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78 results for “multiplicative process”
Effects of Multiple Resource Additions on Community and Ecosystem Processes: NutNet NPP Quadrat Sampling at the Sevilleta National Wildlife Refuge, New Mexico
Two of the most pervasive human impacts on ecosystems are alteration of global nutrient budgets and changes in the abundance and identity of consumers. Fossil fuel combustion and agricultural fertilization have doubled and quintupled, respectively, global pools of nitrogen and phosphorus relative to pre-industrial levels. In spite of the global impacts of these human activities, there have been no globally coordinated experiments to quantify the general impacts on ecological systems. This experiment seeks to determine how nutrient availability controls plant biomass, diversity, and species composition in a desert grassland. This has important implications for understanding how future atmospheric deposition of nutrients (N, S, Ca, K) might affect community and ecosystem-level responses. This study is part of a larger coordinated research network that includes more than 40 grassland sites around the world. By using a standardized experimental setup that is consistent across all study sites, we are addressing the questions of whether diversity and productivity are co-limited by multiple nutrients and if so, whether these trends are predictable on a global scale.
Effects of Multiple Resource Additions on Community and Ecosystem Processes: NutNet Seasonal Biomass and Seasonal and Annual NPP Data at the Sevilleta National Wildlife Refuge, New Mexico
Two of the most pervasive human impacts on ecosystems are alteration of global nutrient budgets and changes in the abundance and identity of consumers. Fossil fuel combustion and agricultural fertilization have doubled and quintupled, respectively, global pools of nitrogen and phosphorus relative to pre-industrial levels. In spite of the global impacts of these human activities, there have been no globally coordinated experiments to quantify the general impacts on ecological systems. This experiment seeks to determine how nutrient availability controls plant biomass, diversity, and species composition in a desert grassland. This has important implications for understanding how future atmospheric deposition of nutrients (N, S, Ca, K) might affect community and ecosystem-level responses. This study is part of a larger coordinated research network that includes more than 40 grassland sites around the world. By using a standardized experimental setup that is consistent across all study sites, we are addressing the questions of whether diversity and productivity are co-limited by multiple nutrients and if so, whether these trends are predictable on a global scale. Above-ground net primary production is the change in plant biomass, represented by stems, flowers, fruit and and foliage, over time and incoporates growth as well as loss to death and decomposition. To measure this change the vegetation variables, including species composition and the cover and height of individuals, are sampled twice yearly (spring and fall) at permanent 1m x 1m plots within each site. Volumetric measurements are made using vegetation data from permanent plots (SEV231, "Effects of Multiple Resource Additions on Community and Ecosystem Processes: NutNet NPP Quadrat Sampling") and regressions correlating species biomass and volume constructed using seasonal harvest weights from SEV157, "Net Primary Productivity (NPP) Weight Data."
Code to reproduce the analyses of "Multiple stressors alter greenhouse gas concentrations in streams through local and distal processes"
<p>Streams are significant contributors of greenhouse gases (GHG) to the atmosphere, and the increasing number of stressors degrading freshwaters may exacerbate this process, posing a threat to climatic stability. However, it is unclear whether the influence of multiple stressors on GHG concentrations in streams results from increases of in-situ metabolism (i.e., local processes) or from changes in upstream and terrestrial GHG production (i.e., distal processes). Here, we hypothesize that the mechanisms controlling multiple stressor effects vary between <span>carbon dioxide (</span>CO<sub>2</sub>) and <span>methane (</span>CH<sub>4</sub>), with the latter being more influenced by changes in local stream metabolism, and the former mainly responding to distal processes. To test this hypothesis, we measured stream metabolism and the concentrations of CO<sub>2</sub> (<em>p</em>CO<sub>2</sub>) and CH<sub>4</sub> (<em>p</em>CH<sub>4</sub>) in 50 stream sites that encompass gradients of <span>nutrient enrichment, oxygen depletion, thermal stress, riparian degradation and discharge</span>. Our results indicate that these stressors had additive effects on stream metabolism and GHG concentrations, with stressor interactions explaining limited variance. Nutrient enrichment was associated with higher stream heterotrophy and <em>p</em>CO<sub>2</sub>, whereas <em>p</em>CH<sub>4</sub> increased with oxygen depletion and water temperature. Discharge was positively linked to primary production, respiration and heterotrophy but correlated negatively with <em>p</em>CO<sub>2.</sub> Our models indicate that CO<sub>2</sub>-equivalent concentrations can more than double in streams that experience high nutrient enrichment and oxygen depletion, as compared to those with oligotrophic and oxic conditions. Structural equation models revealed that the effects of nutrient enrichment and discharge on <em>p</em>CO<sub>2</sub> were related to distal processes rather than local metabolism. In contrast, <em>p</em>CH<sub>4</sub> responses to nutrient enrichment, discharge and temperature were related to both local metabolism and distal processes. Collectively, our study illustrates <span>potential climatic feedbacks resulting from freshwater degradation and </span>provides insight into the processes mediating stressor impacts on the production of GHG in streams.</p>
Improving the drug discovery process by using multiple classifier systems
<p>High-quality dataset gathered from ChEMBL version 22 based on UniProt accession P34972. Regarding to activity data potential, duplicates were ignored, no activity or data validity comments were allowed, only data from binding assays and with a pCheMBL value were kept. This led to a dataset composed of 3925 chemical compounds (instances) represented using 2132 features. The first 2048 features epitomize different chemical structures fingerprints (represented using FCFP_6 notation), while the remaining 84 are associated with several physicochemical descriptors (such as Fractional Polar Surface Area, Rotatable Bonds or Molecular Weight). Finally, the set was transformed into a binary classification set where the activity cut-off was defined at a pChEMBL value > 7 and written to a tab-delimited text file. The final set contained 1977 active compounds and 1948 inactive compounds. Table 3 shows the codification of each feature grouped by type.</p>
Supplementary Material on "Processes, Methods, and Tools in Model-based Engineering --- A Qualitative Multiple-Case Study"
<p>This dataset provides the supplementary material that we applied for all interviews conducted in the context of our qualitative study resulting in the JSS article mentioned in the title:</p> <ul> <li>The semi-structured interview guide,</li> <li>the codebook,</li> <li>the blank consent form that our interviewees signed,</li> <li>and the blank invitation mail that we used to ask our interviewees to participate in our study.</li> </ul>
Testing relationships between multiple regional features and biogeographic processes of speciation, extinction, and dispersal
<p>The spatial and environmental features of regions where clades are evolving are expected to impact biogeographic processes such as speciation, extinction, and dispersal. Any number of regional features (such as altitude, distance, area, etc.) may be directly or indirectly related to these processes. For example, it may be that distances or differences in altitude or both may limit dispersal rates. However, it is difficult to disentangle which features are most strongly related to rates of different processes. Here, we present an extensible Multi-feature Feature-Informed GeoSSE (MultiFIG) model that allows for the simultaneous investigation of any number of regional features. MultiFIG provides a conceptual framework for incorporating large numbers of features of different types, including categorical, quantitative, within-region, and between-region features, along with a mathematical framework for translating those features into biogeographic rates for statistical hypothesis testing. Using traditional Bayesian parameter estimation and reversible-jump Markov chain Monte Carlo, MultiFIG allows for the exploration of models with different numbers and combinations of feature-effect parameters, and generates estimates for the strengths of relationships between each regional feature and core process. We validate this model with a simulation study covering a range of scenarios with different numbers of regions, tree sizes, and feature values. We also demonstrate the application of MultiFIG with an empirical case study of the South American lizard genus <em>Liolaemus</em>, investigating sixteen regional features related to area, distance, and altitude. Our results show two important feature-process relationships: a negative distance/dispersal relationship, and a negative area/extinction relationship. Interestingly, although speciation rates were found to be higher in Andean versus non-Andean regions, the model did not assign significance to Andean- or altitude-related parameters. These results highlight the need to consider multiple regional features in biogeographic hypothesis testing.</p>
Testing relationships between multiple regional features and biogeographic processes of speciation, extinction, and dispersal
Open the record for dataset details and reuse information.
Riparian forests and macroinvertebrates support multiple ecosystem processes across temperate and tropical streams
Open the record for dataset details and reuse information.
Forecasts, score summary files, target observational data and meteorological driver files to accompany the manuscript "Skill of process-based forecasts relative to multiple null models varies across time and depth for water temperature and dissolved oxygen"
<p>This data publication includes raw ensemble forecast output (forecasts.zip), as well as summary score files (scores.zip) for process-based forecasts produced with the Forecasting Lake and Reservoir Ecosystems (FLARE) framework. In addition, it includes scores for climatology (climatology_scores.csv) and random walk (RW_scores.csv) null forecasts, formatted observational data of target variables (sunp-targets-insitu.csv), and meteorological driver files required for analysis to accompany the manuscript "Skill of process-based forecasts relative to multiple null models varies across time and depth for water temperature and dissolved oxygen". Forecasts were made of water temperature and dissolved oxygen at Lake Sunapee, NH in 2021 and 2022.</p>
A case study of the dimensional effects in an additive manufacturing process with multiple operations
<p>This dataset provides a case study for the dimension changes of the prints in an additive manufacturing process with multiple operations. The operations are Stereolithography (SLA) printing and its two post-processing processes (washing and post-curing). The dataset contains the measured dimensions of the prints after each operation, which allows the modeling of each operation individually.<br> </p>
Consistent Modeling of GS 1826-24 X-Ray Bursts for Multiple Accretion Rates Demonstrates the Possibility of Constraining rp-process Reaction Rates
<p>MESA inlists and run_star_extras associated with <a href="https://ui.adsabs.harvard.edu/#abs/2018arXiv180505552M/abstract">Meisel (2018)</a>. MESA version 9793.</p> <p>Publication DOI: <a href="https://doi.org/10.3847/1538-4357/aac3d3">10.3847/1538-4357/aac3d3</a></p>
Efficacy and Safety of BIIB019 (Daclizumab High Yield Process) Versus Interferon β 1a in Participants With Relapsing-Remitting Multiple Sclerosis
ClinicalTrials.gov study NCT01064401. IPD Sharing: Not stated. Countries: 28. Publications: 7.
Safety and Efficacy Extension Study of Daclizumab High Yield Process (DAC HYP) (BIIB019) in Participants Who Have Completed Study 205MS202 (NCT00870740) to Treat Relapsing Remitting Multiple Sclerosis
ClinicalTrials.gov study NCT01051349. IPD Sharing: Not stated. Countries: 8. Publications: 3.
Safety and Efficacy Extension Study of Daclizumab High Yield Process (DAC HYP) in Participants With Multiple Sclerosis Who Have Completed Study 205MS201 (NCT00390221) to Treat Relapsing-Remitting Mult
ClinicalTrials.gov study NCT00870740. IPD Sharing: Not stated. Countries: 8. Publications: 2.
An Open-Label Immunogenicity and Pharmacokinetics Study of Daclizumab High Yield Process Prefilled Syringe in Relapsing Remitting Multiple Sclerosis
ClinicalTrials.gov study NCT01462318. IPD Sharing: Not stated. Countries: 4. Publications: 1.
Safety and Efficacy Study of Daclizumab High Yield Process (DAC HYP) to Treat Relapsing-Remitting Multiple Sclerosis
ClinicalTrials.gov study NCT00390221. IPD Sharing: Not stated. Countries: 8. Publications: 2.
Hidden in the DNA: insights on how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae).
Aim: To investigate cryptic diversity and diversification timing in the putatively low-dispersal Amazonian leaf-litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation. Location: Central Amazonia, Brazil. Taxon: Squamata; Gymnophthalmidae; Loxopholis osvaldoi. Methods: We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographic distance among localities, the environment, and the position of localities in relation to main rivers were tested by Redundancy Analysis (RDA). Results: We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE, and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE, or historical factors. Main conclusions: Our results strongly suggest that L. osvaldoi is a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history of L. osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that non-linear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.
Data from: The multiple roles of β–diversity help untangle community assembly processes affecting recovery of temperate rocky shores
Metacommunity theory highlights the potential of β–diversity as a useful link to empirical research, especially in diverse systems where species exhibit a range of stage-dependent dispersal characteristics. To investigate the importance of different components and scales of β–diversity in community assembly we conducted a large-scale disturbance experiment and compared relative recovery across multiple sites and among plots within sites on the rocky shore. Six sites were spread along 80 km of coastline and, at each site, 5 plots were established, matching disturbed and undisturbed quadrats. Recovery was not complete at any of the sites after 1 year for either epibenthos (mostly composed of macroalgae and, locally, mussels) or infauna. Significant differences in recovery among sites were observed for epibenthos but not for infauna suggesting different community assembly processes were operating. This was supported by epibenthos in the recovering plots having higher species turnover than in undisturbed sediment, and recovery well predicted by local diversity, while infaunal recovery was strongly influenced by the epibenthic community's habitat complexity. However, infaunal community recovery did not simply track formation of habitat by recovering epibenthos, but appeared to be overlain by within-site and among-site aspects of infaunal -diversity. These results suggest that documenting changes in the large plants and animals alone will be a poor surrogate for rocky shore community assembly processes. No role for ecological connectivity (negative effect of among-site β–diversity) in driving recovery was observed, suggesting a low risk of effects from multiple disturbances propagating along the coast, but a limited resilience at the site scale to large-scale disturbances such as landslides or oil spills.
Data from: Ant diversity in Neotropical savannas: hierarchical processes acting at multiple spatial scales
1. Understanding what creates and maintains macroscale biodiversity gradients is a central focus of ecological and evolutionary research. Spatial patterns in diversity are driven by a hierarchy of factors operating at multiple scales. Historical and climatic factors drive large-scale patterns of diversity by affecting the size of regional species pools, while habitat heterogeneity or microhabitat characteristics further influence species coexistence at small scales. 2. We tested the degree to which the species-energy, historical factors, habitat heterogeneity and local environment hypotheses explain observed patterns of ant diversity across hierarchical spatial scales. 3. We sampled ground-dwelling ants at 29 sites within a Neotropical savanna region, the Brazilian Cerrado. We measured species density – an abundance-dependent diversity metric – and rarefied species richness – an abundance-independent metric – at spatial scales with varying grain sizes. For each hypothesis, two correlates were used to predict ant diversity patterns: i) species-energy: rainfall and productivity; ii) historical factors: historical variation in rainfall and refugial areas; iii) habitat heterogeneity: heterogeneity in greenness and diversity of land cover; iv) local factors: contents of sand and coarse fragments in the soil. 4. Ant diversity patterns correlated to net primary productivity and to the proportion of coarse fragments in the soil, corroborating the species-energy and local environment hypotheses, respectively. Soil negatively influenced species density, but not rarefied species richness, which was positively influenced by productivity. We found scale dependencies in the effects of soil/productivity on species density; productivity best predicted species density patterns at large scales, since sampling completeness offset the abundance-driven effects of soil. 5. Considering abundance differences may help to discern the mechanisms underlying the relationship between macroscale diversity patterns and its ecological drivers. Plant productivity affected ant diversity independently of abundance, possibly by limiting the size of regional species pools. On the other hand, soil properties had an abundance-dependent effect on ant diversity, indicating a sampling mechanism. Our findings are consistent with predictions of the hierarchical theory of diversity. Large-scale patterns of productivity limit regional diversity, an effect that cascades down to finer spatial scales, where soil properties influence the number of coexisting species.
Data from: Accounting for observation processes across multiple levels of uncertainty improves inference of species distributions and guides adaptive sampling of environmental DNA
Understanding factors that influence observation processes is critical for accurate assessment of underlying ecological processes. When indirect methods of detection, such as environmental DNA, are used to determine species presence, additional levels of uncertainty from observation processes need to be accounted for. We conducted a field trial to evaluate observation processes of a terrestrial invasive species (wild pigs- Sus scrofa) from DNA in water bodies. We used a multi-scale occupancy analysis to estimate different levels of observation processes (detection, p): the probability DNA is available per sample (θ), the probability of capturing DNA per extraction (γ), and the probability of amplification per qPCR run (δ). We selected four sites for each of three water body types and collected 10 samples per water body during two months (September and October 2016) in central Texas. Our methodology can be used to guide sampling adaptively to minimize costs while improving inference of species distributions. Using a removal sampling approach was more efficient than pooling samples, and was unbiased. Availability of DNA varied by month, was considerably higher when water pH was near neutral, and was higher in ephemeral streams relative to wildlife guzzlers and ponds. To achieve a cumulative detection probability greater than 90% (including availability, capture, and amplification), future studies should collect 20 water samples per site, conduct at least 2 extractions per sample, and conduct 5 qPCR replicates per extraction. Accounting for multiple levels of uncertainty of observation processes improved estimation of the ecological processes and provided guidance for future sampling designs.
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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.