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6,859 results for “parasite”
A droplet digital polymerase chain reaction assay to detect rare helminth parasites infecting natural host populations (Vancouver Island 2023, University of Wisconsin Madison Laboratory colony 2024)
Helminth infections represent a significant challenge to human, livestock, and wildlife health, yet they remain relatively under-studied, especially in terms of their ecological impacts. Better understanding of how these parasites spread in wildlife populations could improve our ability to predict and manage disease transmission across various species. Traditional detection methods, such as visually identifying parasites in environmental samples or infected hosts, often fall short, especially during the early stages of infection when parasite loads are minimal. In this study, we introduce a highly sensitive and precise droplet digital PCR (ddPCR) assay that quantifies helminth DNA in aquatic habitats, focusing on the 18S rRNA gene as a marker. These data utilize the model host-parasite system between the tapeworm Schistocephalus solidus, and its cyclopoid copepod host, Acanthocyclops robustus. The molecular assays are built around creating an infection standard in the lab, where copepods were singly infected with a single tapeworm parasite. We extracted DNA from 100 infected adults and used this as a standard to translate gene copy numbers from the ddPCR reactions to actual animal values. After creating a known lab standard, we then use the generated probes and primers to detect (and quantify!) infection burdens in field samples, which include both water filter samples (eDNA) and zooplankton tows from several lakes around Vancouver Island, B.C. The data presented here include well-specific data from ddPCR runs (amplitude of individual level oil droplets in the reaction) as well as each ddPCR analysis in its entirety. In order to prove the specificity of probes and probe-primers, we include here ddPCR runs of closely related helminth species, Schistocephalus cotti and Schistocephalus pungitii. We also consider the binding to another genera of copepod, the calanoid Eurytomora. All of the data wrangling, analysis, and data visualization are included as .Rmd files in th
Laboratory study on microplastic fiber size and concentration effects on leopard frog (Lithobates pipiens) tadpole survival, development, behavior, and parasite susceptibility
This dataset contains comprehensive raw data from a completed laboratory experiment conducted from May 24 to June 30, 2021 (with additional analysis performed in 2025), investigating the effects of polyester microplastic (MP) fiber exposure on northern leopard frog (Lithobates pipiens) tadpoles and their interactions with echinostome trematodes (Echinostoma sp.). Tadpole egg masses were collected from a wetland in Indiana, USA, and ramshorn snails (Helisoma trivolvis), serving as trematode hosts, were collected from Tioga County, New York, USA. The experiment was conducted under controlled laboratory conditions using a static-renewal design, exposing tadpoles to short (~0.24 mm) or long (~1.50 mm) polyester MP fibers at concentrations of 0, 10, or 40 µg L⁻¹ for 32 days, followed by controlled exposure to echinostome cercariae. The dataset includes measurements of tadpole mortality, developmental traits (mass, snout-to-vent length, Gosner stage), behavioral activity (number of moving pre- and post-parasite exposure), MP fiber ingestion, and susceptibility to trematode infection (metacercarial cyst counts in kidneys). These data provide a resource for studying the ecological and toxicological impacts of microplastics on amphibian health, and host-parasite dynamics in freshwater ecosystems, making the dataset suitable for researchers in ecotoxicology, and disease ecology. The dataset is complete, with no ongoing data collection, and is designed to support analyses of microplastic-mediated effects on aquatic organisms.
Herbivore dung and parasite counts, Ol Pejeta Conservancy and Mpala Research Centre, Kenya (2015-2018)
Data package contains two datasets of dung surveys, one dataset of parasite egg measurements, and two camera trap datasets collected from Mpala Research Centre and Ol Pejeta Conservancy, Laikipia County, Kenya from November 2015-September 2018. Datasets are provided as part of the publication `Watering sources aggregate parasites with increasing effects in more arid conditions`. Source data files for figures in the manuscript are also provided here.
Diffraction images used to solve the structures published in the article "A Family of Dual-Activity Glycosyltransferase-Phosphorylases Mediates Mannogen Turnover and Virulence in Leishmania Parasites"
<p>Raw diffraction images used for generating the structures published in the article A Family of Dual-Activity Glycosyltransferase-Phosphorylases Mediates Mannogen Turnover and Virulence in Leishmania Parasites" (available <a href="https://doi.org/10.1016/j.chom.2019.08.009">here</a>). The software used for the processing of each dataset is listed in their respective PDB entries.</p> <p> </p> <p>If you find this useful, please contact me at <a href="mailto:lukasz.sobala@hirszfeld.pl">lukasz.sobala@hirszfeld.pl</a>, I am just interested in how these data are used!</p>
Dataset - Sex and Habitat effects on Verrallia aucta parasitism in Philaenus spumarius in Scotland
<p>This csv file contains data for analysis on the sex and habitat effects on <i>Verrallia aucta</i> parasitism in <i>Philaenus spumarius</i> in Scotland. <i>P. spumarius</i> were sampled from three different habitat types within eleven sites across Scotland and molecularly screened for <i>V. aucta</i> parasitism using qPCR. Csv file contains total number of <i>P. spumarius </i>samples, total number of <i>V. aucta </i>positive <i>P. spumarius </i>samples and percent positive, per sex and habitat, within each site.</p>
Explosive networking: the role of adaptive host radiations and ecological opportunity in a species-rich host-parasite assembly
<p>Dataset for Cruz-Laufer et al. (2021) Explosive networking: the role of adaptive host radiations and ecological opportunity in a species-rich host-parasite assembly.</p> <p><strong>Abstract: </strong>Many species-rich ecological communities emerge from adaptive radiation events. The effects of this explosive speciation on community assembly remain poorly understood. Here, we explore the well-documented radiations of African cichlid fishes and their interactions with the flatworm gill parasites <em>Cichlidogyrus </em>spp., including 10529 reported infections and 477 different host-parasite combinations collected through a survey of peer-reviewed literature. We assess how evolutionary, ecological, and morphological parameters determine host-parasite meta-communities affected by adaptive radiation events through network metrics, host repertoire measures, and network link prediction. The hosts’ evolutionary history mostly determined host repertoires of the parasites. Ecological and evolutionary parameters determined host-parasite interactions. Generally, ecological opportunity and fitting have shaped cichlid-<em>Cichlidogyrus</em> meta-communities suggesting an invasive potential for hosts used in aquaculture. Meta-communities affected by adaptive radiations are increasingly specialised with higher environmental stability. These trends should be verified across other systems to infer generalities in the evolution of species-rich host-parasite networks.</p>
Data from: Land use, season, and parasitism predict metal concentrations in Australian flying fox fur
<p>There are two .csv files in this upload. The "Pteropus_metal_data_wide.csv" file contains metal concentrations (reported in ng/g) measured in fur samples collected from <em>Pteropus </em>flying foxes (<em>P. alecto</em>, <em>P. conspicillatus</em>, <em>P. poliocephalus</em>). Flying foxes were captured from 2015-2018 at multiple sites across Australia. The file also contains capture information (e.g. date, location) and biological information (e.g. species, sex, age class, parasitism) for each flying fox. The "Pteropus_metadata.csv" file provides further details on all column names in the primary data file, including the specific metals that were quantified. Detailed information on the study methods and results can be found in the associated Science of the Total Environment publication, "Land use, season, and parasitism predict metal concentrations in Australian flying fox fur" by Sánchez et al.</p>
Graphic Illustration of Kelly Speer's Keynote Talk: Hosts, parasites, and microbiomes: A system for studying natural complexity in a changing world
<p><a href="https://lib.ku.edu/people/courtney-foat" target="_blank" rel="noopener">Courtney Foat</a>, Advisor for Strategic Initiatives & Organizational Engagement at the University of Kansas, graphically recorded and synthesized the Keynote Talk by Kelly Speer at the Digital Data 2024 Conference in Lawrence, Kansas in May of 2024. We include this resource, with permission, because of its relevance to our NSF-supported Workshop: Digital Collections Data and Tracking Disease.</p>
Graphic Illustration of Litsa Wooten's Talk: Visualizing Mongolian Mammal Specimens and their Parasites Through Time
<p><a href="https://lib.ku.edu/people/courtney-foat" target="_blank" rel="noopener">Courtney Foat</a>, Advisor for Strategic Initiatives & Organizational Engagement at the University of Kansas, graphically recorded this talk by Litsa Wooten at the Digital Data 2024 Conference in Lawrence, Kansas in May of 2024. We include this resource, with permission, because of its relevance to our NSF-supported Workshop: Digital Collections Data and Tracking Disease.</p>
Python code for "Evolutionary epidemiology consequences of trait-dependent control of heterogeneous parasites"
<p>The file contains the Python code used to run the agent-based simulation of the selection-mutation model presented in "Evolutionary epidemiology consequences of trait-dependent control of heterogeneous parasites"</p>
Datasets and R source code of manuscript "Parasites make hosts more profitable but less available to predators"
<p>Data about experimentations of DIV-1 (virus) infection on Daphnia magna.</p> <p>Linked article: Parasites make hosts more profitable but less available to predators</p>
Sex-specific relationships between urbanization, parasitism, and plumage coloration in house finches
Historically, studies of condition-dependent signals in animals have been male-centric, but recent work suggests that female ornaments can also communicate individual quality (e.g., disease state, fecundity). There also has been a surge of interest in how urbanization alters signaling traits, but we know little about if and how cities affect signal expression in female animals. We present data of carotenoid-based plumage coloration and coccidian (Isospora spp.) parasite burden in desert and city populations of house finches Haemorhous mexicanus to examine links between urbanization, health state, and feather pigmentation in males and females. In earlier work, we showed that male house finches are less colorful and more parasitized in the city, and we again detected such patterns in this study for males; however, urban females were less colorful, but not more parasitized, than rural females. Moreover, contrary to rural populations, we found that urban birds (regardless of sex) with larger patches of carotenoid coloration were also more heavily infected with coccidia. These results show that urban environments can disrupt condition-dependent color expression and highlight the need for more studies on how cities affect disease and signaling traits in both male and female animals.
CSM08 Small mammal host-parasite sampling data for 16 linear trapping transects located in 8 LTER burn treatment watersheds at Konza Prairie
Data set contains summaries (summer) of the number of individuals of each species of small mammal captured (relative abundance) on each transect. Each record contains date, treatment, transect, trap station, species, specimen number, recapture status, specimen disposition, external body measurements (where applicable), reproductive information, and miscellaneous associated comments. These sampling records are based on nightly captures during one 4-night trapping period in summer (June through August) for each of 16 permanent transects established on eight fire treatments (two transects per treatment). These treatments include two seasonal burn watersheds (SpB, SuB), two reversal burn watersheds (R1A, R20A), one annual burn watershed (1D), two 4-year burn watersheds (4B, 4F, and one 20-year burn watershed (20B). None of these treatments implement bison grazing.
Chickadee breeding and parasite survey from Boulder, Sugarloaf, and MRS nest boxes, 2019 - 2021.
Between the years 2019 and 2021 chickadees were sampled at the NWT LTER as part of a broader study encompassing multiple projects (The Boulder Chickadee Study). Here we provide data on the presence of infections with haemosporidian parasites for Black-capped Chickadees (Poecile atricapillus) and Mountain Chickadees (P. gambeli). Haemosporidian parasites are a diverse group of apicomplexans that infect vertebrate hosts during a portion of their life cycle (Valkiunas, G. 2004). We screened chickadees for infections with three haemosporidian genera: Leucocytozoon, Plasmodium, and Haemoproteus using a nested PCR protocol (Hellgren et al. 2004). Both nestlings and adults were screened for parasites in 2019 and 2020 but we only screened adults in 2021. Chickadees sampled at NWT LTER did not have detectable infections with Haemoproteus or Plasmodium, however, we found multiple infections with Leucocytozoon. In conjunction with findings at other field sites, infections with Leucocytozoon parasites appear more common for adult chickadees sampled at higher elevation, while Plasmodium parasites were almost exclusively found in the city of Boulder (Theodosopoulos et al. 2023).
Data for: The immunogenetics of sexual parasitism
<p>Aligned amino acid sequences of 946 orthologous exon loci that were used to obtain a phylogeny of 13 anglerfish species. The locus sequences were obtained using a best hit search using TBLASTN v2.9.0 with the consensus amino acid sequences of the exons from Hughes et al. (PNAS 2013) as queries against databases of whole-genome shotgun sequencing reads (published with the study by Swann et al. (2020) that this dataset belongs to). The sequences for each locus were then aligned using MAFFT v7.464 with the L-INS-i strategy.</p>
Phenotypic data related to genetic architecture of transmission stage production and virulence in schistosome parasites
<p>These data were generated related to the study of the <strong>Genetic architecture of transmission stage production and virulence in schistosome parasites</strong>.</p> <p><strong>Abstract:</strong> Both theory and experimental data from multiple pathogens suggest that the production of transmission stages should be strongly associated with virulence, but the genetic bases of parasite transmission/virulence traits are poorly understood. In the blood fluke <em>Schistosoma mansoni</em>, parasite genotypes show extensive variation in numbers of cercariae larvae shed from infected snails. Furthermore, high shedding parasites cause high mortality to snails while low shedding parasites cause low mortality, consistent with expected trade-offs between parasite transmission and virulence. To understand the genetic basis of transmission stage production/virulence, we conducted reciprocal crosses between schistosomes from two laboratory populations that differ 8-fold in cercarial shedding and in their virulence to inbred snail hosts. Each parasite generation, we determined four-week cercarial shedding profiles in inbred <em>Biomphalaria glabrata</em> snails infected with single parasite larvae. We sequenced the whole genome of the F0 parents and the exome of the F1 progeny and 188 F2 progeny from each cross, and used linkage mapping to reveal quantitative trait loci (QTLs) underlying transmission stage production. Cercarial production is polygenic: we found three major QTLs on chromosome 1, 3 and 5 (Log-of-the-odds (LOD) = 5.61, 8.19, 6.25) and two minor QTLs on chromosome 2 and 4. These QTLs act additively and explained 28.56% of the phenotypic variation in cercarial shedding. Alleles inherited from the high and low shedding parents were co-dominant at all QTLs, except for chr. 1 and chr. 4 where the “high cercarial shedding” allele is recessive. These results demonstrate that the genetic architecture of key traits directly relevant to schistosome ecology can be dissected using classical linkage mapping approaches, and set the stage for fine mapping and functional validation of the genes involved using the growing armory of functional and cell biology tools available for this parasite.</p> <p> </p> <p>This dataset is made of 4 tables:</p> <ul> <li>F0_parental_populations.csv</li> <li>F1.csv</li> <li>F2.csv</li> <li>sex.tsv</li> </ul> <p> </p> <p><strong>F0_parental_populations.csv</strong></p> <p> </p> <p>This table contains the number of cercariae produced by each individual <em>Biomphalaria glabrata</em> Bg26 snails infected with single genotypes of <em>Schistosoma mansoni</em> parasite. We have compared the transmission stage production between two different populations of <em>S. mansoni</em> parasite. This dataset was originally published in Le Clec'h et al., 2019 (Striking differences in virulence, transmission and sporocyst growth dynamics between two schistosome populations. Parasites and Vectors. 2019 Oct 16;12(1):485. doi: 10.1186/s13071-019-3741-z).</p> <p> </p> <p>This table is made of 9 columns:</p> <ul> <li><strong>id</strong>: the unique identifier of each sample.</li> <li><strong>schistosoma_population</strong>: the population of schistosome used for the infection of the snail. Each snail was infected with a single parasite genotype. We have used SmLE (high shedder/highly virulent population) and SmBRE (low shedding/low virulent population).</li> <li><strong>Shed.1</strong>: the number of cercariae produced by each parasite genotype at the first shedding week (4 weeks after exposure to parasite).</li> <li><strong>Shed.2</strong>: the number of cercariae produced by each parasite genotype at the second shedding week (5 weeks after exposure to parasite).</li> <li><strong>Shed.3</strong>: the number of cercariae produced by each parasite genotype at the third shedding week (6 weeks after exposure to parasite).</li> <li><strong>Shed.4</strong>: the number of cercariae produced by each parasite genotype at the fourth shedding week (7 weeks after exposure to parasite).</li> <li><strong>sum</strong>: the sum of the cercariae produced by each parasite genotype over the 4 weeks of shedding (Shed.1 + Shed.2 + Shed.3 + Shed.4).</li> <li><strong>average</strong>: the average number of cercariae produced by each parasite genotype over the 4 weeks of shedding.</li> <li><strong>sex</strong>: the sex of each parasite genotype determined by PCR <sup>1</sup>.</li> </ul> <p> </p> <p><strong>F1.csv</strong></p> <p> </p> <p>This table contains the number of cercariae produced by each individual <em>Biomphalaria glabrata</em> Bg26 snails infected with single genotypes of F1 progeny from the cross SmLE x SmBRE (see the manuscript for details).</p> <p> </p> <p>This table is made of 11 columns:</p> <ul> <li><strong>id</strong>: the unique identifier of each sample.</li> <li><strong>cross</strong>: F1A or F1B cross. Each snail was infected with a single parasite genotype from either F1A or F1B progeny.</li> <li><strong>Shed.1</strong>: the number of cercariae produced by each parasite genotype at the first shedding week (4 weeks after exposure to parasite).</li> <li><strong>Shed.2</strong>: the number of cercariae produced by each parasite genotype at the second shedding week (5 weeks after exposure to parasite).</li> <li><strong>Shed.3</strong>: the number of cercariae produced by each parasite genotype at the third shedding week (6 weeks after exposure to parasite).</li> <li><strong>Shed.4</strong>: the number of cercariae produced by each parasite genotype at the fourth shedding week (7 weeks after exposure to parasite).</li> <li><strong>sum</strong>: the sum of the cercariae produced by each parasite genotype over the 4 weeks of shedding (Shed.1 + Shed.2 + Shed.3 + Shed.4).</li> <li><strong>average</strong>: the average number of cercariae produced by each parasite genotype over the 4 weeks of shedding.</li> <li><strong>PO</strong>: the total phenoloxidase activity in infected snail hemolymph, measured at 7.5 weeks post-exposure <sup>2</sup>.</li> <li><strong>Hb</strong>: the hemoglobin rate in infected snail hemolymph, measured at 7.5 weeks post-exposure <sup>3</sup>.</li> <li><strong>sex</strong>: the sex of each parasite genotype determined by PCR <sup>1</sup>.</li> </ul> <p> </p> <p><strong>F2.csv</strong></p> <p>This table contains the number of cercariae produced by each individual <em>Biomphalaria glabrata</em> Bg26 snails infected with single genotypes of F2 progeny from the cross SmLE x SmBRE (see the manuscript for details).</p> <p> </p> <p>This table is made of 10 columns:</p> <ul> <li><strong>id</strong>: the unique identifier of each sample.</li> <li><strong>cross</strong>: F2A or F2B cross. Each snail was infected with a single parasite genotype from either F2A or F2B progeny.</li> <li><strong>Shed.1</strong>: the number of cercariae produced by each parasite genotype at the first shedding week (4 weeks after exposure to parasite).</li> <li><strong>Shed.2</strong>: the number of cercariae produced by each parasite genotype at the second shedding week (5 weeks after exposure to parasite).</li> <li><strong>Shed.3</strong>: the number of cercariae produced by each parasite genotype at the third shedding week (6 weeks after exposure to parasite).</li> <li><strong>Shed.4</strong>: the number of cercariae produced by each parasite genotype at the fourth shedding week (7 weeks after exposure to parasite).</li> <li><strong>sum</strong>: the sum of the cercariae produced by each parasite genotype over the 4 weeks of shedding (Shed.1 + Shed.2 + Shed.3 + Shed.4)</li> <li><strong>average</strong>: the average number of cercariae produced by each parasite genotype over the 4 weeks of shedding.</li> <li><strong>PO</strong>: the total phenoloxidase activity in infected snail hemolymph, measured at 7.5 weeks post-exposure <sup>2</sup>.</li> <li><strong>Hb</strong>: the hemoglobin rate in infected snail hemolymph, measured at 7.5 weeks post-exposure <sup>3</sup>.</li> </ul> <p> </p> <p><strong>sex.csv</strong></p> <p> </p> <p>This table contains the <em>in silico</em> sexing of F0 parents, F1 parents and F2 progeny of <em>S. mansoni</em> parasites.</p> <p>This table is made of 4 columns:</p> <ul> <li><strong>id</strong>: the unique identifier of each sample</li> <li><strong>read_depth</strong>: the read depth ratio between the Z-linked and pseudo-autosomal regions.</li> <li><strong>ratio</strong>: computed ratio between the Z-linked and pseudo-autosomal regions.</li> <li><strong>sex</strong>: the sex of each parasite genotype determined <em>in silico</em>: a ratio around 1 corresponds to a male carrying two Z chromosomes while a ratio around 0.5 corresponds to a female carrying only one Z chromosome.</li> </ul> <p><strong>Notes:</strong></p> <p><sup>1</sup>. Le Clec’h W, Chevalier F et al. Real-time PCR for sexing Schistosoma mansoni cercariae. Mol Biochem Parasitol. Jan-Feb 2016; 205(1-2):35-8.doi: 10.1016/j.molbiopara.2016.03.010. Epub 2016 Mar 26.</p> <p><sup>2</sup>. Le Clec’h W et al. Characterization of hemolymph phenoloxidase activity in two Biomphalaria snail species and impact of Schistosoma mansoni infection. Parasit Vectors. 2016 Jan 22; 9:32.doi: 10.1186/s13071-016-1319-6.</p> <p><sup>3</sup>. Le Clec'h et al. Striking differences in virulence, transmission and sporocyst growth dynamics between two schistosome populations. Parasit Vectors. 2019 Oct 16; 12(1):485. doi: 10.1186/s13071-019-3741-z.</p>
Data for: Prior exposure of a fungal parasite to cyanobacterial extracts does not impair infection of its Daphnia host
<p>This dataset supports the findings of the study 'Prior exposure of a fungal parasite to cyanobacterial extracts does not impair infection of its <em>Daphnia</em> host', published in Hydrobiologia (https://doi.org/10.1007/s10750-022-04889-7)</p>
Sample accession list for "Malaria protection due to sickle haemoglobin depends on parasite genotype"
<p>This dataset contains a list of sample accessions and associated metadata for <em>P.falciparum</em><br> DNA samples sequenced for the analysis presented in the paper:</p> <p><strong>Malaria protection due to sickle haemoglobin depends on parasite genotype</strong></p> <p>Gavin Band, Ellen M. Leffler, Muminatou Jallow, Fatoumatta Sisay-Joof, Carolyne<br> M. Ndila, Alexander W. Macharia, Christina Hubbart, Anna E. Jeffreys, Kate Rowlands, Thuy<br> Nguyen, Sónia Gonçalves, Cristina V. Ariani, Jim Stalker, Richard D. Pearson, Roberto<br> Amato, Eleanor Drury, Giorgio Sirugo, Umberto d'Alessandro, Kalifa A. Bojang, Kevin<br> Marsh, Norbert Peshu, Joseph W. Saelens, Mahamadou Diakité, Steve M. Taylor10, David J.<br> Conway, Thomas N. Williams, Kirk A. Rockett, Dominic P. Kwiatkowski</p> <p>Nature (2021) doi: <a href="https://doi.org/10.1038/s41586-021-04288-3">10.1038/s41586-021-04288-3</a> <strong>bioRxiv link</strong>: <a href="http://doi.org/10.1101/2021.03.30.437659">doi.org/10.1101/2021.03.30.437659</a>.</p> <p>The data contains: i. a single tab-delimited text file containing accessions and sequence read quality control-related information related to the processing described in [1], and ii. a README file describing the contents of the data in markdown and HTML format. Please see the enclosed README file for full details.</p> <p>A full list of datasets which have been released with this manuscript can be found on the <a href="https://www.malariagen.net/resource/32">MalariaGEN website</a>.</p> <p> </p>
Data files: Single-cell RNA profiling of Plasmodium vivax-infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets
<p>Scripts, preprocessed count matrices, and single-cell data objects generated in <strong>“Single-cell RNA profiling of <em>Plasmodium vivax</em><em>-</em>infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets” </strong></p>
Data from randomized control trials released hatchery salmon treated with anti-parasitic treatment
<p>Data used in the article "<strong>Parasite spillback from fish farms reduce return rate of wild salmon"</strong></p> <p> </p> <p>Each release group has been used as a randomized control trials (RCT) of hatchery reared salmon smolts where half of the fish has been treated with an antiparasitic drug. Description of this method has been given in various other publications (Vollset et al. 2014, Vollset et al 2016, Skilbrei et al. 2013). The method involves rearing salmon eggs originating from the national Gene Bank to smolt size in hatchery facilities during one year, and then treating the salmon smolts with fish feed pellets coated with emamectin benzoate (SLICE®). These fish are then released into the river or transported in tanks or mobile net pens further out in the fjord before release. The fish are tagged with either coded-wire-tags (CWT; years 2000-2017) or Passive Integrated Transponders (PIT; 2015-2019) so that it is possible to identify them as they are recaptured or registered on an antenna upon their return as adults. In a few trials, another antiparasitic treatment (Substance EX) has been used, but in most cases the EB has been the only available treatment. Releases of hatchery reared salmon in freshwater have not been successful in this system, i.e. very few fish have returned from any group released in the river, lakes or estuary of Vosso. Since the release groups are also a part of a restoration effort of the Vosso salmon, some years fish have only been released in the fjord. There has been some variation in the release sites in the fjords, but for the purpose of this study we group the release groups in either group that has been released in the outer fjord (70-105 km from the river mouth) and the inner fjord (15-70 km from the river mouth), and freshwater (approx -10 to 15 km from the river mouth). The two most prevalent locations are at Manger (WGS84; 60.63918, 4.92149) and Arna (WGS84; 60.50812, 5.37777).</p> <p> </p> <p><em>Sea lice surveillance</em></p> <p> </p> <p>Sea lice surveillance on sea trout has been conducted at Herdla, the northern peninsula of the island Askøy (WGS84; 60.568972, 4.963010) since 2009. Here, trout have been caught using a trap net that has been developed specifically to capture and treat trout while minimizing sea lice loss during handling (Barlup et al. 2013). From an earlier study by Vollset et al. (2018), it has been shown that the lice numbers on sea trout on this site correlate with the infestation pressure of fish farms in the outer region of the fjord. This area is also one of the largest fish farm zones with coordinated production and fallowing in the outer fjord system where all the released salmon smolts must migrate (see Vollset et al. 2018). This is also the area where surface salinity layers permit salmon lice to overlap with out-migrating salmon smolts (Vollset et al. 2016).</p> <p> </p> <p>The number of trout caught during the monitoring season has varied with weather conditions, sampling intensity, and number of traps operated. The way that trout are handled is described in more detail in Vollset et al. (2018), but in brief, the trap chambers are checked daily, and individual trout are transferred from the trap using a hand held dip net and are either euthanized and placed in zip-lock bag or transported in a large bucket with aerated water to land. Euthanized samples are kept cold and frozen when at land, and later thawed and counted in the lab, while live samples are counted after being sedated with half dose (0.05 g/L) of MS222 and then assessed for salmon lice in a high-contrast bucket using a headlamp by trained personnel. Since 2015 the sea lice surveillance at Herdla is also operated as a part of the Norwegian national sea lice monitoring program.</p> <p>We aimed to use a standardized time period from which to assess sea lice numbers on sea trout that can be representative of the lice infestation pressure from when the tagged hatchery salmon smolts are released. When counting sea lice on sea trout, the most observable lice are large chalimus and mobile stages, while recently attached copepods are more likely to be missed. Therefore, we use total lice counts on sea trout from Julian day 135 to 165 as an assessment of the infestation pressure the salmon smolts must experience. This corresponds to approximately 15 May to 15 of June, and is based on a study on progression rate of salmon smolts from hatchery smolt in this area (Vollset et al. 2016). To account for the fact that larger fish will attract more parasites, we use parasites per gram fish per individual and average data to get one index per year. This method is expected to provide a fair index of interannual variation of the infestation pressure.</p> <p> </p> <p>Table 1 Description of column names in csv file</p> <table> <tbody> <tr> <td>Name</td> <td>Description</td> </tr> <tr> <td>release_year</td> <td>Year of release as smolts</td> </tr> <tr> <td>release_place</td> <td>Name of release place location</td> </tr> <tr> <td>release_date</td> <td>Date of release as smolts</td> </tr> <tr> <td>Released</td> <td>Number of hatchery smolt released</td> </tr> <tr> <td>Recaptured</td> <td>Number of hatchery smolt recaptured as adults</td> </tr> <tr> <td>treat</td> <td>Treatment (either treatment or control)</td> </tr> <tr> <td>tag</td> <td>Tag type (either CWT or PIT)</td> </tr> <tr> <td>release_category</td> <td>Release place (either river, outer fjord or inner fjord)</td> </tr> <tr> <td>lpg</td> <td>Lice per gram fish on trout during surveillance from 15 of May to 15 of June the year of release</td> </tr> <tr> <td>pr</td> <td>Percent (%) recaptures as adults</td> </tr> </tbody> </table> <p> </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.