Computational systems bioinformatics :: CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 /
This volume contains about 40 papers covering many of the latest developments in the fast-growing field of bioinformatics. The contributions span a wide range of topics, including computational genomics and genetics, protein function and computational proteomics, the transcriptome, structural bioinf...
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Format: | Elektronisch Tagungsbericht E-Book |
Sprache: | English |
Veröffentlicht: |
London : Singapore ; Hackensack, NJ :
Imperial College Press ; Distributed by World Scientific,
2007.
|
Schriftenreihe: | Series on advances in bioinformatics and computational biology.
|
Schlagworte: | |
Online-Zugang: | DE-862 DE-863 |
Zusammenfassung: | This volume contains about 40 papers covering many of the latest developments in the fast-growing field of bioinformatics. The contributions span a wide range of topics, including computational genomics and genetics, protein function and computational proteomics, the transcriptome, structural bioinformatics, microarray data analysis, motif identification, biological pathways and systems, and biomedical applications. Abstracts from the keynote addresses and invited talks are also included. The papers not only cover theoretical aspects of bioinformatics but also delve into the application of n. |
Beschreibung: | 1 online resource (xvi, 454 pages :) |
Bibliographie: | Includes bibliographical references and index. |
ISBN: | 9781860948732 1860948731 1281867594 9781281867599 9786611867591 6611867597 |
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245 | 1 | 0 | |a Computational systems bioinformatics : |b CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 / |c editors, Peter Markstein, Ying Xu. |
246 | 3 | |a CSB 2007 Conference proceedings | |
246 | 3 | 0 | |a CSB2007 Conference proceedings |
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504 | |a Includes bibliographical references and index. | ||
588 | 0 | |a Print version record. | |
505 | 0 | |a Preface; Committees; Referees; Keynote Address; Quantitative Aspects of Gene Regulation in Bacteria: Amplification. Threshold, and Combinatorial Control Terry Hwa; Whole-Genome Analysis of Dorsal Gradient Thresholds in the Drosophila Embryo Julia ZeitlingeK Rob Zinzen, Dmitri Papatsenko et al.; Invited Talks; Learning Predictive Models of Gene Regulation Christina Leslie; The Phylofacts Phylogenomic Encyclopedias: Structural Phylogenomic Analysis Across the Tree of Life Kimmen Golander; Mapping and Analysis of the Human Interactome Network Kavitha Venkatesan; 1. INTRODUCTION | |
505 | 8 | |a Gene-Centered Protein-DNA lnteractome Mapping A.J. Marian WalhoutProteomics; Algorithm for Peptide Sequencing by Tandem Mass Spectrometry Based on Better Preprocessing and Anti-S ymmetric Computational Model Kang Ning and Hon Wai Leong; 1. INTRODUCTION; Preprocessing to remove noisy peaks; The anti-symmetric problem; 2. ANALYSIS OF PROBLEMS AND CURRENT ALGORITHMS; 2.1. General Terminologies; 2.2. Datasets; 2.3. Problems Analysis; 3. NEW COMPUTATIONAL MODELS AND ALGORITHM; 3.1. Preprocessing to remove noisy peaks and introduce pseudo peaks; 3.2. The Anti-symmetric Problem | |
505 | 8 | |a 3.3. Novel Peptide Sequencing Algorithm4. EXPERIMENTS; 4.1. Experiment Settings; 4.2. Results; 5. CONCLUSIONS; References; Algorithms for Selecting Breakpoint Locations to Optimize Diversity in Protein Engineering by Site-Directed Protein Recombination Wei Zheng, Xiaoduan Ye, Alan A4 Friedman and Chris Bailey-Kellogg; 1. INTRODUCTION; 2. METHODS; 2.1. Library Diversity; 2.2. Metrics for Breakpoint Selection; 2.3. Dynamic Programming for Breakpoint Selection; 3. RESULTS A N D DISCUSSION; 4. CONCLUSION; ACKNOWLEDGMENTS; References | |
505 | 8 | |a An Algorithmic Approach to Automated High-Throughput Identification of Disulfide Connectivity in Proteins Using Tandem Mass Spectrometry Timothy Lee, Rahul Singh, Ten-Yang Yen and Bruce Macher1. INTRODUCTION; 1.1. Comparison of the Proposed Approach with Related Works; 2. THE PROPOSED METHOD; 2.1. Problem Formulation; 2.2. Algorithmic Framework; 2.2.1. Finding the MS spectrum match; 2.2.2. Finding the MS/MS spectrum match; 2.2.3. Finding a perfect matching of maximum weight for a fully connected graph; 2.2.4. Consideration of missed proteolytic cleavages and intra-molecular bonded cysteines | |
505 | 8 | |a 2.2.5. Peak finding in the presence of noise2.2.6. Addressing isotopic variation and neutral loss; 2.2.7. Interpretation of peaks given charge state uncertainty; 2.2.8. Overall complexity; 3. EXPERIMENTAL RESULTS; 3.1. Description of the Data and Experimental Procedures; 3.2. Summary of Results; 3.2.1. Analysis of the effect of varying threshold t on results; 3.2.2. Comparison with MS2Assign program; 4. CONCLUSIONS AND DISCUSSION; Acknowledgments; References; Biomedical Application; Cancer Molecular Pattern Discovery by Subspace Consensus Kernel Classification Xiaoxu Hun; 1. INTRODUCTION | |
520 | |a This volume contains about 40 papers covering many of the latest developments in the fast-growing field of bioinformatics. The contributions span a wide range of topics, including computational genomics and genetics, protein function and computational proteomics, the transcriptome, structural bioinformatics, microarray data analysis, motif identification, biological pathways and systems, and biomedical applications. Abstracts from the keynote addresses and invited talks are also included. The papers not only cover theoretical aspects of bioinformatics but also delve into the application of n. | ||
546 | |a English. | ||
650 | 0 | |a Bioinformatics |v Congresses. | |
650 | 0 | |a Biological systems |x Computer simulation |v Congresses. | |
650 | 0 | |a Biological systems |x Simulation methods |v Congresses. | |
650 | 0 | |a Computational biology |v Congresses. | |
650 | 0 | |a Systems biology. |0 http://id.loc.gov/authorities/subjects/sh2008002926 | |
650 | 1 | 2 | |a Computational Biology |
650 | 2 | 2 | |a Systems Biology |
650 | 2 | 2 | |a Models, Genetic |
650 | 2 | 2 | |a Models, Molecular |
650 | 6 | |a Bio-informatique |v Congrès. | |
650 | 6 | |a Systèmes biologiques |x Simulation par ordinateur |v Congrès. | |
650 | 6 | |a Systèmes biologiques |x Méthodes de simulation |v Congrès. | |
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contents | Preface; Committees; Referees; Keynote Address; Quantitative Aspects of Gene Regulation in Bacteria: Amplification. Threshold, and Combinatorial Control Terry Hwa; Whole-Genome Analysis of Dorsal Gradient Thresholds in the Drosophila Embryo Julia ZeitlingeK Rob Zinzen, Dmitri Papatsenko et al.; Invited Talks; Learning Predictive Models of Gene Regulation Christina Leslie; The Phylofacts Phylogenomic Encyclopedias: Structural Phylogenomic Analysis Across the Tree of Life Kimmen Golander; Mapping and Analysis of the Human Interactome Network Kavitha Venkatesan; 1. INTRODUCTION Gene-Centered Protein-DNA lnteractome Mapping A.J. Marian WalhoutProteomics; Algorithm for Peptide Sequencing by Tandem Mass Spectrometry Based on Better Preprocessing and Anti-S ymmetric Computational Model Kang Ning and Hon Wai Leong; 1. INTRODUCTION; Preprocessing to remove noisy peaks; The anti-symmetric problem; 2. ANALYSIS OF PROBLEMS AND CURRENT ALGORITHMS; 2.1. General Terminologies; 2.2. Datasets; 2.3. Problems Analysis; 3. NEW COMPUTATIONAL MODELS AND ALGORITHM; 3.1. Preprocessing to remove noisy peaks and introduce pseudo peaks; 3.2. The Anti-symmetric Problem 3.3. Novel Peptide Sequencing Algorithm4. EXPERIMENTS; 4.1. Experiment Settings; 4.2. Results; 5. CONCLUSIONS; References; Algorithms for Selecting Breakpoint Locations to Optimize Diversity in Protein Engineering by Site-Directed Protein Recombination Wei Zheng, Xiaoduan Ye, Alan A4 Friedman and Chris Bailey-Kellogg; 1. INTRODUCTION; 2. METHODS; 2.1. Library Diversity; 2.2. Metrics for Breakpoint Selection; 2.3. Dynamic Programming for Breakpoint Selection; 3. RESULTS A N D DISCUSSION; 4. CONCLUSION; ACKNOWLEDGMENTS; References An Algorithmic Approach to Automated High-Throughput Identification of Disulfide Connectivity in Proteins Using Tandem Mass Spectrometry Timothy Lee, Rahul Singh, Ten-Yang Yen and Bruce Macher1. INTRODUCTION; 1.1. Comparison of the Proposed Approach with Related Works; 2. THE PROPOSED METHOD; 2.1. Problem Formulation; 2.2. Algorithmic Framework; 2.2.1. Finding the MS spectrum match; 2.2.2. Finding the MS/MS spectrum match; 2.2.3. Finding a perfect matching of maximum weight for a fully connected graph; 2.2.4. Consideration of missed proteolytic cleavages and intra-molecular bonded cysteines 2.2.5. Peak finding in the presence of noise2.2.6. Addressing isotopic variation and neutral loss; 2.2.7. Interpretation of peaks given charge state uncertainty; 2.2.8. Overall complexity; 3. EXPERIMENTAL RESULTS; 3.1. Description of the Data and Experimental Procedures; 3.2. Summary of Results; 3.2.1. Analysis of the effect of varying threshold t on results; 3.2.2. Comparison with MS2Assign program; 4. CONCLUSIONS AND DISCUSSION; Acknowledgments; References; Biomedical Application; Cancer Molecular Pattern Discovery by Subspace Consensus Kernel Classification Xiaoxu Hun; 1. INTRODUCTION |
ctrlnum | (OCoLC)646769053 |
dewey-full | 572.80285 |
dewey-hundreds | 500 - Natural sciences and mathematics |
dewey-ones | 572 - Biochemistry |
dewey-raw | 572.80285 |
dewey-search | 572.80285 |
dewey-sort | 3572.80285 |
dewey-tens | 570 - Biology |
discipline | Biologie |
format | Electronic Conference Proceeding eBook |
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genre_facet | Congress proceedings (reports) Conference papers and proceedings Conference papers and proceedings. Actes de congrès. |
id | ZDB-4-EBA-ocn646769053 |
illustrated | Illustrated |
indexdate | 2025-03-18T14:15:09Z |
institution | BVB |
institution_GND | http://id.loc.gov/authorities/names/nb2006023686 |
isbn | 9781860948732 1860948731 1281867594 9781281867599 9786611867591 6611867597 |
language | English |
oclc_num | 646769053 |
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spelling | Computational Systems Bioinformatics Conference (6th : 2007 : San Diego, Calif.) Computational systems bioinformatics : CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 / editors, Peter Markstein, Ying Xu. CSB 2007 Conference proceedings CSB2007 Conference proceedings London : Imperial College Press ; Singapore ; Hackensack, NJ : Distributed by World Scientific, 2007. 1 online resource (xvi, 454 pages :) text txt rdacontent computer c rdamedia online resource cr rdacarrier data file rda Series on advances in bioinformatics and computational biology Series on Advances in Bioinformatics and Computational Biology ; v.6 Includes bibliographical references and index. Print version record. Preface; Committees; Referees; Keynote Address; Quantitative Aspects of Gene Regulation in Bacteria: Amplification. Threshold, and Combinatorial Control Terry Hwa; Whole-Genome Analysis of Dorsal Gradient Thresholds in the Drosophila Embryo Julia ZeitlingeK Rob Zinzen, Dmitri Papatsenko et al.; Invited Talks; Learning Predictive Models of Gene Regulation Christina Leslie; The Phylofacts Phylogenomic Encyclopedias: Structural Phylogenomic Analysis Across the Tree of Life Kimmen Golander; Mapping and Analysis of the Human Interactome Network Kavitha Venkatesan; 1. INTRODUCTION Gene-Centered Protein-DNA lnteractome Mapping A.J. Marian WalhoutProteomics; Algorithm for Peptide Sequencing by Tandem Mass Spectrometry Based on Better Preprocessing and Anti-S ymmetric Computational Model Kang Ning and Hon Wai Leong; 1. INTRODUCTION; Preprocessing to remove noisy peaks; The anti-symmetric problem; 2. ANALYSIS OF PROBLEMS AND CURRENT ALGORITHMS; 2.1. General Terminologies; 2.2. Datasets; 2.3. Problems Analysis; 3. NEW COMPUTATIONAL MODELS AND ALGORITHM; 3.1. Preprocessing to remove noisy peaks and introduce pseudo peaks; 3.2. The Anti-symmetric Problem 3.3. Novel Peptide Sequencing Algorithm4. EXPERIMENTS; 4.1. Experiment Settings; 4.2. Results; 5. CONCLUSIONS; References; Algorithms for Selecting Breakpoint Locations to Optimize Diversity in Protein Engineering by Site-Directed Protein Recombination Wei Zheng, Xiaoduan Ye, Alan A4 Friedman and Chris Bailey-Kellogg; 1. INTRODUCTION; 2. METHODS; 2.1. Library Diversity; 2.2. Metrics for Breakpoint Selection; 2.3. Dynamic Programming for Breakpoint Selection; 3. RESULTS A N D DISCUSSION; 4. CONCLUSION; ACKNOWLEDGMENTS; References An Algorithmic Approach to Automated High-Throughput Identification of Disulfide Connectivity in Proteins Using Tandem Mass Spectrometry Timothy Lee, Rahul Singh, Ten-Yang Yen and Bruce Macher1. INTRODUCTION; 1.1. Comparison of the Proposed Approach with Related Works; 2. THE PROPOSED METHOD; 2.1. Problem Formulation; 2.2. Algorithmic Framework; 2.2.1. Finding the MS spectrum match; 2.2.2. Finding the MS/MS spectrum match; 2.2.3. Finding a perfect matching of maximum weight for a fully connected graph; 2.2.4. Consideration of missed proteolytic cleavages and intra-molecular bonded cysteines 2.2.5. Peak finding in the presence of noise2.2.6. Addressing isotopic variation and neutral loss; 2.2.7. Interpretation of peaks given charge state uncertainty; 2.2.8. Overall complexity; 3. EXPERIMENTAL RESULTS; 3.1. Description of the Data and Experimental Procedures; 3.2. Summary of Results; 3.2.1. Analysis of the effect of varying threshold t on results; 3.2.2. Comparison with MS2Assign program; 4. CONCLUSIONS AND DISCUSSION; Acknowledgments; References; Biomedical Application; Cancer Molecular Pattern Discovery by Subspace Consensus Kernel Classification Xiaoxu Hun; 1. INTRODUCTION This volume contains about 40 papers covering many of the latest developments in the fast-growing field of bioinformatics. The contributions span a wide range of topics, including computational genomics and genetics, protein function and computational proteomics, the transcriptome, structural bioinformatics, microarray data analysis, motif identification, biological pathways and systems, and biomedical applications. Abstracts from the keynote addresses and invited talks are also included. The papers not only cover theoretical aspects of bioinformatics but also delve into the application of n. English. Bioinformatics Congresses. Biological systems Computer simulation Congresses. Biological systems Simulation methods Congresses. Computational biology Congresses. Systems biology. http://id.loc.gov/authorities/subjects/sh2008002926 Computational Biology Systems Biology Models, Genetic Models, Molecular Bio-informatique Congrès. Systèmes biologiques Simulation par ordinateur Congrès. Systèmes biologiques Méthodes de simulation Congrès. Bio-informatique. Biologie systémique. COMPUTERS Bioinformatics. bisacsh Systems biology fast Bioinformatics fast Biological systems Computer simulation fast Biological systems Simulation methods fast Computational biology fast Congress proceedings (reports) aat Conference papers and proceedings fast Conference papers and proceedings. lcgft http://id.loc.gov/authorities/genreForms/gf2014026068 Actes de congrès. rvmgf Markstein, Peter. http://id.loc.gov/authorities/names/n00003671 Xu, Ying, 1960- https://id.oclc.org/worldcat/entity/E39PCjFYcHcxtgCf7GqKbwvd73 http://id.loc.gov/authorities/names/no2002057065 Life Sciences Society. http://id.loc.gov/authorities/names/nb2006023686 has work: Computational systems bioinformatics (Text) https://id.oclc.org/worldcat/entity/E39PCGPf9mwVCHkry8MG6yPh9C https://id.oclc.org/worldcat/ontology/hasWork Print version: Computational Systems Bioinformatics Conference (6th : 2007 : San Diego, Calif.). Computational systems bioinformatics. London : Imperial College Press ; Singapore ; Hackensack, NJ : Distributed by World Scientific, 2007 (DLC) 2008295420 Series on advances in bioinformatics and computational biology. http://id.loc.gov/authorities/names/no2005039596 |
spellingShingle | Computational systems bioinformatics : CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 / Series on advances in bioinformatics and computational biology. Preface; Committees; Referees; Keynote Address; Quantitative Aspects of Gene Regulation in Bacteria: Amplification. Threshold, and Combinatorial Control Terry Hwa; Whole-Genome Analysis of Dorsal Gradient Thresholds in the Drosophila Embryo Julia ZeitlingeK Rob Zinzen, Dmitri Papatsenko et al.; Invited Talks; Learning Predictive Models of Gene Regulation Christina Leslie; The Phylofacts Phylogenomic Encyclopedias: Structural Phylogenomic Analysis Across the Tree of Life Kimmen Golander; Mapping and Analysis of the Human Interactome Network Kavitha Venkatesan; 1. INTRODUCTION Gene-Centered Protein-DNA lnteractome Mapping A.J. Marian WalhoutProteomics; Algorithm for Peptide Sequencing by Tandem Mass Spectrometry Based on Better Preprocessing and Anti-S ymmetric Computational Model Kang Ning and Hon Wai Leong; 1. INTRODUCTION; Preprocessing to remove noisy peaks; The anti-symmetric problem; 2. ANALYSIS OF PROBLEMS AND CURRENT ALGORITHMS; 2.1. General Terminologies; 2.2. Datasets; 2.3. Problems Analysis; 3. NEW COMPUTATIONAL MODELS AND ALGORITHM; 3.1. Preprocessing to remove noisy peaks and introduce pseudo peaks; 3.2. The Anti-symmetric Problem 3.3. Novel Peptide Sequencing Algorithm4. EXPERIMENTS; 4.1. Experiment Settings; 4.2. Results; 5. CONCLUSIONS; References; Algorithms for Selecting Breakpoint Locations to Optimize Diversity in Protein Engineering by Site-Directed Protein Recombination Wei Zheng, Xiaoduan Ye, Alan A4 Friedman and Chris Bailey-Kellogg; 1. INTRODUCTION; 2. METHODS; 2.1. Library Diversity; 2.2. Metrics for Breakpoint Selection; 2.3. Dynamic Programming for Breakpoint Selection; 3. RESULTS A N D DISCUSSION; 4. CONCLUSION; ACKNOWLEDGMENTS; References An Algorithmic Approach to Automated High-Throughput Identification of Disulfide Connectivity in Proteins Using Tandem Mass Spectrometry Timothy Lee, Rahul Singh, Ten-Yang Yen and Bruce Macher1. INTRODUCTION; 1.1. Comparison of the Proposed Approach with Related Works; 2. THE PROPOSED METHOD; 2.1. Problem Formulation; 2.2. Algorithmic Framework; 2.2.1. Finding the MS spectrum match; 2.2.2. Finding the MS/MS spectrum match; 2.2.3. Finding a perfect matching of maximum weight for a fully connected graph; 2.2.4. Consideration of missed proteolytic cleavages and intra-molecular bonded cysteines 2.2.5. Peak finding in the presence of noise2.2.6. Addressing isotopic variation and neutral loss; 2.2.7. Interpretation of peaks given charge state uncertainty; 2.2.8. Overall complexity; 3. EXPERIMENTAL RESULTS; 3.1. Description of the Data and Experimental Procedures; 3.2. Summary of Results; 3.2.1. Analysis of the effect of varying threshold t on results; 3.2.2. Comparison with MS2Assign program; 4. CONCLUSIONS AND DISCUSSION; Acknowledgments; References; Biomedical Application; Cancer Molecular Pattern Discovery by Subspace Consensus Kernel Classification Xiaoxu Hun; 1. INTRODUCTION Bioinformatics Congresses. Biological systems Computer simulation Congresses. Biological systems Simulation methods Congresses. Computational biology Congresses. Systems biology. http://id.loc.gov/authorities/subjects/sh2008002926 Computational Biology Systems Biology Models, Genetic Models, Molecular Bio-informatique Congrès. Systèmes biologiques Simulation par ordinateur Congrès. Systèmes biologiques Méthodes de simulation Congrès. Bio-informatique. Biologie systémique. COMPUTERS Bioinformatics. bisacsh Systems biology fast Bioinformatics fast Biological systems Computer simulation fast Biological systems Simulation methods fast Computational biology fast |
subject_GND | http://id.loc.gov/authorities/subjects/sh2008002926 http://id.loc.gov/authorities/genreForms/gf2014026068 |
title | Computational systems bioinformatics : CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 / |
title_alt | CSB 2007 Conference proceedings CSB2007 Conference proceedings |
title_auth | Computational systems bioinformatics : CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 / |
title_exact_search | Computational systems bioinformatics : CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 / |
title_full | Computational systems bioinformatics : CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 / editors, Peter Markstein, Ying Xu. |
title_fullStr | Computational systems bioinformatics : CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 / editors, Peter Markstein, Ying Xu. |
title_full_unstemmed | Computational systems bioinformatics : CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 / editors, Peter Markstein, Ying Xu. |
title_short | Computational systems bioinformatics : |
title_sort | computational systems bioinformatics csb2007 conference proceedings volume 6 university of california san diego 13 17 august 2007 |
title_sub | CSB2007 Conference proceedings, volume 6, University of California, San Diego, 13-17 August 2007 / |
topic | Bioinformatics Congresses. Biological systems Computer simulation Congresses. Biological systems Simulation methods Congresses. Computational biology Congresses. Systems biology. http://id.loc.gov/authorities/subjects/sh2008002926 Computational Biology Systems Biology Models, Genetic Models, Molecular Bio-informatique Congrès. Systèmes biologiques Simulation par ordinateur Congrès. Systèmes biologiques Méthodes de simulation Congrès. Bio-informatique. Biologie systémique. COMPUTERS Bioinformatics. bisacsh Systems biology fast Bioinformatics fast Biological systems Computer simulation fast Biological systems Simulation methods fast Computational biology fast |
topic_facet | Bioinformatics Congresses. Biological systems Computer simulation Congresses. Biological systems Simulation methods Congresses. Computational biology Congresses. Systems biology. Computational Biology Systems Biology Models, Genetic Models, Molecular Bio-informatique Congrès. Systèmes biologiques Simulation par ordinateur Congrès. Systèmes biologiques Méthodes de simulation Congrès. Bio-informatique. Biologie systémique. COMPUTERS Bioinformatics. Systems biology Bioinformatics Biological systems Computer simulation Biological systems Simulation methods Computational biology Congress proceedings (reports) Conference papers and proceedings Conference papers and proceedings. Actes de congrès. |
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