You will be shown an abstract from a biomedical research paper. Given this abstract, your task is to extract all unique entities of the following types: ["HealthCareActivity", "InjuryOrPoisoning", "BodySubstance", "IntellectualProduct", "AnatomicalStructure", "SpatialConcept", "Chemical", "Bacterium", "MedicalDevice", "Organization", "BiomedicalOccupationOrDiscipline", "Finding", "BiologicFunction", "Virus", "ResearchActivity", "ClinicalAttribute", "PopulationGroup", "Eukaryote", "BodySystem", "Food", "ProfessionalOrOccupationalGroup"].

Please return the output as a JSON object of the format: {"Virus": ["HIV", ...], "Bacterium": ["MRSA", ...], "AnatomicalStructure": ["Lung", ...], "BodySystem": ["CNS", ...], "BodySubstance": ["Serum", ...], "Finding": ["Headache", ...], "InjuryOrPoisoning": ["Fracture", ...], "BiologicFunction": ["Death", ...], "HealthCareActivity": ["Biopsy", ...], "ResearchActivity": ["Clinical trial", ...], "MedicalDevice": ["Lenses", ...], "SpatialConcept": ["Camps", ...], "BiomedicalOccupationOrDiscipline": ["Forensic medicine", ...], "Organization": ["WHO", ...], "ProfessionalOrOccupationalGroup": ["Provider", ...], "PopulationGroup": ["Swimmers", ...], "Chemical": ["Gold", ...], "Food": ["Rice", ...], "IntellectualProduct": ["RPAM", ...], "ClinicalAttribute": ["Biomarker", ...], "Eukaryote": ["Dogs", ...]}. The keys should be entity types and values should be lists of extracted entities belonging to the corresponding type. If you cannot find entities belonging to a specific type, the value should be [].

Only output the JSON object and do not include any additional text.

Abstract:

Stalk versus base invasion in pT1 papillary cancers of the bladder: improved substaging system predicting risk of progression Pathologic stage T1 (pT1) bladder cancers are a clinically heterogeneous group. However, current staging guidelines for superficially invasive cancers do not acknowledge the variability in type and extent of lamina propria invasion in papillary urothelial carcinomas (PUC), and historically proposed substaging systems showed either high inter-observer variation or limited value in predicting patient outcomes. Herein we reappraise pT1 PUC substaging, aiming to identify a novel scheme which is reproducible and prognostically meaningful. Stage pT1 PUC diagnosed during years 1999-2015 were retrospectively reviewed and characterized as focal invasion confined to papillary stalk, focal invasion of tumor base, or extensive invasion of tumor base. Cases with concurrent flat carcinoma in-situ, angiolymphatic invasion, absent muscularis propria, or clinically advanced disease were excluded. We calculated cumulative incidence of recurrence, progression, and death by tumor subtype and evaluated differential risks using log-rank tests and Kaplan-Meier curves stratified by type and extent of invasion. Among 62 patients satisfying inclusion criteria, 22 of 29 patients with base extensive invasion progressed while 4 of 13 with base focal and 0 of 20 with stalk only invasion progressed. There was strong evidence that base extensive patients had higher risk of progression and death due to bladder cancer than base focal or stalk only counterparts (P<0.0001). However, tumor subtype was not significantly associated with risk of recurrence (P=0.21). We propose an innovative substaging approach for reporting site and extent of lamina propria invasion in patients with pT1 PUC allowing patient stratification for risk of progression. This article is protected by copyright. All rights reserved.
{"AnatomicalStructure": ["base", "Stalk", "stalk", "papillary stalk", "muscularis propria"], "Bacterium": [], "BiologicFunction": ["death", "PUC", "tumor", "bladder cancer", "invasion", "bladder cancers", "papillary urothelial carcinomas", "progression", "papillary cancers of the bladder", "invasive cancers"], "BiomedicalOccupationOrDiscipline": [], "BodySubstance": [], "BodySystem": [], "Chemical": [], "ClinicalAttribute": ["extent of invasion"], "Eukaryote": [], "Finding": ["diagnosed", "lamina propria invasion", "differential risks", "pT1", "invasion", "recurrence", "flat carcinoma in-situ", "Pathologic stage T1", "Stage pT1", "angiolymphatic invasion"], "Food": [], "HealthCareActivity": ["evaluated", "patient outcomes"], "InjuryOrPoisoning": [], "IntellectualProduct": ["log-rank tests", "scheme", "tumor subtype", "prognostically", "staging"], "MedicalDevice": [], "Organization": [], "PopulationGroup": [], "ProfessionalOrOccupationalGroup": [], "ResearchActivity": ["retrospectively reviewed"], "SpatialConcept": ["superficially", "focal"], "Virus": []}