Abstract: A process, apparatus, and method for computerized detection, tracking, and feedback control of nutritional supplements in an animal, including humans relies on Raman scattering effects on skin or other tissues to determine the content of carotenoids or other nutrients as evidenced in that skin. Serum levels of nutrients may vary dramatically with time, but skin tissues may average such nutrition over time. Skin and other tissues may be scanned with light to produce accurate measurements of carotenoids or other nutrients accumulated in the skin based on the Raman scattering affect of those nutrients in the skin. A score can be derived from a properly calibrated bio-photonic scanner to reflect an averaged effective uptake of the detected nutrient (e.g. such as the carotenoid example).

Abstract: Chemical compositions may be selectively or preferentially excited by the application of scores comprising a series of at least four differing energy inputs. The differing energy inputs of the specified series are selected to resonate each of a group of resonant structures among a group of proximate atoms, including at least one bond.

Abstract: The present invention provides the crystal structure of the Trypanosoma cruzi PRACA proline racemase. Methods of modelling drugs that treat or prevent infection by T. cruzi are also provided, as are the drugs that are identified.

Abstract: A system for providing animal test information is disclosed that comprises: test devices; and a central device communicably connected to the test devices, wherein each of the terminal test devices comprises: an input receiving section for receiving input of attribution information of a sample; a measurement section for measuring the sample and acquiring a measurement result; an information transmitting section for transmitting a data set of the attribution information and the measurement result to the central device, wherein the central device comprises: an information receiving section for receiving the data set; a data storage for storing a plurality of the data set; a standard value calculation section for calculating a standard value to be used for determining a treatment of an animal, based on a plurality of the measurement result included in a plurality of the data set which have common attribution information.

Abstract: A method, computer system, and computer program product for determining N disulphide bond connections in a protein having 2N bonded sulphur atoms. Each sulphur atom is available for forming the N disulphide bond connections through use of an undirected graph having the 2N sulphur atoms as nodes and having an edge connecting each pair of nodes. Each sulphur atom is comprised by a cysteine of the protein. The cysteines are sequenced along a chain in the protein as ordered list of position indexes. A weight W of each edge between cysteine position indexes I1 and I2 is calculated as decreasing with increasing separation d between I1 and I2, wherein d is |I1?I2|/100. The N disulphide bond connections are determined by optimizing an objective function formed from the calculated weights W.

Abstract: A method for evaluating the binding of an evaluation target molecule with respect to a macromolecular compound based on numerical calculations and which detects the binding sites of the evaluation target molecule with respect to the macromolecular compound as a site where electronic states in a predetermined restricted region including the evaluation target molecule and the part of the macromolecular compound, which is adjacent to the evaluation target molecule, are unstable.

Abstract: The teachings relates to the three-dimensional structure of a crystal of a cytochrome protein complexed with a ligand. The three-dimensional structure of four cytochrome P450 2A6-ligand complexes are disclosed. Cytochrome P450 2A6-ligand crystal structures, wherein the ligand is an inhibitor molecule, are useful for providing structural information that may be integrated into drug screening and drug design processes. Thus, the teachings also relate to methods for utilizing a crystal structure of a cytochrome P450 2A6-ligand complex for identifying, designing, selecting, or testing inhibitors of the cytochrome protein. Such inhibitors are useful as therapeutics for the treatment or modulation of i) diseases; ii) disease symptoms; or iii) the effect of other physiological events mediated by the cytochrome.

Abstract: In one embodiment, a system and a method relate to generating a summed ion spectrum for a test sample, the summed ion spectrum identifying ion intensities at multiple different mass-to-charge ratios, and comparing the summed ion spectrum of the test sample with multiple reference summed ion spectra to identify a potential match.

Abstract: A method for discriminating particle groups comprises generating, by a particle analyzer, a particle characteristic distribution histogram in which the abscissa indicates respective channels for representing the characteristics of the particles, and the ordinate indicates the particle count; setting a valid area selection height in the particle characteristics distribution histogram; and generating an equivalent negative histogram based on the set height and the particle characteristic distribution histogram.

Abstract: The crystal structure of ligand-bound EGLN1 catalytic domain of prolyl hydroxylase is disclosed. These coordinates are useful in computer aided drug design for identifying compounds that regulate EGLN1 prolyl hydroxylase and thereby regulate HIF-regulated disorders.

Abstract: A spectral image processing system and method of performing robust unmixing on measurement noise. Based on an observed spectral image acquired from a specimen and emission spectral data of each of plural materials contained in the specimen, a contribution of each of the plural materials to the observed spectral image is unmixed by a process, including an evaluating step of evaluating reliability of each component of the observed spectral image based on a predicted spectral image of the observed spectral image, and a reflecting step of reflecting a result of the evaluation in a content of the unmixing.

Abstract: Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

Abstract: A biosensor system determines the presence and/or concentration of an analyte in a sample using one or more calibrated correlation equations. The analysis may be electrochemical, optical, or a combination thereof. The biosensor system may be implemented using a measurement device and a sensor strip. The measurement device applies test signals to a multi-layered encoding area of the sensor strip. Calibration information is determined from the patterns generated by the interaction of the test signals with the multi-layered encoding area.

Abstract: Embodiments of this invention relate to the analysis of mass spectral data in the quiet zones.

Abstract: Techniques for analyzing protein structures, such as a tertiary protein structure, are provided. A centroid of the residue centroids is calculated. The centroid of the residue centroids is used as a spatial origin of a global linear hydrophobic moment. The correlation between residue centroid magnitude and residue solvent accessibility is enhanced. The global linear hydrophobic moment is defined, wherein each of the residue centroids contributes a magnitude and direction to the global linear hydrophobic moment. A method for comparing at least two tertiary protein structures is also disclosed.

Abstract: Method of identifying compounds that modulate intermolecular interactions between a target protein and a modifier are disclosed. Pharmaceutical composition comprising compounds that inhibit intermolecular interactions between a target protein and a modifier are disclosed. Methods of treating individual suffering from inflammatory conditions, undesirable immune responses, immunological conditions and bacterial infections are disclosed.

Abstract: Techniques for analyzing one or more protein structures. In one aspect of the invention, the technique comprises the following steps. A normalized second-order hydrophobic moment is determined for a protein structure. The normalized second-order hydrophobic moment is then used for analysis of the protein structure. A scoring function in accordance with the normalized second-order hydrophobic moment for the protein structure may be determined. A score for the protein structure may then be generated using the scoring function. The scoring function may represent an integral of the normalized second-order hydrophobic moment. The scores may be generated for a plurality of protein structures. The scores generated for the plurality of protein structures may then be compared.

Abstract: Methods for using modified single wall carbon nanotubes (“SWCNTs”) to detect presence and/or concentration of a gas component, such as a halogen (e.g., Cl2), hydrogen halides (e.g., HCl), a hydrocarbon (e.g., CnH2n+2), an alcohol, an aldehyde or a ketone, to which an unmodified SWCNT is substantially non-reactive. In a first embodiment, a connected network of SWCNTs is coated with a selected polymer, such as chlorosulfonated polyethylene, hydroxypropyl cellulose, polystyrene and/or polyvinylalcohol, and change in an electrical parameter or response value (e.g., conductance, current, voltage difference or resistance) of the coated versus uncoated SWCNT networks is analyzed. In a second embodiment, the network is doped with a transition element, such as Pd, Pt, Rh, Ir, Ru, Os and/or Au, and change in an electrical parameter value is again analyzed. The parameter change value depends monotonically, not necessarily linearly, upon concentration of the gas component.

Abstract: The present invention refers to a method for evaluating, comparing and selecting entities over a broad variety of technical fields. Preferably, the entities are pharmaceutical drugs.

Abstract: A computer-based method for identifying at least one pair of similar chemical reactions between a plurality of reactions each related to preparation of at least one product from at least one reagent may include generating for each reaction a structural representation involving dynamic and conventional bonds and, based on the this structural representation, generating for each reaction a set of fragment descriptors of a predetermined length comprising the dynamical bonds and a corresponding descriptor vector. The method may further include calculating similarity indices between descriptor vectors of the plurality of reactions and comparing the similarity indices to identify at least one pair of similar reactions.

Abstract: A scanning electron microscope having a charged particle beam that when in a state being irradiated toward a sample, a voltage is applied to the sample so that the charged particle beam does not reach the sample. The scanning electron microscope also detects information on a potential of a sample using a signal obtained, and a device for automatically adjusting conditions based on the result of measuring.

Abstract: A method and system for the evaluation of the probability for the presence of suspicious materials is presented. The proposed system will be able to continuously monitor a large area or a gate passage, without a specific need for a manual full-body search or manual inspection or the use of sniffers or sniffing dogs (although the system can be embedded within such a gate), and will allow to detect suspicious materials, not by identifying the specific material, but rather by at least one of the chemical and/or physical analysis of the commonality of all detected materials against the statistical accumulation database of all material properties that were presented to the system in the past.

Abstract: The invention relates to methods for analyzing the miscibility of compositions. The methods may further quantify the degree of miscibility of the compositions.

Abstract: A method of analyzing data from a mass spectrometer provides data-dependent acquisition. An extracted ion chromatogram (XIC) is created for each m/z data point of mass spectral scans and the XIC for each m/z data point are correlated to a model function to obtain a XIC correlation value. A weighting function is applied to the XIC correlation value to obtain a current weighted intensity for each m/z point, which is used to reconstruct a weighted mass spectrum. The value or range of intensities of interest of the weighted intensity data or raw data is transformed from the time domain into the frequency domain, and the transformed data is used to make a real-time decision for the data-dependent acquisition. The data-dependent acquisition can be the performance of tandem mass spectrometry. A sample processing apparatus receives the sample and a computer readable medium provides instructions to the apparatus.

Abstract: At least one type of carbon material susceptible to generate a gas G is selected. Then, a model is built from the carbon isotopic composition of a gas P generated by thermal degradation of this type of carbon material. The model is calibrated by calibrating the kinetic effect independently of the precursor effect. In order to achieve that, pyrolyses are performed on compounds modeling the type of carbon material, said compounds being synthesized and labeled with 13C. Using said model, a carbon isotopic composition of gas P generated is estimated. Finally, it is determined whether gas G has been generated from the selected type of carbon material, by comparing a measured isotopic composition of gas G to the estimated isotopic composition.

Abstract: Peptides are identified from a list of candidates using collision-induced dissociation tandem mass spectrometry data. A probabilistic model for the occurrence of spectral peaks corresponding to frequently observed partial peptide fragment ions is applied. As part of the identification procedure, a probability score is produced that indicates the likelihood of any given candidate being the correct match. The statistical significance of the score is known without necessarily having reference to the actual identity of the peptide. In one form of the invention, a genetic algorithm is applied to candidate peptides using an objective function that takes into account the number of shifted peaks appearing in the candidate spectrum relative to the test spectrum.

Abstract: A method and apparatus for performing time of flight mass spectrometry wherein the number of sums of transients taken for generating a given spectra is determined as a function of a characteristic of the incoming data for that spectrum. For instance, the number of transient measurements taken for a given spectrum output can be determined as a function of the abundance of ions in the sample or the abundance of ions corresponding to a base peak or another selected peak. In yet another embodiment, the collection of transients is terminated when a threshold signal to noise ratio is attained.

Abstract: The use of a robust statistical method for self-calibration of a measuring instrument, such as a mass spectrometer, is disclosed. The method involves the use of differences in mass and complementary pairs for example, to estimate calibration parameters. Self-calibration of various mass spectra is described. Related systems and computer-readable media are also described.

Abstract: The invention provides devices and methods for acoustically determining the properties of the contents of one or more reservoirs in a plurality of reservoirs. Each reservoir is adapted to contain a fluid. An acoustic radiation generator can be positioned in acoustic coupling relationship to each of the reservoirs. Acoustic radiation generated by the acoustic radiation generator is transmitted through each reservoir to an analyzer. The analyzer is capable of analyzing a characteristic of the transmitted acoustic radiation and optionally correlating the characteristic to a property of the reservoirs' contents. Properties that may be determined include volume, temperature, and composition. The invention is particularly suited to determining the properties of the contents of a plurality of reservoirs to allow for accuracy and control over the dispensing of fluids therefrom.

Abstract: Described is a technique to exhaustively enumerate the thermodynamic properties of the water molecules solvating the active site of a protein in its apostate and calculate the relative binding affinities of congeneric compounds that bind to this protein. The subject matter includes sampling the configurations of the solvating water in the active site; extracting the thermodynamic information about the solvating water from these configurations by clustering the observed water configurations into regions of high water occupancy (e.g.

Abstract: Described is a technique to exhaustively enumerate the thermodynamic properties of the water molecules solvating the active site of a protein in its apostate and calculate the relative binding affinities of congeneric compounds that bind to this protein. The subject matter includes sampling the configurations of the solvating water in the active site; extracting the thermodynamic information about the solvating water from these configurations by clustering the observed water configurations into regions of high water occupancy (e.g.

Abstract: A system for receiving, analyzing and communicating results of sensing chemical and/or physical parameter values, using wireless transmission of the data. Presence or absence of one or more of a group of selected chemicals in a gas or vapor is determined, using suitably functionalized carbon nanostructures that are exposed to the gas. One or more physical parameter values, such as temperature, vapor pressure, relative humidity and distance from a reference location, are also sensed for the gas, using nanostructures and/or microstructures. All parameter values are transmitted wirelessly to a data processing site or to a control site, using an interleaving pattern for data received from different sensor groups, using I.E.E.E. 802.11 or 802.15 protocol, for example. Methods for estimating chemical concentration are discussed.

Abstract: Methods, systems and computer program products for identifying components of an unknown mixture using spectral analysis techniques. The method includes comparing the spectrum of the unknown mixture with the spectra of library compounds to obtain candidate mixture combinations. A model is generated for each of the candidate mixture combinations based on a modeling metric. A residual spectrum is computed corresponding to each of the candidate mixture combinations by removing the spectrum of each of the compounds of the candidate mixture combination from the spectrum of the unknown mixture. One or more potential compounds are identified by comparing the residual spectrum with the spectrum of library compounds. The potential compounds are added to the candidate mixture combinations to generate an updated list of the candidate mixture combinations. The search algorithm repeats the steps described above on the updated candidate mixture combinations, until a first termination condition is satisfied.

Abstract: The invention provides crystalline O-methyltransferases and isolated non-native O-methyltransferases as well as sets of their structural coordinates. Also provided are methods of predicting the activity or substrate specificity of putative O-methyl-transferases, methods of identifying potential substrates of O-methyltransferases, and methods of identifying potential inhibitors of methyltransferases.

Abstract: A device for downloading data from a machine having a touch screen or PLC to govern its operation, the device includes a handheld control unit that is operably associated with the touch screen or PLC such that the touch screen or PLC can be downloaded from the touch screen onto the device and information from the device can be transmitted to a personal computer to be viewed or printed. Additionally, a method of downloading the data from a machine having a touch screen or PLC to a handheld control unit and downloading this information to a personal computer such that the information can be viewed or printed.

Abstract: Some embodiments an infusion pump system can be used to determine a user's total insulin load (TIL) that provides an accurate indication of the insulin previously delivered to the user's body which has not yet acted. In particular embodiments, the TIL can account for both the bolus deliveries and the basal deliveries that have occurred over a period of time. Such information may be useful, for example, when the infusion pump is operated in conjunction with a continuous glucose monitoring device.

Abstract: The present invention provides a c-Met inhibition model. The invention further provides a method to derive inhibition models for other kinases. The kinase inhibition models of the present invention can be used to design or screen for inhibitors for kinases.

Abstract: The invention comprises for methods of identifying pharmacophores based on the spleen tyrosine kinase (SYK) protein or fragment thereof. The invention further provides methods of identifying SYK inhibitors using pharmacophores that are identified from co-crystals of SYK and its ligands. Further, the invention comprises methods of inhibiting SYK comprising contacting the residues lining the binding site with an inhibitor compound identified from pharmacophores.

Abstract: The teachings relates to the three-dimensional structure of a crystal of a cytochrome protein complexed with a ligand. The three-dimensional structure of four cytochrome P450 2A6-ligand complexes are disclosed. Cytochrome P450 2A6-ligand crystal structures, wherein the ligand is an inhibitor molecule, are useful for providing structural information that may be integrated into drug screening and drug design processes. Thus, the teachings also relate to methods for utilizing a crystal structure of a cytochrome P450 2A6-ligand complex for identifying, designing, selecting, or testing inhibitors of the cytochrome protein. Such inhibitors are useful as therapeutics for the treatment or modulation of i) diseases; ii) disease symptoms; or iii) the effect of other physiological events mediated by the cytochrome.

Abstract: A method and a system is disclosed for determining cetane values from constant volume combustion chamber apparatuses capable of producing pressure versus time combustion profiles having a fast combustion region and a slow combustion region, where data from the two regions is used to compute cetane values for middle distillate fluid samples using a series expansion equation.

Abstract: A molecular force field assignment method for assigning a molecular force field to a molecule having a desired molecular structure, includes a step of specifying a combination according to whether or not an interatomic distance between a first and second atoms, obtained by analyzing a molecular structure with a molecular orbital method, exceeds a prescribed threshold value.

Abstract: The spectral method for determining the concentrations of a substance in a mixture of any number of substances is defined by a chemical image having a plurality of pixels (520). The method includes steps of providing a spectrum for each of the n number of substances in the mixture (530), and obtaining the spectrum for one of the plurality of pixels, and calculating a plurality of estimated concentrations of each substance in the mixture as a function of the spectrum for each substance and the spectrum for the pixel, and calculating a deviation value for each of the plurality of estimated concentrations as a function of the spectrum of each of the number of substances in the mixture, and selecting the estimated concentration with the lowest deviation factor as a most likely concentration of each substance in the mixture (550).

Abstract: This invention is an algorithm for estimating the topology of a protein by determination of the free energy from a global entropy evaluation model combined with local correction methods.

Abstract: The present invention discloses a suite of G2FT and GFT NMR experiments that can be used for complete resonance assignments of proteins and for obtaining structural (conformational and orientational) constraints for determining high resolution three-dimensional structures of biomolecules.

Abstract: The present invention related to a method for crystallizing a CMY-10 being a ?-lactamase with extended-substrate spectrum, a crystal of CMY-10, and a crystal structure of CMY-10. With utilization of three-dimensional structure of CMY-10 protein provided by the present invention, it is possible to develop novel antibiotics or inhibitors that can prevent an emergence of resistance bacteria appeared by plasmidic class C ?-lactamases having extended-substrate specificity.

Abstract: Sequence alignment and sequence database similarity searching are among the most important and challenging task in bio informatics, and are used for several purposes, including protein function prediction. An efficient parallelisation of the Smith-Waterman sequence alignment algorithm using parallel processing in the form of SIMD (Single-Instruction, Multiple-Data) technology is presented. The method has been implementation using the MMX (MultiMedia eXtensions) and SSE (Streaming SIMD Extensions) technology that is embedded in Intel's latest microprocessors, but the method can also be implemented using similar technology existing in other modern microprocessors. Near eight-fold speed-up relative to the fastest previously an optimised eight-way parallel processing approach achieved know non-parallel Smith-Waterman implementation on the same hardware. A speed of about 200 million cell updates per second has been obtained on a single Intel Pentium III 500 MHz microprocessor.

Abstract: The method and system for identifying a biological sample generates a data set indicative of the composition of the biological sample. In a particular example, the data set is DNA spectrometry data received from a mass spectrometer. The data set is denoised, and a baseline is deleted. Since possible compositions of the biological sample may be known, expected peak areas may be determined. Using the expected peak areas, a residual baseline is generated to further correct the data set. Probable peaks are then identifiable in the corrected data set, which are used to identify the composition of the biological sample. In a disclosed example, statistical methods are employed to determine the probability that a probable peak is an actual peak, not an actual peak, or that the data are too inconclusive to call.

Abstract: A computer readable medium comprising atomic coordinates for the human ?2 adrenoreceptor is provided. The computer readable medium programming for displaying a molecular model of the human ?2 adrenoreceptor, programming for identifying a compound that binds to said human ?2 adrenoreceptor and/or a database of structures of known test compounds. Also provided is a method comprising computationally identifying a compound that binds to the human ?2 adrenoreceptor using the atomic coordinates.

Abstract: The inventors have modified the amino acid sequence of a maltogenic alpha-amylase to obtain variants with improved properties, based on the three-dimensional structure of the maltogenic alpha-amylase Novamyl. The variants have altered physicochemical properties, e.g. an altered pH optimum, improved thermostability, increased specific activity, an altered cleavage pattern or an increased ability to reduce retrogradation of starch or staling of bread.

Abstract: A method for determining elemental composition of ions from mass spectral data, comprising obtaining at least one mass measurement from mass spectral data; obtaining a search list of candidate elemental compositions whose exact masses fall within a given mass tolerance range from the accurate mass; reporting a probability measure based on a mass error; calculating an isotope pattern for each candidate elemental composition from the search list; constructing a peak component matrix including at least one of the isotope pattern and mass spectral data; performing a regression against at least one of isotope pattern, mass spectral data, and the peak component matrix; reporting a second probability measure for at least one candidate elemental composition based on the isotope pattern regression; and combining the two the probability measures into an overall probability measure. A method for determining elemental isotope ratios from mass spectral data.