JP5907880B2 - クラスタリングを用いて生物学的持続状態の存在を検出するためのシステムおよび方法 - Google Patents

クラスタリングを用いて生物学的持続状態の存在を検出するためのシステムおよび方法 Download PDF

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JP5907880B2
JP5907880B2 JP2012539000A JP2012539000A JP5907880B2 JP 5907880 B2 JP5907880 B2 JP 5907880B2 JP 2012539000 A JP2012539000 A JP 2012539000A JP 2012539000 A JP2012539000 A JP 2012539000A JP 5907880 B2 JP5907880 B2 JP 5907880B2
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meca
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JP2013510579A (ja
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ジュリュ ル，
ジュリュ ル，
ジフア ワン，
ジフア ワン，
アントニオ アレバロ レイス，
アントニオ アレバロ レイス，
エリック アラン グスタフソン，
エリック アラン グスタフソン，
ジョン スティーブン ライリー，
ジョン スティーブン ライリー，
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Beckman Coulter Inc
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    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • G—PHYSICS
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    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
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    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/30—Unsupervised data analysis

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JP2012539000A 2009-11-13 2010-11-12 クラスタリングを用いて生物学的持続状態の存在を検出するためのシステムおよび方法 Expired - Fee Related JP5907880B2 (ja)

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US26114709P 2009-11-13 2009-11-13
US61/261,147 2009-11-13
PCT/US2010/056455 WO2011060222A2 (en) 2009-11-13 2010-11-12 Systems and methods for detecting the presence of a biological status using clustering

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JP2015080636A Division JP2015165413A (ja) 2009-11-13 2015-04-10 クラスタリングを用いて生物学的持続状態の存在を検出するためのシステムおよび方法

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JP2013510579A JP2013510579A (ja) 2013-03-28
JP2013510579A5 JP2013510579A5 (https=) 2013-12-12
JP5907880B2 true JP5907880B2 (ja) 2016-04-26

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JP2015080636A Pending JP2015165413A (ja) 2009-11-13 2015-04-10 クラスタリングを用いて生物学的持続状態の存在を検出するためのシステムおよび方法

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US (3) US8442924B2 (https=)
EP (1) EP2499591A2 (https=)
JP (2) JP5907880B2 (https=)
KR (1) KR20120101065A (https=)
CN (1) CN102713919B (https=)
BR (1) BR112012011262A2 (https=)
RU (1) RU2012124051A (https=)
WO (1) WO2011060222A2 (https=)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2010076013A1 (de) * 2008-12-30 2010-07-08 Qiagen Gmbh Verfahren zum nachweis methicillin-resistenter staphylococcus aureus (mrsa)-stämme
JP5907880B2 (ja) 2009-11-13 2016-04-26 ベックマン コールター， インコーポレイテッド クラスタリングを用いて生物学的持続状態の存在を検出するためのシステムおよび方法
EP2617836A1 (en) * 2012-01-23 2013-07-24 Steffen Mergemeier Method for detecting a methicillin resistant coagulase positive Staphylococcus aureus strain
EP2887245A1 (en) * 2013-12-20 2015-06-24 Dassault Systèmes A computer-implemented method for designing a biological model
WO2022260129A1 (ja) * 2021-06-09 2022-12-15 国立大学法人京都大学 情報処理装置、情報処理方法、及びプログラム

Family Cites Families (27)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5210015A (en) 1990-08-06 1993-05-11 Hoffman-La Roche Inc. Homogeneous assay system using the nuclease activity of a nucleic acid polymerase
US6335184B1 (en) * 1993-07-23 2002-01-01 Bio-Rad Laboratories, Inc. Linked linear amplification of nucleic acids
US5702895A (en) 1995-01-19 1997-12-30 Wakunaga Seiyaku Kabushiki Kaisha Method and kit for detecting methicillin-resistant Staphylococcus aureus
JP3957338B2 (ja) * 1996-02-23 2007-08-15 株式会社カイノス 診断薬
US6358519B1 (en) * 1998-02-16 2002-03-19 Ruth S. Waterman Germ-resistant communication and data transfer/entry products
JP2003523175A (ja) * 1999-08-04 2003-08-05 ファルマシア・アンド・アップジョン・カンパニー スタフィロコッカスアウレウスＵＤＰ−Ｎ−アセチルエノールピルビルグルコサミン＝リダクターゼ（Ｓ．ａｕｒｅｕｓＭｕｒＢ）の結晶化および構造決定
ES2281520T3 (es) 2001-03-15 2007-10-01 Jacques Schrenzel Deteccion de staphylococcus aureus resistente a meticilina (sarm).
US20030014420A1 (en) * 2001-04-20 2003-01-16 Jessee Charles B. Method and system for data analysis
FR2844807B1 (fr) * 2002-09-23 2005-11-11 Rambach Alain Procede de detection de microorganismes resistants a la meticilline
EP1603674B1 (en) * 2003-02-05 2016-01-06 Iquum, Inc. Sample processing
EP1529847B1 (en) 2003-11-07 2006-04-05 Federal Rep. of Germany repr. by the Ministry of Health & Soc. Security, the latter repr. by the Pres. of the Robert Koch Ins. Method for detecting methicillin resistant Staphylococcus aureus (MRSA)
EP1541696A1 (en) 2003-12-09 2005-06-15 Institut Pasteur A DNA macro-array for staphylococcus aureus identification and typing
EP1776458A2 (en) 2004-07-30 2007-04-25 Agencourt Bioscience Corporation Methods of isolating nucleic acids using multifunctional group-coated solid phase carriers
US7368422B2 (en) * 2005-02-28 2008-05-06 Novartis Vaccines And Diagnostics Inc. Semi-synthetic rearranged vancomycin/desmethyl-vancomycin-based glycopeptides with antibiotic activity
GB0504537D0 (en) * 2005-03-04 2005-04-13 Blaze Venture Technologies Ltd Method and device for bacterial sampling
US20070196820A1 (en) * 2005-04-05 2007-08-23 Ravi Kapur Devices and methods for enrichment and alteration of cells and other particles
US7838221B2 (en) * 2005-10-11 2010-11-23 Geneohm Sciences, Inc. Sequences for detection and identification of methicillin-resistant Staphylococcus aureus (MRSA)
AU2007249812B2 (en) 2006-05-12 2013-08-15 Cepheid DNA recombination junction detection
JP5183635B2 (ja) * 2006-10-18 2013-04-17 ビオメリュー Ｐｖｌ産生黄色ブドウ球菌のインビトロにおける診断方法
WO2008129428A2 (en) 2007-04-19 2008-10-30 Molecular Detection Inc. Methods, compositions and kits for detection and analysis of antibiotic-resistant bacteria
US7888075B2 (en) * 2007-07-31 2011-02-15 Quest Diagnostics Investments Incorporated Detection of methicillin-resistant and methicillin-sensitive Staphylococcus aureus in biological samples
US8229678B2 (en) * 2008-07-25 2012-07-24 Beckman Coulter, Inc. Methods and systems for transforming particle data
US8000940B2 (en) * 2008-10-08 2011-08-16 Beckman Coulter, Inc. Shape parameter for hematology instruments
US8154273B2 (en) * 2008-10-10 2012-04-10 Beckman Coulter, Inc. Detecting and handling coincidence in particle analysis
US8581927B2 (en) * 2008-11-04 2013-11-12 Beckman Coulter, Inc. Multidimensional particle analysis data cluster reconstruction
PL2356465T3 (pl) * 2008-11-13 2015-04-30 Beckman Coulter Inc Sposób korekcji interferencji cząsteczkowej przy oznaczaniu hemoglobiny
JP5907880B2 (ja) 2009-11-13 2016-04-26 ベックマン コールター， インコーポレイテッド クラスタリングを用いて生物学的持続状態の存在を検出するためのシステムおよび方法

Also Published As

Publication number Publication date
WO2011060222A9 (en) 2011-07-14
US20130196334A1 (en) 2013-08-01
JP2013510579A (ja) 2013-03-28
US20110131159A1 (en) 2011-06-02
EP2499591A2 (en) 2012-09-19
US8442924B2 (en) 2013-05-14
RU2012124051A (ru) 2013-12-20
CN102713919A (zh) 2012-10-03
BR112012011262A2 (pt) 2019-09-24
CN102713919B (zh) 2016-07-06
WO2011060222A2 (en) 2011-05-19
US20170140096A1 (en) 2017-05-18
JP2015165413A (ja) 2015-09-17
KR20120101065A (ko) 2012-09-12
US9519751B2 (en) 2016-12-13

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