Roskilde University

Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for complex carbohydrate metabolism. With an increasing number of plant and plant-associated microbial genomes and metagenomes being sequenced, there is an urgent need of automatic tools for genomic data mining of CAZymes. We developed the dbCAN web server in 2012 to provide a public service for automated CAZyme annotation for newly sequenced genomes. Here, dbCAN2 (http://cys.bios.niu.edu/dbCAN2) is presented as an updated meta server, which integrates three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against the CAZy pre-annotated CAZyme sequence database and (iii) Hotpep search against the conserved CAZyme short peptide database. Combining the three outputs and removing CAZymes found by only one tool can significantly improve the CAZome annotation accuracy. In addition, dbCAN2 now also accepts nucleotide sequence submission, and offers the service to predict physically linked CAZyme gene clusters (CGCs), which will be a very useful online tool for identifying putative polysaccharide utilization loci (PULs) in microbial genomes or metagenomes.

Click to increase image sizeClick to decrease image size Notes 1. H. van Lente, Promising technology. The dynamics of expectations in technological developments, PhD Thesis, University of Twente, Enschede, 1993. 2. M. Michael, Futures of the present: from performativity to prehension, in: N. Brown, B. Rappert & A. Webster (Eds) Contested Futures: A Sociology of Prospective Techno-Science (Aldershot, UK, Ashgate, 2000). 3. M. Sturken, D. Thomas & S. J. Ball-Rokeach (Eds), Technological Visions. The Hopes and Fears that Shape New Technologies (Philadelphia, PA, Temple University Press, 2004). 4. N. Brown, B. Rappert & A. Webster (Eds), Contested Futures: A Sociology of Prospective Techno-Science (Aldershot, UK, Ashgate, 2000). 5. W. Bijker & J. Law (Eds), Shaping Technology/Building Society (Cambridge, MA, MIT Press, 1992); A. Pickering (Ed.), Science as Practice and Culture (Chicago, IL, University of Chicago Press, 1992); B. 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Thompson, The biotech mode of reproduction, Paper prepared for the School of American Research Advanced Seminar 'Animation and Cessation: Anthropological Perspectives on Changing Definitions of Life and Death in the Context of Biomedicine', Santa Fe, New Mexico, 2000. 47. P. Weingart, A. Engels & P. Pansegrau, Risks of communication: discourses on climate change in science, politics, and mass medi, Public Understanding of Science, 9(3), 2000, pp. 261–283. 48. H. Nowotny, P. Scott & M. Gibbons, Re-thinking Science—Knowledge and the Public in an Age of Uncertainty (Cambridge, UK, Polity Press, 2001), p. 232. 49. Brown et al., op. cit., Ref. 4.

"Participatory Design is about the direct involvement of people in the co-design of the technologies they use. Its central concern is how collaborative design processes can be driven by the participation of the people affected by the technology designed. Embracing a diverse collection of principles and practices aimed at making technologies, tools, environments, businesses, and social institutions more responsive to human needs, the International Handbook of Participatory Design is a state-of-the-art reference handbook for the subject. The Handbook brings together a multidisciplinary and international group of highly recognized and experienced experts to present an authoritative overview of the field and its history and discuss contributions and challenges of the pivotal issues in Participatory Design, including heritage, ethics, ethnography, methods, tools and techniques and community involvement. The book also highlights three large-scale case studies which show how Participatory Design has been used to bring about outstanding changes in different organisations. The book shows why Participatory Design is an important, highly relevant and rewarding area for research and practice. It will be an invaluable resource for students, researchers, scholars and professionals in Participatory Design"--

The striking similarity of ac conduction in quite different disordered solids is discussed in terms of experimental results, modeling, and computer simulations. After giving an overview of experiment, a macroscopic and a microscopic model are reviewed. For both models the normalized ac conductivity as a function of a suitably scaled frequency becomes independent of details of the disorder in the extreme disorder limit, i.e., when the local randomly varying mobilities cover many orders of magnitude. The two universal ac conductivities are similar, but not identical; both are examples of unusual non-power-law universalities. It is argued that ac universality reflects an underlying percolation determining dc as well as ac conductivity in the extreme disorder limit. Three analytical approximations to the universal ac conductivities are presented and compared to computer simulations. Finally, model predictions are briefly compared to experiment.

The objective of this Personal View is to compare transmissibility, hospitalisation, and mortality rates for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with those of other epidemic coronaviruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), and pandemic influenza viruses. The basic reproductive rate (R 0 ) for SARS-CoV-2 is estimated to be 25 (range 18-36) compared with 20-30 for SARS-CoV and the 1918 influenza pandemic, 09 for MERS-CoV, and 15 for the 2009 influenza pandemic. SARS-CoV-2 causes mild or asymptomatic disease in most cases; however, severe to critical illness occurs in a small proportion of infected individuals, with the highest rate seen in people older than 70 years. The measured case fatality rate varies between countries, probably because of differences in testing strategies. Population-based mortality estimates vary widely across Europe, ranging from zero to high. Numbers from the first affected region in Italy, Lombardy, show an all age mortality rate of 154 per 100 000 population. Differences are most likely due to varying demographic structures, among other factors. However, this new virus has a focal dissemination;

Basic characteristics of the liquid-glass transition are reviewed, emphasizing its universality and briefly summarizing the most popular phenomenological models. Discussion is focused on a number of alternative models which one way or the other connect the fast and slow degrees of freedom of viscous liquids. It is shown that all these ``elastic'' models are equivalent in the simplest approximation.

In the past decade, use of the circular economy (CE) concept by scholars and practitioners has grown steadily. In a 2017 article, Kirchherr et al. found that the CE concept is interpreted and implemented in a variety of ways. While multiple interpretations of CE can enrich scholarly perspectives, differentiation and fragmentation can also impede consolidation of the concept. Some scholarship has discussed these trends in context-specific cases, but no large-scale, systematic study has analysed whether such consolidation has taken place across the field. This article fills this gap by analysing 221 recent CE definitions, making several notable findings. First, the concept has seen both consolidation and differentiation in the past five years. Second, definitional trends are emerging that potentially have more meaning for scholarship than for practice. Third, scholars increasingly recommend a fundamental systemic shift to enable CE, particularly within supply chains. Fourth, sustainable development is frequently considered the principal aim of CE, but questions linger about whether CE can mutually support environmental sustainability and economic development. Finally, recent studies argue that CE transition relies on a broad alliance of stakeholders, including producers, consumers, policymakers, and scholars. This study contributes an updated systematic analysis of CE definitions and conceptualizations that serves as an empirical snapshot of current scholarly thinking. It thereby provides a basis for further research on whether conceptual consolidation is needed and how it can be facilitated for practical purposes.

Aims to renew and refocus the political and scholarly debate on the use of governance networks in public policy making by raising and answering a series of questions about the dynamics of governance networks, the conditions for governance network success and failure, the forms and functions of metagovernance, and more

Summary This paper presents CO 2 flux data from 18 forest ecosystems, studied in the European Union funded EUROFLUX project. Overall, mean annual gross primary productivity (GPP, the total amount of carbon (C) fixed during photosynthesis) of these forests was 1380 ± 330 gC m −2 y −1 (mean ±SD). On average, 80% of GPP was respired by autotrophs and heterotrophs and released back into the atmosphere (total ecosystem respiration, TER = 1100 ± 260 gC m −2 y −1 ). Mean annual soil respiration (SR) was 760 ± 340 gC m −2 y −1 (55% of GPP and 69% of TER). Among the investigated forests, large differences were observed in annual SR and TER that were not correlated with mean annual temperature. However, a significant correlation was observed between annual SR and TER and GPP among the relatively undisturbed forests. On the assumption that (i) root respiration is constrained by the allocation of photosynthates to the roots, which is coupled to productivity, and that (ii) the largest fraction of heterotrophic soil respiration originates from decomposition of young organic matter (leaves, fine roots), whose availability also depends on primary productivity, it is hypothesized that differences in SR among forests are likely to depend more on productivity than on temperature. At sites where soil disturbance has occurred (e.g. ploughing, drainage), soil espiration was a larger component of the ecosystem C budget and deviated from the relationship between annual SR (and TER) and GPP observed among the less‐disturbed forests. At one particular forest, carbon losses from the soil were so large, that in some years the site became a net source of carbon to the atmosphere. Excluding the disturbed sites from the present analysis reduced mean SR to 660 ± 290 gC m −2 y −1 , representing 49% of GPP and 63% of TER in the relatively undisturbed forest ecosystems.

A brief review of the history of ac ionic and electronic conduction in disordered solids is given, followed by a detailed discussion of the simplest possible realistic model: the random free-energy barrier model. This model assumes conduction takes place by hopping, where the hopping charge carriers are subject to spatially randomly varying energy barriers. The model is solved in the continuous time random walk and in the effective medium approximation, and it is shown that the two solutions are almost indistinguishable. In the random free-energy barrier model, the frequency-dependent conductivity is completely determined by the dc conductivity and the dielectric loss strength. The model correctly predicts all qualitative features of ac conduction in disordered solids, and a comparison to experiment on a large number of solids shows that the model is also quantitatively satisfactory.

In response to the growing discrepancy between the steadily rising steering ambitions and the increasing fragmentation of social and political life, governance networks are mushrooming. Governance through the formation of networks composed of public and private actors might help solve wicked problems and enhance democratic participation in public policy‐making, but it may also create conflicts and deadlocks and make public governance less transparent and accountable. In order to ensure that governance networks contribute to an effective and democratic governing of society, careful metagovernance by politicians, public managers and other relevant actors is necessary. In this paper, we discuss how to assess the effective performance and democratic quality of governance networks. We also describe how different metagovernance tools can be used in the pursuit of effective and democratic network governance. Finally, we argue that public metagovernors must develop their strategic and collaborative competences in order to become able to metagovern governance networks.

Evaluation of design artefacts and design theories is a key activity in Design Science Research (DSR), as it provides feedback for further development and (if done correctly) assures the rigour of the research. However, the extant DSR literature provides insufficient guidance on evaluation to enable Design Science Researchers to effectively design and incorporate evaluation activities into a DSR project that can achieve DSR goals and objectives. To address this research gap, this research paper develops, explicates, and provides evidence for the utility of a Framework for Evaluation in Design Science (FEDS) together with a process to guide design science researchers in developing a strategy for evaluating the artefacts they develop within a DSR project. A FEDS strategy considers why, when, how, and what to evaluate. FEDS includes a two-dimensional characterisation of DSR evaluation episodes (particular evaluations), with one dimension being the functional purpose of the evaluation (formative or summative) and the other dimension being the paradigm of the evaluation (artificial or naturalistic). The FEDS evaluation design process is comprised of four steps: (1) explicate the goals of the evaluation, (2) choose the evaluation strategy or strategies, (3) determine the properties to evaluate, and (4) design the individual evaluation episode(s). The paper illustrates the framework with two examples and provides evidence of its utility via a naturalistic, summative evaluation through its use on an actual DSR project.

Public authority does not always fall within the exclusive realm of government institutions; in some contexts, institutional competition is intense and a range of ostensibly a-political situations become actively politicized. Africa has no shortage of institutions which attempt to exercise public authority: not only are multiple layers and branches of government institutions present and active to various degrees, but so-called traditional institutions bolstered by government recognition also vie for public authority, and new emerging institutions and organizations also enter the field. The practices of these institutions make concepts such as public authority, legitimacy, belonging, citizenship and territory highly relevant. This article proposes an analytical strategy for the understanding of public authority in such contexts. It draws on research from anthropologists, geographers, political scientists and social scientists working on Africa, in an attempt to explore a set of questions related to a variety of political practices and their institutional ramifications.

The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking of software for metagenome assembly, binning and taxonomic profiling. Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.

The term 'bioturbation' is frequently used to describe how living organisms affect the substratum in which they live. A closer look at the aquatic science literature reveals, however, an inconsistent usage of the term with increasing perplexity in recent years. Faunal disturbance has often been referred to as particle reworking, while water movement (if considered) is re ferred to as bioirrigation in many cases. For consistency, we therefore propose that, for contemporary aquatic scientific disciplines, faunal bioturbation in aquatic environments includes all transport processes carried out by animals that directly or indirectly affect sediment matrices. These processes include both particle reworking and burrow ventilation. With this definition, bioturbation acts as an 'umbrella' term that covers all transport processes and their physical effects on the substratum. Particle reworking occurs through burrow construction and maintenance, as well as ingestion and defecation, and causes biomixing of the substratum. Organic matter and microorganisms are thus displaced vertically and laterally within the sediment matrix. Particle reworking animals can be categorized as biodiffusors, upward conveyors, downward conveyors and regenerators depending on their behaviour, life style and feeding type. Burrow ventilation occurs when animals flush their open-or blind-ended burrows with overlying water for respiratory and feeding purposes, and it causes advective or diffusive bioirrigation ex change of solutes between the sediment pore water and the overlying water body. Many bioturbating species perform reworking and ventilation simultaneously. We also propose that the effects of bioturbation on other organisms and associated processes (e.g. microbial driven biogeochemical transformations) are considered within the conceptual framework of ecosystem engineering.

Encouraged by the proliferation of governance networks and the growing demands for public innovation, this article aims to advance “collaborative innovation” as a cross-disciplinary approach to studying and enhancing public innovation. The article explains the special conditions and the growing demand for public innovation, and demonstrates how it can be enhanced through multiactor collaboration. The case for collaborative innovation is supported by insights from three different social science theories. The theoretical discussion leads to the formulation of an analytical model that can be used in future studies of collaborative innovation in the public sector.

Size selectivity spectra of 28 planktonic predators from 18 studies in the literature are compared. The linear size ratio between predators and their optimal prey is 1 : 1 for a dinoflagellate, 3 : 1 for other flagellates, 8 : 1 for ciliates, 18 : 1 for rotifers and copepods, and ∼50: 1 for cladocerans and meroplankton larvae. These size ratios seem consistent within groups, and their validity is supported by quantitative information from the literature. However, a difference between filter feeders and raptorial‐interception feeders, preferring relatively smaller and larger prey respectively, is evident across the taxonomic groups. A classification of planktonic predators into functional groups is therefore crucial for the construction of models of pelagic food webs.

The article discusses two issues. The first is whether service firms innovate at all; the second is how they organise the innovation activities. The basis for the analysis is a series of case studies in Danish service firms. The first issue is discussed theoretically. Of the several paradigms within traditional innovation theory, the strategic innovation paradigm is the most adequate to explain service innovations. Organisational learning must be separated from innovation whereby the latter means a jump in turnover and profit while the first means a lower and continuous growth. The emphirical analysis demonstrates that the service firms innovate. The second issue is analysed empirically. Different ways of organising the innovation activities are set placed a taxonomy. It is concluded that the service firms rarely have R&D departments and innovation generally is an unsystematic search-and-learn process.

Governance has become one of the most commonly used concepts in contemporary political science. It is, however, often used to mean a variety of different things. This book helps to clarify this conceptual muddle by concentrating on one variety of governance – interactive governance. We argue that although the State may remain important for many aspects of governing, interactions between State and society represent an important, and perhaps increasingly important, dimension of governance. These interactions may be with social actors such as networks, with market actors, or with other governments, but all these forms represent means of governing involving mixtures of State action with the actions of other entities. This book explores thoroughly this meaning of governance, and links it to broader questions of governance. In the process of explicating this dimension of governance, we also explore some of the more fundamental question about governance theory. For example, although we talk about governance a great deal political science has done relatively little about how to measure this concept. Likewise, the term multilevel governance has become widely used but we also need to understand that idea more fully and how it functions in the context of interactive forms of governance. We also link governance to some very fundamental questions in political science and the social sciences more broadly. How is power exercised in interactive governance? How democratic is interactive governance, and is democratic governance always advanced through transparency?

In order to study the size dependency of grazing and growth rates in zooplankton, data were collected from laboratory studies in the literature, covering both limnic and marine organisms. Data were obtained from about 60 species of nano‐, micro‐, and mesozooplankton, representing flagellates, ciliates, rotifers, meroplankton larvae, copepods, and cladocerans. Estimates of maximum ingestion and clearance were extracted from functional responses (ingestion rates as a function of food density) established from laboratory experiments. Maximum specific rates were expressed as a function of predator body volume. Maximum specific clearance and ingestion rates decreased with predator volume within each group of zooplankton, with a common exponent (scaling factor) of −0.23 (SE = ±0.12) in accordance with previous findings. However, significant differences were found between groups. In particular, among the protists, ciliates display maximum ingestion, growth, and clearance rates that exceed those of dinoflagellates by a factor of 2–4. Among the metazooplankton, calanoid copepods have maximum clearance rates that exceed those of filter‐feeding cladocerans and meroplankton larvae by a factor of 10. Because of these differences between the groups, the entire set of observations could not be fitted by an overall regression.