cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ng76g
title: Data from: Anatomy and affinities of a new 535-million-year-old medusozoan from the Kuanchuanpu Formation, South China

description: We describe here Sinaster petalon gen. et sp. nov., a new embryonic form
 from the c. 535 million-year-old Kuanchuanpu Formation of South China
 (Ningqiang, Shaanxi Province). The excellent three-dimensional, phosphatic
 preservation of these microfossils allowed us to use x-ray
 microtomographic techniques to make accurate reconstructions of their
 internal structures and to compare their anatomy point-by-point with that
 of extant cnidarians and other animal groups. Sinaster petalon has
 anatomical features typical of extant Medusozoa (Cnidaria), such as
 coronal muscles, perradial and adradial frenula, interradial septa,
 accessory septa, gonad-lamellae, tentacle buds and perradial pockets.
 Although Sinaster cannot be straightforwardly assigned to any crown-group
 within Medusozoa, the presence of marginal lappets and endodermal lamellae
 suggests that it is closer to Cubozoa and Scyphozoa than to any other
 group of modern cnidarians. The tentative placement of Sinaster within the
 stem-group Cubozoa is justified by the presence of a velarium supported by
 a frenulum. The cubozoan affinities of Sinaster are also supported by
 cladistic analysis.
description: Appendix
 1S.
 petalon gen. et sp. nov. from the Lower Cambrian Kuanchuanpu Formation,
 Shaanxi Province, China; ELISN 89-107, holotype, colourless
 microtomographic sections (same as in Fig. 2). A. axial section through
 the manubrium. B–I. Horizontal sections from oral to aboral part,
 positioned as B to I in (A). *, perradius; →,
 interradius.appendix 1
 .tifAppendix
 2S.
 petalon gen. et sp. nov. from the Lower Cambrian Kuanchuanpu Formation,
 Shaanxi Province, China; ELISN 115-39, paratype, colourless
 microtomographic sections (same as in Fig. 4). A. axial section through
 the middle of the aperture. B–I. Horizontal sections from oral to aboral
 part, positioned as B' to I' in (A). *, perradius; →,
 interradius.appendix
 2.tifAppendix
 3Raw
 data and processing (PAUP* 4.0 b10) used in the cladistic
 analysis.appendix
 3.txt
DOI: 10.5061/dryad.75r10
title: Data from: Flexible transparent electrodes based on silver nanowires synthesized via a simple method

description: Silver nanowires (Ag NWs) with the length of ～60 μm and the diameter of
 ～300 nm are prepared via a simple, cost-effective, high-yield and
 eco-friendly procedure under a high molar concentration ratio of silver
 nitrate (AgNO3) solution to Poly(vinyl pyrrolidone) (PVP) solution. The
 pre-synthesized Ag NWs were analyzed by scanning electron microscopy
 (SEM), X-ray diffraction (XRD) and UV-Visible spectrophotometer.
 Furthermore, the as-prepared silver nanowires were roll-coated on the
 surfaces of the polyethylene terephthalate (PET) substrates. By optimizing
 the concentration of silver nanowire solution, the flexible Ag NW/ PET
 transparent electrodes with a sheet resistance of 3.8 Ω sq-1 at a
 transmittance of 70% can be fabricated. The results reported in this paper
 provide a basis for optimizing the growth of silver nanowires and
 performances of transparent electrodes.
description: data
 file
DOI: 10.5061/dryad.5fr18
title: Data from: Mutation predicts 40 million years of fly wing evolution

description: Mutation enables evolution, but the idea that adaptation is also shaped by
 mutational variation is controversial. Simple evolutionary hypotheses
 predict such a relationship if the supply of mutations constrains
 evolution, but it is not clear that constraints exist, and, even if they
 do, they may be overcome by long-term natural selection. Quantification of
 the relationship between mutation and phenotypic divergence among species
 will help to resolve these issues. Here we use precise data on over 50,000
 Drosophilid fly wings to demonstrate unexpectedly strong positive
 relationships between variation produced by mutation, standing genetic
 variation, and the rate of evolution over the last 40 million years. Our
 results are inconsistent with simple constraint hypotheses because the
 rate of evolution is very low relative to what both mutational and
 standing variation could allow. In principle, the constraint hypothesis
 could be rescued if the vast majority of mutations are so deleterious that
 they cannot contribute to evolution, but this also requires the
 implausible assumption that deleterious mutations have the same pattern of
 effects as potentially advantageous ones. Our evidence for a strong
 relationship between mutation and divergence in a slowly evolving
 structure challenges the existing models of mutation in evolution.
description: Houle et al.
 Nature.Data used in Houle et
 al. Nature "Mutation predicts 40 million years of fly wing
 evolution"NatureDryad.zip
DOI: 10.5061/dryad.46fr1
title: Data from: Pollen limitation, reproductive success and flowering frequency in single-flowered plants

description: 1. Flowering plants exhibit striking interspecific and intraspecific
 variation in flower number, which strongly influences the reproductive
 success of animal-pollinated plants. However, the reproductive
 consequences of producing a single flower are poorly understood. 2. Here,
 we test if plants producing a single flower have a reproductive
 disadvantage compared to plants producing multiple flowers by combining
 field investigation of five deceptive orchids and a survey of published
 literature. Pollen limitation was estimated by comparing fruit production
 between hand pollination and open pollination. Flowering frequency was
 monitored over years to assess the potential advantage of producing a
 single flower. 3. Both single- and multiple-flowered species suffered
 strong pollen limitation. However, single-flowered species had
 significantly lower fruit set and produced fewer seeds per individual,
 though they had a significantly higher pollen removal than species with
 multiple flowers. A phylogenetically independent contrast (PIC) of 28
 species representing four out of the five subfamilies of Orchidaceae
 revealed that fruit set was significantly positively associated with
 flower number. Both pollen removal and fruit set had a positive
 relationship with flower number within the multiple-flowered species. 4.
 Synthesis Current data and PIC support the hypothesis that producing a
 single flower has reproductive disadvantages. Single-flowered species may
 compensate for low female success through high flowering frequency over
 years. This study provides insight into costs and benefits of producing a
 single flower in deceptive orchids.
description: all data for
 JEcol-2016-0832.R1Sun et al_all data for
 JEcol-2016-0832.R1.xlsx
DOI: 10.18150/26oh09
title: The role of oxidative and nitrative stress and inflammation in the molecular mechanism of urolithiasis and bladder cancer development

description: Urolithiasis and bladder cancer are the most common urological diseases worldwide with an unclear aetiology. However, a growing body of evidence suggests the potential role of molecular disturbances of the inflammation as well as oxidative and nitrative stresses, in the pathogenesis of urolithiasis and bladder cancer. Moreover, it may be of particular importance to pay attention to the common pathomechanism of these diseases, as epidemiological reports indicate the occurrence of many similarities, and among them, apart from the high rate of recurrence, risk factors common for urolithiasis and BC, such as male sex or smoking, deserve attention. Therefore, we aimed to detect the potential association between six selected single-nucleotide polymorphisms (-597 A&gt;G (rs1800797) and c.3331 G&gt;A (rs2069845) in IL-6, c.+396 T&gt;G (rs2227307) in IL-8, c.47T &gt; C (p.Val16Ala) (rs4880) in SOD2, c.1823C &gt; T (p.Ser608Leu) (rs2297518) and g.-1026 C&gt;A (rs2779249) in NOS2) and the development of nephrolithiasis and bladder cancer (the TaqMan SNP genotyping assay and real-time PCR were used to genotype profiling). Moreover, we verified the association of urolithiasis or bladder cancer development and mRNA expression of IL-6, IL-8, SOD2, and NOS2 in peripheral blood mononuclear cells (the evaluation of mRNA expression was performed using real-time PCR and 2-ΔCt methods). In addition, data from the structural questionnaire to determine demographic and potential risk factors for urolithiasis and bladder cancer were obtained from patients. Patients and healthy volunteers provided information on their age, lifestyle habits (e.g. the number of fluids consumed daily, including coffee, type of diet), smoking, body mass index (BMI), and co-occurrence disease (e.g. hypertension, diabetes, hypercholesterolaemia). Moreover, the results of blood and urine analyses for each study participant were also studied. Finally, the presented experiments were conducted in cooperation with the Department of Urology of the Provincial Hospital of M. Kacprzak in Płock. In this study, it has been qualified 116 patients diagnosed with BC, 112 with urolithiasis hospitalised at the Department of Urology of the Provincial Hospital of M. Kacprzak in Płock and a homologous group of 114 healthy volunteers based on consent Bioethics Committee of the University of Lodz No. 12/KBBN-UŁ/II/2020-21. The data were obtained for the project, the aim of which was to identify potential prognostic markers of urolithiasis and bladder cancer, indicating at the same time potential common stages in the development mechanisms of the studied diseases.
DOI: 10.5061/dryad.qn7d3
title: Data from: Identification of any structure-specific hepatotoxic potential of different pyrrolizidine alkaloids using Random Forest and artificial Neural Network

description: Pyrrolizidine alkaloids (PAs) are characteristic metabolites of some plant
 families and form a powerful defence mechanism against herbivores. More
 than 600 different PAs are known. PAs are ester alkaloids composed of a
 necine base and a necic acid, which can be used to divide PAs in different
 structural subcategories. The main target organs for PA metabolism and
 toxicity are liver and lungs. Additionally, PAs are potentially genotoxic,
 carcinogenic and exhibit developmental toxicity. Only for very few PAs, in
 vitro and in vivo investigations have characterised their toxic potential.
 However, these investigations suggest that structural differences have an
 influence on the toxicity of single PAs. To investigate this structural
 relationship for a large number of PAs, a quantitative structural-activity
 relationship (QSAR) analysis for hepatotoxicity of over 600 different PAs
 was performed, using Random Forest- and artificial Neural
 Networks-algorithms. These models were trained with a recently established
 dataset specific for acute hepatotoxicity in humans. Using this dataset, a
 set of molecular predictors was identified to predict the hepatotoxic
 potential of each compound in validated QSAR models. Based on these
 models, the hepatotoxic potential of the 602 PAs was predicted and the
 following hepatotoxic rank order in three main categories defined: (i) for
 necine base: otonecine &gt; retronecine &gt; platynecine; (ii) for
 necine base modification: dehydropyrrolizidine &gt;&gt; tertiary
 PA = N-oxide and (iii) for necic acid: macrocyclic diester ≥ open-ring
 diester &gt; monoester. A further analysis with combined structural
 features revealed that necic acid has a higher influence on the acute
 hepatotoxicity than the necine base.
description: Supplementary
 1Information on the
 substructure search performed in PubChem to obtain the PA
 datasetSupplementary
 2Applicability domain of
 the DILI and the PA dataset, showing the four first principal components
 (PC1 – PC4)
DOI: 10.5061/dryad.tr3d8
title: Data from: Evolution and conservation of Characidium sex chromosomes

description: Fish species exhibit substantial variation in the degree of genetic
 differentiation between sex chromosome pairs, and therefore offer the
 opportunity to study the full range of sex chromosome evolution. We used
 restriction-site associated DNA sequencing (RAD-seq) to study the sex
 chromosomes of Characidium gomesi, a species with conspicuous
 heteromorphic ZW/ZZ sex chromosomes. We screened 9863 single-nucleotide
 polymorphisms (SNPs), corresponding to ~1 marker/100 kb distributed across
 the genome for sex-linked variation. With this data set, we identified 26
 female-specific RAD loci, putatively located on the W chromosome, as well
 as 148 sex-associated SNPs showing significant differentiation (average
 FST=0.144) between males and females, and therefore in regions of more
 recent divergence between the Z and W chromosomes. In addition, we
 detected 25 RAD loci showing extreme heterozygote deficiency in females
 but which were in Hardy–Weinberg equilibrium in males, consistent with
 degeneration of the W chromosome and therefore female hemizygosity. We
 validated seven female-specific and two sex-associated markers in a larger
 sample of C. gomesi, of which three localised to the W chromosome, thereby
 providing useful markers for sexing wild samples. Validated markers were
 evaluated in other populations and species of the genus Characidium, this
 exploration suggesting a rapid turnover of W-specific repetitive elements.
 Together, our analyses point to a complex origin for the sex chromosome of
 C. gomesi and highlight the utility of RAD-seq for studying the
 composition and evolution of sex chromosomes systems in wild populations.
description: Characidium filtered
 RADtagsFasta file containing
 the sequences of the 9,863 final filtered Radtags (biallelic SNPs with a
 minimum depth of 10 reads and genotyped in at least 28
 individuals)9863_characidium.selectedRAD.fa
DOI: 10.5061/dryad.32152
title: Data from: Genome-wide sensitivity analysis of the microsymbiont Sinorhizobium meliloti to symbiotically important, defensin-like host peptides

description: The model legume species Medicago truncatula expresses more than 700
 nodule-specific cysteine-rich (NCR) signaling peptides that mediate the
 differentiation of Sinorhizobium meliloti bacteria into nitrogen-fixing
 bacteroids. NCR peptides are essential for a successful symbiosis in
 legume plants of the inverted-repeat-lacking clade (IRLC) and show
 similarity to mammalian defensins. In addition to signaling functions,
 many NCR peptides exhibit antimicrobial activity in vitro and in vivo.
 Bacterial resistance to these antimicrobial activities is likely to be
 important for symbiosis. However, the mechanisms used by S. meliloti to
 resist antimicrobial activity of plant peptides are poorly understood. To
 address this, we applied a global genetic approach using transposon
 mutagenesis followed by high-throughput sequencing (Tn-seq) to identify S.
 meliloti genes and pathways that increase or decrease bacterial
 competitiveness during exposure to the well-studied cationic NCR247
 peptide and also to the unrelated model antimicrobial peptide polymyxin B.
 We identified 78 genes and several diverse pathways whose interruption
 alters S. meliloti resistance to NCR247. These genes encode the following:
 (i) cell envelope polysaccharide biosynthesis and modification proteins,
 (ii) inner and outer membrane proteins, (iii) peptidoglycan (PG) effector
 proteins, and (iv) non-membrane-associated factors such as transcriptional
 regulators and ribosome-associated factors. We describe a previously
 uncharacterized yet highly conserved peptidase, which protects S. meliloti
 from NCR247 and increases competitiveness during symbiosis. Additionally,
 we highlight a considerable number of uncharacterized genes that provide
 the basis for future studies to investigate the molecular basis of
 symbiotic development as well as chronic pathogenic interactions.
description: Total Tn-seq read counts
 for all annotated S. meliloti genesTable shows the total
 number of Illumina reads obtained for each S. meliloti gene for all tested
 conditions. The raw results are shown as observed and then the normalized
 read counts per gene are also included.all genes Tn-seq
 results.xlsxAll S. meliloti genes
 Tn-seq results highlighting all Tn insertionsThe table shows all Tn
 insertions that have been observed by Illumina sequencing and their
 corresponding read counts for each condition. The dataset includes raw
 read counts for each Tn insertion as well as the normalized read counts.
 The dataset also includes the location of each transposon in each
 corresponding gene.all genes Tn-seq results Tn
 insertions.xlsx
DOI: 10.5061/dryad.tk1v8
title: Data from: Seed origin and warming constrain lodgepole pine recruitment, slowing the pace of population range shifts

description: Understanding how climate warming will affect the demographic rates of
 different ecotypes is critical to predicting shifts in species
 distributions. Here we present results from a common garden, climate
 change experiment in which we measured seedling recruitment of lodgepole
 pine, a widespread North American conifer that is also planted globally.
 Seeds from a low-elevation provenance had greater recruitment to their
 third year (by 323%) than seeds from a high-elevation provenance across
 sites within and above its native elevation range and across climate
 manipulations. Heating reduced (by 49%) recruitment to the third year of
 both low- and high-elevation seed sources across the elevation gradient,
 while watering alleviated some of the negative effects of heating (108%
 increase in watered plots). Demographic models based on recruitment data
 from the climate manipulations and long-term observations of adult
 populations revealed that heating could effectively halt modeled upslope
 range expansion except when combined with watering. Simulating fire and
 rapid post-fire forest recovery at lower elevations accelerated lodgepole
 pine expansion into the alpine, but did not alter final abundance rankings
 among climate scenarios. Regardless of climate scenario, greater
 recruitment of low-elevation seeds compensated for longer dispersal
 distances to treeline, assuming colonization was allowed to proceed over
 multiple centuries. Our results show that ecotypes from lower elevations
 within a species’ range could enhance recruitment and facilitate upslope
 range shifts with climate change.
description: Conlisk_etal_GCB2017_model_archive06282017The models and results shown in manuscript figures 4-6 are archived as text files for use with RAMAS GIS (Version 5).
DOI: 10.5061/dryad.t9888
title: Data from: Sharing is caring? measurement error and the issues arising from combining 3D morphometric datasets

description: Geometric morphometrics is routinely used in ecology and evolution and
 morphometric datasets are increasingly shared among researchers, allowing
 for more comprehensive studies and higher statistical power (as a
 consequence of increased sample size). However, sharing of morphometric
 data opens up the question of how much nonbiologically relevant variation
 (i.e., measurement error) is introduced in the resulting datasets and how
 this variation affects analyses. We perform a set of analyses based on an
 empirical 3D geometric morphometric dataset. In particular, we quantify
 the amount of error associated with combining data from multiple devices
 and digitized by multiple operators and test for the presence of bias. We
 also extend these analyses to a dataset obtained with a recently developed
 automated method, which does not require human-digitized landmarks.
 Further, we analyze how measurement error affects estimates of
 phylogenetic signal and how its effect compares with the effect of
 phylogenetic uncertainty. We show that measurement error can be
 substantial when combining surface models produced by different devices
 and even more among landmarks digitized by different operators. We also
 document the presence of small, but significant, amounts of nonrandom
 error (i.e., bias). Measurement error is heavily reduced by excluding
 landmarks that are difficult to digitize. The automated method we tested
 had low levels of error, if used in combination with a procedure for
 dimensionality reduction. Estimates of phylogenetic signal can be more
 affected by measurement error than by phylogenetic uncertainty. Our
 results generally highlight the importance of landmark choice and the
 usefulness of estimating measurement error. Further, measurement error may
 limit comparisons of estimates of phylogenetic signal across studies if
 these have been performed using different devices or by different
 operators. Finally, we also show how widely held assumptions do not always
 hold true, particularly that measurement error affects inference more at a
 shallower phylogenetic scale and that automated methods perform worse than
 human digitization.
description: Landmark
 coordinatesLandmark coordinates in
 tab delimited format. The name of each observation is formatted as
 Genus_species_device_operatorFruciano_et_al_2017-Ecology_and_Evolution-Measurement_Error-rawcoordinates.txtTree posterior distributionsPosterior distribution of trees used in the analyses of variation in estimates of phylogenetic signal due to measurement error and phylogenetic uncertainty.Fruciano_et_al_2017-Tree_Posterior_distributions.zipGPSA dataOrdinations and singular values used for the analyses of measurement error in GPSA.GPSA.zip
DOI: 10.5061/dryad.tn36j
title: Data from: A framework for the identification of long-term social avoidance in longitudinal datasets

description: Animal sociality is of significant interest to evolutionary and
 behavioural ecologists, with efforts focused on the patterns, causes and
 fitness outcomes of social preference. However, individual social patterns
 are the consequence of both attraction to (preference for) and avoidance
 of conspecifics. Despite this, social avoidance has received far less
 attention than social preference. Here, we detail the necessary steps to
 generate a spatially explicit, iterative null model which can be used to
 identify non-random social avoidance in longitudinal studies of social
 animals. We specifically identify and detail parameters which will
 influence the validity of the model. To test the usability of this model,
 we applied it to two longitudinal studies of social animals (Eastern water
 dragons (Intellegama leseurii) and bottlenose dolphins (Tursiops aduncus)
 to identify the presence of social avoidances. Using this model allowed us
 to identify the presence of social avoidances in both species. We hope
 that the framework presented here inspires interest in addressing this
 critical gap in our understanding of animal sociality, in turn allowing
 for a more holistic understanding of social interactions, relationships
 and structure.
description: <strong>dryad_dolphin_data</strong><br> Data -
 dolphins
 <strong>dryad_dolphin_availability</strong><br>
 Availability file for dolphin model
 <strong>digidolph</strong><br> R code for
 creation of null model - dolphins
 <strong>digidolph_helper_functions</strong><br>
 R code - custom functions for use with creation of dolphin model
 <strong>dragon permutations</strong><br> R code
 for creation of null model for dragons
 <strong>hwi_functions</strong><br> R code -
 custom functions for use in creation of dragon model
 <strong>README_dragondata_RSOScorrection.txt</strong> <strong>dragon_data_dryad_corrected.csv</strong>