cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4382039
title: Ancient Greek Literature for Advanced Data Processing: A Text Fabric Representation of Open Access Texts in TEI XML

description: This data set contains a full conversion of Greek texts available in the Perseus Digital Library and the Open Greek and Latin Project to the Text Fabric data format. The main advantage of the Text Fabric datatype over the original TEI XML format is that it utilizes a strict separation of text and annotation in a flat data structure. At the same time, it permits multiple distinct formats of the same text as well as an unlimited depth of (embedded) annotations. Because of its flat data structure, it facilitates easy and clean procedures to analyze, transform, and enrich the available data. Many of these processes are very difficult to conduct while departing from the hierarchically organized XML tree representation.
description: License notes are attached to the metadata of each .tf-file (@availability). If no availability note exists, the license attributed to the data set as a whole is to be followed. License notes attached to each .tf-file are always to be followed over the general license.
DOI: 10.5281/zenodo.4382038
title: Ancient Greek Literature for Advanced Data Processing: A Text Fabric Representation of Open Access Texts in TEI XML

description: This data set contains a full conversion of Greek texts available in the Perseus Digital Library and the Open Greek and Latin Project to the Text Fabric data format. The main advantage of the Text Fabric datatype over the original TEI XML format is that it utilizes a strict separation of text and annotation in a flat data structure. At the same time, it permits multiple distinct formats of the same text as well as an unlimited depth of (embedded) annotations. Because of its flat data structure, it facilitates easy and clean procedures to analyze, transform, and enrich the available data. Many of these processes are very difficult to conduct while departing from the hierarchically organized XML tree representation.
description: License notes are attached to the metadata of each .tf-file (@availability). If no availability note exists, the license attributed to the data set as a whole is to be followed. License notes attached to each .tf-file are always to be followed over the general license.
DOI: 10.6084/m9.figshare.13190816
title: pf_stull_smith.tgz

description: gene trees, dated species trees, morphological datasets
DOI: 10.6084/m9.figshare.13190816.v1
title: pf_stull_smith.tgz

description: gene trees, dated species trees, morphological datasets
DOI: 10.25955/5f7ac4bdb1c1d
title: Challenges for ECRs in STEMM - On-line survey data supporting BioRxiv manuscript

description: This data set supports the article Survey of Australian STEMM Early Career Researchers published in BioRxiv in February 2020<br>Abstract:We sought to understand the pressures on Early Career Researchers (ECR) in the Science, Technology, Engineering, Mathematics, & Medicine (STEMM) disciplines, collecting data from 658 ECRs working in Australia. Respondents indicated a “<em>love of science</em>”, but most also indicated an intention to leave their position. Decisions were primarily motivated by job insecurity (52%), while grievances included poor supervision (60%), bullying or harassment (34%), inequitable hiring practices (39%) and poor support for families (9.6%). A concerning rate of “<em>questionable research practices</em>” by colleagues (34.1% to 41.1%) was reported to have impacted ECR career advancement. Our study links recent reports that characterise the health of the research industry, providing direct insight from ECRs on job insecurity, workplace culture challenges, and the logical rise of questionable research practices. Internationally, nationally and institutionally the research community needs to improve job security (care for our people) and the quality of research data (our product).<br><br>
DOI: 10.6092/unibo/amsacta/6572
title: Inventory of Urban Agriculture Projects in the Global North

description: Interoperable file of the inventory of urban agriculture projects in the Global North used in the publication: Orsini, F., Pennisi, G., Michelon, N., Minelli, A., Bazzocchi, G., Sanyé-Mengual, E., Gianquinto, G. (2020). Features and functions of urban agriculture in the Global North: a review. Frontiers in Sustainable Food Systems, 4:562513. https://www.doi.org/10.3389/fsufs.2020.562513
DOI: 10.6092/unibo/amsacta/6570
title: The Free-Ranging Italian Wolf (Canis lupus italicus): A Study of the Circulation of DNA and RNA Viruses in Three Italian Regions

description: This dataset is part of my Ph.D. research, which assesses the presence and the spread of DNA and RNA viruses in the free-ranging wolves found dead in Emilia-Romagna, Tuscany, and Calabria from August 2017 to July 2020. The research investigated through molecular methods the genomic DNA presence of three important DNA viruses (CPV-2 Canine Parvovirus type-2, CAdV-1 Canine Adenovirus type-1, CAdV-2 Canine Adenovirus type-2). Furthermore, the presence of genomic RNA of the important RNA viruses, Canine Coronavirus (CCoV) and Canine Distemper Virus (CDV), was also investigated. This dataset information will contribute to improve the knowledge of dog-wolf interface infectious diseases.
DOI: 10.5066/p9aq364r
title: Science to Inform Management of Floodplain Conservation Lands on the Middle Mississippi River

description: Within large-river ecosystems, floodplains serve a variety of important ecological functions. A recent survey of 80 managers of floodplain conservation lands along the Upper and Middle Mississippi and Lower Missouri Rivers in the central United States found that the most critical information needed to improve floodplain management centered on metrics for characterizing depth, extent, frequency, duration, and timing of inundation. These metrics can be delivered to managers efficiently through cloud-based interactive maps. To calculate these metrics, we interpolated an existing one-dimensional HEC-RAS hydraulic model for the Middle Mississippi River, which simulated water surface elevations at cross sections spaced (less than 1 kilometer) to sufficiently characterize water surface profiles along an approximately 800 kilometer stretch upstream from the confluence with the Mississippi River over an 80-year record at a daily time step. To translate these water surface elevations to inundation depths, we subtracted a merged terrain model consisting of floodplain LIDAR and bathymetric surveys of the river channel. We completed these calculations for an 800 kilometer stretch of the Missouri River, spanning from Rulo, Nebraska to the river's confluence with the Mississippi River. Analyzed areas include the entirety of the Mississippi River floodplain, with the exception of the St. Louis metropolitan area in which analysis was constrained to currently unleveed areas only. This approach resulted in a 29,000 plus day time series of inundation depths across the floodplain using grid cells with 30 meter spatial resolution. This dataset presents 14 metrics for each of two scenarios, one using a baseline timeseries of stages from the HEC-RAS simulation and one using a timeseries of stages adjusted to account for removal of existing levees from the floodplain. These metrics are calculated on a per pixel basis and encompass a variety of temporal criteria generally relevant to flora and fauna of interest to floodplain managers, including, for example, the average number of days inundated per year within a growing season. We also include the base elevation layer that we generated to calculate depth of inundation from interpolated water-surface elevations.
DOI: 10.5281/zenodo.4396257
title: The Future of Large Dams in Global Food and Energy Systems

description: Global basin scale data on current and future demands for irrigation and hydropower, as well as available resources in terms of solar photovoltaic and existing storage.
DOI: 10.6084/m9.figshare.13493721
title: 34 new Lak phage genomes

description: The new Lak phage genomes reconstructed from animal metagenomic datasets.
DOI: 10.6084/m9.figshare.13493721.v3
title: 34 new Lak phage genomes

description: The new Lak phage genomes reconstructed from animal metagenomic datasets.
DOI: 10.6084/m9.figshare.13260020
title: Hourly gridded precipitation product in (CHI)llon, (RI)mac and (LU)rin basins (CHIRILU v2)

description: Hourly gridded precipitation product in (CHI)llon, (RI)mac and (LU)rin basins (CHIRILU v2) at 0.1° from 2014 (nov) - 2019 (dec). CHIRILU v2 is developed through the merging of automatic meteorological stations and GPM-IMERG-Early satellite using 8 methods.
DOI: 10.6084/m9.figshare.13260020.v2
title: Hourly gridded precipitation product in (CHI)llon, (RI)mac and (LU)rin basins (CHIRILU v2)

description: Hourly gridded precipitation product in (CHI)llon, (RI)mac and (LU)rin basins (CHIRILU v2) at 0.1° from 2014 (nov) - 2019 (dec). CHIRILU v2 is developed through the merging of automatic meteorological stations and GPM-IMERG-Early satellite using 8 methods.
DOI: 10.5281/zenodo.4396210
title: Ultrafast TCR clustering and accurate repertoire classification using isometric transformation

description: hcXXsXX.txt files are raw reference data containing XX healthy controls and XX COVID-19 patient samples. hcXXsXX--RotationEncodingBL62.txt are the related clustering file required to perform GIANA query. qXX_XX.zip contains the output data after GIANA query of the corresponding reference (hcXXsXX.txt). HC100_COVID300 files are the large reference data containing cancer, COVID-19 and multiple sclerosis patients, and healthy controls. Query.zip contains the output data of additional TCR-seq samples (of the same diseases) using the above reference data.
DOI: 10.5281/zenodo.4055780
title: A quantitative analysis of the interplay of environment, neighborhood and cell state in 3D spheroids - Dataset

description: This is the umbrella archive that contains all the datasets and code associated with: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Datasets: Brightfield plate images: Contains all plate acquisitions for the individual sphere plates before pooling 4 cellline experiment: p173: 10.5281/zenodo.3991929 p176: 10.5281/zenodo.3991931 Overexpression experiment: p161: 10.5281/zenodo.3991925 p165: 10.5281/zenodo.3991927<br> Slidescan images: Contains all fluorescent slidescan images of the cuts derived from the pooled spheroid sample blocks 4 cellline experiment: p173: 10.5281/zenodo.3991921 p176: 10.5281/zenodo.3991923 Overexpression experiment: p161: 10.5281/zenodo.4066430 p165: 10.5281/zenodo.3991919<br> Spillover acquisitions: Contains all spillover acquisitions associated with the two experiments: 4 cellline experiment: p173/p176: 10.5281/zenodo.3991945 Overexpression experiment: p161/p165: 10.5281/zenodo.3991947<br> Imaging mass cytometry acquisitions: 4 cellline experiment: p173: 10.5281/zenodo.3991937 p176: 10.5281/zenodo.3991939 Overexpression experiment: p161: 10.5281/zenodo.3991933 p165: 10.5281/zenodo.3991935<br> Processed data set: 4 cellline experiment: 10.5281/zenodo.3991942 Overexpression experiment: 10.5281/zenodo.4271917 Code: A snakemake pipeline to reproduce the analyses from this raw data can be found at: http://github.com/BodenmillerGroup/SpheroidPublication A version already containing all the containers can be found at: 10.5281/zenodo.4071861
DOI: 10.5281/zenodo.3991925
title: Brightfield images: p161, p163

description: This repository constains all the brightfield plate scans plate p161, p163 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each plate acquisition follows the naming scheme: '{date}-{operator}-Spheroid-{plate}[rev]-{dps}-ac{acnr}_Plate_{acquisitionid} eg. 20180203-Vito-Spheroid-p173-2dps-ac1_Plate_13146 20180204-Vito-Spheroid-p173rev-3dps-ac1_Plate_1315 With: date: acquisition date operator: microscope operator plate: plate number rev: optional, if there indicates that the plate has been rotated 180 degree. E.g. well A01 will be well H12. dps: days post seeding ac: manual acquisition number (e.g. if acquisition needed to be repeated) acquisitionid: machine provided unique acquisition id Each folder contains: HTD files which contains acquisition metadata in text form. TimePoint_1: a folder containing all the acquisitions in .tiff form with the suffix _{wellname}_w{channel} In this acquisition channels 1-3 correspond to 3 brightfield acquisitions at different z positions.<br> Acquisition channel 4 corresponds to an acquisition of the GFP channel. An ImageXpress Micro XL Widefield High Content Imaging microscope (Molecular Devices, 4x objective, NA 0.20) was used for the acquisition.
DOI: 10.5281/zenodo.3991924
title: Brightfield images: p161, p163

description: This repository constains all the brightfield plate scans plate p161, p163 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each plate acquisition follows the naming scheme: '{date}-{operator}-Spheroid-{plate}[rev]-{dps}-ac{acnr}_Plate_{acquisitionid} eg. 20180203-Vito-Spheroid-p173-2dps-ac1_Plate_13146 20180204-Vito-Spheroid-p173rev-3dps-ac1_Plate_1315 With: date: acquisition date operator: microscope operator plate: plate number rev: optional, if there indicates that the plate has been rotated 180 degree. E.g. well A01 will be well H12. dps: days post seeding ac: manual acquisition number (e.g. if acquisition needed to be repeated) acquisitionid: machine provided unique acquisition id Each folder contains: HTD files which contains acquisition metadata in text form. TimePoint_1: a folder containing all the acquisitions in .tiff form with the suffix _{wellname}_w{channel} In this acquisition channels 1-3 correspond to 3 brightfield acquisitions at different z positions.<br> Acquisition channel 4 corresponds to an acquisition of the GFP channel. An ImageXpress Micro XL Widefield High Content Imaging microscope (Molecular Devices, 4x objective, NA 0.20) was used for the acquisition.
DOI: 10.5281/zenodo.3991927
title: Brightfield images: p165, p171, p169, p167

description: This repository constains all the brightfield plate scans plate p165, p171, p169, p167 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each plate acquisition follows the naming scheme: '{date}-{operator}-Spheroid-{plate}[rev]-{dps}-ac{acnr}_Plate_{acquisitionid} eg. 20180203-Vito-Spheroid-p173-2dps-ac1_Plate_13146 20180204-Vito-Spheroid-p173rev-3dps-ac1_Plate_1315 With: date: acquisition date operator: microscope operator plate: plate number rev: optional, if there indicates that the plate has been rotated 180 degree. E.g. well A01 will be well H12. dps: days post seeding ac: manual acquisition number (e.g. if acquisition needed to be repeated) acquisitionid: machine provided unique acquisition id Each folder contains: HTD files which contains acquisition metadata in text form. TimePoint_1: a folder containing all the acquisitions in .tiff form with the suffix _{wellname}_w{channel} In this acquisition channels 1-3 correspond to 3 brightfield acquisitions at different z positions.<br> Acquisition channel 4 corresponds to an acquisition of the GFP channel. An ImageXpress Micro XL Widefield High Content Imaging microscope (Molecular Devices, 4x objective, NA 0.20) was used for the acquisition.
DOI: 10.5281/zenodo.3991926
title: Brightfield images: p165, p171, p169, p167

description: This repository constains all the brightfield plate scans plate p165, p171, p169, p167 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each plate acquisition follows the naming scheme: '{date}-{operator}-Spheroid-{plate}[rev]-{dps}-ac{acnr}_Plate_{acquisitionid} eg. 20180203-Vito-Spheroid-p173-2dps-ac1_Plate_13146 20180204-Vito-Spheroid-p173rev-3dps-ac1_Plate_1315 With: date: acquisition date operator: microscope operator plate: plate number rev: optional, if there indicates that the plate has been rotated 180 degree. E.g. well A01 will be well H12. dps: days post seeding ac: manual acquisition number (e.g. if acquisition needed to be repeated) acquisitionid: machine provided unique acquisition id Each folder contains: HTD files which contains acquisition metadata in text form. TimePoint_1: a folder containing all the acquisitions in .tiff form with the suffix _{wellname}_w{channel} In this acquisition channels 1-3 correspond to 3 brightfield acquisitions at different z positions.<br> Acquisition channel 4 corresponds to an acquisition of the GFP channel. An ImageXpress Micro XL Widefield High Content Imaging microscope (Molecular Devices, 4x objective, NA 0.20) was used for the acquisition.
DOI: 10.5281/zenodo.3991921
title: Slidescans: p173

description: This repository constains all the slidescans associated with slide block p173 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each acquisition follows the naming scheme: "{operator}_{date}_{slideblock}_{slidescan_flo_number}{suffix}" e.g. v.zanotelli_20190509_p161_025.czi With: operator: the slidescan operator date: the acquisition date slideblock: the block cut to produce these slides slidescan_fluo_nr: arbitrary index. Is matched to actual slide number using the metadata file: '20190506_bigstain_selection_final_if_imcalign_v1.csv' suffix: '.czi': main slidescan '_pt1.czi': scan of handwritten slide label '_pt2.csi': coarse slide overview scan Each 'main slidescan' is usually composed of multiple 'scenes' (regions that were scanned with high resolution). The convention is that each scene corresponds to unique cut that is independently stained. Note that scene numbering is not sequential but rather random. The slidescans were acquired using an AxioScan.Z1 microscope with: Objective: Plan-Apochromat 20x/0.8 M27 Resolution: nominal 0.325 um/pixel Channels: 1) DAPI: Excitation Wavelength: 353 nm, Emission Wavelength: 465 nm
DOI: 10.5281/zenodo.3991920
title: Slidescans: p173

description: This repository constains all the slidescans associated with slide block p173 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each acquisition follows the naming scheme: "{operator}_{date}_{slideblock}_{slidescan_flo_number}{suffix}" e.g. v.zanotelli_20190509_p161_025.czi With: operator: the slidescan operator date: the acquisition date slideblock: the block cut to produce these slides slidescan_fluo_nr: arbitrary index. Is matched to actual slide number using the metadata file: '20190506_bigstain_selection_final_if_imcalign_v1.csv' suffix: '.czi': main slidescan '_pt1.czi': scan of handwritten slide label '_pt2.csi': coarse slide overview scan Each 'main slidescan' is usually composed of multiple 'scenes' (regions that were scanned with high resolution). The convention is that each scene corresponds to unique cut that is independently stained. Note that scene numbering is not sequential but rather random. The slidescans were acquired using an AxioScan.Z1 microscope with: Objective: Plan-Apochromat 20x/0.8 M27 Resolution: nominal 0.325 um/pixel Channels: 1) DAPI: Excitation Wavelength: 353 nm, Emission Wavelength: 465 nm
DOI: 10.5281/zenodo.3991923
title: Slidescans: p176

description: This repository constains all the slidescans associated with slide block p176 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each acquisition follows the naming scheme: "{operator}_{date}_{slideblock}_{slidescan_flo_number}{suffix}" e.g. v.zanotelli_20190509_p161_025.czi With: operator: the slidescan operator date: the acquisition date slideblock: the block cut to produce these slides slidescan_fluo_nr: arbitrary index. Is matched to actual slide number using the metadata file: '20190506_bigstain_selection_final_if_imcalign_v1.csv' suffix: '.czi': main slidescan '_pt1.czi': scan of handwritten slide label '_pt2.csi': coarse slide overview scan Each 'main slidescan' is usually composed of multiple 'scenes' (regions that were scanned with high resolution). The convention is that each scene corresponds to unique cut that is independently stained. Note that scene numbering is not sequential but rather random. The slidescans were acquired using an AxioScan.Z1 microscope with: Objective: Plan-Apochromat 20x/0.8 M27 Resolution: nominal 0.325 um/pixel Channels: 1) DAPI: Excitation Wavelength: 353 nm, Emission Wavelength: 465 nm