cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.2v82b5
title: Occurrence Download

description: A dataset containing 0 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.basisofrecord = 'PRESERVED_SPECIMEN'
 AND (occurrence.level0gid = 'BRA.13_1' OR occurrence.level1gid = 'BRA.13_1' OR occurrence.level2gid = 'BRA.13_1' OR occurrence.level3gid = 'BRA.13_1')
 AND occurrence.hascoordinate = TRUE
 AND occurrence.hasgeospatialissues = FALSE
 AND GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '2945500', TRUE)
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 0 records were derived from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003243-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.tht76hf2n
title: RNA seq of PR10.5D1 OE vs WC (mock, 12, 24, 48 hpi)

description: As an important family of pathogenesis-related (PR) proteins, the
 functional diversification and roles of PR10s in biotic stress have been
 well documented. However, the molecular basis of PR10s in plant defense
 responses against pathogens remains to be further understood. To measure
 the biological changes caused by the overexpression of GbPR10.5D1 in
 cotton, an RNA-seq experiment was performed to measure the transcriptome
 changes between the cotton recipient line (WT) and GbPR10.5D1-OE
 transgenic line (OE-17), under normal and V. daliae-infected conditions at
 12, 24, and 48 hpi. The DEGs were identified by comparing the expression
 levels in inoculated samples with those in mock controls in WT and OE-17
 line or mock controls between the two cotton lines, using an FDR threshold
 of 0.05, and a log2 FC ≥1.
DOI: 10.5061/dryad.bnzs7h4dw
title: Annual egg productivity predicts female-biased mortality in avian species

description: Among avian species, the differential cost entailed by either sex in
 competition for mates have been regarded as the main evolutionary
 influence on sex differences in mortality rates. However, empirical
 evidence suggests that sex-biased adult mortality is mainly related to
 differential energy investment in gamete production, a greater annual mass
 devoted to egg production leading to higher female mortality. We
 explicitly tested the generality of this pattern in a comparative
 framework. Annual egg production can be relatively large in some species
 (up to 200% of female body mass) and annual mortality is generally biased
 towards females. We showed that greater annual egg productivity resulted
 in higher mortality rates of females relative to males. Mating system was
 secondarily important, species where males were more involved in mating
 competition having more equal mortality rates between the sexes. However,
 both traits explained only a limited fraction of the interspecific
 variation in female-biased mortality. Other traits, such as sexual size
 dimorphism and parental care, had much weaker influences on female-biased
 mortality. Our results suggest that both annual mass devoted to gamete
 production by females and mating system contribute to the evolution of the
 fundamental life-history trade-off between reproduction and survival in
 avian taxa.
DOI: 10.5061/dryad.crjdfn377
title: Raw data: Association and functional analysis of angiotensin-converting enzyme 2 gene genetic variants with the pathogenesis of pre-eclampsia

description: These data were generated to investigate the association and functional
 analysis of angiotensin-converting enzyme 2 genetic variants with the
 pathogenesis of pre-eclampsia(PE). This study conducted a case-control
 study involving 327 PE patients and 591 healthy pregnant women to explore
 the associations between candidate variants in the ACE2 gene 
 variants and the pathogenesis of PE.This study collected clinical samples
 and data, and used logistic regression, false positive report rate, multi
 factor dimension reduction, functional analysis and other analysis methods
 to process the research data. Potential functional ACE2 gene
 variants (rs2106809 A&gt;G, rs6632677 G&gt;C, and rs2074192
 C&gt;T) were selected and genotyped using kompetitive allele-specific
 PCR. The strength of the associations between the studied genetic variants
 and the risk of PE were evaluated using odds ratios (ORs) and
 corresponding 95% confidence intervals (CIs). Finally,it showed
 that the rs2106809 A&gt;Gis significantly associated with the risk of
 PE via individual locus effects and/or complex gene-gene and
 gene-environment interactions.
DOI: 10.5061/dryad.p8cz8w9tb
title: Original recordings from voltage clamp fluorometry analyses of ANAP-containing P2X7 mutants

description: The large intracellular C-terminus of the pro-inflammatory P2X7 ion
 channel receptor (P2X7R) is associated with diverse P2X7R-specific
 functions. Cryo-EM structures of the closed and ATP-bound open full-length
 P2X7R recently identified a membrane-associated anchoring domain, an
 open-state stabilizing “cap” domain, and a globular “ballast domain”
 containing GTP/GDP and dinuclear Zn2+-binding sites with unknown
 functions. To investigate protein dynamics during channel activation, we
 improved incorporation of the environment-sensitive fluorescent unnatural
 amino acid L-3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (ANAP)
 into Xenopus laevis oocyte-expressed P2X7Rs and performed voltage clamp
 fluorometry (VCF). While we confirmed predicted conformational changes
 within the extracellular and the transmembrane domains, only three out of
 41 mutants containing ANAP in the C-terminal domain resulted in
 ATP-induced fluorescence changes. We conclude that the ballast domain
 functions rather independently from the extracellular ATP binding domain
 and might require activation by additional ligands and/or protein
 interactions. Novel tools to study these are presented.
DOI: 10.5061/dryad.kh189328x
title: Ability of the ash dieback pathogen to reproduce and to induce damage on its host are controlled by different environmental parameters

description: Ash dieback, induced by an invasive ascomycete, Hymenoscyphus fraxineus,
 has emerged in the late 1990s as a severe disease threatening ash
 populations in Europe. Future prospects for ash are improved by the
 existence of individuals with natural genetic resistance or tolerance to
 the disease and by limited disease impact in many environmental conditions
 where ash is common. Nevertheless, it was suggested that, even in those
 conditions, ash trees are infected and enable pathogen transmission. We
 studied the influence of climate and local environment on the ability of
 H. fraxineus to infect, be transmitted and cause damage on its host. We
 showed that healthy carriers, i.e. individuals showing no dieback but
 carrying H. fraxineus, exist and may play a significant role in ash
 dieback epidemiology. The environment strongly influenced H. fraxineus
 with different parameters being important depending on the life cycle
 stage. The ability of H. fraxineus to establish on ash leaves and to
 reproduce on the leaf debris in the litter (rachises) mainly depended on
 total precipitation in July-August and was not influenced by local tree
 cover. By contrast, damage to the host, and in particular shoot mortality
 was significantly reduced by high summer temperature in July-August and by
 high autumn average temperature. As a consequence, in many situations, ash
 trees are infected and enable H. fraxineus transmission while showing
 limited or even no damage. We also observed a decreasing trend of severity
 (leaf necrosis and shoot mortality probability) with the time of disease
 presence in a plot that could be significant for the future of ash
 dieback.
description: Data collected by visual observation in the field (dieback score,
 leaf necrosis, shoot mortality) Data from DNA
 extraction / qPCR with specific primers for detection of
 <em>Hymenoscyphus</em> <em>fraxineus</em> in
 infected tissues Data on the ability of <em>H.
 fraxineus</em> to produce apothecia on rachises collected at leaf
 fall. Rachises that were just shed were collected in autumn and placed
 outdoors for overwintering in common gardens on the soil in a forest
 situation. They were retrieved in spring and placed in humid chamber to
 assess the ability of <em>Hymenoscyphus</em>
 <em>fraxineus</em> to produce apothecia on them. The part
 producing / not producing apothecia were separated and the proportion of
 rachises-producing apothecia were computed
DOI: 10.5061/dryad.f4qrfj701
title: The effect of a temperature‐sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen

description: Viruses are key actors of ecosystems and have major impacts on global
 biogeochemical cycles. Prophages deserve particular attention as they are
 ubiquitous in bacterial genomes and can enter a lytic cycle when triggered
 by environmental conditions. We explored how temperature affects the
 interactions between prophages and other biological levels by using an
 opportunistic pathogen, the bacterium Serratia marcescens, that harbours
 several prophages and that had undergone an evolution experiment under
 several temperature regimes. We found that the release of one of the
 prophages was temperature-sensitive and malleable to evolutionary changes.
 We further discovered that the virulence of the bacterium in an insect
 model also evolved and was positively correlated with phage release rates.
 We determined through analysis of genetic and epigenetic data that changes
 in the bacterial outer cell wall structure possibly explain this
 phenomenon. We hypothezise that the temperature-dependent phage release
 rate acted as a selection pressure on S. marcescens and that it resulted
 in modified bacterial virulence in the insect host. Our study system
 illustrates how viruses can mediate the influence of abiotic environmental
 changes to other biological levels and thus be involved in ecosystem
 feedback loops.
description: Phage particle quantification by qPCR.
 Bacterial virulence estimated from survival of infected waxmoth
 larvae. PacBio sequencing data and other bacterial
 phenotypic data, based on previously published articles.
 All Methods are described in detail in the original
 paper, available as an Open Access article from https://doi.org/10.1111/mec.16638.
description: All dataset files are plain text, tab-separated tabular
 files. R scripts are also provided to reproduce the
 analyses and the figures reported in the article. Those scripts can be
 executed using the R program (https://www.r-project.org/). A pdf file ("pipeline.pdf") is provided to give an overview of the dependencies between dataset files, R scripts, and output files.
DOI: 10.5061/dryad.b2rbnzsjs
title: Biocrust impacts on dryland soil water balance: A path towards the whole picture

description: As a crucial living feature inhabiting the soil-atmosphere boundary,
 biocrusts play a vital role in liquid water or vapor transport through
 surface soil and thus have strong effects on soil water regimes. However,
 it remains unclear how biocrusts affect annual or multi-year soil water
 budgets through the regulation of evaporation outputs and NRW or
 infiltration inputs. Thus, we used automated microlysimeters to
 continually investigate the differences in evaporation and NRW rates
 between moss-dominated biocrusts and bare soil at 0−5 cm depth for two
 years. The upper 30 cm of soil moisture (θ) and water storage (W) of bare
 soil and biocrusts were also monitored. Our results showed that the daily
 evaporation rate (E) of biocrusts was 17% higher than bare soil.
 Especially after rainfall events, biocrusts had higher E and larger
 cumulative evaporation than bare soil. Besides, the daily NRW of biocrusts
 averaged 15% higher than bare soil over two years. Furthermore, biocrusts
 increased θ by 11%−76% at 0−10 cm depth but decreased θ by 32%−56% at
 20−30 cm depth in comparison to bare soil, and they subsequently decreased
 W by 20% at 0−30 cm depth. Summarized annually, the NRW amount of
 biocrusts was 19% higher than bare soil, but at the same time the
 cumulative evaporation of biocrusts was also 19% higher than bare soil.
 Finally, biocrusts resulted in more water loss at shallow depth through
 evaporation and lessened total W throughout 0−30 cm depth of soil. These
 findings demonstrate that although biocrusts input more NRW into surface
 soil, these water inputs partially offset their intensified evaporation.
 Given that all rainfall water infiltrates into the soil in our study
 system, our findings indicate that biocrusts may have an overall negative
 effect on soil water balance there, while at the same time increasing
 water storage and availability of the deeper soil underlying biocrusts.
DOI: 10.5061/dryad.4j0zpc8ft
title: Data from: Species of Dickinsonia Sprigg from the Ediacaran of South Australia

description: An iconic member of the Ediacara Biota, Dickinsonia Sprigg is one of few
 such taxa with multiple species. Here we use gaussian finite mixture
 models to assess the validity of species distinctions for this genus. Our
 results indicate that the five described species of Dickinsonia from the
 Ediacara Member, South Australia are better classified as two based on
 multiple approaches. Two different methods for dimension reduction both
 provide strong support for two groups, with overlapping but distinct
 mixture models. The variable selection method produces the most
 biologically realistic clusters, indicating that the two species can be
 primarily differentiated based on the greater relative size of the
 anteriormost unit of Dickinsonia costata Sprigg compared with Dickinsonia
 tenuis Glaessner & Wade. Despite differences in aspect ratio and
 number of modules, both species regulated growth to maintain overall
 shape. The greater likelihood of preservation of a midline and an
 irregular outer margin in D. tenuis highlights differential structural
 integrity and flexibility. Co-occurrence in the Ediacara Member indicates
 that both species occupied the same environments and temporal
 distribution. Smaller maximum and average size, combined with higher
 abundance of D. costata, may suggest a comparatively shorter lifespan and
 increased rates of reproduction.
description: This dataset consists of measurements obtained from digital
 photographs. See the main text for more details.  
description: The Supplementary Data and associated ReadMe files were created
 in Excel. Code used for mixture model analysis was written and conducted
 using R. See main text for further details.
DOI: 10.5061/dryad.8gtht76s8
title: Factors affecting delay in the presentation of breast cancer symptoms among women in Gaza, occupied Palestinian territory: A cross-sectional survey

description: Objective: To identify factors related to women’s delay in
 presenting with breast cancer symptoms to improve earlier diagnosis in the
 occupied Palestinian territory (oPt). Design: Cross-sectional Setting: Two
 government cancer hospitals. Participants: A consecutive sample of 130
 Palestinian women living in Gaza with newly diagnosed breast cancer were
 approached in the waiting rooms of cancer hospitals in Gaza between 1
 January and 31 December 2017. 120 women took part and returned the
 completed questionnaire. Primary and secondary outcome measures: Clinical
 information about breast cancer were collected from hospital cancer
 records. An interval of three months or more between women’s
 self-discovery of symptoms and their first presentation to a medical
 provider was considered as a delay. Results: 94% (122/130) of women
 attending cancer hospitals in Gaza agreed to take part in the study. Their
 mean age was 51 years (range: 23-72), 33.6% (31/122) had a family history
 of breast cancer, and 74.5% (41/55) of those whose cancer stage was known
 had been diagnosed at stage III or IV. Around one half (62/122) said they
 had not recognised the seriousness of their breast changes but only 20%
 (24/122) of women delayed seeking healthcare by three months and more.
 Considering that the symptom was not serious (X2= 13.94, p&gt; 0.05),
 and lack of pain (X2= 6.63, p&gt; 0.05) were the only two factors
 statistically associated with later presentation. Lower socio-economic
 status, older age, lower education, and negative family history of breast
 cancer were not statistically associated with women’s delay. Conclusions:
 Women’s awareness about the seriousness of breast changes and the critical
 importance of seeking prompt diagnosis needs to be improved using
 context-relevant and evidence-based awareness campaigns. This should be
 accompanied with training of female nurses on promoting early detection
 and improvement in diagnostic facilities to ensure timely diagnosis of
 cancer in the oPt.
description: This data was collected from two oncology centres in Gaza,
 occupied Palestinian territory.
description: Microsoft Word.
DOI: 10.5061/dryad.2bvq83btc
title: Comparing climatic suitability and niche distances to explain populations responses to extreme climatic events

description: Habitat suitability calculated from Species Distribution Models (SDMs) has
 been used to assess population performance, but empirical studies have
 provided weak or inconclusive support to this approach. Novel approaches
 measuring population distances to niche centroid and margin in
 environmental space have been recently proposed to explain population
 performance, particularly when populations experience exceptional
 environmental conditions that may place them outside of the species niche.
 Here, we use data of co-occurring species’ decay, gathered after an
 extreme drought event occurring in the SE of the Iberian Peninsula which
 highly affected rich semiarid shrubland communities, to compare the
 relationship between population decay (mortality and remaining green
 canopy) and (1) distances between populations’ location and species niche
 margin and centroid in the environmental space, and (2) climatic
 suitability estimated from frequently used SDMs (here MaxEnt) considering
 both the extreme climatic episode and the average reference climatic
 period before this. We found that both SDMs-derived suitability and
 distances to species niche properly predict populations performance when
 considering the reference climatic period; but climatic suitability failed
 to predict performance considering the extreme climate period. In
 addition, while distance to niche margins accurately predict both
 mortality and remaining green canopy responses, centroid distances failed
 to explain mortality, suggesting that indexes containing information about
 the position to niche margin (inside or outside) are better to predict
 binary responses. We conclude that the location of populations in the
 environmental space is consistent with performance responses to extreme
 drought. Niche distances appear to be a more efficient approach than the
 use of climate suitability indices derived from more frequently used SDMs
 to explain population performance when dealing with environmental
 conditions that are located outside the species environmental niche. The
 use of this alternative metrics may be particularly useful when designing
 conservation measures to mitigate impacts of shifting environmental
 conditions.
DOI: 10.5061/dryad.qz612jmjz
title: Research gaps limit understanding of invasion-fire cycles

description: These files provide the data underlying our publication that reviews what
 is currently known about plant invasion-fire cycles, including complete
 lists of all papers and the data we gathered from them.
DOI: 10.15468/dl.8cbqe9
title: Occurrence Download

description: A dataset containing 85 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ecuadendron acosta-solisianum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 85 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003269-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hx3ffbghc
title: Temporal data from camera trap captures of raccoons (Procyon lotor) and coyote (Canis latrans) across urban-rural gradient Michigan 2015-2020

description: Temporal data and trap success for raccoons (Procyon lotor) and coyotes
 (Canis latrans) across an urban-rural gradient in Michigan, from 2015 to
 2020. These data are associated with the article "Temporal refuges of
 a subordinate carnivore vary across rural-urban gradient" in the
 journal Ecology and Evolution. 
description: This data was collected using repeated camera trap surveys across
 four sites in Michigan. The data was processed in the R package camtrapR,
 and a 30 minute quiet period was introduced between subsequent triggers of
 the same species. 
description: None (we used R to process the temporal data, and ArcGIS pro to
 general kernel densities from the trap success data).