Nagata et al. Supplementary Figure S1
Bibliographic record
Abstract
Supplemental Figure S1. Representative images of inducible nitric oxide synthase-expressing (iNOS+) cells on postinjury day 5. A-B: Images were obtained from the damaged muscle in the icing group. A: A transverse section of injured muscle was analyzed by immunohistochemical staining for iNOS, counterstained with hematoxylin. Black arrowheads indicate iNOS+ regenerating muscle cells with central nuclei. B: A transverse section of injured muscle was analyzed by immunofluorescence for CD68 (green) and iNOS (red). Nuclei were stained with 4′-6-diamino-2-phenylindole (DAPI, blue). Arrows indicate macrophages identified as positive color of CD68 surrounding a nucleus (blue). White arrowheads indicate iNOS+ cells excluding macrophages identified as single positive color of iNOS surrounding a nucleus (blue). Scale bars = 30 μm. Method for (A): Immunohistochemical staining was performed on the cross section of injured extensor digitorum longus muscle. Cryosection was fixed with 4% paraformaldehyde, washed in phosphate-buffered saline (PBS), blocked and permeabilized with PBS containing 10% normal goat serum at room temperature for 1 h, and incubated with primary antibodies at 4°C overnight. The primary antibody: rabbit polyclonal anti-iNOS antibody (1:50, ab3523, lot# GR3382908-1; Abcam, Cambridge, UK; RRID: AB_303872) was diluted in PBS containing 5% normal goat serum. After washing the section three times in PBS, endogenous peroxidase activity was quenched with 0.3 % hydrogen peroxide diluted in methanol for 30 min at room temperature. The section was then washed three times in PBS and was incubated with MAX-PO (R) (Nichirei Biosciences Inc., Tokyo, Japan) secondary antibodies for 30 min at room temperature. After washing with PBS, the section was placed in the 3,3′-diaminobenzidine reaction solution, counterstained with hematoxylin. The sample was viewed on an Olympus BX50 microscope (Olympus, Tokyo, Japan) with objectives and image was taken with a digital camera (DP20; Olympus). Method for (B): Immunofluorescence was performed on the cross section of injured extensor digitorum longus muscle. Cryosection was fixed with 4% paraformaldehyde, washed in PBS, blocked and permeabilized with PBS containing 10% normal goat serum and 1% Triton X-100 at room temperature for 1 h, and incubated with primary antibodies at 4°C overnight or at room temperature for 1 h. The primary antibodies: mouse monoclonal anti-CD68 antibody (1:200, MCA341GA, lot# 0515; Bio-Rad, Hercules, CA, USA; RRID: AB_566872), and rabbit polyclonal anti-iNOS antibody (1:50, ab3523, lot# GR3382908-1; Abcam, Cambridge, UK; RRID: AB_303872) were diluted in PBS containing 5% normal goat serum. After washing the section three times in PBS, the sample was incubated with the appropriate species-specific (anti-mouse and/or anti-rabbit) fluorescence-conjugated (Alexa Fluor 488 and/or 594) secondary antibodies (Thermo Fisher Scientific, Waltham, MA, USA), diluted (1:1000) in PBS containing 5% normal goat serum, at room temperature for 2 h. After washing with PBS, the section was mounted using Vectashield mounting medium (Vector Laboratories, Burlington, ON, Canada) containing 4′-6-diamino-2-phenylindole to visualize the nuclei. The sample was viewed for the fluorescent labels on a ZEISS Axio Vert. A1 microscope (Zeiss, Oberkochen, Germany) and photographed with an AxioCam MRm (Zeiss) camera (max resolution 1388 × 1040 pixels) using AxioVision Rel. 4.8 (Zeiss) software.
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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 | 0.004 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.003 | 0.002 |
| Insufficient payload (model declined to judge) | 0.651 | 0.273 |
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; the direct Gemma label and the distilled Codex classifier agree on what is shown here.
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".