@synsci/cli-darwin-x64 1.1.70 → 1.1.72

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

@@ -0,0 +1,269 @@
+# 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

@@ -0,0 +1,290 @@
+# 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.