cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.23816190
title: Zebrafish OCM imagery

description: Optic cup morphogenesis (OCM) generates the basic structure of the vertebrate eye. Although it is commonly depicted as a series of epithelial sheet folding events, this does not represent an empirically supported model. Here, we combine four-dimensional imaging with custom cell tracking software and photoactivatable fluorophore labeling to determine the cellular dynamics underlying OCM in zebrafish. Although cell division contributes to growth, we find it dispensable for eye formation. OCM depends instead on a complex set of cell movements coordinated between the prospective neural retina, retinal pigmented epithelium (RPE) and lens. Optic vesicle evagination persists for longer than expected; cells move in a pinwheel pattern during optic vesicle elongation and retinal precursors involute around the rim of the invaginating optic cup. We identify unanticipated movements, particularly of central and peripheral retina, RPE and lens. From cell tracking data, we generate retina, RPE and lens subdomain fate maps, which reveal novel adjacencies that might determine corresponding developmental signaling events. Finally, we find that similar movements also occur during chick eye morphogenesis, suggesting that the underlying choreography is conserved among vertebrates.
DOI: 10.25378/janelia.23816190.v1
title: Zebrafish OCM imagery

description: Optic cup morphogenesis (OCM) generates the basic structure of the vertebrate eye. Although it is commonly depicted as a series of epithelial sheet folding events, this does not represent an empirically supported model. Here, we combine four-dimensional imaging with custom cell tracking software and photoactivatable fluorophore labeling to determine the cellular dynamics underlying OCM in zebrafish. Although cell division contributes to growth, we find it dispensable for eye formation. OCM depends instead on a complex set of cell movements coordinated between the prospective neural retina, retinal pigmented epithelium (RPE) and lens. Optic vesicle evagination persists for longer than expected; cells move in a pinwheel pattern during optic vesicle elongation and retinal precursors involute around the rim of the invaginating optic cup. We identify unanticipated movements, particularly of central and peripheral retina, RPE and lens. From cell tracking data, we generate retina, RPE and lens subdomain fate maps, which reveal novel adjacencies that might determine corresponding developmental signaling events. Finally, we find that similar movements also occur during chick eye morphogenesis, suggesting that the underlying choreography is conserved among vertebrates.
DOI: 10.25378/janelia.23816295
title: Drosophila GAL4 brain imagery

description: Precise, repeatable genetic access to specific neurons via GAL4/UAS and related methods is a key advantage of <i>Drosophila</i> neuroscience. Neuronal targeting is typically documented using light microscopy of full GAL4 expression patterns, which generally lack the single-cell resolution required for reliable cell type identification. Here, we use stochastic GAL4 labeling with the MultiColor FlpOut approach to generate cellular resolution confocal images at large scale. We are releasing aligned images of 74,000 such adult central nervous systems. An anticipated use of this resource is to bridge the gap between neurons identified by electron or light microscopy. Identifying individual neurons that make up each GAL4 expression pattern improves the prediction of split-GAL4 combinations targeting particular neurons. To this end, we have made the images searchable on the NeuronBridge website. We demonstrate the potential of NeuronBridge to rapidly and effectively identify neuron matches based on morphology across imaging modalities and datasets.
DOI: 10.25378/janelia.23816295.v1
title: Drosophila GAL4 brain imagery

description: Precise, repeatable genetic access to specific neurons via GAL4/UAS and related methods is a key advantage of <i>Drosophila</i> neuroscience. Neuronal targeting is typically documented using light microscopy of full GAL4 expression patterns, which generally lack the single-cell resolution required for reliable cell type identification. Here, we use stochastic GAL4 labeling with the MultiColor FlpOut approach to generate cellular resolution confocal images at large scale. We are releasing aligned images of 74,000 such adult central nervous systems. An anticipated use of this resource is to bridge the gap between neurons identified by electron or light microscopy. Identifying individual neurons that make up each GAL4 expression pattern improves the prediction of split-GAL4 combinations targeting particular neurons. To this end, we have made the images searchable on the NeuronBridge website. We demonstrate the potential of NeuronBridge to rapidly and effectively identify neuron matches based on morphology across imaging modalities and datasets.
DOI: 10.6084/m9.figshare.23826450.v1
title: Supplementary files for generalization manuscript

description: Figures and raw data for manuscript: "Smaller models do not exhibit superior generalization performance". Includes the following files:best_vs_smallest.zip: TSV files containing results of "best" vs. "smallest good" experiments (LASSO parameters and performance measurements), for each gene in Vogelstein et al. 2013 datasettcga_ccle_all_genes_figures.zip: Figures (performance curves, model sparsity, best vs. smallest good results) for TCGA &lt;-&gt; CCLE generalization, for each gene in Vogelstein et al. 2013 datasetcancer_type_all_genes_figures.zip: Figures for cancer type generalization experiments, for each gene/cancer type combination in the datasettcga_ccle_raw_results.zip: TSV files containing performance results (AUROC, AUPR) for TCGA -&gt; CCLE generalization, for each gene on each of 8 cross-validation folds (4-fold CV x 2 random seeds), for each LASSO parameterccle_tcga_raw_results.zip: Same as above, for CCLE -&gt; TCGA generalizationcancer_type_raw_results.zip: Same as above, for cancer type holdout generalization experiments on TCGAtcga_ccle_nn_raw_results.zip: Same as above, for TCGA -&gt; CCLE generalization using a fully-connected neural network, with hidden layer size (rather than LASSO parameter) as the regularization axis
DOI: 10.6084/m9.figshare.23826450
title: Supplementary files for generalization manuscript

description: Figures and raw data for manuscript: "Smaller models do not exhibit superior generalization performance". Includes the following files:best_vs_smallest.zip: TSV files containing results of "best" vs. "smallest good" experiments (LASSO parameters and performance measurements), for each gene in Vogelstein et al. 2013 datasettcga_ccle_all_genes_figures.zip: Figures (performance curves, model sparsity, best vs. smallest good results) for TCGA &lt;-&gt; CCLE generalization, for each gene in Vogelstein et al. 2013 datasetcancer_type_all_genes_figures.zip: Figures for cancer type generalization experiments, for each gene/cancer type combination in the datasettcga_ccle_raw_results.zip: TSV files containing performance results (AUROC, AUPR) for TCGA -&gt; CCLE generalization, for each gene on each of 8 cross-validation folds (4-fold CV x 2 random seeds), for each LASSO parameterccle_tcga_raw_results.zip: Same as above, for CCLE -&gt; TCGA generalizationcancer_type_raw_results.zip: Same as above, for cancer type holdout generalization experiments on TCGAtcga_ccle_nn_raw_results.zip: Same as above, for TCGA -&gt; CCLE generalization using a fully-connected neural network, with hidden layer size (rather than LASSO parameter) as the regularization axis
DOI: 10.6084/m9.figshare.23837865
title: 3869Maqam_dataset.zip

description: Dataset number 2 of Maqam Classification of Quranic Recitations using Deep Learning article, By Faisal Omari.3869 audio samples of Quranic recitations, including 8 reciteres and 8 maqams.
DOI: 10.6073/pasta/ffc74da864178596e85030c41242e0c6
title: Larval euphausiids collected using a 1 x 1 m square frame net with 333-μm mesh aboard Palmer LTER annual cruises off the coast of the Western Antarctic Peninsula, 1993-2013

description: Euphausiids (krill) are abundant along the Western Antarctic Peninsula where they have important impacts on the marine ecosystem and biogeochemical cycling. Euphausiids develop through a series of morphologically distinct larval stages within the first year of their life cycle. The calyptopis stages are followed by the furcilia stages before individuals recruit to the post-larval population. Larvae collected during Janury were most likely spawned during the preceding weeks or months of Antarctic spring/summer. Euphausia superba and Thysanoessa macrura are the most abundant euphausiid species along the Western Antarctic Peninsula. Euphausia crystallorophias, Euphausia frigida, and Euphausia triacantha are present but less abundant in the region. Samples were collected with a 1 x 1 m square frame net with 333-μm mesh towed obliquely to a depth of typically 300 m. Density of total calyptopis and furcilia larvae (all species combined) was determined for a subset of samples collected on the annual Palmer LTER cruises to cover the latitudinal and cross-shelf gradients of the study region. Larval euphausiid abundance varies spatially as spawning output is not homogeneous across the region. Larval euphausiid abundance also varies year-to-year due to changes in population demographics and environmental conditions.
DOI: 10.25345/c5bn9xd23
title: MassIVE MSV000092589 - GNPS_positive-mode_cashew-nut_Mikael
title: Analise de extrato de castanha de caju no modo ion positivo
DOI: 10.5517/ccdc.csd.cc2fxzw7
title: CCDC 2262190: Experimental Crystal Structure Determination

description: Related Article: Sipra Sucharita Sahoo, Pradeepta K. Panda|2023|Chem.Commun.|59|9603|doi:10.1039/D3CC02336B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15482/usda.adc/1529364
title: Data from: Effects of solar energy development on ants in the Mojave Desert

description: Data files for manuscript titled "Effects of solar energy development on ants in the Mojave Desert".
Excel file with 4 tabs: Metadata; Abundance, Richness, Shannon; Community Composition; and Functional Traits. Metadata is contained within Excel file that describes all variables for each tab.
Abstract from paper:
Land-use change from solar energy development may affect desert ecosystems and the soils, plants, and animals therein, yet our understanding of these interactions is nascent. With their ubiquity, criticality as ecosystem constituents, and sensitivity to environmental variation, ants may be useful study organisms for elucidating ecological effects of solar energy development in deserts. Our objectives were to disentangle the response of a desert ant community to solar energy development decisions and test the efficacy of ants as bioindicators at Ivanpah Solar Electric Generating System (ISEGS, 392 MW) in the Mojave Desert, USA. We used pitfall traps to collect ants in treatments representing different solar energy development decisions, including variably intense site preparation practices: blading (i.e., bulldozing) and mowing, and establishment of undeveloped patches in solar fields replicated across three power blocks comprising ISEGS and in undeveloped control sites surrounding ISEGS. We determined that ant abundance, species richness, Shannon Diversity Index, and functional richness was lower in bladed treatments than in all other treatments and controls. For most taxonomic and functional ant responses, we detected no difference between non-bladed treatments and controls; these results suggest that less intensive site preparation and increased spatial heterogeneity (i.e., undeveloped patches in solar fields) reduce negative effects of solar energy development on desert ants. However, our results suggest that ants may serve as useful bioindicators of the severity of anthropogenic disturbance from solar energy development in deserts, and indicator analysis signifies that solar energy infrastructure may negatively affect some species with high ecological value (e.g., harvester ants). Negative effects of solar energy development on ants can have significant implications for desert ecosystem function and integrity, but conservation-minded solar facility design and construction may lead to avoidance of “bottom-up” ecological ramifications of increased solar production during the renewable energy transition.
DOI: 10.5281/zenodo.8208294
title: Unit-cell-thick zeolitic imidazolate framework films for membrane application

description: raw data for the manuscript with title of Unit-cell-thick zeolitic imidazolate framework films for membrane application
description: {"references": ["https://repository.kaust.edu.sa/handle/10754/690396"]}
DOI: 10.5281/zenodo.8208295
title: Unit-cell-thick zeolitic imidazolate framework films for membrane application

description: raw data for the manuscript with title of Unit-cell-thick zeolitic imidazolate framework films for membrane application
DOI: 10.5281/zenodo.8212765
title: Unit-cell-thick zeolitic imidazolate framework films for membrane application

description: raw data for the manuscript with title of Unit-cell-thick zeolitic imidazolate framework films for membrane application
description: {"references": ["https://repository.kaust.edu.sa/handle/10754/690396"]}
DOI: 10.6084/m9.figshare.23154923.v3
title: Datafiles

description: These are all of the datafiles use to produce the figures and data reported in the manuscript.
DOI: 10.6084/m9.figshare.23826144
title: Data files for "Phylogenomics reveals the history of host use in mosquitoes," Soghigian et al. 2023.

description: Data files for "Phylogenomics reveals the history of host use in mosquitoes," Soghigian et al. 2023. These are raw alignment and R data/analysis files that we presented in our manuscript. For code and other resources, refer to our GitHub repository (https://github.com/jsoghigian/culicitree).Soghigian_etal_NatComm_Culicidae_pcm_R.tar.gz - The scripts, inputs, and outputs for our phylogenetic comparative methods.aa_pruned_75.aa.phy.tar.bz2 - The amino acid alignment used to generate the maximum likelihood topology discussed in the manuscript and used for subsequent analyses.nt_pruned_75.phy.tar.bz2 - The nucleotide alignment discussed in the manuscript. Due to saturation, we focus analyses on codon position two.pres90.aa.noog.phy.tar.bz2 - The alignment used in MCMCTree for divergence time analyses.aa_pruned_75.aa.parts - Partition file for the amino acid alignment.nt*.parts files - Partition files for the nucleotide alignment.
DOI: 10.6073/pasta/9bdd05f6cddcfe9218658d7c03ad6683
title: McMurdo Dry Valleys LTER: Lake level surveys in the McMurdo Dry Valleys, Antarctica from 1991 to present

description: Manual lake level measurements are conducted for the lakes in the McMurdo Dry Valleys, Antarctica. The survey includes Lakes Fryxell, Hoare, Bonney, Vida, Vanda, Don Juan Pond, Miers, House, and Joyce.
DOI: 10.7910/dvn/gxx1ts/o7ahau
title: data_reg_irt3.csv

description: Main data-set for analysis.
DOI: 10.7910/dvn/gxx1ts/oblvuz
title: analysis.R

description: :unav
DOI: 10.7910/dvn/gxx1ts/vo8p3x
title: adj.R

description: :unav
DOI: 10.15129/3f9b4f09-c509-4b23-98de-cdf3c3123fa1
title: Data for: "Generation of the atomic spin orientation with a linearly polarised beam in room-temperature alkali-metal vapour"

description: Fig2: 2D rf spectra recorded while changing probe detuning. Fig3: rf spectra recorded at different laser powers. Fig4: (a) rf spectra with linearly polarised probe beam only, probe beam with + circularly polarised pump beam and probe beam with - circularly polarised pump beam. (b) amplitude data for the three cases listed in (a) as probe beam power is scanned. Fig5: rf spectra as bias magnetic field is increased.
DOI: 10.25345/c5pd5r
title: MassIVE MSV000084453 - GNPS_Cyanobacteria extracts and fractions - LC-MSMS
title: Cyanobacteria extracts and SPE fractions. LC MSMS analysis was performed in an UltiMate 3000 UPLC system (Thermo Scientific) using a Kinetex 1.7 mm C18 reversed phase UHPLC column (50 X 2.1 mm) and Maxis Impact HD Q-TOF mass spectrometer (Bruker Daltonics) equipped with ESI source.
DOI: 10.17632/6sfbdpympy.1
title: Data for: Effect of Al, Ti and C additions on Widmanstätten microstructure and mechanical properties of cast Al0.6CoCrFeNi compositionally complex alloys.

description: The XRD data present in this paper are 2θ versus intensity data obtained from our diffractometer for all investigated alloys. The XRD data are provided in attached Excel files and a summary of the plotted diffraction patterns is shown in Fig. A1 of supplementary material. The calculated lattice parameters together with their standard deviation for each detected phase are listed in Table 1 for all studied alloys. BSE micrographs taken at different magnifications are presented to document the effect of microalloying on microstructure. For all CCAs, five BSE micrographs are provided, one low magnification image with a remnant indent spanning all phases present in the alloy and four other high magnification micrographs. From some of these BSE images, the microstructural parameters, i.e. mean prior grain size d and average thickness of FCC plates λ listed in Table 2, were determined. The overall chemical composition averaged over all phases present in the studied CCAs were determined in an external laboratory and are listed for some alloys in Table 3. In addition, the local chemical composition of the phases measured at three different locations in a transmission electron microscope (TEM) for the Ti3C0.25 CCA are given in Table 4. The mean volume fraction of the FCC phase provided in Table 2 were determined from a mass balance, see section B of supplementary material. The raw tensile results data obtained at different temperatures are provided in the attached Excel files.
DOI: 10.25919/5da49ca4932aa
title: Parkes observations for project P860 semester 2019APRS_06

description: This is a request for observing time for the initial follow-up of pulsar discoveries from the low-latitude Galactic plane section of the HTRU survey (P630). We have now completed a first pass processing of the entire survey with our periodicity search algorithm as well as the partially-coherent segmented acceleration search pipeline, and have discovered 106 previously unknown pulsars. Interesting science can usually only be derived from a new pulsar after confirmation and a follow-up timing campaign is carried out. One year of initial timing is the minimum timespan required to fully characterise any newly-discovered pulsars, essential for deriving pulsar parameters such as the characteristic age, magnetic ?eld strength, spin-down rate, as well as to detect any unexpected behaviour of the pulsar which might result from emission instabilities. This follow-up timing project is necessary for following up on any interesting pulsar systems discovered from the HTRU Galactic plane survey. Since all of the pulsars on the observing list here are being followed-up for the first time, they will produce completely new and exciting results. In addition, this timing project will enable a large-scale examination of the Galactic plane pulsar population, exploring the true boundaries of pulsar parameter space.
DOI: 10.25919/5da47a9596891
title: Parkes observations for project P895 semester 2019APRS_03

description: Since the year 2005, the Parkes Pulsar Timing Array (PPTA) project has been placing ever more stringent constraints on the amplitude of a gravitational wave background signal. Such upper bounds on the amplitude of the gravitational wave signal are currently dominated by a single pulsar: PSR J1909-3744. The upper bound with this pulsar alone already cuts into the range of tenable theoretical models. Further reducing the amplitude bound (by continued regular observations of this pulsar) will significantly narrow that range. The first evidence of gravitational waves in the pulsar data are likely to be observed in the timing for PSR J1909-3744, but with only a single pulsar we will not be able to make an unambiguous detection. However, knowledge of the likely signal strength (derived from this pulsar) will help to optimise the observing strategy for the detection of the gravitational wave signals with existing or future pulsar timing arrays.
DOI: 10.5281/zenodo.3485211
title: driverMAPS run results for 20 tumor types from TCGA

description: driverMAPS run results for 20 tumor types from TCGA, fixed a formatting error in this version.
DOI: 10.17632/w6mcyb75nv.1
title: Data for: Electronic structure and magnetism of Al-doped tris(8-hydroxyquinoline)iron investigated by experiment and first-principle calculation

description: The uploaded data include raw data of experimental FTIR, XPS, M-H and theoretical molecule and cell structure, electron density, TDOS, PDOS, energy difference for the manuscript "Electronic structure and magnetism of Al-doped tris(8-hydroxyquinoline)iron investigated by experiment and first-principle calculation".
DOI: 10.5281/zenodo.630004
title: SRTM elevation data for the SAFE Project

description: <b>Description: </b>These files contain processed data from the Shuttle Radar Topograpy Mission (SRTM), providing 30 metre resolution elevation data across the research areas used in the SAFE Project .<br><br>The SRTM data used in these datasets was collected by NASA and the NGI and is freely downloadable. These files combine four panes of SRTM data to cover the SAFE sampling region and carry out some simple geoprocessing to produce a set of output files in the UTM 50N projection. Details of the geoprocessing can be found here: https://www.safeproject.net/dokuwiki/safe_gis/srtm.<b>Project: </b>This dataset was collected as part of the following SAFE research project: <b>SAFE CORE DATA</b><b>XML metadata: </b>GEMINI compliant metadata for this dataset is available here<b>Files: </b>This dataset consists of 6 files: SAFE_SRTM_metadata.xlsx, SRTM_UTM50N_processed.tif, SRTM_UTM50N_contour.zip, SRTM_UTM50N_aspect.tif, SRTM_UTM50N_seamask.tif, SRTM_UTM50N_slope.tif<b>SAFE_SRTM_metadata.xlsx</b>This file only contains metadata for the files below<b>SRTM_UTM50N_processed.tif</b>Description: Elevation data in UTM 50N geotiff<b>SRTM_UTM50N_contour.zip</b>Description: Zipped shapefile of 100 metre contours generated from raster data<b>SRTM_UTM50N_aspect.tif</b>Description: Derived slope aspect data in UTM 50N geotiff<b>SRTM_UTM50N_seamask.tif</b>Description: Seamask used in data processing in UTM 50N geotiff<b>SRTM_UTM50N_slope.tif</b>Description: Derived slope angle data in UTM 50N geotiff<b>Date range: </b>2010-10-01 to 2019-10-01<b>Latitudinal extent: </b>4.0223 to 5.9761<b>Longitudinal extent: </b>116.0242 to 117.9758
DOI: 10.25919/5da48f774cf2a
title: Parkes observations for project P958 semester 2019APRS_95

description: Fast radio bursts (FRBs) continue to raise more questions than they answer. Until a few months ago, only one burst – the only one known to repeat - had been localized to a bright radio nebula (either a young supernova remnant or pulsar wind nebulae) in a distant dwarf galaxy. Over the last year searches with the Australian Square Kilometre Array Pathfinder (ASKAP) have detected 28 bursts, two of which have been localised to host galaxies at redshifts &gt; 0.3. These bursts and their hosts are very unlike the repeater, suggesting there may be a dichotomy in the population. Over the next six months we expect to detect another 12 FRBs, which will also have sub-arcsecond localisations. Here we propose to search this population for repeats. Our comprehensive sample and a dense monitoring campaign of well localised bursts, at a fluence limit more than 60 times lower than that of their detections, will either confirm the presence of additional repeating FRBs or the uniqueness of FRB 121102 amongst the population.