cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11301722.v1
title: Reducing uncertainty in species management - expert estimates for 60 aquatic invasive species in the Laurentian Great Lakes.

description: Demographic parameter values elicited from 24 North American experts for 60 aquatic invasive species present in the Laurentian Great Lakes. Values represent the minimum, mean, and maximum for a 95% probability of establishment for two parameters: alpha, the per propagule probability of establishment, and X0, the time it would take to reach half maximum population size. These values were subsequently incorporated in an existing mechanistic model (Drake et al., 2015), to examine the potential for secondary spread within the Great Lakes (Chenery et al., 2019).
DOI: 10.6084/m9.figshare.11301677
title: Supplementary Data Bibliometric Inmmersive Virtual Reality, Augmented Reality and Mixed Reality.pdf

description: Supplementary data for a paper named "Bibliometric analysis about the activities of robotic in Primary Education from STEM approach" presented in the XIII International Congress of Education and Innovation celebrated in University of Granada, Spain.
DOI: 10.6084/m9.figshare.11301677.v2
title: Supplementary Data Bibliometric Inmmersive Virtual Reality, Augmented Reality and Mixed Reality.pdf

description: Supplementary data for a paper named "Bibliometric analysis about the activities of robotic in Primary Education from STEM approach" presented in the XIII International Congress of Education and Innovation celebrated in University of Granada, Spain.
DOI: 10.6084/m9.figshare.11301677.v1
title: Supplementary_Data_Bibliometric_IVR_AR_MR.pdf

description: Supplementary data for a paper named "Bibliometric analysis about the activities of robotic in Primary Education from STEM approach" presented in the XIII International Congress of Education and Innovation celebrated in University of Granada, Spain.
DOI: 10.6084/m9.figshare.11301506
title: aqp1new1.sav

description: Data set for urinary aquaporin-1 - diagnostic accuracy in RCC
DOI: 10.6084/m9.figshare.11301549
title: De novo organelle genome and transcriptome assemblies of the common ornamental plant Ligustrum quihoui

description: We reconstruct the phylogenetic relationships of the family Oleaceae using PCGs of 37 complete chloroplast genomes . The protein-coding genes of 37 chloroplast genomes were extracted, aligned separately, and recombined to construct a matrix using PhyloSuite_v1.1.15. The matrix was used to perform phylogenetic analyses, and <i>Utricularia foliosa</i> was set as the outgroup. RA × ML version 8.2.4 was used to conduct ML analyses with 1000 bootstrap replicates and GTR + G + I substitution model.
DOI: 10.6084/m9.figshare.11301578
title: De novo organelle genome and transcriptome assemblies of the common ornamental plant Ligustrum quihoui

description: We performed the phylogenetic relationships of <i>L. quihoui</i> using 13 conserved PCGs (<i>cox1</i>, <i>cox2</i>, <i>cox3</i>, <i>cytB</i>, <i>nad1</i>, <i>nad2</i>, <i>nad3</i>, <i>nad4</i>, <i>nad4L</i>, <i>nad5</i>, <i>nad6</i>, <i>nad7</i> and <i>nad9</i>) shared in the mitochondrial genomes of four Oleaceae species, and <i>Utricularia reniformis</i> was set as the outgroup. We conducted ML analyses with 1,000 bootstrap replicates and GTR + G substitution model using RA × ML version 8.2.4
DOI: 10.6084/m9.figshare.11301506.v1
title: aqp1new1.sav

description: Data set for urinary aquaporin-1 - diagnostic accuracy in RCC
DOI: 10.6084/m9.figshare.11301503
title: ds01

description: The dataset are analyzed the relationship between atmospheric CO<sub>2</sub> concentrations and air temperature at 500 hPa.
DOI: 10.6084/m9.figshare.11301549.v2
title: De novo organelle genome and transcriptome assemblies of the common ornamental plant Ligustrum quihoui

description: We reconstruct the phylogenetic relationships of the family Oleaceae using PCGs of 37 complete chloroplast genomes . The protein-coding genes of 37 chloroplast genomes were extracted, aligned separately, and recombined to construct a matrix using PhyloSuite_v1.1.15. The matrix was used to perform phylogenetic analyses, and <i>Utricularia foliosa</i> was set as the outgroup. RA × ML version 8.2.4 was used to conduct ML analyses with 1000 bootstrap replicates and GTR + G + I substitution model.
DOI: 10.6084/m9.figshare.11301578.v1
title: The organelle genome and transcriptome of Ligustrum quihoui

description: We performed the phylogenetic relationships of <i>L. quihoui</i> using 13 conserved PCGs (<i>cox1</i>, <i>cox2</i>, <i>cox3</i>, <i>cytB</i>, <i>nad1</i>, <i>nad2</i>, <i>nad3</i>, <i>nad4</i>, <i>nad4L</i>, <i>nad5</i>, <i>nad6</i>, <i>nad7</i> and <i>nad9</i>) shared in the mitochondrial genomes of four Oleaceae species, and <i>Utricularia reniformis</i> was set as the outgroup. We conducted ML analyses with 1,000 bootstrap replicates and GTR + G substitution model using RA × ML version 8.2.4
DOI: 10.6084/m9.figshare.11301549.v1
title: The organelle genome and transcriptome of Ligustrum quihoui

description: We reconstruct the phylogenetic relationships of the family Oleaceae using PCGs of 37 complete chloroplast genomes . The protein-coding genes of 37 chloroplast genomes were extracted, aligned separately, and recombined to construct a matrix using PhyloSuite_v1.1.15. The matrix was used to perform phylogenetic analyses, and <i>Utricularia foliosa</i> was set as the outgroup. RA × ML version 8.2.4 was used to conduct ML analyses with 1000 bootstrap replicates and GTR + G + I substitution model.
DOI: 10.6084/m9.figshare.11301578.v2
title: De novo organelle genome and transcriptome assemblies of the common ornamental plant Ligustrum quihoui

description: We performed the phylogenetic relationships of <i>L. quihoui</i> using 13 conserved PCGs (<i>cox1</i>, <i>cox2</i>, <i>cox3</i>, <i>cytB</i>, <i>nad1</i>, <i>nad2</i>, <i>nad3</i>, <i>nad4</i>, <i>nad4L</i>, <i>nad5</i>, <i>nad6</i>, <i>nad7</i> and <i>nad9</i>) shared in the mitochondrial genomes of four Oleaceae species, and <i>Utricularia reniformis</i> was set as the outgroup. We conducted ML analyses with 1,000 bootstrap replicates and GTR + G substitution model using RA × ML version 8.2.4
DOI: 10.6084/m9.figshare.12865895
title: Supplementary Material for: Lysophosphatidic Acid Regulates the Differentiation of Th2 Cells and Its Antagonist Suppresses Allergic Airway Inflammation

description: <b><i>Background:</i></b> Lysophosphatidic acid (LPA), a prototypic member of a large family of lysophospholipids, has been recently shown to play a role in immune responses to respiratory diseases. The involvement of LPA in allergic airway inflammation has been reported, but the mechanism remains unclear. <b><i>Object:</i></b> We analyzed the biological activity of LPA in vitro and in vivo and investigated its role in allergic inflammation in mice using an LPA receptor 2 (LPA2) antagonist. <b><i>Methods:</i></b> We used a murine model with acute allergic inflammation, in which mice are sensitized and challenged with house dust mite, and analyzed airway hyperresponsiveness (AHR), pathological findings, Th2 cytokines, and IL-33 in bronchoalveolar lavage fluid (BALF) and lung homogenates. The effect of LPA on Th2 differentiation and cytokine production was examined in vitro using naive CD4<sup>+</sup> T cells isolated from splenocytes. We also investigated in vivo the effects of LPA on intranasal administration in mice. <b><i>Results:</i></b> The LPA2 antagonist suppressed the increase of AHR, the number of total cells, and eosinophils in BALF and lung tissue. It also decreased the production of IL-13 in BALF and IL-33 and CCL2 in the lung. LPA promoted Th2 cell differentiation and IL-13 production by Th2 cells in vitro. Nasal administration of LPA significantly increased the number of total cells and IL-13 in BALF via regulating the production of IL-33 and CCL-2-derived infiltrating macrophages. <b><i>Conclusion:</i></b> These findings suggest that LPA plays an important role in allergic airway inflammation and that the blockade of LPA2 might have therapeutic potential for bronchial asthma.
DOI: 10.6084/m9.figshare.11301245
title: Ecology Project Datasheet.xlsx

description: Dataset for the project titled "The Ability of Lemna minor and Azolla caroliniana to Regulate Water Quality"
DOI: 10.6084/m9.figshare.11301098
title: Tricholoma_matsutake_assembly.fna.gz

description: Genomic data of <i>Tricholoma matsutake</i>. - Genome assembly (FASTA) - Masked genome assembly (FASTA) - Gene features (GFF3) - Transcript sequences (FASTA) - Protein sequences (FASTA) - Pfam annotation (TSV) - CAZymes (TSV) - Psort (TSV) - RepeatModeler consensi.fa.classified - RepeatMasker .out - RepeatMasker .tbl
DOI: 10.6084/m9.figshare.11300978
title: Lower ilium length in anthropoids

description: This dataset reports lower ilium length measurements shown in Figure 2 of "Insights into the lower torso in late Miocene hominoid Oreopithecus bambolii."<br>The comparative anthropoid data in this dataset originally appeared in Hammond and Almecija (2017, Anatomical Record, https://doi.org/10.1002/ar.23545). Authors request that use of this dataset also includes citation to the original work. Values in dataset represent anthropoid lower ilium height from the center of the acetabular fossa to the point where the linea arcuata meets the auricular surface. Acetabulum diameter is the superoinferior dimension. Detailed methodology is described in Hammond and Almecija (2017).
DOI: 10.6084/m9.figshare.11300711
title: Matlab solver to solve the G-DIM Partial Differential Equation from A geometric diffuse-interface method for droplet spreading

description: This paper exploits the theory of geometric gradient flows to introduce an alternative regularization of the thin-film equation valid in the case of large-scale droplet spreading—the geometric diffuse-interface method. The method possesses some advantages when compared with the existing models of droplet spreading, namely the slip model, the precursor-film method and the diffuse-interface model. These advantages are discussed and a case is made for using the geometric diffuse-interface method for the purpose of numerical simulations. The mathematical solutions of the geometric diffuse interface method are explored via such numerical simulations for the simple and well-studied case of large-scale droplet spreading for a perfectly wetting fluid—we demonstrate that the new method reproduces Tanner's Law of droplet spreading via a simple and robust computational method, at a low computational cost. We discuss potential avenues for extending the method beyond the simple case of perfectly wetting fluids.
DOI: 10.6084/m9.figshare.11300711.v1
title: Matlab solver to solve the G-DIM Partial Differential Equation from A geometric diffuse-interface method for droplet spreading

description: This paper exploits the theory of geometric gradient flows to introduce an alternative regularization of the thin-film equation valid in the case of large-scale droplet spreading—the geometric diffuse-interface method. The method possesses some advantages when compared with the existing models of droplet spreading, namely the slip model, the precursor-film method and the diffuse-interface model. These advantages are discussed and a case is made for using the geometric diffuse-interface method for the purpose of numerical simulations. The mathematical solutions of the geometric diffuse interface method are explored via such numerical simulations for the simple and well-studied case of large-scale droplet spreading for a perfectly wetting fluid—we demonstrate that the new method reproduces Tanner's Law of droplet spreading via a simple and robust computational method, at a low computational cost. We discuss potential avenues for extending the method beyond the simple case of perfectly wetting fluids.
DOI: 10.6084/m9.figshare.11300687
title: Stage-III geotaxis data from Ocean acidification changes the vertical movement of stone crab larvae

description: Contains the directional responses of stage-III larvae during geotaxis trails.
DOI: 10.6084/m9.figshare.11300678
title: Water chemistry data from Ocean acidification changes the vertical movement of stone crab larvae

description: Contains the environmental conditions, carbonate chemistry, and sampling dates for the experimental treatments during these experiments.
DOI: 10.6084/m9.figshare.11300681
title: Stage-III swimming data all from Ocean acidification changes the vertical movement of stone crab larvae

description: Contains the directional movement and swimming speeds for all stage-III larvae (individual larval responses) during geotaxis trails.
DOI: 10.6084/m9.figshare.11300687.v1
title: Stage-III geotaxis data from Ocean acidification changes the vertical movement of stone crab larvae

description: Contains the directional responses of stage-III larvae during geotaxis trails.
DOI: 10.6084/m9.figshare.11300675
title: Stage-V geotaxis data from Ocean acidification changes the vertical movement of stone crab larvae

description: Contains the directional responses of stage-V larvae during geotaxis trails.
DOI: 10.6084/m9.figshare.11300678.v1
title: Water chemistry data from Ocean acidification changes the vertical movement of stone crab larvae

description: Contains the environmental conditions, carbonate chemistry, and sampling dates for the experimental treatments during these experiments.
DOI: 10.6084/m9.figshare.11300681.v1
title: Stage-III swimming data all from Ocean acidification changes the vertical movement of stone crab larvae

description: Contains the directional movement and swimming speeds for all stage-III larvae (individual larval responses) during geotaxis trails.
DOI: 10.6084/m9.figshare.11300672
title: Stage-V swimming data all from Ocean acidification changes the vertical movement of stone crab larvae

description: Contains the directional movement and swimming speeds for all stage-V larvae during geotaxis trails (individual larval responses) during geotaxis trials.
DOI: 10.6084/m9.figshare.11300672.v1
title: Stage-V swimming data all from Ocean acidification changes the vertical movement of stone crab larvae

description: Contains the directional movement and swimming speeds for all stage-V larvae during geotaxis trails (individual larval responses) during geotaxis trials.
DOI: 10.6084/m9.figshare.11300675.v1
title: Stage-V geotaxis data from Ocean acidification changes the vertical movement of stone crab larvae

description: Contains the directional responses of stage-V larvae during geotaxis trails.
DOI: 10.6084/m9.figshare.11300534
title: Tree species traits affect the Janzen-Connell effect.rar

description: R code files and associated data for analysis supporting the manuscript, "<b>Tree species traits affect which natural enemies drive the Janzen-Connell effect in a temperate forest</b>".
DOI: 10.6084/m9.figshare.11300426
title: Spacer sequence for targeting gyrA gene in Bacillus subtilis strain 168 using CRISPR-Cas9

description: Guide RNA provides unique targeting capability to CRISPR-Cas9 genome editing system through complementary base pairing with the DNA strand at specific locus. Thus, design of the guide RNA sequence plays an important role in achieving precise editing at any location in the genome. But, what defines the guide RNA sequence? The chief component of guide RNA is the spacer sequence that lies immediately adjacent to the protospacer adjacent motif (PAM) sequence in DNA. Design of guide RNA would thus comprise the appending of the spacer sequence to a RNA sequence that forms stem-loop structures complementary to structural motifs in Cas9. Using an in-house MATLAB algorithm, a database comprising all the spacer sequence capable of targeting gyrA gene in <i>Bacillus subtilis</i> strain 168 was created. Collectively, the database of spacer sequences in <i>gyrA </i>gene of <i>B. subtilis</i> 168 should find use in genetic engineering or metabolic engineering studies aiming to modulate <i>gyrA </i>expression through targeted knockdown, knockout or CRISPR mediated gene activation.<br><br>
DOI: 10.6084/m9.figshare.11300426.v1
title: Spacer sequence for targeting gyrA gene in Bacillus subtilis strain 168 using CRISPR-Cas9

description: Guide RNA provides unique targeting capability to CRISPR-Cas9 genome editing system through complementary base pairing with the DNA strand at specific locus. Thus, design of the guide RNA sequence plays an important role in achieving precise editing at any location in the genome. But, what defines the guide RNA sequence? The chief component of guide RNA is the spacer sequence that lies immediately adjacent to the protospacer adjacent motif (PAM) sequence in DNA. Design of guide RNA would thus comprise the appending of the spacer sequence to a RNA sequence that forms stem-loop structures complementary to structural motifs in Cas9. Using an in-house MATLAB algorithm, a database comprising all the spacer sequence capable of targeting gyrA gene in <i>Bacillus subtilis</i> strain 168 was created. Collectively, the database of spacer sequences in <i>gyrA </i>gene of <i>B. subtilis</i> 168 should find use in genetic engineering or metabolic engineering studies aiming to modulate <i>gyrA </i>expression through targeted knockdown, knockout or CRISPR mediated gene activation.<br><br>
DOI: 10.6084/m9.figshare.11300360
title: MOESM6 of Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

description: Additional file 6. Demultiplexing information for the two sample sets.
DOI: 10.6084/m9.figshare.11300360.v1
title: MOESM6 of Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

description: Additional file 6. Demultiplexing information for the two sample sets.
DOI: 10.6084/m9.figshare.11300345
title: MOESM4 of Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

description: Additional file 4. Analyses of paralogs/contaminations.
DOI: 10.6084/m9.figshare.11300348
title: MOESM5 of Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

description: Additional file 5. Details on specimens with &gt;3% divergence from Illumina barcodes for final consolidated barcode sets.
DOI: 10.6084/m9.figshare.11300345.v1
title: MOESM4 of Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

description: Additional file 4. Analyses of paralogs/contaminations.
DOI: 10.6084/m9.figshare.11300348.v1
title: MOESM5 of Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

description: Additional file 5. Details on specimens with &gt;3% divergence from Illumina barcodes for final consolidated barcode sets.
DOI: 10.6084/m9.figshare.11300336
title: MOESM2 of Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

description: Additional file 2. Tag sequences used in this study.
DOI: 10.6084/m9.figshare.11300339
title: MOESM3 of Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

description: Additional file 3. Details on incongruent clusters.
DOI: 10.6084/m9.figshare.11300339.v1
title: MOESM3 of Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

description: Additional file 3. Details on incongruent clusters.
DOI: 10.6084/m9.figshare.11300336.v1
title: MOESM2 of Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

description: Additional file 2. Tag sequences used in this study.
DOI: 10.6084/m9.figshare.11300312
title: MOESM9 of Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR

description: Additional file 9: Table S2. Translational efficiencies in control and treated animals for all tested genes.
DOI: 10.6084/m9.figshare.11300312.v1
title: MOESM9 of Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR

description: Additional file 9: Table S2. Translational efficiencies in control and treated animals for all tested genes.
DOI: 10.6084/m9.figshare.11300309
title: MOESM8 of Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR

description: Additional file 8: Table S1. Mapping statistics of ribosome protected fragment and total RNA libraries.
DOI: 10.6084/m9.figshare.11300309.v1
title: MOESM8 of Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR

description: Additional file 8: Table S1. Mapping statistics of ribosome protected fragment and total RNA libraries.
DOI: 10.6084/m9.figshare.11300264
title: MOESM11 of Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR

description: Additional file 11: Table S4. Primers used for RT-qPCR validation.
DOI: 10.6084/m9.figshare.11300255
title: MOESM10 of Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR

description: Additional file 10: Table S3. Translational control of O. dioica mRNAs associated with genes that are orthologous to human genes encoding TOP mRNAs.
DOI: 10.6084/m9.figshare.11300264.v1
title: MOESM11 of Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR

description: Additional file 11: Table S4. Primers used for RT-qPCR validation.
DOI: 10.6084/m9.figshare.11300255.v1
title: MOESM10 of Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR

description: Additional file 10: Table S3. Translational control of O. dioica mRNAs associated with genes that are orthologous to human genes encoding TOP mRNAs.
DOI: 10.6084/m9.figshare.11300144
title: MOESM4 of Characterizing the interplay between gene nucleotide composition bias and splicing

description: Additional file 4 Table S3. Annotation of isochores, LADs, and TADs.
DOI: 10.6084/m9.figshare.11300144.v1
title: MOESM4 of Characterizing the interplay between gene nucleotide composition bias and splicing

description: Additional file 4 Table S3. Annotation of isochores, LADs, and TADs.
DOI: 10.6084/m9.figshare.11300126
title: MOESM2 of Characterizing the interplay between gene nucleotide composition bias and splicing

description: Additional file 2: Table S2. List of exons activated by each analyzed splicing factors and lists of the GC-exons and AT-exons.
DOI: 10.6084/m9.figshare.11300120
title: MOESM1 of Characterizing the interplay between gene nucleotide composition bias and splicing

description: Additional file 1: Table S1. GEO number of publicly available large-scale datasets analyzed in this work and siRNA-, AON-, and primer-sequences.
DOI: 10.6084/m9.figshare.11300126.v1
title: MOESM2 of Characterizing the interplay between gene nucleotide composition bias and splicing

description: Additional file 2: Table S2. List of exons activated by each analyzed splicing factors and lists of the GC-exons and AT-exons.
DOI: 10.6084/m9.figshare.11300120.v1
title: MOESM1 of Characterizing the interplay between gene nucleotide composition bias and splicing

description: Additional file 1: Table S1. GEO number of publicly available large-scale datasets analyzed in this work and siRNA-, AON-, and primer-sequences.
DOI: 10.6084/m9.figshare.11300060
title: MOESM3 of Modern contraceptive methods knowledge and practice among blind and deaf women in Ethiopia. A cross-sectional survey

description: Additional file 3. Dataset.
DOI: 10.6084/m9.figshare.11300060.v1
title: MOESM3 of Modern contraceptive methods knowledge and practice among blind and deaf women in Ethiopia. A cross-sectional survey

description: Additional file 3. Dataset.
DOI: 10.6084/m9.figshare.11300048
title: MOESM1 of Spatial quantile regression with application to high and low child birth weight in Malawi

description: Additional file 1. Child birth weight data.
DOI: 10.6084/m9.figshare.11300048.v1
title: MOESM1 of Spatial quantile regression with application to high and low child birth weight in Malawi

description: Additional file 1. Child birth weight data.
DOI: 10.6084/m9.figshare.11300015
title: MOESM6 of Transcriptome profiling of posterior kidney of brown trout, Salmo trutta, during proliferative kidney disease

description: Additional file 6: Table S4. List of all pathways mapped in KEGG pathway analysis.