cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9s4mw6mdh
title: Data from: Diabetes mellitus, glycemic traits, and cerebrovascular disease: A Mendelian randomization study

description: Objective: We employed Mendelian randomization (MR) to explore
 the effects of genetic predisposition to type 2 diabetes (T2D),
 hyperglycemia, insulin resistance, and β-cell dysfunction on risk
 of stroke subtypes and related cerebrovascular phenotypes.
 Methods: We selected instruments for genetic predisposition to
 T2D (74,124 cases, 824,006 controls), HbA1c levels (n=421,923), fasting
 glucose levels (n=133,010), insulin resistance (n=108,557),
 and β-cell dysfunction (n=16,378) based on published genome-wide
 association studies. Applying two-sample MR, we examined associations with
 ischemic stroke (60,341 cases, 454,450 controls), intracerebral hemorrhage
 (1,545 cases, 1,481 controls), and ischemic stroke subtypes (large artery,
 cardioembolic, small vessel stroke), as well as with related phenotypes
 (carotid atherosclerosis, imaging markers of cerebral white matter
 integrity, and brain atrophy).  Results: Genetic
 predisposition to T2D and higher HbA1c levels were associated with higher
 risk of any ischemic stroke, large artery stroke, and small vessel stroke.
 Similar associations were also noted for carotid atherosclerotic plaque,
 fractional anisotropy, a white matter disease marker, and markers of brain
 atrophy. We further found associations of genetic predisposition to
 insulin resistance with large artery and small vessel stroke, whereas
 predisposition to β-cell dysfunction was associated with small
 vessel stroke, intracerebral hemorrhage, lower grey matter volume, and
 total brain volume. Conclusions: This study supports causal
 effects of T2D and hyperglycemia on large artery and small vessel
 stroke. We show associations of genetically predicted insulin
 resistance and β-cell dysfunction with large artery and small
 vessel stroke that might have implications for anti-diabetic treatments
 targeting these mechanisms. Classification of Evidence: This
 study provides Class II evidence that genetic predisposition to T2D and
 higher HbA1c levels are associated with a higher risk of large artery and
 small vessel ischemic stroke.
DOI: 10.5061/dryad.pnvx0k6k1
title: Size-dependent male mating tactics and their morphological correlates in Poecilia gillii

description: Male alternative reproductive strategies are found in some species of most
 major animal taxa, but are especially widespread in fishes. Mature males
 of the shortfin molly, Poecilia gillii, display extensive variation in
 size and morphology. We devised a field test of a priori hypotheses
 regarding the interrelationships between male size, colouration,
 morphology, and mating tactics. Males did not occur in discrete size
 classes, but instead occurred in a size and morphological continuum. Large
 males exhibited darker and more orange coloured dorsal and caudal fins,
 while small males exhibited lighter and more inconspicuous fin
 colouration. Furthermore, larger males had proportionately deeper bodies,
 larger dorsal and caudal fins, and shorter gonopodia than smaller males.
 Our field study of male mating behaviour revealed a lack of courtship in
 this species, and similar levels of mating attempts (gonopodial thrusts)
 irrespective of male size. Instead, small males were significantly more
 likely to chase females than were large males. In contrast, large males
 exhibited higher rates of gonoporal nibbling (a likely means by which
 males determine, through chemical factors, whether a female is carrying
 fertilizable ova) and higher likelihood of chasing other males away. In
 total, we found evidence for the predicted associations between male size,
 colouration, morphology and mating behaviour – associations that appear
 likely to maximize mating success for males of a given body size and
 phenotype.
DOI: 10.5061/dryad.7wm37pvr2
title: Asymmetric contextual effects in age perception dataset

description: Perception is context dependent. For example, the perceived orientation of
 a bar changes depending on the presence of oriented bars around it.
 Contextual effects have also been demonstrated for more complex
 judgements, such as facial attractiveness or expression, although it
 remains unclear how these contextual facial effects depend on the types of
 faces surrounding the target face.To examine this, we measured the
 perceived age (a quantifiable measure) of a target face in the presence of
 differently aged faces in the surround. Using a unique database
 of standardized passport photos, participants were asked to estimate the
 age of a target face which was viewed either on its own or
 surrounded by two different identity flanker faces. The flanker
 faces were either both younger or both older than the target face, with
 different age offsets between flankers and targets of ±5, ±10, ±15, ±20
 years. We find that when a target face is surrounded by younger faces, it
 systematically appears younger than when viewed on its own, and
 when it is surrounded by older faces, it systematically appears
 older than when viewed on its own. Surprisingly, we find that the
 magnitude of the flanker effects on perceived age of the target
 is asymmetric with younger flankers having a greater
 influence than older flankers, a result that may reflect the
 participants’ own-age bias, since all participants were young.
 This result holds irrespective of gender or race of the faces and is
 consistent with averaging.
description: Participants viewed target faces (of different ages) on their
 own, surrounded by younger flankers and surrounder by older faces. The
 task was to give a numerical age estimate of the target face. The data set
 is the raw responses.
description: This is a dataset of the raw estimations given in the
 experiments. Each excel tab represents one of the target-flankers age
 difference for the two main experiments. In each tab, all the target ages
 teseted are organised from younger to older. For example, in the first
 excel tab is experiment 1 raw data of age difference (between target and
 flankers)  for target ages from 15 years old to 65 years old. Each 3
 columns are age estimtes of a target age (for example 15 years old). And
 those 3 columns are when the target age is viewed alone (for example the
 column @15_A), when the target age is viewed with younger flankers (for
 example @15_Y), and, when the target age is viewed with older flankers
 (for example, @15_O).
DOI: 10.5061/dryad.1vhhmgqr0
title: National bat monitoring programme roost counts dataset

description: Many long-term wildlife population monitoring programmes rely on citizen
 scientists for data collection. This can offer several benefits over
 traditional monitoring practices as it is a cost-effective, large-scale
 approach capable of providing long time series data and raising public
 environmental awareness. Whilst there is a debate about the quality of
 citizen science data, a standardised sampling design can allow citizen
 science data to be of a similar quality to those collected by
 professionals. However, many programmes use subjective, opportunistic
 selection of monitoring sites and this introduces several types of bias,
 which are not well understood. Using bat roost counts as a case study, we
 took a ‘virtual ecologist’ approach to simulate the effect of
 opportunistic site selection and uneven observer retention on our ability
 to accurately detect abundance trends. We simulated populations with
 different levels of temporal variability and site fidelity. Our
 simulations reveal that opportunistic site selection and low observer
 retention can result in biased trends and that these biases are magnified
 when monitored populations exhibit high levels of inter-annual variation
 and low site fidelity. These results show that the synergistic effects of
 observer behaviour, site selection, and population dynamics lead to biased
 abundance trends in monitoring programmes. This study highlights the value
 of engaging and retaining citizen science observers, a standardised
 sampling design, and the collection of meta-data. We conclude that
 monitoring programmes need to be aware of their focal species’ temporal
 variability and site fidelity to adequately assess the potential bias
 caused by opportunistic site selection and low observer retention.
 Synthesis and applications. Accurate data on population changes are key
 for conservation success. Therefore, it is important that citizen science
 monitoring programmes assess and potentially quantify the biases present
 in their data. We demonstrate the applicability of an established
 simulation framework to assess the effect of biases on our ability to
 correctly detect abundance trends. Our findings highlight that monitoring
 programmes need to be aware of their study species’ temporal variability
 and site fidelity to assess and account for the effects of biased site
 selection and observer retention. The National Bat Monitoring Programme
 (NBMP) is run by Bat Conservation Trust, in partnership with the Joint
 Nature Conservation Committee, and supported and steered by Natural
 England, Natural Resources Wales, Northern Ireland Environment Agency, and
 Scottish Natural Heritage. The NBMP is indebted to all observers who
 contribute data to the programme.
description: This is not the full NBMP dataset but a reduced version used for
 the manuscript. Complete and up-to-date data from the National Bat
 Monitoring Programme can be accessed by contacting nbmp@bats.org.uk.
DOI: 10.5061/dryad.1zcrjdfq9
title: Data from: Learning to see the wood for the trees: machine learning, decision trees and the classification of isolated theropod teeth

description: Taxonomic identification of fossils based on morphometric data
 traditionally relies on the use of standard linear models to classify such
 data. Machine learning and decision trees offer powerful alternative
 approaches to this problem but are not widely used in palaeontology. Here,
 we apply these techniques to published morphometric data of isolated
 theropod teeth in order to explore their utility in tackling taxonomic
 problems. We chose two published datasets consisting of 886 teeth from 14
 taxa and 3020 teeth from 17 taxa, respectively, each with five
 morphometric variables per tooth. We also explored the effects that
 missing data have on the final classification accuracy. Our results
 suggest that machine learning and decision trees yield superior
 classification results over a wide range of data permutations, with
 decision trees achieving accuracies of 96% in classifying test data in
 some cases. Missing data or attempts to generate synthetic data to
 overcome missing data seriously degrade all classifiers predictive
 accuracy. The results of our analyses also indicate that using ensemble
 classifiers combining different classification techniques and the
 examination of posterior probabilities is a useful aid in checking final
 class assignments. The application of such techniques to isolated theropod
 teeth demonstrate that simple morphometric data can be used to yield
 statistically robust taxonomic classifications and that lower
 classification accuracy is more likely to reflect preservational
 limitations of the data or poor application of the methods.
description: Data to test the models was sourced from: HENDRICKX, C.,
 MATEUS, O. and ARAÚJO, R. 2015. The dentition of megalosaurid theropods.
 <i>Acta Palaeontologica Polonica</i>, <b>60</b>,
 627–642. LARSON,
 DEREK W., BROWN, CALEB M. and EVANS, DAVID C. 2016. Dental Disparity and
 Ecological Stability in Bird-like Dinosaurs prior to the End-Cretaceous
 Mass Extinction. <i>Current Biology</i>,
 <b>26</b>, 1325–1333.
description: Please read the README file for detailed instructions.
 A R-script is also included which has been tested on R version
 3.6.0 and 4.0.2
DOI: 10.5061/dryad.0rxwdbrxf
title: Extreme developmental instability is associated with the pea aphid wing plasticity

description: A key focus of evolutionary developmental biology is on how phenotypic
 diversity is generated. In particular, both plasticity and developmental
 instability can contribute to phenotypic variation among genetically
 identical individuals, but the interactions between the two phenomena and
 their general fitness impacts are unclear. We discovered a striking
 example of asymmetry in pea aphids: the presence of wings on one side and
 the complete or partial absence of wings on the opposite side. We used
 this asymmetric phenotype to study the connection between plasticity,
 developmental instability, and fitness. We found that this asymmetry
 equally affects both sides and thus is a developmental instability; is
 present in some genetically unique lines but not others and thus has a
 genetic basis; and has intermediate levels of fecundity, and thus does not
 necessarily have negative fitness consequences. We conclude that this
 dramatic asymmetry may arise from incomplete switching between
 developmental targets, linking plasticity and developmental instability.
 We posit that what we have observed may be a more widespread phenomenon,
 occurring across species that routinely produce distinct, alternative
 phenotypes.
DOI: 10.5061/dryad.zkh189382
title: Effects of soil preservation for biodiversity monitoring using environmental DNA

description: Environmental DNA metabarcoding is becoming a key tool for biodiversity
 monitoring over large geographical or taxonomic scales and for elusive
 taxa like soil organisms. Increasing sample sizes and interest in remote
 or extreme areas often require the preservation of soil samples and thus
 deviations from optimal standardized protocols. However, we still ignore
 the impact of different methods of soil sample preservation on the results
 of metabarcoding studies and there is no guidelines for best practices so
 far. Here, we assessed the impact of four methods of soil sample
 preservation commonly used in metabarcoding studies (preservation at room
 temperature for 6h, preservation at 4°C for three days, desiccation
 immediately after sampling and preservation for 21 days, and desiccation
 after 6h at room temperature and preservation for 21 days). For each
 preservation method, we benchmarked resulting estimates of taxon diversity
 and community composition of three different taxonomic groups (bacteria,
 fungi and eukaryotes) in three different habitats (forest, river bank and
 grassland) against results obtained under optimal conditions (i.e.
 extraction of eDNA right after sampling). Overall, the different
 preservation methods only marginally impaired results and only under
 certain conditions. When rare taxa were considered, we detected small but
 significant changes in MOTU richness of bacteria, fungi and eukaryotes
 across treatments, while the exclusion of rare taxa led to robust results
 across preservation methods. The differences in community structure among
 habitats were evident for all treatments, and the communities retrieved
 using the different preservation conditions were extremely similar. We
 propose guidelines on the selection of the optimal soil sample
 preservation conditions for metabarcoding studies, depending on the
 practical constraints, costs and ultimate research goals.
description: Data has been processed following the pipeline described in
 Script 1 and Script 2 for Euka02, as example.
description: <strong>1. BIOINFORMATIC TREATMENT</strong>
 Script1: bioinformatic treatment of raw data using the Obitools
 software suite raw data
 description:  library GWM-1521
 contains sequences for Euka02 library GWM-1525 contains
 sequences for Bact02 library GWM-1526 contains
 sequences for Fung02  
 <strong>2. DATA FILTERING</strong>
 script2: additional data filtering performed in R
 GWM-1521_tag.obitab is converted to .txt, renamed as
 "bact02.txt" and used as input file
 GWM-1525_tag.obitab is converted to .txt, renamed as
 "fung02_EDP1.txt" and used as input file
 GWM-1526_tag.obitab is converted to .txt, renamed as
 "euka02.txt" and used as input file
 output files:
 bact02_prop.txt euka02_prop.txt
 fung02_prop.txt
DOI: 10.5061/dryad.tx95x69vz
title: Biosonar spatial resolution along the distance axis: revisiting the clutter interference zone

description: Many echolocating bats forage close to vegetation - a chaotic arrangement
 of prey and foliage where multiple targets are positioned behind one
 another. Bats excel at determining distance: they measure the delay
 between outgoing call and returning echo. In their auditory cortex,
 delay-sensitive neurons form a topographic map, suggesting that bats can
 resolve echoes of multiple targets along the distance axis - a skill
 crucial for the forage-amongst-foliage scenario. We tested this hypothesis
 combining an auditory virtual reality with formal psychophysics: We
 simulated a prey item embedded in two foliage elements, one in front of
 and one behind the prey. The simulated spacing between "prey"
 (target) and "foliage" (maskers) was defined by the inter-masker
 delay (IMD). We trained Phyllostomus discolor bats to detect the target in
 the presence of the maskers, systematically varying both loudness and
 spacing of the maskers. We show that target detection is impaired when
 maskers are closely spaced (IMD &lt; 1 ms), but remarkably improves
 when the spacing is increased: the release from masking is about 5 dB for
 intermediate IMDs (1-3 ms) and increases to over 15 dB for large IMDs (≥ 9
 ms). These results are well comparable to earlier work on bats'
 clutter interference zone (Simmons et al., 1988). They suggest that prey
 would enjoy considerable acoustic protection from closely spaced foliage,
 but also that the range resolution of bats would let them "peek into
 gaps". Our study puts target ranging into a meaningful context and
 highlights the limitations of computational topographic maps.
description: Data S1 contains 1) a README file describing the file
 contents, 2)psychophysical data used to determine masking thresholds and
 derive range resolution limits in echolocating bats (Phyllostomus
 discolor) and 3) acoustic data used to investigate echolocation
 strategies.
DOI: 10.25338/b8q04h
title: Estimating the costs of new mobility travel options: monetary and non-monetary factors

description: UC Davis researchers have developed a cost model of travel choices that
 individuals make related to urban vehicle travel. These choices can
 include deciding to own, ride in, and drive a private vehicle or use
 pooled or solo ridesourcing (e.g., Uber). The model considers both
 monetary and non-monetary factors that affect travel choice. Monetary
 factors include the costs of purchasing, maintaining, and fueling
 different types of privately owned vehicles; and the cost of using
 ridesourcing services. Non-monetary (or “hedonic”) factors include travel
 time, parking time/inconvenience, willingness to drive or be a passenger
 in a driven or automated vehicle, and willingness to travel with
 strangers. The travel choices affected by these factors impact broader
 society through traffic congestion, pollution, greenhouse gas emissions,
 accidents, etc. and thus may be an important focus of policy. This report
 reviews recent literature, considers factors affecting travel choices, and
 reports, on a conjoint pilot survey or stated preferences. Finally, it
 considers approaches to apply time value to factors that are not typically
 associated with specific trips, such as time spent on vehicle maintenance
 and parking. The results should enable a deeper understanding of the
 likelihood that individuals will own and use private vehicles or use
 shared (solo and pooled) ridesourcing, and how automated vehicle services
 could affect these choices in the future. The study also highlights
 additional research needs, such as a large scale stated preference study
 covering more factors than have been included in previous studies.
description: The project involved
 convening focus groups and administering a pilot survey (sample size, 37)
 of professionals (21 to 47 years). This group reflected a convenience
 sample and one that is relatively likely to have experience with
 ridesharing and an awareness of automated vehicle concepts. The
 discussions and surveys were focused on commuting trips. Three travel modes were
 considered for this study: Solo
 ridesourcing Pooled ridesourcing (door-to-door with
 stops to pick up and drop off other riders)  “Express” pooled ridesourcing
 (short walk to common pickup and drop off point, without any additional
 stops along the way) A set of hypothetical trip
 situations were presented to participants, with trip characteristics
 varying by: Trip time uncertainty
 (minimum/maximum trip time range) Maximum number of
 other passengers allowed on trip Trip cost
 Whether driven or
 automated vehicle trip The research was undertaken in
 two parts, with a qualitative and quantitative (survey)
 component.
description: The numbered responses in the survey database relate to the order
 of the choices in the survey.  So first option = 1, second option =2, etc.
 All else should be self explanatory from reading the survey instrument,
 included here.
DOI: 10.5061/dryad.qz612jmck
title: R code for: The joint evolution of learning and dispersal maintains intraspecific diversity in metapopulations

description: To get a better understanding of the joint evolution of dispersal
 tendencies and of cognitive abilities, we built an individual-based
 simulation. Both learning speed and dispersal tendency were free to
 evolve. Results show that both positive and negative correlations could
 evolve between these traits, depending on properties both of local patches
 and of the metapopulation as a whole. Furthermore, we found that dispersal
 stabilized the co-existence of different cognitive types in the
 metapopulation, thereby helping to maintain biodiversity within species.
 Here we provide the R code for the function with which the simulation for
 the study "The joint evolution of learning and dispersal maintains
 intraspecific diversity in metapopulations" has been conducted.
 Description of the code is given as comments in the code itself.
description: The results are deriving from IMBs.  Description of the code is
 given as comments in the code itself.
description: Datafiles ending with ~run* are .rds files. Here, for each of the patches within a metapopulation a table is given with one row for each individual. Columns are described in the R code of the simulation which is provided in file: “RCode_Dryad.R”. Files can be loaded in R using e.g. : data&lt;-readRDS("/Users/jannisliedtke/Desktop/ Neg_Correlation_Run1") Files named “Tab_Summary_*” are summary tables in .csv format which provided summary statistics (e.g. mean values and std.err. of traits) of metapopulations. Files can be loaded in R using e.g. : data&lt;-read.csv("/Users/jannisliedtke/Desktop/ Neg_Correlation_Run1")