cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18401566
title: LINF_320014100

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.5x69p8d6f
title: Differential effects of vegetation and climate on termite diversity and damage

description: Species diversity shapes ecosystem services. Despite the advantages that
 this relationship has for pest management, few studies have investigated
 the links between infrastructure damage (i.e. the percentage amount of
 infrastructures infested by termites), species richness and the
 environment. Moreover, it is not clear that which proportion of species
 richness (total/functional-dominant/common/rare) contributes most to
 infrastructure damage. We correlated termite species richness with termite
 infestation throughout 83 cities in Zhejiang Province, eastern China.
 Species were classified according to whether or not they fed on wood, and
 based upon their distributional range, whether they were common or rare.
 We analyzed the relative importance and the direct/indirect effects of
 climate, vegetation, anthropogenic activities, and the species richness of
 four functional categories of termites on the damage levels of eight
 infrastructure types in populated (i.e. urban and rural building, green
 space and sea wall) and remote areas (i.e. ancient building, large-old
 tree, agroforest and reservoir dam). Common species favoured populated
 areas, whereas rare species favoured remote areas. Common species, with
 preferences for deciduous vegetation, caused more damage to the
 infrastructures of populated areas. Rare species, with preferences for
 evergreen vegetation, caused more damage in remote areas. Reforestation
 project which emphasised evergreen trees increased the number of rare
 species but reduced the number of common species. Elevation and drought
 risk were positively correlated with rare species richness but neutrally
 with common species richness. Structural equation models showed that
 vegetation predominantly influenced infrastructure damage in populated
 areas via altering common species richness, whereas climate predominantly
 and directly influenced infrastructure damage in remote areas. Notably,
 elevation and drought risk were positively correlated with infrastructure
 damage especially in remote areas. Synthesis and applications. Termites
 cause global economic losses of 15~40 billion dollars per year. Our study
 reveals that managing city forests and green space, for example increasing
 the proportion of evergreen trees, is a sustainable means of suppressing
 common termites and thereby reducing infrastructure damage in populated
 areas. Conservation strategies, supported by regular inspections, will
 become increasingly important as climate change not only threatens the
 survival of less harmful rare species, but also increases
 infrastructure damage in remote areas.
description: This dataset was compiled from literatures, books and existing
 databases (e.g. climate and vegetation data).
DOI: 10.7291/d1968h
title: Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription

description: Fluctuations in the initiation rate of transcription, the first step in
 gene expression, ensue from the stochastic behavior of the molecular
 process that controls transcription. In steady state, the regulatory
 process is often assumed to operate reversibly, i.e., in equilibrium.
 However, reversibility imposes fundamental limits to information
 processing. For instance, on the assumption of equilibrium, it is
 difficult to explain the precision with which the process executes its
 task in eukaryotes. Here we provide evidence -- from microscopic analyses
 of the transcription dynamics at a single gene copy of yeast -- that the
 regulatory process for transcription is cyclic and irreversible (out of
 equilibrium). The necessary coupling to reservoirs of free energy occurs
 via sequence-specific transcriptional activators and the recruitment, in
 part, of ATP-dependent chromatin remodelers. Our findings may help
 explainhow eukaryotic cells reconcile the dual but opposing requirements
 for fast regulatory kinetics and high regulatory specificity.
description: Raw MFM microscopy images have been sliced and registered
 according to z position into an image stack. Subsequently, a maximum
 intensity projection and background subtraction was completed using a
 darkfield image. Puncta were detected, intensities quantified and
 molecular traces were obtained. These traces are captured in this dataset.
 In addition, "on" and "off" states were assigned to
 each frame in each trace. These binerized traces are also
 present. 
description: Hinrich Boeger, Corrosponding author. hboerger@ucsc.edu.
DOI: 10.5061/dryad.kh189328s
title: Microsatellite profile of Plasmopara viticola isolates collected in Italy

description: Downy mildew, caused by the oomycete Plasmopara viticola, is one of the
 most serious threat to viticulture. P. viticola is native to North America
 and causes the most severe damages to the Eurasian grapevine, Vitis
 vinifera. In this work, we investigated the genetic structure of the
 pathogen in Italy by collecting 96 P. viticola strains in twelve different
 regions. Based on microsatellite characterization (19 microsatellites), we
 confirmed that the Italian population of P. viticola is composed of two
 separate subpopulations and determined that these two cluster differ for
 geographic and climatic conditions. These populations could have been
 originated from the introduction of two separate populations or, more
 likely, from the evolution of the original population that reached Europe
 at the end of the XIX century. The pathogen showed a great evolutionary
 potential, as highlighted by the regular occurrence of sexual
 reproduction, panmictic structure within cluster and absence of clones.
 These results confirm that the P. viticola has a strong potential for
 adaptation and suggest the integration of all the tools (genetic,
 agronomic and chemical) for achieving a proper disease management.
description: In this file, you can find
 information on the origin of the 96 strains analysed and their
 microsatellite profiles (19 microsatellites). Detailed information on the
 isolate and their characterization are provided in the paper
 (https://doi.org/10.1111/aab.12567). Briefly, the 96 isolates analysed in
 this study were collected from 96 different vineyards located in twelve
 different Italian regions. The isolates, derived from single lesions on a
 randomly chosen leaf, were maintained in the culture collection of the
 Department of Agricultural and Environmental Sciences (DiSAA, University
 of Milan, Italy). Following DNA extraction, the isolates were genotyped 
 at INRA Centre de Bordeaux-Aquitaine, UMR Santé et Agroécologie du
 Vignoble, France with 31 microsatellites but only the results of 19 of
 them (PV14, ISA, PV17, PV39, PV31, PV16, PV91, PV147, PV148, PV93, PV141,
 PV65, PV104, PV88, PV83, PV142, PV139, PV127, PV101) were retained due to
 missing data problems. The software GENEMAPPER 4.0 (Applied Biosystems)
 was used to analyse the chromatograms and record the allele sizes in
 bp.   
description: The dataset consists of a csv format file that can be opened with
 excel, where the isolate N, geographic origin, grapevine variety, cluster
 and length of the 19 microsatellite markers are reported.
DOI: 10.5061/dryad.zs7h44jd0
title: Freshwater connectivity transforms spatially integrated signals of biodiversity

description: Aquatic ecosystems offer a continuum of water flow from headwater streams
 to inland lakes and coastal marine systems. This spatial connectivity
 influences the structure, function and dynamics of aquatic communities,
 which are among the most threatened and degraded on earth. Here, we
 determine the spatial resolution of eDNA in dendritic freshwater networks,
 which we use as a model for connected metacommunities. Our intensive
 sampling campaign comprised over 430 eDNA samples across 21 connected
 lakes, allowing us to analyse detections at a variety of scales, from
 different habitats within a lake to entire lake networks. We found strong
 signals of within-lake variation in eDNA distribution reflective of
 typical habitat use by both fish and zooplankton. Most importantly, we
 also found that connecting channels between lakes resulted in an
 accumulation of downstream eDNA detections in lakes with a higher number
 of inflows, and as networks increased in length. Environmental DNA
 achieves biodiversity surveys in these habitats in a high-throughput,
 spatially integrated way. These findings have profound implications for
 the interpretation of eDNA detections in aquatic ecosystems in
 global-scale biodiversity monitoring observations.
description: Raw sequence files are .gz format; can be opened with WinZip or
 similar. R and R studio for opening statistical
 analysis scripts
description: 23/08/2022 Dr Joanne Littlefair, Queen Mary University of London Further
 edits to describe statistical analysis on 12/09/2023 This README file
 relates to the manuscript "Freshwater connectivity transforms
 spatially integrated signals of biodiversity" by. Joanne E.
 Littlefair, José S. Hleap, Vince Palace, Michael D. Rennie, Michael J.
 Paterson, Melania E. Cristescu See README.txt file.
DOI: 10.5061/dryad.r2280gbgj
title: Mass spectrometric data for chaperone-ligand interactions

description: The assembly of proteins and peptides into amyloid fibrils is causally
 linked to serious disorders such as Alzheimer’s Disease. Multiple proteins
 have been shown to prevent amyloid formation in
 vitro and in vivo, ranging from highly specific
 chaperone-client pairs to completely non-specific binding of
 aggregation-prone peptides. The underlying interactions remain elusive.
 Here, we turn to the machine learning-based structure prediction algorithm
 AlphaFold2 (AF2) to obtain models for the non-specific interactions
 of b-lactoglobulin (bLG), transthyretin (TTR), or Thioredoxin 80
 (T80) with the model amyloid peptide Amyloid b (Ab), and
 the highly specific complex between the BRICHOS chaperone domain of lung
 surfactant protein C (CTC) and its polyvaline target. Using a combination
 of native mass spectrometry (MS) and ion mobility MS, we show that
 non-specific chaperoning is driven predominantly by hydrophobic
 interactions of Ab with hydrophobic surfaces in bLG,
 TTR, and T80, and in part regulated by oligomer stability. For CTC, native
 MS and hydrogen-deuterium exchange MS reveal that a disordered region
 recognizes the polyvaline target by forming a
 complementary b-strand. Hence, we show that AF2 and MS can yield
 atomistic models of hard-to-capture protein interactions that reveal
 different chaperoning mechanisms based on separate ligand properties and
 may provide possible clues for specific therapeutic intervention.
description: The dataset contains two folders: IMMS data in
 PULSAR file format, which can be analyzed using the freely available
 PULSAR software package http://pulsar.chem.ox.ac.uk/download.html HDX-MS data in .txt format, which can be analyzed using the freely available mMAss software package http://www.mmass.org
DOI: 10.15468/dl.ydgfcy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Penardochlamys",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003251-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.jsxksn0d1
title: Population structure and demographic history of the gastropod Thaisella chocolata (Duclos, 1832) from the Southeast Pacific inferred from mitochondrial DNA analyses

description: The present-day population structure of a species reflects the combination
 of oceanographic currents, life-history traits, and historical events.
 However, little is known about the mechanisms that have shaped the gene
 lineage distribution of marine species inhabiting the Southeast Pacific.
 Here we provide a comprehensive phylogeographical study of a species
 distributed along the Southeast Pacific coastal region by analyzing the
 endemic gastropod Thaisella chocolata (Duclos, 1832). Sequencing of
 mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S rRNA revealed
 strikingly high haplotypic nucleotide and genetic diversity but a lack of
 significant population differentiation within the survey area. In
 addition, a star-shaped phylogeny and significantly negative Tajima’s D
 and Fu’s Fs tests of neutrality suggested historical occurrence of rapid
 demographic expansion. Mismatch distributions and Bayesian inference
 analyses also confirmed T. chocolata to have undergone two ancestral
 demographic expansions. Calculations suggested that these expansions began
 in the lower and middle Pleistocene epoch, likely due to continental shelf
 development and climatic conditions. These findings could help establish a
 genetic baseline for T. chocolata as the first step toward sustainable
 spatial management of this species, as well as understand this species’
 response to future climate change.
description: The genomic datasets can be opened with any program that opens
 fasta files
DOI: 10.5061/dryad.h44j0zpp8
title: Data from: Visual and motor signatures of locomotion dynamically shape a population code for feature detection in Drosophila

description: Natural vision is dynamic: as an animal moves, its visual input changes
 dramatically. How can the visual system reliably extract local features
 from an input dominated by self-generated signals? In Drosophila, diverse
 local visual features are represented by a group of projection neurons
 with distinct tuning properties. Here we describe a connectome-based
 volumetric imaging strategy to measure visually evoked neural activity
 across this population. We show that local visual features are jointly
 represented across the population, and that a shared gain factor improves
 trial-to-trial coding fidelity. A subset of these neurons, tuned to small
 objects, is modulated by two independent signals associated with
 self-movement, a motor-related signal and a visual motion signal. These
 two inputs adjust the sensitivity of these feature detectors across the
 locomotor cycle, selectively reducing their gain during saccades and
 restoring it during intersaccadic intervals. This work reveals a strategy
 for reliable feature detection during locomotion. This dataset contains
 GCaMP6f and syt1GCaMP6f calcium responses from identified optic glomeruli
 in the Drosophila central brain, as well as walking behavior tracking
 data. It accompanies the manuscript Visual and motor signatures of
 locomotion dynamically shape a population code for feature detection in
 Drosophila, by MH Turner et al.
description: Visually evoked responses from optic glomeruli were extracted
 using the pan-glomerulus imaging and alignment approach described in
 <em>Visual and motor signatures of locomotion dynamically shape a
 population code for feature detection in Drosophila</em>, by MH
 Turner et al. Briefly, raw imaging data were motion corrected and aligned
 to a connectome-based map of optic glomeruli in the central brain.
 Fluorescence signals from the corresponding voxels for each optic
 glomerulus were averaged to produce the optic glomerulus response trace.
 These response traces are included in .hdf5 datafiles that are accompanied
 by animal, experimental and stimulus metadata as well as stimulus timing
 information requried to align visual stimuli with fluorescence
 traces.
description: The main analysis, modeling and figure generation code, which
 produced and can interact with the datafiles included in this dataset, can
 be found here. You
 may also interact with the .hdf5 datafiles using general purpose hdf5
 tools like HDFView.
DOI: 10.5061/dryad.cvdncjt71
title: Fluorescence spectra presenting kinetic photodegradation of ciprofloxacin and levofloxacin

description: First derivative synchronous fluorescence spectroscopy (FDSFS) was applied
 to detect and quantify ciprofloxacin (CIP) and levofloxacin (LEV)
 simultaneously with their photodegradation products, where the photolytic
 pathway for each analyte was found to be pH dependant. Under the guidance
 of early published articles, the structure of the produced photolytic
 products could be concluded, and further related to their resultant
 fluorescence spectra. The proposed method was subjected to a full
 validation procedure which enables its application in investigating the
 photodegradation kinetics for both drugs. The obtained kinetic parameters
 were in accordance with previous reports and could be linked to predict
 the antibacterial activity of the resultant photodegradation products.
 These facts prove the suitability of the suggested FDSFS to serve as a
 stability-indicating assay method and to trace the photofate of CIP and
 LEV in the ecosystem as potential contaminants. Furthermore, the greenness
 of the suggested analytical methodology was evaluated via the ˝ Green
 Analytical Procedure Index˝ (GAPI), which classifies it as an eco-friendly
 assay. Eventually, no extraction, treatment, or preparation steps were
 needed during all analysis steps, which renders the proposed assay an
 appealing tool in environmental analysis.  
description: Fluorescence spectra were recorded, the readings were collected
 and statistically analyzed.
DOI: 10.5061/dryad.cfxpnvx8f
title: Testing the assumption of environmental equilibrium in an invasive plant species over a 130 year history

description: Invasive plants are an increasing threat to global biodiversity. Effective
 management depends on accurate predictions of their spread. However,
 modelling the geographic distribution of invasive species, particularly
 with correlative species distribution models (SDMs), is challenging. SDMs
 assume that species are in equilibrium with their environment (i.e., they
 occur in all suitable environments); this assumption is likely to be
 violated for a species that is actively invading new environments. This
 assumption is rarely assessed, and when violated can have consequences for
 model reliability. Using the invasive vine Vincetoxicum rossicum, we
 tested the hypotheses that: 1) invasive species’ distribution in
 environmental and geographic space increase to a plateau over time; 2)
 this plateau is a useful proxy for equilibrium distribution, a key
 assumption underlying SDMs. We compare V. rossicum’s expansion in
 environmental and geographic space between historical and current time
 periods and infer equilibrium when its distribution has remained stable
 for an extended period. We also compare the performance of SDMs from
 historical time periods in predicting the current geographic distribution
 of V. rossicum. We found that V. rossicum has reached equilibrium in
 environmental space, but is still expanding its geographic distribution.
 SDM performance was poor in the first 30 years following introduction, but
 improved as V. rossicum approached environmental equilibrium. Our findings
 demonstrate the power of including temporal dynamics and the need to
 consider environmental and geographic equilibrium separately when
 modelling the distribution of invasive species. In light of our findings,
 we address shortcomings of the current approach to defining an equilibrium
 distribution and present a new perspective for reconciling the potentially
 confounding influence of dispersal limitation when assessing equilibrium
 distribution.
DOI: 10.5061/dryad.3ffbg79n1
title: Open-population SCR model to estimate spatiotemporal variation in individual birth locations, detection rates, and survival

description: This is an open population SCR model developed by R. Chandler and K.
 Engebretsen. The full model incorporates 4 spatial covariates in birth
 location density submodel, 3 location-specific, temporal
 covariates in the detection submodel, and 4 spatial covariates in
 the survival submodel.  Formatted data is provided for the 2015
 and 2016 fawning season in south Florida and the model can be fit using
 the script fitFawnModel.R.
description: 180 passive trail cameras were deployed during 2015 and 2016 in
 South Florida to collect images of spotted white-tailed deer fawns.
 Individuals were identified by spot patterns, and capture histories were
 made for each individual fawn. Water depth values were extracted from
 hydrologic depth gauges (Everglades Depth Estimation Network). Landcover
 was derived from Florida Natural Areas Inventory Cooperative Land Cover
 (FNAI CLC) 3.2 site-level data at 10m resolution and reclassified into
 four categories. Trail status was binary, indicating if a camera was
 on-trail or off-trail. Human activity was derived from the number of
 photos of humans taken by each camera on each day. 
 These data and covariates were formatted and packaged within the
 "formattedData_2015.RData" and
 "formattedData_2016.RData" objects. These objects contain all
 the data and covariates needed to fit the models using the script
 "fitFawnModel.R". 
description: Program R is required to open these files and run the model.
DOI: 10.5061/dryad.f4qrfj6zz
title: Quantitative and qualitative methods complementing: Bridging modelling and policy-making efforts to realise the European bioeconomy

description: The European Bioeconomy Strategy aims to facilitate the transition from a
 take-make-dispose fossil economy into one fostering circular bio-based
 value chains linking sustainable land use with cutting-edge products.
 Optimised designs, implementation and monitoring rely on continuous
 interactions between policymakers and modellers who run multiple scenarios
 for environmentally, economically and socially desirable futures.
 "Bridging modelling and policy-making efforts to realise the European
 bioeconomy" leverages a multi-layered framework that cross-references
 39 policies and 32 models to assess how they address the five principle
 objectives of the Bioeconomy Strategy in terms of accompanying sectors,
 value-chains, and multi-dimensional indicators. The framework identifies
 gaps in bioeconomy knowledge both in policy and modelling. The analysis
 stemming from this framework matching policies and models based on their
 scope and aim, and reviewing how each addresses bioeconomy objectives,
 sectors, value chain stages and indicators, was built using mixed methods.
 The files complement the Supplementary Files of "Bridging modelling
 and policy-making efforts to realise the European bioeconomy" to
 produce a comprehensive compendium of the key findings extracted from the
 main publication.
DOI: 10.15468/dl.7rsj97
title: Occurrence Download

description: A dataset containing 711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Duparquetia orchidacea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 711 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003252-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jh9w0vtfc
title: Terrain- and climate-based habitat suitability indices for the reef-building coral Lophelia pertusa on the Blake Plateau (southeastern United States)

description: Habitat suitability model outputs from Gasbarro et al. (2022) covering the
 Blake Plateau region of the southeastern United States margin. These
 include raster surfaces of ensemble mean, median, and standard deviation
 habitat suitability indices. Bathymetry-derived terrain variables were
 used to generate the terrain suitability layers, while climate model
 outputs were used to generate the climatic suitability layers. Rasters are
 in WGS84. See Gasbarro et al. (2022) for full modeling details.
DOI: 10.18112/openneuro.ds007327.v1.0.2
title: Basketball Motor Observation and Motor Imagery EEG Dataset