cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d10h6q
title: Photoionization and electron impact ionization frequencies in the dayside ionosphere of Mars, calculated from MAVEN in situ data

description: The following data set contains valid photoionization frequencies and
 electron impact ionization frequencies for the primary neutral species
 CO2, O, CO, N2, and Ar in the dayside ionosphere of Mars, calculated from
 MAVEN in situ data from November 1, 2014 until December 12,
 2019.  It also contains necessary ancillary data, including Time
 UTC, Mars season, solar zenith angle, spacecraft altitude, atmospheric
 pressure, normalized on attenuated CO2 photoionization frequency (as a
 proxy for solar activity), the neutral densities of the primary neutral
 species, and the magnitude and elevation angle of a model magnetic field
 calculated by Morschhauser et al. [2014] (DOI: 10.1002/2013JE004555) and
 normalized to 400 km altitude.  It is the primary source for the
 figures contained in the
 manuscript 2021JE006923: "Ionization efficiency in
 the dayside ionosphere of Mars: structure and variability", by Robert
 J Lillis, Shaosui Xu, David Mitchell, Ed Thiemann, Frank Eparvier, Mehdi
 Benna, Meredith Elrod.
description: The methods for calculating both the photoionization frequencies
 and electron impact ionization frequencies are contained
 within manuscript 2021JE006923: , "Ionization efficiency in the
 dayside ionosphere of Mars: structure and variability", by Robert J
 Lillis, Shaosui Xu, David Mitchell, Ed Thiemann, Frank Eparvier, Mehdi
 Benna, Meredith Elrod.
DOI: 10.5061/dryad.xsj3tx9gg
title: Atmospheric pollutant concentrations and leaf chemistry variables collected along gradients of median household income and traffic density in Salt Lake Valley, UT

description: We utilize traffic density and Convolvulus arvensis leaf chemistry to
 understand spatial patterns linking atmospheric pollution and household
 income in the Salt Lake City metropolitan area, USA. We hypothesize that
 traffic density will explain variation in atmospheric NOx and O3
 concentrations. In addition, we expect foliar %N and nitrogen isotope
 ratios (δ15N) to be elevated and carbon isotope ratios (δ13C) to be
 depleted on high traffic density roads. These hypotheses were supported:
 we found the highest NOx and lowest O3 concentrations on high-traffic
 density roads. Also, NOx concentrations were higher in low-income
 neighborhoods. Low-income neighborhoods contained a greater density of
 high-traffic roads than high-income neighborhoods. Foliar %N was highest
 in low-income neighborhoods and was correlated with NOx and O3, while δ15N
 was more depleted with increasing O3. These findings indicate that the
 distribution of high-traffic density roads plays a significant role in
 inequities in pollution exposure between high- and low-income
 neighborhoods, which is reflected in leaf chemistry.
description: Details on the methodology can be found in the
 "Metadata" tab in the attached excel file and in Cobley et al.
 2021.
DOI: 10.5061/dryad.tdz08kq0z
title: Alpha: A Fortran program for simulating porewater radiolysis

description: The radiolysis of porewaters by uranium, thorium, and potassium in mineral
 grains is a recognised source of molecular hydrogen in rock- and
 sediment-hosted fluids. This radiolytic hydrogen is of geomicrobiological
 interest as a potential energy source (electron donor) for microbial
 metabolism, especially in energy-limited settings such as the marine deep
 biosphere or the subsurface of Mars. Previous efforts to predict the
 production of radiolytic hydrogen from columns of rock and sediment have
 tended to rely upon analytic models that cannot account for the
 attenuation of mineral radiation by grains larger than ~30 microns. To
 address this, we have developed a Monte Carlo method to simulate the
 physics of mineral radiation and evaluate the production of H2 as a
 function of mineral grain size and radioisotope composition. The results
 confirm that grain size is a major control on radiolytic H2 yield. For
 example, using the standard geological classification of grain sizes, we
 find that clay can produce up to an order of magnitude more H2 per unit
 time than sand. The magnitude of this effect is illustrated using
 compositional data from real geological units in order to demonstrate the
 dependence of radiolytic hydrogen flux on natural radionuclide
 concentration and bulk porosity.
DOI: 10.5061/dryad.f4qrfj6x0
title: Nonlinear responses of ecosystem carbon fluxes to nitrogen deposition in an old-growth boreal forest

description: Nitrogen (N) deposition is known to increase carbon (C) sequestration in
 N-limited boreal forests. However, the long-term effects of N deposition
 on ecosystem carbon fluxes have been rarely investigated in old-growth
 boreal forests. Here we show that decade-long experimental N additions
 significantly stimulated net primary production (NPP) but the effect
 decreased with increasing N loads. The effect on soil heterotrophic
 respiration (Rh) shifted from a stimulation at low-level N additions to an
 inhibition at higher levels of N additions. Consequently, low-level N
 additions resulted in a neutral effect on net ecosystem productivity
 (NEP), due to a comparable stimulating effect on NPP and Rh, while NEP was
 increased by high-level N additions. Moreover, we found nonlinear temporal
 responses of NPP, Rh and NEP to low-level N additions. Our findings imply
 that actual N deposition in boreal forests likely exerts a minor
 contribution to their soil C storage.
description: Detailed methods concerning how the dataset were collected can be
 found in the related article.
DOI: 10.5061/dryad.h18931zmt
title: Plant community legacy effects on nutrient cycling, fungal decomposer communities and decomposition in a temperate grassland

description: Soil legacies mediated by plant species-specific microbial communities are
 major drivers of plant community dynamics. Most soil legacy studies focus
 on the role of pathogens and mutualists in driving these processes, while
 much less is known about plant litter-mediated changes to the soil
 microbial community. Here, we used an existing plant-soil feedback field
 experiment in which plant communities with different growth strategies
 (i.e., fast versus slow) and different proportions of functional groups
 (grasses versus forbs) were allowed to condition the soil over contrasting
 temporal scales (i.e., one versus two years) in a natural grassland. In
 the feedback phase, we removed the existent plant community, and replaced
 it with a standardized response plant community. We then tested the legacy
 effects of these different soil conditioning treatments on decomposition
 processes, nutrient cycling and soil decomposer community composition.
 Soil legacy effects on decomposition and the soil decomposer community
 composition were most evident right after the start of the feedback phase,
 but disappeared soon after the new community established. The soil
 conditioning time and years since disturbance affected most of the soil
 functions consistently, while no strong effects of plant functional group
 and plant growth strategy were found. We conclude that after disturbance,
 it is recovery time, not soil legacy effects, that is the most important
 factor driving soil functions.
description: A plant-soil feedback field
 experiment comprised of plant communities with different growth strategies
 (i.e., fast versus slow) and different proportions of functional groups
 (grasses versus forbs) that were allowed to condition the soil over
 contrasting temporal scales (i.e., one versus two years) was conducted.
 The experiment consisted of a conditioning phase and a feedback phase.
 During the conditioning phase, each plot was divided into three subplots.
 We removed the existent plant community and replaced it with target plant
 communities in two successive years in two different subplots. During the
 feedback phase, all plots were sown with a standard species-rich plant
 community and characteristics of the plant community and the soil were
 measured. Here, standardized decomposition rate measurements, nutrient
 concentrations extracted from resin capsules, soil chemistry, soil organic
 matter content and above-ground plant biomass are reported for both
 consecutive years of the feedback phase.
DOI: 10.5061/dryad.2bvq83br7
title: Disease data of Triphragmium ulmariae on Filipendula ulmaria in the Skeppsvik archipelago

description: The data set provides information on the incidence, prevalence and
 severity of a rust fungus Triphragmium ulmariae occurring in populations
 of the herbaceous perennial Filipendula ulmaria growing on a range of
 islands in the Skeppsvik archipelago, northern Sweden. These data,
 together with information on the size of individual host populations, has
 been used to monitor the impact of the disease on host population growth
 rates and temporal and spatial dynamics in a natural plant pathogen - host
 metapopulation system. See Zhan, J., Ericson, L., González-Jiménez, J.
 & Burdon, J.J. (202*). Disease affecting host population growth
 rates in a natural wild plant-pathogen association over a 30-year period.
 Journal of Ecology, accepted. And Smith, David L., Ericson, Lars &
 Burdon, Jeremy J. (2003) Epidemiological patterns at multiple spatial
 scales: an 11-year study of a Triphragmium ulmariae– Filipendula ulmaria
 metapopulation. Journal of Ecology 91 (5), 890-903. for further details.
DOI: 10.5061/dryad.31zcrjdmr
title: Data from: Informing conservation strategies with museum genomics: Long-term effects of past anthropogenic persecution on the elusive European wildcat

description: Like many carnivore species, European wildcats (Felis silvestris) have
 suffered severe anthropogenic population declines in the past, resulting
 in a strong population bottleneck in the beginning of the 20th century. In
 Germany, the species has managed to survive its near-extinction in small
 isolated areas and is currently recolonizing former habitats owing to
 legal protection and concerted conservation efforts. Here, we SNP
 genotyped and mtDNA sequenced 56 historical and 650 contemporary samples
 to assess the impact of massive persecution on genetic diversity,
 population structure and hybridization dynamics of wildcats.
 Spatiotemporal analyses suggest that the presumed postglacial
 differentiation between two genetically distinct metapopulations in
 Germany is in fact the result of the anthropogenic bottleneck followed by
 re-expansion from few secluded refugia. We found that, despite the
 bottleneck, populations experienced no severe genetic erosion, nor
 suffered from elevated inbreeding or showed signs of increased
 hybridization with domestic cats. Our findings have significant
 implications for current wildcat conservation strategies, as the data
 analyses show that the two presently recognized wildcat population
 clusters should be treated as a single conservation unit. Although current
 populations appear under no imminent threat from genetic factors,
 fostering connectivity through the implementation of forest corridors will
 facilitate the preservation of genetic diversity and promote long-term
 viability. The present study documents how museum collections can be used
 as essential resource for assessing long-term anthropogenic effects on
 natural populations, e.g., regarding population structure and the
 delineation of appropriate conservation units, potentially informing
 todays’ species conservation.
description: The SNP data was genotyped with microfluidic 96.96 Dynamic
 Arrays™ (Fluidigm Corp., South San Francisco, USA) using a panel of 96 SNP
 markers described in a previous study (von Thaden et al. 2020).
description: The SNP genotypes are provided in variant call format (.vcf). The
 dataset consists of genotypes for 175 museum and 650 contemporary wildcat
 samples. Sample names include (separated by
 underscore): Sample ID (as referred to in
 corresponding article) Sample type (F1, skin; G1,
 dried tissue remains; FB1, footpad; K1, bone; NMK1, turbinal bone; Z1,
 tooth) Genotyping replicate (coded with
 "r1" to "r7")
DOI: 10.5061/dryad.76hdr7sxs
title: The soil microbiome increases plant survival and modifies interactions with root endosymbionts in the field

description: Evidence is accumulating that the soil microbiome—the community of
 microorganisms living in soils—has a major effect on plant traits and
 fitness. However, most work to date has taken place under controlled
 laboratory conditions and has not experimentally disentangled the effect
 of the soil microbiome on plant performance from the effects of key
 endosymbiotic constituents. As a result, it is difficult to extrapolate
 from existing data to understand the role of the soil microbiome in
 natural plant populations. To address this gap, we performed a field
 experiment using the black medick Medicago lupulina to test how the soil
 microbiome influences plant performance and colonization by two root
 endosymbionts (the mutualistic nitrogen-fixing bacteria Ensifer spp. and
 the parasitic root-knot nematode Meloidogyne hapla) under natural
 conditions. We inoculated all plants with nitrogen-fixing bacteria and
 factorially manipulated the soil microbiome and nematode infection. We
 found that plants grown in microbe-depleted soil exhibit greater
 mortality, but that among the survivors there was no effect of the soil
 microbiome on plant performance (shoot biomass, root biomass, or
 shoot-to-root ratio). The soil microbiome also impacted parasitic nematode
 infection and affected colonization by mutualistic nitrogen-fixing
 bacteria in a plant genotype-dependent manner, increasing colonization in
 some plant genotypes and decreasing it in others. Our results demonstrate
 the soil microbiome has complex effects on plant-endosymbiont interactions
 and may be critical for survival under natural conditions.
DOI: 10.5061/dryad.fj6q573w3
title: Environmental effects on the genetic architecture of fitness components in a simultaneous hermaphrodite

description: Understanding how environmental change affects genetic variances and
 covariances of reproductive traits is key to formulate firm predictions on
 evolutionary responses. This is particularly true for sex-specific
 variance in reproductive success, which has been argued to affect how
 populations can adapt to environmental change. Our current knowledge on
 the impact of environmental stress on sex-specific genetic architecture of
 fitness components is still limited and restricted to separate-sexed
 organisms. However, hermaphroditism is widespread across animals and may
 entail interesting peculiarities with respect to genetic constraints
 imposed on the evolution of male and female reproduction. We explored how
 food restriction affects the genetic variance-covariance (G) matrix of
 body size and reproductive success of the simultaneously hermaphroditic
 freshwater snail Physa acuta. Our results provide strong evidence that the
 imposed environmental stress elevated the opportunity for selection in
 both sex functions. However, the G matrix remained largely stable across
 the tested food treatments. Importantly, our results provide no support
 for cross-sex genetic correlations suggesting no strong evolutionary
 coupling of male and female reproductive traits. We discuss potential
 implications for the adaptation to changing environments and highlight the
 need for more quantitative genetic studies on male and female fitness
 components in simultaneous hermaphrodites.
DOI: 10.5061/dryad.p5hqbzkqj
title: Maximum entropy model estimates functional connectivity

description: Tools to estimate brain connectivity have been useful to improve our
 understanding of brain functioning. Reduced models ofcultured neurons are
 often used to study the behavior of neuronal networks, including
 functional connectivity and how it mightbe affected by external stimuli.
 Cultured neurons tend to be active in ensembles, and when pairs of neurons
 show significantsynchronicity in their firing patterns they are said to be
 functionally connected. The most common methods to infer
 functionalconnections are based on pair-wise cross correlation between
 activity patterns of (small groups of) neurons. However, thesemethods are
 not designed to be used during external stimulation, and they are
 relatively insensitive to inhibitory connections.Maximum Entropy (MaxEnt)
 models may provide a conceptually different method to infer functional
 connectivity, with thepotential benefit to estimate functional
 connectivity in the presence of an external stimulus and to infer
 excitatory as well asinhibitory connections. These models do not use
 pairwise comparison, but are based on probability distributions of sets
 ofneurons that are synchronously active in discrete time bins. We
 investigate the ability of the MaxEnt models to infer
 functionalconnectivity, using electrophysiological recordings fromin
 vitroneuronal cultures on micro electrode arrays. We comparefunctional
 connectivity as inferred by MaxEnt models to that obtained by conditional
 firing probabilities (CFP), an establishedcross-correlation based method.
 We show that MaxEnt models provide connectivity estimates that correlate
 well with CFPoutcomes. In addition, stimulus-induced connectivity changes
 were detected by MaxEnt models, and were of the samemagnitude as those
 detected by CFP.
DOI: 10.5061/dryad.dz08kprzg
title: Data from: Experimental evidence for neonicotinoid driven decline in aquatic emerging insects

description: There is an ongoing unprecedented loss in insects, both in terms of
 richness and biomass. The usage of pesticides, especially
 neonicotinoid insecticides, has been widely suggested to be a contributor
 to this decline. However, the risks of neonicotinoids to natural insect
 populations have remained largely unknown due to lack of field-realistic
 experiments. Here, we used an outdoor experiment to
 determine effects of field-realistic concentrations of the commonly
 applied neonicotinoid thiacloprid on the emergence of naturally assembled
 aquatic insect populations. Following application, all major orders of
 emerging aquatic insects (Coleoptera, Diptera, Ephemeroptera, Odonata,
 Trichoptera) declined strongly in both abundance and biomass. At
 the highest concentration (10 μg/L), emergence of most orders was
 nearly absent. Diversity of the most species-rich family,
 Chironomidae, decreased by 50% at more commonly observed
 concentrations (1 μg/L) and was generally reduced to a single
 species at the highest concentration. Our experimental findings
 thereby showcase a causal link of neonicotinoids and the ongoing insect
 decline. Given the urgency of the insect decline, our results highlight
 the need to reconsider the mass usage of neonicotinoids to
 preserve freshwater insects as well as the life and services depending on
 them.
DOI: 10.5061/dryad.5hqbzkh6q
title: The value of increased spatial resolution of pesticide usage data for assessing risk to endangered species: Data, notebooks, and results

description: Decision makers often cite data quality as a limitation in environmental
 management. Value of information approaches evaluates the benefit
 of new data collection for management outcomes. Pesticide exposure risk
 assessment for endangered species is one context where data limitations
 may affect decisions and a value of information type approach could be
 useful for identifying optimal data quality and resolution. Under
 the U.S. Federal Insecticide, Fungicide and Rodenticide Act, the U.S.
 Environmental Protection Agency (EPA) is responsible for registering
 pesticides before they can be sold and regularly reviewing pesticides.
 Section 7 of the Endangered Species Act requires that the EPA consider
 potential impacts of pesticides to listed endangered species and critical
 habitats in this process, and for the Services—U.S. Fish and Wildlife
 Service and National Marine Fisheries Service—to complete a formal Section
 7 consultation if the EPA deems it necessary. The current process is
 time‐intensive, lacks transparency and confidence among stakeholders, and
 leaves hundreds of unreviewed pesticides on the market. Increasing the
 resolution of pesticide usage data could address these concerns by
 improving estimated overlaps between species ranges and pesticide usage.
 Thus, we evaluated the relative importance of different resolutions of
 pesticide usage data for assessing expected carbaryl exposure to
 endangered plant species endemic to California. We found that spatially
 explicit, township resolution usage data (~36 mile2) excluded 33%
 of terrestrial plants (55/168) and 51% their critical habitats (27/53)
 from requiring a Section 7 consultation, while coarser resolution data
 excluded none. In contrast, the EPA's biological evaluation for
 carbaryl only excludes 4% of terrestrial plants (nationally) from
 requiring formal Section 7 consultation. This suggests high‐resolution
 data could increase pesticide review efficiency and decrease the amount of
 time pesticides remain on the market without a formal evaluation.
DOI: 10.5061/dryad.gb5mkkwqr
title: Bayesian N-mixture and occupancy modeling code for songbirds

description: The proliferation of energy rights-of-way (pipelines and powerlines; ROWs)
 in the central Appalachian region has prompted wildlife management
 agencies to consider ways to use these features to manage and conserve
 at-risk songbird species. However, little empirical evidence exists
 regarding best management strategies to enhance habitat surrounding ROWs
 for the songbird community during stopover or breeding periods. We used a
 before-after-control-impact design to study cut-back border (linear tree
 cuttings along abrupt forest edges) harvest width (15 m, 30 m, and 45 m
 wide into the forest) and harvest intensity (14 m2/ha and 4.5 m2/ha basal
 area retention) prescriptions along ROWs and assessed their effects on
 mature forest and young forest songbird species and avian guilds (forest
 gap habitat, forest interior habitat, young forest habitat, and species of
 regional conservation priority) up to two years after treatment throughout
 West Virginia. Species richness during the spring stopover period
 initially decreased at one-year post-treatment but returned to
 pre-treatment levels by two-year post-treatment. Breeding season responses
 to cut-back border treatments varied across harvest width, harvest
 intensity, and time, but all responses of focal species abundance and
 guild richness were neutral or positive. Cut-back border harvest intensity
 had a stronger influence (i.e., more positive responses) than harvest
 width on breeding focal species abundances and guild richness. For harvest
 intensity, the more intense, 4.5 m2/ha retention treatment had a stronger
 influence (i.e., more positive responses) than the less intense, 14 m2/ha
 retention treatment. For harvest width, the narrowest treatment (15-m
 wide) had the strongest influence (i.e., more positive responses) of all
 width treatments, followed by the widest (45-m wide treatment) with the
 least influence from the 30-m wide treatment. Abundances and richness
 increased from pre-treatment to two-year post-treatment across all species
 and guilds that exhibited a response. These results suggest that cut-back
 borders increase breeding season habitat suitability along ROWs for the
 mature forest and young forest songbird community as well as for species
 of regional conservation priority in the short-term. These findings can
 aid development of management guidelines for the forest songbird community
 along abrupt forest edges of man-made habitat features in forest-dominated
 landscapes.
DOI: 10.21979/n9/mry6xo
title: HAST: A Hardware-efficient Spatio-Temporal Correlation Near-Sensor Noise Filter for Dynamic Vision Sensors - Supplementary Material

description: Supplementary Material for the journal paper: "HAST: A Hardware-efficient Spatio-Temporal Correlation Near-Sensor Noise Filter for Dynamic Vision Sensors"