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integration_instructions Research softwarekeyboard_double_arrow_right Software 2022Publisher:Zenodo Authors: Nam, Christine; Eggert, Daniel; Pfeiffer, Susanne;de-climate-change-analysis provides statistical analysis and plotting functions to determine absolute and relative changes in climate variables. It is used by the Digital Earth Climate Change Backend Module as part of the Digital Earth Flood Event Explorer. It is developed at the Helmholtz-Zentrum Hereon (https://www.hereon.de) in collaboration with the GFZ German Research Centre for Geosciences (https://www.gfz-potsdam.de) and funded by the Initiative and Networking Fund of the Helmholtz Association through the Digital Earth project (https://www.digitalearth-hgf.de/). We acknowledge funding from the Initiative and Networking Fund of the Helmholtz Association through the project "Digital Earth". {"references": ["Gitlab Repository: https://git.geomar.de/digital-earth/de-climate-change/de-climate-change-analysis"]}
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You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5281/zenodo.5833042&type=result"></script>'); --> </script>
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visibility 66visibility views 66 download downloads 3 Powered bymore_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2022Publisher:Zenodo Minoli, Sara; Jägermeyr, Jonas; Asseng, Senthold; Urfels, Anton; Müller, Christoph;Content: Workflow (data and code) to reproduce the results presented in Minoli et al. (2022): Source code of the crop calendar model (./code/01_crop_calendars) Source code of the LPJmL model (./code/02_LPJmL5.0-gsadapt) Scripts for data analysis (./code/03_data_analysis) LPJmL model outputs (./lpjml_output_*) Outputs of the GGCMI crop model evaluation tool (./ggcmi_yield_evaluation_tool_output) # LPJmL outputs in ./data refer to the following climate scenarios gfd = GFDL-ESM2M had = HadGEM2-ES ips = IPSL-CM5A-LR mir = MIROC5 wfd = WFDEI Manuscript Reference: Sara Minoli, Jonas Jägermeyr, Senthold Asseng, Anton Urfels, Christoph Müller. Global crop yields can be lifted by timely adaptation of growing periods to climate change. Nature Communications.
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visibility 352visibility views 352 download downloads 251 Powered bymore_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5281/zenodo.7038162&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2022Publisher:Zenodo Authors: Koussoroplis, Apostolos-Manuel; Sperfeld, Erik; Pincebourde, Sylvain; Bec, Alexandre; +1 AuthorsKoussoroplis, Apostolos-Manuel; Sperfeld, Erik; Pincebourde, Sylvain; Bec, Alexandre; Wacker, Alexander;The increasing frequency and intensity of summer heat waves is pushing freshwater zooplankton towards their upper thermal tolerance limits. At the same time, higher temperatures and prolonged water column stratification can favor the dominance of cyanobacteria in phytoplankton. Even when not toxic or grazing resistant, these prokaryotes lack phytosterols as essential precursors for cholesterol, the main sterol in animal tissues. Cholesterol plays a crucial role in the physiological adaptation of ectotherms to high temperature. Therefore, the shift to cyanobacteria-dominated systems may increase the vulnerability of zooplankton to heatwaves by intensifying cholesterol limitation. Here, we used death time curves that take into consideration the intensity and duration of a thermal challenge and a dynamic model to study the effects of cholesterol limitation on the heat tolerance of the keystone species Daphnia magna and to simulate the cumulative mortality that could occur in a fluctuating environment over several days of heatwave. We show that increasing cholesterol limitation does not affect the slope between time-to-immobilization and temperature, but does decrease the maximal temperature that Daphnia can withstand by up to 0.74°C. This seemingly small difference is sufficient to halve the time individuals can survive heat stress. Our simulations predicted that, when facing heatwaves over several days, the differences in survival caused by cholesterol limitation build up rapidly. Considering the anticipated intensity and duration of future (2070-2099) heatwaves, cholesterol limitation could increase mortality by up to 45% and 72% under low- and medium-greenhouse-gas-emission scenarios, respectively. These results suggest that the increasing risk of cholesterol limitation due to more frequent cyanobacterial blooms could compromise the resistance of zooplankton populations to future heatwaves. More generally, this study shows the importance of considering the nutritional context in any attempt to predict ectotherm mortality with increasing temperatures in the field. We used death time curves to study the effects of cholesterol limitation on the heat tolerance of the keystone species Daphnia magna and to simulate the cumulative mortality that could occur in a fluctuating environment over several days of heatwave. In that aim, D. magna neonates were grown under controlled laboratory condition on a sterol-free, non-toxic cyanobacterial diet (Synnechococcus obliquus) supplemented with different amounts of cholesterol-containing liposomes to obtain four cholesterol concentrations of 0.25, 2.5, 5, and 8 µg per mg C. In all treatments, a small amount of eicosapentaenoic acid (20:5ω3) was also added via liposomes (resulting in 0.25 µg 20:5ω3 per mg C) in order to prevent severe 20:5ω3 limitation, thereby aiding the development of daphnids. The daphnids were grown at 27°C, a non-lethal yet super-optimal temperature. Heat tolerance (time to immobilization) of the daphnids from the different cholesterol treatments was tested on day seven at five different constant temperatures (34.5°, 35.5°, 36.5°, 37.5°, 38.5°C). Here, we provide the raw data, as well as the R scripts used to analyze the data. Funding provided by: Deutsche ForschungsgemeinschaftCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659Award Number: KO5330/1-1Funding provided by: GDR CNRS 3716 GRET*Crossref Funder Registry ID: Award Number:
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visibility 9visibility views 9 download downloads 10 Powered bymore_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5281/zenodo.7225881&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2020Publisher:Zenodo Funded by:EC | PETA-CARBEC| PETA-CARBAuthors: Jongejans, Loeka L.; Strauss, Jens;This script was created to facilitate analysis of data (see data publication) pertaining to the publication: Jongejans, L. L., Strauss, J., Lenz, J., Peterse, F., Mangelsdorf, K., Fuchs, M. and Grosse, G. (2018). Organic matter characteristics in yedoma and thermokarst deposits on Baldwin Peninsula, west Alaska. Biogeosciences 15, 6033-6048. doi:10.5194/bg-15-6033-2018. The input data stem from sediment samples taken from two permafrost exposures in west Alaska. The input parameters are total organic carbon content, bulk density, wedge ice volume, deposit thickness and coverage. The script calculates the organic carbon storage of the permafrost sediments using a bootstrapping approach. The script was written for statistical software R (version 3.6.1). The current code and the required files are available on GitHub.
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You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5281/zenodo.3734246&type=result"></script>'); --> </script>
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visibility 270visibility views 270 download downloads 38 Powered bymore_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2023Publisher:Zenodo Authors: Nielsen, Matthew; Nylin, Soren; Wiklund, Christer; Gotthard, Karl;Photoperiod is a common cue for seasonal plasticity and phenology, but climate change can create cue-environment mismatches for organisms that rely on it. Evolution could potentially correct these mismatches, but phenology often depends on multiple plastic decisions made during different life stages and seasons that may evolve separately. For example, Pararge aegeria (Speckled wood butterfly) has photoperiod-cued seasonal life history plasticity in two different life stages: larval development time and pupal diapause. We tested for climate-change-associated evolution of this plasticity by replicating common garden experiments conducted on two Swedish populations 30 years ago. We found evidence for evolutionary change in the contemporary larval reaction norm—although these changes differed between populations—but no evidence for evolution of the pupal reaction norm. This variation in evolution across life stages demonstrates the need to consider how climate change affects the whole life cycle to understand its impacts on phenology. Please see the main paper and readme files for full details on the methods associated with this dataset. Data on the historic experiment was digitized for this study from the original data sheets associated with Nylin et al 1989, 1995 (see main text for full citations). Data for the contemporary experiment was generated by the authors for this study, following the methods of the historic experiment. Temperature data came from the Swedish Hydrological and Meteorological Institute weather stations and was restructured, but otherwise used as provided by SHMI. Readme file is also plain text compatible (.txt). Data files are comma-separated values (.csv) format. Software files (.R) are written in in R.Funding provided by: VetenskapsrådetCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100004359Award Number: 2017-04500Funding provided by: Bolin Centre for Climate Research*Crossref Funder Registry ID: Award Number:
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You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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visibility 3visibility views 3 download downloads 2 Powered bymore_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5281/zenodo.7967310&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2023Publisher:Zenodo Authors: Serra Yosmaoglu; Krajzewicz, Daniel; Nieland, Simon; Heldt, Benjamin;About NaMIx ("Sustainable mobility index to assess the location-related mobility potential", in German: "Nachhaltige-Mobilität-Index zur Bewertung des standortbezogenen Mobilitätspotentials") is a project that aims to develop an index for sustainable mobility at locations and for neighborhoods that incorporates existing data and indices and maps different spatial levels. You can find out more about the project here: https://verkehrsforschung.dlr.de/de/projekte/namix. Most of the needed data can be retrieved from OpenStreetMap (OSM). Public transport stops can be obtained from OpenStreetMap (OSM) or General Transit Feed Specification (GTFS). Please note that due to restrictions regarding the distribution of some of the used datatypes, we had to limit the functionality in comparison to what has been shown during the final project presentation. Given the current version, the locations of buildings are retrieved from OSM instead of using the BKG address dataset. In addition, schools are retrieved from OSM as well and instead of using access by foot to elementary schools and access by bike to secondary schools NaMIx version 0.2.0 computes the access to all schools obtained from OSM by walk and by bike. Installation The current version is "NaMIx-0.2.0". It computes ten indicators almost (see above) as presented at the final project presentation. Please note that current NaMIx is realised as a Jupyter Notebook and that it is currently available in German only. To run the computation, please do the following Download a version of NaMIx : You may download a copy or fork the code at NaMIx' github page. : Besides, you may download the current release here: NaMIx-0.2.0.zip NaMIx-0.2.0.tar.gz Depack the obtained file into a folder of your choice (named from now on) Open the command line in this folder Optionally create a virtual python environment (recommended) run python -m venv venv_namix run venv_namix\Scripts\activate.bat Run pip install -r requirements.txt to install all necessary dependencies Download the 0.6.0 version of UrMoAC from UrMoAC-0.6.0.zip. Extract the contents into /demo/tools so that the jar file is located directly within this folder. Download GTFS data (e.g. from MVG). Extract the contents so that can be found in /demo/input/GTFS. Start the jupyter notebook You should have a command line open in Run python -m jupyter notebook open "namix_demo.ipynb" in the notebook The notebook processes the input data, computes the individual indicators and the joined NaMIx indicator, and stores the result in a geopackage file named "/demo/namix.gpkg". Authors NaMIx was developed and implemented by Serra Yosmaoglu, Benjamin Heldt, Daniel Krajzewicz, and Simon Nieland. ChangeLog NaMIx 0.2.0 (31.10.2023) initial version License NaMIx is licensed under the Eclipse Public License 2.0. When using it, please cite it via the DOI: https://doi.org/10.5281/zenodo.8328622 (v 0.2.0) Support If you have a usage question, please contact us via email (serra.yosmaoglu@dlr.de). Disclaimer We are not responsible for the contents of the pages we link to. The software is provided "AS IS". We cannot guarantee that the software works as you expect. References Boeing, G. (2017). OSMnx: New Methods for Acquiring, Constructing, Analyzing, and Visualizing Complex Street Networks. Computers, Environment and Urban Systems 65, 126-139. doi:10.1016/j.compenvurbsys.2017.05.004 Krajzewicz, D., Heinrichs, D. & Cyganski, R. (2017). Intermodal Contour Accessibility Measures Computation Using the 'UrMo Accessibility Computer'. International Journal On Advances in Systems and Measurements, 10 (3&4), Seiten 111-123. IARIA. Heldt, B., Yosmaoglu, S. (2023). Neues Planungswerkzeug für Quartiere: Der Nachhaltige-Mobilität-Index. Emmett. https://emmett.io/article/der-nachhaltige-mobilitaet-index.
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more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2020Publisher:Zenodo Funded by:EC | FIThydroEC| FIThydrovan Treeck, Ruben; Radinger, Johannes; Noble, Richard; Geiger, Franz; Wolter, Christian;Hydroelectricity is critical for decarbonizing global energy production, but hydropower plants affect rivers, disrupt their continuity, and threaten migrating fishes. This puts hydroelectricity production in conflict with efforts to protect threatened species and re-connect fragmented ecosystems. Assessing the impact of hydropower on fishes will support informed decision-making during planning, commissioning, and operation of hydropower facilities. Few methods estimate mortalities of single species passing through hydropower turbines, but no commonly agreed tool assesses hazards of hydropower plants for fish populations. The European Fish Hazard Index bridges this gap. This assessment tool for screening ecological risk considers constellation specific effects of plant design and operation, the sensitivity and mortality of fish species and overarching conservation and environmental development targets for the river. Further, it facilitates impact mitigation of new and existing hydropower plants of various types across Europe. The tool does not yet support VBAs. In order to use it and produce reliable results, all input fields have to be reset manually before making a new assessment. The input window contains examplary dummy data.
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You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5281/zenodo.4071822&type=result"></script>'); --> </script>
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visibility 336visibility views 336 download downloads 154 Powered bymore_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.5281/zenodo.4071822&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2021Publisher:Zenodo Trondrud, L. Monica; Pigeon, Gabriel; Król, Elżbieta; Albon, Steve; Evans, Alina L.; Arnold, Walter; Hambly, Catherine; Irvine, R. Justin; Ropstad, Erik; Stien, Audun; Veiberg, Vebjørn; Speakman, John R.; Loe, Leif Egil;1. The fasting endurance hypothesis (FEH) predicts strong selection for large body size in mammals living in environments where food supply is interrupted over prolonged periods of time. The Arctic is a highly seasonal and food restricted environment, but contrary to predictions from the FEH, empirical evidence shows that Arctic mammals are often smaller than their temperate conspecifics. Intraspecific studies integrating physiology and behaviour of different-sized individuals, may shed light on this paradox. 2. We tested the FEH in free-living Svalbard reindeer (Rangifer tarandus platyrhynchus). We measured daily energy expenditure (DEE), subcutaneous body temperature (Tsc) and activity levels during the late winter in 14 adult females with body masses ranging from 46.3 to 57.8 kg. Winter energy expenditure (WEE) and fasting endurance (FE) were modelled dynamically by combining these data with body composition measurements of culled individuals at the onset of winter (14 years, n = 140) and variation in activity level throughout winter (10 years, n = 70). 3. Mean DEE was 6.3±0.7 MJ day−1. Lean mass, Tsc and activity had significantly positive effects on DEE. Across all 140 individuals, mean FE was 85±17 days (range 48–137 days). In contrast to the predictions of the FEH, the dominant factor affecting FE was initial fat mass, while body mass and FE were not correlated. Furthermore, lean mass and fat mass were not correlated. FE was on average 80% (45 days) longer in fat than lean individuals of the same size. Reducing activity levels by ~16% or Tsc by ~5% increased FE by 7%, and 4%, respectively. 4. Our results fail to support the FEH. Rather, we demonstrate that (i) the size of fat reserves can be independent of lean mass and body size within a species, (ii) ecological and environmental variation influence FE via their effects on body composition, and (iii) physiological and behavioural adjustments can improve FE within individuals. Altogether, our results suggest that there is a selection in Svalbard reindeer to accumulate body fat, rather than to grow structurally large. The methods used to collect the data are described in Trondrud et al. 2021: "Fat storage influences fasting endurance more than body size in an ungulate. Accepted in Functional Ecology. Funding provided by: Norges ForskningsrådCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100005416Award Number: KLIMAFORSK 267613
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You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2023Publisher:Zenodo Londoñ-Nieto, Claudia; García-Roa, Roberto; Garcia-Co, Clara; González, Paula; Carazo, Pau;Fitness assays: quantifying male harm To study whether male harm is affected by temperature, we established a factorial design to measure survival and lifetime reproduction success (LRS) of female flies under monogamy (i.e., one male and one female per vial) vs. polyandry (i.e., three males and one female per vial), across three stable temperature treatments typical of this population during their reproductively active period in the wild: 20, 24, and 28°C. Comparison of female fitness at monogamy vs. polyandry is a common way to gauge male harm in Drosophila and other organisms (Yun, Agrawal, & Rundle, 2021), and our treatments reflect the low and high-end of the spectrum of sex ratios that are typical of D. melanogaster at mating patches in the wild (Dukas, 2020). We first randomly divided virgin flies into three groups that we allocated to the three different stable temperature treatments 48 hours before starting the experiment. Flies remained at those temperatures until the end of the experiment. To estimate LRS, we transferred flies to fresh vials twice a week using mild CO2 exposure anaesthesia. We incubated the vials containing female eggs at 24 ± 4°C for 15–20 days (~15 days for 28°C, ~17 days for 24°C and ~20 days for 20°C) to allow F1 offspring emergence, after which we froze them at -21°C for later counting. The differences in incubation time are due to differences in developmental time because of temperature differences in the first 3-4 days of each vial (i.e., before flipping females to new fresh vials). We discarded and replaced males by young (2 to 4 days old) virgin males three weeks after starting (at the same time for all treatments). We kept a stock of replacement males maintained at each of the three temperatures (20, 24 and 28°C) to replace dead male flies if needed. We kept flies under these conditions during six weeks, after which we discarded males and followed females until they died. We started the experiment with 468 females (78 per each temperature x mating system treatment) and 936 males (234 per each temperature x polyandry and 78 per each temperature x monogamy). Final sample sizes were: a) at 20°C: 74 females for polyandry and 76 females for monogamy; b) at 24°C: 72 females for polyandry and 77 females for monogamy; c) at 28°C: 70 females for polyandry and 75 females for monogamy. Differences between start and final sample sizes across treatments are due to discarded/escaped flies since the start of the experiment. We estimated the overall degree of male harm by calculating the relative harm (H) following Yun et al. (2021): H = (Wmonogamy - Wpolyandry) / Wmonogamy Finally, and using the data collected above, we partitioned overall effects on LRS into effects of temperature x mating system (i.e., male-male competition level) on early reproductive rate (i.e., offspring produced during the first two weeks of age) and reproductive (i.e., offspring produced over weeks 1–2 vs. 3–4) and actuarial senescence (i.e., survival). Behavioural assays: quantifying male-male aggression and harassment of females Immediately after the fitness experiment started, we conducted behavioural observations on the first day of the experiment across all treatments, to investigate the behavioural mechanisms that might underlie the potential fitness effects evaluated above. Due to logistic limitations, we conducted behavioural observations in the same temperature control room, so we had to conduct trials at 20, 24 and 28°C in three consecutive days (with both monogamy and polyandry treatments evaluated at the same time for each temperature), in randomized order (i.e., 20, 28 and 24°C). However, all flies were 5 days old at the start of the experiment. We measured the following behaviours: (a) courtship intensity (number of courtships experienced by a female per hour), (b) male-male aggression behaviours and (c) female rejection behaviours (Bastock & Manning, 1955; Connolly & Cook, 1973). We also recorded the number of total matings during the observation period. Observations started at lights‐on (10 a.m.) and lasted for 8 hr, during which time we continuously recorded reproductive behaviours using scan sampling of vials. Each complete scan lasted approximately 8 min, so that we always conducted one complete scan every 10 min to ensure recording of all matings (see below). Scans consisted in observing all vials in succession for ca. 3s each and recording all occurrences of the behaviours listed above. We interspersed these behavioural scans with very quick (<1 min) mating scans where we rapidly swept all vials for copulas at the beginning, in the middle and at the end of each behavioural scan. This strategy ensured that we recorded all successful matings (>10min), which typically last between 15 and 25min in our population of D. melanogaster, during our 8‐hr observation. We obtained a total of 49 scans per vial. Behavioural observations were conducted only once, on day 1 of the fitness experiment, as prior experiments have shown that courtship, aggressive and female rejection behaviours are stable over time in D. melanogaster, so that our behavioural indexes are representative of long-term treatment differences (e.g., Carazo, Perry, Johnson, Pizzari, & Wigby, 2015; Carazo, Tan, Allen, Wigby, & Pizzari, 2014). In contrast to courtship and aggression indexes, note that total mating frequency over the first day cannot be taken as a reliable measure of mating rate (Wolfner, 1997), and thus our rationale in recording this variable was just to ensure that early mating ensued normally across treatments (which was the case, see SI2). Female reproduction and survival assays: quantifying male ejaculate "toxicity" To examine post-mating mechanisms that might underlie the fitness effects observed in our first experiment, we conducted four additional assays to test whether temperature modulates the previously well-documented effects of male ejaculates on female reproduction and survival in D. melanogaster. Briefly, males of this species transfer seminal fluid proteins (SFPs) produced by their accessory glands that increase short-term female fecundity, as well as decrease female receptivity and survival (Chapman, Liddle, Kalb, Wolfner, & Partridge, 1995; Wigby & Chapman, 2005). In addition, prior studies have shown that males are able to tailor investment into SFPs according to the expected sperm competition risk and intensity (Hopkins et al., 2019). Thus, we set up a factorial design where we manipulated the temperature (i.e., 20, 24 and 28ºC) and perceived sperm competition risk levels (i.e., males kept alone vs. with 7 more males in a vial) at which adult males were kept prior to mating, for two temperature treatment durations (i.e., 48 hours or 13 days), and then measured how reception of their ejaculate in a common garden environment (i.e., 24ºC) affected female fecundity, survival and reproduction. Receptivity assays We first collected experimental males as virgins (i.e., within 6 h of eclosion) under ice anesthesia and randomly placed them either individually or in a same-sex group of 8 in medium containing plastic vials. Next, we randomly divided them into three groups that we allocated to the different stable temperature treatments for either 48 hours (experiment 1) or 13 days (experiment 2) immediately before the beginning of each experiment. In experiment 2 (treatment duration of 13 days), we emptied the seminal fluid of experimental males before we allocated them to the different temperature / competition treatments. To do so, we housed individually experimental males with four standard virgin females for 24 hours. This strategy ensured that spermatogenesis took place over the 13 days under the temperature / competition treatments. We collected all females and competitor males used in receptivity assays as virgins and held them in groups of 15 to 20 flies at 24 ± 4°C. Experiments started by exposing all virgin females to single experimental males for 2.5 h at 24°C. After a successful copulation, we separated the mated females from the males and kept them individually in medium-containing vials until the next mating trial. We discarded unmated females and experimental males. 72 h after the first mating, we individually exposed females to single virgin competitor males for 12 h. After each trial, we transferred unmated females into a new medium containing vial, until the next mating assay 24 h later. We repeated remating trials every 24 h for three consecutive days. We calculated the cumulative percentage of remated females for each of the three days of each experiment. We conducted the experiments in two blocks each: with n = 390 females for each batch in experiment 1 (n = 436 rematings) and n = 420 females for each batch in experiment 2 (n = 676 rematings). We also recorded mating duration for the first mating and mating latency (i.e., time between males being introduced into the female-containing vial and copulation) and mating duration for re-matings. Females that did not remate within those three days were right-censored. Females and all experimental males were 4 days old at the start of experiment 1. In experiment 2, females and "re-mating" competitor males were 4 days old, while experimental males were 18 days old. Fecundity and survival assays To gauge effects on female short-term fecundity and long-term survival, we performed two experiments (experiments 3 and 4) where we compared the oviposition and egg fertility of females mated with male flies subject to the same factorial design imposed in receptivity experiments. We collected and treated all experimental males as in the receptivity assays described above, and then proceeded to mate ~4-day-old virgin females in single pairs to either 4- (experiment 3, 48h temperature treatment duration) or 18-day-old experimental males (experiment 4, 13d temperature treatment duration) for 2.5h at 24°C. After copulation, we separated mated females from males and kept them individually in medium-containing vials. We discarded unmated females. We then transferred females to fresh vials every 24h for 4 days, and then every 3 days twice. Later, we transferred female flies to fresh vials once a week, and we combined vials to maintain density at ten flies per vial. We kept female flies under these conditions until they died. We removed dead flies at each transfer and recorded female deaths. We counted eggs laid the first 3 days and vials from days 1, 2, 3, 4, 5, and 8 after mating were retained to count progeny to determine egg viability. We tested 545 females at the starting point of the experiment 3, and 480 females at the starting point of the experiment 4. Statistical analyses We performed all statistical analyses using R statistical software (version 3.5.2). In all models, we assessed fit by visual inspections of diagnostic plots on raw and residual data (Zuur, Ieno, & Elphick, 2010). To examine temperature effects on male harm, we evaluated the interaction between mating system and temperature on female fitness (LRS), survival and male and female reproductive behaviours. We fitted generalized linear models (GLMs) with temperature, mating system and their interaction as fixed effects. We also used Cox proportional hazards survival model to analyse potential differences in mortality risk across treatments, using the survival and survminer packages, including the females lost during manipulations as "right censored" individuals (i.e., individuals that are taken into account for demographic analysis until the day they disappear, Kleinbaum & Klein, 2012). We also censored any remaining females after the six weeks of the experiment. Graphical inspection of LRS and reproductive behaviours (courtship intensity, intersexual aggression behaviours and female rejection) revealed that the normality assumption was apparently violated, as well as the independence assumption for LRS. Box–Cox transformation (Quinn & Keough, 2002) solved these problems and allowed us to run a GLM with a Gaussian error distribution. In all these afore mentioned cases, fitted models were subsequently validated. In addition, we compared GLMs with their corresponding null GLMs using likelihood ratio test. In all models, we used ANOVA type III to compute p-values. We detected a problem of collinearity between mating system and the interaction in the LRS model. We fitted the model again without the main mating system effect (which was not our main interest) and also ran models separately for each temperature level. As a complementary analysis, we ran a model with temperature as factor with a quadratic contrast table predetermined (note that the relation between LRS and temperature does not seem to be linear, Fig 1), obtaining similar results. For the total matings recorded across the 8h observation period (i.e., mating rate), we initially used a GLM with Poisson errors. However, the dataset contained many zero values. We therefore analysed the data using a Hurdle model, in which the zero values are modelled separately from the nonzero values (Zuur et al., 2010). Additionally, we compared GLM and Hurdle models using an information-theoretic approach based on Akaike's Information Criterion (AIC). The minimum AICc value indicates the best-supported model given the trade-off between fit to the data and model complexity (Konishi & Kitagawa, 2008). To estimate how male harm impact estimated population growth across varying demographic scenarios (i.e., decreasing, stable and growing populations), based on our LRS measures, we calculated rate-sensitive fitness estimates (Edward, Fricke, Gerrard, & Chapman, 2011) against different population background growth rates of r = -0.1, r = -0.05, r = 0, r = 0.05 and r = 0.1. For receptivity (mating duration and remating latency) and fecundity (total adults) analyses, we fitted generalized linear models (GLMs) with temperature, sperm competition risk level, treatment duration and their interaction as fixed effects. For egg production data, we fitted a generalized linear mixed model (GLMM) with temperature, sperm competition risk level, treatment duration and their interaction as fixed effects and day number as a random effect, with a zero inflated distribution, in which the zero values are modelled separately from the nonzero values (Zuur et al., 2010). We assessed significance of factors by dropping individual terms from the full model using the "drop1" function, refitting where the interaction was nonsignificant. We also used Cox proportional hazards survival model to analyse potential differences in mortality risk across treatments, using the survival and survminer packages, including the females lost during manipulations as "right censored" individuals. Finally, we also ran models separately for each temperature level for the cases in which a significant interaction between sperm competition risk level and temperature treatment was detected. Strong sexual selection frequently leads to sexual conflict and ensuing male harm, whereby males increase their reproductive success at the expense of harming females. Male harm is a widespread evolutionary phenomenon with a strong bearing on population viability. Thus, understanding how it unfolds in the wild is a current priority. Here, we sampled a wild Drosophila melanogaster population and studied male harm across the normal range of temperatures under which it reproduces optimally in nature by comparing female lifetime reproductive success and underlying male harm mechanisms under monogamy (i.e., low male competition/harm) vs. polyandry (i.e., high male competition/harm). While females had equal lifetime reproductive success across temperatures under monogamy, polyandry resulted in a maximum decrease of female fitness at 24°C (35%), reducing its impact at both 20°C (22%), and 28°C (10%). Furthermore, female fitness components and pre- (i.e., harassment) and post-copulatory (i.e., ejaculate toxicity) mechanisms of male harm were asymmetrically affected by temperature. At 20ºC, male harassment of females was reduced, and polyandry accelerated female actuarial ageing. In contrast, the effect of mating on female receptivity (a component of ejaculate toxicity) was only modulated at 28ºC, where the mating costs for females decreased and polyandry mostly resulted in accelerated reproductive ageing. We thus show that, across a natural thermal range, sexual conflict processes and their effects on female fitness components are plastic and complex. As a result, the net effect of male harm on overall population viability is likely to be lower than previously surmised. We discuss how such plasticity may affect selection, adaptation and, ultimately, evolutionary rescue under a warming climate. Data files included are .xlsx. We performed all statistical analyses using R statistical software.Funding provided by: MCIN/AEI/10.13039/501100011033*Crossref Funder Registry ID: Award Number: PID2020-118027GB-I00Funding provided by: Ministerio de Educación Cultura y Deportes*Crossref Funder Registry ID: Award Number: Juan de la Cierva Formación FJC2018-037058-IFunding provided by: MINECO Spanish Goverment*Crossref Funder Registry ID: Award Number: PRE2018-084009Funding provided by: Generalitat ValencianaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100003359Award Number: AICO/2021/113
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2024Publisher:Zenodo Shu, David Yang; Reinert, Christiane; Mannhardt, Jacob; Leenders, Ludger; Lüthje, Jannik; Mitsos, Alexander; Bardow, André;Referencing If you use our software or any part of it, please cite Shu et al. (2023). The full information on the publication is also shown below: Shu, D.Y. *; Reinert, C. *; Mannhardt, J.*; Leenders, L.; Lüthje, J.; Mitsos, A.; and Bardow, A. (2023): "Overcoming the Central Planner Approach – Bilevel Optimization of the European Energy Transition". Accepted in iScience. *Equal contribution. Since the publication above and this repository mainly describe the extensions compared to the linear SecMOD, please also refer to Reinert et al. (2022) for further information. The full information on the SecMOD publication is also shown below: Reinert, C.; Schellhas, L.; Mannhardt, J.; Shu, D.; Kämper, A.; Baumgärtner, N.; Deutz, S., and Bardow, A. (2022): "SecMOD: An open-source modular framework combining multi-sector system optimization and life-cycle assessment". Frontiers in Energy Research. DOI: https://doi.org/10.3389/fenrg.2022.884525. Documentation and Support Please find the full documentation of the SecMOD LP framework here. You can further find a video about SecMOD and some example applications here. In case you need help using Git, please refer to the git documentation here. Installation A brief instruction to install SecMOD can also be found below: Clone a copy of the whole repository to your computer: git clone git@git-ce.rwth-aachen.de:ltt/secmod-bilevel.git Open a terminal with a python enviroment (e.g. Anaconda promt) and install the secmod package with: pip install --user -e '' The path should point to the directory where secmod is saved (repository folder). Make sure that the setup.py file is located in your repository folder. You can use this installation for several projects in multiple working directories. For further installation instruction please go here. The code was tested with Python 3.7.5.
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integration_instructions Research softwarekeyboard_double_arrow_right Software 2022Publisher:Zenodo Authors: Nam, Christine; Eggert, Daniel; Pfeiffer, Susanne;de-climate-change-analysis provides statistical analysis and plotting functions to determine absolute and relative changes in climate variables. It is used by the Digital Earth Climate Change Backend Module as part of the Digital Earth Flood Event Explorer. It is developed at the Helmholtz-Zentrum Hereon (https://www.hereon.de) in collaboration with the GFZ German Research Centre for Geosciences (https://www.gfz-potsdam.de) and funded by the Initiative and Networking Fund of the Helmholtz Association through the Digital Earth project (https://www.digitalearth-hgf.de/). We acknowledge funding from the Initiative and Networking Fund of the Helmholtz Association through the project "Digital Earth". {"references": ["Gitlab Repository: https://git.geomar.de/digital-earth/de-climate-change/de-climate-change-analysis"]}
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2022Publisher:Zenodo Minoli, Sara; Jägermeyr, Jonas; Asseng, Senthold; Urfels, Anton; Müller, Christoph;Content: Workflow (data and code) to reproduce the results presented in Minoli et al. (2022): Source code of the crop calendar model (./code/01_crop_calendars) Source code of the LPJmL model (./code/02_LPJmL5.0-gsadapt) Scripts for data analysis (./code/03_data_analysis) LPJmL model outputs (./lpjml_output_*) Outputs of the GGCMI crop model evaluation tool (./ggcmi_yield_evaluation_tool_output) # LPJmL outputs in ./data refer to the following climate scenarios gfd = GFDL-ESM2M had = HadGEM2-ES ips = IPSL-CM5A-LR mir = MIROC5 wfd = WFDEI Manuscript Reference: Sara Minoli, Jonas Jägermeyr, Senthold Asseng, Anton Urfels, Christoph Müller. Global crop yields can be lifted by timely adaptation of growing periods to climate change. Nature Communications.
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visibility 352visibility views 352 download downloads 251 Powered bymore_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2022Publisher:Zenodo Authors: Koussoroplis, Apostolos-Manuel; Sperfeld, Erik; Pincebourde, Sylvain; Bec, Alexandre; +1 AuthorsKoussoroplis, Apostolos-Manuel; Sperfeld, Erik; Pincebourde, Sylvain; Bec, Alexandre; Wacker, Alexander;The increasing frequency and intensity of summer heat waves is pushing freshwater zooplankton towards their upper thermal tolerance limits. At the same time, higher temperatures and prolonged water column stratification can favor the dominance of cyanobacteria in phytoplankton. Even when not toxic or grazing resistant, these prokaryotes lack phytosterols as essential precursors for cholesterol, the main sterol in animal tissues. Cholesterol plays a crucial role in the physiological adaptation of ectotherms to high temperature. Therefore, the shift to cyanobacteria-dominated systems may increase the vulnerability of zooplankton to heatwaves by intensifying cholesterol limitation. Here, we used death time curves that take into consideration the intensity and duration of a thermal challenge and a dynamic model to study the effects of cholesterol limitation on the heat tolerance of the keystone species Daphnia magna and to simulate the cumulative mortality that could occur in a fluctuating environment over several days of heatwave. We show that increasing cholesterol limitation does not affect the slope between time-to-immobilization and temperature, but does decrease the maximal temperature that Daphnia can withstand by up to 0.74°C. This seemingly small difference is sufficient to halve the time individuals can survive heat stress. Our simulations predicted that, when facing heatwaves over several days, the differences in survival caused by cholesterol limitation build up rapidly. Considering the anticipated intensity and duration of future (2070-2099) heatwaves, cholesterol limitation could increase mortality by up to 45% and 72% under low- and medium-greenhouse-gas-emission scenarios, respectively. These results suggest that the increasing risk of cholesterol limitation due to more frequent cyanobacterial blooms could compromise the resistance of zooplankton populations to future heatwaves. More generally, this study shows the importance of considering the nutritional context in any attempt to predict ectotherm mortality with increasing temperatures in the field. We used death time curves to study the effects of cholesterol limitation on the heat tolerance of the keystone species Daphnia magna and to simulate the cumulative mortality that could occur in a fluctuating environment over several days of heatwave. In that aim, D. magna neonates were grown under controlled laboratory condition on a sterol-free, non-toxic cyanobacterial diet (Synnechococcus obliquus) supplemented with different amounts of cholesterol-containing liposomes to obtain four cholesterol concentrations of 0.25, 2.5, 5, and 8 µg per mg C. In all treatments, a small amount of eicosapentaenoic acid (20:5ω3) was also added via liposomes (resulting in 0.25 µg 20:5ω3 per mg C) in order to prevent severe 20:5ω3 limitation, thereby aiding the development of daphnids. The daphnids were grown at 27°C, a non-lethal yet super-optimal temperature. Heat tolerance (time to immobilization) of the daphnids from the different cholesterol treatments was tested on day seven at five different constant temperatures (34.5°, 35.5°, 36.5°, 37.5°, 38.5°C). Here, we provide the raw data, as well as the R scripts used to analyze the data. Funding provided by: Deutsche ForschungsgemeinschaftCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659Award Number: KO5330/1-1Funding provided by: GDR CNRS 3716 GRET*Crossref Funder Registry ID: Award Number:
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visibility 9visibility views 9 download downloads 10 Powered bymore_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2020Publisher:Zenodo Funded by:EC | PETA-CARBEC| PETA-CARBAuthors: Jongejans, Loeka L.; Strauss, Jens;This script was created to facilitate analysis of data (see data publication) pertaining to the publication: Jongejans, L. L., Strauss, J., Lenz, J., Peterse, F., Mangelsdorf, K., Fuchs, M. and Grosse, G. (2018). Organic matter characteristics in yedoma and thermokarst deposits on Baldwin Peninsula, west Alaska. Biogeosciences 15, 6033-6048. doi:10.5194/bg-15-6033-2018. The input data stem from sediment samples taken from two permafrost exposures in west Alaska. The input parameters are total organic carbon content, bulk density, wedge ice volume, deposit thickness and coverage. The script calculates the organic carbon storage of the permafrost sediments using a bootstrapping approach. The script was written for statistical software R (version 3.6.1). The current code and the required files are available on GitHub.
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2023Publisher:Zenodo Authors: Nielsen, Matthew; Nylin, Soren; Wiklund, Christer; Gotthard, Karl;Photoperiod is a common cue for seasonal plasticity and phenology, but climate change can create cue-environment mismatches for organisms that rely on it. Evolution could potentially correct these mismatches, but phenology often depends on multiple plastic decisions made during different life stages and seasons that may evolve separately. For example, Pararge aegeria (Speckled wood butterfly) has photoperiod-cued seasonal life history plasticity in two different life stages: larval development time and pupal diapause. We tested for climate-change-associated evolution of this plasticity by replicating common garden experiments conducted on two Swedish populations 30 years ago. We found evidence for evolutionary change in the contemporary larval reaction norm—although these changes differed between populations—but no evidence for evolution of the pupal reaction norm. This variation in evolution across life stages demonstrates the need to consider how climate change affects the whole life cycle to understand its impacts on phenology. Please see the main paper and readme files for full details on the methods associated with this dataset. Data on the historic experiment was digitized for this study from the original data sheets associated with Nylin et al 1989, 1995 (see main text for full citations). Data for the contemporary experiment was generated by the authors for this study, following the methods of the historic experiment. Temperature data came from the Swedish Hydrological and Meteorological Institute weather stations and was restructured, but otherwise used as provided by SHMI. Readme file is also plain text compatible (.txt). Data files are comma-separated values (.csv) format. Software files (.R) are written in in R.Funding provided by: VetenskapsrådetCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100004359Award Number: 2017-04500Funding provided by: Bolin Centre for Climate Research*Crossref Funder Registry ID: Award Number:
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2023Publisher:Zenodo Authors: Serra Yosmaoglu; Krajzewicz, Daniel; Nieland, Simon; Heldt, Benjamin;About NaMIx ("Sustainable mobility index to assess the location-related mobility potential", in German: "Nachhaltige-Mobilität-Index zur Bewertung des standortbezogenen Mobilitätspotentials") is a project that aims to develop an index for sustainable mobility at locations and for neighborhoods that incorporates existing data and indices and maps different spatial levels. You can find out more about the project here: https://verkehrsforschung.dlr.de/de/projekte/namix. Most of the needed data can be retrieved from OpenStreetMap (OSM). Public transport stops can be obtained from OpenStreetMap (OSM) or General Transit Feed Specification (GTFS). Please note that due to restrictions regarding the distribution of some of the used datatypes, we had to limit the functionality in comparison to what has been shown during the final project presentation. Given the current version, the locations of buildings are retrieved from OSM instead of using the BKG address dataset. In addition, schools are retrieved from OSM as well and instead of using access by foot to elementary schools and access by bike to secondary schools NaMIx version 0.2.0 computes the access to all schools obtained from OSM by walk and by bike. Installation The current version is "NaMIx-0.2.0". It computes ten indicators almost (see above) as presented at the final project presentation. Please note that current NaMIx is realised as a Jupyter Notebook and that it is currently available in German only. To run the computation, please do the following Download a version of NaMIx : You may download a copy or fork the code at NaMIx' github page. : Besides, you may download the current release here: NaMIx-0.2.0.zip NaMIx-0.2.0.tar.gz Depack the obtained file into a folder of your choice (named from now on) Open the command line in this folder Optionally create a virtual python environment (recommended) run python -m venv venv_namix run venv_namix\Scripts\activate.bat Run pip install -r requirements.txt to install all necessary dependencies Download the 0.6.0 version of UrMoAC from UrMoAC-0.6.0.zip. Extract the contents into /demo/tools so that the jar file is located directly within this folder. Download GTFS data (e.g. from MVG). Extract the contents so that can be found in /demo/input/GTFS. Start the jupyter notebook You should have a command line open in Run python -m jupyter notebook open "namix_demo.ipynb" in the notebook The notebook processes the input data, computes the individual indicators and the joined NaMIx indicator, and stores the result in a geopackage file named "/demo/namix.gpkg". Authors NaMIx was developed and implemented by Serra Yosmaoglu, Benjamin Heldt, Daniel Krajzewicz, and Simon Nieland. ChangeLog NaMIx 0.2.0 (31.10.2023) initial version License NaMIx is licensed under the Eclipse Public License 2.0. When using it, please cite it via the DOI: https://doi.org/10.5281/zenodo.8328622 (v 0.2.0) Support If you have a usage question, please contact us via email (serra.yosmaoglu@dlr.de). Disclaimer We are not responsible for the contents of the pages we link to. The software is provided "AS IS". We cannot guarantee that the software works as you expect. References Boeing, G. (2017). OSMnx: New Methods for Acquiring, Constructing, Analyzing, and Visualizing Complex Street Networks. Computers, Environment and Urban Systems 65, 126-139. doi:10.1016/j.compenvurbsys.2017.05.004 Krajzewicz, D., Heinrichs, D. & Cyganski, R. (2017). Intermodal Contour Accessibility Measures Computation Using the 'UrMo Accessibility Computer'. International Journal On Advances in Systems and Measurements, 10 (3&4), Seiten 111-123. IARIA. Heldt, B., Yosmaoglu, S. (2023). Neues Planungswerkzeug für Quartiere: Der Nachhaltige-Mobilität-Index. Emmett. https://emmett.io/article/der-nachhaltige-mobilitaet-index.
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2020Publisher:Zenodo Funded by:EC | FIThydroEC| FIThydrovan Treeck, Ruben; Radinger, Johannes; Noble, Richard; Geiger, Franz; Wolter, Christian;Hydroelectricity is critical for decarbonizing global energy production, but hydropower plants affect rivers, disrupt their continuity, and threaten migrating fishes. This puts hydroelectricity production in conflict with efforts to protect threatened species and re-connect fragmented ecosystems. Assessing the impact of hydropower on fishes will support informed decision-making during planning, commissioning, and operation of hydropower facilities. Few methods estimate mortalities of single species passing through hydropower turbines, but no commonly agreed tool assesses hazards of hydropower plants for fish populations. The European Fish Hazard Index bridges this gap. This assessment tool for screening ecological risk considers constellation specific effects of plant design and operation, the sensitivity and mortality of fish species and overarching conservation and environmental development targets for the river. Further, it facilitates impact mitigation of new and existing hydropower plants of various types across Europe. The tool does not yet support VBAs. In order to use it and produce reliable results, all input fields have to be reset manually before making a new assessment. The input window contains examplary dummy data.
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You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2021Publisher:Zenodo Trondrud, L. Monica; Pigeon, Gabriel; Król, Elżbieta; Albon, Steve; Evans, Alina L.; Arnold, Walter; Hambly, Catherine; Irvine, R. Justin; Ropstad, Erik; Stien, Audun; Veiberg, Vebjørn; Speakman, John R.; Loe, Leif Egil;1. The fasting endurance hypothesis (FEH) predicts strong selection for large body size in mammals living in environments where food supply is interrupted over prolonged periods of time. The Arctic is a highly seasonal and food restricted environment, but contrary to predictions from the FEH, empirical evidence shows that Arctic mammals are often smaller than their temperate conspecifics. Intraspecific studies integrating physiology and behaviour of different-sized individuals, may shed light on this paradox. 2. We tested the FEH in free-living Svalbard reindeer (Rangifer tarandus platyrhynchus). We measured daily energy expenditure (DEE), subcutaneous body temperature (Tsc) and activity levels during the late winter in 14 adult females with body masses ranging from 46.3 to 57.8 kg. Winter energy expenditure (WEE) and fasting endurance (FE) were modelled dynamically by combining these data with body composition measurements of culled individuals at the onset of winter (14 years, n = 140) and variation in activity level throughout winter (10 years, n = 70). 3. Mean DEE was 6.3±0.7 MJ day−1. Lean mass, Tsc and activity had significantly positive effects on DEE. Across all 140 individuals, mean FE was 85±17 days (range 48–137 days). In contrast to the predictions of the FEH, the dominant factor affecting FE was initial fat mass, while body mass and FE were not correlated. Furthermore, lean mass and fat mass were not correlated. FE was on average 80% (45 days) longer in fat than lean individuals of the same size. Reducing activity levels by ~16% or Tsc by ~5% increased FE by 7%, and 4%, respectively. 4. Our results fail to support the FEH. Rather, we demonstrate that (i) the size of fat reserves can be independent of lean mass and body size within a species, (ii) ecological and environmental variation influence FE via their effects on body composition, and (iii) physiological and behavioural adjustments can improve FE within individuals. Altogether, our results suggest that there is a selection in Svalbard reindeer to accumulate body fat, rather than to grow structurally large. The methods used to collect the data are described in Trondrud et al. 2021: "Fat storage influences fasting endurance more than body size in an ungulate. Accepted in Functional Ecology. Funding provided by: Norges ForskningsrådCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100005416Award Number: KLIMAFORSK 267613
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You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2023Publisher:Zenodo Londoñ-Nieto, Claudia; García-Roa, Roberto; Garcia-Co, Clara; González, Paula; Carazo, Pau;Fitness assays: quantifying male harm To study whether male harm is affected by temperature, we established a factorial design to measure survival and lifetime reproduction success (LRS) of female flies under monogamy (i.e., one male and one female per vial) vs. polyandry (i.e., three males and one female per vial), across three stable temperature treatments typical of this population during their reproductively active period in the wild: 20, 24, and 28°C. Comparison of female fitness at monogamy vs. polyandry is a common way to gauge male harm in Drosophila and other organisms (Yun, Agrawal, & Rundle, 2021), and our treatments reflect the low and high-end of the spectrum of sex ratios that are typical of D. melanogaster at mating patches in the wild (Dukas, 2020). We first randomly divided virgin flies into three groups that we allocated to the three different stable temperature treatments 48 hours before starting the experiment. Flies remained at those temperatures until the end of the experiment. To estimate LRS, we transferred flies to fresh vials twice a week using mild CO2 exposure anaesthesia. We incubated the vials containing female eggs at 24 ± 4°C for 15–20 days (~15 days for 28°C, ~17 days for 24°C and ~20 days for 20°C) to allow F1 offspring emergence, after which we froze them at -21°C for later counting. The differences in incubation time are due to differences in developmental time because of temperature differences in the first 3-4 days of each vial (i.e., before flipping females to new fresh vials). We discarded and replaced males by young (2 to 4 days old) virgin males three weeks after starting (at the same time for all treatments). We kept a stock of replacement males maintained at each of the three temperatures (20, 24 and 28°C) to replace dead male flies if needed. We kept flies under these conditions during six weeks, after which we discarded males and followed females until they died. We started the experiment with 468 females (78 per each temperature x mating system treatment) and 936 males (234 per each temperature x polyandry and 78 per each temperature x monogamy). Final sample sizes were: a) at 20°C: 74 females for polyandry and 76 females for monogamy; b) at 24°C: 72 females for polyandry and 77 females for monogamy; c) at 28°C: 70 females for polyandry and 75 females for monogamy. Differences between start and final sample sizes across treatments are due to discarded/escaped flies since the start of the experiment. We estimated the overall degree of male harm by calculating the relative harm (H) following Yun et al. (2021): H = (Wmonogamy - Wpolyandry) / Wmonogamy Finally, and using the data collected above, we partitioned overall effects on LRS into effects of temperature x mating system (i.e., male-male competition level) on early reproductive rate (i.e., offspring produced during the first two weeks of age) and reproductive (i.e., offspring produced over weeks 1–2 vs. 3–4) and actuarial senescence (i.e., survival). Behavioural assays: quantifying male-male aggression and harassment of females Immediately after the fitness experiment started, we conducted behavioural observations on the first day of the experiment across all treatments, to investigate the behavioural mechanisms that might underlie the potential fitness effects evaluated above. Due to logistic limitations, we conducted behavioural observations in the same temperature control room, so we had to conduct trials at 20, 24 and 28°C in three consecutive days (with both monogamy and polyandry treatments evaluated at the same time for each temperature), in randomized order (i.e., 20, 28 and 24°C). However, all flies were 5 days old at the start of the experiment. We measured the following behaviours: (a) courtship intensity (number of courtships experienced by a female per hour), (b) male-male aggression behaviours and (c) female rejection behaviours (Bastock & Manning, 1955; Connolly & Cook, 1973). We also recorded the number of total matings during the observation period. Observations started at lights‐on (10 a.m.) and lasted for 8 hr, during which time we continuously recorded reproductive behaviours using scan sampling of vials. Each complete scan lasted approximately 8 min, so that we always conducted one complete scan every 10 min to ensure recording of all matings (see below). Scans consisted in observing all vials in succession for ca. 3s each and recording all occurrences of the behaviours listed above. We interspersed these behavioural scans with very quick (<1 min) mating scans where we rapidly swept all vials for copulas at the beginning, in the middle and at the end of each behavioural scan. This strategy ensured that we recorded all successful matings (>10min), which typically last between 15 and 25min in our population of D. melanogaster, during our 8‐hr observation. We obtained a total of 49 scans per vial. Behavioural observations were conducted only once, on day 1 of the fitness experiment, as prior experiments have shown that courtship, aggressive and female rejection behaviours are stable over time in D. melanogaster, so that our behavioural indexes are representative of long-term treatment differences (e.g., Carazo, Perry, Johnson, Pizzari, & Wigby, 2015; Carazo, Tan, Allen, Wigby, & Pizzari, 2014). In contrast to courtship and aggression indexes, note that total mating frequency over the first day cannot be taken as a reliable measure of mating rate (Wolfner, 1997), and thus our rationale in recording this variable was just to ensure that early mating ensued normally across treatments (which was the case, see SI2). Female reproduction and survival assays: quantifying male ejaculate "toxicity" To examine post-mating mechanisms that might underlie the fitness effects observed in our first experiment, we conducted four additional assays to test whether temperature modulates the previously well-documented effects of male ejaculates on female reproduction and survival in D. melanogaster. Briefly, males of this species transfer seminal fluid proteins (SFPs) produced by their accessory glands that increase short-term female fecundity, as well as decrease female receptivity and survival (Chapman, Liddle, Kalb, Wolfner, & Partridge, 1995; Wigby & Chapman, 2005). In addition, prior studies have shown that males are able to tailor investment into SFPs according to the expected sperm competition risk and intensity (Hopkins et al., 2019). Thus, we set up a factorial design where we manipulated the temperature (i.e., 20, 24 and 28ºC) and perceived sperm competition risk levels (i.e., males kept alone vs. with 7 more males in a vial) at which adult males were kept prior to mating, for two temperature treatment durations (i.e., 48 hours or 13 days), and then measured how reception of their ejaculate in a common garden environment (i.e., 24ºC) affected female fecundity, survival and reproduction. Receptivity assays We first collected experimental males as virgins (i.e., within 6 h of eclosion) under ice anesthesia and randomly placed them either individually or in a same-sex group of 8 in medium containing plastic vials. Next, we randomly divided them into three groups that we allocated to the different stable temperature treatments for either 48 hours (experiment 1) or 13 days (experiment 2) immediately before the beginning of each experiment. In experiment 2 (treatment duration of 13 days), we emptied the seminal fluid of experimental males before we allocated them to the different temperature / competition treatments. To do so, we housed individually experimental males with four standard virgin females for 24 hours. This strategy ensured that spermatogenesis took place over the 13 days under the temperature / competition treatments. We collected all females and competitor males used in receptivity assays as virgins and held them in groups of 15 to 20 flies at 24 ± 4°C. Experiments started by exposing all virgin females to single experimental males for 2.5 h at 24°C. After a successful copulation, we separated the mated females from the males and kept them individually in medium-containing vials until the next mating trial. We discarded unmated females and experimental males. 72 h after the first mating, we individually exposed females to single virgin competitor males for 12 h. After each trial, we transferred unmated females into a new medium containing vial, until the next mating assay 24 h later. We repeated remating trials every 24 h for three consecutive days. We calculated the cumulative percentage of remated females for each of the three days of each experiment. We conducted the experiments in two blocks each: with n = 390 females for each batch in experiment 1 (n = 436 rematings) and n = 420 females for each batch in experiment 2 (n = 676 rematings). We also recorded mating duration for the first mating and mating latency (i.e., time between males being introduced into the female-containing vial and copulation) and mating duration for re-matings. Females that did not remate within those three days were right-censored. Females and all experimental males were 4 days old at the start of experiment 1. In experiment 2, females and "re-mating" competitor males were 4 days old, while experimental males were 18 days old. Fecundity and survival assays To gauge effects on female short-term fecundity and long-term survival, we performed two experiments (experiments 3 and 4) where we compared the oviposition and egg fertility of females mated with male flies subject to the same factorial design imposed in receptivity experiments. We collected and treated all experimental males as in the receptivity assays described above, and then proceeded to mate ~4-day-old virgin females in single pairs to either 4- (experiment 3, 48h temperature treatment duration) or 18-day-old experimental males (experiment 4, 13d temperature treatment duration) for 2.5h at 24°C. After copulation, we separated mated females from males and kept them individually in medium-containing vials. We discarded unmated females. We then transferred females to fresh vials every 24h for 4 days, and then every 3 days twice. Later, we transferred female flies to fresh vials once a week, and we combined vials to maintain density at ten flies per vial. We kept female flies under these conditions until they died. We removed dead flies at each transfer and recorded female deaths. We counted eggs laid the first 3 days and vials from days 1, 2, 3, 4, 5, and 8 after mating were retained to count progeny to determine egg viability. We tested 545 females at the starting point of the experiment 3, and 480 females at the starting point of the experiment 4. Statistical analyses We performed all statistical analyses using R statistical software (version 3.5.2). In all models, we assessed fit by visual inspections of diagnostic plots on raw and residual data (Zuur, Ieno, & Elphick, 2010). To examine temperature effects on male harm, we evaluated the interaction between mating system and temperature on female fitness (LRS), survival and male and female reproductive behaviours. We fitted generalized linear models (GLMs) with temperature, mating system and their interaction as fixed effects. We also used Cox proportional hazards survival model to analyse potential differences in mortality risk across treatments, using the survival and survminer packages, including the females lost during manipulations as "right censored" individuals (i.e., individuals that are taken into account for demographic analysis until the day they disappear, Kleinbaum & Klein, 2012). We also censored any remaining females after the six weeks of the experiment. Graphical inspection of LRS and reproductive behaviours (courtship intensity, intersexual aggression behaviours and female rejection) revealed that the normality assumption was apparently violated, as well as the independence assumption for LRS. Box–Cox transformation (Quinn & Keough, 2002) solved these problems and allowed us to run a GLM with a Gaussian error distribution. In all these afore mentioned cases, fitted models were subsequently validated. In addition, we compared GLMs with their corresponding null GLMs using likelihood ratio test. In all models, we used ANOVA type III to compute p-values. We detected a problem of collinearity between mating system and the interaction in the LRS model. We fitted the model again without the main mating system effect (which was not our main interest) and also ran models separately for each temperature level. As a complementary analysis, we ran a model with temperature as factor with a quadratic contrast table predetermined (note that the relation between LRS and temperature does not seem to be linear, Fig 1), obtaining similar results. For the total matings recorded across the 8h observation period (i.e., mating rate), we initially used a GLM with Poisson errors. However, the dataset contained many zero values. We therefore analysed the data using a Hurdle model, in which the zero values are modelled separately from the nonzero values (Zuur et al., 2010). Additionally, we compared GLM and Hurdle models using an information-theoretic approach based on Akaike's Information Criterion (AIC). The minimum AICc value indicates the best-supported model given the trade-off between fit to the data and model complexity (Konishi & Kitagawa, 2008). To estimate how male harm impact estimated population growth across varying demographic scenarios (i.e., decreasing, stable and growing populations), based on our LRS measures, we calculated rate-sensitive fitness estimates (Edward, Fricke, Gerrard, & Chapman, 2011) against different population background growth rates of r = -0.1, r = -0.05, r = 0, r = 0.05 and r = 0.1. For receptivity (mating duration and remating latency) and fecundity (total adults) analyses, we fitted generalized linear models (GLMs) with temperature, sperm competition risk level, treatment duration and their interaction as fixed effects. For egg production data, we fitted a generalized linear mixed model (GLMM) with temperature, sperm competition risk level, treatment duration and their interaction as fixed effects and day number as a random effect, with a zero inflated distribution, in which the zero values are modelled separately from the nonzero values (Zuur et al., 2010). We assessed significance of factors by dropping individual terms from the full model using the "drop1" function, refitting where the interaction was nonsignificant. We also used Cox proportional hazards survival model to analyse potential differences in mortality risk across treatments, using the survival and survminer packages, including the females lost during manipulations as "right censored" individuals. Finally, we also ran models separately for each temperature level for the cases in which a significant interaction between sperm competition risk level and temperature treatment was detected. Strong sexual selection frequently leads to sexual conflict and ensuing male harm, whereby males increase their reproductive success at the expense of harming females. Male harm is a widespread evolutionary phenomenon with a strong bearing on population viability. Thus, understanding how it unfolds in the wild is a current priority. Here, we sampled a wild Drosophila melanogaster population and studied male harm across the normal range of temperatures under which it reproduces optimally in nature by comparing female lifetime reproductive success and underlying male harm mechanisms under monogamy (i.e., low male competition/harm) vs. polyandry (i.e., high male competition/harm). While females had equal lifetime reproductive success across temperatures under monogamy, polyandry resulted in a maximum decrease of female fitness at 24°C (35%), reducing its impact at both 20°C (22%), and 28°C (10%). Furthermore, female fitness components and pre- (i.e., harassment) and post-copulatory (i.e., ejaculate toxicity) mechanisms of male harm were asymmetrically affected by temperature. At 20ºC, male harassment of females was reduced, and polyandry accelerated female actuarial ageing. In contrast, the effect of mating on female receptivity (a component of ejaculate toxicity) was only modulated at 28ºC, where the mating costs for females decreased and polyandry mostly resulted in accelerated reproductive ageing. We thus show that, across a natural thermal range, sexual conflict processes and their effects on female fitness components are plastic and complex. As a result, the net effect of male harm on overall population viability is likely to be lower than previously surmised. We discuss how such plasticity may affect selection, adaptation and, ultimately, evolutionary rescue under a warming climate. Data files included are .xlsx. We performed all statistical analyses using R statistical software.Funding provided by: MCIN/AEI/10.13039/501100011033*Crossref Funder Registry ID: Award Number: PID2020-118027GB-I00Funding provided by: Ministerio de Educación Cultura y Deportes*Crossref Funder Registry ID: Award Number: Juan de la Cierva Formación FJC2018-037058-IFunding provided by: MINECO Spanish Goverment*Crossref Funder Registry ID: Award Number: PRE2018-084009Funding provided by: Generalitat ValencianaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100003359Award Number: AICO/2021/113
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For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2024Publisher:Zenodo Shu, David Yang; Reinert, Christiane; Mannhardt, Jacob; Leenders, Ludger; Lüthje, Jannik; Mitsos, Alexander; Bardow, André;Referencing If you use our software or any part of it, please cite Shu et al. (2023). The full information on the publication is also shown below: Shu, D.Y. *; Reinert, C. *; Mannhardt, J.*; Leenders, L.; Lüthje, J.; Mitsos, A.; and Bardow, A. (2023): "Overcoming the Central Planner Approach – Bilevel Optimization of the European Energy Transition". Accepted in iScience. *Equal contribution. Since the publication above and this repository mainly describe the extensions compared to the linear SecMOD, please also refer to Reinert et al. (2022) for further information. The full information on the SecMOD publication is also shown below: Reinert, C.; Schellhas, L.; Mannhardt, J.; Shu, D.; Kämper, A.; Baumgärtner, N.; Deutz, S., and Bardow, A. (2022): "SecMOD: An open-source modular framework combining multi-sector system optimization and life-cycle assessment". Frontiers in Energy Research. DOI: https://doi.org/10.3389/fenrg.2022.884525. Documentation and Support Please find the full documentation of the SecMOD LP framework here. You can further find a video about SecMOD and some example applications here. In case you need help using Git, please refer to the git documentation here. Installation A brief instruction to install SecMOD can also be found below: Clone a copy of the whole repository to your computer: git clone git@git-ce.rwth-aachen.de:ltt/secmod-bilevel.git Open a terminal with a python enviroment (e.g. Anaconda promt) and install the secmod package with: pip install --user -e '' The path should point to the directory where secmod is saved (repository folder). Make sure that the setup.py file is located in your repository folder. You can use this installation for several projects in multiple working directories. For further installation instruction please go here. The code was tested with Python 3.7.5.
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