| 1. |
- Alneberg, Johannes, et al.
(författare)
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BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
- 2018
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .
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| 2. |
- Ammar, Yosr, et al.
(författare)
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Long-term dataset for contaminants in fish, mussels, and bird eggs from the Baltic Sea
- 2024
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Ingår i: Scientific Data. - 2052-4463. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Widespread persistent contaminants are a global environmental problem. In the Baltic Sea, wildlife contamination was first noticed in the 1960s, prompting the Swedish Environmental Protection Agency to establish a comprehensive Swedish National Monitoring Programme for Contaminants in Marine Biota (MCoM) in 1978 run by the Swedish Museum of Natural History. Eight species have been analysed, four fish species (Atlantic herring, Atlantic cod, European perch, viviparous eelpout), one bivalve species (blue mussel), and egg from three bird species (common guillemot, common tern, Eurasian oystercatcher). Here, we present a dataset containing MCoM data from its start until 2021. It includes 36 sets of time-series, each analysed for more than 100 contaminants. The longest time-series is for common guillemot and starts in 1968. We describe the structure of MCoM including historic changes to the number of stations, sample treatment, analytical methods, instruments, and laboratories. The MCoM data is available at the Bolin Centre repository and on GitHub through our R package mcomDb. The latter will be updated yearly with new MCoM records.
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| 3. |
- Buchanan, E. M., et al.
(författare)
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The Psychological Science Accelerator's COVID-19 rapid-response dataset
- 2023
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- In response to the COVID-19 pandemic, the Psychological Science Accelerator coordinated three large-scale psychological studies to examine the effects of loss-gain framing, cognitive reappraisals, and autonomy framing manipulations on behavioral intentions and affective measures. The data collected (April to October 2020) included specific measures for each experimental study, a general questionnaire examining health prevention behaviors and COVID-19 experience, geographical and cultural context characterization, and demographic information for each participant. Each participant started the study with the same general questions and then was randomized to complete either one longer experiment or two shorter experiments. Data were provided by 73,223 participants with varying completion rates. Participants completed the survey from 111 geopolitical regions in 44 unique languages/dialects. The anonymized dataset described here is provided in both raw and processed formats to facilitate re-use and further analyses. The dataset offers secondary analytic opportunities to explore coping, framing, and self-determination across a diverse, global sample obtained at the onset of the COVID-19 pandemic, which can be merged with other time-sampled or geographic data.
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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. |
- Burgos, María A., et al.
(författare)
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A global view on the effect of water uptake on aerosol particle light scattering
- 2019
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- A reference dataset of multi-wavelength particle light scattering and hemispheric backscattering coefficients for different relative humidities (RH) between RH = 30 and 95% and wavelengths between lambda = 450 nm and 700 nm is described in this work. Tandem-humidified nephelometer measurements from 26 ground-based sites around the globe, covering multiple aerosol types, have been re-analysed and harmonized into a single dataset. The dataset includes multi-annual measurements from long-term monitoring sites as well as short-term field campaign data. The result is a unique collection of RH-dependent aerosol light scattering properties, presented as a function of size cut. This dataset is important for climate and atmospheric model-measurement inter-comparisons, as a means to improve model performance, and may be useful for satellite and remote sensing evaluation using surface-based, in-situ measurements.
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| 6. |
- Clements, Harley S., et al.
(författare)
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The bii4africa dataset of faunal and floral population intactness estimates across Africa's major land uses
- 2024
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Ingår i: Scientific data. - 2052-4463. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species' population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate 'intactness scores': the remaining proportion of an 'intact' reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region's major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems.
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| 7. |
- Dorschel, Boris, et al.
(författare)
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The International Bathymetric Chart of the Southern Ocean Version 2
- 2022
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- The Southern Ocean surrounding Antarctica is a region that is key to a range of climatic and oceanographic processes with worldwide effects, and is characterised by high biological productivity and biodiversity. Since 2013, the International Bathymetric Chart of the Southern Ocean (IBCSO) has represented the most comprehensive compilation of bathymetry for the Southern Ocean south of 60 degrees S. Recently, the IBCSO Project has combined its efforts with the Nippon Foundation - GEBCO Seabed 2030 Project supporting the goal of mapping the world's oceans by 2030. New datasets initiated a second version of IBCSO (IBCSO v2). This version extends to 50 degrees S (covering approximately 2.4 times the area of seafloor of the previous version) including the gateways of the Antarctic Circumpolar Current and the Antarctic circumpolar frontal systems. Due to increased (multibeam) data coverage, IBCSO v2 significantly improves the overall representation of the Southern Ocean seafloor and resolves many submarine landforms in more detail. This makes IBCSO v2 the most authoritative seafloor map of the area south of 50 degrees S.
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| 8. |
- Fitzpatrick, John, et al.
(författare)
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SpermTree, a species-level database of sperm morphology spanning the animal tree of life
- 2022
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Sperm are the most morphologically variable cell type known, despite performing the same functional role of fertilizing eggs across all sexually reproducing species. Sperm morphology commonly varies among individuals, populations, closely related species, and across animal phyla. Sperm morphology has long been used as a tool for placing species in a phylogenetic context and a range of selective forces are hypothesized to influence sperm evolution and diversification. However, we currently lack robust examinations of macroevolutionary (i.e. across phyla) patterns of sperm evolution, due largely to the challenges of comparing sperm morphological data across the animal tree of life. Here we describe the SpermTree database, which currently represents 5,675 morphological descriptions of sperm morphology from 4,705 unique species from 27 animal phyla. This dataset includes measurements of sperm head, midpiece, flagellum and total length, the latter of which spans four orders of magnitude. All entries in the dataset are matched to currently accepted scientific names in taxonomic databases, facilitating the use of these data in analyses examining sperm evolution in animals.
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| 9. |
- Gnacek, Michal, et al.
(författare)
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AVDOS-VR : Affective Video Database with Physiological Signals and Continuous Ratings Collected Remotely in VR
- 2024
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Ingår i: Scientific Data. - 2052-4463. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Investigating emotions relies on pre-validated stimuli to evaluate induced responses through subjective self-ratings and physiological changes. The creation of precise affect models necessitates extensive datasets. While datasets related to pictures, words, and sounds are abundant, those associated with videos are comparatively scarce. To overcome this challenge, we present the first virtual reality (VR) database with continuous self-ratings and physiological measures, including facial EMG. Videos were rated online using a head-mounted VR device (HMD) with attached emteqPRO mask and a cinema VR environment in remote home and laboratory settings with minimal setup requirements. This led to an affective video database with continuous valence and arousal self-rating measures and physiological responses (PPG, facial-EMG (7x), IMU). The AVDOS-VR database includes data from 37 participants who watched 30 randomly ordered videos (10 positive, neutral, and negative). Each 30-second video was assessed with two-minute relaxation between categories. Validation results suggest that remote data collection is ecologically valid, providing an effective strategy for future affective study designs. All data can be accessed via: www.gnacek.com/affective-video-database-online-study.
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| 10. |
- 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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