Raking Kappa: Describing Potential Impact of Marginal Distributions on Measures of Agreement

Several authors have noted the dependence of kappa measures of inter-rater agreement on the marginal distributions of contingency tables displaying the joint ratings. This paper introduces a smoothed version of kappa computed after raking the table to achieve pre-specified marginal distributions. A comparison of kappa with raked kappa for various margins can indicate the extent of the dependence on the margins, and can indicate how much of the lack of agreement is due to marginal heterogeneity.     

Effect of medium composition, agitation and the presence of EDTA on the antimicrobial activity of cryptolepine

The antimicrobial activity of cryptolepine is influenced by the type of medium employed, agitation and the presence of non-inhibitory concentrations of EDTA. The use of Mueller–Hinton broth (MHB), iso-sensitest broth and tryptone soya broth (TSB) produced lower minimum inhibitory concentrations (MICs) for some of the test organisms compared with nutrient broth or yeast dextrose broth (YDB). For example, a fourfold drop in MIC was recorded for Saccharomyces cerevisiae in MHB compared with the same organism tested in YDB. Agitation of the broths during incubation nearly always produced lower MICs for the bacteria, an eightfold decrease in MIC being recorded for Escherichia coli cultured in nutrient broth with agitation compared with a statically maintained culture. A non-inhibitory concentration (10⁻³ mol l⁻¹) of disodium EDTA enhanced the antimicrobial activity of cryptolepine. Against E. coli NCTC 11560, an eightfold decrease in MIC and minimum bactericidal concentration (MBC) was recorded when tested in the presence of EDTA.     

Identification of a 13-kDa protein associated with the polyhydroxyalkanoic acid granules from Acinetobacter spp.

Abstract Transferrin-binding proteins from Neisseria meningitidis vary among different isolates. We have identified and studied a hypervariable region adjacent to the carboxyl-end of the transferrin-binding domain of the Tbp2 molecule. The tbp2 genes from six strains of N. meningitidis were cloned and sequenced in this particular region. Sequence analysis of these regions along with five other sequences available from pathogenic Neisseria showed a common organisation of seven highly variable nucleotide stretches interspersed with six conserved nucleotide stretches. The variable regions correlated with the location of immunoreactive epitopes in polyclonal antisera raised to transferrin-binding proteins identified by peptide pin technology. Sequence analysis suggested a mosaic-like organisation of the tbp2 genes. Taken together, these data suggest that the antigenic variation in this part of the protein may result from a strong host immune pressure.     

The Mitogen-activated Protein (MAP) Kinases p38 and Extracellular Signal-regulated Kinase (ERK) Are Involved in Hepatocyte-mediated Phenotypic Switching in Prostate Cancer Cells

The greatest challenge for the seeding of cancer in metastatic sites is integration into the ectopic microenvironment despite the lack of an orthotopic supportive environment and presence of pro-death signals concomitant with a localized “foreign-body” inflammatory response. In this metastatic location, many carcinoma cells display a reversion of the epithelial-to-mesenchymal transition that marks dissemination in the primary tumor mass. This mesenchymal to epithelial reverting transition (MErT) is thought to help seeding and colonization by protecting against cell death. We have previously shown that hepatocyte coculture induces the re-expression of E-cadherin via abrogation of autocrine EGFR signaling pathway in prostate cancer (PCa) cells and that this confers a survival advantage. Herein, we show that hepatocytes educate PCa to undergo MErT by modulating the activity of p38 and ERK1/2. Hepatocytes inhibited p38 and ERK1/2 activity in prostate cancer cells, which allowed E-cadherin re-expression. Introduction of constitutively active MEK6 and MEK1 to DU145 cells cocultured with hepatocytes abrogated E-cadherin re-expression. At least a partial phenotypic reversion can be achieved by suppression of p38 and ERK1/2 activation in DU145 cells even in the absence of hepatocytes. Interestingly, these mitogen-activated protein kinase activities were also triggered by re-expressed E-cadherin leading to p38 and ERK1/2 activity in PCa cells; these signals provide protection to PCa cells upon challenge with chemotherapy and cell death-inducing cytokines. We propose that distinct p38/ERK pathways are related to E-cadherin levels and function downstream of E-cadherin allowing, respectively, for hepatocyte-mediated MErT and tumor cell survival in the face of death signals.     

Simultaneous Quantification of Multiple Urinary Naphthalene Metabolites by Liquid Chromatography Tandem Mass Spectrometry

Naphthalene is an environmental toxicant to which humans are exposed. Naphthalene causes dose-dependent cytotoxicity to murine airway epithelial cells but a link between exposure and human pulmonary disease has not been established. Naphthalene toxicity in rodents depends on P450 metabolism. Subsequent biotransformation results in urinary elimination of several conjugated metabolites. Glucuronide and sulfate conjugates of naphthols have been used as markers of naphthalene exposure but, as the current studies demonstrate, these assays provide a limited view of the range of metabolites generated from the parent hydrocarbon. Here, we present a liquid chromatography tandem mass spectrometry method for measurement of the glucuronide and sulfate conjugates of 1-naphthol as well as the mercapturic acids and N-acetyl glutathione conjugates from naphthalene epoxide. Standard curves were linear over 2 log orders. On column detection limits varied from 0.91 to 3.4 ng; limits of quantitation from 1.8 to 6.4 ng. The accuracy of measurement of spiked urine standards was -13.1 to + 5.2% of target and intra-day and inter-day variability averaged 7.2 (± 4.5) and 6.8 (± 5.0) %, respectively. Application of the method to urine collected from mice exposed to naphthalene at 15 ppm (4 hrs) showed that glutathione-derived metabolites accounted for 60-70% of the total measured metabolites and sulfate and glucuronide conjugates were eliminated in equal amounts. The method is robust and directly measures several major naphthalene metabolites including those derived from glutathione conjugation of naphthalene epoxide. The assays do not require enzymatic deconjugation, extraction or derivatization thus simplifying sample work up.     

Decadal Changes in the Abundance and Length of Snapper (Chrysophrys auratus) in Subtropical Marine Sanctuaries

Abundance and length of the highly-targeted snapper Chysophrys auratus were compared between sites in ''no take'' areas (Sanctuary Zones: SZ), partial protected areas which are fished (Habitat Protection Zones: HPZ), and areas outside (Outside) the Solitary Islands Marine Park (SIMP), Australia. Baited Remote Underwater Video (BRUV) sampling on shallow rocky reef (15 - 25 m) was conducted annually from 2002 until 2014 in the Austral-winter, covering the decade after these marine park zones were established (2002). Additional deeper sites (25 - 40 m) were sampled in 2010-2011 to assess if findings were more-broadly applicable. Lengths were measured using stereo-BRUVs from 2011-2014. Snapper were significantly more abundant in SZ overall and in most years compared with the other two management types, which did not significantly differ. Snapper rapidly increased after 2 - 3 years protection in all management types, especially SZ. Snapper were present on more SZ deployments than HPZ and Outside after the same period. The positive SZ response in snapper abundance on shallower reef was also found at a broader spatial scale on deeper sites. Again the two fished management types did not show significant differences among each other. There was considerable variation in snapper abundance between years, with strong peaks in 2005, 2009 and 2014 especially in SZ. Abundances remained higher in SZ in the year or two following a strong peak, but decreased to similar abundances to fished areas before the next peak. Snapper length frequency distribution significantly differed between SZ and both fished management types, with more larger snapper within SZ including a higher proportion (58%) that were legal-sized (>25.7 cm FL). HPZ and Outside did not significantly differ from each other, and were dominated by individuals below legal size. Overall, SZ''s have positively influenced abundance and length of snapper on these subtropical rocky reefs.