cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7280/d1wt11
title: Glacier catchments/basins for the Greenland Ice Sheet

description: We divide Greenland, including its peripheral glaciers and ice caps, into
 260 basins grouped in seven regions:  southwest (SW), central
 west (CW), (iii) northwest (NW), north (NO), northeast
 (NE), central east (CE), and southeast (SE). These
 regions are selected based on ice flow regimes, climate, and the need to
 partition the ice sheet into zones comparable in size (200,000 km2
 to 400,000 km2) and ice production (50 Gt/y to 100 Gt/y, or
 billion tons per year). Out of the 260 surveyed glaciers, 217 are
 marine-terminating, i.e., calving into icebergs and melting in contact
 with ocean waters, and 43 are land-terminating.The actual number of
 land-terminating glaciers is far larger than 43, but we lump them into
 larger units for simplification. Each glacier catchment is defined using a
 combination of ice flow direction and surface slope. In areas of fast flow
 (&gt; 100 m), we use a composite velocity mosaic (Mouginot et al.
 2017). In slowmoving areas, we use surface slope using the GIMP DEM
 (https://nsidc.org/data/nsidc- 0715/versions/1) (Howat et al. 2014)
 smoothed over 10 ice thicknesses to remove shortwavelength undulations.
 References: Mouginot J, Rignot E, Scheuchl B, Millan R (2017)
 Comprehensive annual ice sheet velocity mapping using landsat-8,
 sentinel-1, and radarsat-2 data. Remote Sensing 9(4). Howat IM, Negrete A,
 Smith BE (2014) The greenland ice mapping project (gimp) land
 classification and surface elevation data sets. The Cryosphere
 8(4):1509–1518.
DOI: 10.5061/dryad.5tc40vg
title: Data from: Road avoidance and its energetic consequences for reptiles

description: Roads are one of the most widespread human-caused habitat modifications
 that can increase wildlife mortality rates and alter behaviour. Roads can
 act as barriers with variable permeability to movement and can increase
 distances wildlife travel to access habitats. Movement is energetically
 costly, and avoidance of roads could therefore impact an animal's
 energy budget. We tested whether reptiles avoid roads or road crossings
 and explored whether the energetic consequences of road avoidance
 decreased individual fitness. Using telemetry data from Blanding's
 turtles (Emydoidea blandingii; 11,658 locations of 286 turtles from 15
 sites) and eastern massasaugas (Sistrurus catenatus; 1868 locations of 49
 snakes from 3 sites), we compared frequency of observed road crossings and
 use of road-adjacent habitat by reptiles to expected frequencies based on
 simulated correlated random walks. Turtles and snakes did not avoid
 habitats near roads, but both species avoided road crossings. Compared to
 simulations, turtles made fewer crossings of paved roads with low speed
 limits, and more crossings of paved roads with high speed limits. Snakes
 made fewer crossings of all road types than expected based on simulated
 paths. Turtles travelled longer daily distances when their home range
 contained roads, but the predicted energetic cost was negligible:
 substantially less than the cost of producing one egg. Snakes with roads
 in their home range did not travel further per day than snakes without
 roads in their home range. We found that turtles and snakes avoided
 crossing roads, but road avoidance is unlikely to impact fitness through
 energetic expenditures. Therefore, mortality from vehicle strikes remains
 the most significant impact of roads on reptile populations.
description: READMEbltu_dataData on Blanding's turtle road crossing frequency, mean distance to a road, and daily distance travelledbltu_roadclass_dataCrossing frequency of Blanding's turtles and simulated turtles over different road typesmass_dataMassasauga road crossing frequency, mean distance to a road, and daily distance travelledmass_roadclass_dataCrossing frequency of massasaugas and simulated snakes over different road types
DOI: 10.15468/dl.j9ewwc
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Iran (Islamic Republic of)",
 "Issue is one of (Zero coordinate, Coordinate out of range, Coordinate invalid, Coordinate rounded, Geodetic datum invalid, Geodetic datum assumed WGS84, Continent coordinate mismatch, Footprint WKT invalid, Footprint WKT mismatch, Country coordinate mismatch, Footprint SRS invalid)",
 "Month is one of (December, November, October, September, August, July, June, May, April, March, February, January)",
 "TaxonKey is Falco tinnunculus",
 "Year 2000-2026"
 ]
}

 The dataset includes 126 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001897-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kbz396
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lichonycteris obscura"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001893-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6078/d1rq4v
title: Supporting data for "Direct observation of changing NOx lifetime in North American cities"

description: NOx lifetime can be directly observed from space, and has a nonlinear
 relationship with its own concentration. At high NOx concentrations, NOx
 lifetime decreases with decreasing concentration, but at intermediate
 concentrations, the reverse is true. Here we show that urban NOx lifetime
 in North America has changed between 2005 and 2014. The shape of these
 changes is qualitatively consistent with a steady-state model of NOx
 lifetime with decreasing NOx emissions. The pattern of change suggests
 that NOx-limited chemistry now controls urban NOx lifetime.
description: This dataset was produced by doi: 10.5281/zenodo.2629580 Briefly, NO2 column densities from the Berkeley High Resolution (BEHR) NO2 product, v3.0B (daily) were aligned according to wind direction and integrated in the across-wind direction to product line densities. These line densities were fit with exponentially modified Gaussian functions, and NOx lifetimes derived from the characteristic distance of the exponential and the average wind speed.
description: This dataset consists of both the native Matlab .mat files and
 netCDF versions of those files that contain the line densities and EMG
 fitting results for 49 cities in North America.  The analysis code at
 doi: 10.5281/zenodo.2629580 uses the .mat files; the netCDF files are provided for users without access to Matlab.
DOI: 10.6078/d1g67b
title: Xenon hydrate as an analogue of methane hydrate in geologic systems out of thermodynamic equilibrium

description: This data set contains simulation results of hydrate growth on a
 gas-liquid interface for both methane and xenon hydrate systems. The
 simulations are performed on a 1D domain of 115 micron in length and for a
 duration of 40 minutes. The data set contains two MATLAB data files
 (methane_data.mat and xenon_data.mat) and one file to help users to
 visualize the data (plot_data.m). In the file plot_data.m, we also use
 experimental data from Taylor et al. 2007, which measures methane hydrate
 film thickness as a function of time at three different
 subcoolings. The discussion of the results are presented in the
 manuscript titled "Xenon hydrate as an analogue of methane hydrate in
 geologic systems out of thermodynamic equilibrium" (in review in
 G-cubed).
DOI: 10.6078/d15q4k
title: Synthetic Log-Conductivity

description: This dataset contains the baseline fields for the case study described in
 the manuscript Hydrogeological Modeling and Water Resources Management:
 Improving the Link between Data, Prediction, and Decision-Making (Water
 Resources Research, under review). The data are described in the files
 readme.txt and example_code.R.
DOI: 10.5061/dryad.kd2b16c
title: Tropical niche conservatism explains the Eocene migration from India to Southeast Asia in Ochyroceratid spiders

description: Biological migrations between India and Southeast (SE) Asia provide an
 ideal system for exploring the effects of geology and climate on species
 ranges. Geologists have confirmed that the direct collision between India
 and Eurasia occurred in the Early Eocene, but most migrations occurred
 between the Indian subcontinent and SE Asia rather than the former and the
 southern margin of Eurasia. To explain this seemingly paradoxical
 disconnect between the routes of plate movement and biological migration,
 we studied the evolutionary history of the tropical spider family
 Ochyroceratidae based on 101 globally distributed species. We infer a
 robust dated phylogeny using both transcriptomic data and a dataset of
 classical markers and relate these to biogeographic and climatic analyses.
 Our results indicate that the monophyly of Ochyroceratidae is strongly
 supported, and the divergence times suggest a Cretaceous Gondwanan origin
 of the family. Reconstructed biogeographic histories support a dispersal
 event from the Indian subcontinent to islands of SE Asia 55–38 million
 years ago. Climatic analyses and the fossil record reveal that
 ochyroceratids are characterized by a high degree of tropical niche
 conservatism, and that the ancestor of the Indian and SE Asian clades
 originated in very warm, wet environments. Early Eocene tropical, perhumid
 climates in India and SE Asia may have facilitated ochyroceratid
 migration, whereas the dry or seasonal climate extending from the eastern
 coast of China to Central Asia may have acted as a barrier, preventing
 dispersal. Our analyses suggest that climate plays a more important role
 than geology in biological migration from the Indian subcontinent to SE
 Asia, providing new insights into the Indian–Asian biogeographic link.
description: SI File
 appendices.rar
DOI: 10.6078/d12099
title: Intensification of the Pre‐Meiyu Rainband in the Late 21st Century

description: This contains the SST forcing files and model output for the CESM
 idealized runs used in  Chiang, JCH, J Fisher, W Kong, and MJ
 Herman, "Intensification of the pre-Meiyu rainband in the late 21st
 century", submitted to Geophysical Research Letters, April
 2019 
description: Forcing files for CESM1 fixed SST
 runs
 sst_HadOIBl_bc_0.9x1.25_clim_c040926_20062015.nc
 and sst_HadOIBl_bc_0.9x1.25_clim_c040926_20912100.nc contain the SST
 boundary condition files for the early and late 21st century runs,
 respectively. Greenhouse gas concentrations used
 for (early / late 21st century) are: CO2 391.92 / 899.233 ppm, CH4 1793.32
 / 3712.32 ppb, and N2O 323.884 / 429.625 ppb.
 Model output These output
 are used for figures 4c, 4d, S5c, and S5d of the paper.  Daily
 climatological fields averaged over the last 30 years of
 35-year simulations.     early_21st.30yr.dayclim.U.nc -
 early 21st century run, daily zonal wind climatology.
 early_21st.30yr.dayclim.T.nc - early 21st century run, daily air
 temperature climatology.
 late_21st_GHGs.30yr.dayclim.U.nc - late 21st century GHGs
 only run, daily zonal wind climatology.
 late_21st_GHGs.30yr.dayclim.T.nc  - late 21st century GHGs
 only run, daily air temperature climatology.
 late_21st_SST.30yr.dayclim.U.nc - late 21st century SST only run,
 daily zonal wind climatology.
 late_21st_SST.30yr.dayclim.T.nc  - late 21st century
 SST only run, daily air temperature climatology.
DOI: 10.15146/r3wt2n
title: Estimation of methane emissions from the U.S. ammonia fertilizer industry using a mobile sensing approach (supplemental data)

description: This is the supplemental data for the paper entitled "Estimation of
 methane emissions from the U.S. ammonia fertilizer industry using a mobile
 sensing approach" 1) Ammonia fertilizer plant (CH4 and GPS).zip: is
 the time series of above-ambient methane mixing ratios and GPS collected
 by the Google Street View (GSV) car near the visited ammonia fertilizer
 plants. 2) Wind statistics.xlsx: report the wind statistics collected by
 a small meteorological tower establised near the visited ammonia
 fertilizer plants. 3) Example plume measurements.kmz: the KML files of
 example plume measurements for visited ammonia fertilzier plants.
DOI: 10.5061/dryad.9rh2873
title: Data from: Utilization of metakaolin based geopolymer as a mud-cake solidification agent to enhance the bonding strength of oil well cement-formation interface

description: This research work designed a novel mud-cake solidification method to
 improve zonal isolation of oil and gas wells. The calculation methodology
 of mud-cake compressive strength was proposed. The optimal formula of
 activator and solid precursors, the proper activating time and the best
 activator concentration were selected by compressive strength test. The
 effects of solid precursors on the properties of drilling fluid were
 evaluated. The performances of this novel method were measured. Test
 results show that the respective percentage of bentonite, metakaolin, slag
 and activator is 1:1:0.3:0.8, as well as the optimum ratio of Na2SiO3/NaOH
 is 40:1. The optimum concentration of activator is 0.21 due to the limited
 proportion of solid precursors in mud-cake, and the activating time should
 not lower than 10 min. The solid precursors did not show bad influence on
 the rheological property of drilling fluids in different conditions. Even
 though the compressive strength decreased when the solid precursors blend
 with barite or other drilling fluid additives, the strength values can
 still achieve 8 MPa. The reaction of metakaolin and activator formed
 crosslink structure in the mud-cake matrix, which enhanced the connection
 of the loose bentonite particles, lead to the significant enhancement of
 shear bonding strength and hydraulic bonding strength. This mud-cake
 solidification method provides a new approach to improve the quality of
 zonal isolation.
description:
DOI: 10.25349/d99g6f
title: Halite precipitation from double-diffusive salt fingers in the Dead Sea: Numerical simulations

description: We employ direct numerical simulations in order to analyze the role of
 double-diffusive salt fingering in halite precipitation from hypersaline
 lakes. Guided by field observations from the Dead Sea, which represents
 the only modern deep stratified lake that precipitates halite under
 hydrological crisis, we consider a saturated layer of warm, salty brine
 (epilimnion) overlying a layer of colder, less salty brine (hypolimnion)
 that is also saturated. The double-diffusive instability originating in
 the metalimnion gives rise to an asymmetrical pattern of less salty
 ascending fingers, accompanied by descending salt fingers that lose heat
 as they propagate through the metalimnion. The net result is a strong,
 downward salinity flux that leads to the undersaturation of the
 epilimnion, while the hypolimnion becomes oversaturated and precipitates
 halite. These interfacial processes within deep, hypersaline watercolumns
 in warm and dry regions suggest a potential route towards the formation of
 thick halite layers found in the geological record.
DOI: 10.6071/m3pq1w
title: Growth rate assays reveal fitness consequences of β-lactamases

description: Clinical resistance determination is critical for monitoring the spread of
 antibiotic resistance. However, clinical methods of detecting resistance
 lack the sensitivity necessary to make strong conclusions about fitness.
 Growth rates are a far more sensitive method of measuring resistance, but
 they differ from clinical methods in that a single concentration of
 antibiotic is used for the assay. Here we show that in spite of this key
 difference, the results of growth rates correlate well with clinical
 determination of resistance by MIC, while providing the sensitivity
 required for direct input as fitness values into mathematical models. By
 measuring the growth rates of sequenced clinical isolates obtained from
 Dignity Health Mercy Medical Center, we additionally detected the fitness
 effects of individual resistance genes on bacteria as they are exposed to
 different antibiotics. In our study, the CTX-M-15 gene conferred the
 highest fitness; the TEM-1 gene decreased fitness and the OXA-1 gene had
 no detectable effect on fitness. These results could explain the
 increasing presence of CTX-M-15 in clinical isolates across the world.
DOI: 10.6071/m3d95s
title: Assessing the impact of product inhibition in a chromogenic assay

description: Chromogenic substrates (CS) are synthetic substrates used to monitor the
 activity of a target enzyme. It has been reported that some CSs display
 competitive product inhibition with their target enzyme. Thus, in assays
 where enzyme activity is continuously monitored over long periods of time,
 the product inhibition may significantly interfere with the reactions
 being monitored. Despite this knowledge, it is rare for CSs to be directly
 incorporated into mathematical models that simulate these assays. This
 devalues the predictive power of the models. In this study, we examined
 the interactions between a single enzyme, coagulation factor Xa, and its
 chromogenic substrate. We developed, and experimentally validated, a
 mathematical model of a chromogenic assay for factor Xa that explicitly
 included product inhibition from the CS. We employed Bayesian inference,
 in the form of Markov-Chain Monte Carlo, to estimate the strength of the
 product inhibition and other sources of uncertainty such as pipetting
 error and kinetic rate constants. Our model, together with carefully
 calibrated biochemistry experiments, allowed for full characterization of
 the strength and impact of product inhibition in the assay.  The
 effect of CS product inhibition in more complex reaction mixtures was
 further explored using mathematical models.
description: Experimental data for both continuous and subsampled experiments
 are stored as an excel file but is readable by a large number of
 programs.     Markov-chain monte
 carlo posterior distributions for parameters of both models (with and
 without product inhibition) are stored as Matlab .mat files.
DOI: 10.7280/d1vt0b
title: Supporting data for Formation of Highly Oxidized Molecules from NO3 Radical Oxidation of Δ-3-Carene: A Computational Mechanism

description: NO3 radical oxidation of most monoterpenes is a significant source of
 secondary organic aerosol (SOA) in many regions influenced by both
 biogenic and anthropogenic emissions, but there are very few published
 mechanistic studies of NO3 chemistry beyond simple 1st generation
 products. Here, we present a computationally-derived mechanism detailing
 the unimolecular pathways available to the 2nd generation of peroxy
 radicals following NO3 oxidation of Δ-3-carene, defining generations based
 on the sequence of peroxy radicals formed rather than number of oxidant
 attacks. We assess five different types of unimolecular reactions,
 including peroxy and alkoxy radical (RO2 and RO) hydrogen shifts, RO­2 and
 RO ring closing (e.g. endoperoxide formation), and RO decomposition. Rate
 constants calculated using quantum chemical methods indicate that this
 chemical system has significant contribution from both bimolecular and
 unimolecular pathways. The dominant unimolecular reactions are
 endoperoxide formation, RO H-shifts, and RO decomposition. However, the
 complexity of the overall reaction is tempered as only 1 or 2 radical
 propagation pathways dominate the fate of each radical intermediate.
 Chemical Ionization Mass Spectrometry (CIMS) measurements using the NO3-
 reagent ion during Δ-3-carene + NO3 chamber experiments show products
 consistent with each of the three types of unimolecular reactions
 predicted to be important from the computational mechanism. Moreover, the
 SIMPOL group contribution method for predicting vapor pressures suggests
 that a majority of the closed-shell products inferred from these
 unimolecular reactions are likely to have low enough vapor pressure to be
 able to contribute to SOA formation.
description: please refer to paper
DOI: 10.7280/d1kd47
title: Aerosol particle measurements taken during the airborn ARISTO 2016 campaign.

description: Several different types of measurements of particle size and concentration
 were compared during the 2016 Airborne Research Instrumentation Testing
 Opportunity (ARISTO) campaign.  The scanning mobility particle
 sizer (SMPS) measured number-size distributions for mobility diameters
 between ~20-350 nm or ~8-110 nm, depending on the mobility analyzer
 chosen.  Also included were two stand-alone condensation particle
 counters (CPC) for determining size-integrated particle
 concentrations.  A wing-mounted and a rack-mounted Ultra-High
 Sensitivity Aerosol Spectrometer (UHSAS) were used to measure size
 distributions between 60 and 1000 nm.  Lastly, two different
 sampling inlets were used to investigate performance and observe any
 systematic biases.  Most sampling occurred during cloud-free
 summer conditions in the western United States.  Number
 concentrations from the two CPCs typically agreed within 12% once the
 flows in the ultrafine particle counter were corrected as a function of
 pressure.  As expected, the size-integrated number concentrations
 from the SMPS and UHSAS were generally less than those of the CPCs, as the
 former cover only part of the total range of particle sizes measured by
 the CPCs.  Integrated number concentrations from the wing-mounted
 and rack-mounted UHSAS generally agreed within 20% for all diameter ranges
 analyzed.  The overlap region between the SMPS and the UHSAS
 showed reasonable agreement of +/- 20%.  Some of the uncertainty
 regarding these measurement comparisons originates from a variety of
 factors, including sampling frequency, particle refractive index,
 differences between physical and mobility diameters, and counting
 efficiency uncertainties in the UHSAS optical cavity, especially for the
 smallest diameters (60-100 nm).
description: Data from diffferent particle measuring techniques (sizing and
 concentration) were taken from the C130 aircraft during the 2016 ARISTO
 campaign.  Data has been processed as indicated in Ortega et al., Aerosol
 Science and Technology, 2019.  DOI:  https://doi.org/10.1080/02786826.2019.1610554
description: The read me file, "Aristo2016_data_files_read_me.txt"
 is included to guide the user for any data processing.
DOI: 10.25338/b8801b
title: Genomes From Bacteria Associated with the Canine Oral Cavity: a Test Case for Automated Genome-Based Taxonomic Assignment

description: Taxonomy for bacterial isolates is commonly assigned via sequence
 analysis. However, the most common sequence-based approaches (e.g. 16S
 rRNA gene-based phylogeny or whole genome comparisons) are still labor
 intensive and subjective to varying degrees. Here we present a set of 33
 bacterial genomes, isolated from the canine oral cavity. Taxonomy of these
 isolates was first assigned by PCR amplification of the 16S rRNA gene,
 Sanger sequencing, and taxonomy assignment using BLAST. After genome
 sequencing, taxonomy was revisited through a manual process using a
 combination of average nucleotide identity (ANI), concatenated marker gene
 phylogenies, and 16S rRNA gene phylogenies. This taxonomy was then
 compared to the automated taxonomic assignment given by the recently
 proposed Genome Taxonomy Database (GTDB). We found the results of all
 three methods to be similar (25 out of the 33 had matching genera), but
 the GTDB approach was less subjective, and required far less labor. The
 primary differences in the remaining taxonomic assignments related to
 proposed taxonomy changes by the GTDB team.