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CASP8 results in context of previous experiments.

ABSTRACT: The quality of structure models submitted to CASP8 is analyzed in the context of previous CASPs. To compare models from the latest experiment with their predecessors, we use the approaches consistent with the previous articles in this series. Using the basic evaluation measures accepted in CASP, there were no noticeable advances in the quality of the methods in any of the target difficulty categories. At the same time, there were three positive developments: (1) for set of the best models on each target, CASP8 registered the highest number of cases from all CASPs where alignment accuracy exceeded the maximum possible from the best template; (2) modeling accuracy of regions not present in the best template has improved; and (3) the loss in modeling quality from selection of nonoptimal models as the best ones submitted on the target has decreased.

SUBMITTER: Kryshtafovych A

PROVIDER: S-EPMC5479686 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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CASP8 results in context of previous experiments.

Kryshtafovych Andriy A Fidelis Krzysztof K Moult John J

Proteins 20090101

The quality of structure models submitted to CASP8 is analyzed in the context of previous CASPs. To compare models from the latest experiment with their predecessors, we use the approaches consistent with the previous articles in this series. Using the basic evaluation measures accepted in CASP, there were no noticeable advances in the quality of the methods in any of the target difficulty categories. At the same time, there were three positive developments: (1) for set of the best models on eac ...[more]

PMID: 19722266

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Project description:BackgroundPatients with previous tuberculosis may have residual DNA in sputum that confounds nucleic acid amplification tests such as Xpert MTB/RIF. Little is known about the frequency of Xpert-positive, culture-negative ("false positive") results in retreatment patients, whether these are distinguishable from true positives, and whether Xpert's automated filter-based wash step reduces false positivity by removing residual DNA associated with nonintact cells.MethodsPretreatment patients (n = 2889) with symptoms of tuberculosis from Cape Town, South Africa, underwent a sputum-based liquid culture and Xpert. We also compared Xpert results from dilutions of intact or heat-lysed and mechanically lysed bacilli.ResultsRetreatment cases were more likely to be Xpert false-positive (45/321 Xpert-positive retreatment cases were false-positive) than new cases (40/461) (14% [95% confidence interval {CI}, 10%-18%] vs 8% [95% CI, 6%-12%];P= .018). Fewer years since treatment completion (adjusted odds ratio [aOR], 0.85 [95% CI, .73-.99]), less mycobacterial DNA (aOR, 1.14 [95% CI, 1.03-1.27] per cycle threshold [CT]), and a chest radiograph not suggestive of active tuberculosis (aOR, 0.22 [95% CI, .06-.82]) were associated with false positivity. CThad suboptimal accuracy for false positivity: 46% of Xpert-positives with CT> 30 would be false positive, although 70% of false positives would be missed. CT's predictive ability (area under the curve, 0.83 [95% CI, .76-.90]) was not improved by additional variables. Xpert detected nonviable, nonintact bacilli without a change in CTvs controls.ConclusionsOne in 7 Xpert-positive retreatment patients were culture negative and potentially false positive. False positivity was associated with recent previous tuberculosis, high CT, and a chest radiograph not suggestive of active tuberculosis. Clinicians may consider awaiting confirmatory testing in retreatment patients with CT> 30; however, most false positives fall below this cut-point. Xpert can detect DNA from nonviable, nonintact bacilli.

Project description:The aim of this study was to analyze whether the activity of the autonomic nervous system (ANS) differs between two regrouping procedures in goats, which would indicate stimulus specificity of these stressors. Applying two regrouping procedures, we evaluated heart rate and heart rate variability (RMSSD, SDNN, and RMSSD/SDNN). The two regrouping procedures were (1) introduction of individual goats into established groups ("introduction experiment") and (2) temporary separation and subsequent reintegration of individuals from/into their group with two levels of contact during separation ("separation experiment"). In the "introduction experiment," the heart rate of introduced goats while lying decreased continuously from an average 78 to 68?beats/min from before the introduction to the last day of the introduction period. Inversely, RMSSD increased continuously from 41 to 62?ms, which, on its own, would indicate an adaptation to the situation. During the "separation experiment," heart rate while lying was higher when goats were separated in the "acoustic contact treatment" (82?beats/min on average) compared with the "restricted physical contact treatment" (75?beats/min on average). This difference reflected a higher level of arousal during the "acoustic contact treatment." However, heart rate activity did not allow detecting effects of separation or reintegration. Even though it can be assumed that both the separation and introduction of goats are stressful for goats, the ANS reactions observed in this study differed between the two management procedures indicating that the ANS activation was specific to each situation. In addition, we discuss the ANS results in context with earlier findings of variables of the hypothalamic pituitary adrenal (HPA) axis (fecal cortisol metabolites) and behavior (lying and feeding). As correspondence between ANS, HPA, and behavioral reactions was limited both within and across experiments, the results of this study underline the concept that stress response patterns are context specific.

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CASP8 results in context of previous experiments.

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CASP8 results in context of previous experiments.

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