Find research datasets worth reusing

Data for V1298 Tau TESS Transit Fits

Light curve and Gaussian-process model data for the TESS observations of V1298 Tau. See our GitHub repository (<a href="https://github.com/afeinstein20/v1298tau_tess">https://github.com/afeinstein20/v1298tau_tess</a>) for Jupyter Notebooks on how to interact with these files.

Direct observation of a dynamical glass transition in a nanomagnetic artificial Hopfield network

Source files used to produce the publication "Direct observation of a dynamical glass transition in a nanomagnetic artificial Hopfield network."

Dataset for "Quantifying the effects of bed roughness on transit time distributions via direct numerical simulations of turbulent hyporheic exchange"

This dataset contains the sediment models, DNS flow field data, subsurface path data, and calculated transit time distributions for both the regular- and random-interface cases used in the paper: "Quantifying the effects of bed roughness on transit time distributions via direct numerical simulations of turbulent hyporheic exchange" by Guangchen Shen, Junlin Yuan, and Mantha S. Phanikumar (Submitted to Water Resources Research).  Detailed introduction of each data file is as follows. 1. DNS flow field data Flowfield_Reg.h5 and Flowfield_Ran.h5 contains the following fields for the regular and random cases, respectively. 'ni', 'nj', 'nk' are the numbers of grid points along x, y, and z directions. 'xc', 'yc', 'zc' are the cell center locations. 'u3d','v3d','w3d' are the three-dimensional time-averaged velocities at each grid point. 'vof' is the volume-of-fluid field used by the immersed-boundary method to prescribe the fluid-solid interface (vof=1 in fluid and 0 in solid), at each grid point. 'vof' contains the information of sediment grain distribution and bed roughness geometry. Only the subsurface data (those below the sediment crest) are shared due to dataset size limit. 2. Particle-tracked subsurface flow paths and corresponding transit time distributions The mat files “xxx_pathline” store the (x,y,z) location of each point (saved as 'StrX', 'StrY, 'StrZ') along the subsurface paths, discretized by uniform steps of travel time (with time intervals of 0.1 for 'A' and 0.01 for 'MD' cases, normalized by channel height and friction velocity). The files “xxx_TT” store the array of transit times corresponding to the tracked paths, where the 1d array T is the transit time. 'A' denotes calculations based on time-mean advection only, while 'MD' denotes calculations accounting for additional molecular diffusion. 'Interface' and '3DiameterBelow' indicate that the particles were released at the interface and -3 D below the interface, respectively.

opencc-by-4.0Feb 2022View details →

Complementary observations aid identification of the mountain rain-snow transition elevation

If data have a time stamp, all data are in UTC Includes: <ul> <li>precipitation gauge [meters] data from California Data Exchange (CDEC)</li> <li>SNOTEL data (soil moisture [%], snow water equivalent [meters])</li> <li>snow depth [meters] data from snow pillow sites from CDEC</li> <li>snow water equivalent [meters] from snow pillow sites from CDEC</li> <li>temperature [degrees C] data from snow pillow sites from CDEC</li> <li>FMCW radar freezing level [km above the surface] data from NOAA</li> <li>MODSCAG remote sensing data [rgb, grain size, snow covered area, zenith angle] from JPL</li> </ul>

Transitive groups of degree 48

This database contains the transitive groups of degree 48. It is intended to be used in GAP, but also to be accessible more generally. The groups were originally computed by Derek Holt using MAGMA; this computation was reported in the following paper: Derek Holt, Gordon Royle and Gareth Tracey, The transitive groups of degree 48 and some applications. Journal of Algebra, 2022. (https://doi.org/10.1016/j.jalgebra.2021.06.018) The groups were subsequently made available as one of MAGMA's Optional Databases (http://magma.maths.usyd.edu.au/magma/download/db/). Installing the MAGMA database enables the use of the command "TransitiveGroup(48,i)" for where i is a positive integer at most 195826352 (which is the number of transitive groups of degree 48). The data files and accompanying functions in this archive provide a similar mechanism to access the groups in GAP.  In order for researchers to refer to groups unambiguously (either formally, in research papers, or informally, while communicating with colleagues), it is desirable that the numbering of the groups is independent of the system used to access them.  On these grounds, the numbering used here is consistent with the numbering established by MAGMA. The full data set is very large, because there are 195826352 transitive groups of degree 48. As a result, the data has been split into 1959 files with names of the form "TransitiveGroupsOfDegree48_X.gz", where X is an integer between 1 and 1959. All but the last of these files contains 100000 transitive groups, and each of them is compressed (using gzip) to save space. These files have been combined into 10 tar files, with names such as Trans48Part1.tar, Trans48Part2.tar etc., each containing 200 compressed files (except for the last which contains 159 files). By group identification numbers, the 10 tar files contains the following groups: Trans48Part1.tar 1 - 20000000 Trans48Part2.tar 20000001 - 40000000 Trans48Part3.tar 40000001 - 60000000 Trans48Part4.tar 60000001 - 80000000 Trans48Part5.tar 80000001 - 100000000 Trans48Part6.tar 100000001 - 120000000 Trans48Part7.tar 120000001 - 140000000 Trans48Part8.tar 140000001 - 160000000 Trans48Part9.tar 160000001 - 180000000 Trans48Part10.tar 180000001 - 195826352 The group with transitive identification number n is found in the file "TransitiveGroupsOfDegree48_X", where X = floor( n-1 / 100000) + 1, and as each file has a 13-line descriptive header, group n is located on line (n-1 mod 100000) + 14.  The groups are given as [ id, gens ] where "id" is the Transitive Identification number of the group, and "gens" is a list of permutations which generate the group. The following GAP function provides a reasonably fast way to access a group by its identification number without having to read in all the data. The function identifies which of the 1959 compressed files contains the group, and then reads only that one file. The file can remain compressed because GAP 4.11.1+ can automatically decompress the file as it is read. TransitiveGroup48 := function(id)     local file_number, pos, strm, i, x, g;     file_number := QuoInt(id-1, 100000)+1;;     pos := (id-1) mod 100000 + 1;     strm := InputTextFile(Concatenation("TransitiveGroupsOfDegree48_", String(file_number), ".gz"));;     for i in [1 .. pos+14] do         x:=ReadLine(strm);;     od;     x:=EvalString(x);;     CloseStream(strm);;     if x[1] <> id then         Error("Somehow we got the wrong group!!!\n");     else         g:=Group(x[2]);;         SetTransitiveIdentification(g, id);;         return g;     fi; end; To use this function, download the database and untar each part (or the parts that you are interested in) and move all the "TransitiveGroupsOfDegree48_X.gz" files into a single directory. DO NOT DECOMPRESS THESE FILES. Then change to that directory, start GAP, and create the function "TransitiveGroup48" function using the above code. Finally, remember that the command is "TransitiveGroup48(i)" and not "TransitiveGroup(48,i)".

opencc-by-4.0Mar 2022View details →

Low-cost prediction of molecular and transition state partition functions via machine learning

This dataset contains the vibrational, rotational, translational, and electronic partition functions for 35,883 organic chemistry molecular structures taken from the Grambow et. al dataset [1]. It was used to train ML deep neural networks to predict unknown transition state partition functions as well as partition functions for known molecular structures [2] The partition functions were computed at temperatures in the range T= [50, 2000] K with the rigid rotor, rigid body, harmonic oscillator approximations. Reactions involve no more than 7 C, N, or O atoms. Frequencies for the vibrational partition functions were taken from [1] where they were computed with DFT at the ωB97X-D3/def2-TZVP level of theory. For the rotational partition function, symmetry numbers were obtained by evaluating proper and improper invariant rotations of the structures. We note that structures involving two molecules were not separated: vibrational frequencies and symmetry numbers were computed for the aggregate structure. For each reaction, partition functions were calculated at 50 temperatures sampled uniformly from the inverse temperature range 1/T = [1/2000, 1/50] K-1. This corresponds to 11,961 reactions, 35,883 total structures, and 1,794,150 total partition function examples. The file Partition_Functions.tar.gz contains directories entitled “rxnXXXXXX” where XXXXXX is a reaction number identifier. Each contain three files “rXXXXXX.csv”, “pXXXXXX.csv”, “tsXXXXXX.csv” corresponding to data from the reactant (“r”), product (“p”), and transition state (“ts”) for reaction XXXXXX. Note that the directory structure and the reaction identifiers are the same as used in the original structure dataset by Grambow et al. and the corresponding structures can easily be extracted from that dataset. Each comma separated value (csv) file contains 50 rows and the following columns: <table> <tbody> <tr> <td>  Column label </td> <td>  Values </td> </tr> <tr> <td>  T [K] </td> <td>  Temperature </td> </tr> <tr> <td>  qpart_ele [unitless] </td> <td>  Electronic partition function </td> </tr> <tr> <td>  qpart_trans [unitless] </td> <td>  Translational partition function </td> </tr> <tr> <td>  qpart_vib [unitless] </td> <td>  Vibrational partition function </td> </tr> <tr> <td>  qpart_rot [unitless] </td> <td>  Rotational partition function </td> </tr> <tr> <td>  qpart [unitless] </td> <td>  Partition function </td> </tr> <tr> <td>  log_qpart_trans [unitless]  </td> <td>  Natural logarithm of translational partition function </td> </tr> <tr> <td>  log_qpart_rot [unitless] </td> <td>  Natural logarithm of rotational partition function </td> </tr> <tr> <td>  log_qpart_vib [unitless] </td> <td>  Natural logarithm of vibration partition function </td> </tr> <tr> <td>  log_qpart [unitless] </td> <td>  Natural logarithm of partition function </td> </tr> </tbody> </table>   [1]      C. A. Grambow, L. Pattanaik, and W. H. Green, “Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry,” Sci. Data, 7:1–8, 2020. [2]      Komp, E. Valleau, S. “Low-cost prediction of molecular and transition state partition functions via machine learning”, arXiv:, 2022.

opencc-by-4.0Oct 2021View details →

From structural phase transition to highly sensitive lifetime based luminescent thermometer: multifaceted modification of thermometric performance in Y0.9xNdxYb0.1PO4 nanocrystals

The development of a highly sensitive luminescent thermometer requires a deep understanding of the correlation between the structural properties of the host material and the temperature-dependent luminescence properties of lanthanide emitters embedded in these matrices. In some cases, the presence or increased concentration of the co-dopant ions can alter not only the spectral features, but may additionally cause far-ranging structural changes that further, even more tremendously, modify the luminescence properties of the phosphor. In this work, the temperature dependent luminescence kinetics in response to structural changes induced by increasing Nd3+ ion doping in Y0.9−xNdxYb0.1PO4 nanocrystals are investigated, which correspondingly demonstrated phase transitions from xenotime to monazite structures. Consequently, the low temperature lifetime of the 2F5/2 state of Yb3+ elongates. Moreover, by increasing the Nd3+ amount, the relative sensitivity of the Yb3+ luminescence lifetime-based luminescent thermometer was enhanced and, simultaneously, the temperature at which high sensitivity is achieved was reduced. The maximal relative sensitivity was found to be 2%/K at 273 K for Nd0.9Yb0.1PO4 nanocrystals.

opencc-by-4.0Mar 2022View details →

Dataset for: Pressure-driven symmetry transitions in dense H2O ice

This dataset comprises of all of the XRD patterns for ice and gold used for the equation of state in "Pressure-driven symmetry transitions in dense H2O ice."  Also included is a key for correlating ice and gold as well as the calibration files and CeO2 diffraction patterns for obtaining the calibration

opencc-by-4.0Jun 2021View details →

Safety of Vulnerable Road Users (VRU's) in Light-Rail Transit (LRT) Environment

Light-rail transit (LRT), which includes modern streetcars, trolleys, and heritage trolleys, is one of the fastest growing modes of public transportation in the United States. To reduce the cost and complexity of construction, most LRT systems have their tracks placed on city streets, in medians, or in separate at-grade rights-of-way with at-grade crossings. Operating light-rail vehicles (LRVs) along these alignments introduces new conflicts and increases the risk of collisions with vulnerable road users (VRUs) including pedestrians, bicyclists, and electric scooter riders. This study has two main objectives: (1) to review and evaluate the existing body of knowledge and the state of practice regarding safety of VRUs in LRT environments; and (2) to synthesize this information and package the results in a “Best Practices Resource Guide” and a companion “PowerPoint Presentation” for use in improving the safety of VRUs in existing LRT systems and advancing the professional capacity of transit workforce. Metropolitan Planning Organizations and State DOTs should also benefit from this resource information in the planning and design of new LRT systems. This report presents a wide range of physical, educational, and enforcement treatments for improving the safety of VRUs in LRT environments. The selection of a particular treatment for use at an LRT grade crossing or station should be based on an engineering study whose scope and complexity depend on local conditions. Factors that should be considered during device selection include 1) pedestrian‐LRV collision experience, 2) pedestrian volumes and peak flow rates, 3) train speeds, frequency of trains, number of tracks, and railroad traffic patterns, 4) sight distances available to pedestrians and LRV operators approaching the crossing, and 5) skew angle, if any, of the crossing relative to the LRT tracks.

dryad36/100

Transitioning from environmental genetics to genomics using mitogenome reference databases

Species detection using eDNA is revolutionizing the global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information—especially sequence information that includes intraspecific variation—creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of complete mitogenomic sequence information to evaluate the effectiveness of such data to differentiate, identify and detect taxa. We created the Oregon Biodiversity Genome Project working group to utilize recent advances in sequencing technology to create a database of complete, near error-free mitogenomic sequences for all of Oregon's resident freshwater fishes. So far, we have successfully assembled the complete mitogenomes of 313 specimens of freshwater fish representing 7 families, 55 genera, and 129 (88%) of the 146 resident species and lineages. Our comparative analyses of these sequences illustrate that the short (~150 bp) mitochondrial "barcode" regions typically used for eDNA assays are not consistently diagnostic for species-level identification and that no single region is best for metabarcoding Oregon's fishes. However, often-overlooked intergenic regions of the mitogenome such as the D-loop have the potential to reliably diagnose and differentiate species. This project provides a blueprint for other researchers to follow as they build regional databases. It also illustrates the taxonomic value and limits of complete mitogenomic sequences, and how current eDNA assays and the "PCR-free" environmental genomics methods of the future can best leverage this information.

opencc-zeroApr 2022View details →

Figure 2 from: Keller D., Radivojević N., Lazzarini V. (2022). Issues in ubimus archaeology: Beyond pure computing and precision during the analogue-digital transition

Figure2_W20_003_2_P92 Fonds Jean-Claude Risset, Laboratoire PRISM (UMR 7061 – France). The copyright applies to documents digitized by the PRISM laboratory.

Figure 3 from: Keller D., Radivojević N., Lazzarini V. (2022). Issues in ubimus archaeology: Beyond pure computing and precision during the analogue-digital transition

Figure3. W20_003_3_P10 Fonds Jean-Claude Risset, Laboratoire PRISM (UMR 7061 – France). The copyright applies to documents digitized by the PRISM laboratory

Figure 1 from: Keller D., Radivojević N., Lazzarini V. (2022). Issues in ubimus archaeology: Beyond pure computing and precision during the analogue-digital transition

Figure 1. W20_003_2_P20 Fonds Jean-Claude Risset, Laboratoire PRISM (UMR 7061 – France). The copyright applies to documents digitized by the PRISM laboratory

openother-openMay 2022View details →

Linking land-use and land-cover transitions to their ecological impact in the Amazon

Authors: Cássio Alencar Nunes, Erika Berenguer, Filipe França, Joice Ferreira, Alexander C. Lees, Julio Louzada, Emma J. Sayer, Ricardo Solar, Charlotte C. Smith, Luiz E. O. C. Aragão, Danielle de Lima Braga, Plinio Camargo, Carlos Eduardo Pellegrino Cerri, Raimundo Cosme, Mariana Durigan, Nárgila Moura, Victor Hugo Fonseca Oliveira, Carla Ribas, Fernando Vaz-de-Mello, Ima Vieira, Ronald Zanetti, Jos Barlow Code repository for the paper: Nunes et al. Linking land-use and land-cover transitions to their ecological in the Amazon. Proceedings of the National Academy of Sciences. 2022. In this repository we included codes and data that we used to run the all the analyses presented in the paper.

opencc-by-4.0May 2022View details →

Models and simulation results of "A relatively dry mantle transition zone revealed by geomagnetic diurnal variations"

Data and models used in Zhang et al. 2022: A relatively dry mantle transition zone revealed by geomagnetic diurnal variations. See ReadMe for more detailed description of file contents. Files includes: 1. 3D Conductivity models (ascii)  and corresponding perturbed magnetic field on the surface (Matalab Mat format): Global*Model, Secondary*Hs_1cpd.mat 2. inhomogeneous surface conductance layer for thin-sheet modeling (Matlab Mat format): SurfaceCond1degx1deg.mat 3. 1D inversion profiles to generate Figure 1 (Matalab Mat format) depth.mat, MultiMode*.mat 4.  PCA used for the data analysis (Matalab Mat format).  Data_1-4cpd_Mode_1-5.mat 5. Source estimates results used for the preferred conductivity model (Matalab Mat format). SphereCoeff_PerferedSource.mat

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Global distribution and evolutionary transitions of floral symmetry in angiosperms

Floral symmetry plays a crucial role in plant-pollinator interactions and has remarkable impacts on angiosperm evolution. However, the spatiotemporal patterns in floral symmetry and drivers of these patterns remain poorly known. Here, using global distributions and floral symmetry data of 280,140 angiosperm species, we presented the global geographic and evolutionary patterns of floral symmetry composition and demonstrated the climatic drivers of these patterns. We found that the frequency of actinomorphic (radial) species increased with latitude, while that of zygomorphic (bilateral) species decreased. Solar radiation, present-day temperature and Quaternary temperature change explained the geographic variation in floral symmetry. Evolutionary transitions from actinomorphy to zygomorphy dominated floral symmetry evolution, although the rate of this transition decreased through the Cenozoic associated with decreasing paleo-temperature. Our study provides novel insights into the ecology and evolution of angiosperm floral symmetry and suggests that climate change may influence species distributions via its effect on floral symmetry.

opencc-zeroMay 2022View details →

opencc-by-4.0May 2022View details →

Data set for the article "Self-oscillation and Synchronisation Transitions in Elasto-Active Structures"

This is the data set for the article "Self-oscillation and Synchronisation Transitions in Elasto-Active Structures",  <table summary="Additional metadata"> <tbody> <tr> <td><a href="https://doi.org/10.48550/arXiv.2106.05721">https://doi.org/10.48550/arXiv.2106.05721</a>   </td> </tr> </tbody> </table> Is contains raw images and processed data from images used to describe the self-oscillations under study in this article. All zip files corresponds to the single chain experiment except "Double_chain_Experiment.zip".

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Data from: Habitat change and its consequences on reef fish specialization in biogeographic transition zones

Aim Reef fishes are commonly recognized as sentinels of the ongoing tropicalization in biogeographic transition zones between temperate and tropical areas. Despite the reliance of these marine ectotherms on the benthos, the importance of benthic habitat has rarely been considered as a factor constraining fish distribution. Therefore, our study aims at examining the consequences of both temperature and benthic variations on the fish fauna and diagnosing potential sentinels of these environmental changes. Location Taiwan, West Pacific. Taxon Teleostei (184 species). Methods We examined how the partitioning of habitats can influence the specialization of fish fauna along a latitudinal gradient. We diagnosed 'specialist' and 'generalist' fishes in this partitioning. For each specialist, we further evaluated whether its distribution is constrained by temperature, benthic habitat, or both factors combined. The change in sea surface temperature over the last three decades was also monitored. Results Fish fauna showed the highest specialization when tropical and subtropical partitions of habitat were considered. Fifty-one tropical specialists, seven subtropical specialists, and 21 possible generalists were identified. Among specialists, 13 species were associated with temperature, 19 with habitat, and 26 with both factors. Steady warming occurred across latitudes but was accentuated in the winter of subtropical habitat. Main conclusions Our results suggested that the distribution of some specialist fishes was constrained only by temperature while the distribution of some others also depended on the availability of benthic habitats. Consequently, under global warming, the distribution of some specialists might shift in a manner that follows the movement of isotherms, while the distribution of others might also be conditioned by the poleward shifts of benthos. A temporal mismatch between the emergence of suitable thermal environments and the arrival of some specialists may exist. Therefore, the tropicalization of high-latitude areas may be characterized by different waves of colonization.

opencc-zeroMay 2022View details →

Dataset to "Legendre-Fenchel transforms capture layering transitions in porous media"

This is the dataset presented in the article "Legendre-Fenchel transforms capture layering transitions in porous media" [1]. This dataset contains three files, "isobaric_compression.csv", "isobaric_expansion.csv", and "isometric.csv". The columns are the same in each file. They are flow left to right <ol> <li>Temperature</li> <li>Standard deviation of the temperature</li> <li>Number of fluid particles</li> <li>Normal pressure</li> <li>Standard deviation of the normal pressure</li> <li>Height</li> <li>Standard deviation of the height</li> <li>Potential energy</li> <li>Standard deviation of the potential energy</li> <li>Kinetic energy</li> <li>Standard deviation of the kinetic energy</li> </ol> [1] https://doi.org/10.1039/D1NA00846C