Find research datasets worth reusing

opencc-by-4.0Feb 2022View details →

Raw output data for "Covalency in actinide(IV) hexachlorides in relation to the chlorine K-edge X-ray absorption structure", DOI: 10.1039/D1SC06454A

This repository contains raw output files related to the following article: Authors: Dumitru-Claudiu Sergentu and Jochen Autschbach Title: Covalency in Actinide(IV) Hexachlorides in Relation to Chlorine K-Edge X-ray Absorption Structure DOI: https://doi.org/10.1039/D1SC06454A Each archive: 1) ThCl6.rar 2) UCl6.rar 3) NpCl6.rar and 4) PuCl6.rar contains output data produced by ADF (raw DFT outputs associated with the article, the ADF program can be found at: https://www.scm.com/product/adf/) and OpenMolcas (raw RASSCF and RASSI outputs associated with the article, the OpenMolcas program can be found at: https://gitlab.com/Molcas/OpenMolcas). Each folder in the archives contains 00README.txt files describing its content(s).

opencc-by-4.0Feb 2022View details →

Data of " Micromechanical characterization of the material response in a PA12-SLS fabricated lattice structure and its correlation with bulk behavior"

<pre>Data related to the publication (we would be grateful if you could cite the paper in the case in which you are using the data) title = "Micromechanical characterization of the material response in a PA12-SLS fabricated lattice structure and its correlation with bulk behavior", journal = "Polymer Testing", pages = " ", year = "2022", issn = "####", doi = "<a href="https://doi.org/10.1016/j.polymertesting.2022.107556">https://doi.org/10.1016/j.polymertesting.2022.107556</a>", author = "L. Cobian, M. Rueda-Ruiz, J.P. Fernandez-Blazquez, V. Martinez, F. Galvez, F. Karayagiz, T. Lück, J. Segurado, M.A. Monclus"</pre> This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 862015

Data of the protocol paper: Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST

The archived file contains data of the test cases used used in the protocol paper. For each protocol, there's a folder containing input files the protocol takes, and a folder for the protocol output files.

opencc-by-4.0Mar 2022View details →

Research Data For "Structure and Interactions at the Mg(0001)/Water Interface: An ab initio Study" Paper

This folder contains data used in the paper "Structure and Interactions at the Mg/Water Interface: An ab initio Study". Some details on the structure are as follows: The folder "figures" contains data to create various figures in the main paper. The folder "md_traj" contains the molecular dynamics trajectory. The file "traj.exyz" is a standard format which can be opened with various software. "traj.json" contains the same information in an in-house format used by the author. The "thermo_data.json" contains various thermodynamics properties over the simulation, such as temperatures and kinetic energies. Units are femtoseconds, Angstrom, electron-volts and Kelvin. The folders "mg_plus_clusters"/"mg_plus_monomer"/"misc_reference_structs" contain geometries for various structures used in the paper (in *.exyz format). These also contain *.json files; these contain information on how the calculations were carried out in a format used by the author (they are small files primarily included for the benefit of the author).

opencc-zeroMar 2022View details →

Data from: Trait hierarchies are stronger than trait dissimilarities in structuring spatial co-occurrence patterns of common tree species in a subtropical forest

1. The dissimilarity and hierarchy of trait values that characterize niche and fitness differences, respectively, have been increasingly applied to infer mechanisms driving community assembly and to explain species co-occurrence patterns. Here, we predict that limiting similarity should result in the spatial segregation of functionally similar species, while functionally similar species will be more likely to co-occur either due to environmental filtering or competitive exclusion of inferior competitors (hereafter hierarchical competition). 2. We used a fully mapped 50-ha subtropical forest plot in southern China to explore how pairwise spatial associations between saplings and between adult trees were influenced by trait dissimilarity and hierarchy in order to gain insight into assembly mechanisms. We assessed pairwise spatial associations using two summary statistics of spatial point patterns at different spatial scales and compared the effects of trait dissimilarity and trait hierarchy of different functional traits on the interspecific spatial associations. These comparisons allow us to disentangle the effects of limiting similarity, environmental filtering and hierarchical competition on species co-occurrence. 3. We found that trait dissimilarity was generally negatively related with interspecific spatial associations for both saplings and adult trees across spatial scales, meaning that species with similar trait values were more likely to co-occur and thus supporting environmental filtering or hierarchical competition. We further found that trait hierarchy outweighed trait dissimilarity in structuring pairwise spatial associations, suggesting that hierarchical competition played a more important role in structuring our forest community than environmental filtering across life stages. 4. This study employed a novel method, by offering the integration of pairwise spatial association and trait dissimilarity as well as trait hierarchy, to disentangle the relative importance of multiple assembly mechanisms in structuring co-occurrence patterns, especially the mechanisms of environmental filtering and hierarchical competition, which lead to indistinguishable co-occurrence patterns. This study also reinforced the importance of trait hierarchy rather than trait dissimilarity in driving neighborhood competition.

opencc-by-4.0Jan 2022View details →

Data and code for the article "Hierarchical tensile structures with ultralow mechanical dissipation"

Data and code for the article "Hierarchical tensile structures with ultralow mechanical dissipation", consisting of all the ringdown measurements, spectra and codes for data analysis and generation of the fabrication GDS masks.

opencc-zeroApr 2022View details →

Data from: Do experimental pH increases alter the structure and function of a lowland tropical stream?

Disturbances can alter the structure and function of ecosystems. In stream ecosystems, changes in discharge and physicochemistry at short, intermediate, and long recurrence intervals can affect food webs and ecosystem processes. In this paper, we compare pH regimes in streams at La Selva Biological Station, Costa Rica, where episodic acidification frequency across the stream network varies widely due to buffering from inputs of bicarbonate-rich inter-basin groundwater. To examine the effects of acidification on ecosystem structure and function, we experimentally increased the buffering capacity of a headwater stream reach, and compared it to an unbuffered upstream reach. We compared these reaches to a naturally buffered and unbuffered reaches of a second headwater stream. We quantified ecosystem structural (macroinvertebrate assemblages on leaf litter and coarse woody debris), and functional responses (leaf litter and coarse woody debris decomposition rates, and growth rates of a focal insect taxon (Diptera: Chironomidae)). Non-metric multidimensional scaling and analysis of similarity revealed that macroinvertebrate assemblages were relatively homogenous across the four study reaches, although the naturally buffered reach was the most dissimilar. Ecosystem function, as measured by chironomid growth rates, was greater in the naturally buffered reach, while decomposition rates did not differ across the four reaches. Our results indicate that biological assemblages are adapted to pH regimes of frequently acidified stream reaches. Our experiment informs the effects on structure and function at short time scales in streams that experience moderate acidification, but larger magnitude acidification events in response to hydroclimatic change, as projected under climate change scenarios, may induce stronger responses in streams.

opencc-zeroApr 2022View details →

Improving landscape-scale productivity estimates by integrating trait-based models and remotely-sensed foliar-trait and canopy-structural data

Assessing the impacts of anthropogenic degradation and climate change on global carbon cycling is hindered by a lack of clear, flexible, and easy-to-use productivity models along with scarce trait and productivity data for parameterizing and testing those models. We provide a simple solution: a mechanistic framework (RS-CFM) that combines remotely-sensed foliar-trait and canopy-structural data with trait-based metabolic theory to efficiently map productivity at large spatial scales. We test this framework by quantifying net primary productivity (NPP) at high-resolution (0.01-ha) in hyper-diverse Peruvian tropical forests (30,040 hectares) along a 3,322-m elevation gradient. Our analysis captures hotspots and elevational shifts in productivity more accurately and in greater detail than alternative empirical- and process-based models that use plant functional types. This result exposes how high-resolution, location-specific variation in traits and light competition drive variability in productivity, opening up possibilities to fully harness remote sensing data and reliably scale up from traits to map global productivity in a more direct, efficient, and cost-effective manner.

opencc-by-4.0Apr 2022View details →

Result files (ALLDATA): "Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data with LC-MS²Struct"

Result files associated with the publication: "Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data" by Bach et al. The following files are included in the archive: <ul> <li>Raw max-marginal predictions using LC-MS²Struct for all LC-MS² experiments of the ALLDATA setup</li> <li>Averaged max-marginals for the LC-MS²Struct over all SSVM models</li> <li>Top-k accuracies for the comparison methods (MS²+RT, ...)</li> <li>Ranks for the ground-truth structures predicted by Only MS² and LC-MS²Struct (molecule class analysis)</li> </ul> Instructions: <ul> <li>clone the repository containing the experimental scripts and analysis notebooks: <a href="https://github.com/aalto-ics-kepaco/lcms2struct_exp">https://github.com/aalto-ics-kepaco/lcms2struct_exp</a></li> <li>download the archive in this repository</li> <li>unpack the archive in the git-repository root directory</li> <li>follow the instructions given in the <a href="https://github.com/aalto-ics-kepaco/lcms2struct_exp/blob/main/README.md">README.md</a> of the git-repository to reproduce the figures, etc.</li> </ul> Version history: <ul> <li>Version 1: Experimental results for "Method comparison" and "Molecule classification analysis" where performed with 2D fingerprints (<a href="https://www.biorxiv.org/content/10.1101/2022.02.11.480137v1">preprint v1</a>)</li> <li>Version 2 (this version): Experimental results for "Method comparison" and "Molecule classification analysis" where performed with 3D fingerprints</li> </ul>

Data from: Variations in bark structural properties affect both water loss and carbon economics in neotropical savanna trees in the Cerrado region of Brazil

Even after complete stomatal closure, plants lose water through the leaf cuticles and bark. This residual water conductance of leaves (gleaf-res) and stems (gbark) can negatively impact plant water balance and affect plant survival in seasonally dry environments. However, little is known about the costs and benefits associated with such water leaks, especially on stem level. Here, we characterized the structural and functional determinants of the variability in gbark across tropical savanna species to elucidate how variations in this trait are related to contrasting growth strategies. The high variability in gbark across species was associated with morphoantomical properties of the outer bark (thickness, density, and lenticel investment), and such characteristics influenced both stem transpiration and respiration, suggesting the existence of a trade-off between water conservation and oxygen permeability, which reflected contrasting growth and dehydration tolerance strategies. For instance, species with higher gbark and gleaf-res presented a fast resource acquisition strategy but were more prone to drought-induced mortality by hydraulic failure. However, model simulations revealed that the relative contribution of gleaf-res and gbark to overall water balance depended on whether leaves were less or more resistant to cavitation than the stems. Synthesis. By combining correlative studies, experimental results, and a modeling exercise, we provide a new understanding of the costs and benefits associated with the variability in gbark across tropical savanna species, and a new perspective for studies of water relations and carbon economics in species from a hyperdiverse savanna.

Data from: Flowering overlap and floral trait similarity help explain the structure of pollination network

Co-flowering communities are usually characterized by high plant generalization but knowledge of the underlying factors leading to high levels of generalization and pollinator sharing, and how these may contribute to network structure is still limited. Flowering phenology and floral trait similarity are considered among the most important factors determining plant generalization and pollinator sharing. However, these have been evaluated independently even though they can act in concert with each other. Moreover, the importance of flowering phenology and floral similarity, via their effects on plant generalization, in the structure of plant–pollinator networks have been scarcely studied. Here, we aim to evaluate the effect of flowering phenology and floral similarity in mediating the degree of pollinator sharing and plant generalization in two coastal communities and uncover their importance as drivers of plant–pollinator network structure. We recorded flower production per species, as well as the identity and frequency of floral visitors along the entire flowering season. We estimated the degree of flowering overlap, the degree of floral similarity (using floral traits associated with size and color), and the degree of pollinator sharing among plant species within both communities. Structural equation models (SEM) showed a positive effect of flowering overlap on pollinator sharing and plant generalization. Pollinator sharing and plant generalization positively affected network nestedness. Furthermore, SEM showed a direct positive effect of flowering overlap on network modularity. The SEM analyses also revealed a significant interaction effect of floral similarity and flowering overlap on pollinator sharing, with consequences for network nestedness in one community. Our results highlight the importance of integrating multiple axes of differentiation such as flowering phenology and floral similarity into our understanding of the drivers of plant–pollinator network structure.

Data and scripts from: Long term analysis of social structure: evidence of age-based consistent associations in male Alpine ibex

The folder contains the data and scripts used to produce the manuscript: "Long term analysis of social structure: evidence of age-based consistent associations in Alpine ibex" by Alice Brambilla, Achaz von Hardenberg, Claudia Canedoli, Francesca Brivio, Cédric Sueur and Christina R Stanley.

Load, pressure, rubble pile geometry and video data from model-scale tests on shallow water ice-structure interaction

The data is obtained from model-scale experiments on shallow water ice-structure interaction. During the conducted experiments, a ten-meter wide initially intact ice sheet was pushed against a sloping structure of the same width. As the ice failed against the structure, a grounded rubble pile accumulated in front of it. The structure consisted of ten identical one-meter-wide segments and the horizontal load on each of these segments was measured independently with load cells. These measurements are presented as load-time datasets. The horizontal load acting on the false bottom was measured with load cells and are also presented as load-time datasets. Furthermore, the ice pressure on two of the segments was measured with tactile sensors. These pressure measurements are presented as array-based pressure-time datasets. Video footage filmed from two different video angles is included in the data. In addition, the coordinates of the rubble pile geometries at the end of each experiment are published. The data includes the top and side rubble pile geometries. In total, seven experiments were conducted. The data can be used by researchers, engineers and designers who work with ice structure interaction related issues in order to, for instance, optimize the design of offshore structures, improve ice load predictions or develop future experiments and simulations. A full description of the experimental set-up and the published data is submitted to the journal Data in Brief.

Data for: Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks

The persistence of mutualisms is paradoxical, as there are fitness incentives for exploitation. This is particularly true for plant-microbe mutualisms like arbuscular mycorrhizae (AM), which are promiscuously horizontally-transmitted. Preferential allocation by hosts to the best mutualist can stabilize horizontal mutualisms, however, preferential allocation is imperfect, with its fidelity likely depending upon the spatial structure of symbionts in plant roots. In this study, we tested AM mutualisms' dependence on two dimensions of spatial structure: the initial spatial association of fungi and the ease of fungal dispersal, through three complementary experiments. We found that fitness of the beneficial AM fungus increased when fungi were initially separate, while initial spatial mixing benefited the fitness of the non-beneficial fungus. These effects were strongest when dispersal was limited, and hosts could discriminate. Additionally, we found that changes in AM fungal proportional abundance induced by spatial structure in roots of a preferentially allocating host produced positive feedbacks on plant growth, showing that interactions between spatial structure and host choice can determine the direction of plant-soil feedbacks. Our results suggest that symbiont spatial structure within plant roots may act as an important modifier of plant preferential allocation and the dynamics of mycorrhizal mutualisms, with potentially cascading effects on plant-plant interactions.

Research data: "Effects of Network Structures on the Production Planning in Closed-loop Supply Chains – A Case Study based Analysis for Lithium-ion Batteries in Europe"

This data set belongs to the paper Effects of Network Structures on the Production Planning in Closed-loop Supply Chains – A Case Study based Analysis for Lithium-ion Batteries in Europe in the International Journal of Production Economics (DOI). The BatPac model, as well as, the model for the economic assessment of the recycling route are not included. The needed data can be found in the file (name). Further, the BatPaC model can be gather from the website of Argonne National Laboratory and the assessment tool for the recycling routes via this DOI: 10.5281/zenodo.6500946.   This work is part of the research project Recycling 4.0 (EFRE | ZW 6-85018080), which is funded by the European Regional Development Fund and managed by the development bank for the German federal state of Lower Saxony (NBank).

Data from: Convergent evolution of disordered lipidic structural color in the fruits of Lantana strigocamara (syn. L. camara hybrid cultivar)

Research conducted: The majority of plant colors are produced by anthocyanin and carotenoid pigments, but coloration obtained by nanostructured materials (i.e., structural colors) is increasingly reported in plants. Here, we identify a multilayer photonic structure in the fruits of Lantana strigocamara and compare it to a previously described origin in Viburnum tinus. Methods: We used a combination of transmission electron microscopy, serial EM tomography, scanning force microscopy, and optical simulations to characterize the photonic structure in L. strigocamara. We also examine the development of the structure during maturation. Key results: We find that the structural color derives from a disordered, multilayered reflector consisting of lipid droplets of ~105 nm that form a plate-like structure in 3D. This structure begins to form early in development and reflects blue wavelengths of light with increasing intensity over time as the structure develops. The lipids used are likely polymers of lipid monomers. Main conclusions: Lantana strigocamara is the second origin of a lipid-based photonic structure, convergently evolved with the structure in Viburnum tinus. Chemical differences between the lipids in L. strigocamara and those of V. tinus suggest a distinct evolutionary trajectory with implications for the signaling function of structural colors in fruits.

Data set for the article "Self-oscillation and Synchronisation Transitions in Elasto-Active Structures"

This is the data set for the article "Self-oscillation and Synchronisation Transitions in Elasto-Active Structures",  <table summary="Additional metadata"> <tbody> <tr> <td><a href="https://doi.org/10.48550/arXiv.2106.05721">https://doi.org/10.48550/arXiv.2106.05721</a>   </td> </tr> </tbody> </table> Is contains raw images and processed data from images used to describe the self-oscillations under study in this article. All zip files corresponds to the single chain experiment except "Double_chain_Experiment.zip".

opencc-by-4.0Jun 2022View details →

Gravity data used in the paper "Imaging the volcanic structures beneath Gran Canaria Island using new gravity data"

This file includes the values of gravity and complete Bouguer gravity anomaly calculated for the land gravity stations in Gran Canaria Island (Canary Islands, Spain). Each station has the corresponding UTM coordinates (Zone 28N) in metres (Datum WGS84).   This gravity data set has been used in the paper: Montesinos, F. G., Arnoso, J., Gómez-Ortiz, D., Benavent, M., Blanco-Montenegro, I., Vélez, E., et al. (2022). Imaging the volcanic structures beneath Gran Canaria Island using new gravity data. Journal of Geophysical Research: Solid Earth, 127, e2022JB024863. <a href="https://doi.org/10.1029/2022JB024863">https://doi.org/10.1029/2022JB024863</a>

opencc-zeroJun 2022View details →

Data accessibility for conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon

The quillwort Isoetes cangae is a critically endangered species occurring in a single lake in Serra dos Carajás, Eastern Amazon. Low genetic diversity and small effective population sizes (Ne) is expected for narrow endemic species (NES). Here, we evaluated genetic diversity, population structure, and Ne of I. cangae to provide information for conservation programs. Conservation biology studies centered in a single‐species show some limitations but they are still useful considering the limited time and resources available for the protection of species at risk of extinction. Our analyses were based on 55 individuals collected from the Amendoim lake and 35,638 neutral SNPs. Our results indicated a single panmictic population, moderate levels of genetic diversity, and effective population size (Ne) in the order of thousands, contrasting the expected for NES. Negative FIS values were also found, suggesting that I. cangae is not under risk of inbreeding depression. Our findings imply that I. cangae contains enough genetic diversity to ensure evolutionary potential, all individuals should be treated as one demographic unit.