cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10203149
title: SMAP Daily Seamless Soil Moisture Products from 2015 to 2022 (Physics-constrained Gap-filling Method,PhyFill)

description: The launch of Soil Moisture Active Passive (SMAP) satellite in 2015 has resulted in significant achievements in global soil moisture mapping. Nonetheless, spatiotemporal discontinuities in the soil moisture products have arisen due to the limitations of its orbit scanning gap and retrieval algorithms. To address this issue, this dataset presents a physics-constrained gap-filling method, shortly named PhyFill. The PhyFill method employs a partial convolutional neural network to explore spatial domain features of the original SMAP soil moisture data. Then, it incorporates variations in soil moisture induced by precipitation events and dry-down events as penalty terms in the loss function, thereby accounting for monotonicity and boundary constraints in the physical processes governing the dynamic fluctuations of soil moisture. The PhyFill model was applied to SMAP soil moisture data, resulting in continuous daily soil moisture data on a global scale. The core validation sites demonstrated that the reconstructed soil moisture data has a consistent ubRMSE compared with the original SMAP soil moisture data. The PhyFill method can generate globally continuous, high-accuracy soil moisture estimates, providing remarkable support for advanced hydrological applications, e.g., global soil moisture dry-down events and patterns.
description: <PhyFill_YYYY_AM. h5>, <PhyFill > represents the Physics-constrained Gap-filling Method; <YYYY> Indicates the year of the data, including the data of the corresponding year.  <AM> means the reconfiguration is at 6 a.m. local time. It will be updated continuously according to your valuable suggestions. Usage method: Data can be read in MATLAB, Python, IDL and other programming languages, and can also be visualized in HDFView and Panoply. We provide code to read the data in MATLAB.
description: 'SM' is soil moisture data, if there are 365 days in a year, the data storage dimension is 964×406×365.
'latitude' is the latitude of soil moisture data with a storage dimension of 406×1.
'longitude'' is the longitude of soil moisture data with a storage dimension of 964×1.
'time' is the date. For example, if there are 365 days in a year, the data storage dimension is 365×1.
The reading method of data can be referred to the matlab code read_2015.m.
description: Please cite our paper on PhyFill published in Remote Sensing of Environment (RSE):

Wei Z, Miao L, Peng J, et al. Bridging spatio-temporal discontinuities in global soil moisture mapping by coupling physics in deep learning[J]. Remote Sensing of Environment, 2024, 313: 114371.
DOI: 10.5281/zenodo.10203150
title: SMAP Daily Seamless Soil Moisture Products from 2015 to 2022 (Physics-constrained Gap-filling Method,PhyFill)

description: The launch of Soil Moisture Active Passive (SMAP) satellite in 2015 has resulted in significant achievements in global soil moisture mapping. Nonetheless, spatiotemporal discontinuities in the soil moisture products have arisen due to the limitations of its orbit scanning gap and retrieval algorithms. To address this issue, this dataset presents a physics-constrained gap-filling method, shortly named PhyFill. The PhyFill method employs a partial convolutional neural network to explore spatial domain features of the original SMAP soil moisture data. Then, it incorporates variations in soil moisture induced by precipitation events and dry-down events as penalty terms in the loss function, thereby accounting for monotonicity and boundary constraints in the physical processes governing the dynamic fluctuations of soil moisture. The PhyFill model was applied to SMAP soil moisture data, resulting in continuous daily soil moisture data on a global scale. The core validation sites demonstrated that the reconstructed soil moisture data has a consistent ubRMSE compared with the original SMAP soil moisture data. The PhyFill method can generate globally continuous, high-accuracy soil moisture estimates, providing remarkable support for advanced hydrological applications, e.g., global soil moisture dry-down events and patterns.
description: <PhyFill_YYYY_AM. h5>, <PhyFill > represents the Physics-constrained Gap-filling Method; <YYYY> Indicates the year of the data, including the data of the corresponding year.  <AM> means the reconfiguration is at 6 a.m. local time. It will be updated continuously according to your valuable suggestions. Usage method: Data can be read in MATLAB, Python, IDL and other programming languages, and can also be visualized in HDFView and Panoply. We provide code to read the data in MATLAB.
description: 'SM' is soil moisture data, if there are 365 days in a year, the data storage dimension is 964×406×365.
'latitude' is the latitude of soil moisture data with a storage dimension of 406×1.
'longitude'' is the longitude of soil moisture data with a storage dimension of 964×1.
'time' is the date. For example, if there are 365 days in a year, the data storage dimension is 365×1.
The reading method of data can be referred to the matlab code read_2015.m.
description: Please cite our paper on PhyFill published in Remote Sensing of Environment (RSE):

Wei Z, Miao L, Peng J, et al. Bridging spatio-temporal discontinuities in global soil moisture mapping by coupling physics in deep learning[J]. Remote Sensing of Environment, 2024, 313: 114371.
DOI: 10.6084/m9.figshare.c.3605042_d1
title: Additional file 3: of ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research

description: Target file (mandatory input file) to run ClinQC. (TXT 1 kb)
DOI: 10.15468/dl.hnqb7p
title: Occurrence Download

description: A dataset containing 202 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anaphalis sinica var. morii (Nakai) Ohwi"
 ]
}

 The dataset includes 202 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032691-241126133413365/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.3605069_d1
title: Additional file 3: Table S1. of deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution

description: The mutational signature contribution to each TCGA tumor sample studied as determined by deconstructSigs and WTSI Mutational Signature Framework. Signatures used as input to deconstructSigs were limited to those extracted using the WTSI Mutational Signature Framework approach. (TXT 464 kb)
DOI: 10.6084/m9.figshare.c.3605069_d2
title: Additional file 7: Table S3. of deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution

description: Mutations from TCGA ESCA cohort and their timing (early/late). (TXT 811 kb)
DOI: 10.6084/m9.figshare.c.3605021_d10
title: Additional file 12: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

description: Key differentially expressed genes discussed in the manuscript, based on their functional categories and expression profiles. Each sheet contains the genes in each cluster discussed. (XLSX 23094 kb)
DOI: 10.15468/dl.5pnrqe
title: Occurrence Download

description: A dataset containing 28049 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lonicera caerulea L."
 ]
}

 The dataset includes 28049 records from 426 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032690-241126133413365/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.3605069_d6
title: Additional file 6: Table S2. of deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution

description: The mutational signature contribution to each TCGA tumor sample studied as determined by deconstructSigs and WTSI Mutational Signature Framework. The full published set of mutational signatures [4] was allowed to be used as input to deconstructSigs. Tumor types considered were limited to those where only unambiguous signatures could be extracted using the WTSI Mutational Signature Framework to allow for direct comparison with the input reference signature set. (TXT 359 kb)
DOI: 10.6084/m9.figshare.c.3605021_d11
title: Additional file 9: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

description: Distribution of differentially expressed genes of each soil microorganism in 18 clusters, based on the expression profiles. (XLSX 12 kb)
DOI: 10.15468/dl.d5gd9b
title: Occurrence Download

description: A dataset containing 274 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aster hayatae H.Lév. & Vaniot"
 ]
}

 The dataset includes 274 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032692-241126133413365/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.3605162_d1
title: MOESM1 of A comparison of work-related physical activity levels between inpatient and outpatient physical therapists: an observational cohort trial

description: Additional file 1. Â Accelerometry data.
DOI: 10.6084/m9.figshare.c.3605153_d2
title: Additional file 27: Table S18. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: List of the primers used for the qPCR and qRT-PCR reactions. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.c.3605153_d3
title: Additional file 12: Table S7. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: List of genes with significant differential expression between FCB and FCB pfmdr1_3â ˛KD in a stage-specific manner. Genes with significantly higher expression displayed absolute fold change values &gt;1.5 and normalized fold changes values two standard deviations above the median normalized fold change value. Fold change for each gene at the designated stage is indicated. No gene appeared to be significantly differently expressed between the two strains during both ring and schizont stages. Genes from antigenic variant families have been removed. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.c.3605168_d1
title: MOESM1 of The kdr-bearing haplotype and susceptibility to Plasmodium falciparum in Anopheles gambiae: genetic correlation and functional testing

description: Additional file 1: Table S1. Catalogue of polymorphic SNPs used in the study.
DOI: 10.15468/dl.8pbbtu
title: Occurrence Download

description: A dataset containing 166 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cirsium rhinoceros (H.Lév. & Vaniot) Nakai"
 ]
}

 The dataset includes 166 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032693-241126133413365/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.3605153_d4
title: Additional file 23: Table S15. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Gene expression correlation between P. falciparum genes and either pfcrt or pfmdr1. Pearson correlation coefficients were calculated between pfcrt/pfmdr1 expression values and those of other 2,600 P. falciparum genes across 110 pairwise comparisons. These correspond to bi-directional comparisons between 11 parasite transcriptome data sets, including FCB and 7G8 data sets. (A) List of genes whose expression is highly correlated (PCC &gt;0.7) to that of pfcrt. (B) List of genes whose expression is highly anti-correlated (PCC 0.7) to that of pfmdr1. (D) List of genes whose expression is highly anti-correlated (PCC
DOI: 10.6084/m9.figshare.c.3605153_d5
title: Additional file 18: Table S12. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Genes with significant differential expression between 7G8 pfcrt_CTL and 7G8 pfcrt_T76K in a stage-specific manner. Genes with significantly higher expression displayed absolute fold changes &gt;1.5 and normalized fold changes values two standard deviations above the median normalized fold change value. Genes with significantly lower expression had absolute fold change values lower than 0.6 and a normalized fold change three standard deviations below the median value. Fold change for each gene at the designated stage is indicated. (XLSX 58 kb)
DOI: 10.60656/34e0672bbc7e4826
title: Custom collection of MWR brightness temperature data from Jülich between 5 Oct 2017 and 12 Dec 2024
DOI: 10.6084/m9.figshare.c.3605153_d6
title: Additional file 13: Table S8. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: List of genes with significant differential expression between FCB and 106/1 in a stage-specific manner. Genes with significantly higher expression displayed absolute fold changes &gt;1.5 and normalized fold changes values two standard deviations above the median normalized fold change value. Genes with significantly lower expression had absolute fold change values lower than 0.6 and a normalized fold change three standard deviations below the median value. Fold change for each gene at the designated stage is indicated. (XLSX 66 kb)
DOI: 10.6084/m9.figshare.c.3605153_d14
title: Additional file 20: Table S13. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Hierarchical clustering, which was performed using Pearson correlation coefficients between ~2600 gene pairs across 55 pairwise comparisons of 11 parasite transcriptome data sets, including FCB and 7G8 data sets. Cluster 1 corresponding to gene pairs with high Pearson correlation (PCC &gt;0.7), containing pfmdr1 and pfcrt as well as a transcription factor of the ApiAP2 family PF3D7_0516800. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.c.3605153_d17
title: Additional file 2: Table S1. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Validation of the data point imputation. Using the publically available transcriptome datasets for 3D7, Dd2 and HB3 from (Llinas et al. NAR 2007), we validated whether the density of the data in our time series (of eight points, at a 6-hour resolution) was sufficient to impute data to a 7.5Â min resolution. For each strain, we selected eight time points evenly spread (6-hrs apart) from which we generated an imputed curve of 384 points. Using Pearson correlation values for gene expression, we then compared each actual hourly time point to the imputed curve to identify the closest matching time point. The imputed percentage column shows where the match occurred in the time series. Actual time points from the original time courses match imputed time points that are fairly evenly spread along the imputation-derived curve. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3605153_d18
title: Additional File 26: Table S17.

description: Table summarizing all the gene sets, extracted from various databases or built by our group, that were used in this study. (XLSX 688 kb)
DOI: 10.6084/m9.figshare.c.3605153_d19
title: Additional file 7: Table S3. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Results of quantitative real time PCR to estimate gene copy numbers associated with gene expression variations between FCB and both FCB_3â ˛KD and 106/1 in the pfmdr1-containing amplicon region on chromosome 5. These data suggest dosage compensation for the gene Pf3D7_0521300. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.c.3605153_d20
title: Additional file 15: Table S9. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Genes (A-F, I-K) and gene sets (G-H, L-M) differentially expressed in the pfcrt data set. For each pairwise comparison, 7G8 vs 7G8 pfcrt_CTL , 7G8 vs 7G8 pfcrt_T76K , and 7G8 pfcrt_CTL vs 7G8 pfcrt_T76K , we listed genes with significant differential expression, i.e. with a fold change greater than 1.5 and a normalized fold change two standard deviations above the median values. We listed the gene sets significantly enriched and depleted in 7G8 in comparison with both 7G8 pfcrt_CTL and 7G8 pfcrt_T76K , and in 7G8 and 7G8 pfcrt_CTL in comparison to 7G8 pfcrt_T76K . (XLSX 48 kb)
DOI: 10.6084/m9.figshare.c.3605153_d21
title: Additional file 17: Table S11. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Genes with significant differential expression between 7G8 and 7G8 pfcrt_T76K in a stage-specific manner. Genes with significantly higher expression displayed absolute fold changes &gt;1.5 and normalized fold changes values two standard deviations above the median normalized fold change value. Genes with significantly lower expression had absolute fold change values lower than 0.6 and a normalized fold change three standard deviations below the median value. Fold change for each gene at the designated stage is indicated. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.c.3605153_d23
title: Additional file 21: Table S14. of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Cluster 2 from the Hierarchical clustering, corresponds to another group of gene pairs with high Pearson correlation (PCC &gt;0.7) and includes pfmdr1 and pfcrt. (XLSX 46 kb)
DOI: 10.15468/dl.yct6s4
title: Occurrence Download

description: A dataset containing 3096 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Tantilla gracilis Baird & Girard, 1853"
 ]
}

 The dataset includes 3096 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032694-241126133413365/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.3605153_d24
title: Additional file 11: Table S6 of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

description: Genes (A-D) and gene sets (E-H) differentially expressed in the pfmdr1 data set. For each pairwise comparison, we listed genes with significant differential expression, i.e. with a fold change greater than 1.5 and a normalized fold change two standard deviations above the median values and genes with a fold change lower than 0.6 and a normalized fold change three standard deviations below the median value, which generally represented the quasi-totality of genes with a fold change below 0.6. Normalization was performed using the average fold change computed across a background pool of 11 transcriptome data sets as a scaling factor. This normalization allowed us to identify and filter out most of the hypervariable genes (e.g. var, rifin, stevor, phist, and hyp). Antigenically variant genes not detected by automatic filtering were manually removed. We listed the gene sets with significant differential expression (based on the mean rank of enrichment score &gt;0.9 (significantly enriched) or &lt;0.1 (significantly impoverished)) that are found in both FCB vs. FCB pfmdr1_3â ˛KD and FCB vs. 106/1 pairwise comparisons. (XLSX 65 kb)
DOI: 10.34740/kaggle/dsv/10185552
title: 🇬🇧 Reddit r/CasualUK Subreddit Dataset
DOI: 10.6084/m9.figshare.c.3605246_d3
title: Additional file 4: of A probabilistic algorithm to process geolocation data

description: R script for sensitivity analyses. (TXT 9 kb)
DOI: 10.6084/m9.figshare.c.3605273_d1
title: MOESM1 of Species delimitation in the White-faced Cuckoo-dove (Turacoena manadensis) based on bioacoustic data

description: Additional file 1: Appendix. Master data sheet. Abbreviations: AVoCet - Avian Vocalizations Center at http://avocet.zoology.msu.edu ; xeno-canto - Xeno-Canto Sound Library at http://www.xeno-canto.org ; McCauley - McCauley Sound Library at http://www.mccauleysound.com ; IBC - Internet Bird Collection at http://www.ibc.lynxeds.com .
DOI: 10.6084/m9.figshare.c.3605333_d1
title: Additional file 4: of Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch)

description: List of subset of the differentially expressed genes. Summary of up and down-regulations of differentially expressed genes and annotated by Swiss-Prot and KEGG between BR vs 2D4W, BR vs 7D4W and 2D4W vs. 7D4W filtered based on p-value and an adjusted FDR of less than 0.05. (XLSX 2681Â kb)
DOI: 10.6084/m9.figshare.c.3605327_d2
title: Additional file 3: Table S1. of Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus

description: Lists of p values of principal component analysis with known covariates. Table S2. A list of differentially expressed genes. Table S3. Lists of differentially methylated HpaII sites in each model. Table S4. A list of differentially methylated HpaII sites with previously reported Infinium HumanMethylation450 BeadChip differentially methylated probes. Table S5. A list of variably methylated HpaIIs. Table S6. A list of var-HpaII sites harboring genes. (XLSX 374 kb)
DOI: 10.6084/m9.figshare.c.3605333_d2
title: Additional file 3: of Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch)

description: List of all set of the differentially expressed genes. Summary of all set data and annotated by Swiss-Prot between BR vs 2D4W, BR vs 7D4W and 2D4W vs. 7D4W. (XLSX 15168Â kb)
DOI: 10.6084/m9.figshare.c.3605309_d7
title: Additional file 9: Table S7. of Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

description: Summarized list of differentially expressed genes between inoculated and mock-inoculated data with annotations. (TSV 68 kb)
DOI: 10.6084/m9.figshare.c.3605309_d8
title: Additional file 8: Table S6. of Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

description: EBSeq differential expression analysis results comparing expression between inoculated and mock-inoculated data. (TSV 6517 kb)
DOI: 10.6084/m9.figshare.c.3605345_d1
title: Additional file 1: of mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics

description: Package â  mAPKL_1.1.1.tar.gzâ   including source code, documentation. (GZ 1979 kb)
DOI: 10.6084/m9.figshare.c.3605333_d8
title: Additional file 7: of Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch)

description: GO enrichment analysis. Raw data of Enrichment of gene ontology terms in differentially expression sequences in Prunus persica (L.) Batsch. (XLSX 93Â kb)