Find research datasets worth reusing

opencc-by-4.0Dec 2019View details →

Observational data and numerical experimental files for subglacial discharge plume in Bowdoin Fjord, northwestern Greenland

The dataset includes observational data and all the files used in the numerical experiments. Additionally, this includes the codes to generate the figures and analysis. Please see Ohashi et al. (2019) for details (<a href="https://www.ocean-sci-discuss.net/os-2019-33/">https://www.ocean-sci-discuss.net/os-2019-33/</a>).

opencc-by-4.0Feb 2020View details →

Experimental data from the ICAPS 2020 paper "Incremental Search for Counterexample-Guided Cartesian Abstraction Refinement"

This data set contains the raw experiment data, parsed values and basic reports for the experiments in the paper. For each experiment there are two directories. The first directory contains the raw data of all experiment runs. The code directories and benchmark files have been removed to avoid duplication and to save space. The second directory (*-eval) contains a "properties" file with all parsed values and an HTML report.

opencc-by-4.0Mar 2020View details →

TesCaV: An Approach for Learning Model-based Testing and Coverage in Practice, Experimental Data

The data in this sheet provides the result of the exploratory experiment presented in the following paper: Beatriz Marín, Sofía Alarcón, Giovanni Giachetti, and Monique Snoeck. (2020) TesCaV: An Approach for Learning Model-based Testing and Coverage in Practice, in  Fabiano Dalpiaz, Jelena Zdravkovic, Pericles Loucopoulos (eds), Proceedings of the 14th International Conference on Research Challenges in Information Science, LNCS, Springer.

opencc-by-4.0Dec 2019View details →

Data collected from the project "Experimental Investigation of Sediment Stability at Reservoirs on the Rhône River"

----------------------------------------------------------------------------------------------------------------------------------------------------------------- Data collected from the project "Experimental Investigation of Sediment Stability at Reservoirs on the Rhône River" Details on the project including information on the materials and methods applied are provided in the available technical report ----------------------------------------------------------------------------------------------------------------------------------------------------------------- A_Bulk_Density     - contains the vertical bulk density measurements of all withdrawn sediment cores from the Motz and Logis-Neuf reservoir       Motz:             MZ08, MZ09, MZ10, MZ11, MZ12, MZ13, MZ14, MZ15, MZ16       Logis-Neuf:     LN01, LN02, LN03, LN04, LN05, LN06, LN07, LN08, LN09, LN10, LN11, LN12, LN14 ----------------------------------------------------------------------------------------------------------------------------------------------------------------- --> selected cores for detailed experimental investigations: MZ09, MZ14 and LN10, LN14        B_Sediment_Composition_and_ParticleSizes     - contains the results of the depth-dependent particle size analyses (distribution curves)     - contains the derived sediment composition over core depth      C_TOC_and_CEC     - contains the results of the Total Organic Carbon (TOC) measurements over core depth     - contains the results of the Cation Exchange Capacity (CEC) measurements over core depth D_Sediment_Stability     - contains the results of the measured sediment stability over core depth   E_Sediment_Erosionrates     - contains the results of the measured erosion rates over core depth     --> two methods are considered: "last measured erosion rate" and "mean erosion rate"          F_Sediment_Erosion_Volumes     - contains the raw data of the erosion volume measurements conducted with SETEG/PHOTOSED     --> the data is provided separately for each investigated sediment layer over core depth (denoted by "D**")     --> the data is evaluated for five considered time intervals dt =15s, dt =30s, dt =60s, dt =100s, dt =120s      -----------------------------------------------------------------------------------------------------------------------------------------------------------------

opencc-by-4.0May 2020View details →

Noise study data for: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation

This dataset contains noise study data used in the paper: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation. These include raw CT scans and processed digital volume correlation data. This dataset is part of another dataset which covers other aspects of the paper DOI: <a href="http://www.doi.org/10.5281/zenodo.3352268">10.5281/zenodo.3352268</a> The structure of the dataset is as follows: <ul> <li>Noise study CT raw volumes are contained in a zip file. There are four raw files corresponding to the four noise study steps. These files are 8-bit unsigned, dimensions are 1800 x 1800 x 1400 pixels. A txt file giving more details to the data is included. <ul> <li>CT_Raw_data_Noise_Scans.zip</li> </ul> </li> <li>Metadata files generated for each scan given details of scan parameters are found in the zip file: <ul> <li>CT_Scan_Metadata.zip</li> </ul> </li> <li>Tabulated digital volume data for the noise study scans are contained in the zip file. Tabulated data for each subset size is included in subfolders. A .txt file explains the structure of the tab separated .dat files, i.e. what each column of data represents, and what CT scan each of the four .dat files relate to. <ul> <li>DVC_Noise_Study_Data.zip</li> </ul> </li> </ul>

opencc-by-4.0Jun 2020View details →

Gassert: Evolutionary Improvement of Assertion Oracles - experimental data

This dataset contains the data of our experiments that we conducted in our paper "Evolutionary Improvement of Assertion Oracles" published at ESEC/FSE 2020.

opencc-by-4.0Jun 2020View details →

STEG data of manuscript "Electrical Generation of a Ground Level Solar Thermoelectric Generator: Experimental Tests and One-year Cycle Simulation" submitted to Energies

Figure_7_data: laboratory data of TEG output power working at low temperature differences. Data used in Figure 7 of manuscript "Electrical Generation of a Ground Level Solar Thermoelectric Generator: Experimental Tests and One-year Cycle Simulation" submitted to Energies. Figure_9_data: experimental data of TEG temperature differences from July 24 to July 31, 2017. Data used in Figure 9 of manuscript "Electrical Generation of a Ground Level Solar Thermoelectric Generator: Experimental Tests and One-year Cycle Simulation" submitted to Energies. Figures_11_14_data: input and output data of the STEG model. One-year cycle data. Used to obtain figures 11 to 14 of manuscript "Electrical Generation of a Ground Level Solar Thermoelectric Generator: Experimental Tests and One-year Cycle Simulation" submitted to Energies

opencc-by-4.0May 2020View details →

Experimental Data for "What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way" at SIGIR2020

This deposit contains data used for the experiments reported in the paper "<a href="https://doi.org/10.1145/3397271.3401048">What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way</a>", most notably the ElasticSearch 5.4 indices used for the reported experiments. To load the indices into an ElasticSearch cluster of your own, use the restore function described in the <a href="https://www.elastic.co/guide/en/elasticsearch/reference/5.4/modules-snapshots.html">ElasticSearch documentation</a>. The names of the index snapshots contained here are <ul> <li>ct1718 for the indexed ClinicalTrials data used in the TREC-PM challenges in <a href="http://www.trec-cds.org/2017.html">2017</a> and <a href="http://www.trec-cds.org/2018.html">2018</a>.</li> <li>ct19 for the indexed ClinicalTrials data used in the TREC-PM challenge in <a href="http://www.trec-cds.org/2019.html">2019</a>.</li> <li>ba1718 for the indexed PubMed data used in the TREC-PM challenges in <a href="http://www.trec-cds.org/2017.html">2017</a> and <a href="http://www.trec-cds.org/2018.html">2018</a>.</li> <li>ba19 for the indexed PubMed data used in the TREC-PM challenge in <a href="http://www.trec-cds.org/2019.html">2019</a>.</li> </ul> The other file contains the original output that <a href="https://www.automl.org/automated-algorithm-design/algorithm-configuration/smac/">SMAC</a> wrote to disc during the parameter optimization process. There are directories for the biomedical abstracts (BA) and clinical trials (ct) and for each respective 10 fold cross validation split. Those file contain the exact parameter configurations and their evalation score (the infNDCG metric was used) in live-runXX.json files. The code to these files is located in <a href="https://zenodo.org/record/3856403">this Zenodo deposit</a>.

opencc-by-4.0Jun 2020View details →

Raw experimental data

The uploaded zip file contains two datasets: 1. Interleaved TR-NUS NMR measurement  (raw data) 2. Interleaved NMR measurement with uniform sampling (raw data). Both datasets can be easily processed using TReNDS software (M. Urbańczyk, A. Shchukina, D. Gołowicz, K. Kazimierczuk, Magn. Reson. Chem. 2018, 57, 4–12).

opencc-by-4.0May 2020View details →

Overcoming information reduced data and experimentally uncertain parameters in ptychography with regularized optimization

These are the datasets used for the publication <a href="https://arxiv.org/abs/2005.01530">https://arxiv.org/abs/2005.01530</a>. The bin files are the actual data, and the other files are the configuration files used to generate the datasets. In more detail, the Forward_Params*.cnf files were used in combination with FDES (<a href="https://doi.org/10.1016/j.ultramic.2015.07.005">https://doi.org/10.1016/j.ultramic.2015.07.005</a>) to generate diffraction patterns. The Reconstruction_Params*.cnf files were used with the code outlined in the main publication to generate the simulated results. The Simulation*.bin files are the raw simulated CBEDs, stored in a binary format. The eCount portion of the filename corresponds to the Poissonian statistics applied to simulate real data. The ground truth file is upsampled, with larger diffraction pattern sizes, while the eCountInf has infinite dose, and therefore no noise. If you want more information, please contact the corresponding author of the publication, at vandenbroek@physik.hu-berlin.de.

opencc-by-4.0Jul 2020View details →

Experimental data for 'The transfer of forces through rough surface contact in concrete'

The data contained in this archive was produced within the research project described in the following thesis:     Tirassa M. (2020). The transfer of forces through rough surface contact in concrete. Ph.D. Thesis, EPFL, Lausanne, Switzerland. The research project was funded by the Swiss National Science Foundation through research grant 200021_169649. The data relates to the topic of force transfer across concrete cracks and interfaces (rebar-to-concrete) subjected to mixed mode kinematics with constant opening angle. It comprises the measured forces (normal and tangential) and displacements (crack opening and sliding). Moreover, some of the resulting surfaces (scanned using a digital microscope) are included.

opencc-zeroJul 2020View details →

Data from: Predators drive community reorganization during experimental range shifts

1. Increased global temperatures caused by climate change are causing species to shift their ranges and colonize new sites, creating novel assemblages that have historically not interacted. Species interactions play a central role in the response of ecosystems to climate change, but the role of trophic interactions in facilitating or preventing range expansions are largely unknown. 2. The goal of our study was to understand how predators influence the ability of range-shifting prey to successfully establish in newly available habitat following climate warming. We hypothesized that fish predation facilitates the establishment of colonizing zooplankton populations, because fish preferentially consume larger species that would otherwise competitively exclude smaller bodied colonists. 3. We conducted a mesocosm experiment with zooplankton communities and their fish predators from lakes of the Sierra Nevada Mountains in California, USA. We tested the effect of fish predation on the establishment and persistence of a zooplankton community when introduced in the presence of higher- and lower-elevation communities at two experimental temperatures in field mesocosms. 4. We found that predators reduce the abundance of larger bodied residents from the alpine and facilitate the establishment of new lower-elevation species. In addition, fish predation and warming independently reduced the average body size of zooplankton by up to 30%. This reduction in body size offset the direct effect of warming induced increases in population growth rates, leading to no net change in zooplankton biomass or trophic cascade strength. 5. We found support for a shift to smaller species with climate change through two mechanisms: 1) the direct effects of warming on developmental rates and, 2) size-selective predation that altered the identity of species' that could colonize new higher elevation habitat. Our results suggest that predators can amplify the rate of range shifts by consuming larger bodied residents and facilitating the establishment of new species. However, the effects of climate warming were dampened by reducing the average body size of community members, leading to no net change in ecosystem function, despite higher growth rates. This work suggests that trophic interactions play a role in the reorganization of regional communities under climate warming.

opencc-by-4.0Aug 2020View details →

Experimental data for "Cohesional slip on a plate subduction boundary during a large earthquake"

This deposit contains raw data used for the study reported in the paper "Cohesional slip on a plate subduction boundary during a large earthquake".

Data from: Rapid generation of ecologically relevant behavioural novelty in experimental cichlid hybrids

The East African cichlid radiations are characterised by repeated and rapid diversification into many distinct species with different ecological specialisations and by a history of hybridization events between non-sister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second-generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialised on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialised on sand sifting. We combined experimental behavioural and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behaviour related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioural traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behaviour in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behaviour, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations.

Data from: Experimental demonstration of the importance of keystone communities for maintaining metacommunity biodiversity and ecosystem functioning

As local communities within a metacommunity may differ considerably in their contributions to biodiversity and ecosystem functioning, it has been suggested that conservation priority should be given to disproportionately important local communities (i.e., keystone communities). However, we know little about what characterizes a keystone community. Using laboratory protist microcosms as the model system, we examined how the environmental uniqueness and location of a local community affect its contributions to the metacommunities. We found that the removal of local communities with unique environmental conditions, which supported endemic species, reduced regional-scale diversity, qualifying them as regional-scale keystone communities. In addition, the local communities possessing unique environmental conditions had greater impacts on ecosystem functions, including biovolume production and particulate organic matter decomposition. We also found that keystone communities for biovolume production were not keystone for organic matter decomposition, and vice versa. Our study, therefore, demonstrates the important role of keystone communities in maintaining biodiversity and functioning of metacommunities.

Data from: Experimental reduction of plant abundance changes interaction frequency of a tri-trophic micro-food web: contrasting responses of generalists and specialists

1. Species abundance is vulnerable to climate change and anthropogenic impact. Although numerous studies have examined the food web response to species loss, their response (e.g. in network topology and interaction frequency) to changes in species abundance has received little attention. 2. We experimentally reduced the abundance (by ca. 60%) of one host plant species (Saussurea nigrescens) in a tri-trophic micro-food web consisting of two common Asteraceae species (S. nigrescens and Anaphalis flavescens), their pre-dispersal seed predators (tephritid flies), and the parasitoid wasps that feed on these seed predators. 3. The neutral process hypothesis posits that network topology and interaction frequency are determined by the relative abundances of the participating species. Accordingly, we hypothesized that interaction frequency (indicated by the rate of flies infesting plants and of parasitoid wasps parasitizing flies) would decrease with decreasing abundance of host plant abundance. 4. Consistent with the neutral process hypothesis, abundance reduction significantly decreased the rate of generalist flies infesting the manipulated plant host species, but increased the rate on unmanipulated plant species. In contrast, abundance reduction significantly increased the rate of specialist flies infesting the manipulated species, but it had no demonstrable effect on the specialists on the unmanipulated plant host. 5. Moreover, abundance reduction significantly increased the rate of parasitoid wasps (as a species group) parasitizing flies in the manipulated species but decreased the rate of the unmanipulated species. These results were not attributable to neutral processes, but can be explained only by adaptive foraging theory. In addition, experimental manipulation did not shift the qualitative presence/absence of the linkages in the micro-food web, and the change in the abundance of both fly and wasp species was smaller than the abundance changes of the manipulated plant species. 6. These observations are interpreted to indicate that both neutral process and/or adaptive foraging likely contributed to food web stability in responses to changes in species abundance. Because species abundance is vulnerable to abiotic and biotic environmental changes, we suggest more research should be conducted to understand how food webs respond to climate change and anthropogenic disturbance.

Data from the study: Effect of experimental DNA demethylation on phytohormones production and palatability of a clonal plant after induction via jasmonic acid

Many plant species protect themselves against herbivores through mechanical or chemical so-called inducible defences (ID). These are regulated via a hormonal cascade which may be under epigenetic control and in which jasmonic acid (JA) plays a prominent role. In this study, we indirectly tested the role of DNA methylation in the production of ID and the synthesis of hormones involved in the ID signalling cascade. Using different intensities of 5-azacytidine application, we aimed to produce plants of Trifolium repens with different levels of DNA methylation alteration. We then elicited the plants together with controls, i.e. plants with natural DNA methylation status, with JA and then indirectly recorded ID production in herbivore-choice trials in which the leaves of plants with different DNA methylation statuses were provided to caterpillars of a generalist herbivore, Spodoptera littoralis. We also analysed the balance of several key defence hormones such as jasmonates, abscisic acid (ABA), indole-3-acetic acid (IAA) and salicylic acid in the plants. We found that the Spodoptera littoralis preferred demethylated plants over non-demethylated controls. Demethylation also reduced production of JA, ABA and IAA. We conclude that DNA methylation modulates expression of ID likely via regulation of signalling hormones involved in the establishment of defence.

Data from: How relatedness between mates influences reproductive success: an experimental analysis of self-fertilization and biparental inbreeding in a marine bryozoan

Kin associations increase the potential for inbreeding. The potential for inbreeding does not, however, make inbreeding inevitable. Numerous factors influence whether inbreeding preference, avoidance, or tolerance evolves, and, in hermaphrodites where both self-fertilization and biparental inbreeding are possible, it remains particularly difficult to predict how selection acts on the overall inbreeding strategy, and to distinguish the type of inbreeding when making inferences from genetic markers. Therefore, we undertook an empirical analysis on an understudied type of mating system (spermcast mating in the marine bryozoan, Bugula neritina) that provides numerous opportunities for inbreeding preference, avoidance, and tolerance. We created experimental crosses, containing three generations from two populations to estimate how parental reproductive success varies across parental relatedness, ranging from self, siblings, and non-siblings from within the same population. We found that the production of viable selfed offspring was extremely rare (only one colony produced three selfed offspring), and biparental inbreeding more common. Paternity analysis using 16 microsatellite markers confirmed outcrossing. The production of juveniles was lower for sib mating compared to non-sib mating. We found little evidence for consistent inbreeding, in terms of non-random mating, in adult samples collected from three populations, using multiple population genetic inferences. Our results suggest several testable hypotheses that potentially explain the overall mating and dispersal strategy in this species, including early inbreeding depression, inbreeding avoidance through cryptic mate choice, and differential dispersal distances of sperm and larvae.

DNA methylation and phenotypic data from: Environmentally induced phenotypic plasticity and DNA methylation changes in a wild potato growing in two contrasting Andean experimental gardens

DNA methylation can be environmentally modulated and play a role in phenotypic plasticity. To understand the role of environmentally induced epigenetic variation and its dynamics in natural populations and ecosystems, it is relevant to place studies in a real-world context. Our experimental model is the wild potato Solanum kurtzianum, a close relative of the cultivated potato S. tuberosum. It was evaluated in its natural habitat, an arid Andean region in Argentina characterised by spatial and temporal environmental fluctuations. The dynamics of phenotypic and epigenetic variability (with Methyl Sensitive Amplified Polymorphism markers, MSAP) was assayed in three genotypes across three growing seasons. These genotypes were cultivated permanently and also reciprocally transplanted between experimental gardens (EG) differing in ca. 1000 m of altitude. In two seasons, the genotypes presented differential methylation patterns associated to the EG. In the reciprocal transplants, a rapid epigenomic remodelling occurred according to the growing season. Phenotypic plasticity, both spatial (between EGs within season) and temporal (between seasons), was detected. The epigenetic and phenotypic variability were positively correlated. The lack of an evident mitotic epigenetic memory would be a common response to short-term environmental fluctuations. Thus, the environmentally induced phenotypic and epigenetic variation could contribute to populations persistence through time. These results have implications for understanding the great ecological diversity of wild potatoes.