cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12254444.v1
title: File S1. SeqAilgment from Sponge symbiosis is facilitated by adaptive evolution of larval sensory and attachment structures in barnacles

description: Symbiotic relations and range of host usage are prominent in coral reefs and crucial to the stability of such systems. In order to explain how symbiotic relations are established and evolve, we used sponge-associated barnacles to ask (1) Does larval settlement on sponge hosts require novel adaptations facilitating symbiosis? (2) How do larvae settle and start life on their hosts? (3) How has this remarkable symbiotic lifestyle involving many barnacle species evolved? We found that the larvae (cyprids) of sponge-associated barnacles show a remarkably high level of interspecific variation compared with other barnacles. We document that variation in larval attachment devices are specifically related to properties of the surface on which they attach and metamorphose. Mapping of the larval and sponge surface features onto a molecular-based phylogeny showed that sponge symbiosis evolved separately at least three times within barnacles, with the same adaptive features being found in all larvae irrespective of phylogenetic relatedness. Furthermore, the metamorphosis of two species proceeded very differently, with one species remaining superficially on the host and developing a set of white calcareous structures, the other embedding itself into the live host tissue almost immediately after settlement. We argue that such a high degree of evolutionary flexibility of barnacle larvae played an important role in the successful evolution of complex symbiotic relationships in both coral reefs and other marine systems.
DOI: 10.6084/m9.figshare.12254456.v1
title: Table S2a-b. ML+BI parameters from Sponge symbiosis is facilitated by adaptive evolution of larval sensory and attachment structures in barnacles

description: Symbiotic relations and range of host usage are prominent in coral reefs and crucial to the stability of such systems. In order to explain how symbiotic relations are established and evolve, we used sponge-associated barnacles to ask (1) Does larval settlement on sponge hosts require novel adaptations facilitating symbiosis? (2) How do larvae settle and start life on their hosts? (3) How has this remarkable symbiotic lifestyle involving many barnacle species evolved? We found that the larvae (cyprids) of sponge-associated barnacles show a remarkably high level of interspecific variation compared with other barnacles. We document that variation in larval attachment devices are specifically related to properties of the surface on which they attach and metamorphose. Mapping of the larval and sponge surface features onto a molecular-based phylogeny showed that sponge symbiosis evolved separately at least three times within barnacles, with the same adaptive features being found in all larvae irrespective of phylogenetic relatedness. Furthermore, the metamorphosis of two species proceeded very differently, with one species remaining superficially on the host and developing a set of white calcareous structures, the other embedding itself into the live host tissue almost immediately after settlement. We argue that such a high degree of evolutionary flexibility of barnacle larvae played an important role in the successful evolution of complex symbiotic relationships in both coral reefs and other marine systems.
DOI: 10.6084/m9.figshare.12254435
title: Table S3a-c. Statistical analysis from Sponge symbiosis is facilitated by adaptive evolution of larval sensory and attachment structures in barnacles

description: Symbiotic relations and range of host usage are prominent in coral reefs and crucial to the stability of such systems. In order to explain how symbiotic relations are established and evolve, we used sponge-associated barnacles to ask (1) Does larval settlement on sponge hosts require novel adaptations facilitating symbiosis? (2) How do larvae settle and start life on their hosts? (3) How has this remarkable symbiotic lifestyle involving many barnacle species evolved? We found that the larvae (cyprids) of sponge-associated barnacles show a remarkably high level of interspecific variation compared with other barnacles. We document that variation in larval attachment devices are specifically related to properties of the surface on which they attach and metamorphose. Mapping of the larval and sponge surface features onto a molecular-based phylogeny showed that sponge symbiosis evolved separately at least three times within barnacles, with the same adaptive features being found in all larvae irrespective of phylogenetic relatedness. Furthermore, the metamorphosis of two species proceeded very differently, with one species remaining superficially on the host and developing a set of white calcareous structures, the other embedding itself into the live host tissue almost immediately after settlement. We argue that such a high degree of evolutionary flexibility of barnacle larvae played an important role in the successful evolution of complex symbiotic relationships in both coral reefs and other marine systems.
DOI: 10.6084/m9.figshare.12254435.v1
title: Table S3a-c. Statistical analysis from Sponge symbiosis is facilitated by adaptive evolution of larval sensory and attachment structures in barnacles

description: Symbiotic relations and range of host usage are prominent in coral reefs and crucial to the stability of such systems. In order to explain how symbiotic relations are established and evolve, we used sponge-associated barnacles to ask (1) Does larval settlement on sponge hosts require novel adaptations facilitating symbiosis? (2) How do larvae settle and start life on their hosts? (3) How has this remarkable symbiotic lifestyle involving many barnacle species evolved? We found that the larvae (cyprids) of sponge-associated barnacles show a remarkably high level of interspecific variation compared with other barnacles. We document that variation in larval attachment devices are specifically related to properties of the surface on which they attach and metamorphose. Mapping of the larval and sponge surface features onto a molecular-based phylogeny showed that sponge symbiosis evolved separately at least three times within barnacles, with the same adaptive features being found in all larvae irrespective of phylogenetic relatedness. Furthermore, the metamorphosis of two species proceeded very differently, with one species remaining superficially on the host and developing a set of white calcareous structures, the other embedding itself into the live host tissue almost immediately after settlement. We argue that such a high degree of evolutionary flexibility of barnacle larvae played an important role in the successful evolution of complex symbiotic relationships in both coral reefs and other marine systems.
DOI: 10.6084/m9.figshare.12254354
title: Synoptic time-scale variability of sediment

description: data-set for Synoptic time-scale variability of sediment
DOI: 10.6084/m9.figshare.12254354.v1
title: Synoptic time-scale variability of sediment

description: data-set for Synoptic time-scale variability of sediment
DOI: 10.6084/m9.figshare.12254363
title: Sequences

description: The sequence file contains MiSeq 16S sequences from stool samples of women with spontaneous abortion and with normal early pregnancy who elected to have an abortion. All controls had at least one successful pregnancy and no history of SA, preterm labor, or pre-eclampsia. Subjects with a verifiable cause of miscarriage were excluded.<br>
DOI: 10.6084/m9.figshare.12254342
title: gene.expression.symbol.txt

description: Total RNA from U251MG, U87MG, U251TR and U87TR cell lines were extracted and quanlified. A total amount of 3 μg RNA per sample was used as input material for library preparation. The library preparations went through standard Illumina Hiseq platform and 150 bp paired-end reads from transcriptome sequencing were generated. After quality control procedures, the data were mapped to human hg38 reference by STAR (Dobin et al., 2013). And then the expression level (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DOI: 10.6084/m9.figshare.12254363.v1
title: Sequences

description: The sequence file contains MiSeq 16S sequences from stool samples of women with spontaneous abortion and with normal early pregnancy who elected to have an abortion. All controls had at least one successful pregnancy and no history of SA, preterm labor, or pre-eclampsia. Subjects with a verifiable cause of miscarriage were excluded.<br>
DOI: 10.6084/m9.figshare.12254342.v1
title: gene.expression.symbol.txt

description: Total RNA from U251MG, U87MG, U251TR and U87TR cell lines were extracted and quanlified. A total amount of 3 μg RNA per sample was used as input material for library preparation. The library preparations went through standard Illumina Hiseq platform and 150 bp paired-end reads from transcriptome sequencing were generated. After quality control procedures, the data were mapped to human hg38 reference by STAR (Dobin et al., 2013). And then the expression level (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DOI: 10.6084/m9.figshare.12254243
title: biometric patent data

description: This data is collected in PATSTAT database.<br>
DOI: 10.6084/m9.figshare.12254243.v1
title: biometric patent data

description: This data is collected in PATSTAT database.<br>
DOI: 10.6084/m9.figshare.12254030
title: All entities analysis result_betweeness centrality

description: E-mental health entity analysis result of PMC data.
DOI: 10.6084/m9.figshare.12254018
title: Chinese companies in Indonesia 1890-1940 firm data.xlsx

description: This database is mainly derived from: https://www.colonialbusinessindonesia.nl/en (downloaded 01/07/2017)It only contains firms identified by their name and/or the names of their directors as Chinese companies operating in Indonesia during 1890-1940.It contains the data used in the article "Chinese Entrepreneurship in Indonesia: A Business Demography Approach", accepted for publication in the journal "Business History" (2020).In addition to the database source above, the spreadsheet also includes Chinese companies registered during 1890-1900 from the appendices of "Koloniaal Verslag". Several entries from the original database downloaded in 2017 were corrected.<br>
DOI: 10.17608/k6.auckland.12253088
title: Turbulence statistics for an unsteady lock-exchange gravity current during the slumping phase.

description: Dataset of a lock-exchange gravity current propagating over a mild slope for the computation of turbulence statistics. Data available at t =12.5 s after start of the computation (t<sub>adim</sub> = 29.1). The data are saved in the range -0.58 m &lt; x &lt; 2.895 m in the x-direction which encompasses the whole length of the current at this time step. <br> . List of files: - data_t291_vtk.tar.gz -&gt; Contains the 200 simulation results at t<sub>adim</sub> = 29.1 used for the statistics calculation. The data are in dimensional form - fields_turbulence_statistics_ensembleAveraging_t29.1 -&gt; Corresponding ensemble- and spanwise-averaged statistics <br> . Scaling quantities for non-dimensionalisation: - Velocity: u<sub>b</sub> = 0.349 m/s - Length: H/2 = 0.15 m - Time: t<sub>0</sub> = (H/2)/u<sub>b</sub> = 0.43 s <br> . Initial computational domain size: - Lock length: L<sub>x.lock</sub> = 0.58 m - Channel length: L<sub>x,channel</sub> = 5 m - Domain height: H = 0.3 m - Domain width: L<sub>z</sub> = 0.4 m - Inclination: tan(a) = 2% <br> . Physical conditions: - density light fluid: rho<sub>0</sub> = 997.3 kg/m<sup>3</sup> - density dense fluid: rho<sub>1</sub> = 1080 kg/m<sup>3</sup> - kinematic viscosity: nu = 8.7327 10<sup>-7</sup> m<sup>2</sup>/s - density diffusivity: kappa = 8.7327 10<sup>-7</sup> m<sup>2</sup>/s - gravity vector: g = 9.81 m/s<sup>2</sup> - Reynolds number: Re<sub>b</sub> = u<sub>b</sub>(H/2)/nu = 60 000 - Schmidt number: Sc = nu/kappa = 1 <br> . Grid resolution - Uniform mesh spacing: delta = 0.0054 m - first vertical mesh spacing at bottom wall dy<sub>1</sub> = 0.0002 m<br>. Initial conditions:- -0.45 &lt; u<sub>i</sub>/u<sub>b</sub> &lt; 0.45 and m = 1 for x &lt; 0<br>. Boundary conditions- Bottom: no slip wall- side walls: symmetry- Front, back and top walls: slip walls<br> <br>
DOI: 10.17608/k6.auckland.12253088.v1
title: Turbulence statistics for an unsteady lock-exchange gravity current during the slumping phase.

description: Dataset of a lock-exchange gravity current propagating over a mild slope for the computation of turbulence statistics. Data available at t =12.5 s after start of the computation (t<sub>adim</sub> = 29.1). The data are saved in the range -0.58 m &lt; x &lt; 2.895 m in the x-direction which encompasses the whole length of the current at this time step. <br> . List of files: - data_t291_vtk.tar.gz -&gt; Contains the 200 simulation results at t<sub>adim</sub> = 29.1 used for the statistics calculation. The data are in dimensional form - fields_turbulence_statistics_ensembleAveraging_t29.1 -&gt; Corresponding ensemble- and spanwise-averaged statistics <br> . Scaling quantities for non-dimensionalisation: - Velocity: u<sub>b</sub> = 0.349 m/s - Length: H/2 = 0.15 m - Time: t<sub>0</sub> = (H/2)/u<sub>b</sub> = 0.43 s <br> . Initial computational domain size: - Lock length: L<sub>x.lock</sub> = 0.58 m - Channel length: L<sub>x,channel</sub> = 5 m - Domain height: H = 0.3 m - Domain width: L<sub>z</sub> = 0.4 m - Inclination: tan(a) = 2% <br> . Physical conditions: - density light fluid: rho<sub>0</sub> = 997.3 kg/m<sup>3</sup> - density dense fluid: rho<sub>1</sub> = 1080 kg/m<sup>3</sup> - kinematic viscosity: nu = 8.7327 10<sup>-7</sup> m<sup>2</sup>/s - density diffusivity: kappa = 8.7327 10<sup>-7</sup> m<sup>2</sup>/s - gravity vector: g = 9.81 m/s<sup>2</sup> - Reynolds number: Re<sub>b</sub> = u<sub>b</sub>(H/2)/nu = 60 000 - Schmidt number: Sc = nu/kappa = 1 <br> . Grid resolution - Uniform mesh spacing: delta = 0.0054 m - first vertical mesh spacing at bottom wall dy<sub>1</sub> = 0.0002 m<br>. Initial conditions:- -0.45 &lt; u<sub>i</sub>/u<sub>b</sub> &lt; 0.45 and m = 1 for x &lt; 0<br>. Boundary conditions- Bottom: no slip wall- side walls: symmetry- Front, back and top walls: slip walls<br> <br>
DOI: 10.6084/m9.figshare.12253085
title: Assembly and regulation of the chlorhexidine specific efflux pump AceI

description: Raw Mass Spectrometry data for main figures and supplementary figures for the journal article "Assembly and regulation of the chlorhexidine-specific efflux pump AceI".
DOI: 10.6084/m9.figshare.12253082
title: Core Concepts Supplement 2

description: Supplement 2 for Evaluation of Core Concepts of Physiology in Undergraduate Physiology Curricula: Results from Faculty and Student Surveys
DOI: 10.6084/m9.figshare.12253082.v1
title: Core Concepts Supplement 2

description: Supplement 2 for Evaluation of Core Concepts of Physiology in Undergraduate Physiology Curricula: Results from Faculty and Student Surveys
DOI: 10.6084/m9.figshare.12253058
title: Core Concepts Supplement 1

description: Supplement 1 for Evaluation of Core Concepts of Physiology in Undergraduate Physiology Curricula: Results from Faculty and Student Surveys
DOI: 10.6084/m9.figshare.12253058.v1
title: Core Concepts Supplement 1

description: Supplement 1 for Evaluation of Core Concepts of Physiology in Undergraduate Physiology Curricula: Results from Faculty and Student Surveys
DOI: 10.6084/m9.figshare.12253013
title: Data from: POVERTY AND ENVIRONMENTAL DRIVERS EXPLAIN THE SPATIAL HETEROGENEITY OF SNAKEBITE ENVENOMING AND MORTALITY RISK IN COLOMBIA

description: Save all the files in a same folder. They must be in the same folder than the code. Please update the section in the code called setwd to your new folder with all data, this is needed to compile.
DOI: 10.6084/m9.figshare.12252992
title: Slide_depth

description: This folder contains the files used to numerically model submarine landslide wave generation at different slide initiation depths using Fluidity software. <br>Contains .flml files which sets the domain depth, slide initiation depth and acceleration. The acceleration profile was changed at each depth either set to 'Smith', 'Harbtiz' or 'Grilli' within the .flml. The acceleration profiles were described in the slide_movement.py file. Within the .flml, slide depth was changed to determine the influence over wave height. The return depth was increased to increase depth from 50m to 450m.<br>This folder also contains the .py flied that governed slide movement and contains the dimensions of the slide. For each slide depth modelled, the volume was kept constant.
DOI: 10.6084/m9.figshare.12253013.v1
title: Data from: POVERTY AND ENVIRONMENTAL DRIVERS EXPLAIN THE SPATIAL HETEROGENEITY OF SNAKEBITE ENVENOMING AND MORTALITY RISK IN COLOMBIA

description: Save all the files in a same folder. They must be in the same folder than the code. Please update the section in the code called setwd to your new folder with all data, this is needed to compile.
DOI: 10.6084/m9.figshare.12252992.v1
title: Slide_depth

description: This folder contains the files used to numerically model submarine landslide wave generation at different slide initiation depths using Fluidity software. <br>Contains .flml files which sets the domain depth, slide initiation depth and acceleration. The acceleration profile was changed at each depth either set to 'Smith', 'Harbtiz' or 'Grilli' within the .flml. The acceleration profiles were described in the slide_movement.py file. Within the .flml, slide depth was changed to determine the influence over wave height. The return depth was increased to increase depth from 50m to 450m.<br>This folder also contains the .py flied that governed slide movement and contains the dimensions of the slide. For each slide depth modelled, the volume was kept constant.
DOI: 10.1184/r1/12252968
title: Tradeoffs between automation and light vehicle electrification

description: All underlying figure data and MATLAB code for Nature Energy manuscript. The results of the Monte Carlo analysis presented in the paper can be reproduced by running the Monte Carlo code provided in MATLAB/Octave.
DOI: 10.6084/m9.figshare.12252962
title: 500 example structures from Materials Project

description: 500 example structures from Materials Project for machine learning experimentation.
DOI: 10.1184/r1/12252968.v1
title: Tradeoffs between automation and light vehicle electrification

description: All underlying figure data and MATLAB code for Nature Energy manuscript. The results of the Monte Carlo analysis presented in the paper can be reproduced by running the Monte Carlo code provided in MATLAB/Octave.
DOI: 10.6084/m9.figshare.12252956
title: Figure 3AC.xlsx

description: Data presented in Figure 3 A and C.
DOI: 10.6084/m9.figshare.12252953
title: Figure 4AB.xlsx

description: Data presented in Figure 4 A and B.
DOI: 10.6084/m9.figshare.12252959
title: Figure 4C.xlsx

description: Data presented in Figure 4C.
DOI: 10.6084/m9.figshare.12252962.v1
title: 500 example structures from Materials Project

description: 500 example structures from Materials Project for machine learning experimentation.
DOI: 10.6084/m9.figshare.12252953.v1
title: Figure 4AB.xlsx

description: Data presented in Figure 4 A and B.
DOI: 10.6084/m9.figshare.12252956.v1
title: Figure 3AC.xlsx

description: Data presented in Figure 3 A and C.
DOI: 10.6084/m9.figshare.12252959.v1
title: Figure 4C.xlsx

description: Data presented in Figure 4C.
DOI: 10.6084/m9.figshare.12252902
title: Variant calls for Candida duobushaemulonii

description: GATK variant set for <i>C.</i> <i>duobushaemulonii </i>isolates from Gade et al<i> "</i>Understanding the emergence of multidrug-resistant<i> Candida</i>: Using whole-genome sequencing to describe the population structure of <i>Candida haemulonii</i> species complex", 2020.<br><b></b>
DOI: 10.6084/m9.figshare.12252908
title: Variant calls for Candida haemulonii

description: GATK variant set for <i>C.</i> <i>haemulonii </i>isolates from Gade et al<i> "</i>Understanding the emergence of multidrug-resistant<i> Candida</i>: Using whole-genome sequencing to describe the population structure of <i>Candida haemulonii</i> species complex" 2020.
DOI: 10.6084/m9.figshare.12252911
title: Variant calls for Candida pseudohaemulonii

description: GATK variant set for <i>C.</i> <i>pseudohaemulonii </i>isolates from Gade et al<i> "</i>Understanding the emergence of multidrug-resistant<i> Candida</i>: Using whole-genome sequencing to describe the population structure of <i>Candida haemulonii</i> species complex" 2020.
DOI: 10.6084/m9.figshare.12252914
title: Variant calls for Candida vulturna

description: GATK variant set for <i>C.</i> <i>vulturna </i>isolates from Gade et al<i> "</i>Understanding the emergence of multidrug-resistant<i> Candida</i>: Using whole-genome sequencing to describe the population structure of <i>Candida haemulonii</i> species complex" 2020.
DOI: 10.6084/m9.figshare.12252911.v1
title: Variant calls for Candida pseudohaemulonii

description: GATK variant set for <i>C.</i> <i>pseudohaemulonii </i>isolates from Gade et al<i> "</i>Understanding the emergence of multidrug-resistant<i> Candida</i>: Using whole-genome sequencing to describe the population structure of <i>Candida haemulonii</i> species complex" 2020.
DOI: 10.6084/m9.figshare.12252914.v1
title: Variant calls for Candida vulturna

description: GATK variant set for <i>C.</i> <i>vulturna </i>isolates from Gade et al<i> "</i>Understanding the emergence of multidrug-resistant<i> Candida</i>: Using whole-genome sequencing to describe the population structure of <i>Candida haemulonii</i> species complex" 2020.
DOI: 10.6084/m9.figshare.12252908.v1
title: Variant calls for Candida haemulonii

description: GATK variant set for <i>C.</i> <i>haemulonii </i>isolates from Gade et al<i> "</i>Understanding the emergence of multidrug-resistant<i> Candida</i>: Using whole-genome sequencing to describe the population structure of <i>Candida haemulonii</i> species complex" 2020.
DOI: 10.6084/m9.figshare.12861041
title: Computational metadata.zip

description: Date submited for possible publication on Effect and Mechanism on Climate based on Time and Space Scales”
DOI: 10.6084/m9.figshare.12861041.v1
title: Computational metadata.zip

description: Date submited for possible publication on Effect and Mechanism on Climate based on Time and Space Scales”
DOI: 10.6084/m9.figshare.12252824
title: Satellite observations of ammonia and aerosol optical properties during the 2015 Indonesian fire

description: - Daily total column NH3 from the Cross-track Infrared Sounder instrument on the Suomi National Polar-orbiting Partnership (NPP) satellite from September 1st through October 31st 2015 when severity and emission of the wildfires peaked- Daily aerosol optical depth (AOD) and single scattering albedo (SSA) from the Multi-angle Imaging SpectroRadiometer (MISR) V23- Daily cloud motion vectors (CMVs) from MISR- Using the Hybrid Single-Particle Lagrangian Integrated Trajectory model (HYSPLIT), trajectories of the smoke plumes from the 2015 Indonesian fire have been calculated. <br>
DOI: 10.6084/m9.figshare.12252824.v1
title: Satellite observations of ammonia and aerosol optical properties during the 2015 Indonesian fire

description: - Daily total column NH3 from the Cross-track Infrared Sounder instrument on the Suomi National Polar-orbiting Partnership (NPP) satellite from September 1st through October 31st 2015 when severity and emission of the wildfires peaked- Daily aerosol optical depth (AOD) and single scattering albedo (SSA) from the Multi-angle Imaging SpectroRadiometer (MISR) V23- Daily cloud motion vectors (CMVs) from MISR- Using the Hybrid Single-Particle Lagrangian Integrated Trajectory model (HYSPLIT), trajectories of the smoke plumes from the 2015 Indonesian fire have been calculated. <br>
DOI: 10.6084/m9.figshare.12252740
title: sphinx_029.tar.gz

description: 29/33 CAPTCHA data
DOI: 10.6084/m9.figshare.12252731
title: HMT_MAGs

description: Metagenome assembled genomes of heterotrophic marine thaumarchaea. <br>