cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10036196
title: MOESM4 of Tendon-motion tracking in an ultrasound image sequence using optical-flow-based block matching

description: Additional file 4. Ground truth (point coordinates).
DOI: 10.6084/m9.figshare.10036193.v1
title: MOESM3 of Tendon-motion tracking in an ultrasound image sequence using optical-flow-based block matching

description: Additional file 3. Ground truth (point coordinates).
DOI: 10.6084/m9.figshare.10036196.v1
title: MOESM4 of Tendon-motion tracking in an ultrasound image sequence using optical-flow-based block matching

description: Additional file 4. Ground truth (point coordinates).
DOI: 10.6084/m9.figshare.10036184
title: MOESM10 of Tendon-motion tracking in an ultrasound image sequence using optical-flow-based block matching

description: Additional file 10. Source code of the software.
DOI: 10.6084/m9.figshare.10036175
title: Additional file 8: S1 of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: Archive containing the HEC executable file. 7-Zip archive containing the HEC executable file (Windows version). To switch chemotaxiss on pass 0.1 as a second command line parameter (the first is a model script). S2. HEC script 2D_phage.plentiful_edge.early.txt of early-time phage into (1,1) model. Text file with the model script of early-time phage added into (1,1) model. S3. HEC script 2D_phage.center.early.txt of early-time phage into (3,3) model. Text file with the model script of early-time phage added into (3,3) model. S4. HEC script 2D_phage.poor_edge.early.txt of early-time phage into (5,5) model. Text file with the model script of early-time phage added into (5,5) model. S5. HEC script 2D_phage.plentiful_edge.middle.txt of middle-time phage into (1,1) model. Text file with the model script of middle-time phage added into (1,1) model. S6. HEC script 2D_phage.center.middle.txt of middle-time phage into (3,3) model. Text file with the model script of middle-time phage added into (3,3) model. S7. HEC script 2D_phage.poor_edge.middle.txt of middle-time phage into (5,5) model. Text file with the model script of middle-time phage added into (5,5) model. S8. HEC script 2D_phage.plentiful_edge.late.txt of late-time phage into (1,1) model. Text file with the model script of late-time phage added into (1,1) model. S9. HEC script 2D_phage.center.late.txt of late-time phage into (3,3) model. Text file with the model script of late-time phage added into (3,3) model. S10. HEC script 2D_phage.poor_edge.late.txt of late-time phage into (5,5) model. Text file with the model script of late-time phage added into (5,5) model. S11. Data processing script speciesRichnessFluctuation.sce. A Scilab script that plots species richness dynamics. S12. A library SRlib.sce. A Scilab library sources used by such scripts as speciesRichnessFluctuation.sce, averageSRandBiomass.sce and speciation_rate.sce. (ZIP 594Â kb)
DOI: 10.6084/m9.figshare.10036184.v1
title: MOESM10 of Tendon-motion tracking in an ultrasound image sequence using optical-flow-based block matching

description: Additional file 10. Source code of the software.
DOI: 10.6084/m9.figshare.10036175.v1
title: Additional file 8: S1 of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: Archive containing the HEC executable file. 7-Zip archive containing the HEC executable file (Windows version). To switch chemotaxiss on pass 0.1 as a second command line parameter (the first is a model script). S2. HEC script 2D_phage.plentiful_edge.early.txt of early-time phage into (1,1) model. Text file with the model script of early-time phage added into (1,1) model. S3. HEC script 2D_phage.center.early.txt of early-time phage into (3,3) model. Text file with the model script of early-time phage added into (3,3) model. S4. HEC script 2D_phage.poor_edge.early.txt of early-time phage into (5,5) model. Text file with the model script of early-time phage added into (5,5) model. S5. HEC script 2D_phage.plentiful_edge.middle.txt of middle-time phage into (1,1) model. Text file with the model script of middle-time phage added into (1,1) model. S6. HEC script 2D_phage.center.middle.txt of middle-time phage into (3,3) model. Text file with the model script of middle-time phage added into (3,3) model. S7. HEC script 2D_phage.poor_edge.middle.txt of middle-time phage into (5,5) model. Text file with the model script of middle-time phage added into (5,5) model. S8. HEC script 2D_phage.plentiful_edge.late.txt of late-time phage into (1,1) model. Text file with the model script of late-time phage added into (1,1) model. S9. HEC script 2D_phage.center.late.txt of late-time phage into (3,3) model. Text file with the model script of late-time phage added into (3,3) model. S10. HEC script 2D_phage.poor_edge.late.txt of late-time phage into (5,5) model. Text file with the model script of late-time phage added into (5,5) model. S11. Data processing script speciesRichnessFluctuation.sce. A Scilab script that plots species richness dynamics. S12. A library SRlib.sce. A Scilab library sources used by such scripts as speciesRichnessFluctuation.sce, averageSRandBiomass.sce and speciation_rate.sce. (ZIP 594Â kb)
DOI: 10.6084/m9.figshare.10036169
title: Additional file 6: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: Phage.extinction.chemon.xlsx. An Excel spreadsheet containing the data on the extinction of phage populations for the chemotaxis-on cases. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.10036160
title: Additional file 3: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: Data processing script averageSRandBiomass.sce. A Scilab script that calculates averaged by time species richness (number of species) and total biomass of the community. (SCE 9Â kb)
DOI: 10.6084/m9.figshare.10036163
title: Additional file 4: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: SRI.SR.Biomass.chemoff.xlsx. An Excel spreadsheet containing the data on species richness, SRI and biomass for the chemotaxis-off cases. (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.10036166
title: Additional file 5: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: SRI.SR.Biomass.chemon.xlsx. An Excel spreadsheet containing the data on species richness, SRI and biomass for the chemotaxis-on cases. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.10036157
title: Additional file 2: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: Data processing script speciation_rate.sce. A Scilab script that calculates Speciation Rate Index (SRI). (SCE 13Â kb)
DOI: 10.6084/m9.figshare.10036160.v1
title: Additional file 3: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: Data processing script averageSRandBiomass.sce. A Scilab script that calculates averaged by time species richness (number of species) and total biomass of the community. (SCE 9Â kb)
DOI: 10.6084/m9.figshare.10036166.v1
title: Additional file 5: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: SRI.SR.Biomass.chemon.xlsx. An Excel spreadsheet containing the data on species richness, SRI and biomass for the chemotaxis-on cases. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.10036169.v1
title: Additional file 6: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: Phage.extinction.chemon.xlsx. An Excel spreadsheet containing the data on the extinction of phage populations for the chemotaxis-on cases. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.10036154
title: Additional file 1: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: Data processing script addZeros.sce. A Scilab script for data preprocessing of popSize.txt files that is necessary for some other scripts (such as speciation_rate.sce). (SCE 2Â kb)
DOI: 10.6084/m9.figshare.10036157.v1
title: Additional file 2: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: Data processing script speciation_rate.sce. A Scilab script that calculates Speciation Rate Index (SRI). (SCE 13Â kb)
DOI: 10.6084/m9.figshare.10036163.v1
title: Additional file 4: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: SRI.SR.Biomass.chemoff.xlsx. An Excel spreadsheet containing the data on species richness, SRI and biomass for the chemotaxis-off cases. (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.10036154.v1
title: Additional file 1: of Erratum to: Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

description: Data processing script addZeros.sce. A Scilab script for data preprocessing of popSize.txt files that is necessary for some other scripts (such as speciation_rate.sce). (SCE 2Â kb)
DOI: 10.6084/m9.figshare.10036085
title: Additional file 1: of Contextual flexibility in the vocal repertoire of an Amazon parrot

description: Datasets for statistical analyses by context and note-type. (XLSX 116 kb)
DOI: 10.6084/m9.figshare.10036085.v1
title: Additional file 1: of Contextual flexibility in the vocal repertoire of an Amazon parrot

description: Datasets for statistical analyses by context and note-type. (XLSX 116 kb)
DOI: 10.6084/m9.figshare.10036061
title: MOESM1 of A new kymogram-based method reveals unexpected effects of marker protein expression and spatial anisotropy of cytoskeletal dynamics in plant cell cortex

description: Additional file 1. Detailed protocol and ImageJ macros for performing QuACK measurements. The .cab archive file (which can be unpacked using free programs such as e.g. Cabextract or Keka on non-Windows systems, or using free web utilities such as the online version of the B1 archiver at http://online.b1.org/online ) contains three ImageJ/Fiji macros (.ijm) and a documentation (.pdf) file with detailed step-by-step setup and application instructions.
DOI: 10.6084/m9.figshare.10036061.v1
title: MOESM1 of A new kymogram-based method reveals unexpected effects of marker protein expression and spatial anisotropy of cytoskeletal dynamics in plant cell cortex

description: Additional file 1. Detailed protocol and ImageJ macros for performing QuACK measurements. The .cab archive file (which can be unpacked using free programs such as e.g. Cabextract or Keka on non-Windows systems, or using free web utilities such as the online version of the B1 archiver at http://online.b1.org/online ) contains three ImageJ/Fiji macros (.ijm) and a documentation (.pdf) file with detailed step-by-step setup and application instructions.
DOI: 10.6084/m9.figshare.12866657
title: Figure 3 from manuscript Sparsely-Connected Autoencoder (SCA) for single cell RNAseq data mining

description: Dataset used to generate figure 3: COMET analysis of latent space frequency matrix. A) Set of 4 genes (PAX5, NFAT5, RFXANK and CHD4) characterizing cluster 1 (B-cells) (figure3/setA/Results/setATF_SIMLR/5/outputvis/cluster_1_discrete_quads/rank_1.png). B) Set of 4 genes (CEBPA, KHSRP negation, CEBPB, CREBBP) characterizing cluster 2 (Monocytes) (figure3/setA/Results/setATF_SIMLR/5/outputvis/cluster_2_discrete_quads/rank_1.png). Dots are cells, blue and red colour indicates respectively false and true positives (for more information on this type of visualization of cluster specific markers see the COMET paper). C) Rank 1 NK signature specifically characterizing cluster 4 (NK) (figure3/setA/Results/setAIS2_KMEAN/5/outputvis/cluster_4_singleton/rank_1.png). D) Rank 2 Asthma KEGG negation, specifically characterizing Naïve T-cells (Cluster 5) (figure3/setA/Results/setAIS2_KMEAN/5/outputvis/cluster_5_singleton/rank_2.png).
DOI: 10.6084/m9.figshare.10035962
title: Additional file 1: of C. elegans SUP-46, an HNRNPM family RNA-binding protein that prevents paternally-mediated epigenetic sterility

description: Xcel file containing Tables S1â S8. Table S1 Partial rescue of gna-2(qa705) maternal effect embryonic lethality by sup-46(RNAi). Table S2 HNRNPM and MYEF2 SAINT table. Table S3 HNRNPM and MYEF2 proximal proteins in RNA granules and RNA-associated complexes. See also Fig.Â 2. Table S4 Proteins of the nucleolus (cellular compartment GO:0005730; 862 proteins) associated with HNRNPM and MYEF2. Table S5 RNASeq data of transcript abundance in wildtype and sup-46(qa710). Table S6 Transcripts showing splicing differences between wildtype and sup-46(qa710). Table S7 Worm strains generated in this study. Table S8 Sequences used to generate the MYEF2 sequence logo. (XLSX 1939 kb)
DOI: 10.6084/m9.figshare.10035962.v1
title: Additional file 1: of C. elegans SUP-46, an HNRNPM family RNA-binding protein that prevents paternally-mediated epigenetic sterility

description: Xcel file containing Tables S1â S8. Table S1 Partial rescue of gna-2(qa705) maternal effect embryonic lethality by sup-46(RNAi). Table S2 HNRNPM and MYEF2 SAINT table. Table S3 HNRNPM and MYEF2 proximal proteins in RNA granules and RNA-associated complexes. See also Fig.Â 2. Table S4 Proteins of the nucleolus (cellular compartment GO:0005730; 862 proteins) associated with HNRNPM and MYEF2. Table S5 RNASeq data of transcript abundance in wildtype and sup-46(qa710). Table S6 Transcripts showing splicing differences between wildtype and sup-46(qa710). Table S7 Worm strains generated in this study. Table S8 Sequences used to generate the MYEF2 sequence logo. (XLSX 1939 kb)
DOI: 10.6084/m9.figshare.10035926
title: Additional file 9: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: All significant correlations (q &lt;0.05) between subject metadata and microbiota. Table includes â redundantâ correlations involving similar food items and the same OTU cluster (for example, Food:Yogurt and Food:Yogurt:Non-Activia are both correlated with OTU cluster 84). A non-redundant list of correlations is presented in Table 1. (XLS 33 kb)
DOI: 10.6084/m9.figshare.10035926.v1
title: Additional file 9: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: All significant correlations (q &lt;0.05) between subject metadata and microbiota. Table includes â redundantâ correlations involving similar food items and the same OTU cluster (for example, Food:Yogurt and Food:Yogurt:Non-Activia are both correlated with OTU cluster 84). A non-redundant list of correlations is presented in Table 1. (XLS 33 kb)
DOI: 10.6084/m9.figshare.10035905
title: Additional file 2: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: Subject demographic information. Subjects were unrelated men who volunteered for extensive personal tracking. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.10035902
title: Additional file 1: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: Host metadata categories. We processed host daily records into 349 variables grouped into the categories: ailments, bowel movements, exercise, fitness, specific food intake (parsed by a text-mining algorithm modeled on a food frequency questionnaire), location, medication, mood, nutrition (measured via the CalorieKing database), oral hygiene, sleep, urination, and vitamin supplementation. (XLS 82 kb)
DOI: 10.6084/m9.figshare.10035905.v1
title: Additional file 2: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: Subject demographic information. Subjects were unrelated men who volunteered for extensive personal tracking. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.10035899
title: Additional file 18: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: Sample and nutritional metadata. Metadata are provided for nucleotide sequences deposited on the EBI/ENA database under accession number ERP006059. These metadata include Subject Aâ s nutritional data, provided for the day preceding each sample. (CSV 914 kb)
DOI: 10.6084/m9.figshare.10035902.v1
title: Additional file 1: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: Host metadata categories. We processed host daily records into 349 variables grouped into the categories: ailments, bowel movements, exercise, fitness, specific food intake (parsed by a text-mining algorithm modeled on a food frequency questionnaire), location, medication, mood, nutrition (measured via the CalorieKing database), oral hygiene, sleep, urination, and vitamin supplementation. (XLS 82 kb)
DOI: 10.6084/m9.figshare.10035899.v1
title: Additional file 18: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: Sample and nutritional metadata. Metadata are provided for nucleotide sequences deposited on the EBI/ENA database under accession number ERP006059. These metadata include Subject Aâ s nutritional data, provided for the day preceding each sample. (CSV 914 kb)
DOI: 10.6084/m9.figshare.10035878
title: Additional file 11: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: Taxonomy of Subject A gut OTUs correlated with host metadata. Shown are gut bacterial taxa assigned to bacterial clusters that have significant correlations with host health or lifestyle (Table 1). Clusters were defined using hierarchical clustering (Additional file 16) of bacteria with similar temporal dynamics. Taxonomic IDs and Latin names are drawn from the Greengenes database. (XLS 47 kb)
DOI: 10.6084/m9.figshare.10035875
title: Additional file 10: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: Taxonomy of Subject A saliva OTUs correlated with host metadata. Shown are oral bacterial taxa assigned to bacterial clusters that have significant correlations with host health or lifestyle (Table 1). Clusters were defined using hierarchical clustering (Additional file 16) of bacteria with similar temporal dynamics. Taxonomic IDs and Latin names are drawn from the Greengenes database. (XLS 14 kb)
DOI: 10.6084/m9.figshare.10035878.v1
title: Additional file 11: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: Taxonomy of Subject A gut OTUs correlated with host metadata. Shown are gut bacterial taxa assigned to bacterial clusters that have significant correlations with host health or lifestyle (Table 1). Clusters were defined using hierarchical clustering (Additional file 16) of bacteria with similar temporal dynamics. Taxonomic IDs and Latin names are drawn from the Greengenes database. (XLS 47 kb)
DOI: 10.6084/m9.figshare.10035875.v1
title: Additional file 10: of Erratum to: Host lifestyle affects human microbiota on daily timescales

description: Taxonomy of Subject A saliva OTUs correlated with host metadata. Shown are oral bacterial taxa assigned to bacterial clusters that have significant correlations with host health or lifestyle (Table 1). Clusters were defined using hierarchical clustering (Additional file 16) of bacteria with similar temporal dynamics. Taxonomic IDs and Latin names are drawn from the Greengenes database. (XLS 14 kb)
DOI: 10.6084/m9.figshare.10035773
title: MOESM7 of Fish with red fluorescent eyes forage more efficiently under dim, blue-green light conditions

description: Additional file 7. Foraging success data of the second (heavily shaded) experiment.
DOI: 10.6084/m9.figshare.10035770
title: MOESM6 of Fish with red fluorescent eyes forage more efficiently under dim, blue-green light conditions

description: Additional file 6. Foraging success data of the first (shaded) experiment.
DOI: 10.6084/m9.figshare.10035773.v1
title: MOESM7 of Fish with red fluorescent eyes forage more efficiently under dim, blue-green light conditions

description: Additional file 7. Foraging success data of the second (heavily shaded) experiment.
DOI: 10.6084/m9.figshare.10035770.v1
title: MOESM6 of Fish with red fluorescent eyes forage more efficiently under dim, blue-green light conditions

description: Additional file 6. Foraging success data of the first (shaded) experiment.
DOI: 10.6084/m9.figshare.10035647
title: MOESM3 of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

description: Additional file 3: Housekeeping genes. Loci that were observed to be ubiquitously expressed were ordered according to the coefficient of variation in the sum of the observed normalized tag abundance (TPM) of all tags mapping on the same strand and within the boundaries of the gene. Only tags mapping uniquely to the draft genome that passed our filters (Os-fgU; Figure 2b) were considered. (XLSX 503 KB)
DOI: 10.6084/m9.figshare.10035647.v1
title: MOESM3 of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

description: Additional file 3: Housekeeping genes. Loci that were observed to be ubiquitously expressed were ordered according to the coefficient of variation in the sum of the observed normalized tag abundance (TPM) of all tags mapping on the same strand and within the boundaries of the gene. Only tags mapping uniquely to the draft genome that passed our filters (Os-fgU; Figure 2b) were considered. (XLSX 503 KB)
DOI: 10.6084/m9.figshare.10035641
title: MOESM1 of An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

description: Additional file 1: Tissues sampled and annotation. BRENDA tissue ontology terms are given when known, with the hyphenated number at the end of the column headings specifying level of granularity, where 1 is the lowest level of granularity and the broadest scope. Only tags mapping uniquely to the draft genome that passed our filters (Os-fgU; Figure 2b) were considered. Total Sense TPM Within NM & NR Transcripts: sum of normalized tag counts (tags per million) that mapped on the same strand and within the boundaries of NM and NR transcripts. On 3' terminus: sum of normalized tag abundance of those tags that mapped on the same strand and at the 3'-most and next to 3'-most DpnII sites on the NM or NR transcript (Figure 2a). Not on 3' terminus: sum of normalized tag abundance of those tags that did not map to the 3'-most and next to 3'-most DpnII sites on the NM or NR transcript (Figure 2a): Count Sense GeneID: total number of unique GeneIDs associated with the loci that the tags mapped to on the same strand and within the boundaries of the annotated genes. Count Sense Tags within Loci: number of unique tag sequences that mapped within the boundaries of annotated genes. Total Sense TPM within Loci: sum of normalized tag abundance of those tags that mapped on the same strand and within the boundaries of all annotated genes. The headings including the word 'AntiSense' are similarly defined, except that these tags mapped to the strand opposite to that of the annotated gene. (XLSX 41 KB)