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- ItemUncertainty in the measurement of indoor temperature and humidity in naturally ventilated dairy buildings as influenced by measurement technique and data variability(Amsterdam : Elsevier, 2017) Hempel, Sabrina; König, Marcel; Menz, Christoph; Janke, David; Amon, Barbara; Banhazi, Thomas M.; Estellés, Fernando; Amon, ThomasThe microclimatic conditions in dairy buildings affect animal welfare and gaseous emissions. Measurements are highly variable due to the inhomogeneous distribution of heat and humidity sources (related to farm management) and the turbulent inflow (associated with meteorologic boundary conditions). The selection of the measurement strategy (number and position of the sensors) and the analysis methodology adds to the uncertainty of the applied measurement technique. To assess the suitability of different sensor positions, in situations where monitoring in the direct vicinity of the animals is not possible, we collected long-term data in two naturally ventilated dairy barns in Germany between March 2015 and April 2016 (horizontal and vertical profiles with 10 to 5 min temporal resolution). Uncertainties related to the measurement setup were assessed by comparing the device outputs under lab conditions after the on-farm experiments. We found out that the uncertainty in measurements of relative humidity is of particular importance when assessing heat stress risk and resulting economic losses in terms of temperature-humidity index. Measurements at a height of approximately 3 m–3.5 m turned out to be a good approximation for the microclimatic conditions in the animal occupied zone (including the air volume close to the emission active zone). However, further investigation along this cross-section is required to reduce uncertainties related to the inhomogeneous distribution of humidity. In addition, a regular sound cleaning (and if possible recalibration after few months) of the measurement devices is crucial to reduce the instrumentation uncertainty in long-term monitoring of relative humidity in dairy barns. © 2017 The Authors
- ItemUnraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study(London : BioMed Central, 2011) Hempel, Sabrina; Koseska, Aneta; Nikoloski, Zoran; Kurths, Jürgen; Walther, DirkBackground Inferring regulatory interactions between genes from transcriptomics time-resolved data, yielding reverse engineered gene regulatory networks, is of paramount importance to systems biology and bioinformatics studies. Accurate methods to address this problem can ultimately provide a deeper insight into the complexity, behavior, and functions of the underlying biological systems. However, the large number of interacting genes coupled with short and often noisy time-resolved read-outs of the system renders the reverse engineering a challenging task. Therefore, the development and assessment of methods which are computationally efficient, robust against noise, applicable to short time series data, and preferably capable of reconstructing the directionality of the regulatory interactions remains a pressing research problem with valuable applications. Results Here we perform the largest systematic analysis of a set of similarity measures and scoring schemes within the scope of the relevance network approach which are commonly used for gene regulatory network reconstruction from time series data. In addition, we define and analyze several novel measures and schemes which are particularly suitable for short transcriptomics time series. We also compare the considered 21 measures and 6 scoring schemes according to their ability to correctly reconstruct such networks from short time series data by calculating summary statistics based on the corresponding specificity and sensitivity. Our results demonstrate that rank and symbol based measures have the highest performance in inferring regulatory interactions. In addition, the proposed scoring scheme by asymmetric weighting has shown to be valuable in reducing the number of false positive interactions. On the other hand, Granger causality as well as information-theoretic measures, frequently used in inference of regulatory networks, show low performance on the short time series analyzed in this study. Conclusions Our study is intended to serve as a guide for choosing a particular combination of similarity measures and scoring schemes suitable for reconstruction of gene regulatory networks from short time series data. We show that further improvement of algorithms for reverse engineering can be obtained if one considers measures that are rooted in the study of symbolic dynamics or ranks, in contrast to the application of common similarity measures which do not consider the temporal character of the employed data. Moreover, we establish that the asymmetric weighting scoring scheme together with symbol based measures (for low noise level) and rank based measures (for high noise level) are the most suitable choices.
- ItemBlood–Brain Barrier, Lymphatic Clearance, and Recovery: Ariadne’s Thread in Labyrinths of Hypotheses(Basel : Molecular Diversity Preservation International, 2018) Semyachkina-Glushkovskaya, Oxana; Postnov, Dmitry; Kurths, JürgenThe peripheral lymphatic system plays a crucial role in the recovery mechanisms after many pathological changes, such as infection, trauma, vascular, or metabolic diseases. The lymphatic clearance of different tissues from waste products, viruses, bacteria, and toxic proteins significantly contributes to the correspondent recovery processes. However, understanding of the cerebral lymphatic functions is a challenging problem. The exploration of mechanisms of lymphatic communication with brain fluids as well as the role of the lymphatic system in brain drainage, clearance, and recovery is still in its infancy. Here we review novel concepts on the anatomy and physiology of the lymphatics in the brain, which warrant a substantial revision of our knowledge about the role of lymphatics in the rehabilitation of the brain functions after neural pathologies. We discuss a new vision on the connective bridge between the opening of a blood–brain barrier and activation of the meningeal lymphatic clearance. The ability to stimulate the lymph flow in the brain, is likely to play an important role in developing future innovative strategies in neurorehabilitation therapy.
- ItemDiverging importance of drought stress for maize and winter wheat in Europe([London] : Nature Publishing Group UK, 2018) Webber, Heidi; Ewert, Frank; Olesen, Jørgen E.; Müller, Christoph; Fronzek, Stefan; Ruane, Alex C.; Bourgault, Maryse; Martre, Pierre; Ababaei, Behnam; Bindi, Marco; Ferrise, Roberto; Finger, Robert; Fodor, Nándor; Gabaldón-Leal, Clara; Gaiser, Thomas; Jabloun, Mohamed; Kersebaum, Kurt-Christian; Lizaso, Jon I.; Lorite, Ignacio J.; Manceau, Loic; Moriondo, Marco; Nendel, Claas; Rodríguez, Alfredo; Ruiz-Ramos, Margarita; Semenov, Mikhail A.; Siebert, Stefan; Stella, Tommaso; Stratonovitch, Pierre; Trombi, Giacomo; Wallach, DanielUnderstanding the drivers of yield levels under climate change is required to support adaptation planning and respond to changing production risks. This study uses an ensemble of crop models applied on a spatial grid to quantify the contributions of various climatic drivers to past yield variability in grain maize and winter wheat of European cropping systems (1984–2009) and drivers of climate change impacts to 2050. Results reveal that for the current genotypes and mix of irrigated and rainfed production, climate change would lead to yield losses for grain maize and gains for winter wheat. Across Europe, on average heat stress does not increase for either crop in rainfed systems, while drought stress intensifies for maize only. In low-yielding years, drought stress persists as the main driver of losses for both crops, with elevated CO2 offering no yield benefit in these years.
- ItemGenome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation(San Francisco, CA : Public Library of Science (PLoS), 2013) Winck, F.V.; Arvidsson, S.; Riaño-Pachón, D.M.; Hempe, S.; Koseska, A.; Nikoloski, Z.; Gomez, D.A.U.; Rupprecht, J.; Mueller-Roeber, B.The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO 2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2 ), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.
- ItemTrajectories of the Earth System in the Anthropocene(Washington, DC : NAS, 2018) Steffen, Will; Rockström, Johan; Richardson, Katherine; Lenton, Timothy M.; Folke, Carl; Liverman, Diana; Summerhayes, Colin P.; Barnosky, Anthony D.; Cornell, Sarah E.; Crucifix, Michel; Donges, Jonathan F.; Fetzer, Ingo; Lade, Steven J.; Scheffer, Marten; Winkelmann, Ricarda; Schellnhuber, Hans JoachimWe explore the risk that self-reinforcing feedbacks could push the Earth System toward a planetary threshold that, if crossed, could prevent stabilization of the climate at intermediate temperature rises and cause continued warming on a “Hothouse Earth” pathway even as human emissions are reduced. Crossing the threshold would lead to a much higher global average temperature than any interglacial in the past 1.2 million years and to sea levels significantly higher than at any time in the Holocene. We examine the evidence that such a threshold might exist and where it might be. If the threshold is crossed, the resulting trajectory would likely cause serious disruptions to ecosystems, society, and economies. Collective human action is required to steer the Earth System away from a potential threshold and stabilize it in a habitable interglacial-like state. Such action entails stewardship of the entire Earth System—biosphere, climate, and societies—and could include decarbonization of the global economy, enhancement of biosphere carbon sinks, behavioral changes, technological innovations, new governance arrangements, and transformed social values.
- ItemIce roads through lake-rich Arctic watersheds : Integrating climate uncertainty and freshwater habitat responses into adaptive management(London : Taylor & Francis Group, 2019) Arp, Christopher D.; Whitman, Matthew S.; Jones, Benjamin M.; Nigro, D.A.; Alexeev, Vladimir; Gädeke, Anne; Fritz, Stacey; Daanen, Ronald; Liljedahl, Anna K.; Adams, F.J.; Gaglioti, Benjamin V.; Grosse, Guido; Heim, Kurt C.; Beaver, R.; Cai, Lei; Engram, Melanie; Uher-Koch, Hannah R.Vast mosaics of lakes, wetlands, and rivers on the Arctic Coastal Plain give the impression of water surplus. Yet long winters lock freshwater resources in ice, limiting freshwater habitats and water supply for human uses. Increasingly the petroleum industry relies on lakes to build temporary ice roads for winter oil exploration. Permitting water withdrawal for ice roads in Arctic Alaska is dependent on lake depth, ice thickness, and the fish species present. Recent winter warming suggests that more winter water will be available for ice- road construction, yet high interannual variability in ice thickness and summer precipitation complicates habitat impact assessments. To address these concerns, multidisciplinary researchers are working to understand how Arctic freshwater habitats are responding to changes in both climate and water use in northern Alaska. The dynamics of habitat availability and connectivity are being linked to how food webs support fish and waterbirds across diverse freshwater habitats. Moving toward watershed-scale habitat classification coupled with scenario analysis of climate extremes and water withdrawal is increasingly relevant to future resource management decisions in this region. Such progressive refinement in understanding responses to change provides an example of adaptive management focused on ensuring responsible resource development in the Arctic. © 2019, © 2019 The Author(s). Published with license by Taylor & Francis Group, LLC.
- ItemExtending Near-Term Emissions Scenarios to Assess Warming Implications of Paris Agreement NDCs(Chichester : John Wiley and Sons Inc, 2018) Gütschow, J.; Jeffery, M.L.; Schaeffer, M.; Hare, B.In the Paris Agreement countries have agreed to act together to hold global warming well below 2°C over preindustrial levels and to pursue efforts to limit warming to 1.5°C. To assess if the world is on track to meet this long-term temperature goal, countries' pledged emissions reductions (Nationally Determined Contributions, NDCs) need to be analyzed for their implied warming. Several research groups and nongovernmental organizations have estimated this warming and arrived at very different results but have invariably concluded that the current pledges are inadequate to hold warming below 2°C, let alone 1.5°C. In this paper we analyze different methods to estimate 2100 global mean temperature rise implied by countries' NDCs, which often only specify commitments until 2030. We present different methods to extend near-term emissions pathways that have been developed by the authors or used by different research groups and nongovernmental organizations to estimate 21st century warming consequences of Paris Agreement commitments. The abilities of these methods to project both low and high warming scenarios in line with the scenario literature is assessed. We find that the simpler methods are not suitable for temperature projections while more complex methods can produce results consistent with the energy and economic scenario literature. We further find that some methods can have a strong high or low temperature bias depending on parameter choices. The choice of methods to evaluate the consistency of aggregated NDC commitments is very important for reviewing progress toward the Paris Agreement's long-term temperature goal.
- ItemDesign and quality criteria for archetype analysis(Wolfville, Nova Scotia : Resilience Alliance, 2019) Eisenack, Klaus; Villamayor-Tomas, Sergio; Epstein, Graham; Kimmich, Christian; Magliocca, Nicholas; Manuel-Navarrete, David; Oberlack, Christoph; Roggero, Matteo; Sietz, DianaA key challenge in addressing the global degradation of natural resources and the environment is to effectively transfer successful strategies across heterogeneous contexts. Archetype analysis is a particularly salient approach in this regard that helps researchers to understand and compare patterns of (un)sustainability in heterogeneous cases. Archetype analysis avoids traps of overgeneralization and ideography by identifying reappearing but nonuniversal patterns that hold for well-defined subsets of cases. It can be applied by researchers working in inter-or transdisciplinary settings to study sustainability issues from a broad range of theoretical and methodological standpoints. However, there is still an urgent need for quality standards to guide the design of theoretically rigorous and practically useful archetype analyses. To this end, we propose four quality criteria and corresponding research strategies to address them: (1) specify the domain of validity for each archetype, (2) ensure that archetypes can be combined to characterize single cases, (3) explicitly navigate levels of abstraction, and (4) obtain a fit between attribute configurations, theories, and empirical domains of validity. These criteria are based on a stocktaking of current methodological challenges in archetypes research, including: to demonstrate the validity of the analysis, delineate boundaries of archetypes, and select appropriate attributes to define them. We thus contribute to a better common understanding of the approach and to the improvement of the research design of future archetype analyses. © 2019 by the author(s).
- ItemArchetype analysis in sustainability research: meanings, motivations, and evidence-based policy making(Wolfville, Nova Scotia : Resilience Alliance, 2019) Oberlack, Christoph; Sietz, Diana; Bürgi Bonanomi, Elisabeth; de Bremond, Ariane; Dell'Angelo, Jampel; Eisenack, Klaus; Ellis, Erle C.; Epstein, Graham; Giger, Markus; Heinimann, Andreas; Kimmich, Christian; Kok, Marcel TJ; Manuel-Navarrete, David; Messerli, Peter; Meyfroidt, Patrick; Václavík, Tomáš; Villamayor-Tomas, SergioArchetypes are increasingly used as a methodological approach to understand recurrent patterns in variables and processes that shape the sustainability of social-ecological systems. The rapid growth and diversification of archetype analyses has generated variations, inconsistencies, and confusion about the meanings, potential, and limitations of archetypes. Based on a systematic review, a survey, and a workshop series, we provide a consolidated perspective on the core features and diverse meanings of archetype analysis in sustainability research, the motivations behind it, and its policy relevance. We identify three core features of archetype analysis: Recurrent patterns, multiple models, and intermediate abstraction. Two gradients help to apprehend the variety of meanings of archetype analysis that sustainability researchers have developed: (1) understanding archetypes as building blocks or as case typologies and (2) using archetypes for pattern recognition, diagnosis, or scenario development. We demonstrate how archetype analysis has been used to synthesize results from case studies, bridge the gap between global narratives and local realities, foster methodological interplay, and transfer knowledge about sustainability strategies across cases. We also critically examine the potential and limitations of archetype analysis in supporting evidence-based policy making through context-sensitive generalizations with case-level empirical validity. Finally, we identify future priorities, with a view to leveraging the full potential of archetype analysis for supporting sustainable development. © 2019 by the author(s).
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