Patents Examined by Anna Skibinsky
  • Patent number: 10809258
    Abstract: A method for determination of the amount of a specific analyte in a sample which may show a prozone effect by photometric assays, wherein the specific analyte is quantified from the change in the optical signal of the reaction mixture after the interaction of the analyte with analyte specific assay reagents. The optical signal is measured simultaneously for the specific analyte in the sample to be determined at the wavelength used for the determination of the analyte and at least at an additional specific wavelength used for the detection of the prozone effect over the complete reaction time. The reaction rate ratio R is calculated by using the signals obtained at the wavelength used for the detection of the prozone effect. By comparison of the calculated ratio value R with predetermined limit values it is judged if a prozone effect is present in the sample.
    Type: Grant
    Filed: February 12, 2016
    Date of Patent: October 20, 2020
    Assignee: Roche Diagnostics Operations, Inc.
    Inventors: Ewelina Hegel, Georg Kurz, Eloisa Lopez-Calle, Josef Roedl
  • Patent number: 10803144
    Abstract: A processor-implemented method, computer program product and system are provided for predicting drug-drug interactions based on clinical side effects. The method includes constructing a drug-drug interactions training dataset that includes pharmaceutical, pharmacokinetic or pharmacodynamics drug-drug interactions from multiple data sources for each of a plurality of drugs. The method also includes constructing side effect features for each of the drugs from side effects associated with the drugs. The method further includes building, using the drug-drug interactions training dataset, a drug-drug interactions classifier that predicts adverse drug-drug interactions for drug pairs derivable from the drugs.
    Type: Grant
    Filed: May 6, 2014
    Date of Patent: October 13, 2020
    Inventors: Jianying Hu, Robert K. Sorrentino, Fei Wang, Ping Zhang
  • Patent number: 10793895
    Abstract: The invention provides systems and methods for determining patterns of modification to a genome of a subject by representing the genome using a graph, such as a directed acyclic graph (DAG) with divergent paths for regions that are potentially subject to modification, profiling segments of the genome for evidence of epigenetic modification, and aligning the profiled segments to the DAG to determine locations and patterns of the epigenetic modification within the genome.
    Type: Grant
    Filed: January 27, 2016
    Date of Patent: October 6, 2020
    Assignee: Seven Bridges Genomics Inc.
    Inventors: Devin Locke, Wan-Ping Lee
  • Patent number: 10796783
    Abstract: A method and system for selection of a primer set for a set of target sequences includes: identifying candidate fragments upon performance of a comparison operation with the set of target sequences; identifying a forward subset of unique forward candidates and a reverse subset of unique reverse candidates; reducing the forward subset and the reverse subset based on a filtering operation; performing an in silico search operation with the reduced forward subset and the reduced reverse subset; generating a set of candidate degenerate primers based on the in silico search operation and a base mismatch criterion; generating a reduced set of candidate degenerate primers upon filtering the set of candidate degenerate primers according to the set of primer criteria; and selecting forward primer subsets that amplify the set of target sequences and identifying a reverse primer subset for each of the forward primer subsets with an in silico PCR operation.
    Type: Grant
    Filed: August 18, 2016
    Date of Patent: October 6, 2020
    Assignee: PSOMAGEN, INC.
    Inventors: Daniel Almonacid, Zachary Apte, Jessica Richman
  • Patent number: 10783697
    Abstract: One aspect of the invention provides a method for drift correction to correct a 3D point collection dataset to compensate for drift over time. The method includes: (a) separating the 3D dataset into n segments, wherein n>1; (b) for each of the n segments, reconstructing a volume image as a 3D histogram in which a count for each voxel in the histogram equals a number of localization estimates falling within the voxel; (c) performing 3D cross-correlation between pairs of the n segments; (d) identifying a correlation peak in a result of the 3D cross-correlation to determine a shift distance between pairs of the n segments; (e) solving an overdetermined system of shift distances to determine independent shifts; and (f) offsetting positions from a plurality of segments in the 3D point collection dataset with the independent shifts calculated in step (e) to correct for drift.
    Type: Grant
    Filed: February 24, 2017
    Date of Patent: September 22, 2020
    Assignee: Yale University
    Inventors: Fang Huang, Joerg Bewersdorf
  • Patent number: 10769559
    Abstract: The workflow application integrates with a research software application associated with a laboratory instrument to provide a user with step-by-step instructions on how to follow the workflow steps of a laboratory experiment. The instructions are dynamically tailored, according to the nature of the workflow, the samples being experimented upon and/or the operating states of the instrument and/or the research software application. The workflow application significantly reduces the learning curve to operate sophisticated laboratory instruments. In a genetic testing instrument the workflow application can prescribe the need for control samples and can optimize the layout of samples within the instrument's sample receiving plate or fixture.
    Type: Grant
    Filed: September 18, 2015
    Date of Patent: September 8, 2020
    Assignee: Applied Biosystems, LLC
    Inventors: Bruce DeSimas, Leslie Dow
  • Patent number: 10754926
    Abstract: The present invention refers to data management unit comprising a data storage (130) adapted to store a plurality of measurement values of the physiological parameter, preferably a blood glucose level, for each measurement value an associated event tag, for each measurement value an associated time stamp, an associated time range for tagging preselection for each of at least two meal events, each time range is preferably user-settable, preferably also for a fasting event an associated time range for tagging preselection, this time range is preferably user-settable, a processor (140) adapted to receive a new measurement value from the data storage (130) or from a measurement unit (110), which is preferably at least shortly connected for data transfer, assign an associated time stamp to the new measurement value, if an associated time stamp does not yet exist with the new measurement value, receive selection data containing the information that the user has selected and/or confirmed one of a “before meal” tag a
    Type: Grant
    Filed: September 19, 2014
    Date of Patent: August 25, 2020
    Assignee: Sanofi-Aventis Deutschland GMBH
    Inventor: Andrew Tubb
  • Patent number: 10748438
    Abstract: A method and system for interactive patient-specific simulation of liver tumor ablation is disclosed. A patient-specific anatomical model of the liver and circulatory system of the liver is estimated from 3D medical image data of a patient. A computational domain is generated from the patient-specific anatomical model of the liver. Blood flow in the liver and the circulatory system of the liver is simulated based on the patient-specific anatomical model. Heat diffusion due to ablation is simulated based on a virtual ablation probe position and the simulated blood flow in the liver and the circulatory system of the liver by solving a bio-heat equation for each node on the level-set representation using a Lattice-Boltzmann method (LBM) implementation. Cellular necrosis in the liver is computed based on the simulated heat diffusion. Visualizations of a computed necrosis region and temperature maps of the liver are generated.
    Type: Grant
    Filed: February 24, 2014
    Date of Patent: August 18, 2020
    Assignee: Siemens Healthcare GmbH
    Inventors: Chloe Audigier, Tommaso Mansi, Viorel Mihalef, Ali Kamen, Dorin Comaniciu, Puneet Sharma, Saikiran Rapaka
  • Patent number: 10726943
    Abstract: An embodiment of the invention provides a method for determining a patient-specific probability of disease. The method collects clinical parameters from a plurality of patients to create a training database. A fully unsupervised Bayesian Belief Network model is created using data from the training database; and, the fully unsupervised Bayesian Belief Network is validated. Clinical parameters are collected from an individual patient; and, such clinical parameters are input into the fully unsupervised Bayesian Belief Network model via a graphical user interface. The patient-specific probability of the healing rate of an acute traumatic wound is output from the fully unsupervised Bayesian Belief Network model and sent to the graphical user interface for use by a clinician in pre-operative planning. The fully unsupervised Bayesian Belief Network model is updated using the clinical parameters from the individual patient and the patient-specific probability of the healing rate of an acute traumatic wound.
    Type: Grant
    Filed: April 8, 2011
    Date of Patent: July 28, 2020
    Inventors: Alexander Stojadinovic, Eric Elster, Doug K. Tadaki, John S. Eberhardt, III, Trevor Brown, Thomas A. Davis, Jonathan Forsberg, Jason Hawksworth
  • Patent number: 10724110
    Abstract: The invention provides systems and methods for analyzing viruses by representing viral genetic diversity with a directed acyclic graph (DAG), which allows genetic sequencing technology to detect rare variations and represent otherwise difficult-to-document diversity within a sample. Additionally, a host-specific sequence DAG can be used to effectively segregate viral nucleic acid sequence reads from host sequence reads when a sample from a host is subject to sequencing. Known viral genomes can be represented using a viral reference DAG and the viral sequence reads from the sample can be compared to viral DAG to identify viral species or strains from which the reads were derived. Where the viral sequence reads indicate great genetic diversity in the virus that was infecting the host, those reads can be assembled into a DAG that itself properly represents that diversity.
    Type: Grant
    Filed: February 3, 2016
    Date of Patent: July 28, 2020
    Assignee: Seven Bridges Genomics Inc.
    Inventors: Devin Locke, Piotr Szamel
  • Patent number: 10699802
    Abstract: Embodiments of a method and/or system (e.g., for microsatellite instability detection associated with at least one cancer condition; etc.) can include: determining a microsatellite-related background model; determining one or more loci associated with microsatellite instability based on the microsatellite-related background model; and/or determining a microsatellite instability characterization (e.g., a binary status determination between microsatellite instability such as MSI-H, and microsatellite stability such as MSS; etc.) for the user. Additionally or alternatively, embodiments of the method and/or system can include facilitating treatment provision for one or more users based on the microsatellite instability characterization.
    Type: Grant
    Filed: October 9, 2018
    Date of Patent: June 30, 2020
    Assignee: Strata Oncology, Inc.
    Inventors: Bryan Johnson, Dan Rhodes, Scott Tomlins
  • Patent number: 10697975
    Abstract: Gene expression data provides a basis for more accurate identification and diagnosis of lymphoproliferative disorders. In addition, gene expression data can be used to develop more accurate predictors of survival. The present invention discloses methods for identifying, diagnosing, and predicting survival in a lymphoma or lymphoproliferative disorder on the basis of gene expression patterns. The invention discloses a novel microarray, the Lymph Dx microarray, for obtaining gene expression data from a lymphoma sample. The invention also discloses a variety of methods for utilizing lymphoma gene expression data to determine the identity of a particular lymphoma and to predict survival in a subject diagnosed with a particular lymphoma. This information will be useful in developing the therapeutic approach to be used with a particular subject.
    Type: Grant
    Filed: June 22, 2017
    Date of Patent: June 30, 2020
    Assignees: The United States of America, as represented by the Secretary, Department of Health and Human Services, Board of Regents of the University of Nebraska, University of Rochester, Arizona Board of Regents on behalf of the University of Arizona, Universitat de Barcelona, Fundacio Clinic, Hospital Clinic de Barcelona, Julius-Maximilians-University of Würzburg, British Columbia Cancer Agency Branch, Oslo University Hospital HF, Queen Mary and Westfield College, University of London
    Inventors: Louis M. Staudt, George Wright, Sandeep Dave, Bruce Tan, John I. Powell, Wyndham Wilson, Elaine S. Jaffe, Wing C. Chan, Timothy C. Greiner, Dennis Weisenburger, James Armitage, Kai Fu, Richard I. Fisher, Lisa M. Rimsza, Thomas Miller, Thomas Grogan, Elias Campo Guerri, Silvia M. Bea, Itziar Salaverria, Armando Lopez-Guillermo, Emilio Montserrat, Victor Moreno, Andreas Zettl, German Ott, Hans-Konrad Muller-Hermelink, Andreas Rosenwald, Julie Vose, Randy Gascoyne, Joseph Connors, Erlend B. Smeland, Stein Kvaloy, Harald Holte, Jan Delabie, T. Andrew Lister
  • Patent number: 10676791
    Abstract: The present invention relates to a method of testing whether a patient suffering from arge B-cell lymphoma will respond or not to a DNA repair pathway inhibitor comprising: i) determining the expression level (ELi) of several genes Gi-Gn selected from table A in a biological sample obtained from said patient comparing the expression level (ELi) determined at step i) with a predetermined reference level (ELRi) iii) calculating the DNA repair score trough the following formula (I), wherein ?i represent the regression ? coefficient reference value for the gene Gi and Ci=1 if the expression of the gene Gi (ELi) is higher than the predetermined reference level (ELRi) or Ci=?1 if the expression of the gene (ELi) is lower than or equal to the predetermined reference level (ELRi) iv) comparing the score DNARS determined at step iii) with a predetermined reference value DNARSR v) and concluding that the patient will respond to the treatment when the DNARS score is higher than the predetermined reference value DNARSg o
    Type: Grant
    Filed: July 27, 2015
    Date of Patent: June 9, 2020
    Inventors: Jerome Moreaux, Guillaume Cartron, Caroline Bret, Angelos Constantinou, Philippe Pasero
  • Patent number: 10671632
    Abstract: The methods and system disclose an automated pipeline which receives a list of Accession IDs corresponding to transcriptomic, proteomic, genomic, or metabolomic data. Each Accession ID is submitted in parallel, launching a specific cloud computer to carry out a customized, fully automated transcriptome assembly (or proteomic assembly or genome assembly or metabolome assembly) and analysis by the automated pipeline. The output from multiple assemblies is automatically compiled and compared with genes of interest to identify new gene variants. The new gene variants can be used as queries by the automated pipeline to: discover variants of the variants; and determine new studies to analyze.
    Type: Grant
    Filed: September 3, 2019
    Date of Patent: June 2, 2020
    Inventor: Tyrone Jacob Yacoub
  • Patent number: 10663469
    Abstract: A method for diagnosing lung cancer in a subject by using a complex biomarker group is provided. The method includes steps of: (a) a computing system (1) acquiring a model M by using expression level data by individual biomarkers in the complex biomarker group and then (2) acquiring expression level data by the individual biomarkers measured from a biological specimen of the subject or their processed data Bk; and (b) the computing system determining whether lung cancer is detected in the subject by using the acquired data of the subject by referring to the model M; wherein the complex biomarker group includes CEA, HE4, ApoA2, TTR, sVCAM-1 and RANTES.
    Type: Grant
    Filed: February 10, 2017
    Date of Patent: May 26, 2020
    Assignee: BioInfra Life Science Inc.
    Inventors: Chul Woo Kim, Yong Dai Kim, Yong Sung Shin, Eun Hee Yeon, Kyung Nam Kang, Ho Sang Shin, Oh Ran Kwon
  • Patent number: 10665327
    Abstract: A high-throughput hybridization and reading method for biochips uses probes with different marks to specifically connect single nucleotide loci by conducting connection between the probes and target genes at different temperatures, and performing hybridization at the same temperature after the probes are connected, thereby achieving hybridization detection for various loci in a single chip. The method enables fast detection for multiple loci as required by personalized medicine. The detection is high-throughput and systematized and provides highly visualized and highly accurate results. The method allows detection for different loci at different hybridization temperatures to be done simultaneously. The method features highly uniform and repeatable detection, making biochips more efficient and utility in terms of detection. Besides, the chip is easy to prepare and use, thus having a good promotional value.
    Type: Grant
    Filed: February 28, 2019
    Date of Patent: May 26, 2020
    Inventors: Zhiyuan Zhu, Libo Chen
  • Patent number: 10662477
    Abstract: Disclosed herein are markers associated with sensitivity to treatment with therapeutic agents. Methods to identify markers for predicting outcome to treatment with a therapeutic agent are disclosed as well as methods to predict outcome of treatment using markers. Compositions and methods are provided to predict response to NAE inhibition or EGFR inhibition treatment.
    Type: Grant
    Filed: October 1, 2013
    Date of Patent: May 26, 2020
    Assignee: Millennium Pharmaceuticals, Inc.
    Inventors: Stephen J. Blakemore, Bin Li, Hyunjin Shin, William L. Trepicchio
  • Patent number: 10657271
    Abstract: In an example, a method includes obtaining an expected biological sample value at a computing device. The expected biological sample value indicates an expected concentration of a material biologically processed by a courier. The computing device determines whether the measured biological sample value is associated with the courier based on a comparison of the expected biological sample value to the measured biological sample value. The method also includes determining a particular set of operations to be performed at the computing device based on a result of the comparison.
    Type: Grant
    Filed: May 5, 2015
    Date of Patent: May 19, 2020
    Assignee: International Business Machines Corporation
    Inventors: Matthew S. Doyle, Joseph Kuczynski, Kevin A. Splittstoesser, Timothy J. Tofil
  • Patent number: 10636512
    Abstract: Provided herein are systems and methods for generating an immune-oncology profile from a biological sample. The immune-oncology profile can include the proportion or percentage of immune cells, expression of immune escape genes, and/or mutational burden. The immune-oncology profile may allow the generation of classifiers for making prognostic or diagnostic predictions.
    Type: Grant
    Filed: August 6, 2018
    Date of Patent: April 28, 2020
    Inventors: Ryan J. Bloom, Jon R. Armstrong
  • Patent number: 10607717
    Abstract: The invention is directed to methods for selecting a treatment option for an activated B cell-like diffuse large B cell lymphoma (ABC DLBCL) subject, a germinal center B cell-like diffuse large B cell lymphoma (GCB DLBCL) subject, a primary mediastinal B cell lymphoma (PMBL) subject, a Burkitt lymphoma (BL) subject, or a mantle cell lymphoma (MCL) subject by analyzing digital gene expression data obtained from the subject, e.g., from a biopsy sample.
    Type: Grant
    Filed: November 5, 2014
    Date of Patent: March 31, 2020
    Assignees: The United States of America, as represented by the Secretary, Department of Health and Human Services, British Columbia Cancer Agency Branch, Arizona Board of Regents on behalf of the University of Arizona, Universitat de Barcelona, Hospital Clinic de Barcelona, The Cleveland Clinic Foundation, Board of Regents of the University of Nebraska, Oregon Health and Science University, Julius-Maximilians-University of Würzburg, Oslo University Hospital HF
    Inventors: Louis M. Staudt, George W. Wright, David William Scott, Joseph M. Connors, Randy D. Gascoyne, Lisa Rimsza, Elias Campo Guerri, Raymond Tubbs, Timothy C. Greiner, James Robert Cook, Kai Fu, Paul Michael Williams, Chih-Jian Lih, Elaine S. Jaffe, Rita M. Braziel, Andreas Rosenwald, Erlend B. Smeland, Wing C. Chan, German Ott, Jan Delabie, Dennis Weisenburger