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Long-term research in grassland biodiversity experiments has provided empirical evidence that ecological and evolutionary processes are intertwined in determining both biodiversity–ecosystem functioning (BEF) and biodiversity–stability relationships. Focusing on plant diversity, we hypothesize that multifunctional stability is highest in high-diversity plant communities and that biodiversity–stability relationships increase over time due to a variety of forms of ecological complementarity including the interaction with other biota above and below ground. We introduce the multiple-mechanisms hypothesis of biodiversity–stability relationships suggesting that it is not an individual mechanism that drives long-term biodiversity effects on ecosystem functioning and stability but that several intertwined processes produce increasingly positive ecosystem effects. The following six mechanisms are important. Low-diversity plant communities accumulate more plant antagonists over time (1), and use resources less efficiently and have more open, leaky nutrient cycles (2). Conversely, high-diversity plant communities support a greater diversity and activity of beneficial interaction partners across trophic levels (3); diversify in their traits over time and space, within and across species, to optimize temporal (intra- and interannual) and spatial complementarity (4), create a more stable microclimate (5), and foster higher top-down control of aboveground and belowground herbivores by predators (6). In line with the observation that different species play unique roles in ecosystems that are dynamic and multifaceted, the particular mechanism contributing most to the higher performance and stability of diverse plant communities might differ across ecosystem functions, years, locations, and environmental change scenarios. This indicates "between-context insurance" or "across-context complementarity" of different mechanisms. We introduce examples of experiments that will be conducted to test our hypotheses and which might inspire additional work. [ABSTRACT FROM AUTHOR]

Proton computed tomography (pCT) is a promising tomographic imaging modality allowing direct reconstruction of proton relative stopping power (RSP) required for proton therapy dose calculation. In this review article, we aim at highlighting the role of Monte Carlo (MC) simulation in pCT studies. After describing the requirements for performing proton computed tomography and the various pCT scanners actively used in recent research projects, we present an overview of available MC simulation platforms. The use of MC simulations in the scope of investigations of image reconstruction, and for the evaluation of optimal RSP accuracy, precision and spatial resolution omitting detector effects is then described. In the final sections of the review article, we present specific applications of realistic MC simulations of an existing pCT scanner prototype, which we describe in detail. [ABSTRACT FROM AUTHOR]

Cities are designed for humans but are also highly dynamic ecosystems that provide habitats for wild animals. These habitats depend on a city's green infrastructure which is increasingly threatened by urban densification. A commonly studied model taxon for wild animals in cities are birds, and the importance of large green spaces for the diversity of birds in cities has been shown. However, how small-scale green spaces affect bird communities, which local characteristics are important, and whether there are seasonal differences remains unclear. We asked how and to what extent the characteristics of city squares in Munich affect the diversity and abundance of birds and if there are differences between bird communities in spring, autumn, and winter. We monitored birds on 103 city squares in Munich using a search-route method. Sampled squares spanned a spatial gradient from the center to the periphery of the city and differed in sealed surface proportion and vegetation structures, such as trees, shrubs, and lawns. The diversity and abundance of birds increased with a higher proportion of green characteristics on the square. Especially the proportion of grass cover and the density of trees had strong positive effects. Old trees had additional effects on birds beyond the effects of trees in general, while the mean number of people on a square negatively influenced bird abundance and diversity. Despite seasonal changes in bird composition, square characteristics showed consistent effects on bird abundance and diversity over seasons. These results underline that the green characteristics of city squares, and therefore of small-scale green spaces, affect their suitability as habitat for wildlife in cities. Integrating this knowledge into city planning can help to maintain or even increase urban biodiversity in the future. [ABSTRACT FROM AUTHOR]

Seed removal can result in either seed predation or dispersal and is therefore an indicator of important ecosystem functions. To better understand how these variable processes are affected by environmental changes, rapid and reliable assessments with high temporal and spatial replication are needed. We address this need by testing the application of a rapid ecosystem function assessment (REFA) method to investigate seed removal in habitats with differing land use intensity. We recorded seed removal hourly over eight hours at 301 sites in five habitat types in three urban regions in Germany. We calculated seed removal rates per sampling period, traditionally used in seed removal studies, as well as instantaneous seed removal probabilities based on hourly sampling. Across regions, seed removal probabilities and rates were lowest in arable fields, a habitat type with high land-use intensity. Except in urban sealed areas, temperature had a negative effect on seed removal. Additional Cox hazard regressions suggest invertebrates as the main seed removing animals in arable fields, whereas vertebrates were likely removers in other habitat types. We confirm that seed removal is strongly negatively affected by human disturbance, indicating that the tested method is appropriate in different settings. We were able to recognize patterns in highly variable data and the method also has the advantages of low cost, high replication and high temporal resolution. However, there is a trade-off between the high temporal-resolution of instantaneous seed removal probabilities and the sampling effort, but adjustments in the standardized setup can be made depending on the study. To further utilize the extensive data collection in the REFA method, we propose to combine instantaneous seed removal probabilities, seed removal rates and Cox hazard regressions of seed removal to provide complementary information on the extent and temporal patterns of seed removal and indications about potential seed removing guilds. Keywords: Seed predation, seed dispersal, seed removal, granivore, REFA [ABSTRACT FROM AUTHOR]

Highlights • First proposal of an analytical simulator for proton radiography and tomography. • First extension of the MLP algorithm to non-uniform water equivalent materials. • First comparison between list-mode and integration-mode detector configurations. • Superiority of integration-mode detector configuration in radiography with relatively high proton statistics. • Hampered potentiality of integration-mode detector configuration by tomography. Abstract Purpose An analytical simulator of ion Radiography (iRad) and Computed Tomography (iCT) for protons is proposed to serve as imaging benchmark for different detector configurations. Methods The analytical simulator is applied to an anthropomorphic phantom and provides iRad and iCT benchmarks. Proton trajectories are traced relying on the Most Likely Path (MLP) algorithm. To simulate the proton trajectories the Multiple Coulomb Scattering (MCS) model embedded in the MLP algorithm is extended to non-uniform water equivalent materials according to variable substitution in the well-known statistical description in uniform water. The proton trajectories are instead estimated relying on the typical assumption of uniform water, thus causing intrinsic inaccuracies of the MLP algorithm. In this work the analytical simulator is used to explore and firstly compare the imaging performances of list-mode and integration-mode detector configurations with proton pencil beam scanning. Results The intrinsic inaccuracies of the MLP algorithm affect the imaging performances of list-mode detector configuration, which nevertheless remains superior to integration-mode detector configuration for iCTs. For relatively higher proton statistics, comparable or better imaging performances are offered by integration-mode detector configuration for iRads (upto 29.2% of WET difference). Uncertainties of proton trajectories due to beam spot size are shown to compromise the imaging performances of integration-mode detector configuration, but also to affect the accuracy of the MLP algorithm for list-mode detector configuration. Conclusions Based on MCS model in non-uniform water equivalent materials, the proposed simulation environment can serve for development and testing of dedicated imaging methodologies prior to and in combination with realistic Monte Carlo simulations. [ABSTRACT FROM AUTHOR]

This is a contribution to the discussion of Reinhart's "Review of Self-Exciting Spatio-Temporal Point Processes and Their Applications" [Statist. Sci. 33 (2018)], which synthesizes developments from various research fields. Here, I discuss some experiences from modeling the spread of infectious diseases. Furthermore, I try to complement the review with regard to the availability of software for the described models, which I think is essential in "paving the way for new uses.". [ABSTRACT FROM AUTHOR]

Biodiversity-ecosystem function experiments test how species diversity influences fundamental ecosystem processes. Historically, arthropod driven functions, such as herbivory and pest-control, have been thought to be influenced by direct and indirect associations among species. Although a number of studies have evaluated how plant diversity affects arthropod communities and arthropod-mediated ecosystem processes, it remains unclear whether diversity effects on arthropods are sufficiently consistent over time such that observed responses can be adequately predicted by classical hypotheses based on associational effects. By combining existing results from a long-term grassland biodiversity experiment (Jena Experiment) with new analyses, we evaluate the consistency of consumer responses within and across taxonomic, trophic, and trait-based (i.e. vertical stratification) groupings, and we consider which changes in arthropod community composition are associated with changes in consumer-mediated ecosystem functions. Overall, higher plant species richness supported more diverse and complex arthropod communities and this pattern was consistent across multiple years. Vegetation-associated arthropods responded more strongly to changes in plant species richness than ground-dwelling arthropods. Additionally, increases in plant species richness were associated with shifts in the species-abundance distributions for many, but not all taxa. For example, highly specialized consumers showed a decrease in dominance and an increase in the number of rare species with increasing plant species richness. Most ecosystem processes investigated responded to increases in plant species richness in the same way as the trophic group mediating the process, e.g. both herbivory and herbivore diversity increase with increasing plant species richness. In the Jena Experiment and other studies, inconsistencies between predictions based on classic hypotheses of associational effects and observed relationships between plant species richness and arthropod diversity likely reflect the influence of multi-trophic community dynamics and species functional trait distributions. Future research should focus on testing a broader array of mechanisms to unravel the biological processes underlying the biodiversity-ecosystem functioning relationships. [ABSTRACT FROM AUTHOR]

In the past two decades, a large number of studies have investigated the relationship between biodiversity and ecosystem functioning, most of which focussed on a limited set of ecosystem variables. The Jena Experiment was set up in 2002 to investigate the effects of plant diversity on element cycling and trophic interactions, using a multi-disciplinary approach. Here, we review the results of 15 years of research in the Jena Experiment, focussing on the effects of manipulating plant species richness and plant functional richness. With more than 85,000 measures taken from the plant diversity plots, the Jena Experiment has allowed answering fundamental questions important for functional biodiversity research. First, the question was how general the effect of plant species richness is, regarding the many different processes that take place in an ecosystem. About 45% of different types of ecosystem processes measured in the ‘main experiment’, where plant species richness ranged from 1 to 60 species, were significantly affected by plant species richness, providing strong support for the view that biodiversity is a significant driver of ecosystem functioning. Many measures were not saturating at the 60-species level, but increased linearly with the logarithm of species richness. There was, however, great variability in the strength of response among different processes. One striking pattern was that many processes, in particular belowground processes, took several years to respond to the manipulation of plant species richness, showing that biodiversity experiments have to be long-term, to distinguish trends from transitory patterns. In addition, the results from the Jena Experiment provide further evidence that diversity begets stability, for example stability against invasion of plant species, but unexpectedly some results also suggested the opposite, e.g. when plant communities experience severe perturbations or elevated resource availability. This highlights the need to revisit diversity–stability theory. Second, we explored whether individual plant species or individual plant functional groups, or biodiversity itself is more important for ecosystem functioning, in particular biomass production. We found strong effects of individual species and plant functional groups on biomass production, yet these effects mostly occurred in addition to, but not instead of, effects of plant species richness. Third, the Jena Experiment assessed the effect of diversity on multitrophic interactions. The diversity of most organisms responded positively to increases in plant species richness, and the effect was stronger for above- than for belowground organisms, and stronger for herbivores than for carnivores or detritivores. Thus, diversity begets diversity. In addition, the effect on organismic diversity was stronger than the effect on species abundances. Fourth, the Jena Experiment aimed to assess the effect of diversity on N, P and C cycling and the water balance of the plots, separating between element input into the ecosystem, element turnover, element stocks, and output from the ecosystem. While inputs were generally less affected by plant species richness, measures of element stocks, turnover and output were often positively affected by plant diversity, e.g. carbon storage strongly increased with increasing plant species richness. Variables of the N cycle responded less strongly to plant species richness than variables of the C cycle. Fifth, plant traits are often used to unravel mechanisms underlying the biodiversity–ecosystem functioning relationship. In the Jena Experiment, most investigated plant traits, both above- and belowground, were plastic and trait expression depended on plant diversity in a complex way, suggesting limitation to using database traits for linking plant traits to particular functions. Sixth, plant diversity effects on ecosystem processes are often caused by plant diversity effects on species interactions. Analyses in the Jena Experiment including structural equation modelling suggest complex interactions that changed with diversity, e.g. soil carbon storage and greenhouse gas emission were affected by changes in the composition and activity of the belowground microbial community. Manipulation experiments, in which particular organisms, e.g. belowground invertebrates, were excluded from plots in split-plot experiments, supported the important role of the biotic component for element and water fluxes. Seventh, the Jena Experiment aimed to put the results into the context of agricultural practices in managed grasslands. The effect of increasing plant species richness from 1 to 16 species on plant biomass was, in absolute terms, as strong as the effect of a more intensive grassland management, using fertiliser and increasing mowing frequency. Potential bioenergy production from high-diversity plots was similar to that of conventionally used energy crops. These results suggest that diverse ‘High Nature Value Grasslands’ are multifunctional and can deliver a range of ecosystem services including production-related services. A final task was to assess the importance of potential artefacts in biodiversity–ecosystem functioning relationships, caused by the weeding of the plant community to maintain plant species composition. While the effort (in hours) needed to weed a plot was often negatively related to plant species richness, species richness still affected the majority of ecosystem variables. Weeding also did not negatively affect monoculture performance; rather, monocultures deteriorated over time for a number of biological reasons, as shown in plant-soil feedback experiments. To summarize, the Jena Experiment has allowed for a comprehensive analysis of the functional role of biodiversity in an ecosystem. A main challenge for future biodiversity research is to increase our mechanistic understanding of why the magnitude of biodiversity effects differs among processes and contexts. It is likely that there will be no simple answer. For example, among the multitude of mechanisms suggested to underlie the positive plant species richness effect on biomass, some have received limited support in the Jena Experiment, such as vertical root niche partitioning. However, others could not be rejected in targeted analyses. Thus, from the current results in the Jena Experiment, it seems likely that the positive biodiversity effect results from several mechanisms acting simultaneously in more diverse communities, such as reduced pathogen attack, the presence of more plant growth promoting organisms, less seed limitation, and increased trait differences leading to complementarity in resource uptake. Distinguishing between different mechanisms requires careful testing of competing hypotheses. Biodiversity research has matured such that predictive approaches testing particular mechanisms are now possible. [ABSTRACT FROM AUTHOR]

Plant diversity and land-use intensity have been shown to affect invertebrate herbivory. Several hypotheses predict positive (e.g. associational susceptibility) or negative (e.g. associational resistance) relationships of herbivory with plant species richness. Also, the strength and direction of reported relationships vary greatly between studies leading to the conclusion that relationships either depend on the specific system studied or that other unconsidered factors are more important. Here, we hypothesized that plant phylogenetic diversity is a stronger predictor of invertebrate herbivory than plant species richness because it integrates additional information about the phenotypical and functional composition of communities. We assessed the community-wide invertebrate herbivory, plant species richness and phylogenetic diversity across a range of land-use intensities including a total of 145 managed grasslands in three regions in Germany. Increasing land-use intensity decreased plant species richness and phylogenetic diversity. Plant species richness did not predict invertebrate herbivory. By contrast herbivory moderately increased with increasing plant phylogenetic diversity even after accounting for the effects of region and land use. The strength of direct effects of land-use intensity and indirect effects via altered phylogenetic diversity on herbivory, however, varied among regions. Our results suggest that increasing phylogenetic diversity of plant communities increases invertebrate herbivory probably by providing higher resource diversity. Differences between regions underline the need to account for regional peculiarities when attempting to generalize land-use effects on invertebrate herbivory. [ABSTRACT FROM AUTHOR]

Spatio-temporal interaction is inherent to cases of infectious diseases and occurrences of earthquakes, whereas the spread of other events, such as cancer or crime, is less evident. Statistical significance tests of space–time clustering usually assess the correlation between the spatial and temporal (transformed) distances of the events. Although appealing through simplicity, these classical tests do not adjust for the underlying population nor can they account for a distance decay of interaction. We propose to use the framework of an endemic–epidemic point process model to jointly estimate a background event rate explained by seasonal and areal characteristics, as well as a superposed epidemic component representing the hypothesis of interest. We illustrate this new model-based test for space–time interaction by analysing psychiatric inpatient admissions in Zurich, Switzerland (2007–2012). Several socio-economic factors were found to be associated with the admission rate, but there was no evidence of general clustering of the cases. [ABSTRACT FROM AUTHOR]

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Abstract: Deep reductions of greenhouse gas emissions in the automotive sector are difficult and often regarded as expensive. Use of ethanol from bio-resources is a potential way to reduce emissions. Ethanol produced from wheat typically reduces greenhouse gas emission by 35% (well-to-wheel) compared to gasoline. In principle, greenhouse gas emissions may be further reduced by applying carbon capture and storage to store the co-produced carbon dioxide. In this study we assessed the technical, economical, regulatory and greenhouse gas performance aspects of bio-ethanol production from ligno-cellulose for a hypothetical plant in Germany. Reducing greenhouse gas emission by CCS from bio-ethanol plants is potentially economical attractive; for instance costs for a 170 kt sized bio-ethanol plant are estimated at 21 to 32 €/t of CO2 stored. Emissions from ligno-cellulose based ethanol plants can be reduced by 150%, i.e. resulting in negative emission when using biomass and CCS combined. Potential revenues may come from ETS (requires adjustments), voluntary markets (probably not sufficient yet) and increased value of the ethanol (requires additional regulation). In some cases, it might be possible to sell high quality CO2 on the market. At the moment, none of these is applicable except the food-grade sales or will yield sufficient income to cover the costs. However, some of them may provide opportunities in the future when rules or boundary conditions are changed. [Copyright &y& Elsevier]

Background & Aims Intestinal fibrosis is a long-term complication in inflammatory bowel diseases (IBD) that frequently results in functional damage, bowel obstruction, and surgery. Interleukin (IL) 36 is a group of cytokines in the IL1 family with inflammatory effects. We studied the expression of IL36 and its receptor, interleukin 1 receptor like 2 (IL1RL2 or IL36R) in the development of intestinal fibrosis in human tissues and mice. Methods We obtained intestinal tissues from 92 patients with Crohn's disease (CD), 48 patients with ulcerative colitis, and 26 patients without inflammatory bowel diseases (control individuals). Tissues were analyzed by histology to detect fibrosis and by immunohistochemistry to determine the distribution of fibroblasts and levels of IL36R ligands. Human and mouse fibroblasts were incubated with IL36 or control medium, and transcriptome-wide RNA sequences were analyzed. Mice were given neutralizing antibodies against IL36R, and we studied intestinal tissues from Il1rl2 –/– mice; colitis and fibrosis were induced in mice by repetitive administration of DSS or TNBS. Bone marrow cells were transplanted from Il1rl2 –/– to irradiated wild-type mice and intestinal tissues were analyzed. Antibodies against IL36R were applied to mice with established chronic colitis and fibrosis and intestinal tissues were studied. Results Mucosal and submucosal tissue from patients with CD or ulcerative colitis had higher levels of collagens, including type VI collagen, compared with tissue from control individuals. In tissues from patients with fibrostenotic CD, significantly higher levels of IL36A were noted, which correlated with high numbers of activated fibroblasts that expressed α-smooth muscle actin. IL36R activation of mouse and human fibroblasts resulted in expression of genes that regulate fibrosis and tissue remodeling, as well as expression of collagen type VI. Il1rl2 –/– mice and mice given injections of an antibody against IL36R developed less severe colitis and fibrosis after administration of DSS or TNBS, but bone marrow cells from Il1rl2 –/– mice did not prevent induction of colitis and fibrosis. Injection of antibodies against IL36R significantly reduced established fibrosis in mice with chronic intestinal inflammation. Conclusion We found higher levels of IL36A in fibrotic intestinal tissues from patients with IBD compared with control individuals. IL36 induced expression of genes that regulate fibrogenesis in fibroblasts. Inhibition or knockout of the IL36R gene in mice reduces chronic colitis and intestinal fibrosis. Agents designed to block IL36R signaling could be developed for prevention and treatment of intestinal fibrosis in patients with IBD. [ABSTRACT FROM AUTHOR]