{"doi":"10.1186/1471-2105-10-s9-s4","title":"Infection in the intensive care unit alters physiological networks","abstract":"<h4>Background</h4>Physicians use clinical and physiological data to treat patients every day, and it is essential for treating a patient appropriately. However, medical sources of clinical physiological data are only now starting to find use in bioinformatics research.<h4>Results</h4>We collected 29 types of physiological and clinical data on a minute-by-minute basis from trauma patients in the intensive care unit along with whether they contracted an infection during their stay. Dividing the patients into two groups based on this criterion, we determined that the correlational network amongst pairs of physiological variables changes based on whether the patient contracted an infection.<h4>Conclusion</h4>Examining the variable pairs with the largest change in correlation across groups reveals potential changes in the way our treatments affect the patient's physiology and in how our bodies react to physiological insults. These findings highlight the usefulness of physiological informatics and suggest new relationships to study while also validating previously reported relationships.","journal":"BMC Bioinformatics","year":2009,"id":5075,"datarank":0.4970907917894937,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.20520426943119668,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.20520426943119668,"corpus_percentile":51.50528885272579,"corpus_rank":597,"citation_count":6,"citer_count":4,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5971,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2009-09-01","fair_score":27.9167,"fair_percentile":8.839050131926122,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":30634,"name":"Mitchell J. Cohen","orcid":"0000-0001-5883-8752","position":1,"is_corresponding":false},{"id":30635,"name":"Geoffrey T. Manley","orcid":null,"position":2,"is_corresponding":false},{"id":51,"name":"Atul Janardhan Butte","orcid":"0000-0002-7433-2740","position":3,"is_corresponding":false},{"id":30633,"name":"Adam D Grossman","orcid":null,"position":0,"is_corresponding":true}],"reference_count":13,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"19761574","pmcid":"PMC2745691","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":52.5,"fair_a":42.5,"fair_i":0.0,"fair_r":16.6667,"fair_zscore":-1.5644,"fair_rationale":{"fair_score":27.92,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":52.5,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"The paper provides only basic metadata (title, authors, abstract, keywords) in a non-standardized format, with no machine-readable metadata or structured descriptors."}]},"A":{"name":"Accessible","score":42.5,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"The data and code are not made available; no repository, access protocol, or download instructions are mentioned, only a statement about data being stored on a dedicated server."}]},"I":{"name":"Interoperable","score":0.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"No standard formats, controlled vocabularies, or persistent identifiers (e.g., for variables or data types) are used; the data are described in a minimal custom table without reference to any standard ontology."}]},"R":{"name":"Reusable","score":16.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.167,"signal":null,"rationale":"The paper has a Creative Commons Attribution License for the article itself, but no data-availability statement, no code availability, no license for the data/code, and insufficient details to reproduce the analyses (e.g., raw data are not provided)."}]}},"suggestions":["Provide a data-availability statement that links to a public repository (e.g., Dryad, Figshare) where the raw physiological data and analysis code are deposited, in a non-proprietary format (e.g., CSV).","Add a code-availability statement and share the scripts (e.g., R, Python) used for computing correlations, with a license (e.g., MIT) for reuse.","For each physiological variable, include a standard ontology identifier (e.g., LOINC, SNOMED CT) in Table 1 to ensure interoperability.","Describe the data collection infrastructure and file formats in sufficient detail to allow others to parse and reuse the data without contacting the authors."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:52:14.861835Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}