Find research datasets worth reusing

opencc-by-4.0Dec 2023View details →

FIGURE 3 in Dietary shift of a pimelodid catfish in response to the flood pulse in the Xingu River

FIGURE 3 | Non-metric Multidimensional Scaling (nMDS) graphical representation of the diet of Pimelodus blochii collected in different hydrological periods in the middle Xingu River region, Eastern Amazon, Brazil.

opencc-by-4.0Dec 2023View details →

FIGURE 2 in Dietary shift of a pimelodid catfish in response to the flood pulse in the Xingu River

FIGURE 2 | Alimentary index (Ai) of the diet of Pimelodus blochii collected in different hydrological periods in the middle Xingu River region, Eastern Amazon, Brazil. *Less than 5% of contribution.

opencc-by-4.0Dec 2023View details →

FIGURE 1 in Dietary shift of a pimelodid catfish in response to the flood pulse in the Xingu River

FIGURE 1 | Map depicting the Volta Grande do Xingu (Xingu River, Brazil), with emphasis on the reduced flow section created by the construction of the Belo Monte Dam (including the Pimental Dam). The orange circles represent the sampling sites where Pimelodus blochii specimens were collected, and the arrows indicate the direction of water flow. The orange star and triangle represent the Pimental Dam and the Belo Monte Dam, respectively.

Survey questionnaire data on Perceptions, interactions, and responses to urban natural environments through ecological momentary assessment

Data consist of a R file format and contain the cleaned survey quistionaire data where people were asked about their perceptions, interactions, and responses to urban natural environments. For more information please read the following report Published as part of the Regreen Horizon project.  Panduro, T.E., Zandersen, M., Guell, C., Lovell, R., Garrett, J., Taylor, T., Fullam, J., Amegbor, P. (2024) Perceptions, interactions, and responses to urban natural environments through ecological momentary assessment (EMA). Deliverable D4.6. REGREEN - Fostering nature-based solutions for smart, green and healthy urban transitions in Europe and China. Horizon2020 Grant No. 821016.  https://www.doi.org/10.5281/zenodo.10594764

opencc-by-sa-4.0Apr 2024View details →

Binaural Impulse Response Dataset: Square Plate in Anechoic Chamber

The dataset at hand contains impulse responses that have been measured along two discretized trajectories in the vicinity of a 25 mm thick 1 m x 1 m medium density fiberboard plate. Such data can serve as reference for the modelling of acoustic edge diffraction. This dataset was used in the context of research on binaural perception of diffracted sound in a publication that is in press at the Journal of the Acoustical Society of America

Data from: Local environment and coral composition affect recovery and determine long-term coral responses to recurrent mass mortalities in the Lakshadweep Archipelago

A quarter century after the first global coral bleaching event in 1998, reports differ on the relative importance of anthropogenic influences, local environment and bleaching recurrence in determining the resilience of coral reefs. While life history traits largely determine how corals respond to temperature anomalies, it is unclear if these traits also determine how corals fare over time. From 1998 to 2022, we tracked compositional changes in reefs across the Lakshadweep Archipelago to explore how global El Niño events, and local environment (wave climate and depth) influenced coral responses to repeated mass bleaching. From the 1998 to the 2016 bleaching event, the magnitude of coral mortality reduced overall, particularly at deeper reefs (shallow: -38% to -3%; deep: -18% to -0.45%). Post-bleaching recovery correlated positively with higher wave exposure, linked to the creation of stable structures for coral settlement and survival. Across bleaching phases, recovery was initially slow (6-7 years post-mortality), but, given time, showed a much steeper increase, led by space-occupying genera like Acropora. However, recurring mass bleaching maintained coral cover low (~15% across all sites). These broad trends mask dynamic compositional patterns. Genera such as Porites, Pocillopora, and Favia declined less through time compared to Acanthastrea, Turbinaria, Psammocora and Plesiastrea among others. We identified six community clusters that describe contrasting long-term responses to local and global factors, mediated by depth and wave exposure. Interestingly, genera with different functional traits cluster together indicating that bleaching susceptibility interacts with depth and exposure, creating a spatial mosaic of coral assemblages. These clusters serve as a predictive, site-specific framework to understand the dynamically shifting but declining assemblage of Lakshadweep reefs. While local management could help maintain this changing composition, urgent global action is needed to secure the long-term ecological integrity of tropical reefs.

SLABSTRESS: SLAB STructural RESponse for Seismic European Design

The dataset reports results from the full-scale testing of a two-storey flat slab structure, undertaken in the SlabSTRESS research project; the construction and testing were planned and carried out at the ELSA laboratory of the European Commission’s Joint Research Centre. The dimensions are three bays by two, spans 4.5 and 5 m, slab thickness 0.2 m, interstorey height 3.2 m. Two different longitudinal reinforcement details were considered; welded studs shear reinforcement was provided only in the second floor slab. The testing program included seismic tests for service and ultimate actions, using the pseudo-dynamic technique with virtual walls. To this aim, a building structure was designed with primary walls and the flat slab frame as secondary element. Cyclic loading tests followed up to ultimate drift capacity of the structure. The sequence of tests included strengthening of a set of damaged connections using bolted bars in holes drilled through the slab, followed by cyclic testing to failure. The instrumentation was provided for the global response and the connections with local rotations in the columns and slab; cracking around the columns was measured with through-crack sensors; a measurement system for internal forces and moments was included within the columns. The results show the response with deformations and damage for the different loading conditions up to failure. The results obtained on a full-scale structure extend and confirm the knowledge in the literature, mainly based on isolated connections and/or small-scale samples.

Dataset of Raman spectroscopy responses for over-the-counter drugs in Paraguay, including acetylsalicylic acid, paracetamol, and ibuprofen.

Spectra of three over-the-counter pharmaceuticals—acetylsalicylic acid, paracetamol, and ibuprofen—were collected at the Faculty of Exact and Natural Sciences of the National University of Asuncion, with the aim of creating a dataset that serves as a reference for Raman responses from different drug manufacturers. This dataset will also provide the scientific community with data that can be used for multivariate analysis and model training. In the data collection phase, spectra were obtained using a Raman spectroscopy system (iRaman 785s model from BWTEK) equipped with a 785 nm excitation laser. Samples were collected from diverse sales points such as pharmacies, shopping centers, and street vendors. Each spectrum was captured at 50% laser power with a measurement time of 1 second and an accumulation of 10 spectra over a range of 150 to 3200 cm-1. This method preserved the integrity of the raw data, which includes a common column for Raman shifts and additional columns for intensities and labels, detailing the activation modes in the Raman spectrum. The data is structured into specific  xlsx files for each drug, such as "Paracetamol.xlsx", "acetylsalicylic-acid .xlsx", and "Ibuprofen .xlsx", each containing 50 spectra categorized by the type of pharmaceutical but not by brand. Brand-specific categorization is detailed in separate files like "Paracetamol-trademark .xlsx", where samples are classified using codes such as "Par-A" for different brands. This organization aids the scientific community in using clustering methods to analyze the spectral data and differentiate pharmaceutical brands based on their excipients or binders, with consistent codes across different drugs suggesting common manufacturers for various medications.

opencc-by-4.0Jan 2024View details →

Data and code to accompany sugar kelp DEB thermal response manuscript

Data and R code to accompany the manuscript "Improving growth models of cultivated sugar kelp (Saccharina latissima) by accounting for intraspecific variation in thermal tolerance" (Krasnow et al., 2024), published in the Journal of the World Aquaculture Society. Some material was originally created by Celeste Venolia in March 2018-December 2019 for <a href="https://doi.org/10.1016/j.ecolmodel.2020.109151">Venolia et al. (2020)</a>. <ul> <li>cold_validation.R contains the code to validate DEB kelp model against data from Trømso, Norway</li> <li>venolia_validation.R contains the code to validate the model against the data from Rhode Island, USA, reproducing the analysis from the original paper and producing new estimates with the newly-estimated temperature parameters</li> <li>SolveR_R.R includes the function that is used to solve for the specific growth rate (r)</li> <li>KelpDEB_model.R includes the deSolve-structured function used to run the model</li> </ul> Please use the most recent version (3.1) so that all data/code needed to run the analyses are present.

opencc-by-4.0Nov 2023View details →

Data and scripts for: Idiosyncratic responses to biotic and environmental filters in wood-inhabiting fungal communities

These files include the data, the scripts, and the pipeline for bioinformatic analyses for reproducing the results presented in the manuscript "Idiosyncratic responses to biotic and environmental filters in wood-inhabiting fungal communities". Description of the files can be found from the README.docx file.

Data from: Interannual radial growth response of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) to severe droughts: an analysis along a gradient of soil properties and rooting characteristics

Dataset related to the publication: &bdquo;Interannual radial growth response of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) to severe droughts: an analysis along a gradient of soil properties and rooting characteristics” Information on the data and the tree species_site_key used can be found in the attached Read me file.

Data from: Understanding evolutionary rescue and parallelism in response to environmental stress

Evolutionary rescue, the process by which populations facing environmental stress avoid extinction through genetic adaptation, is a critical area of study in evolutionary biology. The order in which mutations arise and get established will be relevant to the population's rescue. This study investigates the degree of parallel evolution at the genotypic level between independent populations facing environmental stress and subject to different demographic regimes. Under density regulation, two regimes exist: in the former, the population can restore positive growth rates by adjusting its population size or through adaptive mutations, whereas in the second regime, the population is doomed to extinction unless a rescue mutation occurs. Analytical approximations for the likelihood of evolutionary rescue are obtained and contrasted with simulation results. We show that the initial level of maladaptation and the demographic regime significantly affect the level of parallelism. There is an evident transition between these two regimes. Whereas in the first regime, parallelism decreases with the level of maladaptation, it displays the opposite behavior in the rescue/extinction regime. These findings have important implications for understanding population persistence and the degree of parallelism in evolutionary responses as they integrate demographic effects and evolutionary processes.

opencc-by-nc-nd-4.0May 2024View details →

Genome editing of LKB1 gene by CRISPR/Cas9 in lung cancer cells and evaluation of its role in metformin and cisplatin response.

<pre>LKB1 is an important upstream inhibitor of the mTOR/S6Ks pathway. Loss of LKB1 is often associated with cancer, including in A549 lung cancer cell line, boosting the transformation of pre-malignant neoplasic cells. Metformin, a natural compound derived from Galega officinalis, is mainly used as a treatment for diabetes mellitus type 2 (DM2), but recently, it has been associated to lower incidence of cancer. One of the main mechanisms is by activation of AMPK through different pathways, including LKB1 activation. Activation of AMPK inhibits the mTOR pathway, protein synthesis and thus cell growth. The combination of metformin and cisplatin, a main chemothepeutic drug for lung cancer, has shown to improve treatment of cancer cells to cisplatin and also to hinder the cisplatin associated resistance common in lung cancer. Here we aim to use the CRISPR/Cas9 technology to correct the mutation presented in A549 lung cancer cells and improve their response to metformin or to the combination between metformin and cisplatin. Besides, we will assess the mTOR signaling pathway status, as well as cell growth, proliferation, cell cycle and sensitivity to apoptosis induction by cisplatin. This project may be useful as a proof of principle that in the future therapies must consider the genomic background of cancer cells before administration of a specific anticancer drug. </pre>

A model of within-host interactions between host resources, macroparasite infection and immune response

This project was designed to mathematically investigate the of different host parasite-mitigation strategies on host condition. The R code herein comprises: <ul> <li>An ODE model of within-host interactions between a macroparasite (e.g. helminth) infection, host resource levels and host immune response, and the consequent effects on host condition. In brief, resources are ingested and utilised by the host, leading to inceased condition. The host is infected by a parasite, which matures and establishes within the host; both age stages cause harm to the host, decreasing host condition. The presence of the parasite stimulates an immune response, which can either target larval or adult parasites (a resistance strategy), or ameliorate the harm they cause (a tolerance strategy). The host can also reduce resource intake in order to also reduce ingestion of parasite infective stages (an avoidance strategy). Resistance responses have an associated immunopathology, in that the immune response also harms the host.</li> <li>Code to plot model trajectories over time.</li> <li>Code to plot multiple trajectories as a heat map, in which the x-axis is time and the y-axis is a parameter representing the host investment in its parasite-mitigation strategy.</li> <li>Code to calculate the optimum host investment for each strategy, over various sets of parameter values, as determined by maximising mean host condition over a given timeframe, and to plot the output.</li> <li>The same are also provided for an ODE model in which the total immune response is allocated between the two resistance responses and tolerance (a combined strategy). The optimisation code optimises both the total investment in immune repsonse, and how much is allocated to the three different individual strategies.</li> </ul> The model and results are described in detail in the associated manuscript. We also provide here the simulated datasets in which the optimum host investments were calculated over a range of different parameter values, as these take several hours to run on a standard desktop computer..

opencc-by-4.0Feb 2024View details →

Human lung cancer harbors spatially-organized stem-immunity hubs that associate with response to immunotherapy

Data associated with Chen, Nieman, Spurrell et al "Human lung cancer harbors spatially-organized stem-immunity hubs that associate with response to immunotherapy" Nature Immunology, 2024.  (1) Multiplex RNA scope. Processed cell-level data from 3 datasets, separated into manually selected "Stem Immunity" regions and "Tumor" regions, in separate files.  (2) GeoMx. Unprocessed GeoMex data, with standard fields provided by Nanostring software.  (3) MERFISH. Transcript-level information, including CellPose and Baysor segmentation.  (4) Co-registered multispectral RNA and protein images. Processed cell-level data from 46 patients. Patient-level meta data information is available in supplementary table 1, tab B_Patient_Metadata. Fluorophore channel information is Figure 1a.  Paper: <a title="https://secure-web.cisco.com/1OQRHTBMPf1SngM0FLdNuKQOPPx7fLOR87kGiirhnF_e0M74duym9zratwJMs0WJXqHJPAlkZoWXBoHafhJ72n9s0edU76bj8nCUblNWpOnoK6c8KGEQgcNuk8OuBqXAooW9yoh6etJ0bq6VGDmoFd95MrgMob6is1GxcOWx-XK996d_j8QDVu1rptbeyI8n08UfqmHA3n0A0P37k_-DYUWMh7VFNSmbLGzVqGG2n-czoFN3vL5JrMDPRvo0LDGJs96rzB6zYiaLdk6UgYXXc6eUV6FI64MTxmuXCbEmVRqONrjLdyG6HJULOrJLmKURM/https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41590-024-01792-2" href="https://secure-web.cisco.com/1OQRHTBMPf1SngM0FLdNuKQOPPx7fLOR87kGiirhnF_e0M74duym9zratwJMs0WJXqHJPAlkZoWXBoHafhJ72n9s0edU76bj8nCUblNWpOnoK6c8KGEQgcNuk8OuBqXAooW9yoh6etJ0bq6VGDmoFd95MrgMob6is1GxcOWx-XK996d_j8QDVu1rptbeyI8n08UfqmHA3n0A0P37k_-DYUWMh7VFNSmbLGzVqGG2n-czoFN3vL5JrMDPRvo0LDGJs96rzB6zYiaLdk6UgYXXc6eUV6FI64MTxmuXCbEmVRqONrjLdyG6HJULOrJLmKURM/https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41590-024-01792-2">https://www.nature.com/articles/s41590-024-01792-2</a>

opencc-by-4.0May 2024View details →

Bumble bee responses to climate and landscapes: Investigating habitat associations and species assemblages across geographic regions in the United States of America

Bumble bees are integral pollinators of native and cultivated plant communities, but species are undergoing significant changes in range and abundance on a global scale. Climate change and land cover alteration are key drivers in pollinator declines; however, limited research has evaluated the cumulative effects of these factors on bumble bee assemblages. This study tests bumble bee assemblage (calculated as richness and abundance) responses to climate and land use by modeling species-specific habitat requirements, and assemblage-level responses across geographic regions. We integrated species richness, abundance, and distribution data for 18 bumble bee species with site-specific bioclimatic, landscape composition, and landscape configuration data to evaluate the effects of multiple environmental stressors on bumble bee assemblages throughout 433 agricultural fields in Florida, Indiana, Kansas, Kentucky, Maryland, South Carolina, Utah, Virginia, and West Virginia from 2018 to 2020. Distinct east vs. west groupings emerged when evaluating species-specific habitat associations, prompting a detailed evaluation of bumble bee assemblages by geographic region. Maximum temperature of warmest month and precipitation of driest month had a positive impact on bumble bee assemblages in the Corn Belt/Appalachian/northeast, southeast, and northern plains regions, but a negative impact in the mountain region. Further, forest land cover surrounding agricultural fields was highlighted as supporting more rich and abundant bumble bee assemblages. Overall, climate and land use combine to drive bumble bee assemblages, but how those processes operate is idiosyncratic and spatially contingent across regions. From these findings, we suggested regionally specific management practices to best support rich and abundant bumble bee assemblages in agroecosystems. Results from this study contribute to a better understanding of climate and landscape factors affecting bumble bees and their habitats throughout the USA.

Data for: Bi-modal response strategy in Daphnia to ambush predation risk

Predation, a well-established major selective force, can manifest through either consumptive or non-consumptive effects. The relative impact of such effects is predicted to vary depending on the predator hunting strategy. In aquatic systems, great attention has been paid to coursing predators, such as fish, and their effects on the behaviour of zooplankton. However, less information is available regarding more ambush-style predators. To remedy this paucity, we utilised a 3D-tracking platform to record groups of Daphnia magna under control or predation risk conditions from the ambush, invertebrate predator Erythromma najas. This design allowed us to test if there are anti-predator responses in multiple metrics of swimming behaviours. Furthermore, we recorded actual predation events allowing the distinction between predator exuded info-chemicals and those produced during the predation event. We demonstrate that predation risk was greatest for those that swam at 85% of the available depth and averaged 8.1 mm/s. Examining each individuals swimming behaviour separately shows that predation risk did not exert an impact on any of the prey response metrics. Interestingly, however, we show that Daphnia conform to one of two strategies whilst under predation risk; either swim fast high up in the water column or swim slowly close to the bottom. Hence, this dichotomous behaviour is driven by strategies combining speed and depth in different constellations. As a result, our study demonstrates that Daphnia can detect the presence of a predator, but not immediately the act of predation. In a broader context, our findings highlight the importance of considering both the spatial and temporal dimensions of predation events in order correctly detect anti-predator responses. The data here is the raw positions of each individual tracked for the above study.

Data from: Coyotes display minimal response to Cougar scent at experimental carcass sites

Interactions among predators can have cascading impacts on communities and ecosystems. These interactions often occur around carrion, where the carrion provides a food reward, but also a risk of encountering other, potentially dominant, predators. Understanding how predators balance risk and reward at carrion, and how perceived risk changes in response to carcass origins and conditions, provides valuable insight into intraguild interactions. We investigated Coyote (Canis latrans) behavior at carrion simulated as cache sites treated with Cougar (Puma concolor) scent versus carrion used as control sites to better understand how Coyotes assess risk while feeding on carrion. Coyotes displayed similar behavior between sites treated and untreated with Cougar scent, suggesting that the presence of Cougar scent did not alter perceived risk by coyotes in our study. Instead, coyote behavior responded to carcass age, elevation, and whether avian scavengers had visited the carcass. Coyotes spent more time feeding, more time on camera, and touched carcasses quicker as carcass age increased. Avian scavengers appeared to compete with Coyotes, and while the presence of avian scavengers reduced time to carcass detection by Coyotes, it also decreased time spent feeding. These results suggest that carcass condition is a more important indicator of risk and reward than the presence of dominant predator scent to Coyotes. Predator scent may be an unreliable cue of immediate predator presence. Alternatively, all carcasses may be risky because dominant predators also scavenge carrion, creating similar risk regardless of previous visitation by dominant predators. These results provide insights into predator interactions and can also inform the use of scent cues in wildlife management.

Responsiveness to cold snaps by turtle embryos depends on exposure timing and duration

Characterizing how organisms respond to transient temperatures may further our understanding of their susceptibility to climate change. In animals with temperature-dependent sex determination (TSD), unusual transient temperatures during incubation result in sex bias and may therefore impair population breeding capacity. Past studies in the red-eared slider turtle (Trachemys scripta) have demonstrated that the timing and duration of heat exposure ("heat waves") can have major implications for the response of genes involved in gonadal development and the production of female hatchlings. Yet, no study has considered how the response of these genes to transient cold exposure ("cold snaps") may affect gene expression and influence the resulting production of males. We investigated how cold snap timing and duration affect gonadal gene expression in T. scripta embryos. Additionally, we explored the effect of early cold snap exposure duration on resulting hatchling sex ratios. Results show that responsiveness to cool temperatures changes rapidly across development, such that genes that responded to cold snaps when exposure began on incubation day 14 responded differently when cold exposure occurred just 4 to 8 days later. The sex ratio experiment revealed that embryos experiencing an early cold snap also require a long exposure (> 20 days) before most commit to testis development, further suggesting that early development under warm temperatures may lower their sensitivity to later cold snaps. These results highlight how individual responses to incubation temperature can change rapidly across development in turtles and have important effects on sex ratios. We discuss how variation in responsiveness to transient temperatures might help maintain mixed-sex ratios under variable thermal conditions in nature and may permit adaptive population responses to climate change.