Crohnʼs Disease and M. paratuberculosis: Whereʼs the Beef?
Bibliographic record
Abstract
Culture of mycobacterium avium subspecies paratuberculosis from the blood of patients with Crohn's disease. Naser SA, Ghobrial G, Romero C, et al. Lancet. 2004;364:1039-1044. Mycobacterium avium subspecies paratuberculosis (MAP) is a fastidious microorganism with a putative causative role in Crohn's disease (CD). To further support this role, Naser et al studied the presence of viable MAP in the peripheral blood of patients with CD. Buffy coat extracts were obtained from 28 patients with CD, 9 patients with ulcerative colitis (UC), and 15 patients without inflammatory bowel disease (IBD) for culture and for direct genomic DNA extraction. Simultaneous demographic and disease-related history was obtained, including concurrent use of immunosuppressive agents. Culture was performed as per a protocol devised in the investigators' laboratory. Cell pellets were obtained serially from all culture bottles during the incubation period for various MAP staining. At the end of the 12-week incubation period, cell pellets were again obtained for staining and for DNA extraction. The DNA directly extracted from the original buffy coat (referred to as polymerase chain reaction [PCR]), as well as that from the cell pellets obtained after culture (culture), subsequently underwent nested PCR targeting the MAP-specific IS900 gene. The amplified fragments were sequenced and confirmed to be identical to IS900.
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 | 0.003 | 0.012 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.005 | 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".