Paper Citation Record · LEDGER

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators

As of 22 August 2026, this Paper Citation Record lists 64 of 64 outbound references and 1 inbound Pith citation observation for arXiv:2602.11216.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2602.11216 v2

Coverage vector

measured 64 of 64 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-03T01:06:05.356121Z

measured 65 of 65 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-22T06:32:14.747728+00:00

measured 1 of 1 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-07-12T02:29:52.764344Z

measured 1 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: pith, observed 2026-08-05T02:28:24.338817Z

Reference resolution

64 of 64 outbound references displayed

verified exact6
verified fuzzy0
unresolved57
parse uncertain0
malformed identifier1
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External citation measurements

0
pith, observed 2026-08-05T02:28:24.338817Z

Outbound references

Observation fd260331-b7e6-4bdf-8cc3-ade8e14322a9 · outbound

This paper cites write newline.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators write newline

Reference 1

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:01.432090Z

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Observation 610d28eb-0153-4e9f-9188-c5dd4cd3b729 · outbound

This paper cites D., Doucet, A., Bronstein, M.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators D., Doucet, A., Bronstein, M

Reference 2

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:01.454367Z

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Observation e2b56bb9-076c-49cd-8946-f664f1869b86 · outbound

This paper cites an unresolved cited work.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Unresolved cited work

Reference 3

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:01.477585Z

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Observation 0a76121d-0c47-4673-b334-cb99d4c6de42 · outbound

This paper cites Kinetic analysis of folding and unfolding the 56 amino acid igg-binding domain of streptococcal protein g.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Kinetic analysis of folding and unfolding the 56 amino acid igg-binding domain of streptococcal protein g

Reference 4

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:01.500039Z

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Observation 5ff28f71-8122-4bc2-9a84-f87af7823dc4 · outbound

This paper cites Pytorch 2: Faster machine learning through dynamic python bytecode transformation and graph compilation.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Pytorch 2: Faster machine learning through dynamic python bytecode transformation and graph compilation

Reference 5

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Observation 3ffe4070-e1ec-440f-98a1-f3fbb8ab41db · outbound

This paper cites U ber die reaktionsgeschwindigkeit bei der inversion von rohrzucker durch s \.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators U ber die reaktionsgeschwindigkeit bei der inversion von rohrzucker durch s \

Reference 6

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:01.897740Z

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Observation d4de0a02-578e-4c2b-aa07-9c67693f5ab0 · outbound

This paper cites Two for one: Diffusion models and force fields for coarse-grained molecular dynamics.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Two for one: Diffusion models and force fields for coarse-grained molecular dynamics

Reference 7

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:02.037313Z

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Observation c2ccbbce-3650-4ca7-a5d4-5eb6dbe5782d · outbound

This paper cites an unresolved cited work.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Unresolved cited work

Reference 8

Resolution: verified exact; doi, observed 2026-08-03T01:08:23.925910Z

Source-reported events for the cited work

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Observation 3755c60b-8705-4803-bbc9-d657ba3364e6 · outbound

This paper cites an unresolved cited work.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Unresolved cited work

Reference 9

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Observation 9f51de2f-db78-4933-8fdc-9ffcaa0659a2 · outbound

This paper cites an unresolved cited work.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Unresolved cited work

Reference 10

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:02.338789Z

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Observation cf2a58a3-ec5d-406c-9d74-4a5361bd4835 · outbound

This paper cites P., Davidson, D., Saremi, S., Rackers, J., and Kleinhenz, J.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators P., Davidson, D., Saremi, S., Rackers, J., and Kleinhenz, J

Reference 11

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Observation 13067e0a-7628-48f5-a131-7bccca64c85b · outbound

This paper cites V., Atance, S.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators V., Atance, S

Reference 12

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:02.522416Z

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Observation 992fce41-89c2-4156-b10e-99c6a4ed3333 · outbound

This paper cites V., Schreiner, M., and Olsson, S.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators V., Schreiner, M., and Olsson, S

Reference 13

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Observation 66273db1-dec4-437b-b5b8-af0a71c5bad5 · outbound

This paper cites V., Schreiner, M.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators V., Schreiner, M

Reference 14

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Observation 57723f2a-c55f-406b-b9e3-6e9f4a645a2c · outbound

This paper cites Esm cambrian: Revealing the mysteries of proteins with unsupervised learning, 2024.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Esm cambrian: Revealing the mysteries of proteins with unsupervised learning, 2024

Reference 15

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:02.746766Z

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Observation d30ae14d-755f-4e36-a003-596911b511ae · outbound

This paper cites K., Brock, K., Gal, Y., and Marks, D.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators K., Brock, K., Gal, Y., and Marks, D

Reference 16

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:02.904406Z

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Observation 764405aa-141d-4794-a29b-1d77bc936549 · outbound

This paper cites M., Bengtsen, T., Olsen, L., Lindorff-Larsen, K., Ferkinghoff-Borg, J., and Boomsma, W.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators M., Bengtsen, T., Olsen, L., Lindorff-Larsen, K., Ferkinghoff-Borg, J., and Boomsma, W

Reference 17

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:03.036712Z

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Observation 95d511c0-85b7-4ac7-a74d-288c22c1fa09 · outbound

This paper cites J., Olsen, B., and Jaakkola, T.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators J., Olsen, B., and Jaakkola, T

Reference 18

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:03.164404Z

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Observation 1bcf7e5a-8f65-4c15-bbb1-5222cd8d02cc · outbound

This paper cites Proteina: Scaling flow-based protein structure generative models.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Proteina: Scaling flow-based protein structure generative models

Reference 19

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:03.220390Z

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Observation 36f77db5-bb71-4257-b6d9-e8665377c9da · outbound

This paper cites DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning

Reference 20

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:03.292396Z

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Observation f227f6e2-3314-4a11-a431-7d4f5f2f010e · outbound

This paper cites J., Oktay, D., Lin, Z., Verkuil, R., Tran, V.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators J., Oktay, D., Lin, Z., Verkuil, R., Tran, V

Reference 21

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Observation b767e513-00b9-4fee-8b72-22b257b26a60 · outbound

This paper cites Markov field models: Scaling molecular kinetics approaches to large molecular machines.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Markov field models: Scaling molecular kinetics approaches to large molecular machines

Reference 22

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This paper cites and Feig, M.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators and Feig, M

Reference 23

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Observation a5b4743c-059c-4152-b582-16de8275792a · outbound

This paper cites Torsional diffusion for molecular conformer generation.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Torsional diffusion for molecular conformer generation

Reference 24

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:03.503485Z

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Observation d589908e-d18c-4e01-aaa7-73fb4b308b00 · outbound

This paper cites Generative modeling of molecular dynamics trajectories.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Generative modeling of molecular dynamics trajectories

Reference 25

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Observation f5100615-ce48-4253-b07a-8e13ccc09269 · outbound

This paper cites and No\' e , F.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators and No\' e , F

Reference 26

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Observation f0900ec6-2a70-4f2d-9aed-3c23601ce57a · outbound

This paper cites Timewarp: Transferable acceleration of molecular dynamics by learning time-coarsened dynamics.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Timewarp: Transferable acceleration of molecular dynamics by learning time-coarsened dynamics

Reference 27

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Observation 72bd59bb-5df4-469b-a034-0e6a887762e6 · outbound

This paper cites B., Osmark, P., Neergaard, T.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators B., Osmark, P., Neergaard, T

Reference 28

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Observation 843221d8-475e-4415-be5e-8b5a9852cf14 · outbound

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Unresolved cited work

Reference 29

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Observation 8bd5c647-7e3a-48f5-af39-5b7108affaab · outbound

This paper cites Y., Satorras, V.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Y., Satorras, V

Reference 30

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Observation 3883330b-a78d-4dc0-9747-4c6009a98ba8 · outbound

This paper cites Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2

Reference 31

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Observation d2298985-c993-4882-9fc7-f4b9d8be5110 · outbound

This paper cites Evolutionary-scale prediction of atomic-level protein structure with a language model.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Evolutionary-scale prediction of atomic-level protein structure with a language model

Reference 32

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This paper cites O., and Shaw, D.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators O., and Shaw, D

Reference 33

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Observation e18ba3c6-6ba0-4748-9a1f-1134861dc591 · outbound

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Unresolved cited work

Reference 34

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This paper cites Flow straight and fast: Learning to generate and transfer data with rectified flow.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Flow straight and fast: Learning to generate and transfer data with rectified flow

Reference 35

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This paper cites Vampnets for deep learning of molecular kinetics.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Vampnets for deep learning of molecular kinetics

Reference 36

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This paper cites Language models enable zero-shot prediction of the effects of mutations on protein function.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Language models enable zero-shot prediction of the effects of mutations on protein function

Reference 37

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This paper cites mdcath: A large-scale md dataset for data-driven computational biophysics.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators mdcath: A large-scale md dataset for data-driven computational biophysics

Reference 38

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Thermodynamic interpolation: A generative approach to molecular thermodynamics and kinetics

Reference 39

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators H., Brotzakis, Z

Reference 40

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Flow matching for accelerated simulation of atomic transport in crystalline materials

Reference 41

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This paper cites Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning

Reference 42

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators G., Pérez-Hernández, G., Mey, A

Reference 43

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators and No \'e , F

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Identification of slow molecular order parameters for markov model construction

Reference 46

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Unresolved cited work

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Consistent sampling and simulation: Molecular dynamics with energy-based diffusion models

Reference 48

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators D., Sch \"u tte, C., and No \'e , F

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators D., Noé, F., and Olsson, S

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators and Weber, M

Reference 51

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Efficient mapping of phase diagrams with conditional boltzmann generators

Reference 53

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators and Schmid, F

Reference 54

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This paper cites Implicit transfer operator learning: Multiple time-resolution models for molecular dynamics.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Implicit transfer operator learning: Multiple time-resolution models for molecular dynamics

Reference 55

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators B., Bose, J., Lin, C., Klein, L., Bronstein, M

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Unresolved cited work

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Alphafold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Reference 58

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Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators N., Kaiser, ., and Polosukhin, I

Reference 59

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Observation c2c18d51-36d5-43a4-8bd9-54982af32561 · outbound

This paper cites R., Zavadlav, J., Praprotnik, M., and Koumoutsakos, P.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators R., Zavadlav, J., Praprotnik, M., and Koumoutsakos, P

Reference 60

Resolution: verified exact; doi, observed 2026-08-03T01:08:23.316719Z

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This paper cites J., and Raleigh, D.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators J., and Raleigh, D

Reference 61

Resolution: verified exact; doi, observed 2026-08-03T01:08:23.236536Z

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Observation 29341d65-99f6-4372-a84d-6fbbb7cc588e · outbound

This paper cites Energy-based diffusion generator for efficient sampling of boltzmann distributions.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Energy-based diffusion generator for efficient sampling of boltzmann distributions

Reference 62

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This paper cites and Noé, F.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators and Noé, F

Reference 63

Resolution: unresolved; no resolver link, observed 2026-08-03T01:06:05.216802Z

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Observation 1b375ed9-3426-4e12-99fe-eb1c3bc34e93 · outbound

This paper cites Projected metastable markov processes and their estimation with observable operator models.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators Projected metastable markov processes and their estimation with observable operator models

Reference 64

Resolution: verified exact; doi, observed 2026-08-03T01:08:23.070670Z

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This paper cites and Bowman, G.

Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators and Bowman, G

Reference 65

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Pith citing papers

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Design-CP: Context Parallelism for Design of Protein Nanoparticles cites this paper.

Design-CP: Context Parallelism for Design of Protein Nanoparticles Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators

Reference 108

Resolution: verified exact; local_arxiv, observed 2026-07-12T02:38:25.609987Z

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