Graph Report - /Users/wonhurk/mitobio (2026-07-14)

Corpus Check

• 426 files · ~0 words
• Verdict: corpus is large enough that graph structure adds value.

Summary

• 426 nodes · 901 edges · 21 communities (20 shown, 1 thin omitted)
• Extraction: 96% EXTRACTED · 3% INFERRED · 0% AMBIGUOUS · INFERRED: 29 edges (avg confidence: 0.77)
• Token cost: 0 input · 302,262 output

Community Hubs (Navigation)

• Mitochondrial Transplant Disease Targets
• Mitophagy & Intercellular Mito Transfer
• Mito Dynamics & Fertility
• Site Automation Pipeline
• Ischemia-Reperfusion & Organ Injury
• MitoCatch Bispecific Delivery
• Mitochondria-Targeted Nanocarriers
• Artificial Mito Transfer Techniques
• Site Generator (update_site.py)
• Lung Injury Mito Protection
• PN-101 Myositis Trials
• Paper Collector (collect_papers.py)
• Minovia Pearson Syndrome Trials
• Trial Collector (collect_trials.py)
• Migrasome Suppression Axis
• Corneal Endothelial Dysfunction
• Periodontitis & Aquaporin
• Spinal Cord Injury Nanoparticles
• Beta-Catenin Signaling
• Luspatercept

God Nodes (most connected - your core abstractions)

1. Mitochondrial Transplantation - 125 edges

2. Compiled Abstracts: Mitochondrial Transplantation & Delivery - 90 edges

3. Intercellular Mitochondrial Transfer - 76 edges

4. Extracellular Vesicles (EVs) - 23 edges

5. Tunneling Nanotubes (TNTs) - 21 edges

6. main (update_site.py) - 16 edges

7. Ischemia-Reperfusion Injury - 14 edges

8. Mesenchymal stem cells (MSCs) - 13 edges

9. Triphenylphosphonium (TPP) - 12 edges

10. Cancer - 11 edges

Surprising Connections (you probably didn't know these)

• Autologous Mitochondrial Transplantation for Pediatric Cardiogenic Shock (Pilot Cohort) --semantically_similar_to--> ECMO / Ischemic Complication [INFERRED] [semantically similar]

refs/abstracts.md → clinicals/trials/NCT02851758.md

• Autologous Mitochondrial Transplant for Acute Cerebral Ischemia (Phase 1 Trial) --semantically_similar_to--> University of Washington [INFERRED] [semantically similar]

refs/abstracts.md → clinicals/trials/NCT04998357.md

• main (update_site.py) --implements--> public/index.html (Recent Papers page) [EXTRACTED]

scripts/update_site.py → public/index.html

• Artificial Mitochondrial Transfer/Transplantation (AMT/T) --semantically_similar_to--> Light-Activated Mitochondrial Isolation (LAMI) [AMBIGUOUS] [semantically similar]

refs/abstracts.md → refs/papers/PMID_42206452.md

• main (update_site.py) --implements--> public/graph.html (Graph Knowledge page) [EXTRACTED]

scripts/update_site.py → public/graph.html

Hyperedges (group relationships)

• Daily mitobio automation pipeline (collect, refresh graph, build site, deploy) — daily_run_main, collect_papers_main, collect_trials_main, update_site_main [EXTRACTED 0.95]
• MitoCatch-Bi bispecific bridging of TOMM20 and CD71 — mitocatch_bi, tomm20, cd71 [INFERRED 0.85]
• update_site.py fan-out to four public pages — update_site_main, public_index_html, public_trials_html, public_graph_html, public_view_html [EXTRACTED 0.95]
• Intercellular Mitochondrial Transfer Delivery Routes — mitochondrial-transfer, tunneling-nanotubes, extracellular-vesicles, gap-junctions [EXTRACTED 1.00]
• Post-Transfer Mitochondrial Fate Checkpoint — pink1-parkin-pathway, pink1, parkin, usp30, miro1 [EXTRACTED 1.00]
• TP53-PinX1-RanBP2-Rab11a Migrasome Suppression Axis — tp53, pinx1, rab11a, migrasomes, nasopharyngeal-carcinoma [EXTRACTED 1.00]

Communities (21 total, 1 thin omitted)

Community 0 - "Mitochondrial Transplant Disease Targets"

Cohesion: 0.05

Nodes (88): 5-Fluorouracil (5-FU), Compiled Abstracts: Mitochondrial Transplantation & Delivery, Acute Kidney Injury (AKI), Acute Respiratory Distress Syndrome (ARDS), Age-Related Macular Degeneration (AMD), Alpha-synuclein, Intracellular Ca2+ signaling, Cardiac fibrosis (+80 more)

Community 1 - "Mitophagy & Intercellular Mito Transfer"

Cohesion: 0.05

Nodes (75): Acute ischemic stroke, Acute Myeloid Leukemia (AML), Adipose-derived stem cells (ASCs), AIEgens (aggregation-induced emission luminogens), Alzheimer's Disease, Artificial mitochondria, Asthma, Astragaloside IV (+67 more)

Community 2 - "Mito Dynamics & Fertility"

Cohesion: 0.08

Nodes (37): Recurrent assisted reproductive technology failure, CRISPR gene editing, Extracellular Vesicles (EVs), Female Infertility / Recurrent Implantation Failure, HEY1, Ion-responsive microneedle patch, Instituto Valenciano de Infertilidad (IVI Valencia), LL37 antimicrobial peptide (+29 more)

Community 3 - "Site Automation Pipeline"

Cohesion: 0.07

Nodes (35): NCT03384420: MNV-BM-BLD Transplantation in Pediatric Pearson Syndrome, NCT04976140: Allogeneic Mitochondria (PN-101) for Refractory Polymyositis/Dermatomyositis, Mitochondrial Clinical Trials Report - 2026-07-14, efetch, esearch, fetch, main (collect_papers.py), parse (+27 more)

Community 4 - "Ischemia-Reperfusion & Organ Injury"

Cohesion: 0.11

Nodes (27): Boston Children's Hospital, Boston Children's Hospital, Cardiogenic Shock, ECMO / Ischemic Complication, Extracorporeal Membrane Oxygenation (ECMO), Ischemia-Reperfusion Injury, Ischemic Stroke, Kidney Organoid Platforms (+19 more)

Community 5 - "MitoCatch Bispecific Delivery"

Cohesion: 0.1

Nodes (26): Caplacizumab (Cablivi), CD71 (transferrin receptor), Diabetes mellitus, Equine metabolic syndrome (EMS), Institute of Molecular and Clinical Ophthalmology Basel (IOB Basel), Ischemic heart disease / myocardial infarction, Islet transplantation, Leber Hereditary Optic Neuropathy (LHON) (+18 more)

Community 6 - "Mitochondria-Targeted Nanocarriers"

Cohesion: 0.14

Nodes (25): Bromocriptine Mesylate, Porous cerium vanadate nanoparticles, Cyclic RGD (cRGD) peptide, Cyclosporin A (CsA), Evodiamine, Hepatocellular Carcinoma (HCC), Inflammatory Bowel Disease (IBD), IR820 (+17 more)

Community 7 - "Artificial Mito Transfer Techniques"

Cohesion: 0.12

Nodes (23): Artificial Mitochondrial Transfer/Transplantation (AMT/T), BCL2, Chimeric antigen receptor T (CAR-T) cell therapy, CAV1 (Caveolin-1), Mitochondrial electron transport chain (ETC), Gold nanoparticles (GNPs), Lipid nanoparticles, MitoCeption (+15 more)

Community 8 - "Site Generator (update_site.py)"

Cohesion: 0.32

Nodes (14): esc(), find_latest(), load_json(), main(), nav_html(), page(), Minimal converter for graphify's own GRAPH_REPORT.md - not general CommonMark,, render_all_papers_table() (+6 more)

Community 9 - "Lung Injury Mito Protection"

Cohesion: 0.33

Nodes (10): Acute Lung Injury (ALI), Fucoidan smart micelles, LAT1 (L-type amino acid transporter 1), Mitochonic Acid 5 (MA-5), MOTS-c, NRF2 (NFE2L2), P-selectin, LAT1-mediated delivery of engineered R13A-MOTS-c attenuates radiation-induced lung injury via Nrf2 activation and mitochondrial protection (+2 more)

Community 10 - "PN-101 Myositis Trials"

Cohesion: 0.4

Nodes (10): Dermatomyositis, Idiopathic Inflammatory Myopathy (IIM), Paean Biotechnology Inc., Mitochondrial Transplantation in Idiopathic Inflammatory Myopathy (PN-101 Phase 1/2a), Therapeutic potential of mitochondrial transfer in reversing mutant-to-wild-type mtDNA ratio and improving mitochondrial dysfunction in 1555A>G mtDNA mutation-associated hearing loss, PN-101, PN-101 (Allogeneic Mitochondria), Polymyositis (+2 more)

Community 11 - "Paper Collector (collect_papers.py)"

Cohesion: 0.38

Nodes (9): efetch(), esearch(), fetch(), main(), parse(), Write refs/recent_papers_YYYYMMDD.md - the daily snapshot public/papers.html rea, text(), write_paper_md() (+1 more)

Community 12 - "Minovia Pearson Syndrome Trials"

Cohesion: 0.36

Nodes (8): Minovia Therapeutics Ltd., Minovia Therapeutics Ltd., Mitochondrial disorders, MNV-BM-BLD (bone marrow mitochondria transplant product), NCT03384420: Safety and Therapeutic Effects of MNV-BM-BLD Transplantation in Pediatric Pearson Syndrome [COMPLETED, PHASE1/PHASE2], NCT06017869: Safety and Therapeutic Effects of Autologous CD34+ Cells Enriched With Allogeneic Placenta-Derived Mitochondria in Pearson Syndrome [RECRUITING, PHASE2], Pearson Syndrome, Pearson Syndrome

Community 13 - "Trial Collector (collect_trials.py)"

Cohesion: 0.52

Nodes (6): fetch_json(), main(), normalize(), search(), slugify(), write_trial_md()

Community 14 - "Migrasome Suppression Axis"

Cohesion: 0.38

Nodes (7): Cisplatin, Migrasomes, Nasopharyngeal Carcinoma (NPC), PinX1, PinX1 Inhibits Migrasome-Mediated Mitochondrial Transfer in NPC, Rab11a, TP53

Community 15 - "Corneal Endothelial Dysfunction"

Cohesion: 0.6

Nodes (6): Adeno-associated virus (AAV), Corneal Endothelial Dysfunction, Choline chloride-fructose deep eutectic solvent (DES), FOXO1, Fuchs endothelial corneal dystrophy, A Viscous DES-AAV-Foxo1 Delivery System With High Transfection Efficiency for the Treatment of Corneal Endothelial Dysfunction by Restoring Mitochondria-ER Contacts

Community 16 - "Periodontitis & Aquaporin"

Cohesion: 0.4

Nodes (6): AQP1 (Aquaporin 1), Aquaporin 1 (AQP1), Periodontitis, Transplantation of AQP1-overexpressing mitochondria attenuates periodontitis-associated bone loss by regulating mitochondria-ER contacts of macrophages, RANKL, SigmaR1

Community 17 - "Spinal Cord Injury Nanoparticles"

Cohesion: 0.7

Nodes (5): Baicalin, CHCHD2, Diselenide-bridged mesoporous silica nanoparticles (Se-MSN), Diselenide-bridged mesoporous silica nanoplatform for baicalin delivery facilitates spinal cord injury repair via CHCHD2-mediated mitochondrial homeostasis restoration, Spinal Cord Injury (SCI)

Community 18 - "Beta-Catenin Signaling"

Cohesion: 0.83

Nodes (4): beta-catenin pathway, Dickkopf-1 (DKK1), Protein Arginine Methyltransferase 6 Regulated Odontogenic Differentiation and Mitochondrial Function of Stem Cells from Apical Papilla Through its Nuclear Localization Sequence via beta-catenin Pathway, PRMT6

Ambiguous Edges - Review These

• Mitochondrial Transplantation → PRMT6 [AMBIGUOUS]

refs/abstracts.md · relation: conceptually_related_to

• Artificial Mitochondrial Transfer/Transplantation (AMT/T) → Light-Activated Mitochondrial Isolation (LAMI) [AMBIGUOUS]

refs/papers/PMID_42206452.md · relation: semantically_similar_to

• FOXO1 → Corneal Endothelial Dysfunction [AMBIGUOUS]

refs/abstracts.md · relation: treats

• Autologous BMSC Mitochondrial Transplantation in Recurrent ART Failure: RCT → Female Infertility / Recurrent Implantation Failure [AMBIGUOUS]

refs/abstracts.md · relation: treats

Knowledge Gaps

• 59 isolated node(s): Gap junction channels, Equine metabolic syndrome (EMS), Regulatory T (Treg) cells, Blood-brain barrier (BBB), HEY1 (+54 more)

These have ≤1 connection - possible missing edges or undocumented components.

• 1 thin communities (<3 nodes) omitted from report — run graphify query to explore isolated nodes.

Suggested Questions

_Questions this graph is uniquely positioned to answer:_

• What is the exact relationship between Mitochondrial Transplantation and PRMT6?

_Edge tagged AMBIGUOUS (relation: conceptually_related_to) - confidence is low._

• What is the exact relationship between Artificial Mitochondrial Transfer/Transplantation (AMT/T) and Light-Activated Mitochondrial Isolation (LAMI)?

_Edge tagged AMBIGUOUS (relation: semantically_similar_to) - confidence is low._

• What is the exact relationship between FOXO1 and Corneal Endothelial Dysfunction?

_Edge tagged AMBIGUOUS (relation: treats) - confidence is low._

• What is the exact relationship between Autologous BMSC Mitochondrial Transplantation in Recurrent ART Failure: RCT and Female Infertility / Recurrent Implantation Failure?

_Edge tagged AMBIGUOUS (relation: treats) - confidence is low._

• Why does Mitochondrial Transplantation connect Mitochondrial Transplant Disease Targets to Mitophagy & Intercellular Mito Transfer, Mito Dynamics & Fertility, Ischemia-Reperfusion & Organ Injury, MitoCatch Bispecific Delivery, Mitochondria-Targeted Nanocarriers, Artificial Mito Transfer Techniques, Lung Injury Mito Protection, PN-101 Myositis Trials, Minovia Pearson Syndrome Trials, Corneal Endothelial Dysfunction, Periodontitis & Aquaporin, Spinal Cord Injury Nanoparticles, Beta-Catenin Signaling?

_High betweenness centrality (0.490) - this node is a cross-community bridge._

• Why does Compiled Abstracts: Mitochondrial Transplantation & Delivery connect Mitochondrial Transplant Disease Targets to Mitophagy & Intercellular Mito Transfer, Mito Dynamics & Fertility, Ischemia-Reperfusion & Organ Injury, MitoCatch Bispecific Delivery, Mitochondria-Targeted Nanocarriers, Artificial Mito Transfer Techniques, Lung Injury Mito Protection, PN-101 Myositis Trials, Corneal Endothelial Dysfunction, Periodontitis & Aquaporin, Spinal Cord Injury Nanoparticles, Beta-Catenin Signaling?

_High betweenness centrality (0.212) - this node is a cross-community bridge._

• Why does Intercellular Mitochondrial Transfer connect Mitophagy & Intercellular Mito Transfer to Mitochondrial Transplant Disease Targets, Mito Dynamics & Fertility, Ischemia-Reperfusion & Organ Injury, MitoCatch Bispecific Delivery, Artificial Mito Transfer Techniques, Migrasome Suppression Axis?

_High betweenness centrality (0.176) - this node is a cross-community bridge._