{"doi":"10.1007/s00134-025-08047-0","title":"Identification of transcriptomic sepsis endotypes in sub-Saharan Africa: derivation, validation, and global alignment in two Ugandan cohorts","abstract":"PURPOSE: Sub-Saharan Africa carries the highest global burden of critical illness, yet transcriptomic sepsis endotypes have not been defined in the region. Their clinical relevance and alignment with endotypes identified in high-income countries (HICs) remain unknown. METHODS: We analyzed data from two prospective observational cohorts of critically ill adults with sepsis in Uganda (discovery cohort [Tororo, rural], N = 243; validation cohort [Entebbe, urban], N = 112). Unsupervised clustering of whole-blood RNAseq data was used to identify endotypes in the discovery cohort. A random forest classifier was used to predict endotype assignment in the validation cohort. Differential gene expression, pathway enrichment, and digital cytometry were used to define endotype pathobiology and determine overlap with HIC-derived endotypes. RESULTS: Two endotypes-Uganda Sepsis Endotypes 1 (USE-1) and 2 (USE-2)-were identified in the discovery cohort. USE-2, marked by neutrophil-driven innate immune activation and lymphocyte suppression, was associated with greater physiological severity and higher mortality (41.3% vs. 22.0%; absolute difference 19.3%, 95% CI 7.6-30.9%), irrespective of HIV, tuberculosis, or malaria infection. A 13-gene classifier (misclassification rate 1.43%) replicated two endotypes in the validation cohort with similar biological and clinical profiles. USE-2 showed strong transcriptional overlap with SRS1 and inflammopathic endotypes but only modest concordance in patient-level assignments. Overlap with Mars1 was variable. CONCLUSIONS: We identified two transcriptomic sepsis endotypes in Uganda that reflect inter-individual differences in targetable pathobiology and confer prognostic enrichment across high-burden infections. Divergence from HIC-derived endotypes highlights the need for sepsis classifications that are both globally relevant and locally responsive.","journal":"Intensive Care Medicine","year":2025,"id":521739,"datarank":0.2935278955896032,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.024763975205394934,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.024763975205394934,"corpus_percentile":44.449601609035355,"corpus_rank":7182,"citation_count":5,"citer_count":4,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7082,"is_data_producer":true,"deposit_databanks":{"dbGaP":["phs003914.v1.p1"],"BioProject":["PRJNA794277"],"Dryad":["10.5061/dryad.b2rbnzsq2"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":56.25,"fair_percentile":71.90461632528279,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":325140,"name":"Julius J. Lutwama","orcid":"0000-0002-3210-722X","position":1,"is_corresponding":false},{"id":331774,"name":"Alin S. Tomoiaga","orcid":"0000-0003-2221-8484","position":2,"is_corresponding":false},{"id":1392626,"name":"Meng Zhao","orcid":"0000-0002-5060-9223","position":3,"is_corresponding":false},{"id":754246,"name":"Nicholas Owor","orcid":null,"position":4,"is_corresponding":false},{"id":1392627,"name":"Xiaohong Lu","orcid":"0000-0001-6417-0250","position":5,"is_corresponding":false},{"id":1393137,"name":"Peter James Eliku","orcid":null,"position":6,"is_corresponding":false},{"id":1101643,"name":"Jesse Ross","orcid":"0009-0008-3405-0897","position":7,"is_corresponding":false},{"id":754248,"name":"Christopher Nsereko","orcid":null,"position":8,"is_corresponding":false},{"id":1103869,"name":"Irene Nayiga","orcid":null,"position":9,"is_corresponding":false},{"id":1103870,"name":"Stephen Kyebambe","orcid":null,"position":10,"is_corresponding":false},{"id":1393138,"name":"John Bosco Nsubuga","orcid":null,"position":11,"is_corresponding":false},{"id":1393139,"name":"Joseph Shinyale","orcid":null,"position":12,"is_corresponding":false},{"id":788543,"name":"Ignatius Asasira","orcid":null,"position":13,"is_corresponding":false},{"id":1393140,"name":"Tonny Kiyingi","orcid":null,"position":14,"is_corresponding":false},{"id":1393141,"name":"Thomas Ochar","orcid":null,"position":15,"is_corresponding":false},{"id":1393142,"name":"Moses Kiwubeyi","orcid":null,"position":16,"is_corresponding":false},{"id":1393143,"name":"Rittah Nankwanga","orcid":null,"position":17,"is_corresponding":false},{"id":301539,"name":"Steven J. Reynolds","orcid":"0000-0002-5403-2759","position":18,"is_corresponding":false},{"id":830597,"name":"Martina Cathy Nakibuuka","orcid":null,"position":19,"is_corresponding":false},{"id":753746,"name":"John Kayiwa","orcid":"0000-0002-1840-1801","position":20,"is_corresponding":false},{"id":1295718,"name":"Mercy Haumba","orcid":"0009-0005-3428-4595","position":21,"is_corresponding":false},{"id":1392628,"name":"Joweria Nakaseegu","orcid":"0000-0001-9864-0679","position":22,"is_corresponding":false},{"id":329990,"name":"Xiaoyu Che","orcid":"0000-0003-0001-4122","position":23,"is_corresponding":false},{"id":225758,"name":"Kai Nie","orcid":"0000-0002-8253-9688","position":24,"is_corresponding":false},{"id":104251,"name":"Seunghee Kim‐Schulze","orcid":"0000-0003-0192-4400","position":25,"is_corresponding":false},{"id":404972,"name":"Sankar Ghosh","orcid":"0000-0002-3227-0588","position":26,"is_corresponding":false},{"id":104439,"name":"W. Ian Lipkin","orcid":"0000-0002-8768-9386","position":27,"is_corresponding":false},{"id":104638,"name":"Max R. O’Donnell","orcid":"0000-0002-1232-3718","position":28,"is_corresponding":false},{"id":753745,"name":"Barnabas Bakamutumaho","orcid":"0000-0003-4259-8509","position":29,"is_corresponding":false},{"id":104624,"name":"Matthew J. Cummings","orcid":"0000-0003-2906-0966","position":0,"is_corresponding":true}],"reference_count":29,"raw_metadata":null,"created_at":"2026-07-19T02:49:49.198144Z","pmid":"40728637","pmcid":"PMC12405036","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":66.6667,"fair_a":43.75,"fair_i":20.0,"fair_r":45.8333,"fair_zscore":0.8629,"fair_rationale":{"fair_score":56.25,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":66.67,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Proteomic data from RESERVE‑U‑2‑TOR and RESERVE‑U‑1‑EBB are available in Dryad at https:// doi. org/ 10. 5061/ dryad. b2rbn zsq2.","grounded":true,"rationale":"The paper provides a DOI for the proteomic data, which is a persistent identifier scheme. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"NIH/NCBI Sequence Read Archive","grounded":true,"rationale":"The paper names established repositories (SRA via dbGaP, and Dryad) as the holders of the data. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"RNAseq data from the RESERVE‑U‑2‑TOR cohort are available in the NIH/NCBI Sequence Read Archive through dbGaP under accession number phs003914.v1.p1.","grounded":false,"rationale":"The data availability statement points to repository records with specific accessions and DOIs, corresponding to Colavizza category 3 (link to archived data in a public repository). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"We analyzed data from two prospective observational cohorts of critically ill adults with sepsis in Uganda (discovery cohort [Tororo, rural], N = 243; validation cohort [Entebbe, urban], N = 112).","grounded":true,"rationale":"The paper describes the dataset content (cohorts, sample sizes) in running prose without an itemized inventory or dedicated section. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"RNAseq data from the RESERVE‑U‑2‑TOR cohort are available in the NIH/NCBI Sequence Read Archive through dbGaP under accession number phs003914.v1.p1.","grounded":false,"rationale":"The dataset identifiers appear only in the body text (Data availability section) and not as reference-list entries. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":43.75,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"In concordance with participant consent and institutional certification of genomic data sharing, RNAseq data from RESERVE‑U‑2‑TOR will be available to investigators with an IRB‑approved protocol.","grounded":true,"rationale":"The paper states a specified, followable access process (IRB protocol and Data Access Committee request) for the controlled-access cohort, which is a precondition. [majority verdict 'partial' (2/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"RNAseq data from the RESERVE‑U‑2‑TOR cohort are available in the NIH/NCBI Sequence Read Archive through dbGaP under accession number phs003914. v1.p1. In concordance with participant consent and institutional certification of genomic data sharing, RNAseq data from RESERVE‑U‑2‑TOR will be available to investigators with an IRB‑approved protocol.","grounded":true,"rationale":"The paper describes the access process but does not apply an explicit access-level label from the standard vocabulary. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"RNAseq data from the RESERVE‑U‑2‑TOR cohort are available in the NIH/NCBI Sequence Read Archive through dbGaP under accession number phs003914.v1.p1.","grounded":false,"rationale":"The paper names the NIH/NIAID Data Access Committee as the institutional gatekeeper for the controlled-access RNAseq data from the RESERVE-U-2-TOR cohort. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not state any persistence commitment or availability timing for the data beyond the fact that they are available now.","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not name any file format for the released data (RNAseq or proteomic).","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Gene set enrichment analysis (GSEA; Gene Ontology resource [c5.all.v2024.1.Hs.symbols.gmt])","grounded":false,"rationale":"The Gene Ontology is a community standard vocabulary applied to the data analysis. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"GRCh38","grounded":false,"rationale":"The paper gives the identifier of an external resource: the human reference genome assembly GRCh38. 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[majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"phs003914.v1.p1","grounded":false,"rationale":"The dbGaP accession includes a version suffix (v1.p1), pinning the snapshot. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Analytic R code is available in Github at https:// github. com/ mjc22 44/ Uganda‑ Sepsis‑ Endot ype‑ Deriv ation‑ and‑ Valid ation.","grounded":true,"rationale":"The paper provides a machine-resolvable GitHub repository URL for the analytic code. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"K23AI163364","grounded":true,"rationale":"The paper lists specific grant numbers (e.g., K23AI163364) from the National Institute of Allergy and Infectious Diseases. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not attach any reuse license or terms to the data; the CC-BY-NC license applies only to the article.","gain":16.67,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For neuroimaging data, deposit in OpenNeuro or NeuroVault.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"In concordance with participant consent and institutional certification of genomic data sharing, RNAseq data from RESERVE‑U‑2‑TOR will be available to investigators with an IRB‑approved protocol.","why":"The paper states a specified, followable access process (IRB protocol and Data Access Committee request) for the controlled-access cohort, which is a precondition. [majority verdict 'partial' (2/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the neuroimaging repository accession (e.g. from OpenNeuro or NeuroVault) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"RNAseq data from the RESERVE‑U‑2‑TOR cohort are available in the NIH/NCBI Sequence Read Archive through dbGaP under accession number phs003914.v1.p1.","why":"The dataset identifiers appear only in the body text (Data availability section) and not as reference-list entries. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open neuroimaging formats such as NIfTI or BIDS.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name any file format for the released data (RNAseq or proteomic).","gain":8.33,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"phs003914.v1.p1","why":"The dbGaP accession includes a version suffix (v1.p1), pinning the snapshot. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":2.08,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"RNAseq data from the RESERVE‑U‑2‑TOR cohort are available in the NIH/NCBI Sequence Read Archive through dbGaP under accession number phs003914.v1.p1.","why":"The data availability statement points to repository records with specific accessions and DOIs, corresponding to Colavizza category 3 (link to archived data in a public repository). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"We analyzed data from two prospective observational cohorts of critically ill adults with sepsis in Uganda (discovery cohort [Tororo, rural], N = 243; validation cohort [Entebbe, urban], N = 112).","why":"The paper describes the dataset content (cohorts, sample sizes) in running prose without an itemized inventory or dedicated section. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"RNAseq data from the RESERVE‑U‑2‑TOR cohort are available in the NIH/NCBI Sequence Read Archive through dbGaP under accession number phs003914. v1.p1. In concordance with participant consent and institutional certification of genomic data sharing, RNAseq data from RESERVE‑U‑2‑TOR will be available to investigators with an IRB‑approved protocol.","why":"The paper describes the access process but does not apply an explicit access-level label from the standard vocabulary. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In neuroimaging, describe the data with BIDS, NIfTI or DICOM.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Gene set enrichment analysis (GSEA; Gene Ontology resource [c5.all.v2024.1.Hs.symbols.gmt])","why":"The Gene Ontology is a community standard vocabulary applied to the data analysis. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No documentation object (README, codebook) is named as accompanying the data. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"RNAseq data from the RESERVE‑U‑2‑TOR cohort are available in the NIH/NCBI Sequence Read Archive through dbGaP under accession number phs003914.v1.p1.","why":"The paper names the NIH/NIAID Data Access Committee as the institutional gatekeeper for the controlled-access RNAseq data from the RESERVE-U-2-TOR cohort. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"GRCh38","why":"The paper gives the identifier of an external resource: the human reference genome assembly GRCh38. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not state any persistence commitment or availability timing for the data beyond the fact that they are available now.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For neuroimaging data, deposit in OpenNeuro or NeuroVault.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the neuroimaging repository accession (e.g. from OpenNeuro or NeuroVault) in the reference list.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open neuroimaging formats such as NIfTI or BIDS.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T12:55:41.331999Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}