cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7284/136564
title: Meteorological Station data collected during research cruise PE19-20A using a RM Young 92000 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136559
title: Transmissometer data collected during research cruise PE19-20A using a WET Labs C-Star instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136558
title: TSG (Thermosalinograph) data collected during research cruise PE19-20A using a Sea-Bird SBE-21 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7350845
title: Additional file 1: of Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics

description: List of genomes included in this study and previously referenced LTR-retrotransposons. The nine genomes of molluscs are listed together with the current URL and the accession numbers from which the genome sequences have been accessed, number of sequences of each genome included in our analysis, combined sequence sizes (in number of base pairs) and some metrics. Additionally we list all reference LTR-retrotransposons used from Repbase, the Gypsy Database, and previous publications; together with the species name they occur in. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.7350845.v1
title: Additional file 1: of Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics

description: List of genomes included in this study and previously referenced LTR-retrotransposons. The nine genomes of molluscs are listed together with the current URL and the accession numbers from which the genome sequences have been accessed, number of sequences of each genome included in our analysis, combined sequence sizes (in number of base pairs) and some metrics. Additionally we list all reference LTR-retrotransposons used from Repbase, the Gypsy Database, and previous publications; together with the species name they occur in. (XLSX 23 kb)
DOI: 10.7284/136704
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise PE19-28 using a Hawaii UHDAS instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136709
title: Fluorometer data collected during research cruise PE19-28 using a WET Labs ECO-FL instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136703
title: GNSS (Global Navigation Satellite System) data collected during research cruise PE19-28 using a Ashtech ADU800 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136710
title: Gyrocompass data collected during research cruise PE19-28 using a Sperry NAVIGAT X MK 1 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136711
title: Meteorological Station data collected during research cruise PE19-28 using a RM Young 92000 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7350365
title: The annotation file of Oxygymnocypris stewartii genome for the manuscript "The sequence and de novo assembly of Oxygymnocypris stewartii genome"

description: The annotation file of <i>Oxygymnocypris stewartii</i> genome for the manuscript "The sequence and de novo assembly of <i>Oxygymnocypris stewartii</i> genome"
DOI: 10.7284/136712
title: Meteorological Station data collected during research cruise PE19-28 using a RM Young 92000 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136701
title: Transmissometer data collected during research cruise PE19-28 using a WET Labs C-Star instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136700
title: TSG (Thermosalinograph) data collected during research cruise PE19-28 using a Sea-Bird SBE-21 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7350287
title: linkedin_files.zip

description: A set of frequency stats for the linkedin password leak
DOI: 10.6084/m9.figshare.7350290.v1
title: On the relativity of stream restoration and the need for reproducible research: comment

description: R code and associated data for a comment on a paper by Christopher Swan and Bryan Brown titled "Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration." I provide a commentary and critique of the paper by offering a re-analysis of the data, with hypotheses and interpretation in the context of stream, metacommunity, and restoration ecology. I show that results can depend on the sites and concomitant restoration treatments. I highlight limitations of the experimental design and how liberal usage of restoration without considering how individual and combinations of treatments could affect the study system. Moreover, I show that the efficacy of restoration is relative, dependent on which sites are included in the analysis. Importantly, I show that the results presented in the original paper and erratum are not reproducible. I evaluate where discrepancies occur and provided explanations for these deviations. I also discuss potential errors in analysis by Swan and Brown (2017, 2018), including the deviations in written statistical methods and what was actually conducted. Given that analytical scripts are not always required or even provided alongside manuscripts, readers assume what has been described in the manuscript is what was done in the actual analysis. Unfortunately, this is not the case for Swan and Brown (2017, 2018), and should be of concern for ethical and reproducible ecological research.<br>These data were provided with the initial manuscript by Christopher M. Swan and Bryan L.Brown (Swan and Brown 2017), and are also provided here for ease of the reader.<br>If the data are re-used, please cite the proper sources:Swan, C. M., and B. L. Brown. 2017. Metacommunity theory meets restoration: isolation may mediate how ecological communities respond to stream restoration. Ecological Applications 27:2209-2219.<br>Swan, C. M., and B. L. Brown. 2018. Erratum for: Metacommunity theory meets restorations: isolation may mediate how ecological communities respond to stream restoration. Ecological Applications 28: 1370-1371.<br>
DOI: 10.7284/136791
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise PE20-06 using a Hawaii UHDAS instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7350284
title: Reference genome anchoring of high density markers for association mapping and genomic prediction in European winter wheat

description: The availability of a high-quality wheat reference genome assembly offers new potential for the mapping and prediction of agronomic traits. In this study, we anchored genotyping-by-sequencing data to the International Wheat Genome Sequencing Consortium Reference Sequence v1.0 assembly to generate over 40,000 high quality single nucleotide polymorphism markers on a panel of 376 elite European winter wheat varieties released between 1946 and 2007. We compared association mapping and genomic prediction accuracy for a range of productivity traits with previous results based on lower density dominant DArT markers. The results demonstrate that the availability of RefSeq v1.0 supports higher precision trait mapping and provides the density of markers required to obtain accurate predictions of traits controlled by multiple small effect loci, including grain yield. <br>
DOI: 10.6084/m9.figshare.7350284.v1
title: Reference genome anchoring of high density markers for association mapping and genomic prediction in European winter wheat

description: The availability of a high-quality wheat reference genome assembly offers new potential for the mapping and prediction of agronomic traits. In this study, we anchored genotyping-by-sequencing data to the International Wheat Genome Sequencing Consortium Reference Sequence v1.0 assembly to generate over 40,000 high quality single nucleotide polymorphism markers on a panel of 376 elite European winter wheat varieties released between 1946 and 2007. We compared association mapping and genomic prediction accuracy for a range of productivity traits with previous results based on lower density dominant DArT markers. The results demonstrate that the availability of RefSeq v1.0 supports higher precision trait mapping and provides the density of markers required to obtain accurate predictions of traits controlled by multiple small effect loci, including grain yield. <br>
DOI: 10.6084/m9.figshare.7350287.v1
title: linkedin_files.zip

description: A set of frequency stats for the linkedin password leak
DOI: 10.7284/136792
title: Fluorometer data collected during research cruise PE20-06 using a WET Labs ECO-FL instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7350263
title: Pre-Processed Gold Standard of 2017

description: The processed gold standard of 2017 for Biomedical Articles and Clinical Trials.
DOI: 10.6084/m9.figshare.7350263.v1
title: Pre-Processed Gold Standard of 2017

description: The processed gold standard of 2017 for Biomedical Articles and Clinical Trials.
DOI: 10.6084/m9.figshare.7350260
title: Graphs based on our Official Results

description: Graphs representing our results for different topics and metrics.
DOI: 10.7284/136790
title: GNSS (Global Navigation Satellite System) data collected during research cruise PE20-06 using a Ashtech ADU800 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136793
title: Gyrocompass data collected during research cruise PE20-06 using a Sperry NAVIGAT X MK 1 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136794
title: Meteorological Station data collected during research cruise PE20-06 using a RM Young 92000 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7350257
title: Submitted Runs for the Challenge

description: Those were the runs our team submitted to the TREC-PM 2018.
DOI: 10.7284/136788
title: Transmissometer data collected during research cruise PE20-06 using a WET Labs C-Star instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136787
title: TSG (Thermosalinograph) data collected during research cruise PE20-06 using a Sea-Bird SBE-21 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7350044
title: Ecological indicators of mammal exposure to Ebolavirus

description: Data and code corresponding to manuscript " Ecological indicators of spillover potential among mammal bridge hosts ofmammal exposure to Ebolavirus"<br>
DOI: 10.6084/m9.figshare.7350257.v1
title: Submitted Runs for the Challenge

description: Those were the runs our team submitted to the TREC-PM 2018.
DOI: 10.7284/136809
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise PE20-07 using a Hawaii UHDAS instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7350041
title: Gas generation from grinding rocks from glacial catchments

description: Gas generated per gram of rock sample ground by a ball mill in the laboratory. The rock samples were collected from glacial catchments and the experiments were used as analogies to glacial abrasion. If using this data, please cite the following paper for which it was generated: Macdonald, M.L., Wadham, J.L., Telling, J., Skidmore, M.L. (2018). Glacial erosion liberates lithologic energy sources for microbes and acidity for chemical weathering beneath glaciers and ice sheets. Frontiers in Earth Science: Geochemistry, 6 (212), doi: 10.3389/feart.2018.00212
DOI: 10.6084/m9.figshare.7350257.v2
title: Submitted Runs for the Challenge

description: Those were the runs our team submitted to the TREC-PM 2018.
DOI: 10.6084/m9.figshare.7350041.v1
title: Gas generation from grinding rocks from glacial catchments

description: Gas generated per gram of rock sample ground by a ball mill in the laboratory. The rock samples were collected from glacial catchments and the experiments were used as analogies to glacial abrasion. If using this data, please cite the following paper for which it was generated: Macdonald, M.L., Wadham, J.L., Telling, J., Skidmore, M.L. (2018). Glacial erosion liberates lithologic energy sources for microbes and acidity for chemical weathering beneath glaciers and ice sheets. Frontiers in Earth Science: Geochemistry, 6 (212), doi: 10.3389/feart.2018.00212
DOI: 10.6084/m9.figshare.7350257.v3
title: Submitted Runs for the Challenge

description: Those were the runs our team submitted to the TREC-PM 2018.
DOI: 10.6084/m9.figshare.7349939
title: Patterns of rice genomic structure, Supplementary Methods, Figures and Table

description: Supplementary Material accompanying the manuscript "Fine scale genomic signals of admixture and alien introgression among Asian rice landraces". This item includes: Supplementary Methods file, detailing the precise nature of the statistics used in the article, as well as of the simulations used to establish the relation of those statistics and population genetic structure; a Supplementary Table providing IDs, names and classificaiton status of Core Asian rice varieties studied; 22 Supplementary Figures, of which 14 (1-14) accompany the simulation work and 8 (15-22) provide local genomic snapshots of classification and structure at regions of interest.
DOI: 10.6084/m9.figshare.7350257.v5
title: Submitted Runs for the Challenge

description: Those were the runs our team submitted to the TREC-PM 2018.
DOI: 10.7284/136810
title: Fluorometer data collected during research cruise PE20-07 using a WET Labs ECO-FL instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7350257.v4
title: Submitted Runs for the Challenge

description: Those were the runs our team submitted to the TREC-PM 2018.
DOI: 10.7284/136808
title: GNSS (Global Navigation Satellite System) data collected during research cruise PE20-07 using a Ashtech ADU800 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136811
title: Gyrocompass data collected during research cruise PE20-07 using a Sperry NAVIGAT X MK 1 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/136813
title: Meteorological Station data collected during research cruise PE20-07 using a RM Young 92000 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7347335
title: Effects of <i>dam</i> and <i>seqA</i> genes on biofilm and pellicle formation in <i>Salmonella</i>

description: In this study, the effects of <i>dam</i> and <i>seqA</i> genes on the formation of pellicle and biofilm was determined using five different <i>Salmonella</i> serovars <i>S</i>. Group C1 (DMC2 encoded), <i>S</i>. Typhimurium (DMC4 encoded), <i>S</i>. Virchow (DMC11 encoded), <i>S</i>. Enteritidis (DMC22 encoded), and <i>S</i>. Montevideo (DMC89 encoded). <i>dam</i> and <i>seqA</i> mutants in <i>Salmonella</i> serovars were performed by the single step lambda red recombination method. The mutants obtained were examined according to the properties of biofilm on the polystyrene surfaces and the pellicle formation on the liquid medium. As a result of these investigations, it was determined that the biofilm formation properties on polystyrene surfaces decreased significantly (p dam and <i>seqA</i> mutants, while the pellicle formation properties were lost in the liquid medium. When pBAD24 vector, containing the <i>dam</i> and <i>seqA</i> genes cloned behind the inducible arabinose promoter, transduced into <i>dam</i> and <i>seqA</i> mutant strains, it was determined that the biofilm formation properties on the polystyrene surfaces reached to the natural strains’ level in all mutant strains. Also, the pellicle formation ability was regained in the liquid media. All these data demonstrate that <i>dam</i> and <i>seqA</i> genes play an important role in the formation of biofilm and pellicle structures in <i>Salmonella</i> serovars.
DOI: 10.6084/m9.figshare.7347341
title: Exploring insecticide resistance mechanisms in three major malaria vectors from Bangui in Central African Republic

description: Malaria remains the main cause of mortality and morbidity in the Central African Republic. However, the main malaria vectors remain poorly characterised, preventing the design of suitable control strategies. Here, we characterised the patterns and mechanisms of insecticide resistance in three important vectors from Bangui. Mosquitoes were collected indoors, using electrical aspirators in July 2016 in two neighborhoods at Bangui. WHO bioassays performed, using F<sub>2</sub> <i>An. gambiae</i> sensu lato (s.l.), revealed a high level of resistance to type I (permethrin) and II (deltamethrin) pyrethroids and dichlorodiphenyltrichloroethane (Anopheles coluzzii (56.8 %) and <i>An. gambiae</i> s.s. (43.2%) within the <i>An. gambiae</i> complex. <i>Anopheles funestus</i> s.s. was the sole species belonging to <i>An. funestus</i> group. Both <i>kdr-w</i> (40% of homozygotes and 60% of heterozygotes/<i>kdr-w</i>/wild type) and <i>kdr-e</i> (37.5% of heterozygotes) mutations were found in <i>An. gambiae</i>. Contrariwise, only the <i>kdr-w</i> (9.5% homozygotes and 85.7% of heterozygotes) was detected in <i>An. coluzzii</i>. Quantitative RT-PCR showed that <i>CYP6M2</i> and <i>CYP6P3</i> are not upregulated in <i>An. coluzzii</i> from Bangui. Analysis of the sodium channel gene revealed a reduced diversity in <i>An. coluzzii</i> and <i>An. gambiae</i> s.s. In <i>An. funestus</i> s.s., the pyrethroid/DDT <i>GSTe2</i> L119F resistance allele was detected at high frequency (54.7%) whereas a very low frequency for <i>Rdl</i> was observed. Polymorphism analysis of <i>GSTe2</i> and <i>GABA</i> receptor gene in <i>An. funestus</i> revealed the presence of one resistant haplotype for each gene. This study provides baseline information to help guide current and future malaria vector control interventions in CAR.
DOI: 10.7284/136806
title: Transmissometer data collected during research cruise PE20-07 using a WET Labs C-Star instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7347335.v2
title: Effects of <i>dam</i> and <i>seqA</i> genes on biofilm and pellicle formation in <i>Salmonella</i>

description: In this study, the effects of <i>dam</i> and <i>seqA</i> genes on the formation of pellicle and biofilm was determined using five different <i>Salmonella</i> serovars <i>S</i>. Group C1 (DMC2 encoded), <i>S</i>. Typhimurium (DMC4 encoded), <i>S</i>. Virchow (DMC11 encoded), <i>S</i>. Enteritidis (DMC22 encoded), and <i>S</i>. Montevideo (DMC89 encoded). <i>dam</i> and <i>seqA</i> mutants in <i>Salmonella</i> serovars were performed by the single step lambda red recombination method. The mutants obtained were examined according to the properties of biofilm on the polystyrene surfaces and the pellicle formation on the liquid medium. As a result of these investigations, it was determined that the biofilm formation properties on polystyrene surfaces decreased significantly (p dam and <i>seqA</i> mutants, while the pellicle formation properties were lost in the liquid medium. When pBAD24 vector, containing the <i>dam</i> and <i>seqA</i> genes cloned behind the inducible arabinose promoter, transduced into <i>dam</i> and <i>seqA</i> mutant strains, it was determined that the biofilm formation properties on the polystyrene surfaces reached to the natural strains’ level in all mutant strains. Also, the pellicle formation ability was regained in the liquid media. All these data demonstrate that <i>dam</i> and <i>seqA</i> genes play an important role in the formation of biofilm and pellicle structures in <i>Salmonella</i> serovars.
DOI: 10.6084/m9.figshare.7347341.v2
title: Exploring insecticide resistance mechanisms in three major malaria vectors from Bangui in Central African Republic

description: Malaria remains the main cause of mortality and morbidity in the Central African Republic. However, the main malaria vectors remain poorly characterised, preventing the design of suitable control strategies. Here, we characterised the patterns and mechanisms of insecticide resistance in three important vectors from Bangui. Mosquitoes were collected indoors, using electrical aspirators in July 2016 in two neighborhoods at Bangui. WHO bioassays performed, using F<sub>2</sub> <i>An. gambiae</i> sensu lato (s.l.), revealed a high level of resistance to type I (permethrin) and II (deltamethrin) pyrethroids and dichlorodiphenyltrichloroethane (Anopheles coluzzii (56.8 %) and <i>An. gambiae</i> s.s. (43.2%) within the <i>An. gambiae</i> complex. <i>Anopheles funestus</i> s.s. was the sole species belonging to <i>An. funestus</i> group. Both <i>kdr-w</i> (40% of homozygotes and 60% of heterozygotes/<i>kdr-w</i>/wild type) and <i>kdr-e</i> (37.5% of heterozygotes) mutations were found in <i>An. gambiae</i>. Contrariwise, only the <i>kdr-w</i> (9.5% homozygotes and 85.7% of heterozygotes) was detected in <i>An. coluzzii</i>. Quantitative RT-PCR showed that <i>CYP6M2</i> and <i>CYP6P3</i> are not upregulated in <i>An. coluzzii</i> from Bangui. Analysis of the sodium channel gene revealed a reduced diversity in <i>An. coluzzii</i> and <i>An. gambiae</i> s.s. In <i>An. funestus</i> s.s., the pyrethroid/DDT <i>GSTe2</i> L119F resistance allele was detected at high frequency (54.7%) whereas a very low frequency for <i>Rdl</i> was observed. Polymorphism analysis of <i>GSTe2</i> and <i>GABA</i> receptor gene in <i>An. funestus</i> revealed the presence of one resistant haplotype for each gene. This study provides baseline information to help guide current and future malaria vector control interventions in CAR.
DOI: 10.7284/136805
title: TSG (Thermosalinograph) data collected during research cruise PE20-07 using a Sea-Bird SBE-21 instrument system onboard the platform RV Pelican

description: Original (unprocessed) data collected during a Field_expedition