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Chemical variables - stream from Mycklemossen, S-stream-5
No full textManual grab samples from the stream for chemical analysis are taken on a biweekly basis during ice-free conditions, and on a monthly basis in the presence of stream ice.
Skogaryd Research Catchment (2025). Chemical variables - stream from Mycklemossen, S-stream-5, 2019-01-14–2019-12-30 [Data set]. Swedish Infrastructure for Ecosystem Science (SITES). https://hdl.handle.net/11676.1/84u3N2CFBmT6B9c9lf0z8VM
Chemical variables - stream from Följemaden, outlet-stream-4
No full textManual grab samples from the stream for chemical analysis are taken on a biweekly basis during ice-free conditions, and on a monthly basis in the presence of stream ice.
Skogaryd Research Catchment (2025). Chemical variables - stream from Följemaden, outlet-stream-4, 2019-01-14–2019-12-11 [Data set]. Swedish Infrastructure for Ecosystem Science (SITES). https://hdl.handle.net/11676.1/w_ob4JitaWHZOg3yRYkp0BR
Data för: Landscape-scale drivers of insect pest regulation in sugar beet
No full textWe studied the effects of different landscape parameters at three spatial scales on the densities of and damage caused by five major insect pests of sugar beet in 134 sugar beet fields monitored across five years in Denmark and Sweden. The landscape parameters investigated include the cover of cropland as measure of landscape simplification, the absolute inter-annual change in host crop cover (sugar beet), the landscape-level crop diversity in the previous year and the edge-density in the surrounding landscapes. The pests were monitored in a standardised monitoring scheme with one observation plot in each field and the respective values represent the maximum observed densities or damage at economically relevant development stages (see detailed description below). Pest densities and damage were recorded in five clusters of five plants selected at random within the observation plot avoiding plot edges and tractor tracks.
Landscape parameters were extracted from the official land-use maps provided by the Danish Agricultural Agency (Landbrugsstyrelsen, 2024. Internet Markkort (IMK). Ministeriet for Fødevarer, Landbrug og Fiskeri, København) and the Swedish Board of Agriculture (Jordbruksverket, 2024. Kartor och Geografiska informationssystem - Årslager skiftesdata. Jordbruksverket) at three buffer radii (500 m, 1000 m and 2000 m) around the centre of the observation plots. For further information, see methods in the publication Boetzl et al. (2026) Landscape-scale drivers of insect pest regulation in sugar beet. Agriculture, Ecosystems and Environment.
The data in the 'sugarbeet_pests_data.csv' file have information on the prevalence and damage caused by five major sugar beet pests (black bean aphid, pygmy mangold beetle, flea beetles, beet leafminers and thrips) at the respective economically relevant sugar beet growth stages recorded in 134 fields ('ID') in Denmark and Sweden as well as landscape parameters in the landscapes surrounding these fields at three spatial scales (500 m, 1000 m and 2000 m). 135 rows. 'NA' indicates missing values.
SLU has led data analysis and publication of the scientific article. Nordic Beet Research has coordinated data collection. University of Copenhagen has contributed to data interpretation.Vi studerade effekterna av olika landskapsparametrar på tre rumsliga skalor på tätheten av och skadorna orsakade av fem viktiga skadeinsekter på sockerbetor i 134 sockerbetsfält som övervakades under fem år i Danmark och Sverige. De landskapsparametrar som undersöktes omfattade täckningen av odlingsmark som ett mått på landskapsförenkling, den absoluta förändringen mellan åren i täckningen av värdväxter (sockerbetor), mångfalden av odlade grödor på landskapsnivå under föregående år och kanttätheten i de omgivande landskapen. Skadedjuren övervakades i ett standardiserat övervakningssystem med en observationsruta i varje fält, och respektive värden representerar de maximala observerade tätheterna eller skadorna i ekonomiskt relevanta utvecklingsstadier. Skadedjurstätheter och skador registrerades i fem kluster om fem slumpmässigt utvalda växter inom observationsrutor, med undantag för rutornas kanter och traktorspår.
Landskapsparametrarna hämtades från de officiella markanvändningskartorna som tillhandahålls av det danska jordbruksverket (Landbrugsstyrelsen, 2024. Internet Markkort (IMK). Ministeriet for Fødevarer, Landbrug og Fiskeri, København) och Jordbruksverket (Jordbruksverket, 2024. Kartor och Geografiska informationssystem - Årslager skiftesdata. Jordbruksverket) vid tre buffertradier (500 m, 1000 m och 2000 m) runt centrum av observationsområdena. För ytterligare information, se metoderna i publikationen Boetzl et al. (2025) Landscape-scale drivers of insect pest regulation in sugar beet. Agriculture, Ecosystems and Environment.
Filen ”sugarbeet_pests_data.csv” innehåller information om förekomsten av och skador orsakade av fem viktiga skadedjur på sockerbetor (svart bönbladlus, lilla betbaggen, jordloppor, betflugor och trips) i respektive ekonomiskt relevanta tillväxtstadier för sockerbetor, registrerade på 134 fält (”ID”) i Danmark och Sverige, samt landskapsparametrar i landskapet kring dessa fält på tre rumsliga skalor (500 m, 1000 m och 2000 m). 135 rader. ”NA” anger saknade värden.
SLU har lett analys av data och publicering av den vetenskaplig artikeln. Nordic Beet Research har koordinerat insamling av data. Köpenhamns universitet har bidragit till tolkning av data
Data för: Unraveling the Electronic Control of Hydride Diffusivity in Oxyhydrides from Model Studies on BaTiO3−xHy
No full textThis dataset contains input and output files of the DFT package Vienna Ab initio Simulation Package (VASP) used to generate the results of the related article.
Several supercells and calculation settings are used with the aim to describe different degrees of electron localization in BaTiO3−2xHx. Specifically, the calculations consist of: cell optimization, density of states and band structure calculations, and nudged-elastic band calculations. The results, as discussed in the article, help to understand the impact of localized electron on hydride-ion conduction mechanism of the material.Denna datamängd innehåller in- och utdatafiler från DFT-paketet Vienna Ab initio Simulation Package (VASP) som användes för att generera resultaten i den relaterade artikeln.
Flera superceller och beräkningsinställningar används för att beskriva olika grader av elektronlokalisering i BaTiO3−2xHx. Specifikt omfattar beräkningarna: celloptimering, beräkningar av täthetstillstånd och bandstruktur samt beräkningar med nudged-elastic band-metoden. Resultaten, som diskuteras i artikeln, bidrar till en bättre förståelse av den lokaliserade elektronens inverkan på hydridjoners ledningsmekanism i materialet
Data and codes for "Quantum jumps in amplitude bistability: Tracking a coherent and invertible state localization"
No full textWe investigate the nature of quantum jumps occurring between macroscopic metastable states of light in the open driven Jaynes-Cummings model. We find that, in the limit of zero spontaneous emission considered in Carmichael (2015), the jumps from a high-photon state to the vacuum state entail two stages. The first part is coherent and modelled by the localization of a state superposition, in the example of a null-measurement record predicted by quantum trajectory theory. The underlying evolution is mediated by an unstable state (which often splits to a complex of states), identified by the conditioned density matrix and the corresponding quasiprobability distribution of the cavity field. The unstable state subsequently decays to the vacuum to complete the jump. Coherence in the localization allows for inverting the null-measurement photon average about its initial value, to account for the full switch which typically lasts a small fraction of the average cavity lifetime; an asymptotic law for the jump time is established in high-amplitude bistability. This mechanism is contrasted to the jumps leading from the vacuum to the high-photon state in the bistable signal. Spontaneous emission degrades coherence in the localization, and prolongs the jumps.
The datasets in the .mat files (MATLAB) correspond to the paper figure indicated in each filename. They are primarily generated from the code JCRK4_Amp_Bist.m (solving the matrix elements equations of motion by employing a 4th order Runge-Kutta method) as well as JCBist.cc (refer to the C++ library used for quantum trajectories in the main text). The code JCRK4_Amp_Bist_Kerr.mat is used only for generating data for Fig. 8, while for Fig. 6 a subset of data used for Fig. 5 has been deployed. The conditioned Q functions and density matrix barplots are generated using Qfunction.m, while steady-state results have been generated using Qfunc_bist.m (from Quantum Optics Toolbox). The code neoclassical.m generates the mean-field bistability curve pictured in Fig. 9
Skelettmaterial från senneolitikum - äldre bronsålder i Sydsverige
No full textThe database is the foundation for a study of health in Late Neolithic-Early Bronze Age southern Sweden. Skeletal remains from 46 loclities have been osteologically registered. The database founded studies of paleopathology, paleodemography and stature.
Purpose:
Database for the study of health in Late Neolithic-Early Bronze Age Southern Sweden. Data for PhD dissertation in historical osteology.
Osteological registration. Ocular assessment.Databasen ligger till grund för studien av hälsa i senneolitikum och äldre bronsålder i Sydsverige. Skelettmaterial har osteologiskt registrerats från 46 olika lokaler. Databasen har legat till grund för paleopatologi, paleodemografi och kroppslängdsstudier.
Syfte:
Databas för studie av hälsa i senneolitikum och äldre bronsålder. Underlag för doktorsavhandling i historisk osteologi.
Osteologisk registrering. Okulär bedömning
Ultrasound-guided, magnetothermal wax capsule for localized gastrointestinal drug delivery
No full textOral drug delivery to specific lesions in the gastrointestinal (GI) tract remains a major challenge. The current systems depend on internal physiological triggers such as pH, enzymatic activity, and luminal pressure, which exhibit wide intra- and inter-patient variability. To address this, an ingestible capsule was developed to enable on-demand, site-specific drug release in response to an external alternating magnetic field (AMF), with ultrasound imaging used for real-time localization. The capsule is composed of a low-melting-point wax matrix embedded with superparamagnetic iron oxide nanoparticles (SPIONs), which generate heat upon AMF exposure, resulting in rapid wax melting and burst drug release. SPIONs exhibited no toxicity in zebrafish embryonic development, demonstrating excellent biocompatibility. Capsules were fabricated in a hemispherical shape using a 3D-printed mold, yielding highly reproducible batches with a mass variation within ±10%. A Design of Experiments (DoE) approach identified an optimized formulation comprising a 6:4 docosane:eicosane wax blend, 10 wt% SPION loading, and a 1.5 mm capsule shell thickness, achieving efficient magnetic heating while maintaining mechanical strength (> 2 N), sufficient for withstanding GI transit.
The optimized capsule formulation exhibited no cytotoxicity in vitro and remained intact throughout sequential incubation in simulated gastric, intestinal, and colonic fluids. No drug leakage or significant metal leaching (≤ 0.6%) was obtained. The capsule was successfully visualized in a porcine abdominal model using a handheld ultrasound device commonly used at the bedside in the clinic. AMF exposure triggered complete drug release within 33 seconds in vitro. In vivo studies in mice further demonstrated capsule localization via ultrasound, and AMF-triggered capsule melting in the colon via endoscopy. In conclusion, this magnetothermal capsule platform integrates non-invasive imaging and externally triggered drug release to enable localized GI drug delivery, representing a promising strategy for precision treatment of GI diseases
Arthropod Kraken2 Database v1
No full textKraken2 Arthopod Reference Database v.1Kraken2 (v2.1.2) database containing all 2,593 reference assemblies for Arthropoda available on NCBI as of March 2023.
This database was built for and used in the analysis of shotgun sequencing data of bulkDNA from Malaise trap samples collected by the Insect Biome Atlas, in the context of the manuscript "Small Bugs, Big Data: Metagenomics for arthropod biodiversity monitoring" by authors: López Clinton Samantha, Iwaszkiewicz-Eggebrecht Ela, Miraldo Andreia, Goodsell Robert, Webster Mathew T, Ronquist Fredrik, van der Valk Tom (for submission to Ecology and Evolution).
For custom database building, Kraken2 requires all headers in reference assembly fasta files to be annotated with "kraken:taxid|XXX" at the end of each header. Where "XXX" is the corresponding National Center for Biotechnology Information (NCBI) taxID of the species. The code used to add the taxID information to each fasta file header, and update the accession2taxid.map file required by Kraken2 for database building, is available in this GitHub repository (https://github.com/SamanthaLop/Small_Bugs_Big_Data) (also linked under "Related Materials" below).
ContentBelow is a list of the files in this item (in addition to the README and MANIFEST files), and their description. The first three files (marked with a *) are required to run Kraken2 classifications using the database.
- * hash.k2d.gz - A hash file with all minimiser to taxon mappings (855 GB).
- * opts.k2d - A file containing all options used when building the Kraken2 database (64 B).
- * taxo.k2d - A file containing the taxonomy information used to build the database (385.9 KB).
- seqid2taxid.map.gz - A file containing contig accession numbers and their corresponding taxids (810.6 MB). Note that this file is needed by Kraken2 when building the database, and as it was updated during custom building, it has been included for reference, but it is not required to use the database for classification.
- genome_assembly_metadata.tsv - NCBI-generated table (tsv format, gzipped) of all reference assemblies for Arthropoda as of March 2023, which were used in the database construction. This includes columns: Assembly Accession, Assembly Name, Organism Name, Organism Infraspecific Names Breed, Organism Infraspecific Names Strain, Organism Infraspecific Names Cultival, Organism Infraspecific Names Ecotype, Organism Infraspecific Names Isolate, Organism Infraspecific Names Sex, Annotation Name, Assembly Stats Total Sequence Length, Assembly Level, Assembly Submission, and WGS project accession.
How to use the database- Download the hash.k2d.gz, opts.k2d, and taxo.k2d files to the same directory (e.g. /PATH/TO/DATABASE/).
- Unzip the hash.k2d.gz file.
- Install or load Kraken2 to run classification on sequencing data using the database.
- When running Kraken2, indicate the path to the directory (not the individual files) with the --db flag (e.g. kraken2 --db /PATH/TO/DATABASE/ ...).
Note that the whole database must be loaded into memory by Kraken2 to be able to classify any sequencing reads, so ensure you have access to enough memory before running (the uncompressed hash file is around 1.1 TB).
We also recommend using the Kraken2 option --memory-mapping, as it ensures the database is loaded once for all samples, instead of once for each individual sample, saving considerable time and resources.
For more information on using Kraken2, see the Kraken2 wiki manual (https://github.com/DerrickWood/kraken2/wiki/Manual) .
This database was built by Samantha López Clinton (samantha.lopezclinton@nrm) and Tom van der Valk ([email protected])
Scattering data and the final simulation snapshots
No full textCharacterizing the aggregation behavior of Sodium Caprate using coarse-grained molecular dynamics (CG-MD) simulations (Martini 2 and Martini 3 force fields) in combination with the small-angle scattering techniques.
Structural (final simulation snapshot) and scattering data for various systems composed of compound C10 under different concentrations, compositions, and environmental conditions. The files are organized as PDB structures and scattering data.
The PDB files represent the final snapshot of aggregates generated under various conditions. Each file name follows this convention:
- Concentration: e.g., `300mM`, `50mM`
- Component: C10 surfactant
- FaSSIF: Presence of Fasted State Simulated Intestinal Fluid (optional)
- Ratio: `100:0`, `50:50`, representing the charge: uncharge ratios
- Model: `M2` or `M3` representing Martini 2 and Martini 3 force fields
Examples:
- `300mM_C10_100:0_M2.pdb`: 300 mM C10, 100:0 ratio, studied by Martini 2 force field
- `50mM_C10_FaSSIF_50:50_M3.pdb`: 50 mM C10, with FaSSIF, 50:50 ratio, studied by Martini 3 force field
Text files with small-angle x-ray scattering (SAXS) or small-angle neutron scattering (SANS) data under different pH conditions:
- `SANS_C10_300mM_pH81.txt`: SANS data for C10 at 300 mM, pH 8.1
- `SAXS_C10_300mM_pH65.txt`: SAXS data for C10 at 300 mM, pH 6.5
- `SAXS_C10_300mM_pH85.txt`: SAXS data for C10 at 300 mM, pH 8.5
These files can be used to:
- Analyze aggregate structures under different solution conditions.
- Compare structural models to experimental SAXS/SANS data.
- Validate aggregate formation and stability using different simulation parameters
Phenocam - Region Of Interest (ROI) Time Series from Lönnstorp Experimental Fields, Mast 10m Phenocam 02
No full textDaily aggregated time series containing solar-weighted mean vegetation indices and RGB channel values per Region of Interest, temporal data, solar metrics, and processing statistics for each daily composite.
Lönnstorp Research Station (2025). Phenocam - Region Of Interest (ROI) Time Series from Lönnstorp Experimental Fields, Mast 10m Phenocam 02, 2022-01-24–2025-04-30 [Data set]. Swedish Infrastructure for Ecosystem Science (SITES). https://hdl.handle.net/11676.1/qvLqJAFpDN2XC_C10Qe-i15