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41.
  • Franic, Iva, et al. (författare)
  • Worldwide diversity of endophytic fungi and insects associated with dormant tree twigs
  • 2022
  • Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 9:1
  • Tidskriftsartikel (refereegranskat)abstract
    • International trade in plants and climate change are two of the main factors causing damaging tree pests (i.e. fungi and insects) to spread into new areas. To mitigate these risks, a large-scale assessment of tree-associated fungi and insects is needed. We present records of endophytic fungi and insects in twigs of 17 angiosperm and gymnosperm genera, from 51 locations in 32 countries worldwide. Endophytic fungi were characterized by high-throughput sequencing of 352 samples from 145 tree species in 28 countries. Insects were reared from 227 samples of 109 tree species in 18 countries and sorted into taxonomic orders and feeding guilds. Herbivorous insects were grouped into morphospecies and were identified using molecular and morphological approaches. This dataset reveals the diversity of tree-associated taxa, as it contains 12,721 fungal Amplicon Sequence Variants and 208 herbivorous insect morphospecies, sampled across broad geographic and climatic gradients and for many tree species. This dataset will facilitate applied and fundamental studies on the distribution of fungal endophytes and insects in trees.
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42.
  • Gabriel, M., et al. (författare)
  • A relational database to identify differentially expressed genes in the endometrium and endometriosis lesions
  • 2020
  • Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 7
  • Tidskriftsartikel (refereegranskat)abstract
    • Endometriosis is a common inflammatory estrogen-dependent gynecological disorder, associated with pelvic pain and reduced fertility in women. Several aspects of this disorder and its cellular and molecular etiology remain unresolved. We have analyzed the global gene expression patterns in the endometrium, peritoneum and in endometriosis lesions of endometriosis patients and in the endometrium and peritoneum of healthy women. In this report, we present the EndometDB, an interactive web-based user interface for browsing the gene expression database of collected samples without the need for computational skills. The EndometDB incorporates the expression data from 115 patients and 53 controls, with over 24000 genes and clinical features, such as their age, disease stages, hormonal medication, menstrual cycle phase, and the different endometriosis lesion types. Using the web-tool, the end-user can easily generate various plot outputs and projections, including boxplots, and heatmaps and the generated outputs can be downloaded in pdf-format.
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43.
  • Ghahremanpour, Mohammad M., et al. (författare)
  • The Alexandria library, a quantum-chemical database of molecular properties for force field development
  • 2018
  • Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.
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44.
  • Ghiringhelli, Luca M., et al. (författare)
  • Shared metadata for data-centric materials science
  • 2023
  • Ingår i: Scientific Data. - : NATURE PORTFOLIO. - 2052-4463. ; 10
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • The expansive production of data in materials science, their widespread sharing and repurposing requires educated support and stewardship. In order to ensure that this need helps rather than hinders scientific work, the implementation of the FAIR-data principles (Findable, Accessible, Interoperable, and Reusable) must not be too narrow. Besides, the wider materials-science community ought to agree on the strategies to tackle the challenges that are specific to its data, both from computations and experiments. In this paper, we present the result of the discussions held at the workshop on “Shared Metadata and Data Formats for Big-Data Driven Materials Science”. We start from an operative definition of metadata, and the features that  a FAIR-compliant metadata schema should have. We will mainly focus on computational materials-science data and propose a constructive approach for the FAIRification of the (meta)data related to ground-state and excited-states calculations, potential-energy sampling, and generalized workflows. Finally, challenges with the FAIRification of experimental (meta)data and materials-science ontologies are presented together with an outlook of how to meet them.
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45.
  • Gnacek, Michal, et al. (författare)
  • AVDOS-VR : Affective Video Database with Physiological Signals and Continuous Ratings Collected Remotely in VR
  • 2024
  • Ingår i: Scientific Data. - 2052-4463. ; 11
  • 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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46.
  • Gomez-Cabrero, D, et al. (författare)
  • STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse
  • 2019
  • Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 6:1, s. 256-
  • Tidskriftsartikel (refereegranskat)abstract
    • Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multi-omics projects still include a limited number of molecular assays and there have been very few multi-omic studies that evaluate dynamic processes such as cellular growth, development and adaptation. Hence, we lack formal analysis methods and comprehensive multi-omics datasets that can be leveraged to develop true multi-layered models for dynamic cellular systems. Here we present the STATegra multi-omics dataset that combines measurements from up to 10 different omics technologies applied to the same biological system, namely the well-studied mouse pre-B-cell differentiation. STATegra includes high-throughput measurements of chromatin structure, gene expression, proteomics and metabolomics, and it is complemented with single-cell data. To our knowledge, the STATegra collection is the most diverse multi-omics dataset describing a dynamic biological system.
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47.
  • Gundale, Michael (författare)
  • Global data on earthworm abundance, biomass, diversity and corresponding environmental properties
  • 2021
  • Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 8
  • 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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48.
  • Hahn, Max, et al. (författare)
  • Quantitative 3D OPT and LSFM datasets of pancreata from mice with streptozotocin-induced diabetes
  • 2022
  • Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 9:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Mouse models for streptozotocin (STZ) induced diabetes probably represent the most widely used systems for preclinical diabetes research, owing to the compound's toxic effect on pancreatic beta-cells. However, a comprehensive view of pancreatic beta-cell mass distribution subject to STZ administration is lacking. Previous assessments have largely relied on the extrapolation of stereological sections, which provide limited 3D-spatial and quantitative information. This data descriptor presents multiple ex vivo tomographic optical image datasets of the full beta-cell mass distribution in mice subject to single high and multiple low doses of STZ administration, and in glycaemia recovered mice. The data further include information about structural features, such as individual islet beta-cell volumes, spatial coordinates, and shape as well as signal intensities for both insulin and GLUT2. Together, they provide the most comprehensive anatomical record of the effects of STZ administration on the islet of Langerhans in mice. As such, this data descriptor may serve as reference material to facilitate the planning, use and (re)interpretation of this widely used disease model.
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49.
  • Hall, Ola, et al. (författare)
  • Population centroids of the world administrative units from nighttime lights 1992-2013
  • 2019
  • Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 6:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Knowledge about the past, current and future distribution of the human population is fundamental for tackling many global challenges. Censuses are used to collect information about population within a specified spatial unit. The spatial units are usually arbitrarily defined and their numbers, size and shape tend to change over time. These issues make comparisons between areas and countries difficult. We have in related work proposed that the shape of the lit area derived from nighttime lights, weighted by its intensity can be used to analyse characteristics of the population distribution, such as the mean centre of population. We have processed global nighttime lights data for the period 1992-2013 and derived centroids for administrative levels 0-2 of the Database of Global Administrative Areas, corresponding to nations and two levels of sub-divisions, that can be used to analyse patterns of global or local population changes. The consistency of the produced dataset was investigated and distance between true population centres and derived centres are compared using Swedish census data as a benchmark.
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50.
  • Hantke, Max F., et al. (författare)
  • A data set from flash X-ray imaging of carboxysomes
  • 2016
  • Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
  • Tidskriftsartikel (refereegranskat)abstract
    • Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.
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