Novel <i>Campylobacter lari</i>-like bacteria from humans and molluscs: description of <i>Campylobacter peloridis</i> sp. nov., <i>Campylobacter lari</i> subsp. <i>concheus</i> subsp. nov. and <i>Campylobacter lari</i> subsp. <i>lari</i> subsp. nov.

A polyphasic study was undertaken to clarify the taxonomic position of Campylobacter lari-like strains isolated from shellfish and humans. The diversity within the strain collection was initially screened by means of fluorescent amplified fragment length polymorphism analysis and whole-cell protein electrophoresis, revealing the existence of two clusters distinct from C. lari and other Campylobacter species. The divergence of these clusters was confirmed by phenotypic analysis and by 16S rRNA and hsp60 gene sequence analysis. Phylogenetic analysis identified C. lari, Campylobacter jejuni, Campylobacter coli and Campylobacter insulaenigrae as the closest phylogenetic neighbours of both taxa. DNA–DNA hybridizations revealed that one cluster, comprising 10 strains, represented a novel Campylobacter species, for which the name Campylobacter peloridis sp. nov. is proposed, with 2314BVAT (=LMG 23910T =CCUG 55787T) as the type strain. The second cluster, comprising six strains, represents a novel subspecies within the species C. lari, for which the name Campylobacter lari subsp. concheus subsp. nov. is proposed, with 2897RT (=LMG 21009T =CCUG 55786T) as the type strain. The description of C. lari subsp. concheus has the effect of automatically creating the subspecies Campylobacter lari subsp. lari subsp. nov. (type strain LMG 8846T=NCTC 11352T)

Network Features of the Mammalian Circadian Clock

The mammalian circadian clock is a cell-autonomous system that drives oscillations in behavior and physiology in anticipation of daily environmental change. To assess the robustness of a human molecular clock, we systematically depleted known clock components and observed that circadian oscillations are maintained over a wide range of disruptions. We developed a novel strategy termed Gene Dosage Network Analysis (GDNA) in which small interfering RNA (siRNA)-induced dose-dependent changes in gene expression were used to build gene association networks consistent with known biochemical constraints. The use of multiple doses powered the analysis to uncover several novel network features of the circadian clock, including proportional responses and signal propagation through interacting genetic modules. We also observed several examples where a gene is up-regulated following knockdown of its paralog, suggesting the clock network utilizes active compensatory mechanisms rather than simple redundancy to confer robustness and maintain function. We propose that these network features act in concert as a genetic buffering system to maintain clock function in the face of genetic and environmental perturbation

Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths

Abstract Background Late Pleistocene North America hosted at least two divergent and ecologically distinct species of mammoth: the periglacial woolly mammoth (Mammuthus primigenius) and the subglacial Columbian mammoth (Mammuthus columbi). To date, mammoth genetic research has been entirely restricted to woolly mammoths, rendering their genetic evolution difficult to contextualize within broader Pleistocene paleoecology and biogeography. Here, we take an interspecific approach to clarifying mammoth phylogeny by targeting Columbian mammoth remains for mitogenomic sequencing. Results We sequenced the first complete mitochondrial genome of a classic Columbian mammoth, as well as the first complete mitochondrial genome of a North American woolly mammoth. Somewhat contrary to conventional paleontological models, which posit that the two species were highly divergent, the M. columbi mitogenome we obtained falls securely within a subclade of endemic North American M. primigenius. Conclusions Though limited, our data suggest that the two species interbred at some point in their evolutionary histories. One potential explanation is that woolly mammoth haplotypes entered Columbian mammoth populations via introgression at subglacial ecotones, a scenario with compelling parallels in extant elephants and consistent with certain regional paleontological observations. This highlights the need for multi-genomic data to sufficiently characterize mammoth evolutionary history. Our results demonstrate that the use of next-generation sequencing technologies holds promise in obtaining such data, even from non-cave, non-permafrost Pleistocene depositional contexts.http://deepblue.lib.umich.edu/bitstream/2027.42/112426/1/13059_2011_Article_2544.pd

Interactively solving school timetabling problems using extensions of constraint programming

Timetabling problems have been frequently studied due to their wide range of applications. However, they are often solved manually because of the lack of appropriate computer tools. Although many approaches mainly based on local search or constraint programming seem to have been quite successful in recent years, they are often highly dedicated to specific problems and encounter difficulties to take the dynamic and over-constrained nature of such problems. We were confronted with such an over-constrained and dynamic problem in our institution. This paper deals with a timetabling system based on constraint programming with the use of explanations to offer a dynamic behaviour and to allow automatic relaxations of constraints. Our tool has successfully answered the needs of the current planner by providing solutions in a few minutes instead of a week of manual design.We present in this paper the techniques used, the results obtained and a discussion on the effects of the automation of the timetabling process

Kaon photoproduction: background contributions, form factors and missing resonances

The photoproduction p(gamma, K+)Lambda process is studied within a field-theoretic approach. It is shown that the background contributions constitute an important part of the reaction dynamics. We compare predictions obtained with three plausible techniques for dealing with these background contributions. It appears that the extracted resonance parameters drastically depend on the applied technique. We investigate the implications of the corrections to the functional form of the hadronic form factor in the contact term, recently suggested by Davidson and Workman (Phys. Rev. C 63, 025210). The role of background contributions and hadronic form factors for the identification of the quantum numbers of ``missing'' resonances is discussed.Comment: 11 pages, 7 eps figures, submitted to Phys. Rev.

Population pharmacokinetics of fluconazole in critically ill patients receiving continuous venovenous hemodiafiltration - using Monte Carlo Simulations to predict doses for specified pharmacodynamic targets

Fluconazole is a widely used antifungal agent that is extensively reabsorbed in patients with normal renal function. However, its reabsorption can be compromised in patients with acute kidney injury, thereby leading to altered fluconazole clearance and total systemic exposure. Here, we explore the pharmacokinetics of fluconazole in 10 critically ill anuric patients receiving continuous venovenous hemodiafiltration (CVVHDF). We performed Monte Carlo simulations to optimize dosing to appropriate pharmacodynamic endpoints for this population. Pharmacokinetic profiles of initial and steady-state doses of 200 mg intravenous fluconazole twice daily were obtained from plasma and CVVHDF effluent. Nonlinear mixed-effects modeling (NONMEM) was used for data analysis and to perform Monte Carlo simulations. For each dosing regimen, the free drug area under the concentration-time curve (fAUC)/MIC ratio was calculated. The percentage of patients achieving an AUC/MIC ratio greater than 25 was then compared for a range of MIC values. A two-compartment model adequately described the disposition of fluconazole in plasma. The estimate for total fluconazole clearance was 2.67 liters/h and was notably 2.3 times faster than previously reported in healthy volunteers. Of this, fluconazole clearance by the CVVHDF route (CL(CVVHDF)) represented 62% of its total systemic clearance. Furthermore, the predicted efficiency of CL(CVVHDF) decreased to 36.8% when filters were in use >48 h. Monte Carlo simulations demonstrated that a dose of 400 mg twice daily maximizes empirical treatment against fungal organisms with MIC up to 16 mg/liter. This is the first study we are aware of that uses Monte Carlo simulations to inform dosing requirements in patients where tubular reabsorption of fluconazole is probably nonexistent

Examining the Relevancy and Utility of the American Fisheries Society Certification Program to Prepare Future Fisheries Professionals

Fisheries science is a diverse field that requires individuals to be knowledgeable in many disciplines in addition to fisheries (e.g., economics, sociology, political science, chemistry; Kelso and Murphy 1988). This challenges students attempting to enter a career in fisheries, as well as academic institutions and eventual employers, to develop both depth and breadth of knowledge needed to succeed in the profession (Oglesby and Krueger 1989). The preparedness and competency of young professionals entering the workforce has long been a problem (Stauffer and McMullin 2009). Several constraints and ongoing challenges facing the profession have continued to magnify these issues over time (McMullin et al., this issue). These issues stem from the diversity of skills required or expected across employer groups (e.g., government agencies, private sectors, nongovernment organizations) and degree levels sought (B.Sc., M.Sc., Ph.D.), complexity of fisheries-related problems, and balancing a broad academic focus with specific training. Additionally, employers perceive that students lack welldeveloped critical thinking, communication, and statistical skills that are highly desired in any area of fisheries. The American Fisheries Society’s (AFS) mission of preparing and promoting the development of fisheries professionals has been addressed in many ways, including development of the AFS Professional Certification Program in 1963. This program provides minimum standards for which fisheries professionals are recognized across government, academic, and nongovernment entities. The certification program fosters greater recognition that fisheries professionals are well equipped and prepared to act on the public’s behalf concerning fisheries-related issues. Two tiers of certification exist, with first-tier certification (Associate Fisheries Professional) contingent upon the completion of higher education courses in six broad subject areas. In this article, we focus on the first tier of certification, the basic education determined by AFS to be critical in preparing young professionals for a career in fisheries

Paclitaxel for malignant pleural mesothelioma: a phase II study of the EORTC Lung Cancer Cooperative Group.

The EORTC Lung Cancer Cooperative Group undertook a phase II study of paclitaxel in 25 chemotherapy-naive patients with malignant pleural mesothelioma. Paclitaxel was given intravenously at a dose of 200 mg m-2 as a 3 h infusion every 3 weeks, after standard premedication with corticosteroids and antihistamines. This regimen was well tolerated, with < 4% of cycles resulting in severe toxicity. No major objective responses were observed and ten patients had stable disease. Median survival time was 39 weeks and the 1 year survival rate was 30%. In conclusion, paclitaxel at the dose and schedule investigated in this trial had no major activity in the treatment of malignant pleural mesothelioma