cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31165111
title: <b>Road style simulator: Graph-based representation for </b><b>different styles of road models</b>

description: Here are all the decal assets from Unreal Engine 5.2 used in our experimental process. Readers only need to copy them into the <b>Content </b>directory of the created UE project to use them.<br>
DOI: 10.6084/m9.figshare.31165111.v1
title: <b>Road style simulator: Graph-based representation for </b><b>different styles of road models</b>

description: Here are all the decal assets from Unreal Engine 5.2 used in our experimental process. Readers only need to copy them into the <b>Content </b>directory of the created UE project to use them.<br>
DOI: 10.15468/dl.4t69dw
title: Occurrence Download

description: A dataset containing 655367 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Madagascar",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 655367 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002711-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6wwpzgmxj
title: High spatial resolution mapping identifies habitat characteristics of the invasive vine Antigonon leptopus on St. Eustatius (Lesser Antilles)

description: On the Caribbean island of St. Eustatius, Coralita (Antigonon leptopus) is
 an aggressive invasive vine posing major biodiversity conservation
 concerns.  The generation of distribution maps can address these
 conservation concerns by helping to elucidate the drivers of invasion. We
 test the use of support vector machines to map the distribution of
 Coralita on St. Eustatius at high spatial resolution and use this map to
 identify potential landscape and geomorphological factors associated with
 Coralita presence. This latter step was performed by comparing
 the actual distribution of Coralita patches to a random distribution of
 patches. To train the support vector machine algorithm, we used three
 vegetation indices and seven texture metrics derived from a 2014
 WorldView-2 image. The resulting map shows that Coralita covered 3.18% of
 the island in 2014, corresponding to an area of 64 ha. The mapped
 distribution was highly accurate, with 93.2% overall accuracy (Coralita
 class producer’s accuracy: 76.4%, user’s accuracy: 86.2%). Using this
 classification map, we found that Coralita is not randomly distributed
 across the landscape, occurring significantly closer to roads and drainage
 channels, in areas with higher accumulated moisture, and on flatter
 slopes. Coralita was found more often than expected in grasslands,
 disturbed forest and urban areas, but was relatively rare in natural
 forest. These results highlight the ability of high spatial resolution
 data from sensors such as WorldView-2 to produce accurate invasive
 species, providing valuable information for predicting current and future
 spread risks and for early detection and removal plans.
description: A field survey was conducted in July 2015 to collect
 ground-truthing data to allow for image classification, resulting in a
 distribution map of the invasive species Antigonon leptopus (referred to
 as 'Coralita'). On the Caribbean island of St. Eustatius. The
 resulting distribution of the species on the island comprised 1,852
 patches; from each patch, a random location was selected, and additional
 landscape attributes were calculated for this locations. These
 characteristics, for all the 1,852 'Coralita' locations, were
 then compared to characteristics of 1,852 non-Coralita locations, selected
 randomly on the island of St. Eustatius. The .zip folder contains .txt
 files containing the land mass and Coralita distribution at 2 m
 resolution, and the landscape attributes for the 3,704 (i.e. 2*1,852)
 locations. 
description: Please see the readme file in the .zip folder.
DOI: 10.5061/dryad.nk98sf7sh
title: Data for: Local contributions to beta-diversity in urban pond networks: implications for biodiversity conservation and management

description: Aim: An understanding of how biotic communities are spatially organised is
 necessary to identify and prioritize habitats within landscape-scale
 biodiversity conservation. Local Contribution to Beta diversity (LCBD)
 identifies individual habitats that make a significant contribution to
 beta-diversity and may have important practical implications, particularly
 for conservation of habitat networks. In this study, we develop and apply
 a conservation prioritisation approach based on LCBD in aquatic
 invertebrate communities from 132 ponds. Location: Five urban settlements
 in the UK: Halton, Loughborough, Stockport, Birmingham, Huddersfield.
 Methods: We partition LCBD into richness difference (nestedness:
 RichDiffLCBD) and species replacement (turnover: ReplLCBD) and identify
 key environmental variables driving LCBD. We examine LCBD at two scales
 relevant to conservation planning: within urban settlements and nationally
 across the UK. Results: Significant differences in LCBD values were
 recorded among the five settlements. In four of the five urban settlements
 studied, pond sites with the greatest LCBD values typically showed high
 replacement values. Significant LCBD sites and sites with high taxonomic
 diversity together supported more of the regional species pool (70%-97%)
 than sites with high taxonomic diversity alone (54% to 94%) or what could
 be protected by the random selection of sites. LCBD was significantly
 associated with vegetation shading, surface area, altitude and macrophyte
 cover. Main conclusions: Conservation prioritisation that incorporates
 LCBD and sites with high taxonomic diversity improves the effectiveness of
 conservation actions within pond habitat networks, ensures site supporting
 high biodiversity are protected, and provides a method to define a spatial
 network of protected sites. Identifying new, effective conservation
 approaches, particularly in urban areas where resources may be scarce and
 conflicts regarding land use exist, is essential to ensure biodiversity is
 fully supported and detrimental anthropogenic effects are reduced.
DOI: 10.5061/dryad.sbcc2fr5r
title: Inbreeding depression in artificial selection lines of Ipomoea purpurea

description: Inbreeding depression is a central parameter underlying mating system
 variation in nature and one that can be altered by environmental stress.
 Although a variety of systems show that inbreeding depression tends to
 increase under stressful conditions, we have very little understanding
 across most organisms how the level of inbreeding depression may change as
 a result of adaptation to stressors. In this work we examined the
 potential that inbreeding depression varied among lineages of Ipomoea
 purpurea artificially evolved to exhibit divergent levels of herbicide
 resistance. We examined inbreeding depression in a variety of
 fitness-related traits in both the growth chamber and in the field, paired
 with an examination of gene expression changes. We found that, while
 inbreeding depression was present across many of the traits, lineages
 artificially selected for increased herbicide resistance often showed no
 evidence of inbreeding depression in the presence of herbicide, and in
 fact, showed evidence of outbreeding depression in some traits compared to
 non-selected control lines and lineages selected for increased herbicide
 susceptibility. Further, at the transcriptome level, the resistant
 selection lines had differing patterns of gene expression according to
 breeding type (inbred vs outcrossed) compared to the control and
 susceptible selection lines. Our data together indicate that inbreeding
 depression may be lessened in populations that are adapting to regimes of
 strong selection.
description: Plants were artificially selected for increased or decreased
 resistance (resistant and susceptible lines, respectively) to herbicide;
 control line was randomly mated. After 2 generations of selection, seeds
 were created by either outcrossing (within the line) or selfing. These
 plants were assayed to determine inbreeding depression in a variety of
 traits. Survival and biomass post-herbicide was collected from plants
 grown in growth chamber with varying levels of herbicide. Reproductive
 trait data was collected from field plants, either sprayed or not sprayed
 with herbicide. For a subset of those field-grown plants, transcriptomic
 response was measured at 8 and 32 hours post herbicide spray.
DOI: 10.5061/dryad.b2rbnzsdf
title: Kinematics and EMG to show integration of proprioceptive and visual feedback during online control of reaching

description: Visual and proprioceptive feedback both contribute to optimal perceptual
 decisions, but it remains unknown how these feedback signals are
 integrated together or consider factors such as delays and variance during
 online control. We investigated this question by having participants reach
 to a target with randomly applied mechanical and/or visual disturbances.
 We observed that the presence of visual feedback during a mechanical
 disturbance did not increase the size of the muscle response significantly
 but did decrease variance, consistent with a dynamic Bayesian integration
 model (Experiment 1). In a control experiment we verified that vision had
 a potent influence when mechanical and visual disturbances were both
 present but opposite in sign (Experiment 2). These results highlight a
 complex process for multi-sensory integration, where visual feedback has a
 relatively modest influence when the limb is mechanically disturbed, but a
 substantial influence when visual feedback becomes misaligned with the
 limb. The dataset contains hand kinematics and EMG data recorded
 during each experiment, and information of
 visual/mechanical disturbances that were applied during the
 experiments.
description: The dataset was collected by Kinarm Exoskeleton Lab (Kinarm,
 Kingston ON). The data has been processd by Matlab 2018a (Mathworks Inc.
 Natick MA, USA) for raw data processing, analysis on intermediate files,
 figure creation and statistics.
description: Please refer "Code descriptions Exp*.docx" and
 "Data descriptions Exp*.docx" for more information of analysis
 codes and datasets.
DOI: 10.5061/dryad.9p8cz8wfh
title: Oocyst counts from naturally infected mosquitoes collected in Burkina Faso

description: The population dynamics of human to mosquito malaria transmission in the
 field has important implica- tions for the genetics, epidemiology and
 control of malaria. The number of oocysts in oocyst-positive mosquitoes
 developing from a single, naturally acquired infectious blood meal (herein
 referred to as a single-feed infection load) greatly influences the
 efficacy of transmission blocking interventions but still remains poorly
 documented. During a year-long analysis of malaria parasite transmission
 in Burkina Faso we caught and dissected wild malaria vectors to
 assess Plasmodium oocyst prevalence and load (the number
 of oocysts counted in mosquitoes with detectable oocysts) and the
 prevalence of salivary gland sporozoites. This was compared with malaria
 endemicity in the human population, assessed in cross-sectional surveys.
 Data were analysed using a novel transmission mathematical model to
 estimate the per bite transmission probability and the average single-feed
 infection load for each location. The observed oocyst load and the
 estimated single-feed infection load in naturally infected mosquitoes were
 substantially higher than previous estimates (means ranging from 3.2 to
 24.5 according to seasons and locations) and indicate a strong positive
 association between the single-feed infection load and parasite prevalence
 in humans. This work suggests that highly infected mosquitoes are not rare
 in the field and might have a greater influence on the epidemiology and
 genetics of the parasite, and on the efficacy of novel transmission
 blocking interventions.
description: During a year-long analysis of malaria parasite transmission in
 Burkina Faso, wild malaria vectors were caught and dissected to assess
 Plasmodium oocyst prevalence and load (the number of oocysts counted in
 mosquitoes with detectable oocysts). 
description: The R script attached allows the user to extract the oocyst
 counts observed in each location (Klesso & Longo). Specifically
 the counts for 'normal' (rather than 'broken') were
 used in this analysis. As well as the primary analysis described above,
 the data were also used in the following, forthcoming study (submitted to
 Nature Communications): <strong>Predicting the
 public health impact of a malaria transmission-blocking
 vaccine</strong> by Joseph D. Challenger, Daniela Olivera Mesa, Dari
 F. Da, R. Serge Yerbanga, Thierry Lefèvre, Anna Cohuet, Thomas S. Churcher
 [2021]. Correspondance relating to this analysis of the data should be
 addressed to: j.challenger@imperial.ac.uk
DOI: 10.5061/dryad.fn2z34tsp
title: Natural variation in colony inbreeding does not influence susceptibility to a fungal pathogen in a termite

description: Reduced genetic diversity through inbreeding can negatively affect
 pathogen resistance. This relationship becomes more complicated in social
 species, such as social insects, since the chance of disease transmission
 increases with the frequency of interactions among individuals. However,
 social insects may benefit from social immunity, whereby individual
 physiological defenses may be bolstered by collective-level immune
 responses, such as grooming or sharing of antimicrobial substance through
 trophallaxis. We set out to determine whether differences in genetic
 diversity between colonies of the subterranean termite, Reticulitermes
 flavipes, accounts for colony survival against pathogens. We sampled
 colonies throughout the US (Texas, North Carolina, Maryland, and
 Massachusetts) and determined the level of inbreeding of each colony. To
 assess whether genetically diverse colonies were better able to survive
 exposure to diverse pathogens, we challenged groups of termite workers
 with two strains of a pathogenic fungus, one local strain present in the
 soil surrounding sampled colonies and another naïve strain, collected
 outside the range of this species. We found natural variation in the level
 of inbreeding between colonies, but this variation did not explain
 differences in susceptibility to either pathogen. Although the naïve
 strain was found to be more hazardous than the local strain, colony
 resistance was correlated between two strains, meaning that colonies had
 either relatively high or low susceptibility to both strains regardless of
 their inbreeding coefficient. Overall, our findings may reflect
 differential virulence between the strains, immune priming of the colonies
 via prior exposure to the local strain, or a coevolved resistance toward
 this strain. They also suggest that colony survival may rely more upon
 additional factors, such as different behavioral response thresholds or
 the influence of a specific genetic background, rather than the overall
 genetic diversity of the colony.
description: Each colony of Reticulitermes flavipes was exposed to different
 treatments; Exposure to a local (T2) and a naive (T3) pathogens, and
 expose to a control solution (T1). The survival of each group of 24
 termites was record for a 20 day period. The sampling sites and states are
 also indicated for each colony.
DOI: 10.5061/dryad.2jm63xsnq
title: The hidden influence of communities in collaborative funding of clinical science

description: Every year the National Institutes of Health allocates $10.7 billion
 (one-third of its funds) for clinical science research while the
 pharmaceutical companies spend $52.9 billion (90% of its annual budget).
 However, we know little about funder collaborations and the impact of
 collaboratively funded projects. As an initial effort towards this, we
 examine the cofunding network, where a funder represents a node and an
 edge signifies collaboration. Our core data include all papers that cite
 and receive citations by the Cochrane Database of Systemic Reviews, a
 prominent clinical review journal. We find that 65% of clinical papers
 have multiple funders and discover communities of funders that are formed
 by national boundaries and funding objectives. To quantify success in
 funding, we use a g-index metric that indicates efficiency of funders in
 supporting clinically relevant research. After controlling for authorship,
 we find that funders generally achieve higher success when collaborating
 than when solofunding. We also find that as a funder, seeking multiple,
 direct connections with various disconnected funders may be more
 beneficial than being part of a densely interconnected network of
 co-funders. The results of this paper indicate that collaborations can
 potentially accelerate innovation, not only among authors but also
 funders.
description: The data was collected from https://app.dimensions.ai/.
 We first extracted all publications from the Cochrane Database of
 Systemic Reviews journal. Then we got all the papers that cite this
 journal and all the papers cited by this journal. This gives us an entire
 corpus of ~700k clinical science papers.  Accompanied
 with these papers is funding information. This only includes a subset of
 ~160k papers and 1761 funding organizations. After this, we filter funders
 who have funded at least 25 papers, which gives data of 653 funders
 from 143904 papers. Then, we use this data to create
 the co-funding network, where a node is a funder and a link indicates
 collaboration on a project. The constructed network is of 653 nodes and
 26165 edges, with an average degree of 80.13 - we publicly release this
 network along with the paper. This is the primary source of analysis of
 our work. Additionally, for ego-network and heterophily
 analysis, we further filter this network to indicate strong collaborative
 ties. To do this, we remove edges that have less than 10 papers together.
 Beyond this, we observe a network of 512 nodes and 3312 edges with an
 average degree of 12.93 - we also publicly release this constructed data
 for further analysis.
description: The publication data can be accessed using the Dimensions portal
 using appropriate credentials. We are unable to release the entire
 publication corpus without prior permission.
DOI: 10.5061/dryad.fttdz08rs
title: Biomechanics of the human thumb and the evolution of dexterity

description: Systematic tool production and use is one of humanity’s defining
 characteristics, possibly originating as early as &gt;3 million years
 ago.​1–3​ Although heightened manual dexterity is considered to be
 intrinsically intertwined with tool use and manufacture, and critical for
 human evolution, its role in the emergence of early culture remains
 unclear. Most previous research on this question exclusively relied on
 direct morphological comparisons between early hominin and modern human
 skeletal elements, assuming that the degree of a species’ dexterity
 depends on its similarity with the modern human form. Here, we develop a
 new approach to investigate the efficiency of thumb opposition, a
 fundamental component of manual dexterity, in several species of fossil
 hominins. Our work for the first time takes into account soft tissue as
 well as bone anatomy, integrating virtual modeling of musculus opponens
 pollicis and its interaction with three-dimensional bone shape form.
 Results indicate that a fundamental aspect of efficient thumb opposition
 appeared approximately 2 million years ago, possibly associated with our
 own genus Homo, and did not characterize Australopithecus, the earliest
 proposed stone tool maker. This was true also of the late Australopithecus
 species, Australopithecus sediba, previously found to exhibit human-like
 thumb proportions. In contrast, later Homo species, including the
 small-brained H. naledi, show high levels of thumb opposition
 dexterity, highlighting the increasing importance of cultural processes
 and manual dexterity in later human evolution.
description: Trapezio-metacarpal joint torque calculations were generated
 through virtual biomechanical modeling (see Karakostis et al., 2021).
 Three-dimensional shape variables were generated based on landmark-based
 geometric morphometrics.
DOI: 10.25338/b8fk8d
title: Using Molecular Dynamics Simulations to Interrogate T Cell Receptor Non-Equilibrium Kinetics

description: Prinicipal component analysis was performed on TCR-pMHC steered molecular
 dynamics simulation trajectories. These supplementary videos include
 rendered videos of those trajectories (named:
 mutant_equilibrationtime_pull.mp4), principal component trajectories
 (named: mutant_equilibrationtime_pcx.mp4), and the control trajectory with
 pull from termini (named: termini_control.mp4). These are template names
 for the video trajectories (refer to README file for more details). Note,
 mutants refer to the in silico mutations made to the TCR-pMHC protein
 structures and are abbreviated L1, MART1, and GVA, respectively. In
 addition, the starting configurations for all pull simulations have been
 provided free of charge.
DOI: 10.5061/dryad.15dv41nwj
title: Mimicry in motion and morphology: do information limitation, trade-offs or compensation relax selection for mimetic accuracy?

description: Many animals mimic dangerous or undesirable prey as a defence from
 predators. We would expect predators to reliably and exclusively avoid
 animals that closely resemble dangerous prey, yet imperfect mimics are
 common. There have been many hypotheses suggested to explain imperfect
 mimicry, but comparative tests across multiple mimicry systems are needed
 to determine which are applicable, and which—if any—represent general
 principles of imperfect mimicry. We tested four hypotheses on Australian
 ant mimics and found support for only one of them: the information
 limitation hypothesis. A predator with incomplete information will be
 unable to discriminate some poor mimics from their models. We also show
 that since predators must make decisions while they are learning, they are
 likely to never sample broadly enough to gain and utilise the full
 information needed to discriminate poor mimics from their models. We found
 no evidence that one accurate mimetic trait can compensate for another, or
 that rapid movement reduces selection pressure for good mimicry. Based on
 our results, we argue that information limitation is likely to be a
 general principle behind imperfect mimicry of any complex traits, while
 interactions between components of mimicry may apply to some mimicry
 systems but not others.
description: This data set is a zip file containing both data and code (R
 scripts). Data include videos of walking arthropods, from which
 trajectories are extracted, and outlines derived from still photographs,
 which are used to analyse body shape. The R scripts are used to process
 and analyse the data. The data set contains README.md and README.txt files
 that describe the structure of the data set in more detail.
description: The data set contains README.md and README.txt files that
 describe the data set.