Patents by Inventor David Yu Zhang

David Yu Zhang has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20220090168
    Abstract: The present invention provides an oligonucleotide composition including a blocker and a first primer oligonucleotide. The blocker oligonucleotide includes a first sequence having a target-neutral subsequence and a blocker variable subsequence. The non-target specific subsequence is flanked on its 3? and 5? ends by the target-neutral subsequence and is continuous with the target-neutral subsequence. The first primer oligonucleotide is sufficient to induce enzymatic extension; herein the first primer oligonucleotide includes a second sequence. The second sequence overlaps with the 5? end of the target-neutral subsequence by at least 5 nucleotides; herein the second sequence includes an overlapping subsequence and a non-overlapping subsequence. The second sequence does not include the non-target specific subsequence.
    Type: Application
    Filed: November 29, 2021
    Publication date: March 24, 2022
    Applicant: William Marsh Rice University
    Inventors: David Yu ZHANG, Ruojia WU, Juexiao WANG
  • Publication number: 20220048033
    Abstract: The disclosure describes apparatus and methods for multiplexed amplification and detection of nucleic acid targets in a sample. Embodiments of the present disclosure include a mechanical system configured to provide loading, vertical positioning and clamping of a chip; a thermal control system configured to maintain distinct temperatures of the chip, and an optical fluorescence imaging system.
    Type: Application
    Filed: September 13, 2019
    Publication date: February 17, 2022
    Applicant: William Marsh Rice University
    Inventors: David Yu ZHANG, Dmitriy A. KHODAKOV, Xuemeng ZHANG
  • Publication number: 20220042100
    Abstract: Provided herein are methods for quantifying foreign cell-free DNA (cfDNA) via SNP profiling of low-volume blood sample. The methods allow for monitoring the status of organ transplant rejection through analysis of small volumes of patient capillary blood samples collected non-invasively with fingersticks or other devices. The methods also allow for guiding the dosage of immunosuppressant and for preparing for a new organ transplant in case of imminent organ failure.
    Type: Application
    Filed: December 5, 2019
    Publication date: February 10, 2022
    Inventors: David Yu ZHANG, Xi CHEN, Omid VEISEH, Peng DAI, Kerou ZHANG
  • Patent number: 11236705
    Abstract: A gaseous fuel mixer assembly for an engine includes a mixer housing forming gas delivery openings, and positioned to extend across a flow path formed by an intake conduit for the engine. A spool valve is within a central bore in the mixer housing and includes gas distribution openings selectively connectable to the gas delivery openings by moving the spool valve within the mixer housing using a piezoelectric actuator coupled with the spool valve by way of a pivot arm. Sealing lands of the spool valve are in an alternating arrangement with the gas distribution openings, such that at the closed position the sealing lands block the gas distribution openings from the gas delivery openings, and at the open position the respective openings are fluidly connected.
    Type: Grant
    Filed: June 25, 2020
    Date of Patent: February 1, 2022
    Assignee: Caterpillar Inc.
    Inventor: David Yu Zhang Chang
  • Publication number: 20210404422
    Abstract: A gaseous fuel mixer assembly for an engine includes a mixer housing forming gas delivery openings, and positioned to extend across a flow path formed by an intake conduit for the engine. A spool valve is within a central bore in the mixer housing and includes gas distribution openings selectively connectable to the gas delivery openings by moving the spool valve within the mixer housing using a piezoelectric actuator coupled with the spool valve by way of a pivot arm. Sealing lands of the spool valve are in an alternating arrangement with the gas distribution openings, such that at the closed position the sealing lands block the gas distribution openings from the gas delivery openings, and at the open position the respective openings are fluidly connected.
    Type: Application
    Filed: June 25, 2020
    Publication date: December 30, 2021
    Applicant: Caterpillar Inc.
    Inventor: David Yu Zhang Chang
  • Publication number: 20210388430
    Abstract: Provided herein are primers and primer systems having improved specificity and kinetics over existing primers, and methods of use thereof.
    Type: Application
    Filed: February 5, 2021
    Publication date: December 16, 2021
    Applicant: President and Fellows of Harvard College
    Inventors: David Yu Zhang, Peng Yin
  • Publication number: 20210371911
    Abstract: The present disclosure describes the thermodynamic design and concentrations necessary to design probe compositions with desired optimal specificity that enable enrichment, detection, quantitation, purification, imaging, and amplification of rare-allele-bearing species of nucleic acids (prevalence <1%) in a large stoichiometric excess of a dominant-allele-bearing species (wildtype). Being an enzyme-free and homogeneous nucleic acid enrichment composition, this technology is broadly compatible with nearly all nucleic acid-based biotechnology, including plate reader and fluorimeter readout of nucleic acids, microarrays, PCR and other enzymatic amplification reactions, fluorescence barcoding, nanoparticle-based purification and quantitation, and in situ hybridization imaging technologies.
    Type: Application
    Filed: August 2, 2021
    Publication date: December 2, 2021
    Applicant: William Marsh Rice University
    Inventors: David Yu ZHANG, Juexiao WANG
  • Patent number: 11104936
    Abstract: The present disclosure describes the thermodynamic design and concentrations necessary to design probe compositions with desired optimal specificity that enable enrichment, detection, quantitation, purification, imaging, and amplification of rare-allele-bearing species of nucleic acids (prevalence <1%) in a large stoichiometric excess of a dominant-allele-bearing species (wildtype). Being an enzyme-free and homogeneous nucleic acid enrichment composition, this technology is broadly compatible with nearly all nucleic acid-based biotechnology, including plate reader and fluorimeter readout of nucleic acids, microarrays, PCR and other enzymatic amplification reactions, fluorescence barcoding, nanoparticle-based purification and quantitation, and in situ hybridization imaging technologies.
    Type: Grant
    Filed: October 17, 2016
    Date of Patent: August 31, 2021
    Assignee: William Marsh Rice University
    Inventors: David Yu Zhang, Juexiao Wang
  • Patent number: 11078827
    Abstract: An ignition system for a gaseous fuel engine includes an igniter and an actuator structured to apply an actuating force to a piston within the igniter, to autoignite an ignition charge of fuel and air within the igniter. A housing of the igniter includes a gas orifice having a flow area that is increased between a combustion pre-chamber in the igniter and a main combustion chamber in the engine, to limit velocity of outgoing combustion gases to below a threshold velocity for engine mis-fire.
    Type: Grant
    Filed: October 11, 2018
    Date of Patent: August 3, 2021
    Assignee: Caterpillar Inc.
    Inventor: David Yu Zhang Chang
  • Patent number: 11078826
    Abstract: Operating an internal combustion engine system includes advancing a prechamber piston in a fuel delivery igniter to push a main charge of fuel from a prechamber into a cylinder, and advancing the prechamber piston to compression-ignite a pilot charge within the prechamber. Combustion gases of the pilot charge are conveyed into the cylinder to ignite the main charge. Operation of the engine system provides sparkless gaseous fuel ignition.
    Type: Grant
    Filed: October 28, 2020
    Date of Patent: August 3, 2021
    Assignee: Caterpillar Inc.
    Inventor: David Yu-Zhang Chang
  • Publication number: 20210230691
    Abstract: Compositions and methods for highly specific nucleic acid probes and primers are provided. The probe system comprises a complement strand and a protector stand that form a partially double-stranded probe. The reaction standard free energy of hybridization between the probe and target nucleic acid as determined by Expression 1 (?G°rxn=?G°t-TC??G°nh-PC+(?G°v-TC??G°h-PC)) is from about ?4 kcal/mol to about +4 kcal/mol. Alternatively, the reaction standard free energy of hybridization between the probe and target nucleic acid is determined by Expression 1 to be within 5 kcal/mol of the standard free energy as determined by Expression 2 (?R?ln(([P]0?[C]0)/[C]0)]), where the [P]0 term of Expression 2 equals the concentration of the protector strand and the [C]0 term of Expression 2 equals the concentration of the complement strand. In addition, a method for on-the-fly fine tuning of a reaction using the present probe is provided.
    Type: Application
    Filed: December 30, 2020
    Publication date: July 29, 2021
    Applicant: William Marsh Rice University
    Inventors: David Yu ZHANG, Juexiao WANG, Ruojia WU
  • Publication number: 20210164026
    Abstract: This invention describes a method of controlling the hybridization yield of nucleic acid probes by adjusting the relative concentrations of auxiliary oligonucleotides to the probes and the targets. The auxiliary oligonucleotide is partially or fully complementary to either the probe or the target, and is released upon hybridization of the probe to the target.
    Type: Application
    Filed: February 5, 2021
    Publication date: June 3, 2021
    Applicant: William Marsh Rice University
    Inventors: David Yu ZHANG, Ruojia WU, Juexiao WANG
  • Publication number: 20210142866
    Abstract: Provided herein are methods for encoding information in DNA molecules in a way that allows rapid and permanent erasure of information. As such, methods of erasing such information are also provided. Also provided are compositions that so encode information.
    Type: Application
    Filed: May 23, 2019
    Publication date: May 13, 2021
    Applicant: William Marsh Rice University
    Inventors: David Yu ZHANG, Alessandro PINTO, Jangwon KIM
  • Publication number: 20210024989
    Abstract: Provided herein are reagents and methods for simultaneously enriching many potential rare genetic variants at different genetic loci. The rare variants enriched can include single nucleotide polymorphisms (SNPs), single nucleotide variants, or small insertions and deletions. Embodiments of the invention include procedures for integration with downstream next generation sequencing (NGS) analysis. Embodiments of the invention include analysis of nonpathogenic SNPs for the determination of cell identity and detection of cell contamination using qPCR or NGS.
    Type: Application
    Filed: February 20, 2019
    Publication date: January 28, 2021
    Applicant: William Marsh Rice University
    Inventors: David Yu ZHANG, Ping SONG, Xi CHEN
  • Patent number: 10900079
    Abstract: Compositions and methods for highly specific nucleic acid probes and primers are provided. The probe system comprises a complement strand and a protector stand that form a partially double-stranded probe. The reaction standard free energy of hybridization between the probe and target nucleic acid as determined by Expression 1 (?G°rxn=?G°t-TC??G°nh-PC+(?G°v-TC??G°h-PC)) is from about ?4 kcal/mol to about +4 kcal/mol. Alternatively, the reaction standard free energy of hybridization between the probe and target nucleic acid is determined by Expression 1 to be within 5 kcal/mol of the standard free energy as determined by Expression 2 (?R? ln(([P]0?[C]0)/[C]0)]), where the [P]0 term of Expression 2 equals the concentration of the protector strand and the [C]0 term of Expression 2 equals the concentration of the complement strand. In addition, a method for on-the-fly fine tuning of a reaction using the present probe is provided.
    Type: Grant
    Filed: June 6, 2016
    Date of Patent: January 26, 2021
    Assignee: William Marsh Rice University
    Inventors: David Yu Zhang, Juexiao Wang, Ruojia Wu
  • Publication number: 20200347754
    Abstract: A gas engine is disclosed. The gas engine may include a combustion cylinder. The combustion cylinder may include an intake with an intake valve. The combustion cylinder may include an exhaust with an exhaust valve. The gas engine may include a gas admission valve assembly coupled to the intake. The gas admission assembly may include a trimmable electro-hydraulically actuatable gas admission valve to control a gas flow into the intake.
    Type: Application
    Filed: May 2, 2019
    Publication date: November 5, 2020
    Applicant: Caterpillar Inc.
    Inventors: David Yu Zhang CHANG, David Todd MONTGOMERY, Scott FIVELAND, Scott F. SHAFER
  • Patent number: 10745746
    Abstract: The present disclosure provides, in various aspects and embodiments, methods and compositions for selectively amplifying a rare target nucleic acid and/or suppressing amplification of non-target nucleic acids with sequences similar to the rare target nucleic acid. The methods and composition are useful, for example, for detecting rare alleles among a population of wild-type alleles.
    Type: Grant
    Filed: July 18, 2014
    Date of Patent: August 18, 2020
    Assignee: President and Fellows of Harvard College
    Inventors: Xi Chen, David Yu Zhang, Peng Yin
  • Publication number: 20200116074
    Abstract: An ignition system for a gaseous fuel engine includes an igniter and an actuator structured to apply an actuating force to a piston within the igniter, to autoignite an ignition charge of fuel and air within the igniter. A housing of the igniter includes a gas orifice having a flow area that is increased between a combustion pre-chamber in the igniter and a main combustion chamber in the engine, to limit velocity of outgoing combustion gases to below a threshold velocity for engine mis-fire.
    Type: Application
    Filed: October 11, 2018
    Publication date: April 16, 2020
    Applicant: Caterpillar Inc.
    Inventor: David Yu Zhang Chang
  • Patent number: 10616309
    Abstract: Systems, methods, and non-transitory computer readable media can receive a request to upload a file from a user. A server of a plurality of servers can be determined to process the request to upload the file. An indication of an amount of the file that has been received by the server prior to the request to upload the file can be provided. At least a portion of the file that has not been received by the server prior to the request to upload the file can be received.
    Type: Grant
    Filed: December 30, 2016
    Date of Patent: April 7, 2020
    Assignee: Facebook, Inc.
    Inventors: Eran Ambar, Trevor Charles Armstrong, David Yu Zhang
  • Publication number: 20200002759
    Abstract: Provided are methods for characterizing nucleotide accessibility and nucleic acid structure at single nucleotide resolution, using a combination of low-yield bisulfite conversion and next-generation sequencing (NGS). Cytosine (C) nucleotides that are in base-paired states or bound to proteins, etc. are less accessible to chemical reactions and thus exhibit lower bisulfite conversion yields. Analysis of NGS results of a low-yield bisulfite conversion product can thus inform nucleotide accessibility and nucleic acid structure. Compared to other methods for chemical probing of nucleic acid structure, the present methods provide higher information throughput, because each NGS read simultaneously reports on the base pair status of multiple nucleotides.
    Type: Application
    Filed: June 28, 2019
    Publication date: January 2, 2020
    Applicant: William Marsh Rice University
    Inventors: David Yu ZHANG, Jin-Hyung BAE