Find research datasets worth reusing

Data from: Low-dimensional spatio-temporal dynamics underlie cortex-wide neural activity

Cognition arises from the dynamic flow of neural activity through the brain. To capture these dynamics, we used mesoscale calcium imaging to record neural activity across the dorsal cortex of awake mice. We found that the large majority of variance in cortex-wide activity (~75%) could be explained by a limited set of ~14 'motifs' of neural activity. Each motif captured a unique spatio-temporal pattern of neural activity across the cortex. These motifs generalized across animals and were seen in multiple behavioral environments. Motif expression differed across behavioral states and specific motifs were engaged by sensory processing, suggesting the motifs reflect core cortical computations. Together, our results show that cortex-wide neural activity is highly dynamic, but that these dynamics are restricted to a low-dimensional set of motifs, potentially allowing for efficient control of behavior.

opencc-by-4.0Jun 2020View details →

Original data for: Deracemization of Au38 Clusters: Breaking the Equal Status and Dynamic Inversion of Enantiomers

Original data for Figures 2, 6, S1, S2, S3, S4, S5, S6, S7, S8, S9

opencc-by-4.0May 2020View details →

Ultrafast-Laser-induced precessional dynamics in antiferromagnetically coupled ferromagnetic thin films

Open data of "Ultrafast-Laser-induced precessional dynamics in antiferromagnetically coupled ferromagnetic thin films" published in Physical Review B, xx, yy (2020)

Trade-offs between biodiversity and agriculture are moving targets in dynamic landscapes

<ol> <li>Understanding how biodiversity responds to intensifying agriculture is critical to mitigating the trade-offs between them. These trade-offs are particularly strong in tropical and subtropical deforestation frontiers, yet it remains unclear how changing landscape context in such frontiers alters agriculture-biodiversity trade-offs.</li> <li>We focus on the Argentinean Chaco, a global deforestation hotspot, to explore how landscape context shapes trade-off curves between agricultural intensity and avian biodiversity. We use a space-for-time approach and integrate a large field dataset of bird communities (197 species, 234 survey plots), three agricultural intensity metrics (meat yield, energy yield and profit), and a range of environmental covariates in a hierarchical Bayesian occupancy framework.</li> <li>Woodland extent in the landscape consistently determines how individual bird species, and the bird community as a whole, respond to agricultural intensity. Many species switch in their fundamental response, from decreasing occupancy with increased agricultural intensity when woodland extent in the landscape is low (loser species), to increasing occupancy with increased agricultural intensity when woodland extent is high (winner species).</li> <li>This suggests that landscape context strongly mediates who wins and loses along agricultural intensity gradients. Likewise, where landscapes change, such as in deforestation frontiers, the very nature of the agriculture-biodiversity trade-offs can change as landscapes transformation progresses.</li> <li> Synthesis and applications. Schemes to mitigate agriculture-biodiversity trade-offs, such as land sparing or sharing, must consider landscape context. Strategies that are identified based on a snapshot of data risk failure in dynamic landscapes, particularly where agricultural expansion continues to reduce natural habitats. Rather than a single, fixed strategy, adaptive management of agriculture-biodiversity trade-offs is needed in such situations. Here we provide a toolset for considering changing landscape contexts when exploring such trade-offs. This can help to better align agriculture and biodiversity in tropical and subtropical deforestation <a>frontiers.</a> </li> </ol>

opencc-by-4.0Apr 2020View details →

Supplementary videos for "The mechanical origin of snow avalanche dynamics and flow regime transitions"

We are releasing the videos as the supplementary information for our submitted manuscript to The Cryosphere.  Movie 1. Velocity of the flows in the four typical flow regimes in Fig. 2(a). Frame rate is 24 FPS. Movie 2. Volumetric plastic strain of the flows in the four typical flow regimes in Fig. 2(a). Frame rate is 24 FPS. Movie 3. Velocity of the flow in transition from cold dense to warm shear regimes in Fig. 2(b). Frame rate is 24 FPS. Movie 4. Volumetric plastic strain of the flow in transition from cold dense to warm shear regimes in Fig. 2(b). Frame rate is 24 FPS.

Phonon calculations for "Uncovering design principles for amorphous-like heat conduction using two-channel lattice dynamics"

These are the phonon calculations for R. Hanus, J. George, M. Wood, A. Bonkowski, Y. Cheng, D. L. Abernathy, M. E. Manley, G. Hautier, G. J. Snyder, R. P. Hermann, “Uncovering design principles for amorphous-like heat conduction using two-channel lattice dynamics”, Materials Today Physics, 2021, In Press, <a href="https://doi.org/10.1016/j.mtphys.2021.100344">https://doi.org/10.1016/j.mtphys.2021.100344</a>

Supplement to "Dynamic model of photovoltaic module temperature as a function of atmospheric conditions"

This dataset contains data from two measurement campaigns in autumn 2018 and summer 2019 that were part of the BMWi project "MetPVNet", and serve as a supplement to the paper "Dynamic model of photovoltaic module temperature as a function of atmospheric conditions", published in the special edition of "Advances in Science and Research", the proceedings of the 19th EMS Annual Meeting: European Conference for Applied Meteorology and Climatology 2019. Data are resampled to one minute, and include: <ol> <li>PV module temperature</li> <li>Ambient temperature</li> <li>Plane-of-array irradiance</li> <li>Windspeed</li> <li>Atmospheric thermal emission</li> </ol> The data were used for the dynamic temperature model, as presented in the paper

Data from: Brain states govern the spatio-temporal dynamics of resting-state functional connectivity

Previously, using simultaneous resting-state functional magnetic resonance imaging (fMRI) and photometry-based neuronal calcium recordings in the anesthetized rat, we identified blood oxygenation level-dependent (BOLD) responses directly related to slow calcium waves, revealing a cortex-wide and spatially organized correlate of locally recorded neuronal activity (<a href="#_ENREF_68" title="Schwalm, 2017 #1">Schwalm et al., 2017</a>). Here, using the same techniques, we investigate two distinct cortical activity states: persistent activity, in which compartmentalized network dynamics were observed; and slow wave activity, dominated by a cortex-wide BOLD component, suggesting a strong functional coupling of inter-cortical activity. During slow wave activity we find a correlation between the occurring slow wave events and the strength of functional connectivity between different cortical areas. These findings suggest that down-up transitions of neuronal excitability can drive cortex-wide functional connectivity. This study provides further evidence that changes in functional connectivity are dependent on the brain's current state, directly linked to the generation of slow waves.

Data and code for: Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells

This dataset contains experimental data and custom R code for likelihood-based model-fitting associated with the manuscript "Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells". In particular, we estimate the per-cell establishment probability (i.e. probability that a single cell gives rise to a large population) of a resistant strain, in the presence of antibiotics at concentrations below its standard minimum inhibitory concentration. The experiments are conducted here with Pseudomonas aeruginosa, while the model and methods can be applied more generally.

opencc-zeroOct 2019View details →

Data from: Co-prescription network reveals social dynamics of opioid doctor shopping

This paper examines network prominence in a co-prescription network as an indicator of opioid doctor shopping (i.e., fraudulent solicitation of opioids from multiple prescribers). Using longitudinal data from a large commercially insured population, we construct a network where a tie between patients is weighted by the number of shared opioid prescribers. Given prior research suggesting that doctor shopping may be a social process, we hypothesize that active doctor shoppers will occupy central structural positions in this network. We show that network prominence, operationalized using PageRank, is associated with more opioid prescriptions, higher predicted risk for dangerous morphine dosage, opioid overdose, and opioid use disorder, controlling for number of prescribers and other variables. Moreover, as a patient's prominence increases over time, so does their risk for these outcomes, compared to their own average level of risk. Results highlight the importance of co-prescription networks in characterizing high-risk social dynamics.

Data from: Evolution of multiple sex-chromosomes associated with dynamic genome reshuffling in Leptidea wood-white butterflies

Sex chromosome systems tend to be highly conserved and knowledge about their evolution typically comes from macroevolutionary inferences. Rapidly evolving complex sex chromosome systems represent a rare opportunity to study the mechanisms of sex chromosome evolution at unprecedented resolution. Three cryptic species of wood white butterflies – Leptidea juvernica, L. sinapis, and L. reali – have each a unique set of multiple sex chromosomes with 3–4 W and 3–4 Z chromosomes. Using a transcriptome-based microarray for comparative genomic hybridization (array-CGH) and a library of bacterial artificial chromosome (BAC) clones, both developed in L. juvernica, we identified Z-linked Leptidea orthologs of Bombyx mori genes and mapped them by fluorescence in situ hybridization (FISH) with BAC probes on multiple Z chromosomes. In all three species, we determined synteny blocks of autosomal origin and reconstructed the evolution of multiple sex chromosomes. In addition, we identified W-homologs of Z-linked orthologs and characterized their molecular differentiation. Our results suggest that the multiple sex chromosome system evolved in a common ancestor of these three Leptidea species as a result of dynamic genome reshuffling through repeated rearrangements between the sex chromosomes and autosomes, including translocations and fissions. Thus, the sex chromosome turnover could not play a role in reproductive isolation between the Leptidea species studied. However, we suggest that subsequent species-specific rearrangements of multiple sex chromosomes, along with different rates of neo-W chromosome degeneration and significantly increased number of Z-linked genes could accelerate the accumulation of genetic incompatibilities between populations and promote their divergence resulting in speciation.

Data from: Mating dynamics and multiple paternity in a long-lived vertebrate

Multiple paternity is relatively common across diverse taxa; however, the drivers and implications related to paternal and maternal fitness are not well understood. Several hypotheses have been offered to explain the occurrence and frequency of multiple paternity. One set of hypotheses seeks to explain multiple paternity through direct and indirect benefits including increased genetic diversity or enhanced offspring fitness, whereas another set of hypotheses explains multiple paternity as a byproduct of sexual conflict and population-specific parameters such as density. Here we investigate mating system dynamics in a historically studied population of the American alligator (Alligator mississippiensis) in coastal South Carolina. We examine parentage in 151 nests across 6 years and find that 43% of nests were sired by multiple males and that male reproductive success is strongly influenced by male size. Whereas clutch size and hatchling size did not differ between singly sired and multiple sired nests, fertility rates were observed to be lower in multiply sired clutches. Our findings suggest that multiple paternity may exert cost in regard to female fitness, and raise the possibility that sexual conflict might influence the frequency of multiple paternity in wild alligator populations.

Data from: Plant community dynamics and carbon sequestration in Sphagnum-dominated peatlands in the era of global change

Aim: Hydroclimatic shift and anthropogenic-driven nitrogen deposition are major outcomes of global change that could compromise the functioning of many peatlands as a carbon sink. For Sphagnum-dominated peatlands, an emerging hypothesis is that the change could be triggered by shifts in competitive dominance among plant functional groups, specifically from the currently predominant decay-resistant Sphagnum to the more decomposable vascular plants. However, the relationship between Sphagnum and vascular plant occurrence is notably complex and also includes facilitative interactions that are crucial to the productivity of Sphagnum and therefore carbon sequestration. Location: Global Taxa: Northern peatlands—Sphagnum moss and vascular plants Methods: We use a conceptual review to examine underlying mechanisms for the competitive exclusion hypothesis and the nature of facilitative interactions between Sphagnum and vascular plants under the potential global change conditions. We complement the review with an empirical study of peatlands with contrasting hydrology to provide some critical insights into the potential effects of change in plant communities on carbon sequestration. We also propose a conceptual model that presents probable combinations of global change factors and their implications for carbon sequestration. Results: Vegetation structure in Sphagnum-dominated peatland appears to be driven largely by hydrology, rather than competition among plant functional groups. The peat deposit also exerts some controls (e.g., nutrient immobilization) on biotic structure, thereby acting as resistance against an abrupt shift in plant communities. Main conclusions: Peatland controls that constrain vegetation shifts have developed over a millennial timescale in many peatlands, and the pace of climate change may not allow enough time for the establishment of those mechanisms in younger peatlands. Thus, the persistence of a given peatland as a carbon sink also likely depends on the successional stage of the peatland.

Supplemental Materials for "Formation of interstellar complex polycyclic aromatic hydrocarbons: Insights from molecular dynamics simulations of dehydrogenated benzene"

Supplemental Materials for the article entiled "Formation of interstellar complex polycyclic aromatic hydrocarbons: Insights from molecular dynamics simulations of dehydrogenated benzene" authored by M. Hanine et al. at Laboratory for Relativistic Astrophysics, Department of Physics, Guangxi University, 530004 Nanning, China. email: zw@gxu.edu.cn (Zhao Wang) SuppMater1.zip : Atomistic configurations of the formed PAH molecules (in 4.0 ns) at all studied temperatures are available in .xyz format. These .xyz files contain the atomic coordinates of the formed molecules by giving the total number of atoms that will be read on the first line; the comment text on the second; and the atomic number and three atomic Cartesian coordinates in the following lines. The name of the .xyz file consists of four parts separated by ``\_'' including the source molecule type, the temperature, the formation environment (with NP or in gas phase), and the molecular ID (among multiple molecules formed in a simulation). For instance, ``C6H2\_300K\_gas\_2.xyz'' stands for the 2nd molecule formed from C6H at 300K in the gas phase. Please read the 'readme.txt' file before using the data.   SuppMater2.pdf: A data file that contains the DFT-calculated optimized structures and their atomic coordinates.   SuppMater3.mp4: An animation demonstrating the formation process of PAHs on a carbon NP.

Data from: Metabarcoding on planktonic larval stages: an efficient approach for detecting and investigating life cycle dynamics of benthic aliens

High-throughput sequencing (HTS) technologies offer new promise to support surveillance programs targeting marine non-indigenous species (NIS). Metabarcoding might surpass traditional monitoring methods, for example through its ability to detect rare species, a key feature in early detection of NIS. Another interest of this approach is the identification of organisms difficult to identify based on morphology only (e.g., early developmental stages), making it relevant in the context of management programs. Because many marine benthic NIS have a bi-phasic bentho-pelagic life cycle, targeting their pelagic larval stages in zooplankton may allow early detection and assessment of their establishment and potential spread. We illustrate this approach with an analysis of bulk-DNA retrieved from a time-series of zooplankton samples collected over 22 months in one bay in Brittany (France). Using HTS of amplicons obtained with two markers (COI and 18S) and a metabarcoding approach, 12 NIS were identified and their temporal larval dynamics were monitored. Importantly, we chose to focus on a closed list of species, from four metazoan classes encompassing 52 NIS reported within the study area or nearby seas, with molecular references available or obtained locally for 42 of them. The use of a custom-designed database allowed the detection of three NIS otherwise not detected when using public databases. Interestingly, NIS known to have a short-lived larval stage were detected (e.g., the bryozoan Bugula neritina or the tunicate Corella eumyota). For two molluscs Ruditapes philippinarum and Crepidula fornicata, metabarcoding results were compared to those obtained using traditional methods (i.e., barcoding of individual larvae and morphology, respectively) to show the reliability of the approach in detecting and assessing the extent of their reproductive periods. Our results also revealed that the Pacific oyster Crassostrea gigas, a notorious invasive species, failed to reproduce in the study bay, showing that metabarcoding on larval stages also provides information regarding the establishment success (or failure) of NIS. While metabarcoding has its limitations and biases, this study demonstrates its effectiveness for surveillance of targeted NIS, notably to support management strategies like the European Marine Strategy Framework Directive (MSFD).

Data from: Morphology, performance and fluid dynamics of the crayfish escape response

Sexual selection can result in an exaggerated morphology that constrains locomotor performance. We studied the relationship between morphology and the tail-flip escape response in male and female rusty crayfish (Faxonius rusticus), a species in which males have enlarged claws (chelae). We found that females had wider abdomens and longer uropods (terminal appendage of the tail fan) than males, while males possessed deeper abdomens and larger chelae, relative to total length. Chelae size was negatively associated with escape velocity, whereas longer abdomens and uropods were positively associated with escape velocity. We found no sex-specific differences in maximum force generated during the tail flip, but uropod length was strongly, positively correlated with tail-flip force in males. Particle image velocimetry (PIV) revealed that the formation of a vortex, rather than the expulsion of fluid between two closing body surfaces, generates propulsion in rusty crayfish. PIV also revealed that the pleopods (ventral abdominal appendages) contribute to the momentum generated by the tail. To our knowledge, this is the first confirmation of vortex formation in a decapod crustacean.

Dynamic Load Balancing for Predictions of Storm Surge and Coastal Flooding-Model setup and source code

Source code and model setup/inputs for the paper titled "Dynamic Load Balancing for Predictions of Storm Surge and Coastal Flooding" article.  Simulations were conducted using a modified version of ADCIRC+DLB (ADCIRC + Dynamic Load Balancing) on unstructured triangular meshes. Contains: <ol> <li>Model input files. <ol> <li>ADCIRC model input files for the ideal channel setup and Hurricane Irene simulation (*.13, *.14, *.15)</li> </ol> </li> <li>Zipped archive of the ADCIRC code (adcirc-cg-DLB.zip) used to produce the simulations for the paper.</li> <li>Step-by-step compilation and usage instructions for ADCIRC+DLB.  <ol> <li>Installation.html </li> <li>Usage.html</li> </ol> </li> </ol>

opencc-by-4.0Aug 2020View details →

Holocene plant diversity dynamics shows a distinct biogeographical pattern in temperate Europe

Data for manuscript "Holocene plant diversity dynamics shows a distinct biogeographical pattern in temperate Europe" by Roleček J., Abraham V., Vild O., Svitavská Svobodová H., Jamrichová E., Plesková Z., Pokorný P. & Kune&scaron; P.  Data originate from 18 sites in Czech and Slovak Republic. Original data and further metadata are stored in <a href="https://botany.natur.cuni.cz/palycz/">Czech Quaternary Palynological Database</a>. Data presented here were adjusted by following procedure: Pollen counts of trees were adjusted (divided) by <a href="https://doi.pangaea.de/10.1594/PANGAEA.908862">mean pollen productivity for North Hemisphere</a> : Abies    6.88 Alnus    7.46 Betula    4.4 Carpinus betulus    4.52 Corylus    1.97 Fagus    1.96 Fraxinus excelsior-Typ    1.25 Juniperus    9.8 Picea    2.29 Pinus    10.47 Quercus    3.33 Tilia    1.17 Ulmus    7.32 and subsequently whole spectra were resampled for the same pollen sum (100 grains) in all depths and time windows (300 years). Resampling was done by function "spectra_to_target_sum" at <a href="https://github.com/vojtechabraham/pollen">https://github.com/vojtechabraham/pollen</a>. See repository <a href="https://github.com/vojtechabraham/HolDivTempEur">https://github.com/vojtechabraham/HolDivTempEur</a> for the analysis presented in the paper.

opencc-by-nc-4.0Aug 2020View details →

FUNCERT - Registration dynamics and course certification rates on a Massive Open Online Course (MOOC) platform

The FUNCERT data set describes 1 million course registration events collected over a 2-year period from the MOOC platform FUN (France Université Numérique, fun-mooc.fr). Each registration event is associated with a timestamp and an indication of whether a completion certificate was ultimately awarded. It was used in the referenced manuscript to model the impact of multiple course registrations on certificate rates. The data set is provided as a single file (FUNCERT.csv) with the following fields. Time (min) The time of the registration event reported in minutes elapsed since the beginning of data collection. The time stamp is reported as a relative time only, not an exact calendar date, to enhance anonymization. User ID A unique ID number for each user of the platform during this period. The number has been generated specifically for this data set and does not correspond to user ID numbers used within the FUN platform. Course ID Each of the 140 offered courses is assigned a unique and anonymous ID code. In some cases courses were offered multiple times within the data collection period. The same Course ID is used across multiple instances of the same course. Certificate A boolean variable set to 1 if the registration event is associated with a course completion certificate. Of 140 offered courses, 91 awarded certificates during the study period. Age User age in years at the time of registration. Field may be left blank if data was not provided. Gender User gender as selected from the options m and f. Field may be left blank if data was not provided.