Find research datasets worth reusing

Spike-timing based coding in neuromimetic tactile system enables dynamic object classification

Coding dynamic tactile information in spike timing is essential to human haptic exploration and dexterous object manipulation. Conventional electronic skins generate frames of tactile signals upon interaction with objects and are unfortunately ill-suited for efficient coding of temporal information and rapid feature extraction. Here, we report a neuromorphic tactile system that uses spike timing, especially the first-spike timing, to code dynamic tactile information about touch and grasp. This strategy enables the system to seamlessly code highly dynamic information with millisecond temporal resolution on par with the biological nervous system, yielding dynamic extraction of tactile features. Upon interaction with objects, the system rapidly classifies them in the initial phase of touch and grasp, thus paving the way to fast tactile feedback desired for neuro-robotics and neuro-prosthetics.

The paradigm of tax-reward and tax-punishment strategies in the advancement of public resource management dynamics

In contemporary society, the effective utilization of public resources remains a subject of significant concern. A common issue arises from defectors seeking to obtain an excessive share of these resources for personal gain, potentially leading to resource depletion. To mitigate this tragedy and ensure sustainable development of resources, implementing mechanisms to either reward those who adhere to distribution rules or penalize those who do not, appears advantageous. We introduce two models: a tax-reward model and a tax-punishment model, to address this issue. Our analysis reveals that in the tax-reward model, the evolutionary trajectory of the system is influenced not only by the tax revenue collected but also by the natural growth rate of the resources. Conversely, the tax-punishment model exhibits distinct characteristics when compared to the tax-reward model, notably the potential for bistability. In such scenarios, the selection of initial conditions is critical, as it can determine the system's path. Furthermore, our study identifies instances where the system lacks stable points, exemplified by a limit cycle phenomenon, underscoring the complexity and dynamism inherent in managing public resources using these models.

Data from: Spatiotemporal dynamics of Nektonic biodiversity and vegetation shifts during the Smithian–Spathian Transition: Conodont and Palynomorph insights from Svalbard

The dataset includes an Excel file with sporomorph counting of samples from the Stensiöfjellet section, Svalbard. Furthermore, it includes additional taxonomic notes on conodonts from the Stensiöfjellet section, Svalbard.

Data from: Ring species dynamics in California mygalomorph spiders (Nemesiidae, Calisoga)

Idealized ring species, with approximately continuous gene flow around a geographic barrier but singular reproductive isolation at a ring terminus, are rare in nature. A broken ring species model preserves the geographic setting and fundamental features of an idealized model but accommodates varying degrees of gene flow restriction over complex landscapes through evolutionary time. Here we examine broken ring species dynamics in Calisoga spiders, which like classic Ensatina salamanders, are distributed around the Central Valley of California. Using nuclear and mitogenomic data we test key predictions of common ancestry, ring-like biogeography, biogeographic timing, population connectivity and terminal overlap. We show that a ring complex of populations shares a single common ancestor, and from an ancestral area in the Sierra Nevada mountains, two distributional and phylogenomic arms encircle the Central Valley. Isolation by distance occurs along these distributional arms, although gene flow restriction is also evident. Where divergent lineages meet in the South Coast Ranges we find rare lineage sympatry, without evidence for nuclear gene flow, and with clear evidence for morphological and ecological divergence. We discuss general insights provided by broken ring species, and how such a model could be explored and extended in other systems and future studies.

Molecular Dynamics Trajectories for the D3 receptor (D3R) complexes bound with a GαOβγ heterotrimer and 1) FOB02-04A bitopic agonist; 2) pramipexole.

Molecular Dynamics Data for publication "Structure of the dopamine D3 receptor bound to a bitopic agonist reveals a new specificity site in an expanded allosteric pocket". Sandra Arroyo-Urea, Antonina L. Nazarova, Ángela Carrión-Antolí et al., Nat. Comm., revision (2024). https://doi.org/10.21203/rs.3.rs-3433207/v1 This directory includes the PDB (Protein Data Bank) format file detailing the topology and the XTC (eXtended Trajectory) format file outlining the trajectories for two distinct complexes: 1) the FOB02-04A-bound structure of D3 receptor (D3R) complexes in association with a GαOβγ heterotrimer, and 2) the pramipexole-bound structures of D3R complexes also coupled to a GαOβγ heterotrimer. The data is organized in a strided trajectory with a timestep of 0.5 nanoseconds per frame. To reapply periodic boundary conditions, users can employ the standard periodic boundary condition commands available in Visual Molecular Dynamics (VMD) package.   The MD trajectory data for this study was acquired as well as uploaded by Antonina L. Nazarova.

Prediction model of the temporal dynamics of severe pest cashew Anacampsis phytomiella using artificial neural networks

Open the record for dataset details and reuse information.

Dataset: Intercavity polariton slows down dynamics in strongly coupled cavities

Dataset for the experimental data of article:  Intercavity polariton slows down dynamics in strongly coupled cavities

Calcium dynamics upon heating in murine neonatal cardiomyocytes transduced with truncated human TRPV1(−109 a.a.) and the localization of TRPV1 in these cells

<h3>Abstract</h3> The expression of truncated human TRPV1(−109 a.a.) in cardiomyocytes allowed us to induce action potentials (APs) by pulse irradiation with an infrared (IR) diode laser. We studied the calcium dynamics in these cells (Ca_TRPV.zip image set). Murine cardiomyocytes were transducted by AAV-based vectors bearing construction of TRPV1(−109 a.a.) with mRuby (for expression detection) and vectors bearing GCaMP6s calcium sensor. Cardiomyocytes were heated by IR laser with a repetition rate of 2 Hz and 30 ms pulse width in a calcium-free medium. To explain the observed calcium dynamics, we also studied the subcellular localization of human TRPV1 in Murine cardiomyocytes ER_a-flag_100x_param1_Z-stack002.nd2 <h3>Primary cell production and transformation</h3> Experiments were carried out using C57Bl/6J mice (The Jackson Laboratory, #000664, RRID: IMSR_JAX:000664). The mixed mouse primary neonatal cardiomyocyte cell culture was obtained using a neonatal heart dissociation kit (Miltenyi Biotec, 130-098-373) according to the manufacturer’s instructions. The cells were cultured in DMEM/F12, 1:1 mixture (BioloT,  1.3.7.2.) supplemented with 10% FBS, penicillin 100 U/ml /streptomycin 100 mg/ml, and L-glutamine 0.365 g/l. The culture was seeded on 10mm coverslips coated with 10 mg/ml gelatin diluted in PBS and maintained at 37℃ in 5% CO2. For transient expression of the hTRPV1 channel, a reporter protein, and a fluorescent Ca2+ sensor GCaMP6s, we used AAV-based vectors with the encoded genes above. We used the AAV-DJ serotype at a MOI of 12,000 VG/cells for cTnT_hTRPV1(sh)_P2A_mRuby based viruses, and a MOI of 2,500 VG/cells for cTnT_GCaMP6s ones. The cells were infected on the next day after plating, and the transgene expression peak was observed on the third day after the infection. <h3>Distant heating system</h3> The system was equipped with a fiber coupled laser diode (LD) 4PN-117 (SemiNex) as a powerful heating laser, providing radiation at a wavelength of 1375 nm with an average power of up to 4.3 W through a multimode fiber with a core diameter of 105 μm and 0.22NA. The LD was mounted onto a TEC-controlled plate “264 TEC HP LaserMount” (A.I.), which was operated by TEC driver TECSource 5305 (A.I.); current stabilization and control for LD were performed with LD driver LaserSource 4320 (A.I.). The laser was controlled via the TTL output from the HEKA EPC-10 amplifier. Different laser intensities and pulse widths were used. Laser power, P, can be computed from trigger voltage, U, by an equation: P [W] = -0.28 + 1.42 * U [V]. Intracellular calcium recordings of single cardiac cells Neonatal cardiomyocyte cells transduced with GCaMP6s sensor were viewed and acquired under a water immersion Olympus LUMPLFLN40×W objective with 40X magnification. Data acquisition was performed at 20 fps using a Scientifica SliceScopePro 2000 microscope (Scientifica, UK) equipped with a Hamamatsu Orca Flash 4.0 CMOS monochrome digital camera (Hamamatsu Photonics) connected to a PC running the free software uManager. A CoolLED pE-300ultra was used as a light source. It was synchronized with the laser heating system via BNC-TTL output from the Heka Elektronik EPC 10 USB Patch Clamp Amplifier. To synchronize the pacing and the GCamp6s signal registration, the light source was switched off for one acquisition cycle at the beginning of the pacing. The GCamp6s signal was analyzed using Fiji software. <h3> TRPV1 channel localization</h3> To understand the localization of the expressed TRPV1 channels in neonatal mice cardiomyocytes, we utilized cells infected with AAV-PHP.S serotype viruses with pAAV_cTnT_hTRPV1_P2A_FLAG-tag at a MOI of 2500 VG/cells. To visualize endoplasmic reticulum, we stained the live cells with ER-Tracker™ Red (BODIPY™ TR Glibenclamide, Thermo Fisher Scientific, E34250) according to the manufacturer’s instructions. After the staining with ER-tracker, cardiomyocytes were fixed with 4% paraformaldehyde (Sigma-Aldrich, 158127-100G) for 5 minutes at room temperature and washed trice with 0.3% Tween 20 (Sigma-Aldrich, P1379-250ML) diluted in PBS (5 minutes each). The fixed cells then were blocked with PBS containing 0.12% tween 20, 1% bovine serum albumin (BSA, PanEko, 68100.10г), and 10% goat serum (Thermo Fisher Scientific, 16210072) for 40 minutes at room temperature. After the buffer removal, the cardiomyocytes were labeled with of DYKDDDDK Tag Recombinant Rabbit Monoclonal Antibody (8H8L17, Invitrogen, MA1-142-A488) at 1:500 dilution in 1% BSA, 10% goat serum, and 89% PBS for 2 hours at room temperature. The samples were washed three times with PBS after the incubations. Then, the cells were stained with Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody Alexa Fluor™ 488 (Invitrogen, A-11008) at dilution 1:500 for 1 hour at room temperature. The removal of non-conjugated antibodies was performed in parallel with cell nuclei staining. The cells were incubated with PBS supplemented with 2 μg/ml DAPI (Miltenyi Biotec, 130-111-570) for 15 minutes at room temperature. For further experiments, glasses with the labeled cells were placed onto the Superfrost Plus adhesion slides (Epredia, EPBRSF41296SP) in 20 µl VECTASHIELD Vibrance Antifade Mounting Media (Vector Laboratories, H-1700-2) and stored at +4℃ in the dark. The samples were analyzed using an inverted Nikon A1 confocal microscope and visualized using Nikon NIS-Elements software. We pictured the sample in each channel individually exciting DAPI, DYKDDDDK Tag-Alexa Fluor 488, and ER-tracker by laser lines 405 nm, 488 nm and 561 nm, respectively. Colocolization analysis was performed using ImageJ software.

An ulvophycean marine green alga produces large parthenogenetic isogametes as predicted by the gamete dynamics model for the evolution of anisogamy

In eukaryotes, the gamete size difference between the two sexes (anisogamy) evolved from gametes of equal size in both mating types (isogamy) and is plausibly claimed to generate sexual selection in morphology and behaviour. The gamete dynamics (GD) model for anisogamy evolution combines gamete limitation and competition and predicts that, if gametes of both mating types can develop parthenogenetically (i.e. without fusing with the opposite mating type), large isogamy can evolve under gamete-limited conditions. Ulvophycean marine green algae that exhibit various gametic systems from isogamy to anisogamy are important models for testing such theories. However, in most previous papers, whether a species is isogamous or anisogamous has not been examined statistically, which leaves the above theoretical prediction untested. We reveal (i) that the gametic system of Struvea okamurae is large isogamy using a generalized linear mixed model (GLMM), which accounted for the variation of gamete size among individual gametophytes, and (ii) that gametes of this alga can actually develop parthenogenetically, contrary to a previous report. Habitat environments and gametic behaviour suggest that this alga might experience gamete-limited conditions. S. okamurae seems to produce large parthenogenetic isogametes following GD model predictions, as an adaptation to deep waters.

Investigating the truthfulness of autobiographical events through mouse dynamics

This repository contains the dataset associated with the original paper "Investigating the truthfulness of autobiographical events through mouse dynamics”, by M. Monaro, A. Guiotto, G. Sartori. Data are organized as follows: - the dataset used by the authors to perform statistical analysis (ANOVAs) (.xls) - the training sets used by the authors to train and validate ML models (.arff) - the test sets used by the authors to test the ML models (.arff) The "Data dictionary" file contains the description of the variables in each data file. .arff files can be directly run in WEKA software 3.9. The "Details on ML classifiers parameters" file contains the algorithm parameters used to tun ML classifiers.

Funnel Control for Langevin Dynamics

<div> <div>Data and codes to re-create the results in</div> <div>T. Berger and F. Nüske, Funnel Control for Langevin Dynamics, arXiv:2211.07232 (2022)</div> <div> </div> <div>See README.md for detailed instructions.</div> </div>

opencc-by-4.0Apr 2024View details →

Vortex loop dynamics and dynamical quantum phase transitions in 3D fermion matter

Supplemental Material and data corresponding to the article 'Vortex loop dynamics and dynamical quantum phase transitions in 3D fermion matter'. File description: <ul> <li>_sm.pdf - Supplemental Material to the article</li> <li>fig_2_rate.txt - rate function corresponding to Fig. 2</li> <li>fig_3_rate.txt - rate function $\lambda$ corresponding to Fig. 3</li> <li>fig_3_rate_G.txt - rate function $\lambda_G$ corresponding to Fig. 3</li> <li>fig_3a.txt - phase of the Green's function corresponding to Fig. 3a</li> </ul>

Selective dynamic band gap tuning in metamaterials using graded photoresponsive resonator arrays

Raw Data for figures: Fig. 2: Dispersion diagrams for non-illuminated (off) and illuminated (on) pillars of different heights (hp). hp1 = 7 mm, hp2 = 9 mm, hp3 = 11 mm, hp4 = 13 mm; p = 0 (1) for purely in- (out-of-plane) behavior Fig. 4: Computed transmission spectrum of a finite structure. a) Numerically simulated transmission spectrum for the considered 8-pillar specimen, both without ("Laser off") and with laser illumination ("Laser on 7th pillar"). Fig. 5: Transmission spectrum of the finite structure considered experimentally. a) Measured spectra before (blue) and after (red) illumination of pillar 1. Band gaps are highlighted in light blue and numbered from I to IV; b) Corresponding colour map representing transmission vs. frequency and time (vertical axis) when switching laser illumination on (t = 700 s) and off (t = 2300 s); c) same as a), with illumination of pillar 6; d) same as b), with illumination on pillar 6. Fig. 6: Dynamic modulation of signal frequencies (f1 = 21.5 kHz, f2 = 71.5 kHz) in a graded pillar structure. The different temporal intervals depict tunable suppression and enhancement of specific frequencies through selective pillar illumination.

Dataset for the SFmodel, applied in Evapotranspiration dynamics and partitioning in a grassed vineyard: ecophysiological and computational modelling approaches

Dataset used for the SFmodel, applied in the work "Evapotranspiration dynamics and partitioning in a grassed vineyard: ecophysiological and computational modelling approaches". For units and nomenclature of the variables refer to Units_and_Nomenclature_for_SFmodel_in_Evapotranspiration_dynamics_and_partitioning_in_a_grassed_vineyard.pdf.

Data from: Foraging-induced craniofacial plasticity is associated with an early, robust, and dynamic transcriptional response

Phenotypic plasticity is the ability of a single genotype to vary its phenotype in response to the environment. Plasticity of the skeletal system in response to mechanical input is widely studied, but the timing of its transcriptional regulation is not well-understood. Here we used the cichlid feeding apparatus to examine the transcriptional dynamics of skeletal plasticity over time. Using three closely related species that vary in their ability to remodel bone and a panel of 11 genes, including well studied skeletal differentiation markers and newly characterized environmentally sensitive genes, we examined plasticity at 1, 2, 4 and 8 weeks following the onset of alternate foraging challenges. We found that the plastic species exhibited environment-specific bursts in gene expression at 1 week, followed by a sharp decline in levels, while the species with more limited plasticity exhibited consistently low levels of gene expression. This trend held across nearly all genes, suggesting that it is a hallmark of the larger plasticity regulatory network. We conclude that plasticity of the cichlid feeding apparatus is not the result of slowly accumulating gene expression difference over time, but rather is stimulated by early bursts of environment-specific gene expression followed by a return to homeostatic levels.

Jupyter Notebook and comprising data for GRL2023GL106264R: Understanding the Cascade: Removing GCM biases improves dynamically downscaled climate projections

This notebook and attendant files allows users to interface with a small subset of the data used to create the data in GRL2023GL106264R. Also feel free to check out the overall description of the non-bias corrected dynamically downscaled GCMs in WUS-D3 here: https://zenodo.org/records/10635867. This DOI also contains version of WRF 4.1.3 allowing for yearly CH4, CO2, and N2O updates, as well as a 360-day calendar version.

opencc-by-4.0Oct 2023View details →

Size-Dependent Dynamics of the Internal Carbon Pool Drive Isotopic Vital Effects in Calcifying Phytoplankton

Isotopic offsets in biogenic calcite from equilibrium values can provide unique insights into the physiology and mechanisms of carbon regulation in calcifying phytoplankton. This study examines the impact of varying CO2 (controlled via pH) on five coccolithophore species chosen for varied cell sizes, physiology, and calcification. The study investigates isotopic offsets in coccolith calcite and organic matter, in relation to carbon demand and supply (µ/CO2). Species-specific CO2/pH optima for growth (µopt) were derived from variations in growth rates with varying CO2 concentrations. Growth rates for all species declined with rising CO2 (decreasing pH) due to H+-driven inhibition. C. braarudii and C. leptoporus exhibited high µopt values (suggesting high carbon-demand) and limited growth under low CO2 (high pH) suggesting carbon limitation. Under low CO2 supply, when growth rates were CO2-limited, both species exhibited coincident isotopic depletion in calcite and organic matter as a consequence of CO2 diffusion into the cell that experienced no equilibration as a result of a highly depleted internal carbon pool. In these two species, isotopic values in calcite  remained unaffected by growth rates and CO2 concentration (µ/CO2) when CO2 was sufficient for optimal growth. G. huxleyi and G. oceanica displayed optima for growth (µopt) at low CO2 concentrations and showed no growth limitation under low CO2 (indicating low carbon-demand). Both species experienced depleted (negative) vital effects caused by an excess of CO2 diffusion into the small internal carbon pool of the cell when diffusive carbon supply outpaced low demand (low µ/CO2). Enriched (positive) vital effects were observed under low carbon supply and high demand, likely due to diffusive loss of CO2 from the cell's intracellular carbon pool due to a lower intracellular pH. C. carterae exhibited an intermediate µopt and isotopically equilibrated intracellular carbon pool such that δ13C values in calcite and organic matter suggested a shared carbon pool. This study illustrates that pH-CO2 driven vital effects and fractionation into organic matter indicate the residence time for carbon in the intracellular carbon pool, and the size of this pool is proportional to cell size. C. leptoporus and C. carterae can elevate intracellular pH to minimise CO2 leakage, whereas vital effects in G. huxleyi and G. oceanica are caused by diffusive CO2 due to the small size of their internal carbon pool.

Data generated from calculations in "Gauge Field Dynamics in a Multilayer Kitaev Spin Liquid"

The Kitaev honeycomb model hosts a quantum spin liquid in its ground state, where the excitations are gapless Majorana fermions and static Z2 gauge fluxes called visons. We consider Kitaev models stacked on top of each other, weakly coupled by Heisenberg interaction linear in J&perp;. This inter-layer coupling breaks the integrability of the model and makes the gauge fields dynamic. While single visons stay static in this model, an inter-layer pair of visons can hop with a hopping amplitude linear in J&perp;, but remains confined to a single plane. An intra-layer vison-pair, in contrast, is constrained to move along the stacking direction only. Depending on the anisotropy of the Kitaev couplings Kx,Ky,Kz, the intra-layer vison pairs show completely different dynamical behaviours. While coherent intra-layer tunnelling is possible for sufficiently strong anisotropies, only incoherent processes are possible in the isotropic case. When a magnetic field opens a gap for Majorana fermions, one can identify two types of intra-layer vison pairs, one bosonic and one fermionic. Only the bosonic pair obtains a hopping rate linear in J&perp;. We argue that our results can be used to identify leading instabilities of the Kitaev phase induced by the inter-layer coupling.

Data from: Forecasting nocturnal bird migration for dynamic aeroconservation: the value of short-term dataset

Placing wind turbines within large migration flyways, such as the North Sea basin, can contribute to the decline of vulnerable migratory bird populations by increasing mortality through collisions. Curtailment of wind turbines limited to short periods with intense migration can minimize these negative impacts, and near-term bird migration forecasts can inform such decisions. Although near-term forecasts are usually created with long-term datasets, the pace of environmental alteration due to wind energy calls for urgent development of conservation measures that rely on existing data, even when it does not have long temporal coverage. Here, we use five years of tracking bird radar data collected off the western Dutch coast, weather, and phenological variables to develop seasonal near-term forecasts of low-altitude nocturnal bird migration over the southern North Sea. Overall, the models explained 71% of the variance and correctly predicted migration intensity above or below a threshold for intense hourly migration in more than 80% of hours in both seasons. However, the percentage of correctly predicted intense migration hours (top 5% of hours with the most intense migration) was low, likely due to the short-term dataset and their rare occurrence. We, therefore, advise careful consideration of a curtailment threshold to achieve optimal results. Synthesis and applications: Near-term forecasts of migration fluxes evaluated against measurements can be used to define curtailment thresholds for offshore wind energy. We show that to minimize collision risk for 50% of migrants, if predicted correctly, curtailments should be applied during 18 hours in spring and 26 in autumn in the focal year of model assessments, resulting in an estimated annual wind energy loss of 0.12%. Drawing from the Dutch curtailment framework, which pioneered the 'international first' offshore curtailment, we argue that using forecasts developed from limited temporal datasets alongside expert insight and data-driven policies can expedite conservation efforts in a rapidly changing world. This approach is particularly valuable in light of increasing interannual variability in weather conditions.

A hierarchical model for eDNA fate and transport dynamics accommodating low concentration samples

Environmental DNA (eDNA) sampling is an increasingly important tool for answering ecological questions and informing aquatic species management . Challenges of using eDNA include determining species source location(s) and accurately and precisely measuring low concentration eDNA samples, especially considering inhibitory compounds and multiple sources of ecological and measurement variability. These challenges must be overcome to optimize our use of modeling frameworks like the eDNA Integrating Transport and Hydrology (eDITH) model. To better understand eDNA fate and transport dynamics, our ability to estimate parameters within the eDITH framework, and our ability to reliably quantify low concentration samples, we developed a hierarchical model and used it to evaluate a fate and transport experiment. Our model addresses several low concentration challenges by modeling the number of copies in each PCR replicate as latent variables with a count distribution and conditioning detection and quantification on replicate copy number. We provide evidence that the eDNA removal rate was not constant through time, estimating that over 80% of eDNA was removed over the first 10 m, traversed in 41 seconds. After this initial period of rapid decay, eDNA decayed slowly with consistent detection through our furthest site 1km from the release location, traversed in 250 seconds. We show that the eDITH model parameters can be difficult to estimate in this scenario. Our model further allowed us to detect extra-Poisson variation in the allocation of copies to replicates. Despite not observing evidence for inhibition as typically quantified using internal positive controls in conjunction with a binary decision rule (e.g., $\Delta$Cq>3), we hypothesized this overdispersion could be due to inhibitors. We extended our hierarchical model to accommodate a continuous effect of inhibitors, and used our model to provide evidence for the inhibitor hypothesis and explore the implications, if true. We show that inhibitors can cause substantial underestimation of eDNA site concentration, bias eDITH model parameter estimates, and attribute measurement variability erroneously to ecological variability. While our model is not a panacea for all challenges faced when quantifying low eDNA concentrations, it provides a framework for a more complete accounting of uncertainty that can be further tested and refined.