Variable legend

This document provides a detailed legend for variables present in the flu_fighters.csv dataset. Variables are grouped by analytical category or biological measurement type.

Blood Gene Expression (Baseline and Fold Change) 🩸🧪

Variables:

• blood_baseline_go.*

Description:

• These variables represent the expression levels of genes associated with specific Gene Ontology (GO) terms in blood samples.

• Baseline Measurements (blood_baseline_go.*): Indicate the initial gene expression levels before vaccination.

• Gene Ontology (GO): A standardized system that classifies genes based on their biological processes, cellular components, and molecular functions.

Nasal Gene Expression (Baseline and Fold Change) 👃🧪

Variables:

• nasal_baseline_go.*

Description:

• Similar to the blood gene expression variables, these represent gene expression levels in nasal samples.

• Importance: Nasal mucosa is a primary site for respiratory infections like influenza, making nasal gene expression critical for understanding mucosal immunity.

Hemagglutination Inhibition (HAI) Responses 🦠💉

Variables:

• h1_hai_v0_gmt, h1_hai_v21_gmt, h3_hai_v0_gmt, h3_hai_v21_gmt, b_hai_v0_gmt, b_hai_v21_gmt

• h1_hai_gmt_fold_change, h3_hai_gmt_fold_change, b_hai_gmt_fold_change

Description:

• HAI Assay: Measures the ability of antibodies in the serum to prevent the agglutination of red blood cells by the influenza virus, indicating neutralizing antibody levels.

• Viruses:

  • h1_: HAI against H1N1

  • h3_: HAI against H3N2

  • b_: HAI against Influenza B

• Timepoints:

  • _v0_gmt: Geometric Mean Titer (across all three vaccine influenza strains) at baseline (pre-vaccination).

  • _v21_gmt: Geometric Mean Titer (across all three vaccine influenza strains) 21 days post-vaccination.

• Interpretation:

  • Seroconversion: An increase in HAI titer of more than 4-fold post-vaccination is considered seroconversion, and is associated with the 50% reduction in influenza disease severity.

  • Seropositivity: An HAI titer above 40 is considered seropositive, suggesting protective immunity.

• Assay Procedure:

  • Patient serum is mixed with standardized virus amounts.

  • Red blood cells are added; if antibodies are present, they inhibit hemagglutination.

Immunoglobulin A (IgA) Responses 🧫🛡️

Variables:

• ph1n1_ha_iga_v0, ph1n1_ha_iga_v21, h3n2_ha_iga_v0, h3n2_ha_iga_v21, bvic_ha_iga_v0, bvic_ha_iga_v21

• ph1n1_na_iga_v0, ph1n1_na_iga_v21, h3n2_na_iga_v0, h3n2_na_iga_v21, bvic_na_iga_v0, bvic_na_iga_v21

• ph1n1_ha_iga_fold_change, h3n2_ha_iga_fold_change, bvic_ha_iga_fold_change

• max_iga_responder

Description:

• IgA Antibodies: Play a crucial role in mucosal immunity by neutralizing pathogens at entry points.

• Measurements:

  • Levels of IgA specific to hemagglutinin (HA) and neuraminidase (NA) antigens of influenza viruses.

• Timepoints:

  • _v0: Baseline levels.

  • _v21: Levels 21 days post-vaccination.

• Fold Change: Indicates the increase in IgA levels post-vaccination.

T Cell Responses (CD4⁺ and CD8⁺ Cells) 🦠🔬

Variables:

• h1_v0_cd4_ifng, h1_v21_cd4_ifng, h1_v0_cd4_il2, h1_v21_cd4_il2

• Similar variables for cd8 cells and other influenza strains (h3, hmnp, hab, bmnp)

• Fold change variables like h1_cd4_ifng_fold_change

• max_mnp_cd4_responder, max_mnp_cd8_responder

Description:

• Function: Measure cytokine production by T cells in response to influenza antigens.

• Cytokines:

  • IFN-γ (Interferon gamma): Indicates Th1 response, important for antiviral immunity.

  • IL-2 (Interleukin-2): Supports T cell proliferation.

• Cell Types:

  • CD4⁺ T Cells: Helper cells that orchestrate immune responses.

  • CD8⁺ T Cells: Cytotoxic cells that kill infected cells.

• Assay Procedure:

  • Cells are stimulated with antigens and cytokine production is measured via flow cytometry or ELISPOT.

Influenza Virus Protein Microarray (IVPM) Responses 🦠🧬

Variables:

• nc99_ivpm_h1_v0, nc99_ivpm_h1_v21, mich15_h1_ivpm_v0, etc.

• Fold change variables like nc99_ivpm_h1_fold_change

Description:

• IVPM Assay: Detects antibody responses to multiple influenza strains simultaneously using microarray technology.

• Purpose: Evaluates the breadth of the immune response.

Antibody-Dependent Cellular Cytotoxicity (ADCC) and Secretory IgA (SIgA) Responses 🛡️🔬

Variables:

• ch6_adcc_auc_v0, ch6_adcc_auc_v21, ch6_adcc_auc_fold_change

• ch6_siga_v0, ch6_siga_v21, ch6_siga_fold_change

• Similar variables for ch7

Description:

• ADCC:

  • Function: Assesses the ability of antibodies to recruit natural killer (NK) cells to destroy infected cells.

  • Measurement: Area Under the Curve (AUC) represents the overall ADCC activity.

• SIgA:

  • Function: Secretory IgA antibodies protect mucosal surfaces by neutralizing pathogens.

Neuraminidase binding assay titers 🧪🧬

Variables:

• n1_titer_v0, n1_titer_v21, n2_titer_v0, n2_titer_v21

• n1_titer_fold_change, n2_titer_fold_change

Description:

• NI Assay: Measures antibodies that bind neuraminidase (NA) from group 1 (H1N1) and group 2 (H3N2) flu viruses.

• Importance: NA antibodies have cross-reactivity.

Viral Shedding 🌬️🦠

Variables:

• h1_v2_shed, h3_v2_shed, b_v2_shed

• h1_v7_shed, h3_v7_shed, b_v7_shed

Description:

• Definition: Detection of virus in nasal swabs post-vaccination.

• Timepoints:

  • _v2_shed: Viral shedding at day 2.

  • _v7_shed: Viral shedding at day 7.

• Significance: Indicates active viral replication and potential transmissibility.

Demographics and Baseline Characteristics 👤📋

Variables:

• year, sex, age_months, z_score_continuous

Description:

• Year: Study year or participant's birth year.

• Sex: Male or Female.

• Age in Months: Participant's age at the time of study.

• Z-Score: Standardized score indicating nutritional status or growth parameters.

Seropositivity and Seroconversion Status 🛡️🧪

Variables:

• h1_v0_seropositive, h3_v0_seropositive, b_v0_seropositive

Description:

• Seropositivity: Indicates the presence of protective antibody levels at baseline.

• Criteria: HAI titer above 40 is considered seropositive.

• Implication: Participants already have some immunity prior to vaccination.

Monocyte and Dendritic Cell Counts 🧪🔬

Variables:

• Myeloid Dendritic Cells (mDCs):

  • v0_mdcs

• Plasmacytoid Dendritic Cells (pDCs):

  • v0_pdcs

• Monocytes:

  • v0_classical_monocytes

  • v0_nonclassical_monocytes

  • v0_intermediate_monocytes

Description:

• Function: Dendritic cells and monocytes are crucial for antigen presentation and initiating immune responses.

• Timepoints: Counts at baseline

T Follicular Helper (Tfh) Cells 🦠🔬

Variables:

• tfh_cxcr3_icos_pd1_v0

Description:

• Role: Tfh cells assist B cells in producing high-affinity antibodies.

• Markers:

  • CXCR3, ICOS, PD-1: Surface proteins used to identify activated Tfh cells.

• Significance: Increased Tfh cells correlate with better antibody responses.

Baseline Respiratory Virus and Pneumococcus Detection 🦠🩺

Variables:

• v0_resp_virus_positive

• v0_pneumo_ng_log10copies_ul

Description:

• Respiratory Virus Positive: Indicates the presence of 14 respiratory viruses at baseline, which could affect immune responses.

• Pneumococcus Load: Quantifies nasal carriage of Streptococcus pneumoniae.

Fold Change in Immune Responses 📈🧪

Variables:

• Variables ending with _fold_change for various assays (e.g., h1_cd4_ifng_fold_change)

Description:

• Calculation: Post-vaccination value divided by baseline value.

• Purpose: Assesses the magnitude of the immune response induced by vaccination.