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from north","zero_display":626,"alpha_circle_positions":1884,"beta_circle_positions":626,"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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This is an editorial assessment, without calibration or independent peer review.","components":{"design":{"range":[0,3],"criteria":{"3":"Controlled mechanistic test or quantitative prediction tested by manipulation","2":"Structured measurement or comparative design","1":"Descriptive observation","0":"Insufficient information"}},"validation":{"range":[0,3],"criteria":{"3":"Independent replication appraised","2":"Complementary evidence within the paper","1":"Limited or abstract-level corroboration","0":"Unassessed"}},"review":{"range":[0,3],"criteria":{"3":"Main text, relevant methods/results and captions reviewed","2":"Selected full-text sections","1":"Abstract, metadata or figure descriptions","0":"Unreviewed"}},"provenance":{"range":[0,1],"criteria":{"1":"Verified primary peer-reviewed publication","0":"Unverified"}}},"independent_replication_appraisal":"Not yet completed for this collection","citation_policy":"Crossref cited-by counts are a dated contextual snapshot and contribute no points. Coverage depends on deposited references. Unavailable counts remain null.","journal_policy":"Journal reputation and impact factor contribute no points.","jadad_policy":"Jadad concerns reporting of randomised clinical trials. It is not applicable to these fourteen study designs; no numeric Jadad score is assigned."},"publications":[{"id":"E01","title":"Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro","author":"Nakajima et al.","year":"2005","journal":"Science","doi":"10.1126/science.1108451","theme":"Alpha · circadian timing","hero":null,"methods":"Purified cyanobacterial clock proteins; biochemical reconstitution","finding":"KaiA, KaiB, KaiC and ATP supported self-sustaining phosphorylation oscillation. Temperature compensation and agreement between mutant periods in vitro and in vivo strengthened the biological interpretation.","relevance":"direct evidence for a molecular timing mechanism; a broad Alpha reference independent of OXTR.","limit":"biochemical reconstruction is more informative about mechanism than visual analogy. It is a cyanobacterial system, not a mammalian receptor study, and does not support a universal exact 24-hour period or M9 correspondence.","access":"primary abstract and publication metadata. Replication and detailed methods require full-text appraisal before a formal quality rating.","scoreParts":{"design":3,"validation":1,"review":1,"provenance":1},"score":6,"scoreReason":"Molecular reconstitution tests a timing mechanism; appraisal currently covers the abstract and metadata.","jadad":"Not applicable","citationCount":1020,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Reconstitution of Circadian Oscillation of Cyanobacterial KaiC Phosphorylation in Vitro"},{"id":"E02","title":"Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle","author":"Feillet et al.","year":"2014","journal":"PNAS","doi":"10.1073/pnas.1320474111","theme":"Alpha / Beta · cycle coupling","hero":null,"methods":"Mouse fibroblasts; live-cell imaging and modelling","finding":"live imaging of proliferating mouse fibroblasts, combined with modelling, identified phase locking and additional clock states under different conditions.","relevance":"direct support for studying relationships between biological cycles; connects the Alpha and Beta research themes without making them equivalent.","limit":"single-cell observations support the dynamical interpretation. Culture conditions and synchronisation matter, and related cells are not automatically independent replicates. No modular doubling or Atlas geometry was tested.","access":"primary abstract and selected results, including period distributions. A phase-space representation is not evidence of a physical toroidal cell structure.","scoreParts":{"design":2,"validation":2,"review":2,"provenance":1},"score":7,"scoreReason":"Live-cell observations and modelling provide complementary evidence for phase locking; selected results appraised.","jadad":"Not applicable","citationCount":216,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle"},{"id":"E03","title":"Interaction between time-of-day and oxytocin efficacy in mice and humans with and without gestational diabetes","author":"Duong et al.","year":"2026 (online 2025)","journal":"Molecular Metabolism","doi":"10.1016/j.molmet.2025.102269","theme":"Alpha · circadian regulation","hero":"alpha","methods":"Mouse genetics; human cells; retrospective human records","finding":"mouse experiments support BMAL1 regulation of Oxtr and time-dependent oxytocin responsiveness. Human myometrial-cell experiments and records from 2,367 patients add distinct translational observations.","relevance":"a direct OXTR connection to the Alpha theme.","limit":"genetic perturbation and promoter experiments strengthen mechanism. Animal, cell and retrospective components need separate appraisal; the human observations can be confounded. Uterine findings do not establish effects in brain tissue.","access":"final publication abstract and selected full-text results. The 2024 preprint is superseded for this register and is not counted as another study.","scoreParts":{"design":3,"validation":2,"review":2,"provenance":1},"score":8,"scoreReason":"Genetic and promoter experiments support mechanism; the human observational component has separate confounding limits.","jadad":"Not applicable","citationCount":3,"citationSource":"Crossref cited-by count","citationChecked":"17 October 2026","crossrefTitle":"Interaction between time-of-day and oxytocin efficacy in mice and humans with and without gestational diabetes"},{"id":"E04","title":"Cryptochromes mediate rhythmic repression of the glucocorticoid receptor","author":"Lamia et al.","year":"2011","journal":"Nature","doi":"10.1038/nature10700","theme":"Alpha · receptor regulation","hero":null,"methods":"Mouse cells and mice; genetic and biochemical experiments","finding":"Cry1/Cry2 interacted with the glucocorticoid receptor and altered glucocorticoid-responsive transcription in mouse cells, with related metabolic phenotypes in mice.","relevance":"direct circadian–receptor evidence provides a natural NR3C1 example beyond oxytocin.","limit":"molecular interactions, genetic perturbations and physiological observations complement one another. Multiple pathways change in knockout animals; the results do not isolate a universal geometric explanation or establish human clinical effects.","access":"primary abstract and selected experimental/results text. 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/m626/alpha.svg","png":"pilot-v1/views/m626/alpha.png"},{"id":"beta","name":"Beta","svg":"pilot-v1/views/m626/beta.svg","png":"pilot-v1/views/m626/beta.png"},{"id":"gamma","name":"Gamma","svg":"pilot-v1/views/m626/gamma.svg","png":"pilot-v1/views/m626/gamma.png"},{"id":"fibonacci-m626p1884","name":"Fibonacci M626P1884","svg":"pilot-v1/views/m626/fibonacci-m626p1884.svg","png":"pilot-v1/views/m626/fibonacci-m626p1884.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}}