v2 phase 1: TiCS scaffold via manuscript-formatting (#58)

Author: neuromechanist

manuscript/narrative-review/STRUCTURE.md

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+# Structure — TiCS Forum Review
+
+Built by the `manuscript:manuscript-formatting` skill (v0.5.0) in v2 Phase 1. This document maps each file to the *Trends in Cognitive Sciences* (TiCS, Cell Press) Forum Review submission element it serves. The next phase (`manuscript:manuscript-writing`) fills the placeholders.
+
+## Files and TiCS compliance map
+
+| File | TiCS element | Word budget | Notes |
+|---|---|---|---|
+| `frontmatter.yaml` | Title, authors, affiliations, corresponding author, ORCID | n/a | Per skill's "Title page" checklist item |
+| `highlights.md` | Highlights | 3-5 bullets, <=85 chars each | TiCS / Cell Press convention |
+| `abstract.md` | Abstract | ~80-120 words, no citations | TiCS abstract limit |
+| `sections/01_introduction.md` | Section 1: Introduction (the per-shot turn) | ~450 | |
+| `sections/02_scaffold.md` | Section 2: Four-perspective scaffold | ~600 | |
+| `sections/03_psychophysics.md` | Section 3: Psychophysics (bottom-up floor) | ~500 | |
+| `sections/04_action.md` | Section 4: Action (mu-band ERD and event segmentation) | ~500 | |
+| `sections/05_language.md` | Section 5: Language (5a non-transfer + 5b silent-narrative) | ~600 | I5 split applied |
+| `sections/06_emotion.md` | Section 6: Emotion (two latency-distinct predictions) | ~500 | |
+| `sections/07_synthesis.md` | Section 7: Synthesis (integration, falsifiability, open questions) | ~450 | F4/F5 applied |
+| `boxes/box1_anchor.md` | Box 1 (HBN-EEG R3 anchor cohort) | ~180 | F4 anchor case rebuilt |
+| `boxes/trends.md` | Trends Box (recent developments) | ~200-250 | TiCS convention |
+| `boxes/outstanding-questions.md` | Outstanding Questions Box | 5-7 questions | TiCS convention |
+| `glossary.md` | Glossary | 10-15 terms | TiCS convention |
+| `figures.md` | Figure legends | ~400 (not in main count) | 4 figures planned (Phase 3) |
+| `references.md` | References | 80-120 entries | Cell Press numbered (Vancouver-like) |
+| `refs.bib` | Source BibTeX | 94 entries | Already built (Phase 1) |
+
+## Main-text budget total
+
+Sections 1-7: ~3610 words. Inside the TiCS Forum Review ~3500-4000-word ceiling.
+
+## Submission checklist (from `manuscript:manuscript-formatting` SKILL.md)
+
+This section tracks the submission checklist items the skill enumerates. Each item is marked with the phase that will satisfy it.
+
+- [ ] **Manuscript formatted per journal template** — Phase 5 (final assembly via the formatting skill again)
+- [x] **Title page: title, authors, affiliations, corresponding author, ORCID** — `frontmatter.yaml` (Phase 1; placeholders to be filled by author)
+- [ ] **Abstract within word limit** — Phase 2 (manuscript-writing produces; Phase 5 verifies)
+- [ ] **Keywords provided (if required)** — TiCS does not require keywords for Forum Reviews; not applicable
+- [ ] **Main text within page/word limit** — Phase 2 budget + Phase 5 verification
+- [ ] **Figures as separate high-resolution files (typically 300+ DPI)** — Phase 3 via `figures:scientific-figure` composer
+- [ ] **Figure captions in a separate list** — `figures.md` (Phase 2 drafts; Phase 5 finalises)
+- [ ] **Tables formatted per journal style** — no tables planned for this review
+- [x] **References complete and consistently formatted** — `refs.bib` built (Phase 1); numbering applied in Phase 5
+- [ ] **Supplementary materials prepared separately** — none planned
+- [ ] **Cover letter drafted** — Phase 5 (skill's cover-letter template, then humanizer pass)
+- [ ] **`manuscript:humanizer` natural-writing pass** — Phase 4
+- [ ] **Conflict of interest statement** — Phase 5 (author-provided)
+- [ ] **Data availability statement** — Phase 5 (HBN-EEG R3 is public; statement noted in Phase 5)
+- [ ] **Ethics approval statement** — n/a (review article; no new data)
+- [ ] **Author contributions (CRediT format if required)** — Phase 5
+- [ ] **Suggested reviewers** — Phase 5 (author-provided)
+
+## TiCS scaffolding decisions not covered by the skill
+
+The skill provides a generic IMRAD framework plus journal-specific templates for IEEE / Nature / PNAS / PLoS ONE / Elsevier. TiCS (Cell Press) Forum Reviews use a non-IMRAD structure that the skill does not enumerate explicitly. The following TiCS-specific decisions are applied on top of the skill's framework based on public TiCS author guidelines:
+
+- **No IMRAD.** TiCS Forum Reviews use thematic sections, not Introduction/Methods/Results/Discussion. The seven sections here are thematic (Introduction, Scaffold, Psychophysics, Action, Language, Emotion, Synthesis).
+- **Highlights**: 3-5 short bullets at the top, each <=85 characters (Cell Press / Elsevier house style enforced via the skill's Elsevier checklist row).
+- **Trends Box**: a callout box listing recent developments that make the topic timely.
+- **Outstanding Questions Box**: 5-7 forward-looking research questions.
+- **Glossary**: 10-15 defined terms accessible to non-specialist readers.
+
+## Carry-forwards from v1 self-review
+
+From `direction-papers/movie-ersp-direction-review.md` (kept in the project for reference):
+
+- **F1 (Category G cardinality 12 -> 7)**: Section 5a will state "all seven Category G cards (and 12 cards corpus-wide) carry `transfer-to-silent: no`".
+- **F2 (Schubring vs Codispoti DOI)**: `refs.bib` header documents; body prose cites Codispoti.
+- **F3 (stray refs)**: 3 stray keys removed from `refs.bib` (already applied).
+- **F4 (anchor case)**: Section 7.2 + Box 1 rebuild around Petroni-Cohen 2018 + partly-validated pipeline.
+- **F5 (falsifiability)**: Section 7.3 names a topographic-and-band rejection region.
+- **I1-I5**: handled in the per-section placeholders.
+- **S2 (italicised *The Present*)**: enforced throughout via copy-edit.
+
+## Next phase
+
+`manuscript:manuscript-writing` is invoked per section file. Each invocation will receive the placeholders here, the source material under `direction-papers/` and `research/`, and the TiCS section budget for that file.

manuscript/narrative-review/abstract.md

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+<!-- TiCS Abstract. ~80-120 words. No in-text citations. Filled by
+manuscript:manuscript-writing in v2 Phase 2. -->
+
+# Abstract
+
+[Opening sentence: the field has moved from whole-clip ISC to event-locked methods.]
+
+[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.]
+
+[Sentence 3: we review the four-perspective corpus that constrains the design space.]
+
+[Sentence 4: psychophysics, action, language, and emotion make divergent and partly-falsifiable predictions about the 0 to 500 ms post-shot-onset window.]
+
+[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.]
+
+<!-- Verify <= 120 words at Phase 5. -->

manuscript/narrative-review/boxes/box1_anchor.md

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+<!-- Box 1: HBN-EEG R3 anchor cohort. Budget: ~180 words.
+Filled by manuscript:manuscript-writing in v2 Phase 2.
+
+Carry-forwards from v1 self-review:
+- F4 (anchor case): descriptive surface attributes live here, NOT as evidential support for the direction.
+-->
+
+# 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.]

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

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+<!-- Outstanding Questions Box. 5-7 forward-looking research questions.
+TiCS convention; not in the manuscript-formatting SKILL.md.
+Filled by manuscript:manuscript-writing in v2 Phase 2.
+-->
+
+# 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.
+
+1. [Q1: per-shot ERSP in developmental cohort survives LLR and motion-energy partialling at 0-500 ms?]
+
+2. [Q2: mu-band ERD over central rolandic clusters elicited by animated-character action observation as it is by adult hand-action observation?]
+
+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?]
+
+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?]
+
+5. [Q5: can a multimodal vision-language embedding regressor substitute for language-model surprisal on silent stimuli?]
+
+6. [Q6: does within-stimulus narrative position (three-act trajectory) explain condition-level effects that survive low-level partialling in single-stimulus designs?]
+
+7. [Q7: residual saccade-locked variance contamination without synchronous eye tracker, and the cohort size at which ICA-only artifact rejection becomes sufficient?]]

manuscript/narrative-review/boxes/trends.md

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+<!-- Trends Box. ~200-250 words. Recent developments that make the topic timely.
+TiCS convention; not in the manuscript-formatting SKILL.md but is required for TiCS Forum Reviews.
+Filled by manuscript:manuscript-writing in v2 Phase 2.
+-->
+
+# Trends Box: recent developments enabling the per-shot framing
+
+[Budget: ~200-250 words. Bullet list of 5-7 recent developments.
+
+- **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.
+
+- **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.
+
+- **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.
+
+- **Silent abstract animation for MRI compliance.** Vanderwal et al. 2015: Inscapes, used by HBN itself; reliable network-level activity from a silent stimulus.
+
+- **Multi-level cinematic-feature regression.** Kauttonen et al. 2015: multi-level cinematic features regressed against fMRI ISC; methodological template for shot-level feature annotation.
+
+- **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.]

manuscript/narrative-review/figures.md

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+<!-- Figure legends. ~400 words total (not counted in main text).
+Figures themselves are built in v2 Phase 3 via /figures:scientific-figure composer.
+Figure legends drafted by manuscript:manuscript-writing in v2 Phase 2.
+-->
+
+# 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.]
+
+## 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.]
+
+## 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.]
+
+## 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.]
+
+## 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.
+- **QA**: `/figures:figure-qa` on every panel and on the composed figure. Address all findings before completion. No deferrals.

manuscript/narrative-review/frontmatter.yaml

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+# TiCS Forum Review — frontmatter.
+#
+# Built by manuscript:manuscript-formatting in v2 Phase 1.
+# Matches the skill's "Title page" submission-checklist item.
+
+title: "Per-shot EEG during naturalistic film: a four-perspective developmental review"
+short_title: "Per-shot EEG in development"
+article_type: "Forum Review"
+target_journal: "Trends in Cognitive Sciences"
+
+authors:
+  - name: "Seyed Yahya Shirazi"
+    affiliation: 1
+    email: "shirazi@ieee.org"
+    orcid: ""    # to be filled by author
+    corresponding: true
+
+affiliations:
+  - id: 1
+    name: "Open Science Collective"
+
+keywords: []   # TiCS Forum Reviews do not require keywords; left empty intentionally
+
+status: "v2 Phase 1 scaffold (manuscript-formatting)"
+date: "2026-05-20"
+
+# Word budget map (TiCS Forum Review)
+word_budget:
+  main_text: 4000        # ceiling
+  abstract: 120          # ceiling
+  highlights_chars_per_bullet: 85
+  references_target_low: 80
+  references_target_high: 120
+  figures_min: 3
+  figures_max: 5
+
+# Compliance flags for Phase 5 verification
+compliance:
+  no_em_dashes: true
+  no_emojis: true
+  abbreviations_defined_on_first_use: true
+  italicise_film_titles: true

manuscript/narrative-review/glossary.md

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+<!-- Glossary. 10-15 defined terms. Each definition <=50 words.
+TiCS convention; not in the manuscript-formatting SKILL.md but is required for TiCS Forum Reviews.
+Filled by manuscript:manuscript-writing in v2 Phase 2.
+-->
+
+# Glossary
+
+[Each entry follows the pattern: **Term (acronym if any).** Definition sentence(s), <=50 words.]
+
+**Event-related spectral perturbation (ERSP).** [Definition placeholder.]
+
+**Inter-subject correlation (ISC).** [Definition placeholder.]
+
+**Log luminance ratio (LLR).** [Definition placeholder.]
+
+**Adaptive mixture independent component analysis (AMICA).** [Definition placeholder.]
+
+**IC classification (ICLabel).** [Definition placeholder.]
+
+**Mu rhythm.** [Definition placeholder.]
+
+**Event-related desynchronisation (ERD).** [Definition placeholder.]
+
+**Frontal alpha asymmetry.** [Definition placeholder.]
+
+**Default-mode network (DMN).** [Definition placeholder.]
+
+**Theory of mind (ToM).** [Definition placeholder.]
+
+**Temporal response function (TRF).** [Definition placeholder.]
+
+**Baby schema.** [Definition placeholder.]
+
+**Naturalistic stimulus.** [Definition placeholder.]
+
+**Event segmentation.** [Definition placeholder.]
+
+**Temporal receptive window.** [Definition placeholder.]

manuscript/narrative-review/highlights.md

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+<!-- TiCS Highlights. 3-5 bullets. Each <=85 characters. Per Cell Press / Elsevier
+house style. Verified at Phase 5. Filled by manuscript:manuscript-writing
+in v2 Phase 2. -->
+
+# Highlights
+
+- [bullet 1: 1-line claim about the per-shot turn in naturalistic EEG]
+- [bullet 2: 1-line claim that four perspectives diverge in their per-shot predictions]
+- [bullet 3: 1-line claim about LM-regressor non-transfer to silent stimuli]
+- [bullet 4: 1-line claim about the developmental empty-cell]
+- [bullet 5: 1-line claim about HBN-EEG R3 as the testbed]

manuscript/narrative-review/references.md

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+<!-- References. Numbered Cell Press style.
+Sources: refs.bib (94 entries).
+Built in Phase 5 by extracting cited keys from the assembled manuscript in order of first appearance, then formatting per Cell Press house style.
+-->
+
+# References
+
+[Cell Press numbered references go here in Phase 5 final assembly. Format per Cell Press house style (numbered, Vancouver-like).
+
+Build process:
+1. Concatenate per-section files plus boxes plus glossary into a single body text.
+2. Extract `[CiteKey]` references in order of first appearance.
+3. Map each key to its `refs.bib` entry.
+4. Emit a numbered list using Cell Press format.
+5. Replace `[CiteKey]` and `[Key1; Key2]` in the body with `[N]` and `[N,M]` respectively.
+
+The `refs.bib` file (94 entries) is the source of truth.]
+
+## Note on F2 carry-forward (Schubring vs Codispoti)
+
+The body cites the alpha-band-and-emotion review under "Codispoti and colleagues (2023), Psychophysiology, DOI 10.1111/psyp.14438". The BibTeX key is `Codispoti2023AlphabandOA`. The internal corpus slug `schubring-schupp-2023-alpha-emotion` is retained inside `research/collection/emotion/` for stable cross-references and does not appear in published prose.