cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xwdbrv19m
title: Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity

description: Rational drug design for G protein-coupled receptors (GPCRs) is limited by
 the small number of available atomic resolution structures. We assessed
 the use of homology modeling to predict the structures of two
 therapeutically relevant GPCRs and strategies to improve the performance
 of virtual screening against modeled binding sites. Homology models of the
 D2 dopamine (D2R) and serotonin 5-HT2A receptors (5-HT2AR) were
 generated based on crystal structures of 16 different GPCRs. Comparison of
 the homology models to D2R and 5-HT2AR crystal structures showed that
 accurate predictions could be obtained, but not necessarily using the most
 closely related template. Assessment of virtual screening performance was
 based on molecular docking of ligands and decoys. The results demonstrated
 that several templates and multiple models based on each of these must be
 evaluated to identify the optimal binding site structure. Models based on
 aminergic GPCRs displayed ligand enrichment and there was a trend toward
 improved virtual screening performance with increasing binding site
 accuracy. The best models even displayed ligand enrichment better than
 that of the D2R and 5-HT2AR crystal structures. Methods to consider
 binding site plasticity were explored to further improve predictions.
 Molecular docking to ensembles of structures did not outperform the best
 individual binding site models, but could increase the diversity of hits
 from virtual screens and be advantageous for GPCR targets with few known
 ligands. Molecular dynamics refinement resulted in moderate improvements
 of structural accuracy and the virtual screening performance of snapshots
 was either comparable to or worse than that of the raw homology models.
 These results provide guidelines for successful application of
 structure-based ligand discovery using GPCR homology models.
description: This data was obtained running unrestrained molecular dynamics
 simulations of the the D<sub>2</sub>R and
 5-HT<sub>2A</sub>R homology models with ACEMD in a hydrated
 POCP membrane.
DOI: 10.5061/dryad.7wm37pvpq
title: Structural disconnectivity and the risk of dementia in the general population

description: Objective: The disconnectivity hypothesis postulates that partial loss of
 connecting white matter fibers between brain regions contributes to the
 development of dementia. Using diffusion-magnetic resonance imaging (MRI)
 to quantify global and tract-specific white matter microstructural
 integrity, we tested this hypothesis in a longitudinal population-based
 setting. Methods: Global and tract-specific measures of fractional
 anisotropy (FA) and mean diffusivity (MD) were obtained in 4,415
 non-demented persons (mean age 63.9 years (SD 11.0), 55.0% women) from the
 prospective population-based Rotterdam Study with brain MRI (2005-2011).
 We modelled the association of these diffusion measures with risk of
 dementia (follow-up until 2016), and with changes on repeated cognitive
 assessment over 5.4 years of follow-up, adjusting for age, sex, education,
 macrostructural MRI markers, depressive symptoms, cardiovascular risk
 factors, and APOE genotype. Results: During a mean follow-up of 6.7 years,
 101 participants had incident dementia, of whom 83 had AD. Lower global
 values of FA and higher values of MD associated with an increased risk of
 dementia (adjusted hazard ratio (95% confidence interval) per standard
 deviation increase in MD: 1.79 (1.44-2.23), per standard deviation
 decrease in FA: 0.65 (0.52;0.80)). Similarly, lower global values of FA
 and higher values of MD related to more cognitive decline in non-demented
 individuals (difference in global cognition per standard deviation
 increase in MD (95% CI) was: -0.04 (-0.07;-0.01)). Associations were most
 profound in the projection, association and limbic system tracts.
 Conclusions: Structural disconnectivity is associated with and an
 increased risk of dementia and more pronounced cognitive decline in the
 general population.
description: Supplemental data with the main manuscript in Neurology.
DOI: 10.5061/dryad.wm37pvmj6
title: Synthetic soil crusts against green-desert transitions: a spatial model

description: Semiarid ecosystems are threatened by global warming due to longer
 dehydration times and increasing soil degradation. Mounting evidences
 indicate that, given the current trends, drylands are likely to expand and
 possibly experience catastrophic shifts from vegetated to desert states.
 Here we explore a recent suggestion based on the concept of ecosystem
 terraformation, where a synthetic organism is used to counterbalance some
 of the nonlinear effects causing the presence of such tipping points.
 Using an explicit spatial model incorporating facilitation and considering
 a simplification of states found in semiarid ecosystems i.e., vegetation,
 fertile and desert soil, we investigate how engineered microorganisms can
 shape the fate of these ecosystems. Specifically, two different, but
 complementary, terraformation strategies are proposed: Cooperation-based:
 C-terraformation; and Dispersion-based: D-terraformation. The first
 strategy involves the use of soil synthetic microorganisms to introduce
 cooperative loops (facilitation) with the vegetation. The second one
 involves the introduction of engineered microorganisms improving their
 dispersal capacity, thus facilitating the transition from desert to
 fertile soil. We show that small modifications enhancing cooperative loops
 can effectively change the location of the critical transition found at
 increasing soil degradation rates, also identifying a stronger protection
 against soil degradation by using the D-terraformation strategy. The same
 results are found in a mean field model providing insights into the
 transitions and dynamics tied to these terraformation strategies. The
 potential consequences and extensions of these models are discussed.
description: This is the code of the cellular automation
DOI: 10.5061/dryad.jq2bvq867
title: Nectar robbers deter legitimate pollinators by mutilating flowers

description: Nectar robbing – harvesting nectar illegitimately – can have a variety of
 outcomes for plant sexual reproduction and for the pollinator community.
 Nectar robbers can damage flowers while robbing nectar, which could affect
 the behavior of subsequent flower visitors and, consequently, plant
 reproduction. However, only nectar manipulation by nectar robbers has so
 far received attention. We found a short-tongued bee, Hoplonomia sp.
 (Halictidae), mutilating the conspicuous lower petal of the zygomorphic
 flowers of Leucas aspera (Lamiaceae) while robbing nectar. We hypothesized
 that the mutilation of the conspicuous lower petal deters legitimate
 pollinators on L. aspera flowers, which, in turn, might affect plant
 reproduction. We first assessed the proportion of naturally-robbed flowers
 in plant populations for three years to confirm that it was not a purely
 local phenomenon due to a few individual bees. We then studied diversity,
 community and visitation characteristics of pollinators, nectar dynamics,
 and fruit set in unrobbed and robbed open flowers in naturally-robbed
 populations. The proportion of robbed flowers varied significantly across
 sites and years. Robbing did not affect nectar dynamics in flowers, but it
 did alter flower morphology, so much so that it reduced pollinator
 visitation and altered the pollinator community on robbed flowers.
 However, the maternal function of plant reproduction was not affected by
 nectar robbing. This study for the first time shows that a nectar robber
 can have an ecologically significant impact on floral morphology.
description: Please refer Material and Methods of the paper
description: All data labels are given in header rows. Please take prior
 permission before using data; we, rather encourage collaborating while
 using data
DOI: 10.5061/dryad.69p8cz8xt
title: Fine-scale root community structure in the field: species aggregations change with root density

description: 1 Roots are capable of strong plastic responses to environmental signals,
 but the extent of such responses in the field is essentially unknown.
 Here, we aimed to identify interspecific root aggregations and
 segregations as indicators of plastic responses to the presence of other
 species. Further, we asked whether aggregations change with heterogeneity
 in overall root density along soil depth and whether root communities show
 any relationship to species' functional traits. 2 We used
 quantitative Real-Time PCR to estimate root quantities of nine grassland
 species in soil blocks at a centimetre scale. We combined these estimates
 with fine-scale recording of species' positions aboveground. We used
 deviations between measured root density and that expected from the
 relationship to aboveground species abundance to correct for different
 chances of individual species to meet due to the non-random distribution
 of their individuals. This approach allows us to identify whether species
 associations belowground are due to plastic response of their roots. 3 We
 showed that while there were signals of both interspecific aggregation and
 segregation, prevalence of aggregation over segregation strongly increased
 with increasing soil depth. In shallow layers, where root density is high
 and its heterogeneity low, roots are likely to respond to a number of
 signals which produce both interspecific aggregation and segregation. In
 contrast, in deeper layers, where root density is low and its
 heterogeneity higher, root distribution is likely to be driven primarily
 by foraging for resources, producing aggregations. Species composition of
 the root community did not show any relationship to functional traits
 (SLA, shoot lifespan, spreading distance and rooting depth) of the
 examined species. 4 Synthesis. The results imply that processes that
 determine interspecific root associations change at a scale of centimetres
 which is close to the scale of individual fine roots. They also imply that
 while root foraging might explain root co-occurrence under low root
 density, very different processes determine it when root density is high.
 Our findings also support the notion that roots, while extremely plastic,
 may not receive sufficient signals to elicit a response in the field if
 overall root density is high and homogeneous
DOI: 10.5061/dryad.zw3r22853
title: Spatio-temporal variability of tidal-stream energy in north-western Europe

description: Initial selection of tidal stream energy sites is primarily based on
 identifying areas with the maximum current speeds. However, optimal design
 and deployment of turbines requires detailed investigations of the
 temporal variability of the available resource, focusing on areas with
 reduced variability, and hence the potential for more continuous energy
 conversion. These aspects were investigated in some of the most promising
 sites for tidal array development across the north-western European shelf
 seas: the Alderney Race, the Fromveur Strait, the Pentland Firth, and the
 Orkney channels. Particular attention was dedicated to asymmetry between
 the flood and ebb phases of the tidal cycle (due to the phase relationship
 between M2 and M4 constituents), and spring-neap variability of the
 available resource (due to M2 and S2 compound tides). A series of high
 resolution models were exploited to (i) produce a detailed harmonic
 database of these three components, and (ii) characterize, using energy
 resource metrics, temporal variability of the available power density.
 There was a clear contrast between the Alderney Race, with reduced
 temporal variability over semi-diurnal and fortnightly time scales, and
 sites in western Brittany and North Scotland which, due to increased
 variability, appeared less attractive for optimal energy conversion.
description: Tidal harmonic components from the analysis of numerical
 predictions in western Brittany, the western English Channel, the Pentland
 Firth and the Orkney archipelago.
description: See README file for further instructions
DOI: 10.34740/kaggle/dsv/14643520
title: List Benchmarks Kaggle
DOI: 10.5061/dryad.08kprr4zn
title: Genetic Adaptation in New York City Rats

description: Brown rats (Rattus norvegicus) thrive in urban environments by navigating
 the anthropocentric environment and taking advantage of human resources
 and by-products.  From the human perspective, rats are a chronic
 problem that causes billions of dollars in damage to agriculture, health
 and infrastructure.  Did genetic adaptation play a role in the
 spread of rats in cities?  To approach this question, we
 collected whole-genome sequences from 29 brown rats from New York City
 (NYC) and scanned for genetic signatures of adaptation.  We
 tested for (i) high-frequency, extended haplotypes that could indicate
 selective sweeps and (ii) loci of extreme genetic differentiation between
 the NYC sample and a sample from the presumed ancestral range of brown
 rats in northeast China.  We found candidate selective sweeps
 near or inside genes associated with metabolism, diet, the nervous system
 and locomotory behavior.  Patterns of differentiation between NYC
 and Chinese rats at putative sweep loci suggests that many sweeps began
 after the split from the ancestral population. Together, our results
 suggest several hypotheses on adaptation in rats living in close proximity
 to humans.
description: Note that in merging the NYC and 9 of the Chinese samples of
 Deinum et al. 2015, we have used the
 option <em>--missing-to-ref</em> in the
 <em>vcf-merge</em> command of <em>vcftools</em>. 
 Therefore, sites that were polymorphic in one sample but either
 monomorphic or of low quality in the other sample were imputed as the
 reference allele of the Rn5 reference.
description: The
 file <b>nyc_and_china_ref_for_missing_fixedploidy.vcf.gz</b> is in Variant Calling Format (VCF) in its zipped form. To unzip the file, use the bgzip command from the Samtools software package.  The file nyc_and_china_ref_for_<b>missing_fixedploidy.vcf.gz.tbi </b>is the corresponding tabix index file.
DOI: 10.7280/d1xm31
title: Getz Ice Shelf Model Setup and Results

description: Model results presented in manuscript 2019GL086522 (submitted to Geophys.
 Res. Lett.) by Romain Millan et al. The results are obtained from the
 numerical model described in detail in St-Laurent et al. 2017 (
 https://doi.org/10.1002/2017jc013162 ). The horizontal grid has a
 resolution of 1.5km by 1.5km. The vertical dimension has 20
 topography-following levels. The horizontal/vertical positions of the grid
 points are stored in the variables lonr,latr,zr. The suffixes 1,2,3 refer
 to the three `Cases` described in Section Methods of the manuscript
DOI: 10.5061/dryad.nvx0k6dnr
title: Dispersal predicts hybrid zone widths across animal diversity: Implications for species borders under incomplete reproductive isolation

description: Hybrid zones occur as range boundaries for many animal taxa. One model for
 how hybrid zones form and stabilize is the tension zone model, a version
 of which predicts that hybrid zone widths are determined by a balance
 between random dispersal into hybrid zones and selection against hybrids.
 Here, we examine whether random dispersal and proxies for selection
 against hybrids (genetic distances between hybridizing pairs) can explain
 variation in hybrid zone widths across 131 hybridizing pairs of animals.
 We show that these factors alone can explain ~40% of the variation in zone
 width among animal hybrid zones, with dispersal explaining far more of the
 variation than genetic distances. Patterns within clades were
 idiosyncratic. Genetic distances predicted hybrid zone widths particularly
 well for reptiles, while this relationship was opposite tension zone
 predictions in birds. Lastly, the data suggest that dispersal and
 molecular divergence set lower bounds on hybrid zone widths in animals,
 indicating there are geographic restrictions on hybrid zone formation.
 Overall, our analyses reinforce the fundamental importance of dispersal in
 hybrid zone formation, and more generally in the ecology of range
 boundaries.
description: These data were culled from a meta-analysis of over 150 studies
 of 131 hybrid zone systems.   Also
 included are the scripts available on GitHub, zipped for archival
 purposes: https://github.com/singhal/hz_metaanalysis 
description: Data on column descriptions are available as Appendix Table A1
 & A2. Inline citations are referenced in the 'References for
 Online Enhancement Only'.
DOI: 10.5061/dryad.d51c59zzn
title: Growth acceleration results in faster telomere shortening later in life

description: There is a wealth of evidence for a lifespan penalty when environmental
 conditions influence an individual´s growth trajectory such that growth
 rate is accelerated to attain a target size within a limited time period.
 Given this empirically demonstrated relationship between accelerated
 growth and lifespan, and the links between lifespan and telomere dynamics,
 increased telomere loss could underpin this growth-lifespan trade. We
 experimentally modified the growth trajectory of nestling zebra finches
 (Taeniopygia guttata), inducing a group of nestlings to accelerate their
 growth between 7 and 15 days of age, the main phase of body growth. We
 then sequentially measured their telomere length in red blood cells at
 various time points from 7 days to full adulthood (120 days). Accelerated
 growth between 7 and 15 days was not associated with a detectable increase
 in telomere shortening during this period compared with controls. However,
 only in the treatment group induced to show growth acceleration, the rate
 of growth during the experimental period was positively related to the
 amount of telomere shortening between 15 and 120 days. Our findings
 provide evidence of a long-term influence of growth rate on later-life
 telomere shortening, but only when individuals have accelerated growth in
 response to environmental circumstances.
description: Experimental manipulation: growth acceleration induced by diet
 switch; Growth: body mass measurements; Telomere dynamics: red blood cells
 using Southern Blot Telomere Restriction Fragment
 analysis (TRF).
description: Data uploaded in wide format.
DOI: 10.5061/dryad.j6q573n98
title: No evidence for single-copy immune-gene specific signals of selection in termites

description: Selection pressures from pathogens appear to play an important role in
 shaping social evolution. Social behavior, in particular brood care, is
 associated with pathogen pressure in wood-dwelling “lower” termites. Yet,
 generally pathogen pressure is predicted to be low in wood-dwelling
 termite species that never leave the nest except for the mating flight. In
 comparison, pathogen pressure is predicted to be higher in species that
 leave the nest to forage, and thus constantly encounter a diversity of
 microbes from their environment. We hypothesized that such differences in
 predicted pathogen pressure are also reflected by differences in the
 intensity of natural selection on immune genes. We tested this hypothesis
 in a phylogenetic framework, analyzing rates of non-synonymous and
 synonymous substitutions on single-copy immune genes. Therefore, we
 leveraged recent genomic and transcriptomic data from eight termite
 species, representing wood-dwelling and foraging species as well as 14
 additional species spanning the winged insects (Pterygota). Our results
 provide no evidence for a role of pathogen pressure in selection intensity
 on single-copy immune genes. Instead, we found evidence for a genome-wide
 pattern of relaxed selection in termites.
description: Supplementary Data: No evidence for single-copy immune-gene
 specific signals of selection in termites.
DOI: 10.5061/dryad.59zw3r241
title: Data from: Latitudinal clines in the timing and temperature-sensitivity of photoperiodic reproductive diapause in Drosophila montana

description: Reproductive diapause is a primary mechanism used by arthropods to
 synchronize their life cycle with seasonal changes in temperate regions.
 Our study species, Drosophila montana, represents the northern insect
 species where flies enter reproductive diapause under short day conditions
 and where the precise timing of diapause is crucial for both survival and
 offspring production. We have studied clinal variation in the critical day
 length for female diapause induction (CDL) and their overall
 susceptibility to enter diapause (diapause incidence), as well as the
 temperature sensitivity of these traits. The study was performed using
 multiple strains from four latitudinal clines of the species – short
 clines in Finland and Alaska and long clines in the Rocky Mountains and
 the western coast of North America - and from one population in Kamchatka,
 Russia. CDL showed strong latitudinal clines on both continents,
 decreasing by one hour per five degrees decline in latitude, on average.
 CDL also decreased in all populations along with an increase in fly
 rearing temperature postponing the diapause to later calendar time, the
 effects of temperature being stronger in southern than in northern
 population. Female diapause incidence was close to 100 % under short day /
 low temperature conditions in all populations, but decreased below 50 %
 even under short days in 19°C in the southern North American western coast
 populations and in 22°C in most populations. Comparing a diversity of
 climatic data for the studied populations showed that while CDL is under a
 tight photoperiodic regulation linked with latitude, its length depends
 also on climatic factors determining the growing season length. Overall,
 the study deepens our understanding of how spatial and environmental
 parameters affect the seasonal timing of an important biological event,
 reproductive diapause, and helps to estimate the evolutionary potential of
 insect populations to survive in changing climatic conditions.
description:
DOI: 10.5061/dryad.nvx0k6dns
title: Kenyan reference values for chemistry and immunoassay tests

description: This data set contains reference values for several chemistry and
 immunoassay tests. The samples tha were analysed were from healthy adults
 aged 18-65 years recruited from selected counties in Kenya as part of a
 reference interval study carried out by the International Federation of
 Clinical Chemistry committee on reference intervals and decision
 limits.