Patents Examined by Russell S. Negin
  • Patent number: 11911769
    Abstract: The instant disclosure provides nucleic acid amplification systems and multi-reaction analysis systems useful in the efficient processing of samples, including clinical samples. Integrated systems that include nucleic acid amplification devices functionally combined with multi-reaction analysis systems are also included. Also provided are methods for monitoring multiple concurrent nucleic acid amplification reactions that include the use of devices and systems described herein.
    Type: Grant
    Filed: September 30, 2020
    Date of Patent: February 27, 2024
    Assignee: Abbott Laboratories
    Inventors: Sonal Sadaria Nana, Eric B. Shain, Michael S. Hazell, Eric D. Yeaton, Michael Giraud, Timothy J. Patno, Ali Attarwalla, Dean Khan, Matthew J. Hayes
  • Patent number: 11913068
    Abstract: Disclosed herein are data processing and calculating annotation systems and devices, and corresponding methods, for nucleic acid analysis. In particular, disclosed herein are methods for sizing a repeat region of a nucleic acid sample. For example, the methods disclosed herein use a ladder of amplification products to determine nucleic acid size.
    Type: Grant
    Filed: August 23, 2019
    Date of Patent: February 27, 2024
    Assignee: Asuragen, Inc.
    Inventors: Eran Bram, Raghav Shroff, Andrew Hadd, Blake Printy
  • Patent number: 11894107
    Abstract: Systems and techniques that facilitate precision-preserving qubit reduction based on spatial symmetries in fermionic systems are provided. In one or more embodiments, a symmetry component can generate a diagonalized second quantization representation of a spatial point group symmetry operation. The spatial point group symmetry operation can be associated with a molecule (e.g., a geometrical rotation, reflection, and/or inversion of a physical molecule that results in a new molecular orientation that is substantially the same as the original molecular orientation). In one or more embodiments, a transformation component can convert the diagonalized second quantization representation into a single Pauli string. In one or more embodiments, a tapering component can taper off qubits in a computational quantum algorithm that models properties of the molecule, based on the single Pauli string.
    Type: Grant
    Filed: October 22, 2019
    Date of Patent: February 6, 2024
    Assignee: INTERNATIONAL BUSINESS MACHINES CORPORATION
    Inventors: Kanav Setia, Sergey Bravyi, Antonio Mezzacapo, Richard Chen, Marco Pistoia, Julia Elizabeth Rice
  • Patent number: 11893475
    Abstract: Neural network inference may be performed by configuration of a device including an accumulation memory, a plurality of convolution modules configured to perform mathematical operations on input values, a plurality of adder modules configured to sum values output from the plurality of convolution modules, and a plurality of convolution output interconnects connecting the plurality of convolution modules, the plurality of adder modules, and the accumulation memory. The accumulation memory is an accumulation memory allocation of a writable memory block having a reconfigurable bank width, and each bank of the accumulation memory allocation is a virtual combination of consecutive banks of the writable memory block.
    Type: Grant
    Filed: October 11, 2021
    Date of Patent: February 6, 2024
    Assignee: EDGECORTIX INC.
    Inventors: Nikolay Nez, Hamid Reza Zohouri, Oleg Khavin, Antonio Tomas Nevado Vilchez, Sakyasingha Dasgupta
  • Patent number: 11885821
    Abstract: A method of measuring and calculating (preferably by a computer with output to a user) tGSH (total glutathione very particularly defined) with sample preparation and assay methods that have been confirmed to provide accurate and reliable tGSH and related diagnostic assays in blood or tissue from a patient.
    Type: Grant
    Filed: February 18, 2021
    Date of Patent: January 30, 2024
    Assignee: Definitek, Inc.
    Inventors: Howard M. Kingston, Mehmet Pamukcu
  • Patent number: 11875878
    Abstract: The present disclosure relates to a machine learning method and apparatus using steps feature selection based on a genetic algorithm, and the machine learning method includes defining a feature set including a plurality of features, generating a plurality of feature combinations including n-dimensional features (n is a natural number) for the feature set, independently constructing feature models for the plurality of feature combinations and calculating prediction accuracy for each of the feature models as a prediction result for a predetermined data set, arranging the feature models according to the prediction accuracy to determine at least one good feature model that satisfies a preset criterion, determining at least one good feature from among features included in a corresponding feature set of the at least one good feature model, and updating the feature set to include only the at least one good feature and re-determining a good feature model for a (n+1)-dimensional feature combination based on the update
    Type: Grant
    Filed: November 8, 2021
    Date of Patent: January 16, 2024
    Assignees: IMEDISYNC. LTD., THE CATHOLIC UNIVERSITY OF KOREA INDUSTRY-ACADEMIC COOPERATION FOUNDATION
    Inventors: Seung Wan Kang, Namheon Kim, Dong Won Yang
  • Patent number: 11872032
    Abstract: A method of estimating a concentration of an analyte may include obtaining a plurality of in vivo estimation spectra, generating a plurality of noise detection models by varying a number of principal components based on the plurality of in vivo estimation spectra, comparing the generated plurality of noise detection models with a plurality of concentration estimation models for each number of principal components, extracting a noise spectrum and a concentration estimation model for use in estimating the concentration of the analyte based on the comparison, updating the extracted concentration estimation model based on the extracted noise spectrum, and estimating the concentration of the analyte by using the updated concentration estimation model and an in vivo estimation spectrum from among the plurality of in vivo estimation spectra.
    Type: Grant
    Filed: January 13, 2020
    Date of Patent: January 16, 2024
    Assignee: SAMSUNG ELECTRONICS CO., LTD.
    Inventors: Sang Kon Bae, So Young Lee
  • Patent number: 11867690
    Abstract: Embodiments herein described provide methods for determining phenotypic parameters of cell populations and expressing them in terms of tensors that can be compared with one another. Embodiments provide methods for determining phenotypic parameters of cell populations in response to an agent. Embodiments provide methods for comparing effects of an agent on phenotypic parameters to effects of reference standards whose in vivo effects are known. Embodiments provide methods for predicting the effect of an agent by the comparison with the known effects of reference standards. Embodiments provide methods for classifying agents by their effects on phenotypic parameters. Embodiments provide software and computer systems for calculating multiparametric tensors, compressing their complexity and comparing them after compression.
    Type: Grant
    Filed: August 5, 2021
    Date of Patent: January 9, 2024
    Assignee: ASEDASCIENCES AG
    Inventors: Bartlomiej Rajwa, Vincent T Shankey
  • Patent number: 11866768
    Abstract: This disclosure provides methods, systems, compositions, and kits for the multiplexed detection of a plurality of analytes in a sample. In some examples, this disclosure provides methods, systems, compositions, and kits wherein multiple analytes may be detected in a single sample volume by acquiring a cumulative measurement or measurements of at least one quantifiable component of a signal. In some cases, additional components of a signal, or additional signals (or components thereof) are also quantified. Each signal or component of a signal may be used to construct a coding scheme which can then be used to determine the presence or absence of any analyte.
    Type: Grant
    Filed: July 23, 2020
    Date of Patent: January 9, 2024
    Assignee: California Institute of Technology
    Inventors: Emil P. Kartalov, Aditya Rajagopal, Axel Scherer
  • Patent number: 11851704
    Abstract: A method for sequencing biopolymers. The method includes selecting with a sequence generator module an input nucleotide sequence having plural k-mers; simulating with a deep learning simulator, actual electrical current signals corresponding to the input nucleotide sequence; identifying reads that correspond to the actual electrical current signals; and displaying the reads. The deep learning simulator includes a context-dependent deep learning model that takes into consideration a position of a k-mer of the plural k-mers on the input nucleotide sequence when calculating a corresponding actual electrical current.
    Type: Grant
    Filed: June 23, 2021
    Date of Patent: December 26, 2023
    Assignee: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY
    Inventors: Xin Gao, Yu Li, Sheng Wang, Renmin Han
  • Patent number: 11854707
    Abstract: An apparatus in one embodiment comprises a distributed data processing system in which multiple processing devices communicate with one another over at least one network. The distributed data processing system is configured to obtain reads of biological samples of respective sample sources, with each of the biological samples containing genomic material from a plurality of distinct microorganisms within an environment of a corresponding one of the sample sources, and to perform distributed data analytics to provide surveillance functionality characterizing at least one of a disease, an infection and a contamination as involving genomic material from multiple ones of the sample source. Performing distributed data analytics illustratively comprises performing local analytics in respective ones of a plurality of data zones, and performing global analytics utilizing results of the local analytics performed in the respective data zones.
    Type: Grant
    Filed: March 30, 2022
    Date of Patent: December 26, 2023
    Assignee: EMC IP Holding Company LLC
    Inventors: Patricia Gomes Soares Florissi, Michal Ziv Ukelson, Ran Dach, Arnon Benshahar
  • Patent number: 11847532
    Abstract: Systems and methods that analyze blood-based cancer diagnostic tests using multiple classes of molecules are described. The system uses machine learning (ML) to analyze multiple analytes, for example cell-free DNA, cell-free microRNA, and circulating proteins, from a biological sample. The system can use multiple assays, e.g., whole-genome sequencing, whole-genome bisulfite sequencing or EM-seq, small-RNA sequencing, and quantitative immunoassay. This can increase the sensitivity and specificity of diagnostics by exploiting independent information between signals. During operation, the system receives a biological sample, and separates a plurality of molecule classes from the sample. For a plurality of assays, the system identifies feature sets to input to a machine learning model. The system performs an assay on each molecule class and forms a feature vector from the measured values.
    Type: Grant
    Filed: February 11, 2021
    Date of Patent: December 19, 2023
    Assignee: Freenome Holdings, Inc.
    Inventors: Adam Drake, Daniel Delubac, Katherine Niehaus, Eric Ariazi, Imran Haque, Tzu-Yu Liu, Nathan Wan, Ajay Kannan, Brandon White
  • Patent number: 11842799
    Abstract: Systems, architectures, devices, and methods for matching experimentally acquired mass spectrometry data with a peptide database are provided. The system architecture can include a host central processing unit (CPU) system, a bridge connecting the CPU system with a core control register (or registers), a plurality of processing elements (PEs), and a bus arbiter. The PEs can execute the computations in a parallel and asynchronous manner. The bus arbiter can be a first-come first-serve (FCFS)-based bus arbiter (i.e., can utilize an FCFS-based arbitration scheme).
    Type: Grant
    Filed: April 20, 2023
    Date of Patent: December 12, 2023
    Assignee: THE FLORIDA INTERNATIONAL UNIVERSITY BOARD OF TRUSTEES
    Inventors: Sumesh Kumar, Fahad Saeed
  • Patent number: 11827921
    Abstract: This disclosure provides methods, systems, compositions, and kits for the multiplexed detection of a plurality of analytes in a sample. In some examples, this disclosure provides methods, systems, compositions, and kits wherein multiple analytes may be detected in a single sample volume by acquiring a cumulative measurement or measurements of at least one quantifiable component of a signal. In some cases, additional components of a signal, or additional signals (or components thereof) are also quantified. Each signal or component of a signal may be used to construct a coding scheme which can then be used to determine the presence or absence of any analyte.
    Type: Grant
    Filed: May 1, 2020
    Date of Patent: November 28, 2023
    Assignee: California Institute of Technology
    Inventors: Emil P. Kartalov, Aditya Rajagopal, Axel Scherer
  • Patent number: 11810644
    Abstract: In variants, a method for genomic association can include: determining observed variable values and observed phenotype values for each organism in a population, removing information from variables of interest, determining a phenotype-variable association model, identifying causal variables associated with a phenotype, and/or any other suitable steps.
    Type: Grant
    Filed: March 8, 2023
    Date of Patent: November 7, 2023
    Assignee: Avalo, Inc.
    Inventors: Mariano Alvarez, Cynthia Rudin
  • Patent number: 11810648
    Abstract: Systems and methods for analyzing genomic information can include obtaining a sequence read including genetic information; identifying, within a graph representing a reference genome, a plurality of candidate mapping positions that relate to the genetic information, the graph comprising nodes representing genetic sequences and edges connecting pairs of nodes; determining, by means of a computer system, whether an alignment with the graph surrounding each of the plurality of candidate mapping positions is advanced or basic; and performing for each candidate mapping position, by means of the computer system, a local alignment based on whether the local alignment is advanced or basic. The advanced local alignment can include a first-local-alignment algorithm, and the basic local alignment includes a second-local-alignment algorithm. Based on the local alignments, the mapped position of the sequence read can be identified within the genome.
    Type: Grant
    Filed: October 24, 2019
    Date of Patent: November 7, 2023
    Assignee: Seven Bridges Genomics Inc.
    Inventors: Kaushik Ghose, Wan-Ping Lee
  • Patent number: 11804284
    Abstract: A modulo based alignment system for aligning genetic material sequences is provided. The modulo based alignment system reduces the size of data required for the genetic material sequence alignment, reduces the number of the registers required for processing, reduces the power requirements, and reduces the amount of heat generated during processing. The modulo based alignment system provides methods of performing dynamic programs for global, overlapping and local alignments using modular arithmetic. The methods produce smaller parameters requiring fewer processor register bits. In addition, with customized hardware optimized for 8-bit arithmetic, the dynamic programs are sped up.
    Type: Grant
    Filed: July 22, 2022
    Date of Patent: October 31, 2023
    Assignee: OmniTier, Inc.
    Inventor: Razmik Karabed
  • Patent number: 11798654
    Abstract: Systems, architectures, devices, and methods for matching experimentally acquired mass spectrometry data with a peptide database are provided. The system architecture can include a host central processing unit (CPU) system, a bridge connecting the CPU system with a core control register (or registers), a plurality of processing elements (PEs), and a bus arbiter. The PEs can execute the computations in a parallel and asynchronous manner. The bus arbiter can be a first-come first-serve (FCFS)-based bus arbiter (i.e., can utilize an FCFS-based arbitration scheme).
    Type: Grant
    Filed: July 28, 2022
    Date of Patent: October 24, 2023
    Assignee: THE FLORIDA INTERNATIONAL UNIVERSITY BOARD OF TRUSTEES
    Inventors: Sumesh Kumar, Fahad Saeed
  • Patent number: 11790629
    Abstract: The present invention relates generally to a species (analyte) separation and analysis system, for instance a spectrometry system, comprising a processor for receiving and processing signals from said its detector to remove undesirable variation or noise before further processing into a spectrum, whereby the processor is programmed by a novel program for a normalization preprocessing of the signals of said separation and analysis system.
    Type: Grant
    Filed: April 10, 2019
    Date of Patent: October 17, 2023
    Assignee: KATHOLIEKE UNIVERSITEIT LEUVEN
    Inventors: Bart De Moor, Raf Van De Plas, Etienne Waelkens
  • Patent number: 11783914
    Abstract: Embodiments of a system and method for characterizing a panel of conditions associated with a set of taxa related to microorganisms can include a taxonomic database including reference microbiome features for the set of taxa associated with the panel of conditions; a handling operable to collect a container including biological material from a user, the handling system comprising a sequencer system operable to determine a microorganism sequence dataset; and a panel characterization system operable to: determine user microbiome features for the set of taxa for the user based on the microorganism sequence dataset, generate a comparison between the user microbiome features and the reference microbiome features, and determine a panel characterization for the panel of conditions for the user based on the comparison; and a treatment system operable to promote a therapy for a condition of the panel of conditions based on the panel characterization.
    Type: Grant
    Filed: September 18, 2017
    Date of Patent: October 10, 2023
    Assignee: PSOMAGEN, INC.
    Inventors: Zachary Apte, Jessica Richman, Daniel Almonacid, Laurens Kraal, Francisco Ossandon, Juan Pablo Cardenas, Elisabeth Bik, Audrey Goddard