cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7538512
title: Grasshopper genome reveals long-term conservation of the X chromosome and temporal variation in X chromosome evolution

description: We present the first chromosome-level genome assembly of the grasshopper, <em>Locusta migratoria</em>, one of the largest insect genomes. We use coverage differences between females (XX) and males (X0) to identify the X chromosome gene content, and find that the X chromosome shows both complete dosage compensation in somatic tissues and an underrepresentation of testes-expressed genes. Remarkably, X-linked gene content from <em>L. migratoria </em>is highly conserved across four insect orders, namely Orthoptera, Hemiptera, Coleoptera and Diptera, and the 800 Mb grasshopper X chromosome is homologous to the fly ancestral X chromosome despite 400 million years of divergence, suggesting either repeated origin of sex chromosomes with highly similar gene content, or long-term conservation of the X chromosome. We use this broad conservation of the X chromosome to test for temporal dynamics to Fast-X evolution, and find evidence of a recent burst evolution for new X-linked genes in contrast to slow evolution of X-conserved genes. Additionally, our results reveal the X chromosome represents a hotspot for adaptive protein evolution related migration and the locust swarming phenotype. Overall, our results reveal a remarkable case of conservation and adaptation on the X chromosome.
DOI: 10.5281/zenodo.7538511
title: Grasshopper genome reveals long-term conservation of the X chromosome and temporal variation in X chromosome evolution

description: We present the first chromosome-level genome assembly of the grasshopper, <em>Locusta migratoria</em>, one of the largest insect genomes. We use coverage differences between females (XX) and males (X0) to identify the X chromosome gene content, and find that the X chromosome shows both complete dosage compensation in somatic tissues and an underrepresentation of testes-expressed genes. Remarkably, X-linked gene content from <em>L. migratoria </em>is highly conserved across four insect orders, namely Orthoptera, Hemiptera, Coleoptera and Diptera, and the 800 Mb grasshopper X chromosome is homologous to the fly ancestral X chromosome despite 400 million years of divergence, suggesting either repeated origin of sex chromosomes with highly similar gene content, or long-term conservation of the X chromosome. We use this broad conservation of the X chromosome to test for temporal dynamics to Fast-X evolution, and find evidence of a recent burst evolution for new X-linked genes in contrast to slow evolution of X-conserved genes. Additionally, our results reveal the X chromosome represents a hotspot for adaptive protein evolution related migration and the locust swarming phenotype. Overall, our results reveal a remarkable case of conservation and adaptation on the X chromosome.
DOI: 10.5281/zenodo.7552538
title: Data from: Indices of Extremes: Geographic patterns of change in extreme temperature and precipitation under climate intervention

description: This dataset comprises the python notebooks and associated data used to produce Figures 1-9, 12-14, and all supplemental figures in Tye et al. 2022 "Indices of Extremes: Geographic patterns of change in extremes and associated vegetation impacts under climate intervention" Earth System Dynamic, 13, 1233-1257. https://doi.org/10.5194/esd-13-1233-2022 Script is also included to process data from NCAR's HPC Campaign archive and produce figures 10 and 11. The full output from the GLENS simulation are available from from https://data.ucar.edu/dataset/stratospheric-aerosol-geoengineering-large-ensemble-project-glens
description: More information can also be found here: https://www.cesm.ucar.edu/community-projects/glens Computing resources (doi:10.5065/D6RX99HX) were provided by NCAR's Computational and Information Systems Laboratory, sponsored by the National Science Foundation.
DOI: 10.5281/zenodo.7552537
title: Data from: Indices of Extremes: Geographic patterns of change in extreme temperature and precipitation under climate intervention

description: This dataset comprises the python notebooks and associated data used to produce Figures 1-9, 12-14, and all supplemental figures in Tye et al. 2022 "Indices of Extremes: Geographic patterns of change in extremes and associated vegetation impacts under climate intervention" Earth System Dynamic, 13, 1233-1257. https://doi.org/10.5194/esd-13-1233-2022 Script is also included to process data from NCAR's HPC Campaign archive and produce figures 10 and 11. The full output from the GLENS simulation are available from from https://data.ucar.edu/dataset/stratospheric-aerosol-geoengineering-large-ensemble-project-glens
description: More information can also be found here: https://www.cesm.ucar.edu/community-projects/glens Computing resources (doi:10.5065/D6RX99HX) were provided by NCAR's Computational and Information Systems Laboratory, sponsored by the National Science Foundation.
DOI: 10.5281/zenodo.7551676
title: Algal Blooms Sweden - 2022

description: Dataset containing images of algal blooms in the Baltic Sea. The data is provided with a metadata description containing time spotted, comments, municipality, county and coordinates of each image. The images and metadata file are archived in a zip package. Images show various summer surface accumulations of so-called harmful algal blooms (HABs) or nuisance blooms. Typically, these blooms consists of species of cyanobacteria of the order of Nostocales, including toxic Nodularia and Aphanizomenon. These blooms were verified by Informationscentralen (Länstyrelsen Stockholm and Länstyrelsen Västerbotten). However, the blooms seen in the images have not been taxonomically annotated by microscopy nor genetic analysis. The following data fields are contained in the metadata files (provided in both json and csv format): report_id: unique identifier for reporting record, <em>type: string</em><br> time_spotted: date that bloom was spotted, <em>type: datetime</em><br> algae_overview_photo: url to overview photo submitted, <em>type: string</em><br> algae_detail_photo: url to detailed photo submitted, <em>type: string</em><br> comments: Any additional information relating to the bloom, <em>type: string</em><br> lat: Latitude of position where bloom was seen, <em>type: float</em><br> long: Longitude of position where bloom was seen, <em>type: float</em><br> place: County where bloom was spotted, <em>type: string</em><br> kommun: Municipality where bloom was spotted, type: string <strong>Total observations</strong>: 161<br> <em>Note</em>: Not every observation has an accompanying image and others were verified using other information provided.
description: Part of subproject "Algal Blooms Sweden" within Ocean Data Factory Sweden. See Facebook page (https://www.facebook.com/algalbloomssweden/) and project website (https://oceandatafactory.se/) for more information.
DOI: 10.5281/zenodo.7234158
title: Algal Blooms Sweden - 2022

description: Dataset containing images of algal blooms in the Baltic Sea. The data is provided with a metadata description containing time spotted, comments, municipality, county and coordinates of each image. The images and metadata file are archived in a zip package. Images show various summer surface accumulations of so-called harmful algal blooms (HABs) or nuisance blooms. Typically, these blooms consists of species of cyanobacteria of the order of Nostocales, including toxic Nodularia and Aphanizomenon. These blooms were verified by Informationscentralen (Länstyrelsen Stockholm and Länstyrelsen Västerbotten). However, the blooms seen in the images have not been taxonomically annotated by microscopy nor genetic analysis. The following data fields are contained in the metadata files (provided in both json and csv format): report_id: unique identifier for reporting record, <em>type: string</em><br> time_spotted: date that bloom was spotted, <em>type: datetime</em><br> algae_overview_photo: url to overview photo submitted, <em>type: string</em><br> algae_detail_photo: url to detailed photo submitted, <em>type: string</em><br> comments: Any additional information relating to the bloom, <em>type: string</em><br> lat: Latitude of position where bloom was seen, <em>type: float</em><br> long: Longitude of position where bloom was seen, <em>type: float</em><br> place: County where bloom was spotted, <em>type: string</em><br> kommun: Municipality where bloom was spotted, type: string <strong>Total observations</strong>: 161<br> <em>Note</em>: Not every observation has an accompanying image and others were verified using other information provided.
description: Part of subproject "Algal Blooms Sweden" within Ocean Data Factory Sweden. See Facebook page (https://www.facebook.com/algalbloomssweden/) and project website (https://oceandatafactory.se/) for more information.
DOI: 10.5281/zenodo.7551670
title: Algal Blooms Sweden - 2021

description: Dataset containing images of algal blooms in the Baltic Sea. The data is provided with a metadata description containing time spotted, comments, municipality, county and coordinates of each image. The images and metadata file are archived in a zip package. Images show various summer surface accumulations of so-called harmful algal blooms (HABs) or nuisance blooms. Typically, these blooms consists of species of cyanobacteria of the order of Nostocales, including toxic Nodularia and Aphanizomenon. These blooms were verified by Informationscentralen (Länstyrelsen Stockholm and Länstyrelsen Västerbotten). However, the blooms seen in the images have not been taxonomically annotated by microscopy nor genetic analysis. The following data fields are contained in the metadata files (provided in both json and csv format): report_id: unique identifier for reporting record, <em>type: string</em><br> time_spotted: date that bloom was spotted, <em>type: datetime</em><br> algae_overview_photo: url to overview photo submitted, <em>type: string</em><br> algae_detail_photo: url to detailed photo submitted, <em>type: string</em><br> comments: Any additional information relating to the bloom, <em>type: string</em><br> lat: Latitude of position where bloom was seen, <em>type: float</em><br> long: Longitude of position where bloom was seen, <em>type: float</em><br> place: County where bloom was spotted, <em>type: string</em><br> kommun: Municipality where bloom was spotted, type: string <strong>Total observations</strong>: 251<br> <em>Note</em>: Not every observation has an accompanying image and others were verified using other information provided.
description: Part of subproject "Algal Blooms Sweden" within Ocean Data Factory Sweden. See Facebook page (https://www.facebook.com/algalbloomssweden/) and project website (https://oceandatafactory.se/) for more information.
DOI: 10.5281/zenodo.7234132
title: Algal Blooms Sweden - 2021

description: Dataset containing images of algal blooms in the Baltic Sea. The data is provided with a metadata description containing time spotted, comments, municipality, county and coordinates of each image. The images and metadata file are archived in a zip package. Images show various summer surface accumulations of so-called harmful algal blooms (HABs) or nuisance blooms. Typically, these blooms consists of species of cyanobacteria of the order of Nostocales, including toxic Nodularia and Aphanizomenon. These blooms were verified by Informationscentralen (Länstyrelsen Stockholm and Länstyrelsen Västerbotten). However, the blooms seen in the images have not been taxonomically annotated by microscopy nor genetic analysis. The following data fields are contained in the metadata files (provided in both json and csv format): report_id: unique identifier for reporting record, <em>type: string</em><br> time_spotted: date that bloom was spotted, <em>type: datetime</em><br> algae_overview_photo: url to overview photo submitted, <em>type: string</em><br> algae_detail_photo: url to detailed photo submitted, <em>type: string</em><br> comments: Any additional information relating to the bloom, <em>type: string</em><br> lat: Latitude of position where bloom was seen, <em>type: float</em><br> long: Longitude of position where bloom was seen, <em>type: float</em><br> place: County where bloom was spotted, <em>type: string</em><br> kommun: Municipality where bloom was spotted, type: string <strong>Total observations</strong>: 251<br> <em>Note</em>: Not every observation has an accompanying image and others were verified using other information provided.
description: Part of subproject "Algal Blooms Sweden" within Ocean Data Factory Sweden. See Facebook page (https://www.facebook.com/algalbloomssweden/) and project website (https://oceandatafactory.se/) for more information.
DOI: 10.5281/zenodo.7550751
title: SS-DBEM model results for main tuna commercial species

description: Projected body size and potential biomass changes (in %) for the main commercial tuna species and swordfish by each RFMO by the mid- and the end-of-the-century. The changes have been estimated as the difference between the future and the reference period. A multi-species ecosystem model which integrates a species-based model (DBEM, Dynamic Bioclimatic Envelope Model) with the size-spectrum approach (SS) was used in this study. The code for the model is available here.
description: Maite Erauskin_Extramiana was funded with postdoc grant by the Government of Spain Ministry of Science and Innovation (EU-Eranet PCI2018-092995)
DOI: 10.5281/zenodo.7550750
title: SS-DBEM model results for main tuna commercial species

description: Projected body size and potential biomass changes (in %) for the main commercial tuna species and swordfish by each RFMO by the mid- and the end-of-the-century. The changes have been estimated as the difference between the future and the reference period. A multi-species ecosystem model which integrates a species-based model (DBEM, Dynamic Bioclimatic Envelope Model) with the size-spectrum approach (SS) was used in this study. The code for the model is available here.
description: Maite Erauskin_Extramiana was funded with postdoc grant by the Government of Spain Ministry of Science and Innovation (EU-Eranet PCI2018-092995)
DOI: 10.5281/zenodo.7520353
title: Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 3 FOV2

description: <strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 3 FOV2)</strong> Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.
description: Funding: Deutsche Forschungsgemeinschaft HA5354/10-1, SPP1937 (HA5354/8-2) and TRR130 P17 and C01 (to Anja Hauser)
description: {"references": ["Mothes, R. and Pascual-Reguant, A. et al. Local CCL18 and CCL21 expand lung fibrovascular niches and recruit lymphocytes, leading to tertiary lymphoid structure formation in prolonged COVID-19. medRxiv 2022.03.24.22272768 (2022) doi:10.1101/2022.03.24.22272768."]}
DOI: 10.5281/zenodo.7520293
title: Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 3 FOV1

description: <strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 3 FOV1)</strong> Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.
description: Funding: Deutsche Forschungsgemeinschaft HA5354/10-1, SPP1937 (HA5354/8-2) and TRR130 P17 and C01 (to Anja Hauser)
description: {"references": ["Mothes, R. and Pascual-Reguant, A. et al. Local CCL18 and CCL21 expand lung fibrovascular niches and recruit lymphocytes, leading to tertiary lymphoid structure formation in prolonged COVID-19. medRxiv 2022.03.24.22272768 (2022) doi:10.1101/2022.03.24.22272768."]}
DOI: 10.5281/zenodo.7520352
title: Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 3 FOV2

description: <strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 3 FOV2)</strong> Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.
description: Funding: Deutsche Forschungsgemeinschaft HA5354/10-1, SPP1937 (HA5354/8-2) and TRR130 P17 and C01 (to Anja Hauser)
description: {"references": ["Mothes, R. and Pascual-Reguant, A. et al. Local CCL18 and CCL21 expand lung fibrovascular niches and recruit lymphocytes, leading to tertiary lymphoid structure formation in prolonged COVID-19. medRxiv 2022.03.24.22272768 (2022) doi:10.1101/2022.03.24.22272768."]}
DOI: 10.5281/zenodo.7520292
title: Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 3 FOV1

description: <strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 3 FOV1)</strong> Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.
description: Funding: Deutsche Forschungsgemeinschaft HA5354/10-1, SPP1937 (HA5354/8-2) and TRR130 P17 and C01 (to Anja Hauser)
description: {"references": ["Mothes, R. and Pascual-Reguant, A. et al. Local CCL18 and CCL21 expand lung fibrovascular niches and recruit lymphocytes, leading to tertiary lymphoid structure formation in prolonged COVID-19. medRxiv 2022.03.24.22272768 (2022) doi:10.1101/2022.03.24.22272768."]}
DOI: 10.6084/m9.figshare.21821001
title: Supplementary Material for: Microglial characterisation in transient human neurodevelopmental structures

description: Human neurodevelopment is characterised by the appearance, development and disappearance or transformation of various transient structures that underlie the establishment of connectivity within and between future cortical and subcortical areas. Examples of transient structures in the forebrain (amongst many others) include the subpial granular layer and the subplate zone. We have previously characterised the precise spatiotemporal dynamics of microglia in the human telencephalon. Here, we describe the diversity of microglial morphologies in the subpial granular layer and the subplate zone. Where possible, we couple the predominant morphological phenotype with functional characterisations to infer tentative roles for microglia in a changing neurodevelopmental landscape. We interpret these findings within the context of relevant morphogenetic and neurogenetic events in humans. Due to the unique genetic, molecular and anatomical features of the human brain and because many human neurological and psychiatric diseases have their origins during development, these structures deserve special attention.
DOI: 10.34934/dvn/1rgbdr
title: Enquête sur l'hésitation vaccinale

description: Dans le cadre du suivi de l’épidémie, un questionnaire relatif à la vaccination est élaboré par une équipe pluridisciplinaire. Ce questionnaire est administré sur le territoire de la ville de Namur, en Belgique, entre le 12 avril 2021 et le 31 mai 2022. L’objectif de cette enquête est de percevoir les attitudes et motivations de la population face à la vaccination contre la COVID-19.
DOI: 10.6084/m9.figshare.19735501.v1
title: Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes

description: This project aims to use comparative genomics via profiling of unassembled short reads to understand the conservation of sex determining genes in dioecious amaranths and also to explore the relationship between the dioecious species. Files shared on Figshare include RepeatExplorer2 annotations, nonredundant TE libraries for repeat analyses in previously assembled genomes of <em>Amaranthus</em> species, raw tree file (.dnd) for Fig. 2 and R codes used in the manuscript plots.
DOI: 10.6084/m9.figshare.21983261.v1
title: A high quality de novo genome assembly for Clapper Rail (Rallus crepitans)

description: Rallids (Aves: Rallidae) include 37 genera and 159 globally distributed species that occur primarily in wetlands, jungle lowlands, and montane forests (Garcia–R et al. 2019, Winkler et al. 2020). Despite their global distribution, most rallid species remain poorly understood because of their secretive nature. The type genus <em>Rallus</em> includes thirteen species of slim bodied, long-billed rails that occur in the Americas, Eurasia, Africa, and Madagascar (Winkler et al. 2020). Clapper Rail (<em>Rallus crepitans</em>) and King Rail (<em>Rallus elegans</em>) are two closely related species that occur along the eastern coast of North America, south to the Caribbean (Figure 1; del Hoyo et al. 2016, Rush et al. 2020). Clapper and King rails are similar in plumage, vocalization, and morphology (Maley and Brumfield 2013), but they exhibit different habitat preferences for saltwater (Clapper Rail) and freshwater (King Rail) wetlands, although Clapper and King Rail populations hybridize where they co-occur in brackish marsh (Olson 1997, Maley 2012). To facilitate molecular investigations of the underlying mechanisms of saltwater tolerance and adaptive divergence between Clapper and King rail populations, we completed the first genome assembly for Clapper Rail using DNA from a vouchered, wild female bird collected in Louisiana.
DOI: 10.6084/m9.figshare.21983261.v2
title: A high quality de novo genome assembly for Clapper Rail (Rallus crepitans)

description: Rallids (Aves: Rallidae) include 37 genera and 159 globally distributed species that occur primarily in wetlands, jungle lowlands, and montane forests (Garcia–R et al. 2019, Winkler et al. 2020). Despite their global distribution, most rallid species remain poorly understood because of their secretive nature. The type genus <em>Rallus</em> includes thirteen species of slim bodied, long-billed rails that occur in the Americas, Eurasia, Africa, and Madagascar (Winkler et al. 2020). Clapper Rail (<em>Rallus crepitans</em>) and King Rail (<em>Rallus elegans</em>) are two closely related species that occur along the eastern coast of North America, south to the Caribbean (Figure 1; del Hoyo et al. 2016, Rush et al. 2020). Clapper and King rails are similar in plumage, vocalization, and morphology (Maley and Brumfield 2013), but they exhibit different habitat preferences for saltwater (Clapper Rail) and freshwater (King Rail) wetlands, although Clapper and King Rail populations hybridize where they co-occur in brackish marsh (Olson 1997, Maley 2012). To facilitate molecular investigations of the underlying mechanisms of saltwater tolerance and adaptive divergence between Clapper and King rail populations, we completed the first genome assembly for Clapper Rail using DNA from a vouchered, wild female bird collected in Louisiana.
DOI: 10.5281/zenodo.7595570
title: Supplementary Table 1. Antibodies used in the study.

description: Dasen et al. Supplementary Table 1. Antibodies used in the study.