Find research datasets worth reusing

opencc-by-4.0Jan 2023View details →

Video supplement for Lagrangian transport simulations using the extreme convection parametrization: an assessment for the ECMWF reanalyses

We provide a video supplement for the paper "Lagrangian transport simulations using the extreme convection parametrization: an assessment for the ECMWF reanalyses" submitted to the journal Geoscientific Model Development.

opencc-zeroJan 2023View details →

Immediate and long-term genetic consequences of linear transport infrastructure: Can fauna crossing mitigate its cost?

The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human-impacted landscapes. Here, we provide a rare, and to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic dataset collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12–69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of 8 koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human-impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.

opencc-by-4.0Jan 2023View details →

Data for Intra-seasonal variability in sediment provenance and transport processes in the Brahmaputra basin

No description provided.

opencc-zeroJan 2023View details →

A mechanism of uncompetitive inhibition of the serotonin transporter

The serotonin transporter (SERT/SLC6A4) is arguably the most extensively studied solute carrier (SLC). During its eponymous action - i.e., the retrieval of serotonin from the extracellular space - SERT undergoes a conformational cycle. Typical inhibitors (antidepressant drugs and cocaine), partial and full substrates (amphetamines and their derivatives) and atypical inhibitors (ibogaine analogues) bind preferentially to different states in this cycle. This results in competitive or non-competitive transport inhibition. Here, we explored the action of N-formyl-1,3-bis (3,4-methylenedioxyphenyl)-prop-2-yl-amine (ECSI#6) on SERT: inhibition of serotonin uptake by ECSI#6 was enhanced with increasing serotonin concentration. Conversely, the KM for serotonin was lowered by augmenting ECSI#6. ECSI#6 bound with low affinity to the outward-facing state of SERT but with increased affinity to a potassium-bound state. Electrophysiological recordings showed that ECSI#6 preferentially interacted with the inward-facing state. Kinetic modeling recapitulated the experimental data and verified that uncompetitive inhibition arose from preferential binding of ECSI#6 to the K+-bound, inward-facing conformation of SERT. This binding mode predicted a pharmacochaperoning action of ECSI#6, which was confirmed by examining its effect on the folding-deficient mutant SERT-PG601,602AA: pre-incubation of HEK293 cells with ECSI#6 restored export of SERT-PG601,602AA from the endoplasmic reticulum and substrate transport. Similarly, in transgenic flies, administration of ECSI#6 promoted delivery of SERT-PG601,602AA to the presynaptic specialization of serotonergic neurons. To the best of our knowledge, ECSI#6 is the first example of an uncompetitive SLC inhibitor. Pharmacochaperones endowed with the binding mode of ECSI#6 are attractive because they can rescue misfolded transporters at concentrations, which cause modest transport inhibition.

opencc-zeroJan 2023View details →

Data from: A study on the Influence of submergence ratio on the transportation of suspended sediment in a partially vegetated channel flow

Riparian or aquatic vegetation thrives with seasons. The understanding of canopies' Submergence-Ratio SR (stems' height to water depth) influence on suspended sediments' transportation is still limited. Thus, Large Eddy Simulations (LES) coupled with the Discrete Phase Method (DPM) are used to investigate the particles' 3-dimensional distribution in a partially vegetated straight channel. The spanwise distribution of particles is quantified by the Probability Density Function (PDF), showing a non-uniformity of particles in time as quantified by the PDF variance. The findings and conclusions: (Ⅰ) With SR rising, the particles' depletion effects exerted by the vegetation-side mixing layer are improved along the interface between vegetated and vegetation-side bare channel region. However, the SR has little effect on the variance of the particles' PDF in the spanwise direction when the mixing layer is fully developed. (Ⅱ) During the developing stage of the over-canopy mixing layer, submerged vegetation with higher SR gain a stronger upwards (vertical) entrainment capability. The case (SR=60%) has a higher sediment concentration than other cases in the fully developed vertical mixing layer region above canopy. (III) The vertical suspension of particles in the vegetation-side bare channel region is analysed. Particles migrating from the vegetated region are entrained into the vegetation-side bare channel region by turbulent structures. Nevertheless, the vertical concentration profile is more uniform in the vegetated region than in the vegetation-side bare channel at the same streamwise location. The cases SR=40% and 60% still have higher sediment concentrations than other cases in the vegetation-side bare channel's upper region.

Data for "Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota"

MD simulation data of OxlT. Trajectory data and NAMD input files are included. The first 500 ns trajectory that starts from the occluded conformation with a transition to the outward-open conformation is in the OxlT-occ directory. The 200 ns trajectories that start from the outward-open conformation with different protonation states of K355 are in the  OxlT-out directory.

opencc-by-4.0Sep 2021View details →

Greener transport choices

In the third Rebalance Dialogue, <a href="https://rebalancemobility.eu/andrea-ricci/">Andrea Ricci</a> talked with <a href="https://rebalancemobility.eu/andreu-ulied/">Andreu Ulied</a> and <a href="https://rebalancemobility.eu/robert-braun/">Robert Braun </a>about signs towards greener transport choices. In Europe, these signs are emerging. Industry is making cleaner vehicles increasingly available and performant (electromobility, cleaner fuels). Government plays an important role through standards, taxation, phasing out, but also, at the local level, through the redesign of urban, greener spaces and infrastructure. Therefore the question is whether these moves are primarily pushed forward by a changing societal attitude towards environmental protection and the pursuance of a healthier life. If not, how effective would be a green mobility transition without a major shift in the attitude of citizens and mobility users? Grassroots initiatives, like “Fridays for Future”, play an important role in raising environmental and health concerns, which in turn could foster modal shifts. To what extent are people driven by knowledge and evidence on the social and environmental benefits of green choices, or is it rather the urge to fulfil social norms that drives them – this will be revealed in the near future. Moreover, the success of such initiatives might also contribute to underline intergenerational differences in awareness and motivation. If we can imagine a new mobility culture based on structural changes, we should ask ourselves whether demand-side policies today in place – such as access regulations, infrastructure charging, standards – will be no longer necessary. <blockquote> The shift towards “active travel” is a major component of the green transition. </blockquote> Active travel is usually defined as travel that requires physical activity (walking, cycling etc.), generating social benefits in both environmental and health terms. REBALANCE aims to comprehend the depth of the changes in values and attitudes that are required to enact a visible move to active travel. This dialogue tried to understand inequalities and how they relate to active travel. While active mobility is great for upper-middle-class men, it might not so much for the majority. It also brings a lot of externalities. However, the participants stressed the importance of walking for socialisation. According to the discussants, industry pushes towards allegedly sustainable modes that are nothing new. Transition to electricity is being forced by coercion, not by awareness. Consequently, mobility systems have an immense resilience and capability of incorporating critique. An additional concerned was flagged on short-haul and city aerial mobility, which will become a major problem in the future. Gender issues were also addressed during the conversation to understand if gender is a meaningful variable in the transition to greener mobility. If so, does this have to do with gender-specific value differences? Women have been proposed as indicator of transport service quality. The discussants also think that transport and public spaces should be evaluated through women’s involvement and the services provided. A contemporary debate cannot omit the influence of COVID-19 on mobility and the plausibility that it yields structural behavioural changes, a “new normal” where substantial modal shifts become permanent, though the participants think that the new normal will be very similar to the old normal. The role of technology is always present; and our discussants agreed that remote technologies impact socialisation, creativity and new projects. Furthermore, we are not in control when entangled with different technologies. Regarding governance, the debate focused on how regime change is necessary to change the ‘details’ (environment, mobility…). New regimes need to be less based on command-control and more based on collaboration moral economy. Top-down approaches are the enemy because they reflect a totalitarian paradigm. To fight these, a transition organised with the people (from legal norms to social norms) was proposed. <blockquote> Paradigm change is extremely slow. Inequalities are hidden by the environmental imaginary. </blockquote> New technologies do not solve all problems and they can create new ones. For instance, we might build clean, circular, sustainable suburbs where people are disconnected and live alone. The conclusion is that there is no culture-nature divide and we must reconceptualise the world around us. Value choices are more important than technology when changing mobility modes.

Targeted Balloon Observations of Stratosphere-to-Troposphere Transport From a Mesoscale Convective System

Data used for analysis in the JGR-Atmospheres Paper Targeted Balloon Observations of Stratosphere-to-Troposphere Transport From a Mesoscale Convective System. Files include ozonesonde data, gridded radar data, and backward trajectory calculations.

The Agulhas Current transports signals of local and remote Indian Ocean nitrogen cycling

All hydrographic and biogeochemical data from the ASCA16, IIEO2, SWINGS and ASCA summer 2018 cruises published in the journal article, "The Agulhas Current transports signals of local and remote Indian Ocean nitrogen cycling" (Marshall, et al., 2023).

Effect of Hydrophobicity of Fluorescent Carbon Nanoparticles on Transport in Porous Media: Column Experiment Data and Modeling

The data contained here are derived from sand column experiments and modeling which investigate the effects of hydrophobicity on the transport of fluorescent carbon nanoparticles (FCN) in porous media. The data consist of outlet concentrations (relative to the inlet concentrations) of FCN for a suite of experiments testing the recovery of FCN synthesized using four different pyrolysis temperatures(190C, 210C, 230C, and 250C), as well as the recovery of FCN when passed through three different sand types (Fine, Medium, and Coarse). Column experiments were tested under both saturated and unsaturated conditions to investigate the role of pore water content on FCN retention. Finally, results from tests using an inert bromide tracer are also included (File: May_et_al_Column_Experiment_Outlet_Concentrations.xlsx). Additionally, the results from modeling the observed breakthrough curves of FCN are included for three different transport models, as well as modelling results for an inert bromide tracer (File: May_et_al_Breakthrough_Curve_Modeling.xlsx). The raw output files for the two-kinetic sites model that was determined to best reproduce the observed breakthrough curves are also provided (File: May_et_al_Two_Kinetic_Sites_Model_Raw_Output.zip) Finally, the results of sand surface characterization for three sands using a scanning electron microscope are included (File: May_et_al_Sand_Surface_Characterization_SEM-DATA.zip). Please see the following paper for more details: May, D.F., B. Hassanpour, L. Sinclair, T.S. Steenhuis, and L.M. Cathles, (2023, pending), Effect of Hydrophobicity of Fluorescent Carbon Nanoparticles on Transport in Porous Media: Column Experiments and Modeling, Water Resources Research, Manuscript Submitted for Review.

opencc-by-4.0Jul 2022View details →

Heat transport across the Antarctic Slope Front controlled by cross-slope salinity gradients

Feb 2023 updates:  <ul> <li>Add code for EKE spectral analysis to MITgcm_ASF-heat-ver3/analysis/spectrum/</li> <li>Add products of 5km and 10km runs to products_new-ver3</li> <li>Add MITgcm source code, copied from <a href="http://mitgcm.org/">http://mitgcm.org</a></li> </ul> This release contains updates on analysis code and products. <ul> <li>MITgcm_ASF-heat-ver3/newexp/: the Matlab scripts used to generate and run the MITgcm simulations</li> <li>MITgcm_ASF-heat-ver3/analysis/cross_slope/ and MITgcm_ASF-heat-ver2/analysis/plots/: the Matlab scripts used to analyze model output and make plots.</li> <li>MITgcm_ASF-heat-ver3/analysis/spectrum/: the Matlab scripts to calculate EKE spectra </li> <li>exps_configuration.zip: the configurations of the MITgcm simulations.</li> <li>products_new-ver3.zip: the products calculated from MITgcm diagnostics, including 7-year means of all the model outputs, overturning streamfunctions, neutral density, shoreward heat transport, kinetic energy, temporal decomposition, isopycnal thickness fluxes of the 5km and 10km runs, etc. </li> <li>ThicknessFlux_FreshShelf.zip: products of isopycnal thickness flux, used to calculate the decomposition of eddy/tidal heat advection/diffusion, for the "fresh-shelf" simulation. </li> <li>ThicknessFlux_ref.zip: as above, but for the reference simulation.</li> <li>ThicknessFlux_DenseShelf.zip: as above, but for the "dense-shelf" simulation. </li> </ul> The source code of the Massachusetts Institute of Technology General Circulation Model (MITgcm) is available at: <a href="http://mitgcm.org/">http://mitgcm.org</a>. All the raw data of the model output are available at: <a href="https://doi.org/10.15144/S47P49">https://doi.org/10.15144/S47P49</a>. To reproduce MITgcm_ASF simulations:  <ol> <li>Start each simulation with a 20-year spin-up integration. Before running each simulation, you need to substitute &OBCS_PARM04 with &OBCS_PARM05 in the file input/data.obcs, and substitute &EXF_NML_05 with &EXF_NML_OBCS  in the file input/data.exf. For simulations with very fresh shelf waters (e.g., shelf salinity = 33 psu), you need to spin up the simulation with a very small time step (e.g., 60s) for ~ two months, and then use a larger time step. </li> <li> Initialize the production run from the corresponding spin-up run, using the Matlab script initialize.m in the folder MITgcm_ASF-heat-ver2/newexp/. When using the LAYERS package, you need to substitute numperlist = 1 with numperlist = 2 in the file code/DIAGNOSTICS_SIZE.h before running the simulations. </li> </ol>   Notes on calculationg the overturning streamfunction and its mean/eddy/tidal decomposition using the MITgcm LAYERS package:  <ul> <li>avg_t: Calculate time averages. It has been modified since the vertical number of layers can be different from Nr. </li> <li>calc_Overturning_pt, usscar_plot_overturning_pt: calculate and plot eddy/mean/isopycnal overturning streamfunction using potential temperature layer fluxes.</li> </ul> <ul> <li>calc_Overturning_rho, usscar_plot_overturning_rho: calculate and plot eddy/mean/isopycnal overturning streamfunction using potential density layer fluxes.</li> </ul> <ul> <li>calc_Overturning_pt_Aocean, usscar_pt_overturning_rho_Aocean (recommended if your bathymetry is not flat): calculate and plot eddy/mean/isopycnal overturning streamfunction using potential temperature layer fluxes. For each latitude, use the total ocean area below a certain level to interpolate the streamfunction from pt space to z space. </li> </ul> <ul> <li>calc_Overturning_rho_Aocean, usscar_plot_overturning_rho_Aocean (recommended if your bathymetry is not flat): calculate and plot eddy/mean/isopycnal overturning streamfunction using potential density layer fluxes. For each latitude, use the total ocean area below a certain level to interpolate the streamfunction from potential density space to z space.</li> </ul> <ul> <li>calc_decomposition_OT, plot_OT_rho_Aocean_TidalEddyMean: decompose the isopycnal overturning streamfunction into tidal/eddy/mean components, using potential density layer fluxes.</li> </ul> Feel free to contact Yidongfang Si via ysi@g.ucla.edu if you have any questions.

Data for The influence of bathymetry over heat transport onto the Amundsen Sea continental shelf

Data and code for producing figures for the paper 'The influence of bathymetry over heat transport onto the Amundsen Sea continental shelf'

PDB files of "Characterization of ligand-induced thermal stability of the human organic cation transporter 2 (OCT2)"

The predicted alphafold structure of OCT2 (Uniprot O15244) was embedded in a DPPC model membrane, solvated with TIP3P water and subjected to 250 ns molecular dynamics simulation using the Desmond module of Schroedingers Drug Discovery Suite. The last 150 ns were used for clustering and the cluster with most of the members (cluster0) was selected as a model for OCT2. Based on that (still predicted, but optimised) model we performed docking with various substrates for which we also provide the obtained docking pose. See Publication in Frontiers in Pharmacology (DOI: 10.3389/fphar.2023.1154213) for details and results.

Calibrating angular momentum transport in intermediate-mass stars from gravity-mode asteroseismology

Best-matching MESA stellar evolution models and GYRE stellar pulsation models of the seven stars presented in Mombarg (2023). 'MESA_inlist_template_for_GYRE' is the inlist for MESA to compute the models used for the asteroseismic modelling, 'GYRE_inlist_template.in' is the inlist for GYRE to compute the eigenmodes.  'MESA_inlist_template_AM_transport' is the inlist for MESA to compute rotating models with angular momentum transport that were used to predict the near-core and surface rotation frequencies.

opencc-zeroMar 2023View details →

Data for: Invasive investigation: Uptake and transport of L-leucine in the gill epithelium of crustaceans

Many aquatic species are well-known as extremely successful invaders. The green crab (Carcinus maenas) is an arthropod native to European waters; however, it is now known to be a globally invasive species. Recently it was discovered that C. maenas could transport nutrients in the form of amino acids across their gill from the surrounding environment, a feat previously thought to be impossible in arthropods. We compared the ability for branchial amino acid transport of crustaceans native to Canadian Pacific waters to that of the invasive C. maenas, determining if this was a novel pathway in an extremely successful invasive species or a shared trait among crustaceans. Active transport of L-leucine was exhibited in Carcinus maenas, Metacarcinus gracilis, Metacarcinus magister, and Cancer productus across their gill epithelia. C. maenas exhibited the highest maximum rate of branchial L-leucine transport at 53.7 ± 6.24 nmolg-1h-1, over twice the rate of two native Canadian crustaceans. We also examined the influence of feeding, gill specificity, and organ accumulation of L-leucine. Feeding events displayed a heavy influence on the branchial transport rate of amino acids, increasing L-leucine transport rates by up to 10-fold in C. maenas. L-leucine displayed a significantly higher accumulation rate in the gills of C. maenas compared to the rest of the body at 4.15 ± 0.78 nmolg-1h-1, with the stomach, hepatopancreas, eyestalks, muscle tissue, carapace, and heart muscle exhibiting accumulation under 0.15 nmolg-1h-1. For the first time, the novel transport of amino acids in Canadian native arthropods is described, suggesting that branchial amino acid transport is a shared trait among arthropods, contrary to existing literature. Further investigation is required to determine the influence of environmental temperature and salinity on transport in each species to outline any competitive advantages of the invasive C. maenas in a fluctuating estuarine environment.

MInTe2 (M=Ag, Cu) thermal and electronic transport properties

HiPhive, ShengBTE and AMSET files that contain thermal and electronic transport properties of MInTe2 (M=Ag, Cu)

Simulation of free fermion transport on 2D lattice using constant-depth quantum circuits

In these simulations, we consider a fermion initialized on a reference lattice site, and observe how it evolves freely through a two-dimensional (2D) lattice.  The lattice comprises 16 sites with closed boundary conditions, and lattice site '0' is considered our reference site, where the fermion is initialized. We examine transport of a fermion on this 16-site lattice both with and without disorder.  To do this, we track the occupation number at varying distances $M$ from the reference site as the fermion evolves freely through time.  When there is no disorder in the system, we expect the fermion to behave ballistically and oscillate back and forth within the lattice. The file '4x4_2DFF_mu=0.0_nsteps=900_t=90.0_backend=ibm_washington_shot=50000_nis_ps_DD_M3.txt' has the results from simulating a free fermion on a 2D lattice with no disorder on the ibmq_washington QPU, while '4x4_2DFF_mu=0.0_nsteps=900_t=90.0_backend=qasm_sim_shot=100000_nis.txt' has the results from the noise-free quantum simulator.  When there is large random disorder in the system, we expect the fermion to exhibit Anderson localization. '4x4_2DFF_mu=10.0_nsteps=900_t=90.0_backend=ibm_washington_shot=50000_nis_ps_DD_M3_Anderson_loc.txt'  shows results from simulating a free fermion on a 2D lattice with large random disorder on the ibmq\_washington QPU,  while '4x4_2DFF_mu=10.0_nsteps=900_t=90.0_backend=qasm_sim_shot=100000_nis.txt' shows results from the noise-free quantum simulator.   Simulations on the the noise-free quantum simulator were performed with 100,000 shots.  Simulations on the QPU were performed with 50,000 shots and any shot that did not conserve particle number was discarded.  Two straightforward error mitigation techniques were also used to reduce noise in the results from the QPU.  The first was a scalable readout error mitigation method implemented with the mthree package, which reduces errors in quantum measurement via calibration.  The second was dynamical decoupling, a method that can suppress qubit decoherence via the application of a set of pulses (which together amount to application of the identity operator) to idling qubits which cancels the system-environment interaction.

ENSO influence on water vapor transport and thermodynamics over Northwestern South America

Datasets used, generated and analysed during the study "ENSO influence on water vapor transport and thermodynamics over Northwestern South America"

Ontology for transport in French

Ontology describing transport in French