A comparison of two methods for developing the linearization of a shallow-water model

We develop the linearization of a semi-implicit semi-Lagrangian model of the one-dimensional shallow-water equations using two different methods. The usual tangent linear model, formed by linearizing the discrete nonlinear model, is compared with a model formed by first linearizing the continuous nonlinear equations and then discretizing. Both models are shown to perform equally well for finite perturbations. However, the asymptotic behaviour of the two models differs as the perturbation size is reduced. This leads to difficulties in showing that the models are correctly coded using the standard tests. To overcome this difficulty we propose a new method for testing linear models, which we demonstrate both theoretically and numerically. © Crown copyright, 2003. Royal Meteorological Society

Incorporating data received after a sequential trial has stopped into the final analysis: implementation and comparison of methods

In a sequential clinical trial, accrual of data on patients often continues after the stopping criterion for the study has been met. This is termed “overrunning.” Overrunning occurs mainly when the primary response from each patient is measured after some extended observation period. The objective of this article is to compare two methods of allowing for overrunning. In particular, simulation studies are reported that assess the two procedures in terms of how well they maintain the intended type I error rate. The effect on power resulting from the incorporation of “overrunning data” using the two procedures is evaluated.

Active-control trials with binary data: a comparison of methods for testing superiority or non-inferiority using the odds ratio

This paper considers methods for testing for superiority or non-inferiority in active-control trials with binary data, when the relative treatment effect is expressed as an odds ratio. Three asymptotic tests for the log-odds ratio based on the unconditional binary likelihood are presented, namely the likelihood ratio, Wald and score tests. All three tests can be implemented straightforwardly in standard statistical software packages, as can the corresponding confidence intervals. Simulations indicate that the three alternatives are similar in terms of the Type I error, with values close to the nominal level. However, when the non-inferiority margin becomes large, the score test slightly exceeds the nominal level. In general, the highest power is obtained from the score test, although all three tests are similar and the observed differences in power are not of practical importance. Copyright (C) 2007 John Wiley & Sons, Ltd.

Protonation of phenylboronic acid: comparison of G3B3 and G2MP2 methods

G3B3 and G2MP2 calculations using Gaussian 03 have been carried out to investigate the protonation preferences for phenylboronic acid. All nine heavy atoms have been protonated in turn. With both methodologies, the two lowest protonation energies are obtained with the proton located either at the ipso carbon atom or at a hydroxyl oxygen atom. Within the G3B3 formalism, the lowest-energy configuration by 4.3 kcal . mol(-1) is found when the proton is located at the ipso carbon, rather than at the electronegative oxygen atom. In the resulting structure, the phenyl ring has lost a significant amount of aromaticity. By contrast, calculations with G2MP2 show that protonation at the hydroxyl oxygen atom is favored by 7.7 kcal . mol(-1). Calculations using the polarizable continuum model (PCM) solvent method also give preference to protonation at the oxygen atom when water is used as the solvent. The preference for protonation at the ipso carbon found by the more accurate G3B3 method is unexpected and its implications in Suzuki coupling are discussed. (C) 2006 Wiley Periodicals, Inc.

Fecal water as a non-invasive biomarker in nutritional intervention: comparison of preparation methods and refinement of different endpoints

The assessment of cellular effects by the aqueous phase of human feces (fecal water, FW) is a useful biomarker approach to study cancer risks and protective activities of food. In order to refine and develop the biomarker, different protocols of preparing FW were compared. Fecal waters were prepared by 3 methods: (A) direct centrifugation; (B) extraction of feces in PBS before centrifugation; and (C) centrifugation of lyophilized and reconstituted feces. Genotoxicity was determined in colon cells using the Comet assay. Selected samples were investigated for additional parameters related to carcinogenesis. Two of 7 FWs obtained by methods A and B were similarly genotoxic. Method B, however, yielded higher volumes of FW, allowing sterile filtration for long-term culture experiments. Four of 7 samples were non-genotoxic when prepared according to all 3 methods. FW from lyophilized feces and from fresh samples were equally genotoxic. FWs modulated cytotoxicity, paracellular permeability, and invasion, independent of their genotoxicity. All 3 methods of FW preparation can be used to assess genotoxicity. The higher volumes of FWobtained by preparation method B greatly enhance the perspectives of measuring different types of biological parameters and using these to disclose activities related to cancer development.

Comparison of two methods of presenting risk information to patients about the side effects of medicines

Objective: To determine whether the use of verbal descriptors suggested by the European Union (EU) such as "common" (1-10% frequency) and "rare" (0.01-0.1%) effectively conveys the level of risk of side effects to people taking a medicine. Design: Randomised controlled study with unconcealed allocation. Participants: 120 adults taking simvastatin or atorvastatin after cardiac surgery or myocardial infarction. Setting: Cardiac rehabilitation clinics at two hospitals in Leeds, UK. Intervention: A written statement about one of the side effects of the medicine (either constipation or pancreatitis). Within each side effect condition half the patients were given the information in verbal form and half in numerical form (for constipation, "common" or 2.5%; for pancreatitis, "rare" or 0.04%). Main outcome measure: The estimated likelihood of the side effect occurring. Other outcome measures related to the perceived severity of the side effect, its risk to health, and its effect on decisions about whether to take the medicine. Results: The mean likelihood estimate given for the constipation side effect was 34.2% in the verbal group and 8.1% in the numerical group; for pancreatitis it was 18% in the verbal group and 2.1% in the numerical group. The verbal descriptors were associated with more negative perceptions of the medicine than their equivalent numerical descriptors. Conclusions: Patients want and need understandable information about medicines and their risks and benefits. This is essential if they are to become partners in medicine taking. The use of verbal descriptors to improve the level of information about side effect risk leads to overestimation of the level of harm and may lead patients to make inappropriate decisions about whether or not they take the medicine.

Comparison of bottom-up protein identification methods

With the rapid development of proteomics, a number of different methods appeared for the basic task of protein identification. We made a simple comparison between a common liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflow using an ion trap mass spectrometer and a combined LC-MS and LC-MS/MS method using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry and accurate peptide masses. To compare the two methods for protein identification, we grew and extracted proteins from E. coli using established protocols. Cystines were reduced and alkylated, and proteins digested by trypsin. The resulting peptide mixtures were separated by reversed-phase liquid chromatography using a 4 h gradient from 0 to 50% acetonitrile over a C18 reversed-phase column. The LC separation was coupled on-line to either a Bruker Esquire HCT ion trap or a Bruker 7 tesla APEX-Qe Qh-FTICR hybrid mass spectrometer. Data-dependent Qh-FTICR-MS/MS spectra were acquired using the quadrupole mass filter and collisionally induced dissociation into the external hexapole trap. Proteins were in both schemes identified by Mascot MS/MS ion searches and the peptides identified from these proteins in the FTICR MS/MS data were used for automatic internal calibration of the FTICR-MS data, together with ambient polydimethylcyclosiloxane ions.

Assessing the accuracy of CME speed and trajectory estimates from STEREO observations through a comparison of independent methods

We have estimated the speed and direction of propagation of a number of Coronal Mass Ejections (CMEs) using single-spacecraft data from the STEREO Heliospheric Imager (HI) wide-field cameras. In general, these values are in good agreement with those predicted by Thernisien, Vourlidas, and Howard in Solar Phys. 256, 111 -aEuro parts per thousand 130 (2009) using a forward modelling method to fit CMEs imaged by the STEREO COR2 coronagraphs. The directions of the CMEs predicted by both techniques are in good agreement despite the fact that many of the CMEs under study travel in directions that cause them to fade rapidly in the HI images. The velocities estimated from both techniques are in general agreement although there are some interesting differences that may provide evidence for the influence of the ambient solar wind on the speed of CMEs. The majority of CMEs with a velocity estimated to be below 400 km s(-1) in the COR2 field of view have higher estimated velocities in the HI field of view, while, conversely, those with COR2 velocities estimated to be above 400 km s(-1) have lower estimated HI velocities. We interpret this as evidence for the deceleration of fast CMEs and the acceleration of slower CMEs by interaction with the ambient solar wind beyond the COR2 field of view. We also show that the uncertainties in our derived parameters are influenced by the range of elongations over which each CME can be tracked. In order to reduce the uncertainty in the predicted arrival time of a CME at 1 Astronomical Unit (AU) to within six hours, the CME needs to be tracked out to at least 30 degrees elongation. This is in good agreement with predictions of the accuracy of our technique based on Monte Carlo simulations.

Comparison of methods for analysis of proteolysis by plasmin in milk

Sensitive methods that are currently used to monitor proteolysis by plasmin in milk are limited due to 7 their high cost and lack of standardisation for quality assurance in the various dairy laboratories. In 8 this study, four methods, trinitrobenzene sulphonic acid (TNBS), reverse phase high pressure liquid 9 chromatography (RP-HPLC), gel electrophoresis and fluorescamine, were selected to assess their 10 suitability for the detection of proteolysis in milk by plasmin. Commercial UHT milk was incubated 11 with plasmin at 37 °C for one week. Clarification was achieved by isoelectric precipitation (pH 4·6 12 soluble extracts)or 6% (final concentration) trichloroacetic acid (TCA). The pH 4·6 and 6% TCA 13 soluble extracts of milk showed high correlations (R2 > 0·93) by the TNBS, fluorescamine and 14 RP-HPLC methods, confirming increased proteolysis during storage. For gel electrophoresis,15 extensive proteolysis was confirmed by the disappearance of α- and β-casein bands on the seventh 16 day, which was more evident in the highest plasmin concentration. This was accompanied by the 17 appearance of α- and β-casein proteolysis products with higher intensities than on previous days, 18 implying that more products had been formed as a result of casein breakdown. The fluorescamine 19 method had a lower detection limit compared with the other methods, whereas gel electrophoresis 20 was the best qualitative method for monitoring β-casein proteolysis products. Although HPLC was the 21 most sensitive, the TNBS method is recommended for use in routine laboratory analysis on the basis 22 of its accuracy, reliability and simplicity.

An introduction to radial basis functions for system identification: a comparison with other neural network methods

A look is taken at the use of radial basis functions (RBFs), for nonlinear system identification. RBFs are firstly considered in detail themselves and are subsequently compared with a multi-layered perceptron (MLP), in terms of performance and usage.

A comparison among four different retrieval methods for ice-cloud properties using data from CloudSat, CALIPSO, and MODIS

The A-Train constellation of satellites provides a new capability to measure vertical cloud profiles that leads to more detailed information on ice-cloud microphysical properties than has been possible up to now. A variational radar–lidar ice-cloud retrieval algorithm (VarCloud) takes advantage of the complementary nature of the CloudSat radar and Cloud–Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) lidar to provide a seamless retrieval of ice water content, effective radius, and extinction coefficient from the thinnest cirrus (seen only by the lidar) to the thickest ice cloud (penetrated only by the radar). In this paper, several versions of the VarCloud retrieval are compared with the CloudSat standard ice-only retrieval of ice water content, two empirical formulas that derive ice water content from radar reflectivity and temperature, and retrievals of vertically integrated properties from the Moderate Resolution Imaging Spectroradiometer (MODIS) radiometer. The retrieved variables typically agree to within a factor of 2, on average, and most of the differences can be explained by the different microphysical assumptions. For example, the ice water content comparison illustrates the sensitivity of the retrievals to assumed ice particle shape. If ice particles are modeled as oblate spheroids rather than spheres for radar scattering then the retrieved ice water content is reduced by on average 50% in clouds with a reflectivity factor larger than 0 dBZ. VarCloud retrieves optical depths that are on average a factor-of-2 lower than those from MODIS, which can be explained by the different assumptions on particle mass and area; if VarCloud mimics the MODIS assumptions then better agreement is found in effective radius and optical depth is overestimated. MODIS predicts the mean vertically integrated ice water content to be around a factor-of-3 lower than that from VarCloud for the same retrievals, however, because the MODIS algorithm assumes that its retrieved effective radius (which is mostly representative of cloud top) is constant throughout the depth of the cloud. These comparisons highlight the need to refine microphysical assumptions in all retrieval algorithms and also for future studies to compare not only the mean values but also the full probability density function.