{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:DBKYZ5CBMYOT527IP6P7DK3WQX","short_pith_number":"pith:DBKYZ5CB","canonical_record":{"source":{"id":"2410.09346","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.MN","submitted_at":"2024-10-12T03:31:05Z","cross_cats_sorted":["q-bio.QM"],"title_canon_sha256":"3351f031a6ad006f8c89fa84e4a48d8b72a6646a1a6cf985fe75f4092d8bb267","abstract_canon_sha256":"fb6ec2f60a9e754f710eb8cdfc06b357031df21dd5f035ed28042cb64f1a241d"},"schema_version":"1.0"},"canonical_sha256":"18558cf441661d3eebe87f9ff1ab7685ea8aaf253e9cb1c7510cc50d8d0cd49d","source":{"kind":"arxiv","id":"2410.09346","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2410.09346","created_at":"2026-07-05T11:49:04Z"},{"alias_kind":"arxiv_version","alias_value":"2410.09346v2","created_at":"2026-07-05T11:49:04Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2410.09346","created_at":"2026-07-05T11:49:04Z"},{"alias_kind":"pith_short_12","alias_value":"DBKYZ5CBMYOT","created_at":"2026-07-05T11:49:04Z"},{"alias_kind":"pith_short_16","alias_value":"DBKYZ5CBMYOT527I","created_at":"2026-07-05T11:49:04Z"},{"alias_kind":"pith_short_8","alias_value":"DBKYZ5CB","created_at":"2026-07-05T11:49:04Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:DBKYZ5CBMYOT527IP6P7DK3WQX","target":"record","payload":{"canonical_record":{"source":{"id":"2410.09346","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.MN","submitted_at":"2024-10-12T03:31:05Z","cross_cats_sorted":["q-bio.QM"],"title_canon_sha256":"3351f031a6ad006f8c89fa84e4a48d8b72a6646a1a6cf985fe75f4092d8bb267","abstract_canon_sha256":"fb6ec2f60a9e754f710eb8cdfc06b357031df21dd5f035ed28042cb64f1a241d"},"schema_version":"1.0"},"canonical_sha256":"18558cf441661d3eebe87f9ff1ab7685ea8aaf253e9cb1c7510cc50d8d0cd49d","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T11:49:04.522553Z","signature_b64":"IfggvabSVwBEWYLlFmBbcrjEp4YCWVX/PnAZHCw3YFCzQYtVD0uySPKGVMFuDixg/E4vGTX2EkQLc5V7s57CDQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"18558cf441661d3eebe87f9ff1ab7685ea8aaf253e9cb1c7510cc50d8d0cd49d","last_reissued_at":"2026-07-05T11:49:04.522101Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T11:49:04.522101Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2410.09346","source_version":2,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T11:49:04Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"3obHFE66jiWF7ts+keyPTmiOcXGh/OVjE8fph4jQDcvTu3SBuF973AHIvg9bOqz2E+IgMe7WXzHcBqupRaQgDg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-23T12:47:21.483231Z"},"content_sha256":"b4fb2335598d98ff32644d40fa2db70b66de7a3bff5f34c5678ce7d6d2cdf9e6","schema_version":"1.0","event_id":"sha256:b4fb2335598d98ff32644d40fa2db70b66de7a3bff5f34c5678ce7d6d2cdf9e6"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:DBKYZ5CBMYOT527IP6P7DK3WQX","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Transcriptome and Redox Proteome Reveal Temporal Scales of Carbon Metabolism Regulation in Model Cyanobacteria Under Light Disturbance","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","headline":"","cross_cats":["q-bio.QM"],"primary_cat":"q-bio.MN","authors_text":"Connah G. M. Johnson, Liam S. Mackey, Margaret S. Cheung, Natalie C. Sadler, Pavlo Bohutskyi, Song Feng, Tong Zhang, Wei-Jun Qian, Xiaolu Li, Zachary Johnson","submitted_at":"2024-10-12T03:31:05Z","abstract_excerpt":"We develop a systems approach based on an energy-landscape concept to differentiate interactions involving redox activities and conformational changes of proteins and nucleic acids interactions in multi-layered protein-DNA regulatory networks under light disturbance. Our approach is a data-driven modeling workflow using a physics-informed machine learning algorithm to train a non-linear mathematical model for interpreting gene expression dynamics and to lead discovery for protein regulators using redox proteome analysis. We distinguish light-responsive elements within central carbon metabolism"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2410.09346","kind":"arxiv","version":2},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2410.09346/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T11:49:04Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"aXoJL5hOj7z25v5/57YhewHC1WKpR1RyOpDMpeRrYmdzR5LUuYdK+rOOXozeyN6P8IDq6lX7jvlcemPzwUAGAA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-23T12:47:21.483574Z"},"content_sha256":"c82877448b23e1eb4316952b7d05a650c9c468a839ecba8b8d80e5333553130e","schema_version":"1.0","event_id":"sha256:c82877448b23e1eb4316952b7d05a650c9c468a839ecba8b8d80e5333553130e"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/DBKYZ5CBMYOT527IP6P7DK3WQX/bundle.json","state_url":"https://pith.science/pith/DBKYZ5CBMYOT527IP6P7DK3WQX/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/DBKYZ5CBMYOT527IP6P7DK3WQX/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-08-23T12:47:21Z","links":{"resolver":"https://pith.science/pith/DBKYZ5CBMYOT527IP6P7DK3WQX","bundle":"https://pith.science/pith/DBKYZ5CBMYOT527IP6P7DK3WQX/bundle.json","state":"https://pith.science/pith/DBKYZ5CBMYOT527IP6P7DK3WQX/state.json","well_known_bundle":"https://pith.science/.well-known/pith/DBKYZ5CBMYOT527IP6P7DK3WQX/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:DBKYZ5CBMYOT527IP6P7DK3WQX","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"fb6ec2f60a9e754f710eb8cdfc06b357031df21dd5f035ed28042cb64f1a241d","cross_cats_sorted":["q-bio.QM"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.MN","submitted_at":"2024-10-12T03:31:05Z","title_canon_sha256":"3351f031a6ad006f8c89fa84e4a48d8b72a6646a1a6cf985fe75f4092d8bb267"},"schema_version":"1.0","source":{"id":"2410.09346","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2410.09346","created_at":"2026-07-05T11:49:04Z"},{"alias_kind":"arxiv_version","alias_value":"2410.09346v2","created_at":"2026-07-05T11:49:04Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2410.09346","created_at":"2026-07-05T11:49:04Z"},{"alias_kind":"pith_short_12","alias_value":"DBKYZ5CBMYOT","created_at":"2026-07-05T11:49:04Z"},{"alias_kind":"pith_short_16","alias_value":"DBKYZ5CBMYOT527I","created_at":"2026-07-05T11:49:04Z"},{"alias_kind":"pith_short_8","alias_value":"DBKYZ5CB","created_at":"2026-07-05T11:49:04Z"}],"graph_snapshots":[{"event_id":"sha256:c82877448b23e1eb4316952b7d05a650c9c468a839ecba8b8d80e5333553130e","target":"graph","created_at":"2026-07-05T11:49:04Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2410.09346/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"We develop a systems approach based on an energy-landscape concept to differentiate interactions involving redox activities and conformational changes of proteins and nucleic acids interactions in multi-layered protein-DNA regulatory networks under light disturbance. Our approach is a data-driven modeling workflow using a physics-informed machine learning algorithm to train a non-linear mathematical model for interpreting gene expression dynamics and to lead discovery for protein regulators using redox proteome analysis. We distinguish light-responsive elements within central carbon metabolism","authors_text":"Connah G. M. Johnson, Liam S. Mackey, Margaret S. Cheung, Natalie C. Sadler, Pavlo Bohutskyi, Song Feng, Tong Zhang, Wei-Jun Qian, Xiaolu Li, Zachary Johnson","cross_cats":["q-bio.QM"],"headline":"","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.MN","submitted_at":"2024-10-12T03:31:05Z","title":"Transcriptome and Redox Proteome Reveal Temporal Scales of Carbon Metabolism Regulation in Model Cyanobacteria Under Light Disturbance"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2410.09346","kind":"arxiv","version":2},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:b4fb2335598d98ff32644d40fa2db70b66de7a3bff5f34c5678ce7d6d2cdf9e6","target":"record","created_at":"2026-07-05T11:49:04Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"fb6ec2f60a9e754f710eb8cdfc06b357031df21dd5f035ed28042cb64f1a241d","cross_cats_sorted":["q-bio.QM"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.MN","submitted_at":"2024-10-12T03:31:05Z","title_canon_sha256":"3351f031a6ad006f8c89fa84e4a48d8b72a6646a1a6cf985fe75f4092d8bb267"},"schema_version":"1.0","source":{"id":"2410.09346","kind":"arxiv","version":2}},"canonical_sha256":"18558cf441661d3eebe87f9ff1ab7685ea8aaf253e9cb1c7510cc50d8d0cd49d","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"18558cf441661d3eebe87f9ff1ab7685ea8aaf253e9cb1c7510cc50d8d0cd49d","first_computed_at":"2026-07-05T11:49:04.522101Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T11:49:04.522101Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"IfggvabSVwBEWYLlFmBbcrjEp4YCWVX/PnAZHCw3YFCzQYtVD0uySPKGVMFuDixg/E4vGTX2EkQLc5V7s57CDQ==","signature_status":"signed_v1","signed_at":"2026-07-05T11:49:04.522553Z","signed_message":"canonical_sha256_bytes"},"source_id":"2410.09346","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:b4fb2335598d98ff32644d40fa2db70b66de7a3bff5f34c5678ce7d6d2cdf9e6","sha256:c82877448b23e1eb4316952b7d05a650c9c468a839ecba8b8d80e5333553130e"],"state_sha256":"3003136acf15ecc74c9a4e678ccd8682fbc59fbcf2d531254c1e9b22fa1e9739"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"9m0fdm7IvzwwJSI1tJi6W+7jO1OaQVkxhQM5OKkWQ3aKTaqZC9luAxme/7SDV2vMnQvp+r0qxMTjMaq7H+nQAQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-23T12:47:21.486850Z","bundle_sha256":"0a22eb4314502329a52cf1b15cb9b0eb48b4e28d7ee4c9077263d35fa897c937"}}