Abstract: Embodiments of a testing method for optimizing a therapy to a diabetic patient comprise collecting at least one sampling set of biomarker data, computing a probability distribution function, a hazard function, a risk function, and a risk value for the sampling set of biomarker data wherein, wherein the probability distribution function is calculated to approximate the probability distribution of the biomarker data, the hazard function is a function which yields higher hazard values for biomarker readings in the sampling set indicative of higher risk of complications, the risk function is the product of the probability distribution function and the hazard function, and the risk value is calculated by the integral of the risk function, minimizing the risk value by adjusting the diabetic patient's therapy, and exiting the testing method when the risk value for at least one sampling set is minimized to an optimal risk level.

Abstract: An improved method for rapid identification of microorganisms is disclosed, along with sequences of PCR primers optimized for this purpose. The primers are designed based on information analysis of sequences from a large number of organism to amplify certain segments of genomic DNA whose sequences are unique among different organisms. The PCR products are compared with a DNA sequence database to obtain the identity of the microorganisms. This approach provides an accurate and fast identification and taxonomic assignment of microbial species.

Abstract: According to embodiments, techniques for selecting a consistent part of a signal, including a photoplethysmograph (PPG) signal, are disclosed. A pulse oximetry system including a sensor or probe may be used to obtain a PPG signal from a subject. Signal peaks may be identified in the PPG signal. Characteristics of the signal peaks, including the amplitude levels of the signal peaks and/or the time-distance between the signal peaks may be used to determine if the PPG signal is consistent. In an embodiment, signal peaks are processed based on a consistency metric, and the processed signal peaks are compared to the consistency metric to determine if the PPG signal is consistent. If the PPG signal is determined to be consistent, the PPG signal may be further analyzed to determine an underlying signal parameter, including, for example, a patient respiration rate.

Abstract: A method for calculating a sample size for a clinical trial of a first treatment can be provided. The method can include reading a survival curve from a clinical trial for a second treatment, wherein the clinical trial may be selected by a user interacting with a user interface. The method can further include selecting a plurality of points on the survival curve and storing coordinates for each of the plurality of points, wherein the plurality of points are selected so as to capture substantial features of the survival curve. Then, a hazard curve is generated based on the coordinates that were stored, wherein the hazard curve may be a step function. The method can further include calculating a sample size for the clinical trial of the first treatment using a Markov model based on the hazard curve.

Abstract: An improved method for specific identification of any organisms by DNA hybridization or amplification is disclosed. Oligonucleotides are designed based on information analysis of sequences from a large number of related species. Oligonucleotide sequences that have the maximal specificity to certain nucleic acids from a particular species (or set of species) or type strain are selected for hybridization or amplification using DNA from the target organism. The presence or absence of a PCR or hybridization product may be used to identify the target organism. The resulting PCR products may also be compared with a DNA sequence database to obtain the identity of the organisms.

Abstract: The quantitative evaluation of biomarker-probe activity is disclosed. In certain embodiments, the biomarker-probe activity may be quantified and analyzed using biodistributions generated using a model. In some embodiments, such biodistributions may be used to generate simulated images from which quantitative thresholds may be derived. In some embodiments, the quantitative thresholds may be used to analyze the biodistributions.

Abstract: A method and system for optimizing post prandial blood glucose excursions for persons with diabetes via computation of time-varying optimal insulin profiles are disclosed. The method builds upon a mathematical model based on the physiologic description of the human glucoregulatory system. Model parameter values are specific for each patient and meal type, and are determined from measured data by minimizing differences between both measurements and model predictions, and which are used to provide the optimal insulin profiles that are useful to diabetics in managing their chronic disease.

Abstract: Systems and methods for modeling a compound formulation are provided.

Abstract: Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Genetic material from the target individual is acquired, amplified and the genetic data is measured using known methods. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment of the invention, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents.

Abstract: A mass spectrometer and a method of spectrometry are disclosed wherein liquid chromatography mass spectral data are probabilistically clustered on the basis of mass to charge ratio and retention time.

Abstract: A system and method for performing similarity searching is disclosed. This includes a programmable logic device configured to include a pipeline that comprises a matching stage, the matching stage being configured to receive a data stream comprising a plurality of possible matches between a plurality of data strings and a plurality of substrings of a query string. The pipeline may further include an ungapped extension prefilter stage located downstream from the matching stage, the prefilter stage being configured to shift through pattern matches between the data strings and the plurality of substrings of a query string and provide a score so that only pattern matches that exceed a user defined score will pass downstream from the prefilter stage. The matching stage may include at least one Bloom filter.

Abstract: A computer-implemented method and system of modeling physical properties of biodiesel feedstock are presented. The invention method and system include (i) estimating values of a physical property of constituent fatty acid fragments of a mono-, di-, or triglyceride, and (ii) computing a value of the physical property of the mono-, di-, or triglyceride by expressing the value of the physical property of the mono-, di-, or triglyceride as a sum of the estimated values of the physical property of constituent fatty acid fragments thereof. The method and system further include repeating steps (i) and (ii) for different mono-, di-, and/or triglycerides, resulting in a plurality of computed values of the physical property of different mono-, di-, and triglycerides. The determined value of the subject physical property enables blending of the biodiesel feedstock in production of biodiesel.

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: The computational drug discovery method disclosed herein permits a user to specify a three dimensional representation of a molecular fragment derived from a query molecule involved in a drug interaction that then serves as a template to which fragments derived from molecules in database libraries may be aligned. The likely activity of the substitution of the fragment from the database library for the fragment from the query molecule may then be predicted by appropriate shape characterization and CoMFA analysis. The spatial three dimensional representation of the query fragment may be developed from binding data, crystallographic data, modeling data, or any other biophysical or biochemical technique.

Abstract: System for recommending an optimal treatment protocol for a specific individual are disclosed. The systems comprise generally a system model, a plurality of treatment protocols, a system model modifier, wherein said system model is modified by the system model modifier based on parameters specific to the individual; and a selector to select an optimal treatment protocol from said plurality of treatment protocols based on the modified system model. Systems embodying the above techniques but for a general patient are also disclosed. Systems for a general patient and an individual for various specific diseases are disclosed. Methods and computer program products embodying the above techniques are also disclosed.

Abstract: The present disclosure relates generally to a structure-modeling approach to identify therapeutic and diagnostic targets on proteins. Means are provided to generate agents which bind and optionally antagonize a particular domain within a protein referred to as a Cleaved_Adhesin Family Domain. In an embodiment, the disclosure is directed to the control of Porphyromonas gingivalis infection or infection by related microorganisms by targeting selected domains on protease-like molecules having a hemagglutinin region. In another embodiment, the present invention enables the modulation or detection of a protein having a Cleaved_Adhesin domain homologous to those in the protease-like molecules.

Abstract: A computer method of characterizing chemical composition of crude oil and crude oil blends, includes determining respective segment type and segment number range of selected classes of hydrocarbon constituent molecules based on physical and chemical property data on each class of hydrocarbon constituent molecules and on crude oil physical and chemical property data. The method determines relative ratio of each class of hydrocarbon constituent molecules that forms a chemical composition representative of the subject crude oil, and therefrom characterizes chemical composition of the subject crude oil. The method/system displays to an end-user, the characterized chemical composition of the subject crude oil. Based on the identified distribution functions and the relative ratio of each class of hydrocarbon constituent molecules, the method estimates chemical composition of the crude oil. Estimates of physical and chemical properties of the crude oil are then based on the estimated chemical composition.

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

Abstract: In one embodiment, a method of modeling interactions with keratinous tissue may comprise the steps of providing a nonwoven mimic and performing an act on the mimic as may be performed on keratinous tissue. The nonwoven mimic has a surface energy representative of keratinous tissue. In another embodiment, a method of modeling interactions with keratinous tissue may comprise the steps of: providing a mimic comprising from about 60% or greater rayon, from about 40% or less polyester, and a surface energy representative of keratinous tissue; and performing an act on the mimic as may be performed on keratinous tissue. The mimic is preferably a nonwoven mimic.

Abstract: The present disclosure concerns methods and compositions relating to mixed-library parallel gene trait mapping. In particular embodiments, the methods concern quantitative microarray hybridization techniques for genome-wide identification of trait conferring genes. In other embodiments, the compositions concern genetic elements that confer or are associated with a trait. In an exemplary embodiment, the trait is enhanced growth rate. In another exemplary embodiment, genetic elements that confer enhanced bacterial growth rate comprise part or all of the sequences of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4 or SEQ ID NO:5. In other embodiments, the genetic elements that confer enhanced bacterial growth rate correspond to the YliF, adrA, yeaP, yddV or ydeH genes of E. coli.

Abstract: Methods and devices to generate a tool for testing, simulating and/or modifying a closed loop control algorithm are provided. Embodiments include receiving glucose data for a predetermined time period, determining a variation in the glucose level based on the received glucose data, filtering a received glucose data based on the determined variation, substituting a negative change in the glucose data value with a predetermined value to generate a sequence of modified glucose values, and integrating the sequence of modified glucose values to determine an uncontrolled blood glucose excursion condition.

Abstract: A system for optimizing a patient's insulin dosage regimen over time, comprising at least a first memory for storing data inputs corresponding at least to one or more components in a patient's present insulin dosage regimen, and data inputs corresponding at least to the patient's blood-glucose-level measurements determined at a plurality of times, and a processor operatively connected to the at least first memory. The processor is programmed at least to determine from the data inputs corresponding to the patient's blood-glucose-level measurements determined at a plurality of times whether and by how much to vary at least one of the one or more components in the patient's present insulin dosage regimen in order to maintain the patient's future blood-glucose-level measurements within a predefined range.

Abstract: A method and a system for searching for a global minimum are provided. First, a subclass of a plurality of space points in a multidimensional space is clustered into a plurality of clusters through a clustering algorithm, wherein each of the space points is corresponding to an error value in an evaluation function. Then, ellipsoids for enclosing the clusters in the multidimensional space are respectively calculated. Next, a designated space corresponding to each of the ellipsoids is respectively inputted into a recursive search algorithm to search for a local minimum among the error values corresponding to the space points within each designated space. Finally, the local minimums of all the clusters are compared to obtain the space point corresponding to the minimum local minimum.

Abstract: The present invention provides a method and model for monitoring the pretreatment process of a low-k block layer. The method comprises measuring film parameters of the film formed on the silicon substrate after applying the pretreatment process for different time periods; creating a statistical process control curve according to the film parameters; setting a SPC control limit; determining the pretreatment process normal when the data point of measurement in the SPC curve is within the control limit while determining the pretreatment process abnormal when the data point of measurement in the SPC curve exceeds the control limit. According to the present invention, the failure of the pretreatment process can be prevented to improve the product reliability and stability.

Abstract: A method and system is disclosed that enables a less error-prone and preferably automatic assignment of pre-prandial and post-prandial blood glucose values associated with a meal to improve determining the difference between pre-prandial and post-prandial blood glucose measurements as follows. Blood glucose measurements are read and provided with a relative or absolute time mark and labeled as pre-prandial and reading out post-prandial blood glucose measurements provided with a relative or absolute time mark from the memory of a blood glucose measuring instrument. The chronological sequence of the blood glucose measurements labeled as pre-prandial are determined. The post-prandial blood glucose measurements that correspond to each of the pre-prandial blood glucose measurements are determined by applying a time selection criterion. The difference between corresponding pre-prandial and post-prandial blood glucose measurements is determined.

Abstract: The present invention provides methods and computer programs for detecting variations in measurements of a biological variable, e.g., variations in cell viability, under different conditions, e.g., with or without treatment of a drug, under the treatments of different drugs, or under different environmental conditions. The methods and programs of the invention determine a metric of difference between measurements under different condition, and make use of predetermined errors of the measurements, e.g., errors determined from an error model, to estimate the errors in the metric of difference. Such an approach provides a more accurate estimate of the errors of measurements, which, in turn, provides a more accurate estimate of the error of the difference metric.

Abstract: As an elegant solution for minimizing false positives returned by a sensor tuned to an analyte molecule, filters constructed of carbon nanotubes are positioned relative to the sensor to limit the sensor to being exposed to molecules within a defined range of sizes, with too-big molecules being excluded from reaching the sensor by one filter, and too-small molecules being pumped out through another, finer filter before the sensor is operated.

Abstract: A system, apparatus, and method are disclosed wherein a reveal request is initiated through a result reveal station by a person (user) who has previously made some purchase or donation and has been assigned one or more sweepstakes entries in an assignment order from a set of available sweepstakes entries for a sweepstakes game. This reveal request represents a request to reveal one or more of the results associated with the corresponding sweepstakes entries that have been assigned to the user. The reveal station employs a game presentation including various graphics and audio effects to show sweepstakes results in an entertaining fashion. In response to the reveal request, or perhaps even prior to the reveal request, one or more sweepstakes entries are selected to be revealed for the reveal request. The sweepstakes entries are selected in an order different from the order in which the sweepstakes entries were assigned to the user.

Abstract: The invention relates to ecological environment monitoring based on native animals functional state control. The method includes exposure a test animal to IR radiation using an optical radiation source and a transmitting optical fiber; receiving the reflected IR radiation using a receiving optical fiber; converting the reflected IR radiation to an electrical signal; determining a sample of values of the signal periods and the sample dispersion; and forming a danger signal when the threshold value exceeds the sample dispersion. The system contains a cardiac activity sensor which includes a transmitting and receiving optical fibers, an optical radiation source and optical radiation receiver; an amplifier, an analog-to-digital converter and a computer. The output end of transmitting fiber and the input end of receiving fiber have the same direction and are positioned at a distance R satisfying the inequality (?d2P)0.07?2.2(1/(?d2P))0.02?R?(?d2P)0.07+2.2(1/(?d2P))0.02.

Abstract: Methods for processing hyphenated chromatographic data to delineate components of a sample are disclosed. According to one aspect, the method includes obtaining hyphenated chromatographic data points for a sample, each data point comprising at least three dimensions, one of the dimensions being a continuous dimension, and subjecting at least a portion of the data points to an algorithm that organizes the data points into discrete clusters according to the data points' continuous dimension values by starting at either a smallest or largest value and delineating at a largest gap between adjacent values within a predetermined resolution window, wherein the resulting clusters are of varying width of less than or equal to the width of the resolution window and wherein at least some of the clusters are indicative of components of the sample.

Abstract: A method, information processing system, and computer readable medium, are provided for analyzing a protein folding process. The method includes conducting an incremental pattern discovery process. The incremental pattern discovery process includes judging multidimensional data from a simulation of a protein folding process. The incremental pattern discovery process captures at least one intermediate data point in at least one pattern associated with the protein folding process.

Abstract: The present invention relates to a method of detecting coliform bacteria in water from reflected light and a method of detecting Eschericha Coli bacteria in water from reflected light, and also includes devices for the measurement, calculation and transmission of data relating to that method.

Abstract: Method of product evaluation comprising the steps of applying at least one substance to a surface of an artificial substrate to form a substance-coated surface, wherein the substrate surface demonstrates at least one physical property selected from the group consisting of a total surface energy of from about 15 mJ/m2 to about 50 mJ/m2, a polar component of the total surface energy of from about 0 mJ/m2 to about 15 mJ/m2, a zeta-potential at a pH of about 5.0 of from about ?30 mV to about 30 mV, and combinations thereof, and performing at least one analysis of the substance-coated surface.

Abstract: The present invention is related to a method for determining the sensitizing potential of a chemical (test) compound, comprising the steps of: (a) Providing a suitable cell culture of a specific cell type and providing a test sample and a control sample thereof, said test sample and said control sample being identical, (b) Exposing said test sample to a chemical compound in a solvent and exposing said control sample to said solvent for a predetermined period of time, (c) Determining for the test sample and the control sample gene expressions xi for a subset of i=1 to n genes selected from the group of genes corresponding to SEQ ID NOs 1 to 153, (d) For this subset of n genes looking up in a database the gene expressions xi for a set of control and test samples, the test samples being exposed for said predetermined period of time to a set of chemical sensitizing model compounds comprising both sensitizers and non-sensitizers, (e) Using the gene expressions of the said test sample and the said control sample

Abstract: Provided herein are methods and compositions for efficient accumulation of structural information (e.g., three dimensional structural information) for amino acid sequences.

Abstract: The present invention provides methods for rapid forensic analysis of mitochondrial DNA by amplification of a segment of mitochondrial DNA containing restriction sites, digesting the mitochondrial DNA segments with restriction enzymes, determining the molecular masses of the restriction fragments and comparing the molecular masses with the molecular masses of theoretical restriction digests of known mitochondrial DNA sequences stored in a database.

Abstract: In a method of synthesizing components to design a system meeting an exergy loss target value, one or more candidate sets of components are synthesized and an exergy loss value for each of the one or more candidate sets of components are calculated. A determination as to whether at least one of the candidate set of components meets the exergy loss target value is made and at least one candidate set of components determined to meet the exergy loss target value is identified as the set of components for use in the design of the system.

Abstract: A particle behavior analysis system includes a calculation section that, regarding a decomposition portion decomposed in accordance with a decomposition method in a range to be analyzed, considers interaction force with another substance that acts on a particle and calculates behavior of the particle, while performing information communication with other devices; and an output processing section that switches output advisability of an analysis result obtained by the calculation section based on priority of the decomposition portion corresponding to the advisability of output processing of the analysis result.

Abstract: Members of the Amyloid Precursor Protein family (APP molecules) and their neurotoxic cleavage product A? are key players in the development of Alzheimer's disease (AD). Proteolytic processing of APP molecules is influenced by metal ions, protein ligands and its oligomerization state. X-ray structures of the metal bound molecule at 2.6-2.0 ? resolution are presented, providing structural and functional bases for the regulation of APP molecules using conformational information. A metal-dependent molecular switch located within the E2 domain of APP coinciding with a high affinity copper and zinc binding site within the monomeric E2 domain was evaluated. The metal specific coordination spheres of this E2 domain comprise four evolutionary conserved histidine residues. Metal binding induces large conformational changes relative to the metal free protein. This conformational change provides a basis for influencing APP molecule processing and thus trafficking and the production of A?.

Abstract: Systems and methods for generating transfer functions associated with calculating local stresses on pipe elements by post processing forces and moments of a pipe model representing the piping system. The transfer functions are reusable and allow recalculation with different sets of user data without requiring regeneration of the transfer functions.

Abstract: A molecular orbital computing device, method, program, and a recording medium recorded with the program, capable of computing electronic states at a high speed by an elongation method, are provided.

Abstract: The present invention relates to a system and a method for constructing and associating a moduli space to a molecule or a model of a molecule. This mathematical representation of molecular structures enables the prediction of actual physical molecular structures. Molecular structures can be structures of macromolecules such as protein molecules and protein globules.

Abstract: The overall material constant of a composite material is computed where the composite material includes multiple kinds of material components in a matrix phase, each of the material constants of the material components and the matrix phase being known. First, for the composite material, an equation, having the material constant of a virtual composite material as an unknown, is prepared by defining the virtual composite material in which each of the material components is dispersed in a form of spherical particles in the matrix phase at a known volume fractions. Next, the overall material constant of the virtual composite material is found as the overall material constant of the composite material by solving the equation. In this case, the equation is a recursive equation which is obtained using the self-consistent method. The volume fraction of a material component in the composite material is computed using the equation.

Abstract: A method for differentiating complex mixtures each having one or more chemical species is provided. The method comprises producing a sample NMR spectrum by subjecting a mixture to a selective spectroscopy process, wherein the NMR spectrum has individual spectral peaks representative of the one or more chemical species within the mixture. The one or more chemical species within the mixture are identified by analyzing the individual spectral peaks, and the individual spectral peaks are then subjected to a multivariate statistical analysis.

Abstract: Included are methods for modeling at least one physical property of a mixture of at least two chemical species. One or more chemical species of the mixture are approximated or represented by at least one conceptual segment. The conceptual segments are then used to compute at least one physical property of the mixture. An analysis of the computed physical properties forms a model of at least one physical property of the mixture. Also included are computer program products and computer systems for implementing the modeling methods.

Abstract: In the present invention the NonRandom Two-Liquid segment activity coefficient model system of the parent application is extended for computation of ionic activity coefficients and solubilities of electrolytes, organic and inorganic, in common solvents and solvent mixtures. The invention method and system may be applied to the chemical and/or pharmaceutical design process. In addition to the three types of molecular parameters defined for organic nonelectrolytes, i.e., hydrophobicity X, polarity Y, and hydrophilicity Z, an electrolyte parameter, E, is introduced to characterize both local and long-range ion-ion and ion-molecule interactions attributed to ionized segments of electrolytes. Successful representations of mean ionic activity coefficients and solubilities of electrolytes, inorganic and organic, in aqueous and nonaqueous solvents are presented.

Abstract: A system for optimizing a patient's insulin dosage regimen over time, comprising at least a first memory for storing data inputs corresponding at least to one or more components in a patient's present insulin dosage regimen, and data inputs corresponding at least to the patient's blood-glucose-level measurements determined at a plurality of times, and a processor operatively connected to the at least first memory. The processor is programmed at least to determine from the data inputs corresponding to the patient's blood-glucose-level measurements determined at a plurality of times whether and by how much to vary at least one of the one or more components in the patient's present insulin dosage regimen in order to maintain the patient's future blood-glucose-level measurements within a predefined range.

Abstract: A method, program and computer system for changing scale of reservoir model permeabilities (for example a hydrocarbon reservoir) are provided. Mini-models of reservoirs are defined (S100) with a number of meshes and cells in these meshes. For each model mesh, a scaling of the permeability values KH of the meshes is carried out (S400-800) via a mean power formula KH?H??kHi?H relating the mesh permeability KH to the local permeabilities kH,i of the cells. According to the invention, the power coefficient ?H appearing therein is analytically modified, relatively to its expression given by the Noetinger-Haas relationship, in order to correct a non-ergodicity bias.

Abstract: A method for predicting petroleum production is provided. An exemplary embodiment of The computer-implemented comprises computing a first approximation of an amount of generated petroleum that is retained with a complex organic product using a Threshold and a Maximum Retention value. The exemplary method also comprises revising the first approximation by approximating a process of chemical fractionation using at least one partition factor to create a revised approximation and predicting petroleum production based on the revised approximation.

Abstract: Included are methods for modeling at least one physical property of a mixture of at least two chemical species. One or more chemical species of the mixture are approximated or represented by at least one conceptual segment. The conceptual segments are then used to compute at least one physical property of the mixture. An analysis of the computed physical properties forms a model of at least one physical property of the mixture. Also included are computer program products and computer systems for implementing the modeling methods.