The Biological Forms of BK DNA (Virions Versus Free DNA) in Urine and Plasma of Kidney Transplant Recipients.
Bibliographic record
Abstract
Background: Current quantitative nucleic acid tests used for routine BK DNA measurements in urine and plasma cannot differentiate BK virions from free BKV DNA. We studied the biologic forms of BK DNA in urine and plasma samples from renal transplant recipients with and without polyoma virus associated nephropathy (PVAN) Methods: Virions in extracted urine and plasma samples were quantified using enzymatic digestion of DNase I that degrades all free viral DNA but not encapsidated BK virions. Free BKV DNA was determined by determining the difference in the BKV DNA level between total BK DNA and virion DNA (residual amount after DNase I digestion). 270 Urine and 238 plasma samples serially collected from 22 adult patients in three groups were studied: 1) patients with high level BK viruria but no viremia (VOP n=10) 2) patients with BK viruria and viremia but no biopsy-proven nephropathy (n=7) and 3) patients with BK viruria and viremia and biopsy proven nephropathy (PVAN n=5). Patient demographic, immunosuppressive drugs used, renal function, and graft outcome data were collected. Results: In the VOP patient group, virions were not detected in urine when the viral load ≤ 1.0E+07 copies/ml and rarely exceed 20% of the proportion of BK DNA detected when viral loads were > 1.0E+07 copies/ml. The free DNA/virion ratio in the urine and plasma of patients with DNAemia (groups 2 and 3) was more variable.Figure: No Caption available.In individual patients the proportion of virions present in urine and plasma could change significantly, even when viral load remained unchanged. In 5 patients who had early high level BK DNAemia (>1.0E+04 copies/ml) early < 2 months after Transplant, a pattern of 100% virions in plasma associated with 100% free DNA in urine on initial testing was observed. Plasma virions and DNA cleared rapidly from plasma on reduction in immunosuppression in these patients; this pattern may represent donor transmitted infection. Conclusion: Assessment of the biologic form of BK DNA in the urine and plasma of kidney transplant warrants further study as a tool to predict risk of PVAN, monitor response to immunosuppression reduction and predict graft outcome.
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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 | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| 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 | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
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".