| 1. |
- Andersen, Casper W., et al.
(författare)
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OPTIMADE, an API for exchanging materials data
- 2021
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Ingår i: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification.
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| 2. |
- Badian, Reza A., et al.
(författare)
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Wide-field mosaics of the corneal subbasal nerve plexus in Parkinsons disease using in vivo confocal microscopy
- 2021
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Ingår i: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- In vivo confocal microscopy (IVCM) is a non-invasive imaging technique facilitating real-time acquisition of images from the live cornea and its layers with high resolution (1-2 mu m) and high magnification (600 to 800-fold). IVCM is extensively used to examine the cornea at a cellular level, including the subbasal nerve plexus (SBNP). IVCM of the cornea has thus gained intense interest for probing ophthalmic and systemic diseases affecting peripheral nerves. One of the main drawbacks, however, is the small field of view of IVCM, preventing an overview of SBNP architecture and necessitating subjective image sampling of small areas of the SBNP for analysis. Here, we provide a high-quality dataset of the corneal SBNP reconstructed by automated mosaicking, with an average mosaic image size corresponding to 48 individual IVCM fields of view. The mosaic dataset represents a group of 42 individuals with Parkinsons disease (PD) with and without concurrent restless leg syndrome. Additionally, mosaics from a control group (n = 13) without PD are also provided, along with clinical data for all included participants.
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| 3. |
- Brlík, Vojtěch, et al.
(författare)
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Long-term and large-scale multispecies dataset tracking population changes of common European breeding birds
- 2021
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Around fifteen thousand fieldworkers annually count breeding birds using standardized protocols in 28 European countries. The observations are collected by using country-specific and standardized protocols, validated, summarized and finally used for the production of continent-wide annual and long-term indices of population size changes of 170 species. Here, we present the database and provide a detailed summary of the methodology used for fieldwork and calculation of the relative population size change estimates. We also provide a brief overview of how the data are used in research, conservation and policy. We believe this unique database, based on decades of bird monitoring alongside the comprehensive summary of its methodology, will facilitate and encourage further use of the Pan-European Common Bird Monitoring Scheme results.
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| 4. |
- Buck, Moritz, et al.
(författare)
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Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds
- 2021
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.
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| 5. |
- Einarsson, Rasmus, 1988, et al.
(författare)
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Crop production and nitrogen use in European cropland and grassland 1961–2019
- 2021
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents EuropeAgriDB v1.0, a dataset of crop production and nitrogen (N) flows in European cropland 1961–2019. The dataset covers 26 present-day countries, detailing the cropland N harvests in 17 crop categories as well as cropland N inputs in synthetic fertilizers, manure, symbiotic fixation, and atmospheric deposition. The study builds on established methods but goes beyond previous research by combining data from FAOSTAT, Eurostat, and a range of national data sources. The result is a detailed, complete, and consistent dataset, intended as a basis for further analyses of past and present agricultural production patterns, as well as construction of scenarios for the future.
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| 6. |
- Falster, Daniel, et al.
(författare)
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AusTraits, a curated plant trait database for the Australian flora
- 2021
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Ingår i: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
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| 7. |
- Gundale, Michael
(författare)
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Global data on earthworm abundance, biomass, diversity and corresponding environmental properties
- 2021
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change.
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| 8. |
- Haytural, Hazal, et al.
(författare)
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Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis
- 2021
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Mass spectrometry (MS)-based proteomics is a powerful tool to explore pathogenic changes of a disease in an unbiased manner and has been used extensively in Alzheimer disease (AD) research. Here, by performing a meta-analysis of high-quality proteomic studies, we address which pathological changes are observed consistently and therefore most likely are of great importance for AD pathogenesis. We retrieved datasets, comprising a total of 21,588 distinct proteins identified across 857 postmortem human samples, from ten studies using labeled or label-free MS approaches. Our meta-analysis findings showed significant alterations of 757 and 1,195 proteins in AD in the labeled and label-free datasets, respectively. Only 33 proteins, some of which were associated with synaptic signaling, had the same directional change across the individual studies. However, despite alterations in individual proteins being different between the labeled and the label-free datasets, several pathways related to synaptic signaling, oxidative phosphorylation, immune response and extracellular matrix were commonly dysregulated in AD. These pathways represent robust changes in the human AD brain and warrant further investigation.
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| 9. |
- Khavari, Babak, et al.
(författare)
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Population cluster data to assess the urban-rural split and electrification in Sub-Saharan Africa
- 2021
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Human settlements are usually nucleated around manmade central points or distinctive natural features, forming clusters that vary in shape and size. However, population distribution in geo-sciences is often represented in the form of pixelated rasters. Rasters indicate population density at predefined spatial resolutions, but are unable to capture the actual shape or size of settlements. Here we suggest a methodology that translates high-resolution raster population data into vector-based population clusters. We use open-source data and develop an open-access algorithm tailored for low and middle-income countries with data scarcity issues. Each cluster includes unique characteristics indicating population, electrification rate and urban-rural categorization. Results are validated against national electrification rates provided by the World Bank and data from selected Demographic and Health Surveys (DHS). We find that our modeled national electrification rates are consistent with the rates reported by the World Bank, while the modeled urban/rural classification has 88% accuracy. By delineating settlements, this dataset can complement existing raster population data in studies such as energy planning, urban planning and disease response.
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| 10. |
- Kluge, Mariana, et al.
(författare)
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Community composition of aquatic fungi across the thawing Arctic
- 2021
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Thermokarst activity at permafrost sites releases considerable amounts of ancient carbon to the atmosphere. A large part of this carbon is released via thermokarst ponds, and fungi could be an important organismal group enabling its recycling. However, our knowledge about aquatic fungi in thermokarstic systems is extremely limited. In this study, we collected samples from five permafrost sites distributed across circumpolar Arctic and representing different stages of permafrost integrity. Surface water samples were taken from the ponds and, additionally, for most of the ponds also the detritus and sediment samples were taken. All the samples were extracted for total DNA, which was then amplified for the fungal ITS2 region of the ribosomal genes. These amplicons were sequenced using PacBio technology. Water samples were also collected to analyze the chemical conditions in the ponds, including nutrient status and the quality and quantity of dissolved organic carbon. This dataset gives a unique overview of the impact of the thawing permafrost on fungal communities and their potential role on carbon recycling.
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