bluuebunny/crossref_metadata_2025 huggingface dataset:
Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology‐based protein structures
Authors: Fan Hao , Mark Alan E.
Published: March 2004

A novel method for the refinement of misfolded protein structures is proposed in which the properties of the solvent environment are oscillated in order to mimic some aspects of the role of molecular chaperones play in protein folding in vivo. Specifically, the hydrophobicity of the solvent is cycled by repetitively altering the partial charges on solvent molecules (water) during a molecular dynamics simulation. During periods when the hydrophobicity of the solvent is increased, intramolecular hydrogen bonding and secondary structure formation are promoted. During periods of increased solvent polarity, poorly packed regions of secondary structures are destabilized, promoting structural rearrangement. By cycling between these two extremes, the aim is to minimize the formation of long‐lived intermediates. The approach has been applied to the refinement of structural models of three proteins generated by using the ROSETTA procedure for ab initio structure prediction. A significant improvement in the deviation of the model structures from the corresponding experimental structures was observed. Although preliminary, the results indicate computationally mimicking some functions of molecular chaperones in molecular dynamics simulations can promote the correct formation of secondary structure and thus be of general use in protein folding simulations and in the refinement of structural models of small‐ to medium‐size proteins.
An improved crystal form of Plasmodium falciparum peptide deformylase
Authors: Robien Mark A. , Nguyen Kiet T. , Kumar Abhinav , Hirsh Irwin , Turley Stewart , Pei Dehua , Hol Wim G.J.
Published: March 2004

An altered version of peptide deformylase from Plasmodium falciparum (PfPDF), the organism that causes the most devastating form of malaria, has been cocrystallized with a synthesized inhibitor that has submicromolar affinity for its target protein. The structure is solved at 2.2 Å resolution, an improvement over the 2.8 Å resolution achieved during the structural determination of unliganded PfPDF. This represents the successful outcome of modifying the protein construct in order to overcome adverse crystal contacts and other problems encountered in the study of unliganded PfPDF. Two molecules of PfPDF are found in the asymmetric unit of the current structure. The active site of each monomer of PfPDF is occupied by a proteolyzed fragment of the tripeptide‐like inhibitor. Unexpectedly, each PfPDF subunit is associated with two nearly complete molecules of the inhibitor, found at a protein–protein interface. This is the first structure of a eukaryotic PDF protein, a potential drug target, in complex with a ligand.
Prediction of functional sites by analysis of sequence and structure conservation
Authors: Panchenko Anna R. , Kondrashov Fyodor , Bryant Stephen
Published: March 2004

We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.
Energy functions for protein design I: Efficient and accurate continuum electrostatics and solvation
Authors: Pokala Navin , Handel Tracy M.
Published: March 2004

Electrostatics and solvation energies are important for defining protein stability, structural specificity, and molecular recognition. Because these energies are difficult to compute quickly and accurately, they are often ignored or modeled very crudely in computational protein design. To address this problem, we have developed a simple, fast, and accurate approximation for calculating Born radii in the context of protein design calculations. When these approximate Born radii are used with the generalized Born continuum dielectric model, energies calculated by the 106‐fold slower finite difference Poisson‐Boltzmann model are faithfully reproduced. A similar approach can be used for estimating solvent‐accessible surface areas (SASAs). As an independent test, we show that these approximations can be used to accurately predict the experimentally determined pKas of >200 ionizable groups from 15 proteins.
Equilibrium thermal transitions of collagen model peptides
Authors: Persikov Anton V. , Xu Yujia , Brodsky Barbara
Published: March 2004

The folding of collagen in vitro is very slow and presents difficulties in reaching equilibrium, a feature that may have implications for in vivo collagen function. Peptides serve as good model systems for examining equilibrium thermal transitions in the collagen triple helix. Investigations were carried out to ascertain whether a range of synthetic triple‐helical peptides of varying sequences can reach equilibrium, and whether the triple helix to unfolded monomer transition approximates a two‐state model. The thermal transitions for all peptides studied are fully reversible given sufficient time. Isothermal experiments were carried out to obtain relaxation times at different temperatures. The slowest relaxation times, on the order of 10–15 h, were observed at the beginning of transitions, and were shown to result from self‐association limited by the low concentration of free monomers, rather than cis–trans isomerization. Although the fit of the CD equilibrium transition curves and the concentration dependence of Tm values support a two‐state model, the more rigorous comparison of the calorimetric enthalpy to the van't Hoff enthalpy indicates the two‐state approximation is not ideal. Previous reports of melting curves of triple‐helical host–guest peptides are shown to be a two‐state kinetic transition, rather than an equilibrium transition.
Assessing natural and cultural influence on soil in remnant tropical woodlands
Authors: Jim C Y , Chan Michael W H
Published: March 2004

Rural Hong Kong contains culturally protected enclaves of remnant woodlands that provide sanctuary for vegetation, wildlife and soil. This study focuses on the influence of natural and cultural factors on soil properties in woodlands with different human activities. At each of the nine selected sites, two pits were dug to collect soil samples for analysis of 24 physical and chemical properties. Analyses of variance between soil attributes and site factors suggest the prominence of woodland size, and important contribution of topography, aspect and parent material. Soil indicators of human impacts and the tenacity of woodland soil towards anthropogenic disturbance were demonstrated.
Putting discourse in its place: planning, sustainability and the urban capacity study
Authors: Murdoch J
Published: March 2004

This article argues that policy discourses need to be set within the heterogeneous resources that governments routinely use to govern across the state/non‐state divide. It employs the governmentality perspective to show how a discursive coalition in the planning for housing sector uses such resources to embed a new rationality of ‘planning for sustainability’ in a host of differing local arenas. The article extends the governmentality approach by proposing that this ‘embedding’ process is geographically uneven as the discourse becomes enmeshed in differing economic and environmental circumstances. The analysis thus reveals a geography of governmentality by showing how local actions intrude upon the functioning of governmental networks.
Moscow, the global city? The position of the Russian capital within the European system of metropolitan areas
Authors: Brade Isolde , Rudolph Robert
Published: March 2004

During the 1990s, the city of Moscow was subject to an extraordinary transformation in its political, economic and social structures, which had consequences for the position of Moscow within the national and international hierarchy of cities. This article is concerned with the trends that can be discerned regarding the position of Moscow on the national and European scales. Without a doubt, the development of Moscow is characterized by an increasing separation from the national urban system and a growing international orientation. The Russian capital has no competitors on the national level: measured against the relevant economic indicators it is a long way ahead of the remaining Russian cities, which are primarily integrated into national and regional economic flows, and participate in the global economy only to a limited degree. Moscow, in contrast, is increasingly striving to integrate itself into transnational and international economic structures. Although the concept of Moscow as a global city is often instrumentalized in municipal politics, the ability of the Russian capital to act as a global centre is in fact limited. At present Moscow's most important function, from a Central European perspective, is to act as a bridging link between Central and Western Europe and Russia. There is a danger that the spatial disparities between Moscow on the one hand, and the remaining Russian cities and regions on the other, will continue to grow.
A decade of council tax inequities? Geographical perspectives and a research agenda
Authors: Alvanides Seraphim
Published: March 2004

Local taxation reform is back on the agenda in the light of the recent Local Government Bill. In reviewing the literature on the council tax, it is noted that researchers tend to view this from one of two perspectives: either as a fiscal policy, focusing on the tax burden, or as a housing policy, focusing on the property price valuations. Recent debate on council tax reform has gone as far as suggesting that there are regional inequities in the council tax, but what tends to be neglected remains the council tax incidence at the local scale. A research agenda is proposed here as a means of promoting geographically conscious inter‐disciplinary research on local taxation.
National carbon dioxide emissions: geography matters
Authors: Neumayer Eric
Published: March 2004

This article examines the role of geographical factors as determinants of cross‐country differences in per capita carbon dioxide emissions. Such differences have been explained by economists mostly in terms of per capita income. Geographical factors on the other hand have been neglected by economic analysis. We examine the effects of cold and hot climates, transportation requirements and the availability of renewable energy sources on emissions. We find that with the exception of cooling requirements as measured by hot climates, all these geographical factors are statistically significant determinants of emissions in accordance with our expectation. Furthermore, cold climates and the availability of renewable resources are also substantively important.
‘What a dolt one is’: language learning and fieldwork in geography
Authors: Watson Elizabeth E
Published: March 2004

This paper discusses aspects of the theory and practice of foreign language learning for fieldwork in geography, a rarely discussed set of issues despite the personal investment that language learning requires from the researcher. In some cases of cross‐cultural research, it may be particularly desirable to learn a vernacular language for which there are few (or no) study aids. However, there is little guidance about how learning such a language should be approached, or discussion of its significance for the subsequent research. Through a discussion of personal experience in Ethiopia, the paper describes one way of learning a vernacular language, and explores the advantages that this brought to the fieldwork and to the resulting research understandings.
More trees in the tropics
Authors: Bass Jerry O ‘Joby’
Published: March 2004

Repeat photography is the process of rephotographing the same scene that appears in an earlier photograph. As a methodology, repeat photography is a valuable tool for investigating and assessing landscape change. Beyond the disadvantages of scale, composition, areal coverage and temporal punctuation, the method is useful. Photographs are comprehensive views that offer a ‘contextualized’ landscape to examine. As well, the unexpected may be revealed through the process. My research in Honduras using this method led me to find a vegetation increase, rather than the decrease that was expected of a tropical area. A few example photographs illustrate the variety of manifestations this increase takes.
On journal publication and professional responsibilities
Authors: Johnston Ron , Pattie Charles
Published: March 2004

Ron Johnston and Charles Pattie identify a growing problem for journal editors and academics whose manuscripts take so long to get refereed.
An Early‐ and Late‐Stage Convolution Model for Disease Natural History
Authors: Pinsky Paul F.
Published: March 2004

Summary.  The standard convolution model of disease natural history posits an asymptomatic (preclinical) and a symptomatic (clinical) state. An augmented model includes, in both the preclinical and clinical states, an early and late stage of disease. In the case of cancer, the early stage would generally correspond to the organ‐confined stages before there is evidence of cancer spread. We compute the number of screen‐detected (preclinical) and clinical cases in the early and late stages expected under a given screening program and show how the model can be fit to data from a screening trial using maximum likelihood. We also develop expressions for sojourn time, lead time, and overdiagnosis in the context of the model, where each of the above concepts incorporates disease stage. As an example, we fit the model to data from the Mayo Lung Cancer Screening trial.
Parametric Spatial Cure Rate Models for Interval‐Censored Time‐to‐Relapse Data
Authors: Banerjee Sudipto , Carlin Bradley P.
Published: March 2004

Summary. Several recent papers (e.g.,Chen, Ibrahim, and Sinha, 1999,Journal of the American Statistical Association94,909–919;Ibrahim, Chen, and Sinha, 2001a,Biometrics57,383–388) have described statistical methods for use with time‐to‐event data featuring a surviving fraction (i.e., a proportion of the population that never experiences the event). Suchcure ratemodels and their multivariate generalizations are quite useful in studies of multiple diseases to which an individual may never succumb, or from which an individual may reasonably be expected to recover following treatment (e.g., various types of cancer). In this article we extend these models to allow for spatial correlation (estimable via zip code identifiers for the subjects) as well as interval censoring. Our approach is Bayesian, where posterior summaries are obtained via a hybrid Markov chain Monte Carlo algorithm. We compare across a broad collection of rather high‐dimensional hierarchical models using the deviance information criterion, a tool recently developed for just this purpose. We apply our approach to the analysis of a smoking cessation study where the subjects reside in 53 southeastern Minnesota zip codes. In addition to the usual posterior estimates, our approach yields smoothed zip code level maps of model parameters related to the relapse rates over time and the ultimate proportion of quitters (the cure rates).
A Bayesian Approach for the Analysis of Panel‐Count Data with Dependent Termination
Authors: Sinha Debajyoti , Maiti Tapabrata
Published: March 2004

Summary. We consider modeling and Bayesian analysis for panel‐count data when the termination time for each subject may depend on its history of the recurrent events. We propose a fully specified semiparametric model for the joint distribution of the recurrent events and the termination time. For this model, we provide a natural motivation, derive several novel properties, and develop a Bayesian analysis based on a Markov chain Monte Carlo algorithm. Comparisons are made to other existing models and methods for panel‐count data. We demonstrate the usefulness of our new models and methodologies through the reanalysis of a data set from a clinical trial.
Joint Analysis of Time‐to‐Event and Multiple Binary Indicators of Latent Classes
Authors: Larsen Klaus
Published: March 2004

Summary. Multiple categorical variables are commonly used in medical and epidemiological research to measure specific aspects of human health and functioning. To analyze such data, models have been developed considering these categorical variables as imperfect indicators of an individual's “true” status of health or functioning. In this article, the latent class regression model is used to model the relationship between covariates, a latent class variable (the unobserved status of health or functioning), and the observed indicators (e.g., variables from a questionnaire). The Cox model is extended to encompass a latent class variable as predictor of time‐to‐event, while using information about latent class membership available from multiple categorical indicators. The expectation‐maximization (EM) algorithm is employed to obtain maximum likelihood estimates, and standard errors are calculated based on the profile likelihood, treating the nonparametric baseline hazard as a nuisance parameter. A sampling‐based method for model checking is proposed. It allows for graphical investigation of the assumption of proportional hazards across latent classes. It may also be used for checking other model assumptions, such as no additional effect of the observed indicators given latent class. The usefulness of the model framework and the proposed techniques are illustrated in an analysis of data from the Women's Health and Aging Study concerning the effect of severe mobility disability on time‐to‐death for elderly women.
Sample Size Calculations for Surveys to Substantiate Freedom of Populations from Infectious Agents
Authors: Johnson Wesley O. , Su Chun‐Lung , Gardner Ian A. , Christensen Ronald
Published: March 2004

Summary. We develop a Bayesian approach to sample size computations for surveys designed to provide evidence of freedom from a disease or from an infectious agent. A population is considered “disease‐free” when the prevalence or probability of disease is less than some threshold value. Prior distributions are specified for diagnostic test sensitivity and specificity and we test the null hypothesis that the prevalence is below the threshold. Sample size computations are developed using hypergeometric sampling for finite populations and binomial sampling for infinite populations. A normal approximation is also developed. Our procedures are compared with the frequentist methods ofCameron and Baldock(1998a,Preventive Veterinary Medicine34,1–17.) using an example of foot‐and‐mouth disease. User‐friendly programs for sample size calculation and analysis of survey data are available athttp://www.epi.ucdavis.edu/diagnostictests/.
Judgement Post‐Stratification with Imprecise Rankings
Authors: MacEachern Steven N. , Stasny Elizabeth A. , Wolfe Douglas A.
Published: March 2004

Summary.  Judgement post‐stratification, which is based on ideas similar to those in ranked set sampling, relies on the ability of a ranker to forecast the ranks of potential observations on a set of units. In practice, the authors sometimes find it difficult to assign these ranks. This note shows how one can borrow techniques from the literature on finite population sampling to allow a probabilistic ranking of the units in a set, thus facilitating use of these sampling plans and improving estimation. The same techniques provide one approach to estimation using a judgement post‐stratified sample with multiple rankers. The technique is illustrated on allometric data relating brain weight to body weight in different species of mammals, and on a study of student performance in graduate school.
Testing for Marginal Independence between Two Categorical Variables with Multiple Responses
Authors: Bilder Christopher R. , Loughin Thomas M.
Published: March 2004

Summary.  Questions that ask respondents to “choose all that apply” from a set of items occur frequently in surveys. Categorical variables that summarize this type of survey data are called both pick any/c variables and multiple‐response categorical variables. It is often of interest to test for independence between two categorical variables. When both categorical variables can have multiple responses, traditional Pearson chi‐square tests for independence should not be used because of the within‐subject dependence among responses. An intuitively constructed version of the Pearson statistic is proposed to perform the test using bootstrap procedures to approximate its sampling distribution. First‐ and second‐order adjustments to the proposed statistic are given in order to use a chi‐square distribution approximation. A Bonferroni adjustment is proposed to perform the test when the joint set of responses for individual subjects is unavailable. Simulations show that the bootstrap procedures hold the correct size more consistently than the other procedures.
Semiparametric Models for Cumulative Incidence Functions
Authors: Bryant John , Dignam James J.
Published: March 2004

Summary.  In analyses of time‐to‐failure data with competing risks, cumulative incidence functions may be used to estimate the time‐dependent cumulative probability of failure due to specific causes. These functions are commonly estimated using nonparametric methods, but in cases where events due to the cause of primary interest are infrequent relative to other modes of failure, nonparametric methods may result in rather imprecise estimates for the corresponding subdistribution. In such cases, it may be possible to model the cause‐specific hazard of primary interest parametrically, while accounting for the other modes of failure using nonparametric estimators. The cumulative incidence estimators so obtained are simple to compute and are considerably more efficient than the usual nonparametric estimator, particularly with regard to interpolation of cumulative incidence at early or intermediate time points within the range of data used to fit the function. More surprisingly, they are often nearly as efficient as fully parametric estimators. We illustrate the utility of this approach in the analysis of patients treated for early stage breast cancer.
The Case‐Only Odds Ratio as a Causal Parameter
Authors: Rosenbaum Paul R.
Published: March 2004

Summary. In the simplest case‐only design, cases of a disease are cross‐classified into a 2 × 2 table describing a genotype attribute and exposure to some environmental agent. In some instances, the genetic attribute has described inherited genes; in other instances, it has described mutations, for instance, damage to proto‐oncogenes or tumor suppressor genes leading to cancer. Here, the population case‐only odds ratio is written as a causal parameter in terms of potential outcomes with and without exposure to the agent. It is shown that the case‐only odds ratio makes sense as a causal parameter with inherited genes, but its magnitude does not have a causal interpretation with mutations, although deviations from 1 do provide information. The difference is that the environmental agent certainly did not cause an individual to inherit particular genes, but it may have caused the mutation.
Loglinear Models for the Robust Design in Mark–Recapture Experiments
Authors: Rivest Louis‐Paul , Daigle Gaétan
Published: March 2004

Summary.  The robust design is a method for implementing a mark–recapture experiment featuring a nested sampling structure. The first level consists of primary sampling sessions; the population experiences mortality and immigration between primary sessions so that open population models apply at this level. The second level of sampling has a short mark–recapture study within each primary session. Closed population models are used at this stage to estimate the animal abundance at each primary session. This article suggests a loglinear technique to fit the robust design. Loglinear models for the analysis of mark–recapture data from closed and open populations are first reviewed. These two types of models are then combined to analyze the data from a robust design. The proposed loglinear approach to the robust design allows incorporating parameters for a heterogeneity in the capture probabilities of the units within each primary session. Temporary emigration out of the study area can also be accounted for in the loglinear framework. The analysis is relatively simple; it relies on a large Poisson regression with the vector of frequencies of the capture histories as dependent variable. An example concerned with the estimation of abundance and survival of the red‐back vole in an area of southeastern Québec is presented.
Properties of the Multiallelic Trend Test
Authors: Czika Wendy , Weir B. S.
Published: March 2004

Summary.  Disease genes can be mapped on the basis of associations between genetic markers and disease status, with the case–control design having the advantage of not requiring individuals from different generations. When the marker loci have multiple alleles, there has been debate on whether the power of tests for association increases or decreases. We show here that the multiple‐allele version of Armitage's trend test has increased power over the two‐allele version under the requirement of equifrequent alleles, but not in general. The trend test has the advantage of remaining valid even when the sampled population is not in Hardy–Weinberg equilibrium. A departure from Hardy–Weinberg means that association tests depend on gametic and nongametic linkage disequilibrium between marker and disease loci, and we illustrate the magnitude of these effects with simulated data.
Bayesian Point Estimation of Quantitative Trait Loci
Authors: Sisson S. A. , Hurn M. A.
Published: March 2004

Summary.  In this article, we consider the problem of the estimation of quantitative trait loci (QTL), those chromosomal regions at which genetic information affecting some quantitative trait is encoded. Generally the number of such encoding sites is unknown, and associations between neutral molecular marker genotypes and observed trait phenotypes are sought to locate them. We consider a Bayesian model for simple experimental designs, and discuss the existing approaches to inference for this problem. In particular, we focus on locating positions of the best candidate markers segregating for the trait, a situation which is of primary interest in comparative mapping. We introduce a loss function for estimating both the number of QTL and their location, and we illustrate its application via simulated and real data.
A Model to Estimate Risk of Infection with Human Herpesvirus 8 Associated with Transfusion from Cross‐Sectional Data
Authors: Pfeiffer Ruth M. , Mbulaiteye Sam , Engels Eric
Published: March 2004

Summary. In cross‐sectional studies of infectious diseases, the data typically consist of: age at the time of study, status (presence or absence) of infection, and a chronology of events possibly associated with the disease. Motivated by a study of how human herpesvirus 8 (HHV‐8) is transmitted among children with sickle cell anemia in Uganda, we have developed a flexible parametric approach for combining current‐status data with a history of blood transfusions. We model heterogeneity in transfusion‐associated risk by a child‐specific random effect. We present an extension of the model to accommodate the fact that there is no gold standard for HHV‐8 infection and infection status was assessed by a serological assay. The parameters are estimated via maximum likelihood. Finally, we present results from applying various parameterizations of the model to the Ugandan study.
Bayesian Semiparametric Modeling for Matched Case–Control Studies with Multiple Disease States
Authors: Sinha Samiran , Mukherjee Bhramar , Ghosh Malay
Published: March 2004

Summary.  We present a Bayesian approach to analyze matched “case–control” data with multiple disease states. The probability of disease development is described by a multinomial logistic regression model. The exposure distribution depends on the disease state and could vary across strata. In such a model, the number of stratum effect parameters grows in direct proportion to the sample size leading to inconsistent MLEs for the parameters of interest even when one uses a retrospective conditional likelihood. We adopt a semiparametric Bayesian framework instead, assuming a Dirichlet process prior with a mixing normal distribution on the distribution of the stratum effects. We also account for possible missingness in the exposure variable in our model. The actual estimation is carried out through a Markov chain Monte Carlo numerical integration scheme. The proposed methodology is illustrated through simulation and an example of a matched study on low birth weight of newborns (Hosmer, D. A. and Lemeshow, S., 2000, Applied Logistic Regression) with two possible disease groups matched with a control group.
Living labour and the labour of living: a little tractate for looking forward in the twenty‐first century
Authors: Suvin Darko
Published: March 2004

An approach to the insights of Marx indispensable for looking forward today understands them as a fusion of three domains and horizons (cognition, liberty, and pleasure), with a set of regulative principles (dialectic, measure, absolute swerve), and a focus on living labour. The discussion progresses from Epicure and Fourier to Marx's form‐giving fire of living labour. Against this horizon, capitalism is discussed as a cultural revolution based on measuring labour by means of quantitative time, opposed to use‐value qualities, as well as through the metaphors from horror fantasy which Marx found to be appropriate to such a revolution. Its alliance with entropy leads to alienation and loneliness, and finally to a death‐bringing economy. An Appendix on political economy and entropy discusses the situation today and a minimum program of counter‐measures, beginning with the rejection of GNP as is.
The emptiness of zero: representations of loss, absence, anxiety and desire in the late twentieth century
Authors: Smith Kathy
Published: March 2004

As the new millenium approached, the anxiety which this moment generated found resonance in various cultural representations, and the appearance of spectral imagery seemed to indicate an anxiety about subjectivity, and about its fragmentation or complete loss. Unable to comtemplate a state beyond this loss, there came into being a crisis in subjectivity itself, and the existence of the destabilized millenium subject. This subject approached the moment by both fixating on the threshold and by disavowing what lay beyond. These strategies, and the underlying anxiety which brought them into existence, were resonated through many of the cultural representations of the time. This paper argues that it is through nachträglichkeit ‐ a 'making sense' in retrospect of earlier disparate experiences ‐ that we can begin to examine, contextualise and account for the phenomenon of 'millenium frenzy' which came about at the end of 1999. It constructs a reading of this moment, and of two particular filmic representations which resonate the concerns of the time, examining in the process how ‐ from a psychoanalytic perspective ‐ culture might be understood through its representations, and how these representations can be understood through culture.
Address to the ASDA Conference 2002: ‘Visions, Illusions and Delusions’
Authors: Sainsbury Peter
Published: March 2004

Addressing a conference with the headline 'The Persistence of Vision' seems a risky undertaking. On one hand, as Donald Crombie reminds us in his welcoming programme note, the phrase describes the optical illusion that makes cinema possible. This is perhaps a blessed delusion, in which we take an almost innocent delight. It's a simple fact of life, and one that provides enormous pleasure. But there is not much more to be said about it. On the other hand, and in the context of this conference, the phrase is used to suggest some kind of ideal, referring to a director's vision, like a kind of extra‐sightedness...
The Schwartz Report
Authors: Maccabe Collin , Smith Anthony
Published: March 2004

The crisis in university admissions which the Government asked the Steven Schwartz Committee to resolve was one largely of its own making. They resorted to the rhetoric of class warfare in an effort to persuade their own backbenchers to support the vital measure of raising university fees. Ministers came to the sensible conclusion that if those who benefit from higher education paid a proportion of the costs, the country could afford to get half of all its young people into universities.
Wash your mouth out
Authors: Green Jonathon
Published: March 2004

The phone rings. It is the BBC, probably some local radio station. Can I help? A royal has done it, a pol. has done it, a tinker, a tailor, a soldier ... someone deemed newsworthy, anyway. Yes: someone's said fuck. In public. Coo‐err. And they want me to comment. I regale the researcher. A little history, a little lexicography, a little obscene publications. We book an interview slot. 'But there's just one thing: you won't actually say the word, you do promise?' And like mother soothing a frightened child, I promise. And keep it. Because I know this dance...
Targeting seasonal climate forecasts for integration into household level decisions: the case of smallholder farmers in Lesotho
Authors: Ziervogel Gina
Published: March 2004

Seasonal climate forecasts have been promoted as a means to increase the resilience of marginal groups in Africa. The manifestations of this are still to be seen. This paper argues that successful dissemination and adoption of the forecast requires an in‐depth profile of the characteristics and needs of user groups. The case study of a mountainous village in southern Lesotho is used to highlight the decisions which one group of marginal users – smallholder farmers – might make in response to the forecast. A participatory role‐play exercise explores what information households presently receive and how new climate forecast information could be integrated into seasonal decision making. Results show that there are a number of low‐input options available to these farmers for responding to the forecast. Adoption, however, is going to require repeated exposure to the forecast in conjunction with forecast development that is suited to users’ needs. The case study is linked back to the larger scale by suggesting paths that seasonal climate forecast development could take if it is to contribute to improving livelihood sustainability among marginal groups.
Land use changes and trends in Human Appropriation of Above Ground Net Primary Production (HANPP) in India (1961–98)
Authors: Prasad V Krishna , Badarinth K V S
Published: March 2004

Land use change has the potential to influence energy flows, standing crop and biomass turnover at a variety of scales. To understand and quantify the impact of land use change on natural systems, interdisciplinary approaches and concepts linking biophysical and socioeconomic factors are needed. One such approach for analysing the socioeconomic energy flows from land use changes is Human Appropriated Net Primary Production (HANPP). HANPP is defined as the difference between the net primary production of potential vegetation and the actual net primary production remaining in vegetation after harvest. In this study, we used HANPP to quantify the energy flows consequent upon land use/land cover change from 1961 to 1998 in India. Data from the Food and Agricultural Organization Statistics (FAOSTAT) covering land use/land cover estimates, crop production, harvest and fertilizer use data have been used to analyse the trends in HANPP. Land use changes between 1961 and 1998 indicate a small increase in agricultural areas from 58.2% to 60.8% and in forest and woodland areas from 19.0% to 23.2%. Actual above ground net primary production of vegetation increased from 1280.58 to 1818.23 Tg, an increase of approximately 1.4 times over 37 years. Although population increased exponentially, human appropriation of photosynthetic products did not rise as much due to increases in forest cover and agricultural production. Although the HANPP concept is a useful approach to analyse the trends in photosynthetic products brought about by land use changes and harvesting, more robust indicators are needed to understand the impacts associated with these changes. We discuss the relevance of the HANPP analysis results by focusing on land use/land cover change and exploring the inter‐linkages between energy flows and environment.
Explaining complexities of environmental management in developing countries: lessons from the Fiji Islands
Authors: Turnbull Jane
Published: March 2004

Development assistance agencies have long urged developing countries to adopt environmental management techniques used in industrialized countries. They have ascribed shortcomings in the way developing states use those techniques to insufficient training, environmental matters being poorly integrated into economic decision making, other institutional weaknesses and lack of capacity. These reductionist explanations ignore the influence that socio‐political and economic factors may have on state environmental management. They afford only a limited understanding of environmental practice in the Fiji Islands, a South Pacific archipelago and republic. The attempts of Fijian chiefly élite to maintain their power base – achieved through political participation in the state and economic development activities as much as through maintaining the communal system – shape the state's environmental management practices. Those practices have far less rational and democratic bases than one would expect either from the underlying logic of the techniques used (such as environmental impact assessment, environmental planning and protected areas), or from the way those techniques are applied in western, industrialized countries.
The cultural context of forest degradation in adjacent Purépechan communities, Michoacán, Mexico
Authors: Works Martha A , Hadley Keith S
Published: March 2004

Recent changes in the cultural and forest landscapes of the Meseta Purépecha in Michoacán, Mexico as a result of forest degradation underscore the complexity of forest change processes in the tropical highlands of Latin America. Differences in community perception and forest structure and composition between the furniture‐making and lumber‐producing towns of Pichátaro and Sevina, Purépechan indigenous communities located amidst pine forests on Michoacán's volcanic plateau illustrate the dynamics of this process. We base our comparisons on interviews and field measures of forest structure. Our results show dramatic changes in the forests and cultural landscapes of both communities during the past decade. Following high regional timber exports during the early 1990s, Sevina shifted from a self‐sufficient to a timber importation community. By comparison, communal forests and individual parcels in Pichátaro continue to provide wood for approximately 300 wood shops. Field data and forest stand maps confirm the perception of forest degradation in both communities. While Pichátaro has maintained a larger and more diverse forest base to date, stand structure data indicate selective harvesting has led to a shift in dominance toward the less economically desirable pine species and oak. Deforestation and degradation of Sevina and Pichátaro's community forests are symptomatic of both the Meseta Purépecha and Mexico in general. Current forest conditions in both communities justify local, regional, and national concerns regarding declining biodiversity and sustainable economies.
Recent protected‐area designation in China: an evaluation of administrative and statutory procedures
Authors: Jim C. Y. , Xu Steve S. W.
Published: March 2004

Past protected‐area (PA) designation in China followed a centralized administrative approach with minimum participation of lower‐echelon governments. A period of deregulation and decentralization in 1979–91 without the benefit of relevant legislation resulted in few designations and poor management. Responding to national and international encouragement to augment the conservation of natural resources, the central government enacted statutory procedures in 1991 to encourage and regulate PA establishments at different administrative levels of government. The study evaluates the effectiveness of the new procedures in fulfilling conservation objectives. The new legislative and administrative regime reinforces deregulation and decentralization by devolving designation power and shifting financial and management responsibilities to lower levels of government, and involving more scientists and objective site assessment in PA design and assessment. Problems have arisen in the designation process due to the omission of key biota and ecosystems, bypassing the scientific assessment stage, too much emphasis on non‐conservation gains, ignoring the needs of local communities, escalating people–park conflicts, intensifying paper‐park syndrome, and the conflicting role of experts. The recently designated Shimentai Provincial Rank Nature Reserve in a mountain area in south China served as a case study to illustrate the procedures and problems.
Livelihoods in transition: transnational gold mining operations and local change in Cajamarca, Peru
Authors: Bury Jeffrey
Published: March 2004

This paper examines how transnational gold mining operations are transforming rural household livelihoods in the Cajamarca region of Peru. In particular, this paper evaluates how Newmont Mining Corporation's Minera Yanacocha (MYSA) mining operations are altering access to the produced, human, natural and social capital resources that households utilize to produce their livelihoods. The paper argues that while access to produced and human capital resources has increased in the past decade, albeit unevenly, access to natural and social capital resources has declined. The paper begins with a discussion of new frameworks for evaluating local livelihood change and household access to resources. Subsequently, the paper describes Peru's new transnational mining sector, livelihoods and livelihood change in the Cajamarca region. The paper then presents the results of case study field research evaluating the impacts of MYSA on household access to resources in three communities. Finally, the paper concludes with a critical discussion of livelihoods frameworks and how they can contribute to geographic studies.
Occupational allergic contact dermatitis from bisphenol A in vinyl gloves
Authors: Matthieu Lucretia , Godoi Ana F. L. , Lambert Julien , Van Grieken René
Published: March 2004

Allergic contact dermatitis caused by polyvinyl chloride gloves is rarely reported, and in only 2 cases was bisphenol A considered to be the responsible sensitizer. We report a patient with occupational hand dermatitis after the use of a new type of high‐density vinyl (HDV) gloves. Patch tests showed positive (++) reactions to both used and new HDV gloves and to bisphenol A. Chemical analysis by gas chromatography‐mass spectrometry demonstrated the presence of bisphenol A in the HDV gloves. Replacement by nitrile rubber gloves resulted in complete clearance of the hand dermatitis.
Delayed‐type hypersensitivity skin reactions due to heparins and heparinoids. Tolerance of recombinant hirudins and of the new synthetic anticoagulant fondaparinux
Authors: Koch Patrick
Published: March 2004

Eczema‐like, infiltrated plaques at subcutaneous heparin‐injection sites are well‐documented side effects of these anticoagulants. They are due to delayed‐type hypersensitivity. In 4 patients, patch, intradermal and subcutaneous tests were performed with a panel of unfractionated heparins (UFHs), low‐molecular‐weight heparins (LMWHs), heparinoids, recombinant hirudins and a new synthetic pentasaccharide anticoagulant fondaparinux sodium, to find safe alternatives. 3 patients were sensitized to all the UFHs and LMWHs. The LMWH tinzaparin sodium and the heparinoid pentosan polysulfate were found to be a possible substitute in patient no. 1 and 2, respectively. The recombinant hirudins and fondaparinux sodium were tolerated without any side effects in all patients tested. Fondaparinux is a synthetic copy of a pentasaccharide sequence in the heparin molecule. It is the first in a new class of antithrombotic agents. Our study suggests that it is a new safe alternative in patients with eczema‐like, infiltrated plaques at subcutaneous heparin‐injection sites.
Return‐to‐work barriers for workers with contact dermatitis
Authors: Holness D. Linn
Published: March 2004

There is little information available regarding barriers to return‐to‐work (RTW) in workers with contact dermatitis. The purpose of this study was to survey occupational health and safety personnel to determine their perceptions regarding RTW barriers for workers with contact dermatitis. The study was conducted during an occupational health and safety research conference attended by stakeholders from labour, management, injured workers, government, safety associations, occupational health and safety practitioners and researchers. The attendees were presented with 3 pictures of varying degrees of work‐related hand contact dermatitis and were asked to list the 3 key barriers or challenges in RTW for individuals with contact dermatitis. 21 individuals completed the survey. Issues identified in descending order of frequency were concern of ongoing dermatitis, ability to do the job safely, appearance, ability to accommodate, personal protective equipment, fear that the rash was contagious, workplace attitudes and pain. While some of these issues are potentially common to RTW situations in general, others are more specific to health problems which have a visible manifestation. Increased awareness of and attention to these possible barriers to RTW may lead to better RTW outcomes.
Marking patch tests sites: description of a practical, clean, durable and inexpensive method
Authors: Coz Christophe‐J. Le , Muller Beatrice , Donnay Carole
Published: March 2004

We propose an original method to mark patch test sites. A transparency is applied on the patient's back, surrounding patch tests, immediately after their application. Marks are performed with an erasable pen on test sites and on permanent skin lesions like naevi. For further readings performed after patch test removal, the transparency applied on the patient's back permits the attribution of a positive reaction. This method is clean (without ink marks on skin and without contamination of clothing), more comfortable for the patient (allowing back washing immediately after the 1st reading, never inducing allergy to inks), durable (permitting delayed readings after several days or weeks) and inexpensive (because transparencies can be reused).