TASK DEFINITION: Given a passage with a context and an answer, construct a question on the basis of the information present in the passage. Construct the question in such a way that (i) it is unambiguous, (ii) it is answerable from the passage, (iii) its answer is unique (iv) it answer uses text phrases from the passage. Avoid creating questions that (i) can't be answered correctly without actually understanding the passage and (ii) uses the same words or phrases given in the passage.
PROBLEM: Context: Concomitant thyroid nodules are the most common reason for false-positive ultrasonography (US) results in primary hyperparathyroidism. The aims of this prospective clinical study were to evaluate false-positive US results according to the characteristics of concomitant thyroid nodules and to determine which characteristics of thyroid nodules are important.', 'This prospective study included 120 consecutive patients with primary hyperparathyroidism. The patients were divided into 2 groups according to preoperative US results. Group 1 consisted of 32 patients with false-positive US results and group 2 consisted of 88 patients with true-positive US results.', 'The risk for false-positive US result was increased 25-fold for patients with parathyroid adenoma weight of more than 500 mg (odds ratio [OR], 25; 95% confidence interval [CI], 8.6-74.5), 75-fold for more than 1 posteriorly located thyroid (OR, 75; 95% CI, 19.3-293.4), 358-fold for the presence of exophytic thyroid nodules (OR, 358; 95% CI, 42.3-3036), and 423-fold for the presence of posteriorly located thyroid nodules (OR, 423; 95% CI, 49-3662).
Answer: Although there was no particular characteristic of concomitant thyroid nodules that contributes to false-positive US results, the posteriorly located thyroid nodules were the strongest correlate for the false-positive US results to other features.

SOLUTION: Do the characteristics of concomitant thyroid nodules cause false-positive ultrasonography results in primary hyperparathyroidism?

PROBLEM: Context: Minimal residual disease (MRD) is defined as the presence of sub-microscopic levels of leukaemia. Measurement of MRD from bone marrow at the end of induction chemotherapy (day 28) for childhood acute lymphoblastic leukaemia (ALL) can highlight a large group of patients (>40%) with an excellent (>90%) short-term event-free survival (EFS). However, follow-up in recent published trials is relatively short, raising concerns about using this result to infer the safety of further therapy reduction in the future.', 'We examined MRD data on 225 patients treated on one of three UKALL trials between 1997 and 2003 to assess the long-term (>10\u2005years follow-up) outcome of those patients who had low-risk MRD (<0.01%) at day 28.', 'Our pilot data define a cohort of 53% of children with MRD <0.01% at day 28 who have an EFS of 91% and long-term overall survival of 97%. Of 120 patients with day-28 MRD <0.01% and extended follow-up, there was one death due to treatment-related toxicity, one infectious death while in complete remission, and four relapse deaths.
Answer: The excellent outcome for childhood ALL in patients with MRD <0.01% after induction chemotherapy is sustained for more than 10 years from diagnosis. This supports the potential exploration of further reduction of therapy in this group, in an attempt to reduce treatment-related mortality and late effects.

SOLUTION: Is excellent outcome of minimal residual disease-defined low-risk patients sustained with more than 10 years follow-up : results of UK paediatric acute lymphoblastic leukaemia trials 1997-2003?

PROBLEM: Context: DNA barcodes are short unique sequences used to label DNA or RNA-derived samples in multiplexed deep sequencing experiments. During the demultiplexing step, barcodes must be detected and their position identified. In some cases (e.g., with PacBio SMRT), the position of the barcode and DNA context is not well defined. Many reads start inside the genomic insert so that adjacent primers might be missed. The matter is further complicated by coincidental similarities between barcode sequences and reference DNA. Therefore, a robust strategy is required in order to detect barcoded reads and avoid a large number of false positives or negatives.For mass inference problems such as this one, false discovery rate (FDR) methods are powerful and balanced solutions. Since existing FDR methods cannot be applied to this particular problem, we present an adapted FDR method that is suitable for the detection of barcoded reads as well as suggest possible improvements.', 'In our analysis, barcode sequences showed high rates of coincidental similarities with the Mus musculus reference DNA. This problem became more acute when the length of the barcode sequence decreased and the number of barcodes in the set increased. The method presented in this paper controls the tail area-based false discovery rate to distinguish between barcoded and unbarcoded reads. This method helps to establish the highest acceptable minimal distance between reads and barcode sequences. In a proof of concept experiment we correctly detected barcodes in 83% of the reads with a precision of 89%. Sensitivity improved to 99% at 99% precision when the adjacent primer sequence was incorporated in the analysis. The analysis was further improved using a paired end strategy. Following an analysis of the data for sequence variants induced in the Atp1a1 gene of C57BL/6 murine melanocytes by ultraviolet light and conferring resistance to ouabain, we found no evidence of cross-contamination of DNA material between samples.
Answer: Our method offers a proper quantitative treatment of the problem of detecting barcoded reads in a noisy sequencing environment. It is based on the false discovery rate statistics that allows a proper trade-off between sensitivity and precision to be chosen.

SOLUTION:
Does enhancing the detection of barcoded read in high throughput DNA sequencing data by controlling the false discovery rate?