{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T09:02:08Z","timestamp":1789549328439,"version":"build-2803163510"},"reference-count":16,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"General System of Royalties of Colombia","award":["2024000100078"],"award-info":[{"award-number":["2024000100078"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Shannon entropy of single-cell transcript counts reflects composition and sampling. We tested whether interferon-beta (IFN-\u03b2) stimulation was associated with donor-consistent diversity changes after employing technical controls. We reanalyzed GSE96583 peripheral blood mononuclear cells from eight donors with lupus, treating donors\u2014not the 8949 target cells obtained from them\u2014as inferential units. Analyses included sampling without replacement at 562 unique molecular identifiers, a 750-molecule sensitivity analysis, Miller\u2013Madow correction, IFN-gene removal, and exact compositional decomposition. Mean paired-donor raw-count plug-in entropy increased by 0.138 bits in CD14+ monocytes and 0.329 bits in FCGR3A+ monocytes and decreased by 0.080 bits in natural killer cells. Directions persisted across prespecified robustness variants. Monocyte increases accompanied higher evenness and lower transcript dominance; natural killer cells showed the opposite pattern, without consistent richness changes. Adding IFN activity to donor-, condition-, and technical-covariate-adjusted models increased R2 by at most 0.0108. Entropy contributions strongly overlapped pseudobulk expression changes. In GSE194122, the implemented binary chromatin-accessibility entropy was determined by open-peak count, precluding biological cross-modality coupling claims. These findings support a lineage-divergent association within this single lupus cohort; independent replication is required before broader biological or diagnostic interpretation.<\/jats:p>","DOI":"10.3390\/ijms27188182","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T14:15:04Z","timestamp":1789395304000},"page":"8182","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Fail-Closed Validation of Lineage-Associated Transcript-Count Diversity After IFN-\u03b2 Stimulation in a Public Human PBMC Dataset"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3604-3702","authenticated-orcid":false,"given":"Roberto Navarro","family":"Quiroz","sequence":"first","affiliation":[{"name":"Center for Research in Critical Dynamics, Barranquilla 080002, Colombia"},{"name":"Facultad de Ingenier\u00eda, Tecnol\u00f3gico de Antioquia\u2014Instituci\u00f3n Universitaria, Medell\u00edn 050036, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3135-6101","authenticated-orcid":false,"given":"Katherine Escorcia","family":"Lindo","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones en Ciencias de la Vida (CICV), Facultad de Ciencias B\u00e1sicas y Biom\u00e9dicas, Universidad Sim\u00f3n Bol\u00edvar, Barranquilla 080002, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"}]},{"given":"Andrea Jaruffe","family":"Pinilla","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones en Ciencias de la Vida (CICV), Facultad de Ciencias B\u00e1sicas y Biom\u00e9dicas, Universidad Sim\u00f3n Bol\u00edvar, Barranquilla 080002, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yirys","family":"D\u00edaz-Olmos","sequence":"additional","affiliation":[{"name":"Programa de Medicina, Divisi\u00f3n de Ciencias de la Salud, Universidad del Norte, Barranquilla 081007, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0027-1703","authenticated-orcid":false,"given":"Cecilia","family":"Fern\u00e1ndez-Ponce","sequence":"additional","affiliation":[{"name":"Instituto de Investigaci\u00f3n e Innovaci\u00f3n Biom\u00e9dica de C\u00e1diz (INiBICA), 11009 C\u00e1diz, Spain"},{"name":"Departamento de Biomedicina, Biotecnolog\u00eda y Salud P\u00fablica, Facultad de Medicina, Universidad de C\u00e1diz, 11003 C\u00e1diz, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eloina Zarate","family":"Pe\u00f1ata","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones en Ciencias de la Vida (CICV), Facultad de Ciencias B\u00e1sicas y Biom\u00e9dicas, Universidad Sim\u00f3n Bol\u00edvar, Barranquilla 080002, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yesit","family":"Bello Lemus","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones en Ciencias de la Vida (CICV), Facultad de Ciencias B\u00e1sicas y Biom\u00e9dicas, Universidad Sim\u00f3n Bol\u00edvar, Barranquilla 080002, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9248-4596","authenticated-orcid":false,"given":"Lisandro Pacheco","family":"Lugo","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones en Ciencias de la Vida (CICV), Facultad de Ciencias B\u00e1sicas y Biom\u00e9dicas, Universidad Sim\u00f3n Bol\u00edvar, Barranquilla 080002, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5770-3706","authenticated-orcid":false,"given":"Leonardo Pacheco","family":"Londo\u00f1o","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones en Ciencias de la Vida (CICV), Facultad de Ciencias B\u00e1sicas y Biom\u00e9dicas, Universidad Sim\u00f3n Bol\u00edvar, Barranquilla 080002, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Acosta Hoyos","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones en Ciencias de la Vida (CICV), Facultad de Ciencias B\u00e1sicas y Biom\u00e9dicas, Universidad Sim\u00f3n Bol\u00edvar, Barranquilla 080002, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2096-7900","authenticated-orcid":false,"given":"Nataly Galan","family":"Freyle","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones en Ciencias de la Vida (CICV), Facultad de Ciencias B\u00e1sicas y Biom\u00e9dicas, Universidad Sim\u00f3n Bol\u00edvar, Barranquilla 080002, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katy Elena Retamoza","family":"Chamorro","sequence":"additional","affiliation":[{"name":"Facultad de Ciencias de la Salud, Universidad de la Costa\u2013CUC, Barranquilla 080002, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose Luis","family":"Villarreal-Camacho","sequence":"additional","affiliation":[{"name":"Facultad de Ciencias de la Salud, Exactas y Naturales, Universidad Libre, Barranquilla P.O. Box 1752, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7567-6409","authenticated-orcid":false,"given":"Elkin","family":"Navarro Quiroz","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones en Ciencias de la Vida (CICV), Facultad de Ciencias B\u00e1sicas y Biom\u00e9dicas, Universidad Sim\u00f3n Bol\u00edvar, Barranquilla 080002, Colombia"},{"name":"Programa de Medicina, Divisi\u00f3n de Ciencias de la Salud, Universidad del Norte, Barranquilla 081007, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"A mathematical theory of communication","volume":"27","author":"Shannon","year":"1948","journal-title":"Bell Syst. Tech. J."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"15599","DOI":"10.1038\/ncomms15599","article-title":"Single-cell entropy for accurate estimation of differentiation potency from a cell\u2019s transcriptome","volume":"8","author":"Teschendorff","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1162\/089976603321780272","article-title":"Estimation of entropy and mutual information","volume":"15","author":"Paninski","year":"2003","journal-title":"Neural Comput."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1186\/s13059-019-1861-6","article-title":"Feature selection and dimension reduction for single-cell RNA-seq based on a multinomial model","volume":"20","author":"Townes","year":"2019","journal-title":"Genome Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s13059-016-0947-7","article-title":"Pooling across cells to normalize single-cell RNA sequencing data with many zero counts","volume":"17","author":"Lun","year":"2016","journal-title":"Genome Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1186\/s13059-019-1874-1","article-title":"Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression","volume":"20","author":"Hafemeister","year":"2019","journal-title":"Genome Biol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1038\/s41587-019-0379-5","article-title":"Droplet scRNA-seq is not zero-inflated","volume":"38","author":"Svensson","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1186\/s13059-016-1077-y","article-title":"A statistical approach for identifying differential distributions in single-cell RNA-seq experiments","volume":"17","author":"Korthauer","year":"2016","journal-title":"Genome Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1038\/s41467-020-14482-y","article-title":"Determining sequencing depth in a single-cell RNA-seq experiment","volume":"11","author":"Zhang","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1038\/s41467-021-21038-1","article-title":"A practical solution to pseudoreplication bias in single-cell studies","volume":"12","author":"Zimmerman","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"5692","DOI":"10.1038\/s41467-021-25960-2","article-title":"Confronting false discoveries in single-cell differential expression","volume":"12","author":"Squair","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"6077","DOI":"10.1038\/s41467-020-19894-4","article-title":"muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data","volume":"11","author":"Crowell","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/nbt.4042","article-title":"Multiplexed droplet single-cell RNA-sequencing using natural genetic variation","volume":"36","author":"Kang","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref_14","unstructured":"Luecken, M.D., Burkhardt, D.B., Cannoodt, R., Lance, C., Agrawal, A., Aliee, H., Chen, A.T., Deconinck, L., Detweiler, A.M., and Granados, A.A. A sandbox for prediction and integration of DNA, RNA, and proteins in single cells. Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks, Available online: https:\/\/datasets-benchmarks-proceedings.neurips.cc\/paper_files\/paper\/2021\/hash\/158f3069a435b314a80bdcb024f8e422-Abstract-round2.html."},{"key":"ref_15","unstructured":"Quastler, H. (1955). Note on the bias of information estimates. Information Theory in Psychology: Problems and Methods, Free Press."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Syst."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8182\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T08:02:45Z","timestamp":1789545765000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8182"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,14]]},"references-count":16,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27188182"],"URL":"https:\/\/doi.org\/10.3390\/ijms27188182","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,14]]}}}