cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7284/108682
title: Fluorometer data collected during research cruise EN484 using a Turner 10-AU instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103249
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN484 using a Northstar 952 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107337
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN484 using a Furuno GP-90D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642643
title: Recycling nutrients contained in human excreta to agriculture: Pathways, processes, and products

description: The need for better nutrient management has spurred efforts towards more comprehensive recycling of nutrients contained in human excreta to agriculture. Research in this direction has intensified throughout the past years, continuously unfolding new knowledge and technologies. The present review aspires to provide a systematic synthesis of the field by providing an accessible overview of terminology, recovery pathways and treatment options, and products rendered by treatment. Our synthesis suggests that, rather than focusing on a specific recovery pathway or product and on a limited set of nutrients, there is scope for exploring how to maximize nutrient recovery by combining individual pathways and products and including a broader range of nutrients. To this end, finding ways to more effectively share and consolidate knowledge and information on recovery pathways and products would be beneficial. The present review aims to provide a template that aims to facilitate designing human excreta management for maximum nutrient recovery, and that can serve as foundation for organizing and categorizing information for more effective sharing and consolidation.
DOI: 10.6084/m9.figshare.7642643.v1
title: Recycling nutrients contained in human excreta to agriculture: Pathways, processes, and products

description: The need for better nutrient management has spurred efforts towards more comprehensive recycling of nutrients contained in human excreta to agriculture. Research in this direction has intensified throughout the past years, continuously unfolding new knowledge and technologies. The present review aspires to provide a systematic synthesis of the field by providing an accessible overview of terminology, recovery pathways and treatment options, and products rendered by treatment. Our synthesis suggests that, rather than focusing on a specific recovery pathway or product and on a limited set of nutrients, there is scope for exploring how to maximize nutrient recovery by combining individual pathways and products and including a broader range of nutrients. To this end, finding ways to more effectively share and consolidate knowledge and information on recovery pathways and products would be beneficial. The present review aims to provide a template that aims to facilitate designing human excreta management for maximum nutrient recovery, and that can serve as foundation for organizing and categorizing information for more effective sharing and consolidation.
DOI: 10.6084/m9.figshare.7642625
title: Supplementary_Tables_Within_Method_Correlations.doc

description: Supplementary tables 1-2. Within method individual-level and phenotypic correlations.
DOI: 10.6084/m9.figshare.7642625.v1
title: Supplementary_Tables_Within_Method_Correlations.doc

description: Supplementary tables 1-2. Within method individual-level and phenotypic correlations.
DOI: 10.7284/111974
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN484 using a Trimble NT-300D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108677
title: Gyrocompass data collected during research cruise EN484 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108678
title: Gyrocompass data collected during research cruise EN484 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107338
title: Singlebeam Echosounder data collected during research cruise EN484 using a Knudsen 320B/R instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108680
title: Speedlog data collected during research cruise EN484 using a EDO MRQ-4015D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108679
title: TSG (Thermosalinograph) data collected during research cruise EN484 using a Sea-Bird SBE-45 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108681
title: TSG (Thermosalinograph) data collected during research cruise EN484 using a Sea-Bird SBE-21 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.15131/shef.data.7642523
title: Resistance training combined with stretching increases tendon stiffness and is more effective than stretching alone in children with cerebral palsy: A randomised controlled trial.

description: Raw data of fascicle lengths and tendon stiffness corresponding to the paper: Resistance training combined with stretching increases tendon stiffness and is more effective than stretching alone in children with cerebral palsy: A randomised controlled trial.<br>
DOI: 10.7284/107232
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise EN485 using a Hawaii UHDAS instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107343
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise EN485 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642490
title: isotopic_data_2013.csv

description: Isotopic signals of soil respiration measured in a dry temperate grassland in May-Nov 2013.Supporting information for manuscript "Separating effects of temperature and carbon allocation on the diel pattern of soil respiration among phenological stages"
DOI: 10.7284/108688
title: Fluorometer data collected during research cruise EN485 using a Turner 10-AU instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642487
title: Time-specific Errors in Growth Curve Modeling: Type-1 Error Inflation and a Possible Solution with Mixed-Effects Models

description: Growth curve modeling (GCM) has been one of the most popular statistical methods to examine participants’ growth trajectories using longitudinal data. In spite of the popularity of GCM, little attention has been paid to the possible influence of time-specific errors, which influence all participants at each timepoint. In this article, we demonstrate that the failure to take into account such time-specific errors in GCM produces considerable inflation of type-1 error rates in statistical tests of fixed effects (e.g., coefficients for the linear and quadratic terms). We propose a GCM that appropriately incorporates time-specific errors using mixed-effects models to address the problem. We also provide an applied example to illustrate that GCM with and without time-specific errors would lead to different substantive conclusions about the true growth trajectories. Comparisons with other models in longitudinal data analysis and potential issues of model misspecification are discussed.
DOI: 10.6084/m9.figshare.7642490.v1
title: isotopic_data_2013.csv

description: Isotopic signals of soil respiration measured in a dry temperate grassland in May-Nov 2013.Supporting information for manuscript "Separating effects of temperature and carbon allocation on the diel pattern of soil respiration among phenological stages"
DOI: 10.6084/m9.figshare.7642481
title: EC_SRS_dataset_2011_2014.csv

description: Soil respiration dataset measured in a dry temperate grassland in 2011-2014.Supporting information for manuscript "Separating effects of temperature and carbon allocation on the diel pattern of soil respiration among phenological stages".
DOI: 10.6084/m9.figshare.7642481.v1
title: EC_SRS_dataset_2011_2014.csv

description: Soil respiration dataset measured in a dry temperate grassland in 2011-2014.Supporting information for manuscript "Separating effects of temperature and carbon allocation on the diel pattern of soil respiration among phenological stages".
DOI: 10.7284/103250
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN485 using a Northstar 952 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642487.v1
title: Time-specific Errors in Growth Curve Modeling: Type-1 Error Inflation and a Possible Solution with Mixed-Effects Models

description: Growth curve modeling (GCM) has been one of the most popular statistical methods to examine participants’ growth trajectories using longitudinal data. In spite of the popularity of GCM, little attention has been paid to the possible influence of time-specific errors, which influence all participants at each timepoint. In this article, we demonstrate that the failure to take into account such time-specific errors in GCM produces considerable inflation of type-1 error rates in statistical tests of fixed effects (e.g., coefficients for the linear and quadratic terms). We propose a GCM that appropriately incorporates time-specific errors using mixed-effects models to address the problem. We also provide an applied example to illustrate that GCM with and without time-specific errors would lead to different substantive conclusions about the true growth trajectories. Comparisons with other models in longitudinal data analysis and potential issues of model misspecification are discussed.
DOI: 10.17045/sthlmuni.7642463
title: dN/dS calculation of Thermus virus NrdJm evolution

description: A log ratio test of significant overrepresentation of non-synonymous to silent (dN/dS) was estimated with codonml from PAML (Yang 1997, https://doi.org/10.1093/bioinformatics/13.5.555 ; Yang 2007, https://doi.org/10.1093/molbev/msm088) by running the program with a fixed and free dN/dS respectively, and the branch leading to the two Thermus virus sequences (marked with “#1” in reftree.newick) designated as the “foreground” branch in the free dN/dS run. This analysis was performed on the Thermus virus/Firmicutes subtree in https://doi.org/10.17045/sthlmuni.7117430.v2, using the same alignment as for the full tree, reverse translated into nucleotides. We could not find correct gene sequences for seven taxa (RefSeq accession numbers: WP_102410887, WP_033167051, WP_054955013, WP_065068364, WP_088370373, WP_087372021, WP_093315575), so they were left out of the analysis.<br>Scripts in files ending with .codeml; output in .codeml.out files.<br>
DOI: 10.7284/107340
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN485 using a Furuno GP-90D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17045/sthlmuni.7642463.v1
title: dN/dS calculation of Thermus virus NrdJm evolution

description: A log ratio test of significant overrepresentation of non-synonymous to silent (dN/dS) was estimated with codonml from PAML (Yang 1997, https://doi.org/10.1093/bioinformatics/13.5.555 ; Yang 2007, https://doi.org/10.1093/molbev/msm088) by running the program with a fixed and free dN/dS respectively, and the branch leading to the two Thermus virus sequences (marked with “#1” in reftree.newick) designated as the “foreground” branch in the free dN/dS run. This analysis was performed on the Thermus virus/Firmicutes subtree in https://doi.org/10.17045/sthlmuni.7117430.v2, using the same alignment as for the full tree, reverse translated into nucleotides. We could not find correct gene sequences for seven taxa (RefSeq accession numbers: WP_102410887, WP_033167051, WP_054955013, WP_065068364, WP_088370373, WP_087372021, WP_093315575), so they were left out of the analysis.<br>Scripts in files ending with .codeml; output in .codeml.out files.<br>
DOI: 10.7284/111973
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN485 using a Trimble NT-300D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642439
title: DataS1 - review table

description: Review table for: Belowground responses to insect herbivory in forest ecosystems: a global meta-analysis
DOI: 10.7284/108683
title: Gyrocompass data collected during research cruise EN485 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108684
title: Gyrocompass data collected during research cruise EN485 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/107342
title: Singlebeam Echosounder data collected during research cruise EN485 using a Knudsen 320B/R instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642373
title: Datasheet2

description: exome data<br>
DOI: 10.7284/108686
title: Speedlog data collected during research cruise EN485 using a EDO MRQ-4015D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7642358
title: Single-nucleotide polymorphism markers in mitochondrial genomes for identifying <i>Varroa destructor</i>-resistant and -susceptible strains of <i>Apis mellifera</i> (Hymenoptera: Apidae)

description: Mitogenome sequences have a high potential for possessing single-nucleotide polymorphisms (SNPs) that can be used to identify different strains of an organism bred based on maternal lines. The European honey bee, <i>Apis mellifera ligustica</i> (Hymenoptera: Apidae), with a high-hygienic behaviour (HHB) against the external parasitic mite <i>Varroa destructor</i> has been bred for several years in Korea. To distinguish this strain from low-hygienic behaviour (LHB) strains, the complete mitogenome of the two strains were sequenced using next-generation sequencing techniques to detect SNPs. The two mitogenomes with lengths of 16,449 and 16,426 base pairs (bp) in the HHB and LHB strains, respectively, contained a typical set of genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes, plus one non-coding region), exhibited similar-nucleotide compositions, and had an identical gene arrangement compared to other available <i>A. mellifera</i> mitogenomes. The major differences between the HHB and LHB strains included the length of the intergenic spacer sequences located at the <i>COIII</i> and <i>trnG</i> junction (88 vs. 70 bp) and <i>ND4</i> and <i>ND4L</i> junction (45 vs. 33 bp) and the presence or absence of a duplicated sequence block (CTTTTTTAAAAAAATAAAAA) in the A + T-rich region. Comparison of the mitogenome sequences from the two strains of <i>A. m. ligustica</i> revealed 23 SNPs in 11 protein-coding genes which were confirmed by sequencing of 10 randomly selected individuals from each strain, indicating the usefulness of these SNP markers for identifying the HHB strain of <i>A. m. ligustica</i>. Therefore, mitogenome sequences are a promising genome source for detecting SNP markers, particularly those in inbred female lines.
DOI: 10.6084/m9.figshare.7642373.v1
title: Datasheet2

description: exome data<br>
DOI: 10.6084/m9.figshare.7642358.v1
title: Single-nucleotide polymorphism markers in mitochondrial genomes for identifying <i>Varroa destructor</i>-resistant and -susceptible strains of <i>Apis mellifera</i> (Hymenoptera: Apidae)

description: Mitogenome sequences have a high potential for possessing single-nucleotide polymorphisms (SNPs) that can be used to identify different strains of an organism bred based on maternal lines. The European honey bee, <i>Apis mellifera ligustica</i> (Hymenoptera: Apidae), with a high-hygienic behaviour (HHB) against the external parasitic mite <i>Varroa destructor</i> has been bred for several years in Korea. To distinguish this strain from low-hygienic behaviour (LHB) strains, the complete mitogenome of the two strains were sequenced using next-generation sequencing techniques to detect SNPs. The two mitogenomes with lengths of 16,449 and 16,426 base pairs (bp) in the HHB and LHB strains, respectively, contained a typical set of genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes, plus one non-coding region), exhibited similar-nucleotide compositions, and had an identical gene arrangement compared to other available <i>A. mellifera</i> mitogenomes. The major differences between the HHB and LHB strains included the length of the intergenic spacer sequences located at the <i>COIII</i> and <i>trnG</i> junction (88 vs. 70 bp) and <i>ND4</i> and <i>ND4L</i> junction (45 vs. 33 bp) and the presence or absence of a duplicated sequence block (CTTTTTTAAAAAAATAAAAA) in the A + T-rich region. Comparison of the mitogenome sequences from the two strains of <i>A. m. ligustica</i> revealed 23 SNPs in 11 protein-coding genes which were confirmed by sequencing of 10 randomly selected individuals from each strain, indicating the usefulness of these SNP markers for identifying the HHB strain of <i>A. m. ligustica</i>. Therefore, mitogenome sequences are a promising genome source for detecting SNP markers, particularly those in inbred female lines.
DOI: 10.7284/108685
title: TSG (Thermosalinograph) data collected during research cruise EN485 using a Sea-Bird SBE-45 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17045/sthlmuni.7642343
title: Metagenomic NrdJm5 sequences placed in full phylogeny

description: To search for sequences from metagenomics projects, we downloaded all TARA Ocean ORFs (Eren 2017, https://doi.org/10.6084/m9.figshare.4902917.v1 ; Delmont 2018, https://doi.org/10.1038/s41564-018-0176-9), all ORFs from the Human Microbiome Project (2019-01-09; HMP 2012a, https://doi.org/10.1038/nature11234 ; HMP 2012b, https://doi.org/10.1038/nature11209 ) the majority of bacterial MAGs and SAGs from IMG/MER (4910 MAGs, 2230 SAGs) plus 53 aquatic and soil metagenomes, in particular those with project names containing “virus”, “phage”, “therm” or “hot“ (see img_sags.tsv, img_metag_samples.tsv and img_mags.tsv) (Markowitz 2008, https://doi.org/10.1093/nar/gkm869). Together, we downloaded a total of 250,881,638 ORFs. We used hmm profiles designed for each clan in the phylogeny to search the sequences. We found 181 sequences with a best match to the profile designed from the TV clan. These were aligned to the original alignment using Clustal Omega in profile mode (all.NrdJm5.co.profile.wa.masked.alnfaa ; Sievers 2014, https://doi.org/10.1038/msb.2011.75) and phylogenetically placed in the phylogeny from https://doi.org/10.17045/sthlmuni.7117430.v2 with RAxML (Stamatakis 2014, https://doi.org/10.1093/bioinformatics/btu033). The resulting tree can be viewed with Dendroscope (Huson et al. 2007, https://doi.org/10.1186/1471-2105-8-460); placed sequences have "QUERY" prepended to their names.<br><br><br>
DOI: 10.17045/sthlmuni.7642343.v1
title: Metagenomic NrdJm5 sequences placed in full phylogeny

description: To search for sequences from metagenomics projects, we downloaded all TARA Ocean ORFs (Eren 2017, https://doi.org/10.6084/m9.figshare.4902917.v1 ; Delmont 2018, https://doi.org/10.1038/s41564-018-0176-9), all ORFs from the Human Microbiome Project (2019-01-09; HMP 2012a, https://doi.org/10.1038/nature11234 ; HMP 2012b, https://doi.org/10.1038/nature11209 ) the majority of bacterial MAGs and SAGs from IMG/MER (4910 MAGs, 2230 SAGs) plus 53 aquatic and soil metagenomes, in particular those with project names containing “virus”, “phage”, “therm” or “hot“ (see img_sags.tsv, img_metag_samples.tsv and img_mags.tsv) (Markowitz 2008, https://doi.org/10.1093/nar/gkm869). Together, we downloaded a total of 250,881,638 ORFs. We used hmm profiles designed for each clan in the phylogeny to search the sequences. We found 181 sequences with a best match to the profile designed from the TV clan. These were aligned to the original alignment using Clustal Omega in profile mode (all.NrdJm5.co.profile.wa.masked.alnfaa ; Sievers 2014, https://doi.org/10.1038/msb.2011.75) and phylogenetically placed in the phylogeny from https://doi.org/10.17045/sthlmuni.7117430.v2 with RAxML (Stamatakis 2014, https://doi.org/10.1093/bioinformatics/btu033). The resulting tree can be viewed with Dendroscope (Huson et al. 2007, https://doi.org/10.1186/1471-2105-8-460); placed sequences have "QUERY" prepended to their names.<br><br><br>
DOI: 10.6084/m9.figshare.7642310
title: Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus <i>Caenorhabditis</i>

description: Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. Since lncRNAs (or a fraction thereof) are expected to be functional, many efforts have been dedicated to catalog lncRNAs in numerous organisms, but our knowledge of lncRNAs in non vertebrate species remains very limited. Here, we annotated lncRNAs using transcriptomic data from the same larval stage of four <i>Caenorhabditis</i> species. The number of annotated lncRNAs in self-fertile nematodes was lower than in out-crossing species. We used a combination of approaches to identify putatively homologous lncRNAs: synteny, sequence conservation, and structural conservation. We classified a total of 1,532 out of 7,635 genes from the four species into families of lncRNAs with conserved synteny and expression at the larval stage, suggesting that a large fraction of the predicted lncRNAs may be species specific. Despite both sequence and local secondary structure seem to be poorly conserved, sequences within families frequently shared BLASTn hits and short sequence motifs, which were more likely to be unpaired in the predicted structures. We provide the first multi-species catalog of lncRNAs in nematodes and identify groups of lncRNAs with conserved synteny and expression, that share exposed motifs.
DOI: 10.7284/108687
title: TSG (Thermosalinograph) data collected during research cruise EN485 using a Sea-Bird SBE-21 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition