Find research datasets worth reusing

opencc-by-4.0Jan 2020View details →

Data for the evaluatino of the influence of active transportation on body mass index

The dataset is centered on the canton of Geneva Switzerland and is divided into four different folders, available in a shapefile format; Cycle lane : This folder contains the cycle lane available in the State of Geneva. Parking : This folder contains the public and private parking of the State of Geneva. Public transport : This folder contains the public transport servicing quality data in the State of Geneva. Road : This folder contains the road used by the car in the State of Geneva.

opencc-by-4.0Jun 2020View details →

Appendix and Figures for the paper "Artificial Intelligence Applications in Transportation: A Meta-Analytic Review"

This collection includes the Appendix and Figures for the paper "Artificial Intelligence Applications in Transportation: A Meta-Analytic Review", written by Daniele Miranda and Pastor Taco. The Appendix consists of a summary table of the publications that were part of the literature review described on the paper.

opencc-zeroJul 2020View details →

Data from: An ECF-type transporter scavenges heme to overcome iron-limitation in Staphylococcus lugdunensis

Energy-coupling factor type (ECF-transporters) represent trace nutrient acquisition systems. Substrate binding components of ECF-transporters are membrane proteins with extraordinary affinity, allowing them to scavenge trace amounts of ligand. A number of molecules have been described as substrates of ECF-transporters, but an involvement in iron-acquisition is unknown. Host-induced iron limitation during infection represents an effective mechanism to limit bacterial proliferation. We identified the iron-regulated ECF-transporter Lha in the opportunistic bacterial pathogen Staphylococcus lugdunensis and show that the transporter is specific for heme. The recombinant substrate-specific subunit LhaS accepted heme from diverse host-derived hemoproteins. Using isogenic mutants and recombinant expression of Lha, we demonstrate that its function is independent of the canonical heme acquisition system Isd and allows proliferation on human cells as sources of nutrient iron. Our findings reveal a unique strategy of nutritional heme acquisition and provide the first example of an ECF-transporter involved in overcoming host-induced nutritional limitation.

Data from: Effects of soil particles and convective transport on dispersion and aggregation of nanoplastics via small-angle neutron scattering (SANS) and ultra SANS (USANS)

Terrestrial nanoplastics (NPs) pose a serious threat to agricultural food production systems due to the potential harm of soil-born micro- and macroorganisms that promote soil fertility and ability of NPs to adsorb onto and penetrate into vegetables and other crops. Very little is known about the dispersion, fate and transport of NPs in soils. This is because of the challenges of analyzing terrestrial NPs by conventional microscopic techniques due to the low concentrations of NPs and absence of optical transparency in these systems. Herein, we investigate the potential utility of small-angle neutron scattering (SANS) and Ultra SANS (USANS) to probe the agglomeration behavior of NPs prepared from polybutyrate adipate terephthalate, a prominent biodegradable plastic used in agricultural mulching, in the presence of vermiculite, an artificial soil. SANS with the contrast matching technique was used to study the aggregation of NPs co-dispersed with vermiculite in aqueous media. We determined the contrast match point for vermiculite was 66% D 2 O / 33% H 2 O. At this condition, the signal for vermiculite was ~50-100%-fold lower that obtained using neat H 2 O or D 2 O as solvent. According to SANS and USANS, smaller-sized NPs (50 nm) remained dispersed in water and did not undergo size reduction or self-agglomeration, nor form agglomerates with vermiculite. Larger-sized NPs (300-1000 nm) formed self-agglomerates and agglomerates with vermiculite, demonstrating their significant adhesion with soil. However, employment of convective transport (simulated by ex situ stirring of the slurries prior to SANS and USANS analyses) reduced the self-agglomeration, demonstrating weak NP-NP interactions. Convective transport also led to size reduction of the larger-sized NPs. Therefore, this study demonstrates the potential utility of SANS and USANS with contrast matching technique for investigating behavior of terrestrial NPs in complex soil systems.

Atmospheric transport is a major pathway of microplastics to remote regions

In the recent years, a large attention has been given to pollution from plastic products as a major environmental problem. Plastics degrade into smaller particles in the environment via photodegradation, physical abrasion, hydrolysis and biodegradation. Microplastics (1 um to 5 mm size particles) have been reported to affect coral reefs, marine and terrestrial animals, as well as humans. It has been reported that about 30% of microplastics in freshwater and oceanic ecosystems are tire wear particles (TWPs), while brake wear particle (BWP) emissions constitute 55% of all non-exhaust traffic-related particle emissions and 21% of all traffic-related PM emissions. There is a general conviction that the relative contribution of TWP and BWP emissions to total transport-related emissions will grow in the near future, due to the continuous reduction of exhaust traffic-related emissions. Although transport of TWPs and BWPs via runoff and wash-out processes to the marine and/or freshwater ecosystem has been studied extensively, very little is known about how these particles are dispersed in the atmosphere and where they are deposited. This is important due to the aforementioned impact in animals and humans. They also have an environmental impact as they are derived by materials made from fossil fuels such as ethylene and propylene. Thus, larger needs of plastics result in larger emissions of greenhouse gases. Since TWPs and BWPs can become airborne and have been detected already in remote areas, they may absorbe light decreasing surface albedo and accelerating ice melting. Here, we present for the first time the results of the atmospheric dispersion and deposition of traffic-related microplastics (TWPs and BWPs). We assess the suggested emissions using two methods, one indirect based on CO2 country ratios with road microplastics and extrapolation, and another employing an emissions model, which has been extensively used to determine global emissions of various substances by IIASA-International Institute for Applied Systems Analysis (GAINS model). We calculate that 34.4–290 kt y-1 (mean: 100 kt y-1), out of 102–787 kt y-1 (mean: 284 kt y-1) of PM10 TWPs emitted, were deposited in the World Ocean, while the respective annual terrestrial and riverine discharges are about 64 kt y-1. This shows that direct deposition of airborne road microplastics is likely the most important source for the ocean and marine biota. The calculated transport of PM10 road microplastics shows a relatively high efficiency over remote regions such as the Arctic Ocean (14%). High latitudes and the Arctic are highlighted as an important receptor of mid-latitude microplastic emissions, which may imply a future climatic risk taking into account that TWPs and BWPs constitute a small portion of the total plastic emissions. As of now, snow concentrations of road microplastics are 100 times lower than those of black carbon or polymers of larger usage (e.g., PVC or PPC). Around 15% of the PM2.5 road microplastic emissions were deposited in the Atlantic Ocean, whereas coarse particles were less efficiently deposited there (10-11%). The efficiency of PM2.5 deposition (TWPs: 19% - BWPs: 18%) over the Pacific Ocean was even more strongly enhanced relative to PM10 deposition (TWPs: 12% - BWPs: 11%), due to their smaller size. Transport efficiencies of coarse particles were up to twice of those for the fine particles in areas surrounded by microplastic emissions sources (e.g., Alps, Mediterranean, Baltic and South China Seas).

Uncovering transport, deposition and impact of radionuclides released after the early spring 2020 wildfires in the Chernobyl Exclusion Zone

In the beginning of April 2020, large fires that started in the Chernobyl Exclusion Zone (CEZ) established after the Chernobyl accident in 1986 caused media and public concerns about the health impact from the resuspended radioactivity. In this paper, the emissions of previously deposited radionuclides from these fires are assessed and their dispersion and impact on the population is examined relying on the most recent data on radioactive contamination and emission factors combined with satellite observations. About 341 GBq of 137Cs, 51 GBq of 90Sr, 2 GBq of 238Pu, 33 MBq of 239Pu, 66 MBq of 240Pu and 504 MBq of 241Am were released in 1st–22nd April 2020 or about 1,000,000,000 times lower than the original accident in 1986 and mostly distributed in Central and East Europe. The large size of biomass burning particles carrying radionuclides prevents long-range transport as confirmed by low concentrations reported in Europe. The highest cumulative effective doses (>15 μSv) were calculated for firefighters and the population living in the CEZ, while doses were much lower in Kiev (2–5 μSv) and negligible in Europe. All doses are radiologically insignificant and no health impact on the European population is expected from the April 2020 fires.

opencc-by-4.0Aug 2020View details →

Trajectories for 'A Lagrangian view of the atmospheric river related to the heavy rainfall of July 2020 in Japan: Importance of moisture gain during transport''

This is the trajectories output for the article  'A Lagrangian view of the atmospheric river related to the heavy rainfall of July 2020 in Japan: Importance of moisture gain during transport''. The settings for FLEXPART-WRF is also included.

ABCB transporters in a leaf beetle respond to sequestered plant toxins

Phytophagous insects can tolerate and detoxify toxic compounds present in their host plants and have evolved intricate adaptations to this end. Some insects even sequester the toxins for their defense. This necessitates specific mechanisms, especially carrier proteins that regulate uptake and transport to specific storage sites or protect sensitive tissues from noxious compounds. We identified three ATP-binding cassette subfamily B (ABCB) transporters from the transcriptome of the cardenolide-sequestering leaf beetle Chrysochus auratus and analyzed their functional role in the sequestration process. These were heterologously expressed and tested for their ability to interact with various potential substrates: verapamil (standard ABCB substrate), the cardenolides digoxin (commonly used), cymarin (present in the species' host plant) and calotropin (present in the ancestral host plants). Verapamil stimulated all three ABCBs and each was activated by at least one cardenolide, however, they differed as to which they were activated by. While the expression of the most versatile transporter fits with a protective role in the blood-brain-barrier, the one specific for cymarin shows an extreme abundance in the elytra, coinciding with the location of the defensive glands. Our data thus suggest a key role of ABCBs in the transport network needed for cardenolide sequestration.

Cellular bicarbonate accumulation and vesicular proton transport promote calcification in the sea urchin larva

The sea urchin embryo develops a calcitic endoskeleton through intracellular formation of amorphous calcium carbonate (ACC). Intracellular precipitation of ACC, requires HCO3-/CO32- concentrating as well as proton export mechanisms to promote calcification. These processes are of fundamental importance in biological mineralization, but remain largely unexplored. Here we demonstrate that the calcifying primary mesenchyme cells (PMCs) utilize Na+/H+- exchange (NHE) mechanisms to control cellular pH homeostasis during maintenance of the skeleton. During skeleton re-calcification, pHi of PMCs is increased accompanied by substantial elevations in intracellular [HCO3-] mediated by the Na+/HCO3-cotransporter Sp-Slc4a10. However, PMCs lower their pHi regulatory capacities associated with a reduction in NHE activity. Live-cell imaging using GFP reporter constructs in combination with intra-vesicular pH measurements demonstrated alkaline and acidic populations of vesicles in PMCs and extensive trafficking of large V-type H+-ATPase (VHA)-rich acidic vesicles in blastocoelar filopodial cells (BFCs). Pharmacological and gene expression analyses underline a central role of the VHA isoforms Sp-ATP6V0a1, Sp-ATP6V01_1 and Sp-ATPa1-4 for the process of skeleton re-calcification. These results highlight novel pH regulatory strategies in calcifying cells of a marine species with important implications for our understanding of the mineralization process in times of rapid changes in oceanic pH.

opencc-by-4.0Dec 2019View details →

Wrong-way migrations of benthic species driven by ocean warming and larval transport: Data

All data used to generate figures, tables, and other results in the publication cited below.  All data are derived from publicly available data archives as indicated in the publication's Data Availability Statement.  Archived data may change over time, and results in the paper are only relevant to data as originally downloaded.  These condensed data were used in the analyses and are provided to ensure that analyses are replicable. If using any code or data, please cite the following publication: Heidi L. Fuchs, Robert J. Chant, Elias J. Hunter, Enrique N. Curchitser, Gregory P. Gerbi, and Emily A. Chen. 2020. Wrong-way migrations of benthic species driven by ocean warming and larval transport. Nature Climate Change. DOI: 10.1038/s41558-020-0894-x The paper is available at: <a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41558-020-0894-x&data=02%7C01%7Chfuchs%40marine.rutgers.edu%7C8f5bf7d8e5744a5353e408d84e6e924e%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C637345584096517620&sdata=Jy%2FD%2FyrfSX6Z0EU1rriqL%2FHnz7KLxpmlqjQmhM6ACAg%3D&reserved=0">https://www.nature.com/articles/s41558-020-0894-x</a>

opencc-by-4.0Aug 2020View details →

Experimental Tuning of Transport Regimes in Hyperuniform Disordered Photonic Materials

This repository contains the videos related to the paper entitled "Experimental Tuning of Transport Regimes in Hyperuniform Disordered Photonic Materials" published in <a href="https://doi.org/10.1103/PhysRevLett.125.127402">Physical Review Letters 125, 127402 (2020)</a>. They show how the how the electromagnetic wave propagates in the cavity for different frequency ranges. <ul> <li>video-1-stealth.mp4: Stealth regime (Gaussian bandpass filter, \(f_0 = 1.75\ \mathrm{GHz}\), \(\Delta \nu = 0.25\ \mathrm{GHz}\))</li> <li>video-2-stealth.mp4: Stealth regime (Gaussian bandpass filter, \(f_0 = 2.25\ \mathrm{GHz}\), \(\Delta \nu = 0.25\ \mathrm{GHz}\))</li> <li>video-3-diffusion.mp4: Wave diffusion (Gaussian bandpass filter, \(f_0 = 3.50\ \mathrm{GHz}\), \(\Delta \nu = 0.25\ \mathrm{GHz}\))</li> <li>video-4-localizationBelowGap.mp4: Dielectric Anderson localized modes just below the bandgap (Gaussian bandpass filter, \(\Delta \nu = 0.25\ \mathrm{GHz}\))</li> <li>video-5-bandgap.mp4: Square filter in the bandgaps</li> <li>video-6-localizationAboveGap.mp4: Air Anderson localized modes just above the bandgap (Gaussian bandpass filter, \(\Delta \nu = 0.25\ \mathrm{GHz}\))</li> <li>video-7-diffusion.mp4: Wave diffusion (Gaussian bandpass filter, \(f_0 = 6.50\ \mathrm{GHz}\), \(\Delta \nu = 0.25\ \mathrm{GHz}\))</li> </ul>

opencc-by-4.0Sep 2020View details →

Trajectory Movie for the article 'A Lagrangian view of the atmospheric river related to the heavy rainfall of July 2020 in Japan: Importance of moisture gain during transport'

The supplement movie for the article 'A Lagrangian view of the atmospheric river related to the heavy rainfall of July 2020 in Japan: Importance of moisture gain during transport'.

opencc-by-4.0Dec 2019View details →

Representation model of wind velocity fluctuations and saltation sand transport in aeolian sand flow

The data of the figures in the article.

opencc-by-4.0Sep 2020View details →

A center of heavy PM2.5 pollution in the Yangtze River middle basin attributed to regional transport of PM2.5 over China

The Multi-resolution Emission Inventory for China (MEIC) emission sources dataset and PM2.5 datasets

opencc-by-4.0Oct 2020View details →

E3SM - Drake Passage Transport, 26.5 AMOC, Northward Heat Transport at 26.5N, from Hewitt et al 2020

E3SM monthly output has been annually averaged and processed to derive the maximum overturning at 26.5 N, the northward heat transport at 26.5N and the drake passage transport.  The model output includes the low resolution configuration and high resolution configuration.  Both runs use the 1950 control from the HighResMIP protocol.

opencc-by-4.0Oct 2020View details →

Dataset for "Sorption, anomalous water transport and dynamic porosity in cement paste: A spatially localised 1H NMR relaxation study and a proposed mechanism"

This record is the dataset for Figures 4, 5, 6, 7, 8 and 9 in the journal article "Sorption, anomalous water transport and dynamic porosity in cement paste: A spatially localised 1H NMR relaxation study and a proposed mechanism" published in Cement and Concrete Research, Volume 133, July 2020, 106045, https://doi.org/10.1016/j.cemconres.2020.106045. Abstract: The link between anomalous water sorption and dynamic porosity in cement pastes is explored using spatially resolved GARField1H nuclear magnetic resonance (NMR) relaxation analysis. A model is developed in which the effective capillary diffusion coefficient is dependent on the instantaneous pore size distribution. This and earlier data show changes in pore size distribution resultant from changes in saturation that do not occur instantaneously with changes in degree of saturation. Therefore, it is assumed that the pore size distribution is always relaxing exponentially towards a (saturation dependent) equilibrium. It follows that the diffusivity is sample history (i.e. time) dependent as well as saturation dependent. This is sufficient to explain anomalies in rapid capillary water sorption. The same concepts are applied to slow drying. In this case, porosity changes occur on a timescale much shorter than drying so the system is always in dynamic equilibrium and anomalies are therefore not seen.

opencc-by-4.0Oct 2020View details →

SGS scalar transport - homogeneous isotropic turbulence

This dataset contains filtered data (spectral cut) from three DNS simulations (train, tests, decay) of 3-dimensional homogeneous isotropic turbulence in a \(512^3\) periodic domain. More precisely, the following fields are available: <ul> <li>Filtered velocities</li> <li>Filtered transported (passive) scalar</li> <li>Divergence of the SGS term from the transport equation obtained from DNS</li> <li>SGS fluxes (in the three directions) from the transport equation obtained from DNS</li> </ul> The scalar is forced on the high spectral wavenumbers, such that filtered data is not impacted in train and tests, while the scalar forcing is removed in the decay simulation. Note that all three simulations are forced on the velocities with an Alvelius-type scheme. The dataset also provide with three different filter sizes: 8, 16 and 32 times from the initial DNS resolution, which give domain sizes of \(64^3, 32^3, 16^3\) respectively. This dataset has been used to train NN models available : https://github.com/hrkz/SubgridTransportNN.

opencc-zeroOct 2020View details →

Glucose transporter expression and regulation following a fast in the ruby-throated hummingbird, Archilochus colubris

Hummingbirds, subsisting almost exclusively on nectar sugar, face extreme challenges to blood sugar regulation. The capacity for transmembrane sugar transport is mediated by the activity of facilitative glucose transporters (GLUTs) and their localisation to the plasma membrane (PM). In this study, we determined the relative protein abundance of GLUT1, GLUT2, GLUT3, and GLUT5 via immunoblot using custom antibodies in whole-tissue and PM fractions of flight-muscle, heart, and liver of ruby-throated hummingbirds (Archilochus colubris). GLUTs examined were detected in nearly all tissues tested. Hepatic GLUT1 was minimally present in whole-tissue and absent in PM fractions. GLUT5 was expressed in flight-muscles at levels comparable to that of their liver, consistent with hummingbird flight-muscles' hypothesised uniquely high fructose-uptake and oxidation capacity. To assess GLUT regulation, we fed ruby-throated hummingbirds 1M sucrose ad libitum for 24 hours followed by either 1 hour of fasting or continued feeding until sampling. We measured relative GLUT abundance and concentrations of circulating sugars. Blood fructose concentration in fasted hummingbirds declined (∼5 mM to ∼0.18 mM), while fructose-transporting GLUT2 and GLUT5 abundance did not change in PM fractions. Blood glucose concentrations remained elevated in fed and fasted hummingbirds (∼30 mM), while glucose-transporting GLUT1 and GLUT3 in flight muscle and liver PM fractions, respectively, declined in fasted birds. Our results suggest that glucose uptake capacity is dynamically reduced in response to fasting, allowing for maintenance of elevated blood glucose levels, while fructose uptake capacity remains constitutively elevated promoting depletion of blood total fructose within the first hour of a fast.

opencc-zeroOct 2020View details →

Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress

The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM's unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin's LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs.