nERdy: network analysis of endoplasmic reticulum dynamics
Bibliographic record
Abstract
Abstract The endoplasmic reticulum (ER) comprises smooth tubules, ribosome-studded sheets, and peripheral sheets that can present as tubular matrices. ER shaping proteins determine ER morphology, however, understanding their role in tubular matrix formation requires reconstructing the dynamic, convoluted ER network. Existing reconstruction methods are sensitive to parameters or require extensive annotation and training for deep learning. We introduce nERdy, an image processing based approach, and nERdy+, a D4-equivariant neural network, for accurate extraction and representation of ER networks and junction dynamics, outperforming previous methods. Comparison of stable and dynamic representations of the extracted ER structure reports on tripartite junction movement and distinguishes tubular matrices from peripheral ER networks. Analysis of live cell confocal and STED time series data shows that Atlastin and Reticulon 4 promote dynamic tubular matrix formation and enhance junction dynamics, identifying novel roles for these ER shaping proteins in regulating ER structure and dynamics.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".