Intravenous midazolam alters short-interval paired-pulse TMS responses differently in younger and older adults.
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- [1] § 2 Methods › 2.7 Statistical comparisons ↔ GABAM_Zenodo_Data_Package/analysis_code.py, lines 1 to 55 · score 0.78 · Shapiro Wilk, Benjamini Hochberg, Single pulse MEP, paired pulse MEP, mixed, ANOVA · Report a mismatch
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The authors' code
Python · 455 lines · 17 KB · CC-BY-4.0 · 1 match
- #!/usr/bin/env python3
- """
- Analysis code for:
- Intravenous midazolam alters short-interval paired-pulse TMS responses differently
- in younger and older adults
- Purpose
- -------
- This script reproduces the article-style statistical analyses for the de-identified
- subject-level TMS dataset. It performs descriptive summaries, Shapiro-Wilk normality
- checks, independent-samples t-tests, paired-samples t-tests, Benjamini-Hochberg p-value
- adjustment, and ANOVA-style models for single-pulse and paired-pulse MEP outcomes.
- Input
- -----
- subject_level_data.csv
- Expected location
- -----------------
- Place this script in the same folder as subject_level_data.csv, or update DATA_FILE below.
- Outputs
- -------
- The script writes CSV output files to an analysis_outputs/ subfolder:
- - descriptive_statistics.csv
- - normality_tests.csv
- - article_style_ttests.csv
- - one_way_anovas.csv
- - repeated_measures_anovas_within_age_group.csv
- - mixed_effects_wald_tests_mep.csv
- - analysis_notes.txt
- Notes
- -----
- The primary manuscript analyses are the t-tests. ANOVA and mixed-model outputs are
- included as supplementary reproducibility checks. The default paired-pulse ratio uses
- the source ratio variables from the workbook because those are the values preserved
- from the manuscript source file. To instead analyze calculated PP/SP ratios, change
- RATIO_MODE from "source" to "calculated" below.
- """
- from pathlib import Path
- import warnings
- import numpy as np
- import pandas as pd
- from scipy import stats
- try:
- import statsmodels.formula.api as smf
- from statsmodels.stats.anova import anova_lm, AnovaRM
- from statsmodels.stats.multitest import multipletests
- STATSMODELS_AVAILABLE = True
- except ImportError:
- STATSMODELS_AVAILABLE = False
- # -----------------------------------------------------------------------------
- # User settings
- # -----------------------------------------------------------------------------
- DATA_FILE = Path("subject_level_data.csv")
- OUTPUT_DIR = Path("analysis_outputs")
- RATIO_MODE = "source" # options: "source" or "calculated"
- EQUAL_VAR_TTESTS = True # True matches conventional Student independent-samples t-tests
- ALPHA = 0.05
- # -----------------------------------------------------------------------------
- # Helper functions
- # -----------------------------------------------------------------------------
- def as_numeric(series):
- return pd.to_numeric(series, errors="coerce")
- def fmt_float(x):
- if pd.isna(x):
- return np.nan
- return float(x)
- def ensure_output_dir():
- OUTPUT_DIR.mkdir(exist_ok=True)
- def load_data():
- if not DATA_FILE.exists():
- raise FileNotFoundError(
- f"Could not find {DATA_FILE}. Place analysis_code.py in the same folder as "
- "subject_level_data.csv or edit DATA_FILE."
- )
- df = pd.read_csv(DATA_FILE)
- # Coerce expected numeric columns.
- numeric_cols = [
- "sp_baseline_mep_uv", "sp_midazolam_mep_uv", "sp_washout_mep_uv",
- "pp_baseline_mep_uv", "pp_midazolam_mep_uv", "pp_washout_mep_uv",
- "baseline_pp_sp_ratio_source", "midazolam_pp_sp_ratio_source",
- "baseline_pp_sp_ratio_calculated", "midazolam_pp_sp_ratio_calculated",
- ]
- for col in numeric_cols:
- if col in df.columns:
- df[col] = as_numeric(df[col])
- if RATIO_MODE == "source":
- df["baseline_pp_sp_ratio"] = df["baseline_pp_sp_ratio_source"]
- df["midazolam_pp_sp_ratio"] = df["midazolam_pp_sp_ratio_source"]
- elif RATIO_MODE == "calculated":
- df["baseline_pp_sp_ratio"] = df["baseline_pp_sp_ratio_calculated"]
- df["midazolam_pp_sp_ratio"] = df["midazolam_pp_sp_ratio_calculated"]
- else:
- raise ValueError('RATIO_MODE must be either "source" or "calculated".')
- # Categorical ordering for readable output.
- df["age_group"] = pd.Categorical(df["age_group"], categories=["younger", "older"], ordered=True)
- return df
- def descriptive_statistics(df):
- variables = [
- "sp_baseline_mep_uv", "sp_midazolam_mep_uv",
- "pp_baseline_mep_uv", "pp_midazolam_mep_uv",
- "baseline_pp_sp_ratio", "midazolam_pp_sp_ratio",
- ]
- rows = []
- for variable in variables:
- for age_group, sub in df.groupby("age_group", observed=False):
- values = sub[variable].dropna()
- rows.append({
- "variable": variable,
- "age_group": age_group,
- "n": int(values.shape[0]),
- "mean": fmt_float(values.mean()),
- "sd": fmt_float(values.std(ddof=1)),
- "median": fmt_float(values.median()),
- "min": fmt_float(values.min()),
- "max": fmt_float(values.max()),
- })
- return pd.DataFrame(rows)
- def shapiro_normality_tests(df):
- variables = [
- "sp_baseline_mep_uv", "sp_midazolam_mep_uv",
- "pp_baseline_mep_uv", "pp_midazolam_mep_uv",
- "baseline_pp_sp_ratio", "midazolam_pp_sp_ratio",
- ]
- rows = []
- for variable in variables:
- for age_group, sub in df.groupby("age_group", observed=False):
- values = sub[variable].dropna()
- if len(values) >= 3:
- stat, p_value = stats.shapiro(values)
- else:
- stat, p_value = np.nan, np.nan
- rows.append({
- "variable": variable,
- "age_group": age_group,
- "n": int(len(values)),
- "shapiro_w": fmt_float(stat),
- "p_value": fmt_float(p_value),
- })
- return pd.DataFrame(rows)
- def independent_ttest(df, label, variable, group_col="age_group", group_a="younger", group_b="older"):
- a = df.loc[df[group_col] == group_a, variable].dropna()
- b = df.loc[df[group_col] == group_b, variable].dropna()
- stat, p_value = stats.ttest_ind(a, b, equal_var=EQUAL_VAR_TTESTS)
- return {
- "test_family": "independent_samples_ttest",
- "comparison": label,
- "variable": variable,
- "group_a": group_a,
- "group_b": group_b,
- "n_a": int(len(a)),
- "mean_a": fmt_float(a.mean()),
- "sd_a": fmt_float(a.std(ddof=1)),
- "n_b": int(len(b)),
- "mean_b": fmt_float(b.mean()),
- "sd_b": fmt_float(b.std(ddof=1)),
- "t_statistic": fmt_float(stat),
- "df": int(len(a) + len(b) - 2) if EQUAL_VAR_TTESTS else np.nan,
- "p_value_raw": fmt_float(p_value),
- "equal_variance_assumed": EQUAL_VAR_TTESTS,
- }
- def paired_ttest(df, label, variable_a, variable_b, age_group=None):
- sub = df.copy()
- if age_group is not None:
- sub = sub.loc[sub["age_group"] == age_group].copy()
- paired = sub[["participant_id", "age_group", variable_a, variable_b]].dropna()
- a = paired[variable_a]
- b = paired[variable_b]
- if len(paired) >= 2:
- stat, p_value = stats.ttest_rel(a, b)
- else:
- stat, p_value = np.nan, np.nan
- return {
- "test_family": "paired_samples_ttest",
- "comparison": label,
- "variable": f"{variable_a} vs {variable_b}",
- "group_a": age_group if age_group is not None else "all",
- "group_b": "within_subject",
- "n_a": int(len(paired)),
- "mean_a": fmt_float(a.mean()),
- "sd_a": fmt_float(a.std(ddof=1)),
- "n_b": int(len(paired)),
- "mean_b": fmt_float(b.mean()),
- "sd_b": fmt_float(b.std(ddof=1)),
- "t_statistic": fmt_float(stat),
- "df": int(len(paired) - 1) if len(paired) >= 2 else np.nan,
- "p_value_raw": fmt_float(p_value),
- "equal_variance_assumed": np.nan,
- }
- def article_style_ttests(df):
- """Primary tests corresponding to the article narrative."""
- tests = []
- # Age-group comparisons.
- tests.append(independent_ttest(
- df, "Baseline single-pulse MEP amplitude: younger vs older",
- "sp_baseline_mep_uv"
- ))
- tests.append(independent_ttest(
- df, "Baseline paired-pulse/single-pulse ratio: younger vs older",
- "baseline_pp_sp_ratio"
- ))
- tests.append(independent_ttest(
- df, "Midazolam paired-pulse/single-pulse ratio: younger vs older",
- "midazolam_pp_sp_ratio"
- ))
- # Within-group single-pulse versus paired-pulse comparisons at baseline.
- for group in ["younger", "older"]:
- tests.append(paired_ttest(
- df, f"Baseline SP versus PP MEP amplitude within {group}",
- "sp_baseline_mep_uv", "pp_baseline_mep_uv", age_group=group
- ))
- # Midazolam effect on single-pulse MEP amplitude within each group.
- for group in ["younger", "older"]:
- tests.append(paired_ttest(
- df, f"Single-pulse baseline versus midazolam MEP amplitude within {group}",
- "sp_baseline_mep_uv", "sp_midazolam_mep_uv", age_group=group
- ))
- # Within-group single-pulse versus paired-pulse comparisons during midazolam.
- for group in ["younger", "older"]:
- tests.append(paired_ttest(
- df, f"Midazolam SP versus PP MEP amplitude within {group}",
- "sp_midazolam_mep_uv", "pp_midazolam_mep_uv", age_group=group
- ))
- # Baseline versus midazolam paired-pulse MEP amplitudes within each group.
- for group in ["younger", "older"]:
- tests.append(paired_ttest(
- df, f"Paired-pulse baseline versus midazolam MEP amplitude within {group}",
- "pp_baseline_mep_uv", "pp_midazolam_mep_uv", age_group=group
- ))
- out = pd.DataFrame(tests)
- pvals = out["p_value_raw"].astype(float).values
- valid = ~np.isnan(pvals)
- out["p_value_bh_adjusted"] = np.nan
- out["reject_bh_0_05"] = False
- if valid.sum() > 0 and STATSMODELS_AVAILABLE:
- reject, p_adj, _, _ = multipletests(pvals[valid], alpha=ALPHA, method="fdr_bh")
- out.loc[valid, "p_value_bh_adjusted"] = p_adj
- out.loc[valid, "reject_bh_0_05"] = reject
- return out
- def one_way_anovas(df):
- if not STATSMODELS_AVAILABLE:
- return pd.DataFrame({"note": ["statsmodels not installed; ANOVAs not run."]})
- variables = [
- "sp_baseline_mep_uv",
- "baseline_pp_sp_ratio",
- "sp_midazolam_mep_uv",
- "midazolam_pp_sp_ratio",
- ]
- rows = []
- for variable in variables:
- sub = df[["age_group", variable]].dropna().copy()
- if sub["age_group"].nunique() < 2:
- continue
- model = smf.ols(f"{variable} ~ C(age_group)", data=sub).fit()
- aov = anova_lm(model, typ=2).reset_index().rename(columns={"index": "term"})
- for _, r in aov.iterrows():
- rows.append({
- "model": f"{variable} ~ age_group",
- "term": r["term"],
- "sum_sq": fmt_float(r.get("sum_sq")),
- "df": fmt_float(r.get("df")),
- "F": fmt_float(r.get("F")),
- "p_value": fmt_float(r.get("PR(>F)")),
- })
- return pd.DataFrame(rows)
- def make_mep_long(df):
- rows = []
- for _, r in df.iterrows():
- for drug_condition, sp_col, pp_col in [
- ("baseline", "sp_baseline_mep_uv", "pp_baseline_mep_uv"),
- ("midazolam", "sp_midazolam_mep_uv", "pp_midazolam_mep_uv"),
- ]:
- for pulse_condition, col in [("single_pulse", sp_col), ("paired_pulse", pp_col)]:
- value = r[col]
- if pd.notna(value):
- rows.append({
- "participant_id": r["participant_id"],
- "age_group": r["age_group"],
- "drug_condition": drug_condition,
- "pulse_condition": pulse_condition,
- "mep_uv": value,
- })
- return pd.DataFrame(rows)
- def repeated_measures_anovas_within_age_group(df):
- """Within-age-group repeated-measures ANOVA for drug condition x pulse condition."""
- if not STATSMODELS_AVAILABLE:
- return pd.DataFrame({"note": ["statsmodels not installed; repeated-measures ANOVAs not run."]})
- long = make_mep_long(df)
- rows = []
- for group in ["younger", "older"]:
- sub = long.loc[long["age_group"] == group].copy()
- # AnovaRM requires complete balanced data for within-subject factors.
- counts = sub.groupby("participant_id").size()
- complete_ids = counts[counts == 4].index
- sub = sub.loc[sub["participant_id"].isin(complete_ids)].copy()
- if sub["participant_id"].nunique() < 2:
- rows.append({
- "age_group": group,
- "term": "not_run",
- "F Value": np.nan,
- "Num DF": np.nan,
- "Den DF": np.nan,
- "Pr > F": np.nan,
- "note": "Insufficient complete cases for repeated-measures ANOVA.",
- })
- continue
- try:
- aov = AnovaRM(
- data=sub,
- depvar="mep_uv",
- subject="participant_id",
- within=["drug_condition", "pulse_condition"],
- ).fit().anova_table.reset_index().rename(columns={"index": "term"})
- for _, r in aov.iterrows():
- rows.append({
- "age_group": group,
- "term": r["term"],
- "F Value": fmt_float(r.get("F Value")),
- "Num DF": fmt_float(r.get("Num DF")),
- "Den DF": fmt_float(r.get("Den DF")),
- "Pr > F": fmt_float(r.get("Pr > F")),
- "note": "Complete-case within-age-group repeated-measures ANOVA.",
- })
- except Exception as exc:
- rows.append({
- "age_group": group,
- "term": "model_error",
- "F Value": np.nan,
- "Num DF": np.nan,
- "Den DF": np.nan,
- "Pr > F": np.nan,
- "note": str(exc),
- })
- return pd.DataFrame(rows)
- def mixed_effects_wald_tests_mep(df):
- """Mixed-effects model for MEP amplitude with random participant intercepts."""
- if not STATSMODELS_AVAILABLE:
- return pd.DataFrame({"note": ["statsmodels not installed; mixed model not run."]})
- long = make_mep_long(df)
- try:
- with warnings.catch_warnings():
- warnings.simplefilter("ignore")
- model = smf.mixedlm(
- "mep_uv ~ C(age_group) * C(drug_condition) * C(pulse_condition)",
- data=long,
- groups=long["participant_id"],
- )
- fit = model.fit(reml=False, method="lbfgs")
- table = fit.wald_test_terms(scalar=True).table.reset_index().rename(columns={"index": "term"})
- table["model"] = "MixedLM: mep_uv ~ age_group * drug_condition * pulse_condition + random participant intercept"
- table = table.rename(columns={"chi2": "wald_chi_square", "P>chi2": "p_value"})
- cols = ["model", "term"] + [c for c in table.columns if c not in ["model", "term"]]
- return table[cols]
- except Exception as exc:
- return pd.DataFrame({
- "model": ["MixedLM: mep_uv ~ age_group * drug_condition * pulse_condition + random participant intercept"],
- "term": ["model_error"],
- "note": [str(exc)],
- })
- def write_analysis_notes(df):
- notes = []
- notes.append("Analysis notes")
- notes.append("==============")
- notes.append("")
- notes.append(f"Input file: {DATA_FILE}")
- notes.append(f"Ratio mode: {RATIO_MODE}")
- notes.append("Primary article-style tests use Student independent-samples t-tests for between-age-group comparisons and paired-samples t-tests for within-subject comparisons.")
- notes.append("Benjamini-Hochberg adjustment is applied across the article_style_ttests.csv p_value_raw column.")
- notes.append("One-way ANOVA outputs are included because a two-group one-way ANOVA is equivalent to the corresponding independent-samples t-test.")
- notes.append("Within-age-group repeated-measures ANOVAs are included for drug condition x pulse condition MEP amplitude as supplementary checks.")
- notes.append("Mixed-effects Wald tests are included as an additional exploratory model because the dataset contains incomplete midazolam data for some older participants.")
- notes.append("")
- notes.append("Important: The manuscript interprets paired-pulse responses as net physiological responses under the stimulation parameters used, not as a direct receptor-specific assay.")
- notes.append("")
- notes.append("Participant counts by age group:")
- counts = df.groupby("age_group", observed=False)["participant_id"].nunique()
- for k, v in counts.items():
- notes.append(f" {k}: {v}")
- notes.append("")
- notes.append("Missingness summary for primary variables:")
- for col in [
- "sp_baseline_mep_uv", "sp_midazolam_mep_uv",
- "pp_baseline_mep_uv", "pp_midazolam_mep_uv",
- "baseline_pp_sp_ratio", "midazolam_pp_sp_ratio",
- ]:
- notes.append(f" {col}: {int(df[col].isna().sum())} missing")
- (OUTPUT_DIR / "analysis_notes.txt").write_text("\n".join(notes), encoding="utf-8")
- def main():
- ensure_output_dir()
- df = load_data()
- descriptive_statistics(df).to_csv(OUTPUT_DIR / "descriptive_statistics.csv", index=False)
- shapiro_normality_tests(df).to_csv(OUTPUT_DIR / "normality_tests.csv", index=False)
- article_style_ttests(df).to_csv(OUTPUT_DIR / "article_style_ttests.csv", index=False)
- one_way_anovas(df).to_csv(OUTPUT_DIR / "one_way_anovas.csv", index=False)
- repeated_measures_anovas_within_age_group(df).to_csv(
- OUTPUT_DIR / "repeated_measures_anovas_within_age_group.csv", index=False
- )
- mixed_effects_wald_tests_mep(df).to_csv(OUTPUT_DIR / "mixed_effects_wald_tests_mep.csv", index=False)
- write_analysis_notes(df)
- print(f"Analysis complete. Output files written to: {OUTPUT_DIR.resolve()}")
- if __name__ == "__main__":
- main()
analysis_code.py, under CC-BY-4.0 · at the source
Overview
- Department of Clinical and Diagnostic Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Anesthesiology, Division of Neuroanesthesiology, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, New York, United States of America
- VA Rehabilitation R&D Center for Visual and Neurocognitive Rehabilitation, Atlanta VA Health Care System, Atlanta, Georgia, United States of America
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Rehabilitation Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Geriatrics & Gerontology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Radiology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Anesthesiology, Neuroanesthesia Division, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States of America
Abstract
The abstract is not reproduced here: the paper's license (none stated) does not allow it. Read it in the paper, at the publisher or on Europe PMC.
Repository
Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.
Zenodo 20734853
Availability: 1 check, the latest on 9 November 2026: the link answers (HTTP 200)
- 9 November 2026: the link answers (HTTP 200)
1 file
- GABAM_Zenodo_Data_Packag
e/ , Python, 455 lines, 1 matchanalysis_code.py
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 1 script, each with its path and the digest of its content;
- 1 match between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Code and data availability statement
The paper has a code and data availability statement. Its license (none stated) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to the authors' code: Zenodo 20734853
Read it in the paper: doi.org/10.1371/journal.pone.0353088.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 9 November 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 15 MeSH terms, 1 funder, 32 references.
Cite
This paper
McGregor, K. M., Safavynia, S. A., Novak, T., Weber, A. M., Wang, J., Nocera, J. R., Woodbury, A., Crosson, B., & García, P. S. (2026). Intravenous midazolam alters short-interval paired-pulse TMS responses differently in younger and older adults. PloS one, 21(11), e0353088. https://
BibTeX
@article{mcgregor2026int
author = {McGregor, Keith M and Safavynia, Seyed A and Novak, Thomas and Weber, Ashton M and Wang, Jessica and Nocera, Joe R and Woodbury, Anna and Crosson, Bruce and García, Paul S},
title = {{Intravenous midazolam alters short-interval paired-pulse TMS responses differently in younger and older adults}},
journal = {PloS one},
year = {2026},
month = nov,
volume = {21},
number = {11},
pages = {e0353088},
publisher = {PLOS},
issn = {1932-6203},
doi = {10.1371/
url = {https://
pmid = {42993790},
pmcid = {PMC13743024}
}
RIS
TY - JOUR
AU - McGregor, Keith M
AU - Safavynia, Seyed A
AU - Novak, Thomas
AU - Weber, Ashton M
AU - Wang, Jessica
AU - Nocera, Joe R
AU - Woodbury, Anna
AU - Crosson, Bruce
AU - García, Paul S
TI - Intravenous midazolam alters short-interval paired-pulse TMS responses differently in younger and older adults
T2 - PloS one
J2 - PLoS One
PY - 2026
DA - 2026/
VL - 21
IS - 11
SP - e0353088
SN - 1932-6203
PB - PLOS
DO - 10.1371/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1371/
"type": "article-journal",
"title": "Intravenous midazolam alters short-interval paired-pulse TMS responses differently in younger and older adults",
"container-title": "PloS one",
"author": [
{
"family": "McGregor",
"given": "Keith M"
},
{
"family": "Safavynia",
"given": "Seyed A"
},
{
"family": "Novak",
"given": "Thomas"
},
{
"family": "Weber",
"given": "Ashton M"
},
{
"family": "Wang",
"given": "Jessica"
},
{
"family": "Nocera",
"given": "Joe R"
},
{
"family": "Woodbury",
"given": "Anna"
},
{
"family": "Crosson",
"given": "Bruce"
},
{
"family": "García",
"given": "Paul S"
}
],
"container-title-short":
"volume": "21",
"issue": "11",
"page": "e0353088",
"DOI": "10.1371/
"PMID": "42993790",
"PMCID": "PMC13743024",
"ISSN": "1932-6203",
"publisher": "PLOS",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
11,
6
]
]
}
}
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