cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.zmsnge
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Leiodes ciliaris (W.L.E.Schmidt, 1841)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 61 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104741-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zzd2kx
title: Occurrence Download

description: A dataset containing 5236 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Xanthogaleruca luteola (O.F.Müller, 1766)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 5236 records from 235 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104742-240626123714530/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.17983000.v1
title: Additional file 2 of Chlorosis seedling lethality 1 encoding a MAP3K protein is essential for chloroplast development in rice

description: Additional file 2: Table S1. Segregation ratio of csl1 heterozygotes. Table S2. The primers used in this study
DOI: 10.6084/m9.figshare.13787584
title: Additional file 7 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 7 The CDS and protein sequences of the cloned MdCAX genes in this study.
DOI: 10.6084/m9.figshare.7497287.v1
title: MOESM4 of A novel deletion in KRT75L4 mediates the frizzle trait in a Chinese indigenous chicken

description: Additional file 4: Table S4. Summary of the differentially expressed genes detected between KRC and HX. Column A = Ensembl IDs of differentially expressed genes; columns B and C = average RPKM of HX and KRC groups, respectively; column D = fold-change both groups; column E = significance P-value.; columns F, G and H = chromosome number and positions of the DEG; column I = gene names.
DOI: 10.6084/m9.figshare.13787524
title: Additional file 10 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 10: Table S3. Cis-elements identified in the promoter regions of MdCAX genes in apple. Plus and minus signs indicate whether the cis-element was located either the plus or minus strand.
DOI: 10.6084/m9.figshare.17983000
title: Additional file 2 of Chlorosis seedling lethality 1 encoding a MAP3K protein is essential for chloroplast development in rice

description: Additional file 2: Table S1. Segregation ratio of csl1 heterozygotes. Table S2. The primers used in this study
DOI: 10.6084/m9.figshare.7497257.v1
title: MOESM1 of A novel deletion in KRT75L4 mediates the frizzle trait in a Chinese indigenous chicken

description: Additional file 1: Table S1. Pedigree and phenotypes of the GWAS population. Description: Columns A and B = sire and dam IDs, respectively; column C = sample IDs; column D = phenotype of the samples.
DOI: 10.6084/m9.figshare.7497287
title: MOESM4 of A novel deletion in KRT75L4 mediates the frizzle trait in a Chinese indigenous chicken

description: Additional file 4: Table S4. Summary of the differentially expressed genes detected between KRC and HX. Column A = Ensembl IDs of differentially expressed genes; columns B and C = average RPKM of HX and KRC groups, respectively; column D = fold-change both groups; column E = significance P-value.; columns F, G and H = chromosome number and positions of the DEG; column I = gene names.
DOI: 10.6084/m9.figshare.7497218.v1
title: Additional file 1: of Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation

description: Figure S1. Multiple sequence alignment of myoglobin genes in the genomes of Clarias batrachus, Danio rerio, Ictalurus punctatus and Astyanax mexicanus. Figure S2. Detailed phylogenetic tree of olfactory receptor related to class A G protein-coupled receptor (ora) with species names and sequence names for Figure 3b. Figure S3. Multiple sequence alignment of olfactory receptor related to class A G protein-coupled receptor 1 (ora1) in the genomes of Clarias batrachus, Danio rerio, Ictalurus punctatus and Astyanax mexicanus. Figure S4. Syntenic analysis of myoglobin gene (mb) using genomic information of Danio rerio, Ictalurus punctatus and Clarias batrachus. Figure S5. Comparison of relative fold changes between air-breathing organ and gill in Clarias batrachus after normalization to 28S rRNA using RNA-Seq datasets and qRT-PCR. Table S1. Completeness of genome assembly assessed by CEGMA and BUSCO. Table S2. Mapping of five longest ABySS scaffolds to genome assembly. Table S3. Repetitive elements in the Clarias batrachus genome. Table S4. Orthogroups shared between species by OrthoFinder. Table S5. Specific genes in the Clarias batrachus genome compared with that of channel catfish (Ictalurus punctatus). Table S6. GO terms significantly enriched in the specific genes in the Clarias batrachus genome compared with that of channel catfish (Ictalurus punctatus). Table S7. Positively selected genes in the Clarias batrachus genome compared with those of 11 non-air-breathing teleost fish. Table S8. GO terms significantly enriched in the positively selected genes in the Clarias batrachus genome. Table S9. Expanded genes in the Clarias batrachus genome. Table S10. Summary of transcriptome sequencing data. Table S11. Expression values (RPKM) of all the genes in the transcriptomes of the gill and the air-breathing organ. Table S12. Differentially expressed genes in the transcriptome of the air-breathing organ compared with that of the gill. Table S13. GO terms significantly enriched in the differentially expressed genes comparing the transcriptome of the air-breathing organ with that of the gill. Table S14. Pathways significantly enriched in the differentially expressed genes comparing the transcriptome of the air-breathing organs with that of the gill. Table S15. Accession numbers of protein sequences and models used in the construction of phylogenetic trees of expanded genes. Table S16. Primer sequences used for qRT-PCR. (ZIP 5238 kb)
DOI: 10.6084/m9.figshare.6973085.v1
title: Additional file 5: of Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)

description: Unigene IDs and primer sequences for selected transcripts used for qPCR validation. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.16934418.v2
title: Exhaustive Goodness of Fit Via Smoothed Inference and Graphics

description: Classical tests of goodness of fit aim to validate the conformity of a postulated model to the data under study. Given their inferential nature, they can be considered a crucial step in confirmatory data analysis. In their standard formulation, however, they do not allow exploring how the hypothesized model deviates from the truth nor do they provide any insight into how the rejected model could be improved to better fit the data. The main goal of this work is to establish a comprehensive framework for goodness of fit which naturally integrates modeling, estimation, inference and graphics. Modeling and estimation focus on a novel formulation of smooth tests that easily extends to arbitrary distributions, either continuous or discrete. Inference and adequate post-selection adjustments are performed via a specially designed smoothed bootstrap and the results are summarized via an exhaustive graphical tool called <i>CD-plot</i>. Technical proofs, codes and data are provided in the supplementary material.
DOI: 10.6084/m9.figshare.6973046
title: Additional file 3: of Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)

description: Functional analysis of unigenes in blue, red and magenta modules enriched in the photosynthesis pathway. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6973067
title: Additional file 4: of Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)

description: Hub genes for each highly significant content-related module. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6973067.v1
title: Additional file 4: of Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)

description: Hub genes for each highly significant content-related module. (XLSX 54 kb)
DOI: 10.15131/shef.data.3827460
title: Data for paper: InGaAs/AlGaAsSb avalanche photodiode with high gain-bandwidth product

description: The files correspond to experimental results in
paper (accepted by Optics Express): “InGaAs/AlGaAsSb avalanche photodiode with high gain-bandwidth product” DOI: 10.1364/OE.24.024242.<br>

There are two groups of
files:

-.PNG/BMP, which
corresponds to the figures

-.CSV, which are raw
data in figures 

The work in this paper mainly focus on the development
of gain-bandwidth product APDsby using novel avalanche material. We demonstrate an InGaAs/AlGaAsSb APD, grown on an InP substrate,
with a GBP of 424 GHz, the highest value reported for InP-compatible APDs,
which is applicable to future optical communication systems at or above 10 Gb/s. 

The data consists of results from InGaAs/AlGaAsSb
avalanche photodiodes: dark current, photocurrent, frequency response and gain-bandwidth
product. More details about these data/figures can be found in README file.
DOI: 10.6084/m9.figshare.6973193.v1
title: Additional file 2: of Functional relevance for central cornea thickness-associated genetic variants by using integrative analyses

description: Table S2. Summary of integrative annotation scores of CCT associated lead SNPs and variants in strong linkage-disequilibrium (LD) (r2â â Ľâ 0.8) with the lead SNPs, using CADD, GWAVA and Eigen tools. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.13787566
title: Additional file 2 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 2. Sequences of the proteins from HMMER screening results.
DOI: 10.6084/m9.figshare.13787560
title: Additional file 18 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 18. qRT-PCR primers of MdCAX genes used in this study.
DOI: 10.6084/m9.figshare.13787539.v1
title: Additional file 13 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 13. The p-value matrix of the intragroup correlation analysis among MdCAX genes.
DOI: 10.6084/m9.figshare.6448787
title: Additional file 1: of A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women

description: Table S1. Association of the top seven miRNA SNPs from the full analyses with p &lt; 5 × 10−6 in case versus control and case-only subtype analyses. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.13787563
title: Additional file 1 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 1: Table S1. HMMER screening results and conservative domain comparison between CaCA family proteins in apple and Arabidopsis.
DOI: 10.6084/m9.figshare.6973220
title: Additional file 1: of Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t

description: Table S1. DEPs in comparisons KJ201-NPB/Mock-NPB, RB22-NPB/Mock-NPB, KJ201-Piz-t/Mock-Piz-t, and RB22-Piz-t//Mock-Piz-t. (XLS 152 kb)
DOI: 10.6084/m9.figshare.6973220.v1
title: Additional file 1: of Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t

description: Table S1. DEPs in comparisons KJ201-NPB/Mock-NPB, RB22-NPB/Mock-NPB, KJ201-Piz-t/Mock-Piz-t, and RB22-Piz-t//Mock-Piz-t. (XLS 152 kb)
DOI: 10.6084/m9.figshare.13787584.v1
title: Additional file 7 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 7 The CDS and protein sequences of the cloned MdCAX genes in this study.
DOI: 10.6084/m9.figshare.13787557.v1
title: Additional file 17 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 17: Table S4. Functional annotation of CAXs and their interacting proteins.
DOI: 10.6084/m9.figshare.13787560.v1
title: Additional file 18 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 18. qRT-PCR primers of MdCAX genes used in this study.
DOI: 10.6084/m9.figshare.13787590
title: Additional file 8 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 8: Table S2. Basic information for the 3D structure prediction of MdCAX proteins in apple.
DOI: 10.6084/m9.figshare.6973193
title: Additional file 2: of Functional relevance for central cornea thickness-associated genetic variants by using integrative analyses

description: Table S2. Summary of integrative annotation scores of CCT associated lead SNPs and variants in strong linkage-disequilibrium (LD) (r2â â Ľâ 0.8) with the lead SNPs, using CADD, GWAVA and Eigen tools. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.13787563.v1
title: Additional file 1 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 1: Table S1. HMMER screening results and conservative domain comparison between CaCA family proteins in apple and Arabidopsis.
DOI: 10.6084/m9.figshare.6448787.v1
title: Additional file 1: of A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women

description: Table S1. Association of the top seven miRNA SNPs from the full analyses with p &lt; 5 × 10−6 in case versus control and case-only subtype analyses. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.6973274
title: Additional file 2: of BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species

description: Reference collection excel file with meta-data. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.13787632
title: Additional file 1 of Efficient CRISPR/Cas9 mediated Pooled-sgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton

description: Additional file 1. List of the selected genes and their predicted function.
DOI: 10.6084/m9.figshare.16934418.v1
title: Exhaustive goodness-of-fit via smoothed inference and graphics

description: Classical tests of goodness-of-fit aim to validate the conformity of a postulated model to the data under study. Given their inferential nature, they can be considered a crucial step in confirmatory data analysis. In their standard formulation, however, they do not allow exploring how the hypothesized model deviates from the truth nor do they provide any insight into how the rejected model could be improved to better fit the data. The main goal of this work is to establish a comprehensive framework for goodness-of-fit which naturally integrates modeling, estimation, inference and graphics. Modeling and estimation focus on a novel formulation of smooth tests that easily extends to arbitrary distributions, either continuous or discrete. Inference and adequate post-selection adjustments are performed via a specially designed smoothed bootstrap and the results are summarized via an exhaustive graphical tool called <i>CD-plot</i>. Technical proofs, codes and data are provided in the Supplementary Material.
DOI: 10.6084/m9.figshare.6973085
title: Additional file 5: of Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis)

description: Unigene IDs and primer sequences for selected transcripts used for qPCR validation. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.13787593.v1
title: Additional file 9 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 9. Sequences of the promoter regions (− 1500 bp) of MdCAX genes.
DOI: 10.6084/m9.figshare.13787539
title: Additional file 13 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 13. The p-value matrix of the intragroup correlation analysis among MdCAX genes.
DOI: 10.6084/m9.figshare.6973205.v1
title: Additional file 1: of TNFAIP3 is required for FGFR1 activation-promoted proliferation and tumorigenesis of premalignant DCIS.COM human mammary epithelial cells

description: Differentially expressed genes identified in DCIS-iFGFR1 cells treated with AP20187 or vehicle for 3Â h. (XLS 365 kb)
DOI: 10.6084/m9.figshare.6973235
title: Additional file 2: of Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t

description: Table S2. GO and KEGG analyses of DEPs in comparisons KJ201-Piz-t/Mock-Piz-t, and RB22-Piz-t//Mock-Piz-t. (XLSX 84 kb)
DOI: 10.6084/m9.figshare.6973310
title: Additional file 4: of BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species

description: Results of validation test. (CSV 2265 kb)
DOI: 10.6084/m9.figshare.17983024
title: Additional file 1 of Transcriptional dynamics of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP-RK transcription factor linked to reproduction

description: Additional file 1.
DOI: 10.6084/m9.figshare.6973226.v1
title: Additional file 2: of TNFAIP3 is required for FGFR1 activation-promoted proliferation and tumorigenesis of premalignant DCIS.COM human mammary epithelial cells

description: Differentially expressed genes identified in DCIS-iFGFR1 cells treated with AP20187 or vehicle for 16Â h. (XLS 273 kb)
DOI: 10.6084/m9.figshare.7497269
title: MOESM2 of A novel deletion in KRT75L4 mediates the frizzle trait in a Chinese indigenous chicken

description: Additional file 2: Table S2. Sequence of the primers used to screen all the exons of the five candidate genes.
DOI: 10.15131/shef.data.3827460.v1
title: Data for paper: InGaAs/AlGaAsSb avalanche photodiode with high gain-bandwidth product

description: The files correspond to experimental results in
paper (accepted by Optics Express): “InGaAs/AlGaAsSb avalanche photodiode with high gain-bandwidth product” DOI: 10.1364/OE.24.024242.<br>

There are two groups of
files:

-.PNG/BMP, which
corresponds to the figures

-.CSV, which are raw
data in figures 

The work in this paper mainly focus on the development
of gain-bandwidth product APDsby using novel avalanche material. We demonstrate an InGaAs/AlGaAsSb APD, grown on an InP substrate,
with a GBP of 424 GHz, the highest value reported for InP-compatible APDs,
which is applicable to future optical communication systems at or above 10 Gb/s. 

The data consists of results from InGaAs/AlGaAsSb
avalanche photodiodes: dark current, photocurrent, frequency response and gain-bandwidth
product. More details about these data/figures can be found in README file.
DOI: 10.6084/m9.figshare.13787551
title: Additional file 16 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 16 The p-value matrix of the intergroup correlation analysis between MdCAX and AtCAX genes.
DOI: 10.6084/m9.figshare.6973190
title: Additional file 1: of Functional relevance for central cornea thickness-associated genetic variants by using integrative analyses

description: Table S1. GWAS reports that included in the current study. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.6973313.v1
title: Additional file 2: of Genetic analysis of seedling root traits reveals the association of root trait with other agronomic traits in maize

description: Table S1. Root trait data of the parental lines at the three time points. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.6973325
title: Additional file 5: of BMScan: using whole genome similarity to rapidly and accurately identify bacterial meningitis causing species

description: BioProject and PubMLST Ids for genome assemblies used in reference collection. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.13787551.v1
title: Additional file 16 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 16 The p-value matrix of the intergroup correlation analysis between MdCAX and AtCAX genes.
DOI: 10.6084/m9.figshare.6973307
title: Additional file 6: of Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t

description: Table S5. GO and KEGG analyses of DEPs in comparison KJ201-Piz-t/KJ201-NPB. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.6973205
title: Additional file 1: of TNFAIP3 is required for FGFR1 activation-promoted proliferation and tumorigenesis of premalignant DCIS.COM human mammary epithelial cells

description: Differentially expressed genes identified in DCIS-iFGFR1 cells treated with AP20187 or vehicle for 3Â h. (XLS 365 kb)
DOI: 10.6084/m9.figshare.6973208.v1
title: Additional file 3: of Functional relevance for central cornea thickness-associated genetic variants by using integrative analyses

description: Table S3. Significant terms of the Gene Ontology, Pathway, and Disease enrichment of 38 CCT-associated genes (FDRâ &lt;â 0.05). (XLSX 55 kb)
DOI: 10.6084/m9.figshare.6973235.v1
title: Additional file 2: of Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t

description: Table S2. GO and KEGG analyses of DEPs in comparisons KJ201-Piz-t/Mock-Piz-t, and RB22-Piz-t//Mock-Piz-t. (XLSX 84 kb)
DOI: 10.6084/m9.figshare.6973241.v1
title: Additional file 3: of TNFAIP3 is required for FGFR1 activation-promoted proliferation and tumorigenesis of premalignant DCIS.COM human mammary epithelial cells

description: Differentially expressed genes identified in DCIS-iFGFR1 cells treated with AP20187 for 16 or 3Â h (XLS 259 kb)
DOI: 10.6084/m9.figshare.13787590.v1
title: Additional file 8 of Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

description: Additional file 8: Table S2. Basic information for the 3D structure prediction of MdCAX proteins in apple.