diff --git a/4-Infrastructure/shim/ingest_ms_myelin_article.py b/4-Infrastructure/shim/ingest_ms_myelin_article.py new file mode 100644 index 00000000..50728c19 --- /dev/null +++ b/4-Infrastructure/shim/ingest_ms_myelin_article.py @@ -0,0 +1,91 @@ +#!/usr/bin/env python3 +"""Ingest MS myelin glucose signaling article into Research Stack database.""" + +import json, time, hashlib +from pathlib import Path + +RESEARCH_STACK = Path("/home/allaun/Documents/Research Stack") + +ARTICLE = { + "id": "ms-myelin-glucose-2026-05-04", + "source": "https://multiplesclerosisnewstoday.com/news-posts/2026/05/04/brain-sugar-levels-act-signal-myelin-growth-study-finds/", + "title": "Brain sugar levels act as signal for myelin growth, study finds", + "date": "2026-05-04", + "publication": "Multiple Sclerosis News Today", + "summary": "Glucose levels in the brain regulate oligodendrocyte progenitor cell (OPC) fate — high glucose drives OPC proliferation via histone acetylation, low glucose triggers maturation into myelin-producing oligodendrocytes. Acetyl-CoA from glucose is required for OPC division; mature oligodendrocytes can source acetyl-CoA from ketone bodies for myelin synthesis. ACLY enzyme knockout reduces early myelin but ketogenic diet rescues it.", + "key_findings": [ + "OPC activity correlates with local brain glucose levels", + "High glucose → acetyl-CoA → histone acetylation → OPC proliferation", + "Low glucose → OPC maturation into myelin-producing oligodendrocytes", + "ACLY enzyme required for glucose-to-acetyl-CoA conversion in OPCs", + "Mature oligodendrocytes use ketone bodies as alternative acetyl-CoA source", + "Ketogenic diet rescues myelin production in ACLY-deficient mice", + "Same cell lineage interprets different metabolic signals at distinct stages" + ], + "relevance_to_research_stack": { + "topics": [ + "metabolic_epigenetic_switch", + "myelin_repair_mechanism", + "glucose_signaling_pathway", + "oligodendrocyte_differentiation", + "ketogenic_metabolic_intervention", + "histone_acetylation_gene_regulation" + ], + "connections": [ + "N-Dimensional Gene Hypothesis: glucose gradient as spatial morphogen signal", + "PIST biological polymorphic shifter: metabolic state → cell fate switch", + "Topological state machine: glucose level as continuous state variable", + "FAMM delay lines: metabolic latency in cell fate decisions", + "Waveprobe manifolds: glucose gradient as scalar field on brain manifold" + ] + }, + "metadata": { + "ingested_at": time.time(), + "content_hash": hashlib.sha256( + "glucose myelin OPC oligodendrocyte acetyl-CoA ACLY ketogenic histone acetylation".encode() + ).hexdigest()[:16], + "tags": ["neuroscience", "metabolism", "myelin", "multiple-sclerosis", "epigenetics", "glucose-signaling"] + } +} + + +def ingest(): + # Save to germane research data + germane_dir = RESEARCH_STACK / "shared-data/data/germane/research" + germane_dir.mkdir(parents=True, exist_ok=True) + + out_path = germane_dir / "ms_myelin_glucose_signaling_2026-05-04.json" + with open(out_path, 'w') as f: + json.dump(ARTICLE, f, indent=2) + + print(f"✓ Ingested: {out_path}") + + # Append to research index + index_path = germane_dir / "research_ingestion_index.json" + index = [] + if index_path.exists(): + with open(index_path) as f: + index = json.load(f) + + index.append({ + "id": ARTICLE["id"], + "title": ARTICLE["title"], + "date": ARTICLE["date"], + "source": ARTICLE["source"], + "ingested_at": ARTICLE["metadata"]["ingested_at"], + "tags": ARTICLE["metadata"]["tags"], + }) + + with open(index_path, 'w') as f: + json.dump(index, f, indent=2) + + print(f"✓ Index updated: {index_path} ({len(index)} entries)") + + # Print connections + print(f"\nResearch Stack connections:") + for conn in ARTICLE["relevance_to_research_stack"]["connections"]: + print(f" → {conn}") + + +if __name__ == "__main__": + ingest() diff --git a/6-Documentation/tiddlywiki-local/wiki/tiddlers/Hutter Critical Analysis.tid b/6-Documentation/tiddlywiki-local/wiki/tiddlers/Hutter Critical Analysis.tid index e9bd93c8..5453ea83 100644 --- a/6-Documentation/tiddlywiki-local/wiki/tiddlers/Hutter Critical Analysis.tid +++ b/6-Documentation/tiddlywiki-local/wiki/tiddlers/Hutter Critical Analysis.tid @@ -29,3 +29,6 @@ counts, decompressor cost, and comparison baselines. * [[Hutter Prize Compression]] * [[Hutter Tensor Field Analysis DAG]] * [[Mass Number Sidecar Rule]] +* [[Pathological Manifold Torus]] +* [[Pathological Menger-Horn Composite]] +* [[Pathological PIST Shells]] diff --git a/6-Documentation/tiddlywiki-local/wiki/tiddlers/Hutter Prize Compression.tid b/6-Documentation/tiddlywiki-local/wiki/tiddlers/Hutter Prize Compression.tid index 30b4ac48..9959d58c 100644 --- a/6-Documentation/tiddlywiki-local/wiki/tiddlers/Hutter Prize Compression.tid +++ b/6-Documentation/tiddlywiki-local/wiki/tiddlers/Hutter Prize Compression.tid @@ -16,6 +16,9 @@ work. * [[PIST Shifters]] * [[Soliton N-Space Path]] * [[Compression and Soliton Mining]] +* [[Pathological Manifold Torus]] +* [[Pathological Menger-Horn Composite]] +* [[Pathological PIST Shells]] !! Durable Sources diff --git a/6-Documentation/tiddlywiki-local/wiki/tiddlers/PIST Shifters.tid b/6-Documentation/tiddlywiki-local/wiki/tiddlers/PIST Shifters.tid index 66b432a5..5fe7ddf0 100644 --- a/6-Documentation/tiddlywiki-local/wiki/tiddlers/PIST Shifters.tid +++ b/6-Documentation/tiddlywiki-local/wiki/tiddlers/PIST Shifters.tid @@ -15,6 +15,9 @@ variants. * [[Hutter Prize Compression]] * [[Soliton N-Space Path]] * [[Compression and Soliton Mining]] +* [[Pathological PIST Shells]] +* [[Pathological Manifold Torus]] +* [[Pathological Menger-Horn Composite]] !! Durable Source diff --git a/6-Documentation/tiddlywiki-local/wiki/tiddlers/Pathological Manifold Torus.tid b/6-Documentation/tiddlywiki-local/wiki/tiddlers/Pathological Manifold Torus.tid new file mode 100644 index 00000000..61c8bb47 --- /dev/null +++ b/6-Documentation/tiddlywiki-local/wiki/tiddlers/Pathological Manifold Torus.tid @@ -0,0 +1,24 @@ +created: 20260506230000000 +modified: 20260506230000000 +tags: ResearchStack Compression Hutter CAD Geometry Torus +title: Pathological Manifold Torus +type: text/vnd.tiddlywiki + +! Pathological Manifold Torus + +3D slice of a hypertorus used as a PIST pathological manifold for Hutter Prize +compression geometry. A 3D projection of the 4D structure, with points sampled +via irrational φ-rotations (Φ, Φ², Φ³) and the psi angle encoded as color. + +The torus provides periodic boundary conditions for routing across the +compression manifold — no endpoints, no zero-mass singularities. + +!! Links + +* [[Hutter Prize Compression]] +* [[Pathological Menger-Horn Composite]] +* [[Pathological PIST Shells]] + +!! Durable Source + +`../../3-Mathematical-Models/cad_models/hypertorus_slice.scad` diff --git a/6-Documentation/tiddlywiki-local/wiki/tiddlers/Pathological Menger-Horn Composite.tid b/6-Documentation/tiddlywiki-local/wiki/tiddlers/Pathological Menger-Horn Composite.tid new file mode 100644 index 00000000..b37d141f --- /dev/null +++ b/6-Documentation/tiddlywiki-local/wiki/tiddlers/Pathological Menger-Horn Composite.tid @@ -0,0 +1,29 @@ +created: 20260506230000000 +modified: 20260506230000000 +tags: ResearchStack Compression Hutter CAD Geometry MengerSponge GabrielHorn +title: Pathological Menger-Horn Composite +type: text/vnd.tiddlywiki + +! Pathological Menger-Horn Composite + +Composite manifold: Menger sponge nodes mounted as structural attachment points +along Gabriel's horn backbone (x-axis curve y = 1/x). PIST shell coordinates are +nested inside each sponge node. + +The horn provides infinite surface area with finite volume — the byte container +surface. The Menger sponge provides fractal addressing (Hausdorff dimension +~2.7268) for routing between shells. Together they form one of three pathological +manifolds for Hutter Prize compression-geometry folding. + +Composite structure is Torus-Menger-Horn, as referenced in +[[04_Hutter_Prize_Equation.md|Hutter Prize Equation §Torus-Menger-Horn folding]]. + +!! Links + +* [[Hutter Prize Compression]] +* [[Pathological Manifold Torus]] +* [[Pathological PIST Shells]] + +!! Durable Source + +`../../3-Mathematical-Models/cad_models/composite_manifold.scad` diff --git a/6-Documentation/tiddlywiki-local/wiki/tiddlers/Pathological PIST Shells.tid b/6-Documentation/tiddlywiki-local/wiki/tiddlers/Pathological PIST Shells.tid new file mode 100644 index 00000000..a5fe4a7c --- /dev/null +++ b/6-Documentation/tiddlywiki-local/wiki/tiddlers/Pathological PIST Shells.tid @@ -0,0 +1,30 @@ +created: 20260506230000000 +modified: 20260506230000000 +tags: ResearchStack Compression Hutter CAD Geometry PIST Shells +title: Pathological PIST Shells +type: text/vnd.tiddlywiki + +! Pathological PIST Shells + +Concentric polygonal rings representing PIST shell encoding. Each shell k is +drawn as a regular (2k+1)-gon with radius proportional to k. Mirror involution +axes are marked at the t = k symmetry points (red markers). + +Inner shells are dense with low curvature; outer shells are sparse with high +curvature — this is the tension gradient used in compression. The mirror +involution (k, t) → (k, 2k+1-t) preserves mass and is self-inverse, providing +the geometric basis for resonance jumps and shell-preserving RG flow. + +One of three pathological manifold structures (Torus-Menger-Horn) for Hutter +Prize compression folding. + +!! Links + +* [[PIST Shifters]] +* [[Hutter Prize Compression]] +* [[Pathological Manifold Torus]] +* [[Pathological Menger-Horn Composite]] + +!! Durable Source + +`../../3-Mathematical-Models/cad_models/pist_shells.scad`