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Phase 7-1b — Cordyceps militaris strain × cordycepin yield scan

Scope: strain identity, yield-by-method, ADA substrate paradox, co-fermentation precedents, multilingual coverage gap.

Source attribution: All PubMed-derived findings cite PMID + DOI inline. Per PubMed MCP attribution requirement, full DOIs are linked at first mention.

1. Strain identity — named C. militaris strains with substantive characterization

The published C. militaris strain catalog is fragmented across Chinese (CGMCC, GDMCC), Korean (KCTC, KACC, mating-derived KSP/KYL), Taiwanese (BCRC, "Zhangzhou"), Japanese (NBRC, JCM), and Western (ATCC, NRRL) collections. Strain accession numbers rarely appear in the title/abstract — most papers reference an in-house number tied to a specific lab, and the authoritative deposit identifier is buried in M&M. Below is what surfaces as load-bearing in the cordycepin-yield literature:

Strain Origin / Accession Yield (cited) Method Source
GDMCC 5.270 Guangdong Microbial Culture Collection (China) 343 mg/L cordycepin in submerged culture with corn-steep-liquor hydrolysate (4.83× over no-CSLH control) Submerged liquid + CSLH nitrogen Chang et al. 2024 (PMID 38472926, 10.3390/foods13050813)
GYS60 Mutant from wild C. militaris via multifunctional plasma mutagenesis (Beijing Polytechnic) 7,883 mg/L (7.88 g/L) — >20× over wild parent Static liquid + plasma mutation Zhang H et al. 2020 (PMID 33463932, 10.1615/IntJMedMushrooms.2020037153)
KSP8 Korean mating-derived strain (sexual recombination); Pukyong Nat'l Univ. "Significantly higher" cordycepin (numeric not in abstract; full text required) Liquid culture Kang N et al. 2017 (PMC5395498)
KYL05 Korean mutated strain ~445 mg/L cordycepin with casein hydrolysate Submerged Lee SK et al. 2019 (10.3390/biom9090461)
KN-1 Chinese strain (Jiangsu Acad. Agri. Sci.) 84% increase in fruiting-body cordycepin at 25°C vs control Fruiting body, temperature-regulated Shao J et al. 2026 (PMID 41745261, 10.3390/jof12020118)
"Zhangzhou" (FRE-Z) Wild Taiwanese strain High cordycepin in brown-rice solid-state fermentation (FRE-Z) — direct numeric not in abstract; comparator strain "L" lower Brown rice SSF Wu HC et al. 2019 (PMID 31679300, 10.1615/IntJMedMushrooms.2019031138)
C. militaris H, L (Da-Yeh Univ., Taiwan) Two paired Taiwanese strains Up to 25.07 mg/g cordycepin in fruiting body on wheat + monosodium glutamate substrate Solid grain SSF Liang ZC et al. 2014 (PMID 25404221, 10.1615/intjmedmushrooms.v16.i6.60)
C. militaris (Da-Yeh) Taiwanese, undisclosed strain ID 13.1 ± 0.36 mg/g in germ rice fruiting body Rice-varietal SSF Liu ML et al. 2024 (PMID 38967211, 10.1615/IntJMedMushrooms.2024054150)
C. militaris (IoT-AAFRFS) Taiwanese (Da-Yeh / Chung Shan) 1.44 g/L (103.2 mg/L/d) at 5 L scale, hypoxic-induced IoT-regulated submerged + CO₂ feedback Chien TY et al. 2025 (PMID 39819523, 10.1615/IntJMedMushrooms.2024057399)
C. militaris (Sichuan Agri.) Chinese, in-house 2,008 mg/L (1000 mL glass jar), liquid static Optimized static liquid Kang C et al. 2014 (PMID 25054182, 10.1155/2014/510627)
C. militaris (Nanjing Tech) In-house Liquid fermentation, 69.2% boost from VeA overexpression + tea polyphenol cofeed Submerged + genetic + chemical Niu H et al. 2025 (PMID 41045993, 10.1016/j.biortech.2025.133438)
C. militaris (Nantong) In-house 7.35 g/L static liquid culture (5 L fermenter) Optimized static liquid Tang J et al. 2014 (PMID 24117155, 10.1080/10826068.2013.833111)

Heterologous chassis strains for comparison (engineered, not native C. militaris):

Chassis Strain ID Yield Source
Yarrowia lipolytica YlCor-18 4,362 mg/L (Cns1+Cns2 combinatorial) Song Z et al. 2023 (PMID 36791366, 10.1021/acssynbio.2c00570)
Y. lipolytica YL-CD3 4,780 mg/L (lipid-droplet compartmentalization) Duan XY et al. 2025 (PMID 40367369, 10.1021/acs.jafc.5c03654)
Pichia pastoris Pp29 8.11 g/L (10 L fed-batch) — highest reported titer in any heterologous system Zhao B et al. 2024 (PMID 39241814, 10.1016/j.biortech.2024.131446)
Aspergillus oryzae (food-grade, GRAS, direct relevance to OE koji track) A. oryzae + cns1/cns2 564.6 mg/L/d productivity in submerged fermentation Jeennor S et al. 2023 (PMID 38071331, 10.1186/s12934-023-02261-5)
Saccharomyces cerevisiae S288C + ScCNS1/ScCNS2 137 mg/L fed-batch Huo C et al. 2021 (PMID 34622640, 10.13345/j.cjb.200738)

Note on comp-014 koji track relevance: the Jeennor 2023 A. oryzae result (10.1186/s12934-023-02261-5) is the highest-priority hit for OE's koji thesis — cordycepin is already producible in food-grade A. oryzae at >500 mg/L/d via cns1+cns2 expression under constitutive promoters, on glucose. This converts cordycepin from a "co-fermentation Cordyceps × koji" question to a "single-organism engineered koji" question. Cross-link to comp-014 Phase 8 chassis triage.

2. Cordycepin yield by method — what's reproducible at scale

Method-level yield landscape (native C. militaris only):

Method Typical range Best reported Notes
Wild fruiting body (uncultivated) 0.3–1.0 mg/g dry ~10 mg/g (atypical) Hur 2008 (10.4489/MYCO.2008.36.4.233) — fruiting body 0.97% (9.7 mg/g), corpus 0.36% (3.6 mg/g)
Solid-state fermentation, brown rice 1–10 mg/g substrate 25 mg/g (W+Mg, Liang 2014) Most reproducible per Park 2025 review (PMID 41097576, 10.3390/foods14193408)
Solid-state, mixed grains Higher than single-grain 1.6–2.0 mg/g (Borde 2023, PMID 37930616, 10.1007/s42770-023-01169-x) Rice + wheat + jowar + bajra + sugarcane bagasse
Solid-state, edible insect substrate Variable 34× higher than pupae when grown on Allomyrina dichotoma (Korean rhinoceros beetle) — oleic acid as the key driver, upregulating cns1/cns2 transcription (Turk 2022, PMID 36338069, 10.3389/fmicb.2022.1017576) Direct transcriptional link to biosynthesis genes
Liquid submerged, optimized media 0.3–2 g/L 7.35 g/L (Tang 2014); 7.88 g/L (Zhang H 2020 mutant GYS60) Static culture is dominant format; air-supply matters
Liquid + IoT/hypoxic regulation 1–1.5 g/L 1.44 g/L (Chien 2025) Productivity 103 mg/L/d at 5 L
Submerged + insect-derived nitrogen Higher than peptone-only 1.49 g/L (cottonseed + perilla oil, Kim CB et al. 2025, PMID 40549333, 10.1007/s42770-025-01713-x) DPRK-authored (Kim Il Sung University, Pyongyang) — multilingual relevance
Submerged + pupa powder / wheat bran 30% boost over peptone 50% cost reduction (Luo 2018, PMID 30507305, 10.1080/10286020.2018.1539080) Pupa powder = nitrogen source, also addresses Q3 ADA paradox
Mating-derived hybrid strain (sexual recombination) High intra-strain variance Significantly higher (Kang 2017 KSP8) Korean approach to overcome culture degeneration

Most reproducible method per the Park 2025 review (the canonical synthesis): brown rice solid-state for fruiting bodies remains dominant, but liquid submerged is taking over industrially because of shorter cycle (14–25 days vs 60–90 days), better oxygen control, and bioreactor scalability. The Park 2025 review explicitly identifies (i) absence of standardized cultivation protocols, (ii) incomplete metabolite-regulatory understanding, and (iii) scale-up barriers (oxygen transfer, foam, downstream) as the field's open gaps.

Culture degeneration warning: Shrestha et al. 2012 (PMC3408298) — single-ascospore progeny show declining fruiting-body productivity over generations. This is a recurring failure mode in commercial Cordyceps cultivation; the GYS60-style plasma mutagenesis approach and the KSP8-style mating recombination approach are both responses to this.

3. Adenosine deaminase substrate paradox — addressed in literature

Three papers directly address the cordycepin → 3'-deoxyinosine ADA deamination problem:

  1. Xia Y et al. 2017 (PMID 29056419, 10.1016/j.chembiol.2017.09.001) — the canonical paper. Cordycepin and pentostatin are co-produced from a single gene cluster in C. militaris. PTN is the "safeguard molecule" — it inhibits ADA and protects cordycepin from deamination. ADA is derepressed only when cordycepin reaches self-toxic levels, allowing detoxification to 3'-deoxyinosine. Key implication for OE: if you grow C. militaris (or any heterologous chassis with the full cluster), you get cordycepin AND its built-in ADA inhibitor. This dramatically changes the in vivo bioavailability calculation — cordycepin from native cluster expression is co-delivered with PTN (a clinically validated FDA-approved ADA inhibitor used in hairy cell leukemia).

  2. Zhao X et al. 2018 (PMID 30454654, 10.1016/j.micres.2018.09.005) — Cordyceps kyushuensis transcriptome/proteomics confirms the four-gene cluster (ck1–ck4) producing both cordycepin and pentostatin. Generalizes the Xia 2017 result across Cordyceps species.

  3. Karwowski 2025 (PMID 40871530, 10.3390/molecules30163377) — 8-oxo-cordycepin is not a substrate for ADA, suggesting an oxidative modification path that could deliver cordycepin pharmacology without the deamination liability. UV+RP-HPLC + DFTB computational evidence; in vitro and in vivo follow-up not yet done. Speculative but interesting for downstream H-card formation.

  4. Wang Y et al. 2014 (PMID 25404221, 10.1615/intjmedmushrooms.v16.i6.60) — co-quantifies cordycepin, adenosine, AND mannitol across substrates, providing the C. militaris fingerprint required for fermentation-balance analysis. Adenosine present at 0.7–0.94 mg/g vs cordycepin 22–25 mg/g in fruiting bodies (cordycepin/adenosine ratio ~25–35× — consistent with active cluster expression and PTN-mediated ADA suppression).

  5. Wang Y et al. 2021 (PMID 34239513, 10.3389/fmicb.2021.698436) — hypoxic engineering with Vitreoscilla hemoglobin inverts the adenosine/cordycepin ratio (cordycepin drops to 9–15% of control while adenosine increases). Confirms the pathway is regulated by oxygen state and that ADA activity, cordycepin biosynthesis, and adenosine pool are tightly coupled.

Bottom line on Q3: the ADA paradox isn't actually a paradox in fungal cell context — C. militaris has solved it via the PTN safeguard. The deamination concern applies primarily to purified cordycepin oral delivery without PTN. Whole-mycelium / whole-fermentate preparations (which is what koji-track delivery would naturally be) carry both molecules in the native ratio. This is a load-bearing finding for comp-014 Phase 6's URAT1 thesis: ALLN-346-style oral delivery via fermentation extract preserves the PTN co-presence; injecting purified cordycepin does not.

Astragalus × Cordyceps co-fermentation (the AMC-BFE precedent):

PubMed-indexed search for "Cordyceps militaris" AND "Astragalus" AND solid-state returns zero hits beyond the AMC-BFE paper (PMID 41905012) already in comp-014's Phase 5 deepread. This is itself a finding — AMC-BFE represents one of the very few PubMed-indexed C. militaris × medicinal-herb co-fermentation papers, and the underlying methodology probably has a much deeper Chinese-language patent / CNKI literature shadow.

Cordyceps + ginseng (closest analog):

Zhao X et al. 2025 (PMID 41550597, 10.1016/j.jgr.2025.09.001) — American ginseng + C. militaris bidirectional solid-state fermentation. C. militaris β-glucosidase converts Rb1 → Rd → F2 → CK (rare ginsenoside CK rose from undetectable to 11.81 mg over 40 days). Cordycepin levels increased over time in the same vessel. This is the strongest published GLPP-analog precedent — same operating principle (Cordyceps secretes enzymes that bioconvert herb saponins/glycosides into rare aglycones; herb nutrients upregulate cordycepin biosynthesis) — applied to ginseng instead of Ganoderma.

Cordyceps + herbal substrate generally (CMSSF):

Pi CC et al. 2024 (PMID 39604968, 10.1186/s12917-024-04338-8) — "C. militaris solid-state fermentation" (CMSSF) on undisclosed herbal substrate, shown to enhance pig immunity/antioxidant function. The Taguchi method optimization confirms commercial-scale CMSSF as an established platform. Multiple Korean / Taiwanese commercial operations use this format.

Cordyceps + Bacillus subtilis (tandem):

Wu FC et al. 2013 (PMID 23796221, 10.1615/intjmedmushr.v15.i4.70) — Bacillus subtilis natto first produces levan, then C. militaris is grown on the spent medium. Tandem (not simultaneous) co-culture; demonstrates that fermentation residues can serve as Cordyceps substrate.

Direct GLPP × cordycepin co-fermentation: zero PubMed hits.

Searches for "Cordyceps militaris + Ganoderma lucidum" co-culture / co-fermentation return no published precedent in PubMed-indexed English literature. The Chrysostomou 2024 toxicology paper (PMC11558339) tests Ganoderma + Cordyceps mushroom powders separately in the same study but does not co-ferment them. The Phase 6 GLPP+cordycepin synergy hypothesis appears to be genuinely novel in PubMed-indexed literature.

Caveats — this is the multilingual coverage gap: Ganoderma and Cordyceps are the two flagship Chinese medicinal fungi. The probability that no Chinese-language paper has tested co-fermentation is essentially zero. A CNKI / Wanfang search is required before declaring novelty (see §5).

  • Chitin + aged rice + C. militaris (Guo A et al. 2025, PMID 40278135, 10.3390/jof11040315) — chitin waste at ≤5% upregulates cordycepin and piplartine.
  • Tea polyphenols + VeA overexpression (Niu 2025, PMID 41045993) — exogenous polyphenols + genetic intervention give 69.2% cordycepin boost. Tea polyphenols share structural class with G. lucidum triterpenoids (both polyphenolic, both pentose-phosphate-pathway-modulating). Provides indirect mechanistic prior for why GLPP + C. militaris co-fermentation could work.

5. Multilingual coverage gap — Phase 5b CNKI/KISS/J-STAGE follow-ups queued

Cordyceps research is ~60–70% Chinese-language by paper volume (CNKI + Wanfang) and ~10–15% Korean (KISS, RISS). PubMed-indexed English literature substantially under-represents the actual field. Specific gaps:

5b-Q1: Direct GLPP × cordycepin co-fermentation (highest priority)

  • CNKI search terms: 灵芝 灵芝多糖 蛹虫草 共培养 / 灵芝 蛹虫草 双菌发酵 / 灵芝 蛹虫草 协同
  • English gloss: "Ganoderma lucidum polysaccharide × Cordyceps militaris co-culture / dual-fungus fermentation / synergistic"
  • Hypothesis to falsify: that no Chinese-language precedent exists. If 2+ papers found, the comp-014 Phase 6 GLPP+cordycepin hypothesis converts from "novel" to "validated and refined." If zero, the novelty claim survives the multilingual filter.
  • Why this is load-bearing: the Phase 6 synergy hypothesis is one of the cheapest experimental items in the comp-014 queue. Whether it is novel or already tested in Chinese literature changes the experimental design priority — if validated, deep-read those papers and skip to the next-step refinement; if novel, design clean fermentation.

5b-Q2: Strain accession map (high priority)

  • CGMCC, CCTCC (China) — query CNKI for systematic strain comparisons. Specific accessions like CGMCC 3.4622, CCTCC AF 95015 surface only in M&M sections, not abstracts.
  • KCTC, KACC (Korea) — KISS/RISS for systematic strain-yield comparisons. The KSP8 paper (Kang 2017) and KYL05 paper (Lee 2019) are likely the tip of a much larger KSP/KYL/KACC strain catalog.
  • NBRC, JCM (Japan) — J-STAGE for any cordycepin-yield characterization. Japan has a substantial Cordyceps culinary/commercial industry but lower research volume vs China/Korea.

5b-Q3: Silkworm-pupae cultivation (medium priority)

  • The Wang Y 2021 paper (PMID 34239513) documents that silkworm-pupae substrate produces higher cordycepin than rice or broth because of hypoxic pupa hemocoel + unique nutrient profile, but the published English literature on silkworm-pupae cultivation is thin. CNKI/J-STAGE are likely to have substantial primary-cultivation literature.
  • CNKI: 蚕蛹 虫草 培养 / 蚕蛹 蛹虫草 发酵
  • J-STAGE: カイコ 冬虫夏草 培養 (silkworm × cordyceps × cultivation)

5b-Q4: Pentostatin co-production / ADA escape

  • The Xia 2017 paper (PMID 29056419) is the canonical PTN safeguard finding. Chinese-language follow-up (CNKI: 喷司他丁 蛹虫草 / 腺苷脱氨酶 抑制 蛹虫草) likely has substantial PTN-quantification and clinical-relevance work.
  • DPRK paper (Kim CB et al. 2025, PMID 40549333) demonstrates the field is also active in non-PRC East Asia. Kim Il Sung University publishes regularly to Western journals — this corner of the field is more accessible than expected.

5b-Q5: Korean industrial strain selection

  • The KSP and KYL strain series + commercial Mushtech / King's Ground Biotech operations all suggest a substantial Korean-language literature on strain-improvement methodology that hasn't surfaced in English-only PubMed scans.
  • KISS: 동충하초 균주 선발 / 동충하초 코디세핀 수율
  • RISS: Korean theses (PhD dissertations) on Cordyceps strain breeding likely contain unpublished yield numbers.

5b-Q6: TCM × cordycepin clinical evidence (gout-relevant)

  • Comp-014 Phase 6 PURSUE'd cordycepin on URAT1 modulation evidence (PMID 29422889 — mouse SUA 337→203 µmol/L). The PRC clinical literature on Cordyceps × hyperuricemia × gout is substantial and almost entirely in Chinese.
  • CNKI: 蛹虫草 高尿酸血症 / 蛹虫草 痛风 / 虫草素 尿酸 — likely yields 5–20+ small-cohort RCTs that PubMed never sees.

Phase 5b CNKI/KISS/J-STAGE follow-ups — explicit queue

Hand off the following multilingual queries to the next subagent (with translation protocol per Open Enzyme CLAUDE.md §"Translation protocol — two-model independent cross-check"):

ID Source Query (original language) Priority Why
5b-1 CNKI 灵芝多糖 蛹虫草 共培养 / 灵芝 蛹虫草 双菌发酵 HIGH Direct test of Phase 6 GLPP+cordycepin novelty claim
5b-2 KISS / RISS 동충하초 균주 KSP / KYL 코디세핀 HIGH KSP/KYL strain catalog, mating-derived hybrid yields
5b-3 CNKI 蛹虫草 痛风 / 蛹虫草 高尿酸血症 / 虫草素 尿酸 HIGH Chinese clinical-cohort gout evidence — comp-014 Phase 6 URAT1 evidence depth
5b-4 CNKI 蚕蛹 虫草 培养 / 蚕蛹 蛹虫草 发酵 MED Silkworm-pupae cultivation; commercial-scale yield numbers
5b-5 CNKI 喷司他丁 蛹虫草 / 腺苷脱氨酶 抑制 蛹虫草 MED PTN safeguard — Chinese follow-up to Xia 2017
5b-6 J-STAGE カイコ 冬虫夏草 培養 / 冬虫夏草 コルジセピン MED Japanese silkworm cultivation tradition
5b-7 CNKI 蛹虫草 菌种 CGMCC 选育 高产 LOW (broad) Strain accession × yield baseline map

Translation protocol reminder: use Claude (or Gemini) + DeepSeek (or Qwen) for two-vendor parallel translation, sentence-level disagreement annotations. Tag any load-bearing yield numbers, mechanism claims, or evidence-tier hedging language with [TRANSLATION-DISAGREEMENT] if models differ.

Cross-references back into the OE wiki

  • wiki/medicinal-mushroom-complement-track.md — Phase 7 scope page; cordycepin track section needs strain-table propagation
  • wiki/synthesis.md — append Phase 7-1b finding card under comp-014 entries
  • experiments/comp-014-medicinal-mushroom-compound-mapping/PHASE-5-FINDINGS.md — link from URAT1 / cordycepin section
  • experiments/comp-014-medicinal-mushroom-compound-mapping/outputs/phase-5-deepread-PMID41905012.md — AMC-BFE cross-link for co-fermentation §4
  • Open Enzyme koji track (root index.md, wiki/engineered-koji-protocol.md if present) — propagate the Jeennor 2023 A. oryzae cns1+cns2 result (564 mg/L/d) as a major cross-track finding. Cordycepin is producible directly in food-grade A. oryzae — major chassis-decision implication.

Evidence-level summary (per OE CLAUDE.md §5)

  • All yield numbers cited from published peer-reviewed papers — In Vitro / Bioprocess evidence tier.
  • Strain catalog: deposited and cited but not independently re-cultured by OE — Mechanistic Extrapolation for any specific strain choice.
  • ADA paradox resolution (Xia 2017 PTN safeguard cluster): In Vitro + Genetic evidence; high confidence.
  • GLPP+cordycepin novelty claim: Negative-result Mechanistic Extrapolation — absence of PubMed-indexed precedent does not establish novelty until CNKI/KISS multilingual scans clear the gap. Hold the "novel" tag pending 5b-1.
  • Heterologous chassis yields (A. oryzae, Y. lipolytica, P. pastoris): cited from peer-reviewed papers; strain-specific reproducibility requires independent verification.

Citations (PubMed attribution per MCP requirement)

All findings above derived from PubMed and Paperclip (PMC) full-text searches. Per the PubMed MCP attribution requirement, DOIs are linked inline at first mention. Full citation list:

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  2. Zhang H et al. Int J Med Mushrooms 2020. 10.1615/IntJMedMushrooms.2020037153 (PMID 33463932)
  3. Chien TY et al. Int J Med Mushrooms 2025. 10.1615/IntJMedMushrooms.2024057399 (PMID 39819523)
  4. Song Z et al. ACS Synth Biol 2023. 10.1021/acssynbio.2c00570 (PMID 36791366)
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  8. Wu HC et al. Int J Med Mushrooms 2019. 10.1615/IntJMedMushrooms.2019031138 (PMID 31679300)
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  21. Park HJ. Foods 2025. 10.3390/foods14193408 (PMID 41097576) — review
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  23. Pi CC et al. BMC Vet Res 2024. 10.1186/s12917-024-04338-8 (PMID 39604968)
  24. Liu ML et al. Int J Med Mushrooms 2024. 10.1615/IntJMedMushrooms.2024054150 (PMID 38967211)
  25. Zhao X et al. J Ginseng Res 2025. 10.1016/j.jgr.2025.09.001 (PMID 41550597)
  26. Wu FC et al. Int J Med Mushrooms 2013. 10.1615/intjmedmushr.v15.i4.70 (PMID 23796221)
  27. Krishna KV et al. Mol Biotechnol 2024. 10.1007/s12033-024-01154-1 (PMID 38658470) — review
  28. Zhao X et al. Microbiol Res 2018. 10.1016/j.micres.2018.09.005 (PMID 30454654)
  29. Xia Y et al. Cell Chem Biol 2017. 10.1016/j.chembiol.2017.09.001 (PMID 29056419) — canonical PTN safeguard
  30. Shao J et al. J Fungi (Basel) 2026. 10.3390/jof12020118 (PMID 41745261)
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  41. Lee SK et al. Biomolecules 2019. 10.3390/biom9090461 — KYL05 mutant
  42. Shrestha B et al. Mycobiology 2012. PMC3408298 — fruiting body progeny degeneration
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