Gygi
Bret Gygi, Brookfield, WI US
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20160050921 | COMPOSITIONS AND METHODS FOR ENHANCING PLANTH GROWTH - Described herein are compositions comprising one or more flavonoids or derivatives thereof for enhancing plant growth and methods for treating plants, plant parts with one or more flavonoids and derivatives thereof. | 02-25-2016 |
Carl Gygi, Colorado Springs, CO US
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20110103439 | APPARATUS AND METHODS FOR IMPROVED HIGH-SPEED COMMUNICATION SYSTEMS - Apparatus and methods for improved high-speed communication by exchanging low-speed information regarding the high-speed exchanges over the same communication medium. In one exemplary embodiment, a communication device includes a high-speed transceiver adapted to exchange high-speed data with another device via a communication medium using high-frequency signals. The device also includes a low-speed component adapted to exchange low-speed information over the same communication medium as low-frequency signals. The low-frequency signals may be applied as common mode signals to a differential communication path so as to not interfere with the high-speed data exchanges. In another embodiment, a high-pass filter may be included in the device to remove the low-frequency signals before the high-speed data is applied to the high-speed transceiver. Responsive to receipt of the low-speed information, a device may adjust parameters of the transceiver to improve the high-speed data exchanges. | 05-05-2011 |
20140052404 | METHODS AND STRUCTURE FOR ANALYZING DIFFERENT SIGNALING PATHWAYS THROUGH A TEST SIGNAL SELECTION HIERARCHY - Methods and structure are disclosed for analyzing different signaling pathways through a test signal selection hierarchy utilizing test patterns. One embodiment comprises an integrated circuit that includes a block of circuitry, a test signal generator, and a test signal selection hierarchy. The block of circuitry generates internal operational (TOP) signals for performing functions. The test signal generator generates test patterns that correspond with the IOP signals. The test signal selection hierarchy receives IOP signals and the test patterns, and selectively routes received signals to test pads. The test signal selection hierarchy routes the test patterns via signaling pathways through the test signal selection hierarchy to provide outputs signals on the test pads. The output signals are usable by an external test system to determine two or more of: a crosstalk, inter-symbol interference, a signal skew, and a threshold voltage for detecting bit transition on signaling pathways. | 02-20-2014 |
Carl E. Gygi, Colorado Springs, CO US
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20120296598 | COMPENSATING FOR JITTER DURING DDR3 MEMORY DELAY LINE TRAINING - A method for compensating for jitter during DDR3 delay line training may include using a computer or processor to perform the steps of executing a plurality of tests for each one of a plurality of delay values for an interconnect delay between a Double-Data-Rate Three (DDR3) memory controller and a DDR3 Synchronous Dynamic Random Access Memory (SDRAM); accumulating a plurality of test results for each plurality of tests for each one of the plurality of delay values; determining a plurality of final test results, where each final test result is associated with an accumulated plurality of test results; and determining a working window edge for the interconnect delay between the DDR3 memory controller and the DDR3 SDRAM utilizing the plurality of final test results. | 11-22-2012 |
20130091388 | HARDWARE QUEUE FOR TRANSPARENT DEBUG - A method for transparent debug of a hardware queue and recreation of an operational scenario comprising: use of a computer device to: monitor a plurality of inputs and outputs from a plurality of hardware queues associated as parts of a design; receive a request to save from an external source; pause one or more hardware queues upon command; receive hardware queue information from at least one of the paused hardware queues; dump said hardware queue information from at least one paused hardware queue; store the hardware queue information in a data storage connected to the computing device; compare the received information to stored data representative of a functional hardware queue; identify errors and failures in each monitored hardware queue from the comparing and; restore the hardware queue to a previous state. | 04-11-2013 |
20130262398 | SCATTER GATHER LIST FOR DATA INTEGRITY - A system and method for improving message passing between a computer and peripheral devices is disclosed. The system and method for improving message passing between a computer and peripheral devices incorporate data checking on the command/message data and each scatter gather list element. The method in accordance with the present disclosure enables a peripheral device to check the integrity of the message and ownership of the scatter gather list element before the data is processed. | 10-03-2013 |
Jeremy Gygi, Foxborough, MA US
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20090055090 | METHODS AND SYSTEMS FOR LOCATING POSITIONS - The methods and systems provide computer-generated software downloadable into cellular phone devices or other devices. The software programs the cellular device to mark and then locate a location based on its longitudinal and latitudinal position and elevation. The software utilizes all of the cellular device's capabilities to precisely identify locations using, but not limited to, GPS global positioning systems and Wi-Fi wireless fidelity data and information. The software informs the user of the marked location by displaying the position and pointing the user back to the marked location, in three dimensions, as needed, for example, to find the user's vehicle parked in a parking garage. | 02-26-2009 |
Jeremy Pace Gygi, Fox Borough, MA US
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20100059969 | Magnetic easy step in/out snow board binding - This invention describes a magnetic boot binding for snowboards. The magnetic boot binding secures a person onto a snowboard by magnetically holding the persons snowboard boots onto the snowboard. The magnetic binding utilizes hard magnets, electromagnets and/or other magnetic materials imbedded into or physically attached to the snowboard and/or the boots. If an electromagnet is used it can be electronically controlled by a remote controller to apply magnetic force, apply varying amount of magnetic force, and to release the magnetic force for quick releasing. | 03-11-2010 |
Steven Gygi, Boston, MA US
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20130004963 | Tyrosine, serine and threonine phosphorylation sites - The invention discloses 155 novel phosphorylation sites identified in carcinoma and leukemia, peptides (including AQUA peptides) comprising a phosphorylation site of the invention, antibodies specifically bind to a novel phosphorylation site of the invention, and diagnostic and therapeutic uses of the above. | 01-03-2013 |
20140336360 | Tyrosine, Serine and Threonine Phosphorylation Sites - The invention discloses 155 novel phosphorylation sites identified in carcinoma and leukemia, peptides (including AQUA peptides) comprising a phosphorylation site of the invention, antibodies specifically bind to a novel phosphorylation site of the invention, and diagnostic and therapeutic uses of the above. | 11-13-2014 |
Steven P. Gygi, Foxboro, MA US
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20090053742 | Capture and release based isotope tagged peptides and methods for using the same - The invention provides non-affinity based isotope tagged peptides, chemistries for making these peptides, and methods for using these peptides. In one aspect, tags comprise a reactive site (RS) for reacting with a molecule on a protein to form a stable association with the peptide (e.g., a covalent bond) and an anchoring site (AS) group for reversibly or removably anchoring the tag to a solid phase such as a resin support. Anchoring may be direct or indirect (e.g., through a linker molecule). Preferably, the anchoring site comprises a biotin compound. Preferably, the tag comprises a mass-altering label, such as a stable isotope, such that association of the tag with the peptide can be monitored by mass spectrometry. The reagents can be used for rapid and quantitative analysis of proteins or protein function in mixtures of proteins. | 02-26-2009 |
20110269161 | Methods, Compositions and Kits for High Throughput Kinase Activity Screening Using Mass Spectrometry and Stable Isotopes - A mass-spectrometry-based method and substrates are provided herein for large scale kinome activity profiling directly from crude lysates using 90 chemically synthesized peptide substrates with amino acid sequences derived from known phosphoproteins. Quantification of peptide phosphorylation rates was achieved via the use of stable isotope labeled synthetic peptides. Half of these peptides immediately or rapidly showed robust and site-specific phosphorylation after incubation with serum-starved HEK293 cell lysate. A method and substrates for obtaining 90 simultaneous activity measurements in a single-reaction format were developed and validated. Activating kinase pathways through insulin or EGF stimulation reproducibly altered the phosphorylation rates of peptides derived from known pathway protein substrates. While examining cell-cycle-specific activities with the panel, a peptide derived from phosphoinositide 3-kinase regulatory subunit demonstrated mitotic and tyrosine-specific phosphorylation, which was confirmed to be a Src kinase site in vivo. The kinome activity profiling strategy was successfully applied with lysates of each of: cells manipulated by various combination of mitogen stimulation, pharmacological perturbation and siRNA-directed kinase knockdown; seven different breast cancer cell lines treated with gefitinib; and each of normal and cancerous tissue samples from renal cell carcinoma patients. This method concurrently measures multiple peptide phosphorylation rates to provide a diagnostic fingerprint pattern for activated kinases, protein phosphatases, modulators of these enzymes, and pathways (kinome) from as little starting material as a few cells. | 11-03-2011 |
20120149883 | Detection and quantification of modified proteins - The invention provides a method detecting and quantifying proteins by mass spectrophotometric analysis using peptide internal standards and provides a highly sensitive way of detecting protein modifications. In one aspect, the invention provides a method for determining a site of ubiquitination in a polypeptide and for evaluating ubiquitination targets in a population of polypeptides. In this way, a proteome ubiquitination map can be obtained which comprises information relating to the ubiquitination states of a plurality of cellular polypeptides. Maps can be obtained for a variety of different types of cells and cell states. For example, ubiquitination targets in normal and diseased cells can be evaluated. Preferably, the map is stored as data files in a database. Individual ubiquitinated polypeptides identified can be used to generate molecular probes diagnostic of a cell state and/or can serve as targets for agents that modulate one or more cellular processes. | 06-14-2012 |
Steven P. Gygi, Foxborough, MA US
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20080214782 | Phosphopeptide compositions and anti-phosphopeptide antibody compositions and methods of detecting phosphorylated peptides - The present invention relates to phosphopeptide compositions and anti-phosphopeptide antibody compositions. Also provided are methods of identifying phosphorylation sites in phosphorylated peptides and phosphorylation site motifs. | 09-04-2008 |
20130252950 | TARGETING MTOR SUBSTRATES IN TREATING PROLIFERATIVE DISEASES - Provided are over 300 mTOR kinase targets identified by a comprehensive phosphoproteomics assay. Methods of targeting mTOR kinase targets, methods to determine the level of mTOR activity by measuring the level of phosphorylation of an mTOR targeted phosphorylation site, methods for distinguishing different classes of mTOR activity in a cell based on phosphoproteomic analysis of mTOR-targeted proteins are also provided. Also provided is the classification of a hyperproliferative disease based on phosphoproteomic analysis of mTOR-targeted proteins, as well as the personalization of therapeutic methods for the treatment of hyperproliferative disease based on phosphoproteomics. Also provided are therapeutic methods including administering to a subject an mTOR inhibitor, an mTOR inhibitor and an additional kinase inhibitor, or a dual inhibitor of mTOR and an additional kinase based on the phosphorylation levels of mTOR targets determined in the subject. Some aspects of this invention relate to the discovery that GrblO is an mTOR-targeted tumor suppressor gene. | 09-26-2013 |
20130334414 | MASS SPECTROMETRY FOR MULTIPLEXED QUANTITATION USING MULTIPLE FREQUENCY NOTCHES - A method of performing a mass spectrometry analysis includes labeling each of a plurality of samples with a corresponding chemical tag; forming a first plurality of ions from molecules in the samples; selecting a subset of the first plurality of ions, the subset being selected by isolating ions of the first plurality of ions in a plurality of ranges of mass-to-charge; forming a second plurality of ions by fragmenting ions in the subset; and measuring information indicative of a quantity of each of the plurality of chemical tags present in each of the plurality of samples. | 12-19-2013 |
20150293058 | ACCURATE AND INTERFERENCE-FREE MULTIPLEXED QUANTITATIVE PROTEOMICS USING MASS SPECTROMETRY - Embodiments are directed to a method, a computer readable medium encoded with instructions that, when executed, perform a method, and a system for performing mass spectrometry analysis. Molecules of different samples may be labeled with a chemical tag, allowing a multiplexed analysis of multiple samples. The labeled molecules may be fragmented, each fragmented molecule creating at least two separate ions. The relative abundance of each of the heavier ions, which may comprise the original molecule from the sample, may be measured. A relative abundance of the labeled molecules in each of the samples may be determined from the measured relative abundances of the heavier ions. | 10-15-2015 |