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M350P1200","modulus":350,"pisano_period":1200,"conventions":{"index_origin":0,"clock_labels":[1200,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663,664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740,741,742,743,744,745,746,747,748,749,750,751,752,753,754,755,756,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,779,780,781,782,783,784,785,786,787,788,789,790,791,792,793,794,795,796,797,798,799,800,801,802,803,804,805,806,807,808,809,810,811,812,813,814,815,816,817,818,819,820,821,822,823,824,825,826,827,828,829,830,831,832,833,834,835,836,837,838,839,840,841,842,843,844,845,846,847,848,849,850,851,852,853,854,855,856,857,858,859,860,861,862,863,864,865,866,867,868,869,870,871,872,873,874,875,876,877,878,879,880,881,882,883,884,885,886,887,888,889,890,891,892,893,894,895,896,897,898,899,900,901,902,903,904,905,906,907,908,909,910,911,912,913,914,915,916,917,918,919,920,921,922,923,924,925,926,927,928,929,930,931,932,933,934,935,936,937,938,939,940,941,942,943,944,945,946,947,948,949,950,951,952,953,954,955,956,957,958,959,960,961,962,963,964,965,966,967,968,969,970,971,972,973,974,975,976,977,978,979,980,981,982,983,984,985,986,987,988,989,990,991,992,993,994,995,996,997,998,999,1000,1001,1002,1003,1004,1005,1006,1007,1008,1009,1010,1011,1012,1013,1014,1015,1016,1017,1018,1019,1020,1021,1022,1023,1024,1025,1026,1027,1028,1029,1030,1031,1032,1033,1034,1035,1036,1037,1038,1039,1040,1041,1042,1043,1044,1045,1046,1047,1048,1049,1050,1051,1052,1053,1054,1055,1056,1057,1058,1059,1060,1061,1062,1063,1064,1065,1066,1067,1068,1069,1070,1071,1072,1073,1074,1075,1076,1077,1078,1079,1080,1081,1082,1083,1084,1085,1086,1087,1088,1089,1090,1091,1092,1093,1094,1095,1096,1097,1098,1099,1100,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1111,1112,1113,1114,1115,1116,1117,1118,1119,1120,1121,1122,1123,1124,1125,1126,1127,1128,1129,1130,1131,1132,1133,1134,1135,1136,1137,1138,1139,1140,1141,1142,1143,1144,1145,1146,1147,1148,1149,1150,1151,1152,1153,1154,1155,1156,1157,1158,1159,1160,1161,1162,1163,1164,1165,1166,1167,1168,1169,1170,1171,1172,1173,1174,1175,1176,1177,1178,1179,1180,1181,1182,1183,1184,1185,1186,1187,1188,1189,1190,1191,1192,1193,1194,1195,1196,1197,1198,1199],"orientation":"clockwise from north","zero_display":350,"alpha_circle_positions":1200,"beta_circle_positions":350,"node_rule":"Native residues divisible by 3, including zero; preserves the approved M6/M9/M12 reference selection. Additional regular formations of all native values are catalogued separately.","m1_convention":"Modulo 1 has period 1 and residue 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NR3C1 identifies the receptor target; the principal genetic perturbations here involved cryptochromes.","scoreParts":{"design":3,"validation":2,"review":2,"provenance":1},"score":8,"scoreReason":"Genetic perturbations, molecular interactions and physiological measurements support the reported mechanism.","jadad":"Not applicable","citationCount":550,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Cryptochromes mediate rhythmic repression of the glucocorticoid receptor"},{"id":"E05","title":"Experimental and theoretical study of mitotic spindle orientation","author":"Théry et al.","year":"2007","journal":"Nature","doi":"10.1038/nature05786","theme":"Beta · mitotic geometry","hero":null,"methods":"Human HeLa cells; controlled adhesion geometry and modelling","finding":"controlled adhesion patterns in human HeLa cells, combined with a physical model, accounted for spindle-orientation distributions across different microenvironment geometries.","relevance":"direct evidence that geometry is a meaningful biological variable; supports interest in the Beta/division theme and related shape families.","limit":"manipulation of the cell environment offers more than an observational resemblance. The model uses specific force assumptions and a transformed cell line. Division orientation is distinct from division rate, population doubling or a Fibonacci sequence.","access":"publisher abstract and figure descriptions. Full methods and sample accounting remain to be appraised.","scoreParts":{"design":3,"validation":1,"review":1,"provenance":1},"score":6,"scoreReason":"Controlled adhesion geometry tests a quantitative model; full methods and sample accounting remain open for appraisal.","jadad":"Not applicable","citationCount":424,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Experimental and theoretical study of mitotic spindle orientation"},{"id":"E06","title":"Oxytocin promotes epicardial cell activation and heart regeneration after cardiac injury","author":"Wasserman et al.","year":"2022","journal":"Frontiers in Cell and Developmental Biology","doi":"10.3389/fcell.2022.985298","theme":"Beta · proliferation","hero":"beta","methods":"Human stem-cell-derived epicardial cells and zebrafish","finding":"OXT promoted activation and proliferation-related outcomes in human stem-cell-derived epicardial cells; OXTR knockdown removed the response. Zebrafish experiments supplied a separate regeneration context.","relevance":"a direct OXTR-related example for the Beta research theme.","limit":"receptor knockdown strengthens causal interpretation within the model. Check independent cell lines and differentiation batches; images are subsamples, not donors. Cultured epicardial cells and fish regeneration do not establish regeneration of adult human hearts.","access":"primary full-text methods/results and relevant figure captions, including OXTR knockdown and proliferation measurements.","scoreParts":{"design":3,"validation":2,"review":3,"provenance":1},"score":9,"scoreReason":"Receptor knockdown provides a mechanistic test alongside cell and zebrafish experiments; methods and results appraised.","jadad":"Not applicable","citationCount":25,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Oxytocin promotes epicardial cell activation and heart regeneration after cardiac injury"},{"id":"E07","title":"Oxytocin stimulates hippocampal neurogenesis via oxytocin receptor expressed in CA3 pyramidal neurons","author":"Lin et al.","year":"2017","journal":"Nature Communications","doi":"10.1038/s41467-017-00675-5","theme":"Beta · survival / proliferation","hero":null,"methods":"Mice; conditional Oxtr deletion","finding":"conditional Oxtr deletion in mouse hippocampal excitatory neurons affected survival and maturation of newly generated neurons, while measured progenitor proliferation and early differentiation were unchanged.","relevance":"direct evidence that the biological outcome must be named precisely. It bounds generalisations from E06 without contradicting a different tissue-specific finding.","limit":"conditional genetics help localise the process. Appraise cell-type specificity, blinding and precision; an unchanged measured outcome does not prove absence of every possible effect.","access":"primary results/discussion. Retained deliberately to avoid presenting all OXTR growth-related findings as evidence of duplication.","scoreParts":{"design":3,"validation":2,"review":2,"provenance":1},"score":8,"scoreReason":"Conditional genetics and cell-outcome measurements distinguish survival from proliferation in this mouse system.","jadad":"Not applicable","citationCount":149,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Oxytocin stimulates hippocampal neurogenesis via oxytocin receptor expressed in CA3 pyramidal neurons"},{"id":"E08","title":"Structural basis for the activation and ligand recognition of the human oxytocin receptor","author":"Waltenspühl et al.","year":"2022","journal":"Nature Communications","doi":"10.1038/s41467-022-31325-0","theme":"Gamma · molecular recognition","hero":"gamma","methods":"Engineered human receptor complex; cryo-EM and functional assays","finding":"cryo-EM at 3.2 Å and functional experiments characterised OXT recognition and receptor activation. All nine peptide residues participate in binding.","relevance":"a direct structural foundation for Gamma's molecular-recognition theme; useful context, but not confirmation, for the OXT-specific Epsilon proposal.","limit":"structure–function comparisons strengthen interpretation. Receptor stabilisation and an engineered G protein affect generalisation. The six-residue disulfide loop is not itself an aromatic hexagon; the reported contacts do not establish an Epsilon trajectory.","access":"full primary article main text, receptor-engineering description and functional-assay captions. No new molecular analysis performed.","scoreParts":{"design":3,"validation":2,"review":3,"provenance":1},"score":9,"scoreReason":"Structural observations and functional residue tests provide complementary evidence; main text and assay descriptions appraised.","jadad":"Not applicable","citationCount":46,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Structural basis for the activation and ligand recognition of the human oxytocin receptor"},{"id":"E09","title":"X-ray structures and mechanism of the human serotonin transporter","author":"Coleman, Green & Gouaux","year":"2016","journal":"Nature","doi":"10.1038/nature17629","theme":"Gamma · molecular recognition","hero":null,"methods":"Engineered human serotonin transporter; crystallography and assays","finding":"structures of human SERT bound to antidepressants identified central and allosteric binding sites and explained aspects of inhibitor recognition.","relevance":"direct structural evidence broadens Gamma beyond OXTR to SLC6A4.","limit":"structural and binding/transport measurements are complementary. Thermostabilised constructs were used; the ts3 construct had no detectable transport activity. Results describe particular inhibitor-bound conformations rather than every physiological state.","access":"publisher abstract and selected primary methods/results. These data concern the protein product and ligand recognition, not regulation of SLC6A4 gene expression.","scoreParts":{"design":2,"validation":2,"review":2,"provenance":1},"score":7,"scoreReason":"Structures and functional measurements complement one another; engineered constructs constrain interpretation.","jadad":"Not applicable","citationCount":674,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"X-ray structures and mechanism of the human serotonin transporter"},{"id":"E10","title":"Structure of a D2 dopamine receptor–G-protein complex in a lipid membrane","author":"Yin et al.","year":"2020","journal":"Nature","doi":"10.1038/s41586-020-2379-5","theme":"Gamma · molecular recognition","hero":null,"methods":"Engineered human DRD2 complex in a lipid membrane; cryo-EM","finding":"cryo-EM characterised an agonist-bound DRD2–Gi complex within a reconstituted phospholipid membrane, identifying receptor, G-protein and lipid interactions.","relevance":"direct evidence for the structural context of molecular recognition; another Gamma hero example.","limit":"including a lipid environment improves contextual relevance relative to isolated detergent structures. The receptor complex is engineered and ligand-bound; it does not represent every receptor state or establish clinical outcomes.","access":"primary abstract and selected full-text structural results, with deposited structural metadata checked. No geometric correspondence to the Atlas was analysed.","scoreParts":{"design":2,"validation":1,"review":2,"provenance":1},"score":6,"scoreReason":"A membrane-reconstituted structural observation provides a defined molecular state; independent functional validation needs fuller appraisal.","jadad":"Not applicable","citationCount":199,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Structure of a D2 dopamine receptor–G-protein complex in a lipid membrane"},{"id":"E11","title":"Assembly of a π–π stack of ligands in the binding site of an acetylcholine-binding protein","author":"Stornaiuolo et al.","year":"2013","journal":"Nature Communications","doi":"10.1038/ncomms2900","theme":"Epsilon · aromatic stacking","hero":"epsilon","methods":"Molluscan binding protein; crystallography and solution assays","finding":"an Aplysia acetylcholine-binding protein accommodated a stack of three aromatic ligands. Solution binding measurements supported the structural observation.","relevance":"direct experimental support for π-stacking as a molecular-recognition phenomenon; an Epsilon reference that does not depend on OXTR.","limit":"crystallography, mutagenesis and solution assays help address crystallographic-artifact concerns. This soluble molluscan protein is a model for receptor ligand-binding domains, not a complete human receptor. Neither the three-ligand count nor the stacked geometry establishes the Atlas traversal.","access":"full primary main text, including solution validation and scope of the receptor model.","scoreParts":{"design":3,"validation":2,"review":3,"provenance":1},"score":9,"scoreReason":"Structures, mutagenesis and solution assays support the binding interpretation; full main text appraised.","jadad":"Not applicable","citationCount":66,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Assembly of a π–π stack of ligands in the binding site of an acetylcholine-binding protein"},{"id":"E12","title":"Targeted disruption of pi–pi stacking in Malaysian banana lectin reduces mitogenicity while preserving antiviral activity","author":"Covés-Datson et al.","year":"2021","journal":"Scientific Reports","doi":"10.1038/s41598-020-80577-7","theme":"Epsilon · aromatic stacking","hero":null,"methods":"Engineered plant lectin; structures and cellular assays","finding":"an F84T mutation disrupted aromatic stacking in Malay BanLec, reduced mitogenic activity and retained antiviral activity in the studied assays.","relevance":"a direct structure–function example for Epsilon; also connects molecular interactions with proliferation as a biological outcome.","limit":"structural checks and functional comparisons strengthen the rationale. Mutation can change several properties simultaneously, so this is not a pure isolation of one energetic contribution. Plant-lectin effects do not establish OXTR behaviour or clinical benefit.","access":"primary abstract and main structural/results sections. Published in 2021 despite “2020” appearing within the DOI.","scoreParts":{"design":3,"validation":2,"review":2,"provenance":1},"score":8,"scoreReason":"Targeted mutation and structural / cellular comparisons connect aromatic organisation with biological outcomes.","jadad":"Not applicable","citationCount":24,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Targeted disruption of pi–pi stacking in Malaysian banana lectin reduces mitogenicity while preserving antiviral activity"},{"id":"E13","title":"Reconstruction of molecular orbital densities from photoemission data","author":"Puschnig et al.","year":"2009","journal":"Science","doi":"10.1126/science.1176105","theme":"Valence electron orbitals","hero":null,"methods":"Organic molecular films; photoemission and calculations","finding":"photoemission measurements and Fourier reconstruction yielded orbital-density distributions for pentacene films and p-sexiphenyl monolayers, compared with density-functional calculations.","relevance":"direct physics evidence for studying spatial electronic structure; contextual to the valence-electron theme and more distant from biological significance.","limit":"comparison of measurement and theory is valuable. Reconstruction is model-dependent and the samples are non-living materials. Orbital densities are not classical electron orbits or evidence of unicursal electron motion.","access":"primary abstract and metadata. No biological role, creation-of-life claim or numeric WSS assignment follows from this paper.","scoreParts":{"design":2,"validation":1,"review":1,"provenance":1},"score":5,"scoreReason":"Measurement and reconstruction are compared with calculations; current appraisal is abstract-level.","jadad":"Not applicable","citationCount":334,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Reconstruction of Molecular Orbital Densities from Photoemission Data"},{"id":"E14","title":"CD38 is critical for social behaviour by regulating oxytocin secretion","author":"Jin et al.","year":"2007","journal":"Nature","doi":"10.1038/nature05526","theme":"Supporting OXT context","hero":null,"methods":"Mice; Cd38 knockout and rescue experiments","finding":"Cd38-knockout mice showed altered oxytocin secretion and behavioural phenotypes. Oxytocin replacement or hypothalamic delivery of human CD38 rescued selected outcomes.","relevance":"direct support for CD38 involvement in the oxytocin system. Retained as supporting hero context without forcing it into a particular sequence family.","limit":"knockout plus rescue strengthens causal interpretation in mice. Global deletion, behavioural measurement and human translation require careful appraisal. This concerns secretion, not proof of OXTR-expression regulation or geometric correspondence.","access":"primary abstract and figure descriptions. Full methods are needed before formal risk-of-bias grading.","scoreParts":{"design":3,"validation":1,"review":1,"provenance":1},"score":6,"scoreReason":"Knockout and rescue experiments test the secretion mechanism; full methods remain open for appraisal.","jadad":"Not applicable","citationCount":585,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"CD38 is critical for social behaviour by regulating oxytocin secretion"}]},"views":[{"id":"alpha","name":"Alpha","svg":"pilot-v1/views/m350/alpha.svg","png":"pilot-v1/views/m350/alpha.png"},{"id":"beta","name":"Beta","svg":"pilot-v1/views/m350/beta.svg","png":"pilot-v1/views/m350/beta.png"},{"id":"gamma","name":"Gamma","svg":"pilot-v1/views/m350/gamma.svg","png":"pilot-v1/views/m350/gamma.png"},{"id":"fibonacci-m350p1200","name":"Fibonacci M350P1200","svg":"pilot-v1/views/m350/fibonacci-m350p1200.svg","png":"pilot-v1/views/m350/fibonacci-m350p1200.png"}],"formation_interval_encoding":{"version":"alpha-endpoints-v1","rule":"For each formation interval, walk clockwise from from_index + 1 to to_index, excluding both endpoints and wrapping modulo P. Read values from alpha.residues. Endpoints, sum and residue are retained."},"family":{"m9":false,"label":null}}