cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6789902
title: Table3

description: Reaction patterns obtained by the balance rule using the stand-alone library reaCTS.<br>
DOI: 10.6084/m9.figshare.6789902.v1
title: Table3

description: Reaction patterns obtained by the balance rule using the stand-alone library reaCTS.<br>
DOI: 10.6084/m9.figshare.6789905.v1
title: Table4

description: Reaction patterns obtained by the count rule using the stand-alone library reaCTS.
DOI: 10.6084/m9.figshare.6789899
title: Table2

description: The file contain reactant pairs predicted by our method, for which an statistic test was not performed.<br>
DOI: 10.6084/m9.figshare.6789899.v1
title: Table2

description: The file contain reactant pairs predicted by our method, for which an statistic test was not performed.<br>
DOI: 10.6084/m9.figshare.6789839
title: data.xlsx

description: Bed load; movement characteristic; image processing;
DOI: 10.6084/m9.figshare.6789839.v1
title: data.xlsx

description: Bed load; movement characteristic; image processing;
DOI: 10.6084/m9.figshare.6789668.v1
title: Analisis de la Situacion de Salud del CMF #51, Sancti Spiritus, Cuba.pages

description: Análisis de la situación de Salud de un Consultorio Medico de la Familia en la provincia de Sancti Spiritus, Cuba. Se detectan principales problemas y se establecen objetivos y un plan de acción para erradicar estos problemas en la comunidad analizada.
DOI: 10.6084/m9.figshare.6789623
title: Additional file 1: of Thermoelectric Properties of Hot-Pressed Bi-Doped n-Type Polycrystalline SnSe

description: Excel source data. (XLSX 196Â kb)
DOI: 10.6084/m9.figshare.6789623.v1
title: Additional file 1: of Thermoelectric Properties of Hot-Pressed Bi-Doped n-Type Polycrystalline SnSe

description: Excel source data. (XLSX 196Â kb)
DOI: 10.6084/m9.figshare.6789578
title: MOESM8 of Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

description: Additional file 8. Haplotypes of the Russian Yakutian animals checked by qPCR. This file shows 42-SNP haplotypes of the 10 Russian Yakutian animals that were checked by qPCR. As in Additional file 1, SNPs that were excluded from the mapping procedure (MAFâ
DOI: 10.6084/m9.figshare.6789578.v1
title: MOESM8 of Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

description: Additional file 8. Haplotypes of the Russian Yakutian animals checked by qPCR. This file shows 42-SNP haplotypes of the 10 Russian Yakutian animals that were checked by qPCR. As in Additional file 1, SNPs that were excluded from the mapping procedure (MAFâ
DOI: 10.6084/m9.figshare.6789551
title: Additional file 1: of Using data-driven sublanguage pattern mining to induce knowledge models: application in medical image reports knowledge representation

description: Annotation manua. Annotation manual includes definitions of 14 semantic categories. It was used for evaluation of knowledge model. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.6789551.v1
title: Additional file 1: of Using data-driven sublanguage pattern mining to induce knowledge models: application in medical image reports knowledge representation

description: Annotation manua. Annotation manual includes definitions of 14 semantic categories. It was used for evaluation of knowledge model. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.6789515
title: Additional file 1: of Comparison of intraoperative handling and wound healing between (NEOSORBÂŽ plus) and coated polyglactin 910 suture (NEOSORBÂŽ): a prospective, single-blind, randomized controlled trial

description: Raw data of study; Raw data of Comparison Between NEOSORB Plus and NEOSORB. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.6789515.v1
title: Additional file 1: of Comparison of intraoperative handling and wound healing between (NEOSORBÂŽ plus) and coated polyglactin 910 suture (NEOSORBÂŽ): a prospective, single-blind, randomized controlled trial

description: Raw data of study; Raw data of Comparison Between NEOSORB Plus and NEOSORB. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.6789464
title: Additional file 4: of Three new species of the fairy shrimp Eubranchipus Verill, 1870 (Branchiopoda: Anostraca) from northern Japan and far Eastern Russia

description: Table S4. Pair-wise nucleotide difference per site in % for 16S rRNA data. (XLS 35 kb)
DOI: 10.6084/m9.figshare.6789464.v1
title: Additional file 4: of Three new species of the fairy shrimp Eubranchipus Verill, 1870 (Branchiopoda: Anostraca) from northern Japan and far Eastern Russia

description: Table S4. Pair-wise nucleotide difference per site in % for 16S rRNA data. (XLS 35 kb)
DOI: 10.6084/m9.figshare.6789461
title: MOESM1 of Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

description: Additional file 1. Inner candidate haplotypes detected by manual analysis of the extended confidence interval. This file shows the 60-SNP haplotypes of the extended candidate interval for all 110 animals that were used for remapping of the belt locus. SNPs that were excluded from the mapping procedure (MAF
DOI: 10.6084/m9.figshare.6789461.v1
title: MOESM1 of Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation

description: Additional file 1. Inner candidate haplotypes detected by manual analysis of the extended confidence interval. This file shows the 60-SNP haplotypes of the extended candidate interval for all 110 animals that were used for remapping of the belt locus. SNPs that were excluded from the mapping procedure (MAF
DOI: 10.6084/m9.figshare.6789455
title: Additional file 3: of Three new species of the fairy shrimp Eubranchipus Verill, 1870 (Branchiopoda: Anostraca) from northern Japan and far Eastern Russia

description: Table S3. 16S rRNA nucleotide sequence data used in the study. (XLS 31 kb)
DOI: 10.6084/m9.figshare.6789455.v1
title: Additional file 3: of Three new species of the fairy shrimp Eubranchipus Verill, 1870 (Branchiopoda: Anostraca) from northern Japan and far Eastern Russia

description: Table S3. 16S rRNA nucleotide sequence data used in the study. (XLS 31 kb)
DOI: 10.6084/m9.figshare.6789434
title: Additional file 2: of Three new species of the fairy shrimp Eubranchipus Verill, 1870 (Branchiopoda: Anostraca) from northern Japan and far Eastern Russia

description: Table S2. Pair-wise nucleotide difference per site in % for COI data. (XLS 36 kb)
DOI: 10.6084/m9.figshare.6789434.v1
title: Additional file 2: of Three new species of the fairy shrimp Eubranchipus Verill, 1870 (Branchiopoda: Anostraca) from northern Japan and far Eastern Russia

description: Table S2. Pair-wise nucleotide difference per site in % for COI data. (XLS 36 kb)
DOI: 10.6084/m9.figshare.6789422
title: Additional file 1: of Three new species of the fairy shrimp Eubranchipus Verill, 1870 (Branchiopoda: Anostraca) from northern Japan and far Eastern Russia

description: Table S1. COI nucleotide sequence data used in the study. (XLS 33 kb)
DOI: 10.6084/m9.figshare.6789422.v1
title: Additional file 1: of Three new species of the fairy shrimp Eubranchipus Verill, 1870 (Branchiopoda: Anostraca) from northern Japan and far Eastern Russia

description: Table S1. COI nucleotide sequence data used in the study. (XLS 33 kb)
DOI: 10.6084/m9.figshare.6783569
title: Scripts for Analysis

description: Scripts used for analysis of V1 and V2 Datasets.<br>seurat_v1.R - initialize seurat object from 10X Genomics cellranger outputs. Includes filtering, normalization, regression, variable gene identification, PCA analysis, clustering, tSNE visualization. Used for v1 datasets. <br>merge_seurat.R - merge two or more seurat objects into one seurat object. Perform linear regression to remove batch effects from separate objects. Used for v1 datasets. <br>subcluster_seurat_v1.R - subcluster clusters of interest from Seurat object. Determine variable genes, perform regression and PCA. Used for v1 datasets.<br>seurat_v2.R - initialize seurat object from 10X Genomics cellranger outputs. Includes filtering, normalization, regression, variable gene identification, and PCA analysis. Used for v2 datasets. <br>clustering_markers_v2.R - clustering and tSNE visualization for v2 datasets. <br>subcluster_seurat_v2.R - subcluster clusters of interest from Seurat object. Determine variable genes, perform regression and PCA analysis. Used for v2 datasets.<br>seurat_object_analysis_v1_and_v2.R - downstream analysis and plotting functions for seurat object created by seurat_v1.R or seurat_v2.R. <br>merge_clusters.R - merge clusters that do not meet gene threshold. Used for both v1 and v2 datasets. <br>prepare_for_monocle_v1.R - subcluster cells of interest and perform linear regression, but not scaling in order to input normalized, regressed values into monocle with monocle_seurat_input_v1.R <br>monocle_seurat_input_v1.R - monocle script using seurat batch corrected values as input for v1 merged timecourse datasets. <br>monocle_lineage_trace.R - monocle script using nUMI as input for v2 lineage traced dataset. <br>monocle_object_analysis.R - downstream analysis for monocle object - BEAM and plotting. <br>CCA_merging_v2.R - script for merging v2 endocrine datasets with canonical correlation analysis and determining the number of CCs to include in downstream analysis. <br>CCA_alignment_v2.R - script for downstream alignment, clustering, tSNE visualization, and differential gene expression analysis.
DOI: 10.6084/m9.figshare.6783563
title: Stirring the Pot: Comparing Stick Input Patterns and Flight-Path Control Strategies in Airline Pilots

description: <b>Objective</b>: This study evaluated airline pilots’ inceptor input patterns and flight-path control strategies during a manual instrument approach as a function of recent flight practice. <b>Background</b>: Manual flying skills erode due to an extensive use of automation and rare opportunity to practice these skills. <b>Method</b>: One hundred and twenty-six randomly selected pilots of a European airline took part in this experiment, performing a simulated manual raw data precision approach. All of the pilots were allocated to 1 of 4 groups according to their fleet and rank: first officers and captains on short haul, as well as first officers and captains on long haul. A new method to analyze flight-path control strategies by differentiating between constant and variable flight-path errors was proposed. Time-domain measures were taken into account to evaluate sidestick inputs. <b>Results</b>: We distinguished between 2 different flight-path control strategies; both differed in the deviations achieved. In addition, the pilots who predominantly used 1-dimensional sidestick inputs also had smaller deviations from the ideal flight-path. <b>Conclusion</b>: Pilots showed a relationship between manual fine-motor flying skills and recent flight practice, especially in long-haul fleets.
DOI: 10.6084/m9.figshare.6783563.v1
title: Stirring the Pot: Comparing Stick Input Patterns and Flight-Path Control Strategies in Airline Pilots

description: <b>Objective</b>: This study evaluated airline pilots’ inceptor input patterns and flight-path control strategies during a manual instrument approach as a function of recent flight practice. <b>Background</b>: Manual flying skills erode due to an extensive use of automation and rare opportunity to practice these skills. <b>Method</b>: One hundred and twenty-six randomly selected pilots of a European airline took part in this experiment, performing a simulated manual raw data precision approach. All of the pilots were allocated to 1 of 4 groups according to their fleet and rank: first officers and captains on short haul, as well as first officers and captains on long haul. A new method to analyze flight-path control strategies by differentiating between constant and variable flight-path errors was proposed. Time-domain measures were taken into account to evaluate sidestick inputs. <b>Results</b>: We distinguished between 2 different flight-path control strategies; both differed in the deviations achieved. In addition, the pilots who predominantly used 1-dimensional sidestick inputs also had smaller deviations from the ideal flight-path. <b>Conclusion</b>: Pilots showed a relationship between manual fine-motor flying skills and recent flight practice, especially in long-haul fleets.
DOI: 10.6084/m9.figshare.6783554
title: Monocle Objects - V2 Dataset

description: E14_fev_lineage_monocle_ob - Resulting monocle objected generated from E14_fev_lineage_endocrine_seur_ob. Used monocle_lineage_trace.R script. Grouped by "res.1.4" in phenoData. Corresponds to Fig. 7a.
DOI: 10.6084/m9.figshare.6783515
title: V2 Datasets Seurat Objects

description: E12_v2_exocrine_seur_ob - E12.5 V2 Dataset. Only exocrine cells. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5d <br><br>E14_v2_exocrine_seur_ob - E14.5 V2 Dataset. Only exocrine cells. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5d <br><br>E17_v2_agg_exocrine_seur_ob - E17.5 aggregated V2 Dataset. Only exocrine cells. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5d <br><br>E12_v2_endocrine_seur_ob - E12.5 V2 Dataset. Only endocrine cells. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5e <br><br>E14_v2_endocrine_seur_ob - E14.5 V2 Dataset. Only endocrine cells. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5e <br><br>E17_v2_agg_endocrine_seur_ob - E17.5 aggregated V2 Dataset. Only endocrine cells. Grouped by "merged" in @meta.data slot. Corresponds to Supplementary Fig. 5e <br><br>merged_v2_endocrine_seur_ob. - E12.5, E14.5, E17.5 (aggregated) V2 Dataset. Only endocrine cells. Grouped by "merged" in @meta.data slot. Corresponds to Fig. 5h. Generated by CCA_aligment_v2.R and CCA_merging_v2.R scripts. <br><br>E14_fev_lineage_endocrine_seur_ob. - E14.5 Fev-Cre;mTmG lineage traced V2 Dataset. Only endocrine cells. Grouped by "res.1.4" in @meta.data slot. Corresponds to Fig. 6h. "GFP" and "GFP_Bi" in @meta.data refer to GFP counts and binary "yes" or "no" for cells with &gt;0 GFP counts.<br>
DOI: 10.6084/m9.figshare.6783554.v1
title: Monocle Objects - V2 Dataset

description: E14_fev_lineage_monocle_ob - Resulting monocle objected generated from E14_fev_lineage_endocrine_seur_ob. Used monocle_lineage_trace.R script. Grouped by "res.1.4" in phenoData. Corresponds to Fig. 7a.
DOI: 10.6084/m9.figshare.6783506
title: V1 Datasets Seurat Objects

description: R objects for the V1 Datasets. Created with R package Seurat.<br>E14_allcells_seur_ob.Rdata - E14.5 V1 Dataset. Includes all cells. Grouped by "ordered_manuscript" in @data.info slot. Corresponds to Fig. 1c. <br><br>E14_mesenchyme_seur_ob.Rdata - E14.5 V1 Dataset. Only mesenchymal cells. Grouped by "ordered_manuscript" in @data.info slot. Corresponds to Fig. 2a. <br><br>merged_mesenchyme_seur_ob.Rdata - E12.5, E14.5, E17.5 merged V1 Dataset. Only mesenchymal cells. Grouped by "ordered_manuscript" in @data.info slot. Corresponds to Fig. 3a. <br><br>E14_epithelial_seur_ob.Rdata - E14.5 V1 Dataset. Only epithelial cells. Grouped by "ordered" in @data.info slot. Corresponds to Fig. 4a. <br><br>E14_endocrine_seur_ob.Rdata - E14.5 V1 Dataset. Only endocrine cells. Grouped by "ordered_res1_5" in @data.info slot. Corresponds to Fig. 4f. <br><br>merged_epithelial_seur_ob.Rdata - E12.5, E14.5, E17.5 merged V1 Dataset. Only epithelial cells. Grouped by "ordered" in @data.info slot. Corresponds to Supplementary Fig.5a
DOI: 10.6084/m9.figshare.6783479
title: Compromised phagosome maturation underlies RPE pathology in cell culture and whole animal models of Smith-Lemli-Opitz Syndrome

description: Treatment of rats with the cholesterol pathway inhibitor AY9944 produces an animal model of Smith-Lemli-Opitz syndrome (SLOS), an autosomal recessive disease caused by defective cholesterol synthesis. This SLOS rat model undergoes progressive and irreversible degeneration of the neural retina, with associated pathological features of the retinal pigmented epithelium (RPE). Here, we provide further insights into the mechanism involved in the RPE pathology. In the SLOS rat model, markedly increased RPE apical autofluorescence is observed, compared to untreated animals, which correlates with increased levels of A2E and other bisretinoids. Utilizing cultured human induced pluripotent stem cell (iPSC)- derived SLOS RPE cells, we found significantly elevated steady-state levels of 7-dehydrocholesterol (7DHC) and decreased cholesterol levels (key biochemical hallmarks of SLOS). Western blot analysis revealed altered levels of the macroautophagy/autophagy markers MAP1LC3B-II and SQSTM1/p62, and build-up of ubiquitinated proteins. Accumulation of immature autophagosomes was accompanied by inefficient degradation of phagocytized, exogenously supplied retinal rod outer segments (as evidenced by persistence of the C-terminal 1D4 epitope of RHO [rhodopsin]) in SLOS RPE compared to iPSC-derived normal human control. SLOS RPE cells exhibited lysosomal pH levels and CTSD activity within normal physiological limits, thus discounting the involvement of perturbed lysosomal function. Furthermore, 1D4-positive phagosomes that accumulated in the RPE in both pharmacological and genetic rodent models of SLOS failed to fuse with lysosomes. Taken together, these observations suggest that defective phagosome maturation underlies the observed RPE pathology. The potential relevance of these findings to SLOS and the requirement of cholesterol for phagosome maturation are discussed.
DOI: 10.6084/m9.figshare.6783485
title: Monocle Objects V1 Datasets - Epithelial

description: Includes V1 seurat objects used for input (regression with no scaling) and resulting monocle object.<br><br>E14_endocrine_mon_input_seur_ob - E14.5 endocrine V1 Dataset. Prepared for monocle, input into monocle_v1_seurat_input.R <br><br>E14_endocrine_monocle_ob - Resulting monocle object generated from E14_endocrine_mon_input_seur_ob. Grouped by "ordered_res1_5" in phenoData. Corresponds to Fig. 4g. <br><br>merge_fev_endocrine_seur_ob - E12.5, E14.5, E17.5 V1 Dataset. Subclustered epithelial dataset for Fev+/Pax4+, FevHi/Chgb+, Alpha, Beta, Epsilon, and Delta populations. Prepared for monocle, input into monocle_v1_seurat_input.R <br><br>merge_fev_endocrine_monocle_ob - Resulting monocle object generated from merge_fev_endocrine_seur_ob. Grouped by "merged_clus" in phenoData. Corresponds to Supplementary Fig. 8a.<br>
DOI: 10.6084/m9.figshare.6783485.v2
title: Monocle Objects V1 Datasets - Epithelial

description: Includes V1 seurat objects used for input (regression with no scaling) and resulting monocle object.<br><br>E14_endocrine_mon_input_seur_ob - E14.5 endocrine V1 Dataset. Prepared for monocle, input into monocle_v1_seurat_input.R <br><br>E14_endocrine_monocle_ob - Resulting monocle object generated from E14_endocrine_mon_input_seur_ob. Grouped by "ordered_res1_5" in phenoData. Corresponds to Fig. 4g. <br><br>merge_fev_endocrine_seur_ob - E12.5, E14.5, E17.5 V1 Dataset. Subclustered epithelial dataset for Fev+/Pax4+, FevHi/Chgb+, Alpha, Beta, Epsilon, and Delta populations. Prepared for monocle, input into monocle_v1_seurat_input.R <br><br>merge_fev_endocrine_monocle_ob - Resulting monocle object generated from merge_fev_endocrine_seur_ob. Grouped by "merged_clus" in phenoData. Corresponds to Supplementary Fig. 8a.<br>
DOI: 10.6084/m9.figshare.6783479.v2
title: Compromised phagosome maturation underlies RPE pathology in cell culture and whole animal models of Smith-Lemli-Opitz Syndrome

description: Treatment of rats with the cholesterol pathway inhibitor AY9944 produces an animal model of Smith-Lemli-Opitz syndrome (SLOS), an autosomal recessive disease caused by defective cholesterol synthesis. This SLOS rat model undergoes progressive and irreversible degeneration of the neural retina, with associated pathological features of the retinal pigmented epithelium (RPE). Here, we provide further insights into the mechanism involved in the RPE pathology. In the SLOS rat model, markedly increased RPE apical autofluorescence is observed, compared to untreated animals, which correlates with increased levels of A2E and other bisretinoids. Utilizing cultured human induced pluripotent stem cell (iPSC)- derived SLOS RPE cells, we found significantly elevated steady-state levels of 7-dehydrocholesterol (7DHC) and decreased cholesterol levels (key biochemical hallmarks of SLOS). Western blot analysis revealed altered levels of the macroautophagy/autophagy markers MAP1LC3B-II and SQSTM1/p62, and build-up of ubiquitinated proteins. Accumulation of immature autophagosomes was accompanied by inefficient degradation of phagocytized, exogenously supplied retinal rod outer segments (as evidenced by persistence of the C-terminal 1D4 epitope of RHO [rhodopsin]) in SLOS RPE compared to iPSC-derived normal human control. SLOS RPE cells exhibited lysosomal pH levels and CTSD activity within normal physiological limits, thus discounting the involvement of perturbed lysosomal function. Furthermore, 1D4-positive phagosomes that accumulated in the RPE in both pharmacological and genetic rodent models of SLOS failed to fuse with lysosomes. Taken together, these observations suggest that defective phagosome maturation underlies the observed RPE pathology. The potential relevance of these findings to SLOS and the requirement of cholesterol for phagosome maturation are discussed.
DOI: 10.6084/m9.figshare.6783485.v1
title: Monocle V1 Datasets - Epithelial

description: E14_endocrine_mon_input_seur_ob - E14.5 endocrine V1 Dataset. Prepared for monocle, input into monocle_v1_seurat_input.R <br><br>E14_endocrine_monocle_ob - Resulting monocle object generated from E14_endocrine_mon_input_seur_ob. Grouped by "ordered_res1_5" in phenoData. Corresponds to Fig. 4g. <br>merge_fev_endocrine_seur_ob - E12.5, E14.5, E17.5 V1 Dataset. Subclustered epithelial dataset for Fev+/Pax4+, FevHi/Chgb+, Alpha, Beta, Epsilon, and Delta populations. Prepared for monocle, input into monocle_v1_seurat_input.R <br><br>merge_fev_endocrine_monocle_ob - Resulting monocle object generated from merge_fev_endocrine_seur_ob. Grouped by "merged_clus" in phenoData. Corresponds to Supplementary Fig. 8a.<br>merge_fev_endocrine_seur_ob - merged timecourse endocrine V1 Dataset. Prepared for monocle, input into monocle_v1_seurat_input.R
DOI: 10.6084/m9.figshare.6783476
title: Unified Consciousness and the Effect of Body Scan Meditation on Happiness

description: Data of the study titled " Unified consciousness and the effect of body scan meditation on happiness"