{"studies":[{"generated":"2026-10-13T21:06:11+00:00","highlights":[{"detail":"95\u2013187 neurons per animal tracked across 126 mapped sessions (111 analysed after excluding day 7).","kind":"info","title":"Cohort","value":"6 mice \u00b7 848 neurons"},{"detail":"Estimated from 86 reliable boundary steps. Correcting the fixed 2,000-frame grid shifts late cuts by up to 11 frames (1.7 s).","kind":"info","title":"Epoch length","value":"2000.24\u20132000.62 frames"},{"detail":"Population activity changes abruptly every 2,000 frames (binomial vs 10% chance, p < 0.001).","kind":"significant","title":"Session boundaries","value":"65% of boundaries > 90th pct"},{"detail":"Neural blocks are better explained by their own session's ethogram than by shuffled assignments (mean diagonal z = 0.96, 4 animals).","kind":"significant","title":"Session order validated","value":"pooled p < 0.001"},{"detail":"Identified by the lab and omitted from the session map. Figure 4 ranks every other single-slot deletion as a check.","kind":"info","title":"Missing epochs","value":"6597 SS9, 6669 SIT11"}],"id":"s00","n_figures":5,"number":0,"question":"How are the calcium recordings organised in time, and can each imaging block be assigned to its behavioral session with evidence rather than assumption?","runtime_s":80.1,"short":"Recovering session boundaries from concatenated recordings and validating them against behavior.","status":"complete","title":"Data provenance, quality control and session mapping"},{"generated":"2026-10-13T21:06:12+00:00","highlights":[{"detail":"Change in time fraction per CSDS day; 6/6 animals positive, exact Wilcoxon p = 0.031 (q = 0.083).","kind":"trend","title":"Attack (SD)","value":"+0.97 %/day"},{"detail":"Change in time fraction per CSDS day; 6/6 animals positive, exact Wilcoxon p = 0.031 (q = 0.083).","kind":"trend","title":"Submissive (SD)","value":"+2.67 %/day"},{"detail":"Change in time fraction per CSDS day; 6/6 animals positive, exact Wilcoxon p = 0.031 (q = 0.083).","kind":"trend","title":"Non-physical interaction (BL)","value":"+2.80 %/day"},{"detail":"Classification provided by the lab; used for all phenotype analyses (S10).","kind":"info","title":"Lab phenotype","value":"3 susceptible \u00b7 3 resilient"},{"detail":"1/6 animals have an annotation-based SI ratio < 1. The proxy does not reproduce the lab classification well and is not used to label animals.","kind":"caution","title":"Ethogram SI proxy vs lab phenotype","value":"4/6 agree"}],"id":"s01","n_figures":3,"number":1,"question":"How does behavior evolve across repeated defeat, and how does social-test behavior relate to the lab's susceptible/resilient classification?","runtime_s":1.3,"short":"Time budgets, the evolution of defeat responses across days, and a social-interaction phenotype.","status":"complete","title":"Behavioral phenotyping across chronic social defeat"},{"generated":"2026-10-13T21:06:14+00:00","highlights":[{"detail":"Median paired change in inferred event rate, 1/6 animals increased, p = 0.094; Friedman p = 0.135.","kind":"null","title":"Firing during defeat","value":"-0.224 Hz (SD \u2212 BL)"},{"detail":"BL+SS sessions, 6 animals, p = 0.062 (q = 0.562).","kind":"null","title":"Population response: Exploring","value":"z = -0.05"},{"detail":"SD sessions, 6 animals, p = 0.094 (q = 0.562).","kind":"null","title":"Population response: Standing","value":"z = +0.03"},{"detail":"Population rate change when the CD-1 is present, p = 0.188.","kind":"null","title":"SIT CD-1 vs empty","value":"+0.121 Hz"}],"id":"s02","n_figures":3,"number":2,"question":"Does the overall level of neural activity differ between baseline, defeat and post-defeat sensory contact, does it change across defeat days, and which behaviors drive population activity?","runtime_s":2.4,"short":"Inferred firing, active-neuron fraction and behavior-locked population responses.","status":"complete","title":"Neural activity across CSDS phases"},{"generated":"2026-10-13T21:37:29+00:00","highlights":[{"detail":"Mean fraction per animal during defeat (chance 1%), p = 0.047, q = 0.474.","kind":"trend","title":"Standing-excited neurons","value":"6.6%"},{"detail":"Mean fraction per animal during defeat (chance 1%), p = 0.156, q = 0.474.","kind":"null","title":"Freezing-excited neurons","value":"3.2%"},{"detail":"Overlap between defeat-excited and SIT-social neurons relative to shifted-label SIT ensembles (1 informative animal; Fisher-combined p = 1.000; Wilcoxon n/a).","kind":"caution","title":"Defeat \u2192 SIT reactivation","value":"\u00d70.00 vs null"},{"detail":"Overlap between neurons excited by non-physical interaction (BL+SS) and SIT-social neurons (Fisher-combined p = 0.280; Wilcoxon n/a; 0/2 animals individually p < 0.05).","kind":"caution","title":"Non-physical \u2192 SIT reactivation","value":"\u00d73.03 vs null"}],"id":"s03","n_figures":3,"number":3,"question":"What fraction of neurons is selectively excited or inhibited during defeat-related behaviors, and do neurons recruited during physical defeat overlap with neurons that respond to the CD-1 in the SIT?","runtime_s":40.8,"short":"Which neurons encode defeat behaviors, and are defeat-responsive neurons re-engaged in the SIT?","status":"complete","title":"Behavior-tuned neurons and ensemble reactivation"},{"generated":"2026-10-13T21:12:19+00:00","highlights":[{"detail":"Median paired change; 5/6 animals increased; p = 0.062, q = 0.750; Friedman p = 0.311.","kind":"null","title":"modularity Q (SD vs BL)","value":"+0.0225"},{"detail":"Median paired change; 4/6 animals increased; p = 0.219, q = 0.750; Friedman p = 0.846.","kind":"null","title":"clustering coefficient (SD vs BL)","value":"+0.0117"},{"detail":"Median paired change; 4/6 animals increased; p = 0.219, q = 0.750; Friedman p = 0.607.","kind":"null","title":"Q \u2212 null Q (SD vs BL)","value":"+0.0352"},{"detail":"No SD vs BL effect was both nominally significant and direction-consistent across sensitivity analyses.","kind":"null","title":"Robust to sensitivity analyses","value":"0 metric(s)"}],"id":"s04","n_figures":4,"number":4,"question":"Does the functional network formed by co-active neurons reorganise during defeat and post-defeat sensory contact relative to baseline, and does topology change as defeats accumulate?","runtime_s":319.8,"short":"Neuron-level co-activity graphs, null-model thresholding and graph-theoretic contrasts.","status":"complete","title":"Functional network topology across CSDS phases"},{"generated":"2026-10-13T21:14:52+00:00","highlights":[{"detail":"Consecutive same-condition partitions agree above label-permutation null (-0.000), p = 0.016.","kind":"significant","title":"Modules persist across days","value":"ARI = 0.337"},{"detail":"vs 0.06 expected for random hub sets, p = 0.016.","kind":"significant","title":"Hub persistence","value":"Jaccard 0.20"},{"detail":"Strongest community/hub effect of defeat; p = 0.031, q = 0.375.","kind":"trend","title":"hub participation P (SD vs BL)","value":"-0.0605"},{"detail":"Mean over sessions in the 70th\u201390th degree percentile range (> 1 = rich-club organisation).","kind":"info","title":"Rich club","value":"normalised \u03c6 = 1.33"}],"id":"s05","n_figures":4,"number":5,"question":"Are neurons organised into stable co-active modules and hub neurons, and does defeat change hub roles, rich-club organisation or the day-to-day stability of modules?","runtime_s":153.7,"short":"Ensemble (module) structure, connector hubs, rich clubs and their stability across days.","status":"complete","title":"Communities, hubs and rich-club organisation"},{"generated":"2026-10-13T21:15:11+00:00","highlights":[{"detail":"Sessions sharing a context are more alike than different-context sessions on other days (within-day permutation p = 0.126; Wilcoxon p = 0.219; OLS \u03b2 = +0.005).","kind":"null","title":"Context-specific networks","value":"\u0394sim = +0.005"},{"detail":"Mean per-animal change in FC similarity per day of separation between SD sessions; 6/6 animals negative, exact Wilcoxon p = 0.031, q = 0.047 (FDR over BL, SD, SS).","kind":"significant","title":"Drift of defeat networks","value":"-0.0249 per day"},{"detail":"SIT (CD-1) FC similarity to defeat 0.588 vs baseline 0.592, p = 1.000.","kind":"null","title":"SIT network resembles\u2026","value":"no preference"}],"id":"s06","n_figures":5,"number":6,"question":"Does each CSDS context (baseline, defeat, sensory contact, SIT) evoke its own network configuration that recurs across days, and how quickly does the functional network drift over the 11 days?","runtime_s":19.0,"short":"Similarity of neuron-level FC across all sessions: context-specific configurations vs slow drift.","status":"complete","title":"Network reorganisation and drift"},{"generated":"2026-10-13T21:16:33+00:00","highlights":[{"detail":"Defeat context, 5 animals, p = 0.188, q = 1.000.","kind":"null","title":"Submissive: modularity vs exploring","value":"-0.124"},{"detail":"Cross-validated (odd vs even days) within-state reliability vs between-state FC similarity, defeat context, 3/4 animals, p = 0.312.","kind":"null","title":"States reconfigure the network","value":"0.57 vs 0.57"}],"id":"s07","n_figures":3,"number":7,"question":"Within the defeat context, does the network configuration depend on what the animal is doing (physical interaction, submission, freezing, escape vs exploration)?","runtime_s":81.7,"short":"Functional networks computed separately within each annotated behavior, frame-count matched.","status":"complete","title":"Behavior-state-dependent networks"},{"generated":"2026-10-13T21:32:09+00:00","highlights":[{"detail":"6/6 animals above their own null; group p = 0.016.","kind":"significant","title":"Decoding behavior (BL+SS)","value":"45% (chance 27%)"},{"detail":"4/6 animals above their own null; group p = 0.016.","kind":"significant","title":"Decoding behavior (SD)","value":"26% (chance 14%)"},{"detail":"4/6 animals above their own null; group p = 0.031.","kind":"significant","title":"Decoding context (BL/SD/SS, leave-one-day-out)","value":"47% (chance 33%)"}],"id":"s08","n_figures":2,"number":8,"question":"How much information about ongoing defeat behavior and about the CSDS context (baseline, defeat, sensory contact) is carried by the population activity of the imaged neurons?","runtime_s":936.0,"short":"Cross-validated linear decoders with temporally structured null models.","status":"complete","title":"Population decoding of behavior and context"},{"generated":"2026-10-13T21:32:28+00:00","highlights":[{"detail":"Median paired change (SD \u2212 BL), 2/6 animals higher, p = 0.219, q = 0.917.","kind":"null","title":"Dimensionality during defeat","value":"-0.002 PR/N"},{"detail":"Occupancy divergence for same- vs different-context sessions (different days), p = 0.078.","kind":"null","title":"Context-specific population states","value":"JS 0.532 vs 0.549"},{"detail":"1/6 animals above circular-shift null; group p = 0.078.","kind":"null","title":"States track defeat behavior","value":"MI z = 0.9"}],"id":"s09","n_figures":4,"number":9,"question":"Does defeat compress or expand the dimensionality of population activity, and does the population visit different discrete states in each context, states that track defensive behavior?","runtime_s":19.6,"short":"Participation-ratio dimensionality and hidden Markov model population states across CSDS.","status":"complete","title":"Population dynamics: dimensionality and hidden states"},{"generated":"2026-10-13T21:32:40+00:00","highlights":[{"detail":"Lab classification: resilient 4703, 6597, 6669; susceptible 6445, 6672, 6675.","kind":"info","title":"Phenotype groups","value":"3 susceptible \u00b7 3 resilient"},{"detail":"Complete separation of susceptible and resilient animals; \u22482.5 expected by chance (binomial p = 0.73, ignoring correlations among features).","kind":"null","title":"Features separating the groups","value":"2/25"},{"detail":"Susceptible lower (-0.107 vs 0.0151), complete separation, exact p = 0.100 (minimum attainable).","kind":"info","title":"event rate (Hz) \u00b7 SS \u2212 BL","value":"g = -3.22"},{"detail":"Susceptible lower (-0.31 vs -0.0536), complete separation, exact p = 0.100 (minimum attainable).","kind":"info","title":"event rate (Hz) \u00b7 SD \u2212 BL","value":"g = -1.90"},{"detail":"No 3-vs-3 comparison can reach p < 0.05; these are candidate markers.","kind":"caution","title":"Power","value":"n = 3 per group"}],"id":"s10","n_figures":3,"number":10,"question":"Do susceptible and resilient mice differ in how their neuronal activity, functional networks and population codes respond to defeat, and in how those responses evolve across days?","runtime_s":11.3,"short":"Which per-animal network, activity and coding measures separate the lab-classified susceptible and resilient mice?","status":"complete","title":"Susceptible vs resilient: neural correlates of the CSDS phenotype"}],"study":{"acronym":"CSDS-CaNet","institution":"Universit\u00e9 Laval","lab":"JDCHS \u2014 Ca2+ imaging / CSDS","short_name":"csds-ca-networks","start_date":"2026-10-09","title":"Network reorganization of single-neuron calcium dynamics during chronic social defeat stress"},"updated":"2026-10-13T21:37:29+00:00"}