Find research datasets worth reusing

opencc-by-4.0Nov 2022View details →

Processed model output used in 'The impact of winds on AMOC in a fully-coupled climate model'

Processed model output from wind-nudging experiments used to investigate the Atlantic Meridional Overturning Circulation.    For further details, see  Roach, L. A, Blanchard-Wrigglesworth E. Ragen, S., Cheng, W., Armour, K. and Bitz, C. M.. (2022). The impact of winds on AMOC in a fully-coupled climate model. In review at Geophysical Research Letters

opencc-by-4.0Nov 2022View details →

Pore-scale modeling and investigation on thermal-hydro-mechanical-chemical coupled rock dissolution and fracturing process

Attached files include the executable file of the pore-scale multi-field coupled LBM-DEM program written by C language, post-processing programs to record the reactive surface area and reactive temperature written by MATLAB, and the simulation results of rock acid fracturing with 20MPa at the injection hole.

openNov 2022View details →

Intermediate data belonging to "Process-based climate change assessment for European winds using EURO-CORDEX and global models"

This dataset contains the intermediate results of Wohland (2022) that are needed to redo the analysis und produce the figures. It allows to bypass those steps that rely on access to the supercomputers at the German Climate Computing Centre (DKRZ). When using this data in academic work, please reference <blockquote> Jan Wohland, Process-based climate change assessment for European winds using EURO-CORDEX and global models, Environmental Research Letters (provisionally accepted on 28/11/2022), 2022 </blockquote> Using this data to reproduce results The data can be used together with the code provided in https://github.com/jwohland/kliwist_modelchain In the above mentioned github repository, there is a `run_all.py` script that repeats the analysis presented in Wohland (2022). After downloading and extracting this data, you can ignore the steps under "calculations", and begin with "plots". Underlying data The dataset draws on output from the CMIP5, CMIP6 and EURO-CORDEX initiatives. I thank the climate modeling groups for making their data openly available. In particular, I acknowledge the World Climate Research Programme’s Working Group on Regional Climate, and the Working Group on Coupled Modelling, former coordinating body of CORDEX and responsible panel for CMIP5. I also acknowledge the Earth System Grid Federation infrastructure an international effort led by the U.S. Department of Energy’s Program for Climate Model Diagnosis and Intercomparison, the European Network for Earth System Modelling and other partners in the Global Organisation for Earth System Science Portals (GO-ESSP). I also acknowledge the World Climate Research Programme, which, through its Working Group on Coupled Modelling, coordinated and promoted CMIP5 and CMIP6. Funding This work is part of the project "The influence of climate change on wind energy site assessments – KliWiSt" funded by the German Federal Ministry for Economic Affairs and Climate Action (BMWK). References to raw data journal articles <blockquote> Jacob, D. et al. EURO-CORDEX: new high-resolution climate change projections for European impact research. Reg Environ Change 14, 563–578 (2014). </blockquote> <blockquote> Taylor, K. E., Stouffer, R. J. & Meehl, G. A. An Overview of CMIP5 and the Experiment Design. Bull. Amer. Meteor. Soc. 93, 485–498 (2012). </blockquote> <blockquote> Hurtt, G. C. et al. Harmonization of land-use scenarios for the period 1500–2100: 600 years of global gridded annual land-use transitions, wood harvest, and resulting secondary lands. Climatic Change 109, 117–161 (2011). </blockquote>

Processed data used for spatial analysis of DMD mouse models

This repository contains seurat objects and .H5AD files that were used in the analysis described in the paper titled "Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models" Authors: L.G.M. Heezen, T. Abdelaal, M. van Putten, A. Aartsma-Rus, A. Mahfouz and P. Spitali It contains datafiles obtained from spatial transcriptomics (Visium, 10x Genomics) experiments on skeletal muscle samples from two wildtypes: C57BL10 and DBA/2J and two DMD mouse models: mdx and D2-mdx. All ten weeks old male mice, 10micron thick sections of the quadriceps.

Pre-processed radial wind: sample data

Sample data for testing and developing wind retrievals. Each file contains one hour of pre-processed (merged) WindCube observations.

opencc-zeroDec 2022View details →

Teaching the process of science with primary literature: Using the CREATE pedagogy in ecological courses

There have been numerous calls for improved pedagogical practices in biological education, and there is a clear need for such improvements in ecology and related curricula. Most ecology-related texts lack pedagogy and are designed to be content-rich. National initiatives, such as Vision & Change, provide guidance on undergraduate biology education, including increasing use of evidence-based active learning, and taking a more conceptual and science practice skills approach. Biology education research is rich with evidence-based teaching practices, which reveal that active learning approaches implemented in thoughtful ways lead to strong learning gains relative to lecture-based course delivery. CREATE (Consider, Read, Elucidate the hypothesis, Analyze and interpret data, Think of the next Experiment) integrates evidence-based active pedagogical practices into one approach to STEM education that focuses heavily on the process of science and science practice skills rather than content delivery by replacing the textbook with selected journal articles. The approach focuses on deep reading and analysis of primary literature; immersing students in the literature is an advantage of the pedagogy. CREATE was developed and tested in other biological disciplines (genetics, molecular biology) that have long been at the forefront of pedagogical best practices in biology. We transformed two upper-level undergraduate ecological courses (Conservation Biology & Biodiversity and Ecology) into CREATE courses. We provide examples of assignments, student work, and assessments of the approach, illustrating the various ways CREATE can be successfully implemented. The approach can be adopted in part, to ease into it and test it out, or in whole. We recommend that ecology teachers consider making their courses more active if they have not already done so; adopting pedagogical practices embedded within CREATE can be a way to achieve active learning. The CREATE approach and other evidence-based pedagogical best practices lead to strong learning gains and more inclusive learning environments.

Processing code and data for ERA5 analysis

Data, processing code, and instructions for ERA5 analysis

opencc-zeroDec 2022View details →

Data for: Foster children's perspectives on participation in child welfare processes

The objective of this meta-synthesis was to systematically synthesise qualitative research that explores foster children's perspectives on participation in child welfare processes. Searches were conducted in Medline (OVID), Embase, PsycINFO, and Social Science Citation Index. Children in non-kinship foster care in any setting (high-income, middle-income, low-income countries) who self-reported their experiences of care (removal from home, foster family processes, placement breakdown) were eligible for inclusion. Selected studies took place in 11 high-income countries. A total of 8436 citations were identified and 25 articles were included in this meta-synthesis. Studies summarized the views of 376 children. Children had been in foster care for between two weeks and 17 years. Findings synthesize 'facets' of children's participation (e.g., being asked vs making decisions), as well as children's perceived barriers and facilitators to participation. One main priority for children was the quality of their relationships, especially in terms of values (e.g., fairness, honesty, inclusivity). No one way of participating in child welfare processes is better than another, as some children more clearly expressed a desire for passive listening roles and others indicated a desire for active roles in decision-making. However, meaningful adults in foster children's lives have a responsibility to act in a way that strengthens the emphasis on children's needs and voices.

THE PRODUCTION PROCESS OF GROWING WINTER CROPS IN RUSSIA

The article discusses the technology of growing winter crops in Russia. When preparing the soil for winter crops, special attention is paid to the degree of soil cutting, since sowing winter crops in lumpy and unsettled soil leads to their mass death. In this regard, when selecting predecessors for winter crops, the timing of their harvesting and the duration of the free period before sowing winter crops are especially taken into account.

Extraction Forms about Challenges and Problems of Software Processes in the Context of Global Software Development: A Systematic Mapping Study

Extraction Forms of the Systematic Mapping Study about Challenges and Problems of Software Processes in the Context of Global Software Development. 50 papers were analized.

opencc-by-4.0Oct 2022View details →

Pulse, Shunt and Storage: Hydrological Contraction Shapes Processing and Export of Particulate Organic Matter in River Networks

This repository hosts the code to run the analysis presented in  "Pulse, Shunt and Storage: Hydrological Contraction Shapes Processing and Export of Particulate Organic Matter in River Networks"  by Catalan et al., Ecosystems, 2022. DOI: https://doi.org/10.1007/s10021-022-00802-4 The code has been tested on Matlab R2019b. Run the Main.m code to produce the results of Figure 3 and 4 of the paper. Each simulation takes about 8 hours on a standard Desktop computer.

Current-driven writing process in antiferromagnetic Mn_2Au for memory applications

Current pulse induced resistance changes in Mn2Au(001) epitaxial thin films associated with Néel vector reorientation.

openother-atDec 2022View details →

Material from a collaborative analysis with young people. Insights into the analysis process of R&I Action #2 Youth Employment of the CoAct project

The collaborative data analysis presented in this document was undertaken in the context of the research project CoAct (Co-designing Citizen Social Science for Collective Action) as part of the R&I Action #2 on Youth Employment. In this R&I Action, using Citizen Social Science as a research approach, young people aged between 15 and 21 years in employment measures in Vienna/Austria participated in collaborative social research activities. The visualisation of data analysis in the form of posters, is a selection of the collaborative analysis of qualitative expert interviews using the the “Stop and Go” (Harrasser, 2017) method. Following this method, audio recording of interviews, done by the young co-researchers themselves, are listened to and summarized as well as connected to the co-researchers’ own experience. The Creative Commons license and a recommendation regarding the citation of the material are provided in the document. For more information please contact veronika.woehrer@univie.ac.at

Processing steps to generate a Digital Surface Model based on SPOT-7 tri-stereo images published in the study "An assessment of the effects of DEM quality and spatial resolution on a model for mapping lahar inundation areas at volcan Copahue (Argentina & Chile)" in the Journal of South American Earth Sciences https://doi.org/10.1016/j.jsames.2022.104138

The Digital Surface Model (DSM) was created from SPOT-7 tri-stereo images for the Copahue volcano between the border of Argentina and Chile. Two versions of the DSM are provided: an unfiltered product and a final, filtered product. The final product has a spatial resolution of 5-m and was used for lahar inundation modeling for the Copahue volcano (Viotto, Toyos, and Bookhagen 2022, <a href="https://doi.org/10.1016/j.jsames.2022.104138">https://doi.org/10.1016/j.jsames.2022.104138</a> : An assessment of the effects of DEM quality and spatial resolution on a model for mapping lahar hazard inundation at Volcán Copahue (Argentina & Chile). Journal of South American Earth Sciences ). The dataset provided should be cited together with the article.  DSM processing  The source images were given by a SPOT-7 snow- and cloud-free triplet (Nadir, Backward and Forward) of 1.5 m spatial resolution from 19 April 2018 (SPOT Image, Airbus Defence and Space GmbH, distributed by CONAE; Dataset ID:  SEN_SPOT7_20180419_142955500_000, delivered by CONAE as DS_SPOT7_20180419). The data were processed with the suite of digital photogrammetry tools AMES Stereo Pipeline ASP (Beyer et al., 2018). The procedure for the generation of the DSM is summarized by following steps:  <ol> <li> The orbital parameters (RCP models) were adjusted using the bundle adjustment tool with no ground control points, since they were unavailable. </li> <li> The scenes were map-projected onto the NASADEM (spatial resolution of 30 m)  elevation dataset, assisted by the results of the orbital adjustment in Step 1. </li> <li>The stereo correlation of the map-projected scenes including the results of the adjusted orbital parameters, was performed three times, using as first scene (i.e., primary image) the nadir (N), backward (B), and forward (F) images . In each run, the order of images to perform the stereo correlation was: N-F-B, F-N-B, and B-N-F. Thus, three point clouds were generated. Specific ASP correlator settings (other than defaults parameters; for details see the provided stereo-default file) were set in the following way:  Correlation Kernel: 15 x 15 pixels; Sub-pixel Refinement Kernel: 21 x 21 pixels; Subpixel Refinement Mode: 2 (Weighted Affine Adaptive Window Correlator EM)</li> <li> The three point clouds were merged into one point cloud with a regular grid of 5 m (unfiltered product, known as DSM_Copahue_UTM19S_WGS84_5m_raw.tif). </li> </ol> The quality of the final point cloud was assessed by comparing the unfiltered DSM with a spatial resolution of 12-m against the WorldDEMTM  elevation dataset (Collins et al., 2015). The WorldDEM was provided by Airbus Defence and Space GmbH under license for the scope of the Viotto et al., 2022 study. The comparison of the pixel-to-pixel heights above the ellipsoid (WGS84) between the two datasets resulted in a mean difference of 0.67 m and a standard deviation of +/- 4.82 m.  Comprehensive details on the methodologies evaluated  to create the dataset with ASP, can be found in the corresponding master's thesis  “Topografía digital y modelado de lahares en el Volcán Copahue, Argentina-Chile” from S. Viotto (link: https://rdu.unc.edu.ar/handle/11086/15384). Recommended literature about processing DEMs from SPOT imagery is given by Mueting et al., 2021 (<a href="https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021JF006330">https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021JF006330</a>).  Creation of the Final, Filtered DSM product The corrections and improvements applied to the unfiltered product to create the final, filtered DSM (named DSM_Copahue_UTM19S_WGS84_5m_VoidFilled.tif) are summarized by following steps.    <ol> <li> Water Bodies Delineation </li> </ol> The delineation of the water bodies was based on a mask created from the free access water bodies datasets provided by the Instituto Geográfico Nacional of Argentina (<a href="https://www.ign.gob.ar/NuestrasActividades/InformacionGeoespacial/CapasSIG">https://www.ign.gob.ar/ NuestrasActividades/InformacionGeoespacia l/CapasSIG</a>) and by the Ministerio de Bienes Nacionales in Chile ( <a href="https://www.ide.cl/index.php/aguas-continentales/item/1508-catastro-de-lagos">https://www.ide.cl/index.php /aguas-continentales/item/1508-catastro-de-lagos</a>). A total of 45 lakes within the area of interest were considered. Lakes with areas below or equal to 25 m2 were smoothed with a median filter in the last step. Lakes with areas  above this threshold were filled in with a constant value and their borders  were smoothed with a median filter to provide smooth shorelines. 2 . Void Filling Voids (other than water bodies) were filled with the tool “Close Gaps” from Saga GIS software.   3. Smoothing Finally, the elevation dataset was smoothed with a median filter using a 3 x 3 pixel  window, excluding water bodies filled in the step 1.   Final Remarks and Suggestion The quality assessment of the final version by visual inspection of the hillshades suggested an improvement of the signal to noise ratio. However, the void filling process may be improved.   Dataset Description <table align="center"> <caption> </caption> <tbody> <tr> <td>Digital Surface Models</td> <td> No Data Value = -9999 Format = float 32 bit File Format = GeoTiff Vertical Datum: WGS84 Projection information: EPSG 32719 (UTM19S) Spatial Resolution: 5m (subfix: _5m)  Versions:  <ul> <li> Unfiltered product: without corrections DSM_Copahue_UTM19S_WGS84_5m_raw.tif </li> <li> Final, filtered product: smoothed and void filled DSM_Copahue_UTM19S_WGS84_5m_VoidFilled.tif </li> </ul> </td> </tr> <tr> <td>Water Bodies Mask</td> <td> No Lake Value = 0 Lakes Values = 1 to 45 File Format= GeoTiff Spatial Resolution: 5m (subfix: _5m) Projection information : EPSG 32719 (UTM19S) WB_mask_5m_UTM19S.tif </td> </tr> </tbody> </table>     Repository structure |__ 01_Scripts     |+ run21_CopahueDSM_AMES_sviotto.sh     |+ stereo.default |__ 02_DSMs     |+ DSM_Copahue_UTM19S_WGS84_5m_raw.tif     |+ DSM_Copahue_UTM19S_WGS84_5m_VoidFilled.tif     |+  WB_mask_5m_UTM19S.tif References Beyer, R. A., Alexandrov, O., & McMichael, S. (2018). The Ames Stereo Pipeline: NASA's open source software for deriving and processing terrain data. Earth and Space Science, 5, 537– 548. <a href="https://doi.org/10.1029/2018EA000409">https://doi.org/10.1029/2018EA000409</a> Collins, J., Riegler, G., Schrader, H., Tinz, M., 2015. Applying terrain and hydrological editing to TanDEM-X data to create a consumer-ready worlddem product. Int. Arch. Photogram. Rem. Sens. Spatial Inf. Sci. 40 (7), 1149. https://doi.org/10.5194/isprsarchives-XL-7-W3-1149-2015. Mueting, A., Bookhagen, B., & Strecker, M. R. (2021). Identification of debris-flow channels using high-resolution topographic data: A case study in the Quebrada del Toro, NW Argentina. Journal of Geophysical Research: Earth Surface, 126, e2021JF006330. <a href="https://doi.org/10.1029/2021JF006330">https://doi.org/10.1029/2021JF006330</a> Viotto, S., Toyos, G., & Bookhagen, B. (2022). An assessment of the effects of DEM quality and spatial resolution on a model for mapping lahar hazard inundation at volcán copahue (Argentina & Chile). Journal of South American Earth Sciences, 104138.  https://doi.org/10.1016/j.jsames.2022.104138

opencc-zeroDec 2022View details →

A basic community dynamics experiment: Disentangling deterministic and stochastic processes in structuring ecological communities

Community dynamics are governed by two opposed processes: species sorting, which produces deterministic dynamics leading to an equilibrium state, and ecological drift, which produces stochastic dynamics. Despite a great deal of theoretical and empirical work aiming to demonstrate the predominance of one or the other of these processes, the importance of drift in structuring communities and maintaining species diversity remains contested. Here we present the results of a basic community dynamics experiment using floating aquatic plants, designed to measure the relative contributions of species sorting and ecological drift to community change over about a dozen generations. We found that species sorting became overwhelmingly dominant as the experiment progressed, and directed communities towards a stable equilibrium state maintained by negative frequency-dependent selection. The dynamics of any particular species depended on how far its initial frequency was from its equilibrium frequency, however, and consequently the balance of sorting and drift varied among species.

opencc-zeroJan 2023View details →

Information theoretic evidence for layer- and frequency-specific changes in cortical information processing under anesthesia

Nature relies on highly distributed computation for the processing of information in nervous systems across the entire animal kingdom. Such distributed computation can be more easily understood if decomposed into the three elementary components of information processing, i.e., storage, transfer and modification, and rigorous information theoretic measures for these components exist. However, the distributed computation is often also linked to neural dynamics exhibiting distinct rhythms. Thus, it would be beneficial to associate the above components of information processing with distinct rhythmic processes where possible. Here we focus on the storage of information in neural dynamics and introduce a novel spectrally-resolved measure of active information storage (AIS). Drawing on intracortical recordings of neural activity in ferrets under anesthesia before and after loss of consciousness (LOC), we show that anesthesia-related modulation of AIS is highly specific to different frequency bands and that these frequency-specific effects differ across cortical layers and brain regions. We found that in the high/low gamma band, the effects of anesthesia result in AIS modulation only in the supergranular layers, while in the alpha/beta band, the strongest decrease in AIS can be seen at infragranular layers. Finally, we show that the increase of spectral power at multiple frequencies, in particular at alpha and delta bands in frontal areas, that is often observed during LOC ('anteriorization') also impacts local information processing – but in a frequency-specific way: Increases in isoflurane concentration induced a decrease in AIS in the alpha frequencies, while they increased AIS in the delta frequency range $<2$Hz. Thus, the analysis of spectrally-resolved AIS provides valuable additional insights into changes in cortical information processing under anaesthesia.

opencc-by-4.0Jan 2023View details →

Dataset - Observation of photon-photon thermodynamic processes under negative optical temperature conditions

Experimental data and simulation results associated with the article: Observation of photon-photon thermodynamic processes under negative optical temperature conditions

opencc-by-4.0Jan 2023View details →

ALL processed data of quantification of Total, viable and VC population

Processed data set of qPCR, PMA-qPCR and agar enumeration of the article. These data are sorted according to the D2O concentration used (0%, 25%, 50% or 75%), and according to the incubation time

GhmCN example processed datasets

This dataset is to be used with the code from https://github.com/ay-lab/GhmCN Download and untar inside the folder GhmCN/src/data