Showing papers by "University of Copenhagen published in 2005"

Trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer

Abstract: background Trastuzumab, a recombinant monoclonal antibody against HER2, has clinical activity in advanced breast cancer that overexpresses HER2. We investigated its efficacy and safety after excision of early-stage breast cancer and completion of chemotherapy. methods This international, multicenter, randomized trial compared one or two years of trastuzumab given every three weeks with observation in patients with HER2-positive and either node-negative or node-positive breast cancer who had completed locoregional therapy and at least four cycles of neoadjuvant or adjuvant chemotherapy. results Data were available for 1694 women randomly assigned to two years of treatment with trastuzumab, 1694 women assigned to one year of trastuzumab, and 1693 women assigned to observation. We report here the results only of treatment with trastuzumab for one year or observation. At the first planned interim analysis (median follow-up of one year), 347 events (recurrence of breast cancer, contralateral breast cancer, second nonbreast malignant disease, or death) were observed: 127 events in the trastuzumab group and 220 in the observation group. The unadjusted hazard ratio for an event in the trastuzumab group, as compared with the observation group, was 0.54 (95 percent confidence interval, 0.43 to 0.67; P<0.0001 by the log-rank test, crossing the interim analysis boundary), representing an absolute benefit in terms of disease-free survival at two years of 8.4 percentage points. Overall survival in the two groups was not significantly different (29 deaths with trastuzumab vs. 37 with observation). Severe cardiotoxicity developed in 0.5 percent of the women who were treated with trastuzumab. conclusions One year of treatment with trastuzumab after adjuvant chemotherapy significantly improves disease-free survival among women with HER2-positive breast cancer. (clinicaltrials.gov number, NCT 00045032.)

Live migration of virtual machines

Abstract: Migrating operating system instances across distinct physical hosts is a useful tool for administrators of data centers and clusters: It allows a clean separation between hard-ware and software, and facilitates fault management, load balancing, and low-level system maintenance.By carrying out the majority of migration while OSes continue to run, we achieve impressive performance with minimal service downtimes; we demonstrate the migration of entire OS instances on a commodity cluster, recording service downtimes as low as 60ms. We show that that our performance is sufficient to make live migration a practical tool even for servers running interactive loads.In this paper we consider the design options for migrating OSes running services with liveness constraints, focusing on data center and cluster environments. We introduce and analyze the concept of writable working set, and present the design, implementation and evaluation of high-performance OS migration built on top of the Xen VMM.

DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis

Abstract: During the evolution of cancer, the incipient tumour experiences 'oncogenic stress', which evokes a counter-response to eliminate such hazardous cells. However, the nature of this stress remains elusive, as does the inducible anti-cancer barrier that elicits growth arrest or cell death. Here we show that in clinical specimens from different stages of human tumours of the urinary bladder, breast, lung and colon, the early precursor lesions (but not normal tissues) commonly express markers of an activated DNA damage response. These include phosphorylated kinases ATM and Chk2, and phosphorylated histone H2AX and p53. Similar checkpoint responses were induced in cultured cells upon expression of different oncogenes that deregulate DNA replication. Together with genetic analyses, including a genome-wide assessment of allelic imbalances, our data indicate that early in tumorigenesis (before genomic instability and malignant conversion), human cells activate an ATR/ATM-regulated DNA damage response network that delays or prevents cancer. Mutations compromising this checkpoint, including defects in the ATM-Chk2-p53 pathway, might allow cell proliferation, survival, increased genomic instability and tumour progression.

Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection

Abstract: Codon-based substitution models have been widely used to identify amino acid sites under positive selection in comparative analysis of protein-coding DNA sequences. The nonsynonymous-synonymous substitution rate ratio (d(N)/d(S), denoted omega) is used as a measure of selective pressure at the protein level, with omega > 1 indicating positive selection. Statistical distributions are used to model the variation in omega among sites, allowing a subset of sites to have omega > 1 while the rest of the sequence may be under purifying selection with omega 1. Current implementations, however, use the naive EB (NEB) approach and fail to account for sampling errors in maximum likelihood estimates of model parameters, such as the proportions and omega ratios for the site classes. In small data sets lacking information, this approach may lead to unreliable posterior probability calculations. In this paper, we develop a Bayes empirical Bayes (BEB) approach to the problem, which assigns a prior to the model parameters and integrates over their uncertainties. We compare the new and old methods on real and simulated data sets. The results suggest that in small data sets the new BEB method does not generate false positives as did the old NEB approach, while in large data sets it retains the good power of the NEB approach for inferring positively selected sites.

Structure of the cross-beta spine of amyloid-like fibrils.

Abstract: Numerous soluble proteins convert to insoluble amyloid-like fibrils that have common properties. Amyloid fibrils are associated with fatal diseases such as Alzheimer's, and amyloid-like fibrils can be formed in vitro. For the yeast protein Sup35, conversion to amyloid-like fibrils is associated with a transmissible infection akin to that caused by mammalian prions. A seven-residue peptide segment from Sup35 forms amyloid-like fibrils and closely related microcrystals, from which we have determined the atomic structure of the cross-β spine. It is a double β-sheet, with each sheet formed from parallel segments stacked in register. Side chains protruding from the two sheets form a dry, tightly self-complementing steric zipper, bonding the sheets. Within each sheet, every segment is bound to its two neighbouring segments through stacks of both backbone and side-chain hydrogen bonds. The structure illuminates the stability of amyloid fibrils, their self-seeding characteristic and their tendency to form polymorphic structures.

Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level

Abstract: Detecting positive Darwinian selection at the DNA sequence level has been a subject of considerable interest. However, positive selection is difficult to detect because it often operates episodically on a few amino acid sites, and the signal may be masked by negative selection. Several methods have been developed to test positive selection that acts on given branches (branch methods) or on a subset of sites (site methods). Recently, Yang, Z., and R. Nielsen (2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917) developed likelihood ratio tests (LRTs) based on branch-site models to detect positive selection that affects a small number of sites along prespecified lineages. However, computer simulations suggested that the tests were sensitive to the model assumptions and were unable to distinguish between relaxation of selective constraint and positive selection (Zhang, J. 2004. Frequent false detection of positive selection by the likelihood method with branch-site models. Mol. Biol. Evol. 21:1332-1339). Here, we describe a modified branch-site model and use it to construct two LRTs, called branch-site tests 1 and 2. We applied the new tests to reanalyze several real data sets and used computer simulation to examine the performance of the two tests by examining their false-positive rate, power, and robustness. We found that test 1 was unable to distinguish relaxed constraint from positive selection affecting the lineages of interest, while test 2 had acceptable false-positive rates and appeared robust against violations of model assumptions. As test 2 is a direct test of positive selection on the lineages of interest, it is referred to as the branch-site test of positive selection and is recommended for use in real data analysis. The test appeared conservative overall, but exhibited better power in detecting positive selection than the branch-based lest. Bayes empirical Bayes identification of amino acid sites under positive selection along the foreground branches was found to be reliable, but lacked power.

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

Abstract: This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional ''kingdoms.'' The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

Molecular Signatures of Natural Selection

Abstract: There is an increasing interest in detecting genes, or genomic regions, that have been targeted by natural selection. The interest stems from a basic desire to learn more about evolutionary processes in humans and other organisms, and from the realization that inferences regarding selection may provide important functional information. This review provides a nonmathematical description of the issues involved in detecting selection from DNA sequences and SNP data and is intended for readers who are not familiar with population genetic theory. Particular attention is placed on issues relating to the analysis of large-scale genomic data sets.

Bioassay analysis using R

Abstract: We describe an add-on package for the language and environment R which allows simultaneous fitting of several non-linear regression models. The focus is on analysis of dose response curves, but the functionality is applicable to arbitrary non-linear regression models. Features of the package is illustrated in examples.

Musculoskeletal ultrasound including definitions for ultrasonographic pathology

Abstract: Ultrasound (US) has great potential as an outcome in rheumatoid arthritis trials for detecting bone erosions, synovitis, tendon disease, and enthesopathy. It has a number of distinct advantages over magnetic resonance imaging, including good patient tolerability and ability to scan multiple joints in a short period of time. However, there are scarce data regarding its validity, reproducibility, and responsiveness to change, making interpretation and comparison of studies difficult. In particular, there are limited data describing standardized scanning methodology and standardized definitions of US pathologies. This article presents the first report from the OMERACT ultrasound special interest group, which has compared US against the criteria of the OMERACT filter. Also proposed for the first time are consensus US definitions for common pathological lesions seen in patients with inflammatory arthritis.

Cost of disorders of the brain in Europe.

Abstract: Patrik Andlin-Sobocki, Bengt Jonsson, Hans-Ulrich Wittchen and Jes Olesen Stockholm Health Economics, Stockholm, Sweden and Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Stockholm, Sweden; Center for Health Economics, Stockholm School of Economics, Stockholm, Sweden; Institute of Clinical Psychology and Psychotherapy, Technische Universitat Dresden, Dresden, Germany; Department of Neurology, Glostrup Hospital, University of Copenhagen, Copenhagen, Denmark

Human cathelicidin antimicrobial peptide (CAMP) gene is a direct target of the vitamin D receptor and is strongly up-regulated in myeloid cells by 1,25-dihydroxyvitamin D3

Abstract: The innate immune system of mammals provides a rapid response to repel assaults from numerous infectious agents including bacteria, viruses, fungi, and parasites. A major component of this system is a diverse combination of cationic antimicrobial peptides that include the alpha- and beta-defensins and cathelicidins. In this study, we show that 1,25-dihydroxyvitamin D3 and three of its analogs induced expression of the human cathelicidin antimicrobial peptide (CAMP) gene. This induction was observed in acute myeloid leukemia (AML), immortalized keratinocyte, and colon cancer cell lines, as well as normal human bone marrow (BM) -derived macrophages and fresh BM cells from two normal individuals and one AML patient. The induction occurred via a consensus vitamin D response element (VDRE) in the CAMP promoter that was bound by the vitamin D receptor (VDR). Induction of CAMP in murine cells was not observed and expression of CAMP mRNA in murine VDR-deficient bone marrow was similar to wild-type levels. Comparison of mammalian genomes revealed evolutionary conservation of the VDRE in a short interspersed nuclear element or SINE in the CAMP promoter of primates that was absent in the mouse, rat, and canine genomes. Our findings reveal a novel activity of 1,25-dihydroxyvitamin D3 and the VDR in regulation of primate innate immunity.

A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees

Abstract: Since the divergence of humans and chimpanzees about 5 million years ago, these species have undergone a remarkable evolution with drastic divergence in anatomy and cognitive abilities. At the molecular level, despite the small overall magnitude of DNA sequence divergence, we might expect such evolutionary changes to leave a noticeable signature throughout the genome. We here compare 13,731 annotated genes from humans to their chimpanzee orthologs to identify genes that show evidence of positive selection. Many of the genes that present a signature of positive selection tend to be involved in sensory perception or immune defenses. However, the group of genes that show the strongest evidence for positive selection also includes a surprising number of genes involved in tumor suppression and apoptosis, and of genes involved in spermatogenesis. We hypothesize that positive selection in some of these genes may be driven by genomic conflict due to apoptosis during spermatogenesis. Genes with maximal expression in the brain show little or no evidence for positive selection, while genes with maximal expression in the testis tend to be enriched with positively selected genes. Genes on the X chromosome also tend to show an elevated tendency for positive selection. We also present polymorphism data from 20 Caucasian Americans and 19 African Americans for the 50 annotated genes showing the strongest evidence for positive selection. The polymorphism analysis further supports the presence of positive selection in these genes by showing an excess of high-frequency derived nonsynonymous mutations.

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi

Abstract: Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. • UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. • UNITE can be searched by taxon name, via sequence similarity using blastn, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a blast search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. • The UNITE database is accessible through the URL http://unite.zbi.ee

Subjectivity and Selfhood: Investigating the First-Person Perspective

Abstract: What is a self? Does it exist in reality or is it a mere social construct -- or is it perhaps a neurologically induced illusion? The legitimacy of the concept of the self has been questioned by both neuroscientists and philosophers in recent years Countering this, in Subjectivity and Selfhood, Dan Zahavi argues that the notion of self is crucial for a proper understanding of consciousness He investigates the interrelationships of experience, self-awareness, and selfhood, proposing that none of these three notions can be understood in isolation Any investigation of the self, Zahavi argues, must take the first-person perspective seriously and focus on the experiential givenness of the self Subjectivity and Selfhood explores a number of phenomenological analyses pertaining to the nature of consciousness, self, and self-experience in light of contemporary discussions in consciousness research Philosophical phenomenology -- as developed by Husserl, Heidegger, Sartre, Merleau-Ponty, and others -- not only addresses crucial issues often absent from current debates over consciousness but also provides a conceptual framework for understanding subjectivity Zahavi fills the need -- given the recent upsurge in theoretical and empirical interest in subjectivity -- for an account of the subjective or phenomenal dimension of consciousness that is accessible to researchers and students from a variety of disciplines His aim is to use phenomenological analyses to clarify issues of central importance to philosophy of mind, cognitive science, developmental psychology, and psychiatry By engaging in a dialogue with other philosophical and empirical positions, says Zahavi, phenomenology can demonstrate its vitality and contemporary relevance

Appropriate Assessment of Neighborhood Effects on Individual Health: Integrating Random and Fixed Effects in Multilevel Logistic Regression

Abstract: The logistic regression model is frequently used in epidemiologic studies, yielding odds ratio or relative risk interpretations. Inspired by the theory of linear normal models, the logistic regression model has been extended to allow for correlated responses by introducing random effects. However, the model does not inherit the interpretational features of the normal model. In this paper, the authors argue that the existing measures are unsatisfactory (and some of them are even improper) when quantifying results from multilevel logistic regression analyses. The authors suggest a measure of heterogeneity, the median odds ratio, that quantifies cluster heterogeneity and facilitates a direct comparison between covariate effects and the magnitude of heterogeneity in terms of well-known odds ratios. Quantifying cluster-level covariates in a meaningful way is a challenge in multilevel logistic regression. For this purpose, the authors propose an odds ratio measure, the interval odds ratio, that takes these difficulties into account. The authors demonstrate the two measures by investigating heterogeneity between neighborhoods and effects of neighborhood-level covariates in two examples--public physician visits and ischemic heart disease hospitalizations--using 1999 data on 11,312 men aged 45-85 years in Malmo, Sweden.

Oxidative stress-induced DNA damage by particulate air pollution.

Abstract: Exposure to ambient air particulate matter (PM) is associated with pulmonary and cardiovascular diseases and cancer. The mechanisms of PM-induced health effects are believed to involve inflammation and oxidative stress. The oxidative stress mediated by PM may arise from direct generation of reactive oxygen species from the surface of particles, soluble compounds such as transition metals or organic compounds, altered function of mitochondria or NADPH-oxidase, and activation of inflammatory cells capable of generating ROS and reactive nitrogen species. Resulting oxidative DNA damage may be implicated in cancer risk and may serve as marker for oxidative stress relevant for other ailments caused by particulate air pollution. There is overwhelming evidence from animal experimental models, cell culture experiments, and cell free systems that exposure to diesel exhaust and diesel exhaust particles causes oxidative DNA damage. Similarly, various preparations of ambient air PM induce oxidative DNA damage in in vitro systems, whereas in vivo studies are scarce. Studies with various model/surrogate particle preparations, such as carbon black, suggest that the surface area is the most important determinant of effect for ultrafine particles (diameter less than 100 nm), whereas chemical composition may be more important for larger particles. The knowledge concerning mechanisms of action of PM has prompted the use of markers of oxidative stress and DNA damage for human biomonitoring in relation to ambient air. By means of personal monitoring and biomarkers a few studies have attempted to characterize individual exposure, explore mechanisms and identify significant sources to size fractions of ambient air PM with respect to relevant biological effects. In these studies guanine oxidation in DNA has been correlated with exposure to PM(2.5) and ultrafine particles outdoor and indoor. Oxidative stress-induced DNA damage appears to an important mechanism of action of urban particulate air pollution. Related biomarkers and personal monitoring may be useful tools for risk characterization.

Natural selection on protein-coding genes in the human genome

Abstract: Comparisons of DNA polymorphism within species to divergence between species enables the discovery of molecular adaptation in evolutionarily constrained genes as well as the differentiation of weak from strong purifying selection. The extent to which weak negative and positive darwinian selection have driven the molecular evolution of different species varies greatly, with some species, such as Drosophila melanogaster, showing strong evidence of pervasive positive selection, and others, such as the selfing weed Arabidopsis thaliana, showing an excess of deleterious variation within local populations. Here we contrast patterns of coding sequence polymorphism identified by direct sequencing of 39 humans for over 11,000 genes to divergence between humans and chimpanzees, and find strong evidence that natural selection has shaped the recent molecular evolution of our species. Our analysis discovered 304 (9.0%) out of 3,377 potentially informative loci showing evidence of rapid amino acid evolution. Furthermore, 813 (13.5%) out of 6,033 potentially informative loci show a paucity of amino acid differences between humans and chimpanzees, indicating weak negative selection and/or balancing selection operating on mutations at these loci. We find that the distribution of negatively and positively selected genes varies greatly among biological processes and molecular functions, and that some classes, such as transcription factors, show an excess of rapidly evolving genes, whereas others, such as cytoskeletal proteins, show an excess of genes with extensive amino acid polymorphism within humans and yet little amino acid divergence between humans and chimpanzees.

Mutations in the endosomal ESCRTIII-complex subunit CHMP2B in frontotemporal dementia

Abstract: We have previously reported a large Danish pedigree with autosomal dominant frontotemporal dementia (FTD) linked to chromosome 3 (FTD3). Here we identify a mutation in CHMP2B, encoding a component of the endosomal ESCRTIII complex, and show that it results in aberrant mRNA splicing in tissue samples from affected members of this family. We also describe an additional missense mutation in an unrelated individual with FTD. Aberration in the endosomal ESCRTIII complex may result in FTD and neurodegenerative disease.

Worldwide Phylogeography of Wild Boar Reveals Multiple Centers of Pig Domestication

Abstract: Mitochondrial DNA (mtDNA) sequences from 686 wild and domestic pig specimens place the origin of wild boar in island Southeast Asia (ISEA), where they dispersed across Eurasia. Previous morphological and genetic evidence suggested pig domestication took place in a limited number of locations (principally the Near East and Far East). In contrast, new genetic data reveal multiple centers of domestication across Eurasia and that European, rather than Near Eastern, wild boar are the principal source of modern European domestic pigs.

Endothelial function and dysfunction. Part II: Association with cardiovascular risk factors and diseases. A statement by the Working Group on Endothelins and Endothelial Factors of the European Society of Hypertension

Abstract: Dysfunction of the vascular endothelium is a hallmark of most conditions that are associated with atherosclerosis and is therefore held to be an early feature in atherogenesis. However, the mechanisms by which endothelial dysfunction occurs in smoking, dyslipidaemia, hyperhomocysteinaemia, diabetes mellitus, arterial hypertension, cerebrovascular diseases, coronary artery disease and heart failure are complex and heterogeneous. Recent data indicate that endothelial dysfunction is often associated with erectile dysfunction, which can precede and predict cardiovascular disease in men. This paper will provide a concise overview of the mechanisms causing endothelial dysfunction in the different cardiovascular risk factors and disease conditions, and of the impact of the intervention measures and treatments.

Simultaneous determination of protein structure and dynamics

Abstract: We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy--for obtaining experimental information at the atomic level about the structural and dynamical features of proteins--with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant advances in our ability to understand and utilize the structures of native proteins.

Bullying and symptoms among school-aged children: international comparative cross sectional study in 28 countries

Abstract: Background: There have been no large-scale international comparisons on bullying and health among adolescents. This study examined the association between bullying and physical and psychological symptoms among adolescents in 28 countries. Methods: This international cross-sectional survey included 123,227 students 11, 13 and 15 years of age from a nationally representative sample of schools in 28 countries in Europe and North America in 1997–98.The main outcome measures were physical and psychological symptoms. Results: The proportion of students being bullied varied enormously across countries. The lowest prevalence was observed among girls in Sweden (6.3%, 95% CI: 5.2–7.4), the highest among boys in Lithuania (41.4%, 95% CI 39.4–43.5). The risk of high symptom load increased with increasing exposure to bullying in all countries. In pooled analyses, with sex stratified multilevel logistic models adjusted for age, family affluence and country the odds ratios for symptoms among students who were bullied weekly ranged from 1.83 (95% CI 1.70–1.97) to 2.11 (95% CI 1.95–2.29) for physical symptoms (headache, stomach ache, backache, dizziness) and from 1.67 (95% CI 1.55–1.78) to 7.47 (95% CI 6.87–8.13) for psychological symptoms (bad temper, feeling nervous, feeling low, difficulties in getting to sleep, morning tiredness, feeling left out, loneliness, helplessness). Conclusion: There was a consistent, strong and graded association between bullying and each of 12 physical and psychological symptoms among adolescents in all 28 countries.

EASE: Examination of Anomalous Self-Experience.

Abstract: for a detailed account of phenomena that have in common a somehow deformed sense of fi rst-person perspective – in brief, a disorder or defi ciency in the sense of being a subject, a self-coinciding center of action, thought, and experience 1 . The scale is mainly designed for conditions in the schizophrenia spectrum, but it cannot be used alone as a diagnostic instrument (self-disorders are not listed by the DSM-IV or ICD-10 as diagnostically crucial or even important features of schizophrenia; derealization and depersonalization are mentioned as nonessential features of schizotypy). The EASE does not cover all potential anomalies of experience, but focuses only on the disorders of the self [in contrast to the BSABS (‘Bonner Skala fur die Beurteilung von Basissymptomen’) [Gross et al., 1987], e.g. perceptual disorders are not explored].

Studying plasmid horizontal transfer in situ : a critical review

Abstract: This review deals with the prospective, experimental documentation of horizontal gene transfer (HGT) and its role in real-time, local adaptation. We have focused on plasmids and their function as an accessory and/or adaptive gene pool. Studies of the extent of HGT in natural environments have identified certain hot spots, and many of these involve biofilms. Biofilms are uniquely suited for HGT, as they sustain high bacterial density and metabolic activity, even in the harshest environments. Single-cell detection of donor, recipient and transconjugant bacteria in various natural environments, combined with individual-based mathematical models, has provided a new platform for HGT studies.