Find research datasets worth reusing

opencc-by-4.0May 2019View details →

Transiting Planet Population Files

Pandas DataFrame files containing the synthesized populations of transiting planets used in Hadden et. al. 2019.

opencc-by-4.0Oct 2017View details →

Database of mixed-mode ventilated transitional spaces

Transitional spaces are meant as “a space in between indoor and outdoor climate, or between two indoor environments, which thermal characteristics can be or not modified by mechanical control system and where occupant may experience the dynamic effect of this change”. Nowadays, transitional spaces are pivotal in non-residential architecture and the proportion of such areas may vary between 10% up to 40% of the total volume depending on the typology. Mixed-mode buildings are desings with by both active and passive systems. The necessity of buildings’ energy demand and consumption reduction is a tangible fact after the entry into force of the EPBD directive 31/2010/EU. As a consequence buildings design went through the improvement of thermal envelope proprieties. In particular, for non-residential buildings this aspect combined with the increased level of internal gains has changed the energy balance: low heating demand compensated by an increased cooling demand not restricted to the only summer season. This evidence has stimulated a renewed interest in designers for the exploitation of natural ventilation as means of passive cooling solutions. Transitional spaces rely on a great potential for natural ventilation exploitation. They have direct connection with the outside, their architecture based on large volume suites with the principles for an effective natural ventilation. Because of the awareness of natural ventilation limitations, which relies on natural forces, the interest has progressively moved towards mixed-mode buildings. Mixed-mode buildings are indeed designed in such way that the HVAC system help to prevent uncomfortable conditions when natural ventilation is not sufficient to guarantee a comfortable environment. With the aim of a better overview about the role of transitional spaces in mixed-modeventilation design, technical information about 17 non-residential mixed-mode buildings among Europe have been recovered and analysed. All the information about transitionals spaces typology, mixed-mode scheme, ventilation strategy, controls and HVAC integration have been collected in a small database presented by an excel factsheet.

opencc-by-nc-nd-4.0Jul 2017View details →

Using progress sets on non-deterministic transition systems for multiple UAV motion planning

In this demonstration, two Aerial Robotic Workers are given a surveillance task where the first drone (red circle) starts in the blue area, the second drone (blue circle) starts in the red area, and the drones need to infinitely often exchange their positions while avoiding collisions and avoiding leaving the flying area. A controller for the multi-agent system guaranteeing the satisfaction of this high-level task is synthesized by first considering a non-deterministic and finite abstraction of the dynamical system, and then using the notion of progress sets corresponding to sets of state-control pairs for which eventual progress towards the desired goal is guaranteed.

opencc-by-4.0Mar 2024View details →

Final data for paper "A nonperturbative test of nucleation calculations for strong phase transitions"

In this Zenodo deposit we include the data used to make three key figures in our paper, showing our final nucleation rate results. The columns of the raw data files are labelled. In each case, the quantity being tabulated is the logarithm of the nucleation rate, typically labelled logGamma in our data files. We also include plotting scripts to generate the figures from the data. <ul> <li> The directory <code>a_limit</code> contains the extrapolation to zero lattice spacing, with the raw data in the file <code>a_limit_data</code>. The temperature T is fixed to our benchmark point of 93.121 GeV. The linear size Nx and the lattice spacing a are varied to give a constant total volume. The file <code>a_limit_lin_op_data</code> contains our comparison measurement using the linear order parameter. The script <code>plot_a_limit.py</code> performs a nonlinear least squares fit to a cubic, writes the continuum extrapolated nuclation rate result to stdout, and plots the data and the fit. </li> <li> The directory <code>vol_limit</code> contains the extrapolation to infinite volume, with the raw data in the file <code>vol_limit_data</code>. Here the temperature T=93.121 GeV and lattice spacing a=1.5 are fixed, while the linear size Nx is varied. The script <code>plot_vol_limit.py</code> performs a nonlinear least squares fit to an exponential function, writes the infinite volume limit nucleation rate result to stdout, and again plots the data and the fit. </li> <li> The directory <code>rate_reweighted</code> contains the data needed to plot the nucleation rate as a function of temperature. This plot combines lattice data and various perturbative estimates of the nucleation rate. The lattice data are in three files: <ul> <li><code>rate_lattice_BM2_vol_limit</code> contains the infinite volume limit result at the simulated lattice temperature T=93.121 GeV and with lattice spacing a=1.5.</li> <li><code>rate_lattice_BM2</code> reweights the lattice data to different temperatures and then takes the infinite volume limit.</li> <li><code>rate_lattice_BM2_Nx40_a1.5</code> contains data reweighted from the simulation at fixed volume Nx=40. In each lattice data file, the temperature, continuum potential parameters and nucleation rate are given.</li> </ul> The perturbative results are in three files, <code>rate_perturbative_BM2_rg_low</code>, <code>rate_perturbative_BM2</code> and <code>rate_perturbative_BM2_rg_high</code>, corresponding to the three RG scales mentioned in the text. These files again contain the temperature and continuum lattice parameters. The column eps gives the dimensionless loop expansion parameter around the metastable phase within the EFT. The column logGamma_0 gives the tree level result, logGamma_A and logGamma_B the LPA results with the two options for dealing with the imaginary parts described in the text, and logGamma_1 is the one loop result. The script <code>plot_rate_reweighted.py</code> plots all of these data together. For the tree level and one loop cases, the error bands plotted correspond to the minimum and maximum values of the nucleation rate across the three RG scales. For the LPA results, the bands include the extreme values for all six options including the two approaches to handling the imaginary parts. </li> </ul> In each case, the plots are saved to PDF and PNG plot files. The figures used in this deposit and in the paper used the following package versions (obtained with the <code>pipreqs</code> package): <pre><code>matplotlib==3.5.1 numpy==1.21.5 scipy==1.8.0 seaborn==0.11.2</code></pre> Note that in <a href="https://doi.org/10.5281/zenodo.10891524">Version v1</a> there was an error in the normalisation of our perturbative tree-level and LPA results which has now been fixed.

Observations of a PT-like phase transition and limit cycle oscillations in non-reciprocally coupled optomechanical oscillators levitated in vacuum

Trajectories of optically levitated particles in vacuum. Trajectories are recorded using quadrant photodiode and ultra-fast CMOS camera. The readme file with more detailed description is added.

openmit-licenseMay 2024View details →

Computing the Committor with the Committor: an Anatomy of the Transition State Ensemble

The study of the kinetic bottlenecks that hinder the rare transitions between long-lived metastable states is a major challenge in atomistic simulations. We propose a method to explore the transition state ensemble, which is the distribution of configurations that the system passes as it translocates from one metastable basin to another. We base our method on the committor function and the variational principle to which it obeys. We find its minimum through a self-consistent procedure that starts from information limited to the initial and final states. Right from the start, our procedure allows sampling very many transition state configurations. With the help of the variational principle, we perform a detailed analysis of the transition state ensemble, ranking quantitatively the degrees of freedom mostly involved in the transition and enabling for a systematic approach for the interpretation of simulation results and the construction of efficient physics-informed collective variables.

Supplementary Data for 'Eastern Australian estuaries will transition to tidal flood regimes in coming decades' by Hague, Thran, Jakob and Jones.

Supplementary data to support Hague et al. (2024) Coastal Futures paper, Eastern Australian estuaries will transition to tidal flood regimes in coming decades. column 'UTC_DT' provides datetime information in UTC in format YYYY-MM-DD hh:mm:ss column 'sea_lvl' provides quality assured water level as described in Hague et al. (2024) column 'sea_lvl'_pred' provides estimate of tidal contribution to water level as described in Hague et al. (2024)

Time-resolved pump-probe ellipsometry of the photoinduced insulator-metal transition in 25 nm VO2 thin films

<h3>Data available</h3> Transient pseudo dielectric function and ellipsometric parameters (\Psi and \Delta) measured with a time-resolved pump-probe ellipsometry on a 25 nm VO2 film deposited on SiO2. The data of the transient pseudo dielectric function and ellipsometric parameters (\Psi and \Delta) are provided for different pump wavelengths and pump fluences. <ul> <li>\lambda_{pump} = 400 nm - F_{pump} = 3.058 mJ/cm2</li> <li>\lambda_{pump} = 400 nm - F_{pump} = 3.823 mJ/cm2</li> <li>\lambda_{pump} = 400 nm - F_{pump} = 5.352 mJ/cm2</li> <li>\lambda_{pump} = 400 nm - F_{pump} = 6.117 mJ/cm2</li> <li>\lambda_{pump} = 400 nm - F_{pump} = 7.646 mJ/cm2</li> </ul> <ul> <li>\lambda_{pump} = 800 nm - F_{pump} = 1.536 mJ/cm2</li> <li>\lambda_{pump} = 800 nm - F_{pump} = 1.919 mJ/cm2</li> <li>\lambda_{pump} = 800 nm - F_{pump} = 2.109 mJ/cm2</li> <li>\lambda_{pump} = 800 nm - F_{pump} = 2.654 mJ/cm2</li> <li>\lambda_{pump} = 800 nm - F_{pump} = 2.793 mJ/cm2</li> </ul> <h3>Naming of the files</h3> In the .zip file that can be downloaded here, there are several folders. Each are named as lambda_pump_XXX_nm_fluence_YYY_mJcm-2 where XXX is either 400 or 800 and YYY is the fluence value. In each folder are four files. <ul> <li>diffdelta.txt - values of the transient ellipsometric parameter \Delta.</li> <li>diffpsi.txt- values of the transient ellipsometric parameter \Delta.</li> <li>diffpseudoepsilon1.txt- values of the real part of the transient pseudo dielectric function.</li> <li>diffpseudoepsilon2.txt- values of the real part of the transient pseudo dielectric function.</li> </ul> <h3>Structure of the files</h3> Each file has the same structure: The first row an array time delays in picosecond for which measurements have been performed. In the rest of rows, the first element of the array are the photon energy, while the rest of the elements are the values of the transient dielectric function or ellipsometric parameters (\Psi and \Delta) at each of the elements in the time delay array. Example: time delay       t1                         t2                           t3 E1(eV)      Delta(E1, t1)        Delta(E1, t2)          Delta(E1, t3) E2(eV)      Delta(E2, t1)       Delta(E2, t2)         Delta(E2, t3) E3(eV)      Delta(E3, t1)       Delta(E3, t2)         Delta(E3, t3)

Combined data file for Jokinen et al. "Depth and intensity of the sulfate-methane transition zone control sedimentary molybdenum and uranium sequestration in a eutrophic low-salinity setting", Applied Geochemistry 122, 2020

The datafile contains all the new raw data presented in the figures in the publication.

Overtone Transition 2ν1 of HCO+ and HOC+: Origin, Radiative Lifetime, Collisional Quenching

Dataset and post processing scripts used in the ChemPhysChem paper entitled: """Overtone Transition 2\nu_1 of HCO+^ and HOC^+: Origin, Radiative Lifetime, Collisional Quenching""" DOI: <a href="https://doi.org/10.1002/cphc.202400106">10.1002/cphc.202400106 </a>

PanIN and CAF Transitions

Dataset includes raw IMC data (.mcd) and H&E slide images (.tiff) related to "PanIN and CAF Transitions in Pancreatic Carcinogenesis Revealed with Spatial Data Integration" by Bell and Mitchell et al., Cell Systems 2024.

Reliable chaotic transition in incompressible fluid simulations - Supplementary Material

Open the record for dataset details and reuse information.

Parallel dynamics of bacterial genome reduction across independent transitions to endosymbiosis.

The establishment of symbiosis dramatically alters the evolution of the associated species, making symbiotic systems ideal models for studying the impact of lifestyle changes on genomes. Here, we focused on Enterobacterales, a large and ancient bacterial lineage that includes endosymbionts with diverse host associations, ranging from gut inhabitants to intracellular environments, and from horizontal to vertical transmission. Leveraging over two hundred genomes, along with cutting-edge single-copy gene concatenation and multi-copy gene family approaches, we inferred a robust phylogenetic framework that supports eleven independent transitions to endosymbiosis. Inferences on patterns of genome evolution confirm previous hypotheses about the processes underlying genome reduction: a substantial spike in gene loss always occurs simultaneously with the establishment of endosymbiosis, while a reduction in gene acquisition mechanisms is associated with the subsequent genome erosion. Furthermore, gene family loss frequencies were correlated across independent endosymbiotic clades; genes with more conserved functions and stronger constraints on sequence evolution are lost less frequently, suggesting that differences in gene essentiality and dispensability drive the observed parallelism. Our analyses contribute to the coming of age of the theory of genome evolution in symbiotic associations and provide novel insights into the importance of recombination as an opposing force against genome erosion.

opencc-by-4.0Jul 2023View details →

Storage and Transit Time Data and Code

Author: Andrew J. Felton Date: 5/5/2024 This R project contains the primary code and data (following pre-processing in python) used for data production, manipulation, visualization, and analysis and figure production for the study entitled: "Global estimates of the storage and transit time of water through vegetation" Please note that 'turnover' and 'transit' are used interchangeably in this project. Data information: The data folder contains key data sets used for analysis. In particular: "data/turnover_from_python/updated/annual/multi_year_average/average_annual_turnover.nc" contains a global array summarizing five year (2016-2020) averages of annual transit, storage, canopy transpiration, and number of months of data. This is the core dataset for the analysis; however, each folder has much more data, including a dataset for each year of the analysis. Data are also available is separate .csv files for each land cover type. Oterh data can be found for the minimum, monthly, and seasonal transit time found in their respective folders. These data were produced using the python code found in the "supporting_code" folder given the ease of working with .nc and EASE grid in the xarray python module. R was used  primarily for data visualization purposes. The remaining files in the "data" and "data/supporting_data"" folder primarily contain ground-based estimates of storage and transit found in public databases or through a literature search, but have been extensively processed and filtered here.  #Code information Python scripts can be found in the "supporting_code" folder. Each R script in this project has a particular function: 01_start.R: This script loads the R packages used in the analysis, sets the directory, and imports custom functions for the project. You can also load in the  main transit time (turnover) datasets here using the `source()` function. 02_functions.R: This script contains the custom function for this analysis,  primarily to work with importing the seasonal transit data. Load this using the   `source()` function in the 01_start.R script.  03_generate_data.R: This script is not necessary to run and is primarily for documentation. The main role of this code was to import and wrangle the data needed to calculate ground-based estimates of aboveground water storage. 04_annual_turnover_storage_import.R: This script imports the annual turnover and storage data for each landcover type. You load in these data from the 01_start.R script using the `source()` function. 05_minimum_turnover_storage_import.R: This script imports the minimum turnover and storage data for each landcover type. Minimum is defined as the lowest monthly estimate.You load in these data from the 01_start.R script using the `source()` function. 06_figures_tables.R: This is the main workhouse for figure/table production and  supporting analyses. This script generates the key figures and summary statistics  used in the study that then get saved in the  manuscript_figures folder. Note that all maps were produced using Python code found in the "supporting_code"" folder.

opencc-zeroJun 2024View details →

EstablishMed: a dataset of transition probabilities for woody plant establishment in the Mediterranean Region

Motivation: Plant establishment is the result of sequential demographic processes, namely post-dispersal seed survival, seed germination, seedling survival and sapling survival. These processes can be quantified as transition probabilities between life stages through field experiments, and their product provides an overall establishment probability. This information is essential to understand demography within populations and plant colonization potential under global change scenarios. The Mediterranean Region constitutes a biodiversity hotspot characterised by severe summer droughts, which suppose a critical demographic bottleneck for perennial plant establishment. Despite many studies have quantified transition probabilities of woody species in this region, information is scattered through literature and has not yet been compiled. To fill this gap, we collated data from a systematic literature review and completed them with new unpublished data to create the EstablishMed dataset. Main types of variables contained: EstablishMed is a compilation of 4728 records of transition probabilities that quantify demographic processes operating during plant establishment. All records belong to native species and were obtained in situ under field conditions. Each record includes information about the specific spatiotemporal context of the study (i.e., year, site, population, habitat and microhabitat) and the experimental procedures employed (e.g., degree of protection against natural enemies). In addition, we included taxonomic and trait information of the study species (i.e., seed mass, dispersal syndrome and life form), and the bioclimate of the study sites. Spatial location and grain: The dataset covers the whole Mediterranean Region. The finest spatial resolution corresponds to microhabitat types within populations. Time period and grain: Data were extracted from 271 studies originated between 1991 and 2024. Major taxa and level of measurement: 134 woody species from 80 genera and 39 families. Software format: EstablishMed is available in .csv format in Dryad repository.

Imaging material yielding and phase transitions in shock-compressed matter

Extended data sources for manuscript "Imaging material yielding and phase transitions in shock-compressed matter"

opencc-zeroDec 2023View details →

Gradual transitions in genetics and songs between coastal and inland populations of Setophaga townsendi

Setophaga townsendi is a species of wood-warbler (family Parulidae) in northwestern North America that has a geographic structure in the mitochondrial and nuclear genomes: while interior populations have differentiated mitonuclear ancestry from the sister species S. occidentalis, coastal populations have a mix of inland and S. occidentalis mitonuclear ancestries. This coastal-to-inland transition in genomic ancestry raises the possibility of similar geographic structure in phenotypic traits, especially those involved in mate choice. Using qualitative and multivariate approaches, we investigated whether there is a sharp transition between coastal and inland populations in both songs and nuclear DNA. We find there is a shallow geographic cline in the Type I song but not in the Type II song. Nuclear DNA shows a gradient between the coast and inland. There is little correlation between variation in song and the isolation-by-distance pattern in the nuclear DNA. The learned songbird song is shaped by both genetic and cultural processes. There has been a debate on whether song learning promotes or slows down population differentiation. By comparing the within-species variation in song and genetic structures, we can expand our understanding of the dynamic interplay between mating signals and population differentiation.

opencc-by-4.0Jul 2024View details →

Freshwater ecosystem transitions due to artisanal sand mining in Rwanda, Africa

Artisanal small-scale mining (ASM) of sand, gravel and crushed stones plays an economically important role through its value as a ‘development mineral’ for a growing population in sub-saharan Africa. The extracted material is used in developing and expanding urban areas and infrastructure and provides income for the population involved in the sector. However, the extraction of aggregates has shown to have large and often complex ecological and socio-economical consequences with potential significant health effects on the miners and the environment in which the mining takes place. Furthermore, the extent in which these negative effects do arise from ASM in sub-Saharan still remains anecdotal and are largely unknown. Here we show that ASM in a river channel in central Rwanda causes a systemic shift in freshwater biodiversity by changing species assemblages from being riverine towards communities representing standing waters. Based on 101 point samples, we find that ponds created due to mining activities act as habitats for freshwater insects associated with wetland habitats. Furthermore, these mining ponds did also act as breeding sites for mosquitoes and thereby potentially increase the presence of vector borne diseases such as malaria. These findings show how ASM can generate a landscape level shift in freshwater biodiversity and introduces the apparent paradox that while aggregates are critical building blocks in mitigating malaria transmissions and prevalence through improved housing, the mining practices unwillingly can create new breeding ground for malaria mosquitos, thus increasing the risk of malaria spreading to nearby communities.

opencc-zeroJul 2024View details →

Data from: Assessing temporal transition between microgranular and hyaline tests of calcareous microplankton during the Late Jurassic

Calcareous microplankton increased in abundance during the latest Jurassic, coinciding with the increase in abundance of calcareous nannofossils and with the onset of deposition of pelagic calcareous oozes. However, the timing and causes of the shift from microgranular tests of the earliest microplankton (chitinoidellids) to hyaline tests of calpionellids are obscured because the ultrastructure of two-layered praecalpionellids that occur during the Tithonian is poorly documented. Here, we investigate the ultrastructure of chitinoidellids and praecalpionellids from Upper Tithonian deposits in the Western Carpathians. We show that (1) the chitinoidellid microgranular layer is formed by elongated, euhedral, densely-packed, nanometric needles rather than by fragments of calcareous nannofossils, (2) two-layered chitinoidellids (Semichitinoidella) are formed by an internal microgranular layer (identical to that of Chitinoidella) and by an external hyaline prismatic layer, and (3) two-layered Praetintinnopsella exhibits an internal hyaline layer (with densely-packed, equant microcrystals) and an external layer formed by a dark organic rim. The external layer in Praetintinnopsella thus does not have any relation to the microgranular layer in chitinoidellids and the external hyaline layer of Semichitinoidella is not equivalent in structure to the hyaline layer of Praetintinnopsella. As both single-layer and two-layered chitinoidellids appear prior to the first appearance of Praetintinnopsella but still co-occur with this genus in the lowermost Upper Tithonian deposits, the origin of two-layered Praetintinnopsella either reflects a major transformation in biomineralization towards larger and more packed crystals during their earlier divergence from the chitinoidellid lineage or an origination of two-layered tests with a hyaline layer from an independent non-chitinoidellid ancestor.