cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7605422.v1
title: panel.CP2.json

description: JSON file for candidate panel 2, mapping variant to list of resistant drugs, in the format required when running mykrobe.
DOI: 10.6084/m9.figshare.7605407
title: variant_counts.tsv

description: A TSV file of the number of true- and false-positive calls for each tool and each reported variant. The columns are as follows.<br>- Tool: the name of the tool/panel- Dataset: the dataset (train, test or validate)- Drug: drug called as resistant- PPV: positive predictive value (TP / (TP+FP))<br>- TP: number of true-positives- FP: number of false-positives- Variants: semi-colon separated list of variants<br>
DOI: 10.6084/m9.figshare.7605416
title: panel.CP1.json

description: JSON file for candidate panel 1, mapping variant to list of resistant drugs, in the format required when running mykrobe.
DOI: 10.6084/m9.figshare.7605416.v1
title: panel.CP1.json

description: JSON file for candidate panel 1, mapping variant to list of resistant drugs, in the format required when running mykrobe.
DOI: 10.6084/m9.figshare.7605419.v1
title: Ten new species of <i>Calonectria</i> from Indonesia and Vietnam

description: Vietnam and Indonesia have rapidly growing and extensive plantation forestry programs, especially of <i>Acacia</i> spp. and <i>Eucalyptus</i> spp. As these plantations expand, the threat from pests and diseases also increases. <i>Calonectria</i> species are among those pathogens causing diseases of trees in plantations and nurseries in these countries. Extensive surveys were conducted across plantations and nurseries of Vietnam and parts of Indonesia, where a large number of <i>Calonectria</i> isolates were retrieved from diseased leaves and soils associated with symptomatic trees. The aim of this study was to identify and resolve the phylogenetic relationships among these isolates using DNA sequence comparisons of four gene regions as well as morphological characters. From a collection of 165 isolates, the study revealed five known and 10 undescribed species. The relatively high diversity of <i>Calonectria</i> species found in this study supports the view that many more species in this genus remain to be discovered in other areas of Southeast Asia.
DOI: 10.6084/m9.figshare.7605398
title: accuracy_stats.tsv

description: This is a TSV file that has the summary statistics for each tool and each drug.The statistics columns are as follows.<br> - TP: number of true-positives - TN: number of true-negatives - FP: number of false-positives - FN: number of false-negatives - FAIL_R: number of failed runs, where the sample phenotype was resistant - FAIL_S: number of failed runs, where the sample phenotype was susceptible - UNK_R: number of unknown calls, where the sample phenotype was resistant - UNK_S: number of unknown calls, where the sample phenotype was susceptibe - Sensitivity: 100 * TP / (TP + FN) - Specificity: 100 * TN / (TN + FP) - PPV: 100 * TP / (TP + FP) - NPV: 100 * TN / (TN + FN) - FNR: 100 * FN / (FN + TP) - FPR: 100 * FP / (FP + TN) - *_conf_low and *_conf_high: confidence intervals for each<br>of the statistics.
DOI: 10.6084/m9.figshare.7605404
title: Detection of cross-contamination and strong mitonuclear discordance in two species groups of sawfly genus Empria (Hymenoptera, Tenthredinidae): ipyrad dataset and an R script

description: The ipyrad dataset contains alignment of 19 413 ddRAD loci of 35 Empria specimens. The script takes as an input the ipyrad dataset and a table is produced for every locus (rows) and specimen (columns) where cells contain list of specimens that are identical to a specimen indicated in the column (the cell is empty if there are no identical specimens for a particular specimen and locus). Additional columns are added to get information per locus about identical specimens between two groups, the number of specimens, maximum, median and mean divergence. The two groups examined are longicornis (including E. tridentis, which taxonomically is not a member of the group, but closely related) and immersa groups. For both groups and for every locus, specimens are recorded that are identical to any member in the other group while different from specimens in its own group. The second table produced by the script lists the specimens in the dataset, the number of loci, and the normalised number of loci per specimen. Normalised numbers of loci were calculated as half of the maximum number of loci divided by the number of loci of a particular specimen in the dataset. Then the script proceeds to produce bar plots (output as pdf) for every specimen showing percent of loci and normalised percent of loci that are identical to a particular specimen while different from all others. Two additional bar plots are produced for longicornis and immersa groups to show percent of loci of a particular specimen that are identical to any specimen in the wrong group while different from specimens in its own group.<br>
DOI: 10.7284/134053
title: Meteorological Station data collected during research cruise EN634 using a RM Young 26800 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7605395
title: panel.final.tsv

description: Final panel TSV file, in the format required by mykrobe to build the probes FASTA file.
DOI: 10.6084/m9.figshare.7605407.v1
title: variant_counts.tsv

description: A TSV file of the number of true- and false-positive calls for each tool and each reported variant. The columns are as follows.<br>- Tool: the name of the tool/panel- Dataset: the dataset (train, test or validate)- Drug: drug called as resistant- PPV: positive predictive value (TP / (TP+FP))<br>- TP: number of true-positives- FP: number of false-positives- Variants: semi-colon separated list of variants<br>
DOI: 10.7284/134050
title: Radiometer data collected during research cruise EN634 using a Eppley RAD instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7605383
title: panel.CP1.tsv

description: Candidate panel 1 TSV file, in the format required by mykrobe to build the probes FASTA file.<br>
DOI: 10.6084/m9.figshare.7605389
title: panel.CP3.tsv

description: Candidate panel 3 TSV file, in the format required by mykrobe to build the probes FASTA file.
DOI: 10.6084/m9.figshare.7605380
title: removed_variants.tsv

description: A TSV file listing the variants removed from candidate panels 1 and 2 during development of the final variant panel. The columns are as follows.<br>- Panel: the panel from which the variant was removed.- Drug: the drug corresponding to the variant.- Gene: gene containing the variant- Variant: variant that was removed- TP: number of true-positive calls caused by the variant- FP: number of false-positive calls caused by the variant
DOI: 10.6084/m9.figshare.7605383.v1
title: panel.CP1.tsv

description: Candidate panel 1 TSV file, in the format required by mykrobe to build the probes FASTA file.<br>
DOI: 10.6084/m9.figshare.7605386
title: panel.CP2.tsv

description: Candidate panel 2 TSV file, in the format required by mykrobe to build the probes FASTA file.
DOI: 10.6084/m9.figshare.7605389.v1
title: panel.CP3.tsv

description: Candidate panel 3 TSV file, in the format required by mykrobe to build the probes FASTA file.
DOI: 10.7284/134051
title: Radiometer data collected during research cruise EN634 using a Eppley RAD instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134049
title: Singlebeam Echosounder data collected during research cruise EN634 using a Knudsen 3260 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134059
title: Singlebeam Echosounder data collected during research cruise EN634 using a Knudsen 320B/R instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134056
title: Speedlog data collected during research cruise EN634 using a Furuno DS-50 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134058
title: Timeserver data collected during research cruise EN634 using a Spectracom SecureSync instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134052
title: TSG (Thermosalinograph) data collected during research cruise EN634 using a Sea-Bird SBE-45 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7605242
title: Food web motif data

description: Supplementary Information for Giling et al. "Plant diversity alters the representation of motifs in food webs".<br><br>The data files provided contain the results used to generate the figures and statistical analysis in the paper, including the frequencies and representation (normalised z-scores) of each motif in each food web. These files can be used in conjunction with the provided code (R scripts 2 and 3; DOI 10.6084/m9.figshare.7605173) to reproduce the results.<br>Three data files are provided:- "Giling_et_all_motif_data_full_network.csv": motif counts in the full food webs- "Giling_et_all_motif_data_sub_network.csv": motif counts in the sub-web of consumers only- "Giling_et_all_motif_data_complexity_scenario.csv": motif counts in the full food webs under the scenario where encounter probability decreases with plant diversity (see Supplementary Note 2).<br>The three files are formatted identically.
DOI: 10.7284/134060
title: TSG (Thermosalinograph) data collected during research cruise EN634 using a Sea-Bird SBE-21 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134062
title: Winch data collected during research cruise EN634 using a PHE Endeavor instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7605227
title: History of subduction erosion and accretion recorded in the Yarlung Suture Zone, southern Tibet

description: : Zircon U–Pb geochronologic analyses.
DOI: 10.6084/m9.figshare.7605242.v1
title: Food web motif data

description: Supplementary Information for Giling et al. "Plant diversity alters the representation of motifs in food webs".<br><br>The data files provided contain the results used to generate the figures and statistical analysis in the paper, including the frequencies and representation (normalised z-scores) of each motif in each food web. These files can be used in conjunction with the provided code (R scripts 2 and 3; DOI 10.6084/m9.figshare.7605173) to reproduce the results.<br>Three data files are provided:- "Giling_et_all_motif_data_full_network.csv": motif counts in the full food webs- "Giling_et_all_motif_data_sub_network.csv": motif counts in the sub-web of consumers only- "Giling_et_all_motif_data_complexity_scenario.csv": motif counts in the full food webs under the scenario where encounter probability decreases with plant diversity (see Supplementary Note 2).<br>The three files are formatted identically.
DOI: 10.7284/134086
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise EN635 using a Hawaii UHDAS instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7605227.v1
title: History of subduction erosion and accretion recorded in the Yarlung Suture Zone, southern Tibet

description: : Zircon U–Pb geochronologic analyses.
DOI: 10.7284/134101
title: Anemometer data collected during research cruise EN635 using a Gill Windsonic instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134103
title: Anemometer data collected during research cruise EN635 using a Gill Windsonic instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134087
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise EN635 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.7605089
title: Dataset 20190118

description: Involvement of gliadin in increased intestinal permeability leading to NSAID-induced small-intestinal damage
DOI: 10.6084/m9.figshare.7605089.v1
title: Dataset 20190118

description: Involvement of gliadin in increased intestinal permeability leading to NSAID-induced small-intestinal damage
DOI: 10.7284/134085
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN635 using a Ashtech ADU2 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7605017
title: Potential of <i>Equisetum ramosissimum</i> Desf. for remediation of antimony flotation tailings: a case study

description: A flooding event caused collapsing of the Stolice flotation tailing dam and spilling of large volumes of sludge into environment. Urgent remediation measures have not been applied due to the lack of financial resources. Remediation values for Sb, Zn, and Pb in the flotation tailing samples were exceeded 20.5, 4.2, and 1.15 times, respectively, emphasizing the need for remediation. Plants growing on mine spoils represent useful tools for environmental monitoring and soil remediation. The appearance of <i>Equisetum ramosissimum</i> as a dominant colonizer on the flotation tailings indicates that biological reclamation of the site is possible. <i>Equisetum ramosissimum</i> shows the ability to phytostabilize and immobilize available fractions of Fe, Mn, Zn, Pb, and Sb. Transfer rate of metals from roots to shoots reveals exclusion of elements from the shoots, preventing their further spreading through the food chain. The results of this study show that <i>E. ramosissimum</i> can be an additional tool for environmental monitoring and remediation of flotation tailings after hazardous events.
DOI: 10.6084/m9.figshare.7605017.v1
title: Potential of <i>Equisetum ramosissimum</i> Desf. for remediation of antimony flotation tailings: a case study

description: A flooding event caused collapsing of the Stolice flotation tailing dam and spilling of large volumes of sludge into environment. Urgent remediation measures have not been applied due to the lack of financial resources. Remediation values for Sb, Zn, and Pb in the flotation tailing samples were exceeded 20.5, 4.2, and 1.15 times, respectively, emphasizing the need for remediation. Plants growing on mine spoils represent useful tools for environmental monitoring and soil remediation. The appearance of <i>Equisetum ramosissimum</i> as a dominant colonizer on the flotation tailings indicates that biological reclamation of the site is possible. <i>Equisetum ramosissimum</i> shows the ability to phytostabilize and immobilize available fractions of Fe, Mn, Zn, Pb, and Sb. Transfer rate of metals from roots to shoots reveals exclusion of elements from the shoots, preventing their further spreading through the food chain. The results of this study show that <i>E. ramosissimum</i> can be an additional tool for environmental monitoring and remediation of flotation tailings after hazardous events.
DOI: 10.7284/134094
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN635 using a Northstar 952 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134095
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN635 using a Furuno GP-33 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134097
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN635 using a Ashtech ADU5 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7604933
title: Theoretical investigation of intramolecular <i>π</i>-type hydrogen bonding and internal rotation of 2-cyclopropen-1-ol, 2-cyclopropen-1-thiol and 2-cyclopropen-1-amine

description: Theoretical computations utilising both CCSD and MP2 methods and the cc-pVTZ basis set have been carried out to determine the structures of several conformations as well as the internal rotation potential energy functions for 2-cyclopropen-1-ol, 2-cyclopropen-1-thiol and 2-cyclopropen-1-amine. The energies and wavefunctions for these potential functions have also been computed. Each of these molecules has an energy minimum corresponding to a conformation with intramolecular <i>π</i>-type hydrogen bonding. The <i>π</i> bonding stabilisation is about 2.3 kcal/mole for the alcohol, 2.1 kcal/mole for the thiol, and about 2.5 kcal/mole for the amine. The results for the thiol demonstrate a rare example of intramolecular <i>π</i>-type hydrogen bonding. The calculated O–H, S–H, N–H, and C=C stretching frequencies have also been compared for the conformations with and without the <i>π</i>-type hydrogen bonding. The C=C stretching frequency is substantially lower in all cases for the hydrogen bonded conformers.
DOI: 10.6084/m9.figshare.7604930
title: Transport properties of bulk water at 243–550 K: a Comparative molecular dynamics simulation study using SPC/E, TIP4P, and TIP4P/2005 water models

description: Molecular dynamics simulations of various water models – SPC/E (extended simple point charge), TIP4P (transferable intermolecular potential 4 points), and TIP4P/2005 – have been carried out in the canonical (NVT fixed) ensemble over the range of temperatures 243–550 K with Ewald summation. The transport properties (self-diffusion coefficients D, viscosities η, and thermal conductivities λ) of SPC/E, TIP4P, and TIP4P/2005 water were evaluated at 243–550 K and compared with experimental data. The temperature dependence of transport properties of SPC/E, TIP4P and TIP4P/2005 water was discussed to determine how reliable the models are over this temperature range.
DOI: 10.6084/m9.figshare.7604933.v1
title: Theoretical investigation of intramolecular <i>π</i>-type hydrogen bonding and internal rotation of 2-cyclopropen-1-ol, 2-cyclopropen-1-thiol and 2-cyclopropen-1-amine

description: Theoretical computations utilising both CCSD and MP2 methods and the cc-pVTZ basis set have been carried out to determine the structures of several conformations as well as the internal rotation potential energy functions for 2-cyclopropen-1-ol, 2-cyclopropen-1-thiol and 2-cyclopropen-1-amine. The energies and wavefunctions for these potential functions have also been computed. Each of these molecules has an energy minimum corresponding to a conformation with intramolecular <i>π</i>-type hydrogen bonding. The <i>π</i> bonding stabilisation is about 2.3 kcal/mole for the alcohol, 2.1 kcal/mole for the thiol, and about 2.5 kcal/mole for the amine. The results for the thiol demonstrate a rare example of intramolecular <i>π</i>-type hydrogen bonding. The calculated O–H, S–H, N–H, and C=C stretching frequencies have also been compared for the conformations with and without the <i>π</i>-type hydrogen bonding. The C=C stretching frequency is substantially lower in all cases for the hydrogen bonded conformers.
DOI: 10.7284/134088
title: Gyrocompass data collected during research cruise EN635 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7604930.v1
title: Transport properties of bulk water at 243–550 K: a Comparative molecular dynamics simulation study using SPC/E, TIP4P, and TIP4P/2005 water models

description: Molecular dynamics simulations of various water models – SPC/E (extended simple point charge), TIP4P (transferable intermolecular potential 4 points), and TIP4P/2005 – have been carried out in the canonical (NVT fixed) ensemble over the range of temperatures 243–550 K with Ewald summation. The transport properties (self-diffusion coefficients D, viscosities η, and thermal conductivities λ) of SPC/E, TIP4P, and TIP4P/2005 water were evaluated at 243–550 K and compared with experimental data. The temperature dependence of transport properties of SPC/E, TIP4P and TIP4P/2005 water was discussed to determine how reliable the models are over this temperature range.
DOI: 10.7284/134089
title: Gyrocompass data collected during research cruise EN635 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134093
title: Meteorological Station data collected during research cruise EN635 using a RM Young 26800 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134090
title: Radiometer data collected during research cruise EN635 using a Eppley RAD instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/134091
title: Radiometer data collected during research cruise EN635 using a Eppley RAD instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7604849
title: Global buffering of temperatures under forest canopies: Data and Code

description: Data and code for figures and statistics reported in Pieter De Frenne, Florian Zellweger, Francisco Rodríguez-Sánchez, Brett Scheffers, Kristoffer Hylander, Miska Luoto, Mark Vellend, Kris Verheyen & Jonathan Lenoir (2019) Global buffering of temperatures under forest canopies. Nature Ecology & Evolution.<br>
DOI: 10.6084/m9.figshare.7604855
title: The structure of viral cathepsin from <i>Bombyx mori Nuclear Polyhedrosis Virus</i> as a target against grasserie: docking and molecular dynamics simulations

description: The viral cathepsin from <i>Bombyx mori <i>Nuclear Polyhedrosis Virus</i></i> (<i>Bm</i>NPV-<i>Cath</i>) is a broad-spectrum protease that participates in the horizontal transmission of this virus in silkworm by facilitating solubilization of the integument of infected caterpillars. When a <i>B. mori</i> farm is attacked by <i>Bm</i>NPV, there are significant sericultural losses because no drugs or therapies are available. In this work, the structure of viral cathepsin <i>Bm</i>NPV-<i>Cath</i> was used as a target for virtual screening simulations, aiming to identify potential molecules that could be used to treat the infection. Virtual screening of the Natural Products library from the Zinc Database selected four molecules. Theoretical calculations of Δ<i>G</i><sub>binding</sub> by the molecular mechanics Poisson–Boltzmann surface analysis (MM-PBSA) method indicated that the molecule Zinc12888007 (Bm5) would have high affinity for the enzyme. The <i>in vivo</i> infection models of <i>B. mori</i> caterpillars with <i>Bm</i>NPV showed that treatment with a dose of 100 μg Bm5 dissolved in Pluronic-F127 0.02% was able to reduce the mortality of caterpillars in 22.6%, however, it did not impede the liquefaction of dead bodies. Our results suggest a role of <i>Bm</i>NPV-<i>Cath</i> in generating a pool of amino acids necessary for viral replication and indicate a mechanism to be exploited in the search for treatments for grasserie disease of the silkworm.
DOI: 10.7284/134099
title: Singlebeam Echosounder data collected during research cruise EN635 using a Knudsen 320B/R instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition