71 research outputs found

    Porphyre et les universaux dans les Communia logice du ms. Paris, BnF, lat. 16617

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    Cet article offre la première édition du début des Communia logice (et grammatice), une substantielle compilation didascalique issue de la Faculté des arts de l’Université de Paris au milieu du xiiie siècle et contenue dans un manuscrit légué par maître Pierre de Limoges († 1306) à l’ancienne bibliothèque de la Sorbonne. Après une présentation générale (section I) et avant des précisions sur la Ratio edendi (section III), l’étude doctrinale (section II) qui précède cette édition (section IV) montre comment l’auteur-compilateur des Communia logice répond — en le reformulant — au célèbre questionnaire porphyrien relatif aux universaux.This article offers the first edition of the beginning of the Communia logice (et grammatice), a substantial didascalical compilation emanating from the Arts faculty of the University of Paris during the first half of the thirteenth century and preserved in a manuscript bequeathed by master Peter of Limoges († 1306) to the old library of the Sorbonne. After a general presentation (section I) and before some clarifications on the Ratio edendi (section III), the doctrinal study (section II) which precedes this edition (section IV) shows how the author-compiler of the Communia logice answers — while reformulating it — to the well known porphyrian set of questions about the universals

    Le problème des universaux dans l'Isagoge de Porphyre selon quelques commentateurs latins du XIIIe siècle (Pseudo-Robertus Anglicus, Jean le Page, Nicolas de Paris et Robert Kilwardby) : édition critique sélective, traduction française, analyses structurelle et formelle et étude historico-philosophique

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    Notre connaissance de l'histoire du problème des universaux, tel qu'il fut initialement formulé par Porphyre, souffre d'une importante lacune : nous ne savons strictement rien concernant le traitement que ce problème a reçu de la part de ceux qui faisaient profession de philosopher à l'Université de Paris entre 1230 et 1260. Notre thèse s'attaque à ce déficit de savoir en suivant une démarche heuristique qui se déploie en trois phases : premièrement, nous éditons, selon les règles de l'ecdotique, une partie substantielle du commentaire du Pseudo-Robertus Anglicus sur l'Isagoge de Porphyre et nous en offrons une traduction française; deuxièmement, nous sondons l'architectonique de ce texte et des écrits parallèles rédigés par des contemporains--nommément Jean le Page, Nicolas de Paris et Robert Kilwardby; troisièmement et finalement, par l'entremise d'une étude comparative qui met à profit ces documents inédits qui composent notre corpus, nous procédons à une étude historico-philosophique du commentaire isagogique du Pseudo-Robertus Anglicus

    Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

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    Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

    Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

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    Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

    Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

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    This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

    Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

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    Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment
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