cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2ngf1vhmn
title: Data from: Early Cambrian (stage 4) brachiopods from the Shipai Formation in the Three Gorges area of South China

description: Diverse and abundant fossil taxa have been described in the lower Cambrian
 Shipai Formation in the Three Gorges area of Hubei province, South China,
 but the diversity of the co-occurring brachiopod fauna and their taxonomy
 is still far from clear. Here we describe the brachiopod fauna recovered
 from the Shipai Formation in the Three Gorges area of South China,
 including representatives of the subphylum Linguliformea:
 linguloids(Lingulellotreta ergalievi, Eoobolus malongensis and Neobolidae
 gen. indet. sp. indet.), and an acrotretoid (Linnarssonia sapushanensis);
 and representatives from the subphylum Rhynchonelliformea: the
 calcareous-shelled Kutorginates (Kutorgina sinensis, Kutorgina sp.,
 Nisusia liantuoensis). This brachiopod assemblage and the first occurrence
 of Linnarssonia sapushanensis shell beds permits correlation of the Shipai
 Formation in the Three Gorges area of Hubei province with the Stage 4
 Wulongqing Formation in the Wuding area of eastern Yunnan. This
 correlation is further strengthened by the first appearance datum (FAD) of
 the rhynchonelliform brachiopod Nisusia in the upper silty mudstone of
 both the Shipai and Wulongqing formations. The new well-preserved
 material, derived from siliciclastic rocks, also gives critical new
 insights into the fine shell structure of L. sapushanensis.
 Microstructural studies on micromorphic acrotretoids (like Linnarssonia)
 have previously been restricted to fossils acid etched from limestones.
 This is the first study to carry out detailed comparative ultrastructural
 studies on acrotretoid shells preserved in siliciclastic rocks. This work
 reveals a hollow tube and solid column microstructure in the acrotretoid
 shells from the Shipai Formation, which are likely to be equivalent of
 traditional column and central canal observed in shells dissolved from
 limestones.
description: Data 1-3 used to demonstrates strong similarities between
 <i>Eoobolus</i> from the Shipai and Wulongqing formations in
 the Three Gorges area and Yunnan province, South China.
 Data 4 used to interpretates the Cambrian Stage 4 brachiopod
 faunal similarities.
DOI: 10.5061/dryad.j3tx95xch
title: Drought sensitivity of Empetrum nigrum shrub growth at the species’ southern lowland distribution range margin

description: The ongoing warming of the Earth’s atmosphere is projected to cause a
 northward shift of species’ distributions, as they track their climatic
 optimum. In the rapidly warming Arctic, this has already led to an
 increase of shrubs in tundra ecosystems. While this northern expansion of
 woody biomass has been studied relatively extensively over the last
 decade, little research has been devoted to shrub growth responses at the
 southern margins of Northern Hemisphere shrubs. Here, we studied shoot
 length growth, its responses to climate over the period 2010-2017, and
 differences in leaf C and N content of the evergreen dwarf shrub Empetrum
 nigrum, as well as the vegetation composition and soil parameters at four
 sites located along a gradient of increasing dune age on the island
 Spiekeroog, northern Germany. The sites are located in the tri-national
 UNESCO world heritage site, the Wadden Sea. E. nigrum has a predominantly
 circum-arctic-boreal distribution and its southern distribution mbargin in
 European lowlands runs through northern Germany, where it is retreating
 northwards. We found a negative response to autumn (surface) temperatures
 and previous summer surface temperatures and/or a positive response to
 summer precipitation of E. nigrum growth, except at the oldest dune with
 the strongest E. nigrum dominance. Growth rates and plant species
 diversity declined with dune age. Our results suggest that E. nigrum
 growth is drought sensitive at its European southern range margin. We
 hypothesize that this sensitivity may form the basis for its northward
 retreat, which is supported by recent observations of E. nigrum dieback in
 Germany after the extreme drought in 2018 and model projections.
description: See published article for methods: Hein et al. (2021) Drought
 sensitivity of Empetrum nigrum shrub growth at the species’ southern
 lowland distribution range margin - Plant Ecology
description: See attached ReadMe.txt for additional information.
DOI: 10.5061/dryad.4f4qrfj9z
title: Spatiotemporal variation of the indoor mycobiome in daycare centers

description: Abstract Background Children spend considerable time in daycare centers in
 parts of the world and are exposed to the indoor micro- and mycobiomes of
 these facilities. The level of exposure to microorganisms varies within
 and between buildings, depending on occupancy, climate, and season. In
 order to evaluate indoor air quality, and the effect of usage and
 seasonality, we investigated the spatiotemporal variation in the indoor
 mycobiomes of two daycare centers. We collected dust samples from
 different rooms throughout a year and analyzed their mycobiomes using DNA
 metabarcoding. Results The fungal community composition in rooms with
 limited occupancy (auxiliary rooms) was similar to the outdoor samples,
 and clearly different from the rooms with higher occupancy (main rooms).
 The main rooms had higher abundance of Ascomycota, while the auxiliary
 rooms contained comparably more Basidiomycota. We observed a strong
 seasonal pattern in the mycobiome composition, mainly structured by the
 outdoor climate. Most markedly, basidiomycetes of the orders Agaricales
 and Polyporales, mainly reflecting typical outdoor fungi, were more
 abundant during summer and fall. In contrast, ascomycetes of the orders
 Saccharomycetales and Capnodiales were dominant during winter and spring.
 Conclusions Our findings provide clear evidences that the indoor
 mycobiomes in daycare centers are structured by occupancy as well as
 outdoor seasonality. We conclude that the temporal variability should be
 accounted for in indoor mycobiome studies and in the evaluation of indoor
 air quality of buildings.
DOI: 10.5061/dryad.mkkwh70z2
title: All simulation results, figures and code regarding the manuscript: Calibrating models of cancer invasion: parameter estimation using Approximate Bayesian Computation and gradient matching

description: We present two different methods to estimate parameters within a partial
 differential equation (PDE) model of cancer invasion. The model describes
 the spatio-temporal evolution of three variables -- tumour cell density,
 extracellular matrix density and matrix degrading enzyme concentration --
 in a one-dimensional tissue domain. The first method is a likelihood-free
 approach associated with Approximate Bayesian Computation (ABC); the
 second is a two-stage gradient matching method based on smoothing the data
 with a Generalized Additive Model (GAM) and matching gradients from the
 GAM to those from the model. Both methods performed well on simulated
 data.  To increase realism, additionally we tested the gradient
 matching scheme with simulated measurement error and found that the
 ability to estimate some model parameters deteriorated rapidly as
 measurement error increased.
description: All related data presented in this repository regarding the
 manuscript Xiao et al. were simulated using R and MATLAB. The detailed
 methods of applying the two schemes can be found in the README files in
 the repository and the comments in each MATLAB or R file. 
description: The primary repository can be found directly on
 Github: https://github.com/ycx12341/Data-Code-Figures-ver-4. Updates to
 the datasets will first be made to this primary repository.
DOI: 10.5061/dryad.j3tx95xcj
title: Constitutive and induced phenolics and volatiles in Quercus pyrenaica

description: With this dataset, we studied elevational gradients and their underlying
 climatic factors in constitutive and induced phenolics and
 volatile organic compounds in Oak trees. Oak defences were measured in
 leaves in a field study.  The dataset includes data for
 18 populations of Quercus pyrenaica spanning a 1300 m elevational
 gradient (from 370 to 1614 m) with their correspondence coordinates. In
 each population we sampled six saplings that were randomly
 assigned to one of two treatments: 1) herbivore inductionwith A.
 quercertorum larvae or 2) no induction (control). For each tree, we
 include an estimation of leaf-herbivory accounting for
 pre-treatment variation in natural herbivory as well as in the amount of
 experimentally-imposed damage by larvae. For each tree, we quantified and
 identify volatile organic compounds. We report 75 individual
 compounds including monoterpenes, sesquiterpenes and other
 compounds of different nature. We also quantify and identify 40 phenolics
 that were classified as condensed tannins, hydrolysable tannins, lignins
 or flavonoids. Finally, the dataset includes eight climatic variables
 extracted from worldClim for the coordinates of each population.
description: Phenolics were extracted from dry leaves using a methanolic
 extraction. For phenolics quantification, we used ultra-high
 performance<br> liquid-chromatography and a UV/VIS photodiode array
 detector. For phenolic identification, we used an ultraperformance liquid
 chromatography coupled with electrospray<br> ionization quadrupole
 time-of-flight mass spectrometry. Volatile Organic
 Compounds (VOCs) were collected from bagged leaves and trapped on charcoal
 filter using air-sampling pumps. After collection, VOCs were eluted
 in dichloromethane. For VOCs quantification, we used gas chromatography
 (GC) coupled with a mass selective detector (MSD). For VOCs
 identification, we used Kovats<br> retention index from published
 work and the NIST Standard Reference Database.
DOI: 10.5061/dryad.np5hqbzrq
title: Data from: Landscape complexity promotes resilience of biological pest control to climate change

description: Increased climate variability as a result of anthropogenic climate change
 can threaten the functioning of ecosystem services. However, diverse
 responses to climate change among species (response diversity) can provide
 ecosystems with resilience to this growing threat. Measuring and managing
 response diversity and resilience to global change are key ecological
 challenges. Here, we develop a novel index of climate resilience of
 ecosystem services, exemplified by calculating the thermal resilience of
 predator communities providing biological pest control. Field assays
 revealed substantial differences in temperature-dependent activity of
 predator species. Based on this information, our index revealed higher
 thermal resilience in predator communities of high response diversity and
 functional evenness (equity in service provisioning). Predator assemblages
 with higher thermal resilience provided more stable pest control in
 microcosms where temperature was experimentally varied, confirming that
 the index of thermal resilience developed here is linked to predator
 function. Importantly, complex landscapes containing a high number of
 non-crop habitat patches were more likely to contain predator communities
 with high thermal resilience. Thus, the conservation and restoration of
 non-crop habitats in agricultural landscapes – practices known to
 strengthen natural pest suppression under current conditions – will also
 confer resilience in ecosystem service provisioning within a changing
 climate.
description: Data obtained from field trapping for ground-dwelling arthropod
 predators in spring barley fields surrouding the city of Uppsala,
 south-central Sweden. Field trapping for temperature
 niche calculations was conducted over five consecutive weeks in the months
 of June and July 2017 with sampling occasions one day per week over a
 total period of five weeks. During each day of sampling, traps were open
 for one 2-hour period in the morning (10:00 -12:00) and one 2-hour period
 in the afternoon (13:00 -15:00), emptied immediately after each 2-hour
 period and kept closed before and after sampling sessions.
 Miniature temperature loggers (SL54TH, Signatrol, Tewkesbury,
 United Kingdom) were used to monitor ambient temperature
 during the surveys. Each logger was located approx. 2
 cm above the soil surface and protected from direct sunlight by a plastic
 tray located an additional 5 cm above the logger. For each transect and
 sampling session, the average of temperature readings of the six loggers
 was calculated and used as ambient temperature for the subsequent analysis
 of predator-specific temperature niches. The data set contains the number
 of individual predators collected at the respective
 temperature.
 Field trapping for activity
 densities for the landscape analysis was conducted over five consecutive
 weeks in the months of May and June in 2011.
 Traps were open for the entire sampling period
 and emptied weekly.
DOI: 10.5061/dryad.612jm642g
title: Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot

description: As human-induced change eliminates natural habitats, it impacts genetic
 diversity and population connectivity for local biodiversity. The South
 African Cape Floristic Region (CFR) is the most diverse extratropical area
 for plant biodiversity, and much of its habitat is protected as a UNESCO
 World Heritage site. There has long been great interest in explaining the
 underlying factors driving this unique diversity, especially as much of
 the CFR is endangered by urbanization and other anthropogenic activity.
 Here, we use a population and landscape genetic analysis of SNP data from
 the CFR endemic plant Leucadendron salignum or “common sunshine conebush”
 as a model to address the evolutionary and environmental factors shaping
 the vast CFR diversity. We found that high population structure, along
 with relatively deeper and older genealogies, are characteristic of the
 southwestern CFR, whereas, low population structure and more recent
 lineage coalescence depicts the eastern CFR. Population network analyses
 show genetic connectivity is facilitated in areas of lower elevation and
 higher seasonal precipitation. These population genetic signatures
 corroborate CFR species-level patterns consistent with high Pleistocene
 biome stability and landscape heterogeneity in the southwest, but with
 coincident instability in the east. Finally, we also find evidence of
 human land-usage as a significant gene flow barrier, especially in
 severely-threatened lowlands where genetic connectivity has been
 historically the highest. These results help identify areas where
 conservation plans can prioritize protecting high genetic diversity
 threatened by contemporary human activities within this unique cultural
 UNESCO site.
description: These data include SNPs collected from nuclear and mitochondrial
 DNA. The data were analyzed in R
DOI: 10.48689/39d577cf-be0e-4fce-9910-f5fef50a981f
title: A Review and History of Major Artificial Salmon Spawning Channels in British Columbia

description: A Review and History of Major Artificial Salmon Spawning Channels in British Columbia.
DOI: 10.5061/dryad.h70rxwdh9
title: Desulfovibrio vulgaris Hildenborough Genetic Constructs

description: The dissimilatory sulfate-reducing Deltaproteobacterium, Desulfovibrio
 vulgaris Hildenborough (ATCC 29579), was chosen by the LBNL-led research
 collaboration ENIGMA to explore tools and protocols for bringing this
 anaerobe to model status.  Here we describe a collection of
 genetic constructs generated by ENIGMA, which are available to the
 research community.
description: Standard molecular tools were used to construct plasmids that
 could be transformed into the <em>D. vulgaris</em> cells for
 selection of double homologous recombination to exchange a gene, operon or
 gene fragment with a selectable marker. These small plasmids were unable
 to replicate in this host and retention of the marker ensured insertion
 into the chromosome or native plasmid, pDV1. We discovered that double
 recombination events were almost 10-fold more frequent than single
 events.  Thus retention of the plasmid backbone occurred
 infrequently.  All PCR generated DNA fragments were sequenced before
 reintroduction into DvH for genetic constructs. Plasmid construction:  Li and
 Elledge (2012;  DOI 10.1007/978-1-61779-564-0_5,) and Gibson Assembly
 (2009; DOI:10.1038/NMETH.1318). Marker replacement
 plasmids:  Keller et al. (2011; DOI
 10.1016/B978-0-12-385075-1.00022-6) Markerless deletion plasmids: Moore
 and Leigh (2005; DOI: 10.1128/JB.187.3.972-979.2005) and Keller et al.
 (2009; DOI 10.1128/AEM.01839-09) Transposon library: Larsen et al.
 (2002; DOI: 10.1007/s00203-002-0442-2).  Deutschbauer et al.
 (2011;DOI:10.1371/journal.pgen.1002385). Kuehl et al. (2014; DOI:
 10.1128/mBio.01041-14).  TAP-tagged protein production:
 Butland et al. (2005; DOI: 10.1038/nature03239).  Shatsky et al. (2016;
 DOI:10.1074/mcp.M115.054692) Plasmids
 <strong>pSC27</strong> (a shuttle vector with a native
 <em>Deltaproteobacteria</em> replicon),
 <strong>pMO9075</strong> (for stable expression of genes for
 complementation studies in DvH), pMO719 (for marker exchange constructs in
 DvH), and <strong>pMO746 </strong>(for delivery of the gene
 for uracilphosphoribosyltransferase to DvH) are all available from
 Addgene, Inc.  These have the features used in our constructs.
description: A ReadMe file is being uploaded which is associated with the
 lists of constructs and provides more detailed descriptions of and
 publications for the protocols used.  Prior to pooling
 a specialized subset of transposon mutants to determine gene fitness data,
 all members should be streaked to determine the lack of aerobic
 contaminants.  A pool of the ca. 11,000 mutants isolated and sequenced was
 found to have contamination.  Of the mutants we have examined, only one or
 two showed contamination.  Often a second transposon mutant interrupting
 the same gene (usually a different site) is part of the collection that
 may show no contamination. Select publications from
 this work are noted in the ReadMe file and in the Excel file "Genetic
 Constructs of <em>Desulfovibrio vulgaris</em> Hildenborough
 final" in sheet 5, "Boutique Deletions," column
 F.
DOI: 10.5061/dryad.0zpc866wp
title: Shade-growing practices lessen the impact of coffee plantations on multiple dimensions of ant diversity

description: 1. Land use management influence changes in biodiversity beyond the
 targeted species. Management practices in coffee plantations have shifted
 from coffee growing below accompanying (shade) trees, to intensified
 monocultures in which coffee grows fully exposed to the sun. Anthropogenic
 disturbance causes changes in species composition relative to adjacent
 natural patches and reduces their biotic heterogeneity. Here, we assessed
 the impact of coffee plantation management practices on the taxonomical,
 phylogenetic, and functional composition of ant communities, an
 ecologically dominant group and crucial biological pest controller in
 these agroecosystems. We hypothesized that shade-grown coffee plantations
 would harbor ant communities similar to those of nearby forest patches,
 but dissimilar to those of intensified monocultures. 2. We surveyed ant
 diversity in eight shade-grown coffee farms, eight intensive coffee
 monocultures and eight forest patches. We used a combination of active and
 passive sampling methods over two field campaigns spanning six months. 3.
 Our results support our hypothesis for all diversity dimensions.
 Additionally, ant communities in intensified monocultures were
 taxonomically and functionally, but not phylogenetically, more homogeneous
 than those found in forest patches and shade-grown plantations. 4.
 Synthesis and applications. Our findings support the idea that practices
 in shade-grown plantations buffer the impoverishment of multiple diversity
 dimensions after forest conversion. By assessing and integrating multiple
 biodiversity dimensions into management strategies, farmers and interested
 parties can minimize future biodiversity and ecosystem service loss.
description: Please see "readme.txt" file for details of files.
DOI: 10.15468/dl.h3q2h2
title: Occurrence Download

description: A dataset containing 115 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cryptosepalum pellegrinianum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 115 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002697-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h18931zjs
title: Data from: Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida)

description: Previous work, using morphological characters, identified a generalist
 copepod parasite (Pharodes tortugensis) at high prevalence on two common
 gobies (Coryphopterus glaucofraenum and C. dicrus) in the British Virgin
 Islands (BVI).  DNA barcoding subsequently revealed C.
 glaucofraenum to be three morphologically similar species (C.
 glaucofraenum, C. venezuelae and C. tortugae), casting doubt on host
 identities in the BVI and the classification of the parasite as a single
 species.  Mitochondrial cytochrome c oxidase subunit I (COI) data
 from 67 gobies in the BVI showed that, in addition to C. dicrus, host
 gobies were a mix of C. glaucofraenum and C. venezuelae, while C. tortugae
 was unexpectedly absent from the study area.  COI data (n = 70)
 indicated that the copepod infecting all three hosts was a single species,
 almost certainly P. tortugensis.  The pharodes–coryphopterus
 interaction has a strong impact on host dynamics in the BVI, and a revised
 understanding of these dynamics must account for any differences among the
 three newly confirmed hosts in transmission of, and susceptibility to, the
 shared parasite.  No other infected hosts were discovered at our
 sites, but P. tortugensis is reportedly widespread and infects 12
 additional host species elsewhere.  Further DNA barcoding is thus
 needed to test whether P. tortugensis is truly a widespread generalist, or
 instead represents a group of more specialized cryptic species.
description: Digital images of gobies taken on SCUBA for species
 identification in the British Virgin Islands.  Lists of GenBank Ascession
 IDs for gobies and copepods collected in the BVI whose DNA was
 sequenced.
description: The CSV file Sample_list_metadata provides metadata for the
 sample lists. The CSV file Goby_sample_list lists the
 fish sampled and gives their GenBank Ascession #.  Each
 JPG image file is named with the goby sample number followed by an image
 identifier (e.g. GOBY_135A.JPG and GOBY_135B.JPG are two images of the
 fish listed as GOBY_135 in the Goby_sample_list CSV file.
 The CSV file Copepod_sample_list lists the copepods sampled and
 gives their GenBank Ascession #.
DOI: 10.5061/dryad.pvmcvdnjv
title: Table e-1: Supplementary materials for association of dementia-related psychosis with long-term care use and death

description: International Classification of Diseases, Ninth and Tenth Revisions,
 Clinical Modification codes for dementia, codes used to define exclusions
 for conditions potentially associated with psychosis, codes for
 manifestations of psychosis used to establish presence of dementia-related
 psychosis, and antipsychotic medications. The dataset is a collection of
 ICD-9 and -10 codes usedd to define exclusions for conditions potentially
 associated with psychosis, codes for manifestations of psychosis used to
 establish presence of dementia-related psychosis, and antipsychotic
 medications used in the analysis of the attached manuscript. Data in this
 table was used to conduct the analyses presented in the manuscript.