cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cc2fqz669
title: Predicting parasite dynamics in mixed-use trans-Himalayan pastures to underpin management of cross-transmission between livestock and bharal

description: The complexities of multi-use landscapes require sophisticated approaches
 to addressing disease transmission risks. We explored gastro-intestinal
 nematode (GINs) infections in the North India Trans-Himalayas through a
 socio-ecological lens, integrating parasite transmission modelling with
 field surveys and local knowledge, and evaluated the likely effectiveness
 of potential interventions. Bharal (blue sheep; Pseudois nayaur), a native
 wild herbivore, and livestock share pasture year-round and livestock
 commonly show signs of GINs infection. While both wild and domestic
 ungulates had GINs infections, egg counts indicated significantly higher
 parasite burdens in bharal than livestock. However, due to higher
 livestock densities, they contributed more to the total count of eggs and
 infective larvae on pasture. Herders also reported health issues in their
 sheep and goats consistent with parasite infections. Model simulations
 suggested that pasture infectivity in this system is governed by
 historical pasture use and gradually accumulated larval development during
 the summer, with no distinct short-term flashpoints for transmission. The
 most effective intervention was consequently predicted to be early-season
 parasite suppression in livestock using temperature in spring as a cue. A
 one-month pause in egg output from livestock could lead to a reduction in
 total annual availability of infective larvae on pasture of 76%,
 potentially benefitting the health of both livestock and bharal. Modelling
 suggested that climate change over the past 33 years has led to no overall
 change in GINs transmission potential, but an increase in the relative
 influence of temperature over precipitation in driving pasture
 infectivity. Our study provides a transferable multi-pronged approach to
 investigating disease transmission, in order to support herders’
 livelihoods and conserve wild ungulates.
DOI: 10.25349/d99p54
title: Covid, Colleges, and Classes

description: At the start of the 2020 school year, some colleges chose to reopen in
 person while others offered primarily online classes. We find that
 colleges responded to financial and other incentives largely as one might
 expect. Larger shares of revenue attributed to in-person activities, such
 as dorms and dining halls, led schools to reopen in person. In general,
 the share of revenue due to tuition and fees had little association with
 reopening in-person, which is consistent with the idea that the effect of
 the mode of reopening on enrollment was ambiguous. However, private
 schools experiencing financial distress due to tuition and fees were more
 likely to reopen in-person while public schools were less likely. Public
 colleges were influenced by political pressures and the fraction of
 students from out of state, while private schools responded to the
 severity of COVID in their local community.
DOI: 10.5061/dryad.31zcrjdm3
title: Plate boundary deformation at the Azores triple junction determined from continuous GPS geodetic measurements, 2002-2017

description: Ground deformation in the Azores, at the triple junction between the
 Eurasian, Nubian, and North American plates, has been mapped with
 continuous GPS (Global Positioning System) geodetic measurements to
 improve tectonic motion estimates and for understanding volcanic unrest.
 We compute daily GPS positions, spanning almost 17 years (2000-2017), from
 18 continuous GPS stations. The GPS time-series are analyzed by searching
 for discontinuities and periodic functions. Results show that Flores and
 Graciosa islands have displacements close to predicted North American and
 Eurasian plate motions, respectively, while São Miguel, Terceira, São
 Jorge, Faial and Pico islands have displacements in between predicted
 Eurasian and Nubian plate motions. The Eurasian-Nubian plate boundary in
 the Azores behaves as a diffuse ultra-slow oblique spreading center with
 focused deformation found in the Central Group and São Miguel Island. The
 velocity field is modeled by approximating segments of the Eurasian-Nubian
 plate boundary with vertical dislocations with right-lateral motion and
 opening below a locking depth. Best fitting models have deep motion in the
 range of 2.4-2.7 mm/yr directed N(76.5-78.8o)E. Such displacement accounts
 for more than half predicted Eurasian-Nubian relative plate motion. The
 modeling results suggest that the locking depth in the Central Group is
 about 17 km while in São Miguel is about 2 km. We found transient
 deformation at Fogo volcano, São Miguel Island, due to unrest activity
 mainly during 2003–2006 and 2011–2012, and local continuous subsidence in
 Terceira Island, attributed to a deflation source centered on the island.
DOI: 10.5061/dryad.6m905qg0n
title: The role of shade in maintaining alternative stable states between open- and closed-canopy vegetation

description: Fire is commonly identified as strong driver of alternative stable states
 such as adjacent open- versus closed-canopy vegetation types. The absence
 of open-canopy species from closed-canopy understoreys, where light
 availability is low and dynamic, however, suggests shade tolerance is an
 integral determinant of such vegetation boundaries. While the importance
 of light dynamics between alternative stable states has been acknowledged,
 the physiological mechanisms behind sun versus shade-tolerance are
 unclear. Here we investigated the differences in light interception and
 carbon assimilation of open- and closed-canopy species, and whether this
 contributes to the maintenance of alternative stable states. Evergreen
 forest and fynbos species were grown under three light availability
 treatments (24%, 54%, 100%) in a glasshouse with their photosynthetic
 response to continuous and fluctuating light, dark respiration, root
 respiration, biomass and leaf traits quantified.   Fynbos species
 displayed smaller, thicker, and tightly aggregated leaves compared to
 forest species. Under low light, fynbos species experienced some
 mortality, and showed lower light-use efficiency with fluctuating light
 and lower in situ photosynthetic rates under the 54%
 light treatment compared to forest species (0.8 versus 4 mmol
 CO2 m-2 s-1).   Synthesis. Contrasting
 light availability in forest and fynbos selects for dissimilar traits,
 where fynbos species are unable to efficiently intercept light and
 maintain a positive carbon balance under low, dynamic light compared to
 forest species. This shade intolerance is exacerbated by divergent
 nutrient and fire regimes in forest and fynbos environments, requiring
 incompatible trait specializations that promote the emergence and
 maintenance of alternative stable states.
description: See published article in the Journal of Ecology for method
 details.
description: Compilation of data recorded in Experiments 1 and 2, and utilized
 in the associated manuscript. To guide interpretation, a brief
 'readme' tab is attached to each file.
DOI: 10.5061/dryad.rv15dv489
title: Data from: Microstructural description of the maniraptoran egg Protoceratopsidovum

description: Since their discovery in the 1920s, the affinity of asymmetric, elongated
 dinosaur eggs from the Late Cretaceous of Mongolian has been
 controversial, with previous hypotheses supporting either a ceratopsian or
 maniraptoran affinity. Recent technical advancements in palaeontology
 provide a novel approach to diagnose maniraptoran eggs, and the discovery
 of soft ceratopsian eggs makes the controversy a timely issue worth
 revisiting. Here, we analysed Protoceratopsidovum eggshell from southern
 Mongolia with electron backscatter diffraction (EBSD) and the results were
 compared with East Asian and North American maniraptoran and ornithischian
 eggs. The microstructure and crystallography of Protoceratopsidovum shows
 diagnostic features of maniraptoran eggs that are absent in ornithischian
 (e.g. hadrosaur) eggs. Additional characters, such as egg shape,
 ornamentation, egg pairing and clutch structure all support a maniraptoran
 affinity. Protoceratopsidovum has both elongatoolithid (oviraptorosaur
 egg) and prismatoolithid (troodontid egg) features, and it may hold
 implications for the evolution of microstructure in non-avian maniraptoran
 and extant palaeognath eggshells. Considering the similarity between
 Protoceratopsidovum and potential dromaeosaur eggs, at least some
 Protoceratopsidovum may be deinonychosaur eggs. Fossil localities that
 yield both deinonychosaurs and Protoceratopsidovum may yield conclusive
 evidence for the true affinity of this ootaxon. Future discovery of the
 egg-layer of Protoceratopsidovum will not only improve our understanding
 of maniraptoran reproductive biology, but also make Protoceratopsidovum a
 reliable indicator of the palaeobiogeography of that maniraptoran clade.
description: Detailed methodologies for EBSD analysis are summarized in Choi
 et al. (2019, Palaeontology). All data were acquired by using AZtec
 software and exported into cpr and crc files. The cpr and crc files are
 uploaded in the Dryad repository.
description: Please contact Seung Choi (corresponding author) for detailed
 information of EBSD data. See also attached README.
DOI: 10.5061/dryad.0k6djhb14
title: Peak power and body mass as indices of bone loading in a healthy adult population

description: Objective: The purpose of this study was to examine whether a common,
 non-invasive, muscular fitness field test was a better predictor of bone
 strength compared to body mass.  Methods: Hierarchical multiple
 regression analyses were used to determine the amount of variance that
 peak power explained for bone strength of the tibia compared to body mass.
 Peak power was estimated from maximal vertical jump height using Sayer’s
 equation. Peripheral quantitative computed tomography scans were used to
 assess bone strength measures.  Results: Peak power (ꞵ=0.541,
 p&lt;0.001) contributed more to the unique variance in bone strength
 index for compression compared to body mass (ꞵ=-0.102, p=0.332). For polar
 strength strain index, the beta coefficient for body mass remained
 significant (ꞵ=0.257, p&lt;0.006), however, peak power’s contribution
 was similar (ꞵ=0.213, p= 0.051). Conclusion: Compared to body mass, peak
 power was a better predictor for trabecular bone strength but similar to
 body mass for cortical bone strength. These data provide additional
 support for the development of a vertical jump test as a simple,
 objective, valid and reliable measure to monitor bone strength among youth
 and adult populations.
description: Recruitment and Participant
 Characteristics:  A convenience
 sample of 142 participants (79 F, 63 M)  (13.3% African American/Black,
 17.9% Latina/o, 28.6% White, 27.6% Asian/Pacific Islander, 1.0% American
 Indian or Alaskan Native and 11.7% Mixed Race or Unknown) was recruited
 for this observational, cross-sectional study, from the faculty, staff,
 and students at a mid-sized regional university.  Participants were
 recruited through flyers, emails to the university community, and
 word-of-mouth advertisement. Participants received no compensation for
 participation. A general health and demographic survey was completed by
 all participants prior to the start of data collection to determine age,
 sex, and ethnicity of the participants. Participants were excluded if they
 had a history of any diseases that might influence bone health (endocrine
 diseases, gastrointestinal disorders, and eating disorders), were under 18
 years of age, smoked, or were pregnant. All participants were informed of
 the risks and benefits of the study and provided written informed
 consent.  The study was approved by the California State University, East
 Bay Institutional Review Board (IRB) (CSUEB-IRB-2016-223-F). The study was
 pre-registered at the Center for Open Science OSF (DOI:
 10.17605/OSF.IO/B5QZC). Peripheral
 quantitative computed tomography (pQCT) (XCT 2000 Stratec Medizintechnik,
 Pforzheim, Germany) scans were used to assess bone strength measures of
 the dominant tibia.  Maximal jump height was measured using a Vertec™
 (JUMPUSA.com, Sunnyvale, CA).
DOI: 10.5061/dryad.qjq2bvqgq
title: The lower airways microbiome and antimicrobial peptides in Idiopathic Pulmonary Fibrosis differ from Chronic Obstructive Pulmonary Disease

description: Background: The lower airways microbiome and host immune response in
 chronic pulmonary diseases are incompletely understood. We aimed to
 investigate possible microbiome characteristics and key antimicrobial
 peptides and proteins in idiopathic pulmonary fibrosis (IPF) and chronic
 obstructive pulmonary disease (COPD). Methods: 12 IPF patients, 12 COPD
 patients and 12 healthy controls were sampled with oral wash (OW),
 protected bronchoalveolar lavage (PBAL) and right lung protected sterile
 brushings (rPSB). The antimicrobial peptides and proteins (AMPs),
 secretory leucocyte protease inhibitor (SLPI) and human beta defensins 1
 and 2 (hBD-1 & hBD-2), were measured in PBAL by enzyme linked
 immunosorbent assay (ELISA). The V3V4 region of the bacterial 16S rDNA
 gene was sequenced. Bioinformatic analyses were performed with QIIME 2.
 Results: hBD-1 levels in PBAL for IPF were lower compared with COPD. The
 predominant phylae in IPF
 were Firmicutes, Bacteroides and Actinobacteria; Proteobacteria were among top three in COPD. Differential abundance analysis at genus level showed significant differences between study groups for less abundant, mostly oropharyngeal, microbes. Alpha diversity was lower in IPF in PBAL compared to COPD (p=0.03) and controls (p=0.01), as well as in rPSB compared to COPD (p=0.02) and controls (p=0.04). Phylogenetic beta diversity showed significantly more similarity for IPF compared with COPD and controls. There were no significant correlations between alpha diversity and AMPs. Conclusions: IPF differed in microbial diversity from COPD and controls, accompanied by differences in antimicrobial peptides. Beta diversity similarity between OW and PBAL in IPF may indicate that microaspiration contributes to changes in its microbiome.
description: The dataset is part of the larger Bergen COPD Microbiome Study
 ("MicroCOPD") and Bergen ILD Microbiome Study
 ("MicroILD"), and the processing is well described in the paper
 & supplement.
description: See the upload Read Me txt file.
DOI: 10.5061/dryad.rr4xgxd8r
title: DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity

description: DNA metabarcoding is an increasingly popular technique to investigate
 biodiversity; however, many methodological unknowns remain, especially
 concerning the biases resulting from marker choice. Regions of the
 cytochrome c oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly
 employed “universal” markers for eukaryotes, but the extent of taxonomic
 biases introduced by these markers and how such biases may impact
 metabarcoding performance is not well quantified. Here, focusing on
 macro-eukaryotes, we use standardized sampling from autonomous reef
 monitoring structures (ARMS) deployed in the world’s most biodiverse
 marine ecosystem, the Coral Triangle, to compare the performance of COI
 and 18S markers. We then compared metabarcoding data to image-based
 annotations of ARMS plates. Although both markers provided similar
 estimates of taxonomic richness and total sequence reads, marker choice
 skewed estimates of eukaryotic diversity. The COI marker recovered
 relative abundances of the dominant sessile phyla consistent with image
 annotations. Both COI and the image annotations provided higher relative
 abundance estimates of Bryozoa and Porifera and lower estimates of
 Chordata as compared to 18S, but 18S recovered 25% more phyla than COI.
 Thus, while COI more reliably reflects the occurrence of dominant sessile
 phyla, 18S provides a more holistic representation of overall taxonomic
 diversity. Ideal marker choice is, therefore, contingent on study system
 and research question, especially in relation to desired taxonomic
 resolution, and a multi-marker approach provides the greatest application
 across a broad range of research objectives. As metabarcoding becomes an
 essential tool to monitor biodiversity in our changing world, it is
 critical to evaluate biases associated with marker choice.
description: All methods are available in the associated manuscript in
 <em>Environmental DNA</em>.
description: This submission is connected to the manuscript entitled,
 "DNA metabarcoding marker choice skews perception of marine
 eukaryotic biodiversity" published in <em>Environmental
 DNA</em>. Files include the metadata
 ("Bali_Metadata.csv"), final COI OTU table
 ("COI_OTU_Taxonomy.csv"), final 18S data OTU table
 ("18S_OTU_Taxonomy.csv"), CoralNet image analysis data
 ("coralnet.csv"), the R script (COIv18S.R) used for all analyses
 in the manuscript, and a README file that defines variables and describes
 data files (CASEY_README.txt).
DOI: 10.5061/dryad.63xsj3v2x
title: Intensity and mode of Lindera melissifolia reproduction are affected by flooding and light availability

description: A water impoundment facility was used to control the duration of soil
 flooding (0, 45, or 90 days) and shade houses were used to control light
 availability (high = 72 %, intermediate = 33 %, or low = 2 % of ambient
 light) received by L. melissifolia established on native soil of the MAV.
 A completely randomized, split-plot design was used to evaluate the
 effects of soil flooding and light availability on L. melissifolia
 reproductive intensity and mode. Analyses were conducted on plot means
 using PROC GLIMMIX with an adjustment in the error term for the whole-plot
 factor (SAS 9.4, SAS Institute, Inc., Cary, North Carolina, USA). PROC
 UNIVARIATE was used to test data normality for each response variable, and
 residual errors were normalized with Box-Cox, natural log, or square root
 transformations where appropriate prior to the PROC GLIMMIX analyses.
 Significance was accepted at ∝ = 0.05, and we used the least significant
 difference (LSD) test to separate significant treatment effect means. When
 a soil flooding and light availability interaction was significant,
 separation of soil flooding level means was conducted by light
 availability level, and separation of light availability level means was
 conducted by soil flooding level.
description: Analysis code and data files are provided for all variables
 presented in Tables and Figures of the manuscript.
DOI: 10.15468/dl.wpjuev
title: Occurrence Download

description: A dataset containing 80729 records in GBIF matching the query:
SELECT
 '463' 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;= 46.479780028101516
 AND decimalLatitude &lt;= 51.21395264452012
 AND decimalLongitude &gt;= -106.90300826225503
 AND decimalLongitude &lt;= -94.41597137694312
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 80729 records were derived from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002909-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6djh9w11t
title: Magnitude and mechanisms of nitrogen-mediated responses of tree biomass production to elevated CO2: a global synthesis

description: 1. Elevated atmospheric CO2 concentration (eCO2) typically stimulates tree
 growth, which is mediated by nitrogen (N) availability; but how N
 regulates tree biomass responses to eCO2 remains uncertain, which limits
 our prediction of forest carbon (C) cycling under future global change
 scenarios. 2. A meta-analysis of a global dataset including 3399
 observations from 283 papers published from 1980s to February 2021 was
 conducted with the aim of elucidating N-mediated responses of tree biomass
 production to eCO2 and the underlying mechanisms. 3. We found that eCO2
 stimulated tree biomass production (+32.0%), while it induced accumulation
 of nonstructural carbohydrates in leaves rather than in woods and roots,
 suggesting that the production may be C-limited but depend on the sink
 strength of organs. Biomass responses to eCO2 of N-fertilized trees
 (+39.6%) were 68.4% greater than those of non-fertilized trees (+25%),
 confirming that tree growth is also N-limited. Such N limitation was
 alleviated by the eCO2-induced increases in N uptake and N-use efficiency
 (NUE), with the former being more important. Increases in tree N pool
 arose from the enhanced production of fine roots with a lower specific
 root length, whereas increases in NUE resulted from the flexibility in
 tissue C:N ratios instead of N resorption efficiency. The positive
 responses of tree biomass production to eCO2 were greater for
 ectomycorrhizal trees and conifers than for arbuscular mycorrhizal trees
 and angiosperms, respectively. 4. Synthesis: Our findings suggest that
 eCO2 stimulates tree biomass production by increasing C availability, and
 alleviating N limitation in a feedback way via enhancing N uptake and NUE;
 and they improve our mechanistic understanding of responses of forest
 productivity and C sequestration to eCO2 under global change.
DOI: 10.5061/dryad.hqbzkh1gr
title: The influence of predator community composition on photoprotective traits of copepods

description: Trait expression of natural populations often jointly depends on
 prevailing abiotic environmental conditions and predation risk. Copepods,
 for example, can vary their expression of compounds that confer protection
 against ultraviolet radiation (UVR), such as astaxanthin and
 mycosporine-like amino acids (MAAs), in relation to predation risk.
 Despite ample evidence that copepods accumulate less astaxanthin in the
 presence of predators, little is known about how the community composition
 of planktivorous fish can affect the overall expression of photoprotective
 compounds. Here, we investigate how the (co-)occurrence of Arctic charr
 (Salvelinus alpinus) and threespine stickleback (Gasterosteus aculeatus)
 affect the photoprotective phenotype of the copepod Leptodiaptomus minutus
 in lake ecosystems in southern Greenland. We found that average
 astaxanthin and MAA contents were lowest in lakes with stickleback, but we
 found no evidence that these photoprotective compounds were affected by
 the presence of charr. Furthermore, variance in astaxanthin among
 individual copepods was greatest in the presence of stickleback and the
 astaxanthin content of copepods was negatively correlated with increasing
 stickleback density. Overall, we show that the presence and density of
 stickleback jointly affect the content of photoprotective compounds by
 copepods, illustrating how the community composition of predators in an
 ecosystem can determine the expression of prey traits that are also
 influenced by abiotic stressors. --