""" Proof: Chronic periodontal disease has been associated with an increased risk of atherosclerotic cardiovascular disease in adults, with consensus reviews pointing to systemic inflammation as a biologically plausible mediating mechanism (Tonetti & Van Dyke, 2013; Sanz et al., 2020; Cullinan & Ford, 2013). Generated: 2026-05-20 """ import os import sys PROOF_ENGINE_ROOT = os.environ.get("PROOF_ENGINE_ROOT") if not PROOF_ENGINE_ROOT: _d = os.path.dirname(os.path.abspath(__file__)) while _d != os.path.dirname(_d): cand = os.path.join(_d, "proof-engine", "skills", "proof-engine", "scripts") if os.path.isdir(cand): PROOF_ENGINE_ROOT = os.path.join(_d, "proof-engine", "skills", "proof-engine") break _d = os.path.dirname(_d) if not PROOF_ENGINE_ROOT: # Fallback for hosted skill location used by the proof-engine plugin. _candidates = [ "/sessions/beautiful-vigilant-dirac/mnt/.remote-plugins/plugin_011ppymzz6m5MeDLUDFMKX53/skills/proof-engine", ] for c in _candidates: if os.path.isdir(os.path.join(c, "scripts")): PROOF_ENGINE_ROOT = c break if not PROOF_ENGINE_ROOT: raise RuntimeError("PROOF_ENGINE_ROOT not set and skill dir not found via walk-up from proof.py") sys.path.insert(0, PROOF_ENGINE_ROOT) from scripts.verify_citations import verify_all_citations from scripts.computations import compare, apply_verdict_qualifier from scripts.proof_summary import ProofSummaryBuilder # --------------------------------------------------------------------------- # 1. CLAIM INTERPRETATION (Hardening Rule 4) # --------------------------------------------------------------------------- CLAIM_NATURAL = ( "Chronic periodontal disease has been associated with an increased risk of " "atherosclerotic cardiovascular disease in adults, with consensus reviews " "pointing to systemic inflammation as a biologically plausible mediating " "mechanism (Tonetti & Van Dyke, 2013; Sanz et al., 2020; " "Cullinan & Ford, 2013)." ) CLAIM_FORMAL = { "subject": "Chronic periodontal disease and atherosclerotic cardiovascular disease (ASCVD)", "property": ( "Consensus reviews in periodontology and cardiology report (a) a " "statistically meaningful association between periodontitis and incident " "ASCVD in adults that is independent of established cardiovascular risk " "factors, and (b) systemic inflammation as a biologically plausible " "mediating mechanism for this association." ), "operator": ">=", "operator_note": ( "Claim is read as ASSOCIATIONAL, not causal — the words 'has been " "associated with' and 'biologically plausible mediating mechanism' are " "deliberately weaker than 'causes'. The claim is supported when ≥ 3 " "independent consensus reviews/scientific statements affirm BOTH (a) an " "independent epidemiological association between periodontitis and " "ASCVD AND (b) systemic inflammation as a biologically plausible " "mediating mechanism. ATTRIBUTION CORRECTION: The cited 'Cullinan & " "Ford, 2013' is treated as a benign mis-citation of the 2013 " "Periodontology 2000 review whose actual authors are 'Cullinan MP, " "Seymour GJ' (doi:10.1111/prd.12007). Patrice Ford is co-author of an " "earlier 2009 Australian Dental Journal review by Cullinan, Ford and " "Seymour, not the 2013 paper. This is documented as an adversarial " "check; the underlying consensus claim is unaffected." ), "threshold": 3, "proof_direction": "affirm", } # --------------------------------------------------------------------------- # 2. FACT REGISTRY # --------------------------------------------------------------------------- FACT_REGISTRY = { "B1": {"key": "tonetti_van_dyke_2013", "label": "Tonetti & Van Dyke 2013, EFP/AAP Joint Workshop consensus report"}, "B2": {"key": "sanz_2020", "label": "Sanz et al. 2020, EFP/WHF Perio-Cardio Workshop consensus report"}, "B3": {"key": "cullinan_seymour_2013", "label": "Cullinan & Seymour 2013, Periodontology 2000 review (treated as the cited 'Cullinan & Ford 2013')"}, "B4": {"key": "aha_2012", "label": "Lockhart et al. 2012, AHA Scientific Statement (Circulation) — independent corroboration"}, "A1": {"label": "Verified source count", "method": None, "result": None}, } # --------------------------------------------------------------------------- # 3. EMPIRICAL FACTS — sources confirming the claim # Each quote was copied verbatim from the rendered PubMed abstract page # (UTF-8 plaintext) — see snapshots/ for archived copies. # --------------------------------------------------------------------------- _PROOF_DIR = os.path.dirname(os.path.abspath(__file__)) def _load_snapshot(fname): fpath = os.path.join(_PROOF_DIR, fname) try: with open(fpath, encoding="utf-8") as f: return f.read() except FileNotFoundError: return None empirical_facts = { "tonetti_van_dyke_2013": { "quote": ( "In longitudinal studies assessing incident cardiovascular events, " "statistically significant excess risk for ACVD was reported in " "individuals with periodontitis. This was independent of " "established cardiovascular risk factors." ), "url": "https://pubmed.ncbi.nlm.nih.gov/23627332/", "source_name": "Tonetti MS, Van Dyke TE (2013), Periodontitis and atherosclerotic cardiovascular disease: consensus report of the Joint EFP/AAP Workshop on Periodontitis and Systemic Diseases. J Clin Periodontol 40(Suppl 14):S24-S29. doi:10.1111/jcpe.12089", "snapshot": _load_snapshot("snapshots/B1_tonetti_van_dyke_2013.txt"), "snapshot_source": "public:pubmed_abstract", }, "sanz_2020": { "quote": ( "There is now a significant body of evidence to support independent " "associations between severe periodontitis and several NCDs, in " "particular CVD." ), "url": "https://pubmed.ncbi.nlm.nih.gov/32011025/", "source_name": "Sanz M, Marco del Castillo A, Jepsen S, et al. (2020), Periodontitis and cardiovascular diseases: Consensus report. J Clin Periodontol 47(3):268-288. doi:10.1111/jcpe.13189", "snapshot": _load_snapshot("snapshots/B2_sanz_2020.txt"), "snapshot_source": "public:pubmed_abstract", }, "cullinan_seymour_2013": { "quote": ( "the weight of evidence from numerous studies conducted over this " "period, together with several systematic reviews and meta-analyses, " "supports an association between periodontitis and cardiovascular " "disease, and between periodontitis and diabetes. The association " "has also been supported by a number of biologically plausible " "mechanisms, including direct infection, systemic inflammation and " "molecular mimicry." ), "url": "https://pubmed.ncbi.nlm.nih.gov/23574472/", "source_name": "Cullinan MP, Seymour GJ (2013), Periodontal disease and systemic illness: will the evidence ever be enough? Periodontol 2000 62(1):271-286. doi:10.1111/prd.12007", "snapshot": _load_snapshot("snapshots/B3_cullinan_seymour_2013.txt"), "snapshot_source": "public:pubmed_abstract", }, "aha_2012": { "quote": ( "Observational studies to date support an association between PD " "and ASVD independent of known confounders. They do not, however, " "support a causative relationship." ), "url": "http://web.archive.org/web/20260128105120/https://pubmed.ncbi.nlm.nih.gov/22514251/", "source_name": "Lockhart PB, Bolger AF, Papapanou PN, et al. (2012), Periodontal Disease and Atherosclerotic Vascular Disease: Does the Evidence Support an Independent Association? A Scientific Statement From the American Heart Association. Circulation 125(20):2520-2544. doi:10.1161/CIR.0b013e31825719f3. PubMed: https://pubmed.ncbi.nlm.nih.gov/22514251/ (live PubMed fetch was intercepted by reCAPTCHA from this environment; Wayback snapshot used instead).", "snapshot": _load_snapshot("snapshots/B4_aha_2012.txt"), "snapshot_source": "public:pubmed_abstract_via_wayback", }, } # --------------------------------------------------------------------------- # 4. CITATION VERIFICATION (Hardening Rule 2) # --------------------------------------------------------------------------- citation_results = verify_all_citations(empirical_facts, wayback_fallback=True) # --------------------------------------------------------------------------- # 5. COUNT SOURCES WITH VERIFIED CITATIONS # --------------------------------------------------------------------------- COUNTABLE_STATUSES = ("verified", "partial") n_confirmed = sum( 1 for key in empirical_facts if citation_results[key]["status"] in COUNTABLE_STATUSES ) print(f" Confirmed sources: {n_confirmed} / {len(empirical_facts)}") # --------------------------------------------------------------------------- # 6. CLAIM EVALUATION (Hardening Rule 7 — compare(), no hardcoded True/False) # --------------------------------------------------------------------------- claim_holds = compare( n_confirmed, CLAIM_FORMAL["operator"], CLAIM_FORMAL["threshold"], label="verified consensus-review count vs. threshold", ) # --------------------------------------------------------------------------- # 7. COI FLAGS # --------------------------------------------------------------------------- # All four sources are peer-reviewed consensus statements or scientific # statements from major medical/dental societies (EFP/AAP, EFP/WHF, AHA, and # the Periodontology 2000 journal). No commercial sponsor steers the # conclusions; the AHA statement is, if anything, the most conservative of # the four (it pushes back on causation). No COI flagged. coi_flags = [] # --------------------------------------------------------------------------- # 8. ADVERSARIAL CHECKS (Hardening Rule 5) # --------------------------------------------------------------------------- adversarial_checks = [ { "question": ( "Do recent reviews or Mendelian-randomization studies overturn the " "epidemiological association between periodontitis and ASCVD?" ), "verification_performed": ( "Searched PubMed and the web (2022–2026) for counter-evidence: " "'periodontitis cardiovascular disease no evidence', " "'periodontitis CVD not causal', 'Mendelian randomization " "periodontitis ASCVD'. Located Carra et al. 2024 ('Periodontitis " "and atherosclerotic cardiovascular disease: A critical " "appraisal', Periodontology 2000, doi:10.1111/prd.12528) and the " "Brodzikowska & Górski 2022 review (PMC9275186). Both papers " "REJECT the stronger causal claim and note that Mendelian " "randomization has so far failed to demonstrate genetic " "causality, but BOTH still affirm the associational link the " "claim asserts. Carra et al. explicitly state that observed " "associations 'may be influenced by various biases, such as " "confounding and collider stratification' — yet still conclude " "the association is real. The claim under proof uses only " "associational and 'biologically plausible' language, not causal " "language, so this counter-evidence does not break the proof." ), "finding": ( "No source overturns the association. Counter-evidence is " "directed at the stronger causal hypothesis (which this claim " "does NOT assert). The associational + 'biologically plausible " "mechanism' framing remains consensus." ), "breaks_proof": False, }, { "question": ( "Is 'Cullinan & Ford, 2013' a real publication, or is the user's " "citation mis-attributed?" ), "verification_performed": ( "Searched PubMed and Google Scholar for any 2012–2013 " "Cullinan-and-Ford periodontal-systemic review. No such paper " "exists. The 2013 Periodontology 2000 review on periodontitis " "and systemic illness is Cullinan MP & Seymour GJ (PMID " "23574472). The Ford co-authorship is on an earlier 2009 " "Australian Dental Journal review (Cullinan, Ford, Seymour; " "doi:10.1111/j.1834-7819.2009.01144.x). This is treated as a " "benign mis-citation: the cited year is correct, the subject " "matter matches, only the second-author attribution is wrong. " "Proof substitutes the actual Cullinan & Seymour 2013 paper as B3." ), "finding": ( "Attribution error confirmed. Does not break the proof because " "the substitute source (Cullinan & Seymour 2013) makes exactly " "the assertion the claim attributes to that citation." ), "breaks_proof": False, }, { "question": ( "Could publication-bias or sponsor capture inflate the apparent " "consensus among periodontology consensus statements?" ), "verification_performed": ( "Checked authorship and convening bodies. Two of the four " "sources are joint perio-cardio workshops with cardiology " "co-leadership (EFP/AAP 2013 included Van Dyke from the Forsyth " "Institute; EFP/WHF 2020 was co-led with the World Heart " "Federation and includes cardiology co-authors such as " "Gonzalez-Juanatey and Vlachopoulos). The AHA 2012 statement " "(B4) is from cardiology, not periodontology, and is the most " "skeptical of the four (rejects causation). The convergence of " "the periodontology consensus reviews with the independent " "cardiology statement reduces the risk that the apparent " "consensus is an artifact of disciplinary self-promotion." ), "finding": ( "Cross-disciplinary corroboration present. The AHA statement, " "from outside periodontology, agrees on the associational claim." ), "breaks_proof": False, }, ] # --------------------------------------------------------------------------- # 9. VERDICT AND STRUCTURED OUTPUT # --------------------------------------------------------------------------- if __name__ == "__main__": any_unverified = any( cr["status"] != "verified" for cr in citation_results.values() ) is_disproof = CLAIM_FORMAL.get("proof_direction") == "disprove" any_breaks = any(ac.get("breaks_proof") for ac in adversarial_checks) confirmed_keys = {k for k in empirical_facts if citation_results[k]["status"] in COUNTABLE_STATUSES} coi_favorable = {f["source_key"] for f in coi_flags if f["direction"] == "favorable_to_subject" and f["source_key"] in confirmed_keys} coi_unfavorable = {f["source_key"] for f in coi_flags if f["direction"] == "unfavorable_to_subject" and f["source_key"] in confirmed_keys} coi_majority = max(len(coi_favorable), len(coi_unfavorable)) if coi_flags else 0 coi_override = (n_confirmed >= CLAIM_FORMAL["threshold"] and coi_majority > n_confirmed / 2) if any_breaks: base_verdict = "UNDETERMINED" elif coi_override: base_verdict = "UNDETERMINED" elif claim_holds: base_verdict = "DISPROVED" if is_disproof else "PROVED" else: base_verdict = "UNDETERMINED" verdict = apply_verdict_qualifier(base_verdict, any_unverified) print(f"\n=== VERDICT: {verdict} ===\n") builder = ProofSummaryBuilder(CLAIM_NATURAL, CLAIM_FORMAL) for fid, info in FACT_REGISTRY.items(): if not fid.startswith("B"): continue ef_key = info["key"] ef = empirical_facts[ef_key] cr = citation_results.get(ef_key, {}) builder.add_empirical_fact( fid, label=info["label"], source_name=ef["source_name"], source_url=ef["url"], source_quote=ef["quote"], ) builder.set_verification( fid, status=cr.get("status", "unknown"), method=cr.get("method", "full_quote"), coverage_pct=cr.get("coverage_pct"), fetch_mode=cr.get("fetch_mode", "live"), credibility=cr.get("credibility", {}), ) builder.set_extraction( fid, value=cr.get("status", "unknown"), value_in_quote=cr.get("status") in COUNTABLE_STATUSES, quote_snippet=ef["quote"][:80], ) builder.add_computed_fact( "A1", label="Verified source count", method=f"count(verified citations) = {n_confirmed}", result=n_confirmed, depends_on=[fid for fid in FACT_REGISTRY if fid.startswith("B")], ) builder.add_cross_check( description=( "Four independent consensus statements consulted: two joint " "perio-cardio workshops (EFP/AAP 2013, EFP/WHF 2020), one " "Periodontology 2000 narrative review (Cullinan & Seymour 2013), " "and one independent AHA cardiology scientific statement (Lockhart " "et al. 2012)." ), fact_ids=[fid for fid in FACT_REGISTRY if fid.startswith("B")], n_sources_consulted=len(empirical_facts), n_sources_verified=n_confirmed, sources={k: citation_results[k]["status"] for k in empirical_facts}, independence_note=( "Sources span three convening bodies (EFP, AAP, WHF), two " "disciplines (periodontology and cardiology), and a 7-year time " "window. AHA 2012 is the most skeptical and was published by a " "cardiology body — its agreement on the associational claim is " "the strongest evidence against discipline-internal bias." ), coi_flags=coi_flags, agreement=claim_holds, ) for ac in adversarial_checks: builder.add_adversarial_check( question=ac["question"], verification_performed=ac["verification_performed"], finding=ac["finding"], breaks_proof=ac["breaks_proof"], ) builder.set_verdict(base_verdict, any_unverified=any_unverified) builder.set_key_results( n_confirmed=n_confirmed, threshold=CLAIM_FORMAL["threshold"], operator=CLAIM_FORMAL["operator"], claim_holds=claim_holds, ) builder.emit()