medsci-skills 4.1.0

package/skills/check-reporting/references/checklists/AMSTAR2.md

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+# AMSTAR 2 Checklist
+
+**A MeaSurement Tool to Assess systematic Reviews, version 2**
+Version: AMSTAR 2 (2017)
+Source: Shea BJ et al. BMJ 2017;358:j4008. doi: 10.1136/bmj.j4008
+
+## Checklist Items (16 items)
+
+### Items
+
+| # | Item | Description | Critical? |
+|---|------|-------------|-----------|
+| 1 | PICO components | Did the research questions and inclusion criteria for the review include the components of PICO? | No |
+| 2 | Protocol registered | Did the report of the review contain an explicit statement that the review methods were established prior to the conduct of the review and did the report justify any significant deviations from the protocol? | Yes |
+| 3 | Study design selection | Did the review authors explain their selection of the study designs for inclusion in the review? | No |
+| 4 | Comprehensive search | Did the review authors use a comprehensive literature search strategy? (searched at least 2 databases, provided search strategy, justified publication restrictions, searched reference lists, searched trial registries, consulted experts, searched grey literature) | Yes |
+| 5 | Duplicate selection | Did the review authors perform study selection in duplicate? | No |
+| 6 | Duplicate extraction | Did the review authors perform data extraction in duplicate? | No |
+| 7 | Excluded studies | Did the review authors provide a list of excluded studies and justify the exclusions? | Yes |
+| 8 | Study descriptions | Did the review authors describe the included studies in adequate detail? (PICO elements, follow-up period, study design, country, setting) | No |
+| 9 | RoB assessment | Did the review authors use a satisfactory technique for assessing the risk of bias (RoB) in individual studies that were included in the review? (For RCTs: randomization, blinding, missing data, selective reporting. For NRSI: confounding, selection, measurement) | Yes |
+| 10 | Funding sources | Did the review authors report on the sources of funding for the studies included in the review? | No |
+| 11 | Statistical methods | If meta-analysis was performed, did the review authors use appropriate methods for statistical combination of results? (effect measures, model choice, heterogeneity assessment) | Yes |
+| 12 | RoB impact on MA | If meta-analysis was performed, did the review authors assess the potential impact of RoB in individual studies on the results of the meta-analysis or other evidence synthesis? | No |
+| 13 | RoB in interpretation | Did the review authors account for RoB in individual studies when interpreting/discussing the results of the review? | Yes |
+| 14 | Heterogeneity | Did the review authors provide a satisfactory explanation for, and discussion of, any heterogeneity observed in the results of the review? | No |
+| 15 | Publication bias | If they performed quantitative synthesis did the review authors carry out an adequate investigation of publication bias (small study bias) and discuss its likely impact on the results of the review? | Yes |
+| 16 | Conflicts of interest | Did the review authors report any potential sources of conflict of interest, including any funding they received for conducting the review? | No |
+
+---
+
+## Overall Confidence Rating
+
+AMSTAR 2 does NOT generate a numerical score. Instead, rate overall confidence:
+
+| Rating | Criteria |
+|--------|----------|
+| **High** | No or one non-critical weakness: the systematic review provides an accurate and comprehensive summary of the results |
+| **Moderate** | More than one non-critical weakness (but no critical flaws): the review provides an accurate summary but may have some weaknesses |
+| **Low** | One critical flaw with or without non-critical weaknesses: the review may not provide an accurate and comprehensive summary |
+| **Critically Low** | More than one critical flaw with or without non-critical weaknesses: the review should not be relied on to provide an accurate and comprehensive summary |
+
+## Critical Domains (7 of 16)
+
+Items 2, 4, 7, 9, 11, 13, 15 are considered **critical domains**. A flaw in any critical domain results in at least "Low" confidence.
+
+## Notes for Assessors
+
+- AMSTAR 2 replaces the original AMSTAR (2007)
+- Designed for systematic reviews of **interventions** (RCTs and/or NRSI)
+- Not designed for DTA reviews (use ROBIS or domain-specific tools)
+- Cannot be used to assess individual primary studies
+- The tool should NOT be used to generate an overall score — use the confidence rating scheme above
+- For reviews including NRSI: Item 9 should assess confounding, selection bias, and information bias

package/skills/check-reporting/references/checklists/ARRIVE_2.md

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+# ARRIVE 2.0 Checklist — Animal Research
+
+**Reference:** Percie du Sert N et al. The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research. PLoS Biol. 2020;18(7):e3000410. PMID: 32663219
+
+**Website:** https://arriveguidelines.org
+
+---
+
+## How to Use This Checklist
+
+ARRIVE 2.0 has two tiers:
+- **Essential 10** (Items 1–10): Non-negotiable. All journals require these. Missing any = REJECTED.
+- **Recommended** (Items 11–21): Best practice. Complete if possible.
+
+For each item: **PRESENT** / **PARTIAL** / **MISSING**
+
+---
+
+## ESSENTIAL 10 — Non-Negotiable
+
+### Item 1 — Study Design ⚠️ commonly missed
+**Description:** For each experiment, provide brief details of the study design.
+**Required content:**
+- Type of study design (e.g., parallel group, crossover, factorial, dose-response)
+- Number of experimental groups and description of each
+- Independent experimental units (e.g., animal, litter, cage)
+- For any within-animal design: outline the design clearly
+
+**Example:** "Animals were randomly allocated to one of three parallel groups: (1) vehicle control (n=10), (2) low-dose treatment (n=10), (3) high-dose treatment (n=10). Each animal was an independent experimental unit."
+
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+**Location:** ___
+
+---
+
+### Item 2 — Sample Size ⚠️ commonly missed
+**Description:** Specify the number of animals used and rationale for this number.
+**Required content:**
+- Total number of animals used AND number per group
+- Method of sample size determination:
+  - Formal power calculation (provide effect size, α, power, formula, software) **OR**
+  - Pragmatic reasons (limited number of animals available, pilot study) — state explicitly
+
+**Power calculation example:**
+"Sample size was estimated using G*Power 3.1 based on a two-sample t-test, assuming an expected effect size of Cohen's d = 1.2 (derived from [Author Year]), α = 0.05 (two-tailed), and 80% power. The calculation indicated 15 animals per group were required. Accounting for 20% expected attrition, 18 animals per group were enrolled."
+
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+**Location:** ___
+
+---
+
+### Item 3 — Inclusion/Exclusion Criteria ⚠️ commonly missed
+**Description:** Describe any criteria used for including or excluding animals or data.
+**Required content:**
+- Criteria for excluding animals from the experiment (pre-specified, not post-hoc)
+- Criteria for excluding data from analysis (e.g., outliers — method for outlier detection)
+- Any animals that were excluded and why
+
+**Example:** "Animals were excluded if: (a) weight loss exceeded 20% at any time point, (b) technical failure of surgical procedure occurred, or (c) infection was detected. Any exclusion was documented in the study log at the time of occurrence. Two animals were excluded (one from Group A due to procedure failure; one from Group C due to infection)."
+
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+**Location:** ___
+
+---
+
+### Item 4 — Randomization ⚠️ commonly missed
+**Description:** Describe how animals were allocated to experimental groups.
+**Required content:**
+- Method of randomization (computer-generated, random number table)
+- Type: simple, block, stratified
+- Who performed randomization (and whether separate from who conducted experiments)
+- If randomization not used, justify
+
+**Example:** "Animals were randomly allocated to groups using computer-generated random numbers (R version 4.2.0). Block randomization (block size = 6) was used to ensure balanced allocation across experimental days. Allocation was performed by a researcher (initials) not involved in data collection."
+
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+**Location:** ___
+
+---
+
+### Item 5 — Blinding ⚠️ commonly missed
+**Description:** Describe who was aware of group allocation during different stages.
+**Required content:**
+State who was blinded (or not) at each stage:
+- During the experiment (treatment administration)
+- During outcome assessment
+- During data analysis
+
+"Outcome assessors were blinded to group allocation during behavioral testing and histological analysis. The researcher administering treatments could not be blinded due to the nature of the procedure; however, outcome assessment was performed by a blinded assessor."
+
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+**Location:** ___
+
+---
+
+### Item 6 — Outcome Measures ⚠️ commonly missed
+**Description:** Clearly define all outcome measures used and how they were assessed.
+**Required content:**
+- Primary outcome: define explicitly (what is measured, how, by whom)
+- Secondary outcomes: same level of detail
+- Timing of measurements (baseline, Day 7, Day 14, etc.)
+- Observer reliability: intra- and inter-observer variability assessed?
+
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+**Location:** ___
+
+---
+
+### Item 7 — Statistical Methods ⚠️ commonly missed
+**Description:** Describe the statistical methods used for each analysis.
+**Required content:**
+- Primary statistical test for primary outcome
+- Rationale for choice (parametric vs. non-parametric, based on what?)
+- Handling of repeated measures (linear mixed-effects model preferred over repeated ANOVA)
+- Multiple comparison correction: which method (Bonferroni, FDR)?
+- Significance threshold (α)
+- Software: R (version), SPSS (version), GraphPad Prism (version)
+
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+**Location:** ___
+
+---
+
+### Item 8 — Experimental Animals ⚠️ commonly missed
+**Description:** Provide details of animals used in the study.
+**Required content:**
+- Species and strain/substrain (with substrain details — this matters!)
+- Source (commercial vendor; in-house breeding)
+- Sex (justify if single sex)
+- Age and weight at start of experiment (mean ± SD or range)
+- Health status (specific pathogen-free, germ-free, defined flora, conventional)
+- For transgenic animals: complete genotype
+
+**Example:** "Male C57BL/6J mice (Jackson Laboratory, Bar Harbor, ME; stock #000664) aged 8–10 weeks (weight: 22.3 ± 1.8 g at enrollment) were used. Only males were used because [biological justification]. All animals were specific pathogen-free."
+
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+**Location:** ___
+
+---
+
+### Item 9 — Experimental Procedures ⚠️ commonly missed
+**Description:** For each experiment and each experimental group, including controls, describe the procedures in enough detail to allow replication.
+**Required content:**
+- Exact procedure steps
+- Anesthesia: agent, dose, route, monitoring (temperature, heart rate)
+- Analgesia: pre- and post-operative
+- Humane endpoints: pre-specified criteria for euthanasia
+- Equipment: manufacturer, model, settings
+- Any details that could affect reproducibility (time of day, number of animals per session)
+
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+**Location:** ___
+
+---
+
+### Item 10 — Results ⚠️ commonly missed
+**Description:** Report the results for each experiment conducted, with a measure of precision (e.g., SD, SEM, 95% CI).
+**Required content:**
+- All pre-specified outcomes (not just significant ones)
+- Effect size with 95% CI
+- Exact p-values
+- N at each time point (with attrition documented)
+- Adverse events (even if none: "No adverse events were observed")
+- Individual data points for small groups (dot plots)
+
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+**Location:** ___
+
+---
+
+## RECOMMENDED ITEMS — Best Practice
+
+### Item 11 — Abstract ⚠️ commonly missed
+**Description:** Provide an accurate summary of the research objectives, animal species used, key methods, principal findings, and study conclusions.
+**Required content:** Abstract should contain enough information for readers to understand: what species, what procedure, primary result with magnitude, conclusion.
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+
+### Item 12 — Background
+**Description:** Explain why the study was done; include sufficient background to inform the reader why this animal model was chosen.
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+
+### Item 13 — Objectives
+**Description:** Clearly describe the research question, hypothesis, and the specific objectives of the study.
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+
+### Item 14 — Ethical Statement ⚠️ commonly missed
+**Description:** Provide the name of the ethics committee or equivalent, and the approval ID.
+**Required content:** "All animal experiments were approved by the Institutional Animal Care and Use Committee of [Institution] (protocol number [XXX])."
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+
+### Item 15 — Housing and Husbandry ⚠️ commonly missed
+**Description:** Describe the conditions under which animals were housed and cared for.
+**Required content:** Cage type and dimensions, group or individual housing (N per cage), temperature (°C), humidity (%), light cycle, food and water access (ad libitum or restricted; diet specification), acclimatization period, enrichment.
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+
+### Item 16 — Animal Care and Monitoring
+**Description:** Describe the welfare assessments that were carried out before, during, and after the experiment.
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+
+### Item 17 — Interpretation
+**Description:** Interpret the results, taking into account the study objectives and hypotheses, current theory, and other relevant studies.
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+
+### Item 18 — Generalisability/Translation
+**Description:** Comment on whether, and how, the findings of this study are likely to translate to other species or systems, and the relevance to human biology.
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+
+### Item 19 — Limitations ⚠️ commonly missed
+**Description:** Discuss the potential limitations of the study.
+**Required content:** At minimum: (a) model limitations relative to human disease, (b) single sex (if applicable), (c) single center/vendor, (d) follow-up duration, (e) sample size for secondary outcomes.
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+
+### Item 20 — Protocol Registration
+**Description:** Provide a statement indicating whether a study protocol was pre-registered.
+**Required content:** OSF (osf.io), PROSPERO for systematic reviews, or equivalent. State registration ID or that registration was not done (with justification if exploratory study).
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+
+### Item 21 — Data Availability ⚠️ commonly missed
+**Description:** Provide a statement describing if and where study data are available.
+**Required content:** "Data supporting this study are available at [repository/DOI]." or "Data are available upon reasonable request from the corresponding author."
+**Status:** [ ] PRESENT [ ] PARTIAL [ ] MISSING
+
+---
+
+## Summary
+
+| Category | PRESENT | PARTIAL | MISSING |
+|----------|---------|---------|---------|
+| Essential 10 | /10 | /10 | /10 |
+| Recommended | /11 | /11 | /11 |
+| **TOTAL** | /21 | /21 | /21 |
+
+**Verdict:** [ ] All Essential 10 PRESENT → proceed to submission
+[ ] Any Essential 10 MISSING → MUST REVISE before submission

package/skills/check-reporting/references/checklists/CARE.md

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+# CARE Checklist
+
+**CAse REports (CARE) guidelines**
+Version: CARE 2013
+Source: https://www.care-statement.org
+Reference: Gagnier JJ, Kienle G, Altman DG, Moher D, Sox H, Riley D. The CARE guidelines: consensus-based clinical case report guideline development. J Clin Epidemiol 2014;67(1):46-51.
+
+## Checklist Items (13 topics)
+
+### Title and Key Words
+
+| # | Item | Description |
+|---|------|-------------|
+| 1 | Title | The words "case report" should appear in the title along with the diagnosis or intervention of primary focus. |
+| 2 | Key Words | Two to five key words that identify topics in this case report, including "case report". |
+
+### Abstract
+
+| # | Item | Description |
+|---|------|-------------|
+| 3a | Abstract — Introduction | What is unique about this case and what does it add to the scientific literature? |
+| 3b | Abstract — Main concerns | The patient's main concerns and important clinical findings. |
+| 3c | Abstract — Diagnoses, interventions, outcomes | The primary diagnoses, interventions, and outcomes. |
+| 3d | Abstract — Conclusion | What are one or more "take-away" lessons from this case report? |
+
+### Introduction
+
+| # | Item | Description |
+|---|------|-------------|
+| 4 | Introduction | One or two paragraphs summarizing why this case is unique (may include references). |
+
+### Patient Information
+
+| # | Item | Description |
+|---|------|-------------|
+| 5a | Patient Information | De-identified demographic and other patient information. |
+| 5b | Patient Information | Main concerns and symptoms of the patient. |
+| 5c | Patient Information | Medical, family, and psychosocial history including relevant genetic information. |
+| 5d | Patient Information | Relevant past interventions and their outcomes. |
+
+### Clinical Findings
+
+| # | Item | Description |
+|---|------|-------------|
+| 6 | Clinical Findings | Describe the significant physical examination and other clinical findings. |
+
+### Timeline
+
+| # | Item | Description |
+|---|------|-------------|
+| 7 | Timeline | Historical and current information from this episode of care organized as a timeline (figure or table). |
+
+### Diagnostic Assessment
+
+| # | Item | Description |
+|---|------|-------------|
+| 8a | Diagnostic Assessment | Diagnostic methods (e.g., physical examination, laboratory testing, imaging, questionnaires). |
+| 8b | Diagnostic Assessment | Diagnostic challenges (e.g., access to testing, financial, or cultural). |
+| 8c | Diagnostic Assessment | Diagnostic reasoning including other diagnoses considered. |
+| 8d | Diagnostic Assessment | Prognostic characteristics (e.g., staging) where applicable. |
+
+### Therapeutic Intervention
+
+| # | Item | Description |
+|---|------|-------------|
+| 9a | Therapeutic Intervention | Types of therapeutic intervention (e.g., pharmacologic, surgical, preventive, self-care). |
+| 9b | Therapeutic Intervention | Administration of therapeutic intervention (e.g., dosage, strength, duration). |
+| 9c | Therapeutic Intervention | Changes in therapeutic intervention (with rationale). |
+
+### Follow-up and Outcomes
+
+| # | Item | Description |
+|---|------|-------------|
+| 10a | Follow-up and Outcomes | Clinician- and patient-assessed outcomes (when appropriate). |
+| 10b | Follow-up and Outcomes | Important follow-up diagnostic and other test results. |
+| 10c | Follow-up and Outcomes | Intervention adherence and tolerability (and how this was assessed). |
+| 10d | Follow-up and Outcomes | Adverse and unanticipated events. |
+
+### Discussion
+
+| # | Item | Description |
+|---|------|-------------|
+| 11a | Discussion | A scientific discussion of the strengths and limitations associated with this case report. |
+| 11b | Discussion | Discussion of the relevant medical literature with references. |
+| 11c | Discussion | The scientific rationale for any conclusions (including assessment of possible causes). |
+| 11d | Discussion | The primary "take-away" lessons of this case report (without references) in a one-paragraph conclusion. |
+
+### Patient Perspective
+
+| # | Item | Description |
+|---|------|-------------|
+| 12 | Patient Perspective | The patient should share their perspective on the treatment(s) they received, when appropriate. |
+
+### Informed Consent
+
+| # | Item | Description |
+|---|------|-------------|
+| 13 | Informed Consent | Did the patient give informed consent? Provide if requested. |
+
+---
+
+*Educational summary of the CARE 2013 checklist (CC BY-NC 4.0). Cite the original guideline (Gagnier et al. 2014) and consult https://www.care-statement.org for the authoritative, full checklist with explanation and elaboration.*

package/skills/check-reporting/references/checklists/CLAIM_2024.md

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+# CLAIM 2024 Checklist
+
+**Checklist for Artificial Intelligence in Medical Imaging**
+Version: CLAIM 2024 Update
+Source: https://pubs.rsna.org/doi/10.1148/ryai.240300
+Reference: Tejani AS, Klontzas ME, Gatti AA, Mongan JT, Moy L, Park SH, Kahn CE Jr. Checklist for Artificial Intelligence in Medical Imaging (CLAIM): 2024 Update. Radiol Artif Intell 2024;6(4):e240300.
+
+> Note: The 2024 update replaces "ground truth" with "reference standard" and discourages "validation" in favour of "internal/external testing". Each item is answered Yes / No / Not Applicable with the manuscript location cited.
+
+## Checklist Items (44 items)
+
+### Title and Abstract
+
+| # | Item | Description |
+|---|------|-------------|
+| 1 | Title | Identify the study as employing AI methodology and name the specific technology category (e.g., deep learning). |
+| 2 | Abstract | Structured summary including study design, methods, results, and conclusions; population details, data partitions, prospective/retrospective status, statistical analysis, outcomes, and availability of resources. |
+
+### Introduction
+
+| # | Item | Description |
+|---|------|-------------|
+| 3 | Background | Scientific and clinical background, current practice, intended use, and clinical role of the AI approach. |
+| 4 | Objectives | Study aims, objectives, and hypotheses (if not data-driven). |
+
+### Methods — Study Design
+
+| # | Item | Description |
+|---|------|-------------|
+| 5 | Study design | Prospective or retrospective study. |
+| 6 | Study goal | Goal of the study (e.g., model creation, feasibility, trial type, intended use for the classification task). |
+
+### Methods — Data
+
+| # | Item | Description |
+|---|------|-------------|
+| 7 | Data sources | State data sources; provide links to publicly available datasets. |
+| 8 | Eligibility | Inclusion and exclusion criteria and selection methodology for the data. |
+| 9 | Preprocessing | Data preprocessing steps (e.g., normalization, resampling, window/level adjustment). |
+| 10 | Subset selection | Selection of data subsets and training of personnel involved. |
+| 11 | De-identification | De-identification methods meeting HIPAA/GDPR/AI Act standards. |
+| 12 | Missing data | How missing data were handled and potential biases from imputation. |
+| 13 | Acquisition protocol | Image acquisition protocol parameters (e.g., manufacturer, sequences, resolution). |
+
+### Methods — Reference Standard
+
+| # | Item | Description |
+|---|------|-------------|
+| 14 | Reference standard definition | Method for obtaining the reference standard, with precise and replicable definitions. |
+| 15 | Reference standard rationale | Rationale for choosing the reference standard versus alternatives. |
+| 16 | Annotators | Source, qualifications, and training materials of annotators. |
+| 17 | Annotation procedures | Test-set annotation procedures, software version, and any NLP/automated approaches. |
+| 18 | Annotation variability | Measurement of inter- and intra-rater variability and method of discrepancy resolution. |
+
+### Methods — Data Partitions
+
+| # | Item | Description |
+|---|------|-------------|
+| 19 | Partition assignment | Partition assignment (train/tune/test), proportions, justification, and class-imbalance handling. |
+| 20 | Partition disjointness | Level of partition disjointness (patient-, series-, or image-level). |
+
+### Methods — Testing Data
+
+| # | Item | Description |
+|---|------|-------------|
+| 21 | Test set size | Testing-set size derived from a power calculation or AUC-based estimation. |
+
+### Methods — Model
+
+| # | Item | Description |
+|---|------|-------------|
+| 22 | Model architecture | Complete model architecture (inputs, outputs, layers, pooling, normalization). |
+| 23 | Software | Software libraries, frameworks, packages, and version numbers. |
+| 24 | Initialization | Parameter initialization; transfer-learning sources, if used. |
+
+### Methods — Training
+
+| # | Item | Description |
+|---|------|-------------|
+| 25 | Training procedures | Training procedures, data augmentation, convergence monitoring, and all hyperparameters. |
+| 26 | Model selection | Method and metrics for selecting the best-performing model. |
+| 27 | Ensembling | If an ensemble approach is used, details of each model and how outputs are combined. |
+
+### Methods — Evaluation
+
+| # | Item | Description |
+|---|------|-------------|
+| 28 | Performance metrics | Performance metrics and comparison to published models. |
+| 29 | Uncertainty | Measures of uncertainty (e.g., standard deviation, confidence intervals) and statistical significance tests. |
+| 30 | Robustness | Robustness or sensitivity analysis. |
+| 31 | Explainability | If applied, explainability/interpretability methods and their validation. |
+| 32 | Internal testing | Internal-data evaluation and consistency between training and test performance. |
+| 33 | External testing | External-data testing, or justification for its omission. |
+| 34 | Trial registration | If applicable, compliance with ICMJE clinical-trial registration requirements. |
+
+### Results — Data
+
+| # | Item | Description |
+|---|------|-------------|
+| 35 | Inclusion/exclusion numbers | Numbers of patients/examinations included and excluded, with a flowchart. |
+| 36 | Demographics | Demographic and clinical characteristics per partition; identify potential sources of bias. |
+
+### Results — Model Performance
+
+| # | Item | Description |
+|---|------|-------------|
+| 37 | Performance reporting | Final model performance benchmarked against the reference standard across partitions and subgroups. |
+| 38 | Accuracy estimates | Diagnostic accuracy estimates with 95% confidence intervals; ROC analysis; address class imbalance. |
+| 39 | Failure analysis | Failure analysis with a confusion matrix; examples of incorrect classifications in the medical context. |
+
+### Discussion
+
+| # | Item | Description |
+|---|------|-------------|
+| 40 | Limitations | Study limitations (methods, materials, biases, generalisability). |
+| 41 | Implications | Clinical implications, intended use, practice changes, and barriers to translation. |
+
+### Other Information
+
+| # | Item | Description |
+|---|------|-------------|
+| 42 | Full protocol | Reference to the full protocol or technical details if exceeding journal word limits. |
+| 43 | Availability | Availability of software, model, and data, and access conditions. |
+| 44 | Funding | Funding sources and the role of funders. |
+
+---
+
+*Educational summary of the CLAIM 2024 Update checklist (© RSNA, open access). Cite the original (Tejani et al., Radiol Artif Intell 2024;6(4):e240300) and consult the RSNA article for the authoritative, full checklist.*

package/skills/check-reporting/references/checklists/CLEAR.md

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+# CLEAR Checklist
+
+**CheckList for EvaluAtion of Radiomics research**
+Version: CLEAR 2023
+Source: https://doi.org/10.1186/s13244-023-01415-8
+Reference: Kocak B, Baessler B, Bakas S, et al. CheckList for EvaluAtion of Radiomics research (CLEAR): a step-by-step reporting guideline for authors and reviewers endorsed by ESR and EuSoMII. Insights Imaging. 2023;14(1):75. doi:10.1186/s13244-023-01415-8
+
+## Checklist Items (58 items)
+
+### Domain 1: Study Design (Items 1-8)
+
+| # | Item | Description |
+|---|------|-------------|
+| 1 | Study hypothesis | State the study hypothesis or objectives clearly. |
+| 2 | Study design | Describe the study design (retrospective/prospective, single/multi-center, development/validation). |
+| 3 | Inclusion criteria | Define the inclusion criteria for the study population. |
+| 4 | Exclusion criteria | Define the exclusion criteria, including imaging quality-related exclusions. |
+| 5 | Sample size | Report the total sample size and per-group sample sizes. Justify the sample size if a power analysis was performed. |
+| 6 | Clinical and demographic data | Report relevant clinical and demographic characteristics of the study population. |
+| 7 | Reference standard | Describe the reference standard (ground truth) used for labeling, including how and by whom it was determined. |
+| 8 | Time frame | Report the time period of data collection and any relevant temporal information. |
+
+### Domain 2: Imaging Data (Items 9-18)
+
+| # | Item | Description |
+|---|------|-------------|
+| 9 | Imaging modality | Specify the imaging modality (CT, MRI, PET, ultrasound, etc.) and rationale for selection. |
+| 10 | Scanner details | Report scanner manufacturer, model, and number of different scanners used. |
+| 11 | Acquisition parameters | Report key acquisition parameters (e.g., slice thickness, pixel spacing, repetition time, echo time, field strength, reconstruction kernel). |
+| 12 | Contrast agent | Report whether contrast agent was used, type, dose, and timing of acquisition relative to injection. |
+| 13 | Image preprocessing | Describe all image preprocessing steps (resampling, normalization, filtering, N4 bias correction, etc.) and their order. |
+| 14 | Image quality control | Describe any image quality assessment or exclusion criteria applied before feature extraction. |
+| 15 | Multi-scanner harmonization | For multi-scanner data: describe any harmonization methods applied (e.g., ComBat, z-scoring) or state that none was used. |
+| 16 | DICOM compliance | State whether the analysis was performed on DICOM-compliant images and report any format conversions. |
+| 17 | Phantom or test-retest data | Report whether phantom or test-retest data were used to assess feature reproducibility. |
+| 18 | Data augmentation | Describe any data augmentation techniques applied to imaging data and at which stage (before/after splitting). |
+
+### Domain 3: Segmentation (Items 19-24)
+
+| # | Item | Description |
+|---|------|-------------|
+| 19 | Segmentation method | Describe the segmentation method (manual, semi-automatic, fully automatic) and software used. |
+| 20 | ROI definition | Define the region of interest (ROI) -- what was segmented, on which sequences/phases, 2D vs 3D. |
+| 21 | Segmentator qualifications | Report the qualifications and experience of the person(s) performing segmentation. |
+| 22 | Segmentation protocol | Describe the segmentation protocol, including any guidelines or training provided to segmentators. |
+| 23 | Inter-reader agreement | Report inter-reader agreement for segmentation (e.g., Dice coefficient, ICC) if multiple readers were used. |
+| 24 | Intra-reader agreement | Report intra-reader agreement for segmentation if assessed. |
+
+### Domain 4: Feature Extraction and Processing (Items 25-34)
+
+| # | Item | Description |
+|---|------|-------------|
+| 25 | Feature extraction software | Report the software name and version used for feature extraction. |
+| 26 | Feature classes | List the feature classes extracted (e.g., first-order, shape, GLCM, GLRLM, GLSZM, GLDM, NGTDM). |
+| 27 | Number of features | Report the total number of features extracted before any selection. |
+| 28 | Extraction parameters | Report feature extraction parameters (e.g., bin width/count, distance for GLCM, voxel size for resampling). |
+| 29 | IBSI compliance | State whether the feature extraction software is IBSI (Image Biomarker Standardisation Initiative) compliant. |
+| 30 | Feature reproducibility | Report feature reproducibility assessment (e.g., ICC from test-retest or multi-reader segmentation). Describe how non-reproducible features were handled. |
+| 31 | Feature standardization | Describe any feature standardization or normalization methods applied (e.g., z-score, min-max). |
+| 32 | Collinearity handling | Describe methods used to address collinearity among features (e.g., correlation threshold, VIF). |
+| 33 | Feature selection method | Describe the feature selection method(s) used (e.g., LASSO, mRMR, recursive feature elimination) and the rationale. |
+| 34 | Number of selected features | Report the number of features selected for the final model. |
+
+### Domain 5: Modeling (Items 35-44)
+
+| # | Item | Description |
+|---|------|-------------|
+| 35 | Model type | Specify the type of model(s) used (e.g., logistic regression, random forest, SVM, neural network). |
+| 36 | Training methodology | Describe the training methodology, including optimization algorithm, loss function, and stopping criteria. |
+| 37 | Data splitting | Describe the data splitting strategy (training/validation/test), including method (random, temporal, institutional) and ratios. |
+| 38 | Cross-validation | If cross-validation was used, specify the type (k-fold, leave-one-out, nested) and number of folds/repetitions. |
+| 39 | Hyperparameter tuning | Describe the hyperparameter tuning approach and which hyperparameters were tuned. |
+| 40 | Class imbalance | Report whether class imbalance existed and how it was handled (oversampling, undersampling, SMOTE, class weights, etc.). |
+| 41 | Clinical feature integration | If clinical features were combined with radiomics features, describe the integration method. |
+| 42 | Comparison models | Describe any comparison models (clinical-only, radiomics-only, combined) and how they were compared. |
+| 43 | External validation | Report whether external validation was performed. If so, describe the external dataset source, size, and key differences from the development set. |
+| 44 | Temporal validation | Report whether temporal (chronological) validation was performed and the time gap between development and validation cohorts. |
+
+### Domain 6: Performance Assessment (Items 45-52)
+
+| # | Item | Description |
+|---|------|-------------|
+| 45 | Discrimination metrics | Report discrimination metrics (e.g., AUC, sensitivity, specificity, accuracy) with confidence intervals. |
+| 46 | Calibration | Report calibration assessment (calibration plot, Hosmer-Lemeshow test, calibration slope/intercept, Brier score). |
+| 47 | Clinical utility | Report clinical utility assessment (e.g., decision curve analysis, net benefit, net reclassification improvement). |
+| 48 | Statistical tests | Report statistical tests used for comparing models and their p-values. |
+| 49 | Subgroup analysis | Report any subgroup analyses performed (e.g., by scanner, institution, patient subgroup). |
+| 50 | Failure analysis | Report any analysis of cases where the model failed or performed poorly. |
+| 51 | Reader comparison | If applicable, compare model performance with radiologist readers. |
+| 52 | Multicollinearity in final model | Report assessment of multicollinearity in the final model (e.g., VIF values). |
+
+### Domain 7: Open Science (Items 53-58)
+
+| # | Item | Description |
+|---|------|-------------|
+| 53 | Code availability | State whether the analysis code is publicly available. If yes, provide the repository URL. |
+| 54 | Data availability | State whether the data are publicly available. If restricted, explain why and how access can be requested. |
+| 55 | Model availability | State whether the trained model is publicly available for external validation. |
+| 56 | Radiomics feature values | State whether extracted feature values are shared (as supplementary material or in a repository). |
+| 57 | Pre-registration | State whether the study was pre-registered (e.g., in a prospective register or protocol). |
+| 58 | Reporting guideline adherence | State which reporting guideline(s) were followed (e.g., CLEAR, CLAIM, TRIPOD+AI). |
+
+---
+
+## Notes for Assessors
+
+- CLEAR is specifically designed for radiomics studies. For deep learning studies without handcrafted radiomics features, CLAIM 2024 or TRIPOD+AI may be more appropriate.
+- Items in Domain 3 (Segmentation) may not apply if the study uses atlas-based or fully automated segmentation without reader involvement.
+- Items 17 (phantom data) and 57 (pre-registration) are aspirational best practices; their absence should be noted but may be scored as N/A if justified.
+- Item 29 (IBSI compliance) is strongly recommended. Non-IBSI-compliant software should be flagged as a potential limitation.
+- For studies combining radiomics with deep learning features, assess both CLEAR (for radiomics components) and CLAIM/TRIPOD+AI (for deep learning components).
+- Domain 7 (Open Science) items are increasingly required by journals. Missing items here are more likely to trigger reviewer comments in high-impact journals.
+- CLEAR was endorsed by the European Society of Radiology (ESR) and the European Society of Medical Imaging Informatics (EuSoMII).