@synsci/cli-darwin-x64 1.1.97 → 1.1.99

package/bin/skills/peer-review/references/paper_mechanics.md

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-# Paper Mechanics Checklist
-
-Comprehensive checklist for presentation details that human reviewers frequently identify. These mechanical issues are often missed by content-focused review but significantly impact paper quality.
-
-## Table Audit
-
-### Numeric Content
-
-| Issue | Example (Fail) | Fix |
-|-------|---------------|-----|
-| Qualitative descriptors | "Higher", "Better", "↑" | Actual numbers: "15.3%", "+2.4" |
-| Missing values | Empty cells, "N/A" without explanation | Complete data or explain missingness |
-| Inconsistent precision | "15.3" vs "15" vs "15.300" | Consistent significant figures |
-| Missing units | "Speed: 15" | "Speed (ms): 15" |
-
-### Structure and Headers
-
-| Issue | Example (Fail) | Fix |
-|-------|---------------|-----|
-| Ambiguous abbreviations | "Acc." without definition | Define in caption or use full words |
-| Inconsistent naming | "BERT" in Table 1, "bert" in Table 2 | Consistent capitalization |
-| Missing baselines | Only proposed method shown | Include relevant baselines |
-| Unclear groupings | Methods and datasets mixed | Logical organization with separators |
-
-### Caption Completeness
-
-| Requirement | Example |
-|-------------|---------|
-| Self-explanatory | Reader understands without text reference |
-| Abbreviation definitions | "ACC: accuracy, F1: F1-score" |
-| Data source | "Results on MNLI dev set" |
-| Statistical info | "Mean ± std over 5 runs" |
-
-### Common Table Issues Checklist
-
-- [ ] All cells contain numeric values (not just "Higher/Lower")
-- [ ] Column headers are clear and complete
-- [ ] Units are specified for all measurements
-- [ ] Significant figures are appropriate and consistent
-- [ ] Best values are clearly indicated (bold, underline)
-- [ ] Statistical uncertainty reported (std, CI, p-values)
-- [ ] Baselines and comparisons are included
-- [ ] Caption is self-explanatory
-
-## Figure Audit
-
-### Legibility
-
-| Issue | Indicator | Standard |
-|-------|-----------|----------|
-| Text too small | Unreadable at 100% zoom | Minimum 8pt in final figure |
-| Axis labels missing | No indication of what's plotted | All axes labeled with units |
-| Legend obscures data | Legend overlaps plot area | Legend in clear space or outside |
-| Low resolution | Pixelation visible | 300+ DPI for print |
-
-### Color and Accessibility
-
-| Issue | Example (Fail) | Fix |
-|-------|---------------|-----|
-| Red-green scheme | Default matplotlib colors | Colorblind-safe palettes |
-| Too many colors | 10+ colors in one plot | Limit to 6-7, use shapes/patterns |
-| Low contrast | Light colors on white | Sufficient contrast for visibility |
-| Inconsistent colors | Same method, different colors across figures | Consistent color scheme |
-
-### Plot Quality
-
-| Issue | Example (Fail) | Fix |
-|-------|---------------|-----|
-| Missing error bars | Point estimates only | Show uncertainty (std, CI) |
-| Truncated axes | Y-axis starting at 90 for 91-95 range | Start at 0 or clearly indicate break |
-| Cluttered | Too many lines/points | Simplify or split into panels |
-| Cherry-picked range | Hiding poor performance region | Show full range |
-
-### Common Figure Issues Checklist
-
-- [ ] Text readable at 100% zoom (minimum 8pt final size)
-- [ ] All axes labeled with units
-- [ ] Legend doesn't obscure data
-- [ ] Colors are colorblind-accessible
-- [ ] Error bars or uncertainty shown
-- [ ] Consistent color scheme across paper
-- [ ] Resolution suitable for print (300+ DPI)
-- [ ] Aspect ratio appropriate for content
-
-## Notation Audit
-
-### Variable Definitions
-
-| Issue | Example (Fail) | Fix |
-|-------|---------------|-----|
-| Undefined variables | "We minimize L" (L never defined) | Define before first use |
-| Delayed definitions | Used on page 3, defined on page 5 | Define at first occurrence |
-| Implicit assumptions | "The standard loss" without specification | Explicitly state the loss function |
-
-### Consistency
-
-| Issue | Example (Fail) | Fix |
-|-------|---------------|-----|
-| Symbol reuse | θ for parameters and temperature | Different symbols for different concepts |
-| Inconsistent notation | x, X, **x** for same concept | Pick one style and maintain |
-| Mixed conventions | 0-indexed and 1-indexed in same paper | Consistent indexing convention |
-
-### Standard Conventions
-
-| Issue | Example (Fail) | Fix |
-|-------|---------------|-----|
-| Non-standard notation | Unusual symbols for common concepts | Use field-standard notation |
-| Missing font conventions | Scalars and vectors same font | Scalars: italic, vectors: bold |
-| Equation numbering | Important equations unnumbered | Number equations that are referenced |
-
-### Notation Checklist
-
-- [ ] All variables defined before first use
-- [ ] No symbol reuse for different concepts
-- [ ] Consistent notation throughout paper
-- [ ] Font conventions followed (italic scalars, bold vectors)
-- [ ] Standard field notation used where applicable
-- [ ] Important equations are numbered
-
-## Structure Audit
-
-### Section Redundancy
-
-| Issue | Indicator | Fix |
-|-------|-----------|-----|
-| Repeated content | Same information in Intro and Related Work | Consolidate or differentiate purpose |
-| Restated results | Discussion repeats Results verbatim | Discussion should interpret, not repeat |
-| Redundant background | Method section re-explains preliminaries | Reference earlier sections |
-
-### Cross-References
-
-| Issue | Example (Fail) | Fix |
-|-------|---------------|-----|
-| Orphan figures | Figure 3 never mentioned in text | Reference all figures in text |
-| Missing references | "As shown above" without citation | Specific section/figure references |
-| Broken references | "See Section ??" | Verify all cross-references |
-
-### Citation Completeness
-
-| Issue | Example (Fail) | Fix |
-|-------|---------------|-----|
-| Unsupported claims | "It is well known that..." | Add citation |
-| Missing seminal work | No citation for foundational methods | Cite original sources |
-| Only self-citations | All citations are author's prior work | Balanced citation of field |
-| Outdated citations | Most recent citation from 5+ years ago | Include recent relevant work |
-
-### Structure Checklist
-
-- [ ] No redundant content across sections
-- [ ] All figures and tables referenced in text
-- [ ] Cross-references are complete and correct
-- [ ] All factual claims are cited
-- [ ] Citation coverage includes recent work
-- [ ] Self-citations are proportionate
-
-## Abstract and Title Audit
-
-### Title Quality
-
-| Issue | Example (Fail) | Fix |
-|-------|---------------|-----|
-| Too vague | "A New Method for NLP" | Specific: "Efficient Attention for Long Documents" |
-| Too long | 20+ words | Target 10-15 words |
-| Clickbait | "Groundbreaking breakthrough in..." | Factual and professional |
-| Acronym-heavy | "BERT-GAN for NER via RL" | Expand key terms |
-
-### Abstract Completeness
-
-| Required Element | Check |
-|-----------------|-------|
-| Problem statement | What gap does this address? |
-| Method summary | What approach is taken? |
-| Key results | What are the main findings? |
-| Significance | Why does this matter? |
-
-### Abstract Issues Checklist
-
-- [ ] Problem clearly stated
-- [ ] Method briefly described
-- [ ] Key results with numbers (not just "improves")
-- [ ] Claims match actual results in paper
-- [ ] Within word limit for venue
-- [ ] Self-contained (no citations needed)
-
-## Methods Reproducibility Audit
-
-### Technical Details
-
-| Required Element | Check |
-|-----------------|-------|
-| Hyperparameters | Learning rate, batch size, etc. |
-| Random seeds | For reproducibility |
-| Compute resources | GPU type, training time |
-| Software versions | PyTorch version, etc. |
-
-### Data Details
-
-| Required Element | Check |
-|-----------------|-------|
-| Dataset sources | Where to obtain |
-| Preprocessing | Exact steps applied |
-| Splits | Train/val/test sizes |
-| Licenses | Usage rights |
-
-### Reproducibility Checklist
-
-- [ ] All hyperparameters specified
-- [ ] Random seeds reported
-- [ ] Compute requirements stated
-- [ ] Software versions listed
-- [ ] Data sources provided
-- [ ] Preprocessing steps documented
-- [ ] Code availability statement present
-
-## Quick Scan Protocol
-
-For efficient paper mechanics review:
-
-### 30-Second Table Scan
-1. Check any table for "Higher"/"Better" instead of numbers
-2. Verify units are present
-3. Check for missing cells
-
-### 30-Second Figure Scan
-1. Zoom to 100% and check text readability
-2. Look for legend/data overlap
-3. Check for error bars
-
-### 30-Second Notation Scan
-1. Find first equation and check if variables defined
-2. Look for repeated symbols
-3. Check for undefined acronyms
-
-### 30-Second Structure Scan
-1. Compare Intro and Related Work for redundancy
-2. Check if all figures referenced in text
-3. Look for unsupported factual claims
-
-## Reporting Format
-
-When reporting mechanics issues:
-
-```markdown
-### Paper Mechanics Issues
-
-**Tables:**
-- [Moderate] Table 1: Uses "Higher" instead of numeric values for improvement column
-- [Minor] Table 2: Missing units for latency column
-
-**Figures:**
-- [Major] Figure 3: Axis labels unreadable at 100% zoom
-- [Minor] Figure 5: Legend overlaps with data points
-
-**Notation:**
-- [Moderate] Variable θ used for both model parameters (p.3) and temperature (p.7)
-
-**Structure:**
-- [Minor] Section 2.1 and 3.2 contain redundant background on transformers
-```
-
-## Severity Guide for Mechanics
-
-| Severity | Criteria | Examples |
-|----------|----------|----------|
-| **Major** | Impedes understanding or evaluation | Illegible figures, undefined key notation |
-| **Moderate** | Reduces quality but comprehensible | Non-numeric table values, minor redundancy |
-| **Minor** | Polish issue, easy to fix | Small legend overlap, missing units |
-
-Mechanics issues are typically Minor or Moderate, rarely Major, and never Critical (unless they hide scientific issues).

package/bin/skills/peer-review/references/reporting_standards.md

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-# Scientific Reporting Standards and Guidelines
-
-This document catalogs major reporting standards and guidelines across scientific disciplines. When reviewing manuscripts, verify that authors have followed the appropriate guidelines for their study type and discipline.
-
-## Clinical Trials and Medical Research
-
-### CONSORT (Consolidated Standards of Reporting Trials)
-**Purpose:** Randomized controlled trials (RCTs)
-**Key Requirements:**
-- Trial design, participants, and interventions clearly described
-- Primary and secondary outcomes specified
-- Sample size calculation and statistical methods
-- Participant flow through trial (enrollment, allocation, follow-up, analysis)
-- Baseline characteristics of participants
-- Numbers analyzed in each group
-- Outcomes and estimation with confidence intervals
-- Adverse events
-- Trial registration number and protocol access
-
-**Reference:** http://www.consort-statement.org/
-
-### STROBE (Strengthening the Reporting of Observational Studies in Epidemiology)
-**Purpose:** Observational studies (cohort, case-control, cross-sectional)
-**Key Requirements:**
-- Study design clearly stated
-- Setting, eligibility criteria, and participant sources
-- Variables clearly defined
-- Data sources and measurement methods
-- Bias assessment
-- Sample size justification
-- Statistical methods including handling of missing data
-- Participant flow and characteristics
-- Main results with confidence intervals
-- Limitations discussed
-
-**Reference:** https://www.strobe-statement.org/
-
-### PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses)
-**Purpose:** Systematic reviews and meta-analyses
-**Key Requirements:**
-- Protocol registration
-- Systematic search strategy across multiple databases
-- Inclusion/exclusion criteria
-- Study selection process
-- Data extraction methods
-- Quality assessment of included studies
-- Statistical methods for meta-analysis
-- Assessment of publication bias
-- Heterogeneity assessment
-- PRISMA flow diagram showing study selection
-- Summary of findings tables
-
-**Reference:** http://www.prisma-statement.org/
-
-### SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials)
-**Purpose:** Clinical trial protocols
-**Key Requirements:**
-- Administrative information (title, registration, funding)
-- Introduction (rationale, objectives)
-- Methods (design, participants, interventions, outcomes, sample size)
-- Ethics and dissemination
-- Trial schedule and assessments
-
-**Reference:** https://www.spirit-statement.org/
-
-### CARE (CAse REport guidelines)
-**Purpose:** Case reports
-**Key Requirements:**
-- Patient information and demographics
-- Clinical findings
-- Timeline of events
-- Diagnostic assessment
-- Therapeutic interventions
-- Follow-up and outcomes
-- Patient perspective
-- Informed consent
-
-**Reference:** https://www.care-statement.org/
-
-## Animal Research
-
-### ARRIVE (Animal Research: Reporting of In Vivo Experiments)
-**Purpose:** Studies involving animal research
-**Key Requirements:**
-- Title indicates study involves animals
-- Abstract provides accurate summary
-- Background and objectives clearly stated
-- Ethical statement and approval
-- Housing and husbandry details
-- Animal details (species, strain, sex, age, weight)
-- Experimental procedures in detail
-- Experimental animals (number, allocation, welfare assessment)
-- Statistical methods appropriate
-- Exclusion criteria stated
-- Sample size determination
-- Randomization and blinding described
-- Outcome measures defined
-- Adverse events reported
-
-**Reference:** https://arriveguidelines.org/
-
-## Genomics and Molecular Biology
-
-### MIAME (Minimum Information About a Microarray Experiment)
-**Purpose:** Microarray experiments
-**Key Requirements:**
-- Experimental design clearly described
-- Array design information
-- Samples (origin, preparation, labeling)
-- Hybridization procedures and parameters
-- Image acquisition and quantification
-- Normalization and data transformation
-- Raw and processed data availability
-- Database accession numbers
-
-**Reference:** http://fged.org/projects/miame/
-
-### MINSEQE (Minimum Information about a high-throughput Nucleotide Sequencing Experiment)
-**Purpose:** High-throughput sequencing (RNA-seq, ChIP-seq, etc.)
-**Key Requirements:**
-- Experimental design and biological context
-- Sample information (source, preparation, QC)
-- Library preparation (protocol, adapters, size selection)
-- Sequencing platform and parameters
-- Data processing pipeline (alignment, quantification, normalization)
-- Quality control metrics
-- Raw data deposition (SRA, GEO, ENA)
-- Processed data and analysis code availability
-
-### MIGS/MIMS (Minimum Information about a Genome/Metagenome Sequence)
-**Purpose:** Genome and metagenome sequencing
-**Key Requirements:**
-- Sample origin and environmental context
-- Sequencing methods and coverage
-- Assembly methods and quality metrics
-- Annotation approach
-- Quality control and contamination screening
-- Data deposition in INSDC databases
-
-**Reference:** https://gensc.org/
-
-## Structural Biology
-
-### PDB (Protein Data Bank) Deposition Requirements
-**Purpose:** Macromolecular structure determination
-**Key Requirements:**
-- Atomic coordinates deposited
-- Structure factors for X-ray structures
-- Restraints and experimental data for NMR
-- EM maps and metadata for cryo-EM
-- Model quality validation metrics
-- Experimental conditions (crystallization, sample preparation)
-- Data collection parameters
-- Refinement statistics
-
-**Reference:** https://www.wwpdb.org/
-
-## Proteomics and Mass Spectrometry
-
-### MIAPE (Minimum Information About a Proteomics Experiment)
-**Purpose:** Proteomics experiments
-**Key Requirements:**
-- Sample processing and fractionation
-- Separation methods (2D gel, LC)
-- Mass spectrometry parameters (instrument, acquisition)
-- Database search and validation parameters
-- Peptide and protein identification criteria
-- Quantification methods
-- Statistical analysis
-- Data deposition (PRIDE, PeptideAtlas)
-
-**Reference:** http://www.psidev.info/
-
-## Neuroscience
-
-### COBIDAS (Committee on Best Practices in Data Analysis and Sharing)
-**Purpose:** MRI and fMRI studies
-**Key Requirements:**
-- Scanner and sequence parameters
-- Preprocessing pipeline details
-- Software versions and parameters
-- Statistical analysis approach
-- Multiple comparison correction
-- ROI definitions
-- Data sharing (raw data, analysis scripts)
-
-**Reference:** https://www.humanbrainmapping.org/cobidas
-
-## Flow Cytometry
-
-### MIFlowCyt (Minimum Information about a Flow Cytometry Experiment)
-**Purpose:** Flow cytometry experiments
-**Key Requirements:**
-- Experimental overview and purpose
-- Sample characteristics and preparation
-- Instrument information and settings
-- Reagents (antibodies, fluorophores, concentrations)
-- Compensation and controls
-- Gating strategy
-- Data analysis approach
-- Data availability
-
-**Reference:** http://flowcyt.org/
-
-## Ecology and Environmental Science
-
-### MIAPPE (Minimum Information About a Plant Phenotyping Experiment)
-**Purpose:** Plant phenotyping studies
-**Key Requirements:**
-- Investigation and study metadata
-- Biological material information
-- Environmental parameters
-- Experimental design and factors
-- Phenotypic measurements and methods
-- Data file descriptions
-
-**Reference:** https://www.miappe.org/
-
-## Chemistry and Chemical Biology
-
-### MIRIBEL (Minimum Information Reporting in Bio-Nano Experimental Literature)
-**Purpose:** Nanomaterial characterization
-**Key Requirements:**
-- Nanomaterial composition and structure
-- Size, shape, and morphology characterization
-- Surface chemistry and functionalization
-- Purity and stability
-- Experimental conditions
-- Characterization methods
-
-## Quality Assessment and Bias
-
-### CAMARADES (Collaborative Approach to Meta-Analysis and Review of Animal Data from Experimental Studies)
-**Purpose:** Quality assessment for animal studies in systematic reviews
-**Key Items:**
-- Publication in peer-reviewed journal
-- Statement of temperature control
-- Randomization to treatment
-- Blinded assessment of outcome
-- Avoidance of anesthetic with marked intrinsic properties
-- Use of appropriate animal model
-- Sample size calculation
-- Compliance with regulatory requirements
-- Statement of conflict of interest
-- Study pre-registration
-
-### SYRCLE's Risk of Bias Tool
-**Purpose:** Assessing risk of bias in animal intervention studies
-**Domains:**
-- Selection bias (sequence generation, baseline characteristics, allocation concealment)
-- Performance bias (random housing, blinding of personnel)
-- Detection bias (random outcome assessment, blinding of assessors)
-- Attrition bias (incomplete outcome data)
-- Reporting bias (selective outcome reporting)
-- Other sources of bias
-
-## General Principles Across Guidelines
-
-### Common Requirements
-1. **Transparency:** All methods, materials, and analyses fully described
-2. **Reproducibility:** Sufficient detail for independent replication
-3. **Data Availability:** Raw data and analysis code shared or deposited
-4. **Registration:** Studies pre-registered where applicable
-5. **Ethics:** Appropriate approvals and consent documented
-6. **Conflicts of Interest:** Disclosed for all authors
-7. **Statistical Rigor:** Methods appropriate and fully described
-8. **Completeness:** All outcomes reported, including negative results
-
-### Red Flags for Non-Compliance
-- Methods section lacks critical details
-- No mention of following reporting guidelines
-- Data availability statement missing or vague
-- No database accession numbers for omics data
-- No trial registration for clinical studies
-- Sample size not justified
-- Statistical methods inadequately described
-- Missing flow diagrams (CONSORT, PRISMA)
-- Selective reporting of outcomes
-
-## How to Use This Reference
-
-When reviewing a manuscript:
-1. Identify the study type and discipline
-2. Find the relevant reporting guideline(s)
-3. Check if authors mention following the guideline
-4. Verify that key requirements are addressed
-5. Note any missing elements in your review
-6. Suggest the appropriate guideline if not mentioned
-
-Many journals require authors to complete reporting checklists at submission. Reviewers should verify compliance even if a checklist was submitted.