Find research datasets worth reusing

Figure 4 in A transitional species of Daspletosaurus Russell, 1970 from the Judith River Formation of eastern Montana

Figure 4 Right jugal of BDM 107. Shown in medial (A) and lateral (B) views. Abbreviations are as follows: cp, cornual process; po, pneumatic opening; pop, postorbital process. Scale is 10 cm. Full-size DOI: 10.7717/peerj.14461/fig-4

Figure 2 in A transitional species of Daspletosaurus Russell, 1970 from the Judith River Formation of eastern Montana

Figure 2 Premaxillae of BDM 107. Shown in lateral (A), medial (B), and rostral (C) views. Abbreviations are as follows: nf, neurovascular foramina; smp, symphysis. Scale is 10 cm. Full-size DOI: 10.7717/peerj.14461/fig-2

Figure 1 in A transitional species of Daspletosaurus Russell, 1970 from the Judith River Formation of eastern Montana

Figure 1 Map of the area of discovery of BDM 107, holotype of D. wilsoni sp. nov. Nearby towns (Hinsdale, Glasgow, Saco) and highways (US-2) are labeled. Dashed lines indicate county boundaries; "Jack's B2" site indicated by star. Full-size DOI: 10.7717/peerj.14461/fig-1

opencc-by-4.0Dec 2022View details →

Phase transitions and light scalars in bottom-up holography—data release

This dataset contains the data points in the plots of the preprint <a href="https://arxiv.org/abs/2212.07954\">Phase transitions and light scalars in bottom-up holography</a>. If you use this data release in the context of your research, please cite the aforementioned paper. Further details are given in the file ReadMe.md.

dryad40/100

Code and data from: A hierarchical approach for estimating state-specific mortality and state transition in dispersing animals with incomplete death records

Unbiased mortality estimates are fundamental for testing ecological and evolutionary theory as well as for developing effective conservation actions. However, mortality estimates are often confounded by dispersal, especially in studies where dead-recovery is not possible. In such instances, missing individuals (i.e. individuals with unobserved time of death) may have died or permanently emigrated from a study area, making inferences about their fate difficult. Mortality before and during dispersal, as well as the decision to disperse, usually depend on a suite of individual, social, and environmental covariates, which in turn can be used to draw conclusions about the fate of missing individuals. Here, we propose a Bayesian hierarchical model that takes into account time-varying covariates to estimate transitions between life-history states and mortality in each state using mark-resighting data with missing individuals. Specifically, our framework estimates mortality rates in two states (resident and dispersing state) by treating the fate of missing individuals as a latent (i.e. unobserved) variable that is statistically inferred based on information from individuals with a known fate and given the individual, social, and environmental conditions at the time of disappearance. Our model also estimates rates of state transition (i.e. emigration) to assess whether a missing individual was more likely to have died or survived due to unobserved emigration from the study area. We used simulations to check the validity of our model and assessed its performance with data of varying degrees of uncertainty. Our modeling framework provided accurate mortality and emigration estimates for simulated data of different sample sizes, proportions of missing individuals, and resighting intervals. Variation in sample size appeared to affect the precision of estimated parameters the most. Our approach offers a solution to estimating unbiased mortality of both resident and dispersing individuals as well as the probability of emigration using mark-resighting data with incomplete death records. Conditional on the availability of data on known-fate individuals and relevant time-varying covariates, our model can reconstruct the fate (death or emigration) of missing individuals. The modularity of our framework allows mortality analyses to be tailored to a variety of species-specific life histories.

opencc-zeroDec 2022View details →

TROVA outputs for the extratropical transition of tropical cyclones in the North Atlantic basin

Output data from the TRansport Of water Vapor (TROVA) tool for the research paper "Evaluating changes in the moisture sources for tropical cyclones precipitation in the North Atlantic that underwent extratropical transition".

opencc-by-4.0Dec 2022View details →

Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms

Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d).

Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata

Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50=4.21 Mb, scaffold N50=75.55 Mb; 2n=24) harbors 31,584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein-protein and DNA-protein interaction assays. Our high-quality genome assembly, metabolome and transcriptome resources further enrich Quercus genomics, and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.

Supporting information for First-row transition metalloporphenes, metallic conductors or not?

Supporting information for First-row transition metalloporphenes, metallic conductors or not?   POSCAR, vasprun.xml, and INCAR files

Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts

Supporting data for Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts Molecular simulations make it possible to predict equilibrium constants and corresponding free energy differences. For a system that exists in two states A and B, the equilibrium constant K can be predicted as K = t_B / t_A, where t_B and t_A are times spent in states B and A, respectively. The free energy can be calculated as Delta G = -kT log(K). Here we propose a new method for calculation of confidence intervals for K and Delta G. The ratio of the true value of K and estimated K follows the F-distribution with degrees of freedom df1 = number of B to A transitions and df2 = number of A to B transitions. This makes it possible to calculated the confidence interval of K solely from the number of transitions. The code in the directory errors was used to calculate Table 1 of the article. The code in the directory type1error was used to generate 10000 first time passage times for a transition from A to B and B to A as random numbers with exponential distribution. This was done for different combinations of number of transition and values of K. Number of confidence intervals not spanning the predefined value of K (type 1 errors) was expected to be 5 % for 95-% confidence intervals. This was in agreement with the result. The code in the directory type1errorodd was used to run similar experiment as type1error, but with number of A to B transitions higher than B to A by one. The code in the directory threestates was used to run similar experiment as type1error and  type1errorodd but for a system with three states A, B and C. The directory glycerol contains a trajectory, evolution of values of torsion angles and the code for analysis of the simulation of glycerol in water. The directory ffmp contains evolution of values of RMSD from the native structure, manual assignments of folded and unfolded states and the code for analysis of simulations of fast folding miniproteins (original data from Lindorf-Larsen et al. Science 2011, 334(6055) 517-520). The directory se contains the code for calculation of standard errors numerically and by the method presented in the article. The directory parallel presents the code for calculations supporting our method to calculate rate and equilibrium constants in parallel simulations. Codes written in R were executed using R version 3.4.4 by running: $ R –no-save < code.R > code.log File md5sums contains md5sum codes for all files.

opencc-by-4.0Feb 2023View details →

X-ray scattering datasets associated with the publication "Molecular Dynamics of Janus Polynorbornenes: Glass Transitions and Nanophase Separation"

X-ray scattering datasets for samples described in the 2020 publication "Molecular Dynamics of Janus Polynorbornenes: Glass Transitions and Nanophase Separation". This dataset includes both raw and processed X-ray scattering data for samples PTCHSiO-Pr, Bu, Hx, Oc and De, alongside background measurements files (BKG).

opencc-by-4.0Feb 2023View details →

CRDS absorption spectra recorded for the P(16) and P(28) transitions of the 20012-00001 band, and the R(24) and R(30) transitions of the 20013-00001 band of 12CO2 in air

The database is made of the set of the CRDS absorption spectra recorded for the P(16) and P(28) transitions of the 20012-00001 band, and the R(24) and R(30) transitions of the 20013-00001 band of 12CO2 in air, following the procedures and with the experimental setups described in the paper entitled "Line shape parameters of air-broadened 12CO2 transitions in the 2.0 µm region, with their temperature dependence" by D. Mondelain, A. Campargue, H. Fleurbaey, S. Kassi, S. Vasilchenko published in JQSRT 298 (2023) 108485.  Each averaged spectrum corresponds to a .csv file including the following columns:  absolute wavenumber (in cm-1), cavity loss rate 1/ct (in 10-6 cm-1), temperature (in °C) and total pressure (in Torr). Two gas mixtures of CO2 in air (Ar : ~1 Mol-% ; O2 :~20.95 Mol-% ; N2 : ~78.05 Mol-%) are used in this work.  The stated sample CO2 mixing ratios are 6.013±0.060 Mol-ppm for the 20012-00001 band and 40.10±0.24 Mol-ppm for the 20013-00001 band.

opencc-by-4.0Feb 2023View details →

CRDS absorption spectra recorded for the R(06), R(12), R(16), R(18) and R(20) transitions of the 30013-00001 band of 12CO2 in air

The database is made of the set of the CRDS absorption spectra recorded for the R(06), R(12), R(16), R(18) and R(20) transitions of the 30013-00001 band of 12CO2 in air  following the procedures and with the experimental setups described in the paper entitled "CRDS measurements of air-broadened lines in the 1.6 µm band of 12CO2: Line shape parameters with their temperature dependence" by D. Mondelain, A. Campargue, H. Fleurbaey, S. Kassi, S. Vasilchenko published in JQSRT 288 (2022) 108267.  Each averaged spectrum corresponds to a .csv file including the following columns:  absolute wavenumber (in cm-1), cavity loss rate 1/ct (in 10-6 cm-1), temperature (in °C) and total pressure (in Torr). A gas mixture of 398.9±2.0 (2sigma) mol-ppm of CO2 in air (Ar: ~1 mol-% ; O2: ~20.95 mol-%; N2: ~ 78.05 mol-%) is used in this work.

Database of the artistic transfer in the building factory in the ancient kingdom of Seville in the transition to the Modern Age [Dataset]

Los datos recopilados se almacenan en una base de datos de Microsoft Access® que se ha diseñado para integrarse físicamente en un sistema SIG y a herramientas para modelos orientado a Grafo, como Gephi®. La estructura de esta base de datos está compuesta por entidades y relaciones que son representadas por tablas de entidades principales (E), tablas de clasificación/valores - entidades secundarias (Ee) y relaciones (RS). Cada una de las tablas está formada por una serie de registros (cada registro corresponde a una entidad o elemento) y por columnas o campos. Existen 5 tablas de entidades principales: “E1 profesionales”, “E2 mecenas”, “E3 edificios”, “E4 parte_edificio” (objetos asociados a arquitectura y estructura); 4 tablas de entidades secundarias: “Ee1 categoria agente”, “Ee2 tipo-clasificacion”, “Ee3 autor-dato” y “Ee4 ref-docu”; y 2 tablas de Relaciones: “RS1 Evento” y “RS2 tiene pariente”. El objetivo es identificar los eventos relacionados con la actividad constructiva durante el fenómeno del Gótico Tardio, mediados del Siglo XV y XVI de los profesionales que han trabajado en el antiguo Reino de Sevilla con el fin de analizar los movimientos, actividades y red de relaciones de los profesionales en el tiempo y espacio.

opencc-by-4.0Mar 2023View details →

The Stability Transition from Stable to Unstable Frictional Slip with Finite Pore Pressure

The datasets for Affinito et al., 2023 manuscript submitted to GRL. Each experiment is was collected on a 24-bit recorder and 16 channels for hydromechanical data. The purpose of these experiments was to document the transition from stable sliding to unstable stick-slip fricitional sliding. Experiments were done on quartz gouges, with constant pore pressure conditions.

opencc-by-4.0Apr 2023View details →

Accompanying Data for the Manuscript "There's more to life than O2: Simulating the detectability of a range of molecules for ground-based high-resolution spectroscopy of transiting terrestrial exoplanets"

This file contains results for all cases considered in the manuscript titled "There's more to life than O2: Simulating the detectability of a range of molecules for ground-based high-resolution spectroscopy of transiting terrestrial exoplanets"

opencc-by-4.0May 2023View details →

Transit Bus Left Side Camera Video Traffic Monitoring Dataset

This dataset contains the raw data used in the research and development study reported in “Automated Traffic Surveillance Using Existing Cameras on Transit Buses”. This dataset consists of 11 video clips, each approximately 20 min. in duration, taken from the driver (left) side read camera of an in-service Ohio State University (OSU) Campus Area Bus Service (CABS) 40-foot transit bus running the West Campus Loop route. One set, consisting of 7 videos, was collected on a sunny day in October 2019. A second set, consisting of 3 videos, was collected during and after periods of rain and heavy rain in March 2022. Each video is accompanied by manually extracted ground truth of vehicles, and some other objects, that are in the roadway and observed by the camera.

opencc-by-4.0Jun 2023View details →

Code and data supplement for "Unveiling the transition from niche to dispersal assembly in ecology"

This repository contains the data and code needed to reproduce the results and figures in the article “Unveiling the transition from niche to dispersal assembly in ecology” published in Nature.

dryad40/100

Genetic and phenotypic consequences of local transitions between sexual and parthenogenetic reproduction in the wild

Transitions from sexual to asexual reproduction have occurred in numerous lineages across the tree of life, but many questions remain about how such transitions occur and why asexual populations rarely persist. In facultatively parthenogenetic animals, all-female populations can arise when males are absent or become extinct and, if such populations can persist asexually for many generations, they could ultimately give rise to obligately asexual species. However, the initial stages of this process remain poorly understood. The facultatively parthenogenetic Australian phasmid Megacrania batesii exhibits a spatial mosaic of mixed-sex populations that reproduce predominantly sexually and all-female sites that reproduce exclusively via parthenogenesis. We used this system to compare genetic and phenotypic parameters among multiple natural populations that vary in reproductive mode and geographic location. Analysis of single nucleotide polymorphisms (SNPs) collected from reduced representation whole genome data showed populations grouping by geographic location rather than reproductive mode, with little gene-flow between them. Mixed-sex populations had drastically higher heterozygosities than all-female populations. Phenotypic analysis revealed considerable inter-population variation in rates of deformities in (non-functional) wings, with higher mean frequency and severity of deformities in all-female sites. All-female sites also harbored more parasites, but only in swamp habitats. However, reproductive mode did not explain variation in mean female fecundity, egg hatching success, or missing appendages. These results indicate that local transitions to parthenogenetic reproduction can lead to increased rates of developmental abnormalities and increased vulnerability to disease but can also occur without substantial fitness consequences despite dramatic reductions in genetic diversity and heterozygosity.

opencc-zeroJun 2023View details →