cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22581694
title: Urban nonresidential building stocks 1978-2020

description: 159,401 records are weight in total and by 11 types of materials embodied in urban nonresidential buildings in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.19959670
title: Additional file 5 of CircSTX6 promotes pancreatic ductal adenocarcinoma progression by sponging miR-449b-5p and interacting with CUL2

description: Additional file 5: Table S5. Antibodies used in the present study.
DOI: 10.6084/m9.figshare.13668219
title: Additional file 5 of A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

description: Additional file 5: Table S4. RNA-seq to identify the target genes of validated enhancers.
DOI: 10.6084/m9.figshare.19959673.v1
title: Additional file 6 of CircSTX6 promotes pancreatic ductal adenocarcinoma progression by sponging miR-449b-5p and interacting with CUL2

description: Additional file 6: Table S6. List of possible circSTX6-interacting proteins identified by mass spectrometry.
DOI: 10.6084/m9.figshare.13668225
title: Additional file 7 of A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

description: Additional file 7: Table S6. Proteomics data analysis of TRAM2-KO in MCF10A-YAP5SA cells.
DOI: 10.6084/m9.figshare.22581700
title: ‘Road stocks 1978-2020

description: 101,437 records are weight in total and by 7 types of materials embodied in roads in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581700.v1
title: ‘Road stocks 1978-2020

description: 101,437 records are weight in total and by 7 types of materials embodied in roads in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581703
title: Urban rail stocks 1978-2020

description: 115,928 records are weight in total and by 8 types of materials embodied in urban rails in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581703.v1
title: Urban rail stocks 1978-2020

description: 115,928 records are weight in total and by 8 types of materials embodied in urban rails in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581709
title: Pipeline stocks 1978-2020

description: 86,946 records are weight in total and by 6 types of materials embodied in pipelines in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581709.v1
title: Pipeline stocks 1978-2020

description: 86,946 records are weight in total and by 6 types of materials embodied in pipelines in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.13668216.v1
title: Additional file 4 of A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

description: Additional file 4: Table S3. CRISPR screen selected hits.
DOI: 10.6084/m9.figshare.13668222
title: Additional file 6 of A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

description: Additional file 6: Table S5. Proteomics data analysis of MCF10A-YAP5SA and MCF10A-TRAM2 cells.
DOI: 10.6084/m9.figshare.13668228
title: Additional file 8 of A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

description: Additional file 8: Table S7. Proteomics data analysis TRAM2-KO in MDA-MB-231 cells.
DOI: 10.6084/m9.figshare.13668225.v1
title: Additional file 7 of A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

description: Additional file 7: Table S6. Proteomics data analysis of TRAM2-KO in MCF10A-YAP5SA cells.
DOI: 10.6084/m9.figshare.13668231.v1
title: Additional file 9 of A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

description: Additional file 9: Table S8. RNA-seq data analysis of MCF10A-YAP5SA and MCF10A-TRAM2 cells.
DOI: 10.6084/m9.figshare.13668228.v1
title: Additional file 8 of A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

description: Additional file 8: Table S7. Proteomics data analysis TRAM2-KO in MDA-MB-231 cells.
DOI: 10.6084/m9.figshare.22581715
title: Other infrastructure stocks 1978-2020

description: 43,473 records are weight in total and by 3 types of materials embodied in other infrastructure (street lamps and telecommunications) in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581718
title: Vehicle stocks 1978-2020

description: 144,910 records are weight in total and by 10 types of materials embodied in vehicles in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581721
title: Agricultural machinery stocks 1978-2020

description: 43,473 records are weight in total and by 3 types of materials embodied in agricultural machinery in 337 cities from 1978 to 2020
DOI: 10.23728/b2share.bbc307a404f54f0e9addf6b7156cb8e0
title: LTER Zöbelboden, Austria, Soil water chemistry 2017

description: Soil water chemistry of two forest stands in the site LTER Zöbelboden from the year 2017
DOI: 10.6084/m9.figshare.22581724
title: Industrial machinery stocks 1978-2020

description: 14,491 records are weight in total and by 1 type of materials embodied in industrial machinery in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581724.v1
title: Industrial machinery stocks 1978-2020

description: 14,491 records are weight in total and by 1 type of materials embodied in industrial machinery in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581727
title: Appliance stocks 1978-2020

description: 188,383 records are weight in total and by 13 types of materials embodied in appliances in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581730
title: Material stock and population 1978-2020

description: 57,964 records are total material stocks, per capita material stocks, urban populations, and household numbers of 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581733
title: Material intensity

description: 654 records are material intensity data and corresponding sources for the 24 materials embodied in 42 types of products, buildings, and infrastructure
DOI: 10.6084/m9.figshare.22581733.v1
title: Material intensity

description: 654 records are material intensity data and corresponding sources for the 24 materials embodied in 42 types of products, buildings, and infrastructure
DOI: 10.6084/m9.figshare.22581736
title: Data source

description: 625,219 records are the original data sources for the population and 42 types of products, buildings, and infrastructure items in the 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.22581739
title: Estimated code

description: The data gap were filled in Python 3.8, using the following libraries: pandas 1.3.4, numpy 1.18.5, statsmodels 0.13.2, sklearn 1.0.2, scipy 1.7.3.
DOI: 10.6084/m9.figshare.22581739.v1
title: Estimated code

description: The data gap were filled in Python 3.8, using the following libraries: pandas 1.3.4, numpy 1.18.5, statsmodels 0.13.2, sklearn 1.0.2, scipy 1.7.3.
DOI: 10.6084/m9.figshare.13668231
title: Additional file 9 of A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

description: Additional file 9: Table S8. RNA-seq data analysis of MCF10A-YAP5SA and MCF10A-TRAM2 cells.
DOI: 10.5281/zenodo.10598419
title: Data and Codes for the article: "Developing an Automated Detection, Tracking and Analysis Method for Solar Filaments Observed by CHASE via Machine Learning"

description: Codes

data_preparation.ipynb

We use this to get our dataset. This includes the function `readchase` for reading CHASE Hα spectral files and the function `keams_process` for preprocessing the spectra. Within this code segment, we employ 'sklearn.cluster.KMeans' for unsupervised clustering of the spectral data. Subsequently, we apply morphological closing operation on the results of K-means to obtain our dataset.

You can get the file list of our dataset in this code, and then download the files from Solar Science Data Center of Nanjing University. The file is too large to be conveniently uploaded here.

train_unet.py

You can run `python train_unet.py` to train the unet model. `UNet` defines our U-Net model. The original code is from labml.ai, and we have made some modifications to their model. 

In addition, the code for model prediction and evaluation is also included in it.

track.ipynb

This is our code for automated filament tracking. You can find the code flow of our tracking algorithm with helpful comments for better understanding.

feature_extraction.py

You can run `python feature_extraction.py` to obtain the Hα line central imaging of the Chase Hα file, the detection result of filaments, the cloud model inversion results of filaments, and the results of straightening the filaments along the main axis. The function `inversion_cloud` is used for cloud model inversion and `straightening_img` is used for straightening the filaments along the main axis.

These codes are provided on GitHub and Zenodo under the MIT license.

Data

detection/data

This folder comprises the training set `train.zip`, validation set `valid.zip`, test set `test.zip`, and the state dictionary of our U-Net model `model.zip`.

tracking

This folder includes 10 groups of results for tracking filaments, along with our accuracy log `result.xlsx`.
DOI: 10.5281/zenodo.10598418
title: Data and Codes for the article: "Developing an Automated Detection, Tracking and Analysis Method for Solar Filaments Observed by CHASE via Machine Learning"

description: Codes

data_preparation.ipynb

We use this to get our dataset. This includes the function `readchase` for reading CHASE Hα spectral files and the function `keams_process` for preprocessing the spectra. Within this code segment, we employ 'sklearn.cluster.KMeans' for unsupervised clustering of the spectral data. Subsequently, we apply morphological closing operation on the results of K-means to obtain our dataset.

You can get the file list of our dataset in this code, and then download the files from Solar Science Data Center of Nanjing University. The file is too large to be conveniently uploaded here.

train_unet.py

You can run `python train_unet.py` to train the unet model. `UNet` defines our U-Net model. The original code is from labml.ai, and we have made some modifications to their model. 

In addition, the code for model prediction and evaluation is also included in it.

track.ipynb

This is our code for automated filament tracking. You can find the code flow of our tracking algorithm with helpful comments for better understanding.

feature_extraction.py

You can run `python feature_extraction.py` to obtain the Hα line central imaging of the Chase Hα file, the detection result of filaments, the cloud model inversion results of filaments, and the results of straightening the filaments along the main axis. The function `inversion_cloud` is used for cloud model inversion and `straightening_img` is used for straightening the filaments along the main axis.

These codes are provided on GitHub and Zenodo under the MIT license.

Data

detection/data

This folder comprises the training set `train.zip`, validation set `valid.zip`, test set `test.zip`, and the state dictionary of our U-Net model `model.zip`.

tracking

This folder includes 10 groups of results for tracking filaments, along with our accuracy log `result.xlsx`.
DOI: 10.6084/m9.figshare.19959697.v1
title: Additional file 1 of circPDE5A regulates prostate cancer metastasis via controlling WTAP-dependent N6-methyladenisine methylation of EIF3C mRNA

description: Additional file 1.
DOI: 10.6084/m9.figshare.19959697
title: Additional file 1 of circPDE5A regulates prostate cancer metastasis via controlling WTAP-dependent N6-methyladenisine methylation of EIF3C mRNA

description: Additional file 1.
DOI: 10.5061/dryad.nf1kf60/1
title: Data

description: The rar file contains the original data of Figure 1 to Figure 6, and Figure S1 to Figure S6.
DOI: 10.5061/dryad.q446n6q/1
title: JEB-201800183_main_data
DOI: 10.5061/dryad.t5sd8c8.1
title: Data from: Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set
DOI: 10.5061/dryad.t5sd8c8.1/1.1
title: All supplemental files and figures referenced in publication

description: Folder contains the following supplemental files:                         SuppFile1.Catalog.pdf
Fig.S6.ASR_Diel_parsimony.pdf
Fig.S5.ASR_Diel_Phytools.pdf
Table.S2.Extraction_loci.xlsx
Table.S1.Sample_localities.xlsx
Table.S3.Quantification.xlsx
Fig.S3.ML_supports.pdf
Fig.S4.Astral_probeonly.pdf
Table.S4.PartModels.xlsx
Fig.S1.MLbest_probe+flank.pdf
Fig.S2.MLbest_probeonly.pdf
DOI: 10.5061/dryad.t5sd8c8.1/2.1
title: Concatenated supermatrix of probe and flanking sequences for all loci and specimens

description: Concatenated supermatrix of probe and flanking sequences for all loci and specimens. This matrix was use to build the phylogeny in the paper.
DOI: 10.5061/dryad.t5sd8c8.2/5.2
title: Hedylid_tree_combined_probe+flank_FINAL

description: Tree file for the final Fig. 1 tree built from using probe and flanking sequences. This tree was uploaded to the Open Tree of Life https://tree.opentreeoflife.org/
DOI: 10.5061/dryad.t5sd8c8.2/6.2
title: Hedylid_tree_UFboot_combined_probe+flank_FINAL

description: Same tree file as Hedylid_tree_combined_probe+flank_FINAL.tre, but with UltraFast bootstrap support values
DOI: 10.5061/dryad.tk8774f/1
title: Tursiops SNP dataset

description: SNP genotype, vcf file. Mapped to the Tursiops truncatus genome (GCA_001922835.1).
DOI: 10.5061/dryad.tk8774f/2
title: Tursiops ref_seqF

description: Forward reference sequences
DOI: 10.5061/dryad.tk8774f/3
title: Tursiops ref_seqR

description: Reverse reference sequences
DOI: 10.5061/dryad.v0cm4k9/1
title: All data for "Anthropogenic increases in nutrients alter sexual selection dynamics: a case study in butterflies"

description: Each tab corresponds to a separate dataset for the study. In general, "population" refers to either Minnesota (MN) or North Dakota (ND, agricultural) populations. "Diet" refers to common garden rearing on either cabbage or artificial diet (low or high nitrogen manipulation within each diet type). "WT" refers to wild type individuals collected in the field (versus common garden reared individuals). Three different "Pterin measures" are described in the methods. For several measures (pterins, butterfly nitrogen content), there are at least two technical replicates for each biological replicate (each listed on a separate line within that file). Additional details can be found in the manuscript methods section.
DOI: 10.17632/499jpr99ks.1
title: Data for: New archeointensity data from NW Argentina (1300-1500 AD)

description: The Thellier and Thellier experiments related to the paleointensity data presented in this study are provided. Numbers indicate the temperature step with R being the step corresponding to the applied field (35 microTeslas) in the Z direction and V in the -Z direction of the sample. P indicate that the step corresponds to a pTRM check. For a detailed information please contact mgomezpaccard@csic.es
DOI: 10.17632/swrny3wt56.1
title: Data for: Exploiting social and local contexts propagation for inducing Chinese microblog-specific sentiment lexicons

description: This data set includes UCI data set (microblogPCU), Weibo data set (my_weibo_data), three general sentiment lexicons. The results of our framework include UCI and Weibo sentiment nouns, UCI sentiment features and Weibo sentiment features.
DOI: 10.5061/dryad.05pr1n8/1
title: Hamilton_etal_2018_Liposcelis_Data

description: Compiled data from 'Genetics and genomics of an unusual selfish sex ratio distortion in an insect'. Contains seven files, including genome and transcriptome assemblies, as well as read mappings. See included outline for more details.
DOI: 10.5061/dryad.18tb602/2
title: Lemna_gibba_R_code

description: Annotated R code to recreate analyses and figures.
DOI: 10.5061/dryad.1b776v2/12
title: TEC sort Figure1a cre positive

description: Figure 1a cre+
DOI: 10.5061/dryad.1c9g5mm/22
title: Figure A2

description: Figure A2. ASTRAL species tree. Nodes have local posterior probability = 1.0 unless otherwise noted. Branch lengths are in coalescent units. ASTRAL cannot estimate terminal branch lenghs, so all terminal branches arbitrarily = 1.0 coalescent units. Black nodes represent topological conflicts between the ASTRAL species tree and the concatenated RAxML tree.
DOI: 10.5061/dryad.1c9g5mm/23
title: Figure A3

description: Figure A3. Primary concordance tree. Species sampled for each clade are indicated below the clade names. Nodes are labeled with concordance factors, 95% CI in parentheses. Dotted lines indicate conflicting topologies with concordance factor 95% CIs that overlap with the concordance factor 95% CI of a bipartition in the primary concordance tree.
DOI: 10.5061/dryad.1c9g5mm/24
title: Figure A4

description: Figure A4. Primary concordance tree. Species sampled for each clade are indicated below the clade names. Nodes are labeled with concordance factors, 95% CI in parentheses.
DOI: 10.5061/dryad.1c9g5mm/25
title: Figure A5

description: Fig. A5. Time-calibrated maximum clade credibility species tree inferred using SNAPP with all unlinked SNPs shared by the eleven sampled taxa. Grey bars on the nodes indicate 95% highest posterior density for the node heights. Bayesian posterior support is 1.0 unless otherwise labeled. Arrows indicate the potential window for introgression between the stem lineage of Allohistium and the stem lineage of Simoperca.
DOI: 10.5061/dryad.1c9g5mm/26
title: Table A4

description: Table A4. Results of the first set of D-statistic tests (Fig. 4).
DOI: 10.5061/dryad.1c9g5mm/27
title: Table A5

description: Table A5. Results of the first set of D-statistic tests, grouped by P2 taxa + P3 clade. Proportion of D-statistic tests significantly different from 0 after adjusting for multiple comparisons (alpha = 0.05).
DOI: 10.5061/dryad.1c9g5mm/28
title: Table A6

description: Table A6. Results of the first set of D-statistic tests, grouped by P3 taxa. Proportion of D-statistic tests significantly different from 0 after adjusting for multiple comparisons (alpha = 0.05).
DOI: 10.5061/dryad.1c9g5mm/31
title: Table A7

description: Table A7. Results of the first set of D-statistic tests (Fig. 4), grouped by P1 taxa + P3 taxa. Proportion of D-statistic tests significantly different from 0 after adjusting for multiple comparisons (alpha = 0.05).
DOI: 10.5061/dryad.1c9g5mm/32
title: Table A8

description: Table A8. Results of the second set of D-statistic tests (Fig. 5).
DOI: 10.5061/dryad.1c9g5mm/33
title: MacGuigan&Near_appendix

description: Online appendix for "Phylogenomic signatures of ancient introgression in a rogue lineage of darters (Teleostei: Percidae)" by Daniel J. MacGuigan and Thomas J. Near. Table A1, A2, and A3 are included in this file.
DOI: 10.5061/dryad.1mf7q9q/1
title: Principal components of shell shape variation

description: 2D Geometric morphometrics was used to document shell shape variation of the marine whelk Buccinulum vittatum-complex. This shape variation is reduced to principal components of variation.
DOI: 10.5061/dryad.1s471m3/4
title: Posterior lobe shape (PC2) under geldanamycin treatment

description: Mean PC2 scores for DGRP strains under the geldanamycin treatment.
DOI: 10.5061/dryad.1s471m3/5
title: Posterior lobe size (mm) under control treatment

description: Mean Posterior lobe size (mm) for DGRP strains under the control treatment.
DOI: 10.5061/dryad.1s471m3/6
title: Posterior lobe size (mm) under geldanamycin treatment

description: Mean Posterior lobe size (mm) for DGRP strains under the geldanamycin treatment.
DOI: 10.5061/dryad.31bc37q/1
title: Data package including genotypes, parentage assignment, and associated data

description: This Excel workbook includes four worksheets that include the microsatellite genotypes for adults and offspring ("G. polyphemus Genotypes", candidate sire ID's with associated siring and size data used in the ZIP analysis ("Candidate Sires+Assoc Data"), the candidate dam ID's used for this analysis ("CandidateDams"), and the final assigned parentage for hatchlings in this analysis ("AssignedParentage"). All column headers included comments that provide further information on the data they contain.
DOI: 10.5061/dryad.44sk691.1
title: Data from: Biting mechanics determines craniofacial morphology among extant diprotodont herbivores: Dietary predictions for the giant extinct short-faced kangaroo, Simosthenurus occidentalis.
DOI: 10.5061/dryad.44sk691.2
title: Data from: Biting mechanics determines craniofacial morphology among extant diprotodont herbivores: dietary predictions for the giant extinct short-faced kangaroo, Simosthenurus occidentalis.
DOI: 10.5061/dryad.44sk691.2/1.2
title: Strain data

description: Strain data collected from semilandmarks
DOI: 10.5061/dryad.44sk691.2/2.2
title: Landmarks

description: Raw shape data
DOI: 10.5061/dryad.44sk691.2/3.2
title: Specimen details

description: Details on specimens used in morphometric analyses
DOI: 10.5061/dryad.44sk691.2/4.2
title: Phylogenetic tree

description: Phylogenetic tree for morphometric analyses
DOI: 10.5061/dryad.44sk691.2/5.2
title: Mitchell and Wroe supplementary material

description: Landmark details for morphometric data and initial FEMs with volume-scaled muscle forces
DOI: 10.5061/dryad.4f8d2.1
title: Data from: Biochemical determinants of litter quality in 15 species of Sphagnum
DOI: 10.5061/dryad.4f8d2.1/1.1
title: bengtsson_etal_2018_LQ

description: Biochemical data for 15 Sphagnum species used to analyse determinants of litter quality of Sphagnum (peat mosses).
DOI: 10.5061/dryad.4f8d2.2
title: Data from: Biochemical determinants of litter quality in 15 species of Sphagnum
DOI: 10.5061/dryad.4f8d2.2/1.2
title: bengtsson_etal_2018_LQ

description: Biochemical data for 15 Sphagnum species used to analyse determinants of litter quality of Sphagnum (peat mosses).
DOI: 10.5061/dryad.4r50gb0/1
title: BARS Fecal Sequences

description: Raw reads obtained from sequencing Barn Swallow fecal samples amplified using arthropod specific primers.Each fasta file represents a single fecal sample.
DOI: 10.5061/dryad.4s4b3nf/1
title: Data for Bou Daher at al. 2018

description: This .zip file contains all raw experimental data associated with the publication of record (produced by Bou Daher, Chen and Braybrook). Data organization is by Figure, then by data type. Details in the README file.
DOI: 10.5061/dryad.54c5q66/1
title: Sample key file, pipeline configuration file and filtered dataset
DOI: 10.5061/dryad.83nj1.1
title: Data from: Spatiotemporal incidence of Zika and associated environmental drivers for the 2015-2016 epidemic in Colombia
DOI: 10.5061/dryad.83nj1.1/24.1
title: Weekly precipitation at 2.5 arc-minutes

description: Raster brick of weekly total precipitation calculated as the total of the daily precipitation (a total of 143 weeks between Jan 5, 2014 and Oct 1, 2016), in GRI format, at a resolution of 2.5 arc-minutes. Layer names indicate the date each week starts on. For example, the layer named precip_wk151025 has precipitation for the week that starts on October 25, 2015.
DOI: 10.5061/dryad.83nj1.1/7.1
title: Aedes aegypti population at 2.5 arc-minutes

description: Raster brick of ratio of Aedes aegypti population to human population at each week of the year (a total of 52 weeks), in GRI format, at a resolution of 2.5 arc-minutes.
DOI: 10.5061/dryad.83nj1.2/16.2
title: Weekly covariates aggregated at national level

description: Time series of weekly covariates aggregated at national level. This .zip file contains eight tables (in .csv format) of time series for aegypti population, maximum temperature, mean temperature, minimum temperature, NDVI MODIS Aqua, NDIV MODIS Terra, precipitation and relative humidity.
DOI: 10.5061/dryad.83nj1.2/17.2
title: Weekly weighted covariates aggregated at municipality level

description: Time series of weekly covariates, weighted by population, aggregated at municipality level. This .zip file contains eight tables (in .csv format) of time series for aegypti population, maximum temperature, mean temperature, minimum temperature, NDVI MODIS Aqua, NDIV MODIS Terra, precipitation and relative humidity.