cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zpc866t63
title: Synthesis of Bi2S3 thin films based on pulse-plating bismuth nanocrystallines and its photoelectrochemical properties

description: The solubility of Bi3+ in aqueous solution is an important factor that
 limits the fabrication of high quality Bi2S3 thin films. In order to find
 a low–cost method to manufacture high quality Bi2S3 thin films, we are
 reporting the preparation of the Bi2S3 thin films based on pulse-plating
 method in this paper for the first time. The nano-bismuth particles were
 obtained by electroplating on fluorine doped SnO2 (FTO) coated conducting
 glass substrates with saturated bismuth potassium citrate solution as the
 electroplating bath, and then it was put into a muffle furnace to oxidize.
 Finally, the thin films depositing on FTO glass substrates were put into
 the thioacetamide solution for vulcanization. In the end, the Bi2S3 thin
 films were successfully prepared on FTO glass substrates. Different
 characterization techniques were used to characterize the structure,
 morphology and photoelectrochemical properties of the prepared thin films.
 The test results revealed that we used this method can synthesize the high
 quality of Bi2S3 thin films, thus the Bi2S3 materials synthesized through
 this method are promising candidates in photoelectrochemical application.
DOI: 10.25338/b8ww41
title: Digitized pear and peach trees with fruits

description: The dataset contains files with sets of point coordinates derived via
 manual digitization of entire trees and all fruits on them. Twenty
 Bartlett pear and twenty cling-peach trees were digitized. Digitization
 was restricted to rigid, thick branches (&gt; 2.5 cm) that present
 obstacles to machinery interacting with trees; robotic harvesting
 simulation and design were the targeted applications. Each branch segment
 that had small enough curvature was considered linear and was approximated
 by a conical frustum. Hence, an entire tree is represented geometrically
 by a set of connected frustums. The tree geometries and topologies were
 successfully encoded, and position RMS accuracy was better than 1.0 cm.
description: The fruit data was collected using Polhemus Digitization
 equipment in California commercial orchards, in the summer of 2017. The
 procedure of data collection and tree representation is the same as the
 one reported in: Arikapudi, R., Vougioukas, S.,
 Saracoglu, T. 2015. Orchard tree digitization for structural-geometrical
 modelling.<br> In Proceedings of the 10th European Conference on
 Precision Agriculture (ECPA), pp. 329 – 336, Volcani Center, Israel. https://doi.org/10.3920/978-90-8686-814-8
description: The Matlab files read the branch and fruit data from the Excel
 files and print the fruit trees for visualization. Each tree segment is
 represented as a conical frustum. More details are given in the Readme.txt
 file.
DOI: 10.5061/dryad.8931zcrmk
title: The old and the large may suffer disproportionately during episodes of high temperature: evidence from a keystone zooplankton species

description: Widespread declines in the body size of aquatic ectotherms have been
 attributed to the poorer ability of older, larger individuals to tolerate
 high temperature. Here, using the thermal death time curve framework, we
 investigate the relationship between temperature tolerance and size/age by
 measuring the change in heat tolerance of the keystone zooplankton species
 Daphnia magna across a range of temperature intensities (and hence
 exposures of varying duration) among individuals that differed up to
 three-fold in size and thus varied in age also. Across the gradient of
 exposure temperatures, younger, smaller individuals were more tolerant
 than older, larger individuals. This suggests that the young and the small
 may be better equipped to withstand temperature challenges that are both
 intense/brief and more moderate/prolonged. Our study generalizes results
 obtained from more acute tolerance assays, providing physiological
 evidence consistent with the observed reductions in ectotherm body size as
 a response to warming in aquatic systems.
description: Data was collected experimentally in laboratory conditions.
DOI: 10.15468/dl.scynjw
title: Occurrence Download

description: A dataset containing 253310 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Flora-On: occurrence data of the flora of mainland Portugal"
 ]
}

 The dataset includes 253310 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002281-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mgqnk98wm
title: Data from: Shells of the bivalve Astarte moerchi give new evidence of a strong pelagic-benthic coupling shift occurring since the late 1970s in the NOW Polynya

description: Climate changes in the Arctic may weaken the currently tight
 pelagic-benthic coupling. In response to decreasing sea ice cover, arctic
 marine systems are expected to shift from a ‘sea-ice algae-benthos’ to a
 ‘phytoplankton-zooplankton’ dominance. We used mollusk shells as
 bioarchives and fatty acid trophic markers to estimate the effects of the
 reduction of sea ice cover on the exported food to the seafloor. Bathyal
 bivalve Astarte moerchi that lives at 600 m depth in northern Baffin Bay
 reveals a clear shift in growth variations and Ba/Ca ratios since the late
 1970s that we relate to a change in food availability. Fatty acid
 compositions of tissues show that this species feeds mainly on microalgae
 exported from the euphotic zone to the seabed. We thus suggest that
 changes in pelagic-benthic coupling are likely due to either local changes
 in sea ice dynamics, mediated through bottom-up regulation exerted by sea
 ice on phytoplankton production or to a mismatch between phytoplankton
 bloom and zooplankton grazing due to change in their phenology. Both
 possibilities allow a more regular and increased transfer of food to the
 seabed.
description: see MS for all the details
DOI: 10.15468/dl.w3r9tb
title: Occurrence Download

description: A dataset containing 333 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Astragalus microcystis"
 ]
}

 The dataset includes 333 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002290-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ypvrt
title: Occurrence Download

description: A dataset containing 65451 records in GBIF matching the query:
SELECT
 '428' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= -113.29916565233177
 AND decimalLongitude &lt;= -101.89927079016302
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 65451 records were derived from 230 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002276-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.866t1g1n7
title: Warming effect on ecosystem stability

description: 1. Ecosystem stability is essential to its sustainable functions and
 services to humanity. Although climate warming is projected to vary from
 1-5ºC by the end of 21st century, how the temporal stability of plant
 community biomass production responds to different warming scenarios
 remains unclear. 2. To fill this knowledge gap, we conducted a 6-year
 field experiment with three levels of warming treatments (control, +
 1.5oC, + 5oC) by using infrared radiators, in an alpine meadow on the
 Qinghai-Tibet Plateau. 3. We found that low-level warming (+ 1.5oC),
 compared to the control, did not significantly change the temporal
 stability of plant community biomass production and its underlying causes,
 including species diversity, compensatory dynamics, mean-variance scaling,
 biomass temporal stability of plant population (the average of temporal
 stability of species biomass production of all species in the community)
 or dominant species. However, high-level warming (+ 2.5oC) significantly
 reduced them. Species diversity was not a significant predictor of
 temporal stability of plant community biomass production in this
 species-rich ecosystem, regardless of the magnitude of warming, while
 co-existing species compensatory dynamics and the biomass temporal
 stability of dominant species determined the response of temporal
 stability of plant community biomass production to warming. 4. Synthesis.
 Our results suggest that the responses of plant community biomass temporal
 stability and its underlying mechanisms to climate warming depend on
 warming magnitudes. The findings highlight the various responses of
 ecosystem functions and services to different warming scenarios and imply
 that ecosystem will fail to maintain and provide stable biomass-related
 services for humanity under high-level climate warming.
DOI: 10.5061/dryad.m0cfxpp0q
title: Compensating for climate change-induced cue-environment mismatches: evidence for contemporary evolution of a photoperiodic reaction norm in Colias butterflies

description: Anthropogenic climate change alters seasonal conditions without altering
 photoperiod and can thus create a cue-environment mismatch for organisms
 that use photoperiod as a cue for seasonal plasticity. We investigated
 whether evolution of the photoperiodic reaction norm has compensated for
 this mismatch in Colias eurytheme. This butterfly’s wing melanization has
 a thermoregulatory function and changes seasonally. In 1971, Hoffmann
 quantified how larval photoperiod determines adult wing melanization. We
 recreated his experiment 47 years later using a contemporary population.
 Comparing our results to his, we found decreased melanization at short
 photoperiods but no change in melanization at long photoperiods, which is
 consistent with the greater increase in spring than summer temperatures
 recorded for this region. Our study shows that evolution can help correct
 cue-environment mismatches but not in the same way under all conditions.
 Studies of contemporary evolution may miss important changes if they focus
 on only a limited range of conditions.
description: See methods and supplemental materials of associated
 manuscript.
description: <strong>See Readme files for more information about each.
 Images can be made available upon request.</strong> CA(Antioch)_Weather_Data_NOAA NOAA climate records used in this study.   CA_spectra_gray Direct reflectance measurements used to compare current and past measurement methods.   CA_spectra_white Supplemental reflectance measurements using a white backing for the wing, rather than gray.   Hoffmann_1973_extracted_data Mean and standard errors extracted from figures in Hoffmann 1973.   photo_idx Treatments and other data on specimens photographed in this study   photo_measurement_data Measurements of Colias eurytheme specimens produced from images   temperatureAnalysis R script for comparison of temperatures between decade preceding past and present studies   wingAnalysis R script for comparison of wing melanization between Hoffmann 1973 and present study, along with other supplemental analyses.   Colias python functions Set of python functions used in other python scripts for wing image analysis. Required to run those scripts. Colias.py   Colias_wings python functions Set of python functions used in other python scripts for wing image analysis. Required to run those scripts. Colias_wings.py   balance_wing_images Python script to standardize brightness and balance color in wing images based on color standard.   image_segmentation Python script to identify each wing in a images.   measure_wings_basic Python script to perform various basic measurements on identified wing areas.
DOI: 10.5061/dryad.kwh70rz14
title: Supplementary Documentation - Epilepsy risk among survivors of intensive care unit hospitalization for sepsis

description: Objective Our objectives were to determine if survivors of intensive care
 unit (ICU) hospitalizations with sepsis experience higher epilepsy risk
 than survivors of ICU hospitalizations without sepsis, and to identify
 sepsis survivors at highest risk. Methods We used linked, administrative
 healthcare databases to conduct a population-based, retrospective matched
 cohort study of adult Ontario residents discharged from an ICU between
 January 1, 2010 and December 31, 2015, identified using the Discharge
 Abstract Database. We used propensity scores to match patients who
 experienced sepsis during their index ICU hospitalization with up to four
 patients who did not experience sepsis. We applied marginal Cox
 proportional hazards regression to estimate the risk of epilepsy within
 two years following the index ICU hospitalization. Among sepsis survivors,
 Cox proportional hazards regression was used to identify factors
 associated with epilepsy. Results 143,892 patients were included, 32,252
 (22.4%) of whom were exposed. Sepsis survivors were at significantly
 higher epilepsy risk (HR=1.44, 95% CI=1.15-1.80). The risk of epilepsy
 marginally decreased with increasing age (HR=0.97, 95% CI=0.96-0.99),
 while those with chronic kidney disease (HR=2.25, 95% CI=1.48-3.43) were
 at highest risk. Conclusions In this real-world analysis, sepsis
 survivors, particularly those who are younger and have chronic kidney
 disease, are at significantly higher epilepsy risk. These findings
 indicate that sepsis may be an unrecognized epilepsy risk factor.
DOI: 10.5061/dryad.31zcrjdh7
title: Targeted conservation genetics of the endangered chimpanzee

description: Populations of the common chimpanzee (Pan troglodytes) are in an impending
 risk of going extinct in the wild as a consequence of damaging
 anthropogenic impact on their natural habitat and illegal pet and bushmeat
 trade. Conservation management programmes for the chimpanzee have been
 established outside their natural range (ex situ), and chimpanzees from
 these programmes could potentially be used to supplement future
 conservation initiatives in the wild (in situ). However, these programmes
 have often suffered from inadequate information about the geographical
 origin and subspecies ancestry of the founders. Here, we present a newly
 designed capture array with 60 000 ancestry informative markers
 used to infer ancestry of individual chimpanzees in ex situ populations
 and determine geographical origin of confiscated sanctuary individuals.
 From a test panel of 167 chimpanzees with unknown origins or subspecies
 labels, we identify 90 suitable non-admixed individuals in the European
 Association of Zoos and Aquaria (EAZA) Ex situ Programme (EEP). Equally
 important, another 46 individuals have been identified with admixed
 subspecies ancestries, which therefore over time, should be naturally
 phased out of the breeding populations. With potential for future
 re-introduction to the wild, we determine the geographical origin of 31
 individuals that were confiscated from the illegal trade and demonstrate
 the promises of using non-invasive sampling in future conservation action
 plans. Collectively, our genomic approach provides an exemplar for ex situ
 management of endangered species and offers an efficient tool in future in
 situ efforts to combat the illegal wildlife trade.
DOI: 10.5061/dryad.zw3r2285j
title: Associational resistance to both insect and pathogen damage in mixed forests is modulated by tree neighbour identity and drought

description: Tree health declines can be caused by interactions between pests and
 pathogens and many studies have shown a reduction in their damage in mixed
 species forests compared to monocultures. Yet few authors have considered
 tree diversity effects on both groups simultaneously. Moreover, it is
 unclear whether diversity effects on tree pests and pathogens are robust
 to changes in abiotic conditions, such as drought. We addressed tree
 diversity effects on foliar insect herbivory, oak powdery mildew and their
 interaction under contrasting water regimes in a large-scale tree
 diversity experiment in SW France. Using an irrigation treatment that
 alleviated drought conditions, we were able to experimentally assess the
 effects of tree diversity under contrasting abiotic environments. We
 surveyed plots along a richness gradient from 1 – 4 tree species, in which
 a focal study species of oak (Q. robur) was mixed with other oak species
 (Q. pyrenaica and Q. ilex) and a taller, broadleaved species (Betula
 pendula). Increasing tree species richness lowered leaf miner abundance,
 leaf chewer damage and oak powdery mildew infection, consistent with a
 protective effect of resource dilution. However, richness effects on leaf
 miners were stronger in irrigated compared to non-irrigated blocks,
 indicating that environmental conditions can modulate diversity effects.
 Separate from the effect of tree species richness, the presence of birch
 in a plot increased damage by leaf chewers and powdery mildew, but lowered
 leaf miner damage, suggesting additional tree neighbour identity effects
 potentially linked to modulation of microclimate. We found a negative
 association between leaf miner abundance and oak powdery mildew,
 consistent with antagonism between oak damage agents. Overall, our study
 illustrates the importance of considering both tree diversity and
 composition (neighbour identity) in designing forests more resistant to
 pest and pathogen damage.
DOI: 10.5061/dryad.1zcrjdfpg
title: Characterising biogeochemical fluctuations in a world of extremes

description: Coastal and intertidal habitats are at the forefront of anthropogenic
 influence and environmental change. The species occupying these habitats
 are adapted to a world of extremes, which may render them robust to the
 changing climate or more vulnerable if they are at their physiological
 limits. We characterised the diurnal, seasonal and interannual patterns of
 flux in biogeochemistry across an intertidal gradient on a temperate
 sandstone platform in eastern Australia over six years (2009–2015) and
 present a synthesis of our current understanding of this habitat in
 context with global change. We used rock pools as natural mesocosms to
 determine biogeochemistry dynamics and patterns of eco-stress experienced
 by resident biota. In situ measurements and discrete water samples were
 collected night and day during neap low tide events to capture diurnal
 biogeochemistry cycles. Calculation of pHT using total alkalinity (TA) and
 dissolved inorganic carbon (DIC) revealed that the mid-intertidal habitat
 exhibited the greatest flux over the years (pHT 7.52–8.87), and over a
 single tidal cycle (1.11 pHT units), while the low-intertidal (pHT
 7.82–8.30) and subtidal (pHT 7.87–8.30) were less variable. Temperature
 flux was also greatest in the mid-intertidal (8.0–34.5˚C) and over a
 single tidal event (14˚C range), as typical of temperate rocky shores.
 Mean TA and DIC increased at night and decreased during the day, with the
 most extreme conditions measured in the mid-intertidal owing to prolonged
 emersion periods. Temporal sampling revealed that net ecosystem
 calcification (NEC) and production (NEP) were highest during the day and
 lowest at night, particularly in the mid-intertidal. Characterisation of
 biogeochemical fluctuations in a world of extremes demonstrates the
 variable conditions that intertidal biota routinely experience and
 highlights potential microhabitat-specific vulnerabilities and climate
 change refugia.
description: Data was collected using in situ temperature loggers and discrete
 water samples over six years at Little Bay, Sydney, Australia. Data was
 collected at low tide for three tidal heights (subtidal, low- and
 mid-intertidal), day and night, and adjacent seawater at high tide. Data
 from two temporal cycles (24 hr) were also collected at each tidal height
 to document daily flux and extremes.
description: There are some missing values due to occastional missing loggers
 or poor weather. These are either left blank in the datasets, or
 NA.
DOI: 10.5061/dryad.w3r2280mq
title: Data from: Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder

description: Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective
 tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity
 in the vast and important open ocean is currently monitored through
 continuous plankton recorder (CPR) surveys, using ship-based bulk plankton
 sampling and morphological identification. We assessed whether eDNA
 metabarcoding (2 L filtered seawater) could capture similar Southern Ocean
 biodiversity as conventional CPR bulk sampling (~1500 L filtered seawater
 per CPR sample). We directly compared eDNA metabarcoding with (i)
 conventional morphological CPR sampling and (ii) bulk DNA metabarcoding of
 CPR collected plankton (two transects for each comparison, 40 and 44
 paired samples respectively). A metazoan‐targeted cytochrome c oxidase I
 (COI) marker was used to characterize species-level diversity. In the 2 L
 eDNA samples this marker amplified large amounts of non‐metazoan
 picoplanktonic algae, but eDNA metabarcoding still detected up to 1.6
 times more zooplankton species than morphologically analysed bulk CPR
 samples. COI metabarcoding of bulk DNA samples mostly avoided non-metazoan
 amplifications and recovered more zooplankton species than eDNA
 metabarcoding. However, eDNA metabarcoding detected roughly two thirds of
 metazoan species and identified similar taxa contributing to community
 differentiation across the subtropical front separating transects. We
 observed a diurnal pattern in eDNA data for copepods which perform diel
 vertical migrations, indicating a surprisingly short temporal eDNA signal.
 Compared to COI, a eukaryote-targeted 18S ribosomal RNA marker detected a
 higher proportion, but lower diversity, of metazoans in eDNA. With
 refinement and standardization of methodology, eDNA metabarcoding could
 become an efficient tool for monitoring open ocean biodiversity.
description: See materials and methods of Molecular Ecology paper
 "Capturing open ocean biodiversity: comparing
 environmental DNA metabarcoding to the continuous plankton
 recorder"
description: All raw fastq files were uploaded (gz compressed). They originate
 from two separate sequencing runs - file names starting with
 "V4..." are from the first run, file names starting with e.g.
 "003_V4..." are from the second run. Sample specific tags are in
 the respective COITags.csv files. The pipeline to
 process the raw data is in the file
 "Pipeline_processing.R". The html output of
 the R markdown code to analyse the data (includes code for all figures and
 supplemental material) is in the file
 Figures_and_Analyses_R_Markdown_2020-06-25.html, and all processed data
 input files are provided in .csv or .fasta format.