Abstract: A method of treating patients having rheumatoid arthritis by administering Product R, a peptide-nucleic acid preparation, is disclosed.

Abstract: The invention provides a computerized storage and retrieval system for storing biological information organized as a protein pathways database and methods for performing pathway searches on nodes (proteins or other molecules), modes (interactions), and nodes-and-modes. The protein pathways database is a relational database that integrates protein sequence, genomic sequence, gene-expression, protein interactions, protein-protein association and pathway data and can be searched using a query pathway to predict homologous or orthologous nodes, modes, and pathways.

Abstract: An interactive system for facilitating hypothesis construction by correlating and presenting gene expression data, bioassay data, and compound activity data, and associating gene and compound function information with product information, and facilitating product purchase, is disclosed.

Abstract: The invention provides for in silico analysis of a virtual combinatorial library. Mapping coordinates for a training subset of products in the combinatorial library, and features of their building blocks, are obtained. A supervised machine learning approach is used to infer a mapping function ƒ that transforms the building block features for each product in the training subset of products to the corresponding mapping coordinates for each product in the training subset of products. The mapping function ƒ is then encoded in a computer readable medium. The mapping function ƒ can be retrieved and used to generate mapping coordinates for any product in the combinatorial library from the building block features associated with the product.

Abstract: A method and apparatus transforms typically differing length text string representations (i.e., sequences) of biological fragments into uniform length representations. A comparison database stores a predefined number of known biological sequences. A comparison routine compares and scores a subject sequence against each known sequence in the database. Each individual score (one for each known sequence in the database) serves as a vector element forming a fixed length vector representation of the subject sequence. Vector length equals the predefined number of known biological sequences in the database. Scoring is a probability or an occurrence count of the known biological sequence in the subject sequence.

Abstract: Where a DNA chip corresponding to a bacterium that is a subsequently added identification object is produced, temporal and pecuniary cost is reduced, and even where a probe unique to the DNA sequence of an identification object cannot be designed, precision in identifying DNA comprised in a sample is maximized. First, on designing a probe, a plurality of different probes are prepared to one kind of bacterium. Where some probes come to be not available by addition of bacteria that are new identification objects, identification is carried out using the remaining probes. Where a probe unique to an identification target bacterium cannot be designed, a probability of correct identification is increased by using multiple probes. Moreover, in consideration with a possibility that multiple kinds of bacteria simultaneously exist, a combination of probes that maximizes a probability of correct identification is selected.

Abstract: The systems and methods described herein relate to nucleic acid probes comprising a a pattern of universal and designate nucleotides, or ‘gapped’ probes, and the use of sets of gapped probes in sequencing by hybridization to determine the sequence of nucleic acid sequences. The inclusion of universal nucleotides in the probes allows for efficient and rapid sequencing of longer nucleotide sequences than can be sequenced using traditional probes. The systems and methods described herein also relate to apparatus for sequencing nucleic acids which include gapped probes, as well as computer systems capable of analyzing data generated using gapped probes in such apparatus.

Abstract: 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 of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data, The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

Abstract: A method for determining relative incidence of a binding substance within two biological samples is provided. The two samples are labeled with luminescent materials having different chromatic properties. An image of the luminescent materials upon a binding site of a microarray is analyzed as two clusters of data points scattered about respective representative pairs of chromatic intensity values. The relative incidence of the binding substance is determined as a ratio of differences between corresponding indices of the representative pairs.

Abstract: A statistical database system can improve error checking of quality control data used to measure the performance of quantitative analysis equipment. The quality control data can be delivered to a centralized database, wherein the database is linked to error checking functions. Data delivery can be flexible, allowing input via scanning, operator keyed summary data, operator keyed raw data, analyzer direct download, Internet-delivered summary data and Internet-delivered raw data. The received quality control data can be verified against specific lot and analyzer parameters, and data falling outside of these specified ranges can be excluded from a peer group. Excluded data can be verified against original submitted data, and excluded data can then appear on final reports. The quality control data can also be entered directly into the database and a peer group report can then be generated. The quality control data is processed in real time with the data entry and the reports are viewable in real time.

Abstract: Optical scanner system approaches are described in which signal saturation data is produced in real-time. The data generated may be used for tuning a subsequent scan, in protection of optical detector components from damage or otherwise. Approaches for obtaining and storing or expressing the data are also disclosed. Also provided are methods of using the subject system is biopolymer array based application, including genomic and proteomic applications.

Abstract: The use is provided of a composition as a feed additive which comprises one or more endoglucanases, and 0–20% by weight, based upon the content of cellulase proteins in the composition, of a cellobiohydrolase. The endoglycanases may be one or more of EGI, EGII, EGIII and any functionally active derivative of any thereof. Such endoglucanases may be obtained from a genetically modified strain of the fungus Trichoderma. Also provided is an enzyme-based feed additive which comprises EGI and/or EGII which lack the cellulose binding domain, and 0–20% by weight, based upon the content of cellulase proteins in the additive, of a cellobiohydrolase. A further enzyme-based feed additive is provided which comprises a cereal-based carrier, one or more endoglucanases, and 0–20% by weight, based upon the content of cellulase proteins in the additive, of a cellobiohydrolase. Such enzyme-based feed additives can be incorporated into a cereal-based feed which includes one or more of barley, wheat, triticale, rye and maize.

Abstract: A microwave extraction method involves the steps of placing biological material in an enclosure without any solvent whatsoever and exposing the solvent-free biological material to microwave radiation to free at least some of the natural product, and then separating any residual biological material from the extracted natural product. Additionally, the microwave extraction method involves the steps of applying reduced pressure in the enclosure during the microwave radiation stage and heating the enclosure during at least most of the microwave radiation stage to compensate for the temperature drop resulting from water evaporation from the biological material.

Abstract: A method of analyzing an evolution of a biological system comprising the steps of determining a series of variables upon which a state of the biological system depends, mapping the variables to an n-dimensional space, and wherein the evolution of the biological system is monitored utilising a trajectory formed from sets of the variables which define the states of the biological system at different times, thereby using time as a parameter in the n-dimensional space in a manner such that every point on the trajectory corresponds to at least one value of time.

Abstract: A method and system for assisting diagnosis and treatment of temporomandibular joint disease. The steps of the method include recording physical symptoms; conducting a plurality of medical examinations related to temporomandibular joint disease; creating a diagnostic criteria based on conditions known to be a factor in diagnosis of temporomandibular joint disease; and determining which of a plurality of patients match the diagnostic criteria.

Abstract: The invention describes a process for determining a biological state through the discovery and analysis of hidden or non-obvious, discriminatory biological data patterns. The biological data can be from health data, clinical data, or from a biological sample, (e.g., a biological sample from a human, e.g., serum, blood, saliva, plasma, nipple aspirants, synovial fluids, cerebrospinal fluids, sweat, urine, fecal matter, tears, bronchial lavage, swabbings, needle aspirantas, semen, vaginal fluids, pre-ejaculate.), etc. which is analyzed to determine the biological state of the donor. The biological state can be a pathologic diagnosis, toxicity state, efficacy of a drug, prognosis of a disease, etc. Specifically, the invention concerns processes that discover hidden discriminatory biological data patterns (e.g., patterns of protein expression in a serum sample that classify the biological state of an organ) that describe biological states.

Abstract: The present invention relates to a method for gene mapping from chromosome and phenotype data, which utilizes linkage disequilibrium between genetic markers mi, which are polymorphic nucleic acid or protein sequences or strings of single-nucleotide polymorphisms deriving from a chromosomal region. All marker patterns P that satisfy a certain pattern evaluation function e(P) are searched from the data, each marker mi of the data is scored by a marker score and the location of the gene is predicted as a function of the scores s(mi) of all the markers mi in the data.

Abstract: The present invention relates to a method for purifying recombinant HCV single or specific oligomeric envelope proteins selected from the group consisting of E1 and/or E1/E2, characterized in that upon lysing the transformed host cells to isolate the recombinantly expressed protein a disulphide bond cleavage or reduction step is carried out with a disulphide bond cleavage agent. The present invention also relates to a composition isolated by such a method. The present invention also relates to the diagnostic and therapeutic application of these compositions. Furthermore, the invention relates to the use of HCV E1 protein and peptides for prognosing and monitoring the clinical effectiveness and/or clinical outcome of HCV treatment.

Abstract: Newly elucidated sequences of hepatitis C virus type 4 and type 5 are described, together with those of a newly discovered type 6. Unique type-specific sequences in the NS4, NS5 and core regions enable HCV detection and genotyping into types 1 to 6. Antigenic peptides and immunoassays are described.

Abstract: A method of identifying and archiving a nucleic acid sequence includes a) creating a directory of files in a computer, for storing information related to the nucleic acid sequence; b) inputting a raw nucleic acid sequence into the computer; c) trimming the raw nucleic acid sequence to obtain a trimmed nucleic acid sequence; d) submitting the trimmed nucleic acid sequence electronically to a nucleic acid identification database having a search program and receiving search results electronically from the nucleic acid identification database; e) choosing selective information from each search result and inserting the selective information from each search result into a first electronic spreadsheet; and f) selecting at least one of the search results from the first electronic spreadsheet and inserting the at least one search result into a second electronic spreadsheet.