Find research datasets worth reusing

opencc-by-4.0Oct 2022View details →

REMODEL. WP4. Vision-Based Perception. T4-2. Dynamic environment reconstruction. Data related to a paper published on IEEE Access (2022)

Dataset with evaluation results of the paper "Point Cloud Registration With Object-Centric Alignment"; DOI: 10.1109/access.2022.3191352

opencc-by-4.0May 2020View details →

REMODEL. WP4. Vision-Based Perception. T4-2. Dynamic environment reconstruction. Data related to a paper published on RA-L (2020)

Dataset with evaluation results of the paper "Extrinsic Calibration of an Eye-In-Hand 2D LiDAR Sensor in Unstructured Environments Using ICP" 10.1109/LRA.2020.2965878

opencc-zeroOct 2022View details →

Data from: Pathways to global-change effects on biodiversity: New opportunities for dynamically forecasting demography and species interactions

In structured populations, persistence under environmental change is threatened when abiotic factors simultaneously negatively affect survival and reproduction of several life-cycle stages. Such effects can then be exacerbated when species interactions generate reciprocal feedbacks between the demographic rates of the different species. Despite the importance of such demographic feedbacks, forecasts that account for them are severely limited as individual-based data on interacting species are perceived to be essential for such mechanistic forecasting - but are rarely available. This dataset is the input to showcase a state-of-the-art Bayesian method to infer and project stage-specific survival and reproduction from abundance data for several interacting species in a Mediterranean shrub community.

opencc-zeroOct 2022View details →

Data from: Spatial consistency in drivers of population dynamics of a declining migratory bird

1. Many migratory species are in decline across their geographical ranges. Single-population studies can provide important insights into drivers at a local scale, but effective conservation requires multi-population perspectives. This is challenging because relevant data are often hard to consolidate, and state-of-the-art analytical tools are typically tailored to specific datasets. 2. We capitalized on a recent data harmonization initiative (SPI-Birds) and linked it to a generalized modeling framework to identify the demographic and environmental drivers of large-scale population decline in migratory pied flycatchers (Ficedula hypoleuca) breeding across Britain. 3. We implemented a generalized integrated population model (IPM) to estimate age-specific vital rates, including their dependency on environmental conditions, and total and breeding population size of pied flycatchers using long-term (34–64 years) monitoring data from seven locations representative of the British breeding range. We then quantified the relative contributions of different vital rates and population structures to changes in short- and long-term population growth rates using transient life table response experiments (LTREs). 4. Substantial covariation in population sizes across breeding locations suggested that change was the result of large-scale drivers. This was supported by LTRE analyses, which attributed past changes in short-term population growth rates and long-term population trends primarily to variation in annual survival and dispersal dynamics, which largely act during migration and/or non-breeding season. Contributions of variation in local reproductive parameters were small in comparison, despite sensitivity to local temperature and rainfall within the breeding period. 5. We show that both short- and longer-term population changes of British-breeding pied flycatchers are likely linked to factors acting during migration and in non-breeding areas, where future research should be prioritized. We illustrate the potential of multi-population analyses for informing management at (inter)national scales and highlight the importance of data standardization, generalized and accessible analytical tools, and reproducible workflows to achieve them.

opencc-by-4.0Aug 2022View details →

Sampling Rare Event Energy Landscapes via Birth-Death Augmented Dynamics

Archive with data supporting the paper "Sampling Rare Event Energy Landscapes via Birth-Death Augmented Dynamics" and the related PhD thesis by B. Pampel

opencc-zeroDec 2021View details →

Data from: Fertiliser application modulates the impact of interannual climate fluctuations and plant-to-plant interactions on the dynamics of annual species in a Mediterranean grassland

Background: Climate and land-use changes, which include the application of various types of organic and inorganic fertilisers, have been reducing the species diversity of Mediterranean grasslands and threatening their conservation. Annual plants are one of the most diverse functional groups of species in these grasslands, despite suffering competitive pressure from perennial herbaceous and woody species, and they are essential for ecosystem functioning and stability. Aims: To quantify how fertilisation modulates the impact of plant-to-plant interactions and climate fluctuations on the dynamics of annuals in Mediterranean grasslands. We hypothesised that the application of sewage sludge would increase competition between functional groups, reducing the abundance of annuals in the long-term, but would buffer the negative impacts of drought on the year-to-year fluctuation of the diversity of annuals. Methods: In a semi-natural species-rich Mediterranean grassland in northern Spain, we analysed the changes in the taxonomical and functional composition and diversity of annuals over 14 years in response to variations in the abundance of perennial herbaceous and woody species, climate fluctuations, and fertilisation with sewage sludge. We quantified separately the patterns of year-to-year fluctuations and long-term trends. Results: The frequency and diversity of annuals decreased with a higher abundance of perennial herbaceous species, drought in June, and cold winters. The addition of sewage sludge decreased the abundance of annuals in the long-term, seemed to promote competition between annuals and other functional groups at an interannual scale, and mitigated the negative effects of drought and cold. Conclusions: Fertilisation influences differently the temporal response of annuals to climate fluctuations and plant-to-plant interactions.

Optimal Dynamic Service Restoration of Distribution Networks Considering Energy Storage System Data

The power distribution system presented is composed with 53 node and 61 branches and can be employed in multi-time service restoration problem, islading operation and energy storage system optimal operation. The system was designed based on a 53 node system (available <a href="https://ieee-dataport.org/documents/optimal-service-restoration-active-distribution-networks-considering-microgrid-formation">here</a>). The dataset was modified to include 6 photovoltaic generation, 3 energy storage system and time-changing demand load nodes.

opencc-zeroDec 2021View details →

Data for: Dynamic coastal pelagic habitat drives rapid changes in growth and condition of juvenile sockeye salmon (Oncorhynchus nerka) during early marine migration

Migrating marine taxa encounter diverse habitats that differ environmentally and in foraging conditions over a range of spatial scales. We examined body (RNA/DNA, length-weight residuals) and nutritional (fatty acid composition) condition of juvenile sockeye salmon (Oncorhynchus nerka) in British Columbia while migrating through oceanographically variable waters. Fish were sampled in the stratified northern Strait of Georgia (NSoG); the highly mixed Johnstone Strait (JS); and the transitional zone of Queen Charlotte Strait (QCS). In 2015, body and nutritional condition were high in the NSoG but rapidly declined to reach the lowest levels in JS where prey availability was low, before showing signs of compensatory growth in QCS. In 2016, juvenile salmon had a significantly lower condition in the NSoG than in 2015, although zooplankton biomass was similar, condition remained low in JS, and no compensatory growth was observed in QCS. We provide evidence that differences in juvenile salmon condition between the two years were due to changes in the food quality available to juvenile fish. We propose that existing hypotheses about fish survival need to be extended to incorporate food quality in addition to quantity to understand changes in fish condition and survival between years.

Annual Dynamic Ice Thickness Change Rate, Greenland 1993-2017

This data set includes annual dynamic ice sheet thickness change rate time series reconstructed at 16,136 locations on the Greenland Ice Sheet. Time series were derived from laser altimetry data collected from 1993 to 2017 by using the Surface Elevation Reconstruction and Change (SERAC) approach (Schenk and Csatho, 2012). Ice thickness changes caused by surface processes were modeled by RACMO 2.3p2 (Noël et al., 2019) and subtracted from the total elevation change to obtain ice thickness changes due to ice dynamics. Annual rates were computed from polynomial fit (max. 3rd, order) or ALPS (Shekhar et al., 2021).   Parameters: <table> <thead> <tr> <th scope="col">Name</th> <th scope="col">Description</th> </tr> </thead> <tbody> <tr> <td>PointID</td> <td>Unique ID assign to location</td> </tr> <tr> <td>X</td> <td>X coordinate of time series given in meter, UTM projection (zone N24, EPSG: 32624)</td> </tr> <tr> <td>Y</td> <td>Y coordinate of time series given in meter, UTM projection (zone N24, EPSG: 32624)</td> </tr> <tr> <td>ObsInt</td> <td>Length of time series (month, from first to last observational epoch used)</td> </tr> <tr> <td>Hrange_flag</td> <td>Set according to the range of thickness change (from original time series before outlier removal).  Hrange_flag=0, range of thickness change less than 5 m, annual rates computed with polynomial modeling (max 3rd order/cubic), Hrange_flag=1, range of thickness change more than 5 m, annual rates computed with ALPS.</td> </tr> <tr> <td>POL9394</td> <td>Annual rate from polynomial interpretation for balance year 1993/94 (September 1 1993 – August 31, 1994), all years until balance year 2016/17.</td> </tr> <tr> <td>ALPS9394</td> <td>Annual rate from ALPS modeling for balance year 1993/94 (September 1 1993 – August 31, 1994), all years until balance year 2015/16.</td> </tr> </tbody> </table>   Laser altimetry used: <ul> <li>ATM/ATM: ATM airborne laser altimetry (Studinger et al., 2018)</li> <li>LVIS/LVIS: LVIS airborne laser altimetry (Blair and Hofton, 2019)</li> <li>ICESat/L2A-L2F: ICESat satellite laser altimetry (Zwally et al., 2014)</li> </ul>   References: <ol> <li>Blair, J. B. and Hofton, M. (2019). IceBridge LVIS L2 Geolocated Surface Elevation Product, Version 2 [Greenland]. Boulder, Colorado USA. NASA National Snow and Ice Data Center Distributed Active Archive Center. https://doi.org/10.5067/E9E9QSRNLYTK. Date Accessed 11-08-2022.</li> <li>Noël, B. P. Y., van de Berg, W. J., Lharmitte, S., and van den Broeke, M. R. 2019. Rapid Ablation Zone Expansion Amplifies North Greenland Mass Loss, Science Advances, 5(9), <a href="https://doi.org/10.1126/sciadv.aaw0123">DOI: 10.1126/sciadv.aaw0123</a></li> <li>Schenk, T. and Csatho, B. (2012). A New Methodology for Detecting Ice Sheet Surface Elevation Changes From Laser Altimetry Data. IEEE Transactions on Geoscience and Remote Sensing, 50, 3302–3316.</li> <li>Shekhar, P., Csathó, B., Schenk, T., Roberts, C. & Patra, A. K. (2021). ALPS: A Unified Framework for Modeling Time Series of Land Ice Changes. IEEE Transactions on Geoscience and Remote Sensing, 59, 6466–6481.</li> <li>Studinger, M. (2018). IceBridge ATM L2 Icessn Elevation, Slope, and Roughness, Version 2 [Greenland]. Boulder, Colorado USA. NASA National Snow and Ice Data Center Distributed Active Archive Center. https://doi.org/10.5067/CPRXXK3F39RV. Date Accessed 11-08-2022.</li> <li>Zwally, H. J., Schutz, R., Dimarzio, J.., and Hancock. D. (2014). GLAS/ICESat L1B Global Elevation Data (HDF5), Version 34 [Greenland]. Boulder, Colorado USA. NASA National Snow and Ice Data Center Distributed Active Archive Center. https://doi.org/10.5067/ICESAT/GLAS/DATA109. Date Accessed 11-08-2022.</li> </ol>

dataset for bioRxiv preprint titled 'Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease'

This data supports the Figures in the preprint titled Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease working abstract The HIV-1 protease is one of several common key targets of combination drug therapies for human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS).  During the progression of the disease, some individual patients acquire -drug resistance due to mutational hotspots on the viral proteins targeted by combination drug therapies.  It has recently been discovered that drug-resistant mutations accumulate on the ‘flap region’ of the HIV-1 protease,  which is a critical dynamic region involved in non-specific polypeptide binding  during invasion and infection of the host cell.  In this study, we utilize machine learning assisted comparative molecular dynamics, conducted at single amino acid site resolution, to investigate the dynamic changes that occur during functional dimerization and polypeptide binding of the main protease. We use a multi-agent machine learning model to identify conserved dynamics of the HIV-1 main protease that are preserved across simian and feline protease orthologs (SIV and FIV).  We also investigate changes in dynamics due to common drug-resistant mutations in many patients. We find that a key functional site in the flap region, a solvent-exposed isoleucine (ILE50) and surrounding sites that control flap dynamics is often targeted by drug-resistance mutations, likely leading to malfunctional molecular dynamics affecting the overall flexibility of the flap region. We conclude that better long term patient outcomes may be achieved by designing drugs that target protease regions which are less dependent upon single sites with large functional binding effects.

opencc-by-4.0Feb 2021View details →

Tailoring the optical and dynamic properties of iminothioindoxyl photoswitches through acidochromism

Multi-responsive functional molecules are key for obtaining user-defined control of the properties and functions of chemical and biological systems. In this respect, pH-responsive photochromes, whose switching can be directed with light and acid–base equilibria, have emerged as highly attractive molecular units. The challenge in their design comes from the need to accommodate application-defined boundary conditions for both light- and protonation-responsivity. Here we combine time-resolved spectroscopic studies, on time scales ranging from femtoseconds to seconds, with density functional theory (DFT) calculations to elucidate and apply the acidochromism of a recently designed iminothioindoxyl (ITI) photoswitch. We show that protonation of the thermally stable Z isomer leads to a strong batochromically-shifted absorption band, allowing for fast isomerization to the metastable E isomer with light in the 500–600 nm region. Theoretical studies of the reaction mechanism reveal the crucial role of the acid–base equilibrium which controls the populations of the protonated and neutral forms of the E isomer. Since the former is thermally stable, while the latter re-isomerizes on a millisecond time scale, we are able to modulate the half-life of ITIs over three orders of magnitude by shifting this equilibrium. Finally, stable bidirectional switching of protonated ITI with green and red light is demonstrated with a half-life in the range of tens of seconds. Altogether, we designed a new type of multi-responsive molecular switch in which protonation red-shifts the activation wavelength by over 100 nm and enables efficient tuning of the half-life in the millisecond–second range.   Article information: <a href="https://doi.org/10.1039/D0SC07000A">https://doi.org/10.1039/D0SC07000A</a>

The supplemental material for "The small-amplitude dynamics of spontaneous tropical cyclogenesis"

This is the supplemental material for the manuscript "The small-amplitude dynamics of spontaneous tropical cyclogenesis," submitted to Journal of the Atmospheric Sciences.

Data on: Dynamics of short-term ecosystem carbon fluxes induced by precipitation events in a semiarid grassland

Data correspond to mean daytime net ecosystem carbon exchange (NEE) obtained through the eddy covariance method along six years from 2011 to 2016 (For more details of data see  <a href="https://doi.org/10.1029/2018JG004799">https://doi.org/10.1029/2018JG004799</a>). Database contain changes of daytime NEE after a precipitation event (difference between previous day and the day after a precipitation event). Moreover, environmental and soil variables are included: 1) daily mean, previous and the change of soil water content at 2.5 and 15 cm depth, 2) previous NEE rate, 3) change of photosynthetic photon flux density, and 4) air temperature. Data was used to test the effect of environmental and soil variables on the daytime net ecosystem exchange. We was interested in short-term effects, i.e. the priming effect or the Birch effect. Manuscript where this database was used is under review.

opencc-zeroNov 2022View details →

Post-weaning survival in kangaroos is high and constant until senescence: Implications for population dynamics

Large herbivores typically have consistently high prime-aged adult survival and lower, more variable, juvenile and senescent survival. Many kangaroo populations undergo greater fluctuations in density than other large herbivores, but age- and sex-specific survival of kangaroos and their response to environmental variation remain poorly estimated. We used long-term capture-mark-recapture data on 920 individuals to investigate the survival component of eastern grey kangaroo (Macropus giganteus) population dynamics. Forage availability and population density were monitored quarterly and included as predictors of survival in Bayesian Cormack-Jolly-Seber models. Annual survival probabilities were estimated for 5 age classes: 0 years (juveniles), 1–2 years (sub-adults), 3–6 years (prime-aged adults), 7–9 years (pre-senescent adults), and ≥10 years (senescent adults). Survival of juveniles varied widely during our 12-year study, ranging from 0.07–0.90 for females and 0.05–0.92 for males. Sub-adult survival was 0.80–0.93 for females and 0.75–0.85 for males, while that of prime-aged adults was ≥0.94 for females and ≥0.83 for males, despite large fluctuations in forage and density. The survival of pre-senescent adults spanned 0.86–0.93 for females and 0.60–0.86 for males. Senescent survival was variable, at 0.49–0.90 for females and 0.49–0.80 for males. Male survival was significantly lower than female survival in prime-aged and pre-senescent adults, but not in other age classes. Although most models supported by WAIC selection included one or a combination of environmental covariates, none of these individual covariates had a discernable effect on survival. Temporal variability in overall survival was mostly due to changes in survival of juvenile and senescent kangaroos. Kangaroo survival patterns are similar to those of ungulates, suggesting a strong role of sex-age structure on population dynamics.

opencc-zeroDec 2022View details →

Data for: Triose phosphate utilization stress during photosynthesis addressed with dynamic assimilation measurements

Oscillations in CO2 assimilation rate and associated fluorescence parameters have been observed alongside the triose phosphate utilization (TPU) limitation of photosynthesis for nearly 50 years. However, the mechanics of these oscillations are poorly understood. Here we utilize the recently developed Dynamic Assimilation Techniques (DAT) for measuring the rate of CO2 assimilation to increase our understanding of what physiological condition is required to cause oscillations. We found that TPU limiting conditions alone were insufficient, and that plants must enter TPU limitation quickly to cause oscillations. We found that ramps of CO2 caused oscillations proportional in strength to the speed of the ramp, and that ramps induce oscillations with worse outcomes than oscillations induced by step change of CO2 concentration. An initial overshoot is caused due to a temporary excess of available phosphate. During the overshoot, the plant out-performs steady state TPU and ribulose 1,5-bisphosphate regeneration limitations of photosynthesis but cannot exceed the rubisco limitation. We performed additional optical measurements which support the role of photosystem I reduction and oscillations in availability of NADP+ and ATP in supporting oscillations.

opencc-by-4.0Sep 2022View details →

Dataset for Fast Li-ion Storage and Dynamics in TiO2 Nanoparticle Clusters Probed by Smart Scanning Electrochemical Cell Microscopy

This dataset provides the raw data to the manuscript  "Fast Li-ion Storage and Dynamics in TiO2 Nanoparticle Clusters Probed by Smart Scanning Electrochemical Cell Microscopy" published in Angewandte Chemie International Edition. Specifically, the following measurements are provided: <ul> <li>Powder XRD data for the commercial anatase TiO2.</li> <li>Cyclic voltammetry data from SECCM measurements.</li> <li>SEM images of the TiO2 nanoparticles after SECCM tip landing and electrochemical measurement.</li> </ul>

Simultaneous dynamic glucose-enhanced (DGE) MRI and fiber photometry measurements of glucose in the healthy mouse brain

This dataset was acquired for the DGE and fiber photometry study published in NeuroImage ( <a href="https://doi.org/10.1016/j.neuroimage.2022.119762">https://doi.org/10.1016/j.neuroimage.2022.119762</a>). Comprises of three datasets: DGE MRI, fiber photometry and two-photon microscopy.

opencc-zeroDec 2022View details →

Dynamic structure of motor cortical neuron co-activity carries behaviorally relevant information

(This is the dataset used in <a href="https://doi.org/10.1101/2022.05.18.492501" rel="noopener" title="Dynamic Structure Of Motor Cortical Neuron Co-Activity Carries Behaviorally Relevant Information">Dynamic Structure Of Motor Cortical Neuron Co-Activity Carries Behaviorally Relevant Information</a>, Abstract below) Skillful, voluntary movements are underpinned by computations performed by networks of interconnected neurons in the primary motor cortex (M1). Computations are reflected by patterns of co-activity between neurons. Using pairwise spike time statistics, co-activity can be summarized as a functional network (FN). Here, we show that the structure of FNs constructed from an instructed-delay reach task in non-human primates are behaviorally specific: low dimensional embedding and graph alignment scores show that FNs constructed from closer target reach directions are also closer in network space. Using short intervals across a trial we constructed temporal FNs and found that temporal FNs traverse a low-dimensional subspace in a reach-specific trajectory. Alignment scores show that FNs become separable and correspondingly decodable shortly after the instruction cue. Finally, we observe that reciprocal connections in FNs transiently decrease following the instruction cue consistent with the hypothesis that information external to the recorded population temporarily alters the structure of the network at this moment.

opencc-zeroDec 2022View details →

Stroke data from: Robust dynamic brain coactivation states estimated in individuals

A confluence of evidence indicates that brain functional connectivity (FC) is not static but rather dynamic. Capturing transient network interactions in the individual brain requires a technology that offers sufficient within-subject reliability. Here, we introduce an individualized network-based dynamics analysis technique and demonstrate that it is reliable in detecting subject-specific brain states during both resting state and a cognitively challenging language task. Moreover, we evaluated the extent to which brain states showed hemispheric asymmetries and how various phenotypic factors such as handedness and gender might influence network dynamics. We discovered a right-lateralized brain state that occurred more frequently in men than in women, and more frequently in right-handed versus left-handed individuals. Lastly, we demonstrated longitudinal brain state changes in 42 patients with subcortical stroke over 6 months. Taken together, this approach could quantify subject-specific dynamic brain states and has potential for use in both basic and clinical neuroscience research.