{"apiVersion":"1","version":"sha256:faade27e0b75b2aca6311142ff65347b4dacc153e8d28cbdf0e8a237319331f9","data":{"id":"S7561","title":"Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging","authors":["Darci Phillips","Christian M Schürch","Michael S Khodadoust","Youn H Kim","Garry P Nolan","Sizun Jiang"],"publishedDate":"2021-05-19","format":"Paper","url":"https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8170307/fullTextXML","summary":"The authors develop a multiplexed imaging panel using eight previously treated tumor specimens. The 25,456 analyzed cells are nested within eight sampled cores, rather than independent patients. Cell types combine clustering with manual refinement; spatial marker patterns do not establish functional causation or clinical treatment prediction. Nolan supervised and revised the study, while Jiang is corresponding author. Channel labels, figure pointers and plotted units remain inconsistent in the supplied source.","subjects":["Scientific background","Tissue imaging","Cohort and validation limits"],"people":["Garry Nolan"],"review":{"label":"Complete supplied text and received apparatus read","scope":"All 128 supplied XML units, 56 references and 531 main resource-table fields were read. Four main figures, all six single-frame supplementary figures and both published workbooks were reviewed. The workbooks supply 457 cell positions and 305 nonempty cells. All 57 expression plots across eight cores and six marker/core heatmaps were visually inspected, without recovering unprinted numeric values. All eight unique offered supplements were received and read within their meaningful scope. Native text and tail audit found no remaining meaningful omissions. The original workbook page layout was not visually reviewed.","gaps":["Original article-layout PDF, complete numbered-version and correction history, revised date, exact CC BY version and separate supplement license notices remain unknown. Four GIF duplicates receive no additional reading credit.","Detailed gating thresholds, raw data and executable analysis were not inspected. Tiny original glyphs and unprinted distribution, median, deviation or heatmap values are not claimed recovered.","CD163 lists Cy5 with channel 3; red-reporter names differ, a figure pointer names the wrong panel, and a percentage axis has fraction-like ticks. Supplement platform footnotes also contain an unresolved cross-reference. The aggregate 51 prior-use and 22 MIBI counts agree.","The small heterogeneous cohort, one region per specimen, manual annotation and shared methods constrain generalization. Generated IHC and Voronoi views depend on the same CODEX data. Precise overlap with cited CTCL research is not mapped; no clinical-response predictor or independent panel validation is established.","Nolan supervision and revision, Akoya stockholding and patent interests, other advisorships and funding remain specifically attributed. They supply no government approach, classified programme, UAP finding or patient-specific recommendation."]},"familyId":"DOI-10.3389-FIMMU.2021.687673","citationUrl":"https://bioparity.io/sources/S7561","citation":"Darci Phillips, Christian M Schürch, Michael S Khodadoust, Youn H Kim, Garry P Nolan, Sizun Jiang. Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging. May 19, 2021. BioParity S7561. https://bioparity.io/sources/S7561"}}