cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k3j9kd54t
title: A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growth

description: Methods to produce protein amyloid fibrils, in vitro, and in
 situ structure characterization, are of primary importance in
 biology, medicine, and pharmacology. We first demonstrated the droplet on
 a super-hydrophobic substrate as the reactor to produce protein amyloid
 fibrils with real-time monitoring of the growth process by using combined
 light-sheet microscopy and thermal imaging. The molecular structures were
 characterized by Raman spectroscopy, X-ray diffraction and X-ray
 scattering. We demonstrated that the convective flow induced by the
 temperature gradient of the sample is the main driving force in the growth
 of well-ordered protein fibrils. Particular attention was devoted to PHF6
 peptide and full-length Tau441 protein to form amyloid fibrils. By a
 combined experimental with the molecular dynamics simulations, the
 conformational polymorphism of these amyloid fibrils were characterized.
 The study provided a feasible procedure to optimize the amyloid fibrils
 formation and characterizations of other types of proteins in future
 studies.
DOI: 10.6086/d11m3q
title: Assessment of genetic diversity and population structure of Eulaema nigrita (Hymenoptera: Apidae: Euglossini) as a factor of habitat type in Brazilian Atlantic forest fragments

description: In many organisms, habitat affects ecological and genetic diversity and,
 for certain species, it is expected that a large population should have
 higher genetic diversity than a smaller population. We analysed the
 genetics of males of the orchid bee, Eulaema nigrita (Hymenoptera:
 Apidae), and examined the links between local abundance and habitat with
 genetic diversity. We also investigated the impact of landscape features
 on genetic population structure, through microsatellite and mitochondrial
 DNA analysis, among populations found across 700 km of Brazilian Atlantic
 forest fragments. We found that genetic variation was not a function of
 local abundance, but it correlated significantly with habitat. There was
 significant but low genetic differentiation among populations. We found a
 single mitochondrial DNA haplotype in all sequenced specimens, which may
 be widespread throughout the Atlantic forest. Our results reinforce the
 idea that orchid bees can fly long distances. High-dispersal capacity,
 together with insufficient time in eventual isolation, can directly
 contribute to the high degree of similarity among populations for this
 species, despite their wide geographical distribution.
description: Raw data for Microsatellites. Markers were scored automatically,
 with results manually corrected in cases of errors in the automatic
 scoring. Peaks were called and binned with the microsatellite plugin of
 Geneious version 7.1.3 (Kearse <i>et al.,</i> 2012).
DOI: 10.5061/dryad.6hdr7sqxq
title: Data from: The impact of anthropogenic disturbances on the genetic diversity of terrestrial species: a global meta-analysis

description: Human activities are primarily responsible for habitat loss and changes in
 natural environments around the world. It has been suggested that
 populations inhabiting human-modified landscapes are subject to reduced
 gene flow, inbreeding depression, and loss of alleles due to genetic
 drift. However, empirical evidence shows contradictory effects of
 anthropogenic disturbances on the genetic diversity of terrestrial
 species. We performed a meta-analysis of 61 studies that compared the
 genetic diversity of plant and/or animal populations in disturbed and
 preserved areas (317 paired comparisons) to investigate general responses
 to different disturbance type. We found significant negative effects of
 disturbance on genetic diversity (effect size: -0.45), in which the loss
 of structural connectivity was the most detrimental disturbance type. The
 choice of the genetic parameter has an influence on the detection of the
 effect (direction and magnitude), and consequently the studies using
 number of effective alleles did not detect genetic erosion, while all
 other indices, especially allelic richness, revealed negative responses to
 disturbances. Yet, only studies performed with transferred or both
 transferred and specific microsatellites showed negative responses to
 disturbances. The general effect was more detrimental in animal than plant
 populations. Only plant species with biotic pollination and seed dispersal
 mode, self-incompatible reproductive system, and shrubs showed negative
 responses to disturbances. Despite all heterogeneity among studies, we
 found an overall negative effect of disturbance on genetic diversity of
 terrestrial populations, which suggests that the remaining populations
 inhabiting anthropogenic landscapes have a reduced evolutionary potential
 being more prone to local extinction.
description: We
 searched for studies that evaluated the effects of anthropogenic
 disturbances on plant and animal genetic diversity published until
 February 07<sup>th</sup>, 2019. The search was performed in
 the Scopus database using the following term sequences: [("Genetic
 diversity") AND (Microsatellite OR SSR) AND
 ("fragmented habitat" OR "habitat fragmentation" OR
 deforest* OR logging OR "habitat disturbance" OR "disturbed
 habitat" OR "habitat loss")]. These terms were searched in
 the title, abstract, and keyword sections of the manuscripts, except for
 the sequence of terms related to the genetic marker that we searched along
 the entire manuscript.
DOI: 10.5061/dryad.jm63xsj7h
title: Data from: Evolutionary trade-offs in the chemical defense of floral and fruit tissues across genus Cornus

description: Premise of the study Defense investment in plant reproductive structures
 is relatively understudied compared to the defense of vegetative organs.
 Here the evolution of chemical defenses in reproductive structures is
 examined in light of the optimal defense, apparency, and resource
 availability hypotheses within the genus Cornus using a phylogenetic
 comparative approach in relation to phenology and native habitat
 environmental data. Methods Individuals representing 25 Cornus species
 were tracked for reproductive phenology over a full growing season at the
 Arnold Arboretum of Harvard University. Floral, fruit, and leaf tissue was
 sampled to quantify defensive chemistry as well as fruit nutritional
 traits relevant to bird dispersal. Native habitat environmental
 characteristics were estimated using locality data from digitized
 herbarium records coupled with global soil and climate datasets. Key
 Results The evolution of later flowering was correlated with increased
 floral tannins, and the evolution of later fruiting was correlated with
 increased total phenolics. Leaves were observed to contain the highest
 tannin activity while inflorescences contained the highest total
 flavonoids. Multiple aspects of fruit defensive chemistry were correlated
 with fruit nutritional traits. Floral and fruit defensive chemistry were
 evolutionarily correlated with aspects of native habitat temperature,
 precipitation, and soil characteristics. Conclusions Results provide
 tentative support for the apparency hypothesis with respect to both flower
 and fruit phenology, while relative concentrations of secondary
 metabolites across organs provide mixed support for the optimal defense
 hypothesis. The evolution of reproductive defense with native habitat
 provides at best mixed support for the resource availability hypothesis.
description: Common garden experiment using the Arnold Arboretum collections
 of <em>Cornus</em> - standardized phenology assessment with
 controlled sampling of reproductive tissues to collect phenotypic data on
 inflorescences and fruits. Native habitat data for each species obtained
 from Mason et al. 2020 (International Journal of Plant Sciences) using
 digitized herbarium record occurrence points to extract climate and soil
 data from global data layers. Phylogeny used obtained from Mason et al.
 2020, itself reconstructed from data published in Xiang et al. 2006. See
 full article for complete methodological details.
description: Please see full text of the journal article and supplementary
 materials for full details on methodology. Also, if needed feel free to
 contact the corresponding author (Chase Mason) with any questions about
 the suitability of specific data types for re-use for other purposes.
 Phenotypic data are straightforward, though specific to the common garden
 study context. Authors would recommend others obtain the phylogeny and
 environmental data from the original sources if being used for a divergent
 purpose.
DOI: 10.25338/b87k75
title: Data for: Genetic architecture modulates diet induced hepatic mRNA and miRNA expression profiles

description: Genetic approaches in model organisms have consistently demonstrated that
 molecular traits such as gene expression are under genetic regulation,
 similar to clinical traits. The resulting expression quantitative trait
 loci (eQTL) have revolutionized our understanding of genetic regulation
 and identified numerous candidate genes for clinically-relevant traits.
 More recently, these analyses have been extended to other molecular traits
 such as protein abundance, metabolite levels, and miRNA expression. Here
 we performed global hepatic eQTL and miRNA expression quantitative trait
 loci (mirQTL) analysis in a population of Diversity
 Outbred (DO) mice fed two different diets. We identified
 several key features of eQTL and mirQTL, namely differences in the mode of
 genetic regulation (cis or trans) between mRNA and
 miRNA. Approximately 50% of mirQTL are regulated by
 a trans-acting factor compared to ~25% of eQTL. We note
 differences in the heritability of mRNA and miRNA expression and variance
 explained by each eQTL or mirQTL. In general, cis-acting variants
 affecting mRNA or miRNA expression explain more phenotypic variance
 than trans-acting variants. Lastly, we investigated the effect of
 diet on the genetic architecture of eQTL and mirQTL highlighting the
 critical effects of environment on both eQTL and mirQTL. Overall, these
 data underscore the complex genetic regulation of two well-characterized
 RNA classes (mRNA and miRNA) that have critical roles in the regulation of
 clinical traits and disease susceptibility.
description: DOeQTL_DataDictionary.xlsx file accompanies the Master Results
 file, masterRes_3_12_20.rds.  Phenotypes
 in mirCross.rds are expressed miRNA.  Phenotypes in are
 DO2_cross2.rds are expressed mRNA.
DOI: 10.5061/dryad.pg4f4qrkn
title: Density estimates of African lions in Queen Elizabeth National Park

description: African lions are declining across much of their range, yet robust
 measures of population densities remain rare. The Queen Elizabeth
 Conservation Area (QECA; 2400 km2) in East Africa’s Albertine Rift has
 potential to support a significant lion population. However, QECA lions
 are threatened, and information on the status of lions in the region is
 lacking. Here, we use a spatially explicit search encounter approach to
 estimate key population parameters of lions in the QECA. We then compare
 home range sizes estimated from our models to those from a radio-collaring
 study implemented a decade earlier. We recorded 8243.5 km of search effort
 over 93 days, detecting 30 individual lions (16 female and 14 male) on 165
 occasions at a rate of 2 lion detections/100 km2. Lion density in the QECA
 was 2.70 adult lions/100 km2(SD=0.47), while mean abundance was 71
 individuals (SD=11.05). Worryingly, the movement parameter for male lions
 was 3.27 km and 2.22 km for females, suggesting &gt;400%, and
 &gt;100% increases in home range size, respectively, compared to a
 decade earlier. Sex ratio of lions in the QECA was lower (1 male: 0.75
 females), when compared to a previously published review (mean=1:2.33).
 The large movements and skewed sex ratios we report on in this paper are
 likely a result of human driven prey depletion. Our results suggest lions
 in the QECA are in a precarious state and the lion densities are
 significantly lower than what they could be. As lions are under pressure
 throughout much of Africa, our study presents the utility of a census
 technique that could be used elsewhere as an early warning of lion
 declines. 
description: The following document provides the user with the R code to generate African lion densities and other state variables for the QECA (and accompanying raw outputs from R) using the csv input files in Supplementary Information 1. We initially ran models at 11000 iterations (with a burn in of 1000) and achieved convergence for the <b>Global </b>(most parameterized), <b>X</b>and <b>Y</b> models. The <b>full</b> (ie. Model with most support but where theta was 1), <b>Sextheta</b>, <b>Sex</b> and <b>Theta</b> models were run for 39000 iterations with a burn in of 1000 to achieve convergence.  *This code is tested and correct as of 12 August 2019. If you experience any problems replicating these results, or have queries about the code, please contact the lead author on alexander.braczkowski@gmail.com.  
description: Please use the accompanying manual (with R code) and RAW csv
 files to generate the results we produce in our paper.
DOI: 10.5061/dryad.vx0k6djp4
title: Data from : Vacant yet invasible niches in forest community assembly

description: It is controversial whether communities are saturated with species, or
 have vacant niches. The prevalence of vacant niches and the processes
 likely to promote their existence are poorly known.  We used a
 process‐based forest gap‐model to simulate plant community dynamics in 11
 sites along a climatic gradient across central Europe. We then used
 hypervolume analyses to study the existence of vacant niches (seen as
 empty volumes in the trait space of local species pools and communities),
 and we tested for the effect of abiotic (environmental filtering) and
 biotic (competition) processes on the functional hypervolumes along the
 climatic gradient. Last, we performed invasion simulations to assess the
 invasibility of detected vacant niches.  Our results suggest that
 empty volumes in trait space are common, can arise from both abiotic and
 biotic processes, and are more likely in cold climates. We also showed
 that most vacant niches are invasible.     
   4. Synthesis: Our work supports the view that niche space is
 unsaturated, and that many viable ecological strategies are absent from
 these forest communities.
description: Datas were not collected but come from simulations of the
 FORCEEPS model. See article for more details about the model, and the
 following references: <em>Bugmann H (1994) On the
 Ecology of mountainous forests in a changing climate: A simulation study.
 PhD Thesis. Eidgenössische Technische Hochschule,
 Zürich.</em> <em>Bugmann H (1996) A simplified forest
 model to study species composition along climate gradients. Ecology, 77,
 2055-2074.</em> <em>Bugmann H (2001) A review of forest gap
 models. Climatic Change, 51, 259-305.Didion M, </em> <em>Kupferschmid AD, Zingg A, Fahse L,
 Bugmann H (2009) Gaining local accuracy while not losing generality —
 extending the range of gap model applications. Canadian Journal of Forest
 Research, 39, 1092-1107.</em>   The R code
 to replicate the analyses and the figures is provided with the
 summarized datasets. Note that raw simulation outputs were too big
 (&gt;20Go) to be archived.  
description: Follow the code, contact me at pierre.gauzere@gmail.com if you
 need any assitance. I will be happy to help.
DOI: 10.5061/dryad.00000001s
title: Data from: Fledging mass is color morph specific and affects local recruitment in a wild bird

description: Early life conditions may have long-lasting effects on life history. In
 color polymorphic species, morph-specific sensitivity to environmental
 conditions may lead to differential fitness. In tawny owl (Strix aluco)
 pheomelanin-based color polymorphism is expected to be maintained because
 the brown morph has higher adult fitness in warmer environments, while
 selection favors the grey morph under colder conditions. Here we
 investigate body mass at fledging and its consequences until adulthood in
 a population at the species’ cold range margin. Using 40 years of data
 (1979-2017), we show that brown pairs, which mainly produce brown
 offspring consistent with a one-locus-two-alleles inheritance model,
 consistently raised heavier offspring than mixed pairs (grey-brown) and
 grey pairs. Offspring mass declined seasonally, except among offspring
 raised by brown pairs. Brown offspring could be heavier due to
 morph-specific parental care and/or offspring growth. Furthermore, mass at
 fledging is associated with fitness: the probability of local recruitment
 into the breeding population increased with higher mass at fledging,
 especially in mild winters and favorable food conditions, although
 recruitment is not morph-specific. Fledgling mass thus provides a fitness
 benefit in terms of recruitment probability that is modulated by
 environmental factors, which appear to level off any direct morph-specific
 recruitment benefits.
description: This is a long-term dataset on tawny owl offspring condition and
 recruitment according to color morph and winter temperature. See accepted
 publication in Am Nat for details on the methods.
description: A read-me file is uploaded explaining the variables in the two
 datasets. Further data on the methodology can be found in the accepted
 manuscript in Am Nat.
DOI: 10.5061/dryad.59zw3r24n
title: Data from: Varietal variation and chromosome behaviour during meiosis in Solanum tuberosum

description: Naturally occurring autopolyploid species such as the autotetraploid
 potato Solanum tuberosum face a variety of challenges during meiosis.
 These include proper pairing, recombination and correct segregation of
 multiple homologous chromosomes, which can form complex multivalent
 configurations at metaphase I, and in turn alter allelic segregation
 ratios through double reduction. Here, we present a reference map of
 meiotic stages in diploid and tetraploid S. tuberosum using fluorescence
 in situ hybridisation (FISH) to differentiate individual meiotic
 chromosomes 1 and 2. A diploid-like behaviour at metaphase I involving
 bivalent configurations was predominant in all three tetraploid varieties.
 The crossover frequency per bivalent was significantly reduced in the
 tetraploids compared with a diploid variety, which likely indicates
 meiotic adaptation to the autotetraploid state. Nevertheless, bivalents
 were accompanied by a substantial frequency of multivalents, which varied
 by variety and by chromosome (7-48%). We identified possible sites of
 synaptic partner switching, leading to multivalent formation, and found
 potential defects in the polymerisation and/or maintenance of the
 synaptonemal complex in tetraploids. These findings demonstrate the rise
 of S. tuberosum as a model for autotetraploid meiotic recombination
 research and highlight constraints on meiotic chromosome configurations
 and chiasma frequencies as an important feature of an evolved
 autotetraploid meiosis.
description: This dataset is collected from fluoresence <em>in
 situ</em> hybridisation (FISH) analysis of pollen mother cells at
 the metaphase I stage of meiosis, from four varieties of <em>Solanum
 tuberosum</em>. 5S and 45S rDNA probes were used to
 identify chromosomes 1 and 2 and to conservatively score chiasma on short
 and long chromosome arms based on the observed configurations and
 localisation of FISH signals. The four varieties analysed include three
 autotetraploids (Sante, Maris Peer and Cara) and one diploid
 (Scapa).
DOI: 10.5061/dryad.kd51c5b3k
title: Data from: Specialized breeding in plants affects diversification trajectories in Neotropical frogs

description: Many animals breed exclusively in plants that accumulate rainwater
 (phytotelma; e.g., bromeliad, bamboo, fruit husk, and tree hole), to which
 they are either physiologically or behaviorally specialized for this
 microhabitat. Of the numerous life-history modes observed in frogs, few
 are as striking or potentially consequential as the transition from pond-
 or stream-breeding to the deposition of eggs or larvae in phytotelmata.
 Such specialization can increase offspring survivorship due to reduced
 competition and predation, representing potential ecological opportunity
 for adaptive radiation, yet few lineages of phytotelma-breeding frogs
 appear to have diversified extensively after such a transition, at least
 in the New World. We use a phylogeny of Neotropical frogs and data on
 breeding microhabitat to understand the evolutionary transitions involved
 with specialized phytotelma-breeding. First, we find that
 phytotelma-breeding is present in at least 168 species in 10 families of
 frogs. Across the phylogeny, we estimate 14 origins of phytotelma-breeding
 and 115 reversals, showing that phytotelma-breeding is a highly labile
 character. Second, phytotelma-breeding lineages overall have higher net
 diversification than non-phytotelma-breeding ones. This specialization
 represents an ecological opportunity resulting in increased
 diversification in most families with phytotelma-breeding lineages,
 whereas phytotelma-breeding toads have restricted diversification
 histories.
description: Supporting information of Tonini et al. "Does specialized
 breeding in plants affect diversification trajectories in Neotropical
 frogs?"
DOI: 10.34740/kaggle/dsv/14644096
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.prr4xgxjb
title: Plastic changes in the brain after human hand allotransplantation

description: The physiological mechanism after hand transplant was investigated using
 magnetic resonance imaging and transcranial magnetic stimulation.
 Somatosensory and motor representations of the upper arm proximal to
 amputation occupied the hand area before surgery and moved back toward
 normal position after the surgery. The absent cortical inhibition with
 amputation increased gradually after surgery. The cortical plastic changes
 preceded functional recovery and can be used to monitor functional
 restoration after hand transplant.
description: This exploratory case study revealed physiological correlates of functional recovery after hand transplant. Changes in somatosensory cortex and primary motor cortex 4 months before and up to 6 months after hand transplantation surgery were compared. Somatosensory map of different body parts from cutaneous electrical stimulation was obtained using functional magnetic resonance imaging 4 months before and 6 months after the transplant surgery. Changes in motor cortical representations for different muscles and changes in the motor cortical circuits 4 months before and up to 6 months after the surgery were tested with transcranial magnetic stimulation.