bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimizing data collection for structure determination
Authors: González Ana
Published: October 2003

The ultimate purpose of diffraction data collection is to produce a data set which will result in the required structural information about the molecule of interest. This usually entails collecting a complete and accurate set of reflection intensities to as high a resolution as possible. In practice, the characteristics of the crystal and properties of the X-ray source can be limiting factors to the data-set quality that can be achieved and a careful strategy has to be used to extract the maximum amount of information from the data within the experimental constraints. In the particular case of data intended for phasing using anomalous dispersion, the synchrotron beamline properties are relevant to determine how many wavelengths (one or more) should be used for the experiment and what the wavelength values should be. This will in turn affect the detailed strategy for data collection, including decisions about the data-collection sequence and how much data to collect at each wavelength. Collection of multiwavelength anomalous dispersion (MAD) data at three different wavelengths can provide very accurate experimental phases. Two-wavelength MAD experiments may offer the best compromise between phase quality and minimizing the effects of radiation damage to the sample. However, MAD experiments are demanding in terms of beamline wavelength range, easy tunability, stability and reproducibility. When the beamline cannot fulfill these demands, single-wavelength experiments may be a better option.
The phase problem
Authors: Taylor Garry
Published: October 2003

Given recent advances in phasing methods, those new to protein crystallography may be forgiven for asking `what problem?'. As many of those attending the CCP4 meeting come from a biological background, struggling with expression and crystallization, this introductory paper aims to introduce some of the basics that will hopefully make the subsequent papers penetrable. What is the `phase' in crystallography? What is `the problem'? How can we overcome the problem? The paper will emphasize that the phase values can only be discovered through some prior knowledge of the structure. The paper will canter through direct methods, isomorphous replacement, anomalous scattering and molecular replacement. As phasing is the most acronymic realm of crystallography, MR, SIR, SIRAS, MIR, MIRAS, MAD and SAD will be expanded and explained in part. Along the way, we will meet some of the heroes of protein crystallography such as Perutz, Kendrew, Crick, Rossmann and Blow who established many of the phasing methods in the UK. It is inevitable that some basic mathematics is encountered, but this will be done as gently as possible.
Phasing the AP2 core complex with Xe, Hg and Se
Authors: Evans Philip
Published: October 2003

The 200 kDa core of the heterotetrameric AP2 clathrin adaptor complex was phased with xenon, mercury and selenomethionine derivatives. The phasing has been analysed in retrospect to determine how many of the derivative data sets were necessary for optimum phasing and what features were most useful in deciding which derivatives would make a positive contribution. The relative contributions of the different derivatives indicate that the most important phasing came from the two Xe data sets collected at long wavelengths (1.74 and 1.98 Å) to enhance the anomalous signal. The mercury derivatives were less powerful but made a useful contribution, although inclusion of a poor second wavelength set was detrimental, probably because of radiation damage. The SeMet data were less useful for phasing because of incomplete incorporation of selenium owing to the expression conditions needed, but they were useful in chain-tracing.
New ways of looking at experimental phasing
Authors: Read Randy J.
Published: October 2003

In the original work by Blow and Crick, experimental phasing was formulated as a least-squares problem. For good data on good derivatives this approach works reasonably well, but we now attempt to extract more information from poorer data than in the past. As in many other crystallographic problems, the assumptions underlying the use of least squares for phasing are not satisfied, particularly for poor derivatives. The introduction of maximum likelihood (and more powerful computers) has led to substantial improvements. For computational convenience, these new methods still make many assumptions about the independence of different measurements and sources of error. A more general formulation for the probability distributions underlying likelihood-based methods for both experimental phasing and molecular-replacement phasing is reviewed. In the new formulation, all the structure factors associated with a particular hkl are considered to be related by a complex multivariate normal distribution. When it is assumed that certain errors are independent, the general formulation reduces to current likelihood targets. However, the new formulation makes the necessary assumptions more explicit and points the way to improving phasing using both isomorphous and anomalous differences.
Selling candles in a post-Edison world: phasing with noble gases bound within engineered sites
Authors: Quillin Michael L. , Matthews Brian W.
Published: October 2003

The utility of noble gases for phase determination has been limited by the lack of naturally occurring binding sites in proteins. Wild-type T4 lysozyme contains one such binding site. By mutating large hydrophobic residues to alanine, additional noble-gas binding sites have been successfully introduced into this protein. Using data from xenon derivatives of the wild type, two single mutants and the corresponding double mutant, experimental phases for T4 lysozyme have been determined using standard multiple isomorphous replacement (MIR) techniques. These phases, which were obtained from room-temperature data collected on a rotating-anode source, are comparable in quality with phases calculated using selenomethionine-based multiwavelength anomalous dispersion (MAD) methods on frozen crystals at a synchrotron. In addition, this method of introducing noble-gas binding sites near specific residues should provide useful information for determining the register of amino acids within electron-density maps and the positions of molecules within the unit cell.
Substructure search procedures for macromolecular structures
Authors: Grosse-Kunstleve R. W. , Adams P. D.
Published: October 2003

This paper accompanies a lecture given at the 2003 CCP4 Study Weekend on experimental phasing. The first part is an overview of the fundamentals of Patterson methods and direct methods with the audience of the CCP4 Study Weekend in mind. In the second part, a new hybrid substructure search is outlined.
Away from the edge: SAD phasing from the sulfur anomalous signal measured in-house with chromium radiation
Authors: Yang Cheng , Pflugrath J. W. , Courville D. A. , Stence C. N. , Ferrara Joseph D.
Published: October 2003

Anomalous scattering with soft X-ray radiation opens new possibilities in phasing for macromolecular crystallography. Anomalous scattering from S atoms collected on an in-house chromium radiation source (λ = 2.29 Å) was used to phase the X-ray diffraction data of thaumatin (22 kDa) and trypsin (24 kDa) crystals. The contribution to the anomalous term, Δf'' = 1.14 e−, from sulfur for Cr Kα radiation is doubled compared with that for Cu Kα radiation, Δf'' = 0.56 e−. The direct-methods programs RANTAN or SHELXD successfully found sulfur positions using data sets with resolution limited to 3.5 Å. The statistical phasing program SHARP was used to produce the electron-density maps using the sulfur anomalous signal alone at low resolution (∼3.5 Å). An interpretable electron-density map for each structure was obtained solely from the phases derived from single-wavelength anomalous dispersion (SAD) data obtained using Cr Kα radiation. Much fewer data (that is, lower redundancy) are required for this sulfur SAD phasing procedure compared with the highly redundant data reported in the sulfur SAD phasing procedure with Cu Kα radiation. Cr Kα radiation can also improve the strength of anomalous scattering of many other intrinsic elements in macromolecules, such as calcium, zinc and phosphorus, because of the increased Δf''. Furthermore, the anomalous scattering of selenium is increased substantially from 1.14 e− with Cu Kα radiation to 2.28 e− with Cr Kα radiation. In order to measure the small Bijvoet differences accurately, several devices were developed for the experiment, including an Osmic Confocal MaxFlux optic optimized for Cr Kα radiation, a helium path and a beam stop. In the cases studied here, radiation damage to the samples and reduction of anomalous signal were observed in some long exposure time data sets. Therefore, an adequate data-collection strategy to maximize the completeness in a short scan range was used in subsequent data collections. The results show that the anomalous signal of S atoms can be collected quickly. Since the absorption of solvent and the loop may no longer be negligible with Cr Kα radiation, the orientation of the crystal and exposure time were taken into account in order to minimize the effects of radiation damage and absorption. This experimental study shows that using Cr Kα radiation from an in-house rotating-anode X-ray generator can provide sufficient phasing power from sulfur anomalous signals to routinely phase protein diffraction data.
A new class of lanthanide complexes to obtain high-phasing-power heavy-atom derivatives for macromolecular crystallography
Authors: Girard Éric , Stelter Meike , Vicat Jean , Kahn Richard
Published: October 2003

Because of their intense white lines and large f'' values, lanthanide atoms are of great interest for solving structures of biological macromolecules using single-wavelength anomalous diffraction (SAD) or multiple-wavelength anomalous diffraction (MAD) methods. In this work, a series of seven gadolinium complexes are described which provide excellent derivatives for anomalous diffraction experiments in biological systems. These highly soluble lanthanide complexes can easily be introduced into protein crystals either by soaking or by co-crystallization, without significantly affecting the crystallization conditions, by employing highly concentrated complex solutions (≃100 mM). De novo phasing by the SAD method was carried out with several proteins of known as well as previously unknown structures by employing this new class of heavy-atom compounds. Diffraction data were collected either with a laboratory source, making use of the high anomalous signal (f'' = 12 e−) of gadolinium with Cu Kα radiation, or with synchrotron radiation at the peak of the gadolinium L
III absorption edge, which exhibits a strong white line (λ = 1.711 Å, f'' = 28 e−). Using one of these gadolinium complexes, Gd-HPDO3A, the structure of a bacterial chimeric ornithine carbamoyl transferase, OTCase3630, a dodecameric protein of 450 kDa, was determined. Employed with the SAD method, these seven complexes could be of particular interest for high-throughput macromolecular crystallography.
Measurement errors and their consequences in protein crystallography
Authors: Borek Dominika , Minor Wladek , Otwinowski Zbyszek
Published: October 2003

This article analyzes the relative impact of various types of measurement uncertainties on different stages of structure determination. The treatment of errors is an important part of the experimental process and becomes critical when data quality is barely sufficient to solve and/or answer detailed questions about the structure. The sources and types of experimental errors are described and methods of minimizing their impact are discussed. Practical calculations of sigma estimates in DENZO and SCALEPACK are presented.
Is it jolly SAD?
Authors: Dodson Eleanor
Published: October 2003

Examples of phasing macromolecular crystal structures based on single-wavelength anomalous dispersion (SAD) have demonstrated that this approach may have general applications in structural biology. With better data-collection facilities and cryogenic techniques, combined with powerful data-processing, phasing and density-modification programs, the SAD approach may prove simpler than phasing from multi-wavelength (MAD) measurements. It can be performed at any wavelength where anomalous scattering can be observed, in many cases using laboratory X-ray sources. However, there is still a need for accurate data, successful phase improvement and a certain amount of luck. This paper extends the discussion of Jolly SAD in Dauter et al. [Dauter, Z., Dauter, M. & Dodson, E. (2002), Acta Cryst. D58, 494–506].
Twinned crystals and anomalous phasing
Authors: Dauter Zbigniew
Published: October 2003

Merohedral or pseudomerohedral twinning of crystals cannot be identified from inspection of the diffraction patterns. Several methods for the identification of twinning and the estimation of the twin fraction are suitable for macromolecular crystals and all are based on the statistical properties of the measured diffraction intensities. If the crystal twin fraction is estimated and is not too close to 0.5, the diffraction data can be detwinned; that is, related to the individual crystal specimen. However, the detwinning procedure invariably introduces additional inaccuracies to the estimated intensities, which substantially increase when the twin fraction approaches 0.5. In some cases, a crystal structure can be solved with the original twinned data by standard techniques such as molecular replacement, multiple isomorphous replacement or multiwavelength anomalous diffraction. Test calculations on data collected from a twinned crystal of gpD, the bacteriophage λ capsid protein, show that the single-wavelength anomalous diffraction (SAD) method can be used to solve its structure even if the data set corresponds to a perfectly twinned crystal with a twin fraction of 0.5.
On symmetries of substructures
Authors: Grosse-Kunstleve R. W. , Adams P. D.
Published: October 2003

This paper accompanies a lecture given at the 2003 CCP4 Study Weekend on experimental phasing. With the audience of the CCP4 Study Weekend in mind, an overview is given of symmetries of substructures and the implications for single isomorphous replacement and single anomalous diffraction phasing procedures, as well as difference Fourier analyses. Pointers are also provided to practical tools for working with substructure symmetries.
MIR phasing using merohedrally twinned crystals
Authors: Terwisscha van Scheltinga Anke C. , Valegård Karin , Hajdu Janos , Andersson Inger
Published: October 2003

Merohedral twinning is a crystal-growth disorder that seriously hinders the determination of macromolecular crystal structures by isomorphous replacement. The strategies used in the structures solved so far are discussed. Several methods can be used to determine the extent of twinning, the twin fraction and to detwin the data. Accurate determination of the twin fraction by analysing heavy-atom refinement statistics is possible, but only influences the resulting phases slightly. It seems more crucial to restrict the variation in twin fractions between data sets, either by making the twin fractions of some data sets artificially higher or by screening crystals to obtain data with a low twin fraction.
'MAD'ly phasing the extracellular domain of the LDL receptor: a medium-sized protein, large tungsten clusters and multiple non-isomorphous crystals
Authors: Rudenko G. , Henry L. , Vonrhein C. , Bricogne G. , Deisenhofer J.
Published: October 2003

The crystal structure of the extracellular domain of the LDL receptor (LDL-R) was determined in a MAD experiment using 12-tungstophosphate clusters as anomalous scatterers. While useful for phasing, the tungsten clusters rendered the crystals radiation-sensitive and non-isomorphous and profoundly altered the diffraction data, causing complications. The work is presented as a case study for phasing a medium-sized protein (700 residues) at low resolution (4 Å) with multiple non-isomorphous crystals containing 31 W atoms in the asymmetric unit.
Using our Geopost culture to create a change and leadership development programme
Authors: Doolin Michael
Published: October 2003

Geopost is a leading distribution and logistics player in the UK and Ireland, employing over 3,800 people. It embarked upon a major change and leadership programme, named “Making A Difference” (MAD). Comprised of four modules, MAD has facilitated the development of change management skills and behaviours amongst 60 managers at MAD. MAD encapsulates modules on personal leadership styles, people management and creative thinking and interpersonal skills. It is underpinned by participation in a 360‐degree exercise. The success of MAD at Geopost has been reflected in real bottom line impact areas, as well as many other softer benefits.
Coaching – the latest buzzword or a truly effective management tool?
Authors: Edwards Linda
Published: October 2003

Coaching enables people to develop new individualised ways of working to increase their performance and the performance of their teams. A great coach will challenge you and enable you to find the resources within yourself to really do the things that you say you want to do and to enjoy doing them. Many people in senior positions find professional support through coaching to be the ideal solution to developing bespoke, flexible, personal training based on their specific individual needs. Selecting a coach is a matter of personal choice. However, it is paramount that you are able to relate to the person and that they will challenge your personal limitations to enable you be the success you desire.
Time out!
Authors: Rabey Gordon
Published: October 2003

The principles of management enshrined in innumerable texts have been developed in the crucibles of business practice through the ages when there was at least some confidence in the predictability of events. Globalisation of production, processing and distribution, facilitated by the 7/24 dissemination of information has confused predictability. One outcome, the critical element of management survival today, is the effectiveness of a continuous creative response to a sequence of challenge, adaptation and learning arising from ever‐changing circumstances. It will call for a more holistic consideration of organisational effectiveness. Initially, this suggests a look at where power now lies, how it can be exercised, and at the dependencies thus created. In the essential quest for cost saving and innovation, it should come as no surprise in these days of performance‐based pay that the matter of reward for special effort will be raised. It cannot be overlooked that poor performance will be inevitable if good performance is not recognised. “Uncertain” describes the future and people are being more cautious in moving towards it. Time out! will give a pause to reflect.
Leadership motivation and the drivers of share price: the business case for measuring organisational climate
Authors: Watkin Chris , Hubbard Ben
Published: October 2003

This article is a summary of consulting field research carried out by Hay Group to answer why leadership motivation matters to the drivers of share price. The summary also aims to explain how measuring organisational climate can help leaders better understand the effect they have on the motivations and performance impact of those they lead. As such it represents the business case for its use by organisations. There are practical guidelines on how to spot the early warning signs when climate starts to deteriorate; the key factors leaders need to focus on in getting it right; and how climate measures can be used as a macro change lever as part of an organisation talent review.
Central conceptual issues in transformational leadership research
Authors: Pawar Badrinarayan S.
Published: October 2003

Transformational leadership is one of the most recent conceptualizations of leadership concepts. It has been specified as an important mechanism of introducing organizational change. Transformational leadership has received substantial research attention over the last two decades. As a result, transformational leadership research has created considerable knowledge about the transformational leadership phenomenon. It, however, has also generated several conceptual issues and addressing these issues is necessary for advancing transformational leadership research. Highlights six important conceptual issues that the research has generated. Also outlines the significance of each of these six issues and then provides a critical commentary based on these issues. In pointing out research implications, outlines the required research for addressing these issues and provides an outline of how research for addressing them can be approached. Finally, indicates some of the implications of this paper for practice.
Leader self‐awareness and its relationship to subordinate attitudes and performance
Authors: Moshavi Dan , Brown F. William , Dodd Nancy G.
Published: October 2003

This study explored the relationships between a leader’s self‐awareness of his/her leadership behavior and the attitudes and performance of subordinates. Following previous research, leaders were categorized as overestimators, underestimators or in‐agreement. Results indicate that subordinates of underestimators reported significantly higher levels of supervisory and job satisfaction than did subordinates of those who were in‐agreement, and both subordinates of underestimators and those in‐agreement reported significantly higher levels of supervisory and job satisfaction than did subordinates of overestimators. No significant differences were found between the self‐awareness categories and transfer intent. Finally, subordinates of underestimators and those in‐agreement achieved a significantly higher level of productivity than did subordinates of leaders who overestimated their leadership ability.
All research is interpretive!
Authors: Gummesson Evert
Published: October 2003

This article advocates recognition of interpretive elements in business research and the need for improvement of the researcher’s interpretive skills. The scientific tradition specifically concerned with interpretation is called hermeneutics. However, interpretation exists in all types of scientific studies, be they quantitative or qualitative. The article presents lessons from hermeneutics and spells out the interpretive content of research in general and with specific focus on business‐to‐business marketing. Interpretive methods, when applied to business, are characterized by efforts to understand the complexity of the business world and its products, services and markets, and to add meaning to strategies, actions and events. A set of methods designated interactive research is discussed. These are more inspired by the humanities, sociology, anthropology and modern natural sciences than by the social sciences research paradigm as it is currently applied in most mainstream research in marketing.
Organizational analysis and information systems design: a road revisited
Authors: Hulbert James M.
Published: October 2003

Looks retrospectively at an article written by the author and his colleagues in 1975 and contributed to the Journal of Business Research. Concludes that the article is still relevant today, where information systems are still an important topic in the field of marketing.
Cross‐border supply chain relationships: interpretive research of maquiladora realized strategies
Authors: Hausman Angela , Haytko Diana L.
Published: October 2003

Maquiladora plants are foreign‐owned plants operating in Mexico and represent a pre‐North American Trade Agreement (NAFTA) mechanism to reduce tariffs on the assembly of component parts and finished products for re‐export. Maquilas first opened along the Mexican‐US border in the mid‐1960s to provide employment for Mexican workers as well as cheap labor for low‐skilled US manufacturers. Beginning in 1999 the industry started experiencing a sharp decline, which cost jobs and closed factories on both sides of the border. This study applies grounded theory to develop an initial understanding of the factors contributing to the success (and failure) of maquiladora realized strategies, that is, performed operating behaviors and the role of culture in the results these operations achieve. Broadly, these factors include internal relationships (with both management and line employees) and external relationships (both organizational and governmental). The study culminates in a series of suggestions for increasing the likelihood of success of maquiladoras and proposes the applicability of these factors in other multinational operations in labor‐intensive industries.
Grounded theory in sales research: an investigation of salespeople’s client relationships
Authors: Geiger Susi , Turley Darach
Published: October 2003

In this paper, grounded theory as an inductive method of theory generation in business research is presented and critically evaluated. The historical and epistemological backgrounds of the method are discussed, its research procedures are briefly outlined, and its suitability for sales research assessed. To illustrate the principles of the method, a study of the nature of business‐to‐business sales relationships is introduced. The results of this study show clearly that grounded theory can yield highly significant findings in areas that deal with phenomena as complex as human relationships, where the construction of theoretical frameworks cannot be achieved at the cost of conceptual density.
Cognition‐in‐context: reorienting research in business market strategy
Authors: Matthyssens Paul , Vandenbempt Koen
Published: October 2003

This paper highlights the usefulness of interpretive methodologies in theorizing over relatively unstructured, dynamic business market strategy issues. It is based on the tenet that interpretive methodologies are appropriate to cope with market strategy formation in dynamic market settings. We argue that in a “context of discovery”, marketing researchers need to uncover new relationships among key dimensions of market strategy and might consider reframing theories. Further, we demonstrate in this paper that interpretive research methods allow for managerial recommendations that are highly contextualized and that lead to more actionable prescriptions. We illustrate the above by reflecting on a concrete research on how companies in a business‐to‐business industry try to reorientate their market strategy. The process of understanding strategic reorientation in business markets should be based on a multiplex of perspectives, such as: multilevel research, fusing content with context and merging theoretical constructs with data and focusing on socially constructed realities.
The work of Chris Argyris as critical organization practice
Authors: Bokeno R. Michael
Published: October 2003

This essay examines the broad thesis of organizational learning theorist Chris Argyris in terms of communicative action, and finds his critical understanding of Model I and the emancipatory potential embedded in double‐loop learning consistent with prominent themes in critical organization study.
Theorizing limits: an exploration of boundaries, learning, and emancipation
Authors: Durant Rita A. , Cashman James F.
Published: October 2003

Seeking to move beyond limits in order to solve problems is an important part of organizational learning and is therefore potentially emancipatory. Communicating across boundaries in order to expand capabilities might contribute to understanding and therefore to community building. When limits to current capacities are experienced, individuals who admit their own limitations set the stage for both organizational learning and emancipatory processes. Stories of two different departments in the same organization are contrasted in terms of the micro‐emancipatory processes that led to deliberate change in one and not the other. Attention to, and respect for, the three key functions of boundaries is proposed to make a difference in experiences of autonomy and community.
Core groups: a theory of power and influence for “learning” organizations
Authors: Kleiner Art
Published: October 2003

Core groups stand as the tangible, but fluid repositories of knowledge, influence and power in organizations. Thus, the core group in any organization is the focal point of organizational learning throughout the organization, because people act to fulfill the perceived needs and priorities of some key group of people. An organization goes wherever its people perceive that the core group needs and wants to go. An organization becomes whatever its people perceive that the core group needs and wants it to become. Core Group Theory holds implications for how the complex of power, knowledge and influence interacts with organizational opportunities for genuine learning and creativity.
Emancipatory firms vs financial fiduciaries
Authors: Gates Jeff
Published: October 2003

In this response to Kleiner's Core Group Theory, the author maintains that any creative or liberatory potential to be found in core group decision making is and probably will remain unrealized unless maximization of financial returns – as the dominant organizational value – can be successfully challenged. The author contends that maximization of financial returns is such a dominant value, that it is currently and dangerously unchallenged, and that it is likely to remain so because it serves core group interests.
Bayesian Semiparametric Regression for Median Residual Life
Authors: Gelfand Alan E. , Kottas Athanasios
Published: October 2003

Abstract. With survival data there is often interest not only in the survival time distribution but also in the residual survival time distribution. In fact, regression models to explain residual survival time might be desired. Building upon recent work of Kottas & Gelfand [J. Amer. Statist. Assoc.96 (2001) 1458], we formulate a semiparametric median residual life regression model induced by a semiparametric accelerated failure time regression model. We utilize a Bayesian approach which allows full and exact inference. Classical work essentially ignores covariates and is either based upon parametric assumptions or is limited to asymptotic inference in non‐parametric settings. No regression modelling of median residual life appears to exist. The Bayesian modelling is developed through Dirichlet process mixing. The models are fitted using Gibbs sampling. Residual life inference is implemented extending the approach of Gelfand & Kottas [J. Comput. Graph. Statist.11 (2002) 289]. Finally, we present a fairly detailed analysis of a set of survival times with moderate censoring for patients with small cell lung cancer.
A Semiparametric Model for Recapture Experiments
Authors: Wang Yan , Yip Paul S. F.
Published: October 2003

Abstract.A two‐step procedure based on the conditional likelihood is proposed to estimate the population size of a closed population using a semiparametric model for recapture studies. An asymptotic variance estimate and numerical results are presented. The method is applied to a bird banding dataset in Hong Kong.
Joint Modelling of Recurrent Infections and Antibody Response by Bayesian Data Augmentation
Authors: Eerola Mervi , Gasbarra Dario , Helena Mäkelä P. , Linden Henri , Andreev Andrei
Published: October 2003

Abstract.  A joint dynamic model for the interdependence between infection, immunity and risk of disease is presented. Recurrent latent infections are modelled as realizations from a renewal process and antibody dynamics as a diffusion with a decreasing drift modified by the stimulating effect of the random infections. The augmented submodels are estimated simultaneously in one large Markov chain Monte Carlo algorithm. As an example, we consider the risk of recurrent ear infections when having only partially observed information on bacterial carriage and antibody concentrations.
Density Estimation for the Metropolis–Hastings Algorithm
Authors: Sköld M. , Roberts G. O.
Published: October 2003

Abstract.Kernel density estimation is an important tool in visualizing posterior densities from Markov chain Monte Carlo output. It is well known that when smooth transition densities exist, the asymptotic properties of the estimator agree with those for independent data. In this paper, we show that because of the rejection step of the Metropolis–Hastings algorithm, this is no longer true and the asymptotic variance will depend on the probability of accepting a proposed move. We find an expression for this variance and apply the result to algorithms for automatic bandwidth selection.
Improved Sampling‐Importance Resampling and Reduced Bias Importance Sampling
Authors: Skare Øivind , Bølviken Erik , Holden Lars
Published: October 2003

Abstract. The sampling‐importance resampling (SIR) algorithm aims at drawing a random sample from a target distribution π. First, a sample is drawn from a proposal distributionq, and then from this a smaller sample is drawn with sample probabilities proportional to the importance ratios π/q. We propose here a simple adjustment of the sample probabilities and show that this gives faster convergence. The results indicate that our version converges better also for small sample sizes. The SIR algorithms are compared with the Metropolis–Hastings (MH) algorithm with independent proposals. Although MH converges asymptotically faster, the results indicate that our improved SIR version is better than MH for small sample sizes. We also establish a connection between the SIR algorithms and importance sampling with normalized weights. We show that the use of adjusted SIR sample probabilities as importance weights reduces the bias of the importance sampling estimate.
A Wavelet Method for Confidence Intervals in the Density Model
Authors: Tribouley Karine
Published: October 2003

Abstract.  We present a wavelet procedure for defining confidence intervals for f(x0), where x0 is a given point and f is an unknown density from which there are independent observations. We use an undersmoothing method which is shown to be near optimal (up to a logarithmic term) in a first order sense. We propose a second order correction using the Edgeworth expansion. The adaptation with respect to the unknown regularity of f is given via a Lepskii type algorithm and has the advantage to be well located. The theoretical results are proved under weak assumptions and concern very irregular or oscillating functions. An empirical study gives some hints for choosing the constant of the threshold level. The results are very encouraging for the length of the intervals as well as for the coverage accuracy.
On Expected Lengths of Predictive Intervals
Authors: Mukerjee Rahul , Chen Zehua
Published: October 2003

Abstract.  We consider the problem of comparing predictive intervals for a future observation via their expected lengths at a given confidence level. A higher order asymptotic theory is developed. This yields an explicit formula for expected length comparison and associated admissibility results. Illustrative examples are given.
Local Influence Analysis for Penalized Gaussian Likelihood Estimators in Partially Linear Models
Authors: Zhu Zhong‐Yi , He Xuming , Fung Wing‐Kam
Published: October 2003

Abstract.Partially linear models are extensions of linear models to include a non‐parametric function of some covariate. They have been found to be useful in both cross‐sectional and longitudinal studies. This paper provides a convenient means to extend Cook's local influence analysis to the penalized Gaussian likelihood estimator that uses a smoothing spline as a solution to its non‐parametric component. Insight is also provided into the interplay of the influence or leverage measures between the linear and the non‐parametric components in the model. The diagnostics are applied to a mouthwash data set and a longitudinal hormone study with informative results.
The Cusum Test for Parameter Change in Time Series Models
Authors: Lee Sangyeol , Ha Jeongcheol , Na Okyoung , Na Seongryong
Published: October 2003

Abstract. In this paper, we consider the problem of testing for parameter changes in time series models based on a cusum test. Although the test procedure is well established for the mean and variance in time series models, a general parameter case has not been discussed in the literature. Therefore, here we develop a cusum test for parameter change in a more general framework. As an example, we consider the change of the parameters in a random coeefficient autoregressive (1) model and that of the autocovariances of a linear process. Simulation results are reported for illustration.
Mean and Variance of Vacancy for Hard‐Core Disc Processes and Applications
Authors: Bondesson Lennart , Fahlén Jessica
Published: October 2003

Abstract.  Hard‐core Strauss disc processes with inhibition distance r and disc radius R are considered. The points in the Strauss point process are thought of as trees and the discs as crowns. Formulas for the mean and the variance of the vacancy (non‐covered area) are derived. This is done both for the case of a fixed number of points and for the case of a random number of points. For tractability, the region is assumed to be a torus or, in one dimension, a circle in which case the discs are segments. In the one‐dimensional case, the formulas are exact for all r. This case, although less important in practice than the two‐dimensional case, has provided a lot of inspiration. In the two‐dimensional case, the formulas are only approximate but rather accurate for r < R. Markov Chain Monte Carlo simulations confirm that they work well. For R ≤ r < 2R, no formulas are presented. A forestry estimation problem, which has motivated the research, is briefly considered as well as another application in spatial statistics.
On a Dualization of Graphical Gaussian Models: A Correction Note
Authors: Banerjee Moulinath , Richardson Thomas
Published: October 2003

Abstract. We correct two proofs concerning Markov properties for graphs representing marginal independence relations.
A systematic review and meta‐analysis of randomised controlled trials evaluating interventions in adult literacy and numeracy
Authors: Torgerson Carole J. , Porthouse Jill , Brooks Greg
Published: October 2003

This paper reports a systematic review of the trial literature in the field of adult literacy and numeracy. The review was undertaken to investigate the effectiveness of teaching strategies and pedagogies designed to increase adult literacy and numeracy. The objectives were to search for and locate, synthesise and quality appraise all the randomised controlled trials aiming to evaluate interventions in adult literacy and/or numeracy, published between 1980 and 2002. Fifty‐nine papers were included in the descriptive map. Twelve papers were included that contained nine randomised controlled trials. All of the trials included in the review were of high quality in the sense that they had adopted an appropriate study design for assessing effectiveness. However, within that study design many of the studies had methodological problems, for example: small sample size and lack of justification of sample size calculation; unclear method of random allocation; high attrition rate and lack of ‘intention to teach’ analysis. There was evidence of publication bias. Pooling three studies that compared teaching against no teaching showed a strong, positive and statistically significant effect on outcome. Two other studies examined the use of computer‐assisted instruction (CAI) on literacy among imprisoned adults. Pooling these two studies showed a modest but not statistically significant benefit. There is a dearth of rigorous RCTs in the field of adult literacy and numeracy. The evidence is suggestive of a benefit of adult literacy and numeracy interventions; however, because of the heterogeneity of studies, the precise role of any intervention is uncertain and this finding may be undermined by the presence of substantial publication bias. We recommend that a series of large, well‐designed and well‐conducted randomised trials should be undertaken in the field of adult literacy and numeracy.
Computerised formative assessment of reading comprehension: field trials in the UK
Authors: Topping Keith J. , Fisher Anna M.
Published: October 2003

Increased curriculum time allocated to reading might not be effective in raising achievement. Teachers need to closely monitor and manage both the quality and quantity of individualised reading of all their pupils for optimal effectiveness. ‘Learning information systems’ (LIS) for reading such as the ‘Accelerated Reader’ (AR) enable this through individualised computerised assessment of pupil comprehension of ‘real books’, with feedback to both pupil and teacher. This study explored the impact of AR on reading achievement in 13 schools of different types spread across the UK, the majority socio‐economically disadvantaged. Participating pupils were aged 7–14 years. Pre‐post norm‐referenced gains in reading achievement were measured by group paper‐reading tests and a computer‐based adaptive reading test. The implementation integrity of AR was assessed by direct observation by researchers and through data generated by the programme itself. On both paper and computer‐based reading tests, on aggregate pupils in the 13 schools gained in reading at abnormally high and statistically significant rates. Boys tended to show larger gains than girls on the paper test. However, implementation integrity was very variable. In particular, some teachers failed to intervene in response to AR data indicating that pupils were reading ineffectively. AR appears to have potential for raising reading achievement, but only if implemented appropriately.
Are all phonemic awareness tests created equally? A comparison of the Yopp‐Singer and the task of auditory analysis skills (TASS)
Authors: Wilde Jerry , Goerss Betty , Wesler Jennifer
Published: October 2003

This study examined two screening instruments designed to measure phonemic awareness (Test of Auditory Analysis Skills‐TAAS and Yopp‐Singer Test of Phoneme Segmentation). Participants included 25 second‐semester kindergarten children who were administered both instruments. The dependent measure (the STAR Reading Test) was administered in February of their First‐Grade year. The investigation was designed to determine if these instruments are both evaluating the same skills and identify which was more effective in predicting success in reading near the end of First Grade. The children's scores from the Yopp‐Singer and the TAAS were correlated (r=0.56, p<0.01) and so were the scores between the TAAS and STAR (r=0.51, p<0.01). Comparison of scores between the Yopp and the STAR produced non‐significant results (r=0.31). Although the TAAS produced a higher correlation with reading achievement than the Yopp‐Singer, the difference between these two measures failed to reach significance (t=1.16). Implications of these findings, along with possible explanations of the results, are discussed.
PASS cognitive processes, phonological processes, and basic reading performance for a sample of referred primary‐grade children
Authors: Joseph Laurice M. , McCachran Megan E. , Naglieri Jack A.
Published: October 2003

The purpose of this study was to explore the relationships among cognitive processing, phonological processing and basic reading skill performance. Cognitive theorists propose that Planning, Attention, Simultaneous and Successive (PASS) processes are related to various phonological skills. A sample of 62 Primary Grade children referred for reading problems were administered measures of cognitive processes (Cognitive Assessment System), phonological processes (Comprehensive Test of Phonological Processing) and basic reading achievement (Woodcock‐Johnson Tests of Academic Achievement‐III). Findings indicated that some cognitive processes were significantly related to phonological processes as well as basic reading skills. The strongest relationships were found between phonological memory and successive processes and between phonological awareness and basic reading performance.
The Perceiver's Share: Realism, Scepticism, and Response Dependence
Authors: Norris Christopher
Published: October 2003

Abstract: Response‐dispositional (RD) properties are standardly defined as those that involve an object's appearing thus or thus to some perceptually well‐equipped observer under specified epistemic conditions. The paradigm instance is that of colour or other such Lockean “secondary qualities”, as distinct from those—like shape and size—that pertain to the object itself, quite apart from anyone's perception. This idea has lately been thought to offer a promising alternative to the deadlocked dispute between hard‐line ‘metaphysical’ realists and subjectivists, projectivists, social constructivists, or hard‐line anti‐realists. A chief source text is Plato's Euthyphro, where the issue is posed in ethical terms: do the gods infallibly approve virtuous acts on account of their divine moral omniscience or are virtuous acts just those the gods approve? Among the areas proposed as amenable to an RD approach are epistemology, ethics, political theory, and philosophy of mathematics. It is claimed that by making due allowance for the involvement of normalised or optimised human responses one can steer a course between the twin poles of an objectivist realism that places truth beyond our cognitive grasp and an epistemic conception that confines truth within the limits of humanly attainable proof, knowledge, or verification. Here I argue—on the contrary—that RD approaches can be shown to offer nothing more than a variant of the same old realist versus anti‐realist dilemma. That is, they work out either as a trivial (tautologous) claim that ‘truth’ simply equates with ‘best judgement’ in the ideal (quasi‐objective) limit or as the claim—advanced by anti‐realists like Michael Dummett—that we cannot form any adequate conception of objective (recognition‐transcendent) truths. After looking at this issue in various contexts of debate, I conclude that one useful (if pyrrhic) outcome is to demonstrate the non‐availability of any middle‐ground stance. We are left with the strictly unavoidable choice between a realist or objectivist approach and one that assimilates truth to the consensus of accredited best opinion. This latter amounts to a roundabout, elaborately qualified version of the anti‐realist case.
Ricoeur versus Taylor on Language and Narrative
Authors: Steele Meili
Published: October 2003

Abstract: Although Ricoeur and Taylor are often grouped together, their conceptions of language, literature, and practical reason are very different. The first half of this essay focuses on Ricoeur's theory of triple mimesis and narrative, showing how his attempt to synthesize Kant, Husserl, and structuralism results in a formalism that blocks out the ontological, hermeneutical, and historical dimensions of literature and practical reason. The second half of the essay develops Taylor's ontological conception of public imagination and illustrates the dynamics of this conception of language and interpretation by showing how literary works debate with each other over language, subjectivity, and reference. Narrative does not just order; it argues.