***TASK*** the task is to summarize an input biomedical literature in six sentences 
    ***INPUT*** the input is a biomedical literature 
    ***OUTPUT*** the output is the summary of an input biomedical literature in six sentences 
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    ***EXAMPLES*** 
    Input: Background Hospitals in sub-Saharan Africa are inun date d with HIV-infected patients and tuberculosis ( TB ) is the commonest opportunistic infection in this sub-group . Up to one third of TB-HIV co-infected patients fail to produce a sputum sample ( sputum scarce ) and diagnosis is thus often delayed or missed . We investigated the sensitivity of urine-based methods ( Xpert MTB/RIF , LAM strip test and LAM ELISA ) in such patients . Methodology /Principal Findings 281 HIV-infected hospitalised patients with clinical ly suspected TB provided a spot urine sample . The reference st and ard was culture positivity for Mycobacterium tuberculosis on ≥1 sputum or extra-pulmonary sample . MTB/RIF was performed using 1 ml of both unprocessed and , when possible , concentrated urine . Each unconcentrated urine sample was also tested using the Clearview LAM ELISA and Alere LAM strip test . 42 % ( 116/242 ) of patients had culture-proven TB . 18 % ( 20/54 ) were sputum scarce . In sputum-scarce patients , the sensitivity of urine MTB/RIF and LAM ELISA was 40 % ( 95%CI : 22–61 ) and 60 % ( 95%CI : 39–78 ) , respectively . Urine MTB/RIF specificity was 98 % ( 95%CI : 95–100 ) . Combined sensitivity of urine LAM ELISA and MTB/RIF was better than MTB/RIF alone [ MTB/RIF and LAM : 70 % ( 95%CI : 48–85 ) vs. MTB/RIF : 40 % ( 95%CI : 22–61 ) , p = 0.03 ] . Significant predictors of urine MTB/RIF positivity were CD4<50 cells/ml ( p = 0.001 ) , elevated protein-to-creatinine ratio ( p<0.001 ) and LAM ELISA positivity ( p<0.001 ) . Urine centrifugation and pelleting significantly increased the sensitivity of MTB/RIF over unprocessed urine in paired sample s [ 42 % ( 95%CI : 26–58 ) vs. 8 % ( 95%CI : 0–16 ) , p<0.001 ] . Urine MTB/RIF-generated CT values correlated poorly with markers of bacillary burden ( smear grade and time-to-positivity ) . Conclusions / Significance This preliminary study indicates that urine-based MTB/RIF , alone or in combination with LAM antigen detection , may potentially aid the diagnosis of TB in HIV-infected patients with advanced immunosuppression when sputum-based diagnosis is not possible . Concentration of urine prior to MTB/RIF-testing significantly improves sensitivity Background Although antiretroviral therapy ( ART ) is known to be associated with time-dependent reductions in tuberculosis ( TB ) incidence , the long-term impact of ART on incidence remains imprecisely defined due to limited duration of follow-up and incomplete CD4 cell count recovery in existing studies . We determined TB incidence in a South African ART cohort with up to 8 years of follow-up and stratified rates according to CD4 cell count recovery . We compared these rates with those of HIV-uninfected individuals living in the same community . Methodology /Principal Findings Prospect ively collected clinical data on patients receiving ART in a community-based cohort in Cape Town were analysed . 1544 patients with a median follow-up of 5.0 years ( IQR 2.4–5.8 ) were included in the analysis . 484 episodes of incident TB ( 73.6 % culture-confirmed ) were diagnosed in 424 patients during 6506 person-years ( PYs ) of follow-up . The TB incidence rate during the first year of ART was 12.4 ( 95 % CI 10.8–14.4 ) cases/100PYs and decreased to 4.92 ( 95 % CI 3.64–8.62 ) cases/100PYs between 5 and 8 years of ART . During person-time accrued within CD4 cell strata 0–100 , 101–200 , 201–300 , 301–400 , 401–500 , 501–700 and ≥700 cells/µL , TB incidence rates ( 95 % CI ) were 25.5 ( 21.6–30.3 ) , 11.2 ( 9.4–13.5 ) , 7.9 ( 6.4–9.7 ) , 5.0 ( 3.9–6.6 ) , 5.1 ( 3.8–6.8 ) , 4.1 ( 3.1–5.4 ) and 2.7 ( 1.7–4.5 ) cases/100PYs , respectively . Overall , 75 % ( 95 % CI 70.9–78.8 ) of TB episodes were recurrent cases . Up date d CD4 cell count and viral load measurements were independently associated with long-term TB risk . TB rates during person-time accrued in the highest CD4 cell count stratum ( > 700 cells/µL ) were 4.4-fold higher that the rate in HIV uninfected individuals living in the same community ( 2.7 versus 0.62 cases/100PYs ; 95%CI 0.58–0.65 ) . Conclusions / Significance TB rates during long-term ART remained substantially greater than rates in the local HIV uninfected population s regardless of duration of ART or attainment of CD4 cell counts exceeding 700 Background Detection of  lipoarabinomannan ( LAM ) , a Mycobacterium tuberculosis ( Mtb ) cell wall antigen , is a potentially attractive diagnostic . However , the LAM-ELISA assay has demonstrated variable sensitivity in diagnosing TB in diverse clinical population s. We therefore explored pathogen and host factors potentially impacting LAM detection . Methods  LAM-ELISA assay testing , sputum smear and culture status , HIV status , CD4 cell count , proteinuria and TB outcomes were prospect ively determined in adults diagnosed with TB and commencing TB treatment at a South African township TB clinic . Sputum TB isolates were characterised by IS61110-based restriction fragment length polymorphism ( RFLP ) and urines were tested for mycobacteriuria by Xpert ® MTB/RIF assay . Results 32/199 ( 16.1 % ) of patients tested LAM-ELISA positive . Median optical density and proportion testing LAM positive remained unchanged during 2 weeks of treatment and then declined over 24 weeks . LAM was associated with positive sputum smear and culture status , HIV infection and low CD4 cell counts but not proteinuria , RFLP strain or TB treatment outcome . The sensitivity of LAM for TB in HIV-infected patients with CD4 counts of ≥ 200 , 100 - 199 , 50 - 99 , and < 50 cells/μl , was 15.2 % , 32 % , 42.9 % , and 69.2 % respectively . Mycobacteriuria was found in 15/32 ( 46.9 % ) of LAM positive patients and in none of the LAM negative controls . Conclusions Urinary LAM was related to host immune factors , was unrelated to Mtb strain and declined steadily after an initial 2 weeks of TB treatment . The strong association of urine LAM with mycobacteriuria is a new finding , indicating frequent TB involvement of the renal tract in advanced HIV infection Background A rapid diagnostic test for active tuberculosis ( TB ) at the clinical point-of-care could expedite case detection and accelerate TB treatment initiation . We assessed the diagnostic accuracy of a rapid urine lipoarabinomannan ( LAM ) test for TB screening among HIV-infected adults in a TB-endemic setting . Methods We prospect ively enrolled newly-diagnosed HIV-infected adults ( ≥18 years ) at 4 outpatient clinics in Durban from Oct 2011-May 2012 , excluding those on TB therapy . A physician evaluated all participants and offered CD4 cell count testing . Trained study nurses collected a sputum sample for acid-fast bacilli smear microscopy ( AFB ) and mycobacterial culture , and performed urine LAM testing using Determine ™ TB LAM in the clinic . The presence of a b and regardless of intensity on the urine LAM test was considered positive . We defined as the gold st and ard for active pulmonary TB a positive sputum culture for Mycobacterium tuberculosis . Diagnostic accuracy of urine LAM was assessed , alone and in combination with smear microscopy , and stratified by CD4 cell count . Results Among 342 newly-diagnosed HIV-infected participants , 190 ( 56 % ) were male , mean age was 35.6 years , and median CD4 was 182/mm3 . Sixty participants had culture-positive pulmonary TB , result ing in an estimated prevalence of 17.5 % ( 95 % CI 13.7 - 22.0 % ) . Forty-five ( 13.2 % ) participants  were urine LAM positive . Mean time from urine specimen collection to LAM test result was 40 minutes ( 95 % CI 34–46 minutes ) . Urine LAM test sensitivity was 28.3 % ( 95 % CI 17.5 - 41.4 ) overall , and 37.5 % ( 95 % CI 21.1 - 56.3 ) for those with CD4 count < 100/mm3 , while specificity was 90.1 % ( 95 % CI 86.0 - 93.3 ) overall , and 86.9 % ( 95 % CI 75.8 - 94.2 ) for those with CD4 < 100/mm3 . When combined with sputum AFB ( either test positive ) , sensitivity increased to 38.3 % ( 95 % CI 26.0 - 51.8 ) , but specificity decreased to 85.8 % ( 95 % CI 81.1 - 89.7 ) . Conclusions In this prospect i ve , clinic-based study with trained nurses , a rapid urine LAM test had low sensitivity for TB screening among newly-diagnosed HIV-infected adults , but improved sensitivity when combined with sputum smear microscopy Background Current tools for the diagnosis of tuberculosis pleural effusions are sub-optimal . Data about the value of new diagnostic technologies are limited , particularly , in high burden setting s. Preliminary case control studies have identified IFN-γ-inducible-10kDa protein ( IP-10 ) as a promising diagnostic marker ; however , its diagnostic utility in a day-to-day clinical setting is unclear . Detection of LAM antigen has not previously been evaluated in pleural fluid . Methods We investigated the comparative diagnostic utility of established ( adenosine deaminase [ ADA ] ) , more recent ( st and ardized nucleic-acid-amplification-test [ NAAT ] ) and newer technologies ( a st and ardized LAM mycobacterial antigen-detection assay and IP-10 levels ) for the evaluation of pleural effusions in 78 consecutively recruited South African tuberculosis suspects . All consenting participants underwent pleural biopsy  unless contra-indicated or refused . The reference st and ard comprised culture positivity for M. tuberculosis or histology suggestive of tuberculosis . Principal Findings Of 74 evaluable subjects 48 , 7 and 19 had definite , probable and non-TB , respectively . IP-10 levels were significantly higher in TB vs non-TB participants ( p<0.0001 ) . The respective outcomes [ sensitivity , specificity , PPV , NPV % ] for the different diagnostic modalities were : ADA at the 30 IU/L cut-point [ 96 ; 69 ; 90 ; 85 ] , NAAT [ 6 ; 93 ; 67 ; 28 ] , IP-10 at the 28,170 pg/ml ROC-derived cut-point [ 80 ; 82 ; 91 ; 64 ] , and IP-10 at the 4035 pg/ml cut-point [ 100 ; 53 ; 83 ; 100 ] . Thus IP-10 , using the ROC-derived cut-point , missed ∼20 % of TB cases and mis-diagnosed ∼20 % of non-TB cases . By contrast , when a lower cut-point was used a negative test excluded TB . The NAAT had a poor sensitivity but high specificity . LAM antigen-detection was not diagnostically useful . Conclusion Although IP-10 , like ADA , has sub-optimal specificity , it may be a clinical ly useful rule-out test for tuberculous pleural effusions . Larger multi-centric studies are now required to confirm our findings Background Reducing mortality from HIV-associated tuberculosis ( TB ) requires diagnostic tools that are rapid and have high sensitivity among patients with poor prognosis . We determined the relationship between disease severity and the sensitivity of new sputum-based and urine-based diagnostic assays . Methods Consecutive ambulatory patients enrolling for antiretroviral 
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Regardless of how people are enrolled , sensitivity is higher in in patients and those with lower CD4 cell , but a concomitant lower specificity .
As a simple point‐of‐care test that does not depend upon sputum evaluation , LF‐LAM may assist with the diagnosis of tuberculosis , particularly when a sputum specimen can not be produced