Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
174
datasets available to search
ShareScore release 0.9.0
Dataset results
174 results for “Dynamic Assessment”
Pseudoproxies for the paper "A pseudoproxy assessment of data assimilation for reconstructing the atmosphere–ocean dynamics of hydroclimate extremes"
<p>Pseudoproxies for the paper “A pseudoproxy assessment of data assimilation for reconstructing the atmosphere–ocean dynamics of hydroclimate extremes” by Steiger and Smerdon 2017.</p> <p>If you have further questions, address them to the author Nathan J. Steiger.</p>
Biophysical larval dispersal models of observed bonefish (Albula vulpes) spawning events in Abaco, The Bahamas: An assessment of population connectivity and ocean dynamics
<p>Biophysical models are a powerful tool for assessing population connectivity of marine organisms that broadcast spawn. <em>Albula</em> <em>vulpes</em> is a species of bonefish that is an economically and culturally important sportfish found throughout the Caribbean and that exhibits genetic connectivity among geographically distant populations. We created ontogenetically relevant biophysical models for bonefish larval dispersal based upon multiple observed spawning events in Abaco, The Bahamas in 2013, 2018, and 2019. Biological parameterizations were informed through active acoustic telemetry, CTD casts, captive larval rearing, and field collections of related albulids and anguillids. Ocean conditions were derived from the Regional Navy Coastal Ocean Model American Seas dataset. Each spawning event was simulated 100 times using the program Ichthyop. Ten thousand particles were released at observed and putative spawning locations and were allowed to disperse for the full 71-day pelagic larval duration for <em>A</em>. <em>vulpes</em>. Settlement densities in defined settlement zones were assessed along with interactions with oceanographic features. The prevailing Northern dispersal paradigm exhibited strong connectivity with Grand Bahama, the Berry Islands, Andros, and self-recruitment to lower and upper Abaco. Ephemeral gyres and flow direction within Northwest and Northeast Providence Channels were shown to have important roles in larval retention to the Bahamian Archipelago. Larval development environments for larvae settling upon different islands showed few differences and dispersal was closely associated with the thermocline. Settlement patterns informed the suggestion for expansion of conservation parks in Grand Bahama, Abaco, and Andros, and the creation of a park in Eleuthera and the Berry Islands to protect fisheries. Further observation of spawning events and the creation of biophysical models will help to maximize protection for bonefish spawning locations and nursery habitat, and may help to predict year-class strength for bonefish stocks throughout the Greater Caribbean.</p>
Dynamic ctDNA Assessment in Cervical and Anal Canal Tumors: Optimizing Follow-up and Clinical Outcomes
ClinicalTrials.gov study NCT06640283. IPD Sharing: NO. Countries: 1. Publications: 6.
Data from high throughput SNP-chip as cost effective new monitoring tool for assessing invasion dynamics in the comb jelly Mnemiopsis leidyi
Open the record for dataset details and reuse information.
Data from: Connections across open water: A bi-organelle, genomics-scale assessment of Atlantic-wide population dynamics in a pelagic, endangered apex predator shark (Isurus oxyrinchus)
Open the record for dataset details and reuse information.
Data and code from: Accounting for unobserved population dynamics and aging error in close-kin mark-recapture assessments
Open the record for dataset details and reuse information.
Using dynamic foodscape models to assess bottom-up constraints on population performance of herbivores
Open the record for dataset details and reuse information.
Biophysical larval dispersal models of observed bonefish (Albula vulpes) spawning events in Abaco, The Bahamas: An assessment of population connectivity and ocean dynamics
Open the record for dataset details and reuse information.
Data from: Assessing Catharus bicknelli (Bicknell’s Thrush) habitat dynamics: A high-resolution model based on LiDAR metrics
Open the record for dataset details and reuse information.
Data from: Assessing stable isotope dynamics of diapausing Calanus finmarchicus and C. hyperboreus during the overwintering period: a laboratory experiment
This study aimed at describing changes in the stable isotopic composition of late copepodite stage V (CV) subarctic marine copepods (Calanus finmarchicus and C. hyperboreus) during overwintering non-feeding periods. Diapausing stage CVs sampled in deep waters of the Lower St. Lawrence Estuary (Québec, Canada) in late-September 2009 were monitored for 4 months under controlled laboratory conditions. CVs and newly moulted adults were analyzed for δ13C and δ15N signatures as well as lipid, carbon and nitrogen content. Lipids were extracted in half of the samples to compare δ13C of individuals with and without lipids and to evaluate the accuracy of mass balance correction models for δ13C under lipid influence. Lipid content generally decreased with time for both species, which was reflected in an increase of δ13C values of CVs but a constant δ13C in newly moulted adults. Accordingly, lipid extraction resulted in an increase of δ13C in CVs and adults. The mean δ13C signature of lipid-extracted individuals remained constant through the time for CVs of both species and for C. finmarchicus adults. δ15N signatures of individuals increased after lipid extraction, but this did not result in a constant value over time, suggesting that several endogenous metabolic processes affected nitrogen isotopic content. The accuracy of the mass balance model differed between species and stages, suggesting that lipid extraction should always be performed prior to applying mathematical corrections.
Data from: Assessing the effect of predator control on an endangered goose population subjected to predator-mediated food web dynamics
1. Assessing the effectiveness of conservation actions to halt population declines is challenging when confounded by other factors. We assessed whether culling of red fox, a predator currently increasing in the sub-Arctic, contributed to recent recovery of the critically endangered Fennoscandian population of Lesser White-fronted Goose Anser erythropus, while controlling for potentially confounding food web dynamics. 2. Using 19 years of data, 10 before and 9 after the implementation of annual red fox culling, we estimated the effect of this action on annual performance of the goose population. We corrected for the potentially confounding effects of cyclic rodent dynamics and semi-domestic reindeer carrion abundance, both of which are expected to trigger predator functional and numerical responses, as well as for annual variation in spring phenology. 3. Goose reproductive success fluctuated in synchrony with the rodent cycle and was negatively related to abundant carrion. When accounting for these aspects of food web dynamics, there was no evidence for an effect of red fox culling on reproductive success. There was, however, a tendency for fox culling to increase adult survival. 4. Our analysis suggests that goose performance in their breeding area is influenced by fluctuating offspring predation, mediated by mainly natural (rodents) and partly anthropogenic (semi-domestic reindeer) dynamic components of the food web. 5. Synthesis and applications. The effect of a decade-long red fox culling on goose reproductive success and survival is currently uncertain. This is despite the fact that predation drives reproductive success through changes in rodent and reindeer carrion abundance. New management actions may consist of regulation of reindeer herd sizes and/or removal of carcasses to reduce the subsidizing effect of reindeer carrion on mesopredators. Getting robust evidence regarding the impact of red fox culling on population recovery depends on continuing research to disentangle food web dynamics and efficiency of management actions.
Data from: Assessing the influence of temporal autocorrelations on the population dynamics of a disturbance specialist plant population in a random environment
Biological populations are strongly influenced by random variations in their environment, which are often autocorrelated in time. For disturbance specialist plant populations, the frequency and intensity of environmental stochasticity (via disturbances) can drive the qualitative nature of their population dynamics. In this article, we extended our earlier model to explore the effect of temporally autocorrelated disturbances on population persistence. In our earlier work, we only assumed disturbances were independent and identically distributed in time. We proved that the plant seed bank population converges in distribution, and we showed that the mean and variance in seed bank population size were both increasing functions of the autocorrelation coefficient for all parameter values considered, but the interplay between increasing population size and increasing variability caused interesting relationships between quasi-extinction probability and autocorrelation. For example, for populations with low seed survival, fecundity, and disturbance frequency, increasingly positive autocorrelated disturbances decreased quasi-extinction probability. Higher disturbance frequency coupled with low seed survival and fecundity caused a nonmontone relationship between autocorrelation and quasi-extinction, where increasingly positive autocorrelations eventually caused an increase in quasi-extinction probability. For higher seed survival, fecundity, and/or disturbance frequency, quasi-extinction probability was generally a monotonically increasing function of the autocorrelation coefficient.
Data from: A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada
Improving our understanding of species responses to environmental changes is an important contribution ecologists can make to facilitate effective management decisions. Novel synthetic approaches to assessing biodiversity and ecosystem integrity are needed, ideally including all species living in a community and the dynamics defining their ecological relationships. Here we present and apply an integrative approach that links high-throughput, multi-character taxonomy with community ecology. The overall purpose is to enable the coupling of biodiversity assessments with investigations into the nature of ecological interactions in a community-level data set. We collected 1,195 gastropods and crabs in British Columbia. First, the General mixed Yule-coalescent (GMYC) and the Poisson Tree Processes (PTP) methods for proposing primary species-hypotheses based on cox1 sequences were evaluated against an integrative taxonomic framework. We then used data on the geographic distribution of delineated species to test species co-occurrence patterns for non-randomness using community-wide and pairwise approaches. Results showed that PTP generally outperformed GMYC and thus constitutes a more effective option for producing species-hypotheses in community-level datasets. Non-random species co-occurrence patterns indicative of ecological relationships or habitat preferences were observed for grazer gastropods, whereas assemblages of opportunistic omnivorous gastropods and crabs appeared influenced by random processes. Species-pair associations were consistent with current ecological knowledge, thus suggesting that applying community assembly within a large taxonomical framework constitutes a valuable tool for assessing ecological interactions. Combining phylogenetic, morphological and co-occurrence data enabled an integrated view of communities, providing both a conceptual and pragmatic framework for biodiversity assessments and investigations into community dynamics.
Data from: A dynamic state model of migratory behavior and physiology to assess the consequences of environmental variation and anthropogenic disturbance on marine vertebrates
Integrating behavior and physiology is critical to formulating new hypotheses on the evolution of animal life-history strategies. Migratory capital breeders acquire most of the energy they need to sustain migration, gestation and lactation before parturition. Therefore, when predicting the impact of environmental variation on such species, a mechanistic understanding of the physiology of their migratory behavior is required. Using baleen whales as a model system, we developed a dynamic state variable model that captures the interplay among behavioral decisions, energy, reproductive needs and the environment. We applied the framework to blue whales (Balaenoptera musculus) in the Eastern North Pacific Ocean, and explored the effects of environmental and anthropogenic perturbations on female reproductive success. We demonstrate the emergence of migration to track prey resources, enabling us to quantify the trade-offs among capital breeding, body condition, and metabolic expenses. We predict that periodic climatic oscillations affect reproductive success less than unprecedented environmental changes do. The effect of localized, acute anthropogenic impacts depended on whales' behavioral response to the disturbance; chronic, but weaker, disturbances had little effect on reproductive success. Because we link behavior and vital rates by modeling individuals' energetic budgets, we provide a general framework to investigate the ecology of migration and assess the population consequences of disturbance, while identifying critical knowledge gaps.
Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags
<p><span>Microbiomes feature recurrent compositional structures under given environmental conditions. </span><span>However, these patterns may conceal diverse underlying population dynamics that require intra-strain resolution. Here, we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative PCR and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags and showed they can be differentiated with high precision. WISH-tags were introduced into model and non-model bacterial members of the mouse and plant microbiota. Intra-strain priority effects were tested using one species of isogenic barcoded bacteria in the murine gut and the <em>Arabidopsis</em> phyllosphere, both with and without microbiota context. We observed colonization resistance against late arriving strains of <em>Salmonella</em> typhimurium in the mouse gut, whereas the phyllosphere accommodated <em>Sphingomonas</em> latecomers in a proportional manner to their presence at the late inoculation timepoint. This demonstrates that WISH-tags are a resource for deciphering population dynamics underlying microbiome assembly across biological systems. </span></p>
Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts
<p>Attached file is the verification data for the submitted manuscript "Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts" .</p>
Supplementary material for "Comprehensive framework for dynamic energy assessment of building systems using IFC graphs and Modelica"
<p>The provided files include the following:</p> <ul> <li>The IFC model of the demo building used in Section 2.</li> <li>The parsed space boundaries graph.</li> <li>The resulting fragmented space boundaries graph.</li> </ul>
Collaboration for conservation: assessing country-wide carnivore occupancy dynamics from sparse data
<p><strong>Aim:</strong> Assessing the distribution and persistence of species across their range is a crucial component of wildlife conservation. It demands data at adequate spatial scales and over extended periods of time, which may only be obtained through collaborative efforts, and the development of methods that integrate heterogeneous datasets. We aimed to combine existing data on large carnivores to evaluate population dynamics and improve knowledge on their distribution nationwide.</p> <p><strong>Location:</strong> Botswana</p> <p><strong>Methods:</strong> Between 2010 – 2016, we collated data on African wild dog, cheetah, leopard, brown and spotted hyaena, and lion gathered with different survey methods by independent researchers across Botswana. We used a multi-species, multi-method dynamic occupancy model to analyse factors influencing occupancy, persistence, and colonisation, while accounting for imperfect detection. Lastly, we used the gained knowledge to predict the probability of occurrence of each species countrywide.</p> <p><strong>Results:</strong> Wildlife areas and communal rangelands had similar occupancy probabilities for most species. Large carnivore occupancy was low in commercial farming areas and where livestock density was high, except for brown hyaena. Lion occupancy was negatively associated with human density; lion and spotted hyena occupancy was high where rainfall was high, while the opposite applied to brown hyaena. Lion and leopard occupancy remained constant countrywide over the study period. African wild dog and cheetah occupancy declined over time in the south and north, respectively, whereas both hyaena species expanded their ranges. Countrywide predictions identified the highest occupancy for leopards and lowest for the two hyaena species.</p> <p><strong>Main Conclusions:</strong> We highlight the necessity of data sharing and propose a generalisable analytical method that addresses the challenges of heterogeneous data common in ecology. Our approach, which enables a comprehensive multi-species assessment at large spatial and temporal scales, supports the development of data-driven conservation guidelines and the implementation of evidence-based management strategies nationally and internationally.</p>
Raw data on dynamic light scattering assessment of small cellular particles isolated from conditioned culture media of Dunaliella tertiolecta and Phaeodactylum tricornutum. Effect of Triton X-100 and temperature
<p>Raw data on dynamic light scattering assessment of small cellular particles isolated from conditioned culture media of microalgae <em>Dunaliella tertiolecta</em> (<em>D. tertiolecta</em>)<em> </em>and <em>Phaeodactylum tricurnutum</em> (<em>P. tricornutum</em>)<em> </em>by dynamic light scattering are presented. The project contains spreadsheet files with the measured dependencies of g2 function on time. We collected several g2 functions for each setting (3 for <em>D. tertiolecta</em> samples, 5 for <em>D. tertiolecta</em> with added TX100, 3 for <em>P. tricornutum</em> samples, 3 for <em>P. tricornutum</em> with added TX100). Curves were analyzed independently and compared with the respective averaged curve fitted by the inverse Laplace transform program CONTIN (freely available at: <a href="http://s-provencher.com/index.shtml">http://s-provencher.com/index.shtml</a>, the code was accessed 25. 1. 2011). The correlation curves were fitted with up to 50 exponents.</p> <p>For analysis of stability of small cellular particles with respect to temperature change, we have overall reports for each microalgae type and reports on the size distribution function, data for the g2 function and dependence of scattered light intensity on time for each temperature measured. There were 14 temperatures chosen for each type of microalgae. The files are marked with respective temperatures.</p> <p>The samples were prepared as described below:</p> <p><strong>Cultivation of the algae:</strong> Cultures of <em>D. tertiolecta</em> CCAP 19/22 and <em>P. tricornutum</em> CCAP 1052/1A from the Culture Collection of Algae and Protozoa (CCAP) of SAMS (Oban, Scotland) were grown in artificial seawater (Reef Crystals, Aquarium Systems, France). 22 g of salt was dissolved in one litre of distilled water, sterile filtered (0.2-micron cellulose filters, ref. 11107-47-CAN, Sartorius Stedim Biotech GmbH, Germany), autoclaved, and supplemented with Guillard’s (F/2) Marine Water Enrichment Solution (ref. G0154, Sigma Aldrich, USA). Cultures were grown in a respirometer (Echo, Slovenia) in 0.5-L borosilicate bottles, at 20 °C and 20 % illumination (approximately 250 μmol/m2s) with a 14-hour light / 10-hour dark cycle, with aeration of 0.2 L/min.</p> <p><strong>Isolation of small cellular nanoparticles:</strong> Small cellular particles were isolated by differential centrifugation, using a protocol widely used for the isolation of extracellular vesicles (Théry C, Amigorena S, Raposo G, Clayton A. Isolation and Characterization of Exosomes from Cell Culture Supernatants and Biological Fluids. Current Protocols in Cell Biology. 2006;30(1). doi:10.1002/0471143030.cb0322s30). Microalgal cells were removed by low-speed centrifugation (300 g, 10 min, 4°C, centrifuge Centric 260R with rotor RA 6/50 (Domel, Slovenia)), using 50 mL conical centrifuge tubes (ref. S.078.02.008.050, Isolab Laborgeräte GmbH, Germany); and 2000 g, 10 min, 4°C (Centric 400R centrifuge with rotor RS4/100 (Domel, Slovenia)), using 15 mL conical centrifuge tubes (ref. S.078.02.001.050, Isolab Laborgeräte GmbH, Germany). Each step was repeated twice. Then, the cell-depleted medium was centrifuged twice at 10 000g and 4°C for 30 min (Beckman L8-70M ultracentrifuge, rotor SW55Ti (Beckman Coulter, USA)), using thin-wall polypropylene centrifuge tubes (ref. 326819, Beckman Coulter, USA) to remove larger cell debris. Finally, small cellular particles were pelleted by centrifugation at 118 000 g and 4°C, for 70 min in the same type of ultracentrifuge and ultracentrifuge tubes. The isolate obtained from about 30 mL of conditioned media was not visible to the eye.</p> <p>For treatment with Triton X-100, the sample was incubated with Triton X-100 at concentration of 0.1%.</p> <p><strong>Dynamic light scattering (DLS): </strong>The average hydrodynamic radius (<em>R</em><sub>h</sub>) of NPs and the average intensity of scattered light (<em>I</em>) were assessed for characterization of small cellular particles by DLS. The value of <em>I</em> was interpreted as a measure of small cellular particles concentration (in the case of preserved particle size distribution) or as a topological change (in the case of altered particle size distribution)(Paterna A, Rao E, Adamo G, et al. Isolation of Extracellular Vesicles From Microalgae: A Renewable and Scalable Bioprocess. <em>Front Bioeng Biotechnol</em>. 2022;10:836747. doi:10.3389/fbioe.2022.836747; Brown W, ed. <em>Dynamic Light Scattering: The Method and Some Applications</em>. Clarendon Press ; Oxford University Press; 1993). For analysis of the samples we used Instrument 3D-DLS-SLS cross-correlation spectrometer from LS Instruments GmbH (Fribourg, Switzerla nd) with a 100 mW DPSS laser (Cobolt Flamenco, Cobolt AB, Sweden) having a wavelength λ<sub>0</sub> = 660 nm. Before measurements, samples were equilibrated in a decalin bath at 25 °C for 15 min. The scattered light was measured at an angle <em>θ</em> = 90° for 120 s. The correlation functions and integral time-averaged intensities <em>I</em>(<em>θ</em>)≡ <em>I</em>(<em>q</em>) (where <em>q</em> is the scattering vector, defined as <em>q</em> =(4π<em>n</em><sub>0</sub>/λ<sub>0</sub>)sin(<em>θ</em>/2), with <em>n</em><sub>0</sub> the refractive index of the medium, in our case estimated by the corresponding value for water, i.e. <em>n</em><sub>0</sub> = 1.33 at 25°C), were recorded simultaneously. The <em>R</em><sub>h</sub> values of small cellular particles were obtained from the diffusion coefficients (<em>D</em>) that were assessed from the correlation function of the scattered electric field (<em>g</em><sub>1</sub>(<em>t</em>)). The <em>g</em><sub>1</sub>(<em>t</em>) function was calculated from the measured correlation function of the scattered light intensity <em>g</em><sub>2</sub>(<em>t</em>) by applying Siegert’s relation (Schärtl W. <em>Light Scattering from Polymer Solutions and Nanoparticle Dispersions</em>. Springer; 2007; Shurer CR, Kuo JCH, Roberts LM, et al. Physical Principles of Membrane Shape Regulation by the Glycocalyx. <em>Cell</em>. 2019;177(7):1757-1770.e21. doi:10.1016/j.cell.2019.04.017).</p> <p>To convert <em>D</em> to <em>R</em><sub>h</sub>, the Stokes-Einstein equation was used (<em>R</em><sub>h</sub> = <em>kT</em>6π<em>ηD</em>, where <em>k</em> is the Boltzmann constant, <em>T</em> is the absolute temperature, and <em>η</em> is the viscosity of the medium in which the particles diffuse). It was assumed that particles have a spherical shape. The viscosity of the medium was not known. We approximated the viscosity value to that of of water at 25°C.To test the effect of Triton X-100 on the samples, 0.1% (V/V) of Triton X-100 was added to the sample before the measurement. The change in <em>R</em><sub>h</sub> distribution and the change of scattered light intensity (Δ<em>I = I</em><sub>sample </sub><em>- I</em><sub>sample<em>+</em>0.1%.TX100</sub>) was determined.</p> <p>The analysis was made with an in-house created software based on the inverse Laplace transform program CONTIN (freely available at: <a href="http://s-provencher.com/index.shtml">http://s-provencher.com/index.shtml</a>, the code was accessed 25. 1. 2011). We collected several intensity correlation functions for each setting. Curves were analyzed independently and compared with the averaged curve. The correlation curves were fitted with up to 50 exponents.</p> <p>To test the effect of Triton X-100 on NPs, 0.1% (V/V) of Triton X-100 was added to the sample before the measurement. The change in <em>R</em><sub>h</sub> distribution and the change of scattered light intensity (Δ<em>I = I</em><sub>sample </sub><em>- I</em><sub>sample<em>+</em>0.1%.TritonX-100</sub>) was determined.</p> <p>Thermal stability analysis was performed using the LitesizerTM 500 instrument (Anton Paar GmbH). Samples were heated from 15 °C to 80 °C in 5 °C steps. When the target temperature was reached, the samples were equilibrated for another 5 minutes before 10 measurements of 20 s duration were performed. The size distributions were determined from the mean correlation function using the Anton Paar Kalliope Professional; Version 2.16.0. (Anton Paar GmbH), <a href="https://www.anton-paar.com/corp-en/products/details/software-for-particle-analysis-kalliopetm/">https://www.anton-paar.com/corp-en/products/details/software-for-particle-analysis-kalliopetm/</a>, applying the CONTIN approach. A new version of Kalliope<sup>TM </sup>4.12.0 <a href="https://www.kalliope.com/2021/05/03/versione-firmware-4-12-0/?lang=en">https://www.kalliope.com/2021/05/03/versione-firmware-4-12-0/?lang=en</a> is freely available online.</p>
Assessing Mammalian population dynamics in Mizoram
Open the record for dataset details and reuse information.
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.