Abstract: The present invention provides prognostic methods for conditions such as cancer, for example, breast cancer, comprising classifying an individual by a plurality of phenotypic, genotypic or clinical characteristics of the condition into a plurality of patient subsets, and analyzing the pattern of expression of prognosis-informative genes identified for that subset in a sample from the individual. The present invention also provides methods for constructing such patient subsets and of identifying prognosis-informative genesets for such subsets. The invention further provides methods of assigning a therapeutic regimen to an individual, microarrays useful for performing prognosis, kits comprising these microarrays, and computer systems and programs for implementing the methods of the invention.

Abstract: The invention provides molecular markers that are associated with the progression of chronic myeloid leukemia (CML), and methods and computer systems for monitoring the progression of CML in a patient based on measurements of these molecular markers. The present invention also provides CML target genes, and methods and compositions for treating CML patients by modulating the expression or activity of these CML target genes and/or their encoded proteins. The invention also provides genes that are associated with resistance to imatinib mesylate (Gleevec™) treatment in CML patients, and methods and compositions for determining the responsiveness of a CML patient to imatinib mesylate treatment based on measurements of these genes and/or their encoded proteins. The invention also provides methods and compositions for enhancing the effect of Gleevec™ by modulating the expression or activity of these genes and/or their encoded proteins.

Abstract: A method of: submitting reference sequences to a taxonomic database to produce taxonomic results; and reporting a taxonomic identification based on the taxonomic results. The reference sequences are the output of genetic database queries that return a score for each reference sequence. A method for processing a biological sequence obtained from an assay by: converting base calls located in a predetermined list of positions within the biological sequence to N; and determining the ratio of single nucleotide polymorphisms in the biological sequence relative to a reference sequence. Each entry in the predetermined list of positions represents the capability of a substance hybridizing to a microarray used to generate the biological sequence. The substance is not the nucleic acid of a target pathogen.

Abstract: The present invention outlines a novel approach to utilizing the results of genomic sequence information by computer-directed polynucleotide assembly based upon information available in databases such as the human genome database. Specifically, the present invention may be used to select, synthesize and assemble a novel, synthetic target polynucleotide sequence encoding a target polypeptide. The target polynucleotide may encode a target polypeptide that exhibits enhanced or altered biological activity as compared to a model polypeptide encoded by a natural (wild-type) or model polynucleotide sequence.

Abstract: A method and system for determining whether a sequence fragment g is atypical with respect to a reference sequence G using compositional methods and including constructing a template from G and g respectively containing a sequence of characters for a comparison with one another, wherein a number of characters contained in the template exceeds two. For the case where the sequences at hand are genetic, the atypicality detection can be used to determine whether a given sequence fragment g is the result of a horizontal transfer event.

Abstract: The present invention provides a method for identifying siRNA target motifs in a transcript using a position-specific score matrix approach. The invention also provides a method for identifying off-target genes of an siRNA using a position-specific score matrix approach. The invention further provides a method for designing siRNAs with higher silencing efficacy and specificity. The invention also provides a library of siRNAs comprising siRNAs with high silencing efficacy and specificity.

Abstract: The present invention provides a weight loss maintenance system. The invention incorporates supplements (dietary, pharmaceutical or neutraceutical) that aid in maintaining weight loss as well as physical activity. The invention further provides a personal plan that can include instruction, ideas and support based on user input, indicated preferences and various calculations. This invention calculates an Energy Gap™ that is produced by a specific amount of weight loss in an individual and fills this quantitative energy gap with activity and/or products which reduce hunger and/or increase metabolic rate.

Abstract: A system and method to search spectral databases to identify unknown materials, specifically pathogenic microorganisms. A library is provided, having sublibraries containing reference data sets of known materials and test data sets, both generated by at least one spectroscopic data generating instrument. For each test data set, each sublibrary associated with the instrument used is searched. A set of scores for each searched sublibrary is produced, representing the likelihood of a match between the reference data set and test data set. Relative probability values are calculated for each searched sublibrary. All relative probability values are fused producing a set of final probability values, used in determining whether the unknown material is represented through a known material in the library. The known material represented in the libraries having the highest final probability value is reported, if the highest final probability value is greater than or equal to the minimum confidence value.

Abstract: Combinations, called matrices with memories, of matrix materials with remotely addressable or remotely programmable recording devices that contain at least one data storage unit are provided. The matrix materials are those that are used in as supports in solid phase chemical and biochemical syntheses, immunoassays and hybridization reactions. The matrix materials may additionally include fluophors or other luminescent moieties to produce luminescing matrices with memories. The data storage units are non-volatile antifuse memories or volatile memories, such as EEPROMS, DRAMS or flash memory. By virtue of this combination, molecules and biological particles, such as phage and viral particles and cells, that are in proximity or in physical contact with the matrix combination can be labeled by programming the memory with identifying information and can be identified by retrieving the stored information. Combinations of matrix materials, memories, and linked molecules and biological materials are also provided.

Abstract: Clinical samples can be analyzed using microparticles to determine the serodiagnosis of a viral infection from two candidate viral infections of the same viral group. Serodiagnosis can be determined via a pooled population of subsets of microparticles, with the particles in the pooled population having a bound viral group-reactive antibody and the particles in each subset having at least one characteristic classification parameter that distinguishes between subsets. Viral antigens of antibodies of interest in the same viral-class as the viral group-reactive antibody can be bound to the viral group-reactive antibody on the microparticles, and subsequently exposed to a clinical sample. Binding and labeling can be used. Automated analysis of data from multiplexed flow analysis can determine the presence or absence of antibodies of interest in the sample, thereby diagnosing for two candidate viral infections in a single assay.

Abstract: A method of easily and speedily determining what structural change is experienced by a target protein upon contact and binding of any arbitrary compound to the target protein; a method of selecting and screening a compound for use in the method; and a computer program for carrying out these methods. In one embodiment, a Saupe order matrix element of domain is obtained from atomic coordinates of domain and an axial-direction variation of NMR signal dependent upon the orientation angle of molecule in magnetic field, and the matrix is diagonalized to thereby obtain the orientation information on the domain. Using of any change of the orientation information as an indicator for structural change enables realization of the intended easy and speedy measurement of structural change of the target protein.

Abstract: A system for generating optimized values for variable inputs to an animal production system. The system includes a simulator engine configured to receive a plurality of animal information inputs and generate a performance projection. At least one of the animal information inputs is designated as a variable input. The system further includes an enterprise supervisor engine configured to generate first and second optimized values for the at least one variable input. The first optimized value is generated based on an optimization criteria and the second optimized value is generated based on empirical feedback after application of the first variable input.

Abstract: A method of morphological reconstruction of biological activity in a tissue sample maps biological data resulting from analysis of tissue samples onto a 3-D morphological rendering of the biological sample. Each slice in a set of histological slices, indexed by a first index, is micro dissected into micro samples indexed by a pair of first and second indices. The indices are utilized to spatially map biological data to the 3-D rendering.

Abstract: Psychopharmacological properties of new therapeutic drugs and highly heritable behavior patterns of test subjects are identified based on analysis of monitored exploratory movement to identify behavioral signatures. A test subject in a pen is allowed to explore for a period of time, after injecting it with a candidate drug or control vehicle. The test subject's movement is monitored and its locations stored. The locations are analyzed to separate them into behavioral patterns that are defined based on combinations of behavioral feature. Relative frequencies of performing each behavioral pattern are determined. In each pattern, differences between the relative frequencies in the candidate drug and control groups are tested, and only patterns in which this difference is highly significant are retained.

Abstract: A data classification supporting method capable of easily discriminating a cell to which unknown data belongs and cells similar to the unknown data from each other is obtained. This classification compares cell vector data of each cell with the unknown data, decides a cell having cell vector data closest to the unknown data and cells having cell vector data secondly to nthly close to the unknown data as a minimum cell and similar cells respectively and displays a minimum cell mark and similar cell marks indicating the minimum cell and the similar cells respectively on a classification map.

Abstract: A system for screening nucleotide sequences, a method therefor, a program, a recording medium, and a server on which the screening of nucleotide sequences is executed. The solution comprises a step of storing target nucleotide sequence data and a probe nucleotide sequence, a step of generating complementary sequence data from a probe nucleotide sequence that may be bound to the target nucleotide sequence, and storing a maximum acceptable edit distance between the target nucleotide sequence and the probe nucleotide sequence, a step of reading out each nucleotide sequence data and the maximum edit distance from each storing unit, and evaluating the binding possibility of the target nucleotide sequence data and the complementary sequence data in descending order of edit distance, and a step of storing the result of the binding evaluation in a storage unit.

Abstract: A method for non-targeted complex sample analysis which involves the following steps. A first step involves providing a database 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 to obtain data regarding the molecules in the complex sample with the identifying data of known molecules in order to arrive at an identification through comparison of the molecules in the sample.

Abstract: A method of designing probes for detecting a target sequence and a method of detecting the target sequence using the probes are provided. The method of designing probes for detecting target sequence includes: selecting an anchoring location in the target sequence; selecting a first probe designing region; selecting a matched probe; and selecting a mismatched probe.

Abstract: A system for screening nucleotide sequences, a method therefor, a program, a recording medium, and a server on which the screening of nucleotide sequences is executed. The solution comprises a step of storing target nucleotide sequence data and a probe nucleotide sequence, a step of generating complementary sequence data from a probe nucleotide sequence that may be bound to the target nucleotide sequence, and storing a maximum acceptable edit distance between the target nucleotide sequence and the probe nucleotide sequence, a step of reading out each nucleotide sequence data and the maximum edit distance from each storing unit, and evaluating the binding possibility of the target nucleotide sequence data and the complementary sequence data in descending order of edit distance, and a step of storing the result of the binding evaluation in a storage unit.

Abstract: Method of preparing a calibration curve and determining the amount of an analyte polynucleotide present in a test sample, particularly using real-time amplification data. The method involves determining indicia of amplification for both the internal calibrator and analyte polynucleotide standards, each as a function of the amount of analyte polynucleotide standard input into the amplification reaction.