estimates of electron density at each grid point in the experimental electron density map.

Abstract: A main object is to cope with an unknown structure substance thereby to identify the structure of a parent ion highly precisely and to derive a supposed structure. A method for analyzing mass spectrometric data is disclosed, which: acquires mass spectrometric data on an ionized sample and dissociated ions dissociated from the sample as a parent ion; derives dissociated ion candidates by analyzing the molecular orbits on the candidates of the structures of the parent ion; and displays the analytical results of the parent ion candidates and the dissociated ion candidates and compares the data of the dissociated ion candidates and the data of dissociated ions actually measured, to evaluate the structures of the parent ion candidates.

Abstract: A method, system, and computer program product for mining mass spectral data to detect chemical-specific characteristic features in large databases and/or files, including specifying spectral characteristics of mass spectra to mine, specifying a relationship between the spectral characteristics, searching the mass spectra for portions of the mass spectra which match the spectral characteristics based on the relationship, and assigning scores to the portions of mass spectra to indicate a degree of correlation between the portions of mass spectra and the spectral characteristics. Exemplary embodiments encompass a user specification of the spectral characteristics and their relationships used to mine the mass spectral data, automated specification of the spectral characteristics and their relationships used to mine the data, and real-time data mining wherein the mass spectrometer is adjusted based on the result.

Abstract: A method is provided for identifying a search model to use in molecular replacement for determining a structure of a target biomolecule, such as a protein, from X-ray diffraction data, the method comprising: employing computer executable logic to perform multiple molecular replacement searches on X-ray diffraction data of the target biomolecule where a group of different biomolecule structures are used as search models for the multiple molecular replacement searches; and employing computer executable logic to compare solutions from the multiple molecular replacement searches, the comparison producing data from which biomolecule structures can be identified as having superior structural identity with the target biomolecule as compared to the other biomolecule structures in the group.

Abstract: This invention is directed to the crystal structure of yqeJ, and to the use of this structure in rational drug design methods to identify agents that may interact with active sites of yqeJ. Such agents may be useful as antibacterial agents.

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.

Abstract: A device for measuring at least one property of a material web, in particular a paper or board web, includes movable measuring probes provided on both sides of the web, which can be pressed against the web with preferably at least substantially equal force, forming a respective air pad, elements for measuring the air pads, in particular the air pad thickness, on both sides, and at least one property sensor, in particular a paper property sensor, fitted to a measuring probe supported by an air pad.

Abstract: A method for modeling samples includes the use of control points to define lines profiles and other geometric shapes. Each control point used within a model influences a shape within the model. Typically, the control points are used in a connect-the-dots fashion where a set of dots defines the outline or profile of a shape. The layers within the sample are typically modeled independently of the shape defined using the control points. The overall result is to minimize the number of parameters used to model shapes while maintaining the accuracy of the resulting scatterometry models.

Abstract: A sample archive method and system implement a plurality of sample carriers configured to support a plurality of sample nodes in a predetermined spatial relationship, sample storage devices for selectively placing the plurality of sample carriers in an archive, and sample node removal apparatus for locating and removing selected ones of the plurality of sample nodes. Alternative embodiments are disclosed wherein the sample node removal apparatus comprises a laser and a mechanical clipping tool, which may be manually operated or automated. An optical component may be operative to detect the location of selected sample carriers in the archive, selected ones of the plurality of sample nodes, or both. A positioning component may position the sample node removal apparatus responsive to signals transmitted by the optical component. Various apparatus and methods of archiving samples and preparing the same for analysis are also disclosed.

Abstract: The instant invention provides methods, reagents, and computational tools for designing non-natural substrate analogs for enzymes, especially for designing unnatural amino acid analogs for aminoacyl tRNA Synthetases (AARSs), such as the Phe tRNA Synthetase. The instant invention also provides methods to incorporate unnatural amino acid analogs, especially those with interesting functional groups, into protein products to generate proteins of modified or novel functions.

Abstract: The invention relates to methods of identifying and characterizing properties of polymers to provide information about the polymer such as the charge of the polymer, the number and types or characteristics of units of the polymer and the sequence of the polymers. The invention also relates to methods of sequencing polymers such as nucleic acids, polypeptides and polysaccharides and methods for identifying a polysaccharide-protein interaction.

Abstract: The problem of how to select out of a large chemically accessible universe molecules representative of the diversity of that universe is resolved by the discovery of a method to validate molecular structural descriptors. Using the validated descriptors, optimally diverse subsets can be selected. In addition, from the universe, molecules with characteristics similar to a selected molecule can be identified. The validated descriptors also enable the generation of a huge virtual library of potential product molecules which could be formed by combinatorial arrangement of structural variations and cores. In this virtual library it is possible to search billions of possible product compounds in relatively short time frames.

Abstract: 5.5 Angstrom resolution x-ray crystallographic structures of 70S ribosome complexes containing messenger RNA and tranfer RNA (tRNA), or tRNA analogs, are provided. The resolution has been enhanced by fitting atomic resolution structures of 30S and 50S subunits onto the 5.5 anstrong electron density map. The enhanced structure reveals regions of structural differences between the 70S complex and the structures of the individual 30S and 50S components. Pharmacophore design to discover novel inhibitors or activators may be carried out using the enhanced 5.5 Angstrom 70S structure.

Abstract: A process is provided for the high throughput screening of binding of ligands to macromolecules using high resolution powder diffraction data including producing a first sample slurry of a selected polycrystalline macromolecule material and a solvent, producing a second sample slurry of a selected polycrystalline macromolecule material, one or more ligands and the solvent, obtaining a high resolution powder diffraction pattern on each of said first sample slurry and the second sample slurry, and, comparing the high resolution powder diffraction pattern of the first sample slurry and the high resolution powder diffraction pattern of the second sample slurry whereby a difference in the high resolution powder diffraction patterns of the first sample slurry and the second sample slurry provides a positive indication for the formation of a complex between the selected polycrystalline macromolecule material and at least one of the one or more ligands.