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3,118 results for “resources”
What could explain 13C signature of dryland biocrusts? Evaluating potential resource transfer between plants and biocrusts.
Dryland ecosystems are increasing in geographic extent and contribute greatly to interannual variability in global carbon dynamics. Disentangling interactions among dominant primary producers can help partition their contributions to dryland C dynamics. We measured the δ13C signatures of biological soil crusts and dominant plant species (C3 and C4) across a regional scale in the southwestern USA to determine if biocrust cyanobacteria were coupled to plant productivity (using plant-derived C mixotrophically), or independent of plant activity (and therefore purely autotrophic).
Temporal Dynamics of Soil Carbon and Nitrogen Resources Within a Grassland-Creosote Ecotone at the Sevilleta National Wildlife Refuge, New Mexico (1992-1994)
Plant communities across large portions of the southwestern United States have shifted from grassland to desert shrubland. Studies have demonstrated that soil nutrient resources become spatially more heterogeneous and are redistributed into islands of fertility with this shift in vegetation. This research addressed the additional question of whether soil resources become more temporally heterogeneous along a grassland-shrubland ecotome. Within adjacent grassland and creosotebush sites, soil profiles were described at 3 pits and samples collected for description of nutrient resources within the profile. Relative cover of plant species and bare soil were determined within each site by line transects. The top 20-cm of bare soil or soil beneath the canopy of grasses/creosotebush were collected 17 times during 1992-1994. Soil samples were analyzed for soil moisture, extractable ammonium and nitrate, nitrogen mineralization potential, microbial biomass carbon, total organic carbon, microbial respiration, dehydrogenase activity, ratio of microbial C to total C (C[mic]-to-C[org]), and microbial respiration to biomass carbon (metabolic quotient). The major differences in the structure of soils between sites were the apparent loss of a 3 to 5-cm depth of sandy surface soil at the creosotebush site and an associated increase in calcium carbonate content at a more shallow depth. Soils under plants at both sites had greater total and available nutrient resources with higher concentrations under creosotebush than under grasses. Greatest temporal variation in available soil resources was shown in soils under creosotebush. When expressed on an area basis, greater temporal variation in the total amount of available soil resources was shown in the grassland site, primarily due to greater plant cover (45% in grassland vs. 8% in creosote).
Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traits
<p>Data for the preprint "Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traits.”, by Legay N. , Grassein F., Arnoldi C., Segura R., Laîné P., Lavorel S., Clément J.C.</p>
Resources for reproducing experiments in "Novel Entity Discovery from Web Tables"
<p>This repository contains resources developed for the paper: "S. Zhang, E. Meij, K. Balog, and R. Reinanda. Novel Entity Discovery from Web Tables. In: Proceeding of the The Web Conference 2020 (WWW ’20), April 2020".</p> <p>It includes the three test collections for novel entity discovery for Web tables, entity type and mention resolution, as well as the mention-entity and heading-property correspondences for 3M tables. The cited datasets were used in this work.</p> <p>Files to recreate the entity linking experiments:</p> <ul> <li>training_el.csv</li> <li>training_el_type.csv</li> <li>training_el_type_wiki.csv</li> <li>training_el_wiki.csv</li> <li>training_schema.csv</li> </ul> <p>Files to recreate the table matching experiments:</p> <ul> <li>me_corres.csv - textual cells algorithmically linked to Wikipedia entities</li> <li>hp_corres.csv - same but only table headings</li> </ul> <p>Files to recreate the entity resolution experiments:</p> <ul> <li>ec_golden.csv - 20K unlinked mentions textual cells, manually linked to Wikipedia</li> <li>er_sf_golden.csv - 1K cell values, manually clustered</li> <li>er_type_golden.csv - 1K cell values, manually linked to DBpedia types</li> </ul>
Fig. 3 in A new and improved electric fish finder with resources for printed circuit board fabrication
Fig. 3. Internal view of electric fish finder.
Deliverable [D4.1] Techno-economic sustainability analysis methodology on resources for bio-based products, conversion routes and end-of-life alternative valorisation options
<p>Techno-economic sustainability analysis (TESA) is a methodology framework to evaluate the performance of a process under technical and economic perspective. A process can be divided into three main sections, the resources required for bio-based products, the conversion routes for the production and finally, the end-of-life alternative valorisation options. Consequently, TESA is carried out separately in the three sections and evaluates the likelihood of their different technology scales and applications and their economic feasibility.</p>
Resource fluctuations inhibit the reproduction and virulence of the human parasite Schistosoma mansoni in its snail intermediate host
Resource availability can powerfully influence host-parasite interactions. However, we currently lack a mechanistic framework to predict how resource fluctuations alter individual infection dynamics. We address this gap with experiments manipulating resource supply and starvation for a human parasite, Schistosoma mansoni, and its snail intermediate host to test a hypothesis derived from mechanistic energy budget theory: resource fluctuations should reduce schistosome reproduction and virulence by inhibiting parasite ingestion of host biomass. Low resource supply caused hosts to remain small, reproduce less, and produce fewer human-infectious cercariae. Periodic starvation also inhibited cercarial production and prevented infection-induced castration. The periodic starvation experiment also revealed substantial differences in fit between two bioenergetic model variants, which differ in their representation of host starvation. Simulations using the best fit parameters of the winning model suggest that schistosome performance substantially declines with resource fluctuations with periods >7 days. These experiments strengthen mechanistic theory that can be readily scaled up to the population level to understand key feedbacks between resources, host population dynamics, parasitism, and control interventions. Integrating resources with other environmental drivers of disease in an explicit bioenergetic framework could ultimately yield mechanistic predictions for many disease systems.
Aligning repository networks to support international sharing of COVID-19 resources and other current issues
<p>Recording of a panel "Aligning repository networks to support international sharing of COVID-19 resources", organized by COAR. This panel presented several national approaches to managing and sharing COVID-19 resources from around the world (Africa, Canada, Europe, Latin America, Asia), followed by a discussion about how we can work more closely across countries and regions to ensure that content can be integrated internationally. Participants: Kathleen Shearer - COAR, Paolo Manghi - OpenAIRE, Europe, Kazuhiro Hayashi, National Institution of Science and Technology Policy, Japan, Ansie Van de Wasthuizen, UNISA, South Africa, Cesar Olivares, CONCYTEC, Peru and LA Referencia, Latin America, Geoff Harder, Canadian Association of Research Libraries<br> <br> Organization Identifiers and Open Repositories: ROR-ing Together – Maria Gould, California Digital Library, University of California Office of the President.<br> <br> Research Data Management: a Stellenbosch University Journey – Samuel Simango, Stellenbosch University Library.<br> <br> Towards Open Data Metrics: enabling data repositories to demonstrate reuse – Kristian Garza, DataCite.</p> <p>DSpace-CRIS 7: What is Coming? – Susanna Mornati, 4Science</p>
Data for: Relatively rare root endophytic bacteria drive plant resource allocation patterns and tissue nutrient concentration in unpredictable ways
<p><span><span><span><span><span><span><span><span><span><span><span><b>Premise of Study</b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Plant endophytic bacterial strains can influence plant traits such as leaf area and root length. Yet, the influence of more complex bacterial communities in regulating overall plant phenotype is less explored. Here, we conducted two complementary experiments to test if we can predict plant phenotype response to changes in microbial community composition. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methods</b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>In the first study, we inoculated a single genotype of <i>Populus deltoides</i>with individual root endophytic bacteria and measured plant phenotype. Next, single inoculation data were used to predict phenotypic traits in mixed three-member community inoculations, which we tested in the second experiment. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Key Results</b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>When in isolation, each bacterial endophyte significantly but weakly altered plant phenotype relative to non-inoculated plants. In mixture, bacterial strain <i>Burkholderia</i>BT03, constituted at least 98% of community relative abundance. Yet, plant resource allocation and tissue nutrient concentrationswere disproportionately influenced by <i>Pseudomonas </i>sp.GM17, GM30, and GM41. We found a 10% increase in leaf mass fraction and a 11% decrease in root mass fraction when replacing<i>Pseudomonas </i>GM17 with GM41 in communities containing both <i>Pseudomonas </i>GM30 and <i>Burkholderia</i>BT03. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Conclusions</b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Our results indicate that interactions among endophytic bacteria may drive plant phenotype over the contribution of each strain individually. Additionally, we have shown that low-abundant strains contribute to plant phenotype challenging the assumption that the dominant strains will drive plant function.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Sierra Nevada mountain lake microbial communities are structured by temperature, resources, and geographic location
<p><span>Warming, eutrophication (nutrient fertilization) and brownification (increased loading of allochthonous organic matter) are three global trends impacting lake ecosystems. However, the independent and synergistic effects of resource addition and warming on autotrophic and heterotrophic microorganisms are largely unknown. In this study, we investigate the independent and interactive effects of temperature, dissolved organic carbon (DOC, both allochthonous and autochthonous), and nitrogen (N) supply, in addition to the effect of spatial variables, on the composition, richness, and evenness of prokaryotic and eukaryotic microbial communities in lakes across elevation and N deposition gradients in the Sierra Nevada mountains of California, USA. We found that both prokaryotic and eukaryotic communities are structured by temperature, terrestrial (allochthonous) DOC and latitude. Prokaryotic communities are also influenced by total and aquatic (autochthonous) DOC, while eukaryotic communities are also structured by nitrate. Additionally, increasing N availability was associated with reduced richness of prokaryotic communities, and both lower richness and evenness of eukaryotes. We did not detect any synergistic or antagonistic effects as there were no interactions among temperature and resource variables. Together, our results suggest that (a) organic and inorganic resources, temperature, and geographic location (based on latitude and longitude) independently influence lake microbial communities; and (b) increasing N supply due to atmospheric N deposition may reduce richness of both prokaryotic and eukaryotic microbes, likely by reducing niche dimensionality. Our study provides insight into abiotic processes structuring microbial communities across environmental gradients and their potential roles in material and energy fluxes within and between ecosystems.</span></p>
Optimal resource allocation and prolonged dormancy strategies in herbaceous plants
<p>1. Understanding the fitness consequences of different life histories is critical for explaining their diversity and for predicting effects of changing environmental conditions. However, current theory on plant life histories relies on phenomenological, rather than mechanistic, models of resource production.</p> <p>2. We combined a well-supported mechanistic model of ontogenetic growth that incorporates differences in the size-dependent scaling of gross resource production and maintenance costs with a dynamic optimization model to predict schedules of reproduction and prolonged dormancy (plants staying below ground for ≥ 1 growing season) that maximize lifetime offspring production.</p> <p>3. Our model makes three novel predictions: First, maintenance costs strongly influence the conditions under which a monocarpic or polycarpic life history evolves and how resources should be allocated to reproduction by polycarpic plants. Second, in contrast to previous theory, our model allows plants to compensate for low survival conditions by allocating a larger proportion of resources to storage and thereby improving overwinter survival. Incorporating this ecological mechanism in the model is critically important because without it our model never predicts significant investment into storage, which is inconsistent with empirical observations. Third, our model predicts that prolonged dormancy may evolve solely in response to resource allocation tradeoffs.</p> <p>4. Significance: Our findings reveal that maintenance costs and the effects of resource allocation on survival are primary determinants of the fitness consequences of different life history strategies, yet previous theory on plant life history evolution has largely ignored these factors. Our findings also validate recent arguments that prolonged dormancy may be an optimal response to costs of sprouting. These findings have broad implications for understanding patterns of plant life history variation and predicting plant responses to changing environments.</p>
Divergent adaptations in resource-use traits explain how pikas thrive on the roof of the world
Life in extreme environments is possible through multilevel adaptations to physical and biotic stresses. At high elevations, species face numerous challenges, besides low oxygen levels, but previous studies have focused on genetic and physiological adaptations to chronic hypoxia while overlooking other key strategies for thriving in alpine landscapes. Here, we investigate resource-use trait adaptations to extreme elevations using pikas as a model, lagomorphs distributed up to 6200 metres and reaching maximum diversity on the Qinghai-Tibet plateau, the highest plateau on Earth. Specifically, we assess cranial evolution in pikas using geometric morphometric and phylogenetic comparative techniques to determine whether adaptations among high-elevation biota shown at the molecular and physiological levels also occur in resource-use traits. We further explore the roles of two contrasting lifestyles (burrowing and rocky-dwelling) in cranial evolution. We found that alpine species exhibit striking phenotypic specialization to distinct microhabitats. Contrary to physiological and genetic adaptive convergence, we show that the cranium has undergone adaptive divergence likely reflecting past resource competition in highlands and long-term association with alpine landscapes. Our analyses also reveal that the evolution of burrowing lifestyle allows high-elevation pikas to explore novel niches and boosts their phenotypic diversification. In addition to cold and hypoxia tolerance, high cranial specialization, the appearance of burrowing habits, and strong niche separation explain how pikas overcome alpine stresses and flourish on the highest plateau on Earth. By contrast, when moving to spatially complex and heterogeneous vegetation zonation, pikas exhibit generalist skull forms able to exploit diverse habitats. These findings mirror previously reported intraspecific patterns in mammals, suggesting a general morphological response in resource-exploiting traits to cope with distinct selection pressures across elevation zones. Phenotypic diversity is further constrained by rocky habitats, resulting in convergent skulls. Our study highlights that adaptations to extreme environments occur at multiple levels of organization, but can lead to distinct evolutionary paths depending on which selective forces they respond to. The evolution of burrowing behaviour represents a landmark in the evolutionary history of pikas. We further show that rocky habitats impose strong ecological pressures, leading to convergent responses in resource-use traits, which is rarely documented in mammals.
Data from: One and two year visual outcomes from the Moorfields age-related macular degeneration database: a retrospective cohort study and an open science resource
Objectives: To analyse treatment outcomes and share clinical data from a large, single-center, well-curated database (8174 eyes / 6664 patients with 120,756 single entries) of patients with neovascular age related macular degeneration (AMD) treated with anti-vascular endothelial growth factor (VEGF). By making our depersonalised raw data openly available, we aim to stimulate further research in AMD, as well as setting a precedent for future work in this area. Setting: Retrospective, comparative, non-randomised electronic medical record (EMR) database cohort study of the UK Moorfields AMD database with data extracted between 2008 and 2018. Participants: Including one eye per patient, 3357 eyes/patients (61% female). Extraction criteria were ≥ 1 ranibizumab or aflibercept injection, entry of "AMD" in the diagnosis field of the EMR, and a minimum of one year of follow-up. Exclusion criteria were unknown date of first injection and treatment outside of routine clinical care at Moorfields before the first recorded injection in the database. Main outcome measures: Primary outcome measure was change in VA at one and two years from baseline as measured in Early Treatment Diabetic Retinopathy Study (ETDRS) letters. Secondary outcomes were the number of injections and predictive factors for VA gain. Results: Mean VA gain at one-year and two years were +5.5 (95%CI:5.0,6.0) and +4.9 (95%CI:4.2,5.6) letters respectively. Fifty-four percent of eyes gained ≥5 letters at two years, 63% had stable VA (±≤14 letters), forty-four percent of eyes maintained good VA (≥70 letters). Patients received a mean of 7.7 (95%CI:7.6,7.8) injections during year one and 13.0 (95%CI:12.8,13.2) injections over two years. Younger age, lower baseline VA, and more injections were associated with higher VA gain at two years. Conclusion: This study benchmarks high quality EMR study results of real life AMD treatment and promotes open science in clinical AMD research by making the underlying data publicly available.
Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment
Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.
GREEN-VARAN scores resources (EIGEN GRCh37)
<p>Processed EIGEN and EIGEN-PC scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 version for EIGEN v1.1 non-coding annotations.</p> <p>See: <a href="http://www.columbia.edu/~ii2135/eigen.html">http://www.columbia.edu/~ii2135/eigen.html</a></p> <p>If you use EIGEN score annotations with GREEN-VARAN don't forget to cite also the original EIGEN paper.</p>
GREEN-VARAN scores resources (FATHMM-XF GRCh37)
<p>Processed FATHMM-XF non-coding scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 version for FATHMM-XF v2.3 non-coding annotations.</p> <p>See: <a href="http://fathmm.biocompute.org.uk/">http://fathmm.biocompute.org.uk/</a></p> <p>If you use FATHMM-XF score annotations with GREEN-VARAN don't forget to cite also the original FATHMM-XF paper.</p>
GREEN-VARAN scores resources (FATHMM-MKL GRCh37)
<p>Processed FATHMM-MKL scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 version for FATHMM-MKL v2.3 non-coding annotations.</p> <p>See: <a href="http://fathmm.biocompute.org.uk/">http://fathmm.biocompute.org.uk/</a></p> <p>If you use FATHMM-MKL score annotations with GREEN-VARAN don't forget to cite also the original FATHMM-MKL paper.</p>
GREEN-VARAN scores resources (CADD GRCh38)
<p>Processed CADD scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh38 version for CADD v.1.5.</p> <p>See: <a href="https://cadd.gs.washington.edu/">https://cadd.gs.washington.edu/</a></p> <p>If you use CADD score annotations with GREEN-VARAN don't forget to cite also the original CADD paper.</p>
GREEN-VARAN scores resources (FIRE GRCh37)
<p>Processed FIRE scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 version for FIRE.</p> <p>See: <a href="https://sites.google.com/site/fireregulatoryvariation/">https://sites.google.com/site/fireregulatoryvariation/</a></p> <p>If you use FIRE score annotations with GREEN-VARAN don't forget to cite also the original FIRE paper.</p>
GREEN-VARAN scores resources (FATHMM-MKL GRCh38)
<p>Processed FATHMM-MKL scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh38 version for FATHMM-MKL v2.3 non-coding annotations.</p> <p>See: <a href="http://fathmm.biocompute.org.uk/">http://fathmm.biocompute.org.uk/</a></p> <p>If you use FATHMM-MKL score annotations with GREEN-VARAN don't forget to cite also the original FATHMM-MKL paper.</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.