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9,522 results for “invasiveness”
Survey of Family Forest Owners Regarding Invasive Insects in the Connecticut River Watershed 2017
Forest insects have significant direct impacts on forest ecosystems; they are also generating new risks, uncertainties, and opportunities for forest landowners. Our research objective is to understand: (1) whether and how insect infestations are shifting land-use regimes in New England by altering human decision-making, (2) how these changes to human decisions may affect regional forest ecosystems and the provisioning of select ecosystem services, and (3) how subsequent changes to forest ecosystems, in turn, affect landowners. The dataset is a result of gathering information from a random sample of family forest owners (FFOs) in the Connecticut River Watershed; FFOs own approximately half of the private forestland in the region. We collected information on characteristics and perceptions of these FFOs as well as their intentions for their land if faced with the presence or threat of invasive forest insects. To better understand FFO intentions, contingent behavior questions populate the conjoint analysis format of the questionnaire. These are the foundational data that form our further efforts to simulate the impacts of insect dynamics and landowner behavior on regional forest ecosystems, including forest carbon stores, forest structure and composition, and timber yields. One of our overarching hypotheses is that forest land-use change in response to insects will have greater near-term ecological consequences than climate change or insects by themselves.
Invasive Species Mapping at Harvard Forest 2005
We are monitoring vegetation at the Harvard Forest for invasive plant populations with respect to land use history and other factors. Using our historical database for the Harvard Forest Prospect Hill tract, we have begun mapping the current distribution of non-native plants as a function of past land use. The 320 ha tract of Prospect Hill is mapped by parcels with known land-use history, soils, vegetation composition, and long-term vegetation dynamics. We plan to conduct annual vegetation surveys at Harvard Forest and the adjacent Quabbin Reservation to document six key non-native species currently present in the area: A. petiolata, the non-native shrubs B. thunbergii, Rhamnus cathartica, R. frangula, Lonicera spp. and the climbing vine, Celastrus orbiculatus. We will map the GPS coordinates and record cover estimates of each species and conduct spatial analyses on these data using our extensive records and GIS maps of land use histories at these locations. Detailed site histories will be determined certain species of interest, using field and archival records. Using similar techniques, we also plan to monitor invasive plant populations at key experimental plots (including the hemlock removal experiment at Simes Tract, and the "recovery phase" of the Chronic N addition plots). Together, these landscape-level studies will provide a novel historical context for understanding biological invasions in a historical context.
Source-Sink Dynamics of Garlic Mustard Invasion at Harvard Forest 2004-2006
We are investigating the role of disturbance history, source-sink metapopulation dynamics, and genetic adaptation to different canopy environments in the invasion success of Alliaria petiolata in the New England understory. In these studies, we employ a combination of population-level experiments, metapopulation studies, and landscape-level historical analyses. We have initiated a statewide survey of forested locations to determine the presence and absence of garlic mustard with respect to major pathways of invasion via past and present habitat disturbances. More explicit spatial analyses will test whether past sites of open canopy could have acted as corridors for the spread of invasive populations to present locations. This broad analysis will enable us to evaluate the generality of emerging conclusions from our population-level studies for predicting the broad-scale factors controlling the distribution, pattern and abundance of non-native species. At the population-level, we have begun long term demographic modeling of A. petiolata and experiments to test for habitat-specific natural selection on physiological, phenological, and allocational traits in sites with different canopy structure (edge or understory). In long term demographic analyses, we will use matrix population models to determine the relative contributions of subpopulations in different habitats to forest invasion. In ongoing reciprocal transplant studies, we will asses whether the maternal source habitat of a propagule contributes to its germination and survival in contrasting habitats.
Data from: Invasion timing affects multiple scales, metrics and facets of biodiversity outcomes in ecological restoration experiments (Missouri, 2009-2016)
Vegetation responses to experimental ecological restoration treatments at Tyson Research Centre of Washington University in Missouri, USA. These data include species-level cover responses to various factorial restoration treatments. Treatments were applied starting in 2009 and were measured in 2016. Treatment responses reflect these long term responses, but the dataset is comprised to one time point.
Impacts of Land Use on Japanese Barberry Invasion in Central Massachusetts 2005
Despite the recognized importance of historical factors in controlling many native species distributions, few studies have incorporated historical landscape changes into models of invasive species distribution and abundance. We explore the possibility that the current distribution of invasive species may reflect legacies of historical land use despite nearly a century of forest succession and subsequent disturbances. We evaluated the modern distribution and abundance of Berberis thunbergii DC. (Japanese barberry), a problematic non-native shrub in forests of the northeastern U.S., relative to two distinct periods of historical land use, modern forest harvesting activity, and environmental and edaphic characteristics. Species questions addressed in this study include: (1) Do patterns of historical land use influence modern barberry distribution and abundance? (2) What is the influence of disturbance type and timing relative to the timing of introduction on current barberry distribution and abundance? (3) Which disturbance, environmental and edaphic variables best predict modern barberry distribution and abundance? Japanese barberry occurred more frequently and was more abundant in sites historically cleared for agriculture than in historically wooded sites. This relationship was strongest for areas in agriculture in the early 20th century after barberry was introduced to the region. The strong relationship between modern distribution patterns and prior land use suggests historical colonization of abandoned agricultural lands and persistence through subsequent reforestation. Contrary to our expectations, recent forest harvesting did not influence the occurrence or abundance of barberry. Our results indicate that interpretations of both native community composition and modern plant invasions must consider the importance of historical landscape changes and the timing of species introduction along with current environmental and edaphic conditions.
Eradication via destratification: whole-lake mixing to selectively remove rainbow smelt, a cold-water invasive species.
Rainbow smelt (Osmerus mordax) are an invasive species associated with several negative changes to lake ecosystems in northern Wisconsin. We combined empirically based bioenergetics models with empirically based hydrodynamic models to assess lake destratification as a potential rainbow smelt eradication method. The dataset reported here is the otolith data from 20 age 1plus individuals.
Native and invasive species abundance distributions in lakes at North Temperate Lakes LTER 1979-2010
These data were compiled from multiple sources. We collated data on the abundance or density of aquatic invasive and native species sampled in more than 20 sites using the same methods. To control for sampling methodology and allow comparisons among native and invasive species, we only included data where both invasive and native species from a taxonomic group were sampled using the same methods across multiple sites. Exceptions were made to include rusty crayfish (Orconectes rusticus) in its native range and zebra mussel (Dreissena polymorpha) data.
Madison community science field campaign to assess abundance and distribution of invasive jumping worms.
Asian pheretimoid earthworms of the genera Amynthas and Metaphire (jumping worms) are leading a new wave of co-invasion into Northeastern and Midwestern states, with potential consequences for native organisms and ecosystem processes. However, little is known about their distribution, abundance, and habitat preferences in urban landscapes – areas which likely influence range expansion via human-driven spread. We led a participatory field campaign to assess jumping worm distribution and abundance in Madison, Wisconsin in September of 2017. By compressing 250 person-hours of sampling effort into a single day, we quantified presence and abundance of three jumping worm species across different land-cover types (forest, grassland, open space, residential lawns and gardens), finding that urban green spaces differed in invasibility. We show that community science can be powerful for researching invasive species while engaging the public in conservation. This approach was particularly effective here, where broad spatial sampling was required within a short temporal window.
The physiological effects of non-invasive brain stimulation fundamentally differ across the human cortex
Open the record for dataset details and reuse information.
Invasion Biology WikiProject Scientific Papers: Text Data Mining and LLM-based Information Extraction of Species, Locations, Habitats, and Ecosystems
<p>This dataset contains the abstract and full-text for publication DOIs from the Invasion Biology WikiProject (DOI: <a href="https://www.doi.org/10.5281/zenodo.12518036">10.5281/zenodo.12518036</a>). The data was retrieved using the <a href="https://ask.orkg.org/">ask.orkg.org</a> <a href="https://api.ask.orkg.org/docs#tag/Semantic-Neural-Search/operation/explore_documents_index_explore_get">API</a>. For the <a href="https://github.com/jd-coderepos/invasion-biology-IE/blob/main/scripts/ask-doi-list-fulltext-search.py">script</a> used to obtain the data, refer to the accompanying GitHub repository: <a href="https://github.com/jd-coderepos/invasion-biology-IE/" target="_blank" rel="noopener">https://github.com/jd-coderepos/invasion-biology-IE/</a>.</p> <p>The resulting CSV file includes the following fields: <code>"ASK ID"</code>, <code>"DOI"</code>, <code>"Title"</code>, <code>"Abstract"</code>, and <code>"Full-text"</code>.</p> <p>Of the 49,438 queried DOIs, the ASK database provided:</p> <ul> <li><strong>Total DOIs processed:</strong> 12,636</li> <li><strong>DOIs with neither abstract nor full-text:</strong> 36 (abstract token count was less than 10)</li> <li><strong>DOIs with abstracts but no full-text:</strong> 12,636</li> <li><strong>DOIs with both abstract and full-text:</strong> 2,834</li> </ul> <p>The second part of the dataset contains structured information extracted from the publications using the GPT-4o Large Language Model. This structured data is included in the zipped folder <code>structured-publications.zip</code>.</p> <p>The accompanying GitHub repository provides access to the code and scripts used at various stages of the information extraction (IE) process.</p> <p><strong>Theme of the Study:</strong><br>"Mining for Species, Locations, Habitats, and Ecosystems from Scientific Papers in Invasion Biology: A Large-Scale Exploratory Study with Large Language Models."</p>
Efficacy and fate of fluridone applications for control of invasive submersed aquatic vegetation in the estuarine environment of the Sacramento-San Joaquin Delta
We conducted a study in the Sacramento-San Joaquin Delta to determine efficacy of the widely used herbicide fluridone in an estuarine ecosystem. The primary goal of SAV removal was restoration of open water habitat for endangered Hypomesus transpacificus (Delta Smelt). Over 18 months and multiple sets of multi-week fluridone applications, we monitored concentrations of fluridone and responses by SAV across pairs of treated and reference sites. Fluridone concentrations in the water were generally below the 2-5 parts per billion required for SAV control. Monitoring demonstrated these low water concentrations were likely due to dissipation by tides, despite use of pelleted fluridone formulations marketed for flowing water environments. Fluridone did, however, accumulate in sediment at concentrations hundreds of times higher than those measured in the water. Nonetheless, we did not observe lasting reductions in SAV abundance or changes in SAV community composition. By demonstrating lack of efficacy of one of the few herbicides permitted for use in this estuary, this study highlights the need for development of SAV management tools tailored to the challenges of hydrologically complex environments like estuaries.
Impacts of invasive species on food web energy pathways and quality, St. Lawrence River, 2018-2021.
This dataset contains field measurements collected between 2018 and 2021 from three fluvial lakes in the Upper St. Lawrence River (Canada), including both invaded systems (with dreissenid mussels and round goby) and uninvaded reference sites. Data include georeferenced sampling information (site, lake, latitude, longitude, month, year), water chemistry (total phosphorus, µg/L; conductivity, µS/cm), and habitat descriptors (substrate). Biological records encompass seston, macroinvertebrates, and fish. Fish data comprise species identity, sex, total length (mm), weight (g), relative weight index (Wr), and detailed fatty acid composition expressed as relative proportions (%) and concentrations (µg/mg), including essential LC-PUFAs (EPA, DHA), n-3 and n-6 polyunsaturated fatty acids. Stable isotope data are provided, including carbon (δ13C) and nitrogen (δ15N) ratios, C:N ratios, and isotopic baselines from pelagic (δ13Cpel, δ15Npel) and benthic (δ13Cben, δ15Nben) sources. Derived variables, such as pelagic diet proportion and trophic position, were calculated using the two-source mixing model described by Post (2002) (DOI: https://doi.org/10.1890/0012-9658(2002)083[0703:USITET]2.0.CO;2). These data provide a comprehensive resource for examining food web structure, energy pathways, and the ecological impacts of invasive species in large river ecosystems.
Finite element method (FEM) models for translational research in non-invasive brain stimulation
<p>Finite element method (FEM) models for non-invasive brain stimulation modeling using SimNIBS or other compatible software.<br> The mouse and monkey models are described in detail in Alekseichuk et al., Comparative modeling of transcranial magnetic and electric stimulation in mouse, monkey, and human, NeuroImage 2019.<br> The Petri dish model follows a typical experimental setup for in-vitro TMS, similar to what is described in Lenz et al. Repetitive magnetic stimulation induces plasticity of inhibitory synapses, Nature Communications 2016.<br> <br> The following files are included:<br> 1. Brain tissue slice in a Petri dish.<br> 2. Normal adult male nude mouse "Digimouse" (brain volume of 0.38 cm3).<br> 3. Normal adult male capuchin monkey "S" (brain volume of 68.31 cm3).<br> <br> The models include the following tissues (coded with numbers):<br> 1. White matter volume<br> 2. Grey matter volume<br> 3. CSF volume<br> 4. Skull volume<br> 5. Soft tissues volume<br> 8. Eyeballs volume<br> 1001. White matter outer surfaces<br> 1002. Grey matter outer surfaces<br> 1003. CSF outer surfaces<br> 1004. Skull outer surfaces<br> 1005. Soft tissues outer surfaces<br> 1008. Eyeballs outer surfaces<br> <br> With any questions, please, contact the corresponding authors of the relevant papers or <a href="mailto:aopitz@umn.edu">aopitz@umn.edu</a> (Alexander Opitz).</p>
Global Naturalized Alien Flora (GloNAF). Open access data to support research on understanding global plant invasions.
<p>This dataset is a snapshot of the Global Naturalized Alien Flora (GloNAF) database, version 2.02. GloNAF is a continuously updated, curated compilation of alien naturalized vascular plant inventories for geographic regions from around the world. The dataset has 16,429 unique taxa reported as naturalized or invasive and covers 1,343 regions (including 427 islands) from 336 data sources. For each region, the status (invasive, naturalized) is provided as listed in the original source. We provide the scientific names included with the original data source, and the matching accepted name or synonym of the taxon as given in the World Checklist of Vascular Plants (WCVP) Version 12. In addition, we provide an ESRI shapefile of polygons for each region. We also provide several variables that can be used to filter the data according to quality and completeness of alien taxon lists, which vary among the combinations of regions and data sources.</p> <p>The 'glonaf_flora2.csv' file lists the IDs ('taxon_wcvp_id') of all naturalized taxa contained in GloNAF and the regions they occur in. The 'glonaf_taxon_wcvp.csv' lists the original taxon names provided in the source data along with the corresponding accepted taxon name from the WCVP (version 12) for all alien taxa in GloNAF, regardless of their naturalization status. To link taxon names with naturalization records, join the 'id' column of the 'glonaf_taxon_wcvp.csv' file to the 'taxon_wcvp_id' column in 'glonaf_flora2.csv' . Additional information regarding the original source of the data ('glonaf_reference.csv'), specific attributes of the taxon lists ('glonaf_list.csv') and the region ('glonaf_region.csv') can also be joined similarly to 'glonaf_flora2.csv '. </p> <p> </p>
Statistical analysis and dataset for: Acute exposure to caffeine improves foraging in an invasive ant
<p>Linked to the journal article published in iScience (https://doi.org/10.1016/j.isci.2024.109935).</p> <p><em><strong>Abstract</strong></em></p> <p>Argentine ants, <em>Linepithema humile</em>, are a particularly concerning invasive species. Control efforts often fall short likely due to a lack of sustained bait consumption. Using neuroactives, such as caffeine, to improve ant learning and navigation could increase recruitment and consumption of toxic baits. Here, we exposed <em>L. humile</em> to a range of caffeine concentrations and a complex ecologically relevant task: an open landscape foraging experiment. Without caffeine, we found no effect of consecutive foraging visits on the time the ants take to reach a reward, suggesting a failure to learn the reward’s location. However, under low to intermediate caffeine concentrations ants were 38% faster with each consecutive visit, implying that caffeine boosts learning. Interestingly, such improvements were lost at high doses. In contrast, caffeine had no impact on the ants’ homing behavior. Adding moderate levels of caffeine to baits could improve ant’s ability to learn its location, improving bait efficacy.</p> <p> </p> <ul> <li><strong>sample_videos.zip</strong>: A subset of the videos used for data extraction. The complete collection of videos is not publicly accessible primarily due to their considerable size (105.35GB). Requests for access to the entire video set are encouraged.</li> <li><strong>Preregistration.pdf</strong>: The preregistration created for data collection and analysis with justifications for deviations from it.</li> <li><strong>OpLan_D1_metadata.csv</strong>: Manually collected metadata pertaining to experimental conditions, subjects, and treatments.</li> <li><strong>OpLan_D2_DLC_coordinates.zip</strong>: Cartesian coordinates obtained from DeepLabCut for each of the videos analysed.</li> <li><strong>OpLan_C1_reproject_coordinates.py</strong>: Python code used to standardise the ants' coordinates by ensuring the same corner of the A4 platform was used as the origin of the cartesian referential of all videos. The known dimensions of the A4 were further used to convert coordinates from pixels to millimetres.</li> <li><strong>OpLan_C2_remove_impossibilities.py</strong>: Python code used to account for DeepLabCut tracking errors, with any ant movement exceeding two millimetres per frame being considered implausible and subsequently removed.</li> <li><strong>OpLan_C3_find_changepoints.py</strong>: Python code used to automatically derive the times at which an ant reached and left the reward from the tracking data.</li> <li><strong>OpLan_C4_inward_outward_data.py</strong>: Python code used to calculate relevant measures for the foodward (inward) and nestward (outward) journey such as journey duration, mean instantaneous speed and path tortuosity.</li> <li><strong>OpLan_C5_Figure_2.R</strong>: R code used to produce the raw elements of Figure 2.</li> <li><strong>OpLan_C6_Figure_4.R</strong>: R code used to produce the raw elements of Figure 4.</li> <li><strong>OpLan_C7_Statistical_Analysis.html</strong>: Complete statistical analysis and code for the manuscript.</li> </ul>
Country Compendium of the Global Register of Introduced and Invasive Species. Dataset.
<p>The Country Compendium of the Global Register of Introduced and Invasive Species (GRIIS) is a collation of data across 196 individual country checklists of alien species, along with a designation of those species associated with evidence of impact at a country level. </p>
Statistical analysis and dataset for: Invasive ants fed spinosad collectively recruit to known food faster yet individually abandon food earlier
<p>Linked to the journal article published in bioRxiv (https://doi.org/10.1101/2024.06.20.599949).</p> <p><em><strong>Abstract</strong></em></p> <p>Current management strategies applied to invasive ants rely on slow-acting insecticides which aim to delay the ant’s ability to detect the poison until its effects are noticeable. Despite this, most control efforts are unsuccessful, likely due to bait abandonment and insufficient sustained consumption. Conditioned taste aversion, a learned avoidance of a particular taste, is a crucial survival mechanism which prevents animals from repeatedly ingesting toxic substances. However, whether ants are capable of this delayed association between food taste and subsequent illness remains largely unexplored. Here, we exposed colonies of the highly invasive Argentine ant, <em>Linepithema humile</em>, to a sublethal dose of the slow-acting insecticide spinosad. We combined measurements of individual-level feeding patterns with quantification of collective preferences and foraging dynamics to investigate the potential effects of the toxicant on behaviour. Collectively, ants preferred an odour associated with a previously experienced food, even if this contained spinosad, over a novel one. However, at the individual-level, previous exposure to spinosad resulted in reduced food consumption, as a consequence of earlier food abandonment. Moreover, while control-treated colonies recruited slower to a food source which tasted like a previously experienced one, spinosad-exposed colonies recruited equally fast to both novel and familiar foods. Although it appears that ants are unable to develop a conditioned taste aversion to sublethal doses of spinosad, ingestion of even small amounts of the toxicant strongly influences foraging behaviour. Understanding the subtle effects of slow-acting pesticides on ant cognition and behaviour can ultimately inspire the development of more efficient control methodologies.</p>
Cisplatin enhances cell stiffness and decreases invasiveness rate in prostate cancer cells by actin accumulation: Confocal and atomic force microscopy
<p><strong>Summary</strong></p> <p>Dataset of imaging data related to the publication Raudenska, M., Kratochvilova, M., Vicar, T., Gumulec, J., Balvan, J., Polanska, H. Pribyl, J. & Masarik, M.:Cisplatin enhances cell stiffness and decreases invasiveness rate in prostate cancer cells by actin accumulation. <em>Scientific Reports </em><strong>2019, </strong>9, 1660</p> <p>This dataset includes image data of <em>atomic force microcopy</em> (Young modulus) and <em>confocal microscopy</em>(staining of F-actin and β-tubulin) of prostate cell lines PNT1A, 22Rv1, and PC-3. </p> <p><strong>Materials and Methods</strong></p> <p><em>Cells, cell culture conditions</em></p> <p>Cells confluent up to 50–60% were washed with a FBS-free medium and treated with a fresh medium with FBS and required antineoplastic drug concentration (IC50 concentration for the particular cell line). The cells were treated with 93 µM (PC-3), 38 µM (PNT1A), and 24 µM (22Rv1) of cisplatin (Sigma-Aldrich, St. Louis, Missouri), respectively. IC50 concentrations used for treatment with docetaxel (Sigma-Aldrich, St. Louis, Missouri) were 200nM for PC-3, 70nM for PNT1A, and 150nM for 22Rv1. </p> <p><em>Long-term zinc (II) treatment of cell cultures</em></p> <p>Cells were cultivated in the constant presence of zinc(II) ions. Concentrations of zinc(II) sulphate in the medium were increased gradually by small changes of 25 or 50 µM. The cells were cultivated at each concentration no less than one week before harvesting and their viability was checked before adding more zinc. This process was used to select zinc resistant cells naturally and to ensure better accumulation of zinc within the cells (accumulation of zinc is usually poor during the short-term treatment of prostate cancer cells). Total time of the cultivation of cell lines in the zinc(II)-containing media exceeded one year. Resulting concentrations of zinc(II) in the media (IC50 for the particular cell line) were 50 µM for the PC-3 cell line, 150 µM for the PNT1A cell line, and 400 µM for the 22Rv1 cell line. The concentrations of zinc(II) in the media and FBS were taken into account. </p> <p><em>Actin and tubulin staining</em></p> <p>β-tubulin was labeled with anti- β tubulin antibody [EPR1330] (ab108342) at a working dilution of 1/300. The secondary antibody used was Alexa Fluor® 555 donkey anti-rabbit (ab150074) at a dilution of 1/1000. Actin was labeled with Alexa Fluor™ 488 Phalloidin (A12379, Invitrogen); 1 unit per slide. For mounting Duolink® In Situ Mounting Medium with DAPI (DUO82040) was used. The cells were fixed in 3.7% paraformaldehyde and permeabilized using 0.1% Triton X-100. </p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><em>Atomic force microscopy</em></p> <p>We used the bioAFM microscope JPK NanoWizard 3 (JPK, Berlin, Germany) placed on the inverted optical microscope Olympus IX‑81 (Olympus, Tokyo, Japan) equipped with the fluorescence and confocal module, thus allowing a combined experiment (AFM‑optical combined images). The maximal scanning range of the AFM microscope in X‑Y‑Z range was 100‑100‑15 µm. The typical approach/retract settings were identical with a 15 μm extend/retract length, Setpoint value of 1 nN, a pixel rate of 2048 Hz and a speed of 30 µm/s. The system operated under closed-loop control. After reaching the selected contact force, the cantilever was retracted. The retraction length of 15 μm was sufficient to overcome any adhesion between the tip and the sample and to make sure that the cantilever had been completely retracted from the sample surface. Force‑distance (FD) curve was recorded at each point of the cantilever approach/retract movement. AFM measurements were obtained at 37°C (Petri dish heater, JPK) with force measurements recorded at a pulling speed of 30 µm/s (extension time 0.5 sec).</p> <p>The Young's modulus (E) was calculated by fitting the Hertzian‑Sneddon model on the FD curves measured as force maps (64x64 points) of the region containing either a single cell or multiple cells. JPK data evaluation software was used for the batch processing of measured data. The adjustment of the cantilever position above the sample was carried out under the microscope by controlling the position of the AFM‑head by motorized stage equipped with Petri dish heater (JPK) allowing precise positioning of the sample together with a constant elevated temperature of the sample for the whole period of the experiment. Soft uncoated AFM probes HYDRA-2R-100N (Applied NanoStructures, Mountain View, CA, USA), i.e. silicon nitride cantilevers with silicon tips are used for stiffness studies because they are maximally gentle to living cells (not causing mechanical stimulation). Moreover, as compared with coated cantilevers, these probes are very stable under elevated temperatures in liquids – thus allowing long-time measurements without nonspecific changes in the measured signal.</p> <p><em>Image analysis</em></p> <p>Fluorescence microscopy data were analyzed in ImageJ 1.52h and Python 3.7.1 as follows: cells were manually segmented using actin fluorescence channel, two regions were created for analysis: whole cell and cell periphery, lining a 4 μm thick region around cell border and including most of periphery actin cytoskeleton. In these two regions following parameters were measured for both actin and tubulin fluorescence: Integrated intensity, median intensity, and following regions were measured to describe cell morphology: Cell area, Maximum caliper (max feret diameter), roundness, and aspect ratio. Moreover, stress fibers were manually segmented in every cell and following parameters were measured: number of fibers per cell, feret angle of fiber, integrated intensity, fiber length, mean intensity. Next, a standard deviation of feret angles of individual fibers was calculated relatively to mean of feret angle using a circstd function from scipy package for Python.</p> <p><strong>Identification of files</strong></p> <p><em>Microscopy data</em></p> <p>Files are separated into individual zip files. The dataset of <em>confocal microscopy </em>is separated based on treatments: untreated control, docetaxel-treated cells, cisplatin-treated cells, zinc-treated cells. Filenames actin_tubulin_Zstack_cisplatin.zip, actin_tubulin_Zstack_untreated_control.zip, actin_tubulin_Zstack_zinc.zip, actin_tubulin_Zstack_docetaxel.zip. Files included in these ZIP archives are named as follows: "cellline_treatment_FOV". Files are 3-layer 16bit tiff files with layer sequence as follows: F-Actin (Phalloidin)/b-tubulin/Hoechst 33342. The dataset contains 242 FOVs of three cell line types/three treatments + one control, files are Z-stacks made of 50 slices.</p> <p>The dataset of <em>atomic force microscopy </em>(AFM) is included in one ZIP archive "AFM_YoungModulus_SetpointHeight.zip", which includes data on Young modulus and Setpoint Height of cell lines 22Rv1, PNT1A and PC-3 and treatments zinc, docetaxel, cisplatin (+control), i.e. identical like for confocal microscopy. The file naming is as follows: "AFM_cellline_treatment_FOV_Youngmodulus.tif" for Young modulus and "AFM_cellline_treatment_FOV_setpointheight.tif" for setpoint height. The data are filtered 32-bit tiff images, where the pixel value correspond to cell stiffness (young modulus) in Pa or setpoint height in m.</p> <p><em>Confocal microscopy analysis files</em></p> <p>Following files are csv tables including image analysis of actin/tubulin staining captured by confocal microscope:</p> <p>Cytoskeleton_fluo_analysis_Cell_Cell_periphery_morphology.csv: table includes analyzed data for actin and tubulin staining in following cellular regions: cell, cell periphery. Standard ImageJ parameters regarding intensity and morphology included.</p> <p>Cytoskeleton_fluo_analysis_Fibers.csv: table includes results of manual segmentation and consequent analysis of actin stres fibers in the cells. Apart from standard ImageJ parameters, also number of stress fibers per cell and standard deviation of fiber angle relative to the cell mean angle (for details see methods) are included.</p>
Supplementary Table S27.1: Animal species native to South Africa that have invasive populations elsewhere.
<p>Animal species native to South Africa that have invasive populations elsewhere. Sorted by expected chronological appearance in the first place they were recorded as alien species. Notes are made on whether the introduction is known to be (Y) or not (N) from South Africa (or unknown U). Pathways are according to the CBD pathway classification scheme (Harrower et al. 2017), along with an indication of whether the introduction was intentional or accidental. Species that have multi-continental distributions, and which may in addition have some introduced populations are shown at the end of the table.</p>
Is there a non-invasive biomarker for the early detection of ovarian torsion? A systematic review and meta-analysis
<p>We have performed a systematic review and meta-analysis and identified multiple biomarkers that warrant further study as part of a broader diagnostic panel for ovarian torsion. These include SCUBE1, s-DD, IL-6, IMA and TNF-a. </p>
ScienceDex guides
Understand access before you commit
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.