cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.866t1g1rd
title: Dataset: lhp1 FLC-Venus time course imaging – Hybrid protein assembly-histone modification mechanism for PRC2-based epigenetic switching and memory

description: The histone modification H3K27me3 plays a central role in
 Polycomb-mediated epigenetic silencing. H3K27me3 recruits and
 allosterically activates Polycomb Repressive Complex 2 (PRC2), which adds
 this modification to nearby histones, providing a read/write mechanism for
 inheritance through DNA replication. However, for some PRC2 targets, a
 purely histone-based system for epigenetic inheritance may be
 insufficient. We address this issue at the Polycomb target Flowering Locus
 C (FLC) in Arabidopsis thaliana, as a narrow nucleation region of only
 ~three nucleosomes within FLC mediates epigenetic state switching and
 subsequent memory over many cell cycles. To explain the memory’s
 unexpected persistence, we introduce a mathematical model incorporating
 extra protein memory storage elements with positive feedback that persist
 at the locus through DNA replication, in addition to histone
 modifications. Our hybrid model explains many features of epigenetic
 switching/memory at FLC and encapsulates generic mechanisms that may be
 widely applicable.
description: Raw images of the FLC-Venus protein levels in Arabidopsis
 thaliana roots of the lhp1 mutant.<br> Plants were grown in ambient
 temperatures for 7 days, vernalized for 10 weeks and returned to ambient
 temperatures for respective time (for methods see
 https://doi.org/10.7554/eLife.66454)<br> Images are bundled in lif
 files per experimental day and labelled in the following way: 
 e.g. 20200120_10W_T14<br> <strong>20200120
 </strong>refers to day the images were taken [here on the 20th of
 January 2020]<br> <strong>10W</strong> refers to the
 growth period in the cold (vernalization) [here 10 weeks]<br>
 <strong>T14</strong> refers to the growth period after cold
 (post-vernalization) [here 14 days]<br> subname:
 <strong>SDB995-5</strong> refers to John Innes Centre internal
 seed batch number. T0 was included to show cold-induced
 autofluorescence.<br> For imaging details and processing see:
 https://doi.org/10.7554/eLife.66454
description: See Methods
DOI: 10.5061/dryad.44j0zpcf2
title: Data for: Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone

description: A potential shortcoming of concatenation methods for species tree
 estimation is their failure to account for incomplete lineage
 sorting. Coalescent methods address this problem but make various
 assumptions that, if violated, can result in worse performance than
 concatenation. Given the challenges of analyzing DNA sequences
 with both concatenation and coalescent methods, retroelement insertions
 (RIs) have emerged as powerful phylogenomic markers for species tree
 estimation. Here, we show that two recently proposed
 quartet-based methods, SDPquartets and ASTRAL_BP, are
 statistically consistent estimators of the unrooted species tree topology
 under the coalescent when RIs follow a neutral infinite-sites model of
 mutation and the expected number of new RIs per generation is constant
 across the species tree. The accuracy of these (and other)
 methods for inferring species trees from RIs has yet to be assessed on
 simulated data sets, where the true species tree topology is
 known. Therefore, we evaluated eight methods given RIs simulated
 from four model species trees, all of which have short branches and at
 least three of which are in the anomaly zone. In our simulation
 study, ASTRAL_BP and SDPquartets always recovered the
 correct species tree topology when given a sufficiently large
 number of RIs, as predicted. A distance-based method (ASTRID_BP)
 and Dollo parsimony also performed well in recovering the species tree
 topology. In contrast, unordered, polymorphism, and Camin-Sokal
 parsimony (as well as an approach based on MDC) typically fail to recover
 the correct species tree topology in anomaly zone situations with more
 than four ingroup taxa. Of the methods studied, only ASTRAL_BP
 automatically estimates internal branch lengths (in coalescent units) and
 support values (i.e., local posterior probabilities). We examined
 the accuracy of branch length estimation, finding that estimated lengths
 were accurate for short branches but upwardly biased
 otherwise. This led us to derive the maximum likelihood (branch
 length) estimate for when RIs are given as input instead of binary gene
 trees; this corrected formula produced accurate estimates of branch
 lengths in our simulation study, provided that a sufficiently large number
 of RIs were given as input. Lastly, we evaluated the impact of
 data quantity on species tree estimation by repeating the above
 experiments with input sizes varying from 100 to 100,000
 parsimony-informative RIs. We found that, when given just 1,000
 parsimony-informative RIs as input, ASTRAL_BP successfully reconstructed
 major clades (i.e clades separated by branches &gt;0.3 CUs)
 with high support and identified rapid radiations (i.e., shorter connected
 branches), although not their precise branching order. The local
 posterior probability was effective for controlling false positive
 branches in these scenarios.
DOI: 10.5061/dryad.0rxwdbs1b
title: Does the white coat influence satisfaction, trust and empathy in the doctor-patient relationship in the general and family medicine consultation? - interventional study

description: Objectives: To understand the influence of the white coat on patient
 satisfaction, opinions about medical clothing, perception about
 confidence, empathy and medical knowledge and the satisfaction and comfort
 level of physicians in consultation. Setting: An interventional study was
 conducted with a representative sample of the population attending primary
 care in central Portugal. Participants: The sample was composed by 286
 patients divided into two groups exposed or not to a doctor wearing a
 white coat. The first and last patients in consultation every day for 10
 consecutive days were included. Interventions: Every other day the
 volunteer physicians consulted with or without the use of a white coat. At
 the end of the consultation, a questionnaire was distributed to the
 patient with simple questions with a Likert scale response, the Portuguese
 version of the "Trust in physician" scale and the JSPPPE-VP
 scale. A questionnaire was also distributed to the physician. Outcomes:
 Planned and measured primary outcomes were patient satisfaction, trust and
 perception about empathy and secondary outcomes were opinion about medical
 clothing, satisfaction and comfort level of physicians in consultation.
 Results: The sample was homogeneous in terms of sociodemographic
 variables. There were no statistically significant differences between the
 groups in terms of satisfaction, trust, empathy and knowledge perceived by
 the patients. There were differences in the opinion of the patients about
 the white coat, and when the physician was wearing the white coat this
 group of patients tended to think that this was the only acceptable attire
 for the physician (p&lt;0.001). But, when the family physician was in
 consultation without the white coat, this group of patients tended to
 agree that communication was easier (p=0.001). Conclusions: There was no
 significant impact of the white coat in patient satisfaction, empathy, and
 confidence in the family physician. Trial Registration: ClinicalTrials.gov
 ID Number: NCT03965416
DOI: 10.5061/dryad.m63xsj42r
title: Data from: Contextual inference underlies the learning of sensorimotor repertoires

description: Humans spend a lifetime learning, storing and refining a repertoire of
 motor memories. For example, through experience, we become proficient at
 manipulating a large range of objects with distinct dynamical
 properties. However, it is unknown what principle underlies how
 our continuous stream of sensorimotor experience is segmented into
 separate memories and how we adapt and use this growing repertoire. Here
 we develop a theory of motor learning based on the key principle that
 memory creation, updating, and expression are all controlled by a single
 computation—contextual inference. Our theory reveals that adaptation can
 arise both by creating and updating memories (proper learning) and by
 changing how existing memories are differentially expressed (apparent
 learning). This insight allows us to account for key features of motor
 learning that had no unified explanation: spontaneous recovery, savings,
 anterograde interference, how environmental consistency affects learning
 rate and the distinction between explicit and implicit learning.
 Critically, our theory also predicts novel phenomena—evoked recovery and
 context-dependent single-trial learning—which we confirm experimentally.
 These results suggest that contextual inference, rather than
 classical single-context mechanisms, is the key principle underlying how a
 diverse set of experiences is reflected in our motor behaviour.
DOI: 10.5061/dryad.d51c5b03z
title: Waterbird solves the cognitive string-pull test

description: String-pulling is amongst the most widespread cognitive tasks used to test
 problem-solving skills in mammals and birds. The task requires animals to
 comprehend that pulling on a non-valuable string moves an otherwise
 inaccessible food reward to within their reach. Although at least 90 avian
 species have been administered the string-pull test, all but five of them
 were perching birds (passeriformes) or parrots (psittaciformes).
 Waterbirds (Aequorlitornithes) are poorly represented in the cognitive
 literature, yet are known to engage in complex foraging behaviours. In
 this study, we tested whether free-living ring-billed gulls (Larus
 delawarensis), a species known for their behavioural flexibility and
 foraging innovativeness, could solve a horizontal string-pull test. Here,
 we show that 25% (26/104) of the ring-billed gulls that attempted to solve
 the test at least once over a maximum of three trials were successful, and
 that 21% of them (22/104) succeeded during their first attempt.
 Ring-billed gulls are thus the first waterbird known to solve a horizontal
 single-string-rewarded string-pull test. Since innovation rate and
 problem-solving are associated with species’ ability to endure
 environmental alterations, we suggest that testing the problem-solving
 skills of other species facing environmental challenges will inform us of
 their vulnerability in a rapidly changing world.
DOI: 10.5061/dryad.0vt4b8h0m
title: Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation

description: Estimating the complex relationship between fitness and genotype or
 phenotype (i.e. the adaptive landscape) is one of the central goals of
 evolutionary biology. However, adaptive walks connecting genotypes to
 organismal fitness, speciation, and novel ecological niches are still
 poorly understood and processes for surmounting fitness valleys remain
 controversial. One outstanding system for addressing these connections is
 a recent adaptive radiation of ecologically and morphologically novel
 pupfishes (a generalist, molluscivore, and scale-eater) endemic to San
 Salvador Island, Bahamas. We leveraged whole-genome sequencing of 139
 hybrids from two independent field fitness experiments to identify the
 genomic basis of fitness, estimate genotypic fitness networks, and measure
 the accessibility of adaptive walks on the fitness landscape. We
 identified 132 SNPs that were significantly associated with fitness in
 field enclosures. Six out of the 13 regions most strongly associated with
 fitness contained differentially expressed genes and fixed SNPs between
 trophic specialists; one gene (mettl21e) was also misexpressed in
 lab-reared hybrids, suggesting a potential intrinsic genetic
 incompatibility. We then constructed genotypic fitness networks from
 adaptive alleles and show that scale-eating specialists are the most
 isolated of the three species on these networks. Intriguingly,
 introgressed and de novo variants reduced fitness
 landscape ruggedness as compared to standing variation, increasing the
 accessibility of genotypic fitness paths from generalist to specialists.
 Our results suggest that adaptive introgression and de
 novo mutations alter the shape of the fitness landscape,
 providing key connections in adaptive walks circumventing fitness valleys
 and triggering the evolution of novelty during adaptive radiation.
DOI: 10.5061/dryad.0cfxpnw2z
title: The influence of the statistical significance of results and spin on readers’ interpretation of the results in an abstract for a hypothetical clinical trial: A randomized trial

description: Objectives: To assess the impact on readers’ interpretation of the results
 reported in an abstract for a hypothetical clinical trial with 1) a
 statistically significant result, 2) spin, 3) both a statistically
 significant result and spin compared to 4) no spin and no statistically
 significant result. Participants: Health students and professionals from
 universities and health institutions in France and the UK. Interventions:
 Participants completed an online questionnaire using Likert scales and
 free text, after reading one of the four versions of an abstract about a
 hypothetical randomized trial evaluating “Naranex” and “Bulofil” (two
 hypothetical drugs) for chronic low back pain. The abstracts differed in
 a) reported result of “mean difference of 1.31 points (95%CI 0.08 to 2.54;
 p= 0.04)“ or “mean difference of 1.31 points (95%CI -0.08 to 2.70;
 p= 0.06)” and b) presence or absence of spin. The effect size for the
 trial’s primary outcome (pain disability score) was the same in each
 abstract; slightly in favour of Naranex. Primary outcome: The reader’s
 interpretation of the trial’s results, based on their answer (1: disagree,
 4: neutral, 7: agree) to the following statement: “About the main findings
 of the study, what is your opinion about the following statement: ‘Naranex
 is better than Bulofil’?” Results: 297 of the 404 people randomized to
 receive one of the four abstracts completed the study. Respondents were
 more likely to favour Narenex when the abstract reported a statistically
 significant result without spin; a statistically significant result with
 spin, a non-statistically significant result with spin, compared to when
 it reported a non-statistically significant result without spin.
 Conclusions: Statistical significance appears to have influenced readers’
 perception whatever the level of spin, while spin influenced readers’
 perception when the results were not statistically significant but did not
 appear to have an impact when results were statistically significant
description: People informed and consenting
 in participating in the study could submit their email address through an
 online form. Participants completed an online questionnaire hosted in
 framaforms.org using Likert scales and free text, after reading one of the
 four versions of the experimental abstract.
DOI: 10.15468/dl.2vavgz
title: Occurrence Download

description: A dataset containing 200 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diplotropis incexis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 200 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002923-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2bvq83bqw
title: Single nucleotide polymorphisms

description: Aim: Understanding the phylogeography of a species complex can provide
 important insights into its evolutionary history. However, phylogeographic
 inference often faces the dilemma of regionally inadequate sampling.
 Pungitius sticklebacks are a case in point: although the highest species
 diversity is found in Northeast Asia, their phylogeography in this region
 is still poorly understood. Location: Northeast Asia Methods: With the aid
 of whole genome resequencing data, we investigated the phylogeography of
 Northeast Asian Pungitius sticklebacks, with newly sampled 83 world-wide
 Pungitius individuals from 11 locations including eight Chinese locations
 reported to host only P. sinensis. Results: We discovered that three of
 these locations hosted populations of P. kaibarae and P. bussei, species
 new to the fauna of China. Phylogeographic analyses further clarified the
 sequence and timing of colonization of Northeast Asia by different
 Pungitius species, shedding new light on their origins and current
 distribution ranges. Colonization of inland Northeast Asia by Pungitius
 sticklebacks occurred in multiple waves, and the widespread P. sinensis
 expanded its range relatively late in the Pleistocene. Main Conclusions:
 This study complements our understanding of the phylogeography of
 Pungitius sticklebacks by extending sampling to cover an area that
 comprises nearly half of the known distribution area of this genus in
 Northeast Asia. The discovery of three Pungitus species from China is of
 particular interest, as translocations to support locally declining
 populations have occurred under the assumption that all sticklebacks in
 China – except the endangered P. stenurus – are P. sinensis, and draws
 attention to local introduction for their conservation.
DOI: 10.5061/dryad.4mw6m90b1
title: Data for spin quantum beats in pump push spectroscopy

description: Spin quantum beats prove the quantum nature of reactions involving radical
 pairs, the key species of spin chemistry. However, such quantum beats
 remain hidden to transient-absorption-based optical observation because
 the spin hardly affects the radical pairs’ absorption properties. We
 succeeded in demonstrating such quantum beats in the photo-induced charge
 separated state (CSS) of an electron-donor-acceptor dyad by using two
 laser pulses, one for pumping the sample, and another one, with variable
 delay, for further exciting the CSS to a higher electronic state, wherein
 ultrafast recombination to distinct, optically detectable products of
 singlet or triplet multiplicity occurs. This represents a spin quantum
 measurement of the spin state of the CSS at the time instant of the second
 (push) pulse.
description: Uv/vis absorption and emission spectroscopy,
 (spectro)electrochemistry, ns-transient absorption spectroscopy, pump push
 spectroscopy, classical and quantum dynamical simulations, NMR
 spectroscopy, mass spectrometry
DOI: 10.5061/dryad.70rxwdbz4
title: Landmark coordinates from: Dubied et al. Commonalities and evolutionary divergences of mandible shape ontogenies in rodents

description: In mammals, significant changes take place during postnatal growth, linked
 to changes in diet (from sucking to gnawing). During this period, mandible
 development is highly interconnected with muscle growth and the epigenetic
 interactions between muscle and bone control the spatialization of bone
 formation and remodeling in response to biomechanical strain. This
 mechanism contributes to postnatal developmental plasticity, and may have
 influenced the course of evolutionary divergences between species and
 clades.  We sought to model postnatal changes at a
 macroevolutionary scale by analyzing ontogenetic trajectories of mandible
 shape across 16 species belonging mainly to two suborders of Rodents,
 Myomorpha and Hystricomorpha, which differ in muscle attachments, tooth
 growth, and life-history traits. Myomorpha species present a much stronger
 magnitude of changes over a shorter growth period. Among Hystricomorpha,
 part of the observed adult shape is set up prenatally, and most postnatal
 trajectories are genus-specific, which agrees with non-linear
 developmental trajectories over longer gestational periods. Beside
 divergence at large scale, we find some collinearities between
 evolutionary and developmental trajectories. A common developmental trend
 was also observed, leading to enlargement of the masseter fossa during
 postnatal growth. The tooth growth, especially hypselodonty, seems to be a
 major driver of divergences of postnatal trajectories. These muscle- and
 tooth-related effects on postnatal trajectories suggest opportunities for
 developmental plasticity in the evolution of the mandible shape,
 opportunities that may have differed across Rodent clades.
description: Ten landmarks were digitized (L1-L10), together with 33
 semilandmarks divided into three curves (with 4 on the coronoid process, 9
 along the lunar notch, and 10 between postcondylar and angular processes)
 using the <i>Digit3DLand</i> R package 0.1.3 (Laffont and
 Navarro 2019).
DOI: 10.5061/dryad.dr7sqv9zv
title: Human-mediated dispersal redefines mangrove biogeography in the Anthropocene

description: Introduction of species by humans breaks down biogeographic boundaries and
 results in the homogenization of species composition, yet empirical tests
 of this impact in marine forest ecosystems are still scarce. Large-scale
 planting aimed at reversing losses of mangroves has been the dominant
 strategy for mangrove restoration adopted by many organizations in the
 past decades, but there is a lack of quantitative understanding of the
 impacts of such large-scale plantings on mangrove biogeography. Here we
 used data collected before and after large-scale planting to compare the
 species richness and compositional similarities among 72 mangrove sites
 over a biogeographic scale (18-28 °N) in China. After the large-scale
 planting, 15 of the mangrove species spread towards the higher latitudes,
 reflecting the geographical barriers of the mangrove plants have been
 broken. Local species richness of mangrove increased by 44.82% and
 biogeographic compositional similarity of mangroves increased by 13.33%,
 reflecting large-scale introduction and planting increase local diversity
 of mangrove but enhance biological homogenization. The dispersal
 limitation of mangrove communities reduced by 11.1%, which indicates that
 the community assemblage process of mangrove changed obviously.
 Worryingly, two alien species, Sonneratia apetala and
 Laguncularia racemose, have dispersal across the biogeographic
 scale studied, reflecting an increase in the risk of biogeographic
 invasion. It is expected that biological homogeneity and species invasion
 will further influence the functional biogeography of mangroves. Our
 results highlight that mangrove biogeography is defined by human
 activities in the Anthropocene.
description: See the Methods of the article.
description: See the Methods of the article.