Find research datasets worth reusing

opencc-zeroJul 2022View details →

Ecological and biogeographic processes drive the proteome evolution of snake venom

The emergence of venom is an evolutionary innovation that favored the diversification and survival of snakes. The composition of snake venoms is known in detail from venom gland proteomic data. However, there is still a gap of knowledge about the forces that lead to the expression of different toxins in different proportions in the venom cocktail across space and time. LOCATION World. TIME PERIOD Modern. MAJOR TAXA STUDIED Elapidae and Viperidae. We integrated proteomic data with phylogenetic comparative methods to understand how ecological and biogeographical processes drive the evolution of snake venom. We observed that more productive environments favor a more complex venom, which presents a higher diversity and similarity on the toxin proportions in its composition. We found that the taxa that live in islands, where there is lower variability of resources, tended to present less complex venom dominated by few toxins. In this case, the island's isolation seems to be a relevant element for a faster fixation of specific venom compositions. We show that ecological and biogeographic processes, which can act differentially over time and space, affect the gene expression of toxins in snake venoms.

opencc-by-4.0Sep 2021View details →

Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes (code)

GP-FBM and GP-Tool codes and algorithms as in publication day. For updated version: https://github.com/guilmont/GP-Tool

opencc-by-4.0Aug 2021View details →

Dataset of Simulations for LBW and PBF processes

This dataset has been created by TU WIEN and belongs to Work Package 2 about Simulations for LBW and PBF processes. © COPYRIGHT 2021 The CUSTODIAN Consortium. All rights reserved. Table of contents including supplementary information: <ul> <li>LBW_G11.png - Comparative image of cross and longitudinal section of simulation and experiment of LBW; primary beam only; conditions G11 (details given in image).</li> <li>LBW_G11_opt.png - Comparative image of cross and longitudinal section of simulation and experiment of LBW; primary and secondary beam; conditions G11 (details given in image).</li> <li>LBW_G7.mp4 - Comparative video: high speed camera recording (top) and simulation result (bottom) of LBW; conditions G7: P = 4kW, gap width = 0.3mm, welding velocity = 100mm/s; primary beam only.</li> <li>LBW_G7_GrainGrowth.mp4 - Video showing coupled simulation of melting, solidification, and crystallographic grain growth; conditions G7; primary beam only.</li> <li>LBW_G9.png - Comparative image of cross and longitudinal section of simulation and experiment of LBW; primary beam only; conditions G9 (details given in image).</li> <li>LBW_G9_opt.png - Comparative image of cross and longitudinal section of simulation and experiment of LBW; primary and secondary beam; conditions G9 (details given in image).</li> <li>PBF_CM247LC_multitrack.mp4 - Video of simulation showing 6 tracks of PBF-LB/M of CM247LC on a 100μm powder bed; bidirectional scanning path; substrate coloured light grey, powder coloured dark grey, meltpool coloured by temperature.</li> <li>PBF_CM247LC_validation.png - Image showing comparison of cross-sectional weld bead obtained experimentally and in simulation for a single track of CM247LC scanned on 100μm powder bed.</li> <li>PBF_IN713LC_balling.mp4 - Video of simulation of PBF-LB/M of IN713LC where insufficient heat input (452W) leads to surface energy-driven defect called balling; accompanying image of experimental result on the right</li> <li>PBF_IN713LC_Q5plus.png - Image of simulation and experimental result of PBF-LB/M of IN713LC with sufficient heat input to prevent balling (520W).</li> <li>PBF_IN713LC_validation.png - Image showing comparison of cross-sectional weld bead obtained experimentally and in simulation for a single track of IN713LC scanned on 50μm powder bed.</li> </ul>

opencc-zeroSep 2021View details →

Data from: Parallel cognitive processing streams in human prefrontal cortex: parsing areal-level brain network for response inhibition

Multiple cognitive processes are recruited to achieve adaptive behavior. However, it is poorly understood how such cognitive processes are implemented in temporal cascades of human cerebral cortical areas as processing streams to achieve behavior. In the present study, we identify cortical processing streams for response inhibition and examine relationships among the processing streams. Functional magnetic resonance imaging (MRI) and time-resolved single-pulse transcranial magnetic stimulation (TMS) reveal three distinct critical timings of transient disruption in the functionally essential cortical areas that belong to two distinct cerebrocortical networks. Furthermore, single-pulse TMS following suppression of the ventral posterior inferior frontal cortex (vpIFC) with repetitive TMS reveals information flow from the vpIFC to the presupplementary motor area (preSMA) within the same network but not to the dorsal posterior inferior frontal cortex (dpIFC) across different networks. These causal behavioral effects suggest two parallel processing streams (vpIFC-preSMA versus dpIFC-intraparietal sulcus) that act concurrently during response inhibition.

opencc-zeroSep 2021View details →

Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics

Constructing phylogenetic relationships among closely related species is a recurrent challenge in evolutionary biology, particularly for long-lived taxa with large effective population sizes and uncomplete reproductive isolation, like conifers. Conifers further have slow evolutionary rates, which raises the question of whether adaptive or non/adaptive processes were predominantly involved when they rapidly diversified after migrating from temperate regions into the tropical mountains. Indeed, fine-scale phylogenetic relationships within several conifer genus remain under debate. Here, we studied the phylogenetic relationships of endemic firs (Abies, Pinaceae) discontinuously distributed in the montane forests from the Southwestern United States to Guatemala, and addressed several hypotheses related to adaptive and non-adaptive radiations. We derived over 80K SNPs from genotyping by sequencing (GBS) for 45 individuals of nine Mesoamerican species to perform phylogenetic analyses. Both Maximum Likelihood and quartets-inference phylogenies resulted in a well-resolved topology, showing a single fir lineage divided in four subgroups that coincided with the main mountain ranges of Mesoamerica; thus having important taxonomic implications. Such subdivision fitted a North-South isolation by distance framework, in which non-adaptive allopatric processes seemed the rule. Interestingly, several reticulations were observed within subgroups, especially in the central-south region, which may explain past difficulties for generating infrageneric phylogenies. Further evidence for non-adaptive processes was obtained from analyses of 21 candidate-gene regions, which exhibited diminishing values of πa/πs and Ka/Ks with latitude, thus indicating reduced efficiency of purifying selection towards the Equator. Our study indicates that non-adaptive allopatric processes may be key generators of species diversity and endemism in the tropics.

opencc-by-4.0Sep 2021View details →

Franck-Hertz experiment , 178 C processed data set

For PHYS 3220 lab, Franck-Hertz experiment for Mercury, 178 C processed data set. An experiment was conducted on 24th September 2021 at York University.

FOSS4G-IT 2021 - Workshop "QGIS: dal modellatore grafico ai plugin di Processing" (a cura di Federico Gianoli)

Workshop "QGIS: dal modellatore grafico ai plugin di Processing" a cura di Federico Gianoli 20 settembre 2021 In questo workshop sarà illustrato come configurare il modellatore grafico di QGIS per l'automatizzazione di processi di analisi e l'esportazione del modello come plugin di Processing pronto per essere redistribuito. Per seguire il workshop è sufficiente QGIS LTR.   ⏰ <a href="https://www.youtube.com/watch?v=2N937a4Rp4w&list=PLk-K8n5iT-AepY_3OOHSjAMFUafBF_Nl3&index=3&t=0s">00:00:00</a> | INIZIO PAOLO DABOVE ⏰ <a href="https://www.youtube.com/watch?v=2N937a4Rp4w&list=PLk-K8n5iT-AepY_3OOHSjAMFUafBF_Nl3&index=3&t=77s">00:01:17</a> | INTRO FEDERICO GIANOLI ⏰ <a href="https://www.youtube.com/watch?v=2N937a4Rp4w&list=PLk-K8n5iT-AepY_3OOHSjAMFUafBF_Nl3&index=3&t=510s">00:08:30</a> | INTRO PYTHON ⏰ <a href="https://www.youtube.com/watch?v=2N937a4Rp4w&list=PLk-K8n5iT-AepY_3OOHSjAMFUafBF_Nl3&index=3&t=835s">00:13:55</a> | QGIS e pyQGIS ⏰ <a href="https://www.youtube.com/watch?v=2N937a4Rp4w&list=PLk-K8n5iT-AepY_3OOHSjAMFUafBF_Nl3&index=3&t=3555s">00:59:15</a> | DOMANDE PRIMA PARTE ⏰ <a href="https://www.youtube.com/watch?v=2N937a4Rp4w&list=PLk-K8n5iT-AepY_3OOHSjAMFUafBF_Nl3&index=3&t=3955s">01:05:55</a> | MODELLATORE GRAFICO ⏰ <a href="https://www.youtube.com/watch?v=2N937a4Rp4w&list=PLk-K8n5iT-AepY_3OOHSjAMFUafBF_Nl3&index=3&t=5737s">01:35:37</a> | PLUGIN BUILDER 3 ⏰ <a href="https://www.youtube.com/watch?v=2N937a4Rp4w&list=PLk-K8n5iT-AepY_3OOHSjAMFUafBF_Nl3&index=3&t=6798s">01:53:18</a> | DOMANDE FINALI Materiale del Workshop 🔗 <a href="https://github.com/fgianoli/wor_foss4g2021">https://github.com/fgianoli/wor_foss4g2021</a> Altri link 🔗 <a href="https://github.com/fgianoli/wor_foss4g2021/blob/main/foss4g.md">https://github.com/fgianoli/wor_foss4g2021/blob/main/foss4g.md</a>

OKLMA processing comparison

<pre>This OKLMA data is processed from up to 10 stations in central Oklahoma (sensors: CDEHILMNWY), and 7 stations in southwest Oklahoma (sensors: APUBORZ). The OKLMA operates by triangulating sources of VHF (60-66 MHz) radiation emitted by lightning (and any other sources) in 80 microsecond windows in space and time, which map out the three-dimensional structure of lightning flashes. The OKLMA has been operated by National Oceanic and Atmospheric Administration / Office of Atmospheric Research / National Severe Storms Laboratory and OU/CIMMS staff. The OKLMA was installed with funding from Office of Naval Research Grant N00014-00-1-0525 and has since been funded in part by the National Oceanic and Atmospheric Administration National Severe Storms Laboratory, National Environmental Satellite, Data, and Information Service, and the National Science Foundation. Funding for this project was provided by NOAA award NA16OAR4320115. This README was last updated: 10 August 2021 #### 2) METHODS The method of data collection and performance is described in: Thomas, R. J., Krehbiel, P. R., Rison, W., Hunyady, S. J., Winn, W. P., Hamlin, T., and Harlin, J. (2004), Accuracy of the Lightning Mapping Array, J. Geophys. Res., 109, D14207, doi:10.1029/2004JD004549. Chmielewski, V. C., and Bruning, E. C. (2016), Lightning Mapping Array flash detection performance with variable receiver thresholds, J. Geophys. Res. Atmos., 121, 8600– 8614, doi:10.1002/2016JD025159. Weiss, S. A., D. R. MacGorman, E. C. Bruning, and V. C. Chmielewski, 2018: Two Methods for Correcting Range-Dependent Limitations of Lightning Mapping Arrays. J. Atmos. Oceanic Technol., 35, 1273–1282, doi:10.1175/JTECH-D-17-0213.1. The results of two processing methods are included in this dataset. The files in the “unified” directories were created by processing the OKLMA as one, unified network. The files in the “separated” directories were created by processing each of the southwest and central station clusters separately before combining the VHF solutions found by each cluster of stations per each 10 minute period into an otherwise identical datafile. #### 3) DATA INFORMATION All data is stored in tabular, fixed-width formatted files compressed with gzip and organized by case and processing method. Case 1 includes 0000-0600 UTC on 16 June 2019; Case 2 includes 0300-0700 UTC on 12 June 2019. Datafiles are organized by case then method directories. Fixed width formatting described at the end of each file's header (e.g., “Data format: 15.9f 12.8f 13.8f 9.2f 6.2f 5.1f 7x”). Each file contains 10 minutes of VHF events observed by the OKLMA and will be titled following a LYLOUT_yymmdd_HHMMSS_0600.dat.gz convention in which *yy* is the two digit year, *yy* month, *dd* day, *HH* hour, *MM* minute, *SS* second at the start of the analysis period. Each file has a series of header lines including lma_analysis version used for processing, active stations, analysis criteria, summary information, creation date and formatting information. Data entries are preceded by “\*** data ***”. **Column Names and Descriptions** 0. Time of VHF event --UTC second of the day 1. lat --decimal degrees 2. lon --decimal degrees 3. altitude --in meters above MSL 4. Reduced Chi^2 --Reduced chi^2 of the Marquart least squares solution for the VHF event 5. power --emitting power of the VHF event in dBW 6. mask --bitwise mask of the contributing stations to the VHF event solution in the order given by the Stations mask order line in the header. #### 4) SHARING AND ACCESS The data are freely available; however, OKLMA’s researchers request the dataset be cited with the DOI above if it is used in published research. This README was prepared by Vanna Chmielewski with funding provided by NOAA/Office of Oceanic and Atmospheric Research under NOAA-University of Oklahoma Cooperative Agreement #NA16OAR4320115, U.S. Department of Commerce. The statements, findings, conclusions, and recommendations are those of the author(s) and do not necessarily reflect the views of NOAA or the U.S. Department of Commerce.</pre>

Table S1 Full factorial combination of laser process parameters and experimental results.

This dataset is experimental results from a research topic of Prediction and optimization of geometrical quality for pulsed laser cutting of non-oriented electrical steel sheet.

Table S1 Full factorial combination of laser process parameters and experimental results.

This dataset is experimental results from a research topic of An improved grey wolf optimizer for process optimization of pulsed laser cutting of electrical steel sheet in different environments.

opencc-zeroOct 2021View details →

Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.

opencc-by-4.0Oct 2022View details →

Cascading rupture process of the 2021 Maduo, China earthquake revealed by the joint inversion of seismic and geodetic data

The coseismic Sentinel-1 line-of-sight (LOS) displacements, strong-motion and teleseismic waveforms used in the joint inversion of the source rupture process for the 2021 Maduo, China earthquake are included in this repository.

opencc-by-4.0May 2022View details →

Melting and melt segregation processes controlling granitic melt composition

Granitic melt composition is controlled by melting reactions and modified by melt segregation process. This is a fundamental but unresolved issue for granite petrogenesis. To investigate the influence of these two processes on granitic melt compositions, we conducted systematic petrographic and geochemical analyses of melanosome and leucosome samples from the Jindong migmatite in the Indosinian orogen, South China. Petrographic observations and zircon U-Pb geochronology indicate that the Jindong migmatite was formed through water-fluxed melting of the Early Paleozoic gneissic granite (437±2 Ma) during the Triassic (238±1 Ma). The Jindong leucosomes can be divided into lenticular and net-structured types. They show increasing Rb with decreasing Ba and Sr, due to fractionation of K-feldspar and plagioclase during melt segregation. Nd isotope and Th, Y and REE contents of leucosomes reveal the complex behavior of phosphates during melting, recorded by the incongruent melting of apatite with precipitation of monazite and xenotime in the source. The leucosomes have similar Nd isotopic compositions with the source due to early dissolution of monazite. Continued dissolution of apatite caused saturation of monazite and decreased εNd(t) values of melts. This interplay also caused sharply reduction of Th, Y and REE contents in melts with increasing P2O5, when saturation of monazite and xenotime due to dissolution of apatite. Thus, dissolution of accessory phase in the source impacts fundamentally on REE geochemistry and Nd isotope of granites. Such patterns are reflected in granites worldwide, illustrating the strong controls of the melting and melt segregation processes on granitic melt compositions.

Table S1. Full factorial combination of laser process parameters and experimental results.

This dataset is experimental results from a research topic of A robust artificial intelligence-based method for predicting and optimizing cut quality of curved laser cutting of electrical steel sheet.

The dataset for the paper "Long-Lived and Continual Volcanic Eruptions, Tectonic Activity, Pit Chains Formation and Boulder Avalanches in Northern Tharsis Region: Implications for Late Amazonian Geodynamics and Seismo-Tectonic Processes on Mars" JGR: Planets.

This dataset pertains to the following paper in Journal of Geophysical Research: Planets. Krishnan, V., and Kumar, P.S. (2022), Long-Lived and Continual Volcanic Eruptions, Tectonic Activity, Pit Chains Formation and Boulder Avalanches in Northern Tharsis Region: Implications for Late Amazonian Geodynamics and Seismo-Tectonic Processes on Mars, Journal of Geophysical Research: Planets (for full citation, please see the journal). AGU Manuscript No. 2022JE007511.

Table S1. Full factorial combination of laser process parameters and experimental results.

This dataset is experimental results from a research topic of A robust artificial intelligence-based method for predicting and optimizing cut quality in curved laser cutting of electrical steel sheet.

opencc-by-4.0Oct 2022View details →

Processed Data for Cell type-specific aging clocks to quantify aging and rejuvenation in regenerative regions of the brain

Seurat objects for data accompanying the publication "Cell type-specific aging clocks to quantify aging and rejuvenation in regenerative regions of the brain". Preprint available at <a href="https://doi.org/10.1101/2022.01.10.475747">https://doi.org/10.1101/2022.01.10.475747</a> <ul> <li>multi_intergrated_seurat_Dec2020.rds is the data from the SVZ of the cohort of 28 mice across different ages</li> <li>pb_combined.rds is the data from the SVZ of both heterochronic parabiosis mouse cohorts</li> <li>Dulken_svz_celltypes_2019-01-31.rda is the data associated with <a href="https://doi.org/10.1038/s41586-019-1362-5">https://doi.org/10.1038/s41586-019-1362-5</a></li> </ul>

Revisiting process versus product metrics: A large scale analysis

Numerous methods can build predictive models from software data. However, what methods and conclusions should we endorse as we move from analytics in-the-small (dealing with a handful of projects) to analytics in-the-large (dealing with hundreds of projects)? To answer this question, we recheck prior small-scale results (about process versus product metrics for defect prediction and the granularity of metrics) using 722,471 commits from 700 Github projects. We find that some analytics in-the-small conclusions still hold when scaling up to analytics in-the-large. For example, like prior work, we see that process metrics are better predictors for defects than product metrics (best process/product-based learners respectively achieve recalls of 98%/44% and AUCs of 95%/54%, median values). That said, we warn that it is unwise to trust metric importance results from analytics in-the-small studies since those change dramatically when moving to analytics in-the-large. Also, when reasoning in-the-large about hundreds of projects, it is better to use predictions from multiple models (since single model predictions can become confused and exhibit a high variance).

Raw data and processing code for resilient supercurrent

The raw data, extracted data, data analysis codes and figure plotting codes for resilient supercurrent

Processed Single-cell RNA-seq Data for Exercise Rejuvenation Intervention on Mouse Subventricular Zone

Exercise single-cell RNA-seq data of mouse subventricular zone (in processed Seurat object) used in the publication "Cell type-specific aging clocks to quantify aging and rejuvenation in regenerative regions of the brain" (preprint available at <a href="https://doi.org/10.1101/2022.01.10.475747">https://doi.org/10.1101/2022.01.10.475747</a>).