# Baseline Data

## Overview

This component contains pre-intervention and early Cycle 1 baseline data for a longitudinal case study of a cyclic hormone protocol in a post-vaginoplasty trans woman. The baseline period spans March 2026 through April 5, 2026 (Cycle 1 Day 5), encompassing the washout period from a prior steady-state hormone regimen and the pre-injection days of Cycle 1.

An additional pre-washout steady-state lab draw from November 2025 is included for comparison.

## Subject Characteristics

- Age at protocol initiation: 37 years
- Sex (lab designation): Female
- Surgical anatomy: Peritoneal flap vaginoplasty with AlloDerm grafting
- Prior HRT regimen: Estradiol Valerate 6mg SubQ weekly + Progesterone 200mg vaginally nightly (steady-state)
- Medical history: Depression, anxiety disorder (including PTSD), ADHD
- Lab results are reported against female reference ranges, consistent with the subject's current endocrine profile and years-long estrogen-based HRT.

## Timeline Context

- **November 5, 2025**: Pre-washout steady-state blood draw (Labcorp). Trough draw, no depot contamination. Represents the endocrine baseline under the prior fixed-dose regimen.
- **Mid March 2026**: Washout initiated. Final EV injection March 15 (4mg SubQ abdomen); final regular progesterone dose approximately March 8. A prior thigh injection (March 1/8, 6mg) created a subcutaneous depot that leaked over approximately 3 weeks and may have contaminated early washout PK estimates.
- **March 19, 2026**: Blood draw during washout (CPL). Day 4 post-injection; values reflect near-peak state, not trough. E2 541 pg/mL includes depot contribution. P4 9.42 ng/mL reflects a single 400mg vaginal progesterone dose inserted the night before as an absorption experiment, confirming effective P4 absorption through peritoneal tissue.
- **March 26-30, 2026**: Spontaneous withdrawal bleed documented via Clue. Peritoneal tissue is the likely source.
- **April 1, 2026**: Cycle 1 Day 1. No injections; baseline Inito readings collected.
- **April 2, 2026**: Cycle 1 Day 2. Out-of-pocket trough blood draw (E2 65.1 pg/mL) paired with Inito FMU (E3G 73.3 ng/mL) for calibration. Evvy vaginal swab collected same day. No Cycle 1 injections had been administered.
- **April 5, 2026**: Cycle 1 Day 5. First cyclic EV injection (3mg SubQ) administered evening.

## Files

| File | Description | Source |
|------|-------------|--------|
| subject_characteristics.csv | Fixed subject attributes: demographics, surgical history, prior regimen, medical history | Investigator-reported |
| baseline_serum_labs.csv | All serum lab results from Nov 2025 and Mar-Apr 2026 draws | CPL and Labcorp reports |
| baseline_inito.csv | Inito fertility monitor FMU readings (E3G, LH, PdG, FSH) | Inito app PDF export |
| baseline_clue_daily.csv | Daily symptom and cycle tracking | Clue app JSON data export |
| baseline_wearables.csv | Apple Watch biometrics (HRV, RHR, skin temp, sleep) | Apple Health via Clue integration |
| baseline_evvy_microbiome.csv | Vaginal microbiome species-level results (PCR + mNGS) | Evvy provider report |
| baseline_evvy_summary.csv | Evvy summary scores, STI panel, antimicrobial resistance | Evvy provider report |
| data_dictionary.csv | Variable definitions, units, sources, and notes for all files | N/A |

## Key Calibration Points

Two paired Inito/serum measurements anchor the E3G-to-E2 conversion:

1. **March 19 (near-peak)**: Inito E3G 480.8 ng/mL paired with serum E2 541 pg/mL. Ratio: E2/E3G = 1.13.
2. **April 2 (trough)**: Inito E3G 73.3 ng/mL paired with serum E2 65.1 pg/mL. Ratio: E2/E3G = 0.89.

These two points provide calibration across the concentration range. The trough-state ratio (0.89) being lower than the peak-state ratio (1.13) is consistent with the known nonlinearity of E3G-to-E2 conversion at different concentration levels.

## Microbiome Baseline

The Evvy swab (April 2) was collected pre-probiotic intervention using the sterile swab from the Evvy kit inserted via the applicator-as-sheath method to ensure primary fluid contact was with deep peritoneal tissue.

Summary: 2% protective score, 96% disruptive score, diversity 2.9. The community is dominated by Prevotella species (multiple), Peptoniphilus, Porphyromonas, and Gardnerella. L. crispatus was detected at 2.29% and L. iners at 1.53%. No Candida, no STIs. Tetracycline resistance gene detected. VagiBiom probiotic suppository loading phase was initiated after swab collection.

## Known Data Quality Issues

- **Inito March 10 reading** was taken at 11:12 AM, not FMU. All other readings are FMU.
- **Apple Watch sleep April 2** shows 2 minutes, which is a detection artifact (likely the watch was removed or not worn to bed).
- **Clue medication logging is incomplete**. Not all medication administrations were recorded in Clue; the protocol schedule is the authoritative source for dosing.
- **Vaginal estradiol cream timing** may affect FMU E3G values. Cream was applied twice weekly (Wed/Sat). On Inito test mornings that fell the morning after a cream application, E3G may include a cream-driven contribution.
- **March 19 serum E2 (541 pg/mL)** reflects near-peak state (day 4 post-injection) and likely includes contribution from a prior thigh depot. It does not represent steady-state or trough.