cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jwstqjq83
title: The impact of data quality filtering of opportunistic citizen science data on species distribution model performance: dataset used for Maxent modelling.

description: This dataset contains all the necessary data to repeat the
 analyses conducted in the article 'The impact of data quality
 filtering of opportunistic citizen science data on species distribution
 model performance'. Per square kilometer in Flanders, the csv-file
 contains (i) the model predictor values, (ii) the filtered and unfiltered
 presence-only occurrences of the 255 considered species used for model
 training and (iii) the presences and absences per species used for model
 testing. Details on how the data was collected and how the
 dataset was formed can be found in the article's Methods and
 Materials and Supplementary Information.
description: Please read the ReadMe text file for a description of the
 dataset.
DOI: 10.5061/dryad.z34tmpgcc
title: Cinchona pubescens Transcriptome

description: The enzymatic basis for quinine 1 biosynthesis was
 investigated. Transcriptomic data from the producing
 plant Cinchona pubescens led to the discovery of three
 enzymes involved in early and late steps of the pathway. A medium-chain
 alcohol dehydrogenase (CpDCS) and an esterase (CpDCE) yielded the
 biosynthetic intermediate dihydrocorynantheal 2 from
 strictosidine aglycone 3. Additionally, the discovery of
 an O-methyltransferase specific for
 6´-hydroxycinchoninone 4 suggested the final steps order
 to be cinchoninone 16/17 hydroxylation, methylation and
 keto-reduction.
description: This transcriptomic dataset was acquired from <em>Cinchona
 </em><i>pubescens.</i> Illumina data were acquired,
 assembled and annotated by BGI-seq.
description: Read Me Tissues isolated for transcriptome Cinchona1_2nd                       Cinchona Plant 1; 2nd Leaf Cinchona1_3rd                       Cinchona Plant 1; 3rd Leaf      Cinchona2_1st                        Cinchona Plant 2; 1st Leaf       Cinchona2_2nd                       Cinchona Plant 2; 2nd Leaf      Cinchona2_3rd                        Cinchona Plant 2; 3rd Leaf      Cinchona4_1st                        Cinchona Plant 4; 1st Leaf       Cinchona5_1st                        Cinchona Plant 5; 1st Leaf       Cinchona5_2nd                       Cinchona Plant 5; 2nd Leaf Cinchona5_3rd                       Cinchona Plant 5; 3rd Leaf      Cinchona_1_root                    Cinchona Plant 1; root             Cinchona_root2                      Cinchona Plant 2; root Cinchona_root5                      Cinchona Plant 5; root Cinchona_stem2                     Cinchona Plant 2; stem Cinchona_stem3                     Cinchona Plant 3; stem Cinchona_stem5                     Cinchona Plant 5; stem
DOI: 10.5061/dryad.sf7m0cg59
title: Nectar values from: Quantifying nectar production by flowering plants in urban and rural landscapes

description: Floral resources (nectar and pollen) provide food for insect pollinators
 but have declined in the countryside due to land use change. Given
 widespread pollinator loss, it is important that we quantify their food
 supply to help develop conservation actions. While nectar resources have
 been measured in rural landscapes, equivalent data are lacking for urban
 areas, an important knowledge gap as towns and cities often host diverse
 pollinator populations. We quantified the nectar supply of urban areas,
 farmland and nature reserves in the UK by combining floral abundance and
 nectar sugar production data for 536 flowering plant taxa, allowing us to
 compare landscape types and assess the spatial distribution of nectar
 sugar among land uses within cities. The magnitude of nectar sugar
 production did not differ significantly among the three landscapes. In
 urban areas the nectar supply was more diverse in origin and predominantly
 delivered by non-native flowering plants. Within cities, urban land uses
 varied greatly in nectar sugar production. Gardens provided the most
 nectar sugar per unit area and 85% of all nectar at a city scale, while
 gardens and allotments produced the most diverse supplies of nectar sugar.
 Floral abundance, commonly used as a proxy for pollinators’ food supply,
 correlated strongly with nectar resources, but left a substantial
 proportion of the variation in nectar supply unexplained. Synthesis. We
 show that urban areas are hotspots of floral resource diversity rather
 than quantity and their nectar supply is underpinned by the contribution
 of residential gardens. Individual gardeners have an important role to
 play in pollinator conservation as ornamental plants, usually non-native
 in origin, are a key source of nectar in towns and cities.
description: <strong>Data: nectar sugar production of plant taxa (data available from 01 August 2022)</strong> <strong>[N.B. See 'Related Works' for data on floral abundance, and nectar production scaled to site level]</strong> <b>Nectar_sugar_per_taxon.xlsx </b>- nectar sugar values (micrograms of sugars per 24 hours per floral unit) and floral traits used in predictive modelling for each plant taxon. <b>Tab 1</b> = ‘Sugar_values’ - native status, floral unit definition, sugar mass per floral unit & data source/comments for each of the 536 recorded taxa (both empirical and modelled values). <b>Tab 2</b> = ‘Predictive_modelling’ - floral traits (plant family, floral unit type, flower shape, floral unit size) for the 326 taxa with empirical values (‘duplicates’ excluded) and 114 taxa that were subsequently modelled.
DOI: 10.5061/dryad.sn02v6x38
title: COVID-19 patient data from a study in Singapore curated for input into an in silico infection model

description: Within-host models of COVID-19 infection dynamics enable the merits of
 different forms of antiviral therapy to be assessed in individual
 patients. A stochastic agent-based model of COVID-19 intracellular
 dynamics is introduced here, that incorporates essential steps of the
 viral life cycle targeted by treatment options. Integration of model
 predictions with an intercellular ODE model of
 within-host infection dynamics, fitted to patient data, generates a
 generic profile of disease progression in patients that have recovered in
 the absence of treatment. This is contrasted with the profiles obtained
 after variation of model parameters pertinent to the immune response, such
 as effector cell and antibody proliferation rates, mimicking disease
 progression in immunocompromised patients. These profiles are then
 compared with disease progression in the presence of antiviral and
 convalescent plasma therapy against COVID-19 infections. The model reveals
 that using both therapies in combination can be very effective in reducing
 the length of infection, but these synergistic effects decline with a
 delayed treatment start. Conversely, early treatment with either therapy
 alone can actually increase the duration of infection, with infectious
 virions still present after the decline of other markers of infection.
 This suggests that usage of these treatments should remain carefully
 controlled in a clinical environment.
description: Viral load (V) values for 12 patients from a COVID-19 study in Singapore (reported in 10.1001/jama.2020.3204) were curated for input into our <i>in silico </i>infection model. Viral load values in this study are measured in Cycle threshold (Ct) values and presented in a table (eTable 2). In order to use these data as input, we converted Ct values to the number of free virus particles per ml (V) using the formula log10(V)=−0.3231*Ct+14.11, and then used those V values for our analysis. We provide here the file Curated_Patient_Data.txt, that we used as input for our algorithm. This file contains the following information, adapted from the above-mentioned study: The first column gives the patient ID and ranges from 1 to 12; the second column indicates the time of the measurement after the onset of symptoms, considering the onset of symptoms as day 0; the third column gives the measurement from (10.1001/jama.2020.3204) in Ct values; the fourth and fifth columns indicate the log10(V) and V values, where V is the number of free virus particles per ml. Note that columns four and five are calculated by converting Ct values as described above.
DOI: 10.6084/m9.figshare.31145869
title: The Stability–Sustainability Turn in China’s Food Security Evolution

description: Despite sustained growth in global food production, rising levels of hunger reveal critical shortcomings in conventional food security assessments. In particular, the roles of stability and sustainability in food systems remain insufficiently captured, especially in the context of regional conflicts and pandemic outbreaks. To address this gap, we construct a comprehensive six-dimensional food security evaluation framework that explicitly integrates stability and sustainability alongside availability, access, utilization, and agency. The framework is developed using a consolidated long-term dataset covering all Chinese provinces (108,320 observations, 1990–2019). Our results reveal a fundamental transformation in China’s food security trajectory. This transformation is characterized not only by a substantial increase in the composite food security index (from 36.6 to 73.5), but also by a shift from growth achieved at the expense of stability and sustainability toward a more comprehensive and balanced development pattern. Specifically, stability and sustainability evolved from being major constraints (with a combined negative contribution of −36.6%) to becoming net positive contributors (+3.4%) after 2015. Spatially, this shift has reduced internal imbalances in food security indicators across provinces, while improved alignment between stability, sustainability, and other dimensions has enhanced overall system synergy. Importantly, excluding stability and sustainability results in a 13.6% overestimation of food security levels after 2005. Overall, this study offers a replicable framework for food security evaluation and provides policy-relevant insights for other major agricultural economies confronting similar trade-offs between sustainability and stability.
DOI: 10.6084/m9.figshare.31145869.v1
title: Data for Highlighting Stability and Sustainability in Food Security Evaluation

description: Despite sustained growth in global food production, rising levels of hunger reveal critical shortcomings in conventional food security assessments. In particular, the roles of stability and sustainability in food systems remain insufficiently captured, especially in the context of regional conflicts and pandemic outbreaks. To address this gap, we construct a comprehensive six-dimensional food security evaluation framework that explicitly integrates stability and sustainability alongside availability, access, utilization, and agency. The framework is developed using a consolidated long-term dataset covering all Chinese provinces (108,320 observations, 1990–2019). Our results reveal a fundamental transformation in China’s food security trajectory. This transformation is characterized not only by a substantial increase in the composite food security index (from 36.6 to 73.5), but also by a shift from growth achieved at the expense of stability and sustainability toward a more comprehensive and balanced development pattern. Specifically, stability and sustainability evolved from being major constraints (with a combined negative contribution of −36.6%) to becoming net positive contributors (+3.4%) after 2015. Spatially, this shift has reduced internal imbalances in food security indicators across provinces, while improved alignment between stability, sustainability, and other dimensions has enhanced overall system synergy. Importantly, excluding stability and sustainability results in a 13.6% overestimation of food security levels after 2005. Overall, this study offers a replicable framework for food security evaluation and provides policy-relevant insights for other major agricultural economies confronting similar trade-offs between sustainability and stability.
DOI: 10.6084/m9.figshare.31145869.v2
title: The Stability–Sustainability Turn in China’s Food Security Evolution

description: Despite sustained growth in global food production, rising levels of hunger reveal critical shortcomings in conventional food security assessments. In particular, the roles of stability and sustainability in food systems remain insufficiently captured, especially in the context of regional conflicts and pandemic outbreaks. To address this gap, we construct a comprehensive six-dimensional food security evaluation framework that explicitly integrates stability and sustainability alongside availability, access, utilization, and agency. The framework is developed using a consolidated long-term dataset covering all Chinese provinces (108,320 observations, 1990–2019). Our results reveal a fundamental transformation in China’s food security trajectory. This transformation is characterized not only by a substantial increase in the composite food security index (from 36.6 to 73.5), but also by a shift from growth achieved at the expense of stability and sustainability toward a more comprehensive and balanced development pattern. Specifically, stability and sustainability evolved from being major constraints (with a combined negative contribution of −36.6%) to becoming net positive contributors (+3.4%) after 2015. Spatially, this shift has reduced internal imbalances in food security indicators across provinces, while improved alignment between stability, sustainability, and other dimensions has enhanced overall system synergy. Importantly, excluding stability and sustainability results in a 13.6% overestimation of food security levels after 2005. Overall, this study offers a replicable framework for food security evaluation and provides policy-relevant insights for other major agricultural economies confronting similar trade-offs between sustainability and stability.
DOI: 10.5061/dryad.dz08kprwn
title: Nutrient conditions are primary drivers of bacterial capsule maintenance in Klebsiella

description: The fitness cost associated with the production of bacterial capsules is
 considered to be offset by the protection provided by these extracellular
 structures against biotic aggressions or abiotic stress. Yet, it is
 unknown if the capsule contributes to fitness in the absence of these.
 Here, we explored conditions favouring the maintenance of the capsule
 inKlebsiella pneumoniae, where the capsule is known to be a major
 virulence factor. Using short term experimental evolution on
 different Klebsiellastrains, we showed that small environmental
 variations have a strong impact on the maintenance of the capsule. Capsule
 inactivation is frequent in nutrient-rich, but scarce in nutrient-poor
 media. Competitions between wild type and capsule mutants in nine
 different strains confirmed that the capsule is costly in nutrient-rich
 media. Surprisingly, they also showed that the presence of a capsule
 provides a clear fitness advantage in nutrient-poor conditions by
 increasing both growth rates and population yields. The comparative
 analyses of the wild-type and capsule mutants reveal complex interactions
 between the environment, genetic background and serotype even in relation
 to traits known to be relevant during pathogenesis. In conclusion, our
 data suggests there are novel roles for bacterial capsules yet to be
 discovered and further supports the notion that the capsule role in
 virulence may be a by-product of its contribution to bacterial adaptation
 outside the host.
DOI: 10.5061/dryad.dfn2z350k
title: Linnaeus' wild plants are under threat in Uppsala

description: Many of the plant species found by Carl Linnaeus and his students around
 Uppsala during the excursions Herbationes Upsalienses are extant in the
 areas they visited. The authors here present the first complete list of
 species registered during these excursions, with added information on
 extant species in the different areas. These Linnaean populations are of
 high cultural value, but they also have a high scientific value as
 potential type specimens. Three of Linnaeus’ excursion areas are therefore
 proposed to be included in the planned world heritage nomination "The
 Rise of Systematic Biology": Hågadalen, Årike Fyris and Fäbodmossen.
 The Linnaean populations are threatened by genetic pollution through the
 extensive sowing and planting of the same species with alien origin in
 connection with plant restauration after ground preparations and building.
 The degree of genetic pollution is not known, since sowing and planting of
 alien material is not registered. The authors give examples of alternative
 plant restauration methods using local plant material in order to preserve
 the Linnaean flora of Uppsala.
description: List of Linnaean species in and around Uppsala based on protocols
 written by Linnaeus' students during his excursions 1747-1762, the
 thesis <i>Herbationes Upsalienses</i> from 1753 and
 <i>Flora Svecica</i> from 1745 and 1755. For each species,
 different columns indicate on which excursion route as listed in
 <i>Herbationes Upsalienses </i>it was found. Exceptions from
 this are 1) the column "Ultuna/Danmark" which includes species
 from both of these excursions, and 2) "Uppsala generellt"
 (Uppsala general) which includes species from excursions with uncertain
 location or species observed in central Uppsala. The information included
 in these columns is as follows: x = the species is found in the area in
 modern times; p = the species could potentially be growing in the area
 since it is reported in the vicinity in the database Artportalen; ? =
 taxonomic or other uncertainty;  † = the Linnaean population is assumed to
 be extinct in and around the Uppsala.
DOI: 10.5061/dryad.m63xsj419
title: Data for: Female-biased sex ratios in urban centres create a fertility trap in post war Finland

description: Because sex ratios are a key factor regulating mating success and
 subsequent fitness both across and within species, there is widespread
 interest in how population-wide sex ratio imbalances affect marriage
 markets and the formation of families in human societies. Although most
 modern cities have more women than men and suffer from low fertility
 rates, the effects of female-biased sex ratios have garnered less
 attention than male-biased ratios. Here, we analyze how sex ratios are
 linked to marriages, reproductive histories, dispersal and urbanization by
 taking advantage of a natural experiment in which an entire population was
 forcibly displaced during World War II to other local Finnish populations
 of varying sizes and sex ratios. Using a discrete time-event generalised
 linear mixed-effects model, and including factors that change across time,
 such as annual sex ratio, we show how sex ratios, reproduction, and
 migration are connected in a female-dominated environment. Young childless
 women migrated toward urban centers where work was available to women, and
 away from male-biased rural areas. In such areas where there were more
 females, women were less likely to start reproduction.  Despite
 this constraint, women showed little flexibility in mate choice, with no
 evidence for an increase in partner age difference in female-biased areas.
 We propose that together these behaviours and conditions combine to
 generate an ‘urban fertility trap’ which may have important consequences
 for our understanding of the fertility dynamics of today including the
 current fertility decline across the developed world.
DOI: 10.5061/dryad.t76hdr807
title: Habitat-specific survival of golden-winged warblers (Vermivora chrysoptera) during the non-breeding season in an agricultural landscape

description: Nearctic-Neotropical migratory birds are considered priority species for
 conservation because they are subject to threats at distinct breeding,
 migratory and stopover locations throughout their annual cycle, and many
 species have undergone severe population declines. Research during the
 non-breeding season has focused on identifying the locations and habitats
 that migrants use, but wintering migrants are known to occupy habitats of
 both high and low quality, especially when the best sites are saturated by
 conspecifics. Thus, the presence or abundance of a species may not be a
 reliable indicator of winter habitat quality. The habitat associations of
 the golden-winged warbler Vermivora chrysoptera, a Nearctic-Neotropical
 migrant bird species of elevated conservation concern, are relatively well
 studied, yet conservation efforts are hindered by lack of information
 about basic demographic rates. In particular, no published estimates exist
 for non-breeding season survival, which can be a key vital rate affecting
 population viability, nor how survival rates vary among habitats, which is
 important to designing conservation programs to support populations during
 the winter period. We studied a color-banded population of golden-winged
 warblers in Costa Rica over a 3-year period and estimated overall survival
 rates, and the effects of habitat characteristics on survival. We found
 that monthly survival of juveniles (0.881) was lower than adult birds
 (0.978). Monthly survival during the non-breeding season (0.967) was
 higher than monthly survival during the rest of the annual cycle (0.930).
 Survival was negatively related to canopy height, and we observed a
 significant quadratic effect where survival peaked at intermediate levels
 of vine tangles and dead hanging leaves, which corresponds to habitat
 features associated with abundance in prior studies at this same site. Our
 findings contribute to our existing knowledge about the potential impacts
 of winter-season events on Nearctic-Neotropical migratory bird
 populations, and also informs potential conservation strategies for
 wintering golden-winged warblers.
description: All models and data are included and should be placed in the same
 working file to then be used with the provided R code.  The program JAGS
 should also be installed on your computer.