Efficient and accurate experimental design for enzyme kinetics: Bayesian studies reveal a systematic approach

In areas such as drug development, clinical diagnosis and biotechnology research, acquiring details about the kinetic parameters of enzymes is crucial. The correct design of an experiment is critical to collecting data suitable for analysis, modelling and deriving the correct information. As classical design methods are not targeted to the more complex kinetics being frequently studied, attention is needed to estimate parameters of such models with low variance. We demonstrate that a Bayesian approach (the use of prior knowledge) can produce major gains quantifiable in terms of information, productivity and accuracy of each experiment. Developing the use of Bayesian Utility functions, we have used a systematic method to identify the optimum experimental designs for a number of kinetic model data sets. This has enabled the identification of trends between kinetic model types, sets of design rules and the key conclusion that such designs should be based on some prior knowledge of K-M and/or the kinetic model. We suggest an optimal and iterative method for selecting features of the design such as the substrate range, number of measurements and choice of intermediate points. The final design collects data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. (C) 2003 Elsevier Science B.V. All rights reserved.

On the Nusselt number for frazil ice growth—a correction to ”Frazil evolution in channels“ by Lars Hammar and Hung-Tao Shen

The growth (melt) rate of frazil ice is governed by heat transfer away from (towards) the ice crystal, which can be represented by the Nusselt number. We discuss choices for the Nusselt number and turbulent length scale appropriate for frazil ice and note an inaccuracy in the study ”Frazil evolution in channels“ by Lars Hammar and Hung-Tao Shen, which has also led to potentially significant errors in several other papers. We correct this error and suggest an appropriate strategy for determining the Nusselt number applicable to frazil ice growth and melting.

A systematic approach to identify the sources of tropical SST errors in coupled models using the adjustment of initialised experiments

Understanding the sources of systematic errors in climate models is challenging because of coupled feedbacks and errors compensation. The developing seamless approach proposes that the identification and the correction of short term climate model errors have the potential to improve the modeled climate on longer time scales. In previous studies, initialised atmospheric simulations of a few days have been used to compare fast physics processes (convection, cloud processes) among models. The present study explores how initialised seasonal to decadal hindcasts (re-forecasts) relate transient week-to-month errors of the ocean and atmospheric components to the coupled model long-term pervasive SST errors. A protocol is designed to attribute the SST biases to the source processes. It includes five steps: (1) identify and describe biases in a coupled stabilized simulation, (2) determine the time scale of the advent of the bias and its propagation, (3) find the geographical origin of the bias, (4) evaluate the degree of coupling in the development of the bias, (5) find the field responsible for the bias. This strategy has been implemented with a set of experiments based on the initial adjustment of initialised simulations and exploring various degrees of coupling. In particular, hindcasts give the time scale of biases advent, regionally restored experiments show the geographical origin and ocean-only simulations isolate the field responsible for the bias and evaluate the degree of coupling in the bias development. This strategy is applied to four prominent SST biases of the IPSLCM5A-LR coupled model in the tropical Pacific, that are largely shared by other coupled models, including the Southeast Pacific warm bias and the equatorial cold tongue bias. Using the proposed protocol, we demonstrate that the East Pacific warm bias appears in a few months and is caused by a lack of upwelling due to too weak meridional coastal winds off Peru. The cold equatorial bias, which surprisingly takes 30 years to develop, is the result of an equatorward advection of midlatitude cold SST errors. Despite large development efforts, the current generation of coupled models shows only little improvement. The strategy proposed in this study is a further step to move from the current random ad hoc approach, to a bias-targeted, priority setting, systematic model development approach.

An investigation of the shortcomings of the CONSORT 2010 statement for the reporting of group sequential randomised controlled trials: a methodological systematic review

Background It can be argued that adaptive designs are underused in clinical research. We have explored concerns related to inadequate reporting of such trials, which may influence their uptake. Through a careful examination of the literature, we evaluated the standards of reporting of group sequential (GS) randomised controlled trials, one form of a confirmatory adaptive design. Methods We undertook a systematic review, by searching Ovid MEDLINE from the 1st January 2001 to 23rd September 2014, supplemented with trials from an audit study. We included parallel group, confirmatory, GS trials that were prospectively designed using a Frequentist approach. Eligible trials were examined for compliance in their reporting against the CONSORT 2010 checklist. In addition, as part of our evaluation, we developed a supplementary checklist to explicitly capture group sequential specific reporting aspects, and investigated how these are currently being reported. Results Of the 284 screened trials, 68(24%) were eligible. Most trials were published in “high impact” peer-reviewed journals. Examination of trials established that 46(68%) were stopped early, predominantly either for futility or efficacy. Suboptimal reporting compliance was found in general items relating to: access to full trials protocols; methods to generate randomisation list(s); details of randomisation concealment, and its implementation. Benchmarking against the supplementary checklist, GS aspects were largely inadequately reported. Only 3(7%) trials which stopped early reported use of statistical bias correction. Moreover, 52(76%) trials failed to disclose methods used to minimise the risk of operational bias, due to the knowledge or leakage of interim results. Occurrence of changes to trial methods and outcomes could not be determined in most trials, due to inaccessible protocols and amendments. Discussion and Conclusions There are issues with the reporting of GS trials, particularly those specific to the conduct of interim analyses. Suboptimal reporting of bias correction methods could potentially imply most GS trials stopping early are giving biased results of treatment effects. As a result, research consumers may question credibility of findings to change practice when trials are stopped early. These issues could be alleviated through a CONSORT extension. Assurance of scientific rigour through transparent adequate reporting is paramount to the credibility of findings from adaptive trials. Our systematic literature search was restricted to one database due to resource constraints.

Systematic and random errors between collocated satellite ice water path observations

There remains large disagreement between ice-water path (IWP) in observational data sets, largely because the sensors observe different parts of the ice particle size distribution. A detailed comparison of retrieved IWP from satellite observations in the Tropics (!30 " latitude) in 2007 was made using collocated measurements. The radio detection and ranging(radar)/light detection and ranging (lidar) (DARDAR) IWP data set, based on combined radar/lidar measurements, is used as a reference because it provides arguably the best estimate of the total column IWP. For each data set, usable IWP dynamic ranges are inferred from this comparison. IWP retrievals based on solar reflectance measurements, in the moderate resolution imaging spectroradiometer (MODIS), advanced very high resolution radiometer–based Climate Monitoring Satellite Applications Facility (CMSAF), and Pathfinder Atmospheres-Extended (PATMOS-x) datasets, were found to be correlated with DARDAR over a large IWP range (~20–7000 g m -2 ). The random errors of the collocated data sets have a close to lognormal distribution, and the combined random error of MODIS and DARDAR is less than a factor of 2, which also sets the upper limit for MODIS alone. In the same way, the upper limit for the random error of all considered data sets is determined. Data sets based on passive microwave measurements, microwave surface and precipitation products system (MSPPS), microwave integrated retrieval system (MiRS), and collocated microwave only (CMO), are largely correlated with DARDAR for IWP values larger than approximately 700 g m -2 . The combined uncertainty between these data sets and DARDAR in this range is slightly less MODIS-DARDAR, but the systematic bias is nearly an order of magnitude.

Implementing systematic review techniques in chemical risk assessment: challenges, opportunities and recommendations

Systematic review (SR) is a rigorous, protocol-driven approach designed to minimise error and bias when summarising the body of research evidence relevant to a specific scientific question. Taking as a comparator the use of SR in synthesising research in healthcare, we argue that SR methods could also pave the way for a “step change” in the transparency, objectivity and communication of chemical risk assessments (CRA) in Europe and elsewhere. We suggest that current controversies around the safety of certain chemicals are partly due to limitations in current CRA procedures which have contributed to ambiguity about the health risks posed by these substances. We present an overview of how SR methods can be applied to the assessment of risks from chemicals, and indicate how challenges in adapting SR methods from healthcare research to the CRA context might be overcome. Regarding the latter, we report the outcomes from a workshop exploring how to increase uptake of SR methods, attended by experts representing a wide range of fields related to chemical toxicology, risk analysis and SR. Priorities which were identified include: the conduct of CRA-focused prototype SRs; the development of a recognised standard of reporting and conduct for SRs in toxicology and CRA; and establishing a network to facilitate research, communication and training in SR methods. We see this paper as a milestone in the creation of a research climate that fosters communication between experts in CRA and SR and facilitates wider uptake of SR methods into CRA.

A systematic method of parameterisation estimation using data assimilation

In numerical weather prediction, parameterisations are used to simulate missing physics in the model. These can be due to a lack of scientific understanding or a lack of computing power available to address all the known physical processes. Parameterisations are sources of large uncertainty in a model as parameter values used in these parameterisations cannot be measured directly and hence are often not well known; and the parameterisations themselves are also approximations of the processes present in the true atmosphere. Whilst there are many efficient and effective methods for combined state/parameter estimation in data assimilation (DA), such as state augmentation, these are not effective at estimating the structure of parameterisations. A new method of parameterisation estimation is proposed that uses sequential DA methods to estimate errors in the numerical models at each space-time point for each model equation. These errors are then fitted to pre-determined functional forms of missing physics or parameterisations that are based upon prior information. We applied the method to a one-dimensional advection model with additive model error, and it is shown that the method can accurately estimate parameterisations, with consistent error estimates. Furthermore, it is shown how the method depends on the quality of the DA results. The results indicate that this new method is a powerful tool in systematic model improvement.

Systematic risk estimation in symmetric models

The aim of this article is to discuss the estimation of the systematic risk in capital asset pricing models with heavy-tailed error distributions to explain the asset returns. Diagnostic methods for assessing departures from the model assumptions as well as the influence of observations on the parameter estimates are also presented. It may be shown that outlying observations are down weighted in the maximum likelihood equations of linear models with heavy-tailed error distributions, such as Student-t, power exponential, logistic II, so on. This robustness aspect may also be extended to influential observations. An application in which the systematic risk estimate of Microsoft is compared under normal and heavy-tailed errors is presented for illustration.

Prevalence and causes of visual impairment in a Brazilian population: The Botucatu Eye Study

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Step by step analyses of Clarke's matrix correction procedure for untransposed three-phase transmission line cases

The correction procedure for Clarke's matrix, considering three-phase transmission line analyzes, is analyzed step by step in this paper, searching to improve the application of this procedure. Changing the eigenvectors as modal transformation matrices, Clarke's matrix has been applied to analyses for transposed and untransposed three-phase transmission line cases. It is based on the fact that Clarke's matrix is an eigenvector matrix for transposed three-phase transmission lines considering symmetrical and asymmetrical cases. Because of this, the application of this matrix has been analyzed considering untransposed three-phase transmission lines. In most of these cases, the errors related to the eigenvalues can be considered negligible. It is not true when it is analyzed the elements that are not in main diagonal of the quasi-mode matrix. This matrix is obtained from the application of Clarke's matrix. The quasi-mode matrix is correspondent to the eigenvalue matrix. Their off-diagonal elements represent couplings among the quasi-modes. So, the off-diagonal quasi-mode element relative values are not negligible when compared to the eigenvalues that correspond to the coupled quasi-modes. Minimizing these relative values, the correction procedure is analyzed in detail, checking some alternatives for the correction procedure application.

Correction procedure applied to a single real transformation matrix -Untransposed three-phase transmission line cases

Clarke's matrix has been used as an eigenvector matrix for transposed three-phase transmission lines and it can be applied as a phase-mode transformation matrix for transposed cases. Considering untransposed three-phase transmission lines, Clarke's matrix is not an exact eigenvector matrix. In this case, the errors related to the diagonal elements of the Z and Y matrices can be considered negligible, if these diagonal elements are compared to the exact elements in domain mode. The mentioned comparisons are performed based on the error and frequency scan analyses. From these analyses and considering untransposed asymmetrical three-phase transmission lines, a correction procedure is determined searching for better results from the Clarke's matrix use as a phase-mode transformation matrix. Using the Clarke's matrix, the relative errors of the eigenvalue matrix elements can be considered negligible and the relative values of the off-diagonal elements are significant. Applying the corrected transformation matrices, the relative values of the off-diagonal elements are decreased. The comparisons among the results of these analyses show that the homopolar mode is more sensitive to the frequency influence than the two other modes related to three-phase lines. © 2006 IEEE.

Mitigating systematic errors for single frequency GPS receivers employing a penalized least squares methodology

Among the positioning systems that compose GNSS (Global Navigation Satellite System), GPS has the capability of providing low, medium and high precision positioning data. However, GPS observables may be subject to many different types of errors. These systematic errors can degrade the accuracy of the positioning provided by GPS. These errors are mainly related to GPS satellite orbits, multipath, and atmospheric effects. In order to mitigate these errors, a semiparametric model and the penalized least squares technique were employed in this study. This is similar to changing the stochastical model, in which error functions are incorporated and the results are similar to those in which the functional model is changed instead. Using this method, it was shown that ambiguities and the estimation of station coordinates were more reliable and accurate than when employing a conventional least squares methodology.

Modifying the stochastic model to mitigate GPS systematic errors in relative positioning

The GPS observables are subject to several errors. Among them, the systematic ones have great impact, because they degrade the accuracy of the accomplished positioning. These errors are those related, mainly, to GPS satellites orbits, multipath and atmospheric effects. Lately, a method has been suggested to mitigate these errors: the semiparametric model and the penalised least squares technique (PLS). In this method, the errors are modeled as functions varying smoothly in time. It is like to change the stochastic model, in which the errors functions are incorporated, the results obtained are similar to those in which the functional model is changed. As a result, the ambiguities and the station coordinates are estimated with better reliability and accuracy than the conventional least square method (CLS). In general, the solution requires a shorter data interval, minimizing costs. The method performance was analyzed in two experiments, using data from single frequency receivers. The first one was accomplished with a short baseline, where the main error was the multipath. In the second experiment, a baseline of 102 km was used. In this case, the predominant errors were due to the ionosphere and troposphere refraction. In the first experiment, using 5 minutes of data collection, the largest coordinates discrepancies in relation to the ground truth reached 1.6 cm and 3.3 cm in h coordinate for PLS and the CLS, respectively, in the second one, also using 5 minutes of data, the discrepancies were 27 cm in h for the PLS and 175 cm in h for the CLS. In these tests, it was also possible to verify a considerable improvement in the ambiguities resolution using the PLS in relation to the CLS, with a reduced data collection time interval. © Springer-Verlag Berlin Heidelberg 2007.

Avaliação de funções para modelagem do efeito da refratação ionosférica na propagação dos sinais GPS

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Cetacean Notes. I. Sei and Rorqual Whales on the Mississippi Coast, a Correction. II. A Dwarf Sperm Whale in Mississippi Sound and Its Helminth Parasites

I. Gunter and Christmas (1973) described the events leading to the stranding of a baleen whale on Ship Island, Mississippi, in 1968, giving the species as Balaenopteru physalus, the Rorqual. Unfortunately the identification was in error, but fortunately good photographs were shown. The underside of the tail was a splotched white, but there was no black margin. The specimen also had fewer throat and belly grooves than the Rorqual, as a comparison with True’s (1904) photograph shows. Dr. James Mead (in litt.) pointed out that the animal was a Sei Whale, Balaenoptera borealis. This remains a new Mississippi record and according to Lowery’s (1974) count, it is the fifth specimen reported from the Gulf of Mexico. The stranding of a sixth Sei Whale on Anclote Keys in the Gulf, west of Tarpon Springs, Florida on 30 May 1974, was reported in the newspapers and by the Smithsonian Institution (1974). II. Gunter, Hubbs and Beal (1955) gave measurements on a Pygmy Sperm Whale, Kogia breviceps, which stranded on Mustang Island on the Texas coast and commented upon the recorded variations of proportional measurements in this species. Then according to Raun, Hoese and Moseley (1970) these questions were resolved by Handley (1966), who showed that a second species, Kogia simus, the Dwarf Sperm Whale, is also present in the western North Atlantic. Handley’s argument is based on skull comparisons and it seems to be rather indubitable. According to Raun et al. (op. cit.), the stranding of a species of Kogia on Galveston Island recorded by Caldwell, Ingles and Siebenaler (1960) was K. simus. They also say that Caldwell (in litt.) had previously come to the same conclusion. Caldwell et al. also recorded another specimen from Destin, Florida, which is now considered to have been a specimen of simus. The known status of these two little sperm whales in the Gulf is summarized by Lowery (op. cit.).