clearai-dsh 0.3.0 → 0.4.0

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  1. package/CHANGELOG.md +147 -0
  2. package/README.md +28 -28
  3. package/README.zh-CN.md +28 -28
  4. package/lib/client.js +861 -2555
  5. package/lib/domain-language.js +552 -48
  6. package/lib/fold.js +351 -1015
  7. package/lib/host.js +47 -557
  8. package/lib/invariant.js +9 -12
  9. package/lib/knowledge-view.js +363 -226
  10. package/lib/lang.js +81 -0
  11. package/package.json +1 -1
  12. package/presets/clearai/agent.cordis.yml +54 -82
  13. package/presets/clearai/clearai.patch.yml +54 -82
  14. package/presets/clearai/plugins/clearai-kernel.js +1590 -5437
  15. package/presets/clearai/plugins/ontology.js +56 -14
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  17. package/presets/clearai/skills/clearai-loop/SKILL.md +73 -59
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  25. package/presets/clearai/template/skills/citation-management/SKILL.md +0 -73
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  27. package/presets/clearai/template/skills/citation-management/references/citation_validation.md +0 -794
  28. package/presets/clearai/template/skills/citation-management/references/google_scholar_search.md +0 -725
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- # Evidence Hierarchy and Quality Assessment
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-
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- ## Traditional Evidence Hierarchy (Medical/Clinical)
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-
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- ### Level 1: Systematic Reviews and Meta-Analyses
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- **Description:** Comprehensive synthesis of all available evidence on a question.
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-
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- **Strengths:**
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- - Combines multiple studies for greater power
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- - Reduces impact of single-study anomalies
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- - Can identify patterns across studies
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- - Quantifies overall effect size
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-
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- **Weaknesses:**
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- - Quality depends on included studies ("garbage in, garbage out")
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- - Publication bias can distort findings
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- - Heterogeneity may make pooling inappropriate
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- - Can mask important differences between studies
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-
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- **Critical evaluation:**
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- - Was search comprehensive (multiple databases, grey literature)?
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- - Were inclusion criteria appropriate and prespecified?
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- - Was study quality assessed?
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- - Was heterogeneity explored?
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- - Was publication bias assessed (funnel plots, fail-safe N)?
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- - Were appropriate statistical methods used?
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-
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- ### Level 2: Randomized Controlled Trials (RCTs)
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- **Description:** Experimental studies with random assignment to conditions.
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-
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- **Strengths:**
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- - Gold standard for establishing causation
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- - Controls for known and unknown confounders
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- - Minimizes selection bias
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- - Enables causal inference
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-
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- **Weaknesses:**
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- - May not be ethical or feasible
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- - Artificial settings may limit generalizability
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- - Often short-term with selected populations
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- - Expensive and time-consuming
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-
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- **Critical evaluation:**
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- - Was randomization adequate (sequence generation, allocation concealment)?
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- - Was blinding implemented (participants, providers, assessors)?
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- - Was sample size adequate (power analysis)?
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- - Was intention-to-treat analysis used?
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- - Was attrition rate acceptable and balanced?
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- - Are results generalizable?
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-
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- ### Level 3: Cohort Studies
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- **Description:** Observational studies following groups over time.
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-
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- **Types:**
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- - **Prospective:** Follow forward from exposure to outcome
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- - **Retrospective:** Look backward at existing data
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-
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- **Strengths:**
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- - Can study multiple outcomes
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- - Establishes temporal sequence
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- - Can calculate incidence and relative risk
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- - More feasible than RCTs for many questions
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-
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- **Weaknesses:**
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- - Susceptible to confounding
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- - Selection bias possible
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- - Attrition can bias results
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- - Cannot prove causation definitively
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-
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- **Critical evaluation:**
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- - Were cohorts comparable at baseline?
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- - Was exposure measured reliably?
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- - Was follow-up adequate and complete?
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- - Were potential confounders measured and controlled?
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- - Was outcome assessment blinded to exposure?
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-
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- ### Level 4: Case-Control Studies
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- **Description:** Compare people with outcome (cases) to those without (controls), looking back at exposures.
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- **Strengths:**
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- - Efficient for rare outcomes
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- - Relatively quick and inexpensive
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- - Can study multiple exposures
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- - Useful for generating hypotheses
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-
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- **Weaknesses:**
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- - Cannot calculate incidence
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- - Susceptible to recall bias
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- - Selection of controls is challenging
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- - Cannot prove causation
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- **Critical evaluation:**
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- - Were cases and controls defined clearly?
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- - Were controls appropriate (same source population)?
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- - Was matching appropriate?
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- - How was exposure ascertained (records vs. recall)?
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- - Were potential confounders controlled?
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- - Could recall bias explain findings?
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-
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- ### Level 5: Cross-Sectional Studies
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- **Description:** Snapshot observation at single point in time.
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- **Strengths:**
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- - Quick and inexpensive
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- - Can assess prevalence
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- - Useful for hypothesis generation
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- - Can study multiple outcomes and exposures
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- **Weaknesses:**
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- - Cannot establish temporal sequence
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- - Cannot determine causation
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- - Prevalence-incidence bias
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- - Survival bias
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- **Critical evaluation:**
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- - Was sample representative?
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- - Were measures validated?
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- - Could reverse causation explain findings?
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- - Are confounders acknowledged?
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-
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- ### Level 6: Case Series and Case Reports
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- **Description:** Description of observations in clinical practice.
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- **Strengths:**
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- - Can identify new diseases or effects
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- - Hypothesis-generating
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- - Details rare phenomena
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- - Quick to report
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-
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- **Weaknesses:**
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- - No control group
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- - No statistical inference possible
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- - Highly susceptible to bias
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- - Cannot establish causation or frequency
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- **Use:** Primarily for hypothesis generation and clinical description.
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-
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- ### Level 7: Expert Opinion
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- **Description:** Statements by recognized authorities.
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- **Strengths:**
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- - Synthesizes experience
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- - Useful when no research available
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- - May integrate multiple sources
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- **Weaknesses:**
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- - Subjective and potentially biased
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- - May not reflect current evidence
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- - Appeal to authority fallacy risk
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- - Individual expertise varies
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- **Use:** Lowest level of evidence; should be supported by data when possible.
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-
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- ## Nuances and Limitations of Traditional Hierarchy
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-
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- ### When Lower-Level Evidence Can Be Strong
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- 1. **Well-designed observational studies** with:
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- - Large effects (hard to confound)
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- - Dose-response relationships
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- - Consistent findings across contexts
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- - Biological plausibility
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- - No plausible confounders
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- 2. **Multiple converging lines of evidence** from different study types
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- 3. **Natural experiments** approximating randomization
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-
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- ### When Higher-Level Evidence Can Be Weak
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- 1. **Poor-quality RCTs** with:
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- - Inadequate randomization
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- - High attrition
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- - No blinding when feasible
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- - Conflicts of interest
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- 2. **Biased meta-analyses**:
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- - Publication bias
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- - Selective inclusion
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- - Inappropriate pooling
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- - Poor search strategy
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- 3. **Not addressing the right question**:
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- - Wrong population
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- - Wrong comparison
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- - Wrong outcome
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- - Too artificial to generalize
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- ## Alternative: GRADE System
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- GRADE (Grading of Recommendations Assessment, Development and Evaluation) assesses evidence quality across four levels:
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- ### High Quality
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- **Definition:** Very confident that true effect is close to estimated effect.
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- **Characteristics:**
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- - Well-conducted RCTs
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- - Overwhelming evidence from observational studies
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- - Large, consistent effects
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- - No serious limitations
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- ### Moderate Quality
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- **Definition:** Moderately confident; true effect likely close to estimated, but could be substantially different.
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- **Downgrades from high:**
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- - Some risk of bias
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- - Inconsistency across studies
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- - Indirectness (different populations/interventions)
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- - Imprecision (wide confidence intervals)
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- - Publication bias suspected
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- ### Low Quality
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- **Definition:** Limited confidence; true effect may be substantially different.
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- **Downgrades:**
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- - Serious limitations in above factors
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- - Observational studies without special strengths
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- ### Very Low Quality
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- **Definition:** Very limited confidence; true effect likely substantially different.
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- **Characteristics:**
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- - Very serious limitations
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- - Expert opinion
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- - Multiple serious flaws
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- ## Study Quality Assessment Criteria
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- ### Internal Validity (Bias Control)
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- **Questions:**
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- - Was randomization adequate?
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- - Was allocation concealed?
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- - Were groups similar at baseline?
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- - Was blinding implemented?
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- - Was attrition minimal and balanced?
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- - Was intention-to-treat used?
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- - Were all outcomes reported?
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-
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- ### External Validity (Generalizability)
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- **Questions:**
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- - Is sample representative of target population?
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- - Are inclusion/exclusion criteria too restrictive?
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- - Is setting realistic?
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- - Are results applicable to other populations?
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- - Are effects consistent across subgroups?
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-
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- ### Statistical Conclusion Validity
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- **Questions:**
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- - Was sample size adequate (power)?
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- - Were statistical tests appropriate?
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- - Were assumptions checked?
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- - Were effect sizes and confidence intervals reported?
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- - Were multiple comparisons addressed?
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- - Was analysis prespecified?
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-
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- ### Construct Validity (Measurement)
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- **Questions:**
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- - Were measures validated and reliable?
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- - Was outcome defined clearly and appropriately?
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- - Were assessors blinded?
259
- - Were exposures measured accurately?
260
- - Was timing of measurement appropriate?
261
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262
- ## Critical Appraisal Tools
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- ### For Different Study Types
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- **RCTs:**
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- - Cochrane RoB 2 (Risk of Bias 2) — current standard for randomized trials
268
- - PEDro Scale (for trials in physical therapy)
269
- - Legacy: Cochrane RoB 1, Jadad Scale (historical; prefer RoB 2 for new reviews)
270
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271
- **Observational Studies:**
272
- - ROBINS-I (Risk of Bias in Non-randomized Studies — of Interventions)
273
- - Newcastle-Ottawa Scale
274
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275
- **Diagnostic Studies:**
276
- - QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies)
277
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278
- **Systematic Reviews:**
279
- - PRISMA 2020 checklist (reporting standard for systematic reviews)
280
- - AMSTAR-2 (A Measurement Tool to Assess Systematic Reviews)
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- **All Study Types:**
283
- - CASP Checklists (Critical Appraisal Skills Programme)
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- ## Domain-Specific Considerations
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- ### Basic Science Research
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- **Hierarchy differs:**
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- 1. Multiple convergent lines of evidence
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- 2. Mechanistic understanding
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- 3. Reproducible experiments
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- 4. Established theoretical framework
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- **Key considerations:**
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- - Replication essential
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- - Mechanistic plausibility
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- - Consistency across model systems
298
- - Convergence of methods
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300
- ### Psychological Research
301
- **Additional concerns:**
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- - Replication crisis
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- - Publication bias particularly problematic
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- - Small effect sizes often expected
305
- - Cultural context matters
306
- - Measures often indirect (self-report)
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- **Strong evidence includes:**
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- - Preregistered studies
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- - Large samples
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- - Multiple measures
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- - Behavioral (not just self-report) outcomes
313
- - Cross-cultural replication
314
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315
- ### Epidemiology
316
- **Causal inference frameworks:**
317
- - Bradford Hill criteria
318
- - Rothman's causal pies
319
- - Directed Acyclic Graphs (DAGs)
320
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321
- **Strong observational evidence:**
322
- - Dose-response relationships
323
- - Temporal consistency
324
- - Biological plausibility
325
- - Specificity
326
- - Consistency across populations
327
- - Large effects unlikely due to confounding
328
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329
- ### Social Sciences
330
- **Challenges:**
331
- - Complex interventions
332
- - Context-dependent effects
333
- - Measurement challenges
334
- - Ethical constraints on RCTs
335
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336
- **Strengthening evidence:**
337
- - Mixed methods
338
- - Natural experiments
339
- - Instrumental variables
340
- - Regression discontinuity designs
341
- - Multiple operationalizations
342
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- ## Synthesizing Evidence Across Studies
344
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345
- ### Consistency
346
- **Strong evidence:**
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- - Multiple studies, different investigators
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- - Different populations and settings
349
- - Different research designs converge
350
- - Different measurement methods
351
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352
- **Weak evidence:**
353
- - Single study
354
- - Only one research group
355
- - Conflicting results
356
- - Publication bias evident
357
-
358
- ### Biological/Theoretical Plausibility
359
- **Strengthens evidence:**
360
- - Known mechanism
361
- - Consistent with other knowledge
362
- - Dose-response relationship
363
- - Coherent with animal/in vitro data
364
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365
- **Weakens evidence:**
366
- - No plausible mechanism
367
- - Contradicts established knowledge
368
- - Biological implausibility
369
-
370
- ### Temporality
371
- **Essential for causation:**
372
- - Cause must precede effect
373
- - Cross-sectional studies cannot establish
374
- - Reverse causation must be ruled out
375
-
376
- ### Specificity
377
- **Moderate indicator:**
378
- - Specific cause → specific effect strengthens causation
379
- - But lack of specificity doesn't rule out causation
380
- - Most causes have multiple effects
381
-
382
- ### Strength of Association
383
- **Strong evidence:**
384
- - Large effects unlikely to be due to confounding
385
- - Dose-response relationships
386
- - All-or-none effects
387
-
388
- **Caution:**
389
- - Small effects may still be real
390
- - Large effects can still be confounded
391
-
392
- ## Red Flags in Evidence Quality
393
-
394
- ### Study Design Red Flags
395
- - No control group
396
- - Self-selected participants
397
- - No randomization when feasible
398
- - No blinding when feasible
399
- - Very small sample
400
- - Inappropriate statistical tests
401
-
402
- ### Reporting Red Flags
403
- - Selective outcome reporting
404
- - No study registration/protocol
405
- - Missing methodological details
406
- - No conflicts of interest statement
407
- - Cherry-picked citations
408
- - Results don't match methods
409
-
410
- ### Interpretation Red Flags
411
- - Causal language from correlational data
412
- - Claiming "proof"
413
- - Ignoring limitations
414
- - Overgeneralizing
415
- - Spinning negative results
416
- - Post hoc rationalization
417
-
418
- ### Context Red Flags
419
- - Industry funding without independence
420
- - Single study in isolation
421
- - Contradicts preponderance of evidence
422
- - No replication
423
- - Published in predatory journal
424
- - Press release before peer review
425
-
426
- ## Practical Decision Framework
427
-
428
- ### When Evaluating Evidence, Ask:
429
-
430
- 1. **What type of study is this?** (Design)
431
- 2. **How well was it conducted?** (Quality)
432
- 3. **What does it actually show?** (Results)
433
- 4. **How likely is bias?** (Internal validity)
434
- 5. **Does it apply to my question?** (External validity)
435
- 6. **How does it fit with other evidence?** (Context)
436
- 7. **Are the conclusions justified?** (Interpretation)
437
- 8. **What are the limitations?** (Uncertainty)
438
-
439
- ### Making Decisions with Imperfect Evidence
440
-
441
- **High-quality evidence:**
442
- - Strong confidence in acting on findings
443
- - Reasonable to change practice/policy
444
-
445
- **Moderate-quality evidence:**
446
- - Provisional conclusions
447
- - Consider in conjunction with other factors
448
- - May warrant action depending on stakes
449
-
450
- **Low-quality evidence:**
451
- - Weak confidence
452
- - Hypothesis-generating
453
- - Insufficient for major decisions alone
454
- - Consider cost/benefit of waiting for better evidence
455
-
456
- **Very low-quality evidence:**
457
- - Very uncertain
458
- - Should not drive decisions alone
459
- - Useful for identifying gaps and research needs
460
-
461
- ### When Evidence is Conflicting
462
-
463
- **Strategies:**
464
- 1. Weight by study quality
465
- 2. Look for systematic differences (population, methods)
466
- 3. Consider publication bias
467
- 4. Update with most recent, rigorous evidence
468
- 5. Conduct/await systematic review
469
- 6. Consider if question is well-formed
470
-
471
- ## Communicating Evidence Strength
472
-
473
- **Avoid:**
474
- - Absolute certainty ("proves")
475
- - False balance (equal weight to unequal evidence)
476
- - Ignoring uncertainty
477
- - Cherry-picking studies
478
-
479
- **Better:**
480
- - Quantify uncertainty
481
- - Describe strength of evidence
482
- - Acknowledge limitations
483
- - Present range of evidence
484
- - Distinguish established from emerging findings
485
- - Be clear about what is/isn't known