cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.931zcrjgw
title: Data from: Urban heavy metal contamination limits bumble bee colony growth

description: 1. Post-industrial shrinking cities contain abundant vacant land and are
 increasingly recognized for their pollinator conservation potential. At
 the same time, the industrial legacies of these urban ecosystems have
 resulted in elevated levels of heavy metals in surface soils, which could
 negatively affect bee populations. 2. We investigated whether foraging
 within heavy metal contaminated landscapes represents a fitness cost for
 the common Eastern bumble bee, Bombus impatiens, by placing colonies in
 residential backyards along an urban to rural gradient extending south and
 east from the city of Cleveland, Ohio, USA. Bees foraged in the landscape
 for three weeks, after which time we counted the total number of workers
 and larvae present in the colony and analyzed castes for the presence of
 heavy metals. We then assessed the relationship between landscape
 composition, heavy metal loads and caste abundance. 3. Colonies located in
 urban landscapes were more likely to be exposed to lead (Pb). Elevated
 concentrations of Pb within workers were negatively correlated with both
 the number of workers and the number of larvae present. 4. Synthesis and
 applications. Our findings raise concern that Pb contamination could
 represent a significant challenge to bee conservation in cities. To
 elucidate risks posed by this pollutant, we highlight a need to quantify
 lethal and sub-lethal effects of Pb exposure using laboratory and
 field-based studies. Further, identifying routes of exposure and landscape
 factors that influence exposure risk are necessary to implement mitigation
 strategies as part of urban conservation initiatives.09-Apr-2020
DOI: 10.5061/dryad.ncjsxksrf
title: Data from: Predicting heterosis and inbreeding depression from population size and density to inform management efforts

description: 1. Effective population size should be positively related to census size
 and density, and is expected to influence the strength of genetic drift,
 inbreeding and response to selection, and thus the distribution of the
 genetic load across populations. 2. We examined if census population size
 and density predicts the strength of inbreeding depression, heterosis and
 population mean fitness at the seed stage in the terrestrial orchid
 Gymnadenia conopsea by conducting controlled crosses (self, outcross
 within and between populations) in 20 populations of varying size
 (7-30,000 individuals) and density (1-12.8 individuals/m2). In the largest
 population, we also examined how local density affects occurrence of
 self-pollination with a pollen staining experiment. 3. The majority of
 populations expressed strong inbreeding depression at the seed stage (mean
 δID: min-max = 0.26: -0.53–0.51), consistent with a mainly outcrossing
 mating system and substantial genetic load. The effect of
 between-population crosses varied from strong outbreeding depression to
 heterosis (mean δOD: min-max= 0.05: -0.22–0.92), indicating varying
 influence of drift and selection among populations. 4. Census population
 size did not significantly predict the strength of inbreeding depression,
 heterosis or population mean fitness. However, inbreeding depression was
 positively and heterosis negatively correlated with population density.
 The proportion of self-massulae deposition was three times higher in
 sparse patches compared to dense ones (41% vs. 14%). 5. Combined effects
 of density-dependent pollinator behavior and limited seed dispersal may
 cause stronger genetic sub-structuring in sparse populations and reduce
 the strength of the correlation between census and effective population
 size. The results point to the importance of considering population
 density in addition to size when evaluating the distribution of recessive
 deleterious alleles across populations. 6. Synthesis and application:
 Management plans for threatened species often involve crosses between
 populations to restore genetic variation, a process termed genetic rescue.
 Such conservation efforts should be more succesful if designed on the
 basis of population density in addition to population size.03-Apr-2020
description: Results of the controlled crossings conducted in 20 populations
 of Gymnadenia conopsea on Öland.
DOI: 10.5061/dryad.kwh70rz19
title: Data from: The rainfall effect onto solidification and stabilization of heavy metal-polluted sediments

description: Rainfall makes impacts on process of solidification/stabilization and the
 long-term safety of solidified matrix. In this study, the effect of
 rainfall on solidification/stabilization process was investigated by
 rainfall test. The unconfined compressive strength (UCS) and toxicity
 characteristic leaching procedure (TCLP) were adopted to characterize the
 properties of S/S sediments before and after rainfall test. The samples
 cured for 28 days were subjected to semi-dynamic leaching tests with a
 simulated acidic leachant prepared at pH of 2.0, 4.0 and 7.0.
 Effectiveness of S/S treatment was evaluated by diffusion coefficient
 (D_e) and leachability index (LX). The results indicated that UCS
 decreased at maximum deterioration rate of 34.29% of the compressive
 strength after 7 days of curing, along with minimum rate of 7.89% after 28
 days by rainfall, with &gt;14 days referred. The rainfall had little
 effect on the leaching characteristics of heavy metals during the curing
 process. The simulated acid rain could make significant impacts on the
 leaching behavior of the heavy metals in the S/S materials. All cumulative
 fraction of leached heavy metals were less than 2.0 % which showed the
 good stabilization of cement. Furthermore, the calculated diffusion
 coefficient (D_e) for Cu was 1.28×10-11〖cm〗^2/s, indicating that its
 mobility was relatively low of heavy in S/S sediments. The calculated
 diffusion coefficient (Di) for Cd, Cu and Pb were 7.44×10-11, 8.18×10-12
 and 7.85×10-12〖cm〗^2/s respectively, indicating that its mobility was
 relatively low of heavy metal in S/S sediments.
description: See manuscript
DOI: 10.5061/dryad.gtht76hhp
title: Accelerated landings in stingless bees are triggered by visual threshold cues

description: Most flying animals rely primarily on visual cues to coordinate and
 control their trajectory when landing. Studies of visually-guided landing
 typically involve animals that decrease their speed before touchdown.
 Here, we investigate the control strategy of the stingless bee
 Scaptotrigona depilis, which instead accelerates when landing on its
 narrow hive entrance. By presenting artificial targets that resemble the
 entrance at different locations on the hive, we show that these
 accelerated landings are triggered by visual cues. We also found that S.
 depilis initiated landing and extended their legs when the angular size of
 the target reached a given threshold. Regardless of target size, the
 magnitude of acceleration was the same and the bees aimed for the same
 relative position on the target suggesting that S. depilis use a
 computationally simple but elegant ‘stereotyped’ landing strategy that
 requires few visual cues.
DOI: 10.5061/dryad.2bvq83bms
title: Balancing selection in Pattern Recognition Receptor signalling pathways is associated with gene function and pleiotropy in a wild rodent

description: Pathogen-mediated balancing selection is commonly considered to play an
 important role in the maintenance of genetic diversity, in particular in
 immune genes. However, there has not been any systematic analysis of what
 factors influence which immune genes are the targets of such selection. To
 address this, we here focus on Pattern Recognition Receptor (PRR)
 signalling pathways, which play a key role in innate immunity. We used
 whole-genome resequencing data from a population of bank voles (Myodes
 glareolus) to test for associations between balancing selection,
 pleiotropy and gene function in a set of 123 PRR signalling pathway genes.
 To investigate the effect of gene function, we compared genes encoding (i)
 receptors for microbial ligands vs downstream signalling proteins, and
 (ii) receptors recognizing components of microbial cell walls, flagella
 and capsids vs receptors recognizing features of microbial nucleic acids.
 Analyses based on the nucleotide diversity of full coding sequences showed
 that balancing selection primarily targeted receptor genes with a low
 degree of pleiotropy. Moreover, genes encoding receptors recognizing
  components of microbial cell walls etc were more important
 targets of balancing selection than receptors recognizing nucleic acids.
 Tests for localized signatures of balancing selection in coding and
 non-coding sequences showed that such signatures were mostly located in
 introns, and more evenly distributed among different functional categories
 of PRR pathway genes. The finding that signatures of balancing selection
 in full coding sequences primarily occur in receptor genes, in particular
 those encoding receptors for components of microbial cell walls etc, is
 consistent with the idea that coevolution between hosts and pathogens is
 an important cause of balancing selection on immune genes.
DOI: 10.5061/dryad.fn2z34tqx
title: Oldest fossil ciliates from the Cryogenian glacial interlude reinterpreted as possible red algal spores

description: The Cryogenian Period experienced two long lived global glaciations known
 as Snowball Earths. While these events were dramatic, eukaryotic life
 persisted through them, and fossil evidence shows that eukaryotes thrived
 during the ca. 30-million-year interlude between the glaciations.
 Carbonate successions have become an important taphonomic window for this
 interval. One of the most notable examples is the ca. 662–635 Ma Taishir
 Formation (Tsagaan Olom Group, Zavkhan Terrane, Mongolia) which has
 yielded a number of eukaryotic fossil taxa. Here, we examine more closely
 the morphology and taxonomic affinity of some of these Taishir fossils
 previously interpreted as remains of ciliate tintinnid loricae
 (purportedly the oldest fossil ciliates). New morphological and
 ultrastructural analyses indicate that these fossils are not ciliate
 tintinnids. Instead, we propose a new interpretation: that they are algal
 reproductive structures related to coeval macroscopic organic warty sheets
 described as putative red algae. We report the first occurrence of these
 fossils in the earliest Ediacaran Ol Formation, indicating that this taxon
 persisted through the Marinoan Snowball Earth. A new interpretation of
 these fossils as putative red algal spores has broad implications for our
 understanding of biodiversity in the Neoproterozoic Era, specifically
 during the Cryogenian Period, and for the antiquity of ciliates. The
 reinterpretation of these fossils also potentially represents the first
 Proterozoic discovery of two components from a multicomponent life cycle.
DOI: 10.5061/dryad.d51c5b004
title: Spine and dine: A key defensive trait promotes ecological success in spiny ants

description: A key focus of ecologists is explaining the origin and maintenance of
 morphological diversity and its association with ecological success. We
 investigate potential benefits and costs of a common and varied
 morphological trait, cuticular spines, for foraging behavior,
 interspecific competition, and predator-prey interactions in naturally
 co-occurring spiny ants (Hymenoptera: Formicidae: Polyrhachis) in an
 experimental setting. We expect that a defensive trait like spines might
 be associated with more conspicuous foraging, a greater number of workers
 sent out to forage, and potentially increased competitive ability.
 Alternatively, consistent with the ecological trade-off hypothesis, we
 expect that investment in spines for anti-predator defense might be
 negatively correlated with these other ecological traits. We find
 little evidence for any costs to ecological traits, instead finding that
 species with longer spines either outperform or do not differ from species
 with shorter spines for all tested metrics, including resource discovery
 rate and foraging effort as well as competitive ability and anti-predator
 defense. Spines appear to confer broad anti-predator benefits and serve as
 a form of defense with undetectable costs to key ecological abilities like
 resource foraging and competitive ability, providing an explanation for
 both the ecological success of the study genus and the large number of
 evolutionary origins of this trait across all ants. This study also
 provides a rare quantitative empirical test of ecological effects related
 to a morphological trait in ants.
description: These data were collected at the Xishuangbanna Tropical Botanical
 Garden (XTBG) in southern Yunnan in southern China. During June and July
 of 2017 and 2018, we collected <em>Polyrhachis</em> colonies
 in and around XTBG. We kept the colonies in the field station laboratory
 in plastic containers (17 × 11.5 × 10 cm), and regularly provided each
 colony a standard liquid sugar diet (50% sugar/50% water solution) as a
 rough approximation of their natural sugary food sources. Species were
 identified in the laboratory using the primary literature and images from
 AntWeb.org (accessed June–July 2017). Species voucher specimens were
 deposited in the Field Museum of Natural History in Chicago, IL, USA, and
 the Southwest Forestry University Specimen Hall in Kunming, Yunnan,
 China. We then conducted a number of resource discovery
 rate, foraging effort, and competitive ability trials, as well as
 anti-predator ability trials using the myrmecophagous
 spide <em>Siler semiglaucus</em>. See the associated
 manuscript for further details about the trials we conducted.
description: The analyses we conducted should run in a self-contained manner,
 as described in the R Script incldued as a file here.
DOI: 10.15468/dl.vk8a2x
title: Occurrence Download

description: A dataset containing 1376 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Quercus parvula"
 ]
}

 The dataset includes 1376 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002331-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7pvmcvdq6
title: Paleocommunity composition, relative abundance, and new camerate crinoids from the Brechin Lagerstätte (Upper Ordovician)

description: The Brechin Lagerstätte of southern Ontario contains an exceptionally
 diverse and well-preserved Late Ordovician (Katian) crinoid fauna. Here,
 we describe four genera and eight species of camerate crinoids from the
 Brechin Lagerstätte, including six new species. Consequently, the total
 diversity of the fauna now stands at 27 genera and 39 nominal species,
 thereby making it the most taxonomically diverse Ordovician crinoid fauna
 known. Taxa described herein include the diplobathrid Pararchaeocrinus
 kiddi n. sp. and the monobathrids Glyptocrinus ramulosus, Periglyptocrinus
 priscus, Periglyptocrinus astricus n. sp., Periglyptocrinus kevinbretti n.
 sp., Periglyptocrinus mcdonaldi n. sp., Periglyptocrinus silvosus n. sp.,
 and Abludoglyptocrinus steinheimerae n. sp. We summarize the taxonomic
 composition, diversity, and abundance distribution of all known crinoids
 from the Brechin Lagerstätte to better characterize the paleoecological
 structure and complexity of the community. We establish that the fauna is
 dominated by the subclass Pentacrinoidea, both in terms of abundance and
 species richness. In addition, we analyze species-level abundance data
 using relative abundance distribution (RAD) models to evaluate the
 ecological complexity of the paleocommunity. We find that community
 structure of the Brechin Lagerstätte is best explained by an ecologically
 “complex” RAD model, which suggests species partitioned niches along
 multiple resource axes and/or the presence of multiple ecological ways of
 life. These results indicate that the Brechin Lagerstätte is significant
 not only for being the most taxonomically diverse Katian crinoid
 assemblage, but also for being an early ecologically complex fauna that
 developed in the wake of the Great Ordovician Biodiversification Event.
DOI: 10.7272/q6vq30vd
title: CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties

description: Management of the COVID-19 pandemic has proven to be a significant
 challenge to policy makers. This is in large part due to uneven reporting
 and the absence of open-access visualization tools to present and analyze
 local trends as well as infer healthcare needs. Here we
 report the development of CovidCounties.org, an interactive web
 application that depicts daily disease trends at the
 level of US counties using time series plots and maps. This application is
 accompanied by a manually curated dataset that catalogs all major public
 policy actions made at the state-level, as well as technical validation of
 the primary data. Finally, the underlying code
 for the site is also provided as open source, enabling others to validate
 and learn from this work. 
description: Data related to state-wide implementation of social-distancing
 policies were manually curated by web search and independently reviewed by
 a second author; disagreements were rare and resolved by
 discussion. Government websites were prioritized as sources of truth where
 feasible; otherwise, news reports covering state-wide proclamations were
 used. All citations are captured in the data file.
 Ground truth data used in the validation were manually curated
 from states’ Department of Public Health websites. Citations of the
 validation data are included in the data file. To
 confirm global accessibility of covidcounties.org, we used dareboost.com
 to perform loading speed tests from 14 cities across the globe using three
 different devices: Google Chrome via desktop, iPhone 6s/7/8, and Samsung
 Galaxy S6.
DOI: 10.15468/dl.9wg3b4
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ocythoe tuberculata",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 31 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002332-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bg79cnp7w
title: Temporal pole responds to subtle changes in local thyroid hormone signaling

description: To study thyroid hormone (TH) signaling in the human brain, we analyzed
 published microarray data sets of the temporal pole (Brodmann area 38) of
 19 deceased donors. An index of TH signaling built on the expression of 19
 well known TH-responsive genes in mouse brains (T3S+) varied from 0.92 to
 1.1. After Factor analysis, T3S+ correlated independently with the
 expression of TH transporters (MCT8, LAT2), TH receptor (TR) beta and TR
 coregulators (CARM1, MED1, KAT2B, SRC2, SRC3, NCOR2a). Unexpectedly, no
 correlation was found between T3S+ vs DIO2, DIO3, SRC1 or TRα. An
 unbiased systematic analysis of the entire transcriptome identified a set
 of 1,649 genes (set #1) with strong positive correlation with
 T3S+ (r&gt;0.75). Factor analysis of set #1 identified two
 sets of genes that correlated independently with T3S+, sets #2 (329 genes)
 and #3 (191 genes). When processed through the Molecular Signatures Data
 Base (MSigDB), both sets #2-3 were enriched with GO-sets related to
 synaptic transmission and metabolic processes. Ranking individual human
 brain donors according to their T3S+ led us to identify 1,262
 genes (set #4) with &gt;1.3-fold higher expression in the top half.
 The analysis of the overlapped genes between sets #1 and #4 resulted in
 769 genes (set #5), which have a very similar MSigDB signature as sets
 #2-3. In conclusion, gene expression in the human temporal pole can be
 assessed through T3S+ and fluctuates with subtle variations in local TH
 signaling.
description: The database was generated based on the analyses of gene
 expression studies of the human temporal pole.
DOI: 10.6078/d1t12t
title: Targeted occupant surveys: A novel method to effectively relate occupant feedback with environmental conditions

description: Occupant satisfaction surveys are widely used in laboratory and field
 research studies of indoor environmental quality. Field studies pose
 several challenges because researchers usually have no control over the
 indoor environments experienced by building occupants, it is difficult to
 recruit and retain participants, and data collection methods can be
 cumbersome. With this in mind, we developed a survey platform that uses
 real-time feedback to send targeted occupant surveys (TOS) at specific
 indoor environmental conditions and stops sending survey requests when
 collected responses reach the maximum surveys required. We performed a
 pilot study of the TOS platform with occupants of a radiant heated and
 cooled building to target survey responses at 16 radiant slab surface
 (infrared) temperatures evenly distributed from 15 to 30 °C. We developed
 metrics and ideal datasets to compare the TOS platform against other
 occupant survey distribution methods. The results show that this novel
 method has a higher approximation to characteristics of an ideal dataset;
 41% compared to 23%, 19%, and 12% of other datasets in previous field
 studies. Our TOS method minimizes the number of times occupants are
 surveyed and ensures a more complete and balanced dataset. This allows
 researchers to more efficiently and reliably collect subjective data for
 occupant satisfaction studies.
description: We recruited eight occupants from a radiant heated and cooled
 building to respond to a ecological momentary assessment, or
 "right-now" survey, for our pilot study. The right-now survey of
 11-questions took about a minute, on average, to complete. We used this
 survey in conjunction with the targeted occupant surveys (TOS) platform
 that we developed to administer surveys based on specific IEQ
 measurements. The goal of the right-now survey was to characterize
 whole-body thermal comfort (thermal sensation, thermal acceptability, and
 thermal preference) and self-reported well-being (ability to concentrate,
 level of sleepiness, and perceived productivity) when subjects completed
 the survey. We used a continuous scale with 7-points (the ASHRAE scale: -3
 - cold; 0 - neutral; +3 - hot) to evaluate subjects’ thermal sensation
 (ASHRAE 2017). For thermal acceptability, subjects marked their responses
 on a continuous scale with 7-points ranging from clearly not acceptable
 (-3) to just unacceptable (-0.1), and from just acceptable (+0.1) to
 clearly acceptable (+3); subjects were required to distinguish between
 acceptable and unacceptable. Subjects were asked to rate their thermal
 preference by selecting if they prefer to be cooler, warmer, or no change.
 Self-reported productivity questions used a 5-point discrete scale. We
 also asked subjects about their level of activity in the past 15-20
 minutes, clothing ensemble, and their use of fans and windows.