cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5068/d1px0k
title: Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation

description: Functional biomolecules, such as RNA, encapsulated inside a protocellular
 membrane are believed to have comprised a very early, critical stage in
 the evolution of life, since membrane vesicles allow selective
 permeability and create a unit of selection enabling cooperative
 phenotypes. The biophysical environment inside a protocell would differ
 fundamentally from bulk solution, due to the microscopic confinement.
 However, the effect of the encapsulated environment on ribozyme evolution
 has not been previously studied experimentally. Here we examine the effect
 of encapsulation inside model protocells on the self-aminoacylation
 activity of tens of thousands of RNA sequences, using a high-throughput
 sequencing assay. We find that encapsulation of these ribozymes generally
 increases their activity, giving encapsulated sequences an advantage over
 non-encapsulated sequences in an amphiphile-rich environment. In
 addition, highly active ribozymes benefit disproportionately more from
 encapsulation. The asymmetry in fitness gain broadens the distribution of
 fitness in the system. Consistent with Fisher’s Fundamental Theorem of
 Natural Selection, encapsulation therefore leads to faster adaptation when
 the RNAs are encapsulated inside a protocell during in
 vitro selection. Thus, protocells would not only provide
 a compartmentalization function, but also promote activity and
 evolutionary adaptation during the origin of life.
description: <strong>File name explanation</strong>
 The file contains the archived raw data from the high-throughput
 sequencing assay in the study. The "InV" and
 "OutV" indicate the encapsulated and unencapsulated conditions,
 respectively. The "kSeq" indicates the data
 for k-Seq experiments of doped RNA pool. The
 "selection" indicates the data for the in-vitro selection
 experiments starting from a random sequence pool. The
 *-fastqs.zip contains the raw data. The dereplicated list created by the
 EasyDIVER pipeline (https://github.com/ichen-lab-ucsb/EasyDIVER) is
 archived in the *-counts.zip files. For the k-Seq data analysis, the
 achieved MATLAB workspace, scripts, and Readme files are included in the
 *-matlab.zip file.
DOI: 10.5061/dryad.ffbg79ct2
title: Data from: First measurements of field metabolic rate in wild juvenile fishes show strong thermal sensitivity but variations between sympatric ecotypes

description: The relationship between physiology and temperature has a large influence
 on population-level responses to climate change. In natural settings,
 direct thermal effects on metabolism may be exaggerated or offset by
 behavioural responses influencing individual energy balance. Drawing on a
 newly developed proxy, we provide the first estimates of the thermal
 performance curve of field metabolism in a wild fish. We investigate the
 thermal sensitivity of field metabolic rate in two sympatric, genetically
 distinct ecotypes of Atlantic cod from the Skagerrak coast of southern
 Norway. The combined ecotype median of field metabolic rate increased with
 increasing temperature until around 16°C, coincident with the thermal
 optimum for growth for juvenile Atlantic cod. Individual cod experienced
 temperatures in excess of the thermal optimum for field metabolic rate,
 indicating some degree of thermal limitation of field metabolism in a
 complex natural environment with the potential for thermal refugia. The
 two cod ecotypes showed different thermal performance curves for field
 metabolic rate, revealing that genetic components to temperature
 sensitivity persist beyond acclimation effects. The cold-adapted fjord
 ecotype maintained higher field metabolic rates at cooler temperatures
 than the warm-adapted North Sea ecotype, which showed clear preference for
 warmer waters around the thermal optimum. Field metabolic rates of the two
 ecotypes were strongly influenced by year and location of sampling,
 implying more complex behavioural responses to environmental conditions.
 We emphasise that the energy uses reflecting physiological conditions in
 the field should be considered in the evaluation of the effect of climatic
 variables on fish population dynamics and demonstrate that otolith
 isotopes provide an analytical framework to answer this question.
DOI: 10.5061/dryad.h18931zjp
title: Wildland-urban interface fire dynamics simulator input files for pyric tree spatial patterning interactions in historical and contemporary mixed conifer forests, California, USA

description: Tree spatial patterns in dry coniferous forests of the western US, and
 analogous ecosystems globally, were historically aggregated, comprising a
 mixture of single trees and groups of trees. Modern forests, in contrast,
 are generally more homogeneous and overstocked than their historical
 counterparts. As these modern forests lack regular fire, pattern formation
 and maintenance is generally attributed to fire. Accordingly, fires in
 modern forests may not yield historically analogous patterns. However,
 direct observations on how selective tree mortality among pre-existing
 forest structure shapes tree spatial patterns is limited. In this study,
 we (1) simulated fires in historical and contemporary counterpart plots in
 a Sierra Nevadan mixed-conifer forest, (2) estimated tree mortality, and
 (3) examined tree spatial patterns of live trees before and after fire,
 and of fire-killed trees. Tree mortality in the historical period was
 clustered and density-dependent, because trees were aggregated and
 segregated by tree size before fire. Thus, fires maintained an aggregated
 distribution of tree groups. Tree mortality in the contemporary period was
 widespread, except for dispersed large trees, because most trees were a
 part of large, interconnected tree groups. Thus, post-fire tree patterns
 were more uniform and devoid of moderately sized tree groups. Post-fire
 tree patterns in the historical period, unlike the contemporary period,
 were within the historical range of variability identified for the western
 US. This divergence suggests that decades of forest dynamics without
 significant disturbances has altered the historical means of pyric pattern
 formation. Our results suggest that ecological silvicultural treatments,
 such as forest restoration thinnings, which emulate qualities of
 historical forests may facilitate the reintroduction of fire as a means to
 reinforce forest structural heterogeneity.
description: These input files are executable by the Wildland-urban interface
 Fire Dyamics Simuator, a computational fluid dynamics computer program.
 Embedded within the input files are tree lines which represent the
 location and size of individual trees.
description: In order to replicate this study, one needs to execute these
 inputs files in Wildland-urban interface Fire Dyamics Simuator. There are
 6 input files, one for each fire scenario. File names are formatted as
 [plotname]_[year].fds (see manuscript for details on individual
 scenarios.
DOI: 10.5061/dryad.c2fqz616n
title: Context dependent benefits of aphids for bacteria in the phyllosphere.

description: Insect herbivores, like aphids, are common on plants yet how they interact
 with plant microbiomes remains largely unknown. For instance, for the
 widespread bacterial epiphyte and potential aphid pathogen Pseudomonas
 syringae, aphids could impact bacterial populations by serving as
 secondary hosts or by altering the epiphytic habitat through feeding
 and/or waste secretion. Here we examined if the pea aphid, Acyrthosiphon
 pisum, could influence epiphytic populations of P. syringae. First, we
 quantified epiphytic growth ability without aphids and virulence to aphids
 across 21 diverse P. syringae strains. For eight strains that varied in
 these traits we then assessed the influence of aphid presence on epiphytic
 bacterial growth. In some cases, P. syringae benefited significantly from
 the presence of aphids, with up to 3.8 times more cell doublings. This
 benefit was not correlated with strain traits, but rather with initial
 population densities; smaller bacterial populations received relatively
 more benefit from aphids, and larger populations received less benefit.
 Honeydew, the sugary waste product of aphids, in the absence of aphids was
 sufficient to increase P. syringae density on leaves. We conclude that
 aphid honeydew can sometimes increase P. syringae epiphytic growth, but
 that the bacteria may not benefit from using aphids as hosts.
DOI: 10.5061/dryad.fttdz08r9
title: U(VI) adsorption in water by sodium alginate modified Bacillus megaterium

description: The surface of Bacillus megaterium was modified by coating sodium
 alginate. The modified Bacillus megaterium before and after adsorption
 were characterized by SEM, FTIR and XPS. The effects of pH, reaction time,
 initial U(VI) concentration and adsorbent dosage on the adsorption of
 U(VI) by the modified Bacillus megaterium were studied by batch adsorption
 experiments. The adsorption process was studied by pseudo-first-order
 kinetics and pseudo-second-order kinetic models, Langmuir and Freundlich
 isotherms. The results showed that the maximum adsorption capacity of
 U(VI) was 74.61 mg/g under the conditions of pH 5.0, adsorbent 0.2 g/L, 30
 ℃ and initial U(VI) concentration of 15 mg/L. The adsorption process
 accords with pseudo-first-order kinetics and Langmuir isotherm. The
 adsorption capacity of U(VI) by the modified Bacillus megaterium was still
 higher than 80% after 5 times of desorption and reuse experiments. In
 conclusion, the sodium alginate modified Bacillus megaterium was an ideal
 material for U(VI) biosorption.
DOI: 10.5061/dryad.pk0p2ngm7
title: SARS-CoV-2 encephalitis presenting as a clinical cerebellar syndrome: a case report

description: This report contributes to the rapidly expanding knowledgebase of
 COVID-19-associated neurological syndromes and highlights uncertainties
 regarding the pathogenesis of cerebellar dysfunction in, and optimal
 management of, patients with COVID-19-associated encephalitis.
DOI: 10.5061/dryad.sj3tx963j
title: Horizontal acquisition of Symbiodiniaceae in the Anemonia viridis genetic data

description: All metazoans are in fact holobionts, resulting from the association of
 several organisms, and organismal adaptation is then due to the composite
 response of this association to the environment. Deciphering the
 mechanisms of symbiont acquisition in a holobiont is therefore essential
 to understanding the extent of its adaptive capacities. In cnidarians,
 some species acquire their photosynthetic symbionts directly from their
 parents (vertical transmission) but may also acquire symbionts from the
 environment (horizontal acquisition) at the adult stage. The Mediterranean
 snakelocks sea anemone, Anemonia viridis (Forskål, 1775), passes down
 symbionts from one generation to the next by vertical transmission, but
 the capacity for such horizontal acquisition is still unexplored. To
 unravel the flexibility of the association between the different host
 lineages identified in A. viridis and its Symbiodiniaceae, we genotyped
 both the animal hosts and their symbiont communities in members of host
 clones in five different locations in the North Western Mediterranean Sea.
 The composition of within-host symbiont populations was more dependent on
 the geographical origin of the hosts than their membership to a given
 lineage or even to a given clone. Additionally, similarities in host
 symbiont communities were greater among genets (i.e. among different
 clones) than among ramets (i.e. among members of the same given clonal
 genotype). Taken together, our results demonstrate that A. viridis may
 form associations with a range of symbiotic dinoflagellates and suggest a
 capacity for horizontal acquisition. A mixed-mode transmission strategy in
 A. viridis, as we posit here, may help explain the large phenotypic
 plasticity that characterises this anemone.
description: The DNA were extracted from sea anemone tentacles.
 The <em>Anemoni viridis</em> SNPs were obtained by
 RADsequencing firstly filtered with ipyrad. The
 symbiont markers were obtained by Illumina sequencing and analysed with
 SymPortal pipeline (ITS2 sequences) or with obiTools and MicNeSs
 (microsatellites).
DOI: 10.15468/dl.2qndsg
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Hopea chinensis"
 ]
}

 The dataset includes 65 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002669-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f4qrfj6v3
title: Differing limb functions and their potential influence upon the diversification of the mustelid hindlimb skeleton

description: Though form-function relationships of the mammalian locomotor system have
 been investigated for over a century, recent models of trait evolution
 have hitherto been seldom used to identify likely evolutionary processes
 underlying the locomotor system’s morphological diversity. Using
 mustelids, an ecologically diverse carnivoran lineage, I investigated
 whether variation in hindlimb skeletal morphology functionally coincides
 with climbing, digging, swimming, and generalized locomotor habits by
 using 15 linear traits of the femur, tibia, fibula, calcaneum, and
 metatarsal III across 44 species in a principal components analysis. I
 subsequently fit different models of Brownian motion and adaptive trait
 diversification individually to each trait. Climbing, digging, and
 swimming mustelids occupy distinct regions of phenotypic space
 characterized by differences in bone robustness. Models of adaptive and
 neutral evolution are, respectively, the best fits for long bone lengths
 and muscle in-levers, suggesting that different kinds of traits may be
 associated with different evolutionary processes. However, simulations
 based upon models of best fit reveal low statistical power to rank the
 models. Though differences in mustelid hindlimb skeletal morphology appear
 to coincide with locomotor habits, further study, with sampling expanded
 beyond Mustelidae, is necessary to better understand to what degree
 adaptive evolution shapes morphological diversity of the locomotor system.
description: Data was collected using digital caliper measurements. Units of
 measurement: mm. Code was written in R.
description: Missing values are highlighted in black in Excel spreadsheet. For
 fitting of trait evolution models, bootstrapping of model parameters, and
 data simulation, the archived R code presents the OU4 model as base code.
 Other models (OU3_SRG, OU3_SNM, etc.) were fit by modifying this base
 code.
DOI: 10.5061/dryad.2bvq83bp7
title: C. rufifacies heat stress data

description: The increased severity and frequency of elevated temperatures due to
 climate change is changing species distributions and driving thermal
 selection for several species, but many potential effects are still
 unknown. Here, we investigated the effects of an acute thermal stress on
 the oviposition performance of the hairy maggot blow fly Chrysomya
 rufifacies (Macquart), an introduced species of ecological, economic, and
 forensic importance. Adult virgins were exposed to 25°C, 42°C, or 44°C for
 1-h, and then maintained at ~25°C in mixed-sex colonies for 14-d.
 Pre-breeding heat exposure had no effect on male or female reproductive
 success, except for females exposed to 44°C. Females exposure to 44°C
 before breeding oviposited sooner (2.5 ± 0.0 days), more frequently (0.52
 ± 0.4), and produced a greater total egg mass (1.18 ± 0.25 g) than any
 other treatment group. Thus, a brief exposure to non-lethal elevated
 temperatures may affect the timing and intensity of insect oviposition,
 potentially affecting ecological processes and related applications.
description: See paper
DOI: 10.15468/dl.jwrvjy
title: Occurrence Download

description: A dataset containing 3611 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Diplachne fusca"
 ]
}

 The dataset includes 3611 records from 189 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002666-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6t1g1jwxj
title: Longitudinal proteomic profiling of high-risk patients with COVID-19 reveals markers of severity and predictors of fatal disease

description: End-stage kidney disease (ESKD) patients are at high risk of severe
 COVID-19. We performed dense serial blood sampling in hospitalised and
 non-hospitalised ESKD patients with COVID-19 (n=256 samples from 55
 patients) and used Olink immunoassays to measure 436 circulating proteins.
 Comparison to 51 non-infected ESKD patients revealed 221 proteins
 differentially expressed in COVID-19, of which 69.7% replicated in an
 independent cohort of 46 COVID-19 patients. 203 proteins were associated
 with clinical severity scores, including IL6, markers of monocyte
 recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g proteinase-3)
 and epithelial injury (e.g. KRT19). Random Forests machine learning
 identified predictors of current or future severity such as KRT19, PARP1,
 PADI2, CCL7, and IL1RL1 (ST2). Survival analysis with joint models
 revealed 69 predictors of death including IL22RA1, CCL28, and the
 neutrophil-derived chemotaxin AZU1 (Azurocidin). Finally, longitudinal
 modelling with linear mixed models uncovered 32 proteins that display
 different temporal profiles in severe versus non-severe disease, including
 integrins and adhesion molecules. Our findings point to aberrant innate
 immune activation and leucocyte-endothelial interactions as central to the
 pathology of severe COVID-19. The data from this unique cohort of
 high-risk individuals provide a valuable resource for identifying drug
 targets in COVID-19.
description: Code available for replication and re-analysis of
 data: https://github.com/jackgisby/longitudinal_olink_proteomics
DOI: 10.6084/m9.figshare.31165003
title: The compiled field-observation database used for ratoon rice yield modelling

description: We compiled a field-observation database to develop a ratoon rice yield prediction model by systematically reviewing studies published between January 1980 and March 2024 in Web of Science and CNKI using keywords including “ratoon rice” and “regenerated rice”. The final dataset contains 1,096 georeferenced observations from field experiments.
DOI: 10.6084/m9.figshare.31165003.v1
title: The compiled field-observation database used for ratoon rice yield modelling

description: We compiled a field-observation database to develop a ratoon rice yield prediction model by systematically reviewing studies published between January 1980 and March 2024 in Web of Science and CNKI using keywords including “ratoon rice” and “regenerated rice”. The final dataset contains 1,096 georeferenced observations from field experiments.
DOI: 10.5061/dryad.7h44j0zsr
title: Data from: Ecological factors influence balancing selection on leaf chemical profiles of a wildflower

description: Balancing selection is frequently invoked as a mechanism to maintain
 variation within and across populations. However, rigorous tests
 demonstrating balancing selection operating in nature are scarce,
 particularly on complex traits, which frequently display high levels of
 variation. Leveraging a focal polymorphism, leaf chemical profile in a
 perennial wildflower (Boechera stricta, Brassicaceae), we investigated the
 ecological and genetic mechanisms that may influence the maintenance of
 variation in this trait. A suite of common garden and greenhouse
 experiments showed that the alleles underlying variation in chemical
 profile have contrasting fitness effects across environments, implicating
 two ecological drivers of selection on chemical profile: herbivory and
 drought. Phenotype-environment associations and molecular genetic analyses
 revealed additional evidence of past selection by these drivers. Together,
 these data are consistent with balancing selection on chemical profile,
 likely caused by pleiotropic effects of genes that influence secondary
 chemical biosynthesis on herbivore defense and drought response.
description: The studies reported here include: analytical chemistry, field
 transplant experiments, field array experiments, a lab herbivory assay,
 two drought tolerance dry-down experiments, Sanger sequencing analysis,
 and analyses of genomic data to characterize linkage disequilibrium,
 flanking genes, and <em>F<sub>ST</sub></em>. Full
 details regarding the study design for each of these components are
 provided in Methods, Results, and Supplementary Information of the
 manuscript.
description: All usage notes are provided in the enclosed README.txt
 file.
DOI: 10.5061/dryad.kprr4xh3h
title: Microsatellite genotypes and associated data for: The contribution of clonality to population genetic structure in the sea anemone Diadumene lineata

description: Ecological and evolutionary processes differ depending on how genetic
 diversity is organized in space. For clonal organisms, the organization of
 both genetic and genotypic diversity can influence the fitness effects of
 competition, the mating system, and reproductive mode, which are key
 drivers of life cycle evolution. Understanding how individual reproductive
 behavior contributes to population genetic structure is essential for
 disentangling these forces, particularly in species with complex and
 plastic life cycles. The widespread sea anemone Diadumene lineata exhibits
 temperature-dependent fission which contributes to predictable variation
 in clonal rate along the Atlantic coast of the United States, part of its
 non-native range. Because warmer conditions lead to higher rates of
 clonality, we expected to find lower genotypic and genetic diversity in
 lower versus higher latitude populations. We developed primers for 11
 microsatellite loci and genotyped 207 anemones collected from 8 sites
 ranging from Florida to Massachusetts. We found clonal influence at all
 sites, and as predicted, the largest clones were found at lower latitude
 sites. We also found genetic signatures of sex in the parts of the range
 where gametogenesis is most common. Evidence of sex outside the native
 range is novel for this species and provides insights into the dynamics of
 this successful invader. Our findings also illustrate challenges that
 partially clonal taxa pose for eco-evolutionary studies, such as
 difficulty sampling statistically robust numbers of genets and
 interpretating common population genetic metrics. For example, we found
 high among-locus variation in Fis, which makes the meaning of mean
 multilocus Fis unclear.
description: See methods of associated article.
 Microsatellite data were generated
 for individuals of
 the sea anemone Diadumene lineata
 by WH Ryan, J Aida and
 SA Krueger-Hadfield using PCR
 primers designed and tested by the same authors. Microsatellite primer
 information is reported in the associated manuscript (Ryan, Aida,
 Krueger-Hadfield 2021, Journal of Heredity). Anemones were collected by WH
 Ryan in 2016. Further details of collection protocol and additional use of
 samples can be found in Ryan and Miller
 2019. Ryan WH and Miller TE. 2019.
 Reproductive strategy changes across
 latitude in a clonal sea anemone. Marine Ecological Progress
 Series. 611: 129 –
 141.
description: See "metadata" tab for column descriptions.