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1,819 results for “Experimental data”
Experimental EBSD data for 035C and 07C lean steel for habit plane determination
<p>Experimental data for demonstrating the habit plane determination algorithms described in:</p> <p>https://arxiv.org/abs/2303.07750</p> <p>The linked resource contains a full description of how the data was obtained and processed, as well as the interpretation of the results.</p>
Data in experimental stand-alone microgrid
<p>In 'Micro Reseau Mafate' project, the PIMENT Laboratory aims to develop microgrid stations in an isolated area called 'Mafate' at Reunion Island. Datasets from the first experimental microgrid at “Roche plate” are shared with the community.</p> <p>https://www.youtube.com/watch?v=dXmV415MmBs</p>
Experimental data of "Elevated concentrations cause upright alpha-synuclein conformation at lipid interfaces" (NatComm)
<p>The experimental data in this dataset is the basis of the article entitled "Elevated concentrations cause upright alpha-synuclein conformation at lipid interfaces", which will hopefully be published in NatComm soon. We will add a DOI then. It contains the vibrational sum-frequency generation (VSFG), atomic-force microscopy (AFM) and surface-pressure datasets of alpha-synuclein interacting with 1,2-Dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) monolayers, at various alpha-synuclein concentrations.</p>
DATA FOR: Carbon starvation following a decade of experimental drought consumes old reserves in Pinus edulis
<ol> <li>Pre-dawn water potential data used in Fig. 2.</li> <li>Gas exchange data (Anet) used in Fig. 2, along with transpiration data used in supplemental Fig. S8.</li> <li>Fv/fm data used in Fig. 2.</li> <li>Needle growth, shoot growth, and browning data used in Fig. 2.</li> <li>Bole respiration rate data used in Fig. 3.</li> <li>NSC concentration data used in Fig. 5.</li> <li>Respired carbon mass used to calculate total NSC pool ages in Fig. 6b, along with radiocarbon calendar dated ages of sapwood NSC.</li> <li>Raw ring widths from all cross dated trees used to generate BAI for analysis presented in Fig. 4.</li> </ol>
Data from: Experimentally simulating the evolution-to-ecology connection: Divergent predator morphologies alter natural food webs
<p class="MsoNormal">The idea that changing environmental conditions drive adaptive evolution is a pillar of evolutionary ecology. But, the opposite—that adaptive evolution alters ecological processes—has received far less attention yet is critical for eco-evolutionary dynamics. We assessed the ecological impact of divergent values in a key adaptive trait using 16 populations of the brown anole lizard (<em class="i">Anolis sagrei</em>). Mirroring natural variation, we established islands with short- or long-limbed lizards at both low and high densities. We then monitored changes in lower trophic levels, finding that on islands with short-limbed lizards at high-density<span class="inserted">,</span> web spider<span class="inserted">s</span> decreased and plants grew more via an indirect positive effect, likely through an herbivore-mediated trophic cascade. Our experiment provides strong support for evolution-to-ecology connections in nature, likely closing an otherwise well-characterized eco-evolutionary feedback loop.</p>
Experimental data and R scripts for simulations and analysis
<p>Zip file including the experimental data and R scripts for simulations and analysis used in the following article: "Colonisation debt: when invasion history impacts current range expansion by Morel-Journel, T., Haond M., Dunan L., Mailleret L. and Vercken E.</p>
Data for: Guppies in large groups cooperate more frequently in an experimental test of the group size paradox
<p><span class="s6">The volunteer's dilemma, in which a single individual is required to produce a public good, predicts that individuals in larger groups will cooperate less frequently. Mechanistically, this could result from trade-offs between costs associated with volunteering and costs incurred if the public good is not produced (nobody volunteers). During predator inspection, one major contributor to the cost of volunteering is likely increased probability of predation; however, a predator also poses a risk to all individuals if nobody inspects. We tested the prediction that guppies in larger groups will inspect a predator less than those in smaller groups. We also predicted that individuals in larger groups would perceive less threat from the predator stimulus because of the protective benefits of larger groups (</span><span class="s6">e.g.</span><span class="s6"> dilution). Contrary to prediction, we found that individuals in large groups inspected more frequently than those in smaller groups </span><span class="s6">but</span><span class="s6"> (as predicted) spent less time in refuges. There was evidence that individuals in intermediate-sized groups made the fewest inspections and spent the most time in refuges, suggesting that any link between group size, risk and cooperation is not driven by simple dilution. Extensions of theoretical models that capture these dynamics will likely be broadly applicable to risky cooperative behaviour.</span></p>
Data for: Weak sex-specific evolution of locomotor activity of Sepsis punctum (Diptera: Sepsidae) thermal experimental evolution lines
<p><span>Elevated temperatures are expected to rise beyond what the physiology of many organisms can tolerate. Behavioural responses facilitating microhabitat shifts may mitigate some of this increased thermal selection on physiology, but behaviours are themselves mediated by physiology, and any behavioural response may trade-off against other fitness-related activities. </span><span>We investigated whether experimental evolution in different thermal regimes (Cold: 15°C; Hot: 31°C; Intergenerational fluctuation 15/31°C; Control: 23°C) resulted in genetic differentiation of standard locomotor activity in the dung fly <em>Sepsis</em> <em>punctum</em>. We assessed individual locomotor performance, an integral part of most behavioral repertoires, across eight warm temperatures from 24°C to 45°C using an automated device. We found no evidence for generalist-specialist trade-offs (i.e. changes in the breadth of the performance curve) for this trait. Instead, at the warmest assay temperatures, hot-selected flies showed somewhat higher maximal performance than all others, especially cold-selected flies, overall more so in males than females. Yet, the flies' temperature optimum was not higher than that of the cold-selected flies, as expected under the 'hotter-is-better' hypothesis. Maximal locomotor performance merely weakly increased with body size. These results suggest that thermal performance curves are unlikely to evolve as an entity according to theory and that locomotor activity is a trait of limited use in revealing thermal adaptation.</span></p>
Data from: Carbon burial in Cornell's experimental ponds
<p>Ponds are globally abundant and important to the global carbon cycle. While ponds have large greenhouse gas emissions, they may also sequester large amounts of carbon in their sediments. Here, we studied carbon burial rates in 22 experimental ponds without watersheds, where carbon sequestration comes solely from autochthonous primary production. The ponds were built identically in 1964 at Cornell University, and have since experienced different management strategies. This dataset includes two files: (1) spreadsheets related to carbon burial calculations (e.g., measuring sediment thickness, estimates of loss-on-ignition, and carbon burial rates), and (2) spreadsheets of historical management practices for our study ponds. These datasets accompany a manuscript accepted at Limnology and Oceanography Letters.</p>
Experimental data and analysis of performances of dual-type temperature probes
<p>Experimental data, VBA software, and data analysis resulted from an investigation of the performances of prototypes of dual-type temperature probes, that were used for testing the new concept of dual-type thermometers. Dual-type thermometers enable in-situ determination of thermocouple drift. The basic idea behind the concept is that thermocouple drift can be continuously monitored in situ by placing an additional and different temperature sensor in close proximity. The essential requirement for this additional sensor is that it experiences a drift that is lower than the drift of the monitored thermocouple. A drift of a thermocouple can be determined by an algorithm that monitors, and over time compares, the differences in its temperature readings and the readings of an additional (reference) sensor.</p>
Data from: Soil nutrient heterogeneity alters productivity and diversity of experimental plant communities under multiple global change factors
<p>Plant communities in nature are often challenged by multiple global change factors (GCFs) and also ubiquitously encountered with soil nutrient heterogeneity. So far, however, we know little about the interactive effect of multiple GCFs and soil nutrient heterogeneity on plant communities.</p> <p>We conducted an outdoor mesocosm experiment in which a plant community was either grown in heterogeneous soils consisting of high- and low-nutrient patches, or in homogeneous soils where the same amount of nutrients was evenly distributed. These plant communities were exposed to none (control), single, or a combination of two or four GCFs (i.e., drought, nitrogen deposition, microplastic and cadmium).</p> <p>Biomass of the plant community exposed to drought and nitrogen deposition were greater in heterogeneous than in homogeneous soils, but evenness of the plant community exposed to microplastics was lower. Increasing the number of GCFs increased community biomass more in heterogeneous than in homogeneous soils, but it generally reduced community evenness, independent of soil nutrient heterogeneity. These contrasting responses were related to changing competitive hierarchies and root foraging responses under different treatments.</p> <p>Our results suggest that soil nutrient heterogeneity can alter community productivity and diversity via changing competitive interactions of the component species, depending on both the identity and the number of GCFs acting on the community. These results have important implications for the maintenance of ecosystem functions and services under rapid and complex ongoing global changes.</p>
Data for: Effects of drought, disturbance, and biotic neighborhood on experimental tree seedling performance
<p>Forest biodiversity is likely maintained by a complex suite of interacting drivers that vary in importance across both space and time. Contributing factors include disturbance, interannual variation in abiotic variables, and biotic neighborhood effects. To probe ongoing uncertainties and potential interactions, we investigated tree seedling performance in a temperate mid-Atlantic forest ecosystem. We planted seedlings of five native tree species in mapped study plots, half of which were subjected to disturbance, and then monitored seedling survival, height growth, and foliar condition.The final year of data collection encompassed a drought, enabling comparison between intervals varying in water availability. Seedling performance was analyzed as a function of canopy cover and biotic neighborhood (conspecific and heterospecific abundance), including interactions, with separate generalized linear mixed models fit for each interval. All species exhibited: a) pronounced declines in height growth during the drought year, b) detrimental effects of adult conspecifics, and c) beneficial effects of canopy openness. However, despite these consistencies, there was considerable variation across species in terms of the relevant predictors for each response variable in each interval. Our results suggest that drought may strengthen or reveal conspecific inhibition in some instances while weakening it or obscuring it in others, and that some forms of conspecific inhibition may manifest only under particular canopy conditions (although given the inconsistency of our findings, we are not convinced that conspecific inhibition is critical for diversity maintenance in our study system). Overall, our work reveals a complex forest ecosystem that appears simultaneously and interactively governed by biotic neighborhood structure (e.g., conspecific and/or heterospecific abundance), local habitat conditions (e.g., canopy cover), and interannual variability (e.g., drought).</p>
Data for: Experimental infections with Euhaplorchis californiensis and a small cyathocotylid increase conspicuous behaviors in California killifish (Fundulus parvipinnis)
<p>Some parasites manipulate their host's phenotype to enhance predation rates by the next host in the parasite's life cycle. Our understanding of this "parasite-increased trophic-transmission" is often stymied by study design challenges. A recurring difficulty has been obtaining uninfected hosts with a coevolutionary history with the parasites, and conducting experimental infections that mimic natural processes. In 1996, Lafferty and Morris provided what has become a classic example of parasite-increased trophic-transmission; they reported a positive association between the intensity of a brain-infecting trematode (<em>Euhaplorchis californiensis</em>) in naturally infected California killifish (<em>Fundulus parvipinnis</em>) and the frequency of "conspicuous behaviors", which was thought to explain the documented 10-30x increase in predation by the final host birds. Here, we address the primary gap in that study by using experimental infections to assess causality of<em> E. californiensis</em> infection for increased conspicuous behaviors in <em>F. parvipinnis</em>. We hatched and reared uninfected <em>F. parvipinnis</em> from a population co-occurring with E. californiensis, and infected them 1-2 times/week over half their life span with <em>E. californiensi</em>s and a "small cyathocotylid" trematode (SMCY) that targets the host's muscle tissue. At 3 time-points throughout the hosts' lives, we quantified several conspicuous behaviors: contorting, darting, scratching, surfacing, and vertical positioning relative to the water's surface. <em>Euhaplorchis californiensi</em>s and SMCY infection caused 1.8 and 2.5-fold overall increases in conspicuous behaviors, respectively. Each parasite was also associated with increases in specific conspicuous behaviors, particularly 1.9 and 1.4-fold more darting. These experimental findings help solidify <em>E. californiensis</em>-<em>F. parvipinnis</em> as a classic example of behavioral manipulation. Yet our findings for <em>E. californiensis</em> infection-induced behavioral change were less consistent and strong than those previously documented. We discuss potential explanations for this discrepancy, particularly the idea that behavioral manipulation may be most apparent when fish are actively attacked by predators. Our findings concerning the other studied trematode species, SMCY, highlight that trophically transmitted parasites infecting various host tissues are known to be associated with conspicuous behaviors, reinforcing calls for research examining how communities of trophically transmitted parasites influence host behavior.</p>
Experimental data for High-temperature Josephson diode
<p>This experimental dataset was used in our study of the "High-temperature Josephson diode".</p>
Lateral interactions govern self-assembly of the bacterial biofilm matrix protein BslA (experimental and simulation data)
<p>The soil bacterium Bacillus subtilis is a model organism to investigate the formation of biofilms, the predominant form of microbial life. The secreted protein BslA self-assembles at the surface of the biofilm to give the B. subtilis biofilm its characteristic hydrophobicity. To understand the mechanism of BslA self-assembly at interfaces, here we built a molecular model based on the previous BslA crystal structure and the newly determined crystal structure of the BslA paralogue YweA. Our analysis revealed two conserved protein-protein interaction interfaces supporting BslA self-assembly into an infinite 2d lattice that fits previously determined transmission microscopy images. Molecular dynamics simulations and in vitro protein assays further support our model of BslA elastic film formation, while mutagenesis experiments highlight the importance of the identified interactions for biofilm structure. Based on this knowledge, YweA was engineered to form more stable elastic films and rescue biofilm structure in bslA deficient strains. These findings shed new light on protein film assembly and will inform the development of BslA technologies which range from surface coatings to emulsions in fast-moving consumer goods.</p>
Data: Female-limited responses in remating rate and mating duration in the experimental evolution of a beetle Callosobruchus chinensis
<p><span>Mating rate optima often differ between the sexes: males may increase their fitness by multiple mating, but for females, multiple mating confers little benefit and can often be costly (especially in taxa without nuptial gifts or mala parental care). Sexually antagonistic evolution is thus expected in traits related to mating rates under sexual selection. This prediction has been tested by multiple studies that applied the experimental evolution technique, which is a powerful tool to directly examine the evolutionary consequences of selection. Yet, the results so far only partly support the prediction. Here we provide another example of experimental evolution of sexual selection, by applying it for the first time to the mating behavior of a seed beetle <em>Callsorobruchus</em> <em>chinensis</em>. We found a lower remating rate in polygamy-line females than in monogamy-line (i.e. no sexual selection) females after 21 generations of selection. Polygamy-line females also showed a longer duration of first mating than monogamy-line females. We found no effect of male evolutionary lines on the remating rate or first mating duration. Though not consistent with the original prediction, the current and previous studies collectively suggest that the observed female-limited responses may be a norm, which is also consistent with the conceptual advances in the last two decades of the advantages and limitations of the experimental evolution technique.</span></p>
RETINAS: experimental data
<p>Data set of the "measuring G" experiment. Parameters:</p> <ul> <li>Number of horizontal pixels: 256</li> <li>Number of vertical pixels: 128</li> <li>Capture rate: 470 Hz</li> <li>Capture duration: 10 minutes</li> <li>Upsampling factor: 256</li> <li>Offset: 100</li> </ul>
Experimental and simulation data on magnetization and magnetization noise in tetris ice
<p>The files contain data presented in the "Deconstructing Magnetization Noise: Degeneracies, Phases, and Mobile Fractionalized Excitations in Tetris Artificial Spin Ice" paper.</p>
Artificial light at night (ALAN) decreases plant diversity and performance in experimental grassland communities – Data on species biomass and traits
<p>Artificial light at night (ALAN) affects many areas of the world and is increasing globally. To date, there has been limited and inconsistent evidence regarding the consequences of ALAN on plant communities as well as the fitness of their constituent species. ALAN could be beneficial for plants as they need light as an energy source, but they also need darkness for regeneration and growth. We created model communities composed of 16 plant species sown, exposed to a gradient of ALAN ranging from 'moonlight only' to conditions like situations typically found directly underneath a streetlamp. We measured plant community composition and its production (biomass), as well as functional traits of three plant species from different functional groups (grasses, herbs, legumes) in two separate harvests. We found that biomass was reduced by 33% in the highest ALAN treatment compared to the control, Shannon diversity decreased by 43% and Evenness by 34% in the first harvest. Some species failed to establish in the second harvest. Specific leaf area, leaf dry matter content and leaf hairiness responded to ALAN. These responses suggest that plant communities will be sensitive to increasing ALAN, and they flag a need for plant conservation activities that consider impending ALAN scenarios.</p>
Data sets and machine learning models for: Machine learning from quantum chemistry to predict experimental solvent effects on reaction rates
<p>The datasets and final machine learning model files for the manuscript "Machine learning from quantum chemistry to predict experimental solvent effects on reaction rates". Citation should refer directly to the manuscript:</p> <ul> <li>Chung, Y.; Green, W. H. Machine learning from quantum chemistry to predict experimental solvent effects on reaction rates. <em>Chemical Science </em><strong>2024,</strong> doi: <a href="https://doi.org/10.1039/D3SC05353A">10.1039/D3SC05353A</a></li> </ul> <p>To use the machine learning models, please refer to the sample files and instructions on <a href="https://github.com/yunsiechung/chemprop/tree/RxnSolvKSE_ML">https://github.com/yunsiechung/chemprop/tree/RxnSolvKSE_ML</a>. </p> <p>Detailed information can be found in README.md file.</p> <p><br><strong>Details on the files</strong></p> <p>In the pretraining and finetuning set csv files, each column represents:</p> <ol> <li>rxn_smiles: atom-mapped reaction SMILES</li> <li>solvent_smiles: solvent SMILES</li> <li>ddGsolv: solvation free energy of activation of a reaction-solvent pair at 298K in kcal/mol (main prediction target)</li> <li>ddHsolv: solvation enthalpy of activation of a reaction-solvent pair at 298K in kcal/mol (main prediction target)</li> <li>dGsolv_reactant: solvation free energy of reactant(s) at 298K in kcal/mol (additional feature)</li> <li>dGsolv_product: solvation free energy of product(s) at 298K in kcal/mol (additional feature)</li> <li>dHsolv_reactant: solvation enthalpy of reactant(s) at 298K in kcal/mol (additional feature)</li> <li>dHsolv_product: solvation enthalpy of product(s) at 298K in kcal/mol (additional feature)</li> </ol> <p><strong>Data sets under 'RxnSolvKSE_dataset_v1.1.zip'</strong></p> <ul> <li>pretraining_set: contains the dataset used for pre-training <ul> <li>all_data: contains all calculated data <ul> <li>pretraining_rxn_solvent_ddGsolv_ddHsolv_with_features_all.csv: contains both main prediction targets and additional feature for reaction-solvent pairs</li> <li>pretraining_solvent_info.csv: list of all solvents</li> <li>pretraining_unique_rxn.csv: list of all reactions, both forward and reverse directions</li> </ul> </li> <li>chosen_500k_data: contains the chosen 500k data <ul> <li>pretraining_rxn_solvent_ddGsolv_ddHsolv_500k.csv: contains main prediction targets for reaction-solvent pairs</li> <li>pretraining_features_react_prod_dGsolv_dHsolv_500k.csv: contains additional features for reaction-solvent pairs</li> <li>train_test_split: contains the 5-fold random split training and test sets.</li> </ul> </li> </ul> </li> <li>finetuning_set: contains the dataset used for fine-tuning <ul> <li>all_data: contains all calculated data <ul> <li>finetuning_rxn_solvent_ddGsolv_ddHsolv_with_features_all.csv: constains both main prediction targets and additional features for reaction-solvent pairs. The rxn_key column indicates whether the reaction is bimolecular hydrogen abstraction (bihabs), unimolecular hydrogen migration (intrahabs), or radical addition to a multiple bond (raddition). The 'fwd' and 'rev' each indicate forward and reverse reactions.</li> <li>finetuning_solvent_info.csv: list of all solvents</li> <li>finetuning_unique_rxn.csv: list of all reactions, both forward and reverse directions</li> </ul> </li> <li>chosen_data: contains chosen data <ul> <li>finetuning_rxn_solvent_ddGsolv_ddHsolv_chosen.csv: contains main prediction targets for reaction-solvent pairs</li> <li>finetuning_features_react_prod_dGsolv_dHsolv_chosen.csv: contains additional features for reaction-solvent pairs</li> </ul> </li> </ul> </li> <li>experimental_set: contains the experimental rate constant data used to test the model. The original experimental data can be found at <a href="../record/7747557">https://zenodo.org/record/7747557</a>. <ul> <li> expt_rxn_atom_mapped_smiles.csv: contains the atom-mapped reaction SMILES used for the experimental data.</li> <li>expt_data_collected.xlsx: contains all experimental data and detailed information</li> <li>expt_rxn_solv_smiles_with_features_all.csv: contains the computed additional features for the experimental reaction-solvent pairs.</li> </ul> </li> </ul> <p><strong>Machine learning model files under 'RxnSolvKSE_ML_model_files.zip'</strong></p> <ul> <li>Contains the Chemprop machine learning model files for predicting ddGsolv and ddHsolv for a reaction-solvent pair. It takes atom-mapped reaction SMILES and solvent SMILES as inputs.</li> <li>To use these ML models, please refer to the sample files and instructions on <a href="https://github.com/yunsiechung/chemprop/tree/RxnSolvKSE_ML">https://github.com/yunsiechung/chemprop/tree/RxnSolvKSE_ML</a></li> </ul>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.