cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qfttdz0m2
title: The evolution, complexity and diversity of models of long-term forest dynamics

description: 1.  To assess the impacts of climate change on
 vegetation from stand to global scales, models of forest dynamics that
 include tree demography are needed. Such models are now available for 50
 years, but the currently existing diversity of model formulations and its
 evolution over time are poorly documented. This hampers systematic
 assessments of structural uncertainties in model-based studies.
 2.  We conducted a meta-analysis of 28 models, focusing
 on models that were used in the past five years for climate change
 studies. We defined 52 model attributes in five groups (basic assumptions,
 growth, regeneration, mortality and soil moisture) and characterized each
 model according to these attributes. Analyses of model complexity and
 diversity included hierarchical cluster analysis and redundancy analysis.
 3.  Model complexity evolved considerably over the past
 50 years. Increases in complexity were largest for growth processes, while
 complexity of modelled establishment processes increased only moderately.
 Model diversity was lowest at the global scale, and highest at the
 landscape scale. We identified five distinct clusters of models, ranging
 from very simple models to models where specific attribute groups are
 rendered in a complex manner and models that feature high complexity
 across all attributes. 4.  Most models in use today are
 not balanced in the level of complexity with which they represent
 different processes. This is the result of different model purposes, but
 also reflects legacies in model code, modelers’ preferences, and the
 ‘prevailing spirit of the epoch’. The lack of firm theories, laws and
 ‘first principles’ in ecology provides high degrees of freedom in model
 development, but also results in high responsibilities for model
 developers and the need for rigorous model evaluation.
 5.  Synthesis. The currently available model diversity
 is beneficial: convergence in simulations of structurally different models
 indicates robust projections, while convergence of similar models may
 convey a false sense of certainty. The existing model diversity – with the
 exception of global models – can be exploited for improved projections
 based on multiple models. We strongly recommend balanced further
 developments of forest models that should particularly focus on
 establishment and mortality processes, in order to provide robust
 information for decisions in ecosystem management and policymaking.
description: The collection and processing of the dataset are fully described
 in the paper.
description: Microsoft Excel to open the data compilation R
 or R Studio to load and execute the script
DOI: 10.5061/dryad.tht76hf2k
title: Parasitism rate differs between herbivore generations in the univoltine, but not bivoltine, range

description: With climate change, plant-feeding insects might increase their number of
 annual generations (voltinism). However, to what degree the emergence of a
 new herbivore generation affects the parasitism rate has not been
 explored. We performed a field experiment to test whether the parasitism
 rate differs between the first and the second generation of a specialist
 leaf miner (Tischeria ekebladella), both in the naturally univoltine and
 bivoltine parts of the leaf miner’s distribution. We found an interactive
 effect between herbivore generation and geographical range on the
 parasitism rate. The parasitism rate was higher in the first compared to
 the second host generation in the part of the range that is naturally
 univoltine, whereas it did not differ between generations in the bivoltine
 range. Our experiment highlights that shifts in herbivore voltinism might
 release top-down control, with major consequences for natural and applied
 systems.
DOI: 10.6084/m9.figshare.30940076
title: Outputs of the phylogenetic analyses

description: Outputs of the phylogenetic analyses
DOI: 10.6084/m9.figshare.30940076.v1
title: Outputs of the phylogenetic analyses

description: Outputs of the phylogenetic analyses
DOI: 10.5061/dryad.tdz08kq2w
title: Adaptive, randomized, non-inferiority trial to evaluate the efficacy of monoclonal antibodies in outpatients with mild or moderate COVID-19

description: The dataset is based on the results of a trial called MANTICO (Clinical
 trial number NCT05205759). The study is a non-inferiority randomised
 controlled trial comparing the clinical efficacy of
 bamlanivimab/etesevimab, casirivimab/imdevimab, and sotrovimab in
 outpatients aged 50 or older with early COVID-19. The primary outcome was
 COVID-19 progression (hospitalisation, need of supplemental oxygen
 therapy, or death through day 14).  
description: Data were collected during the
 implementation of a randomised clinical trial (Clinical trial number
 NCT05205759). Study data were collected and managed using REDCap
 electronic data capture tool hosted at the Verona University Hospital. A
 web-based eCRF (electronic Case Report Form) was developed and patient
 randomisation was centrally managed and monitored by the coordinating
 centre. Data monitoring was also carried out with STATA and the variables
 for the analysis were manipulated and created using the same
 software.   In line with ethics board approval and informed consent signed
 by study participants, some variables, namely age, gender, height, weight,
 smoking habit, were removed from the original dataset used for the
 analysis. Pseudonymization was also used in order to guarantee
 patients' anonymity. In addition, the dataset record order was
 randomised so the resulting dataset is a file very similar in terms of
 length, fields and content to the original version, except for row order
 which is now completely random, and the record ID variable
 deleted.
description: STATA v.17 with an ad hoc
 codebook
DOI: 10.5061/dryad.wm37pvmqw
title: Seasonal variation in impact of non-native species on tropical seed dispersal networks

description: Invasive non-native species can alter animal-mediated seed dispersal
 interactions and ultimately affect the stability of recipient communities.
 The degree of such disturbances, however, is highly variable and depends
 on several factors, two of which have received little attention: the
 relative timing of native and non-native fruiting phenologies, and the
 associated variation in relative resource availability across the fruiting
 period. Both are likely to alter plant-seed disperser interactions
 threatened by biological invasions. Here we investigated the impact of
 plant invasions on the seasonal dynamics of frugivory and seed dispersal
 networks across a large-scale experimental setup and a plant invasion
 gradient on a tropical island. We recorded fruit and frugivore abundances,
 and plant-frugivore interactions across 8 inselbergs (i.e. rocky outcrops)
 with different levels of plant invasion during 10 months on the island of
 Mahé, Seychelles. By combining four sampling methods of plant-frugivore
 interactions we constructed quantitative seed dispersal networks at all
 sites across two 5-month seasons: the on-peak and off-peak fruiting
 season. Our findings showed that, by fruiting mostly synchronously with
 natives, non-native plants compete with natives for dispersal services,
 predominantly carried out by native frugivores. Variation in native seed
 dispersal was driven by plant invasion and seasonality. Specifically,
 native seed dispersal declined with the degree of invasion; dispersal
 frequency increased with fruit abundance more strongly during the off-peak
 fruiting season; and networks became increasingly specialised during
 off-peak. These results indicated that during the main fruiting peak seed
 dispersal services were saturated, which likely intensified the
 competition between native and non-native fruits. When resources were
 scarce during off-peak fruiting season, native and non-native frugivores
 were more selective in their fruit choice at sites dominated by non-native
 plants. We showed that native plant and frugivore populations and native
 seed dispersal interactions were more vulnerable in invaded plant
 communities, where non-native plants compete with natives for dispersal
 services potentially reducing native recruitment. As invasive non-native
 plants dominate many ecosystems worldwide, particularly on islands, our
 findings showed that controlling plant invasions in vulnerable native
 communities can be critical to maintain native ecosystem functions and
 biodiversity.
DOI: 10.15468/dl.kwwvf5
title: Occurrence Download

description: A dataset containing 25 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.basisofrecord = 'PRESERVED_SPECIMEN'
 AND (occurrence.level0gid = 'BRA.13_1' OR occurrence.level1gid = 'BRA.13_1' OR occurrence.level2gid = 'BRA.13_1' OR occurrence.level3gid = 'BRA.13_1')
 AND occurrence.hascoordinate = TRUE
 AND occurrence.hasgeospatialissues = FALSE
 AND GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '2945499', TRUE)
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 25 records were derived from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003229-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.31zcrjdpx
title: Data for: Frequent fire slows microbial decomposition of newly deposited fine fuels in a pyrophilic ecosystem

description: Fire-plant feedbacks engineer recurrent fires in pyrophilic ecosystems
 like savannas. The mechanisms sustaining these feedbacks may be related to
 plant adaptations that trigger rapid responses to fire’s effects on soil.
 Plants adapted for high fire frequencies should quickly regrow, flower,
 and produce seeds that mature rapidly and disperse post-fire. We
 hypothesized that offspring of such plants would germinate and grow
 rapidly, responding to fire-generated changes in soil nutrients and biota.
 We conducted an experiment using longleaf pine savanna plants that were
 paired based on differences in reproduction and survival under annual
 (“more” pyrophilic) vs. less frequent (“less” pyrophilic) fire regimes.
 Seeds were planted in different soil inoculations from experimental fires
 of varying severity. The “more” pyrophilic species displayed high
 germination rates followed by species-specific, rapid growth responses to
 soil location and fire severity effects on soils. In contrast, the “less”
 pyrophilic species had lower germination rates that were not responsive to
 soil treatments. This suggests that rapid germination and growth
 constitute adaptations to frequent fires and that plants respond
 differently to fire severity effects on soil abiotic factors and microbes.
 Further, variable plant responses to post-fire soils may influence plant
 community diversity and fire-fuel feedbacks in pyrophilic ecosystems.
DOI: 10.7272/q6gb229g
title: Chronic e-cigarette use impairs endothelial function on the physiological and cellular levels

description: Background: The harmful vascular effects
 of smoking are well established, but the effects of
 chronic use of electronic cigarettes (e-cigarettes) on endothelial
 func­tion are less understood. We hypothesized that e-cigarette
 use causes changes in blood milieu that impair endothelial
 function.  Methods: Endothelial function was measured
 in chronic e-cigarette users, chronic cigarette smokers, and
 nonusers. We measured the effects of participants’ sera, or e-cigarette
 aerosol condensate, on nitric oxide (NO) and H2O2 release
 and cell permeability in culture endothelial cells
 (ECs).  Results: E-cigarette users and smokers had lower
 FMD than nonusers. Sera from e-cigarette users and smokers
 reduced VEGF-induced NO secretion by ECs relative to nonuser
 sera, without significant reduction in endothelial NO synthase mRNA or
 protein levels. E-cigarette user sera, but not smoker sera, caused
 increased endothelial release of H2O2, and more permeability, than nonuser
 sera. E-cigarette users and smokers exhibited changes in circulating
 biomarkers of inflammation, thrombosis, and cell adhesion relative to
 nonusers, but with distinct profiles. E-cigarette user sera had higher
 concentrations of the RAGE ligands S100A8 and HMGB1 than smoker and
 nonuser sera, and RAGE inhibition reduced permeability induced by
 e-cigarette user sera but did not affect NO production. 
 Conclusion: Chronic vaping and smoking both impair FMD and cause
 changes in the blood that inhibit endothelial NO release. Vaping, but not
 smoking, causes changes in the blood that increase microvascular
 endothelial permeability and may have a vaping-specific effect on
 intracellular oxidative state. Our results suggest a role for RAGE in
 e-cigarette-induced changes in endothelial function. 
description: <strong>FMD measurement</strong>: High-resolution
 ultrasound of the right brachial artery was performed one cm distal to the
 antecubital fossa with a 10 MHz linear array probe coupled to a GE Vivid 7
 Imaging System and Sonosite M-turbo. Digital images for FMD were analyzed
 with dedicated software (Information Integrity Inc.; Iowa City,
 Iowa). <strong>Generation of e-cigarette aerosol
 and its condensates</strong>: A Gram Universal Vaping Machine (Gram
 Research, Oakland, CA) was used to generate aerosol.
 <strong>Measurement of NO production</strong>: The
 amount of NO released by the cells was measured by the chemilumin­escence
 method using an NO analyzer (model 280i, GE/Zysense, Weddington,
 NC) <strong>Measurement of relative expression of
 NOS3 gene</strong>: qPCR was conducted using
 TaqMan<sup>TM</sup> Gene Expression Master Mix with NOS3
 TaqMan<sup>TM</sup> FAM-MGB Probes in a ViiA7 Real-Time PCR
 system (Applied Biosystems). 
description: Excel is required to open the data files.
DOI: 10.5061/dryad.6hdr7sr44
title: Data From: Forabot: Automated Planktic Foraminifera Isolation and Imaging

description: Physical inspection and sorting of foraminifera is a necessity in many
 research labs, as foraminifera serve as paleoenvironmental and
 chronostratigraphic indicators. In order to gain counts of species from
 samples, analyze chemical compositions, or extract morphological
 properties of foraminifera, research labs require human effort and time
 handling and sorting these microscopic fossils. The presented information
 supports Forabot, an open-source system that can physically manipulate
 individual foraminifera for imaging and isolation with minimal human
 interaction. The associated data, codebase, and documentation support
 building a Forabot and confirming results related to processing raw image
 data, error detection results, and proof of concept deep classification
 network.
description: The dataset was collected using the Forabot system.
 The data in the EDF folder is both unprocessed (raw folder) and
 the resulting processed data (example_edfs folder) to show how the EDF
 generation code works.
description: It is recommended to install software using Anaconda, but the
 software can be manually installed by referencing the Anaconda
 installation documents. A markdown viewer such as
 Typora would benefit a reader. A GPU would be helpful
 if training the deep classification network for validating results. It
 could be run on a CPU but would be quite slow.
DOI: 10.5061/dryad.wh70rxwr3
title: An insight into gill microbiome of Eastern Mediterranean wild fish by applying next generation sequencing

description: Bacterial diseases of marine fish inflict significant economic damage to
 fisheries and aquaculture and pose an increasing risk to public health.
 When addressing fish disease, an accumulating body of research suggests
 adding another factor to the classic epidemiological triangle of
 host-environment-pathogen: the microbiome. The gills, being a gateway into
 the fish body and bearing an important role in fish homeostasis, have been
 found to be a proxy of the gut microbiota as well as reflecting the
 microbial communities of surrounding water. In this study, 16S rRNA
 amplicons of bacterial DNA extracted from the gills of 89 asymptomatic
 specimens of three wild fish species (Pagrus caeruleostictus, Scomber
 colias and Saurida lessepsianus) were sequenced using Next Generation
 Sequencing methodology (NGS). Data analyses revealed the presence of 41
 potentially pathogenic species, including several zoonotic agents. Five
 genera known to include widespread and potentially pathogenic species were
 chosen for further investigation – Photobacterium, Shewanella,
 Staphylococcus, Streptococcus and Vibrio. Of these, Photobacterium and
 Shewanella proved the most prevalent and abundant, making up 30.2% and
 11.3% of the Bluespotted seabream (P. caeruleostictus) gill microbiome
 alone. Photobacterium damselae and Shewanella baltica were most common at
 the species level. The remaining genera - Vibrio, Staphylococcus and
 Streptococcus – were less prevalent, and at a species level were comprised
 of only 1−4% potentially pathogenic representatives. Gill microbiomes
 exhibited host species specificity, with strong correlations between
 certain bacterial taxonomic groups. No definite obligatory pathogenic
 bacteria were found in this study, and it was suggested that pathogenic
 species are present as either covert pathobionts or as opportunists of the
 fish found to host them.
description: Fish gill tissue samples were processed and underwent
 PCR.  Amplicons were sent to UIC Sequencing Core
 (Chicago, IL, USA) for library construction and sequencing.
 Sequence data was analyzed using the Dada2 pipeline using R
 package ‘dada2’. For each amplicon sequence variant
 (ASV), taxonomy (up to the species level) was inferred by alignment to the
 Silva non-redundant small subunit ribosomal RNA database.
 For data analysis and generation of figures, the online tool
 MicrobiomeAnalyst
 (https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/home.xhtml) was used. Taxonomy labels were assigned using the SILVA taxonomic framework (https://www.arb-silva.de/documentation/silva-taxonomy/).
DOI: 10.5061/dryad.fttdz08wj
title: Spatiotemporal patterns of male and female white-tailed deer on a hunted landscape

description: Resource selection in sexually dimorphic ungulates is at least partially
 explained by sex-specific resource requirements and risk aversion
 strategies. Females generally spend more time in areas with less risk and
 abundant, high-quality forage due to their smaller body size. However,
 demographically variable responses to risk are context dependent, and few
 have concurrently quantified male and female behavior within areas with
 the same resource base. We captured 111 (54 males, 57 females) adult
 white-tailed deer (Odocoileus virginianus) from 2009–2018 on a site in
 South Carolina, USA, where hunters were the primary source of adult
 mortality. We fit each deer with a GPS collar programmed to collect
 locations at 30-min intervals. Upon collar recovery, we analyzed the data
 to estimate sex- and time-specific selection for, and distance to, various
 cover types. While both sexes generally avoided risky areas (i.e., sites
 hunted more frequently) during the day, females (p = 0.41) were more
 likely than males (p = 0.16) to use risky areas containing abundant food
 resources during the day, where p = probability of selection. Our findings
 indicate that female white-tailed deer may be forced to utilize high risk
 areas during high risk periods due to their smaller body size and
 increased nutritional demands, whereas larger males are better able to
 forgo foraging opportunities during risky periods to mitigate risk,
 however, our study design left room for the possibility that our
 observations were driven by innate sex-specific patterns in white-tailed
 deer. Nonetheless our study contributes information to the literature by
 describing sex-specific resource selection by diel period on a site where
 sexes shared the same resources and were presented with the same landscape
 of risk. --
DOI: 10.25338/b8nd1w
title: Conifer forest plant species composition across nine years following a high severity fire

description: Ecological disturbance regimes across the globe are being altered via
 direct and indirect human influences. Biodiversity loss at multiple scales
 can be a direct outcome of these shifts. Fire, especially in dry forests,
 is an ecological disturbance that is experiencing dramatic changes due to
 climate change, fire suppression, increased human population in fire-prone
 areas, and alterations to vegetation composition and structure. Dry
 western conifer forests that historically experienced frequent, low
 severity fires are now increasingly burning at high severity. Relatively
 little work has been done looking at the effects of this novel disturbance
 type on affected plant communities, and not much is known about how these
 impacts change over time. To fill in these knowledge gaps, we examined a
 fire that burned in a yellow pine and mixed conifer forest in the central
 Sierra Nevada in California, USA. We sampled at five timesteps across the
 nine years following the fire (1, 3, 5, 8 and 9 years post-fire). We found
 a generally unimodal relationship between fire severity and diversity for
 alpha and gamma diversity, but found that areas that burned at high
 severity progressively supported lower plant diversity as time since fire
 increased. Similarly, beta diversity decreased drastically through time
 for the high severity areas, while remaining more static in the other
 severity classes. The combination of these findings indicate that
 significant floristic homogenization can result from high severity fire in
 this ecosystem type. We also saw consistently lower diversity in unburned
 areas in comparison to area burned at low and moderate severity,
 underlining that both lack of fire and high severity fire can have
 negative impacts on postfire plant diversity. Unburned areas that
 experienced forest thinning after the first sample year saw an increase in
 plant diversity over time, suggesting that some – but not all – of the
 effects of fire on diversity can be approximated through forest
 management.
description: Refer to manuscript (Ecosphere ECS22-0223) in revision.
 Will update once in publication. 
description: Refer to manuscript (Ecosphere ECS22-0223) in revision.
 Will update once in publication.
DOI: 10.5281/zenodo.18401565
title: LINF_320014100

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)