manuwright 1.10.6__py3-none-any.whl

manuwright/.agents/plugins/marketplace.json

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+{
+  "name": "manuwright",
+  "interface": { "displayName": "ManuWright" },
+  "plugins": [
+    {
+      "name": "manuwright",
+      "source": { "source": "local", "path": "./" },
+      "policy": { "installation": "AVAILABLE", "authentication": "ON_INSTALL" },
+      "category": "Productivity"
+    }
+  ]
+}

manuwright/.claude-plugin/marketplace.json

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+{
+  "$schema": "https://anthropic.com/claude-code/marketplace.schema.json",
+  "name": "manuwright",
+  "description": "manuwright manuscript engine adapters",
+  "owner": { "name": "Sang-Min Park" },
+  "plugins": [
+    { "name": "manuwright", "description": "Evidence-bound medical manuscript workflow", "source": "./", "category": "productivity" }
+  ]
+}

manuwright/.claude-plugin/plugin.json

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+{
+  "name": "manuwright",
+  "version": "1.10.6",
+  "description": "Evidence-bound medical manuscript workflow: plan-first gates, citation/number grounding, verification profiles. Requires the manuwright CLI of the same version.",
+  "author": { "name": "Sang-Min Park" },
+  "homepage": "https://github.com/grotyx/Academic_writing_c_claudecode",
+  "hooks": "./hooks/hooks.json"
+}

manuwright/.codex-plugin/plugin.json

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+{
+  "name": "manuwright",
+  "version": "1.10.6",
+  "description": "Evidence-bound medical manuscript workflow. Requires the manuwright CLI of the same version.",
+  "author": { "name": "Sang-Min Park" },
+  "homepage": "https://github.com/grotyx/Academic_writing_c_claudecode",
+  "skills": "./skills/",
+  "hooks": "./hooks/hooks.json",
+  "interface": { "displayName": "ManuWright", "shortDescription": "Medical manuscript workflow gates", "category": "Productivity", "capabilities": ["Instructions", "Lifecycle hooks"] }
+}

manuwright/Style/style_guide.md

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+# Style Guide
+
+`Style/` is separate from `knowledge/`.
+
+Use `knowledge/` for manuscript references: reference PDFs, evidence summaries, and citation support. Use `Style/` for writing-style anchors: own papers, landmark papers, and target-journal house style.
+
+PDFs are copyright-protected and must remain local only. Store PDFs under `Style/PDF/`; PDF files in that tree are gitignored.
+
+Measured style: `manuwright style learn <papers>` measures full-text papers (your own, landmark, target journal; PDF, DOCX, MD, TXT) per section and feeds the result, with model paragraphs, into every section style card (`manuwright style card <section>`). That profile stays in the personal library and is never copied into a paper.
+
+Use `Style/terminology.md` as the project vocabulary registry. It defines preferred terms, forbidden terms, first-definition rules, and context of use.
+
+---
+
+## Folder Roles
+
+| Location | Role |
+|---|---|
+| `Style/PDF/own/` | Source PDFs of the author's own published papers |
+| `Style/own/` | Extracted own-paper style anchors: terminology, team voice, reusable Methods phrasing, key claims |
+| `Style/PDF/landmark/` | Source PDFs of landmark/high-quality papers |
+| `Style/landmark/` | Extracted framing anchors: argument structure, gap framing, Discussion logic |
+| `Style/PDF/target_journal/` | Source PDFs from the target journal |
+| `Style/target_journal/` | Extracted house-style anchors: section flow, sentence rhythm, reporting conventions |
+| `Style/terminology.md` | Preferred/forbidden terminology registry used during drafting, polish, and linting |
+
+---
+
+## PDF to MD Mirror Rule
+
+Use matching basenames between PDF and extracted markdown.
+
+```text
+Style/PDF/own/park_2025_bjj_bed_md.pdf
+Style/own/park_2025_bjj_bed_md.md
+
+Style/PDF/landmark/weber_2007_sciatica.pdf
+Style/landmark/weber_2007_sciatica.md
+
+Style/PDF/target_journal/smith_2024_lumbar_rct.pdf
+Style/target_journal/smith_2024_lumbar_rct.md
+```
+
+Use `author_year_keyword` naming.
+
+If a downloaded PDF already has a generic publisher filename and is not renamed, keep the extracted markdown basename identical to the PDF and record the human-readable citation in `Style/landmark/index.md` or the relevant folder index.
+
+---
+
+## Copyright and Extraction Policy
+
+Style anchor markdown files should extract patterns, not reproduce the paper.
+
+Recommended:
+- Short phrases only when necessary
+- Generalized sentence patterns with placeholders
+- Section flow and paragraph function
+- Preferred vocabulary and forbidden vocabulary
+- Quantitative style metrics
+- Qualitative writing observations
+
+Avoid:
+- Full paragraph copying
+- Large verbatim excerpts
+- Reusing distinctive sentences as-is
+
+---
+
+## Extraction Framework
+
+Each style anchor should include both quantitative and qualitative extraction.
+
+### 1. Own Papers
+
+Purpose: preserve the author's research-team voice and field-specific consistency.
+
+Quantitative extraction:
+- Section word counts: Abstract, Introduction, Methods, Results, Discussion
+- Sentence length: mean and range by section
+- Paragraph count by section
+- Abbreviation definitions and first-use pattern
+- Preferred terminology frequency, e.g., BESS, ODI, VAS, CPK
+- Reusable Methods phrase count, e.g., design, ethics, outcomes, statistics
+- Citation density by section, e.g., citations per paragraph
+- Table/Figure count and placement
+
+Qualitative extraction:
+- Team voice: conservative, direct, clinically oriented, methodological
+- Preferred terminology and terms to avoid
+- Reusable Methods boilerplate patterns
+- Standard outcome definitions
+- Standard limitation wording
+- Key claims that can support future Claim -> Citation Mapping
+- Phrasing that should remain consistent across related papers
+
+### 2. Landmark Papers
+
+Purpose: learn argument quality, framing, and Discussion logic.
+
+Quantitative extraction:
+- Introduction paragraph structure, e.g., burden -> treatment -> gap -> aim
+- Number of claims per Introduction paragraph
+- Citation density and citation clustering
+- Discussion paragraph count and function distribution
+- Hedging marker frequency, e.g., may, suggests, appears, indicates
+- Comparison frequency, e.g., consistent with, differs from, in contrast to
+- Limitation count and placement
+
+Qualitative extraction:
+- How the clinical problem is framed
+- How the evidence gap is made important
+- How the study aim follows from the gap
+- How prior studies are compared without overclaiming
+- How negative or neutral findings are framed
+- How limitations are acknowledged without weakening the whole paper
+- Argument moves worth adapting, not copying
+
+### 3. Target-Journal Papers
+
+Purpose: match the target journal's house style.
+
+Quantitative extraction:
+- Title length and structure
+- Abstract word count and subheading style
+- Section word counts
+- Mean sentence length by section
+- Subheading depth and naming conventions
+- Reference style: bracket vs superscript, author cutoff, DOI use
+- Table/Figure density and caption length
+- Results text density, e.g., number of numeric values repeated outside tables
+- P-value and CI formatting patterns
+
+Qualitative extraction:
+- Title and abstract rhythm
+- How early the study design appears
+- How sparse or detailed the Results narrative is
+- Whether Methods are procedural or concise
+- Preferred transition phrases
+- Strength of conclusion language
+- Journal-specific formatting habits
+- Things not to imitate because they are topic-specific rather than journal-style
+
+---
+
+## Recommended Style Anchor Template
+
+```markdown
+# Style Anchor: Author Year Journal Keyword
+
+## Source
+- PDF: Style/PDF/[own|landmark|target_journal]/author_year_keyword.pdf
+- Anchor type: own / landmark / target_journal
+- Reason for inclusion:
+
+## Quantitative Metrics
+| Metric | Value | Notes |
+|---|---:|---|
+| Title words | | |
+| Abstract words | | |
+| Introduction paragraphs | | |
+| Methods paragraphs | | |
+| Results paragraphs | | |
+| Discussion paragraphs | | |
+| Mean sentence length | | |
+| Tables/Figures | | |
+| Citation density | | |
+
+## Qualitative Style Notes
+- Overall tone:
+- Section flow:
+- Claim strength:
+- Hedging style:
+- Results reporting style:
+- Discussion logic:
+
+## Reusable Patterns
+| Context | Generalized Pattern |
+|---|---|
+| Study design | This was a [design] study conducted at [setting] between [dates]. |
+| Primary outcome | The primary outcome was [endpoint] at [time point]. |
+| Main finding | The principal finding was that [finding], suggesting [cautious interpretation]. |
+
+## Preferred Vocabulary
+| Concept | Use | Avoid |
+|---|---|---|
+| | | |
+
+## Do Not Imitate
+-
+```

manuwright/Style/terminology.md

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+# Terminology Registry
+
+> Field-standard terminology for manuscript drafting and lint checks.
+> This file belongs under `Style/` because it controls writing style and vocabulary, not citation evidence.
+> Confirm project-specific terms in `drafts/draft_plan.md` before drafting.
+
+---
+
+## How to Use
+
+- Use the `Preferred Term` exactly unless the target journal requires otherwise.
+- Do not use terms listed under `Forbidden Terms`.
+- Define abbreviations once at first use in the main text. Abstract is treated independently.
+- If two terms are both acceptable, choose one in the draft plan and use it consistently.
+- Add project-specific terminology before drafting when a new procedure, outcome, disease entity, or group name is introduced.
+- Do not substitute one measurement instrument for another. If the dataset measured NRS, report NRS; if it measured VAS, report VAS.
+- If the target journal uses British spelling, record that decision in `drafts/draft_plan.md` before drafting.
+
+---
+
+## Scope and Override Rules
+
+| Rule | Default | Override When |
+|---|---|---|
+| Term source | This registry controls preferred vocabulary | Target journal instructions conflict |
+| Measurement names | Use the exact instrument measured | None; never convert VAS to NRS or NRS to VAS in text |
+| Procedure names | Use specific procedure terms | A broader pooled category is preplanned |
+| Spelling | US spelling default | Journal requires British spelling |
+| Abbreviations | Define once at first use | Very common journal-approved abbreviations may remain undefined only if allowed |
+| Forbidden terms | Replace before submission | A direct quotation or reviewer comment requires the original term |
+
+---
+
+## Surgical Technique Terms
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| BESS technique | biportal endoscopic spine surgery (BESS) | biportal endoscopy; biportal endoscopic surgery; biportal surgery | Define at first main-text use | Introduction, Methods, Discussion | General technique name |
+| BED procedure | biportal endoscopic discectomy (BED) | biportal endoscopic lumbar discectomy | Define if discectomy-specific | Methods, Results | Use BED after definition |
+| Stenosis decompression | biportal endoscopic decompressive laminectomy | biportal endoscopic laminectomy | Define if used repeatedly | Methods | Use full procedural name for stenosis |
+| Microscopic comparator | microscopic discectomy (MD) | open discectomy; conventional discectomy; open microscopic discectomy | Define at first use | Methods, Results | Comparator term for discectomy studies |
+| Microscopic pooled comparator | microscopic spinal surgery (MSS) | conventional microscopic surgery | Define at first use | Methods, Discussion | Pooled comparator term |
+| Bilateral decompression approach | unilateral laminotomy for bilateral decompression (ULBD) | bilateral decompression alone | Define at first use | Methods | Use when describing unilateral approach |
+| Minimally invasive spine surgery | minimally invasive spine surgery (MISS) | MIS spine; MIS | Define at first use | Introduction, Discussion | Avoid standalone MIS |
+
+---
+
+## Anatomy and Operative Field
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Endoscope portal | viewing portal | endoscopic portal | No definition required | Methods | Scope insertion portal |
+| Instrument portal | working portal | instrument portal | No definition required | Methods | Instrument insertion portal |
+| Interlaminar area | interlaminar space | interlaminar window | No definition required | Methods | |
+| Paraspinal muscles | paraspinal muscles | paravertebral muscles | No definition required | Introduction, Methods | Includes multifidus when relevant |
+| Ligament | ligamentum flavum | yellow ligament | No definition required | Methods | |
+| Isthmus | pars interarticularis | pars | No definition required | Methods | Do not confuse with facet joint |
+| Dural sac | thecal sac | dura sac | No definition required | Methods, Complications | |
+| Nerve root direction | traversing root; exiting root | nerve root only when direction matters | No definition required | Methods | Use direction-specific term when needed |
+| Posterior element | spinous process | spinal process | No definition required | Methods | |
+| Laminar structure | lamina | vertebral plate | No definition required | Methods | |
+| Facet | facet joint | zygapophyseal joint | No definition required | Methods | Use facet joint for consistency |
+
+---
+
+## Instruments and Equipment
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Muscle dissector | Cobb elevator | Cobb's elevator | No definition required | Methods | |
+| Bone/ligament remover | Kerrison punch; Kerrison rongeur | Kerrison forceps | No definition required | Methods | Choose one term and use consistently |
+| Disc fragment remover | pituitary rongeur | pituitary forceps | No definition required | Methods | |
+| Hemostasis device | bipolar radiofrequency cautery | bipolar electrocautery | No definition required | Methods | Preferred wording in BESS manuscripts |
+| Microscopic retractor | Taylor retractor | Taylor's retractor | No definition required | Methods | |
+| Bone drill | high-speed burr | high speed drill | No definition required | Methods | |
+| Endoscope | 30-degree arthroscope; 4-mm endoscope | scope | Define specifications if needed | Methods | Avoid special symbols if journal formatting is uncertain |
+| Irrigation | saline irrigation | continuous irrigation | No definition required | Methods | Pressure can be stated as 30-40 mmHg |
+| Drainage | Zimmer Biomet drain system | drain bottle | No definition required | Methods | Brand only when methodologically relevant |
+
+---
+
+## Outcome Measures
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Disability | Oswestry Disability Index (ODI) | Oswestry score; Oswestry index | Define at first use | Methods, Results | Version 2.0 if applicable; MCID 12.8 points when justified |
+| Pain score | visual analog scale (VAS) or numeric rating scale (NRS), according to the instrument measured | mixing VAS and NRS; substituting VAS for NRS; substituting NRS for VAS | Define at first use | Methods, Results | Use the exact measured scale and range |
+| Quality of life | European Quality of Life-5 Dimensions (EQ-5D-5L) | EQ5D; EuroQol only | Define at first use | Methods, Results | Higher scores indicate better health status |
+| Neuropathic pain | painDETECT questionnaire | pain detect; PainDetect | Define at first use | Methods, Results | Score range -1 to 38 |
+| Comorbidity | Charlson Comorbidity Index (CCI) | Charlson score | Define at first use | Methods, Table 1 | |
+| Anesthetic risk | American Society of Anesthesiologists physical status (ASA PS) | ASA score | Define at first use | Methods, Table 1 | |
+| Scar assessment | Patient and Observer Scar Assessment Scale (POSAS) | scar score | Define at first use | Methods, Results | |
+| Patient-reported outcomes | patient-reported outcome measures (PROMs) | patient questionnaire | Define at first use | Introduction, Methods | PRO acceptable as singular concept if defined |
+| Muscle injury marker | creatine phosphokinase (CPK) ratio | CPK index; CK ratio | Define at first use | Methods, Results | Postoperative day 1 CPK divided by preoperative CPK |
+
+---
+
+## CPK and Muscle Injury Terms
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Enzyme name | creatine phosphokinase (CPK) | creatinine phosphokinase | Define at first use | Methods, Results | Creatinine is incorrect |
+| Serum marker | serum CPK level | serum CK level | Define CPK once | Methods, Results | Use CPK consistently |
+| Ratio variable | CPK ratio | CPK index | Define formula | Methods, Results | Ratio = postoperative CPK / preoperative CPK |
+
+---
+
+## Classification Systems
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Lumbar stenosis severity | Schizas classification | Schizas grade only | Define at first use | Methods, Table 1 | Grade B or higher can define central stenosis if protocol states so |
+| Spondylolisthesis | Meyerding classification | Meyerding grade only | Define at first use | Methods | Grade II or higher may be exclusion criterion |
+| Scoliosis angle | Cobb angle | Cobb's angle | No definition required | Methods | State threshold if used |
+| Comorbidity classification | Charlson Comorbidity Index | CCI score only before definition | Define at first use | Methods, Table 1 | |
+| Anesthetic risk classification | ASA physical status | ASA score | Define at first use | Methods, Table 1 | |
+
+---
+
+## Study Design Terms
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Surgical trial blinding | assessor-blind | double-blind | Define in Methods | Title, Abstract, Methods | Surgical RCTs are usually not double-blind |
+| Participant blinding | single-blind | patient-blind | Define in Methods | Methods | Use only if applicable |
+| Analysis set | modified intention-to-treat (mITT) | ITT if not true ITT | Define in Methods | Methods, Results | Use only when randomized patients who underwent surgery were analyzed |
+| Protocol-compliant set | per-protocol (PP) | protocol analysis | Define in Methods | Methods, Sensitivity | |
+| Noninferiority design | non-inferiority trial | equivalence trial | Define in Title/Methods | Title, Methods | One-sided design |
+| Equivalence design | equivalence trial | non-inferiority trial | Define in Title/Methods | Title, Methods | Two-sided design |
+| Noninferiority threshold | non-inferiority margin | equivalence margin | Define in Methods | Methods | Justify clinically, e.g., ODI MCID |
+| Trial structure | parallel-group trial | parallel trial | Define in Methods | Methods | |
+| Center count | multicenter | multi-center | No definition required | Title, Methods | Use multicentre only if target journal uses British spelling |
+| Randomization method | computer-generated randomization | random allocation | Define in Methods | Methods | |
+| Block randomization | block randomization | blocked randomization | Define if used | Methods | Include block size when appropriate |
+| Allocation concealment | allocation concealment | allocation hiding | Define mechanism | Methods | eCRF or sealed envelopes |
+
+---
+
+## Statistical Terms and Reporting
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Mean with variability | mean (SD) | mean +/- SD; mean ± SD | No definition required | Tables, Abstract | Use journal style; current default is parentheses |
+| Median with variability | median (IQR) | median +/- IQR; median ± IQR | No definition required | Tables | |
+| Confidence interval | 95% confidence interval (CI) | 95% confidence limits | Define at first use | Methods, Results | |
+| Exact p-value | p = 0.023 | p < 0.05; p = NS; p = 0.000 | No definition required | Results, Tables | Use exact p when >=0.001; use p < 0.001 when very small |
+| Significance threshold | two-sided p < 0.05 | two-tailed p | No definition required | Methods | |
+| Normality test | Shapiro-Wilk test | Kolmogorov-Smirnov test | No definition required | Methods | Default unless sample-size rationale says otherwise |
+| Small-sample categorical test | Fisher's exact test | chi-square test for small cells | No definition required | Methods | |
+| Nonparametric two-group test | Mann-Whitney U test | Wilcoxon rank-sum test | No definition required | Methods | Same test, but use Mann-Whitney for consistency |
+| Repeated continuous outcomes | linear mixed model | repeated-measures ANOVA | No definition required | Methods | Preferred for repeated outcome trajectories |
+| Missing data method | last observation carried forward (LOCF) | last value carried forward | Define if used | Methods | Only if preplanned |
+| Statistical software | Stata/MP | STATA; Stata MP | No definition required | Methods | Replace if actual software differs |
+
+---
+
+## Complications and Adverse Events
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Safety events | adverse events | complications when broader safety is meant | Define if needed | Methods, Results | Use adverse events for safety analysis |
+| Surgical technical events | complications | adverse events if only technical events are meant | No definition required | Results, Discussion | |
+| Dural injury | dural tear | durotomy if unintended tear | No definition required | Results, Discussion | Dural tear = unintended tear |
+| Dural opening | durotomy | dural tear when intentional | No definition required | Methods, Results | Intentional or unintentional dural incision |
+| Hematoma | epidural hematoma | subdural hematoma | No definition required | Results | Distinguish location |
+| Wound event | wound dehiscence | wound opening | No definition required | Results | |
+| Nerve event | nerve root injury | radicular injury | No definition required | Results | |
+| Recurrent disc event | recurrent disc herniation | re-herniation; reherniation | No definition required | Results, Discussion | |
+| Decompression event | incomplete decompression | inadequate decompression | No definition required | Results | |
+| Additional surgery | reoperation | re-operation | No definition required | Results, Discussion | Distinguish from revision surgery if needed |
+
+---
+
+## Clinical and Hospital Terms
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| RCT enrolled individuals | participants | patients if trial context requires participants | No definition required | Abstract, Methods, Results | For RCTs, participants is often preferred |
+| Clinical-care individuals | patients | subjects | No definition required | Observational studies | |
+| Hospital type | tertiary institution; tertiary referral center | third-level hospital | No definition required | Methods | Choose one and keep consistent |
+| Specialty spelling | orthopedic; orthopaedic | mixed spelling | No definition required | All sections | Choose based on target journal |
+| Disc disease | lumbar disc herniation | herniated nucleus pulposus; HNP | Define if abbreviated | Introduction, Methods | More broadly understood |
+| Stenosis disease | lumbar spinal stenosis | lumbar stenosis | Define LSS if used | Introduction, Methods | Prefer full name at first use |
+| Symptom | radiating pain | radiculopathy when symptom is meant | No definition required | Introduction, Methods | Radiculopathy is a diagnosis, not just a symptom |
+| Limb term | lower extremity | lower limb | No definition required | Methods, Results | US style default |
+
+---
+
+## Spine Disease and Imaging Terms
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Lumbar disc disease | lumbar disc herniation (LDH) | herniated nucleus pulposus; slipped disc | Define abbreviation if used | Introduction, Methods | Use LDH only after definition |
+| Symptomatic disc level | symptomatic segment | painful level | No definition required | Methods, Discussion | Use when differentiating from adjacent/asymptomatic findings |
+| Asymptomatic adjacent disc | asymptomatic lumbar disc herniation (asLDH) | silent herniation; incidental disc | Define if used repeatedly | Methods, Discussion | Avoid implying harmlessness |
+| Recurrent disc event | recurrent disc herniation | re-herniation; reherniation | No definition required | Results, Discussion | Preferred event term |
+| Cauda equina syndrome | cauda equina syndrome (CES) | cauda equine syndrome | Define at first use | Introduction, Methods | High-risk diagnosis |
+| Epidural fat condition | spinal epidural lipomatosis | epidural obesity | Define at first use | Introduction, Methods | Avoid causal language unless supported |
+| Degenerative slip | degenerative spondylolisthesis | listhesis alone | Define if abbreviated | Introduction, Methods | State grade or slip threshold when relevant |
+| Back-pain phenotype | mechanical low back pain | axial pain only | No definition required | Methods, Discussion | Use only if operationally defined |
+| Retrolisthesis | retrolisthesis | posterior instability | Define measurement threshold | Methods | State percentage or mm threshold |
+| Lumbar stenosis | lumbar spinal stenosis (LSS) | lumbar stenosis only before definition | Define abbreviation if used | Introduction, Methods | |
+| Neurogenic symptom | neurogenic claudication | pseudoclaudication unless source uses it | No definition required | Introduction, Methods | |
+| Foraminal stenosis | foraminal stenosis | foraminal narrowing if graded stenosis is meant | Define grading system | Methods | Use Lee classification if applied |
+| Disc degeneration grade | Pfirrmann classification | Pfirrmann grade only before definition | Define at first use | Methods | |
+| Modic changes | Modic changes | endplate signal changes if Modic classification used | Define type if analyzed | Methods, Results | |
+| Bone density test | dual-energy X-ray absorptiometry (DXA) | DEXA if journal prefers DXA; bone scan | Define at first use | Methods | DXA is increasingly preferred; DEXA acceptable if journal style uses it |
+| CT attenuation | Hounsfield unit (HU) value | CT density only | Define at first use | Methods, Results | |
+| MRI bone quality | vertebral bone quality (VBQ) score | bone quality index | Define formula | Methods | |
+| Endplate bone quality | endplate bone quality (EBQ) score | endplate score | Define formula | Methods | |
+| Cage complication | cage subsidence | cage sinking | Define threshold | Results, Discussion | State measurement method |
+| Interbody fusion | oblique lumbar interbody fusion (OLIF) | oblique fusion | Define at first use | Title, Methods | |
+| Adjacent disease | adjacent segment disease (ASD) | adjacent segment degeneration if symptomatic disease is meant | Define distinction | Discussion | Degeneration is radiographic; disease implies symptoms/event |
+
+---
+
+## Trial and Comparative-Effectiveness Terms
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Simple arm | decompression-alone group | non-fusion group unless journal uses it | Define in Methods | Abstract, Methods, Results | Hyphenate as adjectival phrase |
+| Fusion arm | decompression with instrumented fusion; fusion group | fusion surgery alone if decompression included | Define in Methods | Abstract, Methods, Results | Be explicit about instrumentation |
+| Study aim | comparative effectiveness | efficacy if pragmatic real-world comparison | No definition required | Introduction | |
+| Noninferiority result | noninferior to | equivalent to | Define design and margin | Abstract, Results | Noninferiority is not equivalence |
+| Equivalence result | equivalent to | noninferior to | Define design and margin | Abstract, Results | Use only for two-sided equivalence design |
+| No superiority | no evidence of superiority; did not result in better outcomes | equivalent; no difference proved | No definition required | Results, Discussion | Avoid claiming sameness from superiority trials |
+| Clinically important change | minimal clinically important difference (MCID); clinically important improvement | meaningful without threshold | Define threshold | Methods, Results | State source of threshold |
+| Analysis population | full analysis set; modified intention-to-treat set; per-protocol set | ITT if exclusions applied | Define in Methods | Methods, Results | Use exact analysis set name from SAP |
+| Reoperation | subsequent surgery; reoperation | revision if any repeat surgery | No definition required | Results | Distinguish index-level vs adjacent-level surgery |
+| Follow-up | two-year follow-up; five-year follow-up | long term without duration | No definition required | Abstract, Results | Hyphenate adjectival forms |
+| Resource use | length of hospital stay; operating time; surgical costs | burden only | No definition required | Results, Discussion | |
+| Shared decision | shared decision making | patient preference alone | No definition required | Discussion | Hyphenate only as adjective: shared-decision-making process |
+
+---
+
+## AI, Radiomics, and Prediction Model Terms
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Artificial intelligence | artificial intelligence (AI) | A.I. | Define at first use | Introduction | |
+| Deep learning | deep learning | deep-learning when noun | No definition required | Introduction, Methods | Use deep-learning as adjective |
+| Machine learning | machine learning | ML before definition | Define abbreviation if used | Methods | |
+| Radiomics | radiomics | imaging histology unless source/journal uses it | Define at first use | Introduction, Methods | Prefer radiomics for English manuscripts |
+| Image feature | radiomic feature; image-derived feature | imageomics feature | No definition required | Methods | |
+| Image-derived phenotype | image-derived phenotype (IDP) | AI phenotype without definition | Define at first use | Introduction, Methods | |
+| Region annotation | region of interest (ROI) | focus area | Define at first use | Methods | |
+| Model training | training set; validation set; test set | learning group | No definition required | Methods, Results | Keep split terminology consistent |
+| External validation | external validation cohort | outside test only | No definition required | Methods, Results | State center/time separation |
+| Classifier performance | area under the receiver operating characteristic curve (AUC) | ROC value | Define at first use | Results | AUC is the statistic; ROC is the curve |
+| Discrimination metrics | sensitivity; specificity; precision; accuracy | hit rate | No definition required | Results | Report CIs when possible |
+| Calibration | calibration | agreement if calibration not tested | Define if used | Results | Do not claim calibration unless assessed |
+| Overfitting | overfitting | model memorization unless explaining | No definition required | Discussion | Mention when training-test gap is large |
+| Explainability | feature importance; saliency map | AI reasoning if not interpretable | Define method | Methods, Discussion | |
+| Hallucination | hallucination; unsupported generated content | fabrication if model-output context | Define for LLM studies | Methods, Discussion | |
+| Large language model | large language model (LLM) | chatbot if model is not chat-only | Define at first use | Introduction, Methods | |
+| Multimodal LLM | multimodal large language model (MLLM) | LLM when image input is central | Define at first use | Title, Abstract, Methods | |
+| Human oversight | expert verification; clinician review | autonomous diagnosis | No definition required | Discussion | Required for clinical AI safety framing |
+
+---
+
+## Endoscopy and Automated Reporting Terms
+
+| Concept | Preferred Term | Forbidden Terms | First Definition | Context | Notes |
+|---|---|---|---|---|---|
+| Procedure | upper gastrointestinal endoscopy (UGI endoscopy) | gastroscopy if esophagus/duodenum included and journal prefers UGI | Define at first use | Title, Abstract, Methods | |
+| Report output | draft report | final report if clinician review required | No definition required | Abstract, Results, Discussion | |
+| Primary endpoint | clinically acceptable draft report rate | usability rate without definition | Define criteria | Methods, Results | State approval threshold |
+| Expert comparison | junior endoscopists; senior endoscopists; expert endoscopists | novice/expert if years not stated | Define experience threshold | Methods | |
+| Lesion category | high-risk lesion | cancer if ulcers included | Define category | Methods, Results | |
+| Subepithelial lesion | subepithelial lesion (SEL) | submucosal tumor unless pathologically confirmed | Define at first use | Methods, Results | |
+| Atrophy/metaplasia | atrophy and intestinal metaplasia | atrophic gastritis if not equivalent | Define if needed | Results | |
+| Barrett disease | Barrett's esophagus | Barrett esophagus if journal does not use apostrophe | No definition required | Results | Follow journal style |
+| Reflux disease | reflux esophagitis | GERD if endoscopic finding is meant | No definition required | Results | |
+| Report quality | report completeness; report accuracy | report quality alone | Define operationally | Methods, Results | |
+| Error severity | high-risk error; moderate-risk error; low-risk error | serious error without definition | Define grading rules | Methods, Results | |
+| Workflow claim | reporting workflow integration | clinical deployment if not deployed | No definition required | Discussion | Avoid claiming efficiency unless tested |
+
+---
+
+## High-Priority Forbidden Terms
+
+| Forbidden Term | Preferred Term | Reason |
+|---|---|---|
+| creatinine phosphokinase | creatine phosphokinase (CPK) | Creatinine is incorrect |
+| biportal endoscopy | biportal endoscopic spine surgery (BESS) | Procedure naming consistency |
+| double-blind | assessor-blind | Surgical RCTs are structurally not double-blind unless specifically justified |
+| p = NS | exact p-value or p < 0.001 | Non-standard reporting |
+| p = 0.000 | p < 0.001 | P-values are not zero |
+| re-herniation | recurrent disc herniation | Preferred complication terminology |
+| substituting NRS for VAS or VAS for NRS | report the measured instrument exactly | Separate instruments; do not mix |
+| MIS | minimally invasive spine surgery (MISS) | Avoid ambiguous standalone abbreviation |
+| open surgery | microscopic surgery or microscopic discectomy | Use comparator-specific term |
+| compared to | compared with | AMA-style preference for comparisons |
+| equivalent | noninferior or not superior, if that was the actual design/result | Equivalence requires a specific two-sided design |
+| AI replacement | AI-assisted draft or clinician-reviewed output | Clinical AI should not be framed as replacing expert judgment unless proven |
+
+---
+
+## Project-Specific Terminology Log
+
+Add project decisions here before drafting.
+
+| Project/Paper | Term Decision | Rationale | Date |
+|---|---|---|---|
+| Template | Choose VAS vs NRS according to source dataset | Prevent outcome-instrument substitution | YYYY-MM-DD |

manuwright/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,53 @@
+# Third-party notices
+
+## unslop
+
+Several prose-check patterns in `scripts/academic_style.py` (significance inflation, `serves as a
+cornerstone`-type copulas, vague attribution, synonym-cycling groups and the flat-paragraph rhythm
+check) are adapted from unslop (https://github.com/MohamedAbdallah-14/unslop), used under the MIT
+License:
+
+```
+MIT License
+
+Copyright (c) 2026 Mohamed Abdallah
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```
+
+## Ideas (no code copied)
+
+The academic writing mode also follows ideas from these projects; no code or text was copied:
+
+- caveman (https://github.com/JuliusBrussee/caveman): re-inject the rules at SessionStart, including
+  after compaction, and add a one-line reminder on every prompt; switch the mode from the chat.
+- ponytail (https://github.com/dietrichgebert/ponytail): inject the rules into subagents at
+  SubagentStart.
+- humanizer (https://github.com/blader/humanizer) and stop-slop
+  (https://github.com/hardikpandya/stop-slop): a pre-send self-check that no fact, number or
+  citation was added or dropped; Bad/Good example pairs.
+- claude-scholar (https://github.com/Galaxy-Dawn/claude-scholar, MIT): a claim-strength field with
+  allowed wording for each source; weighted metadata matching for citation verification (title 0.4,
+  authors 0.3, year 0.2, venue 0.1).
+- academic-research-skills (https://github.com/Imbad0202/academic-research-skills, CC BY-NC 4.0):
+  the letter-blind, three-phase re-review of a revision. Reimplemented from the idea only; no text
+  or code was copied, as that license is not compatible with this project's.
+- writing-style-skill (https://github.com/jzOcb/writing-style-skill) and the voice-learn skill:
+  learning style rules from the author's edits of AI drafts, with human approval before a rule is
+  applied.