EIS Biomarkers dataset codebook

Permanent identifier



An anonymised dataset containing details of a sub-study of 100 HIV-negative women in 2009. This sub-study was part of a microbicide feasibility study in North-West Tanzania that was carried out between 2008-2010. It contains information on sexual behaviour, vaginal practices, current contraception, STI symptoms, as well as results of a clinical and colposcopic examination.

Data access

This dataset cannot be made available via a repository due to ethical restrictions. Interested researchers may submit request for de-identified data to Saidi.Kapiga@lshtm.ac.uk.


The dataset produced by the study team contains the variables outlined below.

Variable name Variable label Type Format Value label
eisno EIS Study ID str8 %9s  
visit Visit (1-12) float %9.0g  
attend Attended (y/n) float %9.0g binary
labid LIMS Number str13 %13s  
visitdate EIS enrolment date float %td  
age Age (v1) float %9.0g  
healthy Healthy visit float %9.0g  
healthytot Total healthy visits by participant float %9.0g  
healthyev Ever had at least one healthy visit float %9.0g  
menses Menstruating-pc (v1-v12) float %9.0g  
totmen Total menstruations float %9.0g  
menstage_pdg Menstrual cycle stage by PDG float %16.0g stage
ovulatory Signs of ovualation? float %9.0g  
ovulation_study Was this an ovulatory cycle? float %9.0g  
fpuse Contraceptive use (v1) byte %8.0g binary
fpcat Type of contraceptive use (v1) float %16.0g fpcat
hc Hormonal contraception (v1) float %9.0g binary
hc_study Using HC during the study float %9.0g  
fppill Oral contraceptive (v1) byte %8.0g binary
fpdepo Depo-Provera (v1) byte %8.0g binary
hc3cat_fup Hormonal contraception category float %9.0g hc3
ivp1 Cleansing with soap float %9.0g  
ivp2 Cleansing with cloth float %9.0g  
ivp3 Inserting float %9.0g  
cleanse_enr Cleansing - general (v1) byte %8.0g binary
cleanse_fu Cleansing - since last visit (v2-v12) byte %8.0g binary
cleanlast Last time cleanse (v1-v12) float %29.0g cleanlast
cleanfreq Frequency of cleansing (v1-v12) float %20.0g cleanfreq
clean_lowhigh High frequency cleanser (v1-v12) float %38.0g clean_lowhigh
water_enr Cleanse with water - general(v1) float %9.0g binary
water_fu Cleanse with water - since last visit(v2-v12) float %9.0g  
soap_enr Cleanse with soap - general(v1) byte %8.0g binary
soap_fu Cleanse with soap - since last visit(v2-v12) float %9.0g  
fingers_fu Cleanse with fingers - since last visit (v2-v12) float %9.0g  
cloth_fu Cleanse with cloth - since last visit (v2-v12) byte %8.0g binary
cotton_fu Cleanse with cotton - since last visit (v2-v12) float %9.0g  
appoth_fu Cleanse with other applicator - since last visit (v2-v12) float %9.0g  
insert_enr Inserted a substance - Have you ever? (v1) float %9.0g binary
insert_fu Inserted a substance - since last visit(v2-v12) byte %8.0g binary
insert_lowhigh High freq inserters float %9.0g binary
insertfreq Frequency of inserting (v1-v12) float %36.0g infreq
insertsub_fu What substances have your inserted since last visit TXT (v2-v12) float %22.0g insertsub_f
insertlast Last time insert (v1-v12) float %21.0g inlast
sex_fu Sex since last visit (v2-v12) byte %8.0g binary
sexlast Last sex time (v1-v12) float %18.0g sexlast
sex_study Ever had sex during the study float %9.0g  
cleanse_study Ever cleanse during the study float %9.0g  
soap_study Ever used soap during the study float %9.0g  
cloth_study Ever used cloth during the study float %9.0g  
insert_study Ever inserted during the study float %9.0g  
insertsub_study Substance inserted during the study float %22.0g insertsub_study
vagph Vaginal pH (v1-v12) double %10.0g  
phcat Vaginal pH category float %21.0g phcat
cerectopy Cervical ectopy(v1, v12) byte %8.0g ectopy
ectopy Ectopy - binary float %9.0g  
ectopy_fu Cervical ectopy (filled in during f/up) float %9.0g ectopy
colvulva Colposcopic finding: external genitalia (v1, v12) float %18.0g colvulva
colvagina Colposcopic finding: vagina (v1, v12) float %27.0g colvagina
colfornix Colposcopic finding: fornices (v1, v12) float %13.0g colfornix
colcervix Colposcopic finding: cervix (v1, v12) float %13.0g colcervix
colfinding Colposcopic findings float %21.0g colfinding
colfind Any findings on colposcopy float %9.0g  
psa Prostate-specific antigen (ng/mL) float %9.0g  
psa_cat PSA Semi-qualitative results float %24.0g psa_cat
psa_dose PSA category float %12.0g pdose
cvlblood hemastix testing of supernatant byte %23.0g hemastix
menflank Menstruation & flanking visits float %16.0g menflank
leukocytes_lm Total no. of leukocytes found on LM slides float %13.0g leukocytes_lm
lymph_lm Lymphocytes found on LM slide float %9.0g lymph_lm
neutro_lm Neutrophils found on LM slide float %9.0g neutro_lm
prot Was protein done? float %9.0g binary
invol Was involucrin done? float %9.0g binary
il_1alpha IL-1a float %9.0g  
il_1beta IL-1b float %9.0g  
il_6 IL-6 float %9.0g  
il_12 IL-12 float %9.0g  
il_18 IL-18 float %9.0g  
tnf_alpha TNF-a float %9.0g  
il_10 IL-10 float %9.0g  
ifn_gamma Interferon-g float %9.0g  
il_2 IL-2 float %9.0g  
il_4 IL-4 float %9.0g  
il_15 IL-15 float %9.0g  
il_16 IL-16 float %9.0g  
il_17 IL-17 double %10.0g  
mip_1alpha MIP1-a/CCL3 float %9.0g  
mip_1beta MIP1-b/CCL4 float %9.0g  
mcp_1 MCP-1/CCL2 float %9.0g  
mcp_2 MCP-2/CCL8 float %9.0g  
rantes RANTES/CCL5 float %9.0g  
ip_10 IP-10/CXCL10 float %9.0g  
sdf_1beta SDF-1b/CXCL12 float %9.0g  
mig MIG/CXCL9 double %10.0g  
il_8 IL-8/CXCL8 float %9.0g  
gm_csf Granulocyte-macrophage colony-stimulating factor (GM-CSF) float %9.0g  
g_csf Granulocyte colony-stimulating factor (G-CSF) float %9.0g  
tgf_alpha Transforming growth factor-a (TGF-a) float %9.0g  
tgf_beta1 Transforming growth factor-b (TGF-b) float %9.0g  
ifn_beta Interferon-b float %9.0g  
slpi SLPI float %9.0g  
elafin Elafin float %9.0g  
s100a8 Calgranulin A (S100A8) float %9.0g  
hnp_1_3v Human neutrophil alpha-defensins (HNP) 1-3 float %9.0g  
b_df2 Beta-defensin 2 float %9.0g  
b_df3 Beta-defensin 3 float %9.0g  
b_df4 Beta-defensin 4 float %9.0g  
pigr Poly-immunoglobulin receptor float %9.0g  
iga Immunoglobulin A float %9.0g  
igm Immunoglobulin M float %9.0g  
igg1 Immunoglobulin G, subclass 1 double %10.0g  
igg2 Immunoglobulin G, subclass 2 double %10.0g  
igg3 Immunoglobulin G, subclass 3 float %9.0g  
igg4 Immunoglobulin G, subclass 4 float %9.0g  
apolipoa1 apolipoa1protein A1 - Serum control float %9.0g  
scca_1 SCCA-1 - Vaginal control float %9.0g  
albumin Albumin - Serum control double %10.0g  
involucrin Involucrin - Vaginal control float %9.0g  
bradford_assay Total protein (Bradford assay) float %9.0g