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PubMedDate not supplied

Hostility as a predictor of survival in patients with coronary artery disease.

OBJECTIVE: This article presents a reanalysis of an earlier study that reported a nonsignificant relation between the 50-item Cook-Medley Hostility Scale (CMHS) and survival in a sample of coronary patients. Since publication of those results, there have been significant developments in the measurement of hostility that suggest that an abbreviated scale may be a better predictor of health outcomes. This study examined the ability of the total CMHS and an abbreviated form of the CMHS (ACM) to predict survival in a sample of patients with documented coronary artery disease (CAD) with increased statistical power. METHODS: Nine hundred thirty-six patients (83% were male; mean age = 51.48) with CAD who were followed for an average of 14.9 years. The ACM consisted of the combination of the cynicism, hostile attribution, hostile affect, and aggressive responding subscales that were identified in an earlier study (Barefoot et al. [1989]) by a rational analysis of the item content. The relation between hostility and survival was examined with Cox proportional hazard models (hazard ratios [HRs] based on a two standard deviation difference). RESULTS: Controlling for disease severity, the ACM was a significant predictor for both CHD mortality (HR = 1.33, p <.009) and total mortality (HR = 1.28, p <.02). The total CMHS was only a marginally significant predictor of either outcome (p values < 0.06). CONCLUSION: The results of this study suggest that hostility is associated with poorer survival in CAD patients, and it may be possible to refine measures of hostility in order to improve prediction of health outcomes.

Cause of Death↗
PubMed2004

Human leukocyte antigen type as a risk factor for nonmelanomatous skin cancer in patients after renal transplantation.

Renal-transplant recipients are at an increased risk for developing nonmelanomatous skin cancer (NMSC). Recipient human leukocyte antigen (HLA) type has been suggested as a possible risk factor. We studied the association between HLA type and posttransplant NMSC in 2,433 renal-transplant recipients in a Northern climate, for whom HLA type and clinical follow-up were available. One hundred six (4.3%) patients developed NMSC between 1984 and 1997. Of previously reported HLA-associated risk factors, only HLA A11 showed an increased incidence of posttransplant skin cancer, at 8% (P=0.0137, odds ratio 2.03 with 95% confidence interval 1.11-3.53) in 1998. This effect persisted at follow-up, in a limited reanalysis in 2004. HLA A11 may be a useful marker, in some populations, for identifying at the time of transplantation those patients that are at an increased risk for NMSC and who may therefore be good candidates for preventative clinical trials.

Adult↗
PubMed2005

Long-term benefits of mycophenolate mofetil after heart transplantation.

Transplant coronary artery disease and malignancy are the major limitations to survival after heart transplantation. In a randomized trial, mycophenolate mofetil (MMF) significantly improved 3-year survival over azathioprine, but the expected reduction in intracoronary ultrasound evidence of vasculopathy was not found on initial analysis using unmatched sites. On reanalysis using matched sites, a highly significant reduction in maximum intimal thickness was shown with MMF. Malignancy was numerically but not significantly lower at 3 years; in open label experience up to 7 years, it is diminished by 37% on MMF. MMF protects heart transplant recipients against both vasculopathy and malignancy.

Drug Therapy, Combination↗
PubMed2003

Temporal relation between the ADC and DC potential responses to transient focal ischemia in the rat: a Markov chain Monte Carlo simulation analysis.

Markov chain Monte Carlo simulation was used in a reanalysis of the longitudinal data obtained by Harris et al. (J Cereb Blood Flow Metab 20:28-36) in a study of the direct current (DC) potential and apparent diffusion coefficient (ADC) responses to focal ischemia. The main purpose was to provide a formal analysis of the temporal relationship between the ADC and DC responses, to explore the possible involvement of a common latent (driving) process. A Bayesian nonlinear hierarchical random coefficients model was adopted. DC and ADC transition parameter posterior probability distributions were generated using three parallel Markov chains created using the Metropolis algorithm. Particular attention was paid to the within-subject differences between the DC and ADC time course characteristics. The results show that the DC response is biphasic, whereas the ADC exhibits monophasic behavior, and that the two DC components are each distinguishable from the ADC response in their time dependencies. The DC and ADC changes are not, therefore, driven by a common latent process. This work demonstrates a general analytical approach to the multivariate, longitudinal data-processing problem that commonly arises in stroke and other biomedical research.

Animals↗
PubMed2007

Exposure to beryllium and occurrence of lung cancer: a reexamination of findings from a nested case-control study.

OBJECTIVE: Our aim was to reanalyze a nested case-control study of beryllium and lung cancer because we identified analysis and study design issues that could have led to the elevated odds ratios obtained in the study. METHODS: We reanalyzed the data using nontransformed exposure metrics instead of log-transformed metrics used in the publication. We identified and examined effects on estimated odds ratios of imbalances between cases and controls caused by the control selection method. RESULTS: This reanalysis found no elevated odds ratios for any exposure variable. CONCLUSION: : Our conclusions differ from the authors' interpretation that the findings are due to a causal relationship between beryllium exposure and lung cancer. Our alternative explanation is that they may be due to methodological problems that could have been controlled by closer matching of controls to cases. CLINICAL SIGNIFICANCE: This study challenges conclusions made from a large case-control study concerning beryllium-lung cancer associations. Occupational medicine practitioners may want to integrate findings from this study into advice they give beryllium-exposed workers concerned about lung cancer.

Beryllium↗
PubMed2005

Molecular evidence and marine snake origins.

A molecular phylogeny was used to refute the marine scenario for snake origins. Nuclear gene sequences suggested that snakes are not closely related to living varanid lizards, thus also apparently contradicting proposed relationships between snakes and marine mosasaurs (usually considered to be varanoids). However, mosasaurs share derived similarities with both snakes and living varanids. A reanalysis of the morphological data suggests that, if the relationships between living taxa are constrained to the proposed molecular tree, with fossil forms allowed to insert in their optimal positions within this framework, mosasaurs cluster with snakes rather than with varanids. Combined morphological and molecular analyses also still unite marine lizards with snakes. Thus, the molecular data do not refute the phylogenetic evidence for a marine origin of snakes.

Animals↗
PubMed1995

Evidence for a sex-segregated migration in the humpback whale (Megaptera novaeangliae).

Existing population models for humpback whales assume that all individuals within a population undertake the annual migration from feeding areas in high latitudes to breeding areas in tropical waters. An excess of males was recorded in the commercial whaling catches near breeding areas in the southern hemisphere, but no account of this was taken in developing population models, because it was believed that this bias was a result of whalers selecting against females with young calves. Here we demonstrate that the sex ratio of migrating humpback whales near a breeding area is highly skewed towards males. A biopsy study carried out in 1992 throughout the northward and southward migrations revealed a sex ratio of 2.4 males: 1 female in the population of humpback whales migrating along the east Australian coast (n = 180). A reanalysis of the catches made during commercial whaling in this and other areas of the southern hemisphere gave a sex ratio of the same order. The most plausible explanation, supported by some evidence, is that some females remain in the feeding areas throughout winter. The results reported here show that existing management models require major revision to take account of these findings.

Animals↗
PubMed2000

What is not a bird of paradise? Molecular and morphological evidence places Macgregoria in the Meliphagidae and the Cnemophilinae near the base of the corvoid tree.

The cnemophiline 'birds of paradise' (Cnemophilinae) and Macgregor's 'bird of paradise' (Macgregoria) have traditionally been included in the Paradisaeidae although their relationships within the group have been enigmatic and subject to repeated discussion in the literature. Here we use sequences from two mitochondrial genes, cytochrome b and cytochrome oxidase I, along with a suite of morphological characters, to investigate their relationships to paradisaeids and other members of the passerine Parvorder Corvida. The combined data strongly support the removal of both groups from the birds of paradise: the cnemophilines are basal members of the Corvoidea and Macgregoria is a member of the Meliphagoidea and embedded in the honeyeaters (Meliphagidae) close to the genus Melipotes. The amount of sequence divergence among basal passeriforms and members of the Corvida, as well as available fossil evidence for Australian corvidans, suggest that cnemophilines represent an ancient lineage within the corvoid radiation. Because cnemophilines and Macgregoria have been placed at the base of the paradisaeid tree, hypotheses of morphological, behavioural and ecological character-state transformations within the family will require reanalysis.

Animals↗
PubMed2005

An ecological 'footprint' of climate change.

Recently, there has been increasing evidence of species' range shifts due to changes in climate. Whereas most of these shifts relate ground truth biogeographic data to a general warming trend in regional or global climate data, we here present a reanalysis of both biogeographic and bioclimatic data of equal spatio-temporal resolution, covering a time span of more than 50 years. Our results reveal a coherent and synchronous shift in both species' distribution and climate. They show not only a shift in the northern margin of a species, which is in concert with gradually increasing winter temperatures in the area, they also confirm the simulated species' distribution changes expected from a bioclimatic model under the recent, relatively moderate climate change.

Climate↗
PubMed2002

Coastal modelling for flood defence.

This paper reviews practices and trends in hydrodynamic and statistical analyses and modelling in the Netherlands with regard to the risk of coastal flooding. We restrict ourselves to the physical phenomena of tides, storm surges and wind waves. We first give a brief outline of established policy in the Netherlands regarding accepted levels of risk of flooding, and current changes therein. This is followed by a summary of a statistical reanalysis of historical storm-surge data combined with numerical hydrodynamic modelling, aimed at improved estimates of probabilities of occurrence of extreme water levels along the Dutch coast. Recent developments concerning the physical and numerical modelling of inundation of low-lying areas are presented. State-of-the-art modelling of wind waves in coastal areas is also reviewed. Research issues in the area of coastal modelling for flood defence are indicated.

Climate↗
PubMed1989

The biology of mass extinction: a palaeontological view.

Extinctions are not biologically random: certain taxa or functional/ecological groups are more extinction-prone than others. Analysis of molluscan survivorship patterns for the end-Cretaceous mass extinctions suggests that some traits that tend to confer extinction resistance during times of normal ('background') levels of extinction are ineffectual during mass extinction. For genera, high species-richness and possession of widespread individual species imparted extinction-resistance during background times but not during the mass extinction, when overall distribution of the genus was an important factor. Reanalysis of Hoffman's (1986) data (Neues Jb. Geol. Palaont. Abh. 172, 219) on European bivalves, and preliminary analysis of a new northern European data set, reveals a similar change in survivorship rules, as do data scattered among other taxa and extinction events. Thus taxa and adaptations can be lost not because they were poorly adapted by the standards of the background processes that constitute the bulk of geological time, but because they lacked--or were not linked to--the organismic, species-level or clade-level traits favoured under mass-extinction conditions. Mass extinctions can break the hegemony of species-rich, well-adapted clades and thereby permit radiation of taxa that had previously been minor faunal elements; no net increase in the adaptation of the biota need ensue. Although some large-scale evolutionary trends transcend mass extinctions, post extinction evolutionary pathways are often channelled in directions not predictable from evolutionary patters during background times.

Animals↗
PubMed1998

Base-compositional biases and the bat problem. III. The questions of microchiropteran monophyly.

Using single-copy DNA hybridization, we carried out a whole genome study of 16 bats (from ten families) and five outgroups (two primates and one each dermopteran, scandentian, and marsupial). Three of the bat species represented as many families of Rhinolophoidea, and these always associated with the two representatives of Pteropodidae. All other microchiropterans, however, formed a monophyletic unit displaying interrelationships largely in accord with current opinion. Thus noctilionoids comprised one clade, while vespertilionids, emballonurids, and molossids comprised three others, successively more closely related in that sequence. The unexpected position of rhinolophoids may be due either to the high AT bias they share with pteropodids, or it may be phylogenetically authentic. Reanalysis of the data with varying combinations of the five outgroups does not indicate a rooting problem, and the inclusion of many bat lineages divided at varying levels similarly discounts long branch attraction as an explanation for the pteropodid-rhinolophoid association. If rhinolophoids are indeed specially related to pteropodids, many synapomorphies of Microchiroptera are called into question, not least the unitary evolution of echolocation (although this feature may simply have been lost in pteropodids). Further, a rhinolophoid-pteropodid relationship--if true--has serious implications for the classification of bats. Finally, among the outgroups, an apparent sister-group relation of Dermoptera and Primates suggests that flying lemurs do not represent the ancestors of some or all bats; yet, insofar as gliding of the type implemented in dermopterans is an appropriate model for the evolution of powered mammalian flying, the position of Cynocephalus in our tree indirectly strengthens the argument that true flight could have evolved more than once among bats.

Animals↗
PubMed2004

Influenza as a model system for studying the cross-species transfer and evolution of the SARS coronavirus.

Severe acute respiratory syndrome coronavirus (SARS-CoV) moved into humans from a reservoir species and subsequently caused an epidemic in its new host. We know little about the processes that allowed the cross-species transfer of this previously unknown virus. I discuss what we have learned about the movement of viruses into humans from studies of influenza A, both how it crossed from birds to humans and how it subsequently evolved within the human population. Starting with a brief review of severe acute respiratory syndrome to highlight the kinds of problems we face in learning about this viral disease, I then turn to influenza A, focusing on three topics. First, I present a reanalysis of data used to test the hypothesis that swine served as a "mixing vessel" or intermediate host in the transmission of avian influenza to humans during the 1918 "Spanish flu" pandemic. Second, I review studies of archived viruses from the three recent influenza pandemics. Third, I discuss current limitations in using molecular data to study the evolution of infectious disease. Although influenza A and SARS-CoV differ in many ways, our knowledge of influenza A may provide important clues about what limits or favours cross-species transfers and subsequent epidemics of newly emerging pathogens.

Animals↗
PubMed1998

Characterization of the bovine herpesvirus 1 UL8 gene and gene products.

The bovine herpesvirus 1 (BHV-1) strain Schönböken UL8 gene and the 5' flanking region were sequenced. Comparison of the UL8 ORF with the previously reported UL8 ORF of BHV-1 strain Cooper revealed significant differences that were mainly due to three frame-shifted segments. Reanalysis of the Cooper sequence after isolation of the respective segments from genomic DNA by PCR did not confirm the discrepancies; on the contrary, our results indicate a high degree of sequence conservation between the UL8 proteins of different BHV-1 isolates. A monospecific antiserum, raised against a bacterially expressed TrpE-UL8 fusion protein, identified the 80 kDa apparent molecular mass UL8 polypeptide which is localized in the nucleus of infected cells. Analysis of transcripts and time-course studies demonstrated that the UL8 protein is translated from a delayed-early expressed 3.1 kb polyadenylated mRNA which initiates within the UL9 ORF.

Amino Acid Sequence↗
PubMed2003

An evolutionary analysis of orphan genes in Drosophila.

Orphan genes are protein-coding regions that have no recognizable homolog in distantly related species. A substantial fraction of coding regions in any genome sequenced consists of orphan genes, but the evolutionary and functional significance of orphan genes is not understood. We present a reanalysis of the Drosophila melanogaster proteome that shows that there are still between 26% and 29% of all proteins without a significant match with noninsect sequences, and that these orphans are underrepresented in genetic screens. To analyze the characteristics of orphan genes in Drosophila, we used sequence comparisons between cDNAs retrieved from two Drosophila yakuba libraries and their corresponding D. melanogaster orthologs. We find that a cDNA library from adults yields twice as many orphan genes as such a library from embryos. The orphan genes evolve on average more than three times faster than nonorphan genes, although the width of the evolutionary rate distribution is similar for the two classes. In particular, some orphan genes show very low substitution rates that are comparable to otherwise highly conserved genes. We propose a model suggesting that orphans may be involved in the evolution of adaptive traits, and that slow-evolving orphan genes may be particularly interesting candidate genes for identifying lineage-specific adaptations.

Animals↗
PubMed2005

Stochastic modeling of protein motions within cell membranes.

A simple model in which immobilizing events are imposed onto otherwise free Brownian diffusion [R. Metzler and J. Klafter, Phys. Rep. 339, 1 (2000) and a recent adaptation due to S. Khan and A. M. Reynolds, Physica A 350, 183 (2005)] is shown to encapsulate the peculiar transport characteristics of individual cell receptors within plasma membranes observed in single-particle tracking (SPT) experiments. These characteristics include the occurrence of normal diffusion; non-Gaussian subdiffusion; confined diffusion; a superdiffusive mode of transport that is not due to flow of the membrane or molecular motor attachment; and the occurrence of transitions between these transport modes. Model predictions are shown to be in close agreement with a reanalysis of existing SPT data.

Biological Transport↗
PubMed2002

Angular momentum and cross sections for fusion with weakly bound nuclei: breakup, a coherent effect.

Results for the cross section and average angular momentum for complete fusion at energies around the Coulomb barrier are presented for 7Li with 165Ho. Comparison of the cross sections with a one-dimensional barrier penetration model, using a potential consistent with the measured elastic scattering, showed a reduction above the barrier and an enhancement below it. An increase in the measured average angular momentum, , above the barrier and its consistency with that obtained from the fusion excitation function for weakly bound nuclei, is reported. These results together with a reanalysis of existing data conclusively demonstrate that the effect of breakup on fusion is coherent, like coupling to any nonelastic channel.

Journal Article↗
PubMed2006

Roughness-induced critical phenomena in a turbulent flow.

I present empirical evidence that turbulent flows are closely analogous to critical phenomena, from a reanalysis of friction factor measurements in rough pipes. The data collapse found here corresponds to Widom scaling near critical points, and implies that a full understanding of turbulence requires explicit accounting for boundary roughness.

Journal Article↗