Patents Examined by Mary Zeman
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Patent number: 8428884Abstract: The invention provides a high resolution three-dimensional structure of a deacylated transfer RNA protein synthesis modulator in association with a large ribosomal subunit. The protein synthesis modulator binds at least a portion of the E-site of a large ribosomal subunit. The invention provides methods for designing and/or identifying analogs of candidate molecules, for example, analogs or derivatives of the protein synthesis modulator, that bind and/or modulate the protein biosynthetic activity of the ribosome.Type: GrantFiled: February 29, 2008Date of Patent: April 23, 2013Assignee: Rib-X Pharmaceuticals, Inc.Inventor: Brian T. Wimberly
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Patent number: 8428886Abstract: Determining a genetic sequence for a particular site on an individual's genome is disclosed, including: receiving a measurement associated with a particular sequence for the particular site on the individual's genome, receiving contextual information associated with a context of the individual within a larger collection of genetic information, and using the measurement associated with the particular sequence and the contextual information to compute an improved determination of the genetic sequence at the particular site on the individual's genome.Type: GrantFiled: August 25, 2009Date of Patent: April 23, 2013Assignee: 23andMe, Inc.Inventors: Alexander Wong, Oleksiy Khomenko, Serge Saxonov, Brian Thomas Naughton, Lawrence Hon
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Patent number: 8423296Abstract: The invention provides a method for selecting one or more genes from among a predetermined group of genes whose expression level is significantly different among a first group of individuals in a population in comparison with a second group within the population. The first group of individuals may be, a group of individuals suffering from an illness that responded to a predetermined treatment. The second group of individuals may be a group of individuals suffering from the same illness that did not respond to the treatment.Type: GrantFiled: October 5, 2006Date of Patent: April 16, 2013Assignee: Yissum Research Development Company of the Hebrew University of JerusalemInventor: Yoav Smith
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Patent number: 8412459Abstract: The present invention is related to a method for determining the sensitizing potential of a chemical (test) compound, comprising the steps of: (a) Providing a suitable cell culture of a specific cell type and providing a test sample and a control sample thereof, said test sample and said control sample being identical, (b) Exposing said test sample to a chemical compound in a solvent and exposing said control sample to said solvent for a predetermined period of time, (c) Determining for the test sample and the control sample gene expressions xi for a subset of i=1 to n genes selected from the group of genes corresponding to SEQ ID NOs 1 to 153, (d) For this subset of n genes looking up in a database the gene expressions xi for a set of control and test samples, the test samples being exposed for said predetermined period of time to a set of chemical sensitizing model compounds comprising both sensitizers and non-sensitizers, (e) Using the gene expressions of the said test sample and the said control sampleType: GrantFiled: September 28, 2007Date of Patent: April 2, 2013Assignee: Vlaamse Instelling Voor Technologisch Onderzoek (VITO)Inventors: Greet Schoeters, Rosette Van Den Heuvel, Jef Hooyberghs
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Patent number: 8407010Abstract: The present invention provides methods for rapid forensic analysis of mitochondrial DNA by amplification of a segment of mitochondrial DNA containing restriction sites, digesting the mitochondrial DNA segments with restriction enzymes, determining the molecular masses of the restriction fragments and comparing the molecular masses with the molecular masses of theoretical restriction digests of known mitochondrial DNA sequences stored in a database.Type: GrantFiled: March 17, 2008Date of Patent: March 26, 2013Assignee: Ibis Biosciences, Inc.Inventors: Steven A. Hofstadler, Thomas A. Hall, David J. Ecker, Lawrence B. Blyn, Mark W. Eshoo, Vivek Samant, Neill White
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Patent number: 8374794Abstract: The invention provides a high resolution three-dimensional structure of cycloheximide, either alone or in association with a large ribosomal subunit. The invention provides methods for designing and/or identifying cycloheximide analogs and derivatives that bind and/or modulate the protein biosynthetic activity of the ribosome.Type: GrantFiled: February 29, 2008Date of Patent: February 12, 2013Assignee: Rib-X Pharmaceuticals, Inc.Inventor: Brian T. Wimberly
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Patent number: 8370069Abstract: An exemplary object of the present invention is to provide method, predictor and predicting program for predicting secondary structure of nucleic acid sequence capable of evaluating not only overall similarity and but also localized similarity of secondary structure of nucleic acid sequence. A method according to an exemplary aspect of the present invention includes the steps of: extracting a structural element of the secondary structure from the secondary structure of the nucleic acid sequence; and evaluating a similarity of each structural element of the nucleic acid sequence as a subject, based on a feature vector of the structural element.Type: GrantFiled: May 21, 2008Date of Patent: February 5, 2013Assignee: NEC Soft, Ltd.Inventor: Jou Akitomi
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Patent number: 8364418Abstract: 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.Type: GrantFiled: November 16, 2011Date of Patent: January 29, 2013Assignee: Trillium Diagnostics, LLCInventors: Bruce H. Davis, Charles Bruce Bagwell, Benjamin Hunsberger
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Patent number: 8352194Abstract: Numerous cancer fusion genes have been identified and studied, and in some cases therapy or diagnostic techniques have been designed that are specific to the fusion protein encoded by the fusion gene. However, there has been little progress in understanding the general features of cancer fusions genes in a way that could provide the foundation for an algorithm for predicting the occurrence of a fusion gene once the chromosomal translocation points have been identified by karyotype analyses. In this study, characterization of 59 cancer fusion genes indicated that all but a small percentage of the genes involved in fusion events are either relatively large, compared to neighboring genes, or are highly conserved in evolution. These results support a basis for designing algorithms that could have a high degree of predictive value in identifying fusion genes once conventional microscopic analyses have identified the chromosomal breakpoints.Type: GrantFiled: June 17, 2009Date of Patent: January 8, 2013Assignee: University of South FloridaInventor: George Blanck
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Patent number: 8340914Abstract: Systems and methods are disclosed for compressing and comparing data such as genomic data. The disclosed systems and methods may include selecting a segment, creating a delta representation of the segment, the delta representation comprising a script, and storing the script. Furthermore, the disclosed systems and methods may include receiving a first script comprising a compressed version of a first segment and receiving a second script comprising a compressed version of a second segment. The disclosed systems and methods may further include comparing the first script to the second script and determining if the first segment matches the second segment based upon the comparison of the first script to the second script.Type: GrantFiled: November 8, 2004Date of Patent: December 25, 2012Inventors: Joe M. Gatewood, Valerio G. Aimale, Callum J. Bell
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Patent number: 8332159Abstract: A method of enhancing the efficacy of a monoclonal antibody preparation wherein antigens from patients are tested for their reactivity with the antibody. An amino acid sequence of an expressed protein is deuced from a nucleotide sequence determined by isolation and analysis of a target molecule gene in a biopsy from a patient. This is compared with the previously determined amino acid sequence recognized by the monoclonal antibody preparation in order to assess the fitness of patients for administration of the monoclonal antibody preparation.Type: GrantFiled: February 18, 2004Date of Patent: December 11, 2012Assignee: Juridical Foundation The Chemo-Sero-Therapeutic Research InstituteInventors: Toshio Murakami, Hirofumi Higuchi, Keiichi Makizumi, Toshihiro Maeda, Hiroshi Mizokami
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Patent number: 8321152Abstract: 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.Type: GrantFiled: March 2, 2011Date of Patent: November 27, 2012Assignee: GE Healthcare Bio-Sciences ABInventors: Robert Karlsson, Karl Andersson, Christina Wass
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Patent number: 8315818Abstract: 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.Type: GrantFiled: December 10, 2010Date of Patent: November 20, 2012Assignee: Nestec S.A.Inventors: Augusto Lois, Bruce Neri
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Patent number: 8315809Abstract: A method of generating standard brain model from a bio-expression system includes performing steps of registration to input standard surface and individual surface into affine registration; recording a transformation parameters from the affine registration; performing steps of inputting a individual neuropil and transform parameters into an affine transformation; applying the data of the affine transformation to transform individual neuropil to achieve transformed individual neuropil; and performing a step of affine registration to register a standard neuropil to the transformed individual neuropil to achieve a resulting transformation, wherein the resulting transformation can be output as a position and orientation of standard neuropil within the standard surface.Type: GrantFiled: August 18, 2008Date of Patent: November 20, 2012Assignee: National Tsing Hua UniversityInventors: Ann-Shyn Chiang, Yung-Chang Chen, Hsiu-Ming Chang
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Patent number: 8311791Abstract: A system and method for converting static/still medical images of a particular patient into dynamic and interactive images interacting with medical tools including medical devices by coupling a model of tissue dynamics and tool characteristics to the patient specific imagery for simulating a medical procedure in an accurate and dynamic manner.Type: GrantFiled: October 19, 2010Date of Patent: November 13, 2012Assignee: Surgical Theater LLCInventor: Mordechai Avisar
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Patent number: 8306752Abstract: The invention relates to computer-implemented methods and systems for identifying regulatory relationships between expressed regulating polypeptides and targets of the regulatory activities of such regulating polypeptides. More specifically, the invention provides a new method for identifying regulatory dependencies between biochemical species in a cell. In particular embodiments, provided are computer-implemented methods for identifying a regulatory interaction between a transcription factor and a gene target of the transcription factor, or between a transcription factor and a set of gene targets of the transcription factor. Further provided are genome-scale methods for predicting regulatory interactions between a set of transcription factors and a corresponding set of transcriptional target substrates thereof.Type: GrantFiled: November 17, 2008Date of Patent: November 6, 2012Assignee: Trustees of Boston UniversityInventors: Timothy S. Gardner, James J. Collins, Boris Hayete, Jeremiah Faith
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Patent number: 8301390Abstract: Embodiments of the present invention provide, among other things, methods, apparatus, and systems for tuning a semiempirical process for predicting energy for different molecular configurations. In an example method, an energy value and an energy gradient are determined for each of a plurality of molecular configurations using an accurate method. A functional form of the semiempirical process is optimized using the determined energy values and energy gradients via multiobjective optimization. The functional form relates one or more parameters to energy values and energy gradients.Type: GrantFiled: January 31, 2008Date of Patent: October 30, 2012Assignee: The Board of Trustees of the University of IllinoisInventors: Kumara Sastry, Duane D. Johnson, Alexis L. Thompson, Todd J. Martinez, David E. Goldberg
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Patent number: 8296073Abstract: A method for prognosing osteoporosis phenotypes or estimating osteoporosis quantitative traits comprising determining outcomes for selected SNP variables and clinical variables. Products and methods for genotyping multiple osteoporosis associated genetic variations.Type: GrantFiled: July 12, 2007Date of Patent: October 23, 2012Assignees: Progenika Biopharma, S.A., Bioiberica, S.A.Inventors: Ainara Cadaval, Diego Tejedor Hernández, Antonio Martínez Martínez, Laureano Simón Buela
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Patent number: 8296072Abstract: The present invention provides techniques of recording signals. In one aspect of the invention, a method of recording a signal comprises the following steps. One or more errors are selectively introduced during synthesis of a polymer in response to the signal. The one or more occurrences of the one or more errors in the synthesized polymer are recorded. The synthesis of the polymer may comprise a polymer synthetase that can selectively introduce the one or more errors in response to the signal. A method for analyzing signals is also provided.Type: GrantFiled: September 11, 2008Date of Patent: October 23, 2012Assignee: International Business Machines CorporationInventor: James R. Kozloski
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Patent number: 8275552Abstract: The present invention is a method for communicating and forecasting the extent of toxicity of a given treatment program by deploying a uniform multi-modality grading system, and capturing significant high-grade events within defined risk periods to create a treatment-specific summary rating or classification of the toxicity experience.Type: GrantFiled: October 6, 2004Date of Patent: September 25, 2012Assignee: University of South FloridaInventor: Andrea Trotti, III