cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25400047
title: Nanopore data

description: Datasets describing community composition of EcoPlate wells inoculated with lake water analyzed by 16S rRNA gene sequencing with Nanopore MinION. OTUs were assembled with an in-house pipeline by Hofer, C. 2022. Master thesis: Long-read MinION data for microbial community analysis. Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Switzerland. Here we provide OTU and taxonomy table and OTUs_Nanopore lists the sequences of the OTUs.Only syringe samples (see project description) were analyzed by Nanopore sequencing. 24 samples were sequenced, grown on four different subtrates (D-cellobiose, L-serine, N-acetyl-D-glucosamine, putrescine) inoculated with syringe samples from Sampling 1 and 2 (n = 3). Putrescine enrichments were disregarded in the corresponding publication due to a lack of successful enrichments available for Illumina sequencing. More information about the sampling conditions can be found in the project description.Sample_info provides information for the sample names given in the OTU table. Information is formated as barcode_substrate_sampling. Values: Barcode = 01-24, substrate = cellobiose/serine/glucosamine/putrescine, Sampling = S1/S2. For example, 01_cellobiose_S1 describes a community inoculated with lake water from a sampling 1 syringe sample grown in D-cellobiose.
DOI: 10.15468/dl.tehc7w
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Justicia diminuta Benoist"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042418-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.7497500
title: MOESM2 of Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production

description: Additional file 2. Tax MG-RAST—General taxonomic analysis of RefSeq assignments of metagenomic sequences analyzed by MG-RAST; Fun MG-RAST—General functional analysis of Subsystem function assignments of metagenomic sequences analyzed by MG-RAST; Tax-Fun MetAnnotate—Methanogenesis specific phylogenetic assignments of metagenomic sequences analyzed by MetAnnotate; Tax-Fun MetAnnotate—Combined Consolidated key methanogenesis specific phylogenetic assignments of metagenomic sequences analyzed by MetAnnotate.
DOI: 10.6084/m9.figshare.7497503
title: Additional file 5: of The â Clinicianâ s illusionâ and the epidemiology, diagnosis and treatment of depressive disorders

description: A comma delimited ASCII file generated by the NetLogo model. This data file is the output from the model included in with the manuscript as Additional file 2 for use in the analysis leading to a calibration process for the agents, as described in Additional file 4. (CSV 202 kb)
DOI: 10.7284/115164
title: Multibeam Echosounder data collected during research cruise KN221-03 using a SeaBeam 3012-P1 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497500.v1
title: MOESM2 of Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production

description: Additional file 2. Tax MG-RAST—General taxonomic analysis of RefSeq assignments of metagenomic sequences analyzed by MG-RAST; Fun MG-RAST—General functional analysis of Subsystem function assignments of metagenomic sequences analyzed by MG-RAST; Tax-Fun MetAnnotate—Methanogenesis specific phylogenetic assignments of metagenomic sequences analyzed by MetAnnotate; Tax-Fun MetAnnotate—Combined Consolidated key methanogenesis specific phylogenetic assignments of metagenomic sequences analyzed by MetAnnotate.
DOI: 10.6084/m9.figshare.7497503.v1
title: Additional file 5: of The â Clinicianâ s illusionâ and the epidemiology, diagnosis and treatment of depressive disorders

description: A comma delimited ASCII file generated by the NetLogo model. This data file is the output from the model included in with the manuscript as Additional file 2 for use in the analysis leading to a calibration process for the agents, as described in Additional file 4. (CSV 202 kb)
DOI: 10.7284/115169
title: Radiometer data collected during research cruise KN221-03 using a Eppley PIR instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497485
title: Additional file 2: of The â Clinicianâ s illusionâ and the epidemiology, diagnosis and treatment of depressive disorders

description: The agent based model in NetLogo format. This is a basic version of the NetLogo model used in the analysis to explore the effects of different thresholds in different situations. It is designed to generate a large datafile used to explore the effect of model parameters on disutility. A more elaborate version of the model (capable of simulating several agents with different characteristics) was used in generating the animations that accompany the manuscript. (NLOGO 28 kb)
DOI: 10.7284/115170
title: Radiometer data collected during research cruise KN221-03 using a Eppley PSP instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497482
title: Additional file 1: of The “Clinician’s illusion” and the epidemiology, diagnosis and treatment of depressive disorders

description: Basic features of the signal detection concept, depicted in an Excel spreadsheet. This is the spreadsheet used to produce Figures 1-3. Values in the first three rows of the spreadsheet can be modified to explore scenarios different from those presented in in the Figures. To reproduce Fig. 1 in the graphic labeled “A classical signal detection paradigm”, enter the threshold (d-prime) = 2 in the first row of the spreadsheet. To reproduce the values in Fig. 2, make sure that the costs in row 2 & 3 are both set to one and then successively enter the values 1, 1.5 and 3 into the threshold (d-prime) cell in the first row. To reproduce Figure 3, set the cost of severe event to 10 and then enter 1, 2 or 3 in the d-prime field. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.7497485.v1
title: Additional file 2: of The â Clinicianâ s illusionâ and the epidemiology, diagnosis and treatment of depressive disorders

description: The agent based model in NetLogo format. This is a basic version of the NetLogo model used in the analysis to explore the effects of different thresholds in different situations. It is designed to generate a large datafile used to explore the effect of model parameters on disutility. A more elaborate version of the model (capable of simulating several agents with different characteristics) was used in generating the animations that accompany the manuscript. (NLOGO 28 kb)
DOI: 10.6084/m9.figshare.7497479
title: Additional file 9: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S9. List of canonical pathways predicted for C24MC-associated miRNAs with IPA. (XLS 41 kb)
DOI: 10.6084/m9.figshare.7497482.v1
title: Additional file 1: of The “Clinician’s illusion” and the epidemiology, diagnosis and treatment of depressive disorders

description: Basic features of the signal detection concept, depicted in an Excel spreadsheet. This is the spreadsheet used to produce Figures 1-3. Values in the first three rows of the spreadsheet can be modified to explore scenarios different from those presented in in the Figures. To reproduce Fig. 1 in the graphic labeled “A classical signal detection paradigm”, enter the threshold (d-prime) = 2 in the first row of the spreadsheet. To reproduce the values in Fig. 2, make sure that the costs in row 2 & 3 are both set to one and then successively enter the values 1, 1.5 and 3 into the threshold (d-prime) cell in the first row. To reproduce Figure 3, set the cost of severe event to 10 and then enter 1, 2 or 3 in the d-prime field. (XLSX 56 kb)
DOI: 10.7284/115163
title: Singlebeam Echosounder data collected during research cruise KN221-03 using a Knudsen 320B/R instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497473
title: Additional file 8: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S8. List of disease and physiological functions predicted for C24MC-associated miRNAs with IPA. (XLS 127 kb)
DOI: 10.6084/m9.figshare.7497473.v1
title: Additional file 8: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S8. List of disease and physiological functions predicted for C24MC-associated miRNAs with IPA. (XLS 127 kb)
DOI: 10.6084/m9.figshare.7497479.v1
title: Additional file 9: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S9. List of canonical pathways predicted for C24MC-associated miRNAs with IPA. (XLS 41 kb)
DOI: 10.6084/m9.figshare.7497461
title: Additional file 2: of Power in pairs: assessing the statistical value of paired samples in tests for differential expression

description: SAS code to implement the probability distribution method for calculating approximate power with continuous expression (such as miRNA) data (SAS 9 kb)
DOI: 10.7284/115171
title: Water Temperature data collected during research cruise KN221-03 using a Sea-Bird SBE-48 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497458
title: Additional file 6: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S6. Read counts and mapping quality of Illumina RNA-sequencing dataset from CAM at different stages of pregnancy. Information about RNA-sequencing dataset. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7497461.v1
title: Additional file 2: of Power in pairs: assessing the statistical value of paired samples in tests for differential expression

description: SAS code to implement the probability distribution method for calculating approximate power with continuous expression (such as miRNA) data (SAS 9 kb)
DOI: 10.6084/m9.figshare.7497464
title: Additional file 7: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S7. List of putative target mRNAs for analyzed miRNAs and their expression values (FPKM) during different stages of pregnancy. (XLSX 325 kb)
DOI: 10.6084/m9.figshare.7497464.v1
title: Additional file 7: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S7. List of putative target mRNAs for analyzed miRNAs and their expression values (FPKM) during different stages of pregnancy. (XLSX 325 kb)
DOI: 10.6084/m9.figshare.7497452
title: Additional file 1: of Power in pairs: assessing the statistical value of paired samples in tests for differential expression

description: SAS code to implement the probability distribution method for calculating approximate power with count expression (such as RNA-Seq) data (SAS 9 kb)
DOI: 10.6084/m9.figshare.7497458.v1
title: Additional file 6: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S6. Read counts and mapping quality of Illumina RNA-sequencing dataset from CAM at different stages of pregnancy. Information about RNA-sequencing dataset. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7497449
title: Additional file 5: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S5. Primer sequences for genes which were indicated in our dataset to be involved in angiogenesis. (XLSX 10 kb)
DOI: 10.7284/115167
title: TSG (Thermosalinograph) data collected during research cruise KN221-03 using a Sea-Bird SBE-45 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497452.v1
title: Additional file 1: of Power in pairs: assessing the statistical value of paired samples in tests for differential expression

description: SAS code to implement the probability distribution method for calculating approximate power with count expression (such as RNA-Seq) data (SAS 9 kb)
DOI: 10.6084/m9.figshare.7497443
title: Additional file 4: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S4. Differential expression analysis results for C24MC-associated miRNAs during gestation, generated with Illumina miRNA-sequencing. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7497449.v1
title: Additional file 5: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S5. Primer sequences for genes which were indicated in our dataset to be involved in angiogenesis. (XLSX 10 kb)
DOI: 10.7284/115105
title: Multiplexed data collected during research cruise KN221-04 using a WHOI Calliope instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497443.v1
title: Additional file 4: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S4. Differential expression analysis results for C24MC-associated miRNAs during gestation, generated with Illumina miRNA-sequencing. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7497437
title: Additional file 3: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S3. Normalized read count for C24MC-associated miRNAs generated with Illumina miRNA-sequencing. (XLSX 24 kb)
DOI: 10.7284/115102
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KN221-04 using a Hawaii UHDAS instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497437.v1
title: Additional file 3: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S3. Normalized read count for C24MC-associated miRNAs generated with Illumina miRNA-sequencing. (XLSX 24 kb)
DOI: 10.7284/115103
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise KN221-04 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497419
title: Additional file 1: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S1. Comparative list of C14MC associated-miRNAs among different species. The comparative list of C14MC in domestic animals. (XLSX 13 kb)
DOI: 10.7284/115109
title: Fluorometer data collected during research cruise KN221-04 using a WET Labs WETStar instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497419.v1
title: Additional file 1: of Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare

description: Table S1. Comparative list of C14MC associated-miRNAs among different species. The comparative list of C14MC in domestic animals. (XLSX 13 kb)
DOI: 10.7284/115108
title: GNSS (Global Navigation Satellite System) data collected during research cruise KN221-04 using a C&C C-Nav 2000 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/115104
title: Meteorological Station data collected during research cruise KN221-04 using a Vaisala WXT520 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497392
title: Additional file 1: of Using co-design to develop interventions to address health literacy needs in a hospitalised population

description: Cluster analysis, This additional file presents 3â 13 and a 16 cluster solutions. The 8 cluster solution was the solution chosen for analysis as it presented the least amount of variation within clusters (based on the SDâ s). (XLSX 48 kb)
DOI: 10.7284/115111
title: Meteorological Station data collected during research cruise KN221-04 using a Vaisala WXT520 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/115107
title: Multibeam Echosounder data collected during research cruise KN221-04 using a SeaBeam 3012-P1 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/115112
title: Radiometer data collected during research cruise KN221-04 using a Eppley PIR instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/115113
title: Radiometer data collected during research cruise KN221-04 using a Eppley PSP instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/115106
title: Singlebeam Echosounder data collected during research cruise KN221-04 using a Knudsen 320B/R instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/115114
title: Water Temperature data collected during research cruise KN221-04 using a Sea-Bird SBE-48 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497344
title: Additional file 3: of Genomic characterization of Listeria monocytogenes isolates reveals that their persistence in a pig slaughterhouse is linked to the presence of benzalkonium chloride resistance genes

description: Table S2. PRJNA433177 Assembly Details and Institut Pasteur IDof the 29 Listeria monocytogenes strains isolated from an industrial slaughterhouse over a 4â weeks period. (XLSX 11 kb)
DOI: 10.7284/115110
title: TSG (Thermosalinograph) data collected during research cruise KN221-04 using a Sea-Bird SBE-45 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497338
title: Additional file 2: of Genomic characterization of Listeria monocytogenes isolates reveals that their persistence in a pig slaughterhouse is linked to the presence of benzalkonium chloride resistance genes

description: Table S1. complete annotation of the high impact SNV and function prediction for the group A (spreedsheet group A) and group B (spreed sheet group B). (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7497341
title: Additional file 1: of Design and application of a novel two-amplicon approach for defining eukaryotic microbiota

description: Table S1. Accuracy of taxonomic assignments of 18S and 28S rRNA variable genetic regions. Related to Fig. 1. Table S2. Primer characteristics and TestProbe3.0 results. Related to Fig. 2. Table S3. Amplicon sequencing statistics. Table S4. Read counts for eukaryotic microbes detected by two amplicon methods in patients suffering from SAM. Related to Fig. 3. Table S5. Genome and gene accessions used for comparisons with stool sample DNA and phylogenetic trees. Table S6. Differential abundance analysis of bacteria based on of Blastocystis carriage, using ALDEx2. Related to Fig. 5. Table S7. Association between eukaryote carriage or HIV reactivity and bacterial diversity. Related to Fig. 5. Table S8. Association between eukaryote abundance and clinical characteristics of patients hospitalized for SAM. (XLS 162 kb)
DOI: 10.6084/m9.figshare.7497344.v1
title: Additional file 3: of Genomic characterization of Listeria monocytogenes isolates reveals that their persistence in a pig slaughterhouse is linked to the presence of benzalkonium chloride resistance genes

description: Table S2. PRJNA433177 Assembly Details and Institut Pasteur IDof the 29 Listeria monocytogenes strains isolated from an industrial slaughterhouse over a 4â weeks period. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7497341.v1
title: Additional file 1: of Design and application of a novel two-amplicon approach for defining eukaryotic microbiota

description: Table S1. Accuracy of taxonomic assignments of 18S and 28S rRNA variable genetic regions. Related to Fig. 1. Table S2. Primer characteristics and TestProbe3.0 results. Related to Fig. 2. Table S3. Amplicon sequencing statistics. Table S4. Read counts for eukaryotic microbes detected by two amplicon methods in patients suffering from SAM. Related to Fig. 3. Table S5. Genome and gene accessions used for comparisons with stool sample DNA and phylogenetic trees. Table S6. Differential abundance analysis of bacteria based on of Blastocystis carriage, using ALDEx2. Related to Fig. 5. Table S7. Association between eukaryote carriage or HIV reactivity and bacterial diversity. Related to Fig. 5. Table S8. Association between eukaryote abundance and clinical characteristics of patients hospitalized for SAM. (XLS 162 kb)
DOI: 10.7284/115118
title: Multiplexed data collected during research cruise KN222 using a WHOI Calliope instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497338.v1
title: Additional file 2: of Genomic characterization of Listeria monocytogenes isolates reveals that their persistence in a pig slaughterhouse is linked to the presence of benzalkonium chloride resistance genes

description: Table S1. complete annotation of the high impact SNV and function prediction for the group A (spreedsheet group A) and group B (spreed sheet group B). (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7497326
title: Additional file 8: of Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots

description: Table S7. Characteristics of dinucleotide SSRs obtained in RGC-1066 and M-83 varieties of guar. (XLSX 142 kb)
DOI: 10.6084/m9.figshare.7497329
title: Additional file 9: of Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots

description: Table S8. Characteristics of trinucleotide SSRs obtained in RGC-1066 and M-83 varieties of guar. (XLSX 177 kb)
DOI: 10.7284/115115
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KN222 using a Hawaii UHDAS instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7497326.v1
title: Additional file 8: of Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots

description: Table S7. Characteristics of dinucleotide SSRs obtained in RGC-1066 and M-83 varieties of guar. (XLSX 142 kb)