Find research datasets worth reusing

opencc-zeroOct 2022View details →

Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programs: lessons from a 20-year time series of paired data.

Many long-term genetic monitoring programs began before next-generation sequencing became widely available. Older programs can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programs should capitalize on new information without sacrificing continuity of inference across the time series. We combined existing microsatellite-based genetic monitoring information with SNP-based microhaplotypes obtained from archived samples of Rio Grande silvery minnow (Hybognathus amarus) across a 20-year time series to evaluate point estimates and trajectories of key genetic metrics. Demographic and genetic monitoring bracketed multiple collapses of the wild population, and included cases where captive-born repatriates comprised the majority of spawners in the wild. Even with smaller sample sizes, microhaplotypes yielded comparable and in some cases more precise estimates of variance genetic effective population size, multilocus heterozygosity and inbreeding compared to microsatellites because many more microhaplotype loci were available. Microhaplotypes also recorded shifts in allele frequencies associated with population bottlenecks. Trends in microhaplotype-based inbreeding metrics were associated with the fraction of hatchery-reared repatriates to the wild, and should be incorporated into future genomic monitoring. Although differences in accuracy and precision of some metrics were observed between marker types, biological inferences and management recommendations were consistent.

opencc-by-4.0Oct 2022View details →

Burn severity data from: The heterogeneity of burn severity affects bird density in an abandoned mountain landscape of the Atlantic-Mediterranean transition

[Abstract] Fire regimes in mountain landscapes of southern Europe have been shifting from their baselines due to the accumulation of fuel fostered by long-standing rural abandonment and fire exclusion policies. Understanding the role of fire on biodiversity is paramount to implement adequate management to mitigate the impacts of altered fire regimes and land abandonment on biodiversity. Here, we explored to what extent the spatiotemporal variation in burn severity has affected bird abundance of a mountain abandoned landscape located in the Atlantic-Mediterranean transition (NW Iberia). We took advantage of: (1) satellite images of Sentinel 2 and Landsat missions to compute burn severity indicators from 2010 to 2020, and (2) standardized bird surveys carried out over 206 point-counts along the breeding season of 2021. Bird abundance models were built from burn severity metrics together with well-known fire regime attributes (% of burnt area and time since fire). Our results showed that the spatiotemporal variation of burn severity significantly correlated with the abundance of the 39% of the modeled species, supporting the role of pyro-diversity in driving bird populations in our region. The burnt area also explained abundance patterns for 28% of species. Time since fire only correlated with the abundance of 3 species. Our findings confirm the importance of incorporating burn severity indicators into the toolkit of decision makers to anticipate the response of birds to fire management. [Dataset Description] For each year between 2010 and 2020, we used a pair of satellite images, one before (April - July) and one after (September - November) the fire season. In order to use the best available information, we selected different satellites along the study period: for years 2010 and 2011, we used Landsat 5 imagery, whereas for 2012 we used Landsat 7, since Landsat 5 imagery was not useful due to high cloudiness. Since its launch in 2013, we shifted to Landsat 8 data, and finally to Sentinel 2 data from 2015 onwards. For each of these images we calculated the Normalized Burn Ratio (NBR), which is the normalized ratio between near infrared (NIR) and short wave infrared (SWIR) radiation (Eq. 1). NIR and SWIR bands of satellite sensors respond in opposite ways to burned vegetation, allowing to identify burned areas. NBR =(NIR - SWIR) / (NIR +SWIR) (1) To obtain a quantitative measure of change for each year, we calculated the dNBR by subtracting the NBR of the post-fire season image from the NBR of the pre-fire season image (Eq. 2). Finally, dNBR values were used as an estimate for fire severity. dNBR = NBRprefire- NBRpostfire (2)

opencc-by-4.0Nov 2022View details →

Critical transitions in degree mixed networks: A discovery of forbidden tipping regions in networked spin systems

Simulation data of critical transitions obtained by running a networked implementation of the Ising model on networks with different degree sequences.

opencc-by-4.0Oct 2022View details →

Data for Chandnani and Herrick, Influence of Target Properties on Wall Slumping in Lunar Impact Craters within the Simple-to-Complex Transition

Data files for Figures 3 and S1 of the manuscript.  These are craters counted in slump and ejecta units for the purpose of comparing their relative ages. The directory sf_shapefiles contains subdirectories for the 20 craters for which a slump unit and an ejecta unit had crater counts performed.  The AREA_* shapefiles are polygons that outline the area studied, and the CRATER_* files are the individual craters counted.  These files were created using CraterTools (<a href="https://www.geo.fu-berlin.de/en/geol/fachrichtungen/planet/software/_content/software/index.html">https://www.geo.fu-berlin.de/en/geol/fachrichtungen/planet/software/_content/software/index.html</a>) in ArcGIS, but that software is not necessary to use the shapefiles.  The subdirectory SFD_figs_color and SFC_suppl_figs_color are, respectively, the CraterStats (https://www.geo.fu-berlin.de/en/geol/fachrichtungen/planet/software/_content/software/index.html) files used to generate Figure 3 of the main manuscript and Supplemental Figure S1.  Each crater comprises a subdirectory of those main directories.  Within each subdirectory, the *.plt file is the file directing CraterStats how to make the figure.  The *.png file is the output figure from CraterStats, and the *.jpg file is the .png file after it has been cropped and the error bars have been changed from grey to black.  The *.txt file provides the output from CraterStats that, among other things, provides the data fit of isochrons to the data.  The *.diam files are data extracted from the shapefiles and provide the input into Craterstats.  They have the lat-lon-diameter information on the craters and the counting area.  All of these are commented text files, so you don’t need CraterStats to look at them and use them.

opencc-by-4.0Nov 2022View details →

Data for figures in "Observation of resonances in the transition state region of the F + NH3 reaction using anion photoelectron spectroscopy"

Data for all figures in "Observation of resonances in the transition state region of the F + NH3 reaction using anion photoelectron spectroscopy" and the accompanying supporting information, a manuscript accepted by Nature Chemistry.

opencc-by-4.0Dec 2022View details →

Dataset for "Band structures and Z2 invariant of 2D transition metal dichalcogenides from fully relativistic Dirac--Kohn--Sham theory using Gaussian-type orbitals"

Two-dimensional (2D) materials exhibit a wide range of remarkable phenomena, many of which owe their existence to the relativistic spin--orbit coupling (SOC). To understand and predict properties of materials containing heavy elements, such as the transition metal dichalcogenides (TMDs), full account of relativistic effects is mandatory in first-principles calculations. We present an all-electron method based on the four-component Dirac Hamiltonian and Gaussian-type orbitals (GTOs) that overcomes complications associated with linear dependencies and ill-conditioned matrices arising when diffuse functions are included in the basis. Until now, there has been no systematic study of the convergence of GTO basis sets for periodic solids neither at the nonrelativistic nor the relativistic level. Here, we provide such a study of relativistic band structures of the 2D TMDs in the hexagonal (2H), tetragonal (1T), and distorted tetragonal (1T') structural phases while focusing on SOC-driven properties (the Rashba splitting and the $\mathbb{Z}_2$ topological invariant). We demonstrate that our approach is valid even if large basis sets with multiple basis functions corresponding to each valence atomic orbital (denoted triple- and quadruple-$\zeta$) are used in the relativistic regime. The method does not require the use of pseudopotentials and provides access to all electronic states within the same framework, paving the way for direct studies of material properties that depend heavily on the electron density near atomic nuclei where relativistic effects and SOC are strongest, such as the parameters of the spin Hamiltonian.

opencc-zeroDec 2022View details →

Data for: Macroevolution in axial morphospace: Innovations accompanying the transition to marine environments in elapid snakes

Sea snakes in the Hydrophis-Microcephalophis clade (Elapidae) show exceptional body shape variation along a continuum from similar forebody and hindbody girths, to dramatically reduced girths of the forebody relative to hindbody. The latter is associated with specialisations on burrowing prey. This variation underpins high sympatric diversity and species richness and is not shared by other marine (or terrestrial) snakes. Here, we examined a hypothesis that macroevolutionary changes in axial development contribute to the propensity, at clade level, for body shape change. We quantified variation in the number and size of vertebrae in two body regions (pre- and post-apex of the heart) for ~94 terrestrial and marine elapids. We found Hydrophis-Microcephalophis exhibit increased rates of vertebral evolution in the pre- versus post-apex regions compared to all other Australasian elapids. Unlike other marine and terrestrial elapids, axial elongation in Hydrophis-Microcephalophis occurs via the preferential addition of vertebrae pre heart apex, which is the region that undergoes concomitant shifts in vertebral number and size during transitions along the relative fore- to hindbody girth axis. We suggest that this macroevolutionary developmental change has potentially acted as a key innovation in Hydrophis-Microcephalophis by facilitating novel (especially burrowing) prey specialisations that are not shared with other marine snakes.

opencc-zeroDec 2022View details →

4500 years of morphological diversification in Western Europe wild boars (Sus scrofa) and the consequences of the Neolithic transition

Evolutionary biologists have recently solicited archaeologists to help document and understand the morphological evolution of animals in response to human activities and, more globally, to help reconstruct the history and significance of the anthropogenic impact on worldwide ecosystems. Artificial selection associated with domestication is the best-known example of a major anthropogenic morphological evolution preserved in the archaeological record. However, the impact of the domestication process and dispersal on the morphological evolution of animals has been far less explored. To fill this gap, we focused on 5,000 years of Neolithic transition in Western Europe – a major anthropogenic ecological disturbance involving landscape modification and the translocation of domestic mammals. Using geometric morphometrics on key phenotypic markers preserved in the archaeological record associated with isotopic studies, we explored how and according to which cultural drivers the Neolithic niche construction has influenced the morphological evolution of wild boars (Sus scrofa). The decoupling of size and shape components from bone morphological variation has facilitated the identification of several processes of phenotypic diversification of Sus scrofa in response to human behaviour during the Neolithic transition in Western Europe.

opencc-zeroDec 2022View details →

Transition from transperitoneal to retroperitoneal approach in laparoscopic living donor nephrectomy: Team-based and individual learning curve: A cross-sectional study

Background: Laparoscopic living donor nephrectomy (LLDN) is a standard practice for kidney donor transplantation due to fewer complications associated with the treatment. Retroperitoneal approach to LLDN is thought to be more advantageous in preventing injuries to various abdominal organs. However, the transition process from transperitoneal to retroperitoneal LLDN is important to ensure the best outcome for the patients. The aim of this study was to investigate the learning curve for the retroperitoneal approach in LLDN among urologists in an individual and team-based approach Methods: A retrospective analysis of retroperitoneal LLDN was performed on procedures performed by a kidney donor team consisting of four (4) urologists from January 2019 to January 2022 at Cipto Mangunkusumo National General Hospital, Indonesia. The data were taken from pre-existing medical records. The learning curve for the operation time, warm ischemic time, and estimated blood loss were analyzed using cumulative sum (CUSUM) analysis. Phase 1 represents the initial learning curve, the phase 2 plateau represents the period of proficiency, and phase 3 represents the mastery period. Results: A total of 127 retroperitoneal LLDN procedures were done during the study period by four operators with various experience. The average procedure needed to achieve proficiency was 16.5 procedures. Meanwhile, the average procedure needed to achieve mastery was 28 procedures. A shorter learning curve was achieved by operators with more experience in other laparoscopic procedures. Conclusions: The learning curve for transition from transperitoneal to retroperitoneal approach to LLDN is relatively short and feasible for both individuals and teams of urologists. Therefore, the transition to a retroperitoneal approach is a feasible option to reduce the complication rate of LLDN.

IDE Interactions of Novices Transitioning Between Programming Environments

Novices in introductory programming courses typically learn the fundamentals of programming using one of a wide of programming environments. These vary greatly in terms of the mechanisms they employ to assist programmers, including their approaches to compilation and error message presentation. It is yet to be established which, if any, of these mechanisms are more beneficial for learning. In this study, we utilize Java programming process data to investigate the interaction between novices and two different versions of the BlueJ pedagogical IDE, which differ substantially in terms of compilation mechanism and error message presentation. Specifically, we compare novices that used both BlueJ 3 and BlueJ 4 with those who exclusively used either and the effects of the order in which they transition between BlueJ versions. We find substantial differences between different cohorts in terms of error messages and compilation which provides evidence that programming environments play an important part in influencing the programming practices of novices. This work supports the hypothesis that the choice of programming environment significantly affects user behavior with respect to specific programming interactions and therefore it is reasonable to expect a difference in how these environments affect learning.

Model data archive for a model-data intercomparison of the Eocene-Oligocene transition

This data package contains data used for an model-data intercomparison originally published in: D. K. Hutchinson, H. K. Coxall, D. J. Lunt, M. Steinthorsdottir, A. M. de Boer, M. Baatsen, A. von der Heydt, M. Huber, A. T. Kennedy-Asser, L. Kunzmann, J.-B. Ladant, C. H. Lear, K. Moraweck, P. N. Pearson, E. Piga, M. J. Pound, U. Salzmann, H. D. Scher, W. P. Sijp, K. K. Śliwińska, P. A. Wilson, and Z. Zhang, 2021: The Eocene-Oligocene transition: a review of marine and terrestrial proxy data, models and model-data comparisons, Climate of the Past, 17, 269-315. <a href="https://doi.org/10.5194/cp-17-269-2021">https://doi.org/10.5194/cp-17-269-2021</a> These data are also used in a further model-data intercomparison of Antarctic temperatures: Emily Tibbett, Natalie J Burls, David K. Hutchinson, Sarah J Feakins, (2023), Proxy-Model Comparison for the Eocene-Oligocene Transition in Southern High Latitudes, Paleoceanography and Paleocliamtology, In Review. Pre-print avaiable from: <a href="https://www.authorea.com/doi/full/10.1002/essoar.10511735.2">https://www.authorea.com/doi/full/10.1002/essoar.10511735.2</a> The package contains surface air temperature and sea surface temperature from an ensemble of model simulations of the Eocene-Oligocene transition. These data are provided at annual and monthly frequency. They are also provided on the original model grid, and an interpolated common grid used for the intercomparison. (The common grid is based on the HadCM3BL model grid.) All data are provided in NETCDF format with self-describing variable names. The name and explanation of the interpolated data files are contained in: table_of_experiments.xlsx Please read that spreadsheet to interpret the filenames, and see Table 2 (p291) of Hutchinson et al (2021) for experiment descriptions. Please also be mindful to cite the original authors of the simulations when using these data, whose work made this dataset possible. The appropriate citations are listed below: Reference   DOI link     Baatsen et al (2020) <a href="https://doi.org/10.5194/cp-16-2573-2020">https://doi.org/10.5194/cp-16-2573-2020 </a>  Goldner et al (2014) <a href="https://doi.org/10.1038/nature13597">https://doi.org/10.1038/nature13597</a>      Ladant et al (2014a,b) <a href="https://doi.org/10.5194/cp-10-1957-2014">https://doi.org/10.5194/cp-10-1957-2014</a>  <a href="https://doi.org/10.1002/2013PA002593 ">https://doi.org/10.1002/2013PA002593 </a> Hutchinson et al (2018, 2019) <a href="https://doi.org/10.5194/cp-14-789-2018">https://doi.org/10.5194/cp-14-789-2018</a>  <a href="https://doi.org/10.1038/s41467-019-11828-z">https://doi.org/10.1038/s41467-019-11828-z</a>  Kennedy et al (2015) <a href="https://doi.org/10.1098/rsta.2014.0419">https://doi.org/10.1098/rsta.2014.0419</a>  Zhang et al (2012, 2014) <a href="https://doi.org/10.5194/gmd-5-523-2012">https://doi.org/10.5194/gmd-5-523-2012</a>  <a href="https://doi.org/10.1038/nature13705">https://doi.org/10.1038/nature13705</a>  Sijp et al (2009) <a href="https://doi.org/10.1175/2009JCLI3003.1">https://doi.org/10.1175/2009JCLI3003.1</a>

opencc-zeroJan 2023View details →

Data from: Biogeography of curimatid fishes reveals multiple lowland-upland river transitions and differential diversification in the Neotropics (Teleostei, Curimatidae)

The Neotropics harbors a megadiverse ichthyofauna comprising over 6300 species with approximately 80% in just three taxonomic orders within the clade Characiphysi. This highly diverse group has evolved in tropical South America over tens to hundreds of millions of years influenced mostly by re‐arrangements of river drainages in lowland and upland systems. In this study, we investigate patterns of spatial diversification in Neotropical freshwater fishes in the family Curimatidae, a species‐rich clade of the order Characiformes. Specifically, we examined ancestral areas, dispersal events, and shifts in species richness using spatially explicit biogeographic and macroevolutionary models to determine whether lowlands–uplands serve as museums or cradles of diversification for curimatids. We used fossil information to estimate divergence times in BEAST, multiple time‐stratified models of geographic range evolution in BioGeoBEARS, and alternative models of geographic state‐dependent speciation and extinction in GeoHiSSE. Our results suggest that the most recent common ancestor of curimatids originated in the Late Cretaceous likely in lowland paleodrainages of northwestern South America. Dispersals from lowland to upland river basins of the Brazilian and Guiana shields occurred repeatedly across independently evolving lineages in the Cenozoic. Colonization of upland drainages was often coupled with increased rates of net diversification in species‐rich genera such as Cyphocharax and Steindachnerina. Our findings demonstrate that colonization of novel aquatic environments at higher elevations is associated with an increased rate of diversification, although this pattern is clade‐dependent and driven mostly by allopatric speciation. Curimatids reinforce an emerging perspective that Amazonian lowlands act as a museum by accumulating species along time, whereas the transitions to uplands stimulate higher net diversification rates and lineage diversification.

Dataset for publication: ExTrack characterizes transition kinetics and diffusion in noisy single-particle tracks

Dataset related to article  Simon, F., J.-Y. Tinevez, S. van Teeffelen (2023) ExTrack characterizes transition kinetics and diffusion in noisy single-particle tracks. Journal of Cell Biology Movies: example movies for PBP1b and RodZ. G0 = 370% expression level, G1 = 130% expression level, G2 = 30% expression level. Tracks: resulting tracks from the replicates, each replicate is composed of several movies (one xml file per movie). G0 = 370% expression level, G1 = 130% expression level, G2 = 30% expression level. See the material and method section for more details on the experimental conditions and the analysis pipeline.

"Microfossil evidence for trophic changes during the Eocene–Oligocene transition in the South Atlantic (ODP Site 1263, Walvis Ridge)" - calcareous nannofossil census data

This is a data supplement (Dataset A) to the paper "Microfossil evidence for trophic changes during the Eocene–Oligocene transition in the South Atlantic (ODP Site 1263, Walvis Ridge)" by Bordiga et al., 2015a (https://doi:10.5194/cp-11-1249-2015). Note that data are tabulated against depth in core (meters composite depth, mcd). Please refer to Table 1 in Bordiga et al. (2015) for age-depth model. Dataset A. Calcareous nannofossil census data (ODP Site 1263) One file (ODP 1263 dataset A_Bordiga et al. 2015.xls) containing: Sample information; Raw counts, relative (%) and absolute abundances (N/ g) of all species and size-based groups detected (as illustrated in Figure S2 of the original publication).

opencc-by-nc-nd-4.0Jan 2023View details →

Raw data files for "A Simple, Transition Metal Catalyst-Free Method for the Design of Complex Organic Building Blocks Used to Construct Porous Metal-Organic Frameworks" manuscript

Raw data files for a manuscript "A Simple, Transition Metal Catalyst-Free Method for the Design of Complex Organic Building Blocks Used to Construct Porous Metal-Organic Frameworks". All files are organized by instrumental methods, except Figure 1 in the manuscript and Figure S1, S52 in the SI, plots for which are reported as separate files. The file headers contain the necessary information such as column designations, units, etc.

opencc-by-4.0Oct 2022View details →

Late summer transition from a free-tropospheric to boundary layer source of Aitken mode aerosol in the high Arctic, model data

This dataset contains model output that was used in the publication "Late summer transition from a free-tropospheric to boundary layer source of Aitken mode aerosol in the high Arctic" (Price et al., 2022, in prep).   The output is from the UK Earth System Model run in atmosphere-only configuration at N96 resolution. Output is between September 2016 - December 2018 and is given variously as 3D monthly means, surface 3-hourly means, and 3D 2-hourly instantaneous values, depending on the variable in question.

opencc-by-4.0Feb 2023View details →

SourceData for "Correlating the charge transfer gap to the maximum transition temperature in Bi2Sr2Can-1CunO2n+4+x"

SourceData for "Correlating the charge transfer gap to the maximum transition temperature in Bi2Sr2Can-1CunO2n+4+x"

opencc-zeroFeb 2023View details →

Cuisine in transition? Organic residue analysis of domestic containers from 9th-14th century Sicily

From the 9th to 14th centuries AD, Sicily experienced a series of rapid and quite radical changes in political regime, but the impact of these regime changes on the lives of the people that experienced them remains largely elusive within the historical narrative. We use a multi-faceted lipid residue approach to give direct chemical evidence of the use of 248 everyday domestic ceramic containers from Islamic and post-Islamic contexts in western Sicily to aid our understanding of daily habits throughout this period of political change. A range of commodities was successfully identified, including animal fats, vegetable products, fruit products, (potentially including wine), and plant resins. The study highlights the complexity of residues in Early Medieval Mediterranean society, as in many cases mixtures of commodities were observed, reflecting sequential cooking events and/or the complex mixtures reflective of medieval recipes. However, overall there were no clear changes in the composition of the residues following the imposition of Norman control over the island and through subsequent periods, despite some differences between urban centres and rural sites. Thus, lending to the idea that post-Islamic populations largely flourished and benefited from the agricultural systems, resources, and recipes left by their predecessors.

opencc-by-4.0Feb 2023View details →

Dataset for Mapping State Transition Susceptibility in Quantum Annealing Part 2

Dataset for the paper Mapping State Transition Susceptibility in Quantum Annealing, Part 2. README.md file is contained in the tar.gz file.