Source Page Claim-Confidence Rewrite Audit

Why this audit happened

The initial source pages used Claim-Level Confidence to describe ingest reliability, for example whether a PDF was present, whether tags were detected, and whether biological claims still needed review. That was the wrong level for an LLM wiki: claim confidence should describe the strength and directness of knowledge claims from the source, not the status of the file-processing step.

Sources revisited

• 121 ingested paper source pages in wiki/sources/
• Mature reference style consulted from the parent CODEX_notebook/wiki/ source and entity pages
• Local source text from private extracted text artifacts omitted from public export
• Current topic, entity, digest, and project links used to rebuild Pages Updated From This Source

Page families changed

• Source pages: rewritten from conservative file-processing scaffolds into provisional knowledge-oriented notes.
• Source README: updated to describe source pages as knowledge notes derived from title, abstract/early extracted text, and tags.
• Index and log: updated so navigation reflects the corrected source-page role.

Rule or interpretation changes

• Claim-Level Confidence now refers to source-level knowledge claims: direct title/abstract claims, relevant biological cell/context claims, candidate regulatory mechanisms, and limits on extrapolation.
• File-processing caveats now belong in Caveats, not in Claim-Level Confidence.
• Key Findings now records extracted scientific statements from the title/abstract/early source text.
• Pages Updated From This Source now reflects actual incoming links from topic, entity, digest, and project pages when present.
• Automated tags remain provisional and are explicitly treated as possible over-calls.

Follow-up actions

• Manually curate the highest-priority lung ILC2 and ILC3 papers to upgrade provisional source notes into mature source summaries.
• Clean OCR/encoding artifacts in extracted abstracts when a source becomes a focus paper.
• Replace broad automated context labels with manually verified species, tissue, assay, perturbation, and outcome details during focused review.

Rewritten source pages

• A circadian clock is essential for homeostasis of group 3 innate lymphoid cells in the gut
• Activation and Suppression of Group 3 Innate Lymphoid Cells in the Gut
• Activation of Type 3 innate lymphoid cells and interleukin 22 secretion in the lungs during Streptococcus pneumoniae infection
• AHR drives the development of gut ILC22 cells and postnatal lymphoid tissues via pathways dependent on and independent of Notch
• Allergen-Experienced Group 2 Innate Lymphoid Cells Acquire Memory-like Properties and Enhance Allergic Lung Inflammation
• Antigen-presenting innate lymphoid cells orchestrate neuroinflammation
• Aryl Hydrocarbon Receptor Signaling Cell Intrinsically Inhibits Intestinal Group 2 Innate Lymphoid Cell Function
• Autophagy is critical for group 2 innate lymphoid cell metabolic homeostasis and effector function
• Basophils prime group 2 innate lymphoid cells for neuropeptide-mediated inhibition
• BATF promotes group 2 innate lymphoid cell-mediated lung tissue protection during acute respiratory virus infection
• beta(2)-adrenergic receptor-mediated negative regulation of group 2 innate lymphoid cell responses
• Blocking the HIF-1alpha glycolysis axis inhibits allergic airway inflammation by reducing ILC2 metabolism and function
• c-Kit-positive ILC2s exhibit an ILC3-like signature that may contribute to IL-17-mediated pathologies
• Cannabinoid receptor 2 engagement promotes group 2 innate lymphoid cell expansion and enhances airway hyperreactivity
• CGRP-related neuropeptide adrenomedullin 2 promotes tissue-protective ILC2 responses and limits intestinal inflammation
• Characterization and Quantification of Innate Lymphoid Cell Subsets in Human Lung
• Cigarette smoke aggravates asthma by inducing memory-like type 3 innate lymphoid cells
• Circadian circuits control plasticity of group 3 innate lymphoid cells by sustaining epigenetic configuration of RORgammat
• Context-dependent role of group 3 innate lymphoid cells in mucosal protection
• CTLA-4-expressing ILC3s restrain interleukin-23-mediated inflammation
• Cysteinyl leukotriene E(4) activates human group 2 innate lymphoid cells and enhances the effect of prostaglandin D(2) and epithelial cytokines
• Dampening type 2 properties of group 2 innate lymphoid cells by a gammaherpesvirus infection reprograms alveolar macrophages
• Decoding innate lymphoid cells and innate-like lymphocytes in asthma pathways to mechanisms and therapies
• Development, differentiation, and diversity of innate lymphoid cells
• Dichotomous metabolic networks govern human ILC2 proliferation and function
• Dopamine inhibits group 2 innate lymphoid cell-driven allergic lung inflammation by dampening mitochondrial activity
• Dysregulation of ILC3s unleashes progression and immunotherapy resistance in colon cancer
• Enteric GABAergic neuron-derived gamma-aminobutyric acid initiates expression of Igfbp7 to sustain ILC3 homeostasis
• Eosinophils promote effector functions of lung group 2 innate lymphoid cells in allergic airway inflammation in mice
• Feeding-dependent VIP neuron-ILC3 circuit regulates the intestinal barrier
• Fevipiprant, a selective prostaglandin D(2) receptor 2 antagonist, inhibits human group 2 innate lymphoid cell aggregation and function
• Group 2 innate lymphoid cells (ILC2) are regulated by stem cell factor during chronic asthmatic disease
• Group 2 innate lymphoid cells promote inhibitory synapse development and social behavior
• Group 3 Innate Lymphoid Cells A Potential Therapeutic Target for Steroid Resistant Asthma
• Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis
• Group 3 innate lymphoid cells mediate intestinal selection of commensal bacteria–specific CD4+ T cells
• Group 3 innate lymphoid cells secret neutrophil chemoattractants and are insensitive to glucocorticoid via aberrant GR phosphorylation
• Helper-like Innate Lymphoid Cells in Humans and Mice
• Human CD40 ligand-expressing type 3 innate lymphoid cells induce IL-10-producing immature transitional regulatory B cells
• ICOS-ligand interaction is required for type 2 innate lymphoid cell function, homeostasis, and induction of airway hyperreactivity
• IL-17-producing ST2(+) group 2 innate lymphoid cells play a pathogenic role in lung inflammation
• IL-1beta prevents ILC2 expansion, type 2 cytokine secretion, and mucus metaplasia in response to early-life rhinovirus infection in mice
• IL-1beta, IL-23, and TGF-beta drive plasticity of human ILC2s towards IL-17-producing ILCs in nasal inflammation
• ILC 10 years on
• ILC2-derived LIF licences progress from tissue to systemic immunity
• ILC2-driven innate immune checkpoint mechanism antagonizes NK cell antimetastatic function in the lung
• ILC2s are the predominant source of intestinal ILC-derived IL-10
• ILC3-derived acetylcholine promotes protease-driven allergic lung pathology
• ILC3s promote intestinal tuft cell hyperplasia and anthelmintic immunity through RANK signaling
• ILC3s sense gut microbiota through STING to initiate immune tolerance
• Immunotherapy for asthma
• Inflammatory triggers associated with exacerbations of COPD orchestrate plasticity of group 2 innate lymphoid cells in the lungs
• Innate immune crosstalk in asthmatic airways Innate lymphoid cells coordinate polarization of lung macrophages
• Innate lymphoid cells and asthma
• Innate Lymphoid Cells Are Required to Induce Airway Hyperreactivity in a Murine Neutrophilic Asthma Model
• Innate Lymphoid Cells Are the Predominant Source of IL-17A during the Early Pathogenesis of Acute Respiratory Distress Syndrome
• Innate lymphoid cells as regulators of immunity, inflammation and tissue homeostasis
• Innate lymphoid cells contribute to allergic airway disease exacerbation by obesity
• Innate Lymphoid Cells Diversity, Plasticity, and Unique Functions in Immunity
• Innate lymphoid cells in asthma pathophysiological insights from murine models to human asthma phenotypes
• Innate lymphoid cells in lung infection and immunity
• Innate lymphoid cells major players in inflammatory diseases
• Innate lymphoid cells mediate influenza-induced airway hyper-reactivity independently of adaptive immunity
• Innate Lymphoid Cells of the Lung
• Innate lymphoid cells promote lung-tissue homeostasis after infection with influenza virus
• Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria
• Innate lymphoid cells support regulatory T cells in the intestine through interleukin-2
• Innate type 2 lymphocytes trigger an inflammatory switch in alveolar macrophages
• Insulin-like Growth Factor 1 Supports a Pulmonary Niche that Promotes Type 3 Innate Lymphoid Cell Development in Newborn Lungs
• Interleukin-17-producing innate lymphoid cells and the NLRP3 inflammasome facilitate obesity-associated airway hyperreactivity
• Interleukin-17D regulates group 3 innate lymphoid cell function through its receptor CD93
• Kinetics of the accumulation of group 2 innate lymphoid cells in IL-33-induced and IL-25-induced murine models of asthma a potential role for the chemokine CXCL16
• Light-entrained and brain-tuned circadian circuits regulate ILC3s and gut homeostasis
• Lipid-Droplet Formation Drives Pathogenic Group 2 Innate Lymphoid Cells in Airway Inflammation
• Long-acting muscarinic antagonist regulates group 2 innate lymphoid cell-dependent airway eosinophilic inflammation
• Lung type 2 innate lymphoid cells express cysteinyl leukotriene receptor 1 which regulates TH2 cytokine production
• Maturation and specialization of group 2 innate lymphoid cells through the lung-gut axis
• Mechanics-activated fibroblasts promote pulmonary group 2 innate lymphoid cell plasticity propelling silicosis progression
• Mesenchymal Stem Cells Suppress Severe Asthma by Directly Regulating Th2 Cells and Type 2 Innate Lymphoid Cells
• Metabolic features of innate lymphoid cells
• Metabolite-Sensing Receptor Ffar2 Regulates Colonic Group 3 Innate Lymphoid Cells and Gut Immunity
• Microbiota-dependent crosstalk between macrophages and ILC3 promotes intestinal homeostasis
• mTORC1 signaling in group 2 innate lymphoid cells coordinates neuro-immune crosstalk in allergic lung inflammation
• Neuromedin-U Mediates Rapid Activation of Airway Group 2 Innate Lymphoid Cells in Mild Asthma
• Neuropeptide regulation of non-redundant ILC2 responses at barrier surfaces
• Non-redundant functions of group 2 innate lymphoid cells
• Nucleophosmin 1 promotes mucosal immunity by supporting mitochondrial oxidative phosphorylation and ILC3 activity
• Nutrition impact on ILC3 maintenance and function centers on a cell-intrinsic CD71-iron axis
• Orchestration of intestinal homeostasis and tolerance by group 3 innate lymphoid cells
• PAC1 constrains type 2 inflammation through promotion of CGRP signaling in ILC2s
• PD-1 pathway regulates ILC2 metabolism and PD-1 agonist treatment ameliorates airway hyperreactivity
• Plasticity of innate lymphoid cell subsets
• Pulmonary fibroblast-derived stem cell factor promotes neutrophilic asthma by augmenting IL-17A production from ILC3s
• Reciprocal transcription factor networks govern tissue-resident ILC3 subset function and identity
• Recruitment and activation of type 3 innate lymphoid cells promote antitumor immune responses
• Regulatory Innate Lymphoid Cells Control Innate Intestinal Inflammation
• Retinoid X receptor gamma dictates the activation threshold of group 2 innate lymphoid cells and limits type 2 inflammation in the small intestine
• RORalpha is a critical checkpoint for T cell and ILC2 commitment in the embryonic thymus
• S1P-dependent interorgan trafficking of group 2 innate lymphoid cells supports host defense
• Skin-resident innate lymphoid cells converge on a pathogenic effector state
• Spatial and Temporal Mapping of Human Innate Lymphoid Cells Reveals Elements of Tissue Specificity
• The biology of innate lymphoid cells
• The evolution of innate lymphoid cells
• The group 2 innate lymphoid cell (ILC2) regulatory network and its underlying mechanisms
• The interplay between innate lymphoid cells and T cells
• The IRE1alphaXBP1 pathway sustains cytokine responses of group 3 innate lymphoid cells in inflammatory bowel disease
• The molecular and epigenetic mechanisms of innate lymphoid cell (ILC) memory and its relevance for asthma
• The neuropeptide VIP confers anticipatory mucosal immunity by regulating ILC3 activity
• The Role of the TL1ADR3 Axis in the Activation of Group 2 Innate Lymphoid Cells in Subjects with Eosinophilic Asthma
• The Tumor Necrosis Factor Superfamily Member RANKL Suppresses Effector Cytokine Production in Group 3 Innate Lymphoid Cells
• Tissue-Restricted Adaptive Type 2 Immunity Is Orchestrated by Expression of the Costimulatory Molecule OX40L on Group 2 Innate Lymphoid Cells
• Tissue-specific features of innate lymphoid cells in antiviral defense
• Tissue-Specific Features of Innate Lymphoid Cells
• Toll-like receptor 9-dependent interferon production prevents group 2 innate lymphoid cell-driven airway hyperreactivity
• Trained ILC3 responses promote intestinal defense
• Trained immunity and tolerance in innate lymphoid cells, monocytes, and dendritic cells during allergen-specific immunotherapy
• Tuft cell IL-17RB restrains IL-25 bioavailability and reveals context-dependent ILC2 hypoproliferation
• Vasoactive intestinal peptide promotes host defense against enteric pathogens by modulating the recruitment of group 3 innate lymphoid cells
• Vitamin D downregulates the IL-23 receptor pathway in human mucosal group 3 innate lymphoid cells
• Vitamin D(3) resolved human and experimental asthma via B lymphocyte-induced maturation protein 1 in T cells and innate lymphoid cells
• WASH maintains NKp46+ ILC3 cells by promoting AHR expression