{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T08:05:19Z","timestamp":1762761919735,"version":"3.37.3"},"reference-count":120,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2022,7,25]],"date-time":"2022-07-25T00:00:00Z","timestamp":1658707200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","award":["OSR#4129"],"award-info":[{"award-number":["OSR#4129"]}],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","award":["BAS\/1\/1606-01-01"],"award-info":[{"award-number":["BAS\/1\/1606-01-01"]}],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","award":["FCC\/1\/1976-20-01"],"award-info":[{"award-number":["FCC\/1\/1976-20-01"]}],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","award":["BAS\/1\/1059-01-01"],"award-info":[{"award-number":["BAS\/1\/1059-01-01"]}],"id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prominent being Alzheimer\u2019s disease (AD). AD is brain-related local amyloidosis, while another amyloidosis, such as AA amyloidosis, tends to be more systemic. Therefore, we need to know more about the biological entities\u2019 influencing these amyloidosis processes. However, there is currently no support system developed specifically to handle this extraordinarily complex and demanding task. To acquire a systematic view of amyloidosis and how this may be relevant to the brain and other organs, we needed a means to explore \"amyloid network systems\" that may underly processes that leads to an amyloid-related disease. In this regard, we developed the DES-Amyloidoses knowledgebase (KB) to obtain fast and relevant information regarding the biological network related to amyloid proteins\/peptides and amyloid-related diseases. This KB contains information obtained through text and data mining of available scientific literature and other public repositories. The information compiled into the DES-Amyloidoses system based on 19 topic-specific dictionaries resulted in 796,409 associations between terms from these dictionaries. Users can explore this information through various options, including enriched concepts, enriched pairs, and semantic similarity. We show the usefulness of the KB using an example focused on inflammasome-amyloid associations. To our knowledge, this is the only KB dedicated to human amyloid-related diseases derived primarily through literature text mining and complemented by data mining that provides a novel way of exploring information relevant to amyloidoses.<\/jats:p>","DOI":"10.1371\/journal.pone.0271737","type":"journal-article","created":{"date-parts":[[2022,7,25]],"date-time":"2022-07-25T17:35:27Z","timestamp":1658770527000},"page":"e0271737","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["DES-Amyloidoses \u201cAmyloidoses through the looking-glass\u201d: A knowledgebase developed for exploring and linking information related to human amyloid-related diseases"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2333-8245","authenticated-orcid":true,"given":"Vladan P.","family":"Bajic","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adil","family":"Salhi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katja","family":"Lakota","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksandar","family":"Radovanovic","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rozaimi","family":"Razali","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lada","family":"Zivkovic","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Biljana","family":"Spremo-Potparevic","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mahmut","family":"Uludag","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Faroug","family":"Tifratene","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olaa","family":"Motwalli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benoit","family":"Marchand","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir B.","family":"Bajic","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takashi","family":"Gojobori","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Esma R.","family":"Isenovic","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2709-5356","authenticated-orcid":true,"given":"Magbubah","family":"Essack","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2022,7,25]]},"reference":[{"issue":"11","key":"pone.0271737.ref001","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1016\/0166-2236(93)90078-Z","article-title":"Tau protein and the neurofibrillary pathology of Alzheimer\u2019s disease","volume":"16","author":"M Goedert","year":"1993","journal-title":"Trends Neurosci"},{"issue":"11","key":"pone.0271737.ref002","doi-asserted-by":"crossref","first-page":"4044","DOI":"10.1073\/pnas.83.11.4044","article-title":"Microtubule-associated protein tau (tau) is a major antigenic component of paired helical filaments in Alzheimer disease","volume":"83","author":"KS Kosik","year":"1986","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"34","key":"pone.0271737.ref003","doi-asserted-by":"crossref","first-page":"E4976","DOI":"10.1073\/pnas.1600749113","article-title":"Atomic-resolution structure of a disease-relevant Abeta(1\u201342) amyloid fibril","volume":"113","author":"MA Walti","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"30","key":"pone.0271737.ref004","doi-asserted-by":"crossref","first-page":"9663","DOI":"10.1021\/jacs.6b05129","article-title":"Atomic Resolution Structure of Monomorphic Abeta42 Amyloid Fibrils","volume":"138","author":"MT Colvin","year":"2016","journal-title":"J Am Chem Soc"},{"issue":"37","key":"pone.0271737.ref005","doi-asserted-by":"crossref","first-page":"12447","DOI":"10.1021\/jp903106x","article-title":"Cross-beta-sheet structure in amyloid fiber formation","volume":"113","author":"S Xu","year":"2009","journal-title":"J Phys Chem B"},{"issue":"6","key":"pone.0271737.ref006","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1038\/nrm3810","article-title":"The amyloid state and its association with protein misfolding diseases","volume":"15","author":"TP Knowles","year":"2014","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pone.0271737.ref007","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1146\/annurev.biochem.75.101304.123901","article-title":"Protein misfolding, functional Amyloid, and human disease","volume":"75","author":"F Chiti","year":"2006","journal-title":"Annu Rev Biochem"},{"issue":"1","key":"pone.0271737.ref008","doi-asserted-by":"crossref","first-page":"141","DOI":"10.3324\/haematol.2012.068155","article-title":"Amyloidosis of the gastrointestinal tract: a 13-year, single-center, referral experience","volume":"98","author":"AJ Cowan","year":"2013","journal-title":"Haematologica"},{"issue":"9","key":"pone.0271737.ref009","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.2215\/CJN.10491012","article-title":"Renal amyloidosis: origin and clinicopathologic correlations of 474 recent cases","volume":"8","author":"SM Said","year":"2013","journal-title":"Clin J Am Soc Nephrol"},{"issue":"8","key":"pone.0271737.ref010","doi-asserted-by":"crossref","first-page":"e0160546","DOI":"10.1371\/journal.pone.0160546","article-title":"Diagnostic potential of novel salivary host biomarkers as candidates for the immunological diagnosis of tuberculosis disease and monitoring of tuberculosis treatment response","volume":"11","author":"R Jacobs","year":"2016","journal-title":"PloS one"},{"issue":"3","key":"pone.0271737.ref011","doi-asserted-by":"crossref","first-page":"112","DOI":"10.4161\/pri.2.3.7488","article-title":"Amyloid fibrils","volume":"2","author":"RN Rambaran","year":"2008","journal-title":"Prion"},{"issue":"4","key":"pone.0271737.ref012","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1080\/13506129.2016.1257986","article-title":"Amyloid fibril proteins and Amyloidosis: chemical identification and clinical classification International Society of Amyloidosis 2016 Nomenclature Guidelines","volume":"23","author":"JD Sipe","year":"2016","journal-title":"Amyloid"},{"issue":"10","key":"pone.0271737.ref013","doi-asserted-by":"crossref","first-page":"2473","DOI":"10.1016\/j.polymer.2013.02.029","article-title":"Amyloids: From molecular structure to mechanical properties","volume":"54","author":"M Schleeger","year":"2013","journal-title":"Polymer"},{"issue":"6","key":"pone.0271737.ref014","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1016\/j.cell.2012.02.022","article-title":"The amyloid state of proteins in human diseases","volume":"148","author":"D Eisenberg","year":"2012","journal-title":"Cell"},{"key":"pone.0271737.ref015","doi-asserted-by":"crossref","first-page":"29","DOI":"10.3389\/fnmol.2016.00029","article-title":"Key Points Concerning Amyloid Infectivity and Prion-Like Neuronal Invasion","volume":"9","author":"A Espargaro","year":"2016","journal-title":"Front Mol Neurosci"},{"issue":"1","key":"pone.0271737.ref016","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1111\/nan.12197","article-title":"Invited review: Prion\u2010like transmission and spreading of tau pathology","volume":"41","author":"F Clavaguera","year":"2015","journal-title":"Neuropathology and applied neurobiology"},{"issue":"6","key":"pone.0271737.ref017","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1016\/j.neuron.2014.06.004","article-title":"Tau propagation, different tau phenotypes, and prion-like properties of tau","volume":"82","author":"BT Hyman","year":"2014","journal-title":"Neuron"},{"issue":"5","key":"pone.0271737.ref018","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1084\/jem.20120741","article-title":"Prion-like spread of protein aggregates in neurodegeneration","volume":"209","author":"M Polymenidou","year":"2012","journal-title":"Journal of Experimental Medicine"},{"issue":"2","key":"pone.0271737.ref019","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1172\/JCI43366","article-title":"\u03b1-Synuclein propagates from mouse brain to grafted dopaminergic neurons and seeds aggregation in cultured human cells","volume":"121","author":"C Hansen","year":"2011","journal-title":"The Journal of clinical investigation"},{"issue":"11","key":"pone.0271737.ref020","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11910-014-0495-z","article-title":"Prion-like mechanisms in the pathogenesis of tauopathies and synucleinopathies","volume":"14","author":"M Goedert","year":"2014","journal-title":"Current neurology and neuroscience reports"},{"key":"pone.0271737.ref021","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.virusres.2014.10.016","article-title":"Parkinson\u2019s disease as a member of Prion-like disorders","volume":"207","author":"ME Herva","year":"2015","journal-title":"Virus research"},{"issue":"10","key":"pone.0271737.ref022","doi-asserted-by":"crossref","first-page":"3606","DOI":"10.1523\/JNEUROSCI.20-10-03606.2000","article-title":"Evidence for seeding of \u03b2-amyloid by intracerebral infusion of Alzheimer brain extracts in \u03b2-amyloid precursor protein-transgenic mice","volume":"20","author":"MD Kane","year":"2000","journal-title":"Journal of Neuroscience"},{"issue":"26","key":"pone.0271737.ref023","doi-asserted-by":"crossref","first-page":"8767","DOI":"10.1523\/JNEUROSCI.0615-12.2012","article-title":"Spreading of neurodegenerative pathology via neuron-to-neuron transmission of \u03b2-amyloid","volume":"32","author":"S Nath","year":"2012","journal-title":"Journal of Neuroscience"},{"issue":"3","key":"pone.0271737.ref024","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1001\/jamaneurol.2013.1453","article-title":"Mechanisms of protein seeding in neurodegenerative diseases","volume":"70","author":"LC Walker","year":"2013","journal-title":"JAMA neurology"},{"issue":"2","key":"pone.0271737.ref025","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1038\/ncb1830","article-title":"Cytoplasmic penetration and persistent infection of mammalian cells by polyglutamine aggregates","volume":"11","author":"P-H Ren","year":"2009","journal-title":"Nature cell biology"},{"issue":"35","key":"pone.0271737.ref026","doi-asserted-by":"crossref","first-page":"29722","DOI":"10.1074\/jbc.M112.372474","article-title":"Fibrillar structure and charge determine the interaction of polyglutamine protein aggregates with the cell surface","volume":"287","author":"RS Trevino","year":"2012","journal-title":"Journal of Biological Chemistry"},{"issue":"3","key":"pone.0271737.ref027","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1016\/j.cell.2011.10.011","article-title":"The seeds of neurodegeneration: prion-like spreading in ALS","volume":"147","author":"M Polymenidou","year":"2011","journal-title":"Cell"},{"issue":"9","key":"pone.0271737.ref028","doi-asserted-by":"crossref","first-page":"3548","DOI":"10.1073\/pnas.1017275108","article-title":"Prion-like propagation of mutant superoxide dismutase-1 misfolding in neuronal cells","volume":"108","author":"C M\u00fcnch","year":"2011","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"21","key":"pone.0271737.ref029","doi-asserted-by":"crossref","first-page":"18664","DOI":"10.1074\/jbc.M111.231209","article-title":"A seeding reaction recapitulates intracellular formation of Sarkosyl-insoluble transactivation response element (TAR) DNA-binding protein-43 inclusions","volume":"286","author":"Y Furukawa","year":"2011","journal-title":"Journal of Biological Chemistry"},{"issue":"1","key":"pone.0271737.ref030","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.celrep.2013.06.007","article-title":"Prion-like properties of pathological TDP-43 aggregates from diseased brains","volume":"4","author":"T Nonaka","year":"2013","journal-title":"Cell reports"},{"issue":"23","key":"pone.0271737.ref031","doi-asserted-by":"crossref","first-page":"19440","DOI":"10.1074\/jbc.M112.346072","article-title":"Trans-cellular propagation of tau aggregation by fibrillar species","volume":"287","author":"N Kfoury","year":"2012","journal-title":"Journal of Biological Chemistry"},{"issue":"2","key":"pone.0271737.ref032","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1016\/j.neuron.2013.07.046","article-title":"Anti-tau antibodies that block tau aggregate seeding in vitro markedly decrease pathology and improve cognition in vivo","volume":"80","author":"K Yanamandra","year":"2013","journal-title":"Neuron"},{"issue":"19","key":"pone.0271737.ref033","doi-asserted-by":"crossref","first-page":"12845","DOI":"10.1074\/jbc.M808759200","article-title":"Propagation of tau misfolding from the outside to the inside of a cell","volume":"284","author":"B Frost","year":"2009","journal-title":"Journal of Biological Chemistry"},{"issue":"3","key":"pone.0271737.ref034","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1523\/JNEUROSCI.2642-12.2013","article-title":"Synthetic tau fibrils mediate transmission of neurofibrillary tangles in a transgenic mouse model of Alzheimer\u2019s-like tauopathy","volume":"33","author":"M Iba","year":"2013","journal-title":"Journal of Neuroscience"},{"issue":"4","key":"pone.0271737.ref035","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1002\/ana.23747","article-title":"Neuron\u2010to\u2010neuron transmission of \u03b1\u2010synuclein fibrils through axonal transport","volume":"72","author":"EC Freundt","year":"2012","journal-title":"Annals of neurology"},{"key":"pone.0271737.ref036","article-title":"Intracerebral inoculation of pathological \u03b1-synuclein initiates a rapidly progressive neurodegenerative \u03b1-synucleinopathy in mice","author":"KC Luk","year":"2012","journal-title":"Journal of Experimental Medicine"},{"issue":"6006","key":"pone.0271737.ref037","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1126\/science.1194516","article-title":"Peripherally applied A\u03b2-containing inoculates induce cerebral \u03b2-amyloidosis","volume":"330","author":"YS Eisele","year":"2010","journal-title":"Science"},{"issue":"3","key":"pone.0271737.ref038","first-page":"834","article-title":"In vivo seeding and cross-seeding of localized amyloidosis: a molecular link between type 2 diabetes and Alzheimer disease","volume":"185","author":"ME Oskarsson","year":"2015","journal-title":"The American journal of pathology"},{"issue":"10","key":"pone.0271737.ref039","doi-asserted-by":"crossref","first-page":"928","DOI":"10.2174\/1567205011666141107124538","article-title":"Islet amyloid polypeptide (IAPP): a second amyloid in Alzheimer\u2019s disease","volume":"11","author":"J N Fawver","year":"2014","journal-title":"Current Alzheimer Research"},{"issue":"10","key":"pone.0271737.ref040","doi-asserted-by":"crossref","first-page":"1759","DOI":"10.1021\/acschemneuro.5b00192","article-title":"Cross-seeding interaction between \u03b2-amyloid and human islet amyloid polypeptide","volume":"6","author":"R Hu","year":"2015","journal-title":"ACS chemical neuroscience"},{"issue":"3","key":"pone.0271737.ref041","doi-asserted-by":"crossref","first-page":"155","DOI":"10.3233\/JAD-1999-1303","article-title":"Apolipoprotein serum amyloid A in Alzheimer\u2019s disease","volume":"1","author":"MS Kindy","year":"1999","journal-title":"Journal of Alzheimer\u2019s Disease"},{"issue":"6","key":"pone.0271737.ref042","doi-asserted-by":"crossref","first-page":"1683","DOI":"10.2353\/ajpath.2008.070829","article-title":"Co-localization of amyloid beta and tau pathology in Alzheimer\u2019s disease synaptosomes","volume":"172","author":"JA Fein","year":"2008","journal-title":"The American journal of pathology"},{"issue":"10","key":"pone.0271737.ref043","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1038\/nbt1012","article-title":"Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins","volume":"22","author":"A-M Fernandez-Escamilla","year":"2004","journal-title":"Nature biotechnology"},{"issue":"11","key":"pone.0271737.ref044","doi-asserted-by":"crossref","first-page":"4074","DOI":"10.1073\/pnas.0511295103","article-title":"The 3D profile method for identifying fibril-forming segments of proteins","volume":"103","author":"MJ Thompson","year":"2006","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"8","key":"pone.0271737.ref045","doi-asserted-by":"crossref","first-page":"3487","DOI":"10.1073\/pnas.0915166107","article-title":"Identifying the amylome, proteins capable of forming amyloid-like fibrils","volume":"107","author":"L Goldschmidt","year":"2010","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"10","key":"pone.0271737.ref046","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1093\/protein\/gzm042","article-title":"The PASTA server for protein aggregation prediction","volume":"20","author":"A Trovato","year":"2007","journal-title":"Protein Engineering Design and Selection"},{"issue":"suppl 2","key":"pone.0271737.ref047","doi-asserted-by":"crossref","first-page":"W469","DOI":"10.1093\/nar\/gkp351","article-title":"NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation","volume":"37","author":"C Kim","year":"2009","journal-title":"Nucleic acids research"},{"issue":"3","key":"pone.0271737.ref048","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1093\/bioinformatics\/btp691","article-title":"FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence","volume":"26","author":"SO Garbuzynskiy","year":"2010","journal-title":"Bioinformatics"},{"issue":"13","key":"pone.0271737.ref049","doi-asserted-by":"crossref","first-page":"i34","DOI":"10.1093\/bioinformatics\/btr238","article-title":"A method for probing the mutational landscape of amyloid structure","volume":"27","author":"CW O\u2019donnell","year":"2011","journal-title":"Bioinformatics"},{"issue":"2","key":"pone.0271737.ref050","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1002\/prot.23203","article-title":"STITCHER: Dynamic assembly of likely amyloid and prion \u03b2\u2010structures from secondary structure predictions","volume":"80","author":"AW Bryan","year":"2012","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"issue":"1","key":"pone.0271737.ref051","doi-asserted-by":"crossref","first-page":"e54175","DOI":"10.1371\/journal.pone.0054175","article-title":"A consensus method for the prediction of \u2018aggregation-prone\u2019peptides in globular proteins","volume":"8","author":"AC Tsolis","year":"2013","journal-title":"PloS one"},{"issue":"1","key":"pone.0271737.ref052","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1472-6807-5-18","article-title":"Prediction of\" hot spots\" of aggregation in disease-linked polypeptides","volume":"5","author":"NS de Groot","year":"2005","journal-title":"BMC Structural Biology"},{"issue":"10","key":"pone.0271737.ref053","doi-asserted-by":"crossref","first-page":"2723","DOI":"10.1110\/ps.051471205","article-title":"Prediction of aggregation rate and aggregation\u2010prone segments in polypeptide sequences","volume":"14","author":"GG Tartaglia","year":"2005","journal-title":"Protein Science"},{"issue":"8","key":"pone.0271737.ref054","doi-asserted-by":"crossref","first-page":"2149","DOI":"10.1110\/ps.04790604","article-title":"Detecting hidden sequence propensity for amyloid fibril formation","volume":"13","author":"S Yoon","year":"2004","journal-title":"Protein Science"},{"key":"pone.0271737.ref055","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1186\/1471-2105-9-273","article-title":"AMYPdb: a database dedicated to amyloid precursor proteins","volume":"9","author":"S Pawlicki","year":"2008","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"pone.0271737.ref056","doi-asserted-by":"crossref","first-page":"e0152949","DOI":"10.1371\/journal.pone.0152949","article-title":"CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation","volume":"11","author":"AM Thangakani","year":"2016","journal-title":"PLoS One"},{"issue":"1","key":"pone.0271737.ref057","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/13506120802676781","article-title":"AL-Base: a visual platform analysis tool for the study of amyloidogenic immunoglobulin light chain sequences","volume":"16","author":"K Bodi","year":"2009","journal-title":"Amyloid"},{"issue":"D1","key":"pone.0271737.ref058","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"C The UniProt","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pone.0271737.ref059","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"pone.0271737.ref060","unstructured":"[Internet] P: Bethesda (MD): National Library of Medicine (US). In.; 1946."},{"issue":"14","key":"pone.0271737.ref061","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1093\/bioinformatics\/btu167","article-title":"GAP: towards almost 100 percent prediction for beta-strand-mediated aggregating peptides with distinct morphologies","volume":"30","author":"AM Thangakani","year":"2014","journal-title":"Bioinformatics"},{"issue":"9","key":"pone.0271737.ref062","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1021\/acschemneuro.6b00150","article-title":"TANGO-Inspired Design of Anti-Amyloid Cyclic Peptides","volume":"7","author":"X Lu","year":"2016","journal-title":"ACS Chem Neurosci"},{"issue":"D1","key":"pone.0271737.ref063","doi-asserted-by":"crossref","first-page":"D389","DOI":"10.1093\/nar\/gkz758","article-title":"WALTZ-DB 2.0: an updated database containing structural information of experimentally determined amyloid-forming peptides","volume":"48","author":"N Louros","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"pone.0271737.ref064","article-title":"DESM: portal for microbial knowledge exploration systems","author":"A Salhi","year":"2015","journal-title":"Nucleic acids research"},{"issue":"6","key":"pone.0271737.ref065","doi-asserted-by":"crossref","first-page":"e65190","DOI":"10.1371\/journal.pone.0065190","article-title":"Information exploration system for sickle cell disease and repurposing of hydroxyfasudil","volume":"8","author":"M Essack","year":"2013","journal-title":"PLoS One"},{"issue":"Database issue","key":"pone.0271737.ref066","doi-asserted-by":"crossref","first-page":"D820","DOI":"10.1093\/nar\/gkn593","article-title":"Database for exploration of functional context of genes implicated in ovarian cancer","volume":"37","author":"M Kaur","year":"2009","journal-title":"Nucleic Acids Research"},{"key":"pone.0271737.ref067","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1186\/1471-2164-9-622","article-title":"DDESC: Dragon database for exploration of sodium channels in human","volume":"9","author":"S Sagar","year":"2008","journal-title":"BMC Genomics"},{"issue":"1","key":"pone.0271737.ref068","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.reprotox.2011.12.007","article-title":"DESTAF: a database of text-mined associations for reproductive toxins potentially affecting human fertility","volume":"33","author":"AS Dawe","year":"2012","journal-title":"Reproductive Toxicology"},{"issue":"4","key":"pone.0271737.ref069","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1016\/j.meegid.2010.12.006","article-title":"Dragon exploratory system on hepatitis C virus (DESHCV)","volume":"11","author":"SK Kwofie","year":"2011","journal-title":"Infection, Genetics and Evolution"},{"issue":"7","key":"pone.0271737.ref070","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1080\/15476286.2017.1312243","article-title":"DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining","volume":"14","author":"A Salhi","year":"2017","journal-title":"RNA Biol"},{"key":"pone.0271737.ref071","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1186\/1471-2407-9-219","article-title":"DDEC: Dragon database of genes implicated in esophageal cancer","volume":"9","author":"M Essack","year":"2009","journal-title":"BMC Cancer"},{"issue":"Database issue","key":"pone.0271737.ref072","doi-asserted-by":"crossref","first-page":"D980","DOI":"10.1093\/nar\/gkq849","article-title":"DDPC: Dragon Database of Genes associated with Prostate Cancer","volume":"39","author":"M Maqungo","year":"2011","journal-title":"Nucleic Acids Research"},{"issue":"4","key":"pone.0271737.ref073","doi-asserted-by":"crossref","first-page":"1914","DOI":"10.1104\/pp.105.060863","article-title":"Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists","volume":"138","author":"VB Bajic","year":"2005","journal-title":"Plant physiology"},{"key":"pone.0271737.ref074","doi-asserted-by":"crossref","first-page":"1769437","DOI":"10.1155\/2019\/1769437","article-title":"Literature-Based Enrichment Insights into Redox Control of Vascular Biology","volume":"2019","author":"M Essack","year":"2019","journal-title":"Oxid Med Cell Longev"},{"issue":"1","key":"pone.0271737.ref075","doi-asserted-by":"crossref","first-page":"5968","DOI":"10.1038\/s41598-017-05448-0","article-title":"DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species","volume":"7","author":"A Salhi","year":"2017","journal-title":"Sci Rep"},{"issue":"suppl 1","key":"pone.0271737.ref076","first-page":"D54","article-title":"Entrez Gene: gene-centered information at NCBI","volume":"33","author":"D Maglott","year":"2005","journal-title":"Nucleic acids research"},{"issue":"D1","key":"pone.0271737.ref077","doi-asserted-by":"crossref","first-page":"D191","DOI":"10.1093\/nar\/gkt1140","article-title":"Activities at the universal protein resource (UniProt)","volume":"42","author":"Consortium U","year":"2014","journal-title":"Nucleic acids research"},{"issue":"Database issue","key":"pone.0271737.ref078","first-page":"D456","article-title":"The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013","volume":"41","author":"J Hastings","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"pone.0271737.ref079","doi-asserted-by":"crossref","first-page":"D507","DOI":"10.1093\/nar\/gkj122","article-title":"LMPD: LIPID MAPS proteome database","volume":"34","author":"D Cotter","year":"2006","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"pone.0271737.ref080","doi-asserted-by":"crossref","first-page":"D527","DOI":"10.1093\/nar\/gkl838","article-title":"LMSD: LIPID MAPS structure database","volume":"35","author":"M Sud","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"pone.0271737.ref081","article-title":"MetaboLights: An Open-Access Database Repository for Metabolomics Data","volume":"53","author":"NS Kale","year":"2016","journal-title":"Curr Protoc Bioinformatics"},{"issue":"Database issue","key":"pone.0271737.ref082","doi-asserted-by":"crossref","first-page":"D928","DOI":"10.1093\/nar\/gku1004","article-title":"T3DB: the toxic exposome database","volume":"43","author":"D Wishart","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"pone.0271737.ref083","doi-asserted-by":"crossref","first-page":"D1049","DOI":"10.1093\/nar\/gku1179","article-title":"Gene Ontology Consortium: going forward","volume":"43","author":"C Gene Ontology","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pone.0271737.ref084","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/nar\/27.1.29","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"27","author":"H Ogata","year":"1999","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"pone.0271737.ref085","doi-asserted-by":"crossref","first-page":"D481","DOI":"10.1093\/nar\/gkv1351","article-title":"The Reactome pathway Knowledgebase","volume":"44","author":"A Fabregat","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"pone.0271737.ref086","doi-asserted-by":"crossref","first-page":"D761","DOI":"10.1093\/nar\/gkr1023","article-title":"UniPathway: a resource for the exploration and annotation of metabolic pathways","volume":"40","author":"A Morgat","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"pone.0271737.ref087","doi-asserted-by":"crossref","first-page":"D284","DOI":"10.1093\/nar\/gki078","article-title":"The PANTHER database of protein families, subfamilies, functions and pathways","volume":"33","author":"H Mi","year":"2005","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"pone.0271737.ref088","doi-asserted-by":"crossref","first-page":"D1071","DOI":"10.1093\/nar\/gku1011","article-title":"Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data","volume":"43","author":"WA Kibbe","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"pone.0271737.ref089","doi-asserted-by":"crossref","first-page":"D865","DOI":"10.1093\/nar\/gkw1039","article-title":"The Human Phenotype Ontology in 2017","volume":"45","author":"S Kohler","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"pone.0271737.ref090","doi-asserted-by":"crossref","first-page":"D1075","DOI":"10.1093\/nar\/gkv1075","article-title":"The SIDER database of drugs and side effects","volume":"44","author":"M Kuhn","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"pone.0271737.ref091","doi-asserted-by":"crossref","first-page":"D1074","DOI":"10.1093\/nar\/gkx1037","article-title":"DrugBank 5.0: a major update to the DrugBank database for 2018","volume":"46","author":"DS Wishart","year":"2018","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"pone.0271737.ref092","doi-asserted-by":"crossref","first-page":"D52","DOI":"10.1093\/nar\/gkq1237","article-title":"Entrez Gene: gene-centered information at NCBI","volume":"39","author":"D Maglott","year":"2011","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"pone.0271737.ref093","doi-asserted-by":"crossref","first-page":"D619","DOI":"10.1093\/nar\/gkw1033","article-title":"Genenames.org: the HGNC and VGNC resources in 2017","volume":"45","author":"B Yates","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"pone.0271737.ref094","doi-asserted-by":"crossref","first-page":"D54","DOI":"10.1093\/nar\/gki031","article-title":"Entrez Gene: gene-centered information at NCBI","volume":"33","author":"D Maglott","year":"2005","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"pone.0271737.ref095","doi-asserted-by":"crossref","first-page":"D145","DOI":"10.1093\/nar\/gkw1007","article-title":"TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions","volume":"45","author":"S Schmeier","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"pone.0271737.ref096","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1093\/bioinformatics\/btt156","article-title":"tmVar: a text mining approach for extracting sequence variants in biomedical literature","volume":"29","author":"CH Wei","year":"2013","journal-title":"Bioinformatics"},{"issue":"5","key":"pone.0271737.ref097","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/j.molmed.2011.01.005","article-title":"Disease-associated amyloid and misfolded protein aggregates activate the inflammasome","volume":"17","author":"SL Masters","year":"2011","journal-title":"Trends in molecular medicine"},{"issue":"8","key":"pone.0271737.ref098","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1038\/ni.1636","article-title":"The NALP3 inflammasome is involved in the innate immune response to amyloid-\u03b2","volume":"9","author":"A Halle","year":"2008","journal-title":"Nature immunology"},{"issue":"10","key":"pone.0271737.ref099","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1038\/ni.1935","article-title":"Activation of the NLRP3 inflammasome by islet amyloid polypeptide provides a mechanism for enhanced IL-1 [beta] in type 2 diabetes","volume":"11","author":"SL Masters","year":"2010","journal-title":"Nature immunology"},{"issue":"1","key":"pone.0271737.ref100","doi-asserted-by":"crossref","first-page":"e55375","DOI":"10.1371\/journal.pone.0055375","article-title":"Triggering of Inflammasome by Aggregated \u03b1\u2013Synuclein, an Inflammatory Response in Synucleinopathies","volume":"8","author":"G Codolo","year":"2013","journal-title":"PloS one"},{"issue":"29","key":"pone.0271737.ref101","doi-asserted-by":"crossref","first-page":"13046","DOI":"10.1073\/pnas.1002396107","article-title":"Mutant superoxide dismutase 1-induced IL-1\u03b2 accelerates ALS pathogenesis","volume":"107","author":"F Meissner","year":"2010","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"6","key":"pone.0271737.ref102","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1083\/jcb.201503023","article-title":"TRIM-mediated precision autophagy targets cytoplasmic regulators of innate immunity","volume":"210","author":"T Kimura","year":"2015","journal-title":"J Cell Biol"},{"issue":"12","key":"pone.0271737.ref103","doi-asserted-by":"crossref","first-page":"2504","DOI":"10.1080\/15548627.2016.1239679","article-title":"Regulation of lysosomal dynamics and autophagy by CTSB\/cathepsin B","volume":"12","author":"SM Man","year":"2016","journal-title":"Autophagy"},{"issue":"7","key":"pone.0271737.ref104","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1007\/s00109-016-1389-0","article-title":"Far-infrared promotes burn wound healing by suppressing NLRP3 inflammasome caused by enhanced autophagy","volume":"94","author":"HW Chiu","year":"2016","journal-title":"J Mol Med (Berl)"},{"issue":"8","key":"pone.0271737.ref105","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1038\/ni.1631","article-title":"Silica crystals and aluminum salts activate the NALP3 inflammasome through phagosomal destabilization","volume":"9","author":"V Hornung","year":"2008","journal-title":"Nat Immunol"},{"issue":"12","key":"pone.0271737.ref106","doi-asserted-by":"crossref","first-page":"7745","DOI":"10.1074\/jbc.M708362200","article-title":"Inhibitors of cathepsin B improve memory and reduce \u03b2-amyloid in transgenic Alzheimer disease mice expressing the wild-type, but not the Swedish mutant, \u03b2-secretase site of the amyloid precursor protein","volume":"283","author":"VY Hook","year":"2008","journal-title":"Journal of Biological Chemistry"},{"issue":"3","key":"pone.0271737.ref107","doi-asserted-by":"crossref","first-page":"3","DOI":"10.14797\/mdcj-8-3-3","article-title":"The amyloidoses: clinical features, diagnosis and treatment","volume":"8","author":"KR Baker","year":"2012","journal-title":"Methodist Debakey Cardiovasc J"},{"key":"pone.0271737.ref108","first-page":"263","article-title":"MicroRNA expression in Alzheimer blood mononuclear cells","volume":"1","author":"HM Schipper","year":"2007","journal-title":"Gene Regul Syst Bio"},{"key":"pone.0271737.ref109","doi-asserted-by":"crossref","first-page":"153","DOI":"10.3389\/fgene.2019.00153","article-title":"MicroRNAs in Alzheimer\u2019s Disease","volume":"10","author":"M Wang","year":"2019","journal-title":"Front Genet"},{"key":"pone.0271737.ref110","unstructured":"Keller A SC, Meese E, Kappel A, Backes C, Leidinger P, inventors; Siemens AG, assignee.: Diagnostic miRNA markers for Alzheimer. United States patent US 10,138,520 2018 Nov 27."},{"issue":"7","key":"pone.0271737.ref111","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1002\/gps.4881","article-title":"The microRNA-1908 up-regulation in the peripheral blood cells impairs amyloid clearance by targeting ApoE","volume":"33","author":"Z Wang","year":"2018","journal-title":"Int J Geriatr Psychiatry"},{"issue":"2","key":"pone.0271737.ref112","doi-asserted-by":"crossref","first-page":"FSO40","DOI":"10.4155\/fso.15.40","article-title":"The yin and yang of amyloid aggregation","volume":"1","author":"SF Falsone","year":"2015","journal-title":"Future Sci OA"},{"key":"pone.0271737.ref113","doi-asserted-by":"crossref","first-page":"45","DOI":"10.3389\/fncel.2015.00045","article-title":"Legal but lethal: functional protein aggregation at the verge of toxicity","volume":"9","author":"A Falsone","year":"2015","journal-title":"Front Cell Neurosci"},{"issue":"3","key":"pone.0271737.ref114","doi-asserted-by":"crossref","first-page":"503","DOI":"10.3233\/JAD-2012-112015","article-title":"Amyloids as Sensors and Protectors (ASAP) hypothesis","volume":"29","author":"RD Petrofes Chapa","year":"2012","journal-title":"J Alzheimers Dis"},{"issue":"7636","key":"pone.0271737.ref115","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/nature20814","article-title":"Structural variation in amyloid-beta fibrils from Alzheimer\u2019s disease clinical subtypes","volume":"541","author":"W Qiang","year":"2017","journal-title":"Nature"},{"issue":"1","key":"pone.0271737.ref116","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a024323","article-title":"Noncerebral Amyloidoses: Aspects on Seeding, Cross-Seeding, and Transmission","volume":"8","author":"GT Westermark","year":"2018","journal-title":"Cold Spring Harb Perspect Med"},{"issue":"2","key":"pone.0271737.ref117","doi-asserted-by":"crossref","first-page":"81","DOI":"10.3109\/03009734.2011.573884","article-title":"Amyloid in the islets of Langerhans: thoughts and some historical aspects","volume":"116","author":"P Westermark","year":"2011","journal-title":"Ups J Med Sci"},{"issue":"1","key":"pone.0271737.ref118","doi-asserted-by":"crossref","first-page":"194","DOI":"10.2337\/db12-0420","article-title":"Upregulated NLRP3 inflammasome activation in patients with type 2 diabetes","volume":"62","author":"HM Lee","year":"2013","journal-title":"Diabetes"},{"issue":"6","key":"pone.0271737.ref119","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1016\/j.cell.2014.01.063","article-title":"Prion-like polymerization underlies signal transduction in antiviral immune defense and inflammasome activation","volume":"156","author":"X Cai","year":"2014","journal-title":"Cell"},{"issue":"7","key":"pone.0271737.ref120","doi-asserted-by":"crossref","first-page":"1360","DOI":"10.1002\/jnr.23986","article-title":"Inflammasomes, hormesis, and antioxidants in neuroinflammation: Role of NRLP3 in Alzheimer disease","volume":"95","author":"M Pennisi","year":"2017","journal-title":"J Neurosci Res"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0271737","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,25]],"date-time":"2022-07-25T17:37:21Z","timestamp":1658770641000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0271737"}},"subtitle":[],"editor":[{"given":"Maria Grazia","family":"Ortore","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,7,25]]},"references-count":120,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2022,7,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0271737","relation":{},"ISSN":["1932-6203"],"issn-type":[{"type":"electronic","value":"1932-6203"}],"subject":[],"published":{"date-parts":[[2022,7,25]]}}}