https://researchdata.se/en/catalogue Search results en The scoring system for both mucus production and histopathology is described in the research article "A. salmonicida infection inhibits rainbow trout gill mucin production" in the methods section. A. salmonicida (Aeromonas salmonicida). The variables examined in the data set are quantitative data and based on two main histological scoring systems. In tabs 2, 5 and 6 the scoring is based on how far an injected label is transported within the cell from its starting point (perinuclear; around the nucleus) over time or during insult (such as exposure to bacteria). The goblet cell is split into 4 regions from bottom to top of the mucus producing cell; perinuclear, mid cytoplasm, near apical cell surface and at apical cell surface. Each location/compartment received a score from 0-4 based on intensity of the label. This method is executed in vivo fish (tabs 2 and 5); where in tab 2 the label is injected at time 0 and collected at different time points following the injected label to study mucus production over time. In tab 5, a similar method is used, however, for this the fish were grouped into three different timepoints (8 h, 32 h and 7 days after injection of the label) and further subgrouped into non-immersed control fish and immersed fish in different concentrations of bacteria. Hence, allowing for investigation of mucus production over time and under stimulation. In in vitro fish gill cells (tab 6) grown on cell culture plates grouped in either non-infected controls, infected and cytokine-treated groups were analyzed similarly at 6 h after addition of label, added to the growth medium. In tab 4: Histological sections stained with Hematoxylin/Eosin were evaluated for pathology. For this we used the groups of fish investigated in tab 5 (above). On a general basis, the different categories of tissue changes (17 in total) were assigned to two groups; group 1 encompassed tissue changes thought to represent less negative impact on the gill function and/ or that are usually seen as readily reversible, while group 2 contained tissue changes that are thought to possess a greater influence on the gill function and/ or take longer time to heal. To reflect this expected influence on the gill function, categories of tissue changes of group 2 were given a higher score compared to categories of tissue changes of group 1 given the same relative distribution of tissue changes. In theory, the maximum gill histopathology score with this scoring model was 104, but in general terms, a score under 10 was regarded as mild changes, a score from 10 to under 20 as moderate changes, while a score above 20 was regarded as severe change. The data is available in excel-format. Tue, 29 Jul 2025 09:19:32 GMT https://researchdata.se/en/catalogue/dataset/2024-487 https://researchdata.se/en/catalogue/dataset/2024-487 University of Gothenburg Sinan Sharba I studied the divergence pattern of the European minnow (Phoxinus phoxinus), a common freshwater fish that has received little attention despite its large distribution. In many Scandinavian mountain lakes, European minnows are considered as being invasive and were found to pose threats to the native fish populations due to resource competition. Minnows were recently found to show phenotypic adaptations in lake versus stream habitats, but the question remained if this divergence pattern is related to differences in resource use. I therefore studied the patterns of minnow divergence in morphology (i.e., using geometric morphometrics) and trophic niches (i.e., using stomach content analyses) in the lake Ånnsjön and its tributaries to link the changes in body morphology to the feeding on specific resources. In August 2018, minnows were caught from three lake locations (L1, L2, L3; Figure 1) using gill nets (1 × 10 m with 6 mm mesh size), which were exposed for up to 12 hr. Furthermore, minnows were collected from three different slow-flowing tributaries that were less than two km away from the lake: downstream Stor Klockbäcken (location S1), downstream Sjöviksbäcken (location S2), and downstream Kvarnbäcken (location S3) (Figure 1). In the streams, minnows were caught using an electrofishing approach and killed with an overdose of benzocaine. Fish were frozen to −20°C and transported to the laboratory at Uppsala University. In total, 279 minnows were analyzed, 158 from the lake locations (L1: 52, L2: 52, L3: 54), and 121 in the streams (S1: 50, S2: 50, S3:21). In the laboratory, fish were thawed and subsequently individual length (to the nearest mm) was taken. See Morphological and trophic divergence of lake and stream minnows (Phoxinus phoxinus) by Scharnweber (2020) for furhter methodological information. The dataset was originally published in DiVA and moved to SND in 2024. Mon, 15 Jul 2019 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/2024-270 https://researchdata.se/en/catalogue/dataset/2024-270 Uppsala University Kristin Scharnweber List of bones for the osteological analysis performed on the mass material from the Pitted ware culture site Ajvide, Eksta parish, Gotland, Sweden, in Alexander Sjöstrands PhD thesis "Changes, activities and bones". The bone material is derived from archaeological excavations performed by Stockholm University, Gotland University and Uppsala University between the years 1983-2017. The list of bones contains the base dataset from the osteological analysis with information on ID-number, x and y coordinates, layer, area, layer, burnt/unburned, taxa/species, bone element, bone part, part of the body, side, number of fragments, weight, size (divided into three categories, 0-25mm, 26-50mm, 51-75mm and larger than 75mm), bone id (only a few posts where bone fragments fit together and has been linked in the list of bones via a bone id), age (fused/unfused), age assessment, other comments, date for analysis, and 4 variables for the analysis of the osteological material from the 2017 excavation. Trench, which square, context and FFI (fracture freshness index) Thu, 28 Mar 2024 09:37:14 GMT https://researchdata.se/en/catalogue/dataset/2023-107-1 https://researchdata.se/en/catalogue/dataset/2023-107-1 Uppsala University Alexander Sjöstrand The data is used in the study "Pyric herbivory in a temperate European wood-pasture system", in which we introduced fire and herbivory in a full-factorial experiment in a temperate European wood-pasture system to test if pyric herbivory operates in ways comparable to grassy systems elsewhere in the world. The dataset consists of data from photo traps describing the time in seconds per one-minute video that cattle performed a certain behavior and in which part of a study plot they were located, data on fuel height (cm) and fire cover (m2 and %) in each study plot and year, and data on species and life form cover (%) in each study plot in the end of the experiment. Wed, 21 Feb 2024 09:50:04 GMT https://researchdata.se/en/catalogue/dataset/2024-28 https://researchdata.se/en/catalogue/dataset/2024-28 Swedish University of Agricultural Sciences Karin Amsten Joris P. G. M. Cromsigt Dries P. J. Kuijper Jenny M. Loberg Jens Jung My Strömgren Marcin Churski Mats Niklasson The data set consist of amoxicillin plasma concentrations after treatment of six cats with three different pharmaceutical preparations and routes of administration in a non-randomized cross-over study. Moreover, data on binding to plasma proteins are included. Wed, 04 Jun 2025 07:51:45 GMT https://researchdata.se/en/catalogue/dataset/2025-65 https://researchdata.se/en/catalogue/dataset/2025-65 Swedish University of Agricultural Sciences Carl Ekstrand Beatrice Roques The purpose of this data was to evaluate and quantify wetland restoration efficiency for a scientific paper. The data contains pair counts of wetland bird species in wetlands that have been restored. The observations include time series, including Before and After wetland restoration. The data has been compiled from various published reports. Data: data contains bird pair abundance data in created wetlands in Swedish agricultural landscapes. Data collection description: Data from various published reports have been compiled into one dataset. The data contains bird species observations in wetlands that have been restored in the past 50 years. The bird surveys include mainly the estimates of bird pair abundances before and after restoration, but occasionally broods were estimated. The data also include wetland areas, year of restoration and inventory, as well as references to the original reports that reported the bird numbers, but here they are compiled into one data set. The variables are described in detail in the documentation file. Wed, 02 Nov 2022 08:34:41 GMT https://researchdata.se/en/catalogue/dataset/2022-127-1 https://researchdata.se/en/catalogue/dataset/2022-127-1 Swedish University of Agricultural Sciences Ineta Kačergytė Description of the data and file structure: data on fish biomass, fishery landings and hydrographic variables from the Baltic Sea. The data were used to explore the relationships between clupeids and three-spined stickleback, specifically whether reduced predation from herring and competition from both sprat and herring may have contributed to the recent increase of three-spined stickleback in the Baltic Sea. The data is structured in six separate datasets. Each record report values of fish biomass or abiotic variables related to a specific ICES statistical rectangle (ca. 55 × 55 km size, corresponding to 0.5 degrees in latitude × 1 degree in longitude) and a specific year. The datasets can be merged using the field "year" and "ICES". The files have the following dimensions: ICES_Hydrographic_data_by_year.csv, 4465 rows × 20 columns; herring_biomass.csv, 2056 rows × 5 columns; landings_herring.csv, 2867 rows × 3 columns; landings_sprat.csv, 2108 rows × 3 columns; sprat_biomass.csv, 2042 rows × 4 columns; stic Mon, 18 Nov 2024 09:21:07 GMT https://researchdata.se/en/catalogue/dataset/2024-158 https://researchdata.se/en/catalogue/dataset/2024-158 Swedish University of Agricultural Sciences Serena Donadi Olavi Kaljuste Niklas Larson Ronny Fredriksson Mårten Erlandsson Michele Casini Agnes Olin Johan Eklöf Jonas Nilsson Ulf Bergström The dataset contains both data and code associated with the following manuscript: "Estimating pike (Esox lucius) population dynamics and capture probability by recreational angling using spatial capture-recapture models in a Baltic Sea spawning area". This study aimed to estimate the population size, capture probability, and movement patterns of pike in Byviken, a shallow bay in the Stockholm Baltic Sea archipelago. We applied spatial capture-recapture (SCR) methods during the spring season each year from 2017 to 2022. The pike where caught by rod and reel and marked with T-bar tags in order to identify the individuals during subsequent captures. The dataset was created in a collaborative project between the Swedish University of Agricultural Sciences and the County Administrative Board of Stockholm. The following data files are loaded in the "run SCR models.R" script to run all model combinations: ## pike_cost_ssdf.Rdata ## Contains a list of 6 elements (one per year, 2017–2022). Each element includes the cost surface at 20 x 20 meter pixel resolution, with the variables X and Y—that is, the longitude and latitude in SWEREF 99TM. The variables include "Depth" (approximate depth in meters – not used in this analysis), "Shelter" (whether or not the pixel is in a sheltered area – not used in this analysis), and "Vegetation", which is the z-score distance to vegetation and was used as input in the asymmetric space use model. ## pike_scrFrame.Rdata ## Contains a list of 11 elements. 1 caphist: A list of 6 elements (one per year from 2017 to 2022). Each contains an individual-by-trap-by-occasion matrix. 2 traps: A list of 6 elements (one per year from 2017 to 2022). Each contains the names of traps (1 to 155) along with their X and Y coordinates in SWEREF 99TM. 3 trapCovs: A list of 6 elements (one per year from 2017 to 2022). Each contains a list of data frames, one per sampling occasion, with the following variables. Temperature is the degrees Celsius measured by the anglers during each fishing occasion. TEAM is 1 or 0 depending on which team was fishing. SEAL indicates whether seals or signs of seals were detected. This variable was not used in the analysis. 4 indCovs: A list of 6 elements (one per year from 2017 to 2022). Each contains a data frame where each row represents an individual. The data frames include the variable sex, which is explained in the description of sigCovs below, and removed, which shows the number of sampling occasions the individual was present during the session (year). 5 sigCovs: Contains a data frame with session-level covariates for sigma (one per year from 2017 to 2022) and the binary covariate sex. This covariate is used to distinguish between two size classes of pike: greater than or equal to 42 and less than 60 centimeters, and greater than or equal to 60 centimeters. 6 trapOperation: A list of 6 elements (one per year from 2017 to 2022). It indicates whether each trap (1 to 155) was operational during each occasion. 7 occasions: An integer for each session (one per year from 2017 to 2022) representing the number of sampling occasions. 8 type: Not relevant for this description. 9 mmdm: The mean maximum distance moved. 10 mdm: The maximum distance moved. 11 telemetry: Not relevant and was not included in the models. ## pike_ssdf.Rdata ## Includes the state space at 30 x 30 meter pixel resolution. The format is identical to that of pike_cost_ssdf.Rdata, described above. (For a more detailed description on the structure of the files going into the oSCR.fit() function please consult: Sutherland, C., Royle, J. A., & Linden, D. W. (2019). oSCR: a spatial capture–recapture R package for inference about spatial ecological processes. Ecography, 42(9), 1459-1469.) ## run_SCR_models.R ## Runs all SCR model combinations (these will likely take a very long time to run) and saves the models to: PIKE_MODELS_ECOLOGICAL.Rdata PIKE_MODELS_EUCLIDEAN.Rdata The models are loaded in some of but not all of the following scripts: "AIC_table1.R", "table2_variable_importance_and_p_values.R", and "table_3_sensitivity_table.R" → Used to generate Table 1, Table 2, and Table 3 "Fig2_histograms.R" → Produces Figure 2 "Fig3_cap_prob_figures.R" → Produces Figure 3 "Fig4_and_6_density_figures.R" → Produces Figures 4 and 6 "Fig5_observed_captures_and_observed_captured_percentage_of_population.R" → Produces Figure 5 "Fig7_predicted_home_ranges.R" → Produces Figure 7 "Fig1S_simulate_capture_data_under_model_M0.R" → Simulates data (also available in "results_df_N_1000.txt" and "results_df_N_2500.txt") under different population size and capture probability, produces Figure 1S (supplemental figure) "model_averaged_intercepts_with_95_CI.R" → Produces model-averaged intercepts for density, capture probability, and sigma Script for Figure 1 is not included in this dataset. ## "byviken_edf.txt" ## The file "byviken_edf.txt" contains individual capture data, where each row represents a capture event. The columns are as follows: "Session" — 1 to 6, one for each year from 2017 to 2022. "ID" — the ID of the individual. "Occasion" — the sampling occasion within the session when the capture occurred. "Detector" — the trap (1 to 155) where the capture was made. "Sex" — Male, Female, or Unknown. "Length" — the length of the fish in centimeters. "Weight" — the weight of the fish in grams. "Spawn" — indicates if the pike had spawned: UTLEKT = spawned, OLEKT = not spawned, ODEF = undefined. "Date" — the date of the capture. Tue, 14 Oct 2025 11:41:41 GMT https://researchdata.se/en/catalogue/dataset/2025-176 https://researchdata.se/en/catalogue/dataset/2025-176 Swedish University of Agricultural Sciences Konrad Karlsson Henrik C. Andersson Göran Sundblad Data consisting of animations of different temporal aspects of hominin evolution. The aim of the study was to investigate how various representations of time in an animation affect the way undergraduate students comprehend different temporal aspects of hominin evolution. Two factors, differences in timelines (the number of timelines with different scales) and the mode of the default animated time rate– either constant throughout the animation or decreasing as the animation progressed – were combined to give four different time representations. The animations are designed as a map on which animated areas are superimposed. Each area represented the appearance, dispersal and disappearance of a chosen sample of different species, or groups of species in hominin evolution. All animations are three-and-a-half minute long. These features are shared by all versions of the animation. The only difference between the various animations is how time is represented. The visual representation of time is located below the map and consists of two components: one or several timelines with different scales, and an animated cursor moving horizontally along the timeline, indicating current time and rate of time in the animation. Description of the different temporal representations in the animations: Animation A One timeline and a constant time rate. Animation B One timeline and a time rate that decreases as the animation approach present time. Animation C three emerging timelines of increasing scales become visible as the animation approach present time and a constant time rate. Animation D three emerging timelines of increasing scales become visible, and a time rate that decreases as the animation approach present time. NOTE: Using Macintosh computer and the Safari web browser might cause an error loading the videos. In order to guarantee the video function in Macintosh computers, please use another web browser such as Chrome, FireFox or Opera. The dataset was originally published in DiVA and moved to SND in 2024. Tue, 04 Dec 2018 00:00:00 GMT https://researchdata.se/en/catalogue/dataset/2024-254 https://researchdata.se/en/catalogue/dataset/2024-254 Linköping University Jörgen Stenlund Data and R code used in piecewise structural equation modelling for a study that compared the direct and indirect impacts of temperature and precipitation on moose calf mass in northern Sweden. The study was initiated in 1988 in an effort to examine the impacts of climate change on common forage species of the economically and culturally important moose in Sweden. It ran until 1997 and was re-started in 2017. Temperature and precipitation variables are derived from SMHI weather station data. Average moose calf mass for study sites is derived from data from the Swedish Hunter's Association and individual hunting teams. Both weather and moose calf mass represent mean values within a 50km radius of each study site. Nitrogen and neutral detergent fibre measures are the result of near-infrared spectroscopy modelling, using 50 samples to calibrate the model. Samples were collected from 1-ha sites and included material from 30 individuals of either downy birch or fireweed. The dataset contains the following files. DataWeatherVegMoose.tsv is the data itself (TSV format, 236 rows × 10 columns). This includes the following variables: Total precipitation (mm) from the start of the growing season, defined as the first day of the first four consecutive days each calendar year that each have a mean daily temperature greater than or equal to 5 degrees C, to July 17 of that year. This is an average value for all SMHI weather stations within a 50 km radius of a site. Mean daily average temperature from the start of the growing season, defined as the first day of the first four consecutive days each calendar year that each have a mean daily temperature greater than or equal to 5 degrees C, to July 17 of that year. This is an average value for all SMHI weather stations within a 50 km radius of a site. Proportion of days from the start of the growing season, defined as the first day of the first four consecutive days each calendar year that each have a mean daily temperature greater than or equal to 5 degrees C, to July 17 of that year, when the maximum daily temperature was greater than or equal to 20 degrees C. This is an average value for all SMHI weather stations within a 50 km radius of a site. Neutral detergent fibre content of downy birch leaves at the site, based on a representative sample and calculated using Near Infrared Spectroscopy Neutral detergent fibre content of fireweed stems, leaves, and flowers at the site, based on a representative sample and calculated using Near Infrared Spectroscopy Nitrogen content of downy birch leaves at the site, based on a representative sample and calculated using Near Infrared Spectroscopy Nitrogen content of fireweed stems, leaves, and flowers at the site, based on a representative sample and calculated using Near Infrared Spectroscopy Mean date-adjusted moose calf slaughter weight for calves reportedly shot within 50km of the site. Values must represent the mean weight of at least 10 calves to be included. The documentation file Key_DataWeatherVegMoose.tsv contains detailed information about the variables in the dataset. The documentation file sites_no.tsv contains codes for the different sites where data was collected. It corresponds with the variable Site in the dataset DataWeatherVegMoose.tsv. R_code_piecewise_SEM.r is the R script used to calculate the piecewise structural equation models linking weather to moose calf mass directly and via forage chemistry. R_code_piecewise_SEM_log.txt is output of the script with session information. If R , with the packages nlme and piecewiseSEM, is installed, it can be generated by running this from a shell: Rscript R_code_piecewise_SEM.r > R_code_piecewise_SEM_log.txt Wed, 18 Jan 2023 14:57:29 GMT https://researchdata.se/en/catalogue/dataset/2022-245-1 https://researchdata.se/en/catalogue/dataset/2022-245-1 Swedish University of Agricultural Sciences Sheila Holmes Kjell Danell John Ball Göran Ericsson