TY - JOUR A1 - Nickerson, David A1 - Atalag, Koray A1 - de Bono, Bernard A1 - Geiger, Joerg A1 - Goble, Carole A1 - Hollmann, Susanne A1 - Lonien, Joachim A1 - Mueller, Wolfgang A1 - Regierer, Babette A1 - Stanford, Natalie J. A1 - Golebiewski, Martin A1 - Hunter, Peter T1 - The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable JF - Interface focus N2 - Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome. KW - Human Physiome KW - standards KW - repositories KW - service infrastructure KW - reproducible science KW - managing big data Y1 - 2016 U6 - https://doi.org/10.1098/rsfs.2015.0103 SN - 2042-8898 SN - 2042-8901 VL - 6 SP - 57 EP - 61 PB - Royal Society CY - London ER - TY - JOUR A1 - D'Aprile, Iwan-Michelangelo T1 - Costuming Genders: Acting as an Invention of the Enlightenment JF - German history : the journal of the German History Societ Y1 - 2016 U6 - https://doi.org/10.1093/gerhis/ghv109 SN - 0266-3554 SN - 1477-089X VL - 34 SP - 138 EP - 139 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Sperfeld, Erik A1 - Raubenheimer, David A1 - Wacker, Alexander T1 - Bridging factorial and gradient concepts of resource co-limitation: towards a general framework applied to consumers JF - Ecology letters N2 - Organism growth can be limited either by a single resource or by multiple resources simultaneously (co-limitation). Efforts to characterise co-limitation have generated two influential approaches. One approach uses limitation scenarios of factorial growth assays to distinguish specific types of co-limitation; the other uses growth responses spanned over a continuous, multi-dimensional resource space to characterise different types of response surfaces. Both approaches have been useful in investigating particular aspects of co-limitation, but a synthesis is needed to stimulate development of this recent research area. We address this gap by integrating the two approaches, thereby presenting a more general framework of co-limitation. We found that various factorial (co-)limitation scenarios can emerge in different response surface types based on continuous availabilities of essential or substitutable resources. We tested our conceptual co-limitation framework on data sets of published and unpublished studies examining the limitation of two herbivorous consumers in a two-dimensional resource space. The experimental data corroborate the predictions, suggesting a general applicability of our co-limitation framework to generalist consumers and potentially also to other organisms. The presented framework might give insight into mechanisms that underlie co-limitation responses and thus can be a seminal starting point for evaluating co-limitation patterns in experiments and nature. KW - Consumer KW - essential nutrient KW - factorial design KW - food quality KW - growth rate KW - multi-nutrient limitation KW - nutritional ecology KW - performance landscape KW - substitutable resource KW - synergistic effect Y1 - 2016 U6 - https://doi.org/10.1111/ele.12554 SN - 1461-023X SN - 1461-0248 VL - 19 SP - 201 EP - 215 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - de Vinuesa, Amaya Garcia A1 - Abdelilah-Seyfried, Salim A1 - Knaus, Petra A1 - Zwijsen, An A1 - Bailly, Sabine T1 - BMP signaling in vascular biology and dysfunction JF - New journal of physics : the open-access journal for physics N2 - The vascular system is critical for developmental growth, tissue homeostasis and repair but also for tumor development. Bone morphogenetic protein (BMP) signaling has recently emerged as a fundamental pathway of the endothelium by regulating cardiovascular and lymphatic development and by being causative for several vascular dysfunctions. Two vascular disorders have been directly linked to impaired BMP signaling: pulmonary arterial hypertension and hereditary hemorrhagic telangiectasia. Endothelial BMP signaling critically depends on the cellular context, which includes among others vascular heterogeneity, exposure to flow, and the intertwining with other signaling cascades (Notch, WNT, Hippo and hypoxia). The purpose of this review is to highlight the most recent findings illustrating the clear need for reconsidering the role of BMPs in vascular biology. (C) 2015 Elsevier Ltd. All rights reserved. KW - Bone morphogenetic proteins (BMP) KW - Signaling KW - Vasculature KW - Development KW - Disease Y1 - 2016 U6 - https://doi.org/10.1016/j.cytogfr.2015.12.005 SN - 1359-6101 SN - 1879-0305 VL - 27 SP - 65 EP - 79 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Haack, Timm A1 - Abdelilah-Seyfried, Salim T1 - The force within: endocardial development, mechanotransduction and signalling during cardiac morphogenesis JF - Development : Company of Biologists N2 - Endocardial cells are cardiac endothelial cells that line the interior of the heart tube. Historically, their contribution to cardiac development has mainly been considered from a morphological perspective. However, recent studies have begun to define novel instructive roles of the endocardium, as a sensor and signal transducer of biophysical forces induced by blood flow, and as an angiocrine signalling centre that is involved in myocardial cellular morphogenesis, regeneration and reprogramming. In this Review, we discuss how the endocardium develops, how endocardial-myocardial interactions influence the developing embryonic heart, and how the dysregulation of blood flowresponsive endocardial signalling can result in pathophysiological changes. KW - Endocardium KW - Cardiac development KW - Hemodynamics KW - Bmp KW - Kruppel-like factor 2 KW - Vegf KW - Mechanotransduction KW - Zebrafish KW - Mouse Y1 - 2016 U6 - https://doi.org/10.1242/dev.131425 SN - 0950-1991 SN - 1477-9129 VL - 143 SP - 373 EP - 386 PB - Company of Biologists Limited CY - Cambridge ER - TY - JOUR A1 - Yan, Wenhao A1 - Chen, Dijun A1 - Kaufmann, Kerstin T1 - Molecular mechanisms of floral organ specification by MADS domain proteins JF - Current opinion in plant biology N2 - Flower development is a model system to understand organ specification in plants. The identities of different types of floral organs are specified by homeotic MADS transcription factors that interact in a combinatorial fashion. Systematic identification of DNA-binding sites and target genes of these key regulators show that they have shared and unique sets of target genes. DNA binding by MADS proteins is not based on ‘simple’ recognition of a specific DNA sequence, but depends on DNA structure and combinatorial interactions. Homeotic MADS proteins regulate gene expression via alternative mechanisms, one of which may be to modulate chromatin structure and accessibility in their target gene promoters. Y1 - 2016 U6 - https://doi.org/10.1016/j.pbi.2015.12.004 SN - 1369-5266 SN - 1879-0356 VL - 29 SP - 154 EP - 162 PB - Elsevier CY - London ER - TY - JOUR A1 - Gangloff, Niklas A1 - Ulbricht, Juliane A1 - Lorson, Thomas A1 - Schlaad, Helmut A1 - Luxenhofer, Robert T1 - Peptoids and Polypeptoids at the Frontier of Supra- and Macromolecular Engineering JF - Chemical reviews Y1 - 2016 U6 - https://doi.org/10.1021/acs.chemrev.5b00201 SN - 0009-2665 SN - 1520-6890 VL - 116 SP - 1753 EP - 1802 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Terao, Mineko A1 - Romao, Maria Joao A1 - Leimkühler, Silke A1 - Bolis, Marco A1 - Fratelli, Maddalena A1 - Coelho, Catarina A1 - Santos-Silva, Teresa A1 - Garattini, Enrico T1 - Structure and function of mammalian aldehyde oxidases JF - Archives of toxicology : official journal of EUROTOX N2 - Mammalian aldehyde oxidases (AOXs; EC1.2.3.1) are a group of conserved proteins belonging to the family of molybdo-flavoenzymes along with the structurally related xanthine dehydrogenase enzyme. AOXs are characterized by broad substrate specificity, oxidizing not only aromatic and aliphatic aldehydes into the corresponding carboxylic acids, but also hydroxylating a series of heteroaromatic rings. The number of AOX isoenzymes expressed in different vertebrate species is variable. The two extremes are represented by humans, which express a single enzyme (AOX1) in many organs and mice or rats which are characterized by tissue-specific expression of four isoforms (AOX1, AOX2, AOX3, and AOX4). In vertebrates each AOX isoenzyme is the product of a distinct gene consisting of 35 highly conserved exons. The extant species-specific complement of AOX isoenzymes is the result of a complex evolutionary process consisting of a first phase characterized by a series of asynchronous gene duplications and a second phase where the pseudogenization and gene deletion events prevail. In the last few years remarkable advances in the elucidation of the structural characteristics and the catalytic mechanisms of mammalian AOXs have been made thanks to the successful crystallization of human AOX1 and mouse AOX3. Much less is known about the physiological function and physiological substrates of human AOX1 and other mammalian AOX isoenzymes, although the importance of these proteins in xenobiotic metabolism is fairly well established and their relevance in drug development is increasing. This review article provides an overview and a discussion of the current knowledge on mammalian AOX. KW - Aldehyde oxidase KW - Molybdo-flavoenzymes KW - Xanthine oxidoreductase KW - Drug metabolism Y1 - 2016 U6 - https://doi.org/10.1007/s00204-016-1683-1 SN - 0340-5761 SN - 1432-0738 VL - 90 SP - 753 EP - 780 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Schmidt, Katja A1 - Sachse, Rene A1 - Walz, Ariane T1 - Current role of social benefits in ecosystem service assessments JF - Landscape and urban planning : an international journal of landscape ecology, planning and design N2 - Ecosystem services have a significant impact on human wellbeing. While ecosystem services are frequently represented by monetary values, social values and underlying social benefits remain underexplored. The purpose of this study is to assess whether and how social benefits have been explicitly addressed within socio-economic and socio-cultural ecosystem services research, ultimately allowing a better understanding between ecosystem services and human well-being. In this paper, we reviewed 115 international primary valuation studies and tested four hypotheses associated to the identification of social benefits of ecosystem services using logistic regressions. Tested hypotheses were that (1) social benefits are mostly derived in studies that assess cultural ecosystem services as opposed to other ecosystem service types, (2) there is a pattern of social benefits and certain cultural ecosystem services assessed simultaneously, (3) monetary valuation techniques go beyond expressing monetary values and convey social benefits, and (4) directly addressing stakeholdeŕs views the consideration of social benefits in ecosystem service assessments. Our analysis revealed that (1) a variety of social benefits are valued in studies that assess either of the four ecosystem service types, (2) certain social benefits are likely to co-occur in combination with certain cultural ecosystem services, (3) of the studies that employed monetary valuation techniques, simulated market approaches overlapped most frequently with the assessment of social benefits and (4) studies that directly incorporate stakeholder's views were more likely to also assess social benefits. KW - Literature review KW - Non-monetary valuation KW - Monetary valuation KW - Social valuation Y1 - 2016 U6 - https://doi.org/10.1016/j.landurbplan.2016.01.005 SN - 0169-2046 SN - 1872-6062 VL - 149 SP - 49 EP - 64 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Erdossy, Julia A1 - Horvath, Viola A1 - Yarman, Aysu A1 - Scheller, Frieder W. A1 - Gyurcsanyi, Robert E. T1 - Electrosynthesized molecularly imprinted polymers for protein recognition JF - Trends in Analytical Chemistry N2 - Molecularly imprinted polymers (MIPs) for the recognition of proteins are expected to possess high affinity through the establishment of multiple interactions between the polymer matrix and the large number of functional groups of the target. However, while highly affine recognition sites need building blocks rich in complementary functionalities to their target, such units are likely to generate high levels of nonspecific binding. This paradox, that nature solved by evolution for biological receptors, needs to be addressed by the implementation of new concepts in molecular imprinting of proteins. Additionally, the structural variability, large size and incompatibility with a range of monomers made the development of protein MIPs to take a slow start. While the majority of MIP preparation methods are variants of chemical polymerization, the polymerization of electroactive functional monomers emerged as a particularly advantageous approach for chemical sensing application. Electropolymerization can be performed from aqueous solutions to preserve the natural conformation of the protein templates, with high spatial resolution and electrochemical control of the polymerization process. This review compiles the latest results, identifying major trends and providing an outlook on the perspectives of electrosynthesised protein-imprinted MIPs for chemical sensing. (C) 2016 Elsevier B.V. All rights reserved. KW - Molecularly imprinted polymers KW - Proteins KW - Surface imprinting KW - Electropolymerization KW - Nanostructuring KW - Hybrid nanofilms Y1 - 2016 U6 - https://doi.org/10.1016/j.trac.2015.12.018 SN - 0165-9936 SN - 1879-3142 VL - 79 SP - 179 EP - 190 PB - Elsevier CY - Oxford ER -