cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8002817.v1
title: Additional file 4: of RNA-sequencing reveals altered skeletal muscle contraction, E3 ligases, autophagy, apoptosis, and chaperone expression in patients with critical illness myopathy

description: Of these 68 genes, 46 were regulated in the opposite direction, and 22 genes were regulated in the same direction. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8002835.v1
title: Additional file 1: of Genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in Sichuan wheat

description: The 244 wheat accessions used in this study and the evaluation of their infection type (IT) and disease Severity (DS) in six environments. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.8002841.v1
title: Additional file 2: of Genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in Sichuan wheat

description: The distribution of infection type (IT) and disease severity (DS) for stripe rust between landraces and cultivars in adult-plant stage based on BLUP values. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.13245658
title: Additional file 1 of Characterization, validation, and cross-species transferability of EST-SSR markers developed from Lycoris aurea and their application in genetic evaluation of Lycoris species

description: Additional file 1: Table S1. Contig sequence and primer information of 839 microsatellite markers developed for Lycoris.
DOI: 10.6084/m9.figshare.8002796.v1
title: Additional file 1: of RNA-sequencing reveals altered skeletal muscle contraction, E3 ligases, autophagy, apoptosis, and chaperone expression in patients with critical illness myopathy

description: RNA quality number (RQN). (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8002808
title: Additional file 3: of RNA-sequencing reveals altered skeletal muscle contraction, E3 ligases, autophagy, apoptosis, and chaperone expression in patients with critical illness myopathy

description: 182genes_withFDR. (TXT 8 kb)
DOI: 10.6084/m9.figshare.8002808.v1
title: Additional file 3: of RNA-sequencing reveals altered skeletal muscle contraction, E3 ligases, autophagy, apoptosis, and chaperone expression in patients with critical illness myopathy

description: 182genes_withFDR. (TXT 8 kb)
DOI: 10.6084/m9.figshare.8002913.v1
title: Additional file 4: of DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis

description: Table S2. This table compares the p values and q values of differential expression analysis by edgeR from different normalization methods for 12 genes which were PCR-verified positives in the AMPK data. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.14818643
title: Role and function of the <i>Hintw</i> in early sex differentiation in chicken (<i>Gallus gallus</i>) embryo

description: Mono-Sex culturing is an important methodology for intensive livestock and poultry production. Here, <i>Hintw</i> was identified as a potential key gene in sex-determination process in chickens via RNA-seq. Then we developed an effective method to interfere or overexpress <i>Hintw</i> in chicken embryos through the intravascular injection. QRT-PCR, ELISA and H&E staining were used to detect the effects of <i>Hintw</i> on gonadal development of chicken embryos. Results showed that <i>Hintw</i> exhibited a female-biased expression pattern in the early stage of PGCs (primordial germ cells) in embryonic gonads. The qRT-PCR analysis showed that <i>Foxl2</i>, <i>Cyp19a1</i> in females were upregulated under the overexpression of <i>Hintw</i>, while <i>Sox9</i> and <i>Dmrt1</i> were downregulated <i>Hintw</i>. Overexpression of <i>Hintw</i> can promote the development of gonadal cortex, while interference with <i>Hintw</i> show the opposite result. Additionally, we found that overexpression of the <i>Hintw</i> in male chicken embryos could inhibit androgen levels and increase estrogen levels. On the other hand, interfering with <i>Hintw</i> in female chicken embryos decreased estrogen levels and increased androgen levels. In conclusion, this work sets the basis for the understanding of the molecular regulatory network for the sex-determination process in chicken embryos as well as providing the theoretical basis for mono-sex culturing of poultry.
DOI: 10.6084/m9.figshare.8002850
title: Additional file 4: of Genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in Sichuan wheat

description: The phenotypic and genetic diversity analyses of 244 wheat accessions in two sub-populations. (XLSX 9 kb)
DOI: 10.24403/jp.1329037
title: Pilzflora der Deutschen Demokratischen Republik : Basidiomycetes (Gallert-, Hut- und Bauchpilze). Hrsg. H. Kreisel. - Jena : VEB Gustav Fischer Verlag, 1987 / [rezensiert von] G. R. W. Arnold
DOI: 10.6084/m9.figshare.8002910
title: Additional file 3: of DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis

description: Table S1. This table summarizes the number of false positives claimed in differential expression analysis by edgeR from different normalization methods at q value threshold = 0.05 for data sets including SEQC-AA, GBM RIN10 vs. RIN4, GBM RIN6 vs. RIN4, PBMC-S01, DLPFC Br1729 Ribo-zero, DLPFC Br1729 poly(A)+, and breast tumor FF vs. (XLSX 9 kb)
DOI: 10.24403/jp.1329046
title: Exkursion zum Hexenberg, nach Schoppendorf und Gutendorf bei Weimar am 27. April 1986 / W. Heinrich
DOI: 10.6084/m9.figshare.20581080
title: Additional file 2 of A pan-Zea genome map for enhancing maize improvement

description: Additional file 2: Table S1. Estimating WGS de novo assemblies by whole genome comparison between WGS de novo assemblies and reference genome sequences of B73, SK, Mo17 and HZS.
DOI: 10.6084/m9.figshare.20581080.v1
title: Additional file 2 of A pan-Zea genome map for enhancing maize improvement

description: Additional file 2: Table S1. Estimating WGS de novo assemblies by whole genome comparison between WGS de novo assemblies and reference genome sequences of B73, SK, Mo17 and HZS.
DOI: 10.6084/m9.figshare.14818643.v1
title: Role and function of the <i>Hintw</i> in early sex differentiation in chicken (<i>Gallus gallus</i>) embryo

description: Mono-Sex culturing is an important methodology for intensive livestock and poultry production. Here, <i>Hintw</i> was identified as a potential key gene in sex-determination process in chickens via RNA-seq. Then we developed an effective method to interfere or overexpress <i>Hintw</i> in chicken embryos through the intravascular injection. QRT-PCR, ELISA and H&E staining were used to detect the effects of <i>Hintw</i> on gonadal development of chicken embryos. Results showed that <i>Hintw</i> exhibited a female-biased expression pattern in the early stage of PGCs (primordial germ cells) in embryonic gonads. The qRT-PCR analysis showed that <i>Foxl2</i>, <i>Cyp19a1</i> in females were upregulated under the overexpression of <i>Hintw</i>, while <i>Sox9</i> and <i>Dmrt1</i> were downregulated <i>Hintw</i>. Overexpression of <i>Hintw</i> can promote the development of gonadal cortex, while interference with <i>Hintw</i> show the opposite result. Additionally, we found that overexpression of the <i>Hintw</i> in male chicken embryos could inhibit androgen levels and increase estrogen levels. On the other hand, interfering with <i>Hintw</i> in female chicken embryos decreased estrogen levels and increased androgen levels. In conclusion, this work sets the basis for the understanding of the molecular regulatory network for the sex-determination process in chicken embryos as well as providing the theoretical basis for mono-sex culturing of poultry.
DOI: 10.6084/m9.figshare.8002865
title: Additional file 7: of Genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in Sichuan wheat

description: The putative candidate genes of two potentially novel QTLs. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8002913
title: Additional file 4: of DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis

description: Table S2. This table compares the p values and q values of differential expression analysis by edgeR from different normalization methods for 12 genes which were PCR-verified positives in the AMPK data. (XLSX 12 kb)
DOI: 10.24403/jp.1329050
title: Exkursion zu den Ebertsbergen und Wartbergen bei Thal am 11. Mai 1986 / F. K. Meyer
DOI: 10.24403/jp.1329052
title: Exkursion nach Schmiedefeld am Rennsteig und in das Naturschutzgebiet Vessertal im Thüringer Wald am 1. Juni 1986 / L. Meinunger
DOI: 10.6084/m9.figshare.22678368.v1
title: Additional file 1 of Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage

description: Additional file 1: Figure S1. Aerial root mucilage (ARM) and underground root exudate (URE) compound of H. rotundifolia. Figure S2. Fungal diversity and community of aerial root mucilage (mucilage) and underground rhizosphere soil (rhizosphere). Figure S3. Differentiate analysis, function and phenotypic prediction of mucilage and rhizosphere bacteria. Figure S4. Cultured bacteria and their nitrogen-fixing capacity. Figure S5. Cultured bacteria and their nitrogen-fixing capacity. Figure S6. Estimated genome size of H. rotundifolia by flow cytometry. Figure S7. Resistance of mucilage compound to environmental microbes. Figure S8. Resistance of F-XTBG8 to pathogenic and environmental fungi. Figure S9. A candidate in mucilage microhabitat and its defense against environmental microbes but not mucilage bacteria. Figure S10. Genome, transcriptome and metabolome analysis of C. raphigera (Cr).
DOI: 10.6084/m9.figshare.12197133.v1
title: Additional file 2 of A cost-sensitive online learning method for peptide identification

description: Additional file 2 Cross validation results. Details of the Cross validation results (Excel file).
DOI: 10.24403/jp.1329059
title: Exkursion ins Unstruttal zwischen Sömmerda und Bad Tennstedt am 6. Juli 1986 / F. K. Meyer
DOI: 10.24403/jp.1329080
title: Exkursion zum Hexenberg, ins Hengstbachtal, nach Buchfarth und zurück nach Bad Berka am 20. Juli 1986 / D. Weber
DOI: 10.6084/m9.figshare.11673999
title: Optimal Permutation Recovery in Permuted Monotone Matrix Model

description: <b>Motivated by recent research on quantifying bacterial growth dynamics based on genome assemblies, we consider a permuted monotone matrix model</b>Y=ΘΠ+Z<b>, where the rows represent different samples, the columns represent contigs in genome assemblies and the elements represent log-read counts after preprocessing steps and Guanine-Cytosine (GC) adjustment. In this model, Θ is an unknown mean matrix with monotone entries for each row, Π is a permutation matrix that permutes the columns of Θ, and <i>Z</i> is a noise matrix. This article studies the problem of estimation/recovery of Π given the observed noisy matrix <i>Y</i>. We propose an estimator based on the best linear projection, which is shown to be minimax rate-optimal for both exact recovery, as measured by the 0-1 loss, and partial recovery, as quantified by the normalized Kendall’s tau distance. Simulation studies demonstrate the superior empirical performance of the proposed estimator over alternative methods. We demonstrate the methods using a synthetic metagenomics dataset of 45 closely related bacterial species and a real metagenomic dataset to compare the bacterial growth dynamics between the responders and the nonresponders of the IBD patients after 8 weeks of treatment. Supplementary materials for this article are available online.</b>
DOI: 10.6084/m9.figshare.11673999.v1
title: Optimal Permutation Recovery in Permuted Monotone Matrix Model

description: Motivated by recent research on quantifying bacterial growth dynamics based on genome assemblies, we consider a permuted monotone matrix model Y=ΘΠ+Z, where the rows represent different samples, the columns represent contigs in genome assemblies and the elements represent log-read counts after preprocessing steps and Guanine-Cytosine (GC) adjustment. In this model, Θ is an unknown mean matrix with monotone entries for each row, Π is a permutation matrix that permutes the columns of Θ, and <i>Z</i> is a noise matrix. This paper studies the problem of estimation/recovery of Π given the observed noisy matrix <i>Y</i>. We propose an estimator based on the best linear projection, which is shown to be minimax rate-optimal for both exact recovery, as measured by the 0-1 loss, and partial recovery, as quantified by the normalized Kendall’s tau distance. Simulation studies demonstrate the superior empirical performance of the proposed estimator over alternative methods. We demonstrate the methods using a synthetic metagenomics dataset of 45 closely related bacterial species and a real metagenomic dataset to compare the bacterial growth dynamics between the responders and the non-responders of the IBD patients after 8 weeks of treatment.
DOI: 10.6084/m9.figshare.22678368
title: Additional file 1 of Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage

description: Additional file 1: Figure S1. Aerial root mucilage (ARM) and underground root exudate (URE) compound of H. rotundifolia. Figure S2. Fungal diversity and community of aerial root mucilage (mucilage) and underground rhizosphere soil (rhizosphere). Figure S3. Differentiate analysis, function and phenotypic prediction of mucilage and rhizosphere bacteria. Figure S4. Cultured bacteria and their nitrogen-fixing capacity. Figure S5. Cultured bacteria and their nitrogen-fixing capacity. Figure S6. Estimated genome size of H. rotundifolia by flow cytometry. Figure S7. Resistance of mucilage compound to environmental microbes. Figure S8. Resistance of F-XTBG8 to pathogenic and environmental fungi. Figure S9. A candidate in mucilage microhabitat and its defense against environmental microbes but not mucilage bacteria. Figure S10. Genome, transcriptome and metabolome analysis of C. raphigera (Cr).
DOI: 10.24403/jp.1329084
title: Exkursion in den Thüringer Wald zum Sachsenstein und den linken Quellbächen der Ilm am 3. August 1986 / P. Heerlein
DOI: 10.6084/m9.figshare.9576944
title: Profiling and Bioinformatic Analysis of Differentially Expressed Cytokines in Aqueous Humor of High Myopic Eyes – Clues for Anti-VEGF Injections

description: To investigate the aqueous humor growth factor profile in high myopic eyes and analyze the interaction of differentially expressed cytokines. A case–control study including aqueous humor samples from 36 high myopic patients and 32 controls was conducted. Quantibody® Human Growth Factor Array was used to screen the presence of 40 growth factors in aqueous humor. Expressions of differential growth factors were validated by Bio-Plex Pro<sup>TM</sup> multiplex bead-based immunoassay. Protein–protein interaction (PPI) and gene ontology (GO) analyses were performed. Growth differentiation factor 15 (GDF-15), hepatocyte growth factor (HGF), and platelet-derived growth factor (PDGF)-AA were found to be significantly higher and vascular endothelial growth factor (VEGF) was detected to be lower in high myopic eyes (all <i>P</i> = .03). Multi-plex bead-based assay further validated the differential expressions of four growth factors and all of them were significantly correlated with axial length (<i>P</i> &lt; .001). Twenty-six proteins were mapped into PPI network and positive regulation of cell migration, cellular component movement, and cell motility were the most enriched biological processes based on GO analysis. Differential expressed cytokines that indicates a distinctive intraocular microenvironment in high myopic eyes might provide clues for pathological changes within high myopic eyes after anti-VEGF injections.
DOI: 10.6084/m9.figshare.9576944.v1
title: Profiling and Bioinformatic Analysis of Differentially Expressed Cytokines in Aqueous Humor of High Myopic Eyes – Clues for Anti-VEGF Injections

description: To investigate the aqueous humor growth factor profile in high myopic eyes and analyze the interaction of differentially expressed cytokines. A case–control study including aqueous humor samples from 36 high myopic patients and 32 controls was conducted. Quantibody® Human Growth Factor Array was used to screen the presence of 40 growth factors in aqueous humor. Expressions of differential growth factors were validated by Bio-Plex Pro<sup>TM</sup> multiplex bead-based immunoassay. Protein–protein interaction (PPI) and gene ontology (GO) analyses were performed. Growth differentiation factor 15 (GDF-15), hepatocyte growth factor (HGF), and platelet-derived growth factor (PDGF)-AA were found to be significantly higher and vascular endothelial growth factor (VEGF) was detected to be lower in high myopic eyes (all <i>P</i> = .03). Multi-plex bead-based assay further validated the differential expressions of four growth factors and all of them were significantly correlated with axial length (<i>P</i> &lt; .001). Twenty-six proteins were mapped into PPI network and positive regulation of cell migration, cellular component movement, and cell motility were the most enriched biological processes based on GO analysis. Differential expressed cytokines that indicates a distinctive intraocular microenvironment in high myopic eyes might provide clues for pathological changes within high myopic eyes after anti-VEGF injections.
DOI: 10.24403/jp.1329090
title: Bryologische Exkursion in die Orlasenke bei Pößneck anläßlich des 5. Treffens der Bryologen Sozialistischer Länder in Leipzig vom 26.-29. August 1986 am 28. August 1986 / R. Marstaller, L. Meinunger
DOI: 10.6084/m9.figshare.24781737
title: BiocharDS_V1.0.xlsx

description: A global dataset of biochar application effects on crop yield, soil properties, and greenhouse gas emissions
DOI: 10.24403/jp.1329093
title: Exkursion in das Weinbaugebiet des linksseitigen unteren Unstruttales am 7. September 1986 / A. Keding
DOI: 10.6084/m9.figshare.24781740
title: BiocharDS_V1.0.R

description: The R codes to generate the location of the sites (Fig. 2) and check the distribution of key information in the dataset.
DOI: 10.6084/m9.figshare.24781740.v1
title: BiocharDS_V1.0.R

description: The R codes to generate the location of the sites (Fig. 2) and check the distribution of key information in the dataset.
DOI: 10.6084/m9.figshare.24781764
title: BiocharDS_V1.0.csv

description: A global dataset of biochar application effects on crop yield, soil properties, and greenhouse gas emissions
DOI: 10.6084/m9.figshare.24781764.v1
title: BiocharDS_V1.0.csv

description: A global dataset of biochar application effects on crop yield, soil properties, and greenhouse gas emissions
DOI: 10.24403/jp.1329097
title: Exkursion in das Plothener Teichgebiet am 21. September 1986 / E. Gehroldt
DOI: 10.24403/jp.1329100
title: Exkursion ins Hermsdorfer Buntsandsteingebiet am 28. September 1986 / H.-J. Zündorf
DOI: 10.6084/m9.figshare.20581092.v1
title: Additional file 4 of A pan-Zea genome map for enhancing maize improvement

description: Additional file 4: Table S3. Statistics of pan-Zea gene annotations
DOI: 10.15468/dl.x92m79
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sorbus barrandienica Vít, M.Lepsí & P.Lepsí)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0103112-240626123714530/datasets/export for details.
DOI: 10.15468/dl.zg36px
title: Occurrence Download

description: A dataset containing 0 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 Lithobius lorioli Demange, 1962",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0103113-240626123714530/datasets/export for details.
DOI: 10.15468/dl.ccetsn
title: Occurrence Download

description: A dataset containing 59769 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 Mustela erminea Linnaeus, 1758",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 59769 records from 478 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0103109-240626123714530/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.26840851
title: Processed Stereo-seq of mouse iron overloaded ovary

description: This dataset is the processed Stereo-seq file. Please see our paper or Stereopy website for details.
DOI: 10.6084/m9.figshare.26840851.v1
title: Processed Stereo-seq of mouse iron overloaded ovary

description: This dataset is the processed Stereo-seq file. Please see our paper or Stereopy website for details.
DOI: 10.6084/m9.figshare.26840851.v2
title: Processed Stereo-seq of mouse iron overloaded ovary

description: This dataset is the processed Stereo-seq file. Please see our paper or Stereopy website for details.
DOI: 10.15468/dl.xrpng7
title: Occurrence Download

description: A dataset containing 728 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 Oryzaephilus surinamensis (Linnaeus, 1758)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 728 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0103114-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dgevpu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sorbus busambarensis G.Castellano, P.Marino, Raimondo & Spadaro)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0103115-240626123714530/datasets/export for details.