On the use of partial area under the ROC curve for comparison of two diagnostic tests

Evaluation of diagnostic performance is typically based on the receiver operating characteristic (ROC) curve and the area under the curve (AUC) as its summary index. The partial area under the curve (pAUC) is an alternative index focusing on the range of practical/clinical relevance. One of the problems preventing more frequent use of the pAUC is the perceived loss of efficiency in cases of noncrossing ROC curves. In this paper, we investigated statistical properties of comparisons of two correlated pAUCs. We demonstrated that outside of the classic model there are practically reasonable ROC types for which comparisons of noncrossing concave curves would be more powerful when based on a part of the curve rather than the entire curve. We argue that this phenomenon stems in part from the exclusion of noninformative parts of the ROC curves that resemble straight‐lines. We conducted extensive simulation studies in families of binormal, straight‐line, and bigamma ROC curves. We demonstrated that comparison of pAUCs is statistically more powerful than comparison of full AUCs when ROC curves are close to a “straight line”. For less flat binormal ROC curves an increase in the integration range often leads to a disproportional increase in pAUCs’ difference, thereby contributing to an increase in statistical power. Thus, efficiency of differences in pAUCs of noncrossing ROC curves depends on the shape of the curves, and for families of ROC curves that are nearly straight‐line shaped, such as bigamma ROC curves, there are multiple practical scenarios in which comparisons of pAUCs are preferable.     

Isolation of nitrogen deregulated mutants of erythromycin biosynthesis

Summary Ammonium represses erythromycin synthesis bySaccharopolyspora erythraea and insensitive mutants to this effect were isolated. Six mutants were selected and one of them produces 50% more antibiotic than the wild type in 100 mM NH₄Cl as nitrogen source. Glutamine synthetase and alanine dehydrogenase levels in the mutants were determined and no differences with wild type strain were observed.     

Ecological risk assessment in a tropical wetland contaminated with gasoline: Tier 1

To assess natural attenuation and the efficiency of remediation actions after more than two years a large accident with gasoline spill contaminated a wetland in a tropical region, an Ecological Risk Assessment based on the Dutch Triad was applied. In total, eight surface water-sampling points were distributed randomly in the affected area and on reference area upstream the contaminated site, with similar ecological characteristics. Risks based on chemical, ecotoxicological, and ecological lines of evidence (LoE) were calculated to integrate the environmental risk indexes. The chemical risk was derived from toxic pressure coefficients based on the total BTEX and naphthalene concentrations. Ecotoxicological LoE based on acute toxicity with Daphnia similis and Aliivibrio fischeri bioassays and chronic toxicity with Desmodesmus subspicatus bioassay contributed to raise uncertainty due to low sensitivity of acute assays. Genotoxicity and endocrine disruption biomarkers of Oreochromis niloticus were used to calculate the Biomarker Stress Index (BSI) assumed as Ecological Risk Index. The integration of the Chemical Risk Index with BSI to estimate the Biological Vulnerability Index allowed a meaningful analysis of the threats to the aquatic ecosystem, thereby supporting managers and decision-makers.     

Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module

Cellulases are the key enzymes used in the biofuel industry. A typical cellulase contains a catalytic domain connected to a carbohydrate-binding module (CBM) through a flexible linker. Here we report the structure of an atypical trimodular cellulase which harbors a catalytic domain, a CBM46 domain and a rigid CBM_X domain between them. The catalytic domain shows the features of GH5 family, while the CBM46 domain has a sandwich-like structure. The catalytic domain and the CBM46 domain form an extended substrate binding cleft, within which several tryptophan residues are well exposed. Mutagenesis assays indicate that these residues are essential for the enzymatic activities. Gel affinity electrophoresis shows that these tryptophan residues are involved in the polysaccharide substrate binding. Also, electrostatic potential analysis indicates that almost the entire solvent accessible surface of CelB is negatively charged, which is consistent with the halophilic nature of this enzyme.     

Cytokine-induced cell death in immortalized Schwann cells: roles of nitric oxide and cyclic AMP

Tumor necrosis factor-alpha and interferon-gamma are pleiotropic cytokines that regulate Schwann cell responses during injury and inflammatory demyelination. We have previously shown that cyclic AMP (cAMP)-elevating agents decrease the demyelination and Wallerian degeneration in experimental allergic neuritis. In this study, we examined the role of cAMP in cytokine-mediated signaling in a spontaneously immortal Schwann cell clone (iSC). We found that tumor necrosis factor-alpha and interferon-gamma exert synergistic inhibitory action on Schwann cell viability via the production of nitric oxide (NO) and ceramide (cer). Furthermore, we found that: (i) NO synthase inhibitors attenuate the cytokine-induced cer accumulation and cell death indicating that NO acts upstream of cer; and (ii) cytokine-induced cell death is decreased in iSCs pretreated continuously for 48-72 h with forskolin, an activator of adenylate cyclase. Although forskolin modulates the phosphorylation of ERKs and Akt, it decreases the susceptibility of iSC to cytokines via a separate mechanism operating after NO induction and before cer accumulation. We propose that the protective effect of cAMP-elevating agents in experimental allergic neuritis may be mediated in part via modulation of Schwann cell responses to cytokines.     

Methane emission from paddy soils as affected by wheat straw returning mode

To study influence of wheat straw returning mode on CH₄ emission from paddy soils, a field experiment was conducted at Jurong, Jiangsu Province, China in 2006. Five treatments, no wheat straw applied (CK), wheat straw evenly incorporated into the topsoil (WI), wheat straw buried in ditches (WD), wheat straw strip-mulched onto the field surface (WM) and wheat straw burned in-situ (WB), were laid out in a randomized block design. Results showed that seasonal CH₄ emissions ranged from 6.9 to 28.1 g CH₄ m^?2. Wheat straw incorporation significantly increased CH₄ emission. No significant difference was observed between Treatments WI and WD in total CH₄ emission. Compared with Treatment WI, Treatment WM reduced total CH₄ emission by 32% and Treatment WB by 42%. Treatment WM was about 27% higher than Treatment CK in grain yield. Based on the findings, the best management of wheat straw prior to rice cultivation is strip-mulching wheat straw onto the field surface, which largely reduced CH₄ emission from rice fields with no decrease in rice yield.