cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.qbmmkn
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is LACM Invertebrate Paleontology",
 "Geometry POLYGON((-119.1027 34.056,-118.80116 33.98016,-118.60868 34.00504,-118.61944 34.16359,-118.72898 34.16832,-118.75624 34.22274,-118.78473 34.21745,-118.81238 34.15372,-119.06902 34.16973,-119.1027 34.056))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 31 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016648-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bgys22
title: Occurrence Download

description: A dataset containing 7657 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sphyrna lewini",
 "Year 1986-2026"
 ]
}

 The dataset includes 7657 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016647-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15139/s3/bax1o1
title: Data Management and Sharing Plan for: Molecular Therapeutics for Luminal Tumor Subtypes

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.15468/dl.h52tt5
title: Occurrence Download

description: A dataset containing 203 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Croton kongensis",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 203 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016649-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v7a58d
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pachyurus calhamazon",
 "DecimalLatitude is not null",
 "DecimalLongitude is not null"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016650-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r3rsv3
title: Occurrence Download

description: A dataset containing 42846331 records in GBIF matching the query:
SELECT "eventid", "decimallatitude", "decimallongitude", "eventdate", "samplesizevalue", "samplesizeunit", "samplingprotocol", "dynamicproperties" FROM occurrence WHERE datasetKey = '4fa7b334-ce0d-4e88-aaae-2e0c138d049e' AND decimalLatitude &gt;= 1.182312 AND decimalLatitude &lt;= 28.4382935 AND decimalLongitude &gt;= 81.8824189 AND decimalLongitude &lt;= 122.0004883

 The dataset's 42846331 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016635-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18636666
title: Ontogeny-independent expression of LPCAT2 in granuloma macrophages during experimental visceral leishmaniasis

description: This deposit contains the processed data and analysis scripts accompanying the manuscript "Ontogeny-independent expression of LPCAT2 in granuloma macrophages during experimental visceral leishmaniasis" by Dey, Cao et al. The study integrates spatial transcriptomics (10x Visium), mass spectrometry imaging (MSI), single-cell RNA sequencing (scRNA-seq), and proteomics to characterise hepatic granulomas in a murine model of visceral leishmaniasis (Leishmania donovani). A novel role for LPCAT2-mediated phospholipid remodelling in granuloma-associated macrophages is identified, independent of macrophage ontogeny. Deposited files:








File
Description




integrated_sd2705_dims15_res0.4.rds
Pre-processed, integrated scRNA-seq Seurat object (8 samples: 4 infected, 2 naive pools). Used by scRNAseq_downstream_analysis.Rmd.


integrated_d28_cohort_dims30_res_0.4.Rds
Pre-processed, integrated spatial transcriptomics (Visium) Seurat object (7 capture areas: 4 infected, 4 naive). Used by spatial_downstream_analysis.Rmd.


coregistration.zip
Co-registered mass spectrometry imaging (MSI) lipid intensities mapped to Visium spot barcodes. Contains per-sample CSVs for negative and positive ion modes (8 mice: I2, I3, I4, I5, N1, N2, N3, N4), cell2location cell-type abundance estimates, and m/z-to-lipid species identification.


scripts.zip
R Markdown notebooks, Python scripts, and supporting files for reproducing all analyses. Also available on GitHub: https://github.com/jipsi/spatial_lipid_gene







 




 



Raw data availability:



Raw Visium spatial transcriptomics data: GEO accession GSE290324




Raw scRNA-seq data: GEO accession GSE290325


Software requirements:



R ≥ 4.2.2 with Seurat ≥ 4.3.0




Python ≥ 3.8 with cell2location (for spatial deconvolution; GPU recommended)


Keywords: spatial transcriptomics, mass spectrometry imaging, single-cell RNA-seq, visceral leishmaniasis, granuloma, LPCAT2, phospholipid remodelling, cell2location, Seurat License: MIT
DOI: 10.5281/zenodo.18636665
title: Ontogeny-independent expression of LPCAT2 in granuloma macrophages during experimental visceral leishmaniasis

description: This deposit contains the processed data and analysis scripts accompanying the manuscript "Ontogeny-independent expression of LPCAT2 in granuloma macrophages during experimental visceral leishmaniasis" by Dey, Cao et al. The study integrates spatial transcriptomics (10x Visium), mass spectrometry imaging (MSI), single-cell RNA sequencing (scRNA-seq), and proteomics to characterise hepatic granulomas in a murine model of visceral leishmaniasis (Leishmania donovani). A novel role for LPCAT2-mediated phospholipid remodelling in granuloma-associated macrophages is identified, independent of macrophage ontogeny. Deposited files:








File
Description




integrated_sd2705_dims15_res0.4.rds
Pre-processed, integrated scRNA-seq Seurat object (8 samples: 4 infected, 2 naive pools). Used by scRNAseq_downstream_analysis.Rmd.


integrated_d28_cohort_dims30_res_0.4.Rds
Pre-processed, integrated spatial transcriptomics (Visium) Seurat object (7 capture areas: 4 infected, 4 naive). Used by spatial_downstream_analysis.Rmd.


coregistration.zip
Co-registered mass spectrometry imaging (MSI) lipid intensities mapped to Visium spot barcodes. Contains per-sample CSVs for negative and positive ion modes (8 mice: I2, I3, I4, I5, N1, N2, N3, N4), cell2location cell-type abundance estimates, and m/z-to-lipid species identification.


scripts.zip
R Markdown notebooks, Python scripts, and supporting files for reproducing all analyses. Also available on GitHub: https://github.com/jipsi/spatial_lipid_gene







 




 



Raw data availability:



Raw Visium spatial transcriptomics data: GEO accession GSE290324




Raw scRNA-seq data: GEO accession GSE290325


Software requirements:



R ≥ 4.2.2 with Seurat ≥ 4.3.0




Python ≥ 3.8 with cell2location (for spatial deconvolution; GPU recommended)


Keywords: spatial transcriptomics, mass spectrometry imaging, single-cell RNA-seq, visceral leishmaniasis, granuloma, LPCAT2, phospholipid remodelling, cell2location, Seurat License: MIT
DOI: 10.15468/z5h5vx
title: Collembola Recording Scheme

description: The Collembola dataset contains 359 species, records collected between 1808 - 2008, covering Great Britain and Ireland. It contains approximately 10,000 records.
DOI: 10.15468/3kvvxb
title: Ladybird Survey of the UK

description: Records for the UK Ladybird Survey, consisting of surveys for the harlequin ladybird, data from the London Natural History Society (collated by Paul Mabbott), and the UK Ladybird Survey. Data have been collated by the Biological Records Centre. Many people have provided data to both the Harlequin and the UK Ladybird Survey through the on-line surveys. The data from both on-line surveys (www.ladybird-survey.org and www.harlequin-survey.org) are collated within this dataset. Many county recorders, natural history societies and other wildlife groups have contributed to the survey, with the help of Paul Mabbott (London Natural History Society), Nigel Cuming and Jerry Bowdrey (Essex Field Club/Colchester Museum) and Michael Majerus. Many entomologists have provided survey data and this information is available in the Survey section.
DOI: 10.15468/dl.h7chej
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cryptocarya acutifolia",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 43 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016653-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15139/s3/fl3jog
title: Data Management and Sharing Plan for: Nanodelivery of FP polymers to improve treatment of metastatic colorectal cancer

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.15468/dl.uq23cg
title: Occurrence Download

description: A dataset containing 117 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pachyurus junki",
 "DecimalLatitude is not null",
 "DecimalLongitude is not null"
 ]
}

 The dataset includes 117 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016654-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/d3oo4b
title: Nightjar breeding season surveys in Dumfries and Galloway between 1981 and 2011

description: The UK population of nightjar declined by 50% between 1972 and 1992. These surveys were undertaken to monitor the change in range and population of nightjar in Dumfries and Galloway. This dataset contains data collected between 1981 and 2011, and was conducted by the Dumfries and Galloway Nightjar Study Groups. &lt;br /&gt;&lt;br /&gt;
 Absence records are included, and denote areas that were surveyed where no nightjars were seen.
DOI: 10.15468/kdsdew
title: White-tailed eagle reintroduction in Scotland, 1975 onwards - Sightings data

description: The white-tailed eagle (&lt;i&gt;Haliaeetus albicilla&lt;/i&gt;) is a resident breeding bird in Scotland and the largest bird of prey in the UK. It is listed in the Red List of Birds of Conservation Concern in the UK because of its long-term population decline and since it is a rare breeder in the UK and across its European range. &lt;br&gt; 
 Sightings have been collated from the Scottish white-tailed eagle recovery project, begun in 1975 on Rum. A second reintroduction took place between 1993 and 1998 in Wester Ross. &lt;br&gt;
 These reintroduction projects were carried out in collaboration with Scottish Natural Heritage (SNH), also benefiting from expertise from the Centre of Ecology and Hydrology (CEH), the Join Nature Conservation Committee (JNCC) and the National Trust for Scotland (NTS). In Scotland, we gratefully acknowledge support over the years of, among others, Forestry Commission Scotland, Strathclyde Police and Northern Constabulary, as well as landowners, crofters, farmers, fishermen, wildlife tour operators, volunteers and others in rural communities in the west of Scotland. &lt;br&gt; 
 East Scotland Sea Eagles, a partnership between RSPB Scotland, Scottish Natural Heritage and Forestry Commission Scotland, is the third phase of a successful reintroduction programme. Data from this 2007 reintroduction will be added in a future update.&lt;br&gt;
 All records containing references to nests and roost sites have been marked as sensitive and are not available for viewing by the public.
DOI: 10.15468/tlknh5
title: 2012 Onwards Scottish Lowlands and Southern Uplands Black Grouse (excluding Scottish Borders)

description: This dataset is intended to provide an indication of the numbers and distribution of black grouse in the RSPB region of the Scottish Lowland and Southern Uplands, which consists of the counties of Dumfries and Galloway, South and East Ayrshire, South Lanarkshire and the Scottish Borders. Data from the Scottish Borders is not included as this collected and owned by the Southern Uplands Partnership. Records are included from 2012 onwards. Black grouse is a species of conservation concern and as such has been a priority species for monitoring. Surveys are carried out and co-ordinated by RSPB Scotland and Forestry and Land Scotland through a network of staff and volunteers.
DOI: 10.15468/6vvmv4
title: Bittern Annual Surveys in Britain 1990-2019

description: This dataset contains results from annual national surveys that are undertaken to monitor the population of booming Bitterns (Botaurus stellaris) in Britain. The Bittern is a species of conservation concern. Breeding bitterns in Britain are typically restricted to reedbed (Phragmites australis) dominated habitat. Regularly-occupied sites and other sites with suitable breeding habitat within the bittern range are monitored for booming males annually.
This survey is coordinated by the Royal Society for the Protection of Birds (RSPB), under the Action for Birds in England (AfBiE) agreement, a conservation partnership between Natural England and RSPB.
DOI: 10.15468/595lfs
title: Bird Conservation Targeting Project (BCTP) in the UK, 2006-2011 (sensitive records)

description: The Bird Conservation Targeting Project (BCTP) produces breeding distribution maps for a suite of rare and/or declining farmland and woodland birds. The maps can be used to guide the prescription of land management advice based on the species already breeding in an area, or for allocating funding towards sites known to be important for birds. The data cover a 5-year period, and are up-dated annually. Data are collated from a wide range of sources to produce the most comprehensive maps possible. The data are displayed as presence-only records. Absence of a record does not necessarily indicate a true absence record, as there may be no data available.
 &lt;br /&gt;&lt;br /&gt;
 BCTP outputs were first produced in England in 2004, in Wales and Northern Ireland in 2008, and in Scotland in 2009. This dataset contains the sensitive records for England, Scotland and Northern Ireland, compiled in 2012, covering the 2006 - 2010 breeding seasons (plus any 2011 data available). English data were not updated in 2012; English data span 2005 - 2010. The non-sensitive records are in a separate dataset on the NBN. 
 &lt;br /&gt;&lt;br /&gt;
 The species selection varies in each country. There are sensitive records for 3 species in England, 4 species in Scotland, and 4 species in Northern Ireland. Welsh data are not included in this dataset, and will be added when they become available. 
 &lt;br /&gt;&lt;br /&gt;
 Additional data layers are available in Scotland, showing core areas for corncrake (presence in 2007, 2008 and 2009) and black grouse (3 leking males). These are analysed data layers, relevant to the Scottish Rural Development Programme (SRDP), and are not included in this dataset. 
 &lt;br /&gt;&lt;br /&gt;
 The BCTP is a partnership between the British Trust for Ornithology (BTO), the Centre for Environmental Data and Recording (CEDaR), the Countryside Council for Wales (CCW), the Department of Agriculture and Rural Development (DARD), Forestry Commission England (FCE), Forestry Commission Wales (FCW), Forest Service (FS), Natural England (NE), Northern Ireland Environment Agency, the RSPB and Scottish Natural Heritage (SNH). The BCTP partners are grateful to the contributions of the data providers listed at &lt;a href="http://www.rspb.org.uk/targeting"http://www.rspb.org.uk/targeting&gt;&lt;/a&gt;.
DOI: 10.15468/uw7qem
title: Black-throated Diver annual records in North Scotland, 1834-2019

description: This dataset pulls together all available information from a wide range of sources to give a single line summary for Black-throated Diver breeding territories in North Scotland Region in each year where information is available. Principal sources of information are the RSPB's diver raft project and from other landowners; as well as records submitted for inclusion in the Highland Bird Report and public sightings. Other data was sourced from NTS, NS, SWT, RBBP and Forestry and Land Scotland amongst others. Much of the pre-1985 data comes from a historical dataset compiled by Greg Mudge in the early 1990s that sourced many museum collections etc. In the case of multi-territory lochs, some historical data just refers to the whole loch and does not indicate which territory the record is from. In such cases, a separate entry is made like 'loch name' consolidated. The inclusion of a site in this dataset does not neccesarily mean that it is a known breeding site. Some sites are included for future reference as a pair has been noted present in the egg laying period (27 April to 15 June).

The dataset has been split into two different surveys, one contains data from egg collection (Records from egg collection), and the other contains the records from annual surveys (Records from annual surveys).
Royal Society for the Protection of Birds (RSPB), NatureScot (NS), National Trust for Scotland (NTS), Scottish Wildlife Trust (SWT), Rare Breeding Bird Panel (RBBP), Forestry and Land Scotland (FLS), Museum Collections and private landowners and individuals.
DOI: 10.15468/r1xoae
title: Black grouse annual lek surveys in Argyll & Bute, 2002-2011

description: These data were collected to monitor population levels in the Argyll & Bute area as part of the Black Grouse Recovery Project.
 Priority sites were identified for Black Grouse &lt;I&gt;Tetrao tetrix&lt;/I&gt; conservation in the Argyll & Bute area. These priority sites were identified by surveying known (both historical and current) leks in Argyll & Bute between 2002 and 2011. 
 &lt;br /&gt;&lt;br /&gt;
 The recovery project was funded by a partnership of Scottish Natural Heritage, Forestry Commission Scotland, RSPB Scotland, Scottish Power and an award from the Esm饠Fairbairn Foundation. In 2008 additional survey work was organised and funded by RSPB. &lt;br /&gt;&lt;br /&gt;
 Absence records are included, and denote areas that were surveyed where no black grouse were seen.
DOI: 10.15468/zdu5jy
title: Red-throated diver national surveys in Scotland - raw data

description: Red-throated divers are birds of conservation concern due to large declines in the 19th century. While the population increased in the 20th century, there was not considerable change to the breeding range. This dataset contains the results of systematic national surveys in 1994 and 2006. The dataset contains the raw data, i.e. un-interpreted red-throated diver sightings. As such, it does not report any indirect evidence that has been used to indicate presence in the 5km summary dataset, which is also available on the NBN. In addition to the data collected for the national surveys, this dataset also contains data collected on additional visits in the survey years. These data are either from sites that were not included in the surveys, or from sites visited outside the survey period. These data are flagged in the dataset. The surveys were carried out by the Royal Society for the Protection of Birds (RSPB) and Scottish Natural Heritage (SNH) under the Statutory Conservation Agencies and RSPB Breeding Birds Scheme (SCARABBS).
DOI: 10.15468/vu0lve
title: Black-throated diver national surveys in Scotland

description: Black-throated divers are birds of conservation concern due to the small UK population size, and large declines in the European population in the 20th century. This dataset contains records of black-throated divers from the national surveys conducted in 1985, 1994 and 2006. The 2006 survey details unique site visits, and individual birds may be reported in more than one record, recorded on different visits to the same site. The survey indicated a significant increase of 16% between 1994 and 2006. The 1985 and 1994 surveys in this dataset are breeding summaries of summering territories. The 1985 survey is incomplete, and is missing seven summering territories reported by Campbell and Talbot (British Birds, 1987). In addition to the data collected for the national surveys, this dataset also contains data collected on additional visits in the survey years. These data are either from sites that were not included in the surveys, or from sites visited outside the survey period. These data are clearly flagged in the dataset. The surveys were carried out by the Royal Society for the Protection of Birds (RSPB) and Scottish Natural Heritage (SNH) under the Statutory Conservation Agencies and RSPB Breeding Birds Scheme (SCARABBS).
DOI: 10.15468/2yjzyo
title: Black grouse national surveys

description: The male black grouse &lt;I&gt;Tetrao tetrix&lt;/I&gt; population in Britain was surveyed in 1995/96 and 2005, in order to estimate population size. &lt;br /&gt;&lt;br /&gt;The surveys were based on counts of males displaying in the spring. In Wales and Staffordshire, the entire known population was surveyed in 1995. In northern England and Scotland in 1995/96 and 2005, and in Wales in 2005, a stratified random sample of 5 km squares from the breeding range was surveyed. As such the dataset covers around 10% of the UK population overall and does NOT contain all black grouse leks in Britain in the survey years; its aim was to produce a reliable population estimate. &lt;br /&gt;&lt;br /&gt;The 5 km squares where no black grouse were found will be included in the dataset when zero record display becomes available on the NBN. &lt;br /&gt;&lt;br /&gt;The 1995/96 survey estimated a population of 6510 males, the 2005 survey estimated population size to be 5078 males, a non-significant 22% decrease.&lt;br /&gt;&lt;br /&gt;
 The surveys were organised by the Statutory Conservation Agencies and RSPB Breeding Bird Surveys (SCARABBS) scheme. The 1995/96 survey was funded by the RSPB, Scottish Natural Heritage, English Nature (now Natural England), the Joint Nature Conservation Committee and the Game Conservancy Trust (now the Game and Wildlife Conservation Trust). The Perthshire Black Grouse Study Group carried out a substantial part of the fieldwork. The 2005 survey was funded by the RSPB, the Countryside Council for Wales, Forestry Commission Scotland, the Game Conservancy Trust (now the Game and Wildlife Conservation Trust) and the Defra Rural Development Service (now part of Natural England), and organised with substantial help from the Central Scotland Black Grouse & Capercaillie Study Group, the Perthshire Black Grouse Study Group and the Strathspey Black Grouse Study Group.
DOI: 10.15468/dl.d5yhvh
title: Occurrence Download

description: A dataset containing 44267 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bothriochloa ischaemum"
 ]
}

 The dataset includes 44267 records from 847 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016652-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.