cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3636113_d10
title: Additional file 1: of Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides when exposed to the algicide copper sulfate

description: The primers and full name of genes that used in the qRT-PCR validation. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3636113_d7
title: Additional file 9: of Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides when exposed to the algicide copper sulfate

description: DEGs that involved in spliceosome. The genes were identified by KEGG pathway analysis. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3636113_d8
title: Additional file 8: of Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides when exposed to the algicide copper sulfate

description: DEGs that involved in signal transduction. The genes were identified by KEGG pathway analysis. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3636113_d6
title: Additional file 14: of Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides when exposed to the algicide copper sulfate

description: Differentially expressed antioxidant genes. The genes were manually summarized by reviewing GO and NR annotation. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3636113_d4
title: Additional file 11: of Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides when exposed to the algicide copper sulfate

description: DEGs that involved in photosynthsis. The genes were identified by KEGG pathway analysis. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3636113_d1
title: Additional file 15: of Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides when exposed to the algicide copper sulfate

description: Differentially expressed copper binding or transport genes. The genes were manual summarized by reviewing GO and NR annotation. (XLSX 14 kb)
DOI: 10.15468/xjqhra
title: EMBRAPA FLORESTAS | Soil macrofauna communities in various land use systems in Jaguapitã, Paraná, Brazil

description: Soil macrofauna communities were evaluated in a number of land use systems on private farms in Jaguapitã, Paraná, Brazil. Sampling was performed in March and September 2004 in nine land uses: 1) a 15-year old pasture (JM) previously sown with Paspalum sp., and recently renovated with Cynodon sp. grass; 2) a 15-year old degraded pasture of Paspalum sp.; 3) a &gt;15-year old pasture of Paspalum sp., recently renovated with Urochloa brizantha; 4) a degraded &gt;15-year old Paspalum sp. pasture; 5) a six-year old soybean cropping system, established over an old Paspalum sp. pasture; 6) a 2-year old soybean cropping system after long-term Paspalum sp. pasture; 7) a recently renovated Urochloa brizantha + Urochloa decumbens pasture after several years of annual grain cropping; 8) and 9) two recently established (1 year old) sugarcane plantations, converted from &gt;15 year old pastures. In each land use, 25 samples were taken in a square grid of 5x5 samples, with 10 m between sampling points. Of the total, five samples (along the diagonal) were taken down to 30 cm depth, and the remaining only to 0-10 cm depth. Samples were taken using the standard methodology of the Tropical Soil Biology and Fertility Programme (TSBF), where soil and litter fauna were hand-sorted from monoliths of 25x25 cm, and the abundance of a total of 42 taxa was assessed.
DOI: 10.17632/dww54yfmtt.1
title: BIG-600K (Part 2)

description: Paper: BRIDGE: A Multi-organ Foundation Model for Bridging Histology Images to Spatial Transcriptomics
Authors: Zhuo Liang , Weiqin Zhao , Fuying Wang , Guangyong Chen , Yuanhua Huang , Lequan Yu
DOI: 10.6084/m9.figshare.c.3635909_d4
title: Additional file 3: Table S3. of Genomic heterozygosity and hybrid breakdown in cotton (Gossypium): different traits, different effects

description: MHIs in (E3) F2 population. (XLS 14Â kb)
DOI: 10.17632/rrmkf32v5p.1
title: R code used to analyze the data for the paper "Evaluating sustainable practices for certification schemes: herding practices in Mongolia"

description: This is the R code used to analyze the data for the paper "Evaluating sustainable practices for certification schemes: herding practices in Mongolia", which was submitted to Nature Sustainability. 
Specifically, app.r is the R code of the R Shiny app, which allows users to apply our models developed in this study to produce a sustainability score and certification advice for their real herding scenarios.
BP_analysis_models_used_in_app.r is the R code to build the models used in the above R Shiny app.
BP_analysis_overall_final.r is the R code to do the overall assessment of different models using accuracy indices.
BP_analysis_pred_VS_obs_final.r is the R code to compare predicted scores and the observed scores using five-fold cross-validation.
BP_analysis_plotting.r is the R code to plot the results from the above program BP_analysis_overall_final.r.
See the paper for more details.
DOI: 10.6084/m9.figshare.c.3635909_d3
title: Additional file 1: Table S1. of Genomic heterozygosity and hybrid breakdown in cotton (Gossypium): different traits, different effects

description: Markersâ   information in this research. (XLS 42Â kb)
DOI: 10.6084/m9.figshare.c.3635909_d1
title: Additional file 2: Table S2. of Genomic heterozygosity and hybrid breakdown in cotton (Gossypium): different traits, different effects

description: MHIs in (3E) F2 population. (XLS 26Â kb)
DOI: 10.6084/m9.figshare.c.3635909_d2
title: Additional file 4: Table S4. of Genomic heterozygosity and hybrid breakdown in cotton (Gossypium): different traits, different effects

description: The QTL for studied traits searched from the cotton QTL Database. (XLS 25Â kb)
DOI: 10.17632/9f6bh9f736.1
title: Asymmetric Information, Disagreement, and the Valuation of Debt and Equity

description: This Mathematica code generates the figures in "Asymmetric Information, Disagreement, and the Valuation of Debt and Equity."
DOI: 10.17632/9k2xb94vpz.1
title: Early Diagnosis of Type 2 Diabetes Mellitus in Patients with Psoriasis: Construction of a Multifactorial Diagnostic Model

description: This dataset consists of FigS1, TableS1, and Supplementary appendix.
Fig S1. Proportion of Missing Data in Derivation Cohort
Table S1. TRIPOD Checklist Prediction Model Development
Supplementary appendix:Detailed description of the contents of the manuscripts
DOI: 10.6084/m9.figshare.c.3635858_d1
title: Additional file 1: of Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma

description: Supplementary tables. Table S1. Cancer genes in detected amplification regions. Table S2. Cancer genes in detected deletion regions. Table S3. Comparison of results of Frankel to our results. Table S4. Comparison of results of Paulson to our results. Table S5. Comparison of results of Beroukhim to our results. Table S6. Comparison of results of Zack to our results. Table S7. Ploidy information of the 15 EA samples. (XLSX 57.4 kb)
DOI: 10.6084/m9.figshare.c.3635834_d9
title: Additional file 6: of 
                     De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production

description: Differential genes expression in C. sorokiniana. (XLSX 1025Â kb)
DOI: 10.17632/9f6bh9f736.2
title: Asymmetric Information, Disagreement, and the Valuation of Debt and Equity

description: This Mathematica code generates the figures in "Asymmetric Information, Disagreement, and the Valuation of Debt and Equity."
DOI: 10.6084/m9.figshare.c.3635834_d6
title: Additional file 3: of 
                     De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production

description: Contigs assembled using Trinity. (RAR 12595Â kb)
DOI: 10.6084/m9.figshare.c.3635834_d7
title: Additional file 5: of 
                     De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production

description: Predicted coding sequences. (RAR 1699Â kb)
DOI: 10.17632/n5nvf95rw4.1
title: SMC-CH4

description: To investigate the relationship between soil moisture content and methane flux, we display lipids, gene and flux data from grassland soils. This data includes raw data of the 44 soil samples collected along SMC transects in July 2014 (Data S1), and the raw data of the environmental conditions, q-PCR results and methane flux measurements along SMC transects and 2 background sites in August 2020 (Data S2).
DOI: 10.6084/m9.figshare.c.3635834_d3
title: Additional file 4: of 
                     De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production

description: Annotation of contigs. (XLSX 1984Â kb)
DOI: 10.15468/dl.mjvsx4
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pleuronichthys japonicus Suzuki, Kawashima & Nakabo, 2009",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 12 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032123-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/rcnx6smvyt.1
title: Forest Landscape Restoration Study Data

description: The data was collected in the Kakamega Forest Landscape
DOI: 10.6084/m9.figshare.c.3635834_d1
title: Additional file 9: of 
                     De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production

description: Primer paired used in RT-qPCR. (XLSX 10Â kb)
DOI: 10.15468/p86sf9
title: EMBRAPA FLORESTAS | Soil macrofauna communities in various land use systems in Ponta Grossa, Paraná, Brazil

description: Soil macrofauna communities were evaluated in in October 2012 and April of 2013 in a number of land use systems in Ponta Grossa county, Paraná state, Brazil. At the Fazenda Modelo managed by the Instituto Agronômico do Paraná (IAPAR), samples were taken in three land use systems as part of a long-term integrated production systems experiment initiated in 2006: 1) an agrosilvopastoral system with rows of Eucalyptus dunnii and annual grain cropping (maize, soybean) in the summer and Lolium multiflorum (Italian ryegrass) grazed pasture in the winter performed in the interrow; 2) an agropastoral system with grain cropping (maize, soybean) in the summer and grazed Italian ryegrass in the winter; 3) a permanent pasture of native grasses. Each of these systems was replicated 3 times, and eight samples were taken in each plot. At the Embrapa research station, two land uses were evaluated, with 24 samples taken in each area: 1) a minimum-tillage grain crop production system; and 2) a 20-year old Eucalyptus dunnii tree plantation. Samples were taken using the standard methodology of the Tropical Soil Biology and Fertility Programme (TSBF), where soil (down to 20 cm depth) and litter fauna were hand-sorted from monoliths of 25x25 cm, and the abundance of a total of 42 taxa was assessed.
DOI: 10.6084/m9.figshare.c.3635765_d1
title: Additional file 1: of Patient-Reported Outcomes Measurement Information System (PROMIS) instruments among individuals with symptomatic knee osteoarthritis: a cross-sectional study of floor/ceiling effects and construct validity

description: The additional file contains a supplemental table entitled â  Matrix of Spearman correlation coefficients between PROMIS short-form instruments and legacy measures.â   The file also includes the raw data used for the figures and the appropriate references. (XLSX 48 kb)
DOI: 10.5281/zenodo.14418069
title: Code and data for 'Four-dimensional variational data assimilation with a sea-ice thickness emulator'

description: All the codes written to build the datasets, train the emulator and run the 4D--Var minimization are available in nextsim-4dvar-1.

The post-processed dataset for training the emulator are in data/twin_exp. The dataset is based on neXtSIM simulation data and ERA5 forcing data and extracted from the SASIP shared data OpenDAP server:



The neXtSIM simulations were performed by Gauillaume Boutin and published in the paper "Arctic sea ice mass balance in a new coupled ice–ocean model using a brittle rheology framework" (Boutin et al., 2023) and available as Zenodo dataset (Boutin et al., 2022).

The forcing data is based on the ERA5 reanalysis dataset published in the paper: "The ERA5 global reanalysis" (Hersbach et al., 2020) and available as dataset from the Copernicus Climate Change Service (C3S, Copernicus Climate Change Service, 2023). The here used forcing data is based on the hourly reanalysis data on single levels and interpolated with nearest neighbors to the curvilinear grid as used in the output from the neXtSIM simulations. 

The same dataset can then be used to perform 4D-Var minimimzation in twin experiment case

The folder data/cs2smos contains all post-processed datasets necessary to perform real observations with CS2SMOS

CS2SMOS retrievals are publicly available here


The neural network weights are included under models.These neural network weights have been used to generate the results presented in the paper.

 

References:

Guillaume Boutin, Heather Regan, Einar Ólason, Laurent Brodeau, Claude Talandier, Camille Lique, & Pierre Rampal. (2022). Data accompanying the article "Arctic sea ice mass balance in a new coupled ice-ocean model using a brittle rheology framework" (1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7277523

Boutin, G., Ólason, E., Rampal, P., Regan, H., Lique, C., Talandier, C., Brodeau, L., and Ricker, R.: Arctic sea ice mass balance in a new coupled ice–ocean model using a brittle rheology framework, The Cryosphere, 17, 617–638, https://doi.org/10.5194/tc-17-617-2023, 2023.

Copernicus Climate Change Service (2023): ERA5 hourly data on single levels from 1940 to present. Copernicus Climate Change Service (C3S) Climate Data Store (CDS), DOI: 10.24381/cds.adbb2d47.

Hersbach H, Bell B, Berrisford P, et al. The ERA5 global reanalysis. Q J R Meteorol Soc. 2020; 146: 1999–2049. https://doi.org/10.1002/qj.3803
DOI: 10.6084/m9.figshare.c.3635591_d2
title: Additional file 2: Table S2. of Examining the transcriptional response of overexpressing anthranilate synthase in the hairy roots of an important medicinal plant Catharanthus roseus by RNA-seq

description: List of differentially expressed genes. (XLS 648 kb)
DOI: 10.6084/m9.figshare.c.3635441_d2
title: Additional file 1: of Using proteomic analysis to investigate uniconazole-induced phytohormone variation and starch accumulation in duckweed (Landoltia punctata)

description: Up-regulated proteins after application of uniconazole. The up-regulated proteins with &gt;1.2-fold change and p-value less than 0.05 and their ratios among all comparative groups listed in the table. (XLSX 64Â kb)
DOI: 10.6084/m9.figshare.c.3635441_d3
title: Additional file 2: of Using proteomic analysis to investigate uniconazole-induced phytohormone variation and starch accumulation in duckweed (Landoltia punctata)

description: Down-regulated proteins after application of uniconazole. The down-regulated proteins with &lt;0.8-fold change and p-value less than 0.05 and their ratios among all comparative groups listed in the table. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.c.3635441_d1
title: Additional file 3: of Using proteomic analysis to investigate uniconazole-induced phytohormone variation and starch accumulation in duckweed (Landoltia punctata)

description: KEGG pathway analysis of the annotated proteins. The pathway, number of annotated proteins, and pathway ID were listed in the table. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3635378_d13
title: Additional file 2: Table S1. of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

description: Consensus in the location of the OGS2 gene set on the genome assemblies of sibling species Nasonia longicornis and N. giraulti, including recent, high identity paralogs. Almost all OGS2 genes are located on 2 sibling species draft assemblies [4], using GMAP [36] transcript mapping. Paralog locus consensus patterns are tabulated for inparalogs (sharing orthology to other species) and uniquepar (lacking strong homology to other species). Of the total paralog families, each with several genes, most paralogs are on different scaffolds for all species. The counts of tandem paralogs with different separations are indicated. Table S2. A set of 62 orthology groups found in Nasonia transcript assemblies that are poorly mapped onto the current genome, but should be considered as part of a complete Nasonia gene set. Table S3. A total of 75 orthology groups missing from Nasonia but found in 9 other insect genomes. Table S4. Histone genes present in OGS2.0 annotated with presence or absence of lineage-specific expansions. NA entries were not assigned to orthologous groups at the level of Hymenoptera. (ZIP 33Â kb)
DOI: 10.15468/dgjpjs
title: EMBRAPA FLORESTAS | Soil macrofauna communities in various land use systems in Santo Inácio, Paraná, Brazil

description: Soil macrofauna communities were evaluated in a number of land use systems on a private farm (Estância JAE) in Santo Inácio, Paraná, Brazil. Sampling was performed in October 2013 and January 2014 in seven land uses: 1) an agrosilvopastoral system with Eucalyptus urograndis tree rows and Urochloa ruziziensis pasture and annual crops (soybean, maize, oats, wheat) planted in the interrow; 2) a silvopastoral system with rows of Corymbia maculata trees and the interrow planted with Urochloa ruziziensis; 3) a permanent pasture of Urochloa sp.; 4) a sugarcane plantation with conventional tillage; 5) an agropastoral system with soybean in the summer and Urochloa ruziziensis pasture in the winter; 6) a 20-year old Eucalyptus sp. plantation; and 7) a native Atlantic Forest fragment, nearby a stream. Samples were taken using the standard methodology of the Tropical Soil Biology and Fertility Programme (TSBF), where soil (down to 20 cm depth) and litter fauna were hand-sorted from monoliths of 25x25 cm, and the abundance of a total of 42 taxa was assessed.
DOI: 10.6084/m9.figshare.c.3635270_d5
title: Additional file 1: of Biochemical and transcriptomic analyses reveal different metabolite biosynthesis profiles among three color and developmental stages in â  Anji Baichaâ   (Camellia sinensis)

description: Gene Ontology enrichment classifications of the differentially expressed genes up-regulated between the yellow-green and re-greening stages. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3635270_d6
title: Additional file 5: of Biochemical and transcriptomic analyses reveal different metabolite biosynthesis profiles among three color and developmental stages in â  Anji Baichaâ   (Camellia sinensis)

description: Unigenes involved in theanine biosynthesis. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3635270_d4
title: Additional file 2: of Biochemical and transcriptomic analyses reveal different metabolite biosynthesis profiles among three color and developmental stages in â  Anji Baichaâ   (Camellia sinensis)

description: Gene Ontology enrichment classifications of the differentially expressed genes down-regulated between the yellow-green and re-greening stages. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3635270_d2
title: Additional file 4: of Biochemical and transcriptomic analyses reveal different metabolite biosynthesis profiles among three color and developmental stages in â  Anji Baichaâ   (Camellia sinensis)

description: Unigenes involved in chlorophyll biosynthesis. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3635270_d3
title: Additional file 3: of Biochemical and transcriptomic analyses reveal different metabolite biosynthesis profiles among three color and developmental stages in â  Anji Baichaâ   (Camellia sinensis)

description: Unigenes involved in carotenoid biosynthesis. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3635270_d1
title: Additional file 6: of Biochemical and transcriptomic analyses reveal different metabolite biosynthesis profiles among three color and developmental stages in â  Anji Baichaâ   (Camellia sinensis)

description: Primers used for quantitative reverse transcription polymerase chain reaction analyses. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3635261_d1
title: Additional file 1: of A single amino acid substitution alter antigenicity of Glycosylated protein 4 of HP-PRRSV

description: The peptides chip scanning results. (XLS 242 kb)
DOI: 10.6084/m9.figshare.c.3635261_d2
title: Additional file 2: of A single amino acid substitution alter antigenicity of Glycosylated protein 4 of HP-PRRSV

description: The peptide based ELLISA results. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3635225_d1
title: Additional file 1: Table S1. of Identification of recurrent focal copy number variations and their putative targeted driver genes in ovarian cancer

description: Sample information of 587 ovarian patients and normal tissue samples with Copy number variation and mRNA data on different platforms. Table S2. Distributions of focal gains/losses in primary tumors and adjacent normal tissue separately on each of the three microarray platforms. Table S3. List of genes encoded in the recurrent focal event regions. Table S4. Prognostic results of ovarian cancer progression using fCNV on three platforms. (XLSX 20403 kb)
DOI: 10.15468/dl.d5cse9
title: Occurrence Download

description: A dataset containing 397 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pleuronichthys cornutus (Temminck & Schlegel, 1846)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 397 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032124-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3635147_d6
title: Additional file 4: Table S5. of Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

description: 86 DEGs with InDels detected in sterile buds. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3635147_d7
title: Additional file 2: Table S3. of Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

description: Blast results of sesame 1445 DEGs in MapMan pathway analysis. (XLSX 264 kb)
DOI: 10.6084/m9.figshare.c.3635147_d5
title: Additional file 3: Table S4. of Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

description: 52 DEGs with InDels detected in fertile buds. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.c.3635147_d3
title: Additional file 6: Table S7. of Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

description: 77 InDels in 68 DEGs down-regulated in sterile buds. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.c.3635147_d4
title: Additional file 1: Table S2. of Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

description: Expressions and annotations of the 1502 differentially expressed unigenes in sesame. (XLSX 338 kb)
DOI: 10.6084/m9.figshare.c.3635147_d2
title: Additional file 8: Table S1. of Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

description: List of primer sequences for qRT-PCR. (XLSX 11 kb)