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opencc-zeroJan 2022View details →

Cortico-subcortical β burst dynamics underlying movement cancellation in humans

Dominant neuroanatomical models hold that humans regulate their movements via loop-like cortico-subcortical networks, including the subthalamic nucleus (STN), thalamus, and sensorimotor cortices (SMC). Inhibitory commands across these networks are purportedly sent via transient, burst-like signals in the β frequency (15-29Hz). However, since human depth-recording studies are typically limited to one recording site, direct evidence for this proposition is hitherto lacking. Here, we present simultaneous multi-site depth-recordings from SMC and either STN or thalamus in humans performing the stop-signal task. In line with their purported function as inhibitory signals, subcortical β-bursts were increased on successful stop-trials and were followed within 50ms by increased β-bursting over SMC. Moreover, between-site comparisons (including in a patient with simultaneous recordings from all three sites) confirmed that β-bursts in STN precede thalamic β-bursts. This provides first empirical evidence for the role of β-bursts in conveying inhibitory commands along long-proposed cortico-subcortical networks underlying movement regulation in humans.

Grid-graph modeling of emergent neuromorphic dynamics and heterosynaptic plasticity in memristive nanonetworks - Dataset

This is the dataset of "Grid-graph modeling of emergent neuromorphic dynamics and heterosynaptic plasticity in memristive nanonetworks"

The observation of the dynamic sea level (DSL) is available from the AVISO

The observation of the DSL used for the publication about formulation of a new explicit tidal scheme in ocean general circulation model by Jin et al., currently under review for GMD journal. (See https://doi.org/10.5194/gmd-2021-441).

Atomistic spin dynamics simulations of iron and cobalt

Atomistic spin dynamics (ASD) simulations of ultrafast demagnetization in ferromagnetic iron and cobalt. The ASD simulations here are energy-conserving, which means that energy flow into and out of the spin system is considered. The dataset contains simulations at four different pump laser fluences for iron and six different fluences for cobalt. The excitation was assumed to be homogeneous throughout the simulated volume. The heat capacities and electron-phonon coupling parameters which were used in the ASD simulations are provided in the folder "heat capacities and G_ep". More information is available here: - https://arxiv.org/abs/2110.00525 - Zahn et al. Phys. Rev. Research 3, 023032 (2021) https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.3.023032

Reproducing nonlinear seismic response from in-situ soil dynamic parameters: application to the Delaney Park Downhole Array, Alaska

The zip file named 'seismic data at DPDA.zip' contains all the seismic data used in our study. The DEEPSOIL file named 'ground response analysis at DPDA.dp' contains the numerical models used in our study.

Data set for "Relaxation time asymmetry in stator dynamics of the bacterial flagellar motor"

Zipped file containing three python Dictionaries pertaining to the Science Advances publication "Relaxation time asymmetry in stator dynamics of the bacterial flagellar motor," authored by  Ruben Perez-Carrasco, María-José Franco-Oñate, Jean-Charles Walter, Jérôme Dorignac, Fred Geniet, John Palmeri, Andrea Parmeggiani, Nils-Ole Walliser, and Ashley L Nord.

opencc-zeroJan 2022View details →

Incorporating effects of age on energy dynamics predicts non-linear maternal allocation patterns in iteroparous animals

Iteroparous parents face a trade-off between allocating current resources to reproduction versus maximizing survival to produce further offspring. Optimal allocation varies across age, and follows a hump-shaped pattern across diverse taxa, including mammals, birds and invertebrates. This non-linear allocation pattern lacks a general theoretical explanation, potentially because most studies focus on offspring number rather than quality and do not incorporate uncertainty or age-dependence in energy intake or costs. Here, we develop a life history model of maternal allocation in iteroparous animals. We identify the optimal allocation strategy in response to stochasticity when energetic costs, feeding success, energy intake, and environmentally-driven mortality risk are age-dependent. As a case study, we use tsetse, a viviparous insect that produces one offspring per reproductive attempt and relies on an uncertain food supply of vertebrate blood. Diverse scenarios generate a hump-shaped allocation: when energetic costs and energy intake increase with age; and also when energy intake decreases, and energetic costs increase or decrease. Feeding success and mortality risk have little influence on age-dependence in allocation. We conclude that ubiquitous evidence for age-dependence in these influential traits can explain the prevalence of non-linear maternal allocation across diverse taxonomic groups.

Dynamic cone penetration tests conducted at the NBS site in OAL-Austria

Dynamic cone penetration tests conducted at the NBS site in OAL-Austria to infer the regolith depth and penetration resistance A light-weight CPT device was used, dropping a defined weight of 10kg from a defined height, while recording the number of strokes required for penetrating the soil material in vertical increments of 10 cm.

Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations

MD simulations used in the studies of the publication "Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations"

Dataset accompanying manuscript "Correlative imaging of spatio-angular dynamics of biological systems with multimodal instant polarization microscope"

Raw images and microscope calibration metadata for reconstruction of datasets presented in Fig. 1 and Fig. 3 of "Correlative imaging of spatio-angular dynamics of biological systems with multimodal instant polarization microscope". Notebooks demonstrating steps in the label-free and fluorescence anisotropy reconstruction pipelines can be found at https://github.com/mehta-lab/miPolScope.

opencc-zeroFeb 2022View details →

Data and scripts for: Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high-throughput phenotyping

Plant phenotyping under field conditions plays an important role in agricultural research. Efficient and accurate high-throughput phenotyping strategies enable a better connection between genotype and phenotype. Unmanned aerial vehicle-based high-throughput phenotyping platforms (UAV-HTPPs) provide novel opportunities for large-scale proximal measurement of plant traits with high efficiency, high resolution, and low cost. The objective of this study was to use time series normalized difference vegetation index (NDVI) extracted from UAV-based multispectral imagery to characterize its pattern across development and conduct genetic dissection of NDVI in a large maize population. The time series NDVI data from the multispectral sensor were obtained at 5 time points across the growing season for 1,752 diverse maize accessions with a UAV-HTPP. Cluster analysis of the acquired measurements classified 1,752 maize accessions into 2 groups with distinct NDVI developmental trends. To capture the dynamics underlying these static observations, penalized-splines (P-splines) model was used to obtain genotype-specific curve parameters. Genome-wide association study (GWAS) using static NDVI values and curve parameters as phenotypic traits detected signals significantly associated with the traits. Additionally, GWAS using the projected NDVI values from the P-splines models revealed the dynamic change of genetic effects, indicating the role of gene-environment interplay in controlling NDVI across the growing season. Our results demonstrated the utility of ultra-high spatial resolution multispectral imagery, as that acquired using a UAV-based remote sensing, for genetic dissection of NDVI.

Dataset: Tensor-network study of correlation-spreading dynamics in the two-dimensional Bose-Hubbard model

Dataset Tensor-network study of correlation-spreading dynamics in the two-dimensional Bose-Hubbard model Ryui Kaneko, Ippei Danshita

Nitrogen resorption dynamics and slow-fast strategies in 137 Arabidopsis thaliana genotypes

Leaf nitrogen resorption efficiency (R_efficiency, %) and the relative maximum resorption rate of nitrogen (R_rate_max_perN, mg d-1 mg-1) were estimated together with the flowering time (FT, days after germination) and specific leaf area (SLA, m2 kg-1) in 137 Arabidopsis thaliana accessions selected from the 1001 genomes project accession list. The dataset contains genotype means for every measured accession.

"Dynamics of Endothelial Engagement and Filopodia Formation in Complex 3D Microscaffolds" : Raw Data

Raw data of the paper "Dynamics of Endothelial Engagement and Filopodia Formation in Complex 3D Microscaffolds",   International Journal of Molecular Sciences, 2022. Abstract: The understanding of endothelium–extracellular matrix interactions during the initiation of new blood vessels is of great medical importance; however, the mechanobiological principles governing endothelial protrusive behaviours in 3D microtopographies remain imperfectly understood. In blood capillaries submitted to angiogenic factors (such as vascular endothelial growth factor, VEGF), endothelial cells can transiently transdifferentiate in filopodia-rich cells, named tip cells, from which angiogenesis processes are locally initiated. This protrusive state based on filopodia dynamics contrasts with the lamellipodia-based endothelial cell migration on 2D substrates. Using two-photon polymerization, we generated 3D microstructures triggering endothelial phenotypes evocative of tip cell behaviour. Hexagonal lattices on pillars (“open”), but not “closed” hexagonal lattices, induced engagement from the endothelial monolayer with the generation of numerous filopodia. The development of image analysis tools for filopodia tracking allowed to probe the influence of the microtopography (pore size, regular vs. elongated structures, role of the pillars) on orientations, engagement and filopodia dynamics, and to identify MLCK (myosin light-chain kinase) as a key player for filopodia-based protrusive mode. Importantly, these events occurred independently of VEGF treatment, suggesting that the observed phenotype was induced through microtopography. These microstructures are proposed as a model research tool for understanding endothelial cell behaviour in 3D fibrillary networks.

opencc-by-4.0Apr 2020View details →

Data from: Drought and recovery effects on belowground respiration dynamics and the partitioning of recent carbon in managed and abandoned grassland

The supply of soil respiration with recent photoassimilates is an important and fast pathway for respiratory loss of carbon (C). To date it is unknown how drought and land-use change interactively influence the dynamics of recent C in soil respired CO2. In an in situ common-garden experiment, we exposed soil-vegetation monoliths from a managed and a nearby abandoned mountain grassland to an experimental drought. Based on two 13CO2 pulse-labelling campaigns, we traced recently assimilated C in soil respiration during drought, rewetting and early recovery. Independent of grassland management, drought reduced the absolute allocation of recent C to soil respiration. Rewetting triggered a respiration pulse, which was strongly fueled by C assimilated during drought. In comparison to the managed grassland, the abandoned grassland partitioned more recent C to belowground respiration than to root C storage under ample water supply. Interestingly, this pattern was reversed under drought. We suggest that these different response patterns reflect strategies of the managed and the abandoned grassland to enhance their respective resilience to drought, by fostering their resistance and recovery, respectively. We conclude that while severe drought can override the effects of abandonment of grassland management on the respiratory dynamics of recent C, abandonment alters strategies of belowground assimilate investment, with consequences for soil-CO2 fluxes during drought and drought-recovery.

Long-term simulation of snow cover and its potential impacts on seasonal frost dynamics in croplands across southern Canada

In northern climes, accurate simulation of thermal and hydrological budgets for farmlands during overwintering conditions is crucial to both an accurate prediction of spring flooding and the successful management of nutrient losses. As snow cover influences soil freezing dynamics, it has been hypothesized that reduced snow cover due to warmer winters might increase the depth and duration of frozen soil conditions. Nonetheless, such impacts remain poorly understood and, given the difficulty in measuring the depth of frozen soil, no long-term field experiment has documented these potential effects. The present study was designed to test this hypothesis.  Drawing upon observed snow depth and soil temperature data collected from six research farms across Southern Canada over various time spans from 1989 to 2020, the Root Zone Water Quality Model, integrated with the Simultaneous Heat and Water model, was calibrated and validated. The potential influence of warmer winter on shifts in soil frost dynamics was evaluated by estimating the depth and duration of frozen soil for each farmland site under various RCP temperature scenarios using the RZ-SHAW model. Soil frozen depth in Eastern site increased with the increase of RCP temperature scenarios in some years, but decreased under the highest RCP temperature scenario. The monthly relationship between snow depth and soil frozen depth was determined through partial correlation analysis. Snow was most effective in alleviating soil freezing in the months of January and February, a period when snow cover depth was least affected by warming air temperatures. This paper suggests that Global warming induced-snow cover reduction would be site-specific and is more likely to occur in regions where energy lost through reduced snow cover would outweigh the energy gained through warmer air temperature.

Underlying data for IsoAligner: dynamic mapping of amino acidpositions across protein isoforms

The human isoform library (list_of_gene_objects_25th_july_final.txt) for the IsoAligner webtool is generated from these resources.

opencc-zeroMar 2022View details →

Environmental drivers of biseasonal anthrax outbreak dynamics in two multi-host savanna systems

Environmental factors are common forces driving infectious disease dynamics. We compared inter-annual and seasonal patterns of anthrax infections in two multi-host systems in southern Africa: Etosha National Park, Namibia, and Kruger National Park, South Africa. Using several decades of mortality data from each system, we assessed possible transmission mechanisms behind anthrax dynamics, examining 1) within- and between-species case correlations, and 2) associations between anthrax mortalities and environmental factors, specifically rainfall and the Normalized Difference Vegetation Index (NDVI). Anthrax cases in Kruger had wide inter-annual variation in case numbers, and large outbreaks seemed to follow roughly a decadal cycle. In contrast, outbreaks in Etosha were smaller in magnitude and occurred annually. In Etosha, the host species commonly affected remained consistent over several decades, although plains zebra (Equus quagga) became relatively more dominant. In Kruger, turnover of the main host species occurred after the 1990s, where the previously dominant host species, greater kudu (Tragelaphus strepsiceros), was replaced by impala (Aepyceros melampus). In both parks, anthrax infections showed two seasonal peaks, with each species having only one peak in a year. Zebra, springbok (Antidorcas marsupialis), wildebeest (Connochaetes taurinus) and impala cases peaked in wet seasons, while elephant (Loxodonta africana), kudu and buffalo (Syncerus caffer) cases peaked in dry seasons. For common host species shared between the two parks, anthrax mortalities peaked in the same season in both systems. Among host species with cases peaking in the same season, anthrax mortalities were mostly synchronized, which may imply similar transmission mechanisms or shared sources of exposure. Between seasons, outbreaks in one species may contribute to more cases in another species in the following season. Higher vegetation greenness was associated with more zebra and springbok anthrax mortalities in Etosha, but fewer elephant cases in Kruger. These results suggest that host behavioral responses to changing environmental conditions may affect anthrax transmission risk, with differences in transmission mechanisms leading to multi-host biseasonal outbreaks. This study reveals the dynamics and potential environmental drivers of anthrax in two savanna systems, providing a better understanding of factors driving biseasonal dynamics and outbreak variation among locations.

opencc-by-4.0Mar 2022View details →

Training and Testing Data, Associated Code, and WRF Code for ML-based nonhydrostatic alternative scheme in dynamical core of atmosphere

Data and codes for a nonhydrostatic alternative scheme (NAS) in dynamical core of atmosphere based on machine learning. In this new version, the randomly sampled training data samples testing data samples from nonhydrostatic simulations in WRF baraclinic wave test are provided. They are processed into a new data structure, which can be directly utilized in training and testing.  Follow the instructions in README.txt and download the training and testing data, and the associated codes. Here we provide 3 parts of data and codes: 1, Training and testing data from WRF; 2, Training and testing codes for two machine learning emulators: machine learning and neural network 3, WRF application.