# Cycle 1 Data

## Overview

This component contains all data collected during Cycle 1 of a longitudinal case study of a 28-day cyclic hormone protocol in a post-vaginoplasty trans woman. Cycle 1 spans April 1, 2026 (CD1) through April 28, 2026 (CD28).

CD1-CD5 data overlaps with the baseline component, which covers the washout period and the pre-first-injection window. Files in this component begin at CD6 (the first day post first cyclic EV injection). The protocol log file is the exception: it covers CD1-CD28 in full to provide a complete cycle reference.

## Protocol Summary

The cyclic protocol uses four EV injections totaling 11 mg per cycle, with vaginal progesterone luteal support and twice-weekly vaginal estradiol cream. A vaginal microbiome intervention (VagiBiom suppositories) runs in parallel.

| Component | Schedule |
|-----------|----------|
| EV injections (SubQ) | CD5: 2mg / CD10: 4mg / CD15: 3mg / CD22: 2mg |
| Vaginal P4 | 200mg nightly CD15-CD18; 400mg AM+PM CD19-CD26 |
| Vaginal estradiol cream | 0.01% cream, 1g, twice weekly (Wed/Sat) |
| VagiBiom suppositories | 5 days on, 2 days off; midday or bedtime per stacking logic |
| Withdrawal window | CD27-CD28 (no EV, no P4) |

Detailed daily planned and actual administration are in `cycle1_protocol_log.csv`.

## Files

| File | Description | Source |
|------|-------------|--------|
| cycle1_protocol_log.csv | Day-by-day planned and actual protocol administration; deviation flags | Investigator-logged |
| cycle1_inito.csv | Inito fertility monitor FMU readings (E3G, LH, PdG, FSH); CD6-CD19 | Inito API via Cycle Planner MCP |
| cycle1_clue_daily.csv | Daily symptom and cycle tracking; logged dates only | Clue app JSON data export |
| cycle1_wearables.csv | Apple Watch biometrics (HRV, RHR, skin temp, sleep); CD6-CD28 | Apple Health via Clue integration |
| cycle1_data_dictionary_additions.csv | Variable definitions for the protocol log and notes on schema continuity from baseline | N/A |

Schemas for `cycle1_inito.csv`, `cycle1_clue_daily.csv`, and `cycle1_wearables.csv` are identical to the corresponding baseline files. See the baseline data dictionary for column definitions.

## Files Not Included

- **cycle1_serum_labs.csv**: No serum draws were logged under this component. One serum draw was collected on CD2 (April 2, 2026), but it is included in the baseline component (`baseline_serum_labs.csv`) rather than here. The CD2 draw functioned as a washout-endpoint and trough-calibration measurement: confirming that residual estradiol from the prior steady-state regimen had cleared sufficiently to begin the cyclic protocol with the CD5 EV injection. No CD2 cyclic-protocol injection had been administered, so the values represent baseline endogenous activity rather than cyclic-protocol response. The two additional cycle 1 draws originally planned (CD13 ovulatory-peak out-of-pocket; CD21 luteal via insurance) were not collected. Future cycles will resume serum monitoring.
- **cycle1_evvy_microbiome.csv / cycle1_evvy_summary.csv**: No microbiome retest was performed during Cycle 1. The next Evvy test is scheduled for late June or early July 2026 (approximately 12 weeks after baseline).

## Data Quality Notes

### Sources of truth

When the same value appears in more than one source, the following hierarchy applies:

| Data type | Authoritative source |
|-----------|----------------------|
| Inito readings (E3G, LH, PdG, FSH) | Inito API, synced into the Cycle Planner MCP (cycle tracker database) |
| Apple Watch biometrics | Apple Health JSON export (via Clue) |
| Self-reported symptoms and tags | Clue app JSON export |
| Serum lab values | Original lab report PDF |
| Microbiome results | Evvy provider report |
| Protocol administration | Cycle Planner MCP, reconciled against memory and supporting evidence |

See `data_conventions.md` (project root) for the full data source documentation, including Inito API field mappings.

### Logging gaps

Self-reported logging tapered off in the second half of the cycle:

- **Inito readings stopped after CD19** (April 19) due to protocol fatigue. CD20-CD28 are absent. The original cycle plan included continued readings into the late luteal and withdrawal phases.
- **Clue self-reporting** has gaps on CD13 and CD18-CD24 (8 days total in the mid- to late-luteal window). Resumed CD25-CD27 to log the withdrawal bleed. Wearable data is intact through this period.
- **Protocol administration logging** ends at CD23. CD24-CD28 actual administration was not logged in the cycle tracker. Planned values are documented; actuals are blank.

### Protocol deviations (6 days flagged)

| CD | Deviation |
|----|-----------|
| 9  | VagiBiom suppository missed bedtime; administered Apr 10 morning |
| 15 | First scheduled P4 dose (200mg) and estradiol cream missed (fell asleep early) |
| 19 | P4 dose escalation to 400mg AM+PM; only AM dose administered |
| 20 | Only AM P4 dose administered (planned 800mg) |
| 21 | Only PM P4 dose administered (planned 800mg) |
| 22 | Fourth EV injection missed; administered CD23. Only AM P4 dose administered |

### Withdrawal bleed timing

The protocol-designed withdrawal window was CD27-CD28. The actual withdrawal bleed began CD25 (light), continued CD26 (medium), and CD27 (light with red spotting). Onset was approximately 2 days earlier than the protocol-designed window. The deviation may relate to the partial P4 doses during CD19-CD22.

### Other notes

- **CD20 wearable HRV** of 75 ms is meaningfully higher than other Cycle 1 readings (next-highest 55 ms). Value retained as-recorded; no artifact verification available.
- **CD28 wearable sleep_duration_min** of 102 (~1.7 hr) follows the same pattern as the Apr 2 baseline reading flagged as a likely Apple Watch detection artifact (watch removed or not worn to bed).
- **Clue medication logging is incomplete** as noted in baseline. Cycle 1 medication entries reflect only what was recorded in the app; the protocol log is authoritative for dosing.
- **Vaginal estradiol cream timing** may affect FMU E3G values on mornings following a cream application (Wed/Sat evenings).
- **Notes column convention** in `cycle1_inito.csv` was tightened relative to baseline. Notes contain factual events only (chronology, same-day administration timing). Interpretive content moved to this README and to analysis documents.

## File Conventions

- Encoding: UTF-8
- Date format: YYYY-MM-DD
- Time format: HH:MM (24-hour, local time)
- Multi-value cells: semicolon-separated (`;`)
- Empty cells: blank (no placeholder values)
- Phase naming: snake_case (e.g., `early_luteal`)
- License: CC-BY 4.0