Evaluating Autophagy in Preimplantation Embryos
Bibliographic record
Abstract
Autophagy is an essential cellular degradation pathway in the mammalian preimplantation embryo. In this review, the process of autophagy is outlined and its function pertaining to preimplantation embryos is discussed. The current methods of measuring autophagy in preimplantation embryos are also summarized, with highlights of advances and challenges that one may encounter when examining preimplantation embryo autophagy. This article identifies the techniques, assays, and available models that are viable but infrequently used in the context of examining autophagy in preimplantation embryos. We aim to bring attention to alternative assays that could contribute to future analysis of autophagic pathways in preimplantation embryos.Abbreviations: AMBRA1: Activating molecule in Beclin-1-regulated autophagy 1; ATG: Autophagy-related protein; AL: Autolysosome; BCL-2: B-cell lymphoma 2; BECN1: Beclin-1; CQ: Chloroquine; ER: endoplasmic reticulum; ES cells: Embryonic stem cells; GFP: Green fluorescent protein; ICM: Inner cell mass; IF: Immunofluorescence; LC3: Light chain 3; LC3-II: Light chain 3 (lipid-conjugated); MAPK: mitogen-activating protein kinase; mTOR: Mammalian target of rapamycin; p62/SQSTM1: Sequestome 1; PA: Palmitic acid; PG: Phagophore; PtdIns3K: Phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3 phosphate; qPCR: Quantitative polymerase chain reaction; RFP: Red fluorescent protein; ROS: Reactive oxygen species; SNARE: Soluble N-ethylmaleimide-sensitive factor attachment protein receptor; TS cells: Trophoblast stem cells; ULK1: UNC-51-like kinase 1; WB: Western blot
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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 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".