cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11557398.v1
title: Additional file 3: of Establishment of long-term serum-free culture for lacrimal gland stem cells aiming at lacrimal gland repair

description: Table S4. Differential expressed gene list of LGSCs cultured 7 days and 14 days. All the genes expressed differentially between day 7 LGSCs and day 14 LGSCs (XLS 44 kb)
DOI: 10.6084/m9.figshare.16800278
title: Additional file 1 of Development and validation of a radiomics-based model to predict local progression-free survival after chemo-radiotherapy in patients with esophageal squamous cell cancer

description: Additional file 1. The list of radiomics features extracted from the delineated VOIs.
DOI: 10.6084/m9.figshare.16800278.v1
title: Additional file 1 of Development and validation of a radiomics-based model to predict local progression-free survival after chemo-radiotherapy in patients with esophageal squamous cell cancer

description: Additional file 1. The list of radiomics features extracted from the delineated VOIs.
DOI: 10.6084/m9.figshare.11557419
title: MOESM1 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 1: Table S1. Raw data of the time course of biomass, sugar consumption and crude pigment content
DOI: 10.6084/m9.figshare.11557419.v1
title: MOESM1 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 1: Table S1. Raw data of the time course of biomass, sugar consumption and crude pigment content
DOI: 10.6084/m9.figshare.11557425
title: MOESM2 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 2: Table S2. Metabolome data used in this study. Lists of compounds include ion mode, Rt (min), molecular weight (Da), compounds, class, MEAN value at G2 and G8, VIP, P-value, and fold change
DOI: 10.6084/m9.figshare.11557425.v1
title: MOESM2 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 2: Table S2. Metabolome data used in this study. Lists of compounds include ion mode, Rt (min), molecular weight (Da), compounds, class, MEAN value at G2 and G8, VIP, P-value, and fold change
DOI: 10.6084/m9.figshare.16800305
title: Additional file 10 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 10: Table S10. Enrichment analysis of KEGG pathways of miRNAs and their target genes of yellowhorn.
DOI: 10.6084/m9.figshare.16800305.v1
title: Additional file 10 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 10: Table S10. Enrichment analysis of KEGG pathways of miRNAs and their target genes of yellowhorn.
DOI: 10.6084/m9.figshare.16800310
title: Additional file 1 of Evaluation of GnRH antagonist pretreatment before ovarian stimulation in a GnRH antagonist protocol in normal ovulatory women undergoing IVF/ICSI: a randomized controlled trial

description: Additional file 1: Additional Table 1. Changes in hormones at different time points.
DOI: 10.6084/m9.figshare.16800310.v1
title: Additional file 1 of Evaluation of GnRH antagonist pretreatment before ovarian stimulation in a GnRH antagonist protocol in normal ovulatory women undergoing IVF/ICSI: a randomized controlled trial

description: Additional file 1: Additional Table 1. Changes in hormones at different time points.
DOI: 10.6084/m9.figshare.16800313
title: Additional file 2 of Evaluation of GnRH antagonist pretreatment before ovarian stimulation in a GnRH antagonist protocol in normal ovulatory women undergoing IVF/ICSI: a randomized controlled trial

description: Additional file 2: Additional Table 2. Comparison of follicular development characteristics.
DOI: 10.6084/m9.figshare.16800313.v1
title: Additional file 2 of Evaluation of GnRH antagonist pretreatment before ovarian stimulation in a GnRH antagonist protocol in normal ovulatory women undergoing IVF/ICSI: a randomized controlled trial

description: Additional file 2: Additional Table 2. Comparison of follicular development characteristics.
DOI: 10.6084/m9.figshare.11557437
title: MOESM3 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 3: Table S3. Differentially expressed genes (DEGs) (P-value &lt; 0.5 and log2FC &gt; 1) in G2 and G8. Lists of DEGs include gene ID, length, log2FC, P-value, count, and annotation (XLS 694 kb)
DOI: 10.6084/m9.figshare.11557437.v1
title: MOESM3 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 3: Table S3. Differentially expressed genes (DEGs) (P-value &lt; 0.5 and log2FC &gt; 1) in G2 and G8. Lists of DEGs include gene ID, length, log2FC, P-value, count, and annotation (XLS 694 kb)
DOI: 10.6084/m9.figshare.6838850
title: Additional file 20: of Genome-wide analysis of genes encoding core components of the ubiquitin system in soybean (Glycine max) reveals a potential role for ubiquitination in host immunity against soybean cyst nematode

description: Table S6. Soybean UBS genes that are differetially expressed under stresses as revealed by RNA-seq analysis. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6838850.v1
title: Additional file 20: of Genome-wide analysis of genes encoding core components of the ubiquitin system in soybean (Glycine max) reveals a potential role for ubiquitination in host immunity against soybean cyst nematode

description: Table S6. Soybean UBS genes that are differetially expressed under stresses as revealed by RNA-seq analysis. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.11557443
title: MOESM4 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 4: Table S4. Primers used in this study
DOI: 10.6084/m9.figshare.11557443.v1
title: MOESM4 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 4: Table S4. Primers used in this study
DOI: 10.6084/m9.figshare.12081732
title: Randomization-Based Methods for Treatment Comparisons for Dichotomous Outcomes for Multiple Anatomical Regions

description: Some clinical trials in ophthalmology or dermatology randomize patients into two or more treatment groups, and observations are made for one or more anatomical regions (or sites) for each patient. In this case, patients are primary sampling units, and their responses for multiple anatomical sites are usually correlated. Useful randomization-based extensions of the Cochran–Mantel–Haenszel method are discussed here for such studies; and aspects of their application are illustrated with two examples. The first example is a randomized ophthalmology clinical trial with the number of treated eyes as strata and a dichotomous response criterion. The second example is a randomized dermatology clinical trial with three strata for the number of treated anatomical regions among the face, scalp, or chest, one covariable (as disease severity at baseline), and a dichotomous outcome. For these examples, the results are interpretable through the proportions of treated sites with favorable outcome for each treatment and their difference between treatments.
DOI: 10.6084/m9.figshare.12081732.v2
title: Randomization-Based Methods for Treatment Comparisons for Dichotomous Outcomes for Multiple Anatomical Regions

description: Some clinical trials in ophthalmology or dermatology randomize patients into two or more treatment groups, and observations are made for one or more anatomical regions (or sites) for each patient. In this case, patients are primary sampling units, and their responses for multiple anatomical sites are usually correlated. Useful randomization-based extensions of the Cochran–Mantel–Haenszel method are discussed here for such studies; and aspects of their application are illustrated with two examples. The first example is a randomized ophthalmology clinical trial with the number of treated eyes as strata and a dichotomous response criterion. The second example is a randomized dermatology clinical trial with three strata for the number of treated anatomical regions among the face, scalp, or chest, one covariable (as disease severity at baseline), and a dichotomous outcome. For these examples, the results are interpretable through the proportions of treated sites with favorable outcome for each treatment and their difference between treatments.
DOI: 10.6084/m9.figshare.25151156.v1
title: Informed consent for participation

description: This form was utilized for providing written agreement from the suggested person/people into participating in this study.
DOI: 10.6084/m9.figshare.25151156
title: Informed consent for participation

description: This form was utilized for providing written agreement from the suggested person/people into participating in this study.
DOI: 10.6084/m9.figshare.16800326
title: Additional file 3 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 3: Table S3. The known miRNAs identified in yellowhorn.
DOI: 10.6084/m9.figshare.16800326.v1
title: Additional file 3 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 3: Table S3. The known miRNAs identified in yellowhorn.
DOI: 10.6084/m9.figshare.6838856
title: Additional file 21: of Genome-wide analysis of genes encoding core components of the ubiquitin system in soybean (Glycine max) reveals a potential role for ubiquitination in host immunity against soybean cyst nematode

description: Table S7. UBS genes that are differetially expressed after SCN treatment as revealed by RNA-seq analysis. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.6838856.v1
title: Additional file 21: of Genome-wide analysis of genes encoding core components of the ubiquitin system in soybean (Glycine max) reveals a potential role for ubiquitination in host immunity against soybean cyst nematode

description: Table S7. UBS genes that are differetially expressed after SCN treatment as revealed by RNA-seq analysis. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.11557452
title: MOESM5 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 5: Table S5. CHS and C4H blast results show that the plant-derived gene may be responsible for the production of anthocyanins. Lists of the blast results include gene symbols, query names, subject names, subject species, identity, alignment length, mismatch length, gap openings, query start, query end, subject start, subject end, e-value and score
DOI: 10.6084/m9.figshare.11557452.v1
title: MOESM5 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 5: Table S5. CHS and C4H blast results show that the plant-derived gene may be responsible for the production of anthocyanins. Lists of the blast results include gene symbols, query names, subject names, subject species, identity, alignment length, mismatch length, gap openings, query start, query end, subject start, subject end, e-value and score
DOI: 10.6084/m9.figshare.16800332
title: Additional file 5 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 5: Table S5. The novel miRNAs identified in yellowhorn.
DOI: 10.6084/m9.figshare.16800332.v1
title: Additional file 5 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 5: Table S5. The novel miRNAs identified in yellowhorn.
DOI: 10.6084/m9.figshare.16800335
title: Additional file 6 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 6: Table S6. (a) Differentially expressed miRNAs between HO40 and HO54. (b) Differentially expressed miRNAs between HO54 and HO68. (c) Differentially expressed miRNAs between HO68 and HO81.
DOI: 10.6084/m9.figshare.16800335.v1
title: Additional file 6 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 6: Table S6. (a) Differentially expressed miRNAs between HO40 and HO54. (b) Differentially expressed miRNAs between HO54 and HO68. (c) Differentially expressed miRNAs between HO68 and HO81.
DOI: 10.6084/m9.figshare.16800338
title: Additional file 7 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 7: Table S7. (a) Differentially expressed miRNAs between LO40 and LO54. (b) Differentially expressed miRNAs between LO54 and LO68. (c) Differentially expressed miRNAs between LO68 and LO81.
DOI: 10.6084/m9.figshare.16800338.v1
title: Additional file 7 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 7: Table S7. (a) Differentially expressed miRNAs between LO40 and LO54. (b) Differentially expressed miRNAs between LO54 and LO68. (c) Differentially expressed miRNAs between LO68 and LO81.
DOI: 10.6084/m9.figshare.16800341
title: Additional file 8 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 8: Table S8. Targets prediction of all differentially expressed miRNAs.
DOI: 10.6084/m9.figshare.16800341.v1
title: Additional file 8 of Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

description: Additional file 8: Table S8. Targets prediction of all differentially expressed miRNAs.
DOI: 10.6084/m9.figshare.11557464
title: MOESM7 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 7. Total transcript fasta sequences obtained in this study
DOI: 10.6084/m9.figshare.11557464.v1
title: MOESM7 of Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1

description: Additional file 7. Total transcript fasta sequences obtained in this study
DOI: 10.5061/dryad.nj1bp/12
title: Supplementary Table S6
DOI: 10.5061/dryad.nj1bp/7
title: Supplementary Table S1
DOI: 10.5061/dryad.nj1bp/8
title: Supplementary Table S2
DOI: 10.5061/dryad.nj1bp/9
title: Supplementary Table S3
DOI: 10.5061/dryad.p1k03/1
title: Datafile transplant experiment

description: Datafile of the transplant experiment, transplanting 101 species into two experimental gardens on Mount Kilimanjaro, Tanzania. A legend of the variables is included in the file
DOI: 10.5061/dryad.p3215/1
title: Behavior__Analysis_Rfile

description: The R-code for the Analysis performed
DOI: 10.5061/dryad.p3215/2
title: Full_Dataset

description: Full Dataset of the movement of D. melanogaster flies. This Data contains Information about average movement in pixels per second of each fly in 5 minute intervals of each experiment. Each line contains information about a single fly. There is also information about the percentage of time the fly spends close to the walls. This is calculated by dividing the circular arena into 2 equal area circles and finding the percentage of time the fly is in the outer circle. The columns labels dist1 and dist2 refer to the average distance between the male and female and the two male flies in each arena respectively.
DOI: 10.5061/dryad.rf5jp/1
title: Supplementary Information

description: Supplementary information 1 (SEM images) and supplementary information 2 (histograms) from the manuscript Punctuated changes in the morphology of an endemic diatom from Lake Titicaca.
DOI: 10.5061/dryad.rr36r/4
title: chloroplast glutamine synthetase(ncpGS) gene, partial cds; nuclear gene for chloroplast product

description: N1-N22 are both from Sophora moorcroftiana
DOI: 10.5061/dryad.rr36r/5
title: PsbA (psbA) gene, partial cds; and psbA-trnH intergenic spacer, partial sequence; chloroplast

description: PT1-PT9,PT10-PT11,PT12-PT18 and PT19 are from Sophora davidii,Sophora alopecuroides,Sophora moorcroftiana and Sophora tomentosa,respetively.
DOI: 10.5061/dryad.rr36r/6
title: ribosomal protein L32 (rpl32) gene, partial cds; and rpl32-trnL intergenic spacer, partial sequence; chloroplast

description: RT1-RT5,RT6-RT7,RT8,RT9 are from Sophora davidii，Sophora moorcroftiana，Sophora alopecuroides and Sophora tomentosa,respectively
DOI: 10.5061/dryad.sv0q9/5
title: DataForUpload

description: All initial, raw datasets for all 14 databases
DOI: 10.5061/dryad.t9221/3
title: Associated Metadata

description: Includes CSV file with 4 worksheets containing metadata for each specimen used in this study
DOI: 10.5061/dryad.t9221/4
title: Scripts_for_processing_reads

description: Text document containing scripts used to process Illumina sequences, from raw reads to a vcf file
DOI: 10.5061/dryad.t9221/5
title: Scripts_for_SNP_filtering_and_analysis

description: Text document containing scripts used to run all analyses (including scripts to prepare files for analyses)
DOI: 10.5061/dryad.t9221/6
title: Rscripts_and_associated_files
DOI: 10.5061/dryad.t9221/7
title: README
DOI: 10.5061/dryad.tp257/1
title: Physiological and behavioural data on final-instar Pieris napi
DOI: 10.5061/dryad.vc6p9/1
title: Idaho_only_pedigrees_2008_2015

description: Pack composition data for groups analyzed in Ausband et al. JAE 2017
DOI: 10.5061/dryad.12758/1
title: Genotypes_Altja

description: STR genotypes for Salmo trutta individuals from River Altja
DOI: 10.5061/dryad.12758/2
title: Genotypes_Mustoja

description: STR genotypes for Salmo trutta individuals from River Mustoja
DOI: 10.5061/dryad.12758/3
title: MarkerTypeErrorRate

description: STR genotyping error file used in parental reconstruction analysis using the program Colony
DOI: 10.5061/dryad.12758/4
title: PhenotypeData

description: Phenotype and sampling information for Salmo trutta individuals from rivers Altja and Mustoja.
DOI: 10.5061/dryad.12758/5
title: MinerData.All.Ecorr

description: qPCR quantification cycle as inferred by the online tool 'Real-time PCR Miner' http://miner.ewindup.info/ given per plate and well, including amplification efficiencies and efficiency-corrected quantification cycle
DOI: 10.5061/dryad.12758/6
title: PKD.NegativeData

description: Phenotype data on parasite free Salmo trutta individuals from three Estonian rivers.
DOI: 10.5061/dryad.2601h/10
title: CFD simulation file for Parvancorina minchami from South Australia, relief increased by 30%, oriented at 0° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina minchami from South Australia with relief increased by 30% was oriented at 0° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/11
title: CFD simulation file for Parvancorina minchami from South Australia, relief increased by 30%, oriented at 90° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina minchami from South Australia with relief increased by 30% was oriented at 90° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/3
title: 3-D model of Parvancorina sagitta from Russia in STL format

description: A freely-available reconstruction of Parvancorina sagitta from Russia in dorsal view (https://en.wikipedia.org/wiki/Parvancorina#/media/File:Parvancorina_species.png) was imported into the open-source 3-D creation program Blender (http://www.blender.org) and used as a reference to guide box modelling of the shield-shaped base. The file was exported from Blender in STL format and converted into a non-uniform rational basis spline (NURBS) surface (IGES format) in Geomagic Studio 2012 (http://www.geomagic.com). This IGES format file was then imported into the commercial simulation software COMSOL Multiphysics (https://uk.comsol.com/), where the raised T-shaped ridge was digitally modelled with a half torus, a cylinder, and three spheres. The final model was exported from COMSOL in STL format.
DOI: 10.5061/dryad.2601h/4
title: CFD simulation file for Parvancorina minchami from South Australia, original relief, oriented at 0° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina minchami from South Australia with original relief was oriented at 0° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.