cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25338/b8204m
title: Processed carbon mass loading data from DRI and Sunset analyzers

description: This dataset contains thermal-optical analysis (TOA) carbon data from an
 inter-laboratory comparison study described in the paper: Zhang, X.,
 Trzepla, K., White, W., Raffuse, S., and Hyslop, N. P.: Intercomparison of
 thermal–optical carbon measurements by Sunset and Desert Research
 Institute (DRI) analyzers using the IMPROVE_A protocol, Atmos. Meas.
 Tech., 14, 3217–3231, https://doi.org/10.5194/amt-14-3217-2021, 2021.
description: Two sets of Chemical Speciation Network (CSN) carbon samples
 collected on 25mm diameter quartz filters were respectively analyzed by
 thermal-optical reflective analysis with the IMPROVE_A protocol. Set 1
 consists of 303 CSN filters sampled in September and October 2007 that
 were previously analyzed by DRI with the DRI-2001 models in the year 2008.
 Set 2 consists of 4073 CSN samples and 622 CSN field blanks collected
 between May and September 2017, which were sequentially analyzed by the
 Sunset analyzers at UC Davis and by the DRI-2015 analyzers at DRI within a
 year after sample collection. Sunset and DRI-2015 data
 are reported in mass loadings (μg/cm2). Sunset raw data were processed
 using a custom R computing package developed by UC Davis. DRI-2015 data
 were calculated by the program supplied by the manufacturer. DRI-2001 data
 from the archived 2007 CSN samples were downloaded from the EPA
 Air<br> Quality System (AQS) database
 (https://aqs.epa.gov/aqsweb/documents/data_api.html, last access: 28 April
 2021). The concentration data (μgm-3) were converted to mass loadings
 (μg/cm2) using a nominal sample volume (33m3) and filter area (3.53 cm2)
 for direct comparison against the Sunset data.
  
description: This data file contains 5 columns with header.
 Specifically, SampleID = original CSN filter
 identifier Parameter = carbon fractions speciated by
 thermal-optical analysis UCD_massloading =  carbon mass
 loading in the unit of μg/cm2 measured by Sunset analyzers in UC Davis
 laboratory DRI_massloading = carbon mass loading in the
 unit of μg/cm2 measured by DRI analyzers in Desert Research
 Institute laboratory DRI Analyzer = the model type of
 the DRI analyzer, used as a flag to distinguish Set 1 and Set2 specified
 in the Methods section
DOI: 10.5061/dryad.fbg79cnv2
title: Flowering phenology of Nouelia insignis

description: Nouelia insignis Franch (Asteraceae) is a short, narrow endemic
 and endangered tree, growing with a natural population in the dry and hot
 valley of the Jinsha River in the southwest area of China. In this work,
 flowering phenology (time and duration), floral biology, visit frequency
 and behavior of pollinators, and pollination characteristics were studied
 based on investigation in the field and analysis in the laboratory with
 the help of a stereomicroscope, and the relationship between seed setting
 rate and reproductive traits, as well as the relationship between
 flowering time and rainfall before flowering was tested using the method
 of general linear regression model. The results showed that natural
 population of N. insignis exhibited high flowering synchrony with
 relatively stable flowering duration, and the flowering time fluctuated
 greatly depending on the rainfall 5 months before flowering. The
 pollination of N. insignis required pollinators, and insect activities
 played a very important role in the pollination process. However, lack of
 the pollinators was not a limitation for reproductive fitness in N.
 insignis, although the number of pollinators was small and the frequency
 of visits was low. In addition, no pollen limitation was found during
 pollination. The average seed setting rate of N. insignis in the natural
 condition was only 1.52%–3.73%, and it was generally affected by changes
 in flowering phenology between years, and had a higher seed set in early
 flowering year. The annual variation of seed set might be related to the
 annual variations of stamen and pistil functions, such as changes of
 pollen viability and stigma receptivity, which were closely related to
 flowering time. The results of this study are of value for further
 conservation actions on natural population of this threatened endemic
 plant.
DOI: 10.5061/dryad.573n5tb7j
title: Full-length transcriptome analysis reveals candidate genes involved in terpenoid biosynthesis in Artemisia argyi

description: Artemisia argyi is an important medicinal plant widely utilized
 for moxibustion heat therapy in China. The terpenoid
 biosynthesis process in A. argyi is speculated to play a
 key role in conferring its medicinal value. Yet the molecular
 mechanism underlying terpenoid biosynthesis
 remains unclear, in part because the reference genome of
 A. argyi is unavailable. Moreover, the full-length transcriptome
 of A. argyi has yet to be sequenced. Therefore, in this study de
 novo transcriptome sequencing of A.
 argyi’s root, stem and leaf tissues was performed to
 obtain those candidate genes related to terpenoid
 biosynthesis, by combining the PacBio single-molecule real-time
 (SMRT) and Illumina sequencing NGS platforms. These respectively
 generated more than 55.4 Gb of sequencing data and 108,846
 full-length reads (non-chimeric) were generated by the Illumina
 and PacBio platform, respectively. Then, 53,043 consensus isoforms were
 clustered and used to represent 36,820 non-redundant transcripts, of which
 34,839 (94.62%) were annotated in public databases, namely those
 of Nr, eggNOG, GO, Swiss-Prot, KEGG, and Pfam. A differential
 gene expression analysis that compared A.
 argyi leaves with root and stem tissues revealed 13,850
 (7,566 up-regulated, 6,284 down-regulated) and 9,502 (5,284 up-regulated,
 218 down-regulated) uniquely assembled transcripts as differentially
 expressed (DETs) between them. Specifically, the expression
 profile and KEGG functional enrichment analysis of these DETs
 indicated that they were significantly enriched in the
 biosynthesis of amino acids, carotenoids, diterpenoids and
 flavonoids, as well as the metabolism processes of glycine,
 serine, and threonine. Moreover, multiple genes encoding
 significant enzymes or transcription factors related to diterpenoid
 biosynthesis were highly expressed in the A. argyi
 leaf tissue. Additionally, several transcription factor families,
 such as RLK-Pelle_LRR-L-1 and RLK-Pelle_DLSV, were also identified. In
 conclusion, this study offers a valuable resource for
 transcriptome information, providing a functional genomic
 foundation for further research on molecular mechanisms
 underlying the medicinal use of A. argyi leaves.
DOI: 10.5061/dryad.02v6wwq32
title: Auxetic vibration behaviours of periodic tetrahedral units with a shared edge

description: A very low frequency mode supported within an auxetic structure is
 presented. We propose a constrained periodic framework with
 corner-to-corner and edge-to-edge sharing of tetrahedra and develop a
 kinematic model incorporating two types of linear springs to calculate the
 momentum term under infinitesimal transformations. The modal analysis
 shows that the microstructure with its two degrees of freedom has both low
 and high frequency modes under auxetic transformations. The low frequency
 mode approaches zero frequency when the corresponding spring constant
 tends to zero. With regard to coupled eigenmodes, the stress–strain
 relationship of the uniaxial forced vibration covers a wide range. When
 excited, a very slow motion is clearly observed along with a structural
 expansion for almost zero values of the elastic modulus.
DOI: 10.5061/dryad.wstqjq2m3
title: Macroinvertebrate along Vestari-Jökulsá Iceland

description: 1. Background: The impact of climate change on the longitudinal
 distribution of macroinvertebrates in glacier‐fed streams has been the
 subject of increasing awareness in recent years. Despite prior intensive
 research on the longitudinal distribution of macroinvertebrates in
 glacier-fed ecosystems, long-term studies in glacier-fed rivers of arctic
 regions, that investigate the temporal change of macroinvertebrate
 communities during periods of rapid climate change, are largely missing,
 although climate change is expected to cause large shifts in arctic
 ecosystems. Especially in the arctic rivers of Iceland, where the aquatic
 macroinvertebrate fauna is very poor in species, and glacier-fed rivers
 have the lowest density and diversity of benthic invertebrates of all
 river groups, the response of benthic macroinvertebrates to future
 environmental change may differ distinctly from those in low-latitude
 climate regions. Here we present the results of a pilot study
 investigating the changes of the macroinvertebrate communities along the
 longitudinal gradient of the glacial river ecosystem Vestari-Jökulsá in
 Iceland between the years 1996 and 2018, where environmental conditions
 changed rapidly, especially including the recession of its source glacier.
 2. Methods: At the 9 respective locations invertebrate sampling took place
 along a 15 m river reach, where 10 stones were removed while holding a
 surber sampler with a mesh size 250 μm downstream of the stone. Electrical
 conductivity, water temperate, pH-value, dissolved oxygen, turbidity and
 chlorophyll α were measured in-situ and water samples were taken for
 analyzing DOC (concentration, optical properties), POC and nutrients. 3.
 Results: The total number of species and diversity decreased significantly
 from July 1996 to July 2018. The longitudinal distribution of
 macroinvertebrates within the studied Arctic glacial stream did not
 resemble long-term changes as their occur in low-latitude glacial streams.
 While 36 taxa related to 12 different species were found in 1996, their
 number has decreased to 8 in 2018. 4. Conclusions: At present, it is
 difficult to firmly determine the exact mechanisms which control the
 reduction of macroinvertebrates along the unique ecosystem of
 Vestari-Jökulsá with its shows comparatively low biodiversity. Glacier
 retreat may be crucial, but it is imperative to carry out further
 comparative studies, especially investigating the influence of changing
 hydrological conditions on the longitudinal changes of macroinvertebrate
 in artic glacier-fed rivers.
description: At the 9 respective locations invertebrate sampling
 took place along a 15 m river reach, where 10 stones were removed while
 holding a surber sampler with a mesh size 250 μm downstream of the stone.
 Electrical conductivity, water temperate, pH-value, dissolved oxygen,
 turbidity and chlorophyll α were measured in-situ and water samples were
 taken for analyzing DOC (concentration, optical properties), POC and
 nutrients.
DOI: 10.5061/dryad.3bk3j9kjz
title: Difference in rupture risk between familial and sporadic intracranial aneurysms: an individual patient data meta-analysis

description: Objective: We combined individual patient data (IPD) from prospective
 cohorts of patients with unruptured intracranial aneurysms (UIA) to assess
 to what extent patients with familial UIA have a higher rupture risk than
 those with sporadic UIA. Methods: For this IPD meta-analysis we performed
 an Embase and Pubmed search for studies published up to December 1, 2020.
 We included studies that 1) had a prospective study design; 2) included 50
 or more patients with UIA; 3) studied the natural course of UIA and risk
 factors for aneurysm rupture including family history for aneurysmal
 subarachnoid haemorrhage and UIA; and 4) had aneurysm rupture as an
 outcome. Cohorts with available IPD were included. All studies included
 patients with newly diagnosed UIA visiting one of the study centers. The
 primary outcome was aneurysmal rupture. Patients with polycystic kidney
 disease and moyamoya disease were excluded. We compared rupture rates of
 familial versus sporadic UIA using a Cox proportional hazard regression
 model adjusted for the PHASES score and smoking. We performed two
 analyses: 1. only studies defining first-degree relatives as parents,
 children, and siblings and 2. all studies, thus both including and
 excluding siblings as first-degree relatives. Results: We pooled IPD from
 eight cohorts with a low and moderate risk of bias. First-degree relatives
 were defined as parents, siblings and children in six cohorts (29% Dutch,
 55% Finnish, 15% Japanese), totalling 2,297 patients (17% familial, 399
 patients) with 3,089 UIA and 7,301 person-years follow-up. Rupture
 occurred in 10 familial patients (rupture rate: 0·89%/person-year; 95%
 CI:0·45-1·59) and 41 sporadic patients (0·66%/person-year; 95%
 CI:0·48-0·89); adjusted HR for familial patients 2·56 (95% CI: 1·18–5·56).
 After adding also the two cohorts excluding siblings as first-degree
 relatives resulting in 9,511 patients the adjusted HR was 1·44 (95% CI:
 0·86–2·40). Conclusion: The risk of rupture of UIA is two and a half times
 higher, with a range from a 1.2 to 5 times higher risk, in familial than
 in sporadic UIA. When assessing the risk of rupture in UIA, family history
 should be taken into account.
description: Individual patient data
 meta-analysis.
DOI: 10.5061/dryad.7wm37pvsq
title: Mercury accumulation in leaves of different plant types – the significance of tissue age and specific leaf area

description: Mercury, Hg, is one of the most problematic metals from an environmental
 perspective. To assess the problems caused by Hg in the environment it is
 crucial to understand the processes of Hg biogeochemistry, but the
 exchange of Hg between the atmosphere and vegetation is not sufficiently
 well characterised. We explored the mercury concentration, [Hg], in
 foliage from a diverse set of plant types, locations and sampling periods
 to study whether there is a continuous accumulation of Hg in
 leaves/needles over time. Measurements of [Hg] were made in deciduous and
 conifer trees in Gothenburg, Sweden (Botanical Garden and city area) as
 well as of evergreen trees in Rwanda. In addition, data for wheat from an
 ozone experiment conducted at Östad, Sweden, were included. Conifer data
 were quantitatively compared with literature data. In every case where
 older foliage was directly compared with younger, [Hg] was higher in older
 tissue. Covering the range of current year up to four-year old needles,
 there was no sign of Hg saturation in conifer needles with age. Thus, over
 time scales of approximately one month to several years, the Hg uptake in
 foliage from the atmosphere always dominated over Hg evasion. Rwandan
 broadleaved trees had generally older leaves due to lack of seasonal
 abscission and higher [Hg] than Swedish broadleaved trees. The
 significance of atmospheric Hg uptake in plants was shown in a wheat
 experiment where charcoal filtrated air lead to significantly lower leaf
 [Hg]. To search for general patterns, the accumulation rates of Hg in the
 diverse set of tree species in the Gothenburg area were related to the
 specific leaf area (SLA). Leaf area based [Hg] was strongly negatively and
 non-linearly correlated with SLA, while mass-based [Hg] had a somewhat
 weaker positive relationship with SLA (both relationships with p &lt;
 0.001). An elaborated understanding of the relationship behind [Hg] and
 SLA would support large-scale modelling of Hg uptake by vegetation and Hg
 circulation in general.
description: Analyses of mercury in leaves and needles of trees as well as
 wheat collected in the field in Sweden and Rwanda. Chemical analysis was
 made by ICP-MS. Specific leaf area was estimated and used to calculate
 unit leaf area mercury concentration.
description: No missing values but some samples for wheat were below detection
 limit (clearly indicated in the data file). Detailed
 descriptions of sites and sampling methods will be described in a
 manuscript to be submitted to Biogeosciences.
DOI: 10.5061/dryad.fxpnvx0rs
title: Group-size effect on vigilance in mammals

description: Group-size effects, whereby antipredator vigilance decreases as group size
 increases, are widely reported in mammals and birds but a meta-analysis
 has only been conducted in birds. We systematically reviewed the
 literature on mammalian group-size effects, estimated the effect sizes in
 each study, and conducted a phylogenetic meta-analysis. We obtained 296
 effect sizes from 97 species belonging to 10 Orders and 26 Families.
 Overall, effect sizes indicated a moderate negative effect of group size
 (r = - 0.44), but 43% of the effect sizes were compatible with a null
 effect of group size. There was significant heterogeneity in effect sizes.
 Weaker effect sizes occurred when vigilance was measured as a frequency or
 a duration rather than as a percentage of time spent vigilant, when
 measured in closed habitats, during the reproductive season, and in
 mixed-sex groups or during times when juveniles were absent. We infer a
 ‘file drawer problem’ because there were relatively few studies with
 smaller sample sizes reporting small group-size effects. The results
 confirm the importance of group size in explaining variation in mammalian
 vigilance, but also suggests that a substantial amount of variation
 remains unexplained. We suggest that future studies should aim to study
 mammalian group-size effects by quantifying the percentage of time
 allocated to vigilance rather than apparently lower-power methods such as
 frequency or duration of vigilance.
DOI: 10.5281/zenodo.18396996
title: ISD
DOI: 10.5061/dryad.15dv41nx6
title: metabarcoding data for: Benchmark of bioinformatics tools for fast and accurate species identification from environmental DNA metabarcoding

description: This dataset contains fish DNA sequences samples, simulated with Grinder,
 to build a mock community, as well as real fish eDNA metabarcoding data
 from the Mediterranean sea. These data have been used to compare the
 efficiency of different bioinformatic tools in retrieving the species
 composition of real and simulated samples.
description: The archive "simulated_forward_reverse_reads.zip"
 contains the sequence reads simulated with Grinder. The
 archive "species_abundance_per_sample.zip" contains 1 file per
 sample with the relative proportions of reads per species, in the
 simulated samples. The archive
 "real_eDNA_forward_reverse_reads.zip" contains the real eDNA
 metabarcoding data collected in the Mediterranean Sea.
DOI: 10.5281/zenodo.18396995
title: ISD
DOI: 10.5061/dryad.dv41ns1z2
title: Data for: Sex-specific ornament evolution is a consistent feature of climatic adaptation across space and time in dragonflies

description: Adaptation to different climates fuels the origins and maintenance of
 biodiversity. Detailing how organisms optimize fitness for their local
 climate is therefore an essential goal in biology. Although we
 increasingly understand how survival-related traits evolve as organisms
 adapt to climatic conditions, it is unclear if organisms also optimize
 traits that coordinate mating between the sexes. Here, we show that
 dragonflies consistently adapt to warmer climates across space and time by
 evolving less male melanin ornamentation—a mating-related trait that also
 absorbs solar radiation and heats individuals above ambient temperatures.
 Continent-wide macroevolutionary analyses reveal that species inhabiting
 warmer climates evolve less male ornamentation. Community-science
 observations across ten species indicate that populations adapt to warmer
 parts of species’ ranges through microevolution of smaller male ornaments.
 Observations from 2005-2019 detail that contemporary selective pressures
 oppose male ornaments in warmer years; and our climate-warming projections
 predict further decreases by 2070. Conversely, our analyses show that
 female ornamentation responds idiosyncratically to temperature across
 space and time, indicating the sexes evolve in different ways to meet the
 demands of the local climate. Overall, these macro- and microevolutionary
 findings demonstrate that organisms predictably optimize their
 mating-related traits for the climate just as they do their
 survival-related traits.
description: see articles for full details
description: Please see meta-data files for information on variables
DOI: 10.5061/dryad.qrfj6q5fp
title: Data from: Detailed characterization of the UMAMITs proteins provides insight into their evolution, amino acid transport properties, and role in the plant

description: Amino acid transporters play a critical role in distributing amino acids
 within the cell compartments and between the plant organs. Despite this
 importance, relatively few amino acid transporter genes have been
 characterized and their role elucidated with certainty. Two main families
 of proteins encode amino acid transporters in plants: the Amino
 Acid-Polyamine-Organocation superfamily, containing mostly importers, and
 the Usually Multiple Acids Move In and out Transporter family, apparently
 encoding exporters, totaling 63 and 44 genes in Arabidopsis, respectively.
 Knowledge on UMAMITs is scarce, based on six Arabidopsis genes and a
 handful of genes from other species. To get insight into the role of the
 members of this family and provide data to be used for future
 characterization, we studied the evolution of the UMAMITs in plants, and
 determined the functional properties, the structure, and the localization
 of the 47 Arabidopsis UMAMITs. Our analysis showed that the AtUMAMITs are
 essentially localized at the tonoplast or the plasma membrane, and that
 most of them are able to export amino acids from the cytosol, confirming a
 role in intra- and inter-cellular amino acid transport. As an example,
 this set of data was used to hypothesize the role of a few AtUMAMITs in
 the plant and the cell.