Find research datasets worth reusing

opencc-by-4.0Jul 2024View details →

data sets supporting information about rime-splintering experiments

The uploaded data are related to the publication: ' Secondary Ice Production - No Evidence of Efficient Rime-Splintering Mechanism during Dry and Wet Rimer Growth' by Seidel et al. in the journal Atmospheric Chemistry and Physics. Droplet size distributions can be found in DSD.csv. Information on the individual secondary ice production experiments are provided by SIP_experiments_valid.csv. The descriptive information of the parameters can be found in the respective read_me file.

opencc-by-4.0Nov 2023View details →

A step towards understanding plastic complexity: antimony speciation in consumer plastics and synthetic textiles revealed by XAS - supporting data

This dataset contains all data related to "A step towards understanding plastic complexity: antimony speciation in consumer plastics and synthetic textiles revealed by XAS"

Supporting data sets for "Evolutionary analyses of IDRs reveal widespread signals of conservation"

S1: Disorder and order regions of alignments computed from AUCPreD scores which passed the 30 residue minimum length and phylogenetic diversity filters. The "ppids" column indicates the sequences in each alignment which were not excluded due these and other filtering criteria. See the main text methods for more details. S2: Substitution model parameters fit to meta-alignments derived from disorder and order filtered regions. S3: Features of segments in all regions. S4: Contrasts and root estimates of disorder scores in filtered regions computed with Felsenstein's contrasts algorithm. S5: Contrasts and root estimates of features in filtered regions computed with Felsenstein's contrasts algorithm. S6: Estimated BM and OU model parameters of simulated data. S7: Estimated BM and OU model parameters of features in filtered regions computed with maximum likelihood.

Aboveground Biomass (AGB) in the Boreal Region: Dataset for Supporting Biomass Recovery Analysis

This package supplements the following paper submitted to Nature: Biomass recovery carbon gains surpass fire losses over boreal forests during the last decades. This dataset contains the Aboveground Biomass (AGB) map (unit: Mg/ha) for the boreal region in 2020 at ~100m resolution.The global AGB dataset, upon which this regional subset is based, was initially developed by Yu et al. (2023). The preprint version of the corresponding AGB data paper has been made available online and can be accessed at <a href="https://doi.org/10.5281/zenodo.7583611">https://doi.org/10.5281/zenodo.7583611</a>. This paper is currently under peer review. The AGB map for the boreal region, as featured in our Nature submission, is provided here for reference and further research.

SCOPING REVIEW OF EMPIRICAL LITERATURE ON EVALUATION OF EDITORIAL POLICIES SUPPORTING OPEN SCIENCE PRACTICES IN SCHOLARLY JOURNALS

Excel file containing the description of methods & materials used in the scoping review, the whole dataset of included studies, and respective descriptive metadata.

opencc-zeroDec 2023View details →

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Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)

The rapid expansion of wild pigs (Sus scrofa) throughout the United States (US) has been fueled by unlawful introductions, with invasive populations causing extensive crop losses, damaging native ecosystems, and serving as a reservoir for disease. Multiple states have passed laws prohibiting the possession or transport of wild pigs. However, genetic and phenotypic similarities between domestic pigs and invasive wild pigs – which overwhelmingly represent domestic pig-wild boar hybrids – pose a challenge for the enforcement of such regulations. We sought to exploit wild boar ancestry as a common attribute among the vast majority of invasive wild pigs as a means of genetically differentiating wild pigs from breeds of domestic pigs found within the US. We organized reference high-density single nucleotide polymorphism genotypes (1,039 samples from 33 domestic breeds and 382 samples from 16 wild boar populations) into five genetically cohesive reference groups: mixed-commercial breeds, Durocs, heritage breeds, primitive breeds, and wild boar. Building upon well-established genetic clustering approaches, we structured the test statistic to describe the difference in the likelihood of a given genotype's ancestry vectors (sensu genetic clustering analysis) if derived strictly from the four described domestic pig reference groups versus allowing for admixture from the wild boar group. By fitting statistical distributions to test statistics of reference domestic pigs, we characterized the distribution of the null hypothesis – that a given genotype descends strictly from domestic pig reference groups. We tested the approach with simulated genotypes and empirical data from an additional 29 breeds of domestic pig represented by 435 unique genotypes; all associated test statistics for simulated and empirical domestic pig challenge sets fell within the distribution of reference domestic pigs. We then evaluated 6,566 invasive wild pigs sampled across the contiguous United States, of which 63% exceeded the maximum threshold for domestic pigs and could be statistically classified as possessing wild boar ancestry. This approach provides a scientific foundation to enforce regulations prohibiting the possession of this destructive invasive species. Further, this computationally efficient and generalizable approach could be readily adapted to quantify gene flow among ecological systems of conservation or management concern.

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Reclaiming urban vacant land to manage stormwater and support insect habitat

Urban green spaces can provide important wildlife habitat and ecosystem services. In legacy cities, built structures are demolished as populations dwindle, resulting in vacant land. Vacant land constitutes an opportunity to establish green infrastructure that provides multiple ecosystem services. Our objective was to determine whether establishing green infrastructure on vacant land to manage stormwater could provide insect habitat in the legacy city of Cleveland, Ohio, U.S.A. Two green infrastructure treatments were implemented on vacant land in the historic Slavic Village neighborhood in 2014 and 2015: rain gardens (lower cost) and bioswales (higher cost). We hypothesized that rain gardens and bioswales would support more abundant, species rich insect communities compared to unaltered vacant lots. Wild bees (Hymenoptera: Aculeata) and lady beetles (Coleoptera: Coccinellidae), two insect groups of conservation concern, were sampled during the summer (June–August) from 2014 to 2016 using pan traps and yellow sticky card traps. Local vegetation and temporal variables were measured. Generalized linear mixed effects models evaluated whether insect biodiversity varied with treatment, habitat variables, site, and time. We collected 3,004 bees from pan traps and 5,438 lady beetles from yellow sticky card traps during this study. Bee biodiversity was similar among treatments. In 2014, alien Coccinellidae abundance was higher in vacant lots compared to rain gardens. In 2015 and 2016, alien Coccinellidae were marginally more abundant in rain gardens compared to vacant lots and bioswales, while native Coccinellidae abundance was significantly higher in vacant lots. In the short term, establishing green infrastructure on vacant land can improve stormwater management without compromising the quality of vacant land as insect habitat.

opencc-zeroJan 2024View details →

Figure 4 in Histological study of the oral teeth and their bony support in the Mexican Jurassic gar †Nhanulepisosteus mexicanus (Ginglymodii, Lepisosteidae)

Figure 4. – †Nhanulepisosteus mexicanus. A-B: IGM 4902-5. Cross-section (respectively natural and polarized transmitted light) of a small tooth. We can show a crown of dentine (de), with an external crenulated layer of enameloid (arrow-heads). The pulp cavity (pc) is empty and its wall is regular. Scale bar = 100 μm.

Figure 2 in Histological study of the oral teeth and their bony support in the Mexican Jurassic gar †Nhanulepisosteus mexicanus (Ginglymodii, Lepisosteidae)

Figure 2. – †Nhanulepisosteus mexicanus: External view of the sample used for the paleohistological study (IGM 4902). (see Material and Methods chapter for explanations). Scale bar = 5 mm.

Figure 1 in Histological study of the oral teeth and their bony support in the Mexican Jurassic gar †Nhanulepisosteus mexicanus (Ginglymodii, Lepisosteidae)

Figure 1. – †Nhanulepisosteus mexicanus: External view of the fossil sample (IGM 4901) showing four caniniform teeth with their apical cap of acrodine (arrows). Two small teeth are seen between the fangs (arrowheads). Scale bar = 1 mm.

Figure 7 in Histological study of the oral teeth and their bony support in the Mexican Jurassic gar †Nhanulepisosteus mexicanus (Ginglymodii, Lepisosteidae)

Figure 7. – Comparison of the pulp cavity of the fang teeth in four Lepisosteoidei. Cross sections are made in the mid part of the teeth. A: †Nhanulepisosteus mexicanus (specimen IGM 4902; see Brito et al., 2017). B: †Atractosteus sp.* from the Santonian of Hungary (specimen VER 2014.91.3). C: Atractosteus tropicus. D: Lepisosteus platostomus (See fig. 3C in Meunier and Brito, 2017) The pulp cavity is completely invaded by the dentigerous tissue in †N. mexicanus and in the Santonian †Atractosteus whereas the dentine plies let at least the central mid part in the two extant species. The tooth of †Atractosteus sp. has eusthenodont plicidentine whereas teeth of Atractosteus tropicus and Lepisosteus platostomus have polyplocodont plicidentine. Abbreviations: de: dentine; en: collar enamel; er: external ridges; pc: pulp cavity; rd: radial folding of the dentine; vs: vascular space; arrowheads: dentine folds. Scale bars: A, D = 250 μm; B = 500 μm; C = 150 μm * The photo of the ground section was given to us by Dr. Marton Szabó, Department of Paleontology and Geology, Hungarian Natural History Museum, Ludovika têr 2, Budapest 1083, Hungary.

Figure 6 in Histological study of the oral teeth and their bony support in the Mexican Jurassic gar †Nhanulepisosteus mexicanus (Ginglymodii, Lepisosteidae)

Figure 6. – †Nhanulepisosteus mexicanus: Histological organization of the teeth supporting bone. A: Detail of the basal contact of a tooth (pc) and its supporting bone (bo) with vascular canals or cavities (vc). The white arrows point to osteons. B: Detail of the dentigerous plate showing lamellar bone and numerous cementing lines (black arrow-heads) that characterized an intensive remodeling of bone tissue below the tooth. We also show canalicles of Williamson (arrows). The asterisks point to secondary osteons. C-D: Detail of the secondary osteon (**) of Fig. 6B (respectively natural and polarized transmitted light). The secondary bone of the osteons is lamellar bone (black asterisks). The arrow-heads point to cementing line. We also show canalicles of Williamson (black arrows). E: Detail of the secondary osteon (*) of Fig. 6B showing canaliculi of Williamson (black arrows) and osteocytes (black arrowheads). A: IGM 4902-4; B, C, D, E: IGM 4902- 5. Scale bars: A = 200 μm; B = 100 μm; C, D = 50 μm; E = 25 μm.

Figure 5 in Histological study of the oral teeth and their bony support in the Mexican Jurassic gar †Nhanulepisosteus mexicanus (Ginglymodii, Lepisosteidae)

Figure 5. – †Nhanulepisosteus mexicanus: A: Pharyngeal dentigerous plate. We can see cross (white and black arrow-heads) and axial (white and black arrows) sections of minute teeth. We can also see a section of a scale (sc) (bo = bony tissue). B: Axial section of a pharyngeal tooth (white arrow) and its supporting bony plate (bp). A: IGM 4902-4; B: IGM 4902-5. Scale bars: A = 200 μm; B = 100 μm.

opencc-by-4.0Jan 2024View details →

Supporting Dataset (Tables S1-S7, Figure S1) for "Heavy-mineral grain counting: Counting techniques, error estimation, and the number of grains to be counted"

This Dataset comprises Tables S1-S7 for the article "Heavy-mineral grain counting: Counting techniques, error estimation, and the number of grains to be counted" authored by Jan Schönig and submitted to Journal of Geophysical Research: Earth Surface. Figure S1: Error of different counting methods in comparison with theory and without considering the finite population correction Table S1: Heavy-mineral dataset from semi-automated Raman analysis Table S2: Summary of heavy-mineral composition for individual samples in percent Table S3: Computed ribbon compositions for individual samples and ribbon sizes given in numbers of counts Table S4: Relative errors at 95 % quantile for consecutive ribbon counting simulations Table S5: Relative errors at 95 % quantile for maximum distance ribbon counting simulations Table S6: Relative errors at 95 % quantile for cluster counting simulations Table S7: Numerical solution for determining the number of counts required to discriminate the content of two mineral species in an aliquot

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Data from: Exponential history integration with diverse temporal scales in retrosplenial cortex supports hyperbolic behavior

Animals rely on their experience to guide their next choice. In foraging-type tasks guided by history-dependent value, these experiences are typically integrated such that the weights of past events initially decay quickly over time but show a longer tail than expected by exponential decay. Rather, such integration is better described by a hyperbolic function. Hyperbolic integration affords sensitivity to both recent environmental dynamics and long-term trends, however the mechanism by which the brain implements this hyperbolic integration is unknown. We trained mice on a history-dependent, value-based decision task and found that the mice indeed showed hyperbolic decay on their weighting of past experience. However, the activity of history-encoding cortical neurons showed weighting with exponential decay. In resolving this apparent mismatch, we observed that cortical neurons encode history information heterogeneously across a wide variety of exponential time-constants, with the retrosplenial cortex (RSC) overrepresenting longer time-constants compared to other areas. A model that combines these diverse timescales of exponential history integration can recreate the heavy-tailed, hyperbolic history integration observed in behavior. In particular, time-constants of RSC neurons best matched the behavior, and optogenetic inactivation of RSC uniquely reduced the use of history information. These results indicate that behavior-relevant history information is maintained in neurons across multiple timescales in parallel, and suggest that the neural population in RSC is a critical reservoir of this information guiding decision-making.

opencc-zeroJan 2024View details →

opencc-by-4.0Feb 2024View details →

Supporting material for von Fromm et al (2024) Global synthesis of SOC abundance and persistence profile data

This file contains the supporting material for von Fromm et al (2024) Controls and relationships of soil organic carbon abundance and persistence vary across pedo-climatic regions published in Global Change Biology (https://doi.org/10.1111/gcb.17320).  The data comes originally from the International Soil Radiocarbon Database (ISRaD; <a href="https://soilradiocarbon.org/">https://soilradiocarbon.org/</a>). We filtered the data and applied a mass-preserving spline function. For more details see the corresponding manuscript and the github repository (https://github.com/SophievF/Global_SOC_Abundance_Persistence).

Different components of cognitive-behavioural therapy affect specific cognitive mechanisms: supporting data

This repository holds data associated with the manuscript "Different components of cognitive-behavioural therapy affect specific cognitive mechanisms" (<a href="https://osf.io/preprints/psyarxiv/ydct5">https://osf.io/preprints/psyarxiv/ydct5</a>).<ul><li>rew-eff-planningX .csv files represent data from experiments testing effects of a planning/goal-setting intervention on reward-effort decision-making (X=1, initial discovery sample, X=2, replication sample)</li><li>causal-attr-X .csv files represent data from experiments testing the effects of a cognitive restructuring intervention on causal attribution tendencies (X=1, initial discovery sample, X=2, replication sample)</li><li>crossover-study-X .csv files represent data from the crossover-design study (data saved separately for participants randomly allocated to complete the reward-effort vs causal attribution tasks).</li></ul>Data-generating task code and full analysis code can be found at <a href="https://github.com/agnesnorbury/cognitive-mechanisms-psychotherapy">https://github.com/agnesnorbury/cognitive-mechanisms-psychotherapy</a>.

opencc-by-4.0Nov 2023View details →

Images supporting: Nondestructive, quantitative viability analysis of 3D tissue cultures using machine learning image segmentation

Two image datasets (as zip files) including all images analyzed in the manuscript Nondestructive, quantitative viability analysis of 3D tissue cultures using machine learning image segmentation. Images are of pancreatic adenocarcinoma (PDAC) cystic spheroid samples grown in either BME or Matrigel. Some images have background noise in the form of iron oxide nanoparticles introduced to them.

opencc-by-4.0Sep 2023View details →

Code and data to support 'Street view imagery for built environment auditing: a systematic review'

Code and data to support  the manuscript entitled 'Street view imagery for built environment auditing: a systematic review'