Medical Research Wiki

log

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Wiki Log

Chronological record of medical research wiki actions. Append-only. Format: ## [YYYY-MM-DD] action | subject

[2026-06-06] create | Medical Research Wiki initialized

  • Created Obsidian-compatible vault at /Users/paul/Documents/Medical Research Wiki.
  • Primary domain: ulcerative colitis and related medical research.
  • Created schema, index, dashboard, condition hub, directory structure, and backup script.
  • Notion access is configured, but the first API inspection attempt was blocked by the runtime approval layer; ingestion should resume after the user confirms/approves future Notion API calls if prompted.

[2026-06-16] create | Medical research system upgrade plan

  • Created _meta/medical-research-system-upgrade-plan.md.
  • Captured desired architecture for a positive, cure-oriented weekly medical research internet scrub.
  • Noted that current Hermes cron list only contains the daily silent backup job e50d059a0af0; no active research digest cron was found.
  • Planned next steps: Guava export ingestion, personal health profile, expert/protocol pages, YouTube/social scraping workflow, weekly digest archive, and email delivery setup.

[2026-06-16] update | Condition-first notebook model and Notion access

  • Installed and verified Notion CLI ntn 0.16.0 using the existing Notion integration token from Hermes env.
  • Verified Notion search access for health/medical terms.
  • Identified accessible Notion health objects including Ulcerative Colitis, Health Meetings, Ulcerative Colitis Monitoring on Facebook, Health Record Apps, and Colitis Management, Cholesterol, and COPD (Dr. Enos).
  • Updated SCHEMA.md to use top-level condition objects plus a chronological journal/ layer.
  • Created journal/index.md as the research journal home.
  • Created _meta/notion-health-docs-inventory.md with a private-safe inventory and staged import recommendations.
  • Updated _meta/medical-research-system-upgrade-plan.md to incorporate condition-first organization and journal-first weekly digest storage.

[2026-06-17] import | Notion UC export and condition-first UC object

  • Backed up the vault to /Users/paul/Backups/ObsidianMedicalResearch/medical-research-wiki-20260617-092500.zip before import work.
  • Exported the large Notion Ulcerative Colitis page to raw/notion-exports/2026-06-17/ulcerative-colitis-notion.md.
  • Extracted 54 headings and 310 links from the Notion UC page.
  • Created link inventories: ulcerative-colitis-headings.md, ulcerative-colitis-links.csv, and ulcerative-colitis-link-domains.md.
  • Created conditions/ulcerative-colitis/source-digestion-queue.md to process all UC sources one by one.
  • Created the new condition object folder conditions/ulcerative-colitis/ with index, personal history, research map, methods/protocols, coaches/influencers, and journal highlights pages.
  • Captured Paul’s current UC/proctitis observations: dairy-triggered bleeding, gluten sensitivity, stress/sleep exacerbation, mucus/constipation/blood progression, rectal and cecal pain, cholesterol-flare correlation, and ALP-calprotectin/symptom correlation.
  • Added top-level condition placeholders for sleep apnea, high cholesterol, and silent reflux.
  • Created _meta/medical-intake-question-bank.md for the future structured personal-history interview.

[2026-06-17] research | Central UC/proctitis theory and causal mechanism digest 001

  • Created conditions/ulcerative-colitis/central-theory.md as the evolving causal model for UC/proctitis.
  • Created journal/finds/2026-06-17-uc-causal-mechanism-digest-001.md covering mucus phosphatidylcholine/barrier, mitochondrial thiolase/redox, microbial niche/pathobiont localization, coconut water RCT, and IBD-liver/ALP clues.
  • Promoted source implications into conditions/ulcerative-colitis/central-theory.md v0.2 and conditions/ulcerative-colitis/research.md.
  • Added central theory links from conditions/ulcerative-colitis/index.md.
  • Marked processed queue items in conditions/ulcerative-colitis/source-digestion-queue.md where source links matched the digest batch.

[2026-06-17] research | UC distal/proctitis onset causal mechanism digest 002

  • Saved raw PubMed provenance for 20 records to raw/papers/2026-06-17-uc-distal-proctitis-digest-002/.
  • Created journal/finds/2026-06-17-uc-distal-proctitis-onset-digest-002.md covering rectal-first UC, ulcerative proctitis, mucus barrier penetrability, phosphatidylcholine thinning toward rectum, fecal stasis/contact time, diversion colitis/SCFA paradox, and distal metabolite gradients.
  • Created canonical mechanism page mechanisms/distal-proctitis-onset.md.
  • Promoted Digest 002 into conditions/ulcerative-colitis/central-theory.md v0.3, conditions/ulcerative-colitis/research.md, conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/journal-highlights.md, and index.md.

[2026-06-17] planning | Weekly report source-audit requirement

  • Updated _meta/medical-research-system-upgrade-plan.md so the future weekly medical research digest must include Sources browsed and new takeaways and Reviewed but no major new data sections.
  • Added fields for source title/name, URL/platform, source class, why browsed, main new takeaway, novelty status, and affected wiki/condition/theory page.
  • Updated the reusable medical-research-and-anecdote-kb skill and references/uc-cure-oriented-research-system.md so future sessions and cron prompts inherit the source-audit requirement.

[2026-06-17] research | UC dairy/gluten/wheat food-trigger causal mechanism digest 003

  • Backed up the vault to /Users/paul/Backups/ObsidianMedicalResearch/medical-research-wiki-20260617-171301.zip before edits.
  • Saved raw PubMed provenance for 23 records to raw/papers/2026-06-17-uc-dairy-gluten-food-trigger-digest-003/.
  • Created journal/finds/2026-06-17-uc-dairy-gluten-food-trigger-digest-003.md covering dairy/milk protein/casein/lactose, gluten/wheat/fructans/ATIs, patient-reported triggers, objective evidence limits, and Paul’s dairy → blood signal.
  • Created canonical mechanism page mechanisms/dairy-gluten-wheat-food-triggers-uc.md.
  • Promoted Digest 003 into conditions/ulcerative-colitis/central-theory.md v0.4, conditions/ulcerative-colitis/research.md, conditions/ulcerative-colitis/methods.md, conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/journal-highlights.md, and index.md.

[2026-06-17] research | UC sleep/apnea/circadian causal mechanism digest 004

  • Backed up the vault to /Users/paul/Backups/ObsidianMedicalResearch/medical-research-wiki-20260617-234917.zip before edits.
  • Saved raw PubMed provenance for 10 records to raw/papers/2026-06-17-uc-sleep-apnea-circadian-digest-004/.
  • Created journal/finds/2026-06-17-uc-sleep-apnea-circadian-digest-004.md covering sleep quality, sleep duration, OSA prevalence/screening, circadian rhythm disruption, permeability, calprotectin, TNF-α, dysbiosis, melatonin, and Paul’s sleep-exacerbation signal.
  • Created canonical mechanism page mechanisms/sleep-apnea-circadian-uc-barrier.md.
  • Promoted Digest 004 into conditions/ulcerative-colitis/central-theory.md v0.5, conditions/ulcerative-colitis/research.md, conditions/ulcerative-colitis/methods.md, conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/journal-highlights.md, conditions/sleep-apnea/index.md, and index.md.

[2026-06-18] update | UC key insights running list

  • Backed up the vault to /Users/paul/Backups/ObsidianMedicalResearch/medical-research-wiki-20260618-004605.zip before edits.
  • Created conditions/ulcerative-colitis/key-insights.md as the concise, source-linked running list of durable UC/proctitis insights.
  • Added the sleep insight explicitly: poor sleep/sleep apnea/circadian disruption appears important for UC/proctitis barrier resilience, with links to Digest 004, the 2025 poor-sleep UC relapse study, and the circadian actigraphy study.
  • Linked the key-insights page from conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/central-theory.md, and index.md.

[2026-06-18] research | UC ALP/cholesterol/gut-liver-lipid causal mechanism digest 005

  • Saved raw PubMed provenance for 24 records to raw/papers/2026-06-18-uc-alp-cholesterol-gut-liver-digest-005/; corrected DOI parsing to use PubmedData/ArticleIdList only.
  • Created journal/finds/2026-06-18-uc-alp-cholesterol-gut-liver-digest-005.md covering ALP source/fraction logic, PSC screening questions, intestinal alkaline phosphatase/LPS/barrier biology, bile-acid–microbiome signaling, and IBD lipid profile evidence.
  • Created canonical mechanism page mechanisms/alp-cholesterol-gut-liver-lipid-axis-uc.md.
  • Promoted Digest 005 into conditions/ulcerative-colitis/central-theory.md v0.6, conditions/ulcerative-colitis/research.md, conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/journal-highlights.md, conditions/ulcerative-colitis/key-insights.md, conditions/high-cholesterol/index.md, and index.md.

[2026-06-18] research | UC mucus phosphatidylcholine causal mechanism digest 006

  • Backed up the vault to /Users/paul/Backups/ObsidianMedicalResearch/medical-research-wiki-20260618-090519.zip before edits.
  • Saved raw PubMed provenance for 7 records to raw/papers/2026-06-18-uc-mucus-phosphatidylcholine-digest-006/.
  • Created journal/finds/2026-06-18-uc-mucus-phosphatidylcholine-digest-006.md covering mucus PC deficiency, early delayed-release PC trials, the 2021 meta-analysis, 2024 LT-02 multicenter trial contradiction, formulation caveats, and PC34:1/PEMT/PCYT1α lipidomics.
  • Created canonical mechanism/intervention page mechanisms/mucus-phosphatidylcholine-barrier-uc.md.
  • Promoted Digest 006 into conditions/ulcerative-colitis/central-theory.md v0.7, conditions/ulcerative-colitis/research.md, conditions/ulcerative-colitis/methods.md, conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/journal-highlights.md, conditions/ulcerative-colitis/key-insights.md, and index.md.

[2026-06-18] structure | UC key open questions page

  • Created conditions/ulcerative-colitis/key-open-questions.md to track the highest-value unresolved UC/proctitis questions alongside key-insights.md.
  • Linked the page from conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/central-theory.md, and root index.md.
  • Seeded the page with active questions from the central theory: mucus-PC causality/delivery, redox/butyrate oxidation, mucus→constipation→blood sequence, dairy/gluten specificity, sleep/apnea threshold effects, ALP/cholesterol source logic, PSC screening question, microbial niche/location, stool contact-time/pelvic-floor mechanics, and barrier-repair intervention tracking.

[2026-06-18] research | UC redox butyrate Pravda digest 007

  • Saved raw PubMed provenance for 23 records to raw/papers/2026-06-18-uc-redox-butyrate-pravda-digest-007/.
  • Created journal/finds/2026-06-18-uc-redox-butyrate-pravda-digest-007.md covering Santhanam thiolase/butyrate oxidation, Roediger starved-gut hypothesis, Pravda radical-induction/H2O2 theory, H2S nuance, oxidative-stress reviews, and safety filters.
  • Created canonical mechanism page mechanisms/redox-butyrate-thiolase-uc.md.
  • Promoted Digest 007 into conditions/ulcerative-colitis/central-theory.md v0.8, conditions/ulcerative-colitis/research.md, conditions/ulcerative-colitis/methods.md, conditions/ulcerative-colitis/key-insights.md, conditions/ulcerative-colitis/key-open-questions.md, conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/journal-highlights.md, and root index.md.

[2026-06-18] structure | UC top research insights page

  • Created conditions/ulcerative-colitis/top-research-insights.md for the strongest/high-signal UC findings worth remembering verbatim.
  • Seeded it with findings including ~80% mitochondrial acetoacetyl-CoA thiolase impairment in UC biopsies, ~70% mucus PC reduction signal, poor sleep UC relapse signal, penetrable UC mucus, and key biomarker contradictions.
  • Linked the page from conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/central-theory.md, and root index.md.

[2026-06-18] research | UC constipation contact-time digest 008

  • Saved raw PubMed provenance for 18 records to raw/papers/2026-06-18-uc-constipation-contact-time-digest-008/.
  • Created journal/finds/2026-06-18-uc-constipation-contact-time-digest-008.md covering UC-associated constipation, fecal stasis/contact time, tenesmus, pelvic-floor dysfunction, and local rectal therapy evidence.
  • Created canonical mechanism page mechanisms/constipation-contact-time-pelvic-floor-uc.md.
  • Promoted Digest 008 into conditions/ulcerative-colitis/central-theory.md v0.9, conditions/ulcerative-colitis/research.md, conditions/ulcerative-colitis/methods.md, conditions/ulcerative-colitis/key-insights.md, conditions/ulcerative-colitis/top-research-insights.md, conditions/ulcerative-colitis/key-open-questions.md, conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/journal-highlights.md, and root index.md.

[2026-06-18] research | UC pathobiont mucus-layer digest 009

  • Saved raw PubMed provenance for 38 retrieved records and 27 curated records to raw/papers/2026-06-18-uc-pathobiont-mucus-layer-digest-009/.
  • Created journal/finds/2026-06-18-uc-pathobiont-mucus-layer-digest-009.md covering MUC2 mucus spatial barrier, active UC mucus penetrability, Aeromonas/aerolysin emerging subgroup signal, Fusobacterium oral-gut pathobiont literature, sulfate-reducing bacteria/H2S, Akkermansia, Ruminococcus gnavus, and stool-test limitations.
  • Created canonical mechanism page mechanisms/pathobiont-mucus-layer-ecology-uc.md.
  • Promoted Digest 009 into conditions/ulcerative-colitis/central-theory.md v1.0, conditions/ulcerative-colitis/research.md, conditions/ulcerative-colitis/methods.md, conditions/ulcerative-colitis/key-insights.md, conditions/ulcerative-colitis/top-research-insights.md, conditions/ulcerative-colitis/key-open-questions.md, conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/journal-highlights.md, and root index.md.

[2026-06-18] maintenance | Medical TODOs page

  • Created medical-todos.md as the vault-level action/research checklist.
  • Added TODOs to look into pelvic-floor PT/biofeedback for constipation/incomplete evacuation and to investigate food/routine/method options for reducing constipation and ensuring more complete evacuation.
  • Linked the TODO page from root index.md and conditions/ulcerative-colitis/index.md.

[2026-06-18] correction | Faecalibacterium prausnitzii omission

  • User noted Digest 009 did not call out Faecalibacterium prausnitzii despite prior Notion notes.
  • Patched journal/finds/2026-06-18-uc-pathobiont-mucus-layer-digest-009.md, mechanisms/pathobiont-mucus-layer-ecology-uc.md, conditions/ulcerative-colitis/key-insights.md, and medical-todos.md.
  • Framed F. prausnitzii as the beneficial butyrate-producing/anti-inflammatory commensal counterpart to the pathobiont/toxin branch and queued it for Digest 010 on probiotics/prebiotics/butyrate/fiber.

[2026-06-18] research | UC beneficial commensals probiotics prebiotics digest 010

  • Saved curated PubMed provenance for 37 records to raw/papers/2026-06-18-uc-beneficial-commensals-probiotics-prebiotics-digest-010/.
  • Created journal/finds/2026-06-18-uc-beneficial-commensals-probiotics-prebiotics-digest-010.md covering Faecalibacterium prausnitzii, Roseburia hominis, EcN, De Simone/VSL#3-style probiotics, psyllium/Plantago, fiber tolerance, and butyrate delivery evidence.
  • Created canonical page mechanisms/beneficial-commensals-butyrate-ecology-uc.md.
  • Promoted Digest 010 into conditions/ulcerative-colitis/central-theory.md v1.1, research.md, methods.md, key-insights.md, top-research-insights.md, key-open-questions.md, journal-highlights.md, UC/root indexes, and medical-todos.md.

[2026-06-19] research | UC constipation-safe fiber and full evacuation digest 011

  • Saved raw PubMed provenance for 27 records to raw/papers/2026-06-19-uc-constipation-safe-fiber-evacuation-digest-011/.
  • Created journal/finds/2026-06-19-uc-constipation-safe-fiber-evacuation-digest-011.md covering UC-associated constipation, safe fiber options, kiwi/psyllium/PHGG/resistant starch, PEG and guideline options, toileting posture, pelvic-floor mechanics, and tracking variables.
  • Created canonical page mechanisms/constipation-safe-fiber-full-evacuation-uc.md.
  • Promoted Digest 011 into conditions/ulcerative-colitis/central-theory.md v1.2, research.md, methods.md, key-insights.md, top-research-insights.md, key-open-questions.md, journal-highlights.md, UC/root indexes, and medical-todos.md.

[2026-06-25] monitoring | UC community/forum watchlist

  • Created conditions/ulcerative-colitis/community-watchlist.md as the standing watchlist for UC/proctitis forums, boards, Reddit communities, and cure/remission threads.
  • Added user-provided Bluelight and Low-Toxin threads as Tier 2 high-signal leads.
  • Added candidate communities including Reddit r/UlcerativeColitis/r/IBD/r/UlcerativeColitisRDLA, HealingWell UC forum, Smart Patients IBD, MyCrohnsAndColitisTeam, Mayo Clinic Connect digestive group, Low-Toxin Forum, Bluelight, and experimental/diet subreddits.
  • Saved raw Jina/search snapshots under raw/social/2026-06-25-uc-forum-watchlist-candidates/.
  • Linked the watchlist from root index.md, conditions/ulcerative-colitis/index.md, coaches-and-influencers.md, and _meta/medical-research-system-upgrade-plan.md.
  • Access notes: Firecrawl web search failed with billing authorization error; Reddit OpenCLI timed out; Reddit public JSON returned 403; Jina successfully retrieved Bluelight/Low-Toxin and several community pages.

[2026-06-27] update | Medical TODOs dairy/milk rule-out

  • Added a UC/proctitis dairy and milk trigger rule-out TODO to medical-todos.md.
  • Captured lactose vs SIBO vs casein/whey/A1-A2/fat/bile/histamine/additive branches, plus conservative tracking and flare-safety notes.

[2026-06-27] research | Scite validation of UC central theory

  • Confirmed scite MCP literature access and ran searches/DOI lookups across the current UC/proctitis central-theory branches.
  • Created journal/finds/2026-06-27-uc-scite-validation-central-theory.md with validation matrix, source audit, contradictions, and new ideas.
  • Promoted central-theory version to v1.3 and added a scite validation status section.
  • Updated key-insights.md, top-research-insights.md, and key-open-questions.md with functional distal microenvironment, 4-SURE sulfide-reducing diet, IAP/SRB/Snail, and lipid-causality refinements.
  • Updated UC index, research, methods, journal highlights, and root index with links to the validation pass.
  • Safety framing preserved: scite validation does not justify DIY antibiotics, FMT, redox/enema protocols, or high-dose fiber jumps.

[2026-06-27] update | Medical TODOs milk-allergy differential

  • Enhanced medical-todos.md dairy/milk trigger section with compact next steps from the food-allergy/oral-tolerance discussion.
  • Preserved distinctions: lactose intolerance vs milk-protein allergy/hypersensitivity vs additives/fat/histamine vs reproducible UC flare trigger.
  • Added clinician/allergist differential questions and a small objective dairy-free tracking block before any reintroduction decision.

[2026-06-27] update | Expanded milk-allergy TODO definitions

  • Expanded medical-todos.md dairy/milk section so terms like IgE-mediated allergy, non-IgE milk-protein hypersensitivity, eosinophilic GI overlap, lactose intolerance, and milk-triggered UC flare remain understandable later.
  • Added lightweight dairy-free tracking block details: baseline markers, meaningful signal criteria, and one-axis-at-a-time reintroduction distinctions.

[2026-06-28] research | UC milk allergy / oral tolerance digest

  • Created journal/finds/2026-06-28-uc-milk-allergy-oral-tolerance-digest.md from PubMed/NCBI source retrieval after scite MCP and managed web extraction were unavailable.
  • Saved source set to raw/papers/2026-06-28-uc-milk-allergy-oral-tolerance-digest/pubmed-abstracts.md.
  • Created mechanisms/milk-allergy-oral-tolerance-uc.md as the focused branch for milk-protein allergy/hypersensitivity, oral tolerance, non-IgE GI reactions, eosinophils/mast cells, lactose, and dairy-triggered UC amplification.
  • Promoted the refined framing into UC index, research map, methods, central theory, key insights, and key open questions: dairy is a personal trigger/amplifier branch, not proof that milk allergy universally causes UC.
  • Safety framing preserved: no dairy challenge during active bleeding/unstable symptoms/possible immediate allergy without clinician guidance; allergy testing and lactose testing clarify mechanisms but do not prove UC causation alone.

[2026-06-28] research | UC supplement shortlist from email

  • Backed up the vault to /Users/paul/Backups/ObsidianMedicalResearch/medical-research-wiki-20260628-201935.zip before edits.
  • Saved Paul’s emailed shortlist to raw/personal-notes/2026-06-28-uc-supplement-email-berberine-omega-glutathione.md.
  • Created journal/finds/2026-06-28-uc-supplement-shortlist-berberine-omega-glutathione.md covering berberine, Juice+ Omega / omega-3, and liposomal glutathione/NAC.
  • Promoted noteworthy items into conditions/ulcerative-colitis/methods.md, mechanisms/redox-butyrate-thiolase-uc.md, conditions/ulcerative-colitis/key-open-questions.md, and journal/index.md.
  • Main takeaways: berberine has a small phase I human UC tissue/histology signal with liver/interactions caveats; liposomal glutathione lacks direct UC trial evidence in this quick pass but NAC has a more direct UC remission-maintenance signal; omega-3 evidence is mixed and product-label/dose dependent.

[2026-06-28] research | UC carnivore/nicotine X anecdotes from email

  • Saved Paul’s forwarded Grok/X excerpt to raw/social/2026-06-28-grok-x-uc-remission-carnivore-nicotine-keto.md; raw tweet URLs were not accessible because the Grok chat was private and xAI/X search returned a spending-limit error.
  • Created journal/finds/2026-06-28-uc-carnivore-nicotine-x-anecdotes.md triaging carnivore/keto remission anecdotes, the 2024 Frontiers in Nutrition carnivore-ketogenic IBD case series, the 2025 ketogenic UC case report, and older nicotine-patch UC RCT/Cochrane evidence.
  • Promoted lightweight notes into conditions/ulcerative-colitis/methods.md, conditions/ulcerative-colitis/key-open-questions.md, and journal/index.md.
  • Main takeaways: carnivore/keto is a noteworthy low-evidence responder/elimination signal, but mechanism and safety are unresolved; nicotine has older induction-vs-placebo evidence but not maintenance/standard-therapy superiority and has substantial adverse-event/addiction/cardiovascular caveats.

[2026-06-29] monitoring | UC community/forum watchlist digest

  • Used Agent Reach doctor and confirmed Reddit active backend was OpenCLI; Reddit search/read worked this run.
  • Saved raw Reddit snapshots and search outputs under raw/reddit/2026-06-29-uc-community-watchlist/.
  • Saved forum/social Jina snapshots and access notes under raw/social/2026-06-29-uc-community-watchlist/.
  • Created journal/weekly-digests/2026-06-29-uc-community-forum-watchlist-digest.md.
  • Updated conditions/ulcerative-colitis/community-watchlist.md with the 2026-06-29 monitoring summary and access status.
  • Main new signals: a recent antibiotic-remission/Lyme-overlap story, a helminthic-therapy remission-with-harms report, recurring nicotine-responsive UC reports, strong reinforcement of constipation/mucus/blood UCAC patterns, and continued RDLA/Pravda discussion in Bluelight/Low-Toxin.
  • Safety framing preserved: no medication stopping; no smoking initiation; avoid DIY enemas, unregulated FMT/helminths, and unsupervised antibiotics/antimicrobials.

[2026-06-28] validation | Scite pass for UC milk allergy / oral tolerance digest

  • Re-ran scite after MCP recovery and validated the milk/oral-tolerance digest anchor papers and mechanism claims.
  • Scite confirmed the old Wright/Truelove milk-free diet subset signal, including citation context that about 20% of UC patients benefited from milk withdrawal, while also confirming Jewell & Truelove 1972 and Jones 1981 as conservative counterweights against universal milk-allergy causation.
  • Added scite validation addendum to journal/finds/2026-06-28-uc-milk-allergy-oral-tolerance-digest.md.
  • Updated mechanisms/milk-allergy-oral-tolerance-uc.md, key-insights.md, and key-open-questions.md to reflect scite-supported confidence: personal trigger/amplifier branch strengthened; universal milk-allergy-cause claim rejected/refined downward.

[2026-06-29] research | UC functional distal microenvironment scite-heavy pass

  • Created journal/finds/2026-06-29-uc-functional-distal-microenvironment-scite-pass.md from scite-heavy searches covering H₂S/sulfur, indole/protein fermentation, SCFA/butyrate ecology, 4-SURE, reduced-sulfur diet, low-fat/high-fiber diet, F. prausnitzii/Roseburia, and UCAC/contact-time.
  • Created mechanisms/functional-distal-microenvironment-uc.md as the canonical mechanism page.
  • Saved raw scite source audit to raw/papers/2026-06-29-uc-functional-distal-microenvironment-scite-sources.md.
  • Promoted durable findings into central-theory.md, key-insights.md, top-research-insights.md, key-open-questions.md, research.md, methods.md, journal/index.md, and root index.md.
  • Key update: Paul’s microbiome/diet target is now framed as a functional distal microenvironment: lower H₂S/indole/protein-fermentation pressure, stronger SCFA/butyrate ecology, intact mucus exclusion, and lower stool contact time, with UCAC/fiber tolerance as a gating variable.

[2026-07-03] update | Current UC/proctitis care plan and Dr. Snow regimen

  • Backed up the vault to /Users/paul/Backups/ObsidianMedicalResearch/medical-research-wiki-20260703-174652-before-current-care-plan.zip before edits.
  • Created conditions/ulcerative-colitis/current-care-plan.md to track Paul’s current mesalamine enema/suppository alternation, Dr. Snow’s Moss Nutrition supplement regimen, voicemail notes, and daily tracking priorities.
  • Linked the current care plan from conditions/ulcerative-colitis/index.md, conditions/ulcerative-colitis/methods.md, and root index.md.
  • Preserved safety/uncertainty framing: the page is a personal tracking/care-plan record, not medical advice; exact meanings of “2x2” and “1.5 x 2 tablespoon” remain clinician-clarification items.

[2026-07-04] maintenance | Structural cleanup, tooling, and two new mechanism pages

  • Backed up the vault to /Users/paul/Backups/ObsidianMedicalResearch/medical-research-wiki-20260704-143501.zip before edits.

  • Broken navigation fixed: deleted two empty 0-byte raw notes (raw/personal-notes/Ulcerative Colitis.md, raw/personal-notes/Research Dashboard.md) that the homepage’s [[Ulcerative Colitis]]/[[Research Dashboard]] links were silently resolving to; deleted the redundant legacy redirect conditions/ulcerative-colitis.md. Added aliases: to the UC hub and _meta/research-dashboard.md so friendly bare links resolve to the real hubs.

  • Link standardization: removed all ../ relative wikilink prefixes and normalized ~318 internal links to the shortest-unambiguous convention (bare basename when unique, full vault path for colliding index.md names). This also fixed the milk-allergy find’s pubmed-abstracts link, which had been resolving to the wrong digest folder.

  • Schema reconciliation: expanded SCHEMA.md controlled vocabularies to match actual practice (added study-design source_class values and care-plan/journal-find/research-digest/weekly-digest page types); documented the link convention; fixed the offending pages’ type values.

  • New tooling in tools/: check_links.py (dead/ambiguous/orphan link report), validate_structure.py (frontmatter + controlled-vocabulary check), fix_links.py (link normalizer, dry-run/—apply), and README.md. Both checkers exit non-zero on hard errors so they can gate automation.

  • CLAUDE.md added at vault root: orientation for humans/LLMs on structure, link rules, the raw→journal→promote flow, frontmatter, and safety rules.

  • central-theory.md thinned (v1.4): condensed the inline per-digest recaps into a Digest index (detail now lives in the linked journal finds/mechanism pages); added the persistence loop to the causal graph; added model refinements R1–R6 (barrier-reserve threshold + additive-load logging, redox-vs-contact-time delivery-route argument, ALP/cholesterol confound to score, persistence framing, bile-acid node, and the FMT + nicotine levers).

  • Two new evidence-backed mechanism pages (verified via PubMed, DOIs included): mechanisms/fmt-microbiome-transfer-uc.md (Moayyedi 2015, Paramsothy 2017, Costello 2019; note the Fusobacterium→non-remission link to the pathobiont branch) and mechanisms/nicotine-smoking-paradox-uc.md (Sandborn 1997 induction-positive, Thomas 1995 maintenance-negative). Added an “IAP as a lever, not just a biomarker” note to the ALP page and four new entries (bile acids, FMT, nicotine, composite-load logging) to key-open-questions.md.

  • Refreshed root index.md (stale “1 page / 2026-06-16” header → current; populated the previously empty section stubs; added the two new mechanism links).

  • Safety framing preserved throughout: FMT (not DIY, infection risk), nicotine (not an endorsement of smoking; clinician-only), and IAP/bile-acid ideas all flagged clinician-discussion, not self-directed.

  • 2026-07-04 — Redacted signed Notion S3 image URL query strings from raw Notion export before private Git/Quartz publishing.

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