Additional file 2 of Gut microbiome is linked to functions of peripheral immune cells in transition cows during excessive lipolysis
Bibliographic record
Abstract
Additional file 2: Figure S1. The single-cell landscape of the peripheral immune cells in cows with low (LNF) and high lipolysis (HNF). A. T-distributed stochastic neighbor embedding (T-SNE) plot map of cell type clustering from the peripheral immune cells of LNF and HNF cows. B. The violin plot of the marker genes expressed in each clusters. Figure S2. Top ten representative immune biological pathways that enriched from the up-regulated differential expressed genes of immune cells isolated from HNF cow. Pathways are presented as log10 p-value and color scheme is used to indicate immune cell population. MON: monocyte; NEU: neutrophil. Figure S3. The bile acid profile in plasma and feces of cows with low (LNF) and high lipolysis (HNF). A. The percentage of plasma bile acid in two groups. B. The percentage of fecal bile acid in two groups. TDCA: Taurodeoxycholic acid; TCA: Taurocholic acid; CDCA: Chenodeoxycholic acid; CA: Cholic acid; TCDCA: Taurochenodeoxycholic acid; GCA: Glycocholic acid; GCDCA: Glycochenodeoxycholic acid; HDCA: Hyodeoxycholic acid; THDCA: Taurohyodeoxycholic acid; AlloCA: Allocholic acid; UDCA: Ursodeoxycholic acid; DCA: Deoxycholic acid; LCA: Lithocholic acid; ApoCA: Apocholic acid; GDCA: Glycodeoxycholic acid; 7-KDCA: 7-ketodeoxycholic acid; 7-KLCA: 7-Ketolithocholic acid; 12-KLCA: 12-ketolithocholic acid; 3-DHCA: 3-dehydrocholic acid; TLCA: Taurolithocholic acid; GLCA: Glycolithocholic acid; Total α-MCA: α-Muricholic acid; γ-MCA: γ-muricholic acid; isoLCA: Isolithocholic acid; TMCA: Tauro-muricholic acid; TUDCA: Tauroursodeoxycholic acid. LNF: cows with low lipolysis; HNF: cows with high lipolysis. * P-value < 0.05; # 0.05 < P-value < 0.10. Figure S4. The functional changes and associations with bile acid related gene set. A. The enriched decreased biological process of FCGR3A+MON in HFNC compared to LFNC. B. Correlation of bile acid metabolism to the major decreased functions in FCGR3A+MON. LNFC: cow with low lipolysis; HNFC: cow with excessive lipolysis; MON: monocyte.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.024 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.857 | 0.116 |
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".