cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18400810
title: CAMS-REG-UNC-v8.1: A detailed uncertainty product for the gridded CAMS-REG-v8.1 emission inventory

description: This dataset is described in detail in: manuscript submitted to ESSD.

Independent verification of greenhouse gas emission reductions and trends in air pollution levels is receiving increasing attention. Atmospheric observations can provide such a constraint on emission estimates through inverse modelling, which requires a detailed quantification of uncertainties in prior emission inventories, observations and chemical transport models. A detailed methodology was developed to quantify uncertainties in a state-of-the-art European emission inventory: CAMS-REG. Uncertainties are estimated for all input data used to create the emission inventory and propagated to the final product. This results in separate uncertainty estimates for country-level emissions per sector and uncertainties in the spatial allocation of those emissions. Ideally, the gridded emission uncertainties should add up to the country-level emission uncertainties and for this purpose an optimization procedure was developed (only for countries with detailed emission reporting). This results in (scaled) gridded emission uncertainties and spatial error correlation lengths, which are included in the final dataset. This work follows up from previous efforts and details the first comprehensive emission uncertainty dataset for Europe.

The dataset follows the same format as the CAMS-REG inventory and contains relative standard deviations in gridded emissions, per pollutant, sector, and location. Additionally, spatial error correlation lengths (in degrees and km) are provided, per pollutant, country, and sector.
DOI: 10.5061/dryad.3ffbg79nh
title: Effects of yeast strain and juice nitrogen status on glutathione utilisation during fermentation of model media

description: Background and Aims An OIV resolution provides guidelines on using
 glutathione as a prefermentation additive when the amount of yeast
 assimilable nitrogen (YAN) of a juice or must is adequate, to avoid the
 metabolism of glutathione by the yeast. The effect of YAN concentration on
 glutathione metabolism by yeast had not been determined. This study
 explored whether nitrogen management could be used to control glutathione
 consumption during fermentation. Methods and Results An HPLC-UV method was
 developed to quantify reduced L-glutathione (GSH) and oxidised glutathione
 (GSSG) and used to monitor yeast GSH metabolism during alcoholic
 fermentation with two yeast strains (AWRI 1688 and AWRI 2861). The
 addition of GSH had no impact on the fermentation rate of the chemically
 defined medium, even in a limited YAN environment; however, a decrease in
 glutathione concentration occurred regardless of YAN concentration. The
 effect of GSH on volatile sulfur compound formation was yeast
 strain-dependent. Conclusions Increasing the YAN status of a chemically
 defined medium led to a decrease in GSH consumption during fermentation,
 but the loss of GSH could not be prevented entirely, even with a low
 initial GSH concentration and high initial YAN. Significance of the Study
 In the presence of higher concentrations of GSH during fermentation, there
 is a risk of forming undesirable fermentative sulfur compounds that are
 not mitigated through nitrogen supplementation. Thus, it seems unlikely
 that an argument could be made for the inclusion of GSH in relevant food
 standards codes as a wine additive especially if a lack of GSH metabolism
 was a criterion.
description: All methods used to produce this dataset are described in the
 associated manuscript.
description: All files are stored as tab-delimited text. Analysis and
 visualisation of the data was achieved using R. The R code used for data
 visualisation and analysis is provided as an .R file.
DOI: 10.5061/dryad.q83bk3jn2
title: Normative behavioral data from the novel One Trail Trace escape reaction task (OTTER)

description: We designed a behavioral task where rats learn to associate two temporally
 distinct but close-in-time events by means of incidental one-trial
 learning. The task takes advantage of two competing motivations - to avoid
 light places and to avoid painful stimuli (foot shock) predicted by an
 acoustic signal. Motivation to avoid a bright light is constant throughout
 the experiment and is manifested by rats preferring a dark compartment in
 a light/dark shuttle box. Motivation to stay in the dark is overridden (1)
 during the training session: when foot-shock (US) (preceded by the
 acoustic stimulus (CS)) is presented; and (2) during the testing session:
 when CS, that predicts US, is presented. The latter case occurs when rats
 successfully form an association between CS and US in the training session
 and the rat escapes into the light compartment ('responders').
 The rats that do not escape ('non-responders' appear to lack
 this memory as even non-specific fear response (freezing) was absent.
 Generally, &gt;50% of rats escape into the lit compartments following
 CS on the testing day. Importantly, rats do not show a contextual
 association measured by freezing behavior and preference for a light
 compartment on the testing day. Moreover, we observed that several
 putative details in the setup affect the probability of the successful
 formation of a one-trial trace association. Compared to similar tasks, the
 OTTER task tests incidental learning with no requirement for pre-training.
 Moreover, the memory formed in the OTTER task consists of two events that
 do not overlap in time: a characteristic of many episodic memories. The
 OTTER task presents high-throughput means to study neuronal substrates of
 incidental temporal binding.
description: Radostova_OTTER_manuscript_data.csv shows the habituation
 behavior of rats in the OTTER task. This file also identifies ‘responders’
 and ‘non-responders’. Radostova_OTTER_manuscript_data_freezing.csv shows
 the freezing for 1 minute following conditioned stimulus presentation
 during the recall session, and shows no difference in freezing between
 'responders' and 'non-responders'.
DOI: 10.5061/dryad.1zcrjdfwf
title: Transient acetaldehyde production by SO2 producing S. cerevisiae promotes survival of Oenococcus oeni during co-fermentation

description: Stuck or sluggish malolactic fermentation (MLF) can be problematic in
 limiting wine conditions, particularly white and sparkling base musts /
 wines. In these cases, knowledge of yeast-bacteria strain compatibility
 and the amount of sulfur dioxide (SO2) a yeast strain produces are
 important considerations for successful MLF. Here, the effects of
 yeast-derived SO2 production on O. oeni survival was investigated in
 laboratory- and pilot-scale co-fermentations in Chardonnay. Further to the
 S. cerevisiae strain affecting O. oeni survival and MLF, we show
 that SO2 production by yeast (to approximately 65 mg/L) can be
 uncoupled from O. oeni survival in early stages of co-fermentation.
 Bacterial survival with certain SO2-producing yeast strains was correlated
 with early, transient formation of a high concentration of
 acetaldehyde.  Upon co-inoculation, an extremely low
 concentration range (approximately 1–44 µg/L) of calculated molecular SO2
 is indicated to regulate O. oeni survival. Possible strain-dependent
 sensitivity of O. oeni to bound SO2 may also occur, although the
 extent and nature of such inhibition by the SO2 adduct itself
 during co-fermentation remains unclear. Choice of co-inoculation yeast
 strain also influenced wine diacetyl concentration, which was only
 detected in wines co-inoculated with high-SO2-producing S. cerevisiae
 strains. These wines also had comparatively high citation frequency for a
 buttery sensory attribute. Both the SO2 and acetaldehyde production
 capacity of yeasts are therefore seen as meaningful co-inoculation
 selection criteria. The range of yeast strains suitable for MLF induction
 by co-inoculation could be widened to include SO2-producing strains which
 transiently produce an early, high concentration of acetaldehyde. Reliance
 on total / bound SO2 concentration may also potentially provide an
 inaccurate measure of SO2 toxicity towards O. oeni, particularly
 for co-inoculation, and the impact of low, equilibrium concentrations of
 molecular SO2 should also be considered.
DOI: 10.5061/dryad.tx95x6b2f
title: Data from: RockNet: Rockfall and earthquake detection and association via multitask learning and transfer learning

description: Seismological data can provide timely information for slope failure hazard
 assessments, among which rockfall waveform identification is challenging
 for its high waveform variations across different events and stations. A
 rockfall waveform does not have typical body waves as earthquakes do, so
 researchers have made enormous efforts to explore characteristic function
 parameters for automatic rockfall waveform detection. With recent advances
 in deep learning, algorithms can learn to automatically map the input data
 to target functions. We develop RockNet via multitask and transfer
 learning; the network consists of a single-station detection model and an
 association model. The former discriminates rockfall and earthquake
 waveforms. The latter determines the local occurrences of rockfall and
 earthquake events by assembling the single-station detection model
 representations with multiple station recordings. RockNet achieves macro
 F1 scores of 0.990 and 0.981 in terms of discriminating earthquakes and
 rockfalls from other events with the single-station detection and
 association models, respectively.
description: The raw seismic waveforms (.sac files) were recorded by the
 Geophones and DATA-CUBE
 (https://digos.eu/wp-content/uploads/2020/11/2020-10-21-Broschure.pdf) and
 converted to `mseed` format with `cub2mseed` command
 (https://digos.eu/CUBE/DATA-CUBE-Download-Data-2017-06.pdf) of the
 CubeTools utility package (https://digos.eu/seismology/). The .tfrecord files are generated using the scripts host on<strong> Github </strong>and a permanent identifier to <strong>Zenodo.</strong>
description: <strong>Please clone the RockNet project on Github (https://github.com/tso1257771/RockNet) and put the downloaded dataset under the cloned directory.</strong> *The SAC software (Seismic Analysis Code, http://ds.iris.edu/ds/nodes/dmc/software/downloads/sac/102-0/) is used to process and visualize SAC files.  *The ObsPy (https://docs.obspy.org/) package is used to process and manipulate SAC files in the python interface.  *The h5py package (https://docs.h5py.org/en/stable/) is used to store seismic data and header information (i.e., metadata, including station and labeled information) in HDF5 (https://hdfgroup.org/) format for broader usages.  *The ObsPy and TensorFlow packages (https://www.tensorflow.org/) are collaboratively used to convert the SAC files into the `TFRecord` format (https://www.tensorflow.org/tutorials/load_data/tfrecord) for TensorFlow applications.
DOI: 10.5061/dryad.kprr4xh81
title: Expert consensus on core topics of sustainable development online learning module for family physicians: A Delphi study

description: Objectives Medical institutions must provide learning experiences that
 enhance the knowledge and perspectives of Sustainable Development (SD) to
 prepare trainees of family medicine to become competent global citizens.
 The aim of this study was to develop an SD online learning module for
 trainees of family medicine. Design This mixed-methods study was conducted
 from January 2020 to May 2021, beginning with a literature review
 concerning Sustainable Development Goals (SDG) and Education for
 Sustainable Development (ESD) in medicine. In-depth interviews were held
 to assess the relevant needs of family medicine training, followed by a
 two-round Delphi survey with experienced educators (n = 21) in family
 medicine to refine and achieve consensus on the appropriate SDG topics for
 family physicians. Setting All residency training programmes in Thailand.
 Participants Members of the Residency Training Committee, Royal College of
 Family Physicians of Thailand. Results The literature review and in-depth
 interviews identified 12 topics of SD that were required for family
 physicians. The first round of the Delphi survey was concluded by
 identifying 7 core topics with additional suggestions. In the second
 round, a consensus was obtained among the experienced educators regarding
 7 core topics: 1) A definition of SD, 2) Principles of SD, 3) SDG, 4) A
 new concept of SD, 5) SD in the context of Thailand, 6) SD and principles
 of family medicine and 7) SD and family practice. These core topics were
 grouped within three main objectives and three sub-modules. Conclusions An
 online learning module of SD for family physicians was developed using a
 modiﬁed Delphi method. This included three sub-modules: 1) Concept and
 principles of SD, 2) SDG and 3) SD and its integration with family
 practice. This online learning module will provide additional resources
 for trainees of family medicine and Thai family physicians to expand their
 knowledge and perspectives of sustainable development.
description: A Delphi method was used to achieve consensus on the core topics
 of a sustainable development learning module for family physicians. In the
 Delphi method, equal weights are given to the opinions of each individual.
 The surveys are blinded to ensure anonymity and several rounds or
 iterations are conducted so that the experts can consider the results of
 previous rounds and change their answers if they wish.
 We modified the Delphi method. We used both questionnaire survey
 and open-ended questions in the first round. All issues emanating from the
 open-ended questions and free-text comments were added to the
 questionnaire in the second round.
DOI: 10.5061/dryad.z8w9ghxgn
title: Toll-like receptor polymorphism in fan mussels

description: The fan mussel Pinna nobilis is currently on the brink of extinction due
 to a multifactorial disease mainly caused to the highly pathogenic
 parasite Haplosporidium pinnae, meaning that the selection pressure
 outweighs the adaptive potential of the species. Hopefully, rare specimens
 have been observed somehow resistant to the parasite, stretching the need
 to identify the traits underlying this better fitness. Among the candidate
 to explore at first intention are fast-evolving immune genes, of which
 toll-like receptor (TLR). In this study, we examined the genetic diversity
 at 14 TLR loci across Pinna nobilis, Pinna rudis and Pinna nobilis x Pinna
 rudis hybrid genomes, collected at four physically distant regions, that
 were found to be either resistant or sensitive to the parasite H. pinnae.
 We report a high genetic diversity, mainly observed at cell surface TLRs
 compared to that of endosomal TLRs. However, the endosomal TLR-7 exhibited
 unexpected level of diversity and haplotype phylogeny. The lack of
 population structure, associated with a high genetic diversity and
 elevated dN/dS ratio, was interpreted as balancing selection, though both
 directional and purifying selection were detected. Interestingly, roughly
 40% of the P. nobilis identified as resistant to H. pinnae were
 introgressed with P. rudis TLR. Specifically, all these P. nobilis carried
 a TLR-7 of P. rudis origin. On the contrary, sensitive P. nobilis were not
 introgressed, at least at TLR loci, highlighting that TLR-7 might be a
 potent effector of resistance. Small contributions of TLR-6 and TLR-4
 single nucleotide polymorphism to the cluster of resistant and sensitive
 groups could be detected, but their specific role in the resistance
 remains highly speculative. This study brings additional knowledge on the
 molecular processes of resistance to H. pinnae and will likely contribute
 to the conservation efforts carried out to prevent from extinction this
 Mediterranean endemic species.
DOI: 10.5061/dryad.8kprr4xs4
title: Dataset for: The empty forest three decades later: Lessons and prospects

description: The “Empty Forest” paradigm published three decades ago inspired studies
 on biodiversity erosion. Evidence to date continues pessimistic regarding
 the fate of wildlife. This calls for a more proactive approach by several
 societal actors to realign systems of resource exploitation with the goals
 of the Convention on Biological Diversity. In late February 2022, we used
 the Scopus search engine separately using the keywords “defaunation” and
 “empty forest” to aggregate the number of scientific publications using
 these terms in the manuscript title, abstract, and keywords. We thus
 analyzed this dataset using descriptive statistics, such as the number of
 published papers, the author’s keywords, and a pictorial synthesis of the
 major effects of defaunation upon ecosystem functioning. Moreover, we
 briefly illustrate a pantropical overview on this topic by mapping
 defaunation trends (e.g. declines in species richness, abundance and
 population biomass) by selecting several key papers — using our extensive
 knowledge of this literature — and a wider geographic or long-term cover
 or large datasets documenting wildlife declines. We further derive
 estimates of proportional declines (richness, abundance, and biomass) by
 averaging (and SD) the major trends stated in these studies.
description: R
DOI: 10.5061/dryad.s4mw6m99g
title: Data from: Denser and greener cities

description: Green spaces in urban areas-- like remnant habitat, parks, constructed
 wetlands, and street trees-- supply multiple benefits. Many studies show
 green spaces in and near urban areas play important roles harboring
 biodiversity and promoting human well-being. On the other hand, evidence
 suggests that greater human population density enables compact, low-carbon
 cities that spare habitat conversion at the fringes of expanding urban
 areas, while also allowing more walkable and livable cities. How then can
 urban areas have abundant green spaces as well as density?   This
 data archive contains data created as part of a scientific manuscript that
 attempts to answer this question, entitled "Denser and greener
 cities: Green interventions to achieve both urban density and
 nature". Please see that manuscript for details on sources of data
 and details of methodology. We found that there is a negative correlation
 between population density and urban green spaces. For Functional Urban
 Areas in the OECD, a doubling of density is associated with a 2.9% decline
 in tree cover. We argue that there are competing tradeoffs between the
 benefits of density for sustainability and the benefits of nature for
 human well-being. Planners must decide an appropriate density by choosing
 where to be on this tradeoff curve, taking into account city-specific
 urban planning goals and context. However, while the negative correlation
 between population density and tree cover is modest at the level of US
 urbanized areas (R2=0.22), it is weak at the US Census block level
 (R2=0.05), showing that there are significant brightspots, neighborhoods
 that manage to have more tree canopy than would be expected based upon
 their level of density. We then describe techniques for how urban planners
 and designers can create more brightspots, identifying a typology of urban
 forms and listing green interventions appropriate for each form. We also
 analyze policies that enable these green interventions illustrating them
 with the case studies of Curitiba and Singapore. We conclude that while
 there are tensions between density and urban green spaces, an urban world
 that is both green and dense is possible, if society chooses to take
 advantage of the available green interventions and create it.
description: Please see the Methods section in McDonald et al. (People and
 Nature) for details on our methods.
description: All data tables are provided as CSV files, which can be read by a
 number of proprietary (e.g., Excel) and open-source (e.g., LibreOffice)
 software packages.
DOI: 10.5061/dryad.gqnk98ssf
title: Invasion tolerance varies along a topographic gradient irrespective of invader presence

description: Invasive exotic plants often impact native plant species through strong
 competition, yet their effects can vary across different native
 populations. Previous exposure to invasive species but also
 differentiation along abiotic gradients may determine to what extent
 native populations are competitively suppressed by plant invasive species.
 Here, we experimentally investigated whether competitive effects of the
 invasive exotic jewelweed Impatiens parviflora on its native congener
 Impatiens noli-tangere are related to previous exposure to the invader or
 rather to topography of the source populations, i.e., to terrain features
 such as elevation, aspect, or slope. We also asked whether, in return,
 topographic settings of invasive I. parviflora populations may explain
 competitive effects of the native jewelweed. In a common garden
 competition experiment we found that populations of native jewelweed from
 colder, higher altitude sites and from drier sites were on average seven
 and six times, respectively, more tolerant to interspecific competition
 than populations from warmer and wetter sites. In contrast, previous
 exposure of native jewelweed populations to the invader was not a
 significant predictor of invader’s competitive effects. Further,
 topographic settings of populations of invasive jewelweed were not
 significantly related to the native’s competitive effects. Our study
 suggests that the native jewelweed’s population differentiation along
 topographic gradients is more important in determining competitive
 interactions with an invasive congener than invasion-induced selection. As
 fine-scale environmental variation can shape adaptation of native species
 to the effects of invasive species, such variation should be considered
 when predicting invasive species’ impact on native plant communities.
DOI: 10.5061/dryad.msbcc2g2q
title: Conservation measures or hotspots of disease transmission? Agri-environment schemes can reduce disease prevalence in pollinator communities

description: Insects are under pressure from agricultural intensification. To protect
 pollinators, conservation measures such as the EU agri-environment schemes
 (AES) promote planting wildflowers along fields. However, this can
 potentially alter disease ecology by serving as transmission hubs or by
 diluting infections. We tested this by measuring plant-pollinator
 interactions and virus infections (DWV-A, DWV-B and ABPV) across
 pollinator communities in agricultural landscapes over a year. AES had a
 direct effect on DWV-B, reducing prevalence and load in honeybees, with a
 tentative general dilution effect on load in early summer. DWV-A
 prevalence was reduced both under AES and with increasing niche overlap
 between competent hosts, likely via a dilution effect. In contrast, AES
 had no impact on ABPV; its prevalence was driven by the proportion of
 bumblebees in the community. Epidemiological differences were also
 reflected in the virus phylogenies, with DWV-B showing recent rapid
 expansion, while DWV-A and ABPV showed slower growth rates and geographic
 population structure. Phylogenies indicate that all three viruses freely
 circulate across their host populations. Our study illustrates how complex
 interactions between environmental, ecological and evolutionary factors
 may influence wildlife disease dynamics. Supporting pollinator nutrition
 can mitigate the transmission of important bee diseases, providing an
 unexpected boost to pollinator conservation.
description: See paper in Philosophical Transactions, Manley et al.
 Conservation measures or hotspots of disease transmission?
 Agri-environment schemes can reduce disease prevalence in pollinator
 communities.
description: R