{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2019:CKMVSQYM5TODDWYFBFD3YRARQT","short_pith_number":"pith:CKMVSQYM","canonical_record":{"source":{"id":"1907.03351","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.MN","submitted_at":"2019-07-07T21:51:47Z","cross_cats_sorted":[],"title_canon_sha256":"aedcbdb400f3fc3a4d73a7e0edccb8e1f2592265fc01da54ef897b16c16161ea","abstract_canon_sha256":"3992d5f2a49e3f639330b7ef5dd57e0daf3f02e719a301f4172b5788bb98eab3"},"schema_version":"1.0"},"canonical_sha256":"129959430cecdc31db050947bc441184dabc2ef6fa02e069d6b32bf72a92e5f0","source":{"kind":"arxiv","id":"1907.03351","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1907.03351","created_at":"2026-05-17T23:41:16Z"},{"alias_kind":"arxiv_version","alias_value":"1907.03351v1","created_at":"2026-05-17T23:41:16Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1907.03351","created_at":"2026-05-17T23:41:16Z"},{"alias_kind":"pith_short_12","alias_value":"CKMVSQYM5TOD","created_at":"2026-05-18T12:33:15Z"},{"alias_kind":"pith_short_16","alias_value":"CKMVSQYM5TODDWYF","created_at":"2026-05-18T12:33:15Z"},{"alias_kind":"pith_short_8","alias_value":"CKMVSQYM","created_at":"2026-05-18T12:33:15Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2019:CKMVSQYM5TODDWYFBFD3YRARQT","target":"record","payload":{"canonical_record":{"source":{"id":"1907.03351","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.MN","submitted_at":"2019-07-07T21:51:47Z","cross_cats_sorted":[],"title_canon_sha256":"aedcbdb400f3fc3a4d73a7e0edccb8e1f2592265fc01da54ef897b16c16161ea","abstract_canon_sha256":"3992d5f2a49e3f639330b7ef5dd57e0daf3f02e719a301f4172b5788bb98eab3"},"schema_version":"1.0"},"canonical_sha256":"129959430cecdc31db050947bc441184dabc2ef6fa02e069d6b32bf72a92e5f0","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-17T23:41:16.482585Z","signature_b64":"Vsne/RNcrFfkFCCDlNcNDpx8JkgPvT3JUAs0XKmp46SsncdbSV8/upP0KC3NHbDuL15bbW5gURHBm6y+YSfKDw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"129959430cecdc31db050947bc441184dabc2ef6fa02e069d6b32bf72a92e5f0","last_reissued_at":"2026-05-17T23:41:16.481974Z","signature_status":"signed_v1","first_computed_at":"2026-05-17T23:41:16.481974Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1907.03351","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-17T23:41:16Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"35JqEjRONdu4/Na5ve4Jwp1GeaXmqsMpz6romlHCjzhGsYZm023wpTS/0delqUhk/dOCyvDtaKp4dZT6Ci5/Aw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-26T01:44:50.186506Z"},"content_sha256":"e32650d44e9a9d023bb8cea4c600da116f879278970915e5c55e72289360e52d","schema_version":"1.0","event_id":"sha256:e32650d44e9a9d023bb8cea4c600da116f879278970915e5c55e72289360e52d"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2019:CKMVSQYM5TODDWYFBFD3YRARQT","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Network analysis of synonymous codon usage","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.MN","authors_text":"Gabriel Wright, Jacob Piland, Jun Li, Khalique Newaz, Patricia Clark, Scott Emrich, Tijana Milenkovic","submitted_at":"2019-07-07T21:51:47Z","abstract_excerpt":"Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can impact co-translational protein folding and that positions of some rare codons are evolutionary conserved. Analyses of positions of rare codons in proteins' 3-dimensional structures, which are richer in biochemical information than sequences alone, might further explain the role of rare codons in protein folding. We analyze a protein set recently annotated "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1907.03351","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"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":"2026-05-17T23:41:16Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"LlOmfi0NlLAGpAx3iOJXX5hSjJqgLHhKAjpo4C1jOaGp1nYUBlI9PIdxPe9ulieyFbNwHLSZ1U43EszQkIF5BA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-26T01:44:50.187045Z"},"content_sha256":"d929ca81ad6ac7e0b8d9f0286eef167bf5f6226465847b2ecde10637c89dd0df","schema_version":"1.0","event_id":"sha256:d929ca81ad6ac7e0b8d9f0286eef167bf5f6226465847b2ecde10637c89dd0df"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/CKMVSQYM5TODDWYFBFD3YRARQT/bundle.json","state_url":"https://pith.science/pith/CKMVSQYM5TODDWYFBFD3YRARQT/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/CKMVSQYM5TODDWYFBFD3YRARQT/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":"2026-05-26T01:44:50Z","links":{"resolver":"https://pith.science/pith/CKMVSQYM5TODDWYFBFD3YRARQT","bundle":"https://pith.science/pith/CKMVSQYM5TODDWYFBFD3YRARQT/bundle.json","state":"https://pith.science/pith/CKMVSQYM5TODDWYFBFD3YRARQT/state.json","well_known_bundle":"https://pith.science/.well-known/pith/CKMVSQYM5TODDWYFBFD3YRARQT/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2019:CKMVSQYM5TODDWYFBFD3YRARQT","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":"3992d5f2a49e3f639330b7ef5dd57e0daf3f02e719a301f4172b5788bb98eab3","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.MN","submitted_at":"2019-07-07T21:51:47Z","title_canon_sha256":"aedcbdb400f3fc3a4d73a7e0edccb8e1f2592265fc01da54ef897b16c16161ea"},"schema_version":"1.0","source":{"id":"1907.03351","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1907.03351","created_at":"2026-05-17T23:41:16Z"},{"alias_kind":"arxiv_version","alias_value":"1907.03351v1","created_at":"2026-05-17T23:41:16Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1907.03351","created_at":"2026-05-17T23:41:16Z"},{"alias_kind":"pith_short_12","alias_value":"CKMVSQYM5TOD","created_at":"2026-05-18T12:33:15Z"},{"alias_kind":"pith_short_16","alias_value":"CKMVSQYM5TODDWYF","created_at":"2026-05-18T12:33:15Z"},{"alias_kind":"pith_short_8","alias_value":"CKMVSQYM","created_at":"2026-05-18T12:33:15Z"}],"graph_snapshots":[{"event_id":"sha256:d929ca81ad6ac7e0b8d9f0286eef167bf5f6226465847b2ecde10637c89dd0df","target":"graph","created_at":"2026-05-17T23:41:16Z","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"},"paper":{"abstract_excerpt":"Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can impact co-translational protein folding and that positions of some rare codons are evolutionary conserved. Analyses of positions of rare codons in proteins' 3-dimensional structures, which are richer in biochemical information than sequences alone, might further explain the role of rare codons in protein folding. We analyze a protein set recently annotated ","authors_text":"Gabriel Wright, Jacob Piland, Jun Li, Khalique Newaz, Patricia Clark, Scott Emrich, Tijana Milenkovic","cross_cats":[],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.MN","submitted_at":"2019-07-07T21:51:47Z","title":"Network analysis of synonymous codon usage"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1907.03351","kind":"arxiv","version":1},"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:e32650d44e9a9d023bb8cea4c600da116f879278970915e5c55e72289360e52d","target":"record","created_at":"2026-05-17T23:41:16Z","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":"3992d5f2a49e3f639330b7ef5dd57e0daf3f02e719a301f4172b5788bb98eab3","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.MN","submitted_at":"2019-07-07T21:51:47Z","title_canon_sha256":"aedcbdb400f3fc3a4d73a7e0edccb8e1f2592265fc01da54ef897b16c16161ea"},"schema_version":"1.0","source":{"id":"1907.03351","kind":"arxiv","version":1}},"canonical_sha256":"129959430cecdc31db050947bc441184dabc2ef6fa02e069d6b32bf72a92e5f0","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"129959430cecdc31db050947bc441184dabc2ef6fa02e069d6b32bf72a92e5f0","first_computed_at":"2026-05-17T23:41:16.481974Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-17T23:41:16.481974Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"Vsne/RNcrFfkFCCDlNcNDpx8JkgPvT3JUAs0XKmp46SsncdbSV8/upP0KC3NHbDuL15bbW5gURHBm6y+YSfKDw==","signature_status":"signed_v1","signed_at":"2026-05-17T23:41:16.482585Z","signed_message":"canonical_sha256_bytes"},"source_id":"1907.03351","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:e32650d44e9a9d023bb8cea4c600da116f879278970915e5c55e72289360e52d","sha256:d929ca81ad6ac7e0b8d9f0286eef167bf5f6226465847b2ecde10637c89dd0df"],"state_sha256":"e0048ffcdec2c9eb7d1d3485d294ce935459ab528330fafaf5531a7e547b97b4"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"1cOA49T8em/StrgQUIvISFJp8UMQn7Qz7jStDmJq927iHKRV4/eVIgzz6TCveNkcsXAanPCp1NJUiAy4DMvsAw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-26T01:44:50.190832Z","bundle_sha256":"3cc8b6fea9d249c785e53c278ffd0b11da1e8ca65cb070d60613f265b13ad332"}}