Biological Or Biochemical

Biological Or Biochemical patent applications listed are from June 2005 to current and include Date, Patent Application Number, Patent Title, Patent Abstract summary and are linked to the corresponding patent application page.

12/07/06 - 20060276974 - System for remote viewing and display of a slide
A method for creating a virtual slide is provided. A virtual slide is a digital representation of an area of interest of a microscope slide. One method is to use a motorized microscope that can move a specimen with respect to a microscope objective. With such a system, one can ...

12/07/06 - 20060276973 - Predicting animal performance
The invention provides for methods of characterizing animal performance based on the microbial profile of an animal. The invention also provides for methods of monitoring the effect of a feed or feed additive regimen on the microbial profile of one or more animals. The invention further provides for method of ...

12/07/06 - 20060276972 - Method for determining the amount of an analyte in a sample
An automated analyzer for performing multiple diagnostic assays simultaneously includes multiple stations in which discrete aspects of the assay are performed on fluid samples contained in sample vessels. The analyzer includes stations for automatically preparing a sample, incubating the sample, preforming an analyte isolation procedure, ascertaining the presence of a ...

12/07/06 - 20060276971 - Method and device for comparative display of biological data
Embodiments of computer systems for visualizing information and data from samples, such as nucleic acids, proteins, or other bio-polymers, are disclosed. One embodiment of a method comprises displaying first and second display areas on a display, displaying an axis dividing the first display area into first and second sub-areas, and ...

12/07/06 - 20060276970 - Apparatus and method for the ozone preservation of crops
A method for substantially reducing the development of fungal spoilers of perishable produce such as fruit, salads and vegetables comprising the steps of arranging the products in a matrix in a substantially closed environment and introducing to the environment a gaseous mixture containing a prescribed concentration of ozone. ...

11/30/06 - 20060271308 - Identifying statistically linear data
Methods, apparatus, and systems are provided for processing a data set having noise to determine whether the data set exhibits statistically linear behavior. A true data signal is calculated based on local properties of the data, and an estimate of the noise in the data is calculated from the true ...

11/30/06 - 20060271307 - Coding module, a bio sensing meter and a system for operating a bio sensing meter
This invention relates to bio sensing meters for determining the presence of an analyte in a biological sample, and, more particularly, to a bio sensing meter whose operation is controlled by a code provided by a removably pluggable coding module. The invention further relates to a coding module pluggable into ...

11/30/06 - 20060271306 - Method and apparatus for assessing polypeptide aggregation
A method of determining aggregation rate data predicting an aggregation rate of a polypeptide defined by an amino acid sequence, the method comprising determining a hydrophobicity value, a charge value, and at least one shape propensity value for said sequence; identifying one or more aggregation-influencing patterns within said sequence; determining ...

11/30/06 - 20060271305 - Optimal dynamic discrimination of similar molecular scale systems using functional data
Techniques for molecular scale discrimination using functional data are provided. A method for molecular scale discrimination using functional data can include, for example, (a) applying a control pulse to excite one or more molecular species in a molecular scale system, (b) collecting functional data for an observable variable from the ...

11/30/06 - 20060271304 - Systems and methods for fast reachability queries in large graphs
A method which identifies different types of substructures within a graph and encodes them using techniques suitable to the characteristics of each of them. The method is embodied by an efficient two-phase algorithm, where the first phase identifies and encodes strongly connected components as well as tree substructures, and the ...

11/30/06 - 20060271303 - Methods and systems for transferring data
Methods and systems for transferring data, e.g., analytical device consumable data, from a source location to a target location are provided. Also provided are computer program products for executing the subject methods. ...

11/30/06 - 20060271302 - Method of assessing productivity of lactating animals using fitted parameters to a mechanistic lactation model
An analytic method to evaluate performance of lactating animals by use of a parameterized algebraic model based on hypotheses about the physiology of lactation. Observed production data are fitted to the model to generate a set of parameter values which optimize compliance between model and data. Fitted parameter values summarize ...

11/30/06 - 20060271301 - Parallel calculation method and device
A method for executing calculation of the Hartree-Fock method in a molecular orbital method by a distributed memory parallel computing system includes the steps of: using a computer cluster made up of a plurality of computers; dividing a density matrix into multiple density submatrixes and distributing them to the individual ...

11/30/06 - 20060271300 - Systems and methods for microarray data analysis
Clustering is routinely applied in the exploratory analysis of microarray data. Missing entries arise from blemishes on the microarrays. The present invention provides a new method, and computer program and/or computer product thereof to impute missing values. The method involves the steps of clustering microarray data by partitioning the data ...

11/23/06 - 20060265137 - Methods to increase the capacity of high content cell-based screening assays
The present invention involves the pooling of multiple high content cell-based screening assays, and carrying out a primary screen in a one or more channels of a fluorescence detection device, which drastically increases the number of simultaneous high content cell-based screening events that can be carried out. Subsequent deconvolution of ...

11/23/06 - 20060265136 - Treatment effect prediction system, a treatment effect prediction method, and a computer program product thereof
A treatment effect prediction system, comprising: a processor; and a memory, under control of the processor, including instructions enabling the processor to carry out operations comprising: determining a patient pathological condition information, which represents a feature of pathological condition of a patient, based on diagnostic data of the patient; accessing ...

11/23/06 - 20060265135 - Bio-information analyzer, bio-information analysis method and bio-information analysis program
With the use of a bio-information analyzer, a total contribution showing a relationship between a gene expression regulatory sequence and a biological phenomenon is calculated. This total contribution is calculated based on contributions of a gene expression regulatory sequence to a plurality of gene candidates and contributions of the plurality ...

11/23/06 - 20060265134 - Medicine management methods and apparatus
Methods and apparatus are shown for providing information on a pill. A patient specific delivery apparatus for medicine using information on a pill or pills is shown as well, and a database with patient specific information may be provided, resulting in an individualized pharmacopoeia for a patient. ...

11/23/06 - 20060265133 - Analysis system and procedures
A system and apparatus for automation of microscope slide sample staining is disclosed. The slides are labelled with a unique identification, preferably a machine readable code printed onto a label, where the label is affixed to the slide. The label is a pointer to information in a database containing patient ...

11/16/06 - 20060259247 - Apparatus and method for automated protein design
The present invention relates to apparatus and methods for quantitative protein design and optimization. ...

11/16/06 - 20060259246 - Methods for efficiently mining broad data sets for biological markers
A biological marker identification method identifies biological markers within broad sets of biological data containing many more measurements than observations. For example, the data can contain thousands of measurements on each blood sample obtained from fewer than 100 subjects, each of which falls into one of a set of clinical ...

11/16/06 - 20060259245 - Digital x-ray camera for quality evaluation three-dimensional topographic reconstruction of single crystals of biological macromolecules
The present invention provides a digital topography imaging system for determining the crystalline structure of a biological macromolecule, wherein the system employs a charge coupled device (CCD) camera with antiblooming circuitry to directly convert x-ray signals to electrical signals without the use of phosphor and measures reflection profiles from the ...

11/16/06 - 20060259244 - Level 3 fusion engine for detection and tracking of chemical biological, nuclear and radiological hazards
A chemical, biological, radiological and nuclear (CBRN) hazard detecting system. In one embodiment, the CBRN hazard detecting system includes a plurality of sensors, a plurality of acoustic sensors, one or more weather sensors and a level 3 fusion engine. The level 3 fusion engine is in communication with the plurality ...

11/16/06 - 20060259243 - Provision of diagnosis information
The invention relates to a method for generating a system for providing diagnosis information, and to a corresponding system. The aim of the invention is to simplify the provision of information for diagnosing technical installations or technical processes. To this end, components pertaining to an automation system and having diagnosis ...

11/09/06 - 20060253261 - Digitizing biology
A method and apparatus for determining the progress of a disease. A pre-determined vector space is determined where the vector space mathematically describes a reference set of wavelength resolved data at a plurality of time intervals. A sample containing at least one cell is irradiated with light. Target data is ...

11/09/06 - 20060253260 - Methods for establishing and analyzing the conformation of amino acid sequences
The present invention relates to methods for establishing and analyzing the conformation of amino acid sequences. In particular, the invention relates to methods for the validation of the conformation of given amino acid-based molecules, methods for conformation determination starting from a linear amino acid sequence as well as methods for ...

11/09/06 - 20060253259 - Integrated biosensor and simulation system for diagnosis and therapy
BioMEMS/NEMS appliance biologically monitors an individual, using biosensors to detect cellular components. Data is simulated or analyzed using systems-biology software, which provides diagnostic or therapeutic guidance. ...

11/09/06 - 20060253258 - Digital cell
It is intended to provide a method and system for carrying out data production with respect to the actual status of cells as a profile. It is also intended to provide a system and method for presenting time-lapse and/or real-time information of cell interior directly, or as it is, from ...

11/02/06 - 20060247867 - Customized and dynamic association of probe type with feature extraction algorithms
Systems, methods and computer readable media for extracting data from features on a chemical array, using a feature extraction module including feature extraction algorithms configured to calculate characteristics of array features. A reference table is provided that associates probe names of probes contained on the array with at least one ...

11/02/06 - 20060247866 - Setting method of measuring apparatus, analyzing system, data processing apparatus, and storage medium
A setting method relating to measurement of measuring apparatus that minimizes the modification locations in an application program when the setting functions are modified, analyzing system, data processing apparatus, and storage medium are provided. When an application program is executed, setting data are processed to setting item data, setting parameter ...

11/02/06 - 20060247865 - Apparatus for identifying peptides and proteins by mass spectrometry
A method of identifying a protein, polypeptide or peptide by means of mass spectrometry and especially by tandem mass spectrometry is disclosed. The method preferably models the fragmentation of a peptide or protein in a tandem mass spectrometer to facilitate comparison with an experimentally determined spectrum. A fragmentation model is ...

11/02/06 - 20060247864 - Method and system for assessment of biomarkers by measurement of response to surgical implant
In a human or animal organ or other region of interest, specific objects, such as liver metastases and brain lesions, serve as indicators, or biomarkers, of disease. In a three-dimensional image of the organ, the biomarkers are identified and quantified both before and after a surgical implant is implanted, and ...

11/02/06 - 20060247863 - Optimizing maldi mass spectrometer operation by sample plate image analysis
A method and apparatus are described for performing image analysis of a sample target area on a MALDI sample plate to select laser impingement locations for optimal mass spectra acquisition. The target area image is captured and analyzed to determine the incidence distribution of picture element values (representative of luminance ...

11/02/06 - 20060247862 - Determining cell cycle phase data
A method of determining cell cycle phase data for cells comprising at least one luminescent reporter capable of emitting radiation, the at least one luminescent reporter comprising a first luminescent reporter which is capable of being indicative of at least one cell cycle phase, said method comprising: storing classification information ...

10/26/06 - 20060241869 - Computer systems and methods for inferring causality from cellullar constituent abundance data
Methods for determining whether a molecule affects a disorder are provided. A cell from an organism is contacted with the molecule, or the molecule is expressed within the cell. A determination is made as to whether the RNA or protein expression in the cell of at least one open reading ...

10/26/06 - 20060241868 - System, method, and computer product for simplified instrument control and file management
An embodiment of a system for managing files generated from biological probe arrays is described that comprises a first generator that produces a first data file comprising a plurality of raw intensity values, and metadata comprising a first identifier that uniquely identifies the first data file; a second generator that ...

10/19/06 - 20060235623 - Method of processing biological analysis data and expert system of biological analysis applying this method
Expert system of biological analysis includes comprising: a collecting engine to collect and represent data resulting from biological measurements carried out on a human or animal subject and defining a biological profile, and personal data relating to the human or animal subject. ...

10/19/06 - 20060235622 - Statistical methods for analyzing biological sequences
Statistical algorithms that are useful to aid in the identification of evolutionarily conserved amino acid positions within a family of proteins, and in the identification of interacting amino acid positions within a protein sequence are disclosed. The algorithms may also be useful in the analysis of other polymer sequences such ...

10/19/06 - 20060235621 - Imaging techniques and associated apparatus
Imaging techniques of pharmaceutical preparations such as tablets are disclosed. The techniques combine the measurement of reflected/transmitted terahertz radiation originating from within the tablet and data analysis localised in frequency and time in order to enable a three dimensional image indicating composition to be obtained. ...

10/12/06 - 20060229826 - Quantitative structure - activity relationships (qsar)
A method for estimation of the distance from a domain by means of a fragment-based model, the method comprising the steps of identifying the fragments [r1 to rn] in a structure, comparing the or each fragment with one or more fragments in the model, if the or each fragment substantially ...

10/12/06 - 20060229825 - Database system including computer code for predictive cellular bioinformatics
According to the present invention, computer based techniques for using information technology in therapeutics or drug discovery. In an exemplary embodiment, computer based techniques for determining information about the properties of substances based upon information about structure of living or non-living cells exposed to substances are provided. Computer software according ...

10/12/06 - 20060229824 - Arrays of nucleic acid probes for analyzing biotransformation genes
The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three ...

10/12/06 - 20060229823 - Methods and computer software products for analyzing genotyping data
In one aspect of the invention, methods, systems and computer software products are provided for analyzing genotyping data. In exemplary embodiment, genotype data are analyzed using a model based classification method. ...

10/12/06 - 20060229822 - System, method, and software for automated detection of predictive events
A system for the automatic detection and communication of detection of nosocomial infection and/or antimicrobial resistance events in a health care environment includes an input unit that receives nosocomial infection and/or antimicrobial resistance related data, an an event detection machine, and a knowledge discovery unit. The event detection machine sorts ...

10/12/06 - 20060229821 - Method for measuring the incidence of hospital acquired infections
Disclosed is a method and system for analyzing patient hospitalization data to determine a Nosocomial Infection Marker (NIM), the method comprising receiving from a database hospitalization data associated with at least one patient, calculating from the hospitalization data the number of specimens with non-duplicate hospital isolates (SNDHI) markers, calculating from ...

10/12/06 - 20060229820 - Chemical sensor array evaluation method
A method is proposed for identifying a chemical substance from a set of output states provided by a chemical sensor array being exposed to the chemical substance. The method comprises steps for selecting from a set of class descriptions for different chemical substances a first class description and one or ...

10/12/06 - 20060229819 - Method for imaging an array of microspheres
A method for imaging an array of microspheres. The method employs a wavelength tunable light source and camera for detecting and quantifying the presence of biological probes that indicate the presence of specific chemical moieties within a biological system. ...

10/12/06 - 20060229818 - Method for eliminating crosstalk between waveguide grating-based biosensors located in a microplate and the resulting microplate
The present invention includes several methods for modifying the current processes of manufacturing optical sensing microplates that use continuous waveguide films to reduce/eliminate crosstalk between the biosensors that are incorporated within wells. The methods include (1) physically deteriorating/removing the waveguide film between individual biosensors; (2) chemically depositing highly absorbing materials ...

10/12/06 - 20060229817 - Concurrent two-phase completion genetic algorithm system and methods
A genetic algorithm architecture implements a two-stage completion genetic algorithm with respect to an evolving current population data set. The two-stage completion genetic algorithm that includes genotype and phenotype completion loops. The genotype completion loop operates to compete the current population data set based on genotype field fitness scores. The ...

10/05/06 - 20060224327 - System and method for plant selection
Processes, systems and databases are provided for plant selection. The processes may include providing a database of plant species and eliminating a portion of the plant species based on at least two search criteria including a user's desired climate zone or location plant cultivation, plant size, plant type, plant leaf ...

10/05/06 - 20060224326 - Integrated data collection and analysis for clinical study
A data collection system includes remote, implantable sensors for monitoring one or more patient parameters, collecting and processing data from those sensors and utilizing that data in the performance of a clinical study of a drug or other pharmacological agent. The system assists with preparation of a protocol for a ...

10/05/06 - 20060224325 - Predictive indicator model
A predictive indicator tool for predicting the risk of a manufacturing process producing products having defects. Manufacturing sub-processes are identified for the process and s a series of 12 questions is applied to each sub-process. The questions are generated using Six Sigma statistical techniques. The questions are scored and an ...

09/28/06 - 20060217893 - Method for detecting an unknown contaminant concentration in a substance
A method for detecting contaminants in a solution by determining a change in resonant frequency (ΔF) and motional resistance (ΔR) of a crystal microbalance (CM) immunosensor is presented. The method includes measuring ΔF and determining ΔR of a CM immunosenor exposed to various samples including known concentrations and a sample ...

09/28/06 - 20060217892 - Vectorization of dynamic-time-warping computation using data reshaping
A method for comparing data sequences includes accepting first and second data sequences of data elements. A distance matrix is computed. The matrix includes rows and columns of matrix elements, describing distances between the data elements of the first sequence and the data elements of the second data sequence. The ...

09/28/06 - 20060217891 - Method of designing physiologically active peptide and use thereof
The present invention provides a means of economically, quickly and efficiently designing a physiologically active peptide to a target protein. Specifically, the present invention provides a method of designing a physiologically active peptide characterized in that, to design a physiologically active peptide capable of binding to a target site comprising ...

09/21/06 - 20060212229 - Method and system for providing a probe array chip design database
Systems and method for organizing information relating to the design of polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model ...

09/21/06 - 20060212228 - Identification-data setting device, identification-data setting method, and computer product
A device for setting identification information for identifying an intermediary device mounted on a substrate, the device includes an information acquiring unit that acquires position information indicating a position at which the intermediary device is mounted; and an information setting unit that sets the identification information based on the position ...

09/21/06 - 20060212227 - An analysis platform for annotating comprehensive functions of genes on high throughput and integrated bioarray system
This invention presents the analysis platform for annotating comprehensive functions of genes on high throughput and integrated bioarray system. High throughput and Integrated bioarray system produces the integrated information or data as functional patterns of DNA, RNA, protein, cDNA, tissue, and etc. from the same piece of biomaterials in a ...

09/14/06 - 20060206271 - Body composition measuring apparatus
There are provided a hold portion that can be held in a hand of a subject, a cable having one end connected to the hold portion, and a rest portion on which a foot of the subject can be rested. The rest portion includes a reel portion connected to the ...

09/14/06 - 20060206270 - Isomarker system for component analysis of mixtures
A system couples isotope markers to molecules in mixtures to identify and quantitate the molecular components in the mixtures and detects them using nuclear magnetic resonance (NMR) spectroscopy. ...

09/14/06 - 20060206269 - One-dimensional qsar models
A set of molecules, the members of which have the same type of biological activity, are represented as one-dimensional strings of atoms. The one-dimensional strings of all members of the set are aligned, in order to obtain a multiple alignment profile of a consensus active compound. The one-dimensional multiple alignment ...

09/07/06 - 20060200316 - Data correction, normalization and validation for quantitative high-throughput metabolomic profiling
Metabolomic profiling of a biological sample using a separation-molecular ID process, such as gas chromatography-mass spectrometry (“GC-MS”), requires the derivatization of the original sample. Quantitative GC-MS metabolomics is possible if the derivative is in one-to-one proportional relationship with the original concentration profile, wherein the proportionality remaining constant among samples. Two ...

09/07/06 - 20060200315 - High-throughput screening hit selection system and method
A high-throughput screening system and method employing compound relationship characteristics for facilitating hit selection may significantly improve hit confirmation rate and allow direct identification of active compound families exhibiting a certain level of SAR or other relationship characteristic. Valuable family and SAR information obtained at an early stage of the ...

08/31/06 - 20060195268 - Method for determining the titer of biological agents in living target cells
Method for determining the titer (concentration) of biological agents, such as viral vectors for gene transfer, in real time, in living target cells and uses thereof in the field of gene therapy and diagnosis. ...

08/31/06 - 20060195267 - Ellipsoidal gaussian representations of molecules and molecular fields
I describe several techniques for characterizing molecules based on the shapes of their fields. In particular, I describe a way to automatically break molecules into a series of fragments by using an ellipsoidal Gaussian decomposition. These fragments can then be analyzed by a shape metric technique, and the parameters of ...

08/31/06 - 20060195266 - Methods for predicting cancer outcome and gene signatures for use therein
The present invention pertains to specific gene signatures for cancer that are used to predict survival and novel processes for identifying such gene signatures. In one embodiment, gene signatures for human colorectal cancer are identified and outcomes are linked to the specific gene signatures using significance analysis of microarrays (SAM) ...

08/24/06 - 20060190189 - Reagents, devices and methods for proteomic analysis with applications including diagnostics, vaccines, quality control and research
The invention describes methods for proteomic analysis, with multiple applications that involve the mapping of samples in an N-dimensional shape space. The applications include the classification of samples on the basis of the three-dimensional shapes of substances they contain, which leads to novel diagnostic methods that are linked to new ...

08/24/06 - 20060190188 - Methods and systems for determining lot consistency
This invention provides methods for determining lot consistency between a plurality of lots, systems for determining lot consistency between a plurality of lots, and computer-readable media which store a set of instructions which when executed performs a method for determining lot consistency between a plurality of lots. ...

08/24/06 - 20060190187 - Data processing apparatus for measuring apparatus and storage medium
An application program is configured by a tri-layer architecture having a presentation layer, business logic layer, and data access layer. The presentation layer has a communication module for communication between a computer and a measuring device, and a display module for displaying process results of the measurement data on the ...

08/24/06 - 20060190186 - Viral polymerase and modulation thereof
The present invention provides the tertiary structure of a Hepatitis B Virus (HBV) polymerase reverse transcriptase (rt) domain from which a variant HBV polymerase mutations associated with resistance to or having reduced sensitivity to an anti-viral drug have been mapped. The present invention further provides methods of identifying, designing and/or ...

08/24/06 - 20060190185 - Memory management method and apparatus for automated biological reaction system
A reagent management system for an automated biological reaction apparatus including an automated biological reaction apparatus including at least one reagent dispenser for applying a reagent to a sample, a memory device containing data for a reagent device selected from the group consisting of a reagent dispenser or a reagent ...

08/24/06 - 20060190184 - System and method using a visual or audio-visual programming environment to enable and optimize systems-level research in life sciences
The current invention provides a visual or audio-visual programming environment for life science and bioinformatics. It is based on the VIBE platform, which is a flexible, extensible, and integrated workflow construction and management platform. The current invention enables researchers to consolidate molecular profiling data from complementary experimental techniques, intelligently reduce ...

08/24/06 - 20060190183 - Peptide sequencing from peptide fragmentation mass spectra
The invention relates to a method of peptide sequencing from peptide fragment mass data, wherein a step of deriving a plurality of candidate peptide sequences comprises the following steps: calculating peptide fragment masses by adding to masses of a proton, hydronium ion, b1 ion or y1 ion masses of one ...

08/10/06 - 20060178841 - Integrated biosensor and simulation system for diagnosis and therapy
BioMEMS/NEMS appliance biologically monitors an individual, using biosensors to detect cellular components. Data is simulated or analyzed using systems-biology software, which provides diagnostic or therapeutic guidance. ...

08/10/06 - 20060178840 - Method and apparatus for searching molecular structure databases
I describe several methods for organizing databases of molecular structures and searching such structures. Also described are methods for characterizing molecules based on the shapes of their fields that can be used in conjunction with the methods of organizing and searching databases. In particular, the databases of molecular structures can ...

08/10/06 - 20060178839 - Optical measurement instrument and optical measurement method
In order to provide an optical measurement system and an optical measurement method which is suitable for optically measuring a body to be inspected and easily obtaining an image of a desired item based on information obtained by the measurement, an optical measurement method comprising an initial display process for ...

08/10/06 - 20060178838 - Method of receiving and handling a plurality of clinical samples for reporting a sum of diagnostic results for each sample
A method is provided for receiving and handling a plurality of clinical samples and managing information associated therewith for generating and reporting any of a plurality of different diagnostic results from each sample in a timely manner, particularly within about thirty (30) hours. Methods described comprise, for example, receiving a ...

08/10/06 - 20060178837 - Computer-assisted means for assessing lifestyle risk factors
The present invention relates to methods of assessing disease susceptibility associated with dietary and lifestyle risk factors. The invention provides for analysis of alleles at loci of genes associated with lifestyle risk factors, and the disease susceptibility profile of an individual is determined by reference to datasets which further match ...

08/10/06 - 20060178836 - System and method for adaptive bolus chasing computed tomography (ct) angiography
A method of utilizing bolus propagation and control for contrast enhancement comprises measuring with an imaging device a position of a bolus moving along a path in a biological structure. The method further comprises predicting a future position of the bolus using a simplified target model and comparing the predicted ...

08/10/06 - 20060178835 - Normalization methods for genotyping analysis
In arrays and other high density analysis platforms variabilities between data points and/or data sets may arise for a number of reasons. Disclosed are methods for addressing these variabilities and generating correction factors that may be used in conforming the data to expected or desired distributions. The methods may be ...

08/10/06 - 20060178834 - Systems and methods for optimizing crop yield with amino acid chelates and complexes
Systems and methods for optimizing crop yield using amino acid chelates by comparing a crop with collected data about the desired amount of minerals that should be present are described. The system of the invention contains a database with data about the amount and type of minerals for optimum growth ...

08/10/06 - 20060178833 - System for and method of providing diagnostic information through microscopic imaging
A method and apparatus for automated analysis of chromagenic and fluorescently labeled biological samples, wherein the apparatus automatically scans at a low magnification to acquire images which are analyzed to determine candidate cell objects of interest. Once candidate objects of interest are identified, further analysis can be conducted automatically to ...

08/10/06 - 20060178832 - Device for the temporal compression or expansion, associated method and sequence of samples
A device comprising an input memory, in which samples to be processed are stored, in addition to a control unit, which controls a temporal compression or expansion of the sequence of samples in a cyclic manner based on a conversion factor is provided. A skew unit is linked on the ...

08/03/06 - 20060173633 - Crystalline phosphatase and method for use thereof
This disclosure is directed to a crystalline form of a human protein tyrosine phosphatase designated cdc14A and more particularly to a crystal of human cdc14A, a method of crystallization thereof, and its structure, obtained by x-ray diffraction. In addition, the disclosure relates to methods of identifying new PTP binding agents ...

08/03/06 - 20060173632 - Method for predicting effectiveness of chemotherapy
A method for predicting an effectiveness of chemotherapy is described. The method comprises a comparing step and a predicting step. The comparing step is a step of comparing a threshold value with a parameter of a cyclin dependent kinase (CDK) included in a sample containing a tumor cell obtained from ...

08/03/06 - 20060173631 - Methods, software arrangements and systems for aligning sequences which utilizes non-affine gap penalty procedure
Methods, software arrangements and systems are provided which can utilize an exemplary embodiment of a procedure which can enable an efficient alignment of DNA sequences using piecewise-linear gap penalties that closely approximate general and biologically meaningful gap-functions. Accordingly, an exemplary process, software arrangement and system can be provided for obtaining ...

08/03/06 - 20060173630 - Automated method and system for setting image analysis parameters to control image analysis operations
A method and system for setting image analysis parameters to control image analysis operations. The method and system include collecting set of digital training images including a set of states for the set of digital training images. An objective function is defined to determine a relative quality of plural different ...

08/03/06 - 20060173629 - Diagnosis method of hepatic steatosis using biochemical markers
The present invention is drawn to a new diagnosis method for detecting the extent of hepatic steatosis in a patient, in particular in a patient who suffers from a disease involving hepatic steatosis, or who already had a positive diagnosis test of liver fibrosis and/or presence of liver necroinflammatory lesions, ...

08/03/06 - 20060173628 - Method and system for determining feature-coordinate grid or subgrids of microarray images
The present invention provides various embodiments that are directed to methods and systems for determining a feature-coordinate grid of a microarray image so that individual features can be located and isolated for statistical analysis. The method receives microarray-image data and determines centroid coordinates for each feature of the microarray image. ...

07/27/06 - 20060167637 - System and methods for optimized drug delivery and progression of diseased and normal cells
Systems 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 ...

07/27/06 - 20060167636 - System, method, and computer software for the presentation and storage of analysis results
A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure ...

07/27/06 - 20060167635 - Methods for predicting fatty acid enrichment
Methods and equations are provided for predicting the enrichment of polyunsaturated fatty acids in a canine based on a known diet. The methods and equations of the present invention can be used to predict the enrichment of linoleic acid and α-linolenic acid in plasma triglycerides and n-3 and n-6 type ...

07/20/06 - 20060161354 - Drug model explorer
Computer systems and methods facilitate exploring results of drug candidate modeling. In one embodiment, the software is configured to receive raw data simulated by a probabilistic model of clinical safety, tolerability, and efficacy of a drug candidate. Index information is extracted from the raw data and then referenced to generate ...

07/20/06 - 20060161353 - Computer implemented searching using search criteria comprised of ratings prepared by leading practitioners in biomedical specialties
The present invention provides a system and method for creating and maintaining a Biomedical document database, wherein the documents have been reviewed by biomedical and other experts, who have assigned taxonomic based indicia to each document wherein a specialized search engine can rapidly retrieve relevant documents based upon the commnly ...

07/13/06 - 20060155482 - Method for design of polypeptides for nanofabrication of multilayer films, coatings, and microcapsules
A method for designing polypeptides suitable, for example, for the nanofabrication of thin films, coatings, and microcapsules by ELBL for applications in biomedicine and other fields is described. In one embodiment, the method comprises identifying an amino acid sequence motif comprising n+1 amino acids, wherein a balance of charges of ...

07/13/06 - 20060155481 - System and method for reusing project planning data
The invention relates to a system and a method for managing and/or providing partial solutions consisting of elements. With the aid of the system and method, existing partial solutions can be reused and updated. Here at least one partial solution is created, especially by a user, with the at least ...

07/13/06 - 20060155480 - Method for verifying the correct spatial structure of molecules
The current invention concerns a method for quantitative verification of the correct spatial structure of molecules using NMR spectroscopy. Following a comparison between test and reference spectra, a quantitative statement concerning the quality of the sample is made, i.e. the fraction of substance having the correct spatial structure is quantified. ...

07/13/06 - 20060155479 - Efficiently calculating scores for chains of sequence alignments
Each of a plurality of substantially co-linear alignments has a score. Each alignment may comprise a starting alignment that has been diagonally extended to meet a length requirement. Dynamic programming is performed in interalignment regions between the extended alignments to generate a corresponding set of interalignment scores. Alignment scores and ...

07/13/06 - 20060155478 - Method and apparatus for providing signal analysis of a bionems resonator or transducer
An outputs signal, v(t), is generated from a bioNEMs transducer and mixed with a reference signal and then filtered to generate a correlator output, r(t). The correlator output is detected to generate a signal u(t) and then determined whether the signal u(t) satisfies a predetermined threshold. If qualified, it is ...

07/06/06 - 20060149483 - Method and apparatus for determining anticoagulant therapy factors
Methods and apparatus are disclosed for determining a new anticoagulant therapy factor (nATF) for monitoring oral anticoagulant therapy to help prevent excessive bleeding or deleterious blood clots that might otherwise occur before, during or after surgery. In one embodiment, the new anticoagulant therapy factor is based upon a determination of ...

07/06/06 - 20060149482 - Nucleic acids and proteins with thioredoxin reductase activity
The present invention relates to the use of a variety of methods for generating functional thioredoxin reductase variants in which at least one physical, chemical or biological property of the variant is altered in a specific and desired manner when compared to the wild-type protein. ...

07/06/06 - 20060149481 - Quantitative assessment of biological function based on the temporal and spatial organization of subnuclear domains
The present invention provides a method useful for analysis of punctate distribution of supramolecular complexes that are compartmentalized in nuclear microenvironments. In preferred embodiments the method provides quantitative analysis of the assembly of regulatory machinery within the context of nuclear architecture and to provide a mechanistic link with biological control. ...

07/06/06 - 20060149480 - Method of making combination medicament and medicament made thereby
Method of making a medicament, and a medicament made thereby, including identifying at least one morbid condition including a plurality of manifestations for which a plurality of distinct active ingredients may be prescribed for treatment of each of the respective plurality of manifestations; determining a combination of at least two ...

07/06/06 - 20060149479 - Method for improving fluorescence image contrast
There is provided an improved method for enhancing fluorescence images of an object, such as a biological tissue, by selectively eliminating or reducing unwanted fluorescence from fluorophores other than the fluorophore of interest. The method is based on the measurement of the lifetime of fluorophores while preserving information related to ...

06/29/06 - 20060142948 - Multiple-channel bias removal methods with little dependence on population size
Methods, systems and computer readable media for removing labeling-bias factors affecting data from two or more data sources after single source biasing factors have been removed to the extent possible. Respective data points from the data sources are considered in combination to generate a population of data points. The population ...

06/29/06 - 20060142947 - Method and apparatus for reading an assay using low resolution detection
A method of reading an assay includes illuminating a substrate. The substrate includes a sensitive region. The method also includes detecting whether the substrate was exposed to an analyte of interest. The detecting includes using low resolution detection and a priori data about the sensitive region to determine whether a ...

06/22/06 - 20060136141 - Crystallization and structure determination of glycosylated human beta secretase, an enzyme implicated in alzheimer's disease
An inhibitor bound form of human beta secretase, also known as memapsin 2 and BACE, particularly in a glycosylated form as expressed in Chinese hamster ovary (CHO), HEK293 cells, or in insect cells as part of a Baculovirus expression system has been crystallized, and the three dimensional x-ray crystal structure ...

06/22/06 - 20060136140 - Method for identification and functional characterization of agents which modulate ion channel activity
Materials, methods and a computer system are provided which facilitate the identification and characterization of modulators of potassium ion channels, particularly the HERG channel. ...

06/22/06 - 20060136139 - Rapid computational identification of targets
Disclosed are compositions and methods for rapid computational identification of targets. ...

06/22/06 - 20060136138 - Creation and maintenance of a history list in a method and apparatus for integrated modeling, simulation and analysis of chemical and biological systems
A system for modeling, simulating and analyzing chemical and biochemical reactions includes a modeling environment for constructing a model of a chemical or biochemical system comprising a plurality of chemical reactions. The system also includes a simulation engine accepting as input said constructed model of the chemical or biochemical system ...

06/22/06 - 20060136137 - Computerized system and method for safely transfusing blood products
The present invention relates to a system and method for safely transfusing blood to a patient in a computerized healthcare environment is provided. A blood product to be administered to a patient is identified and the patient is identified. A database containing a plurality of blood compatibility test results is ...

06/22/06 - 20060136136 - Crystal structure of baff, and use thereof in drug design
The present invention relates to crystallizable compositions and crystals of BAFF. In addition, this invention relates to the high resolution structure of a BAFF polypeptide as obtained by X-ray crystallography. This invention also relates to a computer (machine) comprising a machine-readable data storage medium comprising a data storage material encoded ...

06/15/06 - 20060129329 - Investigating different physical and/or chemical forms of materials
A method is provided for investigating different physical and/or chemical forms of a material. The material is placed in an array of receptacles. The material in different receptacles is subjected to different treatments under the control of a computer. Any material resulting from the different treatments is then analyzed. The ...

06/15/06 - 20060129328 - Method for designing 3-dimensional porous tissue engineering scaffold
The present invention provides a method for designing three-dimensional scaffold structures that are anatomically accurate and possess the necessary internal porous micro-architecture design, wherein the porous micro-architecture is necessary for the proliferation and colonization of cultured cells that lead to tissue formation. The design method of the present invention utilizes ...

06/15/06 - 20060129327 - Ultrasensitive sensor and rapid detection of analytes
The present invention relates to systems and methods for real time, rapid detection, identification, and enumeration of a wide variety of analytes, which include but are not limited to, cells (Eukarya, Eubacteria, Archaea), microorganisms, organelles, viruses, proteins (recombinant or natural proteins), nucleic acids, prionss, and any chemical, metabolites, or biological ...

06/15/06 - 20060129326 - System for continuous outcome prediction during a clinical trial
The present invention provides a method, apparatus, and computer instructions for improved control of clinical trials. In a preferred embodiment, after a clinical trial is initiated, data is regularly cleaned and processed to statistically analyze the data. The outcome includes a predictive measure of the timing and level by which ...

06/15/06 - 20060129325 - Integration of microarray data analysis applications for drug target identification
An analyzing system for analyzing microarray experiment data showing the arrangement of a gene to identify targets in drug discovery. Remotely located service providers are each configured for analyzing the microarray experiment data in a predetermined sequential manner. Analysis information including at least what type of analysis each service provider ...

06/15/06 - 20060129324 - Comparison of molecules using field points
This invention relates to a method for significantly increasing the accuracy of predicting and selecting an antidepressant agent, or other pharmacological agent for treatment of a disease state, that will be effective based on pre-treatment or baseline, placebo treatment and/or active treatment, or other post-treatment time period data, early changes ...

06/15/06 - 20060129323 - Comparison of molecules using field points
A method of comparing two conformers in which any score is obtained by determining the field value for molecule A at the coordinates of molecule B's field point. Molecule B's field point does not have to be very close to molecule A's field point to get a good overlay score: ...

06/08/06 - 20060122788 - Method of identifying changes in biopolymers
The current invention relates to a method of identifying changes in biopolymers, especially in chromosomal DNA, using two or more different sets of labeled detector molecules, as well as to a diagnostic kit for detecting these changes. ...

06/08/06 - 20060122787 - Protein structure search system and search method of protein structure
A protein structure searching system including a protein database storing structural characteristics proteins wherein the characteristics include structural characteristics of an entire area and a sub-area of each protein; a data processing unit receiving structural characteristics of an entire area and a sub-area of a target protein from the protein ...

06/08/06 - 20060122786 - Prediction model of cadaveric graft survival
Described are methods of predicting graft survival based on pre-transplant variables. A logistic regression (LM) and/or a tree-based model (TBM) are used to identify predictors of graft survival and to generate prediction algorithms. Both the logistic regression model and the tree-based model may be used in clinical practice for long ...

06/08/06 - 20060122785 - Constellation mapping and uses thereof
The present invention features computer methods and systems for comparing biomolecules across biological samples. In these methods, mass spectrometry measurements are obtained on biomolecules in two or more samples. These measurements are then processed and analyzed by the methods described herein to render them more comparable. We refer to this ...

06/08/06 - 20060122784 - System and method for augmenting a humoral immune response
The present application relates, in general, to a system and/or method for detection and/or treatment. ...

06/08/06 - 20060122783 - System and method for heightening a humoral immune response
The present application relates, in general, to a system and/or method for detection and/or treatment. ...

06/08/06 - 20060122782 - Read-write assay system
A read-write assay system includes providing an assay device; and writing assay device information to the assay device for subsequent reading of the assay device information from the assay device; or performing an assay with the assay device and subsequent writing of the assay related information to the assay device ...

06/08/06 - 20060122781 - Method and arrangement for detecting and measuring the phase of periodical biosignals
The invention relates to a method and an arrangement to detect and measure the phase of periodic bio-signals. The aim of the invention is to detect and measure a causal phase response in periodic bio-signals with improved reliability and higher speed compared to conventional methods, simultaneously reducing the computing power ...

06/01/06 - 20060116826 - Crystals of cytochrome p450 2c9, structures thereof and their use
The present invention provides co-crystals of cytochrome P450 2C9 proteins and a ligand such as warfarin which has been crystallised to provide a high resolution structure. The structure may be used for homology modelling of other cytochrome P450 structures such as 2C8, 2C18 and 2C19, and for analysis of the ...

06/01/06 - 20060116825 - Systems and methods for producing chemical array layouts
Systems and methods for using the same to obtain a chemical array layout are provided. Also provided are computer program products for executing the subject methods. ...

06/01/06 - 20060116824 - System and method for modulating a humoral immune response
The present application relates, in general, to a system and/or method related to detection and/or treatment. ...

05/25/06 - 20060111848 - Identification and use of cofactor independent phosphoglycerate mutase as a drug target for pathogenic organisms and treatment of the same
Present embodiments of the invention describe computational methods for performing a systematic, genome-wide search for novel drug targets in pathogenic organisms for example, the human filarial parasites. Cofactor independent phosphoglycerate mutase (iPGM) was identified by this search as a candidate target for identifying therapeutic agents for use in treating animal ...

05/25/06 - 20060111847 - Method, system, and software for analyzing pharmacovigilance data
A computer-implemented method of analyzing a dataset of pharmacovigilance data, includes determining a sample size-independent measure of association between two conditions of interest in the dataset of pharmacovigilance data; using a hypergeometric distribution to determine a measure of statistical unexpectedness between the conditions of interest in said dataset, wherein the ...

05/25/06 - 20060111846 - G-matrix fourier transformation (gft) nuclear magnetic resonance (nmr) experiments for resonance assignment and structure determination of organic molecules
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. ...

05/25/06 - 20060111845 - Method for managing agricultural produce inventories
The present invention relates to a system and method for managing and monitoring agricultural produce inventories from harvest forward in the supply chain, including obtaining data points relating to activity and activity locations that bear on the produce as it moves along the supply chain, and further includes methods for ...

05/18/06 - 20060106545 - Methods of clustering proteins
The invention relates to a method of clustering a set of proteins based on the sequence similarities of functional domain(s) such as pocket(s), functional site(s), allosteric site(s), and active site(s). The functional domain(s) of a protein sequence are identified based on the three-dimensional structure of the protein. Proteins are clustered ...

05/18/06 - 20060106544 - Method and system for predicting functions of compound
Feature of a compound is predicted by using information on interactions between substances. A database of interactions between compounds and genes/proteins is constructed on the base of information collected from bibliographic databases, gene/protein databases, and disease databases, and an interaction network is prepared by mapping the collected information to thereby ...

05/18/06 - 20060106543 - Method for analyzing effectiveness of pharmaceutical preparation
The activity of a pharmaceutical preparation or medicament on a neuronal structure is analyzed by subjecting a neuronal structure to the influence of a pharmaceutical preparation. Signals describing neuronal activities in the neuronal structure under the influence of the pharmaceutical preparation are detected and statistically evaluated to determine indicators for ...

05/11/06 - 20060100789 - Methods for searching stable docking models of biopolymer-ligand molecule complex
Methods for searching stable docking models of biopolymer-ligand molecule complex, which comprise the steps of: (1) searching possible hydrogen-bond schemes between a biopolymer and a ligand molecule by preparing possible combination sets of hydrogen-bonding heteroatoms in the ligand molecule with dummy atoms located at the positions of heteroatoms that can ...

05/11/06 - 20060100788 - Collections of matched biological reagents and methods for identifying matched reagents
Provided herein are collections of matched biological reagents selected from a larger collection of biological reagents, wherein the collection of matched biological reagents relate to a biological element. Also provided are methods for selling an isolated biomolecule or biological research reagent in a collection of matched biological reagents, and methods ...

05/11/06 - 20060100787 - Synthesis of nanocodes, and imaging using scanning probe microscopy
Methods for making nanocodes that can be detected using scanning probe microscopy are provided, as are nanocodes constructed of two or more polymers, including homogeneous polymers such as nucleic acid molecules and heterogeneous polymers such as peptide nucleic acid polymers, and subunits useful for constructing such nanocodes. Also provided are ...

05/11/06 - 20060100786 - Pan coating simulation for determining tablet coating uniformity
A method and computer program product for simulating a pan coating process estimates at least one of tablet coating uniformity or coated tablet weight uniformity for tablets within a tablet bed of a pan. The simulation includes obtaining a plurality of parameters associated with the pan coating process, selecting tablet ...

05/04/06 - 20060095211 - System and method for modulating a cell mediated immune response
The present application relates, in general, to a system and/or method related to detection and/or treatment. ...

04/27/06 - 20060089810 - Biological sample analyzing apparatus and biological sample analyzing method
In a biological sample analyzing apparatus and method, an assay sample is prepared by mixing a reagent with a biological sample which may contain assay material. Then, a first information relating to the assay material is collected from the assay sample, and when the first information satisfies predetermined condition, the ...

04/27/06 - 20060089809 - Data processing apparatus
When receiving prescribed entry data from an input device, a data entry device issues an authenticate request to a biological authentication device. Upon receipt of the authenticate request, the biological authentication device authenticates the biological information transmitted from the input device by collating it with each piece of biological information ...

04/27/06 - 20060089808 - Conformational sampling by self-organization
A self-organizing method, system, and computer program product for generating molecular conformations that are consistent with a set of distance and/or volume constraints. A stochastic proximity embedding (SPE) algorithm evaluates individual distance and/or volume constraints and adjusts the atomic coordinates to minimize violations of such constraints. The method scales linearly ...

04/27/06 - 20060089807 - Identifying peptide modifications
Methods, systems and apparatus implement techniques for identifying modifications in polypeptides. A set of candidate sequences is identified that includes sequence information potentially corresponding to an unmodified variant of the polypeptide. Peptides derived from the polypeptide are sequenced to identify sequence tags. The sequence tags are compared with sequence information ...

04/20/06 - 20060085137 - Micropressors, devices and methods for use in analyte monitoring systems
The present invention comprises one or more microprocessors programmed to execute methods for improving the performance of an analyte monitoring device including prediction of glucose levels in a subject by utilizing a predicted slower-time constant (1/k2). In another aspect of the invention, pre-exponential terms (1/c2) can be used to provide ...

04/20/06 - 20060085136 - Method and system for determining an optimal amount of a pharmaceutical to be administered to a patient during surgery
A method for determining an optimal amount of a pharmaceutical to be administered to a patient during surgery in accordance with an embodiment of the present application includes establishing a desired effect-site concentration of the pharmaceutical, infusing a proper amount of the pharmaceutical into the patient based on the desired ...

04/13/06 - 20060080042 - Method of non-targeted complex sample analysis
A method for non-targeted complex sample analysis which involves the following steps. A first step involves providing a database (16) containing identifying data of known molecules. A second step involves introducing a complex sample containing multiple unidentified molecules into a Fourier Transform Ion Cyclotron Mass Spectrometer (12) to obtain data ...

04/13/06 - 20060080041 - Chemical mixing apparatus, system and method
There is disclosed a system and method of formulating a batch comprising at least two ingredients. An embodiment is disclosed wherein a feedforward algorithm can be used to control the target blend. Subsequently a feedback closed loop control loop algorithm is provided for a multivariant blend. Use of this approach ...

04/13/06 - 20060080040 - Method and system for processing multi-dimensional measurement data
The invention provides a method for grouping measurement data obtained by effecting two or more techniques to provide characterization data characterizing at least one sample with respect to characterizing substances. According to one aspect of the invention, the grouping is effected on the basis of at least one statistical distribution ...

04/06/06 - 20060074564 - Micropressors, devices and methods for use in analyte monitoring systems
The present invention comprises one or more microprocessors programmed to execute methods for improving the performance of an analyte monitoring device including prediction of glucose levels in a subject by utilizing a predicted slower-time constant (1/k2). In another aspect of the invention, pre-exponential terms (1/c2) can be used to provide ...

04/06/06 - 20060074563 - System and method for programatic access to biological probe array data
An applications programming interface is described that includes code libraries that enable transfer of pixel data, intermediate results data, or both, from a data structure or data file directly or indirectly to a user-provided application. The pixel data and intermediate results data may include data from biological experiments related probe ...

03/30/06 - 20060069519 - Method for predicting protein-protein interactions
Method predicting whether protein or polypeptide interacts with another one by the steps of decomposition, database searching, sequence alignment and frequency determination; recording medium for carrying out the method; and obtained proteins. ...

03/30/06 - 20060069518 - Identification of genetic targets for modulation by oligonucleotides and generation of oligonucleotides for gene modulation
Interative, preferably computer based iterative processes for generating synthetic compounds with desired physical, chemical and/or bioactive properties, i.e., active compounds, are provided. During iterations of the processes, a target nucleic acid sequence is provided or selected, and a library of candidate nucleobase sequences is generated in silico according to defined ...

03/30/06 - 20060069517 - Crystal structure of house dust mite allergen der p 1
The present invention relates to a crystal structure of house dust mite allergen proDer p 1, the three-dimensional structure of proDer p 1 and the use of the three-dimensional structure to design a mutant of a protein belonging to the papain-like cysteine proteases. ...

03/30/06 - 20060069516 - Structure-based modulators of b1 g-protein coupled receptors
The present invention relates to a method for identifying modulators of B1 G-protein coupled receptors. The present invention also relates to a method for identifying an antagonist or agonist of the corticotropin-releasing factor receptor 2 (CRFR2). The present invention also relates to a method for improving antagonists or agonists of ...

03/30/06 - 20060069515 - Method and system for protein folding trajectory analysis using patterned clusters
A method (and system) of analyzing protein folding trajectory includes a combinatorial pattern discovery process for analyzing multidimensional data from a simulation of the protein folding trajectory. The method of analyzing protein folding trajectory allows a user to understand the global state changes and folding mechanism of a protein during ...

03/30/06 - 20060069514 - Methods, systems, computer program products and data structures for hierarchical organization of data associated with medical events in databases
Methods of organizing medical data can include hierarchically relating a single type of medical or research event to medical data generated from the single type of medical or research event in a computer database environment. Organizing the data in this way may enable a researcher to access medical data collected ...

03/30/06 - 20060069513 - Repair and protection factor scoring method for bioactive agents
A method of scoring the biological activity of bioactive agents like colostrum comprising conducting separate bioassays for cell restitution and cell proliferation on the bioactive agent, a comparative growth factor stimulating agent, and (preferably) a negative baseline control sample containing the cells and growth medium alone. These values are then ...

03/30/06 - 20060069512 - Gene discovery through comparisons of networks of structural and functional relationships among known genes and proteins
The present invention relates to methods for identifying novel genes comprising: (i) generating one or more specialized databases containing information on gene/protein structure, function and/or regulatory interactions; and (ii) searching the specialized databases for homology or for a particular motif and thereby identifying a putative novel gene of interest. The ...

03/23/06 - 20060064252 - Small molecule mimetics of erythropoietin
The invention features computer-assisted methods for identifying molecules which will bind to the EPO receptor and act as an erythropoietin (EPO) mimetic. Preferred EPO mimetics identified using the method of the invention act as agonists of the EPO receptor in one or more in vitro or in vivo biological assays ...

03/23/06 - 20060064251 - System for extracting compound differently interacting with bioactive polymer of interest
In a compound-extraction system: a storage unit stores first data sets each indicating interactions between one of bioactive polymers for reference and predetermined compounds under consideration, in association with the bioactive polymers for reference and the predetermined compounds under consideration; and an extraction unit receives a second data set indicating ...

03/23/06 - 20060064250 - Methods and systems for providing a nutraceutical program specific to an individual animal
The present invention relates to methods and systems for providing an animal with a nutraceutical program that is specifically tailored to address the deficiencies and/or needs of the particular animal. Blood is drawn from the animal and analyzed at a lab to obtain blood test results. The blood test results ...

03/23/06 - 20060064249 - Method and device for diagnosing and treating insulin-like growth factor deficiency disorders
The present invention provides standard deviation score (SDS) calculators, which SDS calculators are useful for transforming insulin-like growth factor-1 (IGF-1) concentrations to IGF-1 standard deviation scores. In one embodiment, IGF-1 blood levels are calculated so as to take into account IGFBP-3 blood levels (and, optionally, IGF-2 blood levels) to provide ...

03/23/06 - 20060064248 - Systems and methods for automated diagnosis and grading of tissue images
Systems and methods are provided for automated diagnosis and grading of tissue images based on morphometric data extracted from the images by a computer. The morphometric data may include image-level morphometric data such as fractal dimension data, fractal code data, wavelet data, and/or color channel histogram data. The morphometric data ...

03/23/06 - 20060064247 - Methods and systems for in silico experimental design and for providing a biotechnology product to a customer
Provided herein is a method and computer program product for designing and/or simulating a biotechnology experiment in silico; and for providing and generating revenue from a customized list of one or more biotechnology products and/or services related to the in silico designed or simulated biotechnology experiment or the product of ...

03/23/06 - 20060064246 - Automated processing of chemical arrays and systems therefore
Methods, systems and computer readable media for automatically generating information from chemical arrays. A plurality of image files representative pf features contained on a plurality of substrates, respectively, may be automatically and sequentially generated. Automatic and sequential feature extraction of the image files may be carried out, wherein automatic feature ...

03/16/06 - 20060058967 - Method of designing probe set, microarray having substrate on which probe designed by the method is immobilized, and computer readable medium on which program for executing the method is recorded
A method of designing a probe set for identifying a target sequence from a plurality of target sequence groups by a hybridization reaction is provided. The method includes: (a) selecting a first target sequence group including a plurality of target sequences; (b) selecting oligonucleotides specifically binding to the target sequences ...

03/16/06 - 20060058966 - Methods and systems for guiding selection of chemotherapeutic agents
The present invention relates to a systems and methods for selecting agents and combinations of agents for treatment of particular cancer patients or selected groups of cancer patients. These methods of the invention index possible agents and combinations in a ranking indicating the likelihood of their usefulness in the particular ...

03/09/06 - 20060052944 - Particle size distribution analyzer
In a measurement system, by suppressing the environmental changes of counter-flow of air, and temperature changes and the like, measurement can be accomplished with stable high precision and replication, and by providing a transparent cell 2 which stores a particles dispersed in a dispersion medium, and a light source which ...

03/09/06 - 20060052943 - Architectures, queries, data stores, and interfaces for proteins and drug molecules
Architectures, queries, data stores, and interfaces for proteins and drug molecules are provided. Active and binding sites or proteins and drug molecules are modeled and indexed in a data store. The data store may be browsed, searched, and mined to find specific proteins or to find potential drug molecules that ...

03/09/06 - 20060052942 - Integrated knowledge-based reverse engineering of metabolic pathways
A method of enhancing the yield of a product is provided. A host organism that is adapted to produce the product as a function of metabolism in the presence of a substrate is selected and a plurality of optimal reaction pathways are determined by searching a database and executing an ...

03/09/06 - 20060052941 - Crystal of bacterial core rna polymerase and methods of use thereof
A detailed three-dimensional structure for a bacterial core RNA polymerase is provided. Crystals of the bacterial core RNA polymerase are also included in the invention. The present invention further provides procedures for identifying agents that can inhibit bacterial proliferation through the use of rational drug design predicated on the crystals ...

03/09/06 - 20060052940 - System and method for identifying test kit types
An analysis data interpretation system configured to automatically identify a test kit type used to generate a laboratory system output file. The system includes an analysis data interpretation processor configured to receive a laboratory system output file including a test kit identifier to identify the test kit that was used ...

03/09/06 - 20060052939 - Methods for identifying compounds for treating disease states
The process of System Reconstruction is used to integrate sequence data, clinical data, experimental data, and literature into functional models of disease pathways. System Reconstruction models serve as informational “skeletons” for integrating various types of “high throughput” data. ...

03/02/06 - 20060047441 - Semantic gene organizer
A semantic gene classification and annotation system, method and computer program can utilize Latent Semantic Indexing (LSI) to identify conceptually related genes based on textual information in biomedical literature, including MEDLINE citations. In addition, term weights calculated from the usage of the gene terms in and across gene documents can ...

03/02/06 - 20060047440 - Apparatus, method, and computer product for supporting estimation of metabolism
Structure information of an estimation target compound and structure information of an arbitrary unit of CYP are acquired. Stable position information on a stable position in which the estimation target compound is stably disposed in a pocket of the CYP based on the acquired structure information. A distance between an ...

03/02/06 - 20060047439 - System and method for improving a humoral immune response
The present application relates, in general, to a system and/or method for detection and/or treatment. ...

03/02/06 - 20060047438 - Identification of different regions of biopolymer sequences using a denoiser
Various embodiments of the present invention are directed to analysis of biopolymer sequences by introducing artificial noise into the sequences and then applying a denoiser to remove the artificial noise, monitoring the denoisability of each portion of the sequence by comparing the product of the denoiser and the original sequence. ...

03/02/06 - 20060047437 - System and method for heightening an immune response
The present application relates, in general, to a system and/or method for detection and/or treatment. ...

03/02/06 - 20060047436 - System and method for magnifying an immune response
The present application relates, in general, to a system and/or method for detection and/or treatment. ...

03/02/06 - 20060047435 - System and method related to augmenting an immune system
The present application relates, in general, to a system and/or method for detection and/or treatment. ...

03/02/06 - 20060047434 - System and method related to improving an immune system
The present application relates, in general, to a system and/or method for detection and/or treatment. ...

03/02/06 - 20060047433 - System and method related to enhancing an immune system
The present application relates, in general, to a system and/or method related to detection and/or treatment. ...

02/23/06 - 20060041388 - Oligosaccharides fragmentation pattern analysis system and oligosaccharides fragmentation pattern analysis method
Oligosaccharides fragmentation pattern analysis system 10 includes: a geometry optimization part for calculating an optimized structure of an ionized oligosaccharide; a binding parameter extraction part for extracting multiple kinds of binding parameters which relate to bond strengths for respective multiple candidate bonds to be the candidate of the cleavage site ...

02/23/06 - 20060041387 - Smart microarray cancer detection system
A smart microarray detection system for exploring and detecting cancer specific genes. A microarray is constructed using cancer specific genes that can detect, identify, quantify, and discriminate cancers in biological specimens. Data obtained from the microarray is analyzed with questionable signals reanalyzed with real time PCR. This information is then ...

02/23/06 - 20060041386 - Method of analyzing industrial food products, cosmetics, and/or hygiene products, a measurement interface for implementing the method, and an electronic system for implementing the interface
The invention seeks to improve the taking of physical measurements on an industrial product represented by organoleptic perceptions, the method providing a measurement interface that submits descriptors in a relative arrangement such that testers are not influenced by the order in which they appear, regardless of the descriptor and regardless ...

02/23/06 - 20060041385 - Method of quantitating proteins and genes in cells using a combination of immunohistochemistry and in situ hybridization
The disclosure provides a system for and method of accurately determining the status of a protein target and a nucleic acid target in a biological sample (e.g., a tissue or cell sample). Provided are methods of quantitating a protein target and a nucleic acid target in a tissue or cell ...

02/23/06 - 20060041384 - Automated information processing in randomly ordered arrays
The invention relates to the use of a computer system to compare images generated from a randomly ordered array. This system preserves the relative position of each site within the array so that the same site can be compared in different images. ...

02/16/06 - 20060036372 - Method and apparatus for tissue modeling
A method and apparatus for tissue modeling using at least one tissue image having cells therein and derived from biological tissue. Data derived from the tissue image is clustered to generate cluster vectors such that each cluster vector represents a portion of the tissue image. Cell information is generated which ...

02/16/06 - 20060036371 - Method for predicting protein-protein interactions in entire proteomes
The invention is a teachable system and method for predicting the interactions of proteins with other proteins, nucleic acids and small molecules. A database containing protein sequences and information regarding protein interactions is used to “teach” the machine. Proteins with unknown interactions are compared by the machine to proteins in ...

02/16/06 - 20060036370 - Process, system and method for improving the determination of digestive effects upon an ingestable substance
The present invention generally relates to processes, computer programs and systems, methods of making such and methods of using such for improving the determination of one or more digestive effects upon an ingestable substance. The underlying data used in this determination may originate from either an in vitro or in ...

02/16/06 - 20060036369 - Automated histological grading of tubules
A method of grading tubules in a first histological slide image derives a second image of objects in the first image of objects in the first image with boundary characteristics corresponding to tubules. It also derives a third image of second objects in the first image having pixel value characteristic ...

02/16/06 - 20060036368 - Drug discovery methods
Method for identifying disease-related pathways that can used to identify discovery targets, to identify new uses for known drugs, to identify markers for drug response, and related purposes. ...

02/09/06 - 20060031024 - Method of optimizing parameter values in a process of producing a product
A method of optimizing parameter values in a process, which process is essentially controlled by a set of parameters affecting a set of properties characterizing an output of the process. The method may use an analytic hierarchy process (AHP) to associate a weight with each property according to its relative ...

02/09/06 - 20060031023 - Mass intensity profiling system and uses thereof
The present invention is directed to computer automated methods and systems for identifying and characterizing biomolecules in a biological sample. Mass spectrometry measurements are obtained on biomolecules in a sample. These measurements are analyzed to determine the abundance of the biomolecules in the sample, and the abundance measurements are coupled ...

02/09/06 - 20060031022 - Method of planning and performing stability studies
The present invention relates to a method and system for planning a stability study of a pharmaceutical composition. According to the current invention a new statistical principle for designing studies is provided. It addresses directly that the aim of the stability study is to derive more precise and efficient specification ...

02/09/06 - 20060031021 - In vitro predictive method
An in vitro method for predicting in vivo pharmacokinetic parameters such as Cmax for poorly soluble drug compounds in formulations. ...

02/09/06 - 20060031020 - Computational approach for constructing an analyte binding motif
A method for constructing an analyte binding motif by accessing a database that comprises structural data on analyte binding sites, generating at least one preliminary analyte binding site from the structural data, selecting an analyte binding site from the at least one preliminary analyte binding sites, and constructing the analyte ...

02/09/06 - 20060031019 - Methods and compositions for assessing partially saturated pixel signals
Methods for producing data for a partially saturated pixel produced during scanning of a chemical array are provided. In general, an analog signal for a partially saturated pixel is sampled to obtain a set of non-saturated digital signals and a set of saturated digital signals. The saturated digital signals are ...

02/09/06 - 20060031018 - System and method for processing and reporting biologically significant events
A system and method are provided for processing reports of biological events in order to filter the reports and output the reports to appropriate institutions and individuals for reporting. The system includes a primary filter for receiving a record, evaluating an event contained within the record, identifying any potential receiving ...

02/02/06 - 20060025932 - Novel method for chromatographic finger printing and standardization of single medicines and formulations
The present invention provides a method for the chromatographic fingerprinting, chemical and therapeutic standardization, bar-coding of the fingerprints and preparation of a data base for Enterprise Resource Planning (ERP) and Customer Relationship Management (CRM) machines and applications of medicines in general and traditional medicines in particular; this invention includes a ...

02/02/06 - 20060025931 - Method and apparatus for real time predictive modeling for chronically ill patients
Various embodiments of the present invention are directed to a method and apparatus for improving the care of patients (e.g., chronically ill patients). In one example (which example is intended to be illustrative and not restrictive), the invention may be designed to improve such care through real time output (e.g., ...

02/02/06 - 20060025930 - Automated analysis of multiplexed probe-target interaction patterns: pattern matching and allele identification
Disclosed are methods and algorithms (and their implementation) supporting the automated analysis and interactive review and refinement (“redaction”) of the analysis within an integrated software environment, for automated allele assignments. The implementation, preferably with a software system and a program referred to as the Automated Allele Assignment (“AAA”) program, provides ...

02/02/06 - 20060025929 - Method of determining a genetic relationship to at least one individual in a group of famous individuals using a combination of genetic markers
A method for quantifying the genetic relationship of a customer to at least one individual of at least one group of famous individuals, the method includes the following steps. First, receiving genetic information and famous individual group selection criteria from a customer, next, calculating the genetic distance of the customer ...

02/02/06 - 20060025928 - Hydropathy plots and fourier analysis with an ellipsoidal distance metric
Techniques for protein structure analysis are provided. In one aspect, a method of characterizing at least a portion of a protein structure comprising amino acid residues comprises the following steps. A set of values characterizing the protein structure are determined, wherein each value represents a distance from a center of ...

01/26/06 - 20060020396 - Rational directed protein evolution using two-dimensional rational mutagenesis scanning
Rational methods for generating protein variants are provided. Processes and systems for the high throughput directed evolution of peptides and proteins employing the method are provided. ...

01/26/06 - 20060020395 - Method of labeling object, object to which label is attached by the method, and method of distinguishing object by detecting the attached label
A method of labeling an object is effective in attaching many species of labels according to the necessity to a minute object such as a fine particulate substrate that is used for fixing a probe molecule to be used in a bioassay. For a minute object, a labeling material prepared ...

01/26/06 - 20060020394 - Network
A method of optimising a storage network comprising the steps of: defining a plurality F of flows through a set N of fabric nodes; investigating the cost of establishing some routes through the storage network; and updating a route desirability variable as a function of the cost. ...

01/26/06 - 20060020393 - Methods for quantification and de novo polypeptide sequencing by mass spectrometry
The invention provides a method of determining an amino acid sequence of a parent polypeptide. The method consists of: (a) obtaining mass spectra of two or more differentially labeled polypeptide fragments of a parent polypeptide; (b) assigning a mass and a weighting characteristic to two or more paired signals having ...

01/26/06 - 20060020392 - Crystalsym process
The CrystalSym process is a logical process. It enables users of the process to easily construct symmetric systems of objects within a 3D virtual space. This process utilizes the gamut of the crystallographic 3D space filling symmetry groups of which there are 230, as well as subgroups of these 230 ...

01/26/06 - 20060020391 - Method for tracking and controlling infections
The present invention is a system and method for performing real-time infection control over a computer network. The method comprises obtaining a sample of a microorganism at a health care facility, sequencing a first region of a nucleic acid from the microorganism sample, comparing the first sequenced region with historical ...

01/19/06 - 20060015263 - Apparatus for determining association variables
An apparatus, and related method, for determining one or more association variables is described. The apparatus includes at least one processor, at least one memory, and at least one program module. The program module is stored in the memory and is configurable to be executed by the processor. The program ...

01/19/06 - 20060015262 - Method and system for automated quantitation of tissue micro-array (tma) digital image analysis
A method and system for automated quantitation of tissue micro-array image (TMA) digital analysis. The method and system automatically analyze a digital image of a TMA with plural TMA cores created using a needle to biopsy or other techniques to create standard histologic sections and placing the resulting needle cores ...

01/19/06 - 20060015261 - Blood clotting predictor
A computer program product for predicting the speed and efficacy of a blood-clotting agent is disclosed. The product comprises a computer usable medium having computer readable program code means embodied in the medium for causing an application program to execute on a computer with a database for storing data therein. ...

01/12/06 - 20060009915 - Rapid and quantitative proteome analysis and related methods
The invention provides methods for identifying polypeptides. The method can include the steps of simultaneously determining the mass of a subset of parent polypeptides from a population of polypeptides and the mass of fragments of the subset of parent polypeptides; comparing the determined masses to an annotated polypeptide index; and ...

01/12/06 - 20060009914 - Detection and identification of nucleic acid, peptide, and protein modifications
Embodiments of the present invention provide devices and methods for detecting, identifying, distinguishing, and quantifying modifications to nucleic acids, proteins, and peptides using SERS and Raman spectroscopy. Applications of embodiments of the present invention include proteome wide modification profiling and analyses with applications in disease diagnosis, prognosis and drug efficacy ...

01/12/06 - 20060009913 - System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing g-protein coupled receptors
The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling ...

01/12/06 - 20060009912 - Microbiological information system
The present invention relates to an apparatus and a method for the classification of microorganisms. In particular, the invention relates to an apparatus and method for the classification of microorganisms with annotation of clinically and/or industrially relevant information. An apparatus according to the invention comprises a measuring apparatus for classifying ...

01/05/06 - 20060004525 - System and method of determining proteomic differences
The present invention relates to a system and methods for identifying differential peptide expression in one or more peptide populations. Each population is labeled with a discernable label and provides a mechanism to resolve mixed peptide populations using mass spectroscopy-based techniques. Spectra produced by the peptide sample are used to ...

01/05/06 - 20060004524 - Method, apparatus, and computer program product for collecting and securing chain of custody information related to a specimen and generated via specimen collection
A specimen collection system, container device, and a method and computer program product for collecting and securing chain of custody (COC) information related to a specimen is provided. The system, method, and computer program product guides a collector to collect a complete COC data set related to a specimen, detect ...

01/05/06 - 20060004523 - Methods and system for comparing data values across multiple platforms
Methods, systems and computer readable media for imposing monotonic consistency among results of multiple platforms measuring the same specific property for the same/equivalent series of samples, to provide viable comparisons of sensitivity and precision among the platforms as well as provide useful conversion formulas among the platforms to ensure equivalent ...

12/29/05 - 20050288869 - Patient-specific dosimetry
A patient-specific optimally effective radiation dose for administration of a radiopharmaceutical to a patient for treatment of a disease may be established by basing the calculation of the appropriate therapeutic dose on factors such as the desired total body dose, the maximum tolerated dose, the typical clearance profile of the ...

12/29/05 - 20050288868 - Molecular property modeling using ranking
Methods and articles of manufacture for modeling molecular properties using data regarding the partial orderings of compound properties, or by considering measurements of compound properties in terms of partial orderings are disclosed. One embodiment provides for constructing such partial orderings from data that is not already in an ordered form ...

12/29/05 - 20050288867 - Cell tissue culture management method and system
In order to detect the mis-operation of cells or tissues in a culturing step and other working steps to prevent erroneous use in treatment of cultured cell and tissues besides those of the cell donor, a genetic information, held by a cell or tissue, is used as a cell tissue ...

12/29/05 - 20050288866 - Computational method for identifying adhesin and adhesin-like proteins of therapeutic potential
A computational method for identifying adhesin and adhesin-like proteins, said method comprising steps of computing the sequence-based attributes of a neural network software wherein the attributes are (i) amino acid frequencies, (ii) multiplet frequency, (iii) dipeptide frequencies, (iv),charge composition, and (v) hydrophobic composition, training the artificial neural Network (ANN) for ...

12/29/05 - 20050288865 - Peptide and protein identification method
A method for identifying peptides and proteins, starting from corresponding tandem spectrometry data. A structured representation is matched with a biological sequence database, and the best peptide match or matches within the database is determined. MS/MS data is interpreted and structured to allow full exploitation of the information contained in ...

12/29/05 - 20050288864 - Intracellular antibodies
A method of identifying at least one consensus sequence for an intracellular antibody (ICS) comprising the steps of: creating a database comprising sequences of validated intracellular antibodies (VIDA database) and aligning the sequences of validated intracellular antibodies according to Kabat; determining the frequency with which a particular amino acid occurs ...

12/22/05 - 20050283318 - Systems for the detection of short and long samples
Methods and systems are provided for detecting the accidental use of short and long samples in the clinical analysis of a sample, specimen, or assay. The systems can include a clinical analyzer for determining one or more values for one or more measurable characteristics of a sample. These values are ...

12/22/05 - 20050283317 - Characterizing biological stimuli by response curves
A method for generating stimulus response curves (e.g., dose response curves) shows how the phenotype of one or more cells change in response to varying levels of the stimulus. Each “point” on the curve represents quantitative phenotype for cell(s) at a particular level of stimulus (e.g., dose of a therapeutic). ...

12/22/05 - 20050283316 - Silico iterations correlating mass spectrometer outputs with peptides in databases and success of same
Independent of scoring algorithm for matching or correlating mass spectrometer outputs to peptides in database(s), methods for identifying when a scoring algorithm has achieved a successful correlation include identifying criteria indicative of the successful correlation, conducting a plurality of scoring algorithm runs or analyses, and making an in silico determination ...

12/15/05 - 20050278124 - Methods for molecular property modeling using virtual data
Embodiments of the invention provide methods, systems, and articles of manufacture for modeling molecular properties based on information obtained from sources other than direct empirical measurements of the properties. Embodiments of the invention use “virtual data” related to molecular properties to train a molecular properties model. Virtual data about a ...

12/08/05 - 20050273273 - Metrics for characterizing chemical arrays based on analysis of variance (anova) factors
Methods, systems and computer readable media for producing a metric to characterize a chemical array. Effects of terms impacting results of measurement of an output generated from analysis of the array or a procedure performed using the array, are quantified by performing ANOVA analysis and calculating sums of squares quantities ...

12/08/05 - 20050273272 - System and method for laboratory-wide information management
A laboratory information management system includes a process template manager that creates a process template from a plurality of activities. A workflow template generator generates a workflow template from the process template. A process manager starts a process run according to the process template. A workflow component schedules workflow according ...

12/08/05 - 20050273271 - Method of characterizing cell shape
An image analysis method characterizes cells based on the elongation. It analyzes an image of the cells and automatically identifies points or locations of high contrast (i.e., regions where the transition from intense signal to weak signal occurs abruptly, over a short distance). Groups of contiguous high contrast points collectively ...

12/08/05 - 20050273270 - Profile searching in nucleic acid sequences using the fast fourier transformation
One embodiment of the present invention provides methods for detecting known blocks of functionally aligned protein sequences in a test nucleic acid sequence, e.g., in an uncharacterized EST. The method can include the following steps. A) Reverse translate the set of protein sequences to a set of functionally aligned nucleic ...

12/08/05 - 20050273269 - Method and system for analysis of biological and chemical data
In various embodiments of the present invention, initial experimental data is initially partitioned into classes by sample source, concentration or number-of-molecule values are computed with respect to each initial partition, and a rank consistency score or fold-change consistency score is computed for various molecular concentration or number-of-copies determinants with respect ...

12/08/05 - 20050273268 - Method and system for quantifying and removing spatial-intensity trends in microarray data
A method and system for quantifying and correcting spatial-intensity trends for each channel of a microarray data set having one or more channels. The method and system of one embodiment of the present invention selects a set of features from each channel of the microarray data set. Based on the ...

12/08/05 - 20050273267 - Method for identifying markers
The invention is a method for identifying markers associated with the presence of a predetermined characteristic comprising accumulating spectral data from a sample known to have a predetermined characteristic, identifying a spectral feature which is indicative of the predetermined characteristic, and identifying a marker associated with the spectral feature. ...

12/01/05 - 20050267690 - Extracting shape information contained in cell images
Methods and apparatus are provided for the analysis of images of cells and extraction biologically-significant shape-related features from the cell images. The extracted features may be correlated with particular conditions induced by biologically-active agents with which cells have been treated, thereby enabling the automated analysis of cells based on cell ...

12/01/05 - 20050267689 - Method to automatically identify peak and monoisotopic peaks in mass spectral data for biomolecular applications
A method for identifying peaks in mass spectral data includes: eliminating non-constant levels of background noise; detecting all peaks above a user-identified signal-to-noise ration threshold; and compiling a list of all detected peaks. ...

12/01/05 - 20050267688 - Method for enhanced accuracy in predicting peptides elution time using liquid separations or chromatography
A method for predicting the elution time of a peptide in chromatographic and electrophoretic separations by first providing a data set of known elution times of known peptides, then creating a plurality of vectors, each vector having a plurality of dimensions, and each dimension representing positional information about at least ...

12/01/05 - 20050267687 - System for predicting three-dimensional structure of protein
The present invention is to provide a system for measuring the similarity between protein profile matrices which is suitably used for predicting a protein three-dimensional structure. The present invention provides a system for measuring the similarity between protein profile matrices, wherein said profile matrix consists of a group of profile ...

11/24/05 - 20050261837 - Kernel-based system and method for estimation-based equipment condition monitoring
A system for monitoring in real-time the health of equipment or the performance of a process utilizing a universal modeling technique that generates estimates of parameters for gauging early indications of anomalies. A kernel regression model such as the Nadaraya-Watson may be used, and may be in autoassociative form. Kernel ...

11/24/05 - 20050261836 - Crystal structure of mitogen-activated protein kinase-activated protein kinase 2 and binding pockets thereof
The invention relates to crystalline molecules or molecular complexes that comprise binding pockets of mitogen activated protein kinase activated protein kinase 2 (MAPKAPK2) or its homologues. The invention also relates to crystals comprising MAPKAPK2. The present invention also relates to a computer comprising a data storage medium encoded with the ...

11/17/05 - 20050256651 - Algorithm for estimation of multiple faults on a transmission line or waveguide
An algorithm is provided for a frequency domain reflectometer which takes into account both attenuation per unit length of transmission line and phase shift per unit length of transmission line in a modified Inverse Fourier Transform that converts a frequency domain complex reflection coefficient into a more accurate time domain ...

11/17/05 - 20050256650 - System and method for time correlated multi-photon counting measurements
The invention provides a method and a measurement system for characterisation of luminescence properties, the method comprises irradiating the luminescent material with a pulse of excitation light, providing a triggering signal correlated to the pulse of excitation light; detecting with a photodetector such as a photomultiplier tube (PMT) a plurality ...

11/17/05 - 20050256649 - High throughput correlation of polymorphic forms with multiple phenotypes within clinical populations
A computer-assisted method of looking for pharmacologic targets, in which large numbers of persons are enrolled in drugh clinical trials, they are medically examined and documented, tissue samples are taken, the tissue samples are genotyped, and an examination is made of the genotypes to try to ascertain associations between the ...

11/10/05 - 20050251347 - Automatic visual recognition of biological particles
A method and system provide the ability to automatically recognize biological particles. An image of biological particles (e.g., airborne pollen or urine) is obtained. One or more parts of the image are detected as containing one or more particles of interest. Feature vector(s) are extracted from each detected part of ...

11/10/05 - 20050251346 - Method and apparatus for reaction route graphs for reaction mechanism and kinetics modeling
A method and apparatus for reaction route (RR) network analysis is provided in analogy with electrical networks and is based on the combined use of RR theory, graph theory, and Kirchhoff's laws. The result is a powerful new approach of “RR graphs” that is useful in not only topological representation ...

11/10/05 - 20050251345 - Small molecules and a pharmacophore model for inhibition of anthrax lethal factor
Disclosed herein is a pharmacophore model for inhibiting anthrax lethal factor protease activity which comprises a first aromatic center A, a second aromatic center B, a first polar center C, a second polar center D, a third polar center E, and a neutral linker F. In some embodiments, the distance ...

11/10/05 - 20050251344 - Method and apparatus for monitoring a technical installation, especially for carrying out diagnosis
The invention makes use of human perception to derive potential faults of at least one component of the technical installation. A sensor device may be employed for acquiring at least one human physiological reaction whereby said human physiological reaction may include at least one of neuritic currents and changes in ...

11/03/05 - 20050246105 - Interpolated image response
Systems and methods are provided for characterizing a multidimensional distribution of responses from the objects in a populations subject to a perturbation. The methods enable the creation of a “degree of response” scale interpolated from non-perturbed and perturbed reference populations. The methods enables, using the interpolated degree of response scale, ...

10/27/05 - 20050240356 - Method and device for monitoring an analyte concentration in the living body of a human or animal
The present invention generally relates to a method and a device for monitoring an analyte concentration in the living body of a human or animal. In particular to a method and device for determining analyte values y(tn) correlating with the concentration to be determined are determined for consecutive points in ...

10/27/05 - 20050240355 - Molecular entity design method
A method for designing a molecular entity meeting a set of objectives. The method includes: a) providing a set of objectives to be met by the molecular entity; b) providing a population of candidates for the molecular entity; c) predicting properties of each candidate of the population using at least ...

10/27/05 - 20050240354 - Service oriented architecture for an extract function in a data integration platform
An extraction function of an extract-transform-load data integration process is deployed as a service in a services oriented architecture. ...

10/27/05 - 20050240353 - Reagents, devices and methods for proteomic analysis with applications including diagnostics, vaccines, quality control and research
The invention describes methods for proteomic analysis involving the mapping of samples in N-dimensional shape space. The applications include the classification of samples on the basis of the three-dimensional shapes of substances they contain. A panel of P (>>1) reagents, with P≧N, called X(j), with j=1 to P, is used. ...

10/27/05 - 20050240352 - Online procurement of biologically related products/services using interactive context searching of biological information
Systems and methods for procuring biologically related products available on a vendor Website are described which involve user-server interfacing with a Web based browser to retrieve database files representing available target products via processing biological context searches on named annotated text string databases. ...

10/20/05 - 20050234653 - Systems and computer software products for gene expression analysis
Methods and computer software products are provided for analyzing gene expression data. In one embodiment, non-parametric statistics is used to determine whether a transcript is detected in a sample. ...

10/20/05 - 20050234652 - Nuclear magnetic resonance-docking of compounds
The invention provides a method for determining a structure model for a test ligand bound to a macromolecule binding site. Structural constraints for the test ligand are derived from spectroscopic signals arising from interactions between the test ligand and macromolecule. The structure constraints are used as constraints in docking a ...

10/20/05 - 20050234651 - Method for analyzing structure of glycoprotein
The present invention provides a simplified method for analyzing a structure of glycoprotein capable of conducting a peptide sequence analysis, a sugar chain sequence analysis, and an analysis of a sugar chain binding site accurately and rapidly using a mass spectrometer. ...

10/20/05 - 20050234650 - Method and system for normalization of microarray data
One embodiment of the present invention provides a method and system for selecting a subset of normalization features, or biomolecule probes, from multiple data sets generated from a single microarray and from multiple data sets generated from multiple microarrays. In this embodiment, the signal intensities corresponding to common features within ...

10/13/05 - 20050228594 - Quantitative measurements of concentration and solubility using raman spectroscopy
The present invention provides methods which allows for the determination of concentration or solubility in a multi-component system using Raman spectroscopy. The present invention circumvents the necessity of constructing a calibration curve in order to analytically determine the concentration/solubility of a solute in a homogeneous liquid or a homogeneous solid. ...

10/13/05 - 20050228593 - Method, system, and computer program for providing and evaluating medicine information
A system, method, or computer program product may provide medical information to aid users in identifying new treatments for medical conditions, or in identifying adverse affects of drugs, or in locating clinical trials and medical conventions, or in providing prescription refill notification, or in providing information about conditions, drugs, and ...

10/13/05 - 20050228592 - Method and device for partitioning a molecule
A method for partitioning a molecular subset is described. The partitioning method takes into account molecular structure and its manner of storage and transmission, transformations to be applied to the molecular subset and their implementation, and constraints imposed by the implementation of the partitioning method. Using this method, a molecular ...

10/13/05 - 20050228591 - Kernels and kernel methods for spectral data
Support vector machines are used to classify data contained within a structured dataset such as a plurality of signals generated by a spectral analyzer. The signals are preprocessed to ensure alignment of peaks across the spectra. Similarity measures are constructed to provide a basis for comparison of pairs of samples ...

10/06/05 - 20050222778 - System, method, and computer-readable medium for collection of environmental data and generation of user report for compliance with fda requirements
A system, method, and computer-readable medium for the collecting and storing of environmental data, and generating a user report of the environmental data, the user report providing document compliance with U.S. Food and Drug Administration requirements. The collected and stored environmental data includes a wide variety of manufacturing facility parameter ...

10/06/05 - 20050222777 - System, method, and computer software prorduct for specifying parameters associated with a biological probe array
Systems, methods, and computer program products are described for specifying a scanning area of a substrate. In accordance with one method, steps include receiving location data corresponding to a plurality of probe-feature locations on the substrate, storing the location data, accessing the location data, and scanning the substrate based on ...

10/06/05 - 20050222776 - Method for fragment preparation
A method for characterizing a molecular fragment to collect data related to the fragment that allows its evaluation for drug discovery purposes. Starting with a two-dimensional model of the fragment, an initial three-dimensional model of the fragment is derived. Conformers of the fragment are identified. The conformers are then clustered, ...

09/29/05 - 20050216206 - Systems, methods and apparatus for reconstructing phylogentic trees
In one aspect, a tree data structure is reconstructed by reconstructing a local topology from samples of data of known nodes, and estimating the data value of each node in the reconstructed local topology. The reconstructing and estimating are performed iteratively. In another aspect, the topology is reconstructed from pairs ...

09/29/05 - 20050216205 - Method for measuring surface plasmon resonance
An object of the present invention is to suppress variations in measurement values when measuring a specific binding reaction between a physiologically active substance and a tested substance using a surface plasmon resonance measurement device, so that binding detection data with high reliability is obtained. The present invention provides a ...

09/29/05 - 20050216204 - Method and apparatus for tissue modeling
A method and apparatus for tissue modeling using at least one tissue image derived from clinical tissue. The at least one tissue image having cells therein. The method comprises for each tissue image of the at least one tissue image wherein each tissue image is denoted as a sample tissue ...

09/29/05 - 20050216203 - System and method for providing optimal concentrations for medication infusions
Optimum concentrations for a drug administered as a medical infusion to a patient, particularly a pediatric patient, are determined. The determination is made using inputs regarding (1) the drug to be administered; (2) the patient; and (3) the infusion process. The optimum concentrations are displayed to a user, such as ...

09/29/05 - 20050216202 - Method for processing missing values in measured data
A method for processing missing values in measured data is provided. The method includes assigning weights to measured objects or measured items, according to a priority of the measured objects or measured items; selecting a set of the measured objects and measured items including the missing values having the smallest ...

09/29/05 - 20050216201 - Techniques for synthesis integrity evaluation utilizing cycle fidelity probes
Techniques for designing polymer probes to verify the integrity of the probe synthesis are provided. Multiple probes with identical sequences are designed so that the probes will be formed utilizing at least one different monomer addition cycle. Based on the probes affinity to a control target, variations (e.g., errors) in ...

09/29/05 - 20050216200 - Neural network pattern recognition for predicting pharmacodynamics using patient characteristics
Methods are provided for predicting the effect of a drug given the drug dose and individual patient clinical characteristics. A neural network is trained on samples of clinical data including the observed drug dose and effect on patients, as well as their individual clinical characteristics. The neural network is then ...

09/29/05 - 20050216199 - Cuffless blood-pressure monitor and accompanying web services interface
The invention provides a system for monitoring blood pressure that includes: 1) a gateway software system that receives blood pressure information collected with a blood-pressure monitor and transmitted with a wireless interface; 2) a database that receives the blood pressure information from the gateway software system and stores this information ...

09/22/05 - 20050209785 - Systems and methods for disease diagnosis
The present invention is directed to improved systems and methods for distinguishing and classifying subjects based on analysis of biological materials. Methods for the analysis of multivariate data collected from a plurality of subjects of known class are provided. The results of such analyses include a set of intermediate combined ...

09/22/05 - 20050209784 - Method and device for analyzing three-dimensional structure of polysaccharides
The present invention provides a three-dimensional structure analysis method that extracts monosaccharide bonding patterns significant for elucidation of the formation of the three-dimensional structures of polysaccharides when the alignments of local structures are given for those polysaccharides. This three-dimensional structure analysis method comprises inputting the alignment of the local structures ...

09/15/05 - 20050203710 - Parallel reaction executing apparatus, parallel reaction execution planning design apparatus, and parallel reaction executing method
A parallel reaction executing apparatus comprises an electronic computer and a parallel reaction executing section, the electronic computer substantially controlling a function of the parallel reaction executing section in addition to a current computing process, and executing a number of reactions in parallel under the control of the apparatus, wherein ...

09/15/05 - 20050203709 - Methods of analyzing multi-channel profiles
The present invention provides methods for analyzing multi-channel profiles. In the method of the invention, systematic cross-profile (cross-experiment) errors among a plurality of multi-channel profiles having a common reference channel are estimated using profiles of the common reference channel. The cross-profile errors are then removed from profiles of the experiment ...

09/15/05 - 20050203708 - Method and system for microarray gradient detection and characterization
A method and system for detecting and optionally characterizing background intensity gradients is disclosed. Various embodiments of the present invention employ metrics computed for a number of features within an image of a microarray that provide an indication of background intensity gradients within the image of the microarray. In one ...

09/15/05 - 20050203707 - Data measuring device, healthcare data acquiring system, and healthcare data acquiring method
The data measuring unit 11 measures a subject's blood and urine, and acquires numerical data (S501). The communication control unit 12 transmits the acquired numerical data to the data management apparatus 20 (S502). The overall control unit 14 receives the numerical data from the data measuring apparatus 10 (S503), and ...

09/08/05 - 20050197786 - System and method for managing the development and manufacturing of a pharmaceutical drug
A system and method for managing the development and manufacturing process of a pharmaceutical is disclosed. The method comprises capturing and recording the development and manufacturing history of the pharmaceutical drug in order to generate a product history. The product history is stored on a computer and is searchable in ...

09/08/05 - 20050197785 - Apparatus and methods for assessing metabolic substrate utilization
Apparatus and methods for assessing metabolic substrate utilization are described. In one embodiment, a processor-readable medium includes code to receive data indicative of a plasma glucose concentration, a plasma free fatty acid concentration, and a respiratory quotient of a subject. The processor-readable medium also includes code to calculate, based on ...

09/08/05 - 20050197784 - Methods and systems for analyzing term frequency in tabular data
Systems, methods and recordable media for facilitating user-guidance of statistical analysis of large datasets based upon word-based textual annotations associated with the large datasets. Particular applications to large biological datasets are described. ...

09/08/05 - 20050197783 - Methods and systems for extension, exploration, refinement, and analysis of biological networks
Systems, methods and recordable media for facilitating user-guidance of computational analysis and knowledge extraction tools for use with biological data for disambiguation and determination of causation in representations of the data. Systems, methods, tools and computer readable media for user-guided expansion of biological networks and manipulations of the same. Tools ...

09/01/05 - 20050192761 - Physiological profiling
A new analytical strategy, termed physiological profiling, was developed that can capture physiological baselines and reveal relationships between particular phenotypes as a function of genotype in complex disease conditions. Physiological profiling offers a powerful strategy to visualize complex physiological processes. Combined with developing statistical analysis, this analytical tool is likely ...

09/01/05 - 20050192760 - System and method for plant identification
Methods of compiling a database of images of plant species and the use of the database to identify unknown plant species are described. Images of the apical complexes of the plant are obtained and stored in a database to allow a comparison of the apical complexes with unknown plant species. ...

09/01/05 - 20050192759 - Computer program for designing treating member and system for providing service using the program
A computer program embodied on a computer readable medium for designing a treating member contains a first code segment adapted to acquiring a piece of input information containing a treatment sequence; and a second code segment adapted to designing a flow path along which a sample moves, based on the ...

09/01/05 - 20050192758 - Methods for comparing functional sites in proteins
The present invention relates to methods and systems for representing and scoring the similarity of two protein by iteratively rotating and translating one protein surface representation relative to the other protein surface representation in order to maximize (or minimize) a score that represents both the volume between the two surface ...

09/01/05 - 20050192757 - Method of constructing teritiary structure of protein composed of plural chains
A method is provided of constructing a tertiary structure of a protein composed of plural chains having given arbitrary amino acid sequences by extending an comparative modeling method of constructing a tertiary structure of a protein composed of a single chain having a given arbitrary amino acid sequence (extended modeling ...

09/01/05 - 20050192756 - Information management system for biochemical information
An information management system for managing biological information (200). The information management system comprises by structured descriptions of biological pathways (700) that are formed of at least pathways (212), biochemical entities (218), connections (216) and interactions (222), such that each pathway (212) relates to one or more connections (216); each ...

09/01/05 - 20050192755 - Methods and systems for identification of macromolecules
A method is provided for identifying sequences of molecules and sequence modifications from mass spectrometry data. At least one de novo sequence is produced from mass spectrometry data of sequences of molecules,. At least one mass-based alignment is calculated between each de novo sequence and sequences in a sequence database. ...

09/01/05 - 20050192754 - Protein sequence signals and their applications
Just as written languages appear random unless one knows the words, so too protein sequences can appear as random. By statistical measures they are far from random. Protein sequences contain nonrandom signals. Some signals are associated with structure and function. Methods to search for and identify such signals are provided. ...

08/25/05 - 20050187719 - System and method for adding hardware registers to a power management and configuration system
A system for adding multiple GPE blocks (in addition to the system/root GPE block device) to a computing system by creating a device entry in the ACPI namespace, and using a _CRS object to describe the system resources consumed by the device is described. The GPE block device may then ...

08/25/05 - 20050187718 - Novel purified polypeptides from streptococcus pneumoniae
The present invention relates to novel drug targets for pathogenic bacteria. Accordingly, the invention provides purified protein comprising the amino acid sequence set forth in SEQ ID NO: 4. The invention also provides biochemical and biophysical characteristics of the polypeptides of the invention. ...

08/25/05 - 20050187717 - Method and apparatus for integrated modeling, simulation and analysis of chemical and biochemical reactions
An integrated system for modeling, simulating and analyzing chemical and biochemical reactions includes a modeling environment for constructing a model of a chemical or biochemical reaction. The system also includes a simulation engine accepting as input said constructed model of the chemical or biochemical reaction and generating as output an ...

08/25/05 - 20050187716 - Three-dimensional model of a fc region of an ige antibody and uses thereof
The present invention includes three-dimensional models of antibodies, such as Fc-Cε3/Cε4 regions of IgE antibodies, as well as methods to produce such models. The present invention also includes muteins having increased stability and/or antibody receptor binding activity, as well as methods to produce such muteins, preferably using information derived from ...

08/18/05 - 20050182570 - Process for identifying similar 3d substructures onto 3d atomic structures and its applications
The invention pertains to the field of structural biology and relates to a process to compare various three-dimensional (3D) structures and to identify functional similarities among them. The process of comparison of 3D atomic structures of the invention is based on the comparisons of defined chemical groups onto the 3D ...

08/18/05 - 20050182569 - Method for testing for bioaccumulation
For use in estimating or predicting bioaccumulation of a chemical analyte, even a surfactant, log Pow values for the analyte may be determined by calculating the log of the ratio of the concentrations of the analyte in n-octanol and in water, equilibrated using a slow-stir method. In this method, samples ...

08/18/05 - 20050182568 - Method for evaluating a patients biological condition
This invention is concerned with a method for evaluating the dynamic biological state of a patient, said method, which involves measuring several elements or substances contained in the blood and interpreting results of the measurements carried out, comprising the following steps (1°) taking a sample of blood from the patient ...

08/18/05 - 20050182567 - Notebook computer keyboard system
A modular laptop computer for accommodating selective placement and customization of user interface components. The computer includes a cavity having a connection or interface or coupling region, such as a universal serial bus jack for connecting to or mating with a corresponding interface on each component. The interface connections in ...

08/11/05 - 20050177314 - System and method for signal matching and characterization
A system and method for selecting a best match of a received input signal from a set of candidate signals, wherein two or more of the candidate signals are uncorrelated. In a preprocessing phase a signal transform (UST) is determined from the candidate signals. The UST converts each candidate signal ...

08/11/05 - 20050177313 - Method, device and computer program for selecting an intraocular lens for an aphakic eye that has previously been subjected to refractive surgery
A method for selecting an intraocular lens for an aphakic eye that has previously been subjected to refractive surgery by calculating the required power of an IOL to provide the desired refraction using a known formula, and then applying an adjustment based upon the spherical equivalence of the eye prior ...

08/11/05 - 20050177312 - Real-time medical data recording system and method
A medical data recording system and method for real-time storage of medical data received from a plurality of different sources. The system includes a router including an output and a plurality of inputs for connection to a plurality of different medical data sources, and operable to selectively route medical data ...

08/11/05 - 20050177311 - Information server with a database of information about particular locations and a telephone for remotely accessing and querying the same
An information server and corresponding telephone are disclosed wherein the server containing a database of records with each record being identified by a location tag and containing information about a particular location; and wherein at least some of the location tags are neither descriptive of the name of organisations which ...

08/04/05 - 20050171701 - System and method for identifying, reporting, and evaluating presence of substance
A system and method for identifying, reporting, and evaluating a presence of a solid, liquid, gas, or other substance of interest, particularly a dangerous, hazardous, or otherwise threatening chemical, biological, or radioactive substance. The system comprises one or more substantially automated, location self-aware remote sensing units; a control unit; and ...

07/28/05 - 20050165557 - Framework for a biopharmaceutical value chain
An information management framework includes a network of connected processors, an application data server connected to the network, and an infrastructure for interfacing with the application data server. The framework includes a first client accessing the application data server through the infrastructure and making drug candidate data available on the ...

07/28/05 - 20050165556 - Colon cancer biomarkers
Systems and methods for enhancing knowledge discovery from data using multiple learning machines in general and multiple support vector machines in particular. Training data for a learning machine is pre-processed in order to add meaning thereto. Multiple support vector machines, each comprising distinct kernels, are trained with the pre-processed training ...

07/21/05 - 20050159896 - Apparatus and method for analyzing data
In a data analysis system for determining a correlation model between biological conditions and expression levels of a plurality of genes and/or quantities of intracellular substances, A data set is constructed by using the biological conditions or changes of the biological conditions probabilistically generated with time as object variables, and ...

07/14/05 - 20050154537 - Methods, program products, and systems for single and multi-agent dosing and other related methods
Methods, program product, and systems for single and multi-agent dosing are provided. An embodiment of a method for revising a cycle dose of at least one agent for a patient receiving a single or multi-agent therapy includes accepting as a first input the patient's cycle dose(s) of the at least ...

07/14/05 - 20050154536 - Two-part drug discovery system
A mathematical prognostic in which changes in a number of physiologically significant factors are measured and interpolated to determine a “damage fluction” incident to bacterial infection or other serious inflammation, followed by either or both of in vitro or in vivo investigations of a particular active agent (drug) and adjustment ...

07/14/05 - 20050154535 - Method, system and apparatus for assembling and using biological knowledge
Disclosed are methods, systems and apparatus for constructing assemblies of biological knowledge constituting a biological knowledge base, and for subsetting and transforming life sciences-related data and information into biological models to facilitate computation and electronic reasoning on biological information. A subset of data is extracted from a global knowledge base ...

07/14/05 - 20050154534 - Automated media optimization technology
An automated system and method for identifying agents capable of eliciting a phenotypic change in a cell-type. The method includes the steps of providing a statistical design including generic factor names, factor levels and experimental runs, and utilizing a software program to generate a computer representation of the statistical design ...

07/14/05 - 20050154533 - Common protein surface shapes and uses therefor
A method of determining common three-dimensional structural features of protein surfaces is provided, as is use of representations of these common structures in molecular database searching and in designing focussed molecular libraries. The method is particularly concerned with the analysis and representation of protein surfaces such as b-turns, loops and ...

07/07/05 - 20050149270 - Componentware creating method, apparatus and recording medium
It is an object to shorten a time required for a processing of linking components and to reduce the amount of a memory to be used during the linkage. When creating a component to be referred to another component, a declaration of a symbol in a source file is converted ...

07/07/05 - 20050149269 - Browsable database for biological use
The browsable database can allow for high-throughput analysis of protein sequences. One helpful feature may be a simplified ontology of protein function, which allows browsing of the database by biological functions. Biologist curators may have associated the ontology terms with Hidden Markov Models (HMMs), rather than individual sequences, so that ...

07/07/05 - 20050149268 - Methods of data analysis using ranks
Methods of analyzing data using ranks comprise ranking a set of captured data, comparing the ranked set of captured data to another set of ranked data, determining the change in rank between the sets, and defining the change in rank by statistical analysis. ...

06/30/05 - 20050143932 - Meal planning tool
The present invention provides methods, systems, and products which overcome the problems of achieving and maintaining an adequate weight loss in the context of an existing obesity. The present invention makes dietary meal planning easier by eliminating the need to calculate the recommended daily calorie intake. ...

06/30/05 - 20050143931 - System and methods for non-targeted processing of chromatographic data
Methods are provided for non-targeted processing of hyphenated chromatographic data, such that even when the data represent a complex mixture of unknown components, a comprehensive number of the components are detected with minimal information loss and introduction of error. Processing hyphenated chromatographic data by the present methods is compatible with ...

06/30/05 - 20050143930 - Method of acquiring a set of specific elements for discriminating sequence
To provide a method of accurately and efficiently acquiring a candidate for a set of discrimination elements for identification. Provided is a method of acquiring a set of specific elements on a specific sequence for discriminating the specific sequence from a number of sequences, including the steps of acquiring a ...

06/30/05 - 20050143929 - Protein engineering with analogous contact environments
The invention relates to novel methods for engineering protein sequences using structural and homology information. ...

06/30/05 - 20050143928 - Method and apparatus for discovering patterns in binary or categorical data
The present invention relates to a computationally efficient method of finding patterns in any data that can be expressed in the form of arrays of binary features or arrays of categorical features. This includes data represented by continuous-valued attributes that can be transformed to a categorical representation, such as the ...

06/30/05 - 20050143927 - Method for estimating or predicting the anti-tumor activity of a compound and for estimating or predicting the tumor growth in mammals
The present invention relates to a method for estimating or predicting anti-tumor activity of a compound and for estimating or predicting the tumor growth in mammals; the estimation comprises a) measuring the tumor weight in time; b) measuring the concentration of the compound in time; c) calculating kinetic parameters of ...

06/30/05 - 20050143926 - Method and apparatus for generating biologically-active-substance candidate structure, and computer product
Compound fragments in a fragment library are input into an active site to perform initial packing. Using a field of force in which atoms repel each other when they are close energetically and attract each other when they are away, so-called shaking is performed by MD calculation, thereby stabilizing the ...

06/30/05 - 20050143925 - Safety test support system, method and program
A safety test support system comprises application storage 5, an application activating means 7, check program storage 17 and an inspection conducting means 19. The application storage 5 stores applications for safety tests, which are functionally partitioned according to data items and/or operations. The application activating means 7 activates at ...

06/23/05 - 20050137808 - Method for conceptualizing protein interaction networks using gene ontology
Provided is a method for conceptualizing protein interaction networks. The method conceptualizes and simplifies complicated and enormous protein interaction networks wherein the method comprises the steps of (a) conceptualizing protein nodes that form the protein interaction network as gene ontology concepts to reconfigure the network; (b) integrating nodes including the ...

06/23/05 - 20050137807 - Method of visualization of the adme properties of chemical substances
A method is described for selecting chemical compounds and visualizing their ADME properties using an indication-specific target profile. In one embodiment, the method comprises determining and/or selecting molecular properties of one or more compounds in a computer database. This information is used to generate one or more ADME maps describing ...

06/23/05 - 20050137806 - Characterizing biological stimuli by response curves
A method for calculating distances between stimulus response curves (e.g., dose response curves) allows classification of stimuli. The response curves show how the phenotype of one or more cells changes in response to varying levels of the stimulus. Each “point” on the curve represents quantitative phenotype or signature for cell(s) ...

06/23/05 - 20050137805 - Gene expression profiles that identify genetically elite ungulate mammals
Genetically elite ungulate mammals are identified on the basis of gene expression profiles from biological samples such as liver and blood. Methods and compositions are presented to select genetically elite animals with a desired phenotype such as high milk production for breeding to improve production levels. A method to select ...

06/16/05 - 20050131650 - Method and system for interaction analysis
The invention relates to a computer-implemented method for determining at least one kinetic parameter for the interaction of an analyte in solution with an immobilized ligand from a data set comprising a plurality of different binding curves, each of which represents the progress of the interaction of the analyte with ...

06/16/05 - 20050131649 - Advanced databasing system for chemical, molecular and cellular biology
The present invention relates to systems and methods for biomedical drug research, addressing major molecular, cell biological and biochemical information management issues within drug discovery and basic biomedical science. The invention allows scientists to enter biological, chemical, and/or molecular data into a central database, analyze the data entries according to ...

06/16/05 - 20050131648 - Screening assays for agonists or antagonists of cd40 signaling
The present invention provides methods for identifying a molecule that antagonizes or agonizes CD40 activity by screening for molecules that modulate the binding of NEMO and CYLD. Also provided are assays useful in screening for the binding of NEMO and CYLD and databases and methods useful for analyzing the resultant ...

06/16/05 - 20050131647 - Calculating confidence levels for peptide and protein identification
Computer programs and methods for defining a misidentification probability for an experimental protein divisible into experimental peptides. The invention receives data representing a set of matches of experimental peptides to reference peptides that can be derived from a protein in a database of proteins; calculates a probability of observing by ...

06/09/05 - 20050125158 - Generating a mathematical model for diabetes
A mathematical model specifically for diabetes may be generated which may be continuous in time, in that there are no discrete time steps, and any event can occur at any times. The model may be generated using differential equations, object oriented programming, and features. The model may be used to ...

06/02/05 - 20050119835 - Method and apparatus for analysis of molecular combination based on computational estimation of electrostatic affinity using basis expansions
A method and apparatus for analysis of molecular combinations featuring two or more molecular subsets is described. The computational method estimates the electrostatic affinity of the system via utilization of a basis expansion representing charge density and electrostatic potential functions associated with the first and second molecular subsets in a ...

06/02/05 - 20050119834 - Method and apparatus for analysis of molecular combination based on computations of shape complementarity using basis expansions
A method and apparatus for analysis of molecular combinations featuring two or more molecular subsets is described. The method computes the shape complementarity of the system utilizing a basis expansion representing molecular shapes of the first and second molecular subsets in a coordinate system. The precomputed sets of translated expansion ...

06/02/05 - 20050119833 - Health monitor system and method for health monitoring
A mobile health monitor system that includes at least one physiological data sensor; at least one biomechanical data sensor; and a processing unit for correlating between physiological data and biophysical data. A method for health monitoring that includes: determining an occurrence of a measurement-initiating event; initiating an additional measurement in ...

06/02/05 - 20050119832 - Computer system and method for calculating adme properties
The invention relates to a computer system and a method for calculating an ADME property of a substance, which comprises the following steps: a. input of molecular properties of said substance into a biophysical model, whereby said biophysical model describes a correlation between the molecular properties and the ADME property ...

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