bluuebunny/crossref_metadata_2025 huggingface dataset:
Selecting Factors Predictive of Heterogeneity in Multivariate Event Time Data
Authors: Dunson David B. , Chen Zhen
Published: June 2004

Summary. In multivariate survival analysis, investigators are often interested in testing for heterogeneity among clusters, both overall and within specific classes. We represent different hypotheses about the heterogeneity structure using a sequence of gamma frailty models, ranging from a null model with no random effects to a full model having random effects for each class. Following a Bayesian approach, we define prior distributions for the frailty variances consisting of mixtures of point masses at zero and inverse‐gamma densities. Since frailties with zero variance effectively drop out of the model, this prior allocates probability to each model in the sequence, including the overall null hypothesis of homogeneity. Using a counting process formulation, the conditional posterior distributions of the frailties and proportional hazards regression coefficients have simple forms. Posterior computation proceeds via a data augmentation Gibbs sampling algorithm, a single run of which can be used to obtain model‐averaged estimates of the population parameters and posterior model probabilities for testing hypotheses about the heterogeneity structure. The methods are illustrated using data from a lung cancer trial.
Best Linear Unbiased Allele‐Frequency Estimation in Complex Pedigrees
Authors: Sara McPeek Mary , Wu Xiaodong , Ober Carole
Published: June 2004

Summary.  Many types of genetic analyses depend on estimates of allele frequencies. We consider the problem of allele‐frequency estimation based on data from related individuals. The motivation for this work is data collected on the Hutterites, an isolated founder population, so we focus particularly on the case in which the relationships among the sampled individuals are specified by a large, complex pedigree for which maximum likelihood estimation is impractical. For this case, we propose to use the best linear unbiased estimator (BLUE) of allele frequency. We derive this estimator, which is equivalent to the quasi‐likelihood estimator for this problem, and we describe an efficient algorithm for computing the estimate and its variance. We show that our estimator has certain desirable small‐sample properties in common with the maximum likelihood estimator (MLE) for this problem. We treat both the case when parental origin of each allele is known and when it is unknown. The results are extended to prediction of allele frequency in some set of individuals S based on genotype data collected on a set of individuals R. We compare the mean‐squared error of the BLUE, the commonly used naive estimator (sample frequency) and the MLE when the latter is feasible to calculate. The results indicate that although the MLE performs the best of the three, the BLUE is close in performance to the MLE and is substantially easier to calculate, making it particularly useful for large complex pedigrees in which MLE calculation is impractical or infeasible. We apply our method to allele‐frequency estimation in a Hutterite data set.
Bayesian Sample Size Determination for Prevalence and Diagnostic Test Studies in the Absence of a Gold Standard Test
Authors: Dendukuri Nandini , Rahme Elham , Bélisle Patrick , Joseph Lawrence
Published: June 2004

Summary. Planning studies involving diagnostic tests is complicated by the fact that virtually no test provides perfectly accurate results. The misclassification induced by imperfect sensitivities and specificities of diagnostic tests must be taken into account, whether the primary goal of the study is to estimate the prevalence of a disease in a population or to investigate the properties of a new diagnostic test. Previous work on sample size requirements for estimating the prevalence of disease in the case of a single imperfect test showed very large discrepancies in size when compared to methods that assume a perfect test. In this article we extend these methods to include two conditionally independent imperfect tests, and apply several different criteria for Bayesian sample size determination to the design of such studies. We consider both disease prevalence studies and studies designed to estimate the sensitivity and specificity of diagnostic tests. As the problem is typically nonidentifiable, we investigate the limits on the accuracy of parameter estimation as the sample size approaches infinity. Through two examples from infectious diseases, we illustrate the changes in sample sizes that arise when two tests are applied to individuals in a study rather than a single test. Although smaller sample sizes are often found in the two‐test situation, they can still be prohibitively large unless accurate information is available about the sensitivities and specificities of the tests being used.
Bayesian Isotonic Regression and Trend Analysis
Authors: Neelon Brian , Dunson David B.
Published: June 2004

Summary. In many applications, the mean of a response variable can be assumed to be a nondecreasing function of a continuous predictor, controlling for covariates. In such cases, interest often focuses on estimating the regression function, while also assessing evidence of an association. This article proposes a new framework for Bayesian isotonic regression and order‐restricted inference. Approximating the regression function with a high‐dimensional piecewise linear model, the nondecreasing constraint is incorporated through a prior distribution for the slopes consisting of a product mixture of point masses (accounting for flat regions) and truncated normal densities. To borrow information across the intervals and smooth the curve, the prior is formulated as a latent autoregressive normal process. This structure facilitates efficient posterior computation, since the full conditional distributions of the parameters have simple conjugate forms. Point and interval estimates of the regression function and posterior probabilities of an association for different regions of the predictor can be estimated from a single MCMC run. Generalizations to categorical outcomes and multiple predictors are described, and the approach is applied to an epidemiology application.
Bayesian Analysis of Serial Dilution Assays
Authors: Gelman Andrew , Chew Ginger L. , Shnaidman Michael
Published: June 2004

Summary.  In a serial dilution assay, the concentration of a compound is estimated by combining measurements of several different dilutions of an unknown sample. The relation between concentration and measurement is nonlinear and heteroscedastic, and so it is not appropriate to weight these measurements equally. In the standard existing approach for analysis of these data, a large proportion of the measurements are discarded as being above or below detection limits. We present a Bayesian method for jointly estimating the calibration curve and the unknown concentrations using all the data. Compared to the existing method, our estimates have much lower standard errors and give estimates even when all the measurements are outside the “detection limits.” We evaluate our method empirically using laboratory data on cockroach allergens measured in house dust samples. Our estimates are much more accurate than those obtained using the usual approach. In addition, we develop a method for determining the “effective weight” attached to each measurement, based on a local linearization of the estimated model. The effective weight can give insight into the information conveyed by each data point and suggests potential improvements in design of serial dilution experiments.
Accounting for Multiplicities in Assessing Drug Safety: A Three‐Level Hierarchical Mixture Model
Authors: Berry Scott M. , Berry Donald A.
Published: June 2004

Summary. Multiple comparisons and other multiplicities are among the most difficult of problems that face statisticians, frequentists, and Bayesians alike. An example is the analysis of the many types of adverse events (AEs) that are recorded in drug clinical trials. We propose a three‐level hierarchical mixed model. The most basic level is type of AE. The second level is body system, each of which contains a number of types of possibly related AEs. The highest level is the collection of all body systems. Our analysis allows for borrowing across body systems, but there is greater potential—depending on the actual data—for borrowing within each body system. The probability that a drug has caused a type of AE is greater if its rate is elevated for several types of AEs within the same body system than if the AEs with elevated rates were in different body systems. We give examples to illustrate our method and we describe its application to other types of problems.
Self Modeling with Flexible, Random Time Transformations
Authors: Brumback Lyndia C. , Lindstrom Mary J.
Published: June 2004

Summary.  Methods for modeling sets of complex curves where the curves must be aligned in time (or in another continuous predictor) fall into the general class of functional data analysis and include self‐modeling regression and time‐warping procedures. Self‐modeling regression (SEMOR), also known as a shape invariant model (SIM), assumes the curves have a common shape, modeled nonparametrically, and curve‐specific differences in amplitude and timing, traditionally modeled by linear transformations. When curves contain multiple features that need to be aligned in time, SEMOR may be inadequate since a linear time transformation generally cannot align more than one feature. Time warping procedures focus on timing variability and on finding flexible time warps to align multiple data features. We draw on these methods to develop a SIM that models the time transformations as random, flexible, monotone functions. The model is motivated by speech movement data from the University of Wisconsin X‐ray microbeam speech production project and is applied to these data to test the effect of different speaking conditions on the shape and relative timing of movement profiles.
Testing Separability in Spatial‐Temporal Marked Point Processes
Authors: Paik Schoenberg Frederic
Published: June 2004

Summary. Nonparametric tests for investigating the separability of a spatial‐temporal marked point process are described and compared. It is shown that a Cramer–von Mises‐type test is very powerful at detecting gradual departures from separability, and that a residual test based on randomly rescaling the process is powerful at detecting nonseparable clustering or inhibition of the marks. An application to Los Angeles County wildfire data is given, in which it is shown that the separability hypothesis is invalidated largely due to clustering of fires of similar sizes within periods of up to 3.9 years.
A Multiple‐Record Systems Estimation Method that Takes Observed and Unobserved Heterogeneity into Account
Authors: Stanghellini Elena , van der Heijden Peter G. M.
Published: June 2004

Summary. We present a model to estimate the size of an unknown population from a number of lists that applies when the assumptions of (a) homogeneity of capture probabilities of individuals and (b) marginal independence of lists are violated. This situation typically occurs in epidemiological studies, where the heterogeneity of individuals is severe and researchers cannot control the independence between sources of ascertainment. We discuss the situation when categorical covariates are available and the interest is not only in the total undercount, but also in the undercount within each stratum resulting from the cross‐classification of the covariates. We also present several techniques for determining confidence intervals of the undercount within each stratum using the profile log likelihood, thereby extending the work ofCormack(1992,Biometrics48,567–576).
Sensitivity of Bayes Estimators to Hyper‐Parameters with an Application to Maximum Yield from Fisheries
Authors: Millar Russell B.
Published: June 2004

Summary. Priors are seldom unequivocal and an important component of Bayesian modeling is assessment of the sensitivity of the posterior to the specified prior distribution. This is especially true in fisheries science where the Bayesian approach has been promoted as a rigorous method for including existing information from previous surveys and from related stocks or species. These informative priors may be highly contested by various interest groups. Here, formulae for the first and second derivatives of Bayes estimators with respect to hyper‐parameters of the joint prior density are given. The formula for the second derivative provides a correction to a previously published result. The formulae are shown to reduce to very convenient and easily implemented forms when the hyper‐parameters are for exponential family marginal priors. For model parameters with such priors it is shown that the ratio of posterior variance to prior variance can be interpreted as the sensitivity of the posterior mean to the prior mean. This methodology is applied to a nonlinear state‐space model for the biomass of South Atlantic albacore tuna and sensitivity of the maximum sustainable yield to the prior specification is examined.
Multivariate Regression Trees for Analysis of Abundance Data
Authors: Larsen David R. , Speckman Paul L.
Published: June 2004

Summary.  Multivariate regression tree methodology is developed and illustrated in a study predicting the abundance of several cooccurring plant species in Missouri Ozark forests. The technique is a variation of the approach of Segal (1992) for longitudinal data. It has the potential to be applied to many different types of problems in which analysts want to predict the simultaneous cooccurrence of several dependent variables. Multivariate regression trees can also be used as an alternative to cluster analysis in situations where clusters are defined by a set of independent variables and the researcher wants clusters as homogeneous as possible with respect to a group of dependent variables.
Multicentric plasma cell variant of Castleman's disease with cutaneous involvement
Authors: Klein Walter M. , Rencic Adrienne , Munshi Nikhil C. , Nousari Carlos H.
Published: June 2004

Background:  Castleman's disease (CD) is a rare low‐grade B‐cell lymphoproliferative disorder that can be associated with a variety of antibody‐mediated paraneoplastic syndromes. The disease is classified clinically by two forms and three histologic variants.

Methods:  We describe the clinical and pathological features of a 44‐year‐old woman who presented with an autoimmune hemolytic anemia, thrombocytosis, polyclonal gammopathy, axillary lymphadenopathy, hepatosplenomegaly, and several erythematous and violaceous nodules and plaques without scaling involving the trunk and extremities.

Results:  Histologic examination of the skin lesions revealed a deep dermal and subcutaneous nodular mononuclear infiltrate composed primarily of polyclonal plasmacytoid cells without atypia and an increased vascular proliferation. Additional studies including a bone marrow and lymph node biopsy, serum and urine protein electrophoresis, and computed tomography scans supported the diagnosis of multicentric plasma cell variant of CD with an associated autoimmune paraneoplastic hemolytic anemia.

Conclusion:  Cutaneous involvement in CD is part of the multicentric nature and should be considered in the differential diagnosis of a polyclonal plasma cell‐rich lymphoproliferative disorder associated with paraneoplastic autoimmune disease.
Hyperplasia of dermal microvascular pericytes in scleroderma*
Authors: Helmbold Peter , Fiedler Eckhard , Fischer Matthias , Marsch Wolfgang Ch.
Published: June 2004

Background:  Pericytes (PCs) are smooth muscle‐like mural cells of capillaries and venules, which can synthesize matrix components and fibroblast‐activating cytokines, and are thus potential mediators of pathological changes in scleroderma. In this study, alterations in microvessels were quantitatively imaged, taking PC into account for the first time.

Methods:  Skin biopsies from systemic (12) and localized (14) scleroderma forms as well as age‐, sex‐, and body location‐matched controls were examined with respect to capillary and venular densities as well as endothelial cell (EC) and PC counts using a newly developed (in respect of PC and EC) indirect collagen IV immunostaining‐based method.

Results:  Hyperplasia of the PC that doubled the microvascular PC density was the most conspicuous characteristic. In the capillaries of the upper dermal plexus of the periphery of the sclerotic zones, median ratios of PC : EC were 0.23 (controls 0.10) or 0.18 (controls 0.11) in systemic or localized scleroderma, respectively. Furthermore, an increase in capillary density in the upper dermal plexus could be demonstrated in the marginal zones of both types of disease.

Conclusions:  The observed PC increase in the peripheral zones of active disease supports the hypothesis of a vascular pathogenesis of scleroderma and directs the focus to microvascular PC.
Collagenolytic (necrobiotic) granulomas: part II – the ‘red’ granulomas
Authors: Lynch Jane M. , Barrett Terry L.
Published: June 2004

Abstract:  A collagenolytic or necrobiotic non‐infectious granuloma is one in which a granulomatous infiltrate develops around a central area of altered collagen and elastic fibers. The altered fibers lose their distinct boundaries and exhibit new staining patterns, becoming either more basophilic or eosinophilic. Within the area of altered collagen, there may be deposition of acellular substances such as mucin (blue) or fibrin (red), or there may be neutrophils with nuclear dust (blue), eosinophils (red), or flame figures (red). These color distinctions can be used as a simple algorithm for the diagnosis of collagenolytic granulomas, i.e. ‘blue’ granulomas vs. ‘red’ granulomas. Eight diagnoses are included within these two groupings, which are discussed in this two‐part article. In the previously published first part, the clinical presentation, pathogenesis and histologic features of the ‘blue’ collagenolytic granulomas were discussed. These are the lesions of granuloma annulare, Wegener's granulomatosis, and rheumatoid vasculitis. In this second half of the series, the ‘red’ collagenolytic granulomas are discussed; these are the lesions of necrobiosis lipoidica, necrobiotic xanthogranuloma, rheumatoid nodules, Churg–Strauss syndrome, and eosinophilic cellulitis (Well's Syndrome).
Polymorphisms in the genes encoding interferon‐γ and interferon‐γ receptors in multiple sclerosis
Authors: Schrijver H. M. , Hooper‐van Veen T. , Van Belzen M. J. , Crusius J. B. A. , Peña A. S. , Barkhof F. , Polman C. H. , Uitdehaag B. M. J.
Published: June 2004

Genome screens suggest that several genes, each contributing to a small extent, are involved in multiple sclerosis (MS) susceptibility. Simultaneous analysis of related genes may improve the power to detect such small effects. Interferon‐γ (IFN‐γ), mediating its effects through the IFN‐γ receptor, is a pleiotropic, pro‐inflammatory cytokine for which a detrimental effect on the course of MS has been reported. The role of IFN‐γ receptor 1 (IFNGR1) and IFN‐γ receptor 2 (IFNGR2) gene polymorphisms has not been studied in MS, and, for the IFNG gene polymorphism there is only one previous study, which incorporates clinical, but not imaging, data. The aim of this study was to investigate whether polymorphisms in the IFNG and IFNGR1 and IFNGR2 genes are associated with susceptibility to MS, or disease characteristics, as defined by clinical and imaging criteria. Genotypes for IFNG, IFNGR1 and IFNGR2 were determined in 509 patients with MS and in 193 healthy controls. Patient files were reviewed for disease course, age at onset of disease, and rate of progression. Serial magnetic resonance imaging (MRI) data were available for 107 patients. No significant differences in the distribution of IFNG, IFNGR1 and IFNGR2 genotype and allele frequencies were found between patients and controls. A progressive, as opposed to a relapsing, onset was significantly more frequent in carriers of the IFNGR2 allele Arg64 (P = 0.028). Moreover, IFNGR2 allele Arg64 carriers had a lower black hole ratio than non‐carriers (P = 0.016). No other associations with clinical parameters, such as age at onset or rate of progression, or with imaging parameters, were observed. The IFNG intron 1 gene polymorphism studied is unlikely to play a major role in MS susceptibility or disease course. The IFNGR1 and IFNGR2 gene polymorphisms studied do not exert an important influence on MS susceptibility, but allele IFNGR2*Arg64 may be associated with a progressive disease onset.
CA microsatellite polymorphism of the nuclear factor kappa B1 gene in celiac disease
Authors: Rueda B. , López‐Nevot M. A. , Ruiz M. P. , Ortega E. , Maldonado J. , López M. , Martín J.
Published: June 2004

In the present work, we investigate the possible effect of a CAn microsatellite polymorphism in the nuclear factor kappa B1 (NFKB1) gene on predisposition to celiac disease (CD). Seventy‐eight Spanish families with CD were genotyped using a polymerase chain reaction (PCR)‐fluorescent method, and the transmission patterns of different CAn alleles were analysed. Furthermore, in order to type the CAn polymorphism more accurately, samples between 126 and 144 bp were cloned and sequenced. A trend of association with the 132‐bp allele was found (P = 0.02). This allele was more frequently transmitted to affected sibs, although the results of statistical tests were not significant after correction for multiple comparisons. After sequencing, we found that the 132‐, 138‐ and 142‐bp alleles had two As at the end of the CA microsatellite, with the other alleles presenting the described pattern (NCB1 nucleotide U60337) for the microsatellite repeats. These results suggest that the NFKB1 CAn microsatellite does not play a major role in CD susceptibility. In addition, a more detailed molecular characterization of the CA microsatellite is described.
Alport syndrome: HLA association and kidney graft outcome
Authors: Barocci S. , Fiordoro S. , Santori G. , Valente U. , Mossa M. , Antonelli P. , Ferrara G. B. , Cannella G. , Nocera A.
Published: June 2004

Alport syndrome (AS) is a genetic disease of type IV collagen involving non‐homogeneous patterns of inheritance characterized clinically by the presence of progressive haematuric nephritis leading to end‐stage renal disease (ESRD), hearing loss and/or ophthalmologic abnormalities. The aim of this study was to investigate, in a cohort of AS patients who had undergone a kidney graft (KG) or who were still on a waiting list for a KG, (a) whether there is a correlation between AS and HLA antigen expression, and (b) long‐term graft outcome in transplant patients. The AS cohort was represented by 34 ESRD patients, of whom 25 received a KG and the remaining nine were still on a waiting list. AS transplant patients represented 2.78% of 899 first KGs performed at our centre (Transplantation Department at S. Martino Hospital, Genoa) between 1983 and 2002. Grafts were procured from cadaveric donors in 18 cases and from living, related donors in seven cases. All AS transplant patients had a post‐transplant follow‐up period of at least 12 months. Results showed that: (i) the frequency of the HLA‐DRB1*16 antigen was significantly increased in the whole AS cohort as compared to 128 healthy subjects (HS) (corrected P‐value 0.0026; relative risk 7.20) as well as to 232 non‐AS ESRD patients on a waiting list for KG (corrected P‐values 0.0156; relative risk 4.67); (ii) 5‐ and 10‐year graft survivals in the AS transplant patients were 80 and 73%, respectively, and did not differ from those of a control group represented by 25 non‐AS KG recipients matched for sex, age, number of HLA mismatches and immunosuppressive treatment. Increased frequency of HLA‐DRB1*16 in AS patients may reflect a linkage disequilibrium with genes coding for collagen synthesis.
Structure of the BoLA‐DRB3 gene and promoter
Authors: Russell G. C. , Smith J. A. , Oliver R. A.
Published: June 2004

The cattle major histocompatibility complex (MHC) class II DR gene product is a heterodimer encoded by the BoLA‐DRA and ‐DRB3 genes. Several groups have isolated cDNA and genomic clones for these genes, but their full genomic organization has not been described. We used a combination of long‐range polymerase chain reaction (PCR), cloning and sequencing to define the organization of the DRB3 gene on existing genomic clones and in genomic DNA. We estimate the size of the coding region to be 11.4 kbp. Sequencing of full‐length PCR clones from two different haplotypes confirmed that they carried complete DRB3 genes and allowed the design of probes and primers to isolate and characterize the DRB3 promoter and 3′ end. Fragments carrying the 5′ end of the DRB3 gene and its promoter were identified on bacterial artificial chromosome (BAC) clones carrying the BoLA‐DR genes. A 10‐kbp promoter fragment was subcloned from one clone and a 1.7‐kbp region including exon 1 and the promoter was sequenced. A 3‐kbp fragment encoding exons 4–6 and the entire 3′ untranslated region of the DRB3 gene was isolated from lambda clone A1 and sequenced. This provides us with improved characterization of the DRB3*0101 and DRB3*2002 alleles, and also subcloned 5′ and 3′ flanking regions of the polymorphic DRB3 gene for use in functional studies.
Topographic controls on the regional‐scale biodiversity of the south‐western USA
Authors: Coblentz David D. , Riitters Kurt H.
Published: June 2004

Aim  Topography is a fundamental geophysical observable that contains valuable information about the geodynamic, tectonic and climatic history of a region. Here, we extend the traditional uses of topographic analysis to evaluate the role played by topography in the distribution of regional‐scale biodiversity in the south‐western USA. An important aspect of our study is its ability to provide a way to quantify characteristics of the topographic fabric and to construct predictive models that can be used to test hypotheses that relate topography and biodiversity.

Location  South‐western USA region of the North American Cordillera.

Methods  Our approach begins with a quantitative analysis of the topography and the construction of a predicted biodiversity map based on measurable topographic quantities: organization, roughness, slope aspect, grain orientation and mean elevation. We then make a quantitative comparison between the predicted and observed biodiversity, based on the assumption that land‐cover diversity is a plausible measure of regional‐scale biodiversity. Land‐cover information used for this study was collected as part of the U.S.G.S. global land cover characteristics (GLCC) project and is derived from satellite (AVHRR) imagery.

Results  To a first order, the predicted regional‐scale biodiversity based on our topographic model shows a good correlation with the observed biodiversity (as estimated from the land‐cover diversity). Our model overestimates the biodiversity in many parts of the Colorado Plateau, Rio Grande Rift, and the low desert regions of the Southern Basin and Range, suggesting that in these provinces a biodiversity estimate based solely on topography is an over‐simplification. However, much of the Madrean Archipelago and Sierra Madre provinces, which are centres of high biodiversity in this region, show excellent agreement between the observed and predicted biodiversity.

Main conclusions  While we acknowledge that many other factors in addition to topography have an important influence on biodiversity (particularly on a local scale), we conclude that topography plays a primary role in the regional to continental‐scale biodiversity, particularly in regions characterized by insular mountain fabrics.
Historical biogeography and distribution of the freshwater cyclopine copepods (Copepoda, Cyclopoida, Cyclopinae) of the Yucatan Peninsula, Mexico
Authors: Suárez‐Morales Eduardo , Reid Janet W. , Fiers Frank , Iliffe Thomas M.
Published: June 2004

Aim  To determine and analyse the distribution of the freshwater cyclopine copepod fauna of the Yucatan Peninsula (YP) and its relationship with the geological and climatic history of this Neotropical karstic zone.

Location  The Yucatan Peninsula, Mexico.

Methods  Plotting of georeferenced sites, analysis of local and regional geological and climatic history, analysis and comparison of regional and local faunistic records.

Results  Distinct dispersal and/or vicariant processes seem to be linked to the current distributions of the seven genera known in the YP. In general, the endemic hypogean or benthic crevicular forms (i.e. Diacyclops chakan, D. puuc and Mesocyclops chaci), derived from epigean, tropical, widely distributed forms (some of them South American) may have been among the earliest colonizers of the subterranean habitats in the YP. The distribution of these and other endemic forms seem to be related to the Holocene dry periods that desiccated the largest bodies of water and isolated local populations of different species. These vicariant processes resulted in forms with restricted distributional areas; some of these formed sister species that speciated in geographically close localities but related to a common identifiable ancestor. Overall, the processes of cyclopine colonization of the YP show the influence of the South American fauna, as the closest relatives of some species endemic to the YP are South American forms; the Nearctic influence is low. The cyclopine fauna of the YP is formed by a mixture of Nearctic‐derived (species of Acanthocyclops), Neotropical (i.e. M. edax, M. longisetus, A. panamensis, Thermocyclops inversus and T. tenuis), and epigean and hypogean endemic forms. The highly dynamic geomorphology of the YP and the recent climatic changes in the Holocene define the YP as a peculiar subregion that harbours a diverse fauna of cyclopine copepods with a high endemism.

Main conclusion  The current distribution of cyclopine copepods reflects relatively recent, post‐Pliocene biogeographical patterns; probably older patterns are involved as well. The eastern coast of the Yucatan is the most recently colonized by cyclopine copepods. Most of the genera are linked with South American forms, and the Nearctic influence is weakly represented. This group has no marine relatives, but there is evidence of vicariant events involving cave‐dwelling forms.
Do smaller islands host younger populations? A case study on metapopulations of three carabid species
Authors: Zalewski Marcin
Published: June 2004

Aims To test a new concept for island ecology and metapopulation studies: if population persistence is a result of colonization and extinction processes, one would expect remarkable variability in the age of neighbouring populations – there would be both old and young (recently established) populations.

Location The lake Mamry archipelago, Poland.

Methods Forty trap transects with a total of 114 Barber traps were operating from June to September in 1997 and in 1998. The traps (0.5‐L plastic beakers, mouth diameter 120 mm, with a 20 × 20 cm wooden roof) were placed by applying a stratified sampling design into 13 habitat types on the 16 islands and two mainland sites. The frequency of macropterous individuals in wing‐dimorphic populations of three carabid species (Pterostichus melanarius,P. anthracinusandCarabus granulatus) was used as an indicator of population ‘age’.

Results The frequency of macropterous individuals in the populations varied from 0% to 100% forP. melanarius(18.5% on average), from 0% to 91% forP. anthracinus(12.6%) and from 0% to 29% forC. granulatus(8.9%). Populations hosted more long‐winged individuals (and were therefore interpreted as being younger) on smaller islands, compared with those inhabiting large islands and the mainland sites. The results also revealed that the viability of the populations of the autumn‐breedingP. melanariusmight be more affected by population size than that of the two studied spring breeders. Island connectivity did not have a significant effect on the frequency of macropterous individuals in the studied populations.

Main conclusions The inverse relationship between the proportion of macropterous individuals and island size contrasts with the accepted theory of dispersal, which assumes that there is selection against dispersal on small islands. A regression analysis for population age and habitat characteristics reveals the extinction probability of a given population. I suggest that investigations based on variability in population age can help in studies of colonization–extinction processes that would otherwise face logistic and methodological obstacles.
Phylogeography of the widespread Australian freshwater prawn, Macrobrachium australiense (Decapoda, Palaemonidae)
Authors: Murphy Nicholas P. , Austin Christopher M.
Published: June 2004

Aim  To investigate the phylogeographic structure of the widespread freshwater prawn, Macrobrachium australiense, within and between major Australian drainage basins using mitochondrial sequence data. This will enable the investigation of historical connections between major drainages and examination of hypotheses of biogeographic associations among Australian freshwater basins.

Location  Inland, eastern and northern Australia.

Methods  Sequencing 16S rRNA and ATPase 6 protein coding mitochondrial DNA genes from M. australiense from 19 locations from inland, eastern and northern Australia.

Results  Within drainage basins, haplotype trees are monophyletic, with the exception of the Finke River from the Lake Eyre Basin. Macrobrachium australiense from the two main inland drainages, the Murray–Darling and Lake Eyre Basin are divergent from each other and do not form a monophyletic group, instead the Murray–Darling Basin haplotypes clade with eastern coastal haplotypes. Haplotypes from neighbouring eastern coastal drainages were found to be quite divergent from each other.

Main conclusions  The phylogeographic relationships among M. australiense suggest that the two major inland drainages, the Murray–Darling Basin and the Lake Eyre Basin, are not biogeographically closely associated to each other. Instead the Murray–Darling Basin is more closely allied with the eastern coastal drainages across the Great Dividing Range. Despite their proximity the neighbouring southeast Queensland coastal Mary and Brisbane Rivers are also biogeographically divergent from each other. The results also indicate that the Finke River appears to have been isolated from the remainder of the Lake Eyre Basin catchment for a significant period of time.
Patch occupancy of two hemipterans sharing a common host plant
Authors: Biedermann Robert
Published: June 2004

Aim  Two hemipteran species were chosen as a study system for the comparative analysis of patch occupancy and spatial population structure of insects sharing a common host plant. This study tested whether (1) the incidence in the host plant patches differed between the two species, and (2) the two species exhibited a different spatial population structure, i.e. were they affected differentially by isolation and area of the host plant patches.

Location  The porphyry landscape north of Halle (Saale) in Germany comprising 506 patches of the host plant Brachypodium pinnatum.

Methods  The host plant patches were surveyed for the two hemipterans. To assess the influence of patch quality on species occurrence the patches were characterized by mean cover abundance of B. pinnatum, type of subsoil, slope, exposure, and shading. The spatial configuration of the patches was considered by patch area and isolation. The influence of the habitat factors and the spatial configuration on the occupancy of the two species was analysed by logistic regression.

Results  Adarrus multinotatus was found in 441 patches, while Neophilaenus albipennis was found in only 90 patches. While A. multinotatus showed virtually no relationship to the habitat factors, the occupancy of N. albipennis was influenced by subsoil type, cover abundance, and shading. The effects of area and isolation on occupancy of the patches also differed between the two species. The occupancy of N. albipennis was determined largely by area and isolation, whereas in A. multinotatus no considerable effect of spatial configuration was found.

Main conclusions  The study revealed a marked difference between the two hemipteran species in respect of spatial population structure. Adarrus multinotatus built up a ‘patchy population’, whereas N. albipennis showed a ‘metapopulation’ structure within the same set of patches in the same landscape. Spatial population structure was found to be not only a function of spatial configuration of habitat patches, but population structure differed between the habitat generalist A. multinotatus and the habitat specialist N. albipennis.
Review Essay
Authors: Wolfe Arnold S.
Published: June 2004

SOUND EFFECTS: YOUTH, LEISURE, AND THE POLITICS OF ROCK ‘N’ ROLL.
Simon Frith
On the Use of Helmholtz Resonators for Damping Acoustic Pulsations in Industrial Gas Turbines
Authors: Bellucci V. , Flohr P. , Paschereit C. O. , Magni F.
Published: June 2004

In this work, the application of Helmholtz resonators for damping low-frequency pulsations in gas turbine combustion chambers is discussed. We present a nonlinear model for predicting the acoustic response of resonators including the effect of purging air. Atmospheric experiments are used to validate the model, which is employed to design a resonator arrangement for damping low-frequency pulsations in an ALSTOM GT11N2 gas turbine. The predicted damper impedances are used as the boundary condition in the three-dimensional analysis of the combustion chamber. The suggested arrangement leads to a significant extension of the low-pulsation operating regime of the engine.
Flashback in a Swirl Burner With Cylindrical Premixing Zone
Authors: Fritz J. , Kro¨ner M. , Sattelmayer T.
Published: June 2004

Flame flashback from the combustion chamber into the mixing zone is one of the inherent problems of lean premixed combustion and essentially determines the reliability of low NOx burners. Generally, flashback can be initiated by one of the following four phenomena: flashback due to the conditions in the boundary layer, flashback due to turbulent flame propagation in the core flow, flashback induced by combustion instabilities and flashback caused by combustion induced vortex breakdown. In this study, flashback in a swirling tubular flow was investigated. In order to draw maximum benefit from the tests with respect to the application in gas turbines, the radial distribution of the axial and circumferential momentum in the tube was selected such that the typical character of a flow in mixing zones of premix burners without centerbody was obtained. A single burner test rig has been designed to provoke flashback with the preheating temperature, the equivalence ratio and the mean flow rate being the influencing parameters. The flame position within the mixing section is detected by a special optical flame sensor array, which allows the control of the experiment and furthermore the triggering of the measurement techniques. The burning velocity of the fuel has been varied by using natural gas or hydrogen. The characteristics of the flashback, the unsteady swirling flow during the flame propagation, the flame dynamics and the reaction zones have been investigated by applying high-speed video recordings, the laser Doppler anemometry and the laser induced fluorescence. The presented results show that a combustion induced vortex breakdown is the dominating mechanism of the observed flashback. This mechanism is very sensitive to the momentum distribution in the vortex core. By adding axial momentum around the mixing tube axis, the circumferential velocity gradient is reduced and flashback can be prevented.
Reducing Grid Dependency in Droplet Collision Modeling
Authors: Schmidt David P. , Rutland Christopher J.
Published: June 2004

Droplet collision models have been criticized for creating large mesh dependency in spray calculations. These numerical errors are very troublesome; they behave erratically and interfere with the predictive ability of physical models. The collision method used in KIVA can cause mesh dependent changes in average drop size of over 40 microns. In order to reduce mesh dependency, a new method has been developed for calculating the incidence of collision. The solution is to create a special collision mesh that is optimized for accuracy. The mesh is created automatically during the spray calculation. Additionally, a different stochastic collision sampling technique is also used. The new method, called the NTC algorithm, was incorporated into KIVA and found to be much faster than older algorithms. Calculations with 60,000 parcels required only a few CPU minutes. With the new NTC method and collision mesh, the mesh dependence of the drop size is only nine microns. This remaining mesh dependency is found to be due to the drag calculations and is not the fault of the collision algorithm.
Inherent CO2 Capture Using Chemical Looping Combustion in a Natural Gas Fired Power Cycle
Authors: Brandvoll O̸. , Bolland O.
Published: June 2004

In this paper an alternative to the so-called “oxy-fuel” combustion for CO2 capture is evaluated. “Chemical looping combustion” (CLC), is closely related to oxy-fuel combustion as the chemically bound oxygen reacts in a stoichiometric ratio with the fuel. In the CLC process the overall combustion reaction takes place in two reaction steps in two separate reactors. In the reduction reactor, the fuel is oxidized by the oxygen carrier, i.e., the metal oxide MeO. The metal oxide is reduced to a metal oxide with a lower oxidation number, Me, in the reaction with the fuel. In this manner, pure oxygen is supplied to the reaction with the fuel without using a traditional air separation plant, like cryogenic distillation of air. The paper presents a thermodynamic cycle analysis, where CLC is applied in a humid air turbine concept. Main parameters are identified, and these are varied to examine the influence on cycle efficiency. Results on cycle efficiency are presented and compared to other CO2 capture options. Further, an evaluation of the oxygen carrier, metals/oxides, is presented. An exergy analysis is carried out in order to understand where losses occur, and to explain the difference between CLC and conventional combustion. The oxidation reactor air inlet temperature and the oxidation reactor exhaust temperature have a significant impact on the overall efficiency. This can be attributed to the controlling effect of these parameters on the required airflow rate. An optimum efficiency of 55.9% has been found for a given set of input parameters. Crucial issues of oxygen carrier durability, chemical performance, and mechanical properties have been idealized, and further research on the feasibility of CLC is needed. Whether or not the assumption 100% gas conversion holds, is a crucial issue and remains to be determined experimentally. Successful long-term operation of chemical looping systems of this particular type has not yet been demonstrated. The simulation points out a very promising potential of CLC as a power/heat generating method with inherent capture of CO2. Exergy analysis show reduced irreversibilities for CLC compared to conventional combustion. Simulations of this type will prove useful in designing CLC systems in the future when promizing oxygen carriers have been investigated in more detail .
Preliminary Gas Turbine Design Using the Multidisciplinary Design System MOPEDS
Authors: Jeschke P. , Kurzke J. , Schaber R. , Riegler C.
Published: June 2004

A prototype preliminary design task for gas turbines is set up to outline the four major requirements a preliminary design program must typically meet: assessment of all major engine components and their interrelations; inclusion of all relevant disciplines; designing over several operating points; and model fidelity zooming at least for individual components. It is described how the “MOdular Performance and Engine Design System” (MOPEDS)—MTU Aero Engines’ software package for the preliminary design of airborne and stationary gas turbines—fulfills these requirements. The program structure, the graphical user interface, and the physical models are briefly presented. A typical design example is carried out emphasizing the necessity for a numerical procedure to find a solution to the many variables and constraints that the design problem comprises. Finally, some dominating multidisciplinary effects are discussed.
The Selective Non-Catalytic Removal (SNCR) of Nitric Oxides From Engine Exhaust Streams: Comparison of Three Processes
Authors: Caton Jerald A. , Xia Zhiyong
Published: June 2004

Three processes for the selective non-catalytic removal (SNCR) of nitric oxides from engine exhaust gases are compared. The three processes are similar but each uses a different chemical agent: ammonia, urea, or cyanuric acid. A number of operating conditions have been studied. In particular, results for the removal of nitric oxide are significantly different for the three processes as the oxygen concentration varies. Ammonia, urea, and cyanuric acid were found to be most effective at low, intermediate, and high oxygen concentrations, respectively. The implications of these results for a range of engines and engine applications are discussed.
Development of the Radially Stratified Flame Core Low NOx Burner: From Fundamentals to Industrial Applications
Authors: Bee´r J. M. , Toqan M. A. , Haynes J. M. , Borio R. W.
Published: June 2004

Research and development of the low NOx radially stratified flame core (RSFC) burner is followed from its fundamental concept through prototype burner design, pilot scale experiments at M.I.T. and scale-up and commercial design by ABB-CE (now ALSTOM Power) to applications in industrial and utility plant boilers. The principle that turbulence can be significantly damped in a rotating flow field with a strong positive radial density gradient was used to increase the fuel rich zone residence time in internally staged low NOx burners. The continuous interaction of ideas from laboratory experimental and computational studies with those from the commercial design and industrial scale tests played a pivotal role in the development of the final product, the commercial RSFC burner. Examples of application in gas, oil, and coal fired industrial and utility boilers are discussed.
On the Control of Synchronous Vibration in Rotor/Magnetic Bearing Systems Involving Auxiliary Bearing Contact
Authors: Keogh P. S. , Cole M. O. T. , Sahinkaya M. N. , Burrows C. R.
Published: June 2004

During the normal operation of rotor/magnetic bearing systems, contacts with auxiliary bearings or bushes are avoided. However, auxiliary bearings are required under abnormal conditions and in malfunction situations to prevent contact between the rotor and stator laminations. Studies in the open literature deal largely with rotor drop and the requirements of auxiliary bearings design parameters for safe rundown. Rotor drop occurs when the rotor is delevitated and no further means of magnetic bearing control is available. This paper considers the case when full control is still available and rotor/auxiliary bearing contact has been induced by an abnormal operating condition or a temporary fault. It is demonstrated that events leading to contact from a linearly stable rotor orbit can drive the rotor into a nonlinear vibratory motion involving persistent contacts. Furthermore, the phase of the measured vibration response may be changed to such an extent that synchronous controllers designed to minimize rotor vibration amplitudes will worsen the rotor response, resulting in higher contact forces. A modified controller design is proposed and demonstrated to be capable of returning a rotor from a contacting to a noncontacting state.