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Showing papers by "University of Amsterdam published in 2003"


Journal ArticleDOI
TL;DR: It is shown that the first approach can lead to PCR efficiencies that vary over a 0.2 range, whereas the second approach may be off by 0.26, and proposed linear regression on the Log(fluorescence) per cycle number data as an assumption-free method to calculate starting concentrations of mRNAs and PCRefficiencies for each sample.

3,536 citations


Journal ArticleDOI
TL;DR: In this article, an evidence-based quality assessment tool called QUADAS was proposed to assess the quality of primary studies of diagnostic accuracy, based on the results of three previously conducted reviews of the diagnostic literature.
Abstract: Background: In the era of evidence based medicine, with systematic reviews as its cornerstone, adequate quality assessment tools should be available. There is currently a lack of a systematically developed and evaluated tool for the assessment of diagnostic accuracy studies. The aim of this project was to combine empirical evidence and expert opinion in a formal consensus method to develop a tool to be used in systematic reviews to assess the quality of primary studies of diagnostic accuracy. Methods: We conducted a Delphi procedure to develop the quality assessment tool by refining an initial list of items. Members of the Delphi panel were experts in the area of diagnostic research. The results of three previously conducted reviews of the diagnostic literature were used to generate a list of potential items for inclusion in the tool and to provide an evidence base upon which to develop the tool. Results: A total of nine experts in the field of diagnostics took part in the Delphi procedure. The Delphi procedure consisted of four rounds, after which agreement was reached on the items to be included in the tool which we have called QUADAS. The initial list of 28 items was reduced to fourteen items in the final tool. Items included covered patient spectrum, reference standard, disease progression bias, verification bias, review bias, clinical review bias, incorporation bias, test execution, study withdrawals, and indeterminate results. The QUADAS tool is presented together with guidelines for scoring each of the items included in the tool. Conclusions: This project has produced an evidence based quality assessment tool to be used in systematic reviews of diagnostic accuracy studies. Further work to determine the usability and validity of the tool continues.

3,468 citations


Journal ArticleDOI
TL;DR: In this paper, a comprehensive overview of the structure, function and tissue distribution of members of the classical histone deacetylase (HDAC) family, in order to gain insight into the regulation of gene expression through HDAC activity is presented.
Abstract: Transcriptional regulation in eukaryotes occurs within a chromatin setting, and is strongly influenced by the post-translational modification of histones, the building blocks of chromatin, such as methylation, phosphorylation and acetylation. Acetylation is probably the best understood of these modifications: hyperacetylation leads to an increase in the expression of particular genes, and hypoacetylation has the opposite effect. Many studies have identified several large, multisubunit enzyme complexes that are responsible for the targeted deacetylation of histones. The aim of this review is to give a comprehensive overview of the structure, function and tissue distribution of members of the classical histone deacetylase (HDAC) family, in order to gain insight into the regulation of gene expression through HDAC activity. SAGE (serial analysis of gene expression) data show that HDACs are generally expressed in almost all tissues investigated. Surprisingly, no major differences were observed between the expression pattern in normal and malignant tissues. However, significant variation in HDAC expression was observed within tissue types. HDAC inhibitors have been shown to induce specific changes in gene expression and to influence a variety of other processes, including growth arrest, differentiation, cytotoxicity and induction of apoptosis. This challenging field has generated many fascinating results which will ultimately lead to a better understanding of the mechanism of gene transcription as a whole.

2,822 citations


Journal ArticleDOI
04 Jan 2003-BMJ
TL;DR: If medical journals adopt the STARD checklist and flow diagram, the quality of reporting of studies of diagnostic accuracy should improve to the advantage of clinicians, researchers, reviewers, journals, and the public.
Abstract: Objective: To improve the accuracy and completeness of reporting of studies of diagnostic accuracy, to allow readers to assess the potential for bias in a study, and to evaluate a study9s generalisability. Methods: The Standards for Reporting of Diagnostic Accuracy (STARD) steering committee searched the literature to identify publications on the appropriate conduct and reporting of diagnostic studies and extracted potential items into an extensive list. Researchers, editors, and members of professional organisations shortened this list during a two day consensus meeting, with the goal of developing a checklist and a generic flow diagram for studies of diagnostic accuracy. Results: The search for published guidelines about diagnostic research yielded 33 previously published checklists, from which we extracted a list of 75 potential items. At the consensus meeting, participants shortened the list to a 25 item checklist, by using evidence, whenever available. A prototype of a flow diagram provides information about the method of patient recruitment, the order of test execution, and the numbers of patients undergoing the test under evaluation and the reference standard, or both. Conclusions: Evaluation of research depends on complete and accurate reporting. If medical journals adopt the STARD checklist and flow diagram, the quality of reporting of studies of diagnostic accuracy should improve to the advantage of clinicians, researchers, reviewers, journals, and the public. The Standards for Reporting of Diagnostic Accuracy (STARD) steering group aims to improve the accuracy and completeness of reporting of studies of diagnostic accuracy. The group describes and explains the development of a checklist and flow diagram for authors of reports

2,550 citations


Journal ArticleDOI
TL;DR: The diagnostic odds ratio is closely linked to existing indicators, it facilitates formal meta-analysis of studies on diagnostic test performance, and it is derived from logistic models, which allow for the inclusion of additional variables to correct for heterogeneity.

1,921 citations


Journal ArticleDOI
07 Mar 2003-Cell
TL;DR: It is found that activation of HIF-1alpha is essential for myeloid cell infiltration and activation in vivo through a mechanism independent of VEGF, and its direct regulation of survival and function in the inflammatory microenvironment is demonstrated.

1,773 citations


Journal ArticleDOI
TL;DR: Tissue microarray analysis demonstrated that EZH2 protein levels were strongly associated with breast cancer aggressiveness and provided compelling evidence for a functional link between dysregulated cellular memory, transcriptional repression, and neoplastic transformation.
Abstract: The Polycomb Group Protein EZH2 is a transcriptional repressor involved in controlling cellular memory and has been linked to aggressive prostate cancer. Here we investigate the functional role of EZH2 in cancer cell invasion and breast cancer progression. EZH2 transcript and protein were consistently elevated in invasive breast carcinoma compared with normal breast epithelia. Tissue microarray analysis, which included 917 samples from 280 patients, demonstrated that EZH2 protein levels were strongly associated with breast cancer aggressiveness. Overexpression of EZH2 in immortalized human mammary epithelial cell lines promotes anchorage-independent growth and cell invasion. EZH2-mediated cell invasion required an intact SET domain and histone deacetylase activity. This study provides compelling evidence for a functional link between dysregulated cellular memory, transcriptional repression, and neoplastic transformation.

1,555 citations


Journal ArticleDOI
TL;DR: It is becoming increasingly clear that the selective development of T-cell-polarizing DC subsets is related to the ligation of particular receptors that are involved in DC maturation, and several inconsistencies with this concept remain.
Abstract: Dendritic cells (DCs) are central in the orchestration of the various forms of immunity and tolerance. Their immunoregulatory role mainly relies on the ligation of specific receptors that initiate and modulate DC maturation resulting in the development of functionally different effector DC subsets that selectively promote T helper 1 (TH1)-, TH2- or regulatory T-cell responses. These DC-priming receptors include pattern recognition receptors (PRRs), which discriminate between (groups of) pathogens, as well as receptors that bind tissue factors that are produced either constitutively or in response to infection with pathogens, and characterize the type of tissue and the pathogen-specific response pattern of this tissue. Although it is becoming increasingly clear that the selective development of T-cell-polarizing DC subsets is related to the ligation of particular receptors that are involved in DC maturation, several inconsistencies with this concept remain.

1,441 citations


Journal ArticleDOI
TL;DR: If medical journals adopt the STARD checklist and flow diagram, the quality of reporting of studies of diagnostic accuracy should improve to the advantage of clinicians, researchers, reviewers, journals, and the public.
Abstract: OBJECTIVE: To improve the accuracy and completeness of reporting of studies of diagnostic accuracy, to allow readers to assess the potential for bias in the study and to evaluate its generalisability. METHODS: The Standards for Reporting of Diagnostic Accuracy (STARD) steering group searched the literature to identify publications on the appropriate conduct and reporting of diagnostic studies and extracted potential items into an extensive list. Researchers, editors, and members of professional organisations shortened this list during a two-day consensus meeting with the goal of developing a checklist and a generic flow diagram for studies of diagnostic accuracy. RESULTS: The search for published guidelines regarding diagnostic research yielded 33 previously published checklists, from which we extracted a list of 75 potential items. At the consensus meeting, participants shortened the list to a 25-item checklist, using evidence, whenever available. A prototypical flow diagram provides information about th...

1,322 citations


Journal ArticleDOI
TL;DR: This explanatory document aims to facilitate the use, understanding, and dissemination of the checklist and contains a clarification of the meaning, rationale, and optimal use of each item on the checklist.
Abstract: The quality of reporting of studies of diagnostic accuracy is less than optimal. Complete and accurate reporting is necessary to enable readers to assess the potential for bias in the study and to evaluate the generalisability of the results. A group of scientists and editors has developed the STARD (Standards for Reporting of Diagnostic Accuracy) statement to improve the reporting the quality of reporting of studies of diagnostic accuracy. The statement consists of a checklist of 25 items and flow diagram that authors can use to ensure that all relevant information is present. This explanatory document aims to facilitate the use, understanding and dissemination of the checklist. The document contains a clarification of the meaning, rationale and optimal use of each item on the checklist, as well as a short summary of the available evidence on bias and applicability. The STARD statement, checklist, flowchart and this explanation and elaboration document should be useful resources to improve reporting of diagnostic accuracy studies. Complete and informative reporting can only lead to better decisions in healthcare.

1,309 citations


Journal ArticleDOI
04 Apr 2003-Science
TL;DR: It is demonstrated that transient recruitment of the Eed-Ezh2 complex to the inactive X chromosome (Xi) occurs during initiation of X inactivation in both extraembryonic and embryonic cells and is accompanied by H3-K27 methylation.
Abstract: The Polycomb group (PcG) protein Eed is implicated in regulation of imprinted X-chromosome inactivation in extraembryonic cells but not of random X inactivation in embryonic cells. The Drosophila homolog of the Eed-Ezh2 PcG protein complex achieves gene silencing through methylation of histone H3 on lysine 27 (H3-K27), which suggests a role for H3-K27 methylation in imprinted X inactivation. Here we demonstrate that transient recruitment of the Eed-Ezh2 complex to the inactive X chromosome (Xi) occurs during initiation of X inactivation in both extraembryonic and embryonic cells and is accompanied by H3-K27 methylation. Recruitment of the complex and methylation on the Xi depend on Xist RNA but are independent of its silencing function. Together, our results suggest a role for Eed-Ezh2-mediated H3-K27 methylation during initiation of both imprinted and random X inactivation and demonstrate that H3-K27 methylation is not sufficient for silencing of the Xi.

Journal ArticleDOI
TL;DR: Results are consistent with the view that the N2 in go/no-go tasks reflects conflict arising from competition between the execution and the inhibition of a single response, and suggest previous conceptions of the no-go N2 as indexing response inhibition may be in need of revision.
Abstract: Neuroimaging and computational modeling studies have led to the suggestion that response conflict monitoring by the anterior cingulate cortex plays a key role in cognitive control. For example, response conflict is high when a response must be withheld (no-go) in contexts in which there is a prepotent tendency to make an overt (go) response. An event-related brain potential (ERP) component, the N2, is more pronounced on no-go than on go trials and was previously thought to reflect the need to inhibit the go response. However, the N2 may instead reflect the high degree of response conflict on no-go trials. If so, an N2 should also be apparent when subjects make a go response in conditions in which no-go events are more common. To test this hypothesis, we collected high-density ERP data from subjects performing a go/no-go task, in which the relative frequency of go versus no-go stimuli was varied. Consistent with our hypothesis, an N2 was apparent on both go and no-go trials and showed the properties expected of an ERP measure of conflict detection on correct trials: (1) It was enhanced for low-frequency stimuli, irrespective of whether these stimuli were associated with generating or suppressing a response, and (2) it was localized to the anterior cingulate cortex. This suggests that previous conceptions of the no-go N2 as indexing response inhibition may be in need of revision. Instead, the results are consistent with the view that the N2 in go/no-go tasks reflects conflict arising from competition between the execution and the inhibition of a single response.

Book
17 Nov 2003
TL;DR: In this article, two of the leading figures in argumentation theory present a view of argumentation as a means of resolving differences of opinion by testing the acceptability of the disputed positions and propose a practical code of behaviour for discussants who want to resolve their differences in a reasonable way.
Abstract: In this book two of the leading figures in argumentation theory present a view of argumentation as a means of resolving differences of opinion by testing the acceptability of the disputed positions. Their model of a 'critical discussion' serves as a theoretical tool for analysing, evaluating and producing argumentative discourse. They develop a method for the reconstruction of argumentative discourse that takes into account all aspects that are relevant to a critical assessment. They also propose a practical code of behaviour for discussants who want to resolve their differences in a reasonable way. This is a major contribution to the study of argumentation and will be of particular value to professionals and graduate students in speech communication, informal logic, rhetoric, critical thinking, linguistics, and philosophy.

Journal ArticleDOI
TL;DR: The initial drop in mortality and morbidity after the introduction of HAART has been sustained and potential long-term adverse effects associated with HAART have not altered its effectiveness in treating AIDS.

Journal ArticleDOI
TL;DR: In this article, a survey of empirical studies shows that women are worse off than men on some dimensions, better off on others, and similarly placed on yet others, while for some dimensions the evaluation is unclear.
Abstract: This paper investigates how Amartya Sen's capability approach can be applied to conceptualize and assess gender inequality in Western societies. I first argue against the endorsement of a definitive list of capabilities and instead defend a procedural approach to the selection of capabilities by proposing five criteria. This procedural account is then used to generate a list of capabilities for conceptualizing gender inequality in Western societies. A survey of empirical studies shows that women are worse off than men on some dimensions, better off on a few others, and similarly placed on yet others, while for some dimensions the evaluation is unclear. I then outline why, for group inequalities, inequalities in achieved functionings can be taken to reflect inequalities in capabilities, and how an overall evaluation could be arrived at by weighting the different capabilities.

Journal ArticleDOI
TL;DR: Three case studies demonstrate that the adaptive capability of the SCEM‐UA algorithm significantly reduces the number of model simulations needed to infer the posterior distribution of the parameters when compared with the traditional Metropolis‐Hastings samplers.
Abstract: Author(s): Vrugt, JA; Gupta, HV; Bouten, W; Sorooshian, S | Abstract: Markov Chain Monte Carlo (MCMC) methods have become increasingly popular for estimating the posterior probability distribution of parameters in hydrologic models. However, MCMC methods require the a priori definition of a proposal or sampling distribution, which determines the explorative capabilities and efficiency of the sampler and therefore the statistical properties of the Markov Chain and its rate of convergence. In this paper we present an MCMC sampler entitled the Shuffled Complex Evolution Metropolis algorithm (SCEM-UA), which is well suited to infer the posterior distribution of hydrologic model parameters. The SCEM-UA algorithm is a modified version of the original SCE-UA global optimization algorithm developed by Duan et al. [1992]. The SCEM-UA algorithm operates by merging the strengths of the Metropolis algorithm, controlled random search, competitive evolution, and complex shuffling in order to continuously update the proposal distribution and evolve the sampler to the posterior target distribution. Three case studies demonstrate that the adaptive capability of the SCEM-UA algorithm significantly reduces the number of model simulations needed to infer the posterior distribution of the parameters when compared with the traditional Metropolis-Hastings samplers.

Journal ArticleDOI
Ming Li, Xin Chen1, Xin Li, Bin Ma, Paul M. B. Vitányi1 
15 Sep 2003
TL;DR: Evidence of successful application in areas as diverse as genomics, virology, languages, literature, music, handwritten digits, astronomy, and combinations of objects from completely different domains, using statistical, dictionary, and block sorting compressors is reported.
Abstract: We present a new method for clustering based on compression. The method does not use subject-specific features or background knowledge, and works as follows: First, we determine a parameter-free, universal, similarity distance, the normalized compression distance or NCD, computed from the lengths of compressed data files (singly and in pairwise concatenation). Second, we apply a hierarchical clustering method. The NCD is not restricted to a specific application area, and works across application area boundaries. A theoretical precursor, the normalized information distance, co-developed by one of the authors, is provably optimal. However, the optimality comes at the price of using the noncomputable notion of Kolmogorov complexity. We propose axioms to capture the real-world setting, and show that the NCD approximates optimality. To extract a hierarchy of clusters from the distance matrix, we determine a dendrogram (ternary tree) by a new quartet method and a fast heuristic to implement it. The method is implemented and available as public software, and is robust under choice of different compressors. To substantiate our claims of universality and robustness, we report evidence of successful application in areas as diverse as genomics, virology, languages, literature, music, handwritten digits, astronomy, and combinations of objects from completely different domains, using statistical, dictionary, and block sorting compressors. In genomics, we presented new evidence for major questions in Mammalian evolution, based on whole-mitochondrial genomic analysis: the Eutherian orders and the Marsupionta hypothesis against the Theria hypothesis.

Journal ArticleDOI
14 Nov 2003-Science
TL;DR: CLIP reveals that Nova coordinately regulates a biologically coherent set of RNAs encoding multiple components of the inhibitory synapse, an observation that may relate to the cause of abnormal motor inhibition in POMA.
Abstract: Nova proteins are neuron-specific antigens targeted in paraneoplastic opsoclonus myoclonus ataxia (POMA), an autoimmune neurologic disease characterized by abnormal motor inhibition Nova proteins regulate neuronal pre-messenger RNA splicing by directly binding to RNA To identify Nova RNA targets, we developed a method to purify protein-RNA complexes from mouse brain with the use of ultraviolet cross-linking and immunoprecipitation (CLIP)Thirty-four transcripts were identified multiple times by Nova CLIPThree-quarters of these encode proteins that function at the neuronal synapse, and one-third are involved in neuronal inhibitionSplicing targets confirmed in Nova-/- mice include c-Jun N-terminal kinase 2, neogenin, and gephyrin; the latter encodes a protein that clusters inhibitory gamma-aminobutyric acid and glycine receptors, two previously identified Nova splicing targetsThus, CLIP reveals that Nova coordinately regulates a biologically coherent set of RNAs encoding multiple components of the inhibitory synapse, an observation that may relate to the cause of abnormal motor inhibition in POMA

Journal ArticleDOI
TL;DR: In this article, the authors demonstrate the usefulness of two theories for the development of effective health communication campaigns, namely integrative model of behavioral prediction and media priming theory, for the selection of beliefs to target in an intervention.
Abstract: This article demonstrates the usefulness of two theories for the development of effective health communication campaigns. The integrative model of behavioral prediction focuses on changing beliefs about consequences, normative issues, and efficacy with respect to a particular behavior. Media priming theory focuses on strengthening the association between a belief and its outcomes, such as attitude and intention toward performing the behavior. Both the integrative model of behavioral prediction and media priming theory provide guidance with respect to the selection of beliefs to target in an intervention. The article describes the theories, shows how they can be applied to the selection of target beliefs, and, for each theory, defines the criteria for belief selection. The two theories as well as their appropriate analytic strategies are complementary rather than conflicting.

Journal ArticleDOI
TL;DR: This work introduces and test different Bayesian network classifiers for classifying expressions from video, focusing on changes in distribution assumptions, and feature dependency structures, and proposes a new architecture of hidden Markov models (HMMs) for automatically segmenting and recognizing human facial expression from video sequences.

Journal ArticleDOI
TL;DR: In this paper, the authors present definitions of visual attention and awareness that clearly distinguish between the two, yet explain why attention and attention are so intricately related, and why there seems more overlap between mechanisms of memory and awareness than between those of attention.

Journal ArticleDOI
TL;DR: Recent findings that VEGFs secreted by epithelia, including the retinal pigment epithelium (RPE), are likely to mediate paracrine vascular survival signals for adjacent endothelia may explain the pathogenesis of subretinal neovascularisation in AMD.

Journal ArticleDOI
TL;DR: The authors revisited the existing scholarly debate on the possible impact of the principal's leadership on student achievement and conducted a quantitative meta-analysis to examine to what extent principals directly affect student outcomes, finding that small positive effects confirmed earlier research findings on the limitations of the direct effects approach to linking leadership with student achievement.
Abstract: This study revisits the existing scholarly debate on the possible impact of the principal's leadership on student achievement. Both `direct effect' and `indirect effect' models are discussed. A quantitative meta-analysis examines to what extent principals directly affect student outcomes. The small positive effects found in this meta-analysis confirm earlier research findings on the limitations of the direct effects approach to linking leadership with student achievement. Finally, lines of future research inquiry are discussed.

Journal ArticleDOI
TL;DR: It is shown that Socs3 deficiency results in prolonged activation of signal transducer and activator of transcription 1 (STAT1) and STAT3 after IL-6 stimulation but normal activation of STAT1 after stimulation with interferon-γ (IFN-γ).
Abstract: Members of the suppressor of cytokine signaling (SOCS) family are potentially key physiological negative regulators of interleukin-6 (IL-6) signaling. To examine whether SOCS3 is involved in regulating this signaling, we have used conditional gene targeting to generate mice lacking Socs3 in the liver or in macrophages. We show that Socs3 deficiency results in prolonged activation of signal transducer and activator of transcription 1 (STAT1) and STAT3 after IL-6 stimulation but normal activation of STAT1 after stimulation with interferon-gamma (IFN-gamma). Conversely, IL-6-induced STAT activation is normal in Socs1-deficient cells, whereas STAT1 activation induced by IFN-gamma is prolonged. Microarray analysis shows that the pattern of gene expression induced by IL-6 in Socs3-deficient livers mimics that induced by IFN-gamma. Our data indicate that SOCS3 and SOCS1 have reciprocal functions in IL-6 and IFN-gamma regulation and imply that SOCS3 has a role in preventing IFN-gamma-like responses in cells stimulated by IL-6.

Journal ArticleDOI
TL;DR: This paper examines how these processes are influenced by strong and/or weak ties and whether the degree of innovation (incremental versus radical) acts as a contingency factor in the way network ties support entrepreneurial processes.
Abstract: The value of networks as an integral part of the explanation of entrepreneurial success is widely acknowledged. However, the network perspective does not specify the role of networks in the emergence and early growth of a venture. We have distinguished three entrepreneurial processes in new venture development, i.e. discovery of opportunities, securing resources, and obtaining legitimacy, which are of importance for survival and performance. This paper examines how these processes are influenced by strong and/or weak ties and whether the degree of innovation (incremental versus radical) acts as a contingency factor in the way network ties support entrepreneurial processes. In this explorative study three cases on high technology firms in The Netherlands provide empirical material enabling us to develop a number of propositions on the network effect, in particular the mix of strong and weak ties, on the three entrepreneurial processes.

Journal ArticleDOI
TL;DR: Once-daily, subcutaneous administration of fondaparinux without monitoring is at least as effective and is as safe as adjusted-dose, intravenous administration of unfractionated heparin in the initial treatment of hemodynamically stable patients with pulmonary embolism.
Abstract: background The standard initial treatment of hemodynamically stable patients with pulmonary embolism is intravenous unfractionated heparin, requiring laboratory monitoring and hospitalization. methods We conducted a randomized, open-label trial involving 2213 patients with acute symptomatic pulmonary embolism to compare the efficacy and safety of the synthetic antithrombotic agent fondaparinux with those of unfractionated heparin and to document noninferiority in terms of efficacy. Patients received either fondaparinux (5.0, 7.5, or 10.0 mg in patients weighing less than 50, 50 to 100, or more than 100 kg, respectively) subcutaneously once daily or a continuous intravenous infusion of unfractionated heparin (ratio of the activated partial-thromboplastin time to a control value, 1.5 to 2.5), both given for at least five days and until the use of vitamin K antagonists resulted in an international normalized ratio above 2.0. The primary efficacy outcome was the three-month incidence of the composite end point of symptomatic, recurrent pulmonary embolism (nonfatal or fatal) and new or recurrent deep-vein thrombosis. results Forty-two of the 1103 patients randomly assigned to receive fondaparinux (3.8 percent) had recurrent thromboembolic events, as compared with 56 of the 1110 patients randomly assigned to receive unfractionated heparin (5.0 percent), for an absolute difference of i1.2 percent in favor of fondaparinux (95 percent confidence interval, i3.0 to 0.5). Major bleeding occurred in 1.3 percent of the patients treated with fondaparinux and 1.1 percent of those treated with unfractionated heparin. Mortality rates at three months were similar in the two groups. Of the patients in the fondaparinux group, 14.5 percent received the drug in part on an outpatient basis. conclusions Once-daily, subcutaneous administration of fondaparinux without monitoring is at least as effective and is as safe as adjusted-dose, intravenous administration of unfractionated heparin in the initial treatment of hemodynamically stable patients with pulmonary embolism.

Journal ArticleDOI
14 Mar 2003-Science
TL;DR: Expect many new industrial applications of biocatalysis to be realized, from single-step enzymatic conversions to customized multistep microbial synthesis by means of metabolic pathway engineering.
Abstract: Biocatalysis has emerged as an important tool in the industrial synthesis of bulk chemicals, pharmaceutical and agrochemical intermediates, active pharmaceuticals, and food ingredients. However, the number and diversity of the applications are modest, perhaps in part because of perceived or real limitations of biocatalysts, such as limited enzyme availability, substrate scope, and operational stability. Recent scientific breakthroughs in genomics, directed enzyme evolution, and the exploitation of biodiversity should help to overcome these limitations. As a result, we expect many new industrial applications of biocatalysis to be realized, from single-step enzymatic conversions to customized multistep microbial synthesis by means of metabolic pathway engineering.

Journal ArticleDOI
TL;DR: In this article, a two-layer model is proposed for subjective well-being by taking into account different aspects of life, called domains, such as health, financial situation, job, leisure, housing, and environment.
Abstract: This paper contributes to the literature on subjective well-being (SWB) by taking into account different aspects of life, called domains, such as health, financial situation, job, leisure, housing, and environment We postulate a two-layer model where individual total SWB depends on the different subjective domain satisfactions A distinction is made between long-term and short-term effects The individual domain satisfactions depend on objectively measurable variables, such as income The model is estimated using a large German panel data set

Posted Content
TL;DR: The normalized compression distance (NCD) as discussed by the authors is a similarity metric that approximates universality based on the normalized information distance (NIC) metric, which was proposed by the authors of this paper.
Abstract: We present a new method for clustering based on compression. The method doesn't use subject-specific features or background knowledge, and works as follows: First, we determine a universal similarity distance, the normalized compression distance or NCD, computed from the lengths of compressed data files (singly and in pairwise concatenation). Second, we apply a hierarchical clustering method. The NCD is universal in that it is not restricted to a specific application area, and works across application area boundaries. A theoretical precursor, the normalized information distance, co-developed by one of the authors, is provably optimal but uses the non-computable notion of Kolmogorov complexity. We propose precise notions of similarity metric, normal compressor, and show that the NCD based on a normal compressor is a similarity metric that approximates universality. To extract a hierarchy of clusters from the distance matrix, we determine a dendrogram (binary tree) by a new quartet method and a fast heuristic to implement it. The method is implemented and available as public software, and is robust under choice of different compressors. To substantiate our claims of universality and robustness, we report evidence of successful application in areas as diverse as genomics, virology, languages, literature, music, handwritten digits, astronomy, and combinations of objects from completely different domains, using statistical, dictionary, and block sorting compressors. In genomics we presented new evidence for major questions in Mammalian evolution, based on whole-mitochondrial genomic analysis: the Eutherian orders and the Marsupionta hypothesis against the Theria hypothesis.

Journal ArticleDOI
TL;DR: A comprehensive review of methods to measure soil water content with ground penetrating radar (GPR) is presented in this article, where the authors distinguish four methods: reflected wave velocity, ground wave velocity and surface reflection coefficient.
Abstract: We present a comprehensive review of methods to measure soil water content with ground penetrating radar (GPR) We distinguish four methodologies: soil water content determined from reflected wave velocity, soil water content determined from ground wave velocity, soil water content determined from transmitted wave velocity between boreholes, and soil water content determined from the surface reflection coefficient For each of these four methodologies, we discuss the basic principles, illustrate the quality of the data with field examples, discuss the possibilities and limitations, and identify areas where future research is required We hope that this review will further stimulate the community to consider ground penetrating radar as one of the possible tools to measure soil water content