Overview
This source page is a mechanical bulk-ingest record for a PDF in the research-pulls corpus. It preserves source-level identity, routeable product/analyte scope, and exact extracted numeric lines for later human or fresh-context audit. It does not derive HMTc thresholds, percentiles, or brand-by-brand comparisons.
Key numbers
The worker extracted the full PDF text with layout preservation twice and compared extraction hashes before commit. The following lines are copied from numeric/table-bearing regions of the PDF and retain the source units and wording where legible:
- Intestinal fibrosis is a common complication of Crohn’s dis- in over 50% of CD patients.2 The fibrostenotic CD pheno-
- including the sum of squares for the selected component (R2) presented as a median with a 95% confidence interval.
- streptomycin, ampicillin, and gentamicin 1%. The tissue mass
- In addition, a validation experiment was designed to estimate containing digestion media (2.5% FCS, RPMI 1640, liberase,
- cific sample sizes (eg, 5, 10, 15, 50, 100, etc.) were selected tissue was then washed with 10% FBS and RPMI, and filtered
- processed for cDNA synthesis and library preparation using Fibrostenotic CD patients undergoing surgery, N = 9
- tain 5000 cells per sample. Disease duration (years) median (IQR) 14 (3.5-28.5)
- using adapter sequences as described in Table S1. Sequencing Age at diagnosis, n (%)
- CellRanger’s count command. L2 (colonic) 0
- FindAllMarkers() function. Clusters closely apposed in the Previous bowel surgery for CD, n (%) 2 (22)
- resembling fibroblasts, epithelial cells, endothelial cells, and Mesalamine, n (%) 1 (11)
- gene expression levels across cells were generated using the Immunosuppressive, n (%) 3 (33)
- Montreal Classification, all patients were classified as having CRP mcg/mL, median (IQR) 16 (2.5-30)
- a fibrotic B2 behavior and L1 phenotype, confirmed at a mul- Albumin g/dL, median (IQR) 43 (38.5-44)
- tidisciplinary meeting of IBD gastroenterologists, colorectal Fecal calprotectin, median (IQR) 128 (82-248)
- tion on the main characteristics of the study population at Ileo-caecal resection, n (%) 3 (33)
- Ileal resection, n (%) 4 (44)
- and the serine protease inhibitor protein E1 (SERPINE1). differentiating stricture, with a combined AUC of 0.95 (95%
- B (EDNRB), and lymphocyte antigen 96 (LY96). In addi- of at least 75% to diagnose strictures within a sample size of
- fibrostenotic CD surgical patients (Table S2). As illustrated margins compared to strictures, without reaching statistical
- least 75% to diagnose strictures within a sample size of 20 patients.
- (95% CI: 0.56-0.89), while GREM1 showed an AUC of 0.65 thelial cells and Thy1(CD90) + fibroblasts expressing collagen
- (95% CI: 0.47-0.81). When all genes were combined, the di- transcripts (COL1A1 and COL1A2) and platelet-derived
- strictures (Table S3). Across all patients, we sequenced 31.195 margins (Figure S4A). Similarly, SRM showed expression in
- ciated with intestinal barrier integrity, such as KLF5, known Currently, there is a notable absence of biomarkers for
- activation of intestinal fibroblasts through enhanced fatty cell viability and the loss of up to 60% of tissue cells during
Methods (brief)
- samples for bulk transcriptomics. Differentially expressed genes (DEGs) were identified (adj. P value < .05), and machine learning analyses
- samples and do not take into account the different stages of
- relevant demographic and clinical data were collected and
- to microbes-driven tissue remodeling via M2 macrophages.7 Samples Collection
- meticulously dissected fresh samples from 3 sites: 1 from the
- the segments of the strictured intestine. Study samples were
- the adhesion molecule CDH11 was found to be broadly Tissue samples from different segments were stored in RNA
- 1–3 million reads/sample. FastQ files were obtained through To elucidate the biological significance and pathways, enrich-
- adjusted P value < .05 and a fold change of 2 were considered genes and literature evidence. Samples from nine patients
- differentially expressed. Normalized transcripts per million considered in bulk RNA-seq and additional samples from 5
- with < 1 transformed count in any sample were excluded, as was extracted from intestinal samples using the RNeasy
- Tissue samples were stored overnight at 4 °C in MACS
- Sample size estimation × 1 mm2 or less and transferred into gentleMACS C tubes
- In addition, a validation experiment was designed to estimate containing digestion media (2.5% FCS, RPMI 1640, liberase,
- the required number of samples to capture the effect size of deoxyribonuclease I, penicillin-streptomycin, ampicillin and
- selected genes. gentamicin). Digestion was performed at 37 °C shaking at ap-
- cific sample sizes (eg, 5, 10, 15, 50, 100, etc.) were selected tissue was then washed with 10% FBS and RPMI, and filtered
- each group at the specified sample sizes. A defined Cohen’s d counted, stained with propidium iodide to detect dead cells,
Implications
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Verification notes
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Update history
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