Showing papers by "University of Amsterdam published in 2006"
TL;DR: Clonogenic assay or colony formation assay is an in vitro cell survival assay based on the ability of a single cell to grow into a colony that can be used to determine cell reproductive death after treatment with ionizing radiation and the effectiveness of other cytotoxic agents.
Abstract: Clonogenic assay or colony formation assay is an in vitro cell survival assay based on the ability of a single cell to grow into a colony. The colony is defined to consist of at least 50 cells. The assay essentially tests every cell in the population for its ability to undergo "unlimited" division. Clonogenic assay is the method of choice to determine cell reproductive death after treatment with ionizing radiation, but can also be used to determine the effectiveness of other cytotoxic agents. Only a fraction of seeded cells retains the capacity to produce colonies. Before or after treatment, cells are seeded out in appropriate dilutions to form colonies in 1-3 weeks. Colonies are fixed with glutaraldehyde (6.0% v/v), stained with crystal violet (0.5% w/v) and counted using a stereomicroscope. A method for the analysis of radiation dose-survival curves is included.
3,244 citations
TL;DR: The evolutionary conservation of similar defense-related proteins in monocots and dicots, but also their divergent occurrence in other conditions, suggest that these proteins serve essential functions in plant life, whether in defense or not.
Abstract: Inducible defense-related proteins have been described in many plant species upon infection with oomycetes, fungi, bacteria, or viruses, or insect attack. Several types of proteins are common and have been classified into 17 families of pathogenesis-related proteins (PRs). Others have so far been found to occur more specifically in some plant species. Most PRs and related proteins are induced through the action of the signaling compounds salicylic acid, jasmonic acid, or ethylene, and possess antimicrobial activities in vitro through hydrolytic activities on cell walls, contact toxicity, and perhaps an involvement in defense signaling. However, when expressed in transgenic plants, they reduce only a limited number of diseases, depending on the nature of the protein, plant species, and pathogen involved. As exemplified by the PR-1 proteins in Arabidopsis and rice, many homologous proteins belonging to the same family are regulated developmentally and may serve different functions in specific organs or tissues. Several defense-related proteins are induced during senescence, wounding or cold stress, and some possess antifreeze activity. Many defense-related proteins are present constitutively in floral tissues and a substantial number of PR-like proteins in pollen, fruits, and vegetables can provoke allergy in humans. The evolutionary conservation of similar defense-related proteins in monocots and dicots, but also their divergent occurrence in other conditions, suggest that these proteins serve essential functions in plant life, whether in defense or not.
2,747 citations
TL;DR: It is shown that PcG proteins directly repress a large cohort of developmental regulators in murine ES cells, the expression of which would otherwise promote differentiation, and dynamic repression of developmental pathways by Polycomb complexes may be required for maintaining ES cell pluripotency and plasticity during embryonic development.
Abstract: The mechanisms by which embryonic stem (ES) cells self-renew while maintaining the ability to differentiate into virtually all adult cell types are not well understood. Polycomb group (PcG) proteins are transcriptional repressors that help to maintain cellular identity during metazoan development by epigenetic modification of chromatin structure. PcG proteins have essential roles in early embryonic development and have been implicated in ES cell pluripotency, but few of their target genes are known in mammals. Here we show that PcG proteins directly repress a large cohort of developmental regulators in murine ES cells, the expression of which would otherwise promote differentiation. Using genome-wide location analysis in murine ES cells, we found that the Polycomb repressive complexes PRC1 and PRC2 co-occupied 512 genes, many of which encode transcription factors with important roles in development. All of the co-occupied genes contained modified nucleosomes (trimethylated Lys 27 on histone H3). Consistent with a causal role in gene silencing in ES cells, PcG target genes were de-repressed in cells deficient for the PRC2 component Eed, and were preferentially activated on induction of differentiation. Our results indicate that dynamic repression of developmental pathways by Polycomb complexes may be required for maintaining ES cell pluripotency and plasticity during embryonic development.
2,549 citations
TL;DR: It is found that PRC2 target genes are preferentially activated during ES cell differentiation and that the ES cell regulators OCT4, SOX2, and NANOG cooccupy a significant subset of these genes.
2,341 citations
TL;DR: In this paper, the authors proposed a rank test based on matrix perturbation theory, which overcomes deficiencies of existing rank statistics, such as: a Kronecker covariance matrix for the canonical correlation rank statistic of Anderson [Annals of Mathematical Statistics (1951), 22, 327-351] sensitivity to the ordering of the variables for the LDU rank statistics of Cragg and Donald [1996, 91, 1301-1309] and Gill and Lewbel [Journal of the American Statistical Association (1992), 87, 766-776] a limiting
2,125 citations
TL;DR: Range scaling and autoscaling were able to remove the dependence of the rank of the metabolites on the average concentration and the magnitude of the fold changes and showed biologically sensible results after PCA (principal component analysis).
Abstract: Extracting relevant biological information from large data sets is a major challenge in functional genomics research. Different aspects of the data hamper their biological interpretation. For instance, 5000-fold differences in concentration for different metabolites are present in a metabolomics data set, while these differences are not proportional to the biological relevance of these metabolites. However, data analysis methods are not able to make this distinction. Data pretreatment methods can correct for aspects that hinder the biological interpretation of metabolomics data sets by emphasizing the biological information in the data set and thus improving their biological interpretability. Different data pretreatment methods, i.e. centering, autoscaling, pareto scaling, range scaling, vast scaling, log transformation, and power transformation, were tested on a real-life metabolomics data set. They were found to greatly affect the outcome of the data analysis and thus the rank of the, from a biological point of view, most important metabolites. Furthermore, the stability of the rank, the influence of technical errors on data analysis, and the preference of data analysis methods for selecting highly abundant metabolites were affected by the data pretreatment method used prior to data analysis. Different pretreatment methods emphasize different aspects of the data and each pretreatment method has its own merits and drawbacks. The choice for a pretreatment method depends on the biological question to be answered, the properties of the data set and the data analysis method selected. For the explorative analysis of the validation data set used in this study, autoscaling and range scaling performed better than the other pretreatment methods. That is, range scaling and autoscaling were able to remove the dependence of the rank of the metabolites on the average concentration and the magnitude of the fold changes and showed biologically sensible results after PCA (principal component analysis). In conclusion, selecting a proper data pretreatment method is an essential step in the analysis of metabolomics data and greatly affects the metabolites that are identified to be the most important.
1,987 citations
TL;DR: European consensus for the management of patients with differentiated thyroid carcinoma of the follicular epithelium Furio Pacini, Martin Schlumberger, Henning Dralle, Rossella Elisei, Johannes W A Smit, Wilmar Wiersinga and the European Thyroid Cancer Taskforce Section of Endocrinology and Metabolism are presented.
Abstract: European consensus for the management of patients with differentiated thyroid carcinoma of the follicular epithelium Furio Pacini, Martin Schlumberger, Henning Dralle, Rossella Elisei, Johannes W A Smit, Wilmar Wiersinga and the European Thyroid Cancer Taskforce Section of Endocrinology and Metabolism, University of Siena, Via Bracci, 53100 Siena, Italy, Service de Medicine Nucleaire, Institut Gustave Roussy, Villejuif, France, Department of General, Visceral and Vascular Surgery, University of Halle, Germany, Department of Endocrinology, University of Pisa, Italy, Department of Endocrinology and Metabolic Disease, Leiden University Medical Center, The Netherlands and Department of Endocrinology and Metabolism, University of Amsterdam, The Netherlands
1,926 citations
TL;DR: Theoretical studies suggest that the medial entorhinal cortex might perform some of the essential underlying computations by means of a unique, periodic synaptic matrix that could be self-organized in early development through a simple, symmetry-breaking operation.
Abstract: The hippocampal formation can encode relative spatial location, without reference to external cues, by the integration of linear and angular self-motion (path integration). Theoretical studies, in conjunction with recent empirical discoveries, suggest that the medial entorhinal cortex (MEC) might perform some of the essential underlying computations by means of a unique, periodic synaptic matrix that could be self-organized in early development through a simple, symmetry-breaking operation. The scale at which space is represented increases systematically along the dorsoventral axis in both the hippocampus and the MEC, apparently because of systematic variation in the gain of a movement-speed signal. Convergence of spatially periodic input at multiple scales, from so-called grid cells in the entorhinal cortex, might result in non-periodic spatial firing patterns (place fields) in the hippocampus.
1,747 citations
TL;DR: This survey reviews 100+ recent articles on content-based multimedia information retrieval and discusses their role in current research directions which include browsing and search paradigms, user studies, affective computing, learning, semantic queries, new features and media types, high performance indexing, and evaluation techniques.
Abstract: Extending beyond the boundaries of science, art, and culture, content-based multimedia information retrieval provides new paradigms and methods for searching through the myriad variety of media all over the world. This survey reviews 100p recent articles on content-based multimedia information retrieval and discusses their role in current research directions which include browsing and search paradigms, user studies, affective computing, learning, semantic queries, new features and media types, high performance indexing, and evaluation techniques. Based on the current state of the art, we discuss the major challenges for the future.
1,652 citations
TL;DR: This work presents recursive equations that are used to constantly update the parameters of a Gaussian mixture model and to simultaneously select the appropriate number of components for each pixel and presents a simple non-parametric adaptive density estimation method.
1,483 citations
TL;DR: Metacognition and Learning as discussed by the authors is a journal dedicated to the study of metacognitions and all its aspects within a broad context of learning processes, and it is the first issue of MetACognition & Learning Journal.
Abstract: This is the first issue of Metacognition and Learning, a new international journal dedicated to the study of metacognition and all its aspects within a broad context of learning processes. Flavell coined the term metacognition in the seventies of the last century (Flavell, 1979) and, since then, a huge amount of research has emanated from his initial efforts. Do we need metacognition as a concept in learning theory? Already in 1978, Brown posed the question whether metacognition was an epiphenomenon. Apparently, she was convinced otherwise as she has been working fruitfully for many years in the area of metacognition. Moreover, a review study by Wang, Haertel, and Walberg (1990) revealed metacognition to be a most powerful predictor of learning. Metacognition matters, but there are many unresolved issues that need further investigation. This introduction will present ten such issues, which are by no means exhaustive. They merely indicate what themes might be relevant to the journal.
TL;DR: The results suggest that EF component processes develop at different rates, and that it is important to recognize both the unity and diversity ofEF component processes in studying the development of EF.
TL;DR: The discrimination between the four motor imagery tasks based on classification of single EEG trials improved when, in addition to event-related desynchronization (ERD), event- related synchronization (ERS) patterns were induced in at least one or two tasks.
TL;DR: Using structural equation modeling, it is found that the frequency with which adolescents used the site had an indirect effect on their social self-esteem and well-being.
Abstract: The aim of this study was to investigate the consequences of friend networking sites (e.g., Friendster, MySpace) for adolescents' self-esteem and well-being. We conducted a survey among 881 adolescents (10–19-year-olds) who had an online profile on a Dutch friend networking site. Using structural equation modeling, we found that the frequency with which adolescents used the site had an indirect effect on their social self-esteem and well-being. The use of the friend networking site stimulated the number of relationships formed on the site, the frequency with which adolescents received feedback on their profiles, and the tone (i.e., positive vs. negative) of this feedback. Positive feedback on the profiles enhanced adolescents' social self-esteem and well-being, whereas negative feedback decreased their selfesteem and well-being.
TL;DR: A review of the past 25 years of research into time series forecasting can be found in this paper, where the authors highlight results published in journals managed by the International Institute of Forecasters.
TL;DR: An overview of the mechanism of this remarkable reaction is presented as a means to explain the myriad of experimental results, particularly the various methods of catalyst generation, solvent and substrate effects, and choice of base or ligand as discussed by the authors.
Lille University of Science and Technology1, Goddard Space Flight Center2, Goddard Institute for Space Studies3, Texas A&M University4, University of Maryland, Baltimore County5, University of Amsterdam6, Spanish National Research Council7, Royal Netherlands Meteorological Institute8, Radboud University Nijmegen9
TL;DR: In this article, the authors used shape mixtures of randomly oriented spheroids for modeling desert dust aerosol light scattering, and the results indicated that nonspherical particles with aspect ratios similar to 1.5 dominate in desert dust plumes, while in the case of background maritime aerosol spherical particles are dominant.
Abstract: [ 1] The possibility of using shape mixtures of randomly oriented spheroids for modeling desert dust aerosol light scattering is discussed. For reducing calculation time, look-up tables were simulated for quadrature coefficients employed in the numerical integration of spheroid optical properties over size and shape. The calculations were done for 25 bins of the spheroid axis ratio ranging from similar to 0.3 ( flattened spheroids) to similar to 3.0 ( elongated spheroids) and for 41 narrow size bins covering the size parameter range from similar to 0.012 to similar to 625. The look-up tables were arranged into a software package, which allows fast, accurate, and flexible modeling of scattering by randomly oriented spheroids with different size and shape distributions. In order to evaluate spheroid model and explore the possibility of aerosol shape identification, the software tool has been integrated into inversion algorithms for retrieving detailed aerosol properties from laboratory or remote sensing polarimetric measurements of light scattering. The application of this retrieval technique to laboratory measurements by Volten et al. ( 2001) has shown that spheroids can closely reproduce mineral dust light scattering matrices. The spheroid model was utilized for retrievals of aerosol properties from atmospheric radiation measured by AERONET ground-based Sun/sky-radiometers. It is shown that mixtures of spheroids allow rather accurate fitting of measured spectral and angular dependencies of observed intensity and polarization. Moreover, it is shown that for aerosol mixtures with a significant fraction of coarse-mode particles ( radii >= similar to 1 mu m), the nonsphericity of aerosol particles can be detected as part of AERONET retrievals. The retrieval results indicate that nonspherical particles with aspect ratios similar to 1.5 and higher dominate in desert dust plumes, while in the case of background maritime aerosol spherical particles are dominant. Finally, the potential of using AERONET derived spheroid mixtures for modeling the effects of aerosol particle nonsphericity in other remote sensing techniques is discussed. For example, the variability of lidar measurements ( extinction to backscattering ratio and signal depolarization ratio) is illustrated and analyzed. Also, some potentially important differences in the sensitivity of angular light scattering to parameters of nonspherical versus spherical aerosols are revealed and discussed.
TL;DR: Colonoscopy rarely misses polyps ≥10 mm, but the miss rate increases significantly in smaller sized polyps.
TL;DR: The known protein phosphorylation-related regulatory functions of the PTS are summarized, which shows that the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.
Abstract: The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.
TL;DR: It is shown that the time dependence of correlation functions in an extended quantum system in d dimensions, which is prepared in the ground state of some Hamiltonian and then evolves without dissipation according to some other Hamiltonian, may be extracted using methods of boundary critical phenomena in d + 1 dimensions.
Abstract: We show that the time dependence of correlation functions in an extended quantum system in d dimensions, which is prepared in the ground state of some Hamiltonian and then evolves without dissipation according to some other Hamiltonian, may be extracted using methods of boundary critical phenomena in d + 1 dimensions For d = 1 particularly powerful results are available using conformal field theory These are checked against those available from solvable models They may be explained in terms of a picture, valid more generally, whereby quasiparticles, entangled over regions of the order of the correlation length in the initial state, then propagate classically through the system
TL;DR: The hypothesis that simple choices indeed produce better results after conscious thought, but that choices in complex matters should be left to unconscious thought was confirmed in four studies on consumer choice.
Abstract: Contrary to conventional wisdom, it is not always advantageous to engage in thorough conscious deliberation before choosing. On the basis of recent insights into the characteristics of conscious and unconscious thought, we tested the hypothesis that simple choices (such as between different towels or different sets of oven mitts) indeed produce better results after conscious thought, but that choices in complex matters (such as between different houses or different cars) should be left to unconscious thought. Named the "deliberation-without-attention" hypothesis, it was confirmed in four studies on consumer choice, both in the laboratory as well as among actual shoppers, that purchases of complex products were viewed more favorably when decisions had been made in the absence of attentive deliberation.
TL;DR: The Prague C & M Criteria have high overall validity for the endoscopic assessment of visualized Barrett's esophagus lengths.
Space Telescope Science Institute1, University of Hertfordshire2, University of Leicester3, Western Kentucky University4, European Southern Observatory5, University of California, Santa Cruz6, Liverpool John Moores University7, Norwegian Meteorological Institute8, University of Copenhagen9, Spanish National Research Council10, University of Nottingham11, California Institute of Technology12, Stockholm University13, University of Notre Dame14, Vanderbilt University15, Goddard Space Flight Center16, Marshall Space Flight Center17, Renaissance Technologies18, Lawrence Berkeley National Laboratory19, INAF20, University of Amsterdam21
TL;DR: In this article, the authors show that long-duration γ-ray bursts are associated with the most extremely massive stars and may be restricted to galaxies of limited chemical evolution. But they also show that the host galaxies of the long-drone bursts are significantly fainter and more irregular than the hosts of the core-collapse supernovae.
Abstract: When massive stars exhaust their fuel, they collapse and often produce the extraordinarily bright explosions known as core-collapse supernovae. On occasion, this stellar collapse also powers an even more brilliant relativistic explosion known as a long-duration γ-ray burst. One would then expect that these long γ-ray bursts and core-collapse supernovae should be found in similar galactic environments. Here we show that this expectation is wrong. We find that the γ-ray bursts are far more concentrated in the very brightest regions of their host galaxies than are the core-collapse supernovae. Furthermore, the host galaxies of the long γ-ray bursts are significantly fainter and more irregular than the hosts of the core-collapse supernovae. Together these results suggest that long-duration γ-ray bursts are associated with the most extremely massive stars and may be restricted to galaxies of limited chemical evolution. Our results directly imply that long γ-ray bursts are relatively rare in galaxies such as our own Milky Way.
TL;DR: A unifying theory is proposed, which states that stress will only facilitate learning and memory processes when stress is experienced in the context and around the time of the event that needs to be remembered.
TL;DR: A survey of dynamic heterogeneous agent models (HAMs) in economics and finance can be found in this article, where the authors focus on simple models that are tractable by analytic methods in combination with computational tools.
Abstract: This chapter surveys work on dynamic heterogeneous agent models (HAMs) in economics and finance. Emphasis is given to simple models that, at least to some extent, are tractable by analytic methods in combination with computational tools. Most of these models are behavioral models with boundedly rational agents using different heuristics or rule of thumb strategies that may not be perfect, but perform reasonably well. Typically these models are highly nonlinear, e.g. due to evolutionary switching between strategies, and exhibit a wide range of dynamical behavior ranging from a unique stable steady state to complex, chaotic dynamics. Aggregation of simple interactions at the micro level may generate sophisticated structure at the macro level. Simple HAMs can explain important observed stylized facts in financial time series, such as excess volatility, high trading volume, temporary bubbles and trend following, sudden crashes and mean reversion, clustered volatility and fat tails in the returns distribution.
TL;DR: The unconscious-thought theory is applicable to decision making, impression formation, attitude formation and change, problem solving, and creativity, and distinguishes between two modes of thought: unconscious and conscious.
Abstract: We present a theory about human thought named the unconscious-thought theory (UTT). The theory is applicable to decision making, impression formation, attitude formation and change, problem solving, and creativity. It distinguishes between two modes of thought: unconscious and conscious. Unconscious thought and conscious thought have different characteristics, and these different characteristics make each mode preferable under different circumstances. For instance, contrary to popular belief, decisions about simple issues can be better tackled by conscious thought, whereas decisions about complex matters can be better approached with unconscious thought. The relations between the theory and decision strategies, and between the theory and intuition, are discussed. We end by discussing caveats and future directions.
TL;DR: The identification and characterization of yeast mutants defective either in the biogenesis of peroxisomes or in one of its metabolic functions, notably fatty acid beta-oxidation, combined with the recognition of a group of genetic diseases in man, wherein these processes are also defective, have provided new insights in all aspects of perxisomes.
Abstract: In this review, we describe the current state of knowledge about the biochemistry of mammalian peroxisomes, especially human peroxisomes. The identification and characterization of yeast mutants defective either in the biogenesis of peroxisomes or in one of its metabolic functions, notably fatty acid beta-oxidation, combined with the recognition of a group of genetic diseases in man, wherein these processes are also defective, have provided new insights in all aspects of peroxisomes. As a result of these and other studies, the indispensable role of peroxisomes in multiple metabolic pathways has been clarified, and many of the enzymes involved in these pathways have been characterized, purified, and cloned. One aspect of peroxisomes, which has remained ill defined, is the transport of metabolites across the peroxisomal membrane. Although it is clear that mammalian peroxisomes under in vivo conditions are closed structures, which require the active presence of metabolite transporter proteins, much remains to be learned about the permeability properties of mammalian peroxisomes and the role of the four half ATP-binding cassette (ABC) transporters therein.
TL;DR: In this paper, a nonparametric test for Granger non-causality was proposed to avoid the over-rejection observed in the frequently used test proposed by Hiemstra and Jones [1994].
TL;DR: It is argued that introspective or behavioral observations are considered the gold standard, to which neural measures should be fitted, and that this poses serious problems for understanding the mind-brain relationship.
University of Düsseldorf1, VU University Amsterdam2, French Institute of Health and Medical Research3, Mayo Clinic4, University of Amsterdam5, Erasmus University Rotterdam6, University of Newcastle7, Institute of Cancer Research8, Johns Hopkins University9, University of Michigan10, University of New South Wales11
TL;DR: Cancer risks were similar in Peutz-Jeghers syndrome patients with identified STK11/LKB1 mutations and those with no detectable mutation (log-rank test of difference χ2; 1 df; P = 0.43), and the type or site of STK 11/L KB1 mutation did not significantly influence cancer risk.
Abstract: BACKGROUND: Although an increased cancer risk in Peutz-Jeghers syndrome is established, data on the spectrum of tumors associated with the disease and the influence of germ-line STK11/LKB1 (serine/threonine kinase) mutation status are limited. EXPERIMENTAL DESIGN: We analyzed the incidence of cancer in 419 individuals with Peutz-Jeghers syndrome, and 297 had documented STK11/LKB1 mutations. RESULTS: Ninety-six cancers were found among individuals with Peutz-Jeghers syndrome. The risk for developing cancer at ages 20, 30, 40, 50, 60, and 70 years was 2%, 5%, 17%, 31%, 60%, and 85%, respectively. The most common cancers represented in this analysis were gastrointestinal in origin, gastroesophageal, small bowel, colorectal, and pancreatic, and the risk for these cancers at ages 30, 40, 50, and 60 years was 1%, 9%, 15%, and 33%, respectively. In women with Peutz-Jeghers syndrome, the risk of breast cancer was substantially increased, being 8% and 31% at ages 40 and 60 years, respectively. Kaplan-Meier analysis showed that cancer risks were similar in Peutz-Jeghers syndrome patients with identified STK11/LKB1 mutations and those with no detectable mutation (log-rank test of difference chi2 = 0.62; 1 df; P = 0.43). Furthermore, the type or site of STK11/LKB1 mutation did not significantly influence cancer risk. CONCLUSIONS: The results from our study provide quantitative information on the spectrum of cancers and risks of specific cancer types associated with Peutz-Jeghers syndrome.