***TASK***
the task is to simplify the input abstract of a biomedical literature

***INPUT***
the input is the abstract of a biomedical literature

***OUTPUT***
the output is the simplified abstract for the input abstract of a biomedical literature

***DOCUMENTATION***

***EXAMPLES***

Input: We included 29 primary studies (18 from the original review and 11 from this update), corresponding to 34 data sets, published between 2000 and 2018 in the meta-analyses, with a mean prevalence of proven or probable IA of 16.3 (median prevalence 11.1% , range 2.5% to 57.1%). Most patients had received chemotherapy for haematological malignancy or had undergone hematopoietic stem cell transplantation. Several PCR techniques were used among the included studies. The sensitivity and specificity of PCR for the diagnosis of IA varied according to the interpretative criteria used to define a test as positive. The summary estimates of sensitivity and specificity were 79.2% (95% confidence interval (CI) 71.0 to 85.5) and 79.6% (95% CI 69.9 to 86.6) for a single positive test result, and 59.6% (95% CI 40.7 to 76.0) and 95.1% (95% CI 87.0 to 98.2) for two consecutive positive test results. PCR shows moderate diagnostic accuracy when used as screening tests for IA in high-risk patient groups. Importantly the sensitivity of the test confers a high negative predictive value (NPV) such that a negative test allows the diagnosis to be excluded. Consecutive positives show good specificity in diagnosis of IA and could be used to trigger radiological and other investigations or for pre-emptive therapy in the absence of specific radiological signs when the clinical suspicion of infection is high. When a single PCR positive test is used as the diagnostic criterion for IA in a population of 100 people with a disease prevalence of 16.3% (overall mean prevalence), three people with IA would be missed (sensitivity 79.2%, 20.8% false negatives), and 17 people would be unnecessarily treated or referred for further tests (specificity of 79.6%, 21.4% false positives). If we use the two positive test requirement in a population with the same disease prevalence, it would mean that nine IA people would be missed (sensitivity 59.6%, 40.4% false negatives) and four people would be unnecessarily treated or referred for further tests (specificity of 95.1%, 4.9% false positives). Like galactomannan, PCR has good NPV for excluding disease, but the low prevalence of disease limits the ability to rule in a diagnosis. As these biomarkers detect different markers of disease, combining them is likely to prove more useful.
Output:

We conducted our most recent search for studies in March 2018 and combined with an earlier search selected 29 clinical studies reporting the evaluation of PCR tests prospectively in cohorts of people at high risk of IA. None of the companies involved in the diagnosis of invasive fungal diseases funded any of the studies included in the review. Most studies were at low risk of bias and low concern regarding applicability. However, differences in the reference standard may have contributed to differences we found in the distribution of cases as being classified as IA or not. Several PCR techniques were used in the studies. Pooling the data from the studies showed that sensitivity and specificity of PCR for the diagnosis of IA varied (from 59% to 79.2% and from 79% to 95.2%, respectively) depending on the interpretative criteria used to define a test as positive. When used as a diagnostic criterion for IA in a population of 100 people with a disease prevalence of 16.3% (overall mean prevalence), a single PCR positive test would have missed three people with the disease, and falsely classified 17 people as having the disease, who would be treated unnecessarily or referred for further tests. A requirement of two positive tests as a diagnostic criterion in a population with the same disease prevalence would miss nine people with the disease and falsely classify four people as having the disease. These numbers should be interpreted with caution because the reference standard is based on the degree of certainty of diagnosis and is rarely proven so cannot provide consistent assessment of cases as being IA or not. Overall, PCR shows moderate diagnostic accuracy when used as a screening test for IA in high-risk patient groups. Importantly, when the rate of sensitivity is low, the sensitivity of the tests means that a negative result allows the diagnosis to be excluded with confidence except when the patient is receiving certain antifungal drugs. With the low prevalence of the disease, a high negative predictive value such that a negative test allows the diagnosis to be excluded.