Patents Examined by Ardin H. Marschel
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Patent number: 7009041Abstract: A method, composition and kit for synthesizing multiple copies of a target nucleic acid sequence autocatalytically under conditions of substantially constant temperature, ionic strength, and pH are provided in which multiple RNA copies of the target sequence autocatalytically generate additional copies using a mixture of blocked and unblocked primers and/or promoter-primers to initiate DNA and RNA synthesis, preferably with reduced non-specific product formation. The invention is useful for generating copies of a nucleic acid target sequence for purposes that include assays to quantitate specific nucleic acid sequences in clinical, environmental, forensic and similar samples, cloning and generating probes.Type: GrantFiled: June 6, 1995Date of Patent: March 7, 2006Assignee: Gen-Probe IncorporatedInventors: Sherrol H. McDonough, Daniel L. Kacian, Nanibhushan Dattagupta, Diane L. McAllister, Philip W. Hammond, Thomas B. Ryder
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Patent number: 7010431Abstract: A method is described for effecting computer-implemented decision-support in the selection of a drug therapy of patients having a viral disease. A rules database is provided and patient data is entered including genotype data on the viral genome of the viral disease. The rules database comprises a number of associated rules for each available drug for treatment of the viral disease. Each rule indicates the suitability of the drug for treatment of a specific viral genotype. The patient data is entered into the rules database, the database providing an output of drugs suitable for therapy. The drugs suitable for therapy are displayed in a ranking in accordance with their suitability indication, for selection.Type: GrantFiled: January 28, 2002Date of Patent: March 7, 2006Assignee: F. Hoffman-LaRoche Ltd.Inventor: Charles Achim Bernard Boucher
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Patent number: 7006925Abstract: Waveform shaping by Fourier transformation is performed on data of N points from the head of detected data with a parameter of a previously set peak interval (S1, S2), base sequence is determined as to data of M points (M<N) from the head of the data of N points (S3), and a peak interval is obtained from the result of the sequence determination (S4). Waveform shaping by Fourier transformation is performed on data of N points from a position returning by L points (L<M) from final data of M points subjected to the sequence determination with a parameter of a precedently obtained peak interval, and thereafter the sequence determination, peak interval calculation and waveform shaping are similarly repeated. Thus, noise can be removed on the basis of Fourier transformation also as to a data section where a migration speed changes, for precisely determining the base sequence.Type: GrantFiled: December 6, 2001Date of Patent: February 28, 2006Assignee: Shimadzu CorporationInventor: Makoto Hazama
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Patent number: 7005509Abstract: The present invention provides nucleotide and amino acid sequences that identify and encode novel expressed chemokines (PANEC-1 and PANEC-2) from human pancreas cells. The present invention also provides for antisense molecules to the nucleotide sequences which encode PANEC-1 and PANEC-2, expression vectors for the production of purified PANEC-1 and PANEC-2, antibodies capable of binding specifically to PANEC-1 and PANEC-2, hybridization probes or oligonucleotides for the detection of PANEC-1- or PANEC-2-encoding nucleotide sequences, genetically engineered host cells for the expression of PANEC-1 and PANEC-2, diagnostic tests for chemokine activation based on PANEC-1- and PANEC-2-encoding nucleic acid molecules and antibodies capable of binding specifically to the protein.Type: GrantFiled: February 17, 1995Date of Patent: February 28, 2006Assignee: Incyte CorporationInventors: Roger Coleman, Olga Bandman, Craig G. Wilde
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Patent number: 7003440Abstract: A method for use in displaying an expression phenomenon in a living matter that are capable of displaying (printing), in a format directly appealing to the eyes or sense, information indicative of gene expression phenomena occurring with time to assist a researcher with easy elucidation of a gene network mechanism.Type: GrantFiled: July 13, 2001Date of Patent: February 21, 2006Inventors: Takashi Gojobori, Yuzuru Tanaka, Toshitsugu Okayama
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Patent number: 6996472Abstract: Methods of compensating for drift in fingerprint spectra of microorganisms caused by changes in their environment are disclosed. These methods of compensating for drift permit identification of microorganisms from their fingerprint spectra regardless of the environment from which the microorganisms are obtained. Furthermore, the disclosed methods may be used to construct coherent databases of fingerprint spectra that may be expanded even though the standard database conditions are no longer experimentally achievable. In particular embodiments, methods of compensating for drift in pyrolysis mass spectra, constructing coherent pyrolysis mass spectral databases, and identifying bacteria from their pyrolysis mass spectra are disclosed.Type: GrantFiled: October 10, 2001Date of Patent: February 7, 2006Assignee: The United States of America as represented by the Department of Health and Human ServicesInventors: Jon G. Wilkes, Fatemeh Rafii, Katherine L. Glover, Manuel Holcomb, Xiaoxi Cao, John B. Sutherland
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Patent number: 6989434Abstract: The present invention provides certain cationic lipids containing stigmasterol, ergosterol and cholic acid groups. Compounds of the invention are useful, either alone or in combination with other lipid aggregate-forming components (e.g., DOPE, DOSPA, DOTMA or cholesterol) for formulation into liposomes or other lipid aggregates. Such aggregates are cationic, and able to form stable complexes with anionic macromolecules, such as nucleic acids. The cationic lipids of the invention are useful in methods of transfecting cells, particularly to introduce nucleic acids into cells. The invention also related to kits for the preparation of lipid aggregates and to lipid aggregates and compositions for transfection of cells.Type: GrantFiled: June 4, 1999Date of Patent: January 24, 2006Assignee: Invitrogen CorporationInventors: Gulilat Gebeyehu, Joel A. Jessee
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Patent number: 6988041Abstract: An unliganded form of Staphylococcus aureus NAD synthetase (S. aureus NadE) has been crystallized, and the three-dimensional x-ray crystal structure has been solved to 2.3 ? resolution. The x-ray crystal structure is useful for solving the structure of other molecules or molecular complexes, and designing inhibitors of S. aureus NadE activity.Type: GrantFiled: January 30, 2001Date of Patent: January 17, 2006Assignee: Pharmacia & Upjohn CompanyInventors: Timothy E. Benson, Donald Bryan Prince
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Patent number: 6979424Abstract: An analysis device comprises a body having a reaction chamber for chemically reacting a sample, a separation region for separating components of the sample, and a transition region connecting the reaction chamber to the separation region. The transition region includes at least one valve for controlling the flow of fluid between the reaction chamber and the separation region. Further, the transition region thermally isolates the reaction chamber from the separation region. In a preferred embodiment, the reaction chamber is an amplification chamber for amplifying nucleic acid in the sample, and the separation region comprises an electrophoresis channel containing a suitable matrix material, such as electrophoresis gel or buffer, for separating nucleic acid fragments. Electrodes are embedded in the body for separation of sample components. The body may also be surrounded by external, functional components such as an optical detector for detecting separated components of the sample.Type: GrantFiled: August 13, 2001Date of Patent: December 27, 2005Assignee: CepheidInventors: M. Allen Northrup, Kurt E. Petersen, William A. McMillan, Gregory T. A. Kovacs
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Patent number: 6973388Abstract: The present invention provides methods for monitoring disease states in a subject, as well as methods for monitoring the levels of effect of therapies upon a subject having one or more disease states. The methods involve: (i) measuring abundances of cellular constituents in a cell from a subject to obtain a diagnostic profile, (ii) measuring abundances of cellular constituents in a cell of one or more analogous subjects to obtain perturbation response profiles which correlate to a particular disease or therapy, and (iii) determining the interpolated perturbation response profile or profiles which best fit the diagnostic profile. In other aspects, the invention also provides a computer system capable of performing the methods of the invention, databases comprising perturbation response profiles for one or more diseases and/or therapies, and kits for determining levels of disease states and/or therapeutic effects according to the methods of the invention.Type: GrantFiled: February 14, 2001Date of Patent: December 6, 2005Assignee: Rosetta Inpharmatics LLCInventors: Stephen H. Friend, Roland Stoughton
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Patent number: 6960474Abstract: Selective androgen receptor modulators (SARMs) having antagonist activity in hormone-dependent tumors while exhibiting no activity or agonist activity against other nontumor tissues containing the androgen receptor as well as methods for identifying, designing and using SARMs are provided.Type: GrantFiled: June 20, 2001Date of Patent: November 1, 2005Assignee: Bristol-Myers Squibb CompanyInventors: Mark E. Salvati, Marco M. Gottardis, Ricardo M. Attar, Stanley R. Krystek, Jr., John S. Sack
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Patent number: 6953676Abstract: Disclosed are devices for amplifying a preselected polynucleotide in a sample by conducting a polynucleotide polymerization reaction. The devices comprise a substrate microfabricated to define a sample inlet port and a mesoscale flow system, which extends from the inlet port. The mesoscale flow system includes a polynucleotide polymerization reaction chamber in fluid communication with the inlet port which is provided with reagents required for polymerization and amplification of a preselected polynucleotide. In one embodiment the devices may be utilized to implement a polymerase chain reaction (PCR) in the reaction chamber (PCR chamber).Type: GrantFiled: December 15, 1998Date of Patent: October 11, 2005Assignee: Trustees of the University of PennsylvaniaInventors: Peter Wilding, Larry J. Kricka
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Patent number: 6949638Abstract: Systems, methods, and products are described for synthesizing probe arrays of polymers. A mask is used that includes reticle areas, each of which includes a number of reticles associated with a same synthesis area on a substrate. A method includes (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate; (b) coupling monomers on the first synthesis area at locations determined by the first reticle; (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and (d) coupling monomers on the first synthesis area at locations determined by the second reticle. The monomers may be, for example, nucleotides, amino acids or saccharides.Type: GrantFiled: April 3, 2001Date of Patent: September 27, 2005Assignee: Affymetrix, Inc.Inventors: Michael P. Mittmann, Earl A. Hubbell
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Patent number: 6950752Abstract: The invention provides methods for removing unwanted response components (i.e., “artifacts”) from a measured biological profile comprising measurements of a plurality of cellular constituents of a cell or organism in response to a perturbation. The methods involve subtracting from the measured biological profile one or more artifact patterns, each of which comprises measurements of changes in cellular constituents as a result of deviation of one or more experimental variables, such as cell culture density and temperature, hybridization temperature, as well as concentrations of total RNA and/or hybridization reagents, from desired values.Type: GrantFiled: December 23, 1998Date of Patent: September 27, 2005Assignee: Rosetta Inpharmatics LLCInventors: Stephen H. Friend, Roland Stoughton, Yudong He
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Patent number: 6943240Abstract: The invention pertains to murine TLR9 and related TLR9s which include murine-specific amino acids, as well as nucleic acids which encode those polypeptides. The present invention also includes fragments and biologically functional variants of the murine TLR9. The invention further relates to methods of using such murine and non-murine TLR9 nucleic acids and polypeptides, especially in methods for screening for agonists and antagonists of immunostimulatory CpG nucleic acids. Also included are murine TLR9 inhibitors which inhibit murine TLR9 activity by inhibiting the expression or function of murine TLR9. In a further aspect the present invention pertains to murine TLR7 and murine TLR8, as well as related TLR7 and TLR8 molecules which include murine-specific amino acids, as well as nucleic acids which encode those polypeptides. The present invention also includes fragments and biologically functional variants of the murine TLR7 and TLR8.Type: GrantFiled: September 17, 2001Date of Patent: September 13, 2005Assignee: Coley Pharmaceuticals GmbHInventors: Stefan Bauer, Grayson Lipford, Hermann Wagner
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Patent number: 6934639Abstract: The present invention relates to the three dimensional structure of human collagenase 3 (MMP-13), as well as to (i) methods of using the MMP-13 structure to rationally design or identify compounds or molecules that inhibit or activate MMP-13 activity, and (ii) compounds identified using said methods.Type: GrantFiled: February 25, 2000Date of Patent: August 23, 2005Assignee: WyethInventors: James M. Chen, Dominick Mobilio, Franklin J. Moy, Kevin D. Parris, Robert Powers, Zhang Bao Xu
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Patent number: 6931325Abstract: The present invention relates to multi-phase protein separation methods capable of resolving and characterizing large numbers of cellular proteins, including methods for efficiently facilitating the transfer of protein samples between separation phases. In particular, the present invention provides systems and methods for the generation of multi-dimensional protein maps. The present invention thus provides improved methods for the analysis of samples containing large numbers of proteins.Type: GrantFiled: April 26, 2002Date of Patent: August 16, 2005Assignee: Regents of the University of MichiganInventors: Daniel B. Wall, David M. Lubman, Timothy Barder
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Patent number: 6931329Abstract: A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {Fh} is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {FhOBS} if structure factor set {Fh} was correct, and (2) the likelihood that an electron density map resulting from {Fh} is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {Fh} is then adjusted to maximize the likelihood of {Fh} for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.Type: GrantFiled: February 25, 2000Date of Patent: August 16, 2005Assignee: The Regents of the University of CaliforniaInventor: Thomas C. Terwilliger
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Patent number: 6926865Abstract: An apparatus for identifying an unknown DNA sample. The apparatus includes a plurality of detection nodes, each of which is operable for allowing an interaction between a known DNA sample and an unknown DNA sample, and for generating an output signal if hybridization occurs between the known DNA sample and the unknown DNA sample. The apparatus further includes a decoder operative for receiving an input signal indicative of which of the plurality of detection nodes should be selected for processing and for outputting control signals which operate to activate the selected detection node. Further, each of the detection nodes comprises a first floating gate transistor having a conductance value which varies if hybridization occurs between the known DNA sample and the unknown DNA sample contained in the first transistor. This change of conductance value is utilized to generate the output signal which indicates that hybridization has occurred.Type: GrantFiled: February 11, 2002Date of Patent: August 9, 2005Assignee: Matsushita Electric Industrial Co., Ltd.Inventor: John K. Howard
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Patent number: 6925394Abstract: The invention provides an X-ray crystal structure of the 30S ribosome, obtained from Thermus thermophilus 30S subunit, having a tetragonal space group P41212 with unit cell dimensions of a=401.4±4.0 ?, b=401.4±4.0 ?, c=175.9±5.0 ?. An advantageous feature of the structure is that it diffracts beyond 3 ? resolution. The invention also provides a crystal of 30S having the three dimensional atomic coordinates of the 30S ribosome, the coordinates being provided in Tables 1A and 1B. The data may be used for the rational design and modelling of inhibitors for the 30S ribosome, which have potential use as antibiotics.Type: GrantFiled: July 13, 2001Date of Patent: August 2, 2005Assignees: University of Utah Research Foundation, Medical Research CouncilInventors: Venkatraman Ramakrishnan, Ditlev Egeskov Brodersen, Andrew Philip Carter, Brian Thomas Wimberly, William Melvon Clemons, Jr.