cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5441/001/1.fs61hr7v/2
title: Deconstructing the flight paths of hippocampal-lesioned homing pigeons (data from Gagliardo et al. 2022)-reference-data

description: Gagliardo A, Cioccarelli S, Giunchi D, Pollonara E, Colombo S, Casini G, Bingman VP. 2023. Deconstructing the flight paths of hippocampal-lesioned homing pigeons as they navigate near home offers insight into spatial perception and memory without a hippocampus. Behav Brain Res. 436:114073. doi:10.1016/j.bbr.2022.114073
description: The aim of this study was to exploit detailed analyses of GPS-recorded tracks to better characterise the impact of hippocampal (HF) lesion on spatial memory and perception in the context of homing pigeon navigation when reliant on familiar landscape features near the home loft following repeated releases from the same three locations. As reported previously, following HF lesion, a low spatio-temporal resolution analysis revealed that homing pigeons fly less direct paths home once near the loft. We now further show that 1) HF-lesioned pigeons are less likely to display fidelity to a particular flight path home when released from the same locations multiple times, 2) intact pigeons are more likely to exploit leading-line landscape features, e.g., a road or the border of a woodlot, in developing flight-path fidelity and 3) even when flying a straight path HF-lesioned homing pigeons are more likely to display relatively rapid, oscillatory heading changes as if casting about for sensory, presumably visual information. The flight behaviour differences between the intact and HF-lesioned pigeons persisted across the four releases from the three locations, although the differences became smaller with increasing experience. Taken together, the GPS-track data offer a detailed characterisation of the effects of HF lesion on landscape-based, homing pigeon navigation, offering new insight into the role of the hippocampal formation in supporting memory-related, e.g., fidelity to a familiar route home, and perhaps perceptual-related, e.g., oscillating headings, navigational processes.
DOI: 10.5281/zenodo.7034578
title: Computational Prediction and Experimental Realisation of Earth Abundant Transparent Conducting Oxide Ga-doped ZnSb2O6 - computational datasets

description: Additional computational data for our publication on Ga-doped ZnSb2O6. This repository contains two files related to the defect calculations ("new-defect-corrections.json" and "aide-plotter"), which contain data concerning the charge correction schemes and total energies of all defect species, and the charge transition levels (which can be used to repeat the SCFL analysis), respectively. The other two files are the AMSET output files, which can be used to plot all the calculated charge transport data used in this study. Documentation for plotting using these files is provided at https://github.com/hackingmaterials/amset. Contact: joe.willis.15@ucl.ac.uk; d.scanlon@ucl.ac.uk
DOI: 10.5281/zenodo.7034577
title: Computational Prediction and Experimental Realisation of Earth Abundant Transparent Conducting Oxide Ga-doped ZnSb2O6 - computational datasets

description: Additional computational data for our publication on Ga-doped ZnSb2O6. This repository contains two files related to the defect calculations ("new-defect-corrections.json" and "aide-plotter"), which contain data concerning the charge correction schemes and total energies of all defect species, and the charge transition levels (which can be used to repeat the SCFL analysis), respectively. The other two files are the AMSET output files, which can be used to plot all the calculated charge transport data used in this study. Documentation for plotting using these files is provided at https://github.com/hackingmaterials/amset. Contact: joe.willis.15@ucl.ac.uk; d.scanlon@ucl.ac.uk
DOI: 10.6084/m9.figshare.20696533.v1
title: Table S14. Grouping of GbW in haploblock

description: <strong>Table S14. Grouping of GbW in haploblock</strong>
DOI: 10.6084/m9.figshare.20696530.v1
title: Table S13. Putative selected scan region

description: <strong>Table S13. Putative selected scan region</strong>
DOI: 10.6084/m9.figshare.20722438
title: buceros_bicornis_decontaminated_gx.fasta.gz

description: .......
DOI: 10.6084/m9.figshare.20722438.v1
title: buceros_bicornis_decontaminated_gx.fasta.gz

description: .......
DOI: 10.6084/m9.figshare.20696524.v1
title: Table S12. Gene variants annotation within haploblock

description: <strong>Table S12. Gene variants annotation within haploblock</strong>
DOI: 10.6084/m9.figshare.20696521.v1
title: Table S11. Grouping of cultivars in haploblock

description: <strong>Table S11. Grouping of cultivars in haploblock</strong>
DOI: 10.5281/zenodo.7034580
title: COURAGE - SwipeIt - Study 1 & 2 - SwipeIt-Tagging data

description: We have designed a serious mini-game (the mobile app “SwipeIt”) that allows for a playful and controllable interaction with potentially toxic content items. <br> The app was designed to be used in a classroom context to support classroom discussions around example social media items. Given that we know that the classification of social media items regarding different types of discrimination and toxic content varies between individuals, we first wanted to capture such differences and make them available as a resource for classroom discussions. In addition to triggering classroom discussions, this collection of data will also serve as a resource for further analyses using machine learning techniques. In study 1, we provided discrimination, hate speech, cyberbullying (cybermobbing) and verbal violence as labels.<br> In study 2, we provided discrimination, hate speech, cyberbullying (cybermobbing) and sexism as labels.
DOI: 10.5281/zenodo.7034579
title: COURAGE - SwipeIt - Study 1 & 2 - SwipeIt-Tagging data

description: We have designed a serious mini-game (the mobile app “SwipeIt”) that allows for a playful and controllable interaction with potentially toxic content items. <br> The app was designed to be used in a classroom context to support classroom discussions around example social media items. Given that we know that the classification of social media items regarding different types of discrimination and toxic content varies between individuals, we first wanted to capture such differences and make them available as a resource for classroom discussions. In addition to triggering classroom discussions, this collection of data will also serve as a resource for further analyses using machine learning techniques. In study 1, we provided discrimination, hate speech, cyberbullying (cybermobbing) and verbal violence as labels.<br> In study 2, we provided discrimination, hate speech, cyberbullying (cybermobbing) and sexism as labels.
DOI: 10.6084/m9.figshare.20696518.v1
title: Table S8. G. darwinii-specific SV overlapping genes

description: <strong>Table S8. G. darwinii-specific SV overlapping genes</strong>
DOI: 10.6084/m9.figshare.20696509.v1
title: Table S7. SV overlapping genes intorgressed from upland cotton

description: <strong>Table S7. SV overlapping genes intorgressed from upland cotton</strong>
DOI: 10.6084/m9.figshare.20722429
title: amazona_vinacea_decontaminated_gx.fasta.gz

description: ........
DOI: 10.6084/m9.figshare.20722429.v1
title: amazona_vinacea_decontaminated_gx.fasta.gz

description: ........
DOI: 10.6084/m9.figshare.20722432
title: barnardius_zonarius_decontaminated_gx.fasta.gz

description: .......
DOI: 10.6084/m9.figshare.20722432.v1
title: barnardius_zonarius_decontaminated_gx.fasta.gz

description: .......
DOI: 10.5281/zenodo.6866210
title: Stability characterization of microfluidic lipid-stabilized double emulsions under physiologically-relevant conditions

description: Double emulsions (DEs) are water-in-oil-in-water (or oil-in-water-in-oil) droplets with the potential to deliver combinatory therapies due to their ability to co-localize hydrophilic and hydrophobic molecules in the same carrier. However, DEs are thermodynamically unstable and only kinetically trapped. Extending this transitory state, rendering DEs more stable, would widen the possibilities of real-world applications, yet characterization of their stability in physiologically-relevant conditions is lacking. In this work, we used microfluidics to produce lipid-stabilized DEs with reproducible monodispersity and high encapsulation efficiency. We investigated DE stability under a range of physico-chemical parameters such as temperature, pH and mechanical stimulus. Stability through time was inversely proportional to temperature. DEs were significantly stable up to 8 days at 4 oC, 5 days at RT and 2 days at 37 oC. When encapsulating a cargo, DE stability decreased significantly. When exposed to a pH change, unloaded DEs were only significantly unstable at the extremes (pH 1 and 13), largely outside physiological ranges. When exposed to flow, unloaded DEs behaved similarly regardless of the mechanical stimulus applied, with approximately 70% remaining after 100 flow cycles of 10s. These results indicate that lipid-stabilized DEs produced via microfluidics could be tailored to endure physiologically-relevant conditions and act as carriers for drug delivery. Special attention should be given to the composition of the solutions, e.g. osmolarity ratio between inner and outer solutions, and the interaction of the molecules, e.g. carrier and cargo, involved in the final formulation.
DOI: 10.5281/zenodo.6866211
title: Stability characterization of microfluidic lipid-stabilized double emulsions under physiologically-relevant conditions

description: Double emulsions (DEs) are water-in-oil-in-water (or oil-in-water-in-oil) droplets with the potential to deliver combinatory therapies due to their ability to co-localize hydrophilic and hydrophobic molecules in the same carrier. However, DEs are thermodynamically unstable and only kinetically trapped. Extending this transitory state, rendering DEs more stable, would widen the possibilities of real-world applications, yet characterization of their stability in physiologically-relevant conditions is lacking. In this work, we used microfluidics to produce lipid-stabilized DEs with reproducible monodispersity and high encapsulation efficiency. We investigated DE stability under a range of physico-chemical parameters such as temperature, pH and mechanical stimulus. Stability through time was inversely proportional to temperature. DEs were significantly stable up to 8 days at 4 oC, 5 days at RT and 2 days at 37 oC. When encapsulating a cargo, DE stability decreased significantly. When exposed to a pH change, unloaded DEs were only significantly unstable at the extremes (pH 1 and 13), largely outside physiological ranges. When exposed to flow, unloaded DEs behaved similarly regardless of the mechanical stimulus applied, with approximately 70% remaining after 100 flow cycles of 10s. These results indicate that lipid-stabilized DEs produced via microfluidics could be tailored to endure physiologically-relevant conditions and act as carriers for drug delivery. Special attention should be given to the composition of the solutions, e.g. osmolarity ratio between inner and outer solutions, and the interaction of the molecules, e.g. carrier and cargo, involved in the final formulation.
DOI: 10.57745/yc6dx8/b59iq7
title: rpg_complete_2020_d32.zip

description: :unav
DOI: 10.57745/yc6dx8/37mcud
title: rpg_complete_2020_d09.zip

description: :unav
DOI: 10.6084/m9.figshare.20418570
title: Discordance_trees

description: The alternative topologies for six branches. Each file contains three topologies with the relative frequency values.
DOI: 10.6084/m9.figshare.20418570.v3
title: Discordance_trees

description: The alternative topologies for six branches. Each file contains three topologies with the relative frequency values.
DOI: 10.6084/m9.figshare.20418570.v2
title: Discordance_trees

description: The alternative topologies for six branches. Each file contains three topologies with the relative frequency values.
DOI: 10.6084/m9.figshare.20418594
title: Phylogenetic_tree

description: The dataset contains a newick format species tree with RAxML branch lengths and a fasta format file, in which we combinded 9653 alignments into one.
DOI: 10.6084/m9.figshare.20418594.v3
title: Phylogenetic_tree

description: The dataset contains a newick format species tree with RAxML branch lengths and a fasta format file, in which we combinded 9653 alignments into one.
DOI: 10.6084/m9.figshare.20418594.v2
title: Phylogenetic_tree

description: The dataset contains a newick format species tree with RAxML branch lengths and a fasta format file, in which we combinded 9653 alignments into one.
DOI: 10.6084/m9.figshare.20418582
title: one-to-one orthologs

description: The sheet contains 9653 one-to-one orthologs used in phylogeny inferring, with species name in the first row. We used the <em>Taeniopygia guttata</em> gene sets as the reference and performed a reciprocal best hit (RBH) method to get one-to-one orthologs.
DOI: 10.6084/m9.figshare.20418582.v3
title: one-to-one orthologs

description: The sheet contains 9653 one-to-one orthologs used in phylogeny inferring, with species name in the first row. We used the <em>Taeniopygia guttata</em> gene sets as the reference and performed a reciprocal best hit (RBH) method to get one-to-one orthologs.
DOI: 10.6084/m9.figshare.20418582.v2
title: one-to-one orthologs

description: The sheet contains 9653 one-to-one orthologs used in phylogeny inferring, with species name in the first row. We used the <em>Taeniopygia guttata</em> gene sets as the reference and performed a reciprocal best hit (RBH) method to get one-to-one orthologs.
DOI: 10.5281/zenodo.7029994
title: Large eddy simulations of precipitating marine stratocumulus are sensitive to free tropospheric aerosol concentrations

description: A sample of prognostic and diagnostic Control simulation data generated for our study. Data include the time series and vertical profiles used in the analysis of our study into the importance of free tropospheric aerosol in marine stratocumulus clouds. Full datasets are available on request from the author.
DOI: 10.5281/zenodo.7029993
title: Large eddy simulations of precipitating marine stratocumulus are sensitive to free tropospheric aerosol concentrations

description: A sample of prognostic and diagnostic Control simulation data generated for our study. Data include the time series and vertical profiles used in the analysis of our study into the importance of free tropospheric aerosol in marine stratocumulus clouds. Full datasets are available on request from the author.
DOI: 10.6084/m9.figshare.20418621
title: Functional_annotation

description: The dataset contains the functional annotation sheets of four manakins. The translated gene coding sequences were aligned to the SwissProt database (release-2020_05). Motifs and domains of each gene was annotated with modules PRINTS, SMART, PANTHER, ProSiteProfiles, ProSitePatterns, CDD, SFLD, Gene3D, SUPERFAMILY, and TMHMM of InterPro. The pathway in which the gene might be involved was aligned the protein sequence of each gene to the KEGG database (release-93).
DOI: 10.6084/m9.figshare.20418621.v3
title: Functional_annotation

description: The dataset contains the functional annotation sheets of four manakins. The translated gene coding sequences were aligned to the SwissProt database (release-2020_05). Motifs and domains of each gene was annotated with modules PRINTS, SMART, PANTHER, ProSiteProfiles, ProSitePatterns, CDD, SFLD, Gene3D, SUPERFAMILY, and TMHMM of InterPro. The pathway in which the gene might be involved was aligned the protein sequence of each gene to the KEGG database (release-93).
DOI: 10.6084/m9.figshare.20418621.v2
title: Functional_annotation

description: The dataset contains the functional annotation sheets of four manakins. The translated gene coding sequences were aligned to the SwissProt database (release-2020_05). Motifs and domains of each gene was annotated with modules PRINTS, SMART, PANTHER, ProSiteProfiles, ProSitePatterns, CDD, SFLD, Gene3D, SUPERFAMILY, and TMHMM of InterPro. The pathway in which the gene might be involved was aligned the protein sequence of each gene to the KEGG database (release-93).
DOI: 10.6084/m9.figshare.20418603
title: Protein-coding_gene_annotation

description: The dataset contains protein coding gene annotation files of four manakins. We used the homolog-based approach to annotate the protein-coding genes by using the protein sequences of <em>Gallus gallus</em>, <em>Taeniopygia guttata</em> and <em>Homo sapiens</em> downloaded from Ensembl release 105 as the reference gene sets.
DOI: 10.6084/m9.figshare.20418603.v3
title: Protein-coding_gene_annotation

description: The dataset contains protein coding gene annotation files of four manakins. We used the homolog-based approach to annotate the protein-coding genes by using the protein sequences of <em>Gallus gallus</em>, <em>Taeniopygia guttata</em> and <em>Homo sapiens</em> downloaded from Ensembl release 105 as the reference gene sets.
DOI: 10.6084/m9.figshare.20418603.v2
title: Protein-coding_gene_annotation

description: The dataset contains protein coding gene annotation files of four manakins. We used the homolog-based approach to annotate the protein-coding genes by using the protein sequences of <em>Gallus gallus</em>, <em>Taeniopygia guttata</em> and <em>Homo sapiens</em> downloaded from Ensembl release 105 as the reference gene sets.
DOI: 10.6084/m9.figshare.20418615
title: Repeat_annotation

description: The dataset contains repeat annotation files of four manakins. We used Tandem Repeat Finder (TRF, v4.09.1) to identify Tandem repeats. We used de novo methods with RepeatModeler (v2.0.2a) and LTR_Finder (v1.07), and homolog-based RepeatMasker (v4.1.2) to annotate transposable elements (TEs). We merged the annotation for each species separately into the corresponding species file.
DOI: 10.6084/m9.figshare.20418615.v3
title: Repeat_annotation

description: The dataset contains repeat annotation files of four manakins. We used Tandem Repeat Finder (TRF, v4.09.1) to identify Tandem repeats. We used de novo methods with RepeatModeler (v2.0.2a) and LTR_Finder (v1.07), and homolog-based RepeatMasker (v4.1.2) to annotate transposable elements (TEs). We merged the annotation for each species separately into the corresponding species file.
DOI: 10.6084/m9.figshare.20418615.v2
title: Repeat_annotation

description: The dataset contains repeat annotation files of four manakins. We used Tandem Repeat Finder (TRF, v4.09.1) to identify Tandem repeats. We used de novo methods with RepeatModeler (v2.0.2a) and LTR_Finder (v1.07), and homolog-based RepeatMasker (v4.1.2) to annotate transposable elements (TEs). We merged the annotation for each species separately into the corresponding species file.
DOI: 10.6084/m9.figshare.20418627
title: Diploid_genome_assembly

description: The dataset contains four folders corresponding to four manakins and each folder contains two fasta format files. We used the "style=pseudohap2" in Supernova version 2.0.1 to assemble the two ‘parallel’ pseudohaplotypes in separate FASTA files (pseudohap2.1.fasta.gz and pseudohap2.2.fasta.gz).
DOI: 10.6084/m9.figshare.20418627.v4
title: Diploid_genome_assembly

description: The dataset contains four folders corresponding to four manakins and each folder contains two fasta format files. We used the "style=pseudohap2" in Supernova version 2.0.1 to assemble the two ‘parallel’ pseudohaplotypes in separate FASTA files (pseudohap2.1.fasta.gz and pseudohap2.2.fasta.gz).
DOI: 10.6084/m9.figshare.20418627.v3
title: Diploid_genome_assembly

description: The dataset contains four folders corresponding to four manakins and each folder contains two fasta format files. We used the "style=pseudohap2" in Supernova version 2.0.1 to assemble the two ‘parallel’ pseudohaplotypes in separate FASTA files (pseudohap2.1.fasta.gz and pseudohap2.2.fasta.gz).
DOI: 10.25574/49333
title: Chandra X-ray Observatory ObsId 49333
DOI: 10.25574/49396
title: Chandra X-ray Observatory ObsId 49396
DOI: 10.6084/m9.figshare.20730820
title: Kampana Tower

description: Google maps review for Kampana Tower, historical city Kotor, Montenegro
DOI: 10.6084/m9.figshare.20730841
title: Sea Gate

description: Google maps reviews for Sea Kate, Kotor, Montenegrom
DOI: 10.6084/m9.figshare.20730841.v1
title: Sea Gate

description: Google maps reviews for Sea Kate, Kotor, Montenegrom
DOI: 10.6084/m9.figshare.20730649
title: Katedrala Svetog Tripuna - Cathedral of Saint Tryphon (1).xlsx

description: Google maps review for Cathedral of Saint Tryphon in Kotor, Montenegro
DOI: 10.6084/m9.figshare.20730649.v1
title: Katedrala Svetog Tripuna - Cathedral of Saint Tryphon (1).xlsx

description: Google maps review for Cathedral of Saint Tryphon in Kotor, Montenegro
DOI: 10.6084/m9.figshare.20730859
title: Kotor Fortress

description: Kotor Fortress Google maps review
DOI: 10.5281/zenodo.2631823
title: Aeolian saltation fieldwork: values for size-selective transport measurements

description: This excel spreadsheet (‘SizeSelectiveTransport.xlsx’) contains the following information on surface and airborne particle size distributions (PSDs) for size-selective saltation transport analyses at our six field sites (Jericoacoara, Rancho Guadalupe, Oceano N1, Oceano S1, Oceano N2, Oceano S2):


	<strong>“d_lower_mm”</strong> – Lower limit diameter for each particle size bin [mm].
	<strong>“d_mid_mm”</strong> – Midpoint diameter for each particle size bin [mm].
	<strong>“d_upper_mm”</strong> – Upper limit diameter for each particle size bin [mm].
	<strong>“dVdlnd_bed”</strong> – Site-averaged non-dimensionalized volume fraction in each size bin for surface samples, \(\frac{dV_{bed}}{d\ln(d)}\).


The field measurements from which these values were calculated are described in Martin and Kok (2017).


	<strong>“dVdlnd_air”</strong> – Site-averaged non-dimensionalized volume fraction in each size bin for airborne samples, \(\frac{dV_{air}}{d\ln(d)}\).
	Site-averaged non-dimensionalized volume fraction in each size bin for airborne samples, conditioned on each non-dimensionalized shear stress range, \(\frac{dV_{air}}{d\ln(d)}|_{\tau/\tau_{it}}\). Cases in which a PSD is lacking for a shear stress range are marked as “NaN”:
	
		<strong>“dVdlnd_air_taunorm_below_10”</strong> – for \(\tau/\tau_{it} \leq 1.0\)
		<strong>“dVdlnd_air_taunorm_10_15”</strong> – for \(1.0 &lt; \tau/\tau_{it} \leq 1.5\)
		<strong>“dVdlnd_air_taunorm_15_22</strong>” – for \(1.5 &lt; \tau/\tau_{it} \leq 2.2\)
		<strong>“dVdlnd_air_taunorm_22_30”</strong> – for \(2.2 &lt; \tau/\tau_{it} \leq 3.0\)
		<strong>“dVdlnd_air_taunorm_30_40”</strong> – for \(3.0 &lt; \tau/\tau_{it} \leq 4.0\)
	
	
	<strong>“f_bed”</strong> – Fraction of bed surface particles in size bin <em>i</em>, \(f_{bed,i}\). Fraction is computed only for bins with particle diameter <em>d</em> &gt; 1.3 mm. Bins below this value are marked as “NaN”.
	<strong>“f_air_bar”</strong> – Mean fraction of airborne particles in size bin <em>i</em>, \(\langle f_{air,i} \rangle\). Fraction is computed only for bins with particle diameter <em>d </em>&gt; 1.3 mm. Bins below this value are marked as “NaN”.
	<strong>“f_air_sigma”</strong> – Uncertainty on mean fraction of airborne particles in size bin <em>i</em>, \(\sigma_{\langle f_{air,i} \rangle}\). “NaN” values correspond to undefined values for f_air_bar.
description: {"references": ["Martin, R. L. and J. F. Kok (2017), Equal susceptibility and size-selective mobility in aeolian saltation (article in review)"]}