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Available plasmids used in year 1 of ASAP project 2 - Target Enablement.
<p>Collated plasmids used for the ASAP project 2 drug discovery platform in year 1. Details of insert sequence and vector backbone included. These plasmids will be deposited into Addgene shortly.</p> <p>Plasmids will be accessible for use by all. </p> <p>Plasmids used in successful crystal screens to date are highlighted on the sheet.</p> <p>Up to date information on the progress made by the ASAP project 2 team can be found here: https://asapdiscovery.org/outputs/target-enabling-packages/</p> <p> </p> <p> </p> <p>Research reported here was supported in part by NIAID of the National Institutes of Health under award number U19AI171399.The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health</p>
Plant trait responses to variation in N and P availability
<ol> <li><span>Global change drivers such as eutrophication and plant invasions will create novel environments for many plant species. Through adaptive trait plasticity plants may maintain their performance under these novel conditions and may outcompete those showing low adaptive trait plasticity. In a greenhouse study, we determined if plasticity in traits is adaptive or maladaptive in endangered, non-endangered and invasive plant species in response to variation of nitrogen (N) and phosphorus (P) availability (N:P ratios 1.7, 15 and 135) and whether plastic trait responses are adaptive and/or costly for fitness (i.e. biomass). </span></li> <li><span>Species choice comprised 17 species from three functional groups (legumes, non-legume forbs and grasses), either classified as endangered, non-endangered or invasive. After two months plants were harvested and nine traits related to carbon assimilation and nutrient uptake were measured (leaf area, SLA, LDMC, SPAD, RMR, root length, SRL, root surface area and PME activity).</span></li> <li> <span>We found more traits responding plastically to variation in P than in N. Plasticity only created costs when P was varied. Plasticity in traits was mostly adaptively neutral towards fitness, with plasticity in three traits being similarly adaptive across all species groups: SPAD (as a measure of chlorophyll content, adaptive to N and P limitation), leaf area and root surface area (adaptive to P limitation). We found little differences in trait plasticity between endangered, non-endangered and invasive species.</span> </li> <li> <em><span>Synthesis</span></em><span>. Along a gradient from N limitation, balanced N:P supply and P limitation we found that the type of fluctuating nutrient (i.e. if N or P is varied) is decisive for the adaptive value of a trait. Variation in P availability (from balanced supply to P limitation) created both a stronger reduction in fitness as well as created plasticity costs in more traits than variation in N availability (from balanced supply to N limitation). However, the patterns observed in our study may change if nutrient availability is altered, either by nutrient inputs or by a shift in nutrient availabilities, e.g. by decreasing N input as foreseen by European Legislation, but without simultaneously decreasing P input. </span> </li> </ol>
Prey availability influences the effect of boldness on reproductive success in a mammalian predator
<p>Boldness is an important trait in wild populations and among-individual differences can link to individual fitness<span>. </span>The strength and direction of relationships between behavioral and life-history traits may however vary according to environmental conditions, where fluctuating selection acting on behavioral traits contributes to the maintenance of personality differences. <span>We </span>explored sources of variation in <span>Arctic fox (<em>Vulpes</em> <em>lagopus</em>) boldness </span>and <span>investigated how temporal variation in the abundance of a main prey (lemmings) influences the relationship between fox boldness and reproductive success. We measured the behavioral reaction of individuals when escaping after handling, as an indicator of their boldness. We obtained 70 measurements from 42 individuals </span>during two years of low lemming abundance and two years of high lemming abundance<span> and assessed fox litter size as an indicator of reproductive success. First, individual characteristics (age, sex, mass) did not affect Arctic fox boldness, while individual identity generated variation in boldness. Next, </span>we found that during years of low lemming density, individuals behaving boldly had more pups than those behaving less boldly, suggesting boldness may provide an advantage when lemmings are scarce by increasing hunting success or allowing access to alternative resources. However, all <span>individuals tended to show high levels of boldness when lemming density was high, and all produced large litters. </span>Temporal variation in the abundance of a main prey might therefore influence the relation between boldness and reproductive success of a predator, and if individuals consistently differ in their level of boldness, fluctuating selection could contribute to the maintenance of personality.</p>
SPADATAS - OER Available on Internet
<p>List of Open Educational Resources regarding</p> <ul> <li>Raising awareness of the importance of data privacy in schools</li> <li>Enhance data privacy in data academic management in schools</li> </ul>
Data from: Brood size, food availability, and body size affects male care decisions and offspring performance
<p>Parental care strategies do not only vary greatly across species, but also within species, there can be substantial between- and within-individual variation in parental care behaviour. To better understand the evolution of care strategies, it is crucial to determine how and when parents modify their behaviour in response to internal as well as environmental factors. Here, we investigated the effect of brood size, resource size and an individual's quality on care strategies of uniparental males and examined the downstream consequences on offspring performance in the burying beetle <em>Nicrophorus vespilloides</em>. Burying beetles breed on small vertebrate cadavers and, on average, males invest much less in care than females. Nevertheless, we found that uniparentally caring males were responsive to their social and non-social environment and adjusted the amount as well as the type of care to the size of the brood, the size of the cadaver and their own body size. Additionally, we show that the care strategies affected offspring performance. Specifically, males that cared longer had larger and more surviving larvae. Our results add to our understanding of plastic parenting strategies by showing that even the sex that provides less care can evolve a very flexible care behaviour.</p>
Oxygen availability and body mass modulate ectotherm responses to ocean warming
<p>Data and analysis scripts for the following publication: Duncan et al. In press. Oxygen availability and body mass regulate ectotherm responses to ocean warming. Nature communications</p> <p> </p> <p><em>Analysis_script.R</em> is the R script to carry out the main analysis in the manuscript.</p> <p><em>data.csv</em> is the physiology data to carry out the main analysis in the manuscript.</p> <p> </p> <p><em>current_bottom_oxy_monthly.Rda</em> is an environmental layer used to carry out the distribution modelling in the manuscript.</p> <p><em>current_bottom_salt_monthly.Rda</em> is an environmental layer used to carry out the distribution modelling in the manuscript.</p> <p><em>current_bottom_temp_monthly.Rda</em> is an environmental layer used to carry out the distribution modelling in the manuscript.</p> <p><em>future_bottom_oxy_monthly.Rda</em> is an environmental layer used to carry out the distribution modelling in the manuscript.</p> <p><em>future_bottom_salt_monthly.Rda</em> is an environmental layer used to carry out the distribution modelling in the manuscript.</p> <p><em>future_bottom_temp_monthly.Rda</em> is an environmental layer used to carry out the distribution modelling in the manuscript.</p> <p> </p> <p><em>raw respirometry data.zip</em> is the raw respirometry data collected during the experiments for the manuscript.</p> <p><em>raw_meta_data.xlsx</em> is the meta data related to the respirometry data collected during the experiments.</p> <p><em>raw_resp_data_script.R</em> is the R script to quantify physiological metrics from experimental data.</p>
Soil fungal communities contribute to the positive diversity-productivity relationship of tree communities under contrasting water availability
<p><span>Plant diversity has often been linked to increased productivity; however, this apparent diversity-productivity relationship may rely on inter-trophic interactions such as those between plants and soil microbes. Soil fungi can create complementarity between plant species via altered plant resource partitioning, facilitation via fungal networks, or biotic feedbacks, thereby promoting plant diversity-productivity relationships. Furthermore, these relationships are likely to be context-dependent in response to resource availability. </span></p> <p><span>We used a biodiversity-ecosystem function experiment with trees exposed to high and low water availability treatments to determine the contribution of soil fungal communities to the diversity-productivity relationship in tree communities. We used amplicon sequencing of soil fungi to assess fungal richness, community composition, and richness of functional guilds. We then applied structural equation modelling to determine relationships between tree diversity, fungal communities, and tree productivity and the role of water availability in these relationships.</span></p> <p><span>Tree species richness and functional diversity both increased above-ground tree productivity and influenced soil fungal community composition. Fungal community composition had a direct impact on tree productivity and enhanced net diversity effects on productivity. Therefore, fungal communities mediated a positive, indirect effect of tree richness on productivity. While total fungal richness was not associated with tree diversity, pathogen richness decreased and mycorrhizal richness increased with tree richness. Pathogen and mycorrhizal richness had either no impact or a weak negative effect on productivity. Tree species traits strongly affected fungal communities and these changes promoted productivity. Finally, water availability greatly influenced fungal communities but did not interact with tree diversity to affect productivity; indicating possible resilience of tree communities to altered precipitation regimes and associated changes in fungal communities.</span></p> <p><span>Synthesis: Our study highlights the crucial role that fungal communities play in shaping the relationship between tree diversity, traits, and productivity, and resilience to altered water availability. </span></p>
A Great Escape: resource availability and density-dependence shape population dynamics along trailing range edges
<p>Populations along geographical range limits are often exposed to unsuitable climate and low resource availability relative to core populations. As such, there has been a renewed focus on understanding the factors that determine range limits to better predict how species will respond to global change. Using recent theory on range limits and classical understanding of density dependence, we evaluated the influence of resource availability on the snowshoe hare Lepus americanus along its trailing range edge. We estimated variation in population density, habitat use, survival, and parasite loads to test the Great Escape Hypothesis (GEH), i.e. that density dependence determines, in part, a species' persistence along trailing edges. We found that variability in resource availability affected density and population fluctuations and led to trade-offs in survival for snowshoe hare populations in the northeastern USA. Hares living in resource-limited environments had lower and less variable population density, yet higher survival and lower parasitism compared to populations living in resource-rich environments. We suggest that density-dependent dynamics, elicited by resource availability, provide hares a unique survival advantage and partly explain persistence along their trailing edge. We hypothesize that this low-density escape from predation and parasitism occurs for other prey species along trailing edges, but the extent to which it occurs is likely conditional on the quality of matrix habitat. Our work indicates that biotic factors play an important role in shaping species' trailing edges and more detailed examination of non-climatic factors is warranted to better inform conservation and management decisions.</p>
Data from: Hydraulic vulnerability of tropical forests is largely independent of water availability
<p>Tropical rainforest woody plants have been thought to have uniformly low resistance to hydraulic failure and to function near the edge of their hydraulic safety margin, making these ecosystems vulnerable to drought; however, this may not be the case. Using data collected at 30 tropical forest sites for three key traits associated with drought tolerance, we show that site-level hydraulic diversity of leaf turgor loss point, resistance to embolism (P<sub>50</sub>), and hydraulic safety margins (HSMs) is high across tropical forests and largely independent of water availability. Species with high HSMs (>1 MPa) and low P<sub>50</sub> values (<-2 MPa) are common across the wet and dry tropics. This high site-level hydraulic diversity, largely decoupled from water stress, could influence which species are favored and become dominant under a drying climate. High hydraulic diversity could also make these ecosystems more resilient to variable rainfall regimes.</p>
Changes in nitrogen and phosphorus availability driven by secondary succession in temperate forests shape soil fungal communities and function
<p><span>Soil fungal community plays an important role in forest ecosystems, and forest secondary succession is a crucial driver of soil fungal community. However, the driving factors of fungal community and function during temperate forest succession and their potential impact on succession processes are poorly understood. In this study, we investigated the dynamics of the soil fungal community in three temperate forest secondary successional stages (shrublands, coniferous forests, and deciduous broadleaf forests) using high-throughput DNA sequencing coupled with functional prediction via the FUNGuild database. We found that fungal community richness, α-diversity, and evenness decreased significantly during the succession process. Soil available phosphorus and nitrate</span> <span>nitrogen decreased significantly after initial succession occurred, and redundancy analysis showed that both were significant predictors of soil fungal community structure. Among functional groups, fungal saprotrophs as well as pathotrophs represented by plant pathogens were significantly enriched in the early-successional stage, while fungal symbiotrophs represented by ectomycorrhiza were significantly increased in the late-successional stage. The abundance of both saprotroph and pathotroph fungal guilds was positively correlated with soil nitrate</span> <span>nitrogen and available phosphorus content. Ectomycorrhizal fungi were negatively correlated with nitrate</span> <span>nitrogen and available phosphorus content and positively correlated with ammonium</span> <span>nitrogen content.</span> <span>These results indicated that the dynamics of fungal community and function reflected the changes in nitrogen and phosphorus availability caused by the secondary succession of temperate forests. The fungal plant pathogen accumulated in the early-successional stage and ectomycorrhizal fungi accumulated in the late-successional stage may have a potential role in promoting forest succession. These findings contribute to a better understanding of the response of soil fungal communities to the secondary forest succession process and highlight the importance of fungal communities during temperate forest succession.</span></p>
Coursing the mottled mosaic: generalist predators track pulses in availability of neonatal ungulates
<p>The density and distribution of resources shape animal movement and behavior and have direct implications for population dynamics. Resource availability often is "pulsed" in space and time, and individuals should cue in on resource pulses when the energetic gain of doing so exceeds that of stable resources. Birth pulses of prey represent a profitable but ephemeral resource and should thereby result in shifting functional responses by predators. We evaluated movements and resource selection of coyotes (<em>Canis</em> <em>latrans</em>) across a gradient of reproductive stages ranging from late gestation to peak lactation of female mule deer (<em>Odocoileus</em> <em>hemionus</em>) in southwest Wyoming, USA to test whether coyotes exhibited shifts in selection and movement behavior relative to the availability and vulnerability of neonatal mule deer. We expected coyotes to track pulses in availability of neonatal mule deer, and such behavior would be represented by shifts in resource selection and search behavior of coyotes that would be strongest during peak parturition of mule deer. Coyotes selected areas of high relative probability of use by female mule deer and did so most strongly during peak parturition. Further, searching behavior of coyotes intensified during pulses of availability of deer neonates. Our findings support the notion that coyotes exploit pulses of neonatal deer, presumably as an attempt to capitalize on a vulnerable, energy-rich resource. Our work quantifies the behavioral mechanisms by which coyotes consume ungulate neonates and provides one of the first examples of a mammalian predator-prey system centered on a pulsed resource. </p>
Long-term ecological responses of a lowland dipterocarp forest to climate changes and nutrient availability at Bulusan Lake
<p>This data publication encompasses the datasets generated in a study focusing on reconstructing ecological responses to climatic and nutrient availability changes during the late Holocene in northern Philippines. The data comes from samples taken from sediment cores retrieved from Bulusan Lake, located on Luzon Island, Philippines, in March 2013. In these samples, we analyzed fossil pollen and spores (a proxy for plant taxa abundance), charcoal (a proxy for fire activity), stable carbon isotopic composition of terrestrial-lipid biomarkers (a proxy for vegetation cover), stable nitrogen and phosphate isotope composition of bulk sediments, and elemental composition of sediment cores at a high resolution (proxies for nutrient availability and volcanic activity). The dataset also includes links to records generated in a previous study on the same sediments (Prohaska <em>et al.</em> 2023), where we measured the stable hydrogen isotopic composition of terrestrial-lipid biomarkers to reconstruct past hydrological conditions, as well as the magnetic susceptibility record and AMS dates of plant macrofossils to calculate sediment accumulation ages. The data generation spanned the period from April 2013 to September 2020, and the data files are provided in Excel spreadsheet format.</p>
Behavioural thermoregulation and food availability drives fine-scale seasonal habitat partitioning in limpets
<ol> <li>Small-scale spatial variation in temperature plays a key role in limiting the distribution of organisms in thermally heterogeneous environments. In the rocky intertidal zone, intra-day temperature variation at small scales (cm-m) can easily exceed 30°C.</li> <li>To experimentally test the impact of this small-scale temperature heterogeneity on the distribution of an ecologically important limpet species (<em>Cellana</em> <em>denticulata</em>), boulders on an intertidal rocky reef in New Zealand were rotated, and small-scale temperature variability and food availability were measured throughout one year. Small-scale variability in thermal tolerance, heart rate, and heat shock protein expression was also measured to relate in situ limpet distributions with environmental conditions. Temperature variability was measured using limpet bio-mimics and HOBO pendant temperature loggers, while food availability (chlorophyll <em>a</em> concentration) was measured on in situ concrete fiberboard tiles.</li> <li>To measure limpet distributions, every tagged limpet on each of 18 boulders was followed from June 2021–2022. During each sampling, the location of each limpet, compass direction, and slope of the surface that each limpet inhabited were measured. To test for physiological differences among limpets from each microhabitat, thermal tolerance, and heat shock protein expression were measured in collected limpets; in situ heart rates and body temperatures were also measured sporadically on hot days.</li> <li>Maximum predicted body temperatures (36–39°C), heart rates, and actual body temperatures were greatest on equatorial surfaces (i.e., surfaces facing the equator) whereas food availability was greatest on poleward-facing surfaces. During summer, limpets moved towards surfaces that minimised their body temperatures and maximised food availability, namely vertical and poleward facing surfaces and undersides of boulders.</li> <li>Thermal tolerance, measured using Arrhenius breakpoint temperatures (mean ± SE: 34.7–35.8 ± 0.4–0.7°C) and flat line temperatures (36.2–37.4 ± 0.3–0.4°C), were similar among limpets facing different directions. Surprisingly, heat shock protein expression was relatively consistent throughout the year and among directions.</li> <li>Overall, limpet populations are resilient to thermal stress because they effectively use behavioural thermoregulation to exploit cooler microhabitats that also have greater food availability during summer.</li> </ol>
Data for "False trends in Landsat-based vegetation greenness due to increased image availability over time"
<p>Raster data used in this following paper : "False trends in Landsat-based vegetation greenness due to increased image availability over time". The dataset includes observed greening trends for the European Alps, and sum of observations in the european alps and the arctic.</p>
Carbon availability affects already large species-specific differences in chemical composition of ectomycorrhizal fungal mycelia in pure culture
<p>Although ectomycorrhizal (ECM) contribution to soil organic matter processes receives increased attention, little is known about fundamental differences in chemical composition among species, and how that may be affected by carbon (C) availability. Here we study how 16 species (incl. 19 isolates) grown in pure culture at three different C:N ratios (10:1, 20:1 and 40:1) vary in chemical structure, using Fourier transform infrared (FTIR) spectroscopy. We hypothesised that C availability impacts directly on chemical composition, expecting increased C availability to lead to more carbohydrates and less proteins in the mycelia. There were strong and significant effects of ECM species (R<sup>2</sup> = 0.873 and P = 0.001) and large species-specific differences in chemical composition. Chemical composition also changed significantly with C availability, and increased C led to more polysaccharides and less proteins for many species, but not all. Understanding how chemical composition change with altered C availability is a first step towards understanding their role in organic matter accumulation and decomposition.</p>
Available data from South African Voyages in the Southern Ocean
<p>This dataset provides an overview of data produced during South African voyages in the Southern Ocean aboard the <em>R/V S.A. Agulhas II</em> and contains a document detailing the data that are presented (AvailableData.pdf) and an .xlsx file that contains the metadata and links to the published datasets (AvailableData.xlsx). Each voyage has a dedicated sheet within the .xlsx file.</p> <p>This dataset will be updated, and a new version published as more data becomes available. Please refer to the most recent version on <a href="https://zenodo.org/communities/scale_south_africa/">https://zenodo.org/communities/scale_south_africa/</a> </p> <p><strong>This is a data curation document</strong><strong> only</strong><strong>. Any use of the data mentioned in this document should reference the original dataset</strong><strong> and authors</strong><strong>.</strong></p>
A Positive Atmospheric Feedback on the North Atlantic Warming Hole Data Availability
<p>There are three files with the data required to recreate: Figure 1, Figures 2&3, and Figure 4. Contact the corresponding author (sydney.kramer@colorado.edu) for additional information. The MATLAB files contain variables including: Sea Surface Temperature (SST), Zonal Wind (u), Meridional Wind (v), Sea Level Pressure (slp), Geopotential Height (z), Virtual Temperature (VirtualTemp), Latitude (lat), Longitude (lon), Vertical Levels (lev), and coastlines (xcoast/ycoast). These variables are provided for five different experiments, CESM control, CESM NAWH, CESM NAWH-S, ECHAM control, and ECHAM NAWH. </p>
Pacritinib Versus Best Available Therapy to Treat Myelofibrosis
ClinicalTrials.gov study NCT01773187. IPD Sharing: Not stated. Countries: 12. Publications: 2.
A Study of IMC-A12 in Participants With Tumors Who No Longer Respond to Treatment or For Whom No Treatment is Available
ClinicalTrials.gov study NCT00785538. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Research Study to Compare Two Types of Insulin, a New Insulin, Insulin Icodec and an Available Insulin, Insulin Degludec, in People With Type 2 Diabetes Who Have Not Used Insulin Before (ONWARDS 3)
ClinicalTrials.gov study NCT04795531. IPD Sharing: YES. Countries: 12. Publications: 5.
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.