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Montgomery", "lastName": "Pettitt" }, { "creatorType": "author", "firstName": "Paul", "lastName": "Labute" } ], "abstractNote": ", We show that an Ng\nbridge function modified version of the three-dimensional\nreference interaction site model (3D-RISM-NgB) solvation free energy\nmethod can accurately predict the hydration free energy (HFE) of a\nset of 504 organic molecules. To achieve this, a single unique constant\nparameter was adjusted to the computed HFE of single atom Lennard-Jones\nsolutes. It is shown that 3D-RISM is relatively accurate at predicting\nthe electrostatic component of the HFE without correction but requires\na modification of the nonpolar contribution that originates in the\nformation of the cavity created by the solute in water. We use a free\nenergy functional with the Ng scaling of the direct correlation function\n[Ng, K. C. J. Chem. Phys.1974, 61, 2680]. This produces a rapid, reliable small molecule\nHFE calculation for applications in drug design.", "publicationTitle": "Journal of Chemical Theory and Computation", "publisher": "", "place": "", "date": "2014-03-11", "volume": "10", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "934-941", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Chem Theory Comput", "DOI": "10.1021/ct4009359", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3953892/", "accessDate": "2015-08-31T19:46:27Z", "PMID": "", "PMCID": "", "ISSN": "1549-9618", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "00024 \nPMID: 24634616\nPMCID: PMC3953892", "tags": [], "collections": [ "BDD32N4F" ], "relations": {}, "dateAdded": "2015-08-31T19:46:27Z", "dateModified": "2015-09-07T09:20:38Z" } }, { "key": "D4QZUHH5", "version": 8935, "library": { "type": "group", "id": 4336, "name": "Strelcova Zora", "links": { "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4336/items/D4QZUHH5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora/items/D4QZUHH5", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/4336/items/I9GKRS8G", "type": "application/json" } }, "meta": { "createdByUser": { "id": 38526, "username": "zorule", "name": "Zora Strelcova", "links": { "alternate": { "href": "https://www.zotero.org/zorule", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "D4QZUHH5", "version": 8935, "parentItem": "I9GKRS8G", "itemType": "attachment", "linkMode": "imported_url", "title": "PubMed Central Full Text PDF", "accessDate": "2015-08-31T19:46:27Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3953892/pdf/ct4009359.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Truchon et al. - 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The structure determination has been carried out by using an optical analogue instrument which proved to be an adequate and rapid tool for the derivation of Fourier transforms, signs of amplitudes and the production of optical Fourier syntheses. The new model of chitin accounts properly for known chemical and physical properties, including the infrared absorption as well as for x-ray data, but because of the limited resolution of the diffraction patterns it can only be regarded as a good approximation. The stereochemical configuration of the polysaccharide chains has certain implications for the structure of cellulose.", "publicationTitle": "The Journal of Biophysical and Biochemical Cytology", "publisher": "", "place": "", "date": "Sep 25, 1957", "volume": "3", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "669-683", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Biophys Biochem Cytol", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0095-9901", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 13475384\nPMCID: PMC2224123", "tags": [ { "tag": "Polysaccharides", "type": 1 } ], "collections": [ "BDD32N4F" ], "relations": {}, "dateAdded": "2015-07-27T17:34:07Z", "dateModified": "2015-07-27T17:34:07Z" } }, { "key": "E7K2P5EH", "version": 8930, "library": { "type": "group", "id": 4336, "name": "Strelcova Zora", "links": { "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4336/items/E7K2P5EH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora/items/E7K2P5EH", "type": "text/html" } }, "meta": { "createdByUser": { "id": 38526, "username": "zorule", "name": "Zora Strelcova", "links": { "alternate": { "href": "https://www.zotero.org/zorule", "type": "text/html" } } }, "creatorSummary": "Terstappen et al.", "parsedDate": "1990-11-01", "numChildren": 1 }, "data": { "key": "E7K2P5EH", "version": 8930, "itemType": "journalArticle", "title": "Identification and characterization of plasma cells in normal human bone marrow by high-resolution flow cytometry", "creators": [ { "creatorType": "author", "firstName": "L. W.", "lastName": "Terstappen" }, { "creatorType": "author", "firstName": "S.", "lastName": "Johnsen" }, { "creatorType": "author", "firstName": "I. M.", "lastName": "Segers-Nolten" }, { "creatorType": "author", "firstName": "M. R.", "lastName": "Loken" } ], "abstractNote": "The low frequency of plasma cells and the lack of specific cell surface markers has been a major obstacle for a detailed characterization of plasma cells in normal human bone marrow. Multiparameter flow cytometry enabled the identification of plasma cells in normal bone marrow aspirates. The plasma cells were located in a unique position in the correlation of forward light scattering, orthogonal light scattering, and immunofluorescent-labeled CD38. The identity of the sorted cell populations was confirmed by microscopic examination of Wright's stained slides and slides stained for cytoplasmic immunoglobulin using polyclonal antibodies reactive with light chains; ie, anti-kappa fluorescein isothiocyanate and anti lambda phycoerythrin (PE). The purity of the sorted plasma cells was greater than 97% (n = 4). The average frequency of plasma cells in normal bone marrow aspirates was low--0.25% of the nucleated cells (n = 7)--but surprisingly consistent between individuals (SD = .05; range 0.14% to 0.30%). A detailed analysis showed two distinct populations of plasma cells: (1) A population relatively smaller by forward light scattering expressed CD22, CD35, and sigE and was identified as early plasma cells (ie, lymphoplasmacytoid), and (2) a population larger by forward light scattering lacked these markers and was identified as mature plasma cells. The antigenic profile of the normal plasma cells was determined in two-color immunofluorescence studies. The expression of cell surface immunoglobulin G (IgG), IgA, IgE, IgD, IgM, and the cell surface antigens CD10, CD11b, CD13, CD11c, CD14, CD15, CD16, CD19, CD22, CD20, CD33, CD35, CD45, and HLA-DR was determined on the plasma cells. A significant heterogeneity in cell surface antigen expression was observed within the plasma cell population. Unexpectedly, myeloid-specific cell surface antigens such as CD33 and CD13 and the early B-cell antigen identified by CD10 were expressed on a proportion of plasma cells. These observations imply that the association of myeloid and early B-cell markers described in multiple myeloma may not be associated with the neoplasia but is a normal phenomenon.", "publicationTitle": "Blood", "publisher": "", "place": "", "date": "Nov 1, 1990", "volume": "76", "issue": "9", "section": "", "partNumber": "", "partTitle": "", "pages": "1739-1747", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Blood", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0006-4971", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 2224123", "tags": [ { "tag": "ADP-ribosyl Cyclase", "type": 1 }, { "tag": "Antigens, CD", "type": 1 }, { "tag": "Antigens, CD38", "type": 1 }, { "tag": "Antigens, Differentiation", "type": 1 }, { "tag": "Bone Marrow", "type": 1 }, { "tag": "Bone Marrow Cells", "type": 1 }, { "tag": "Cell Membrane", "type": 1 }, { "tag": "Flow Cytometry", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Membrane Glycoproteins", "type": 1 }, { "tag": "Plasma Cells", "type": 1 } ], "collections": [ "BDD32N4F" ], "relations": {}, "dateAdded": "2015-07-27T17:33:44Z", "dateModified": "2015-07-27T17:33:44Z" } }, { "key": "QR3DNNM8", "version": 8930, "library": { "type": "group", "id": 4336, "name": "Strelcova Zora", "links": { "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4336/items/QR3DNNM8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora/items/QR3DNNM8", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/4336/items/E7K2P5EH", "type": "application/json" } }, "meta": { "createdByUser": { "id": 38526, "username": "zorule", "name": "Zora Strelcova", "links": { "alternate": { "href": 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"links": { "alternate": { "href": "https://www.zotero.org/zorule", "type": "text/html" } } }, "creatorSummary": "Beckham and Crowley", "parsedDate": "2011-04-21", "numChildren": 0 }, "data": { "key": "AT8A2WFP", "version": 8930, "itemType": "journalArticle", "title": "Examination of the α-Chitin Structure and Decrystallization Thermodynamics at the Nanoscale", "creators": [ { "creatorType": "author", "firstName": "Gregg T.", "lastName": "Beckham" }, { "creatorType": "author", "firstName": "Michael F.", "lastName": "Crowley" } ], "abstractNote": "", "publicationTitle": "The Journal of Physical Chemistry B", "publisher": "", "place": "", "date": "2011-04-21", "volume": "115", "issue": "15", "section": "", "partNumber": "", "partTitle": "", "pages": "4516-4522", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1021/jp200912q", "citationKey": "", "url": "http://pubs.acs.org/doi/abs/10.1021/jp200912q", "accessDate": "2015-07-27T17:31:43Z", "PMID": "", "PMCID": "", "ISSN": "1520-6106, 1520-5207", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "BDD32N4F" ], "relations": {}, "dateAdded": "2015-07-27T17:31:43Z", "dateModified": "2015-07-27T17:31:43Z" } }, { "key": "JCP6V8AP", "version": 8930, "library": { "type": "group", "id": 4336, "name": "Strelcova Zora", "links": { "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4336/items/JCP6V8AP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora/items/JCP6V8AP", "type": "text/html" } }, "meta": { "createdByUser": { "id": 38526, "username": "zorule", "name": "Zora Strelcova", "links": { "alternate": { "href": "https://www.zotero.org/zorule", "type": "text/html" } } }, "creatorSummary": "Alvarez", "parsedDate": "2014-04-10", "numChildren": 0 }, "data": { "key": "JCP6V8AP", "version": 8930, "itemType": "journalArticle", "title": "The Effect of Chitin Size, Shape, Source and Purification Method on Immune Recognition", "creators": [ { "creatorType": "author", "firstName": "Francisco", "lastName": "Alvarez" } ], "abstractNote": "", "publicationTitle": "Molecules", "publisher": "", "place": "", "date": "2014-04-10", "volume": "19", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "4433-4451", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.3390/molecules19044433", "citationKey": "", "url": "http://www.mdpi.com/1420-3049/19/4/4433/", "accessDate": "2015-07-27T17:24:23Z", "PMID": "", "PMCID": "", "ISSN": "1420-3049", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "BDD32N4F" ], "relations": {}, "dateAdded": 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"IXXJHC9W", "version": 8930, "library": { "type": "group", "id": 4336, "name": "Strelcova Zora", "links": { "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4336/items/IXXJHC9W", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora/items/IXXJHC9W", "type": "text/html" } }, "meta": { "createdByUser": { "id": 38526, "username": "zorule", "name": "Zora Strelcova", "links": { "alternate": { "href": "https://www.zotero.org/zorule", "type": "text/html" } } }, "creatorSummary": "Ravi Kumar", "parsedDate": "2000", "numChildren": 0 }, "data": { "key": "IXXJHC9W", "version": 8930, "itemType": "journalArticle", "title": "A review of chitin and chitosan applications", "creators": [ { "creatorType": "author", "firstName": "Majeti N.V", "lastName": "Ravi Kumar" } ], "abstractNote": "", "publicationTitle": "Reactive and Functional Polymers", "publisher": "", "place": "", "date": "11/2000", "volume": "46", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "1-27", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/S1381-5148(00)00038-9", "citationKey": "", "url": "http://linkinghub.elsevier.com/retrieve/pii/S1381514800000389", "accessDate": "2015-07-27T13:24:26Z", "PMID": "", "PMCID": "", "ISSN": "13815148", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "BDD32N4F" ], "relations": {}, "dateAdded": "2015-07-27T13:24:26Z", "dateModified": "2015-07-27T13:24:26Z" } }, { "key": "SSQVPCHW", "version": 8931, "library": { "type": "group", "id": 4336, "name": "Strelcova Zora", "links": { "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora", "type": "text/html" } } }, "links": { "self": { "href": 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}, { "key": "GQBBGE3P", "version": 8930, "library": { "type": "group", "id": 4336, "name": "Strelcova Zora", "links": { "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4336/items/GQBBGE3P", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora/items/GQBBGE3P", "type": "text/html" } }, "meta": { "createdByUser": { "id": 38526, "username": "zorule", "name": "Zora Strelcova", "links": { "alternate": { "href": "https://www.zotero.org/zorule", "type": "text/html" } } }, "creatorSummary": "Srinivasan et al.", "parsedDate": "1998", "numChildren": 1 }, "data": { "key": "GQBBGE3P", "version": 8930, "itemType": "journalArticle", "title": "Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices", "creators": [ { "creatorType": "author", "firstName": "Jayashree", "lastName": "Srinivasan" }, { "creatorType": "author", "firstName": "Thomas E.", "lastName": "Cheatham" }, { "creatorType": "author", "firstName": "Piotr", "lastName": "Cieplak" }, { "creatorType": "author", "firstName": "Peter A.", "lastName": "Kollman" }, { "creatorType": "author", "firstName": "David A.", "lastName": "Case" } ], "abstractNote": "We apply continuum solvent models to investigate the relative stability of A- and B-form helices for three DNA sequences, d(CCAACGTTGG)2, d(ACCCGCGGGT)2, and d(CGCGAATTCGCG)2, a phosphoramidate-modified DNA duplex, p(CGCGAATTCGCG)2, in which the O3? atom in deoxyribose is replaced with NH, and an RNA duplex, r(CCAACGUUGG)2. Structures were taken as snapshots from multi-nanosecond molecular dynamics simulations computed in a consistent fashion using explicit solvent and with long-range electrostatics accounted for using the particle?mesh Ewald procedure. The electrostatic contribution to solvation energies were computed using both a finite-difference Poisson?Boltzmann (PB) model and a pairwise generalized Born model; nonelectrostatic contributions were estimated with a surface-area-dependent term. To these solvation free energies were added the mean solute internal energies (determined from a molecular mechanics potential) and estimates of the solute entropy (from a harmonic analysis). Consistent with experiment, the relative energies favor B-form helices for DNA and A-form helices for the NP-modified system and for RNA. Salt effects, modeled at the linear or nonlinear PB level, favor the A-form helices by modest amounts; for d(ACCCGCGGGT)2, salt is nearly able to switch the conformational preference to ?A?. The results provide a physical interpretation for the origins of the relative stabilities of A- and B-helices and suggest that similar analyses might be useful in a variety of nucleic acid conformational problems.", "publicationTitle": "Journal of the American Chemical Society", "publisher": "", "place": "", "date": "Září 1, 1998", "volume": "120", "issue": "37", "section": "", "partNumber": "", "partTitle": "", "pages": "9401-9409", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Am. Chem. 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Here, a popular analytical Generalized Born (GB) solvation model is modified to improve its accuracy in calculating the solvent polarization part of free energy changes in large-scale conformational transitions, such as protein folding. In contrast to an earlier GB model (implemented in the AMBER-6 program), the improved version does not overstabilize the native structures relative to the finite-difference Poisson-Boltzmann continuum treatment. In addition to improving the energy balance between folded and unfolded conformers, the algorithm (available in the AMBER-7 and NAB molecular modeling packages) is shown to perform well in more than 50 ns of native-state molecular dynamics (MD) simulations of thioredoxin, protein-A, and ubiquitin, as well as in a simulation of Barnase/Barstar complex formation. For thioredoxin, various combinations of input parameters have been explored, such as the underlying gas-phase force fields and the atomic radii. The best performance is achieved with a previously proposed modification to the torsional potential in the Amber ff99 force field, which yields stable native trajectories for all of the tested proteins, with backbone root-mean-square deviations from the native structures being approximately 1.5 A after 6 ns of simulation time. The structure of Barnase/Barstar complex is regenerated, starting from an unbound state, to within 1.9 A relative to the crystal structure of the complex.", "publicationTitle": "Proteins", "publisher": "", "place": "", "date": "May 1, 2004", "volume": "55", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "383-394", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proteins", "DOI": "10.1002/prot.20033", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1097-0134", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 15048829", "tags": [ { "tag": "Bacterial Proteins", "type": 1 }, { "tag": "Computer Simulation", "type": 1 }, { "tag": "Models, Molecular", "type": 1 }, { "tag": "Poisson Distribution", "type": 1 }, { "tag": "Protein Conformation", "type": 1 }, { "tag": "Protein Folding", "type": 1 }, { "tag": "Proteins", "type": 1 }, { "tag": "Ribonucleases", "type": 1 }, { "tag": "Software", "type": 1 }, { "tag": "Solvents", "type": 1 }, { "tag": "Staphylococcal Protein A", "type": 1 }, { "tag": "Static Electricity", "type": 1 }, { "tag": "Thermodynamics", "type": 1 }, { "tag": "Thioredoxins", "type": 1 }, { "tag": "Ubiquitin", "type": 1 } ], "collections": [ "BDD32N4F" ], "relations": {}, "dateAdded": "2015-06-28T20:04:23Z", "dateModified": "2015-06-28T20:04:23Z" } }, { "key": "9JG7FWIU", "version": 8930, "library": { "type": "group", "id": 4336, "name": "Strelcova Zora", "links": { "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4336/items/9JG7FWIU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/strelcova_zora/items/9JG7FWIU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 38526, "username": "zorule", "name": "Zora Strelcova", "links": { "alternate": { "href": "https://www.zotero.org/zorule", "type": "text/html" } } }, "creatorSummary": "Carlstrom", "parsedDate": "1957-09-25", "numChildren": 2 }, "data": { "key": "9JG7FWIU", "version": 8930, "itemType": "journalArticle", "title": "THE CRYSTAL STRUCTURE OF ?-CHITIN (POLY-N-ACETYL-D-GLUCOSAMINE)", "creators": [ { "creatorType": "author", "firstName": "Diego", "lastName": "Carlstrom" } ], "abstractNote": "A detailed model for the crystal structure of the fibrous polysaccharide chitin is proposed. The structure determination has been carried out by using an optical analogue instrument which proved to be an adequate and rapid tool for the derivation of Fourier transforms, signs of amplitudes and the production of optical Fourier syntheses. The new model of chitin accounts properly for known chemical and physical properties, including the infrared absorption as well as for x-ray data, but because of the limited resolution of the diffraction patterns it can only be regarded as a good approximation. The stereochemical configuration of the polysaccharide chains has certain implications for the structure of cellulose.", "publicationTitle": "The Journal of Biophysical and Biochemical Cytology", "publisher": "", "place": "", "date": "1957-9-25", "volume": "3", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "669-683", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Biophys Biochem Cytol", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2224123/", "accessDate": "2014-08-10T15:10:12Z", "PMID": "", "PMCID": "", "ISSN": "0095-9901", "archive": "", "archiveLocation": "", "shortTitle": "THE CRYSTAL STRUCTURE OF ?", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 13475384\nPMCID: PMC2224123", "tags": [], "collections": [], "relations": {}, "dateAdded": "2015-06-03T18:21:12Z", "dateModified": "2015-06-03T18:21:12Z" } }, { "key": "2F4J784N", "version": 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