Abstract: A method of insuring the integrity of a plurality of updates brought in real-time to a production database concurrently used by one or more software applications is described. The production database includes a plurality of products participating to the definition of objects. The method first includes requesting the issuance of a unique filing number associated to a draft state version of the plurality of updates while keeping them invisible to the end-users of the production database. Then, a set of product items identified as a whole by the unique filing number are created or copied from the production database and gathered under the form of a meta-product on which the plurality of updates is applied. After updating, the meta-product is successively set into a customizable flow of one or more validation states in order to perform a cross-validation of the plurality of updates.

Abstract: The present invention concerns a method for prediction and identification of microRNA precursors (pre-microRNA) and microRNA molecules using data processing programs and databases. The invention also pertains to the isolated form of these pre-microRNAs, microRNA molecules and derived nucleic acids there of. The invention also relates to recombinant vector, host cell, support, pharmaceutical composition or kit comprising such microRNA molecules or there of derivated molecules. The invention also applies to the use of such microRNA molecules and/or their identified targets in research, prognostic, diagnostic tools/methods as well as for therapeutic applications.

Abstract: A method (and an article of manufacture having computer readable program code to implement the method) is disclosed to version a node range and locate a versioned node range in a storage architecture, wherein the method comprises: maintaining a set of node ranges, with each node range being formed from a range of node ID values assigned to each node among a plurality of nodes, receiving a node modification request for a node range from a database system, versioning the node range by copying (to a storage) a node range to which the node modification request is to be made, labeling the copied node range with a timestamp, locating the labeled node range via the timestamp and a hash on the node range, and outputting the located labeled node range. Optionally, versioning is done by shadowing nodes in the range to a version hash table based on a range identifier.

Abstract: The invention relates a method of quantifying CD64 and CD163 expression in leukocytes and, specifically to a kit for use with a flow cytometer including a suspension of quantitative fluorescent microbead standards, fluorescent labeled antibodies directed to CD64 and CD163, and analytical software. The software is used to take information on the microbead suspension and fluorescent labeled antibodies from a flow cytometer and analyse data, smooth curves, calculate new parameters, provide quality control measures and notify of expiration of the assay system.

Abstract: Provided is a member or content search method in a virtual private community (VPC) network including at least one of a first VPC including communication devices owned by a predetermined user, a second VPC that may be positioned in an upper layer of the first VPC, and a third VPC that may be positioned in an upper layer of the second VPC, the method including receiving, by one of the communication devices, a search request comprising one of VPC identifiers of a user, verifying a VPC corresponding to the VPC identifiers that may be included in the search request, in response to the search request, and searching for members included in the verified VPC, a VPC positioned in a lower layer of the verified VPC, or contents owned by the members included in the verified VPC.

Abstract: Embodiments of archival storage system are disclosed. The archival storage system includes one or more removable disk drives that provide random access and are readily expandable. One or more application servers can store archival data to the one or more removable disk drives. Further, the archival storage system provides an audit trail that stores information about actions taken on the archival data. The audit trail data providing a list of the actions and information about the actions that can be used to determine changes to the archival data.

Abstract: Pharmacogenetic methods for determining a predicting responsiveness to antifolate therapy for subjects that present with recent-onset undifferentiated arthritis. The methods are based on the determination of a set of clinical parameter values and determining a predicted responsiveness to antifolate therapy by correlating the parameter values with predefined responsiveness values associated with ranges of parameter values. Parameters values that are decisive for responsiveness to antifolate therapy may include polymorphisms in the methylenetetrahydrofolate dehydrogenase (MTHFD1) gene as well as in three genes involved in the adenosine release pathway, the presence or absence of Rheumatoid factors, gender, pre- or postmenopausal status and/or smoking status.

Abstract: A system is described for ordering oligonucleotides through a network, such as the Internet. The system provides a mechanism for validating the data provided by a customer, and then displaying graphical images to represent any data that has errors. The system can also pool multiple oligonucleotide samples together by providing graphical images representing oligonucleotide containers, and allowing the customer to select the proper containers to pool.

Abstract: A servicing daemon is described herein for providing servicing of a running computer system (such as a filer). The servicing daemon resides and executes on the operating system of the filer and communicates across a network with a debugger that resides and executes on a remote administering computer. A debugging session is performed that complies with a protocol relating to the remote accessing of files. The debugging session provides live servicing of an application executing on the filer without requiring an actual corefile (having copied filer memory data) to be created. Rather, the servicing daemon creates a simulated corefile header that is sent to the debugger, receives requests from the debugger, and maps addresses specified in the requests to filer memory addresses. The servicing daemon then reads and retrieves data directly from filer memory at the determined filer memory addresses and sends the data to the debugger for analysis.

Abstract: The present disclosure relates to methods and systems that may be used for detection of one or more pathogens and determining one or more agents in response to pathogen detection.

Abstract: Generally, computer implemented remote monitoring system which generates a viewable reduced byte data representation for each one of a plurality of analyzed instrument signals. Specifically, a flow cytometer remote monitoring system which generates a viewable reduced byte data representation for each one of a plurality analyzed flow cytometer signals.

Abstract: A correctness verification system receives a query, executes the query using a query logic, and produces a query result. The query result comprises data records that satisfy the query, data verification objects associated with the data records, index segments accessed during the execution of the query, index verification objects associated with the index segments, and the query. The system transfers the query result to a verification system. The verification system verifies correctness of the query result by executing the query using the query logic. The verification system uses the data verification objects to verify integrity of the data objects, uses the index verification objects to verify the integrity of the index segments, and uses the index verification objects and the data verification objects to verify the completeness of the query result.

Abstract: A method provides an index that is indicative of the state of a subject, as to a biological condition, based on a sample from the subject. An embodiment of this method includes: deriving from the sample a profile data set, the profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables evaluation of the biological condition; and in deriving the profile data set, achieving such measure for each constituent under measurement conditions that are substantially repeatable; and applying values from the profile data set to an index function that provides a mapping from an instance of a profile data set into a single-valued measure of biological condition, so as to produce an index pertinent to the biological condition of the subject.

Abstract: 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 sequence data stored in a database, determining a measure of phylogenetic relatedness between the microorganism sample and historical samples stored in the database, and providing infection control information based on the phylogenetic relatedness determination to the health care facility, thereby allowing the health care facility to use the infection control information to control or prevent the spread of an infection.

Abstract: The invention provides a method of determining a comparative expression profile in an individual by comparing the expression levels of a sample of molecules in a population of molecules in a specimen from the individual with a health-associated reference expression region of the sample of molecules, wherein expression levels within the health-associated reference expression region indicate a reference expression profile and wherein expression levels outside the health-associated reference expression region indicate a perturbed expression profile. The invention also provides methods of diagnosing a disease or a health state in an individual by comparing the expression level of a sample of molecules in a specimen from the individual with a health-associated reference expression region of the sample of molecules.

Abstract: Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or comparative genome hybridization microarray, comprising selecting a plurality of potential target sequences, generating a plurality of candidate probes from the target sequences, filtering the plurality of candidate probes by analyzing candidate probes for selected probe properties in silico. Microarrays comprising probes selected by the methods of the invention are particularly useful for comparative genome hybridization and location analysis.

Abstract: Methods and systems for evaluating biological dataset profiles relating to asthma and other atopic conditions are provided, where datasets comprising information for multiple cellular parameters are compared and identified, and used in the evaluation of candidate pharmacologic agents for suitability as therapeutic agents.

Abstract: The present invention encompasses utilizing a model of disease, immune response, and dynamic (time-dependent) drug therapy. In the embodiments an optimal dynamic therapy from one or more compounds is selected for the treatment of infectious disease.

Abstract: A data validation system and method for a fully or partially automated docket management solution. The system may require single-user double entry and/or double user data re-entry for validation and confirmation of data content. Un-validated/un-confirmed data may be quarantined or otherwise hidden from part or all of the rest of the docket management system.

Abstract: Disclosed are methods of identifying microRNA motifs or microRNA precursors for a target gene or a set of target genes. Also disclosed are related computer-readable media.

Abstract: A computerized system and method of building a system of test components for an orderable healthcare procedure is provided. An orderable healthcare procedure is received and associated with a discrete ontology concept. An ontology is traversed for the discrete ontology concept to identify test components related to the discrete ontology concept. The test components related to the discrete ontology concept are identified.

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: Methods of evaluating candidate CGH probe nucleic acid sequences are provided. Aspects of the methods include providing a candidate CGH probe nucleic acid sequence for a target sequence of a copy number variation (CNV) of a genome. A proximity score is then determined for the candidate CGH probe nucleic acid sequence and employed to evaluate the sequence. Aspects of the invention further include computer programming and systems that include the same which are configured to evaluate candidate CGH probe nucleic acid sequences using a proximity score.

Abstract: The present invention relates to genetic analysis and evaluation utilizing copy-number variants or polymorphisms. The methods utilize array comparative genomic hybridization and PCR assays to identify the significance of copy number variations in a subject or subject group.

Abstract: The present invention relates to a method and system for determining whether an ordered genetic test will duplicate at least one existing genetic test result. The method includes receiving an ordered genetic test that is for a particular genetic sequence or variant thereof for an individual. The method further includes determining whether the individual has at least one existing genetic test result for the particular genetic sequence or variant thereof. Upon determining that the individual has at least one existing genetic test result for the particular genetic sequence or variant thereof, a notification of the existence of the at least one existing genetic test result is provided.

Abstract: Disclosed are methods of identifying microRNA motifs or microRNA precursors for a target gene or a set of target genes. Also disclosed are related computer-readable media.

Abstract: The present invention provides methods for the assessment of diseases that result from the combined or interactive effects of two or more genetic variants, and in particular for diagnosing risk of developing such diseases in subjects using an analysis of genetic polymorphisms. Methods for the derivation of a net score indicative of a subject's risk of developing a disease are provided.

Abstract: Detailed information of each analysis subject partial network is displayed on a left pane of a screen. The detailed information includes the number of nodes, the number of edges, and accumulative coverage of the analysis subject partial network for each disease. Based on the detailed information, a user can designate the analysis subject partial network of a disease the user wishes to analyze. When the user has designated the disease, a network diagram indicating a partial network related to the designated disease is displayed on a right pane.

Abstract: Methods and compositions for the identification of breast cancer grade signatures are provided. The signature profiles are identified based upon multiple sampling of reference breast tissue samples from independent cases of breast cancer and provide a reliable set of molecular criteria for identification of cells as being in one or more particular stages and/or grades of breast cancer.

Abstract: A method of determining kinetic parameters for a reversible molecular interaction between a ligand immobilized to a solid support surface and a binding partner to the ligand in solution, comprises sequentially, without intermediate regeneration or renewal of the immobilized ligand, flowing a plurality of fluid volumes containing different known concentrations of the binding partner over the solid support surface, monitoring the momentary amount of binding partner bound to the solid support surface related to time and solution concentration of binding partner and collecting the binding data, and determining the kinetic parameters by globally fitting a predetermined kinetic model for the interaction between the binding partner and the immobilized ligand to the collected binding data, which model allows for mass transport limitation at the solid support surface.

Abstract: The present invention provides systems and methods that utilize an information architecture for disambiguating scientific names and other classification labels and the entities to which those names are applied, as well as a means of accessing data on those entities in a networked environment using persistent, unique identifiers.

Abstract: An apparatus and method for performing similarity searching on a data stream with respect to a query string are disclosed, where the data stream comprises a plurality of data substrings, and where the query string comprises a plurality of query substrings. A programmable logic device is used to filter the data stream to find a plurality of possible matches between the data substrings and a plurality of the query substrings, wherein the data substrings and the query substrings comprise a plurality of characters. From these possible matches, a determination can be made as to a similarity between the query string and at least a portion of the data stream.

Abstract: The present invention provides methods for analyzing a combination of biomarkers to individualize tyrosine kinase inhibitor therapy in patients who have been diagnosed with cancer. In particular, the assay methods of the present invention are useful for predicting, identifying, or monitoring the response of a tumor, tumor cell, or patient to treatment with a tyrosine kinase inhibitor using an algorithm based upon biomarker profiling. The assay methods of the present invention are also useful for predicting whether a patient has a risk of developing toxicity or resistance to treatment with a tyrosine kinase inhibitor. In addition, the assay methods of the present invention are useful for monitoring tyrosine kinase inhibitor therapy in a patient receiving the drug to evaluate whether the patient will develop resistance to the drug.

Abstract: A robust classification method for cancer detection from mass spectrometry data includes inputting the mass spectrometry data, preprocessing the spectrometry data, conducting robust feature selection, generating predictions for the test data sets using multiple data classifiers, the multiple data classifiers including artificial neural networks, support vector machines, weighted voting on data patterns, classification and regression trees, k-nearest neighbor classification, and logistic regression, and constructing and validating a meta-classifier by combining individual predictions of the multiple data classifiers to generate a robust prediction of a phenotype. The test data sets are used exclusively for validation of the meta-classifier.

Abstract: The present embodiments relate to a system and method of measuring the methylation level of DNA. Some embodiments relate to a system and method of measuring methylation level of DNA with a gene array.

Abstract: The invention relates to a method of updating a data storage system. The method updates a raw database using an input data stream based on an input temporal value associated with the input data stream and a raw temporal value associated with the raw database. The method includes updating a derived database associated with the data storage system using the updated raw database based on the input temporal value, a derived temporal value and a user-defined relationship, the derived temporal value being associated with the derived database. The invention also relates to a computer-readable medium. The computer readable medium including instructions, wherein execution of the instructions by at least one computing device updates a data storage system. The invention further relates to a data storage system. The system includes a raw database, a derived database and a computing device operatively coupled to the raw database and the derived database.

Abstract: A query generation using cardinality constraints process including choosing a first set of parameters for a query, calculating an additional set of parameters based on the first set of parameters, executing the query using additional set of parameters, evaluating the cardinality error the additional set of parameters, and refining the additional set of parameters to meet the desired cardinality constraint. Creating a query and selecting parameters for the query to meet a desired cardinality constraint or set of cardinality constraints when the query is executed against a database may be difficult. A query generation using cardinality constraints process may create a set of parameters for a query which satisfies a desired cardinality constraint or set of cardinality constraints. An application of such a query generation using cardinality constraints process may be database component and code testing.

Abstract: Methods and apparatus teach a digital spectrum of a data file. The digital spectrum is used to map a file's position in multi-dimensional space. This position relative to another file's position reveals closest neighbors. Certain of the closest neighbors are grouped together, while others are differentiated. Grouping ceases upon application of a stopping function so that rightly sized, optimum numbers of file groups are obtained. Embodiments of stopping functions relate to curve types in a mapping of numbers of groups per sequential rounds of grouping, recognizing whether groups have overlapping file members or not, and/or determining whether groups meet predetermined numbers of members, to name a few. Properly grouped files can then be further acted upon.

Abstract: The present invention provides methods, systems, and code for accurately classifying whether a sample from an individual is associated with inflammatory bowel disease (IBD) or a clinical subtype thereof. In particular, the present invention is useful for classifying a sample from an individual as an IBD sample using a statistical algorithm and/or empirical data. The present invention is also useful for differentiating between a clinical subtype of IBD such as Crohn's disease (CD) and ulcerative colitis (UC) using a statistical algorithm and/or empirical data. Thus, the present invention provides an accurate diagnostic prediction of IBD or a clinical subtype thereof and prognostic information useful for guiding treatment decisions.

Abstract: A method, system and computer program product for confirming the validity of data returned from a data store. A data store contains a primary data set encrypted using a first encryption and a secondary data set using a second encryption. The secondary data set is a subset of the primary data set. A client issues a substantive query against the data store to retrieve a primary data result belonging to the primary data set. A query interface issues at least one validating query against the data store. Each validating query returns a secondary data result belonging to the secondary data set. The query interface receives the secondary data result and provides a data invalid notification if data satisfying the substantive query included in an unencrypted form of the secondary data result is not contained in an unencrypted form of the primary data result.

Abstract: Least Square Deconvolution (LSD) uses quantitative allele peak data derived obtained from a sample containing the DNA of more than one contributor to resolve the best-fit genotype profile of each contributor. The resolution is based on finding the least square fit of the mass ratio coefficients at each locus to come closest to the quantitative allele peak data. Consistent top-ranked mass ratio combinations from each locus can be pooled to form at least one composite DNA profile at a subset of the available loci. The top-ranked DNA profiles can be used to check against the profile of a suspect or be used to search for a matching profile in a DNA database.

Abstract: The present invention provides a system and method for targeting content to audiences. The audience is defined by rules that may be based on properties as well as organizational structure associated with the users. Each of the rules is compiled to determine the group of members belonging to the rule. Logical operators are then applied to the groups to determine the audience membership. Compiling the rules enhances performance as the rules do not have to be run each time. Instead, a simple check against the rules results is performed. The rules making up the audience may be compiled at predetermined times in order to keep the audience up-to-date. Audiences are then selected and tagged to content so that the content may be viewed by the selected audiences.

Abstract: A system for analyzing a document in a repository is provided. The system receives a document that includes data and a document type. The document type has an associated physical structure. The system determines a logical structure of the document based in part on the data and selects a subset of the data based on at least one of the group including the associated physical structure and the logical structure. The system also stores a document segment that includes the selected subset of the data.

Abstract: A read-write access to a file in a file server includes an initial metadata access step, an asynchronous read or write of file data, and a metadata commit step. In order to parallelize access to a range locking database, an inode and indirect file block mapping database, and a pre-allocation data base, operations are pipelined within the metadata access step and also within the metadata commit step. The pipelined operations within the metadata access step include a first stage of range locking, a second stage of reading block mapping metadata, and a third stage of reading and updating a pre-allocation map for write access. The pipelined operations within the metadata commit step include a first stage of releasing range locks, a second stage of accessing old block metadata for write access, and a third stage of updating metadata and flushing the pre-allocation map for write access.

Abstract: A database comprises a database interface and a database updater. The database interface receives a first set of information and a second set of information to be updated in the database. The database updater updates a second set of information in the database based at least in part on a condition that a first set of information in the database has been previously updated.

Abstract: A database comprises a database interface and a database updater. The database interface enables a reading of a first set of information from the database. The database updater updates a second set of information in the database based at least in part on one or more conditions. The one or more conditions limit changes allowable to the first set of information from the database that occurred after the reading of the first set of information from the database.

Abstract: The disclosed embodiments present a system, method, and computer program product for certifying a timestamp generated by a data processing system. In some embodiments, the method includes receiving a request to certify a timestamp generated by a trusted data processing system, analyzing historical data related to a system time of the data processing system, and certifying the timestamp in response to determining that the historical data indicates a trustworthy system time of the data processing system when the timestamp was generated.

Abstract: An information processor (program processing unit 1) for managing a data sequence in a fixed order comprises a direction array (reference data storage section 2) for storing a reference to each data item of the data sequence in an element of the index associated with the key to the data, and means (CPU 3) for changing all data keys referenced by elements within an arbitrary range of indexes in the direction array by the same amount, where memory contents within the range of the direction array are shifted by the number of indexes corresponding to the changed amount.

Abstract: A dynamic range constraint is defined that has one or more limits that are computed from data residing in the database. In a first embodiment, a dynamic range constraint is defined for a database column that includes at least one limit that is computed from data within that column. In a second embodiment, a dynamic range constraint is defined for a database column that includes at least one limit that is computed from data in a different database column. The limits may be computed using any suitable heuristic or criteria, including statistical analysis of the data in the database. In this manner a range constraint for a column may evolve automatically as the data in the database changes.

Abstract: An application server includes a cache memory that stores in a correlated form a retrieval condition and a retrieval result, an update condition setting unit that sets a cache update condition that indicates when the cache memory is to be updated; and an update processing unit that reads the retrieval condition from the cache memory upon fulfillment of the cache update condition, retrieves data as the retrieval result from the database using the retrieval condition, and updates the retrieval result in the cache memory corresponding to the retrieval condition.