Interlaboratory comparison of real-time polymerase chain reaction methods to detect Coxiella burnetii, the causative agent of Q fever

The bacterium Coxiella burnetii, which has a wide host range, causes Q fever. Infection with C burnetii can cause abortions, stillbirth, and the delivery of weak offspring in ruminants. Coxiella burnetii infection is zoonotic, and in human beings it can cause chronic, potentially fatal disease. Real-time polymerase chain reaction (PCR) is increasingly being used to detect the organism and to aid in diagnosis both in human and animal cases. Many different real-time PCR methods, which target different genes, have been described. To assess the comparability of the C. burnetii real-time PCR assays in use in different European laboratories, a panel of nucleic acid extracts was dispatched to 7 separate testing centers. The testing centers included laboratories from both human and animal health agencies. Each laboratory tested the samples using their in-house real-time PCR methods. The results of this comparison show that the most common target gene for real-time PCR assays is the IS1111 repeat element that is present in multiple copies in the C. burnetii genome. Many laboratories also use additional real-time PCR tests that target single-copy genes. The results of the current study demonstrate that the assays in use in the different laboratories are comparable, with general agreement of results for the panel of samples.

Resistance of Staphylococcus aureus to the cationic antimicrobial agent poly(2-(dimethylamino ethyl)methacrylate) (pDMAEMA) is influenced by cell-surface charge and hydrophobicity

Cationic antimicrobial agents may prevent device-associated infections caused by Staphylococcus epidermidis and Staphylococcus aureus. This study reports that the cationic antimicrobial polymer poly(2-(dimethylamino ethyl)methacrylate) (pDMAEMA) was more effective at antagonizing growth of clinical isolates of S. epidermidis than of S. aureus. Importantly, mature S. epidermidis biofilms were significantly inactivated by pDMAEMA. The S. aureus isolates tested were generally more hydrophobic than the S. epidermidis isolates and had a less negative charge, although a number of individual S. aureus and S. epidermidis clinical isolates had similar surface hydrophobicity and charge values. Fluorescence spectroscopy and flow cytometry revealed that fluorescently labelled pDMAEMA interacted strongly with S. epidermidis compared with S. aureus. S. aureus Delta dltA and Delta mprF mutants were less hydrophobic and therefore more susceptible to pDMAEMA than wild-type S. aureus. Although the different susceptibility of S. epidermidis and S. aureus isolates to pDMAEMA is complex, influenced in part by surface hydrophobicity and charge, these findings nevertheless reveal the potential of pDMAEMA to treat S. epidermidis infections.

A graded BDI agent model to represent and reason about preferences

In this research note, we introduce a graded BDI agent development framework, g-BDI for short, that allows to build agents as multi-context systems that reason about three fundamental and graded mental attitudes (i.e. beliefs, desires and intentions). We propose a sound and complete logical framework for them and some logical extensions to accommodate slightly different views on desires. © 2011 Elsevier B.V. All rights reserved.

"From Indomania to Indophobia":Thomas De Quincey's Providential Orientalism

Thomas De Quincey’s terrifying oriental nightmares, reported to sensational acclaim in his Confessions of an English Opium-Eater (1821), have become a touchstone of romantic imperialism in recent studies of the literature of the period (Leask 1991; Barrell 1992 et al). De Quincey’s collocation of “all creatures, birds, beasts, reptiles, all trees and plants, usages and appearances, that are found in all tropical regions” in the hypnagogic hallucinations that characterized what he called “the pains of opium” seems to anticipate neatly Said’s theory of orientalism, whereby the orient was supplied by the west with “a mentality, a genealogy, an atmosphere,” the attitudinal basis as he argues for the continuing march of imperialism from the late eighteenth century. Yet, as Thomas Trautmann (1997) has pointed out, orientalist scholarship based in India and led by the influential Asiatic Society of Bengal in the late eighteenth century was extremely enthusiastic about Indian classical antiquity. The early orientalist scholarship posited ethnic, linguistic, cultural and religious links between Europe and India, while recognizing the greater antiquity of Indian civilization. This favourable attitude (which Trautmann calls “Indomania”) was overtaken in the nineteenth century by disavowal of that scholarship and repugnance (which he calls “Indophobia”), influenced by utilitarian and evangelical attitudes to colonialism. De Quincey’s lifespan covers this crucial period of change. My paper examines his evangelical upbringing and interest in biblical and orientalist scholarship to suggest his anxious investment in these modes of thinking. I will suggest that the bizarre orientalist fusions of his dreams can be better understood in the context of changing attitudes to the imperialism during the period. An examination of his work provides a far more dynamic understanding of the processes of orientalism than the binary model suggested by Said. The transformation implied from imperial scholarship to governance, I will suggest, is not irrelevant to a world which continues to pull apart on various grounds of race and ethnicity, and reflects on our own role in the academy today.

How to Manipulate an Incompatibilistically Free Agent

A prominent criticism of compatibilist theories of moral responsibility is that they do not deal adequately with cases of manipulation, and particularly with induced desires. So, for example, accounts that give the conditions for responsibility in terms of the reasons-responsiveness of the mechanism governing one's decisions, as Fischer and Ravizza (1998) do, seem to leave the door open to cases such as the following.

A randomised, phase II trial of the DNA-hypomethylating agent 5-aza-2'-deoxycytidine (decitabine) in combination with carboplatin vs carboplatin alone in patients with recurrent, partially platinum-sensitive ovarian cancer.

Background: Our previous laboratory and clinical data suggested that one mechanism underlying the development of platinum resistance in ovarian cancer is the acquisition of DNA methylation. We therefore tested the hypothesis that the DNA hypomethylating agent 5-aza-2'-deoxycytodine (decitabine) can reverse resistance to carboplatin in women with relapsed ovarian cancer.

Methods: Patients progressing 6-12 months after previous platinum therapy were randomised to decitabine on day 1 and carboplatin (AUC 6) on day 8, every 28 days or carboplatin alone. The primary objective was response rate in patients with methylated hMLH1 tumour DNA in plasma.

Results: After a pre-defined interim analysis, the study closed due to lack of efficacy and poor treatment deliverability in 15 patients treated with the combination. Responses by GCIG criteria were 9 out of 14 vs 3 out of 15 and by RECIST were 6 out of 13 vs 1 out of 12 for carboplatin and carboplatin/decitabine, respectively. Grade 3/4 neutropenia was more common with the combination (60% vs 15.4%) as was G2/3 carboplatin hypersensitivity (47% vs 21%).

Conclusions: With this schedule, the addition of decitabine appears to reduce rather than increase the efficacy of carboplatin in partially platinum-sensitive ovarian cancer and is difficult to deliver. Patient-selection strategies, different schedules and other demethylating agents should be considered in future combination studies.

Detectability of bovine TB using the tuberculin skin test does not vary significantly according to pathogen genotype within Northern Ireland

Strains of many infectious diseases differ in parameters that influence epidemic spread, for example virulence, transmissibility, detectability and host specificity. Knowledge of inter-strain variation can be exploited to improve management and decrease disease incidence. Bovine tuberculosis (bTB) is increasingly prevalent among farmed cattle in the UK, exerting a heavy economic burden on the farming industry and government. We aimed to determine whether strains of Mycobacterium bovis (the causative agent of bTB) identified and classified using genetic markers (spoligotyping and multi-locus VNTR analysis) varied in response to the tuberculin skin test; this being the primary method of bTB detection used in the UK. Inter-strain variation in detectability of M. bovis could have important implications for disease control. The skin test is based on a differential delayed type hypersensitivity (DTH) response to intradermal injections of purified protein derivative (PPD) from M. bovis (PPD-B) and Mycobacterium avium (PPD-A). We searched for an association between skin test response (PPD-B skin rise minus PPD-A skin rise) and M. bovis genotype at the disclosing test in culture-confirmed cases using a field dataset consisting of 21,000 isolates belonging to 63 genotypes of M. bovis from cattle in Northern Ireland. We found no substantial variation among genotypes (estimated responses clustered tightly around the mean) controlling for animal sex, breed and test effects. We also estimated the ratio of skin test detected to undetected cases (i.e. cases only detected at abattoir). The skin test detection ratio varied among abattoirs with some detecting a greater proportion of cases than others but this variation was unrelated to the community composition of genotypes within each abattoir catchment. These two lines of evidence indicate that M. bovis genotypes in Northern Ireland have similar detectability using the skin test.

Adaptive uncertain information fusion to enhance plan selection in BDI agent systems

Correctly modelling and reasoning with uncertain information from heterogeneous sources in large-scale systems is critical when the reliability is unknown and we still want to derive adequate conclusions. To this end, context-dependent merging strategies have been proposed in the literature. In this paper we investigate how one such context-dependent merging strategy (originally defined for possibility theory), called largely partially maximal consistent subsets (LPMCS), can be adapted to Dempster-Shafer (DS) theory. We identify those measures for the degree of uncertainty and internal conflict that are available in DS theory and show how they can be used for guiding LPMCS merging. A simplified real-world power distribution scenario illustrates our framework. We also briefly discuss how our approach can be incorporated into a multi-agent programming language, thus leading to better plan selection and decision making.

New genetic loci link adipose and insulin biology to body fat distribution

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.

The CXCR2 antagonist, SCH-527123, shows antitumor activity and sensitizes cells to oxaliplatin in preclinical colon cancer models

Colorectal cancer is the second most common cause of cancer-related death in the United States. Recent studies showed that interleukin-8 (IL-8) and its receptors (CXCR1 and CXCR2) are significantly upregulated in both the tumor and its microenvironment, and act as key regulators of proliferation, angiogenesis, and metastasis. Our previous study showed that IL-8 overexpression in colorectal cancer cells triggers the upregulation of the CXCR2-mediated proliferative pathway. The aim of this study was to investigate whether the CXCR2 antagonist, SCH-527123, inhibits colorectal cancer proliferation and if it can sensitize colorectal cancer cells to oxaliplatin both in vitro and in vivo. SCH-527123 showed concentration-dependent antiproliferative effects in HCT116, Caco2, and their respective IL-8-overexpressing variants colorectal cancer cell lines. Moreover, SCH-527123 was able to suppress CXCR2-mediated signal transduction as shown through decreased phosphorylation of the NF-κB/mitogen-activated protein kinase (MAPK)/AKT pathway. These findings corresponded with decreased cell migration and invasion, while increased apoptosis in colorectal cancer cell lines. In vivo results verified that SCH-527123 treatment decreased tumor growth and microvessel density when compared with vehicle-treated tumors. Importantly, these preclinical studies showed that the combination of SCH-527123 and oxaliplatin resulted in a greater decrease in cell proliferation, tumor growth, apoptosis, and angiogenesis that was superior to single-agent treatment. Taken together, these findings suggest that targeting CXCR2 may block tumor proliferation, migration, invasion, and angiogenesis. In addition, CXCR2 blockade may further sensitize colorectal cancer to oxaliplatin treatment.

Regulation of human dUTPase gene expression and p53-mediated transcriptional repression in response to oxaliplatin-induced DNA damage

Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) catalyzes the hydrolysis of dUTP to dUMP and PPi. Although dUTP is a normal intermediate in DNA synthesis, its accumulation and misincorporation into DNA is lethal. Importantly, uracil misincorporation is a mechanism of cytotoxicity induced by fluoropyrimidine chemotherapeutic agents including 5-fluorouracil (5-FU) and elevated expression of dUTPase is negatively correlated with clinical response to 5-FU-therapy. In this study we performed the first functional characterization of the dUTPase promoter and demonstrate a role for E2F-1 and Sp1 in driving dUTPase expression. We establish a direct role for both mutant and wild-type forms of p53 in modulating dUTPase promoter activity. Treatment of HCT116 p53(+/+) cells with the DNA-damaging agent oxaliplatin induced a p53-dependent transcriptional downregulation of dUTPase not observed in the isogenic null cell line. Oxaliplatin treatment induced enrichment of p53 at the dUTPase promoter with a concomitant reduction in Sp1. The suppression of dUTPase by oxaliplatin promoted increased levels of dUTP that was enhanced by subsequent addition of fluoropyrimidines. The novel observation that oxaliplatin downregulates dUTPase expression may provide a mechanistic basis contributing to the synergy observed between 5-FU and oxaliplatin in the clinic. Furthermore, these studies provide the first evidence of a direct transcriptional link between the essential enzyme dUTPase and the tumor suppressor p53.