A plasmid-based lacZα gene assay for DNA polymerase fidelity measurement

A significantly improved DNA polymerase fidelity assay, based on a gapped plasmid containing the lacZα reporter gene in a single-stranded region, is described. Nicking at two sites flanking lacZα, and removing the excised strand by thermocycling in the presence of complementary competitor DNA, is used to generate the gap. Simple methods are presented for preparing the single-stranded competitor. The gapped plasmid can be purified, in high amounts and in a very pure state, using benzoylated-naphthoylated DEAE-cellulose, resulting in a low background mutation frequency (~1 × 10(-4)). Two key parameters, the number of detectable sites and the expression frequency, necessary for measuring polymerase error rates have been determined. DNA polymerase fidelity is measured by gap filling in vitro, followed by transformation into Escherichia coli and scoring of blue/white colonies and converting the ratio to error rate. Several DNA polymerases have been used to fully validate this straightforward and highly sensitive system

STOCHASTIC EFFICIENCY ANALYSIS USING MULTIPLE UTILITY FUNCTIONS

Evaluating the risk of a particular decision depends on the risk aversion of the decision maker related to the underlying utility function. The objective of this paper is to use stochastic efficiency with respect to a function (SERF) to compare the ranking of risky alternatives using alternative utility functional forms.Research Methods/ Statistical Methods,

Stochastic efficiency analysis with risk aversion bounds: a simplified approach

A method of stochastic dominance analysis with respect to a function (SDRF) is described and illustrated. The method, called stochastic efficiency with respect to a function (SERF), orders a set of risky alternatives in terms of certainty equivalents for a specified range of attitudes to risk. It can be applied for conforming utility functions with risk attitudes defined by corresponding ranges of absolute, relative or partial risk aversion coefficients. Unlike conventional SDRF, SERF involves comparing each alternative with all the other alternatives simultaneously, not pairwise, and hence can produce a smaller efficient set than that found by simple pairwise SDRF over the same range of risk attitudes. Moreover, the method can be implemented in a simple spreadsheet with no special software needed.Risk and Uncertainty,

An X-ray absorption spectroscopic study at the mercury LIII edge on phenylmercury(II) oxygen species

The X-ray absorption spectra of the reference and model compounds HgCl2, PhHgCl, PhHgOAc and [(PhHg)2OH][BF4].H2O have been analysed in both the XANES and EXAFS regions, and the technique was extended to determine the structures of (PhHg)2O, PhHgOH, and the basic salts PhHgOH.PhHgNO3 and PhHgOH.(PhHg)2SO4, which were previously structurally uncharacterised. Results indicate that (PhHg)2O is a molecular species with Hg-O-Hg 135°, while PhHgOH contains the [(PhHg)2OH]+ cation and is better formulated as [(PhHg)2OH]OH. The same cation is also featured in the two basic salts. Electrospray mass spectral studies of PhHgOH in aqueous solutions show that [PhHgOH2]+, [(PhHg)2OH]+ and [(PhHg)3O]+ co-exist in solution in a pH-dependent equilibrium

Nitrogen dynamics in the Irish Sea and adjacent shelf waters: An exploration of dissolved organic nitrogen

AbstractRelatively little is known about dissolved organic nitrogen (DON) in the marine environment because research has historically focused on dissolved inorganic nitrogen (DIN). In this study we combine measurements of dissolved organic matter (DOM), DIN, particulate organic nitrogen (PON), dissolved inorganic phosphorus (DIP) and silicon (DIS), with temperature and salinity data from the western shelf region of the UK and Ireland, and with inorganic and organic nitrogen (N) data from the western Irish Sea to develop an understanding of N dynamics in the Irish Sea and adjacent shelf waters, and investigate the role of DON in the nitrogen budget of the seasonally stratifying western Irish Sea. In January 2013, the sampling area was divided by density fronts into 4 regions of distinct oceanography and homogeneous chemistry. DON concentrations accounted for 25.3 ± 1.8% of total dissolved N (TDN) across all regions. DOM concentrations generally decreased from the freshwater influenced water of Liverpool Bay to the oceanic waters of the Celtic Sea and Malin Shelf. Urea and dissolved free amino acids (DFAA) together made up 27.3 ± 3.1% of DON. Estimated concentrations in the rivers discharging into Liverpool Bay were 8.0 and 2.1 μmol N L−1 respectively: at the high end of reported riverine concentrations. Oceanic nutrient inputs to the Irish Sea only have a small influence on N concentrations. Riverine N inputs to the Irish Sea are substantial but are likely removed by natural N cycling processes. In the western Irish Sea, DON and PON concentrations reached maxima and minima in midsummer and early spring respectively. DIN followed the opposite trend. DON accounted for 38% of the yearly internal N cycling and we estimated that as much as 1.4 ± 1.2 μmol N L−1 of labile DON was available as an N source at the start of the spring bloom. Our study supports the view that DON plays an important role in N cycling in temperate shelf and coastal seas and should be included more often in biogeochemical measurements if we are to have a complete understanding of N dynamics in a changing world

Signal Processing and Propagation for Aeroacoustic Sensor Networking,” Ch

Passive sensing of acoustic sources is attractive in many respects, including the relatively low signal bandwidth of sound waves, the loudness of most sources of interest, and the inherent difficulty of disguising or concealing emitted acoustic signals. The availability of inexpensive, low-power sensing and signal-processing hardware enables application of sophisticated real-time signal processing. Among th

A Reinforcement Learning Based Control Approach for Propofol-Induced Burst Suppression

High-dose propofol is being investigated for its potential antidepressant effect. Propofol is titrated to induce burst suppression, a specific EEG pattern. However, propofol is difficult to dose due to uncertainty in each patient’s pharmacokinetics (PK) and pharmacodynamics (PD), and the lack of a commercially available monitor of propofol concentration. Clinicians currently infer the proper drug dose after observing the EEG response to the given dose. In this report we share our development of an automated controller to optimally administer propofol-induced burst suppression. We designed a deep deterministic policy gradient (DDPG) algorithm, which includes two deep neural networks and relates a 2-dimensional action space with a 3-dimensional state space. Our DDPG prototype did not satisfy our minimum training criteria. However, we share our diagnosis of current limitations in training a DDPG-based RL agent to administer propofol to PK-PD-simulated in silico patients. We also discuss potential solutions to improve RL agent training and performance

Research Fundamentals: V. The Use of Laboratory Animal Models in Research

Animal research has provided important information about many aspects of the pathophysiology of human disease. Well-performed animal studies can determine the potential benefit of many proposed therapeutic interventions, and experimental results from animal studies have served as the basis for many landmark clinical trials. Many animal research models are described in the research literature, and choosing the appropriate model to answer a research question can be a daunting task. Even more challenging is developing a new model when none of the existing systems are relevant to the proposed question. This article was prepared by members of the SAEM Research Committee to provide an overview of animal modeling. Important considerations in choosing, applying, and developing animal research models are outlined. Practical discussions of potential problems with animal models are also provided