cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n02v6wx04
title: Data from: Drivers of foliar 15N trends in southern China over the last century

description: Foliar stable nitrogen (N) isotopes (δ15N) generally reflect N
 availability to plants and have been used to infer about changes thereof.
 However, previous studies of temporal trends in foliar δ15N have ignored
 the influence of confounding factors, leading to uncertainties on its
 indication to N availability. In this study, we measured foliar δ15N of
 1,811 herbarium specimens from 12 plant species collected in southern
 China forests from 1920 to 2010. We explored how changes in atmospheric
 CO2, N deposition and global warming have affected foliar δ15N and N
 concentrations ([N]) and identified whether N availability decreased in
 southern China. Across all species, foliar δ15N significantly decreased by
 0.82‰ over the study period. However, foliar [N] did not decrease
 significantly, implying N homeostasis in forest trees in the region. The
 spatiotemporal patterns of foliar δ15N were explained by mean annual
 temperature (MAT), atmospheric CO2 (PCO2), atmospheric N deposition, and
 foliar [N]. The spatiotemporal trends of foliar [N] were explained by MAT,
 temperature seasonality, PCO2, and N deposition. N deposition within the
 rates from 5.3 – 12.6 kg N ha-1 yr-1 substantially contributed to the
 temporal decline in foliar δ15N. The decline in foliar δ15N was not
 accompanied by changes in foliar [N] and therefore does not necessarily
 reflect a decline in N availability. This is important to understand
 changes in N availability, which is essential to validate and parameterize
 biogeochemical cycles of N.
DOI: 10.15468/dl.pvfduy
title: Occurrence Download

description: A dataset containing 80188 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "Country is Belgium",
 "StateProvince is Antwerpen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 80188 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003047-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6078/d1342b
title: Data from: Linking microenvironment modification to species interactions and demography in an alpine plant community

description: Individual plants can modify the microenvironment within their spatial
 neighborhood. However, the consequences of microenvironment modification
 for demography and species interactions remain unclear at the community
 scale. In a study of co-occurring alpine plants, we (1) determined the
 extent of species-specific microclimate modification by comparing
 temperature and soil moisture between vegetated and non-vegetated
 microsites for several focal species. We (2) determined how vital rates
 (survival, growth, fecundity) of all species varied in response to
 aboveground and belowground vegetative overlap with inter- and
 intraspecific neighbors as proxies for microenvironment modification. For
 (1), surface temperatures were buffered (lower maximums and higher
 minimums) and soil moisture was higher below the canopies of most species
 compared to non-vegetated areas. For (2), vegetative overlap predicted the
 most vital rates, although the effect varied depending on whether
 aboveground or belowground overlap was considered. Vital rate response to
 microenvironment-modification proxies (vegetative overlap) was also
 frequently context-dependent with respect to plant size and macroclimate.
 Microenvironment modification and spatial overlapping of individuals are
 key drivers of demography and species interactions in this alpine
 community.
description: All analyses are conducted in the R programming laguage.
DOI: 10.5061/dryad.kd51c5b7d
title: Underlying data for 'Rapid molecular assays for the detection of the four dengue viruses in infected mosquitoes'

description: The pantropic emergence of severe dengue disease can partly be attributed
 to the co-circulation of different dengue viruses (DENVs) in the same
 geographical location. Effective monitoring for circulation of each of the
 four DENVs is critical to inform disease mitigation strategies. In low
 resource settings, this can be effectively achieved by utilizing
 inexpensive, rapid, sensitive and specific assays to detect viruses in
 mosquito populations. In this study, we developed four rapid DENV tests
 with direct applicability for low-resource virus surveillance in
 mosquitoes. The test protocols utilize a novel sample preparation step, a
 single-temperature isothermal amplification, and a simple lateral flow
 detection. Analytical sensitivity testing demonstrated tests could detect
 down to 1,000 copies/µL of virus-specific DENV RNA, and analytical
 specificity testing indicated tests were highly specific for their
 respective virus, and did not detect closely related flaviviruses. All
 four DENV tests showed excellent diagnostic specificity and sensitivity
 when used for detection of both individually infected mosquitoes and
 infected mosquitoes in pools of uninfected mosquitoes. With individually
 infected mosquitoes, the rapid DENV-1, -2 and -3 tests showed 100%
 diagnostic sensitivity (95% CI = 69% to 100%, n=8 for DENV-1; n=10 for
 DENV 2,3) and the DENV-4 test showed 92% diagnostic sensitivity (CI: 62%
 to 100%, n=12) along with 100% diagnostic specificity (CI: 48–100%) for
 all four tests. Testing infected mosquito pools, the rapid DENV-2, -3 and
 -4 tests showed 100% diagnostic sensitivity (95% CI = 69% to 100%, n=10)
 and the DENV-1 test showed 90% diagnostic sensitivity (55.50% to 99.75%,
 n=10) together with 100% diagnostic specificity (CI: 48–100%). Our tests
 reduce the operational time required to perform mosquito infection status
 surveillance testing from &gt; two hours to only 35 minutes, and have
 potential to improve accessibility of mosquito screening, improving
 monitoring and control strategies in low-income countries most affected by
 dengue outbreaks.
description: The DNA and RNA analytical sensitivity of the DENV 1–4 RPA/LFD
 tests was determined using 10-fold serial dilutions of both plasmid DNA
 and RNA-transcripts. Analytical specificity for
 detection of different dengue serotypes was tested using high
 concentrations (10<sup>5</sup> copies/µL) of RNA transcripts
 from each of the four DENVs Analytical specificity for
 detection of different flaviviruses (FV) was tested using RNA extracted
 from ZIKV, JEV, MVEV, and WNV<sub>KUN</sub> cell culture
 supernatant (5–7 log<sub>10
 </sub>TCID<sub>50</sub>/ml)
 Individual mosquito testing was tested by comparing rapid DENV
 1–4 serotyping tests to qRT-PCR Pooled mosquito testing
 was also tested by comparing rapid DENV 1–4 serotyping tests
 to qRT-PCR
description: The contents of each data file are described in the Readme.txt
 file.
DOI: 10.5061/dryad.8w9ghx3p5
title: The consequences of coastal offsets for fisheries

description: Biodiversity offsetting is increasingly used to mitigate biodiversity
 impacts from development, but the practice of offsetting rarely considers
 how to also mitigate losses of ecosystem services. Offset rules, such as
 how near an offset must be to an impact site, may help ensure biodiversity
 offsets also counterbalance losses of ecosystem services but this has not
 yet well understood. We explored how different rules for siting coastal
 offsets could change net impacts to a provisioning ecosystem service:
 fishery resources in Queensland, Australia. A spatially-explicit model
 incorporating supply, flow and demand of fishery resources was developed
 to simulate contributions of offset sites to commercial fisheries in
 Queensland, Australia. We simulated offsets for losses due to 63 real
 projects that damaged mangroves and 14 projects damaging seagrasses. We
 found that the percentage of species suffering net negative outcomes for
 the whole commercial fishery increased from about 68% when offsets were
 located close to impact sites to &gt; 85% when there were no
 restrictions on offset location. All fisheries for seagrass offsets
 suffered net economic losses under both scenarios, but these were worse
 when offsets were not required to be near to impact sites. Offsetting
 outcomes varied substantially across species. Species with shorter maximum
 dispersal distance and higher dispersal decay parameters suffered greater
 net losses. Synthesis and applications. Our model quantified
 impacts of fishery habitat depletion and offsets on fishery resources and
 the approach can be applied to assess impacts of losses of fishery
 habitats globally. The findings suggest that to minimize losses of fishery
 resources caused by habitat depletion, offset policy should generally
 locate offset sites at the locations available for restoration that are
 nearest to impact sites, unless specific information about the relative
 contributions of sites to impacted fisheries is available to guide offset
 location.
description: The data for traditional boat moorings located in existing
 seagrass habitats in Queensland is provided as potential seagrass offset
 sites in Queensland. Python script for the model.
DOI: 10.5061/dryad.8gtht76r1
title: Tumor-induced Osteomalacia: A Systematic Review and Individual Patient’s Data Analysis

description: Abstract Context Tumor-induced osteomalacia (TIO) is a rare paraneoplastic
 syndrome, usually caused by small, benign, and slow-growing phosphaturic
 mesenchymal tumors. Clinically, TIO is characterized by renal phosphate
 leak, causing hypophosphatemia and osteomalacia. This review was performed
 to assess the clinical characteristics of TIO patients described worldwide
 so far. Evidence Acquisition On June 26, 2021, a systematic search was
 performed in Medline, Google Scholar, Google book, and Cochrane Library
 using the terms: “tumor induced osteomalacia,” “oncogenic osteomalacia,”
 “hypophosphatemia.” There were no language restrictions. This review was
 performed according to Preferred Reporting Items for Systematic reviews
 and Meta-Analyses criteria. Evidence Results Overall, 1725 TIO cases were
 collected. TIO was more frequent in adult men, who showed a higher
 incidence of fractures compared with TIO women. The TIO-causing neoplasms
 were identified in 1493 patients. The somatostatin receptor-based imaging
 modalities have the highest sensitivity for the identification of
 TIO-causing neoplasms. TIO-causing neoplasms were equally located in bone
 and soft tissues; the latter showed a higher prevalence of fractures and
 deformities. The surgery is the preferred TIO definitive treatment
 (successful in &gt; 90% of patients). Promising nonsurgical
 therapies are treatments with burosumab in TIO patients with elevated
 fibroblast growth factor-23 levels, and with radiolabeled somatostatin
 analogs in patients with TIO-causing neoplasm identified by somatostatin
 receptor-based imaging techniques. Conclusion TIO occurs preferentially in
 adult men. The TIO clinical expressiveness is more severe in men as well
 as in patients with TIO-causing neoplasms located in soft tissues.
 Treatments with burosumab and with radiolabeled somatostatin analogs are
 the most promising nonsurgical therapies.
DOI: 10.5061/dryad.4mw6m90c5
title: Morphological measurements Oryzias eversi, Oryzias nigrimas and hybrids

description: The evolution of complex phenotypes like reproductive strategies is
 challenging to understand as they often depend on multiple adaptations,
 which only jointly result in a specific functionality. Sulawesi ricefishes
 (Adrianichthyidae) evolved a reproductive strategy termed pelvic brooding.
 In contrast to the more common transfer brooding, female pelvic brooders
 carry an egg-bundle connected to their body for weeks until the fry
 hatches. To examine the genetic architecture of pelvic
 brooding, we crossed the pelvic brooding Oryzias
 eversi and the transfer brooding O.
 nigrimas (species divergence time: ~ 3.6 my). We hypothesize,
 that a low number of loci and modularity have facilitated the rapid
 evolution of pelvic brooding. Traits associated to pelvic brooding, like
 rib length, pelvic fin length and morphology of the genital papilla were
 correlated in the parental species but correlations were reduced or lost
 in their F1 and F2 hybrids. Using the Castle-Wright estimator, we found
 that generally few loci underlie the studied traits. Further, both
 parental species showed modularity in their body plans. In conclusion,
 morphological traits related to pelvic brooding were based on a few loci
 and the mid-body region likely could evolve independently from the
 remaining body parts. Both factors presumably facilitated the rapid
 evolution of pelvic brooding.
description: We photographed preserved specimen and measured distances using
 ImageJ.
description: There is missing data in the O. eversi backcross hybrids. This is
 due the Covid-19 lockdown and the labs were closed.
DOI: 10.5061/dryad.kkwh70s69
title: Unraveling hierarchical genetic structure of tea green leafhopper, Matsumurasca onukii, in East Asia based on SSRs and SNPs

description: Matsumurasca onukii (Matsuda, 1952), one of the dominant pests in major
 tea production areas in Asia, currently is known to occur in Japan,
 Vietnam, and China, and severely threatens tea production, quality, and
 international export trade. To elucidate the population genetic structure
 of this species, 1633 single nucleotide polymorphisms (SNPs) and 18
 microsatellite markers (SSRs) were used to genotype samples from 27 sites
 representing 18 geographical populations distributed throughout the known
 range of the species in East Asia. Analyses of both SNPs and SSRs showed
 that M. onukii populations in Yunnan exhibit high genetic differentiation
 and structure compared to other populations. The Kagoshima (JJ) and
 Shizuoka (JS) populations from Japan were separated from populations from
 China by SNPs but clustered with Jinhua (JH), Yingde (YD), Guilin (GL),
 Fuzhou (FZ), Hainan (HQ), Leshan (CT), Chongqing (CY) and Zunyi (ZY) tea
 areas in China and the Vietnamese Vinh Phuc (VN) population based on SSR
 data. On the contrary, CT, CY, ZY, and Shaanxi (SX) populations clustered
 together based on SNPs, but were separated by SSRs. Both marker datasets
 identified significant geographic differentiation among the 18
 populations. Various environmental and anthropogenic factors, including
 the geographical barriers to migration, human transport of hosts (Camellia
 sinesis (L.) O. Kuntze), and adaptability of M. onukii to various climatic
 zones possibly account for the rapid spread of this pest in Asia. The
 results demonstrate that SNPs from high-throughput genotyping data can be
 used to reveal subtle genetic substructure at broad scales in r-strategist
 insects.
description: Genotype table for 18 microsatellites generated using AFLP of
 sequences containing repeats (FIASCO). Each row is a microsatellite locus;
 each column starting with the second is an <em>M. onukii</em>
 individual. For these diploid markers, individuals have two alleles per
 locus. Missing data (e.g. due to low reads) are indicated by
 "000". For each locus, haplotypes are uniquely labeled with
 numbers (genotyping by automated capillary electrophoresis).
 Genotype table for 1633 SNPs.  Associated raw sequence data have
 been deposited to the NCBI Sequence Read Archive (BioProject ID:
 PRJNA799739).
description: Genotypic data obtained by 18 microsatellite markers was
 submitted in Genpop format. Genotypic data obtained by
 1633 microsatellite markers was submitted in .vcf.
DOI: 10.5061/dryad.hmgqnk9jq
title: Data from: Novel methods to define invasive procedures at the end-of-life were developed to improve quality of end of life care research: A population-based cohort study in colorectal cancer

description: Background Understanding the use of invasive procedures (IPs) at the
 end-of-life (EoL) is important to avoid under- and overtreatment, but
 epidemiologic analysis is hampered by limited methods to define treatment
 intent and EoL phase. This study applied novel methods to report IPs at
 the EoL using a colorectal cancer (CRC) case study. Methods An English
 population-based cohort of adult patients diagnosed between 2013 and 2015
 was used with follow-up to 2018. Procedure intent (curative, non-curative,
 diagnostic) by cancer site and stage at diagnosis was classified by two
 surgeons independently. Joinpoint regression modelled weekly rates of IPs
 for 36 sub-cohorts of patients with incremental survival of 0-36 months.
 EoL phase was defined by a significant IP rate change before death.
 Zero-inflated Poisson regression explored associations between IP rates
 and clinical/sociodemographic variables. Results Of 87,731 patients
 included, 41,972 (48%) died. 9,492 procedures were classified by intent
 (interrater agreement 99.8%). Patients received 502,895 IPs (1.39 and 3.36
 per person year for survivors and decedents). Joinpoint regression
 identified significant increases in IPs four weeks before death in those
 living 3-6 months, and eight weeks before death in those living 7–36
 months from diagnosis. 7,908 (18.8%) patients underwent IPs at the EoL,
 with stoma formation the most common major procedure. Younger age,
 early-stage disease, men, lower comorbidity, those receiving chemotherapy
 and living longer from diagnosis were associated with IPs. Conclusions
 Methods to identify and classify IPs at the EoL were developed and tested
 within a CRC population. This approach can be now extended and validated
 to identify potential under- and overtreatment. 
description: # Data from: Novel methods to define invasive procedures at the
 end-of-life were developed to improve quality of end of life care
 research: A population-based cohort study in colorectal cancer
 [https://doi.org/10.5061/dryad.hmgqnk9jq](https://doi.org/10.5061/dryad.hmgqnk9jq) This dataset categorizes OPCS codes according to treatment intent (potentially curative, non-curative, diagnostic and metastectomy) ## Description of the data and file structure This data is structured with in rows corresponding to OPCS codes (version 4) by cancer site (ICD10) and stage (UICC TNM). Each permutation is categorized by two independent colorectal surgical specialists with discrepancies reconciled into a final categorization. ## * ##
DOI: 10.5061/dryad.qv9s4mwgb
title: Root traits, root diameter distribution and soil parameters at the community level along a mediterranean successional gradient

description: The data correspond to average root traits at the community level, and
 parameters describing the root diameter distribution at the community
 level. Soil parameters are also indicated. All measurements were conducted
 along a successional gradient on roadsides in the Mediterranean region
 (Montpellier, France, 43°6′N, 3°8′E). These data were used in the article
 entitled "Dissecting fine root diameter distribution at the community
 level captures root morpological diversity" from Erktan, A., Roumet,
 C., Munoz, F (in press) in Oikos (2022).
description: All the information regarding to the dataset collection are
 provided in the associated manuscript entitled "Dissecting fine root
 diameter distribution at the community level captures root morpological
 diversity" from Erktan, A., Roumet, C., Munoz, F (in press) in Oikos
 (2022), and in Erktan, A. et al. 2018. Two dimensions define the variation
 of fine root traits across plant communities under the joint influence of
 ecological succession and annual mowing. – J. Ecol. 106:
 2031–2042.
description: Significance of the variables: age: age of the
 plant community; NM: not mown; M: mown; Mx: average root diameter of the
 mode x (root diameter distribution at the community level); SDx: average
 standard deviation of the mode x (root diameter distribution at the
 community level); Px: average relative proportion of the mode x (root
 diameter distribution at the community level); SoilC: concentration in
 soil organic carbon (g/kg); SoilN: concentration in total nitrogen (g/kg);
 CEC : cation exchange capacity (meq/kg); SoilP: available Phosphorus
 (mg/kg); SRL: specific root length (m/g); MRD: mean root diameter (mm);
 Root_N: concentration in root nitrogen (mg/g); Root_C: concentration in
 root carbon (mg/g); RDMC: root dry matter content (mg/g); variance:
 variance of the root diameter distribution at the community level;
 graminoid: proportion of graminoids in the plant community in %; herb:
 proportion of herbs in the plant community in %; shrub: proportion of
 shrubs in the plant community in %; tree: proportion of trees in the plant
 community in %; Woodiness: proportion of woody species in the plant
 community (%); Cmean: average proportion of plants with a competitive
 strategy; Smean: average proportion of plants with a stress-tolerant
 strategy; Rmean: average proportion of plants with a ruderal strategy.
 Fric: Functional plant richness at the community level; simpson: Simpson
 diversity of the plant communities.
DOI: 10.5061/dryad.xgxd254hz
title: Data from: Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae

description: Species of the mustelid subfamily Guloninae inhabit diverse habitats on
 multiple continents, and occupy a variety of ecological niches. They
 differ in feeding ecologies, reproductive strategies and morphological
 adaptations. To identify candidate loci associated with adaptations to
 their respective environments, we generated a de novo assembly of the
 tayra (Eira barbara), the earliest diverging species in the subfamily, and
 compared this with the genomes available for the wolverine (Gulo gulo) and
 the sable (Martes zibellina). Our comparative genomic analyses included
 searching for signs of positive selection, examining changes in gene
 family sizes, as well as searching for species-specific structural
 variants (SVs). Among candidate loci associated with phenotypic traits, we
 observed many related to diet, body condition and reproduction. For
 example, for the tayra, which has an atypical gulonine reproductive
 strategy of aseasonal breeding, we observe species-specific changes in
 many pregnancy-related genes. For the wolverine, a circumpolar
 hypercarnivore that must cope with seasonal food scarcity, we observed
 many changes in genes associated with diet and body condition. All types
 of genomic variation examined (single nucleotide polymorphisms, gene
 family expansions, structural variants) contributed substantially to the
 identification of candidate loci. This strongly argues for consideration
 of variation other than single nucleotide polymorphisms in comparative
 genomics studies aiming to identify loci of adaptive significance.
DOI: 10.5061/dryad.1g1jwstzg
title: Pycnogonid mitochondrial genomes data

description: Pycnogonida, or sea spiders, is a speciose clade with ~1,300 described
 species that is especially diverse in the Southern Ocean. Evolutionary
 patterns within sea spiders remain unresolved between and within the ten
 putative, extant families due to due to shared morphological traits and
 highly reduced forms. Herein, we find that the order of mitochondrial
 protein coding genes is consistent between all sampled sea spiders, even
 though arrangement of tRNA genes, as well as placement and length of the
 control region, vary. The presence of large noncoding introns present in
 multiple families indicates that pycnogonid mtDNA have a fast evolutionary
 rate. A consensus phylogeny of recognized families is still debated, and
 previous work based on various methodologies has produced contrasting
 hypotheses of relationships. To better understand phylogenetic
 relationships between major clades of sea spiders, we constructed a
 dataset of whole mitochondrial genomes from representatives of all ten
 currently recognized families. Our results suggest a novel familial-level
 phylogeny within Pycnogonida, with a monophyletic clade containing
 Callipallenidae and Nymphonidae placed as the sister to all other
 recognized families.
description: EMBOSS palindrome (Rice et al. 2000) was used to search each
 intron for terminal repeats known to be associated with
 transposons.