Proximity in mice induced by an auditory-conditioned stimulus.
The 5 matches
- [1] § Results › Auditory conditioned stimulus facilitates proximity between familiar mice ↔ distribution_analysis_and_graphs.ipynb, lines 242–381 · score 0.81 · probability mass, bimodal model, Akaike weights, Gaussian Mixture, ePMF, empirical
- [2] § Results › Auditory conditioned stimulus facilitates proximity between familiar mice ↔ distribution_analysis_and_graphs.ipynb, lines 242–381 · score 0.79 · Probability Mass, bimodal model, Akaike weights, Gaussian Mixture, ePMF, smoothed
- [3] § Materials and methods › Data analysis ↔ paper_figures.ipynb, lines 700–771 · score 0.69 · Mann Whitney, unpaired comparisons, Shapiro Wilk, CS
- [4] § Materials and methods › Data analysis ↔ distribution_analysis_and_graphs.ipynb, lines 1–119 · score 0.67 · Akaike weights, Gaussian Mixture, density, AIC, BIC, GMM
- [5] § Results › Oxytocin signaling is required for CS-induced proximity ↔ distribution_analysis_and_graphs.ipynb, lines 1–119 · score 0.57 · Gaussian mixture, ePMF, density, AIC, BIC, bimodality
Paper
Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC
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The authors' code
Jupyter notebook · 384 lines · 13 KB · no license · 4 matches
- # %%
- # Combined code for ECDF, EPMF, and bimodality test. EPMF bins are set at 30.Enter the file name into the file path at 1.SETUP
- import os
- # Fix for Windows MKL memory leak/UserWarning
- os.environ["OMP_NUM_THREADS"] = "1"
- import pandas as pd
- import numpy as np
- import matplotlib.pyplot as plt
- from sklearn.mixture import GaussianMixture
- from scipy.stats import levene
- import warnings
- # Silence the specific KMeans warning if it still persists
- warnings.filterwarnings("ignore", category=UserWarning, module="sklearn.cluster._kmeans")
- # --- 1. SETUP ---
- file_path = r"W:\alexei\jupyter\graphs_jupyter\unfamiliar_vs_familiar.xlsx"
- df = pd.read_excel(file_path)
- base_name = os.path.splitext(os.path.basename(file_path))[0]
- output_dir = os.path.dirname(file_path)
- control = df["control"].dropna().values
- treatment = df["treatment"].dropna().values
- datasets = {"Control": control, "Treatment": treatment}
- # Illustrator-ready settings
- plt.rcParams['svg.fonttype'] = 'none'
- plt.rcParams['pdf.fonttype'] = 42
- # --- 2. ANALYTICS FUNCTIONS ---
- def ecdf(data):
- x = np.sort(data)
- y = np.arange(1, len(x) + 1) / len(x)
- return x, y
- def calculate_weights(ics):
- ics = np.array(ics)
- delta_ic = ics - np.min(ics)
- weights = np.exp(-0.5 * delta_ic)
- return weights / np.sum(weights)
- # --- 3. EXECUTION & PLOTTING ---
- fig, axes = plt.subplots(1, 3, figsize=(18, 5))
- # Common Bins for ePMF (not Freedman-Diaconis rule but a chosen number)
- all_data = np.concatenate([control, treatment])
- bins = np.histogram_bin_edges(all_data, bins=30)
- aic_results = []
- bic_results = []
- print(f"=== Analysis for {base_name} ===\n")
- # Run Levene's Test for Variance
- stat, p_val = levene(control, treatment)
- print(f"Levene’s Test for Equal Variance: p = {p_val:.4f}")
- if p_val < 0.05:
- print("Result: Significant difference in variance detected.\n")
- else:
- print("Result: No significant difference in variance.\n")
- for i, (name, data) in enumerate(datasets.items()):
- data_reshaped = data.reshape(-1, 1)
- # Panel 1: ECDF
- x, y = ecdf(data)
- axes[0].step(x, y, where="post", label=name, lw=2)
- # Panel 2: ePMF (Binned Density)
- counts, edges = np.histogram(data, bins=bins)
- pmf = counts / counts.sum()
- centers = (edges[:-1] + edges[1:]) / 2
- axes[1].plot(centers, pmf, marker='o', label=name, lw=2)
- # Model Comparison (GMM)
- m1 = GaussianMixture(n_components=1, random_state=0).fit(data_reshaped)
- m2 = GaussianMixture(n_components=2, random_state=0).fit(data_reshaped)
- aics = [m1.aic(data_reshaped), m2.aic(data_reshaped)]
- bics = [m1.bic(data_reshaped), m2.bic(data_reshaped)]
- aic_w = calculate_weights(aics)
- bic_w = calculate_weights(bics)
- aic_results.append(aic_w)
- bic_results.append(bic_w)
- print(f"[{name}] Bimodal Evidence: AIC Weight {aic_w[1]:.1%}, BIC Weight {bic_w[1]:.1%}")
- # --- 4. FINALIZE VISUALS ---
- axes[0].set_title("ECDF (Cumulative)")
- axes[0].set_ylabel("Cumulative Probability")
- axes[0].legend()
- axes[1].set_title("ePMF (Density)")
- axes[1].set_ylabel("Probability")
- axes[1].legend()
- # Panel 3: Akaike Weight Bar Chart
- labels = ["Control", "Treatment"]
- x_pos = np.arange(len(labels))
- width = 0.35
- axes[2].bar(x_pos - width/2, [w[1] for w in aic_results], width, label='AIC (Generous)', color='skyblue')
- axes[2].bar(x_pos + width/2, [w[1] for w in bic_results], width, label='BIC (Strict)', color='coral')
- axes[2].set_title("Confidence in Bimodality")
- axes[2].set_xticks(x_pos)
- axes[2].set_xticklabels(labels)
- axes[2].set_ylim(0, 1.1)
- axes[2].axhline(0.95, color='red', linestyle='--', alpha=0.5, label="95% Confidence")
- axes[2].legend()
- plt.tight_layout()
- output_path = os.path.join(output_dir, f"{base_name}_Full_Analysis")
- plt.savefig(output_path + ".svg")
- plt.savefig(output_path + ".pdf")
- print(f"\nFiles saved to: {output_dir}")
- plt.show()
- # %%
- # Combined code for ECDF, EPMF, and bimodality test. EPMF bins are set per Freedman-Diaconis rule. Enter the file name into the file path at 1.SETUP
- import os
- # Fix for Windows MKL memory leak/UserWarning
- os.environ["OMP_NUM_THREADS"] = "1"
- import pandas as pd
- import numpy as np
- import matplotlib.pyplot as plt
- from sklearn.mixture import GaussianMixture
- from scipy.stats import levene
- import warnings
- # Silence the specific KMeans warning if it still persists
- warnings.filterwarnings("ignore", category=UserWarning, module="sklearn.cluster._kmeans")
- # --- 1. SETUP ---
- file_path = r"W:\alexei\jupyter\graphs_jupyter\unfamiliar_vs_familiar.xlsx"
- df = pd.read_excel(file_path)
- base_name = os.path.splitext(os.path.basename(file_path))[0]
- output_dir = os.path.dirname(file_path)
- control = df["control"].dropna().values
- treatment = df["treatment"].dropna().values
- datasets = {"Control": control, "Treatment": treatment}
- # Illustrator-ready settings
- plt.rcParams['svg.fonttype'] = 'none'
- plt.rcParams['pdf.fonttype'] = 42
- # --- 2. ANALYTICS FUNCTIONS ---
- def ecdf(data):
- x = np.sort(data)
- y = np.arange(1, len(x) + 1) / len(x)
- return x, y
- def calculate_weights(ics):
- ics = np.array(ics)
- delta_ic = ics - np.min(ics)
- weights = np.exp(-0.5 * delta_ic)
- return weights / np.sum(weights)
- # --- 3. EXECUTION & PLOTTING ---
- fig, axes = plt.subplots(1, 3, figsize=(18, 5))
- # Common Bins for ePMF (Freedman-Diaconis rule)
- all_data = np.concatenate([control, treatment])
- bins = np.histogram_bin_edges(all_data, bins='fd')
- aic_results = []
- bic_results = []
- print(f"=== Analysis for {base_name} ===\n")
- # Run Levene's Test for Variance
- stat, p_val = levene(control, treatment)
- print(f"Levene’s Test for Equal Variance: p = {p_val:.4f}")
- if p_val < 0.05:
- print("Result: Significant difference in variance detected.\n")
- else:
- print("Result: No significant difference in variance.\n")
- for i, (name, data) in enumerate(datasets.items()):
- data_reshaped = data.reshape(-1, 1)
- # Panel 1: ECDF
- x, y = ecdf(data)
- axes[0].step(x, y, where="post", label=name, lw=2)
- # Panel 2: ePMF (Binned Density)
- counts, edges = np.histogram(data, bins=bins)
- pmf = counts / counts.sum()
- centers = (edges[:-1] + edges[1:]) / 2
- axes[1].plot(centers, pmf, marker='o', label=name, lw=2)
- # Model Comparison (GMM)
- m1 = GaussianMixture(n_components=1, random_state=0).fit(data_reshaped)
- m2 = GaussianMixture(n_components=2, random_state=0).fit(data_reshaped)
- aics = [m1.aic(data_reshaped), m2.aic(data_reshaped)]
- bics = [m1.bic(data_reshaped), m2.bic(data_reshaped)]
- aic_w = calculate_weights(aics)
- bic_w = calculate_weights(bics)
- aic_results.append(aic_w)
- bic_results.append(bic_w)
- print(f"[{name}] Bimodal Evidence: AIC Weight {aic_w[1]:.1%}, BIC Weight {bic_w[1]:.1%}")
- # --- 4. FINALIZE VISUALS ---
- axes[0].set_title("ECDF (Cumulative)")
- axes[0].set_ylabel("Cumulative Probability")
- axes[0].legend()
- axes[1].set_title("ePMF (Density)")
- axes[1].set_ylabel("Probability")
- axes[1].legend()
- # Panel 3: Akaike Weight Bar Chart
- labels = ["Control", "Treatment"]
- x_pos = np.arange(len(labels))
- width = 0.35
- axes[2].bar(x_pos - width/2, [w[1] for w in aic_results], width, label='AIC (Generous)', color='skyblue')
- axes[2].bar(x_pos + width/2, [w[1] for w in bic_results], width, label='BIC (Strict)', color='coral')
- axes[2].set_title("Confidence in Bimodality")
- axes[2].set_xticks(x_pos)
- axes[2].set_xticklabels(labels)
- axes[2].set_ylim(0, 1.1)
- axes[2].axhline(0.95, color='red', linestyle='--', alpha=0.5, label="95% Confidence")
- axes[2].legend()
- plt.tight_layout()
- output_path = os.path.join(output_dir, f"{base_name}_Full_Analysis")
- plt.savefig(output_path + ".svg")
- plt.savefig(output_path + ".pdf")
- print(f"\nFiles saved to: {output_dir}")
- plt.show()
- # %%
- # Combined code for ECDF, EPMF, KS test, and bimodality test. EPMF is slidng window.The ePMF graph has a single shared x_grid
- # Enter the file name into the file path at 1.SETUP.
- # Set sliding window as % of total: in 3 Execution and plotting, Shared window width for PMF comparison (7.5% of range)
- # - 2. ANALYTICS FUNCTIONS --- n points recommended 200
- # The sliding window counts are normalized by the sum of all window counts (pmf / np.sum(pmf)) - see x_grid definition
- import os
- # Fix for Windows MKL memory leak/UserWarning
- os.environ["OMP_NUM_THREADS"] = "1"
- import pandas as pd
- import numpy as np
- import matplotlib.pyplot as plt
- from sklearn.mixture import GaussianMixture
- from scipy.stats import levene, ks_2samp
- import warnings
- # Silence specific KMeans warnings
- warnings.filterwarnings("ignore", category=UserWarning, module="sklearn.cluster._kmeans")
- # --- 1. SETUP ---
- # Update this path to your local file location
- file_path = r"W:\alexei\jupyter\graphs_jupyter\OT_antag_vs_saline_relative.xlsx"
- df = pd.read_excel(file_path)
- base_name = os.path.splitext(os.path.basename(file_path))[0]
- output_dir = os.path.dirname(file_path)
- control = df["control"].dropna().values
- treatment = df["treatment"].dropna().values
- datasets = {"Control": control, "Treatment": treatment}
- # Illustrator-ready font settings
- plt.rcParams['svg.fonttype'] = 'none'
- plt.rcParams['pdf.fonttype'] = 42
- # --- 2. ANALYTICS FUNCTIONS ---
- def ecdf(data):
- """Computes the Empirical Cumulative Distribution Function."""
- x = np.sort(data)
- y = np.arange(1, len(x) + 1) / len(x)
- return x, y
- def sliding_window_epmf(data, window_width, n_points=200):
- """Computes a smoothed ePMF using a sliding window across the global data range."""
- all_vals = np.concatenate([control, treatment])
- # use the line below to plot ePMF considering data ranges of each group separately
- # x_grid = np.linspace(np.min(data), np.max(data), n_points)
- x_grid = np.linspace(np.min(all_vals), np.max(all_vals), n_points)
- pmf = []
- for x in x_grid:
- count = np.sum((data >= x - window_width/2) & (data < x + window_width/2))
- pmf.append(count)
- pmf = np.array(pmf)
- return x_grid, pmf / np.sum(pmf)
- def calculate_weights(ics):
- """Calculates Akaike weights from AIC or BIC values."""
- ics = np.array(ics)
- delta_ic = ics - np.min(ics)
- weights = np.exp(-0.5 * delta_ic)
- return weights / np.sum(weights)
- # --- 3. EXECUTION & PLOTTING ---
- fig, axes = plt.subplots(1, 3, figsize=(18, 5))
- aic_results = []
- bic_results = []
- print(f"=== Statistical Summary for {base_name} ===\n")
- # A. Levene's Test (Checks if the 'spread' or variance changed)
- l_stat, l_p = levene(control, treatment)
- print(f"Levene’s Test (Variance Difference): p = {l_p:.4f}")
- # B. Kolmogorov-Smirnov Test (Checks if the overall distribution changed)
- ks_stat, ks_p = ks_2samp(control, treatment)
- print(f"KS Test (Distributional Shift): D = {ks_stat:.4f}, p = {ks_p:.4e}")
- if ks_p < 0.05:
- print("Result: Significant global shift between Control and Treatment.\n")
- else:
- print("Result: No significant global shift detected.\n")
- # Shared window width for PMF comparison (10 % of range)
- all_data = np.concatenate([control, treatment])
- w_width = (np.max(all_data) - np.min(all_data)) * 0.10
- for i, (name, data) in enumerate(datasets.items()):
- data_reshaped = data.reshape(-1, 1)
- # Panel 1: ECDF
- x_ec, y_ec = ecdf(data)
- axes[0].step(x_ec, y_ec, where="post", label=name, lw=2)
- # Panel 2: Sliding Window ePMF
- x_pmf, y_pmf = sliding_window_epmf(data, window_width=w_width)
- axes[1].plot(x_pmf, y_pmf, label=name, lw=2)
- # GMM Model Comparison for Bimodality
- m1 = GaussianMixture(n_components=1, random_state=0).fit(data_reshaped)
- m2 = GaussianMixture(n_components=2, random_state=0).fit(data_reshaped)
- aics = [m1.aic(data_reshaped), m2.aic(data_reshaped)]
- bics = [m1.bic(data_reshaped), m2.bic(data_reshaped)]
- aic_w = calculate_weights(aics)
- bic_w = calculate_weights(bics)
- aic_results.append(aic_w)
- bic_results.append(bic_w)
- print(f"[{name}] Bimodal Evidence: AIC {aic_w[1]:.1%}, BIC {bic_w[1]:.1%}")
- # --- 4. FORMATTING & SAVING ---
- axes[0].set_title("ECDF (Basis for KS Test)")
- axes[0].set_ylabel("Cumulative Probability")
- axes[0].legend()
- axes[1].set_title(f"Sliding Window ePMF (Width={w_width:.2f})")
- axes[1].set_ylabel("Probability Mass")
- axes[1].legend()
- # Panel 3: Akaike/BIC Weight Bar Chart
- labels = list(datasets.keys())
- x_pos = np.arange(len(labels))
- width = 0.35
- axes[2].bar(x_pos - width/2, [w[1] for w in aic_results], width, label='AIC Weight', color='skyblue')
- axes[2].bar(x_pos + width/2, [w[1] for w in bic_results], width, label='BIC Weight', color='coral')
- axes[2].set_title("Evidence for Bimodal Model")
- axes[2].set_xticks(x_pos)
- axes[2].set_xticklabels(labels)
- axes[2].set_ylim(0, 1.1)
- axes[2].axhline(0.95, color='red', linestyle='--', alpha=0.6, label="95% Threshold")
- axes[2].legend()
- plt.tight_layout()
- output_path = os.path.join(output_dir, f"{base_name}_Integrated_Analysis")
- plt.savefig(output_path + ".svg")
- plt.savefig(output_path + ".pdf")
- print(f"\nSaved analysis plots to: {output_dir}")
- plt.show()
- # %%
distribution_analysis_and_graphs.ipynb at commit 1ceada1, no license · at the source
Overview
- Fralin Biomedical Research Institute Center for Neurobiology Research at Virginia Tech Carilion,Roanoke, VA USA
- Department of Psychiatry and Behavioral Medicine, Virginia Tech Carilion School of Medicine,Roanoke, VA USA
Abstract
Social affiliation promotes survival and well-being across species, and proximity to conspecifics is a necessary precondition for affiliative contact. While innate threats reliably increase proximity among conspecifics, whether learned threats have the same effect remains unknown. Here, we report that an auditory conditioned stimulus (CS) induces proximity in mice. In same-sex dyads, fear-conditioned mice increased proximity during CS presentation, independent of freezing levels. This CS-evoked proximity required familiarity between partners and intact basolateral amygdala-to-ventral hippocampus inputs, demonstrated by DREADD-mediated suppression. It also required oxytocin receptor signaling, demonstrated by systemic administration of the antagonist L368,899. These findings suggest that learned and innate threats engage shared neural circuitry for social proximity.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 5 matches between paragraphs and lines of code.
wataruito/Codes_in_Threat-induced_proximity_Ito_et_al
1ceada176731bb006722dd31c0f8362a9b841cff, 9 July 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
3 files
- distribution_analysis_an
d_graphs.ipynb , Jupyter, 384 lines, 4 matches - paper_figures.ipynb, Jupyter, 1,181 lines, 1 match
- README.md, Text, 55 lines
Code availability
All primary data, including video files, are available from the authors upon reasonable request. Analysis code and example datasets are available at https://
Reproduced under the paper's license (CC BY), from the paper cited above.
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.
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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.
Data availability
All primary data, including video files, are available from the authors upon reasonable request. Analysis code and example datasets will be provided as part of a replication package upon publication.
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
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Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 2 authors, 2 keywords, 12 MeSH terms, 1 funder, 62 references.
Cite
This paper
Ito, W., & Morozov, A. (2026). Proximity in mice induced by an auditory-conditioned stimulus. Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology,
BibTeX
@article{ito2026proximit
author = {Ito, Wataru and Morozov, Alexei},
title = {{Proximity in mice induced by an auditory-conditioned stimulus}},
journal = {Neuropsychopharmacology
year = {2026},
month = jul,
volume = {51},
number = {10},
pages = {1836--1843},
publisher = {Nature Publishing Group},
issn = {0893-133X},
doi = {10.1038/
url = {https://
pmid = {42457949},
pmcid = {PMC13486637}
}
RIS
TY - JOUR
AU - Ito, Wataru
AU - Morozov, Alexei
TI - Proximity in mice induced by an auditory-conditioned stimulus
T2 - Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology
J2 - Neuropsychopharmacology
PY - 2026
DA - 2026/
VL - 51
IS - 10
SP - 1836
EP - 1843
SN - 0893-133X
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1038/
"type": "article-journal",
"title": "Proximity in mice induced by an auditory-conditioned stimulus",
"container-title": "Neuropsychopharmacology
"author": [
{
"family": "Ito",
"given": "Wataru"
},
{
"family": "Morozov",
"given": "Alexei"
}
],
"container-title-short":
"volume": "51",
"issue": "10",
"page": "1836-1843",
"DOI": "10.1038/
"PMID": "42457949",
"PMCID": "PMC13486637",
"ISSN": "0893-133X",
"publisher": "Nature Publishing Group",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
7,
15
]
]
}
}
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