cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rbnzs7hf6
title: Enhanced isohydric behavior decoupled the whole-tree sap flux response to leaf transpiration under nitrogen addition in a subtropical forest

description: Anthropogenic nitrogen deposition has the potential to change the leaf
 water-use strategy in the subtropical region of China. Nevertheless, the
 whole-tree level response crucial for ecosystem functions has not been
 well addressed over the past decades. In this study, the stem sap flux
 density (JS) was monitored for the whole-tree water transport capacity in
 two dominant species (Schima superba and Castanopsis chinensis) in a
 subtropical forest. To simulate the increased nitrogen deposition, the
 NH4NO3 solutions were sprayed onto the forest canopy at 25 kg ha-1 year-1
 (CAN25) and 50 kg ha-1 year-1 (CAN50), respectively, since April 2013. The
 JS and microclimate (monitored since January 2014) derived from the
 whole-tree level stomatal conductance (GS) were used to quantify the
 stomatal behavior (GS sensitive to vapor pressure deficit, GS-VPD) in
 response to the added nitrogen. The maximum shoot hydraulic conductance
 (Kshoot-max) was also measured for both species. After one year of
 monitoring in January 2015, the mid-day (JS-mid) and daily mean (JS-mean)
 sap flux rates did not change under all the nitrogen addition treatments
 (p &gt; 0.05). A consistent decline in the GS-VPD indicated an
 enhanced isohydric behavior for both species. In addition, the GS-VPD in
 the wet season was much lower than that in the dry season. S. superba had
 a lower GS-VPD and decreased JS-mid/JS-mean, implying a stronger
 stomatal control under the fertilization, which might be attributed to the
 low efficient diffuse-porous conduits and a higher JS. In addition, the GS
 for S. superba decreased and the GS-VPD increased more under CAN50 than
 that under CAN25, indicating that the high nitrogen dose restrains the
 extra nitrogen benefits. Our results indicated that the JS for both
 species was decoupled from the leaf transpiration for both species due to
 an enhanced isohydric behavior, and a xylem anatomy difference and
 fertilization dose would affect the extent of this decoupling relation.
description: Please see the README document ("README.md.txt") and
 the accompanying published article: Zhao Z, Zhao P, Zhang Z, et al.
 Enhanced Isohydric Behavior Decoupled the Whole-Tree Sap Flux Response to
 Leaf Transpiration under Nitrogen Addition in a Subtropical Forest[J].
 Forests, 2022, 13(11): 1847. DOI: 10.3390/f13111847
description: Please see the README document ("README.md.txt") and
 the accompanying published article: Zhao Z, Zhao P, Zhang Z, et al.
 Enhanced Isohydric Behavior Decoupled the Whole-Tree Sap Flux Response to
 Leaf Transpiration under Nitrogen Addition in a Subtropical Forest[J].
 Forests, 2022, 13(11): 1847. DOI: 10.3390/f13111847
DOI: 10.5281/zenodo.18401508
title: Machine Learning in Next-Generation AEM Fuel Cells: A Systematic Review
DOI: 10.5061/dryad.z34tmpghw
title: Data: Large old trees increase growth under shifting climatic constraints: Aligning tree longevity and individual growth dynamics in primary mountain spruce forests

description: In a world of accelerating changes in environmental conditions driving
 tree growth, tradeoffs between tree growth rate and longevity could
 curtail the abundance of large, old trees (LOTs), with potentially dire
 consequences for biodiversity and carbon storage. However, the influence
 of tree-level tradeoffs on forest structure at landscape scales will also
 depend on disturbances, which shape tree size and age distribution, and on
 whether LOTs can benefit from improved growing conditions due to climate
 warming. We analyzed temporal and spatial variation in radial growth
 patterns from ~5000 Norway spruce (Picea abies (L.) H. Karst) live and
 dead trees from the Western Carpathian primary spruce forest stands. We
 applied mixed-linear modeling to quantify the importance of LOT growth
 histories and stand dynamics (i.e. competition and disturbance factors) on
 lifespan. Finally, we assessed regional synchronization in radial growth
 variability over the 20th century, and modelled the effects of stand
 dynamics and climate on LOTs recent growth trends. Tree age varied
 considerably among forest stands, implying an important role of
 disturbance as an age constraint. Slow juvenile growth and longer period
 of suppressed growth prolonged tree lifespan, while increasing disturbance
 severity and shorter time since last disturbance decreased it. The highest
 age was not achieved only by trees with continuous slow growth, but those
 with slow juvenile growth followed by subsequent growth releases. Growth
 trend analysis demonstrated an increase in absolute growth rates in
 response to climate warming, with late summer temperatures driving the
 recent growth trend. Contrary to our expectation that LOTs would
 eventually exhibit declining growth rates, the oldest LOTs (&gt;400
 years) continuously increase growth throughout their lives, indicating a
 high phenotypic plasticity of LOTs for increasing biomass, and a strong
 carbon sink role of primary spruce forests under rising temperatures,
 intensifying droughts, and increasing bark beetle outbreaks.
DOI: 10.5281/zenodo.18400719
title: Synthetic Images Flood Scenario

description: Synthetic RGB image dataset depicting 766 images of floods in varied scenarios generated with AI methods. This data can be used to train/evaluate flood segmentation models on RGB images.

FloodsScenarios/├── images/                       (image_00001_.jpg → image_00766_.jpg)├── annotated_images/    (image_00001_.png → image_00766_.png)└── annotated_masks/      (image_00001_.png → image_00766_.png)
DOI: 10.5281/zenodo.18400720
title: Synthetic Images Flood Scenario

description: Synthetic RGB image dataset depicting 766 images of floods in varied scenarios generated with AI methods. This data can be used to train/evaluate flood segmentation models on RGB images.

FloodsScenarios/├── images/                       (image_00001_.jpg → image_00766_.jpg)├── annotated_images/    (image_00001_.png → image_00766_.png)└── annotated_masks/      (image_00001_.png → image_00766_.png)
DOI: 10.5061/dryad.cfxpnvx8p
title: Data for: Effects of biotic interactions on plant fecundity depend on spatial and functional structure of communities and time since disturbance

description: Biotic interactions in plant communities affect individual fitness and
 community dynamics. Interactions between plants vary in space, over time
 and with organisational complexity. Yet it is challenging to quantify
 temporal, spatial and functional determinants of different types of
 interactions between long-lived perennial plant species and their effect
 on lifetime fecundity. We studied how plant-plant, pollinator- and seed
 predator-mediated interactions affect year-to-year variation in three
 fecundity components (cone production, seed set and seed survival) during
 post-fire recovery. Age-stratified data on the three fecundity components
 were collected in 19 even-aged communities comprising 20 serotinous Protea
 shrub species in the South African Fynbos. We analyse data on these
 fecundity components with neighbourhood models to infer the sign and
 strength of interactions throughout post-disturbance recovery, the
 neighbour plant traits that shape them and the spatial scale at which
 interactions take place. For each fecundity component, these models
 describe how neighbourhood effects change over time and with spatial
 distance between plants. For each focal plant, we then predicted
 neighbourhood effects on individual fecundity components and cumulative
 reproductive output at different post-fire stand ages. Competitive effects
 on cone production and seed set increased with post-fire stand age as
 biomass and floral resources for pollinators build up. In contrast,
 neighbourhood effects on seed survival were weak throughout
 post-disturbance recovery. Plant-plant interactions were shaped by
 neighbour traits related to resource acquisition, whereas animal-mediated
 interactions depended on neighbour traits related to resource availability
 for pollinators and seed predators. The spatial scale of the interactions
 increased from plant-plant over predator-mediated to pollinator-mediated
 interactions. The joint effect of these interactions on cumulative
 reproductive output caused the proportion of focal plants experiencing
 competition to increase with time since fire. We show that temporal
 changes in biotic interactions throughout post-disturbance recovery of
 perennial plant communities depend on functional traits and can be
 integrated to neighbourhood effects on lifetime fecundity. Studying the
 temporal, spatial and functional determinants of neighbourhood effects on
 lifetime fecundity is important for predicting not only individual plant
 fitness, but also population and community dynamics in changing
 environments.
DOI: 10.5061/dryad.44j0zpchr
title: Livestock management promotes bush encroachment in savanna systems by altering plant-herbivore feedback

description: This repository contains all code to reproduce the analysis in Koch et al.
 2022 "Livestock management promotes bush encroachment in savanna
 systems by altering plant-herbivore feedback". We use a set of
 coupled differential equations to describe competition between shrubs and
 grasses, as well as plant biomass consumption via grazing and browsing.
 Grazers were assumed to receive a certain level of care from farmers, so
 that grazer densities emerge dynamically from the combined effect of
 vegetation abundance and farmersupport. Our main goal was to understand
 how critical transitions from grass-dominated to shrub-dominated system
 states were affected by the dynamic role of grazing. Our results show that
 bistability emerges for intermediate levels of farmer support due to
 positive feedback that arises from competition between shrubs and grasses
 and from herbivory. We furthermore demonstrate that disturbances, such as
 drought events, trigger abrupt transitions from the grass dominated to the
 shrub dominated state and that the system becomes more susceptible to
 disturbances with increasing farmer support.
description: We used numerical simulations to analyse system dynamics under
 different livestock management and disturbance regimes. Then, we
 quantified all self-reinforcing and self-dampening feedback loops to
 determine their relative importance in shaping system (in)stability. The
 whole analysis was performed in python. For details, see the Methods
 section of the corresponding paper.
DOI: 10.5061/dryad.h70rxwdnd
title: Deciphering the interactions between plant species and their main fungal root pathogens in mixed grassland communities

description: 1. Plant diversity can reduce the risk of plant disease, but positive, and
 neutral effects have also been reported. These contrasting relationships
 suggest that plant community composition, rather than diversity per se,
 affects disease risk. Here, we investigated how diversity and composition
 of plant communities drive root-associated pathogen accumulation
 belowground. 2. In a temperate grassland biodiversity experiment,
 containing 16 plant species (forbs and grasses), we determined the
 abundance of root-associated fungal pathogens in individual plant species
 growing in monocultures and in 4-species mixtures through Illumina MiSeq
 amplicon sequencing. 3. In the plant monocultures, we identified three
 major fungal pathogens that differed in host range: Paraphoma
 chrysanthemicola, associated with roots of forb species of the Asteraceae
 family, Slopeiomyces cylindrosporus, associated with grass species, and
 Rhizoctonia solani, associated with multiple forb and grass species. In
 mixtures, there was no significant reduction in relative abundance of
 these pathogens in their host species as compared to monocultures.
 However, in mixtures, there was a significant increase in relative
 abundance of each pathogen in several non-host and host plant species.
 Across mixtures, plant community composition affected pathogen relative
 abundance in individual plant species. This effect was driven by the
 presence of a particular neighbouring plant species (depending on the
 pathogen), rather than functional group composition (i.e. grass/forb
 ratio) or averaged pathogen pressure (based on monocultures) of all
 neighbours. Specifically, the presence of neighbour host species Achillea
 millefolium significantly increased P. chrysanthemicola, but decreased R.
 solani relative abundance in several host and non-host plant species in
 mixtures. 4. Synthesis: Our results indicate that interactions between
 different plant species – both host and non-hosts – and fungal pathogens
 underlie effects of plant diversity on root pathogen abundance. Non-host
 species may act as pathogen reservoirs in diverse plant communities, as
 they harboured certain pathogens in mixtures, but not in monocultures.
 Additionally, particular host species can strongly affect pathogen
 abundance in other (host and non-host) plant species in plant mixtures,
 suggesting clear effects of species identity in the diversity-disease
 relationship. Belowground disease risk thus depends on plant community
 composition rather than diversity per se, via specific interactions
 between plant species and their root-associated pathogens.
description: Illumina MiSeq sequencing of
 fungal ITS1 region of DNA extracted from root
 samples. <br>Processed as described in the
 manuscript. <br>Three files: metadata; taxonomy, and ASV read
 abundances.
DOI: 10.5061/dryad.t1g1jwt5k
title: Pelagic primary production in northern lakes

description: These datasets present data on pelagic gross primary production (GPP) of
 detailed depth profiles ("GPPzrates") and lake averages
 ("GPPlakeaverages") of summer pelagic GPP together with
 environmental and climatic data across 45 small and shallow lakes across
 northern Sweden. The datasets include 20 boreal, 6 subarctic, and 19
 arctic lakes. 
description: We collected data on pelagic GPP depth profiles and
 GPPlake-averages, together with physico-chemical lake parameters in summer
 (June-August) from 45 lakes in northern Sweden. The lakes were spread over
 three different biomes (20 boreal, 6 subarctic, and 19 Arctic lakes),
 covering a colored DOC gradient from 1.0 to 19.5mg L-1. Pelagic GPP was
 measured at varying depths using 14C as isotopic tracer .
DOI: 10.5061/dryad.m0cfxpp75
title: Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia

description: Internal ribosome entry sites (IRESs) drive translation initiation during
 stress. In response to hypoxia, (lymph)angiogenic factors responsible for
 tissue revascularization in ischemic diseases are induced by the
 IRES-dependent mechanism. Here we searched for IRES trans-acting factors
 (ITAFs) active in early hypoxia in mouse cardiomyocytes. Using knock-down
 and proteomics approaches, we show a link between a stressed-induced
 nuclear body, the paraspeckle, and IRES-dependent translation.
 Furthermore, smiFISH experiments demonstrate the recruitment of
 IRES-containing mRNA into paraspeckle during hypoxia. Our data reveal that
 the long non-coding RNA Neat1, an essential paraspeckle component, is a
 key translational regulator, active on IRESs of (lymph)angiogenic and
 cardioprotective factor mRNAs. In addition, paraspeckle proteins p54nrb
 and PSPC1 as well as nucleolin and Rps2, two p54nrb-interacting proteins
 identified by mass spectrometry, are ITAFs for IRES subgroups. Paraspeckle
 thus appears as a platform to recruit IRES-containing mRNAs and possibly
 host IRESome assembly. Polysome PCR array shows that Neat1 isoforms
 regulate IRES-dependent translation and, more widely, translation of mRNAs
 involved in stress response.
DOI: 10.5061/dryad.f7m0cfz0n
title: Data from: Redefining possible: Combining phylogenomic and supersparse data in frogs

description: The data available for reconstructing molecular phylogenies have become
 wildly disparate. Phylogenomic studies can generate data for thousands of
 genetic markers for dozens of species, but for hundreds of other taxa,
 data may be available from only a few genes. Can these two types of data
 be integrated to combine the advantages of both, addressing the
 relationships of hundreds of species with thousands of genes? Here we show
 that this is possible, using data from frogs. We generated a phylogenomic
 dataset for 138 ingroup species and 3,784 nuclear markers (ultraconserved
 elements, UCEs), including new UCE data from 70 species. We also assembled
 a supermatrix dataset, including data from 97% of frog genera (441 total),
 with 1–307 genes per taxon. We then produced a combined
 phylogenomic-supermatrix dataset (a “gigamatrix”) containing 441 ingroup
 taxa and 4,091 markers, but with 86% missing data overall. Likelihood
 analysis of the gigamatrix yielded a generally well-supported tree among
 families, largely consistent with trees from the phylogenomic data alone.
 All terminal taxa were placed in the expected families, even though 42.5%
 of these taxa each had &gt;99.5% missing data, and 70.2% had
 &gt;90% missing data. Our results show that missing data need not be
 an impediment to successfully combining very large phylogenomic and
 supermatrix datasets, and they open the door to new studies that
 simultaneously maximize sampling of genes and taxa.
DOI: 10.5281/zenodo.17976203
title: PopPUNK-mod real genome pairwise distances

description: Real pairwise distance genome datasets used for fitting PopPUNK-mod.
DOI: 10.5281/zenodo.18129934
title: PopPUNK-mod real genome pairwise distances

description: Real pairwise distance genome datasets used for fitting PopPUNK-mod.
DOI: 10.5061/dryad.k3j9kd5bg
title: Determinants of QuantiFERON Plus-diagnosed tuberculosis infection in adult Ugandan TB contacts: A cross-sectional study

description: Background The tuberculin skin test is commonly used to diagnose latent
 tuberculosis infection (LTBI) in resource-limited settings, but its
 specificity is limited by factors including cross-reactivity with BCG
 vaccine and environmental mycobacteria. Interferon-gamma release assays
 (IGRA) overcome this problem by detecting M. tuberculosis complex-specific
 responses, but studies to determine risk factors for IGRA-positivity in
 high TB burden settings are lacking. Methods We conducted a
 cross-sectional study to determine factors associated with a positive IGRA
 by employing the QuantiFERON-TB® Gold-plus (QFT Plus) assay in a
 cohort of asymptomatic adult TB contacts in Kampala, Uganda. Multivariate
 logistic regression analysis with forward stepwise logit function was
 employed to identify independent correlates of QFT Plus-positivity.
 Results Of the 202 participants enrolled, 129/202 (64%) were female,
 173/202 (86%) had a BCG scar, and 67/202 (33%) were HIV-infected. Overall,
 105/192 (54%, 95% CI 0.48–0.62) participants had a positive QFT Plus
 result. Increased risk of QFT-Plus positivity was independently associated
 with manual employment/unemployment vs. professional employment (adjusted
 odds ratio (aOR) 2.18, 95% CI 1.01–4.72), a family vs. non-family relation
 to the index patient (aOR 2.87, 95% CI 1.33–6.18), living in the same vs.
 a different house as the index (aOR 3.05, 95% CI 1.28–7.29), a higher body
 mass index (BMI) (aOR per additional kg/m2 1.09, 95% CI 1.00–1.18) and
 tobacco smoking vs. not (aOR 2.94, 95% CI 1.00–8.60). HIV infection was
 not associated with QFT-Plus positivity (aOR 0.91, 95% CI 0.42–1.96).
 Conclusion The prevalence of IGRA positivity in this study population was
 lower than previously estimated. Tobacco smoking and raised BMI are
 hitherto unappreciated determinants of LTBI risk in this setting.
description: A cross-sectional study to determine factors associated with a
 positive IGRA by employing the QuantiFERON-TB® Gold-plus (QFT Plus) assay
 in a cohort of asymptomatic adult TB contacts in Kampala, Uganda.
 Multivariate logistic regression analysis with forward stepwise logit
 function was employed to identify independent correlates of QFT
 Plus-positivity.
description: Excel
DOI: 10.5061/dryad.7m0cfxpz1
title: Filial cannibalism leads to chronic nest failure of eastern hellbender salamanders (Cryptobranchus alleganienesis)

description: These data and code support the results in our accompanying manuscript. In
 species that provide parental care, parents will sometimes cannibalize
 their own young. Here, we quantified the frequency of whole-clutch filial
 cannibalism in a species of giant salamander (eastern
 hellbender; Cryptobranchus alleganienesis) that has experienced
 precipitous population declines with unknown causes. We used underwater,
 artificial nesting shelters deployed across a gradient of upstream forest
 cover to assess the fates of 182 nests at 10 sites over 8 years. We found
 strong evidence that nest failure rates increased at sites with low
 riparian forest cover in the upstream catchment. At several sites,
 reproductive failure was 100%, mainly due to cannibalism by the caring
 male. The high incidence of filial cannibalism at degraded sites was not
 explained by evolutionary hypotheses for filial cannibalism based on adult
 body condition or low reproductive value of clutches. Instead, larger
 clutches at degraded sites were most vulnerable to cannibalism. 
 We hypothesize that high frequencies of filial cannibalism of large
 clutches in areas with low forest cover could be related to changes in
 water chemistry or siltation that influence parental physiology or that
 reduce viability of eggs. Importantly, our results identify a possible
 mechanism contributing to population declines and observed geriatric age
 structure in this imperiled species.
description: We used underwater, artificial nesting shelters deployed across a
 gradient of upstream forest cover to assess the fates of 182 nests at 10
 sites over 8 years. We measured nest success using images and videos taken
 at different times of the year. The data included here have been checked
 for quality control. The analysis is available in the R script. 
description: R programming language version 4.1.1 are needed to open and run
 the R software. Rstudio (free version of the IDE) may be useful. Newer
 versions of R may or may not compile Stan; see README for
 details.  For the image files (.jpg) a photo viewer is
 needed. Preview on Mac OS or an open-source image viewer such as Image
 Glass (for Windows 10) can be used to view the photos once
 downloaded.  For the movie files (.mp4) a movie player
 is needed. VLC is an open-source media player that works on
 both Windows and Mac platforms.
DOI: 10.15468/dl.vbd337
title: Occurrence Download

description: A dataset containing 486 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Erythrophleum chlorostachys",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 486 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003296-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.