@pikaa-ai/pikaa 0.2.4 → 0.3.0

package/skills/venue-templates/assets/examples/medical_structured_abstract.md

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+# Medical Journal Structured Abstract Examples
+
+Examples of structured abstracts for NEJM, Lancet, JAMA, and BMJ showing the labeled section format expected at medical journals.
+
+---
+
+## NEJM Style (250 words max)
+
+### Example 1: Clinical Trial
+
+```
+BACKGROUND
+Sodium-glucose cotransporter 2 (SGLT2) inhibitors reduce cardiovascular 
+events in patients with type 2 diabetes and established cardiovascular 
+disease. Whether these benefits extend to patients with heart failure and 
+reduced ejection fraction, regardless of diabetes status, is unknown.
+
+METHODS
+We randomly assigned 4,744 patients with heart failure and an ejection 
+fraction of 40% or less to receive dapagliflozin (10 mg once daily) or 
+placebo, in addition to recommended therapy. The primary outcome was a 
+composite of worsening heart failure (hospitalization or urgent visit 
+requiring intravenous therapy) or cardiovascular death.
+
+RESULTS
+Over a median of 18.2 months, the primary outcome occurred in 386 of 
+2,373 patients (16.3%) in the dapagliflozin group and in 502 of 2,371 
+patients (21.2%) in the placebo group (hazard ratio, 0.74; 95% confidence 
+interval [CI], 0.65 to 0.85; P<0.001). A first worsening heart failure 
+event occurred in 237 patients (10.0%) in the dapagliflozin group and 
+in 326 patients (13.7%) in the placebo group (hazard ratio, 0.70; 95% 
+CI, 0.59 to 0.83). Death from cardiovascular causes occurred in 227 
+patients (9.6%) and 273 patients (11.5%), respectively (hazard ratio, 
+0.82; 95% CI, 0.69 to 0.98). Effects were similar in patients with and 
+without diabetes. Serious adverse events were similar between groups.
+
+CONCLUSIONS
+Among patients with heart failure and a reduced ejection fraction, 
+dapagliflozin reduced the risk of worsening heart failure or 
+cardiovascular death, regardless of the presence of diabetes.
+```
+
+**Key Features**:
+- Four labeled sections (BACKGROUND, METHODS, RESULTS, CONCLUSIONS)
+- Background: 2 sentences (problem + gap)
+- Methods: Study design, population, intervention, primary outcome
+- Results: Primary outcome with HR and 95% CI, key secondary outcomes
+- Conclusions: Clear, measured statement of findings
+
+---
+
+### Example 2: Observational Study
+
+```
+BACKGROUND
+Long-term use of proton-pump inhibitors (PPIs) has been associated with 
+adverse outcomes in observational studies, but causality remains uncertain. 
+The relationship between PPI use and chronic kidney disease is unclear.
+
+METHODS
+We conducted a prospective cohort study using data from 10,482 participants 
+in the Atherosclerosis Risk in Communities study who were free of kidney 
+disease at baseline. PPI use was ascertained at baseline and follow-up 
+visits. The primary outcome was incident chronic kidney disease, defined 
+as an estimated glomerular filtration rate less than 60 ml per minute per 
+1.73 m² of body-surface area.
+
+RESULTS
+Over a median follow-up of 13.9 years, incident chronic kidney disease 
+occurred in 56.0 per 1000 person-years among PPI users and in 42.0 per 
+1000 person-years among non-users (adjusted hazard ratio, 1.50; 95% 
+confidence interval [CI], 1.14 to 1.96). The association persisted after 
+adjustment for potential confounders, including indication for PPI use 
+and baseline kidney function. Sensitivity analyses using propensity-score 
+matching yielded similar results. No association was observed for 
+histamine H2-receptor antagonist use (hazard ratio, 1.08; 95% CI, 0.87 
+to 1.34).
+
+CONCLUSIONS
+PPI use was associated with an increased risk of incident chronic kidney 
+disease in this community-based cohort. These findings warrant cautious 
+use of PPIs and further investigation to establish causality.
+```
+
+**Key Features**:
+- Appropriate hedging for observational study ("associated with")
+- Incidence rates provided (per 1000 person-years)
+- Sensitivity analyses mentioned
+- Negative control (H2-receptor antagonists)
+- Cautious conclusion acknowledging limitation
+
+---
+
+## Lancet Style (300 words max)
+
+### Example 3: Clinical Trial with Summary Box
+
+```
+BACKGROUND
+Dexamethasone has been shown to reduce mortality in hospitalized patients 
+with COVID-19 requiring respiratory support. We aimed to evaluate whether 
+higher doses of corticosteroids would provide additional benefit in 
+patients with severe COVID-19 pneumonia.
+
+METHODS
+In this randomized, controlled, open-label trial conducted at 18 hospitals 
+in Brazil, we assigned patients with moderate-to-severe COVID-19 (PaO2/FiO2 
+≤200 mm Hg) to receive high-dose dexamethasone (20 mg once daily for 5 
+days, then 10 mg once daily for 5 days) or standard dexamethasone (6 mg 
+once daily for 10 days). The primary outcome was ventilator-free days 
+at 28 days.
+
+FINDINGS
+Between June 17, 2020, and September 20, 2021, we enrolled 299 patients 
+(151 assigned to high-dose dexamethasone and 148 to standard 
+dexamethasone). The mean number of ventilator-free days at 28 days was 
+14·2 (SD 10·8) in the high-dose group and 15·5 (SD 10·4) in the standard 
+group (difference, −1·3 days; 95% CI, −3·9 to 1·3; P=0·32). There was 
+no significant difference in 28-day mortality (high dose 35·8% vs 
+standard 31·8%; hazard ratio 1·16; 95% CI, 0·79 to 1·70). Hyperglycemia 
+requiring insulin was more frequent with high-dose dexamethasone (66·0% 
+vs 53·4%; P=0·027).
+
+INTERPRETATION
+In patients with moderate-to-severe COVID-19 pneumonia, high-dose 
+dexamethasone did not improve ventilator-free days and was associated 
+with increased hyperglycemia compared with standard-dose dexamethasone. 
+These findings do not support the use of high-dose corticosteroids in 
+COVID-19.
+
+FUNDING
+Ministry of Health of Brazil.
+```
+
+**Key Features**:
+- Lancet uses "Findings" instead of "Results"
+- Lancet uses "Interpretation" instead of "Conclusions"
+- Includes funding statement in abstract
+- Decimal point (·) instead of period in numbers (Lancet style)
+
+---
+
+## JAMA Style (350 words max)
+
+### Example 4: Diagnostic Study
+
+```
+IMPORTANCE
+Lung cancer screening with low-dose computed tomography (CT) reduces 
+mortality but identifies many indeterminate pulmonary nodules, leading 
+to unnecessary invasive procedures. Improved risk prediction could 
+reduce harms while preserving benefits.
+
+OBJECTIVE
+To develop and validate a deep learning model for predicting malignancy 
+risk of lung nodules detected on screening CT.
+
+DESIGN, SETTING, AND PARTICIPANTS
+This retrospective cohort study included 14,851 participants with 
+lung nodules from the National Lung Screening Trial (NLST) for model 
+development and 5,402 participants from an independent multi-site 
+validation cohort (2016-2019). Data analysis was performed from 
+January to November 2022.
+
+EXPOSURES
+Deep learning model prediction of malignancy risk based on CT imaging.
+
+MAIN OUTCOMES AND MEASURES
+The primary outcome was lung cancer diagnosis within 2 years. Model 
+performance was assessed by area under the receiver operating 
+characteristic curve (AUC), sensitivity, specificity, and comparison 
+with radiologist assessments.
+
+RESULTS
+In the validation cohort (median age, 65 years; 57% male), 312 nodules 
+(5.8%) were diagnosed as lung cancer within 2 years. The deep learning 
+model achieved an AUC of 0.94 (95% CI, 0.92-0.96), compared with 0.85 
+(95% CI, 0.82-0.88) for the Lung-RADS categorization used by radiologists 
+(P<0.001). At 95% sensitivity, the model achieved 68% specificity compared 
+with 38% for Lung-RADS, corresponding to a 49% reduction in false-positive 
+nodules requiring follow-up. The model's performance was consistent across 
+subgroups defined by nodule size, location, and patient demographics.
+
+CONCLUSIONS AND RELEVANCE
+A deep learning model for lung nodule malignancy prediction outperformed 
+current clinical standards and could substantially reduce false-positive 
+findings in lung cancer screening, decreasing unnecessary surveillance 
+and invasive procedures.
+```
+
+**Key Features**:
+- JAMA-specific sections (IMPORTANCE, OBJECTIVE, DESIGN...)
+- "Importance" section required (2-3 sentences on why this matters)
+- Detailed design section
+- "Exposures" clearly stated
+- "Main Outcomes and Measures" explicit
+
+---
+
+## BMJ Style (300 words max)
+
+### Example 5: Cohort Study
+
+```
+OBJECTIVE
+To examine the association between statin use and risk of Parkinson's 
+disease in a large population-based cohort.
+
+DESIGN
+Prospective cohort study.
+
+SETTING
+UK Biobank, 2006-2021.
+
+PARTICIPANTS
+402,251 adults aged 40-69 years without Parkinson's disease at baseline.
+
+MAIN OUTCOME MEASURES
+Incident Parkinson's disease identified through hospital admissions, 
+primary care records, and death certificates. Hazard ratios were 
+estimated using Cox regression, adjusted for age, sex, education, 
+smoking, alcohol, physical activity, body mass index, and comorbidities.
+
+RESULTS
+Over a median follow-up of 12.3 years, 2,841 participants developed 
+Parkinson's disease (incidence rate 5.7 per 10,000 person-years). 
+Statin use at baseline was not associated with incident Parkinson's 
+disease (adjusted hazard ratio 0.95, 95% confidence interval 0.87 to 
+1.04). Results were consistent across analyses stratified by statin 
+type (lipophilic vs hydrophilic), dose, and duration of use, and in 
+sensitivity analyses accounting for reverse causation. No protective 
+association was observed in analyses restricted to participants with 
+high cardiovascular risk or in propensity-score matched cohorts.
+
+CONCLUSIONS
+In this large prospective cohort, statin use was not associated with 
+reduced risk of Parkinson's disease, contrary to findings from some 
+previous observational studies. The null findings were robust across 
+multiple sensitivity analyses. These results do not support a 
+neuroprotective effect of statins against Parkinson's disease.
+
+WHAT IS ALREADY KNOWN ON THIS TOPIC
+Previous observational studies have yielded inconsistent results 
+regarding statin use and Parkinson's disease risk.
+
+WHAT THIS STUDY ADDS
+This large prospective study with long follow-up found no evidence 
+that statin use protects against Parkinson's disease.
+```
+
+**Key Features**:
+- BMJ uses abbreviated section headers
+- Includes "What is already known" and "What this study adds" boxes
+- Design, Setting, and Participants as separate sections
+- Clear Main Outcome Measures section
+
+---
+
+## Key Differences Between Journals
+
+| Element | NEJM | Lancet | JAMA | BMJ |
+|---------|------|--------|------|-----|
+| **Word limit** | 250 | 300 | 350 | 300 |
+| **Results label** | RESULTS | FINDINGS | RESULTS | RESULTS |
+| **Conclusions label** | CONCLUSIONS | INTERPRETATION | CONCLUSIONS AND RELEVANCE | CONCLUSIONS |
+| **Unique sections** | — | Funding in abstract | IMPORTANCE | What is known/adds |
+| **Decimal style** | Period (.) | Centered dot (·) | Period (.) | Period (.) |
+
+---
+
+## Essential Elements for All Medical Abstracts
+
+### Background/Context
+- Disease burden or clinical problem (1 sentence)
+- Knowledge gap or rationale for study (1 sentence)
+
+### Methods
+- Study design (RCT, cohort, case-control)
+- Setting (number of sites, country/region)
+- Participants (N, key inclusion criteria)
+- Intervention or exposure
+- Primary outcome with definition
+
+### Results
+- Number enrolled and analyzed
+- Primary outcome with effect size and 95% CI
+- Key secondary outcomes
+- P-values for primary comparisons
+- Adverse events (if applicable)
+
+### Conclusions
+- Clear statement of main finding
+- Appropriate hedging based on study design
+- Clinical implication (optional, 1 sentence)
+
+---
+
+## Common Mistakes in Medical Abstracts
+
+❌ **Missing confidence intervals**: "HR 0.75, P=0.02" → include 95% CI
+❌ **Relative risk only**: Add absolute risk reduction, NNT
+❌ **Causal language for observational studies**: "PPIs cause kidney disease"
+❌ **Overstated conclusions**: Claims exceeding evidence
+❌ **Missing sample sizes**: Always include N for each group
+❌ **Vague outcomes**: "Improved outcomes" without specific definition
+
+---
+
+## See Also
+
+- `medical_journal_styles.md` - Comprehensive medical writing guide
+- `venue_writing_styles.md` - Style comparison across venues
+

package/skills/venue-templates/assets/examples/nature_abstract_examples.md

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+# Nature/Science Abstract Examples
+
+Examples of well-crafted abstracts for high-impact multidisciplinary journals. These demonstrate the flowing paragraph style with broad accessibility expected at Nature, Science, and related venues.
+
+---
+
+## Example 1: Molecular Biology / Cell Biology
+
+**Topic**: CRISPR gene editing discovery
+
+```
+The ability to precisely edit DNA sequences in living cells has transformed 
+biological research and holds promise for treating genetic diseases. However, 
+current genome editing tools can introduce unwanted mutations at off-target 
+sites, limiting their clinical potential. Here we describe prime editing, a 
+versatile and precise genome editing method that directly writes new genetic 
+information into a specified DNA site using a reverse transcriptase fused to a 
+CRISPR nickase. Prime editing can make all 12 types of point mutations, as 
+well as small insertions and deletions, with minimal off-target editing and 
+without requiring double-strand breaks or donor DNA templates. In human cells, 
+we used prime editing to correct the primary genetic causes of sickle cell 
+disease and Tay-Sachs disease, and to install protective mutations that 
+reduce risk of prion disease. Prime editing expands the scope and capabilities 
+of genome editing and may address approximately 89% of known human genetic 
+disease variants.
+```
+
+**Why this works**:
+- Opens with broad significance (genetic disease treatment)
+- States the problem clearly (off-target mutations)
+- Describes the approach accessibly ("writes new genetic information")
+- Includes specific results (all 12 point mutations, specific diseases)
+- Ends with quantified impact (89% of variants)
+
+---
+
+## Example 2: Neuroscience
+
+**Topic**: Memory consolidation mechanism
+
+```
+Sleep is essential for memory consolidation, yet how the sleeping brain 
+transforms labile memories into stable long-term representations remains 
+poorly understood. We used multi-site electrophysiology in freely behaving 
+mice to record the activity of thousands of neurons across hippocampus and 
+cortex during learning and subsequent sleep. We discovered that specific 
+neurons that encode a newly learned memory reactivate in precisely timed 
+sequences during slow-wave sleep, with hippocampal reactivation preceding 
+cortical reactivation by 10-15 milliseconds. Optogenetic disruption of this 
+temporal coordination impaired memory retention by 78%, whereas artificial 
+enhancement of the temporal relationship strengthened memories beyond normal 
+levels. These results reveal that the temporal ordering of hippocampal-cortical 
+replay is not merely correlative but causally necessary for memory 
+consolidation. Our findings suggest new therapeutic approaches for memory 
+disorders based on optimizing the temporal dynamics of sleep.
+```
+
+**Why this works**:
+- Connects to well-known phenomenon (sleep and memory)
+- States what was unknown
+- Describes approach (multi-site recordings)
+- Key finding with specific number (10-15 ms)
+- Causal evidence (disruption and enhancement experiments)
+- Broader implications (therapeutic approaches)
+
+---
+
+## Example 3: Climate Science
+
+**Topic**: Carbon cycle feedback
+
+```
+Arctic permafrost contains approximately 1,500 billion tonnes of organic 
+carbon—twice the amount currently in the atmosphere. As the Arctic warms, 
+this carbon may be released to the atmosphere, accelerating global warming 
+through a positive feedback loop. However, the magnitude and timing of this 
+feedback remain highly uncertain because microbial decomposition rates in 
+thawing permafrost are poorly constrained. Here we present a 15-year 
+field experiment across 25 sites spanning the Arctic, tracking carbon 
+fluxes in warming permafrost under natural conditions. We find that 
+microbial respiration increases exponentially with temperature until soils 
+reach 3°C, then plateaus due to substrate limitation—a threshold effect 
+not captured by current Earth system models. Our results suggest that 
+permafrost carbon feedback will be 30-50% lower than current projections 
+during this century, providing more time to limit warming, but will 
+accelerate dramatically if deep permafrost begins to thaw.
+```
+
+**Why this works**:
+- Opens with striking number (1,500 billion tonnes)
+- Clear problem statement (feedback uncertainty)
+- Specific methodology (15 years, 25 sites)
+- Novel finding (threshold at 3°C)
+- Implications both reassuring and cautionary
+
+---
+
+## Example 4: Physics / Materials Science
+
+**Topic**: Room-temperature superconductivity
+
+```
+Superconductivity—the flow of electricity without resistance—has been 
+confined to extremely low temperatures since its discovery over a century 
+ago, limiting practical applications. The recent demonstration of 
+superconductivity in hydrogen-rich materials at high pressure has raised 
+hopes for higher transition temperatures, but achieving room-temperature 
+superconductivity at ambient pressure has remained elusive. Here we report 
+superconductivity at 21°C (294 K) in a nitrogen-doped lutetium hydride 
+(Lu-N-H) compound at pressures of approximately 1 GPa—nearly ambient 
+conditions. Electrical resistance drops to zero below the transition 
+temperature with a sharp transition width of 2 K, and we observe the Meissner 
+effect confirming bulk superconductivity. Density functional theory 
+calculations suggest that nitrogen incorporation stabilizes the high-symmetry 
+structure that enables strong electron-phonon coupling. These results 
+establish a pathway toward practical room-temperature superconductors.
+```
+
+**Why this works**:
+- Opens with accessible explanation of significance
+- Historical context (century-old limitation)
+- Precise results (21°C, 1 GPa, 2 K transition width)
+- Multiple lines of evidence (resistance + Meissner effect)
+- Theoretical explanation briefly included
+- Forward-looking conclusion
+
+---
+
+## Example 5: Evolution / Ecology
+
+**Topic**: Rapid evolution in response to climate
+
+```
+Climate change is driving rapid shifts in the geographic distributions of 
+species, but whether organisms can adapt quickly enough to keep pace with 
+warming remains a critical question for biodiversity conservation. Here we 
+document real-time evolution in wild populations of a widespread forest tree, 
+Scots pine, along a 1,000 km latitudinal gradient in Scandinavia. By combining 
+whole-genome sequencing with phenotypic measurements across 25 common gardens, 
+we detect signatures of selection at 47 loci associated with cold tolerance, 
+phenology, and drought resistance over just 50 years—approximately 
+five tree generations. Alleles conferring warmer-adapted phenotypes have 
+increased in frequency by 4-12% across northern populations, matching 
+predictions from models of climate-driven selection. However, migration of 
+warm-adapted genotypes from the south appears limited by geographic barriers. 
+These results demonstrate that trees can evolve rapidly in response to 
+climate change but suggest that assisted gene flow may be necessary to 
+prevent local maladaptation.
+```
+
+**Why this works**:
+- Opens with pressing question (climate adaptation)
+- Specific system (Scots pine) and scale (1,000 km)
+- Methods described briefly (genomics + common gardens)
+- Quantitative results (47 loci, 4-12% frequency shift, 5 generations)
+- Mechanism identified (limited migration)
+- Conservation implications stated
+
+---
+
+## Common Elements Across Examples
+
+### Structure (Implicit)
+1. **Hook**: Why this matters broadly (1-2 sentences)
+2. **Gap**: What was unknown or problematic (1 sentence)
+3. **Approach**: What was done (1 sentence)
+4. **Findings**: Key results with numbers (2-3 sentences)
+5. **Significance**: Why this matters going forward (1 sentence)
+
+### Style Features
+- **Active voice**: "We discovered," "We find," "We report"
+- **Specific numbers**: Exact values, not vague quantities
+- **Accessible language**: Minimal jargon, explained when needed
+- **Compelling opening**: Broad hook before technical details
+- **Strong close**: Implications or future directions
+
+### Word Count
+- Nature: 150-200 words (examples above: 185-210 words)
+- Science: ≤125 words (would need tightening)
+
+---
+
+## What to Avoid
+
+❌ **Too technical opening**:
+> "The CRISPR-Cas9 system with guide RNA targeting PAM sequences..."
+
+✅ **Better opening**:
+> "The ability to precisely edit DNA in living cells..."
+
+---
+
+❌ **Vague results**:
+> "Our method significantly outperformed existing approaches..."
+
+✅ **Better results**:
+> "Our method reduced off-target editing by 78% compared to standard Cas9..."
+
+---
+
+❌ **Weak significance statement**:
+> "These findings may have implications for the field..."
+
+✅ **Better significance**:
+> "These findings suggest new therapeutic approaches for memory disorders..."
+
+---
+
+## See Also
+
+- `nature_science_style.md` - Comprehensive Nature/Science writing guide
+- `venue_writing_styles.md` - Style comparison across venues
+