v2 phase 2: per-section prose via manuscript-writing (#59)

Author: neuromechanist

manuscript/narrative-review/abstract.md

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 # Abstract
 
-[Opening sentence: the field has moved from whole-clip ISC to event-locked methods.]
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-[Sentence 2: most empirical evidence is adult fMRI / iEEG / scalp-EEG ISC; per-shot ERSP in a developmental cohort viewing silent character animation has no precedent.]
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-[Sentence 3: we review the four-perspective corpus that constrains the design space.]
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-[Sentence 4: psychophysics, action, language, and emotion make divergent and partly-falsifiable predictions about the 0 to 500 ms post-shot-onset window.]
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-[Closing sentence: HBN-EEG Release 3 viewing *The Present* (Pixar 2014) sits at this empty intersection; the 100 Hz local working set caps beta-band claims until a 500 Hz validation pass.]
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+Naturalistic-stimulus neuroscience has moved from whole-clip inter-subject correlation (ISC) to event-locked methods that interrogate individual shots. Most empirical evidence is adult functional magnetic resonance imaging (fMRI), adult intracranial electroencephalography (iEEG), or adult scalp electroencephalography (EEG) ISC. Per-shot event-related spectral perturbation (ERSP) in a developmental cohort viewing silent character animation has no published precedent. We review the corpus that constrains this design space and argue that psychophysics, action, language, and emotion make divergent, partly-falsifiable predictions about the 0 to 500 ms post-shot-onset window. The Healthy Brain Network EEG Release 3 cohort viewing *The Present* (Pixar 2014) sits at this empty intersection; the 100 Hz local working set caps beta-band claims until a 500 Hz validation pass.

manuscript/narrative-review/boxes/box1_anchor.md

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 # Box 1: HBN-EEG Release 3 as the anchor cohort
 
-[Paragraph (~180 words). Describe the HBN-EEG R3 cohort:
-- 5-21-year-old participants in a developmental research setting.
-- 128-channel HydroCel Geodesic Sensor Net.
-- Passive viewing of the 3.5-minute Pixar short *The Present* (2014).
-- Local working set: 184 subjects at 100 Hz BDF (Nyquist-aware downsample of original 500 Hz).
-- 56 stimulus-side shots with per-shot `onset`, `duration`, `LLR`, `has_boy`, `has_puppy` annotations.
-- After invalidating 3 high-drift rows (`match_diff_s > 1.0 s`), 49 trusted rows: 20 boy-only + 15 puppy-only shots for mutually exclusive single-agent contrast.
-- Pipeline: BIDS import, 1 Hz HPF, conditional cleanline (gated by Nyquist), `clean_rawdata` channel rejection, AMICA, ICLabel (brain threshold 0.69), dipfit5, std_precomp ERSP.
-- F4 carry-forward statement: the anchor case rests on Petroni-Cohen 2018 (external precedent) + this partly-validated pipeline (internal feasibility). The six-feature uniqueness conjunction is *descriptive*, not evidential.]
+The Healthy Brain Network EEG (HBN-EEG) Release 3 cohort recruits 5- to 21-year-old participants in a developmental research setting and records 128-channel HydroCel Geodesic Sensor Net during passive viewing of the 3.5-minute Pixar short *The Present* (2014). The local working set used in our pipeline development is 184 subjects at 100 Hz Biosignal Data Format (BDF), a Nyquist-aware downsample of the original 500 Hz. The 56 stimulus-side shots carry per-shot `onset`, `duration`, `LLR`, `has_boy`, and `has_puppy` annotations. After invalidating 3 high-drift rows (`match_diff_s > 1.0 s`), 49 rows are trusted, yielding 20 boy-only and 15 puppy-only shots for the mutually exclusive single-agent contrast. The pipeline runs BIDS import, 1 Hz high-pass filter, conditional cleanline (gated by Nyquist), `clean_rawdata` channel rejection, AMICA, ICLabel (brain threshold 0.69), dipfit5, and `std_precomp` ERSP. The anchor case rests on Petroni and colleagues 2018 [Petroni2018TheVO] as the external precedent and this partly-validated pipeline as the internal feasibility proof.

manuscript/narrative-review/boxes/outstanding-questions.md

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 # Outstanding Questions Box
 
-[Budget: 5-7 questions. Each question is one sentence; forward-looking; adjudicates between perspectives or names a gap the field could fill.
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-1. [Q1: per-shot ERSP in developmental cohort survives LLR and motion-energy partialling at 0-500 ms?]
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-2. [Q2: mu-band ERD over central rolandic clusters elicited by animated-character action observation as it is by adult hand-action observation?]
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-3. [Q3: cuteness-driven affective response in children produces a sub-second EEG signature distinguishable from generic arousal? And is the signature compatible with frontal asymmetry at sub-second timescales given reliability concerns?]
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-4. [Q4: can the topographic-and-band rejection region for the four-perspective ranking be pre-registered before group analysis? Is the central-rolandic vs frontal-asymmetric vs language-network discrimination operationalisable from EEG IC clusters?]
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-5. [Q5: can a multimodal vision-language embedding regressor substitute for language-model surprisal on silent stimuli?]
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-6. [Q6: does within-stimulus narrative position (three-act trajectory) explain condition-level effects that survive low-level partialling in single-stimulus designs?]
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-7. [Q7: residual saccade-locked variance contamination without synchronous eye tracker, and the cohort size at which ICA-only artifact rejection becomes sufficient?]]
+1. Does per-shot EEG spectral perturbation in a developmental cohort viewing silent animation survive partialling for log luminance ratio and motion energy at the 0 to 500 ms window?
+2. Is mu-band ERD over central rolandic clusters elicited by animated-character action observation, as it is by hand-action observation in adults?
+3. Does cuteness-driven affective response in children produce a sub-second EEG signature distinguishable from generic arousal in the alpha band, and is the signature compatible with frontal asymmetry at sub-second timescales given the meta-analytic reliability concerns?
+4. Can a topographic-and-band rejection region for the four-perspective ranking be pre-registered before group analysis, and is the central-rolandic-versus-frontal-asymmetric-versus-language-network discrimination operationalisable from EEG IC clusters?
+5. Can a multimodal vision-language embedding regressor substitute for language-model surprisal on silent stimuli?
+6. Does within-stimulus narrative position (three-act trajectory) explain condition-level effects that survive low-level partialling in single-stimulus designs?
+7. What is the residual saccade-locked variance contamination in shot-onset EEG ERSP without a synchronous eye tracker, and at what cohort size does ICA-only artifact rejection become sufficient?

manuscript/narrative-review/boxes/trends.md

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 # Trends Box: recent developments enabling the per-shot framing
 
-[Budget: ~200-250 words. Bullet list of 5-7 recent developments.
+Recent advances make the per-shot framing newly tractable.
 
-- **Whole-brain shot-cut response in adult intracranial EEG.** Nentwich et al. 2023: 6328 contacts in 23 patients across 43.6 minutes of film clips; triple-regressor against optical-flow magnitude, saccade onsets, and film-cut onsets; whole-brain saccade- and cut-locked responses with motion concentrated in occipitoparietal cortex.
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-- **Hidden-Markov-model recovery of event states from fMRI.** Baldassano et al. 2017: hierarchy of event boundaries from Sherlock-movie fMRI; hippocampal boundary signals predict subsequent free recall.
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-- **Cross-sectional developmental EEG-ISC.** Petroni et al. 2018: whole-clip EEG-ISC reliability across ages 6-44 during passive viewing of six naturalistic videos, peaking in childhood.
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-- **Silent abstract animation for MRI compliance.** Vanderwal et al. 2015: Inscapes, used by HBN itself; reliable network-level activity from a silent stimulus.
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-- **Multi-level cinematic-feature regression.** Kauttonen et al. 2015: multi-level cinematic features regressed against fMRI ISC; methodological template for shot-level feature annotation.
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-- **Open developmental EEG releases.** HBN-EEG and Studyforrest (Hanke et al. 2014) make large-N developmental datasets available for naturalistic-stimulus analysis at unprecedented scale.]
+- **Whole-brain shot-cut response in adult intracranial EEG.** Nentwich and colleagues 2023 recorded 6328 contacts in 23 patients across 43.6 minutes of film clips and regressed responses against optical-flow magnitude, saccade onsets, and film-cut onsets simultaneously, finding whole-brain saccade- and cut-locked responses with motion concentrated in occipitoparietal cortex [Nentwich2023SemanticNM].
+- **Hidden Markov model recovery of event states from fMRI.** Baldassano and colleagues 2017 recovered a hierarchy of event boundaries from Sherlock-movie fMRI, with hippocampal boundary signals predicting subsequent free recall [baldassano2017event].
+- **Cross-sectional developmental EEG-ISC.** Petroni and colleagues 2018 reported whole-clip EEG-ISC reliability across ages 6 to 44 during passive viewing of six naturalistic videos, peaking in childhood [Petroni2018TheVO].
+- **Silent abstract animation for MRI compliance.** Vanderwal and colleagues 2015 built Inscapes, used by HBN itself, with reliable network-level activity [Vanderwal2015InscapesAM].
+- **Multi-level cinematic-feature regression.** Kauttonen and colleagues 2015 regressed multi-level cinematic features against fMRI ISC, supplying a methodological template for shot-level feature annotation [Kauttonen2015OptimizingMF].
+- **Open developmental EEG releases.** HBN-EEG and Studyforrest [Hanke2014AH7] make large-N developmental datasets available for naturalistic-stimulus analysis at unprecedented scale.

manuscript/narrative-review/figures.md

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 <!-- Figure legends. ~400 words total (not counted in main text).
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 # Figure legends
 
 ## Figure 1. Four-perspective strand map
 
-[Caption placeholder. Compose in Phase 2 after the Phase 3 figure-qa report is in. Reference the four perspectives, the 15 corpus themes, the colour code (Okabe-Ito), and the legend's redundant shape-and-colour encoding.]
+Four research perspectives (psychophysics, action, language, emotion) mapped against 15 corpus themes. Filled coloured circles indicate substantial contribution from the perspective to the theme; outlined circles indicate absence or peripheral relevance. The four columns are colour-coded by perspective and the legend doubles as a colour key. Theme overlap is intentional: the perspectives interact at the per-shot ERSP level rather than partitioning variance cleanly.
 
 ## Figure 2. Naturalness gradient and developmental cohort coverage
 
-[Caption placeholder. X-axis: stimulus naturalness gradient. Y-axis: participant cohort. Markers: size by number of corpus cards, shape by modality. Highlight the (child, character animation, EEG ERSP) empty cell.]
+Stimulus naturalness on the x-axis (controlled gratings, static photographs, Heider-Simmel triangles, abstract animation, character animation, live-action film) versus participant cohort on the y-axis (adult, adolescent, child). Markers are sized by number of corpus cards and shaped and coloured by modality (fMRI as circle, EEG as square, MEG as triangle, intracranial EEG as diamond; behavioural-only entries as the letter b). The dashed yellow rectangle at (child, character animation) marks the target cell for per-shot EEG ERSP at the 0 to 500 ms window: existing coverage is whole-clip ISC, not per-shot ERSP.
 
 ## Figure 3. Gap matrix
 
-[Caption placeholder. 8 named gaps from `research/synthesis/gap-analysis.md` versus 4 prior-effort axes. Filled cells contain representative card slugs; empty cells highlighted.]
+Eight named gaps from the four-strand corpus (rows) versus four prior-effort axes (cinematic fMRI, naturalistic scalp EEG, intracranial and MEG, behavioural and eye-tracking; columns). Filled cells list a representative card slug; cells marked "no coverage" with a vermillion dashed border indicate uncovered combinations. Thirteen cells across the eight rows carry no coverage, defining the design space for per-shot developmental EEG ERSP.
 
 ## Figure 4. Predictions and falsification regions, per perspective
 
-[Caption placeholder. Each perspective (row) gives topography (with head schematic), band, latency, pre-registered falsification region. Reference the F5 carry-forward.]
+Each perspective (row) is named with its predicted topography (with a head schematic showing the topographic focus), band, latency, and pre-registered falsification region. Psychophysics is the covariate, not the prediction. Action predicts central-rolandic mu-band (8 to 13 Hz) ERD over electrodes C3, Cz, and C4, with possible beta rebound (15 to 25 Hz). Language predicts no signal locally; a surviving cluster in left-frontotemporal IC space (Lipkin atlas negative-control mask) falsifies the four-perspective ranking. Emotion predicts early occipital alpha desynchronisation (80 to 300 ms) and later frontal F3/F4 asymmetry (200 to 500 ms), at incompatible latencies and topographies. The cluster-level alpha for falsification is p < 0.05 corrected by mass-univariate permutation.
 
 ## Figure assembly notes (for Phase 3)
 
 - **Composer**: `/figures:scientific-figure` (multi-panel; the recommended composer per its skill description).
-- **Panel sources**:
-  - `/figures:svg-figure` for the matrix-style schematic panels (Figs 1, 3).
-  - `/figures:transparent-icons` for stimulus thumbnails (Fig 2 x-axis: gratings, photographs, Heider-Simmel triangles, abstract animation, character animation, live-action film) and brain-topo icons (Fig 4 topography column).
-  - `/figures:plot-styling` only if any panel needs data plotting; the current 4 figures are conceptual schematics, so it may not be needed.
+- **Panel sources**: `/figures:svg-figure` for matrix-style schematic panels (Figs 1, 3); `/figures:transparent-icons` for stimulus thumbnails (Fig 2 x-axis) and brain-topo icons (Fig 4 topography column); `/figures:plot-styling` only if any panel needs data plotting.
 - **QA**: `/figures:figure-qa` on every panel and on the composed figure. Address all findings before completion. No deferrals.

manuscript/narrative-review/glossary.md

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 <!-- Glossary. 10-15 defined terms. Each definition <=50 words.
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 # Glossary
 
-[Each entry follows the pattern: **Term (acronym if any).** Definition sentence(s), <=50 words.]
+**Event-related spectral perturbation (ERSP).** A time-frequency representation of the change in spectral power (and optionally inter-trial phase coherence) at each frequency and latency relative to an event, computed by averaging single-trial power spectrograms after subtracting a baseline window.
 
-**Event-related spectral perturbation (ERSP).** [Definition placeholder.]
+**Inter-subject correlation (ISC).** The Pearson correlation between time courses of different participants viewing the same stimulus, computed voxel-wise (fMRI) or component-wise (EEG and MEG); a stimulus-locked reliability metric.
 
-**Inter-subject correlation (ISC).** [Definition placeholder.]
+**Log luminance ratio (LLR).** The base-10 logarithm of the ratio of mean luminance in the first post-shot frame to the mean luminance in the last pre-shot frame; a per-shot stimulus-side regressor of the visual transient at shot onset.
 
-**Log luminance ratio (LLR).** [Definition placeholder.]
+**Adaptive mixture independent component analysis (AMICA).** A multi-model extension of ICA that estimates a mixture of ICA decompositions, used in EEGLAB-style pipelines for artifact-resistant source separation.
 
-**Adaptive mixture independent component analysis (AMICA).** [Definition placeholder.]
+**IC classification (ICLabel).** An automated classifier that labels independent components as brain, muscle, eye, heart, line noise, channel noise, or other.
 
-**IC classification (ICLabel).** [Definition placeholder.]
+**Mu rhythm.** An 8 to 13 Hz oscillation over central rolandic electrodes (C3, Cz, C4) that desynchronises during motor execution and during observation of others' actions.
 
-**Mu rhythm.** [Definition placeholder.]
+**Event-related desynchronisation (ERD).** A decrease in spectral power in a specific frequency band time-locked to an event, interpreted as cortical activation in the band's reference resting state.
 
-**Event-related desynchronisation (ERD).** [Definition placeholder.]
+**Frontal alpha asymmetry.** The difference between right and left frontal alpha-band (8 to 13 Hz) power, traditionally framed as an approach-withdrawal index; recent meta-analyses report smaller effects and reliability concerns.
 
-**Frontal alpha asymmetry.** [Definition placeholder.]
+**Default-mode network (DMN).** A set of cortical regions including medial prefrontal cortex, posterior cingulate cortex, and lateral parietal cortex that show coordinated activity during internally directed cognition, narrative comprehension, and rest.
 
-**Default-mode network (DMN).** [Definition placeholder.]
+**Theory of mind (ToM).** The cognitive capacity to attribute mental states (beliefs, desires, intentions) to self and others.
 
-**Theory of mind (ToM).** [Definition placeholder.]
+**Temporal response function (TRF).** A linear filter that maps a continuous stimulus feature to a continuous neural response, fit via regularised regression.
 
-**Temporal response function (TRF).** [Definition placeholder.]
+**Baby schema.** A set of infantile physical features (large head, large eyes, round cheeks) that elicit attentional, affective, and caregiving responses.
 
-**Baby schema.** [Definition placeholder.]
+**Naturalistic stimulus.** A continuous, ecologically valid stimulus (typically a film, audiobook, or video game) presented without trial-by-trial structuring. Naturalness is a continuum from controlled gratings to live-action film, with character animation and abstract Heider-Simmel triangles as intermediate points (Figure 2).
 
-**Naturalistic stimulus.** [Definition placeholder.]
+**Event segmentation.** The cognitive process of parsing continuous experience into discrete events at moments of high prediction error, organised hierarchically.
 
-**Event segmentation.** [Definition placeholder.]
-
-**Temporal receptive window.** [Definition placeholder.]
+**Temporal receptive window.** The span of preceding time over which a brain region integrates information; ranges from milliseconds in primary sensory cortex to tens of seconds in default-mode regions.