cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mc810bq
title: Data from: Photocatalytic activity of graphene oxide–TiO2 thin films sensitized by natural dyes extracted from Bactris guineensis

description: This study synthesized and characterized composites of graphene oxide and
 TiO2 (GO-TiO2). GO-TiO2 thin films were deposited using the Doctor Blade
 technique. Subsequently, the thin films were sensitized with a natural dye
 extracted from a Colombian source (Bactris guineensis). Thermogravimetric
 analysis, X-ray diffraction, Raman spectroscopy, scanning electron
 microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and diffuse
 reflectance measurements were used for physicochemical characterization.
 All the samples were polycrystalline in nature, and the diffraction
 signals corresponded to the TiO2 anatase crystalline phase. Raman
 spectroscopy and FT-IR verified the synthesis of composite thin films, and
 the SEM analysis confirmed the TiO2 films morphological modification after
 the process of GO incorporation and sensitization. XPS results suggested a
 possibility of appearance of Titanium (III) through the formation of
 oxygen vacancies (Ov). Furthermore, the optical results indicated that the
 presence of the natural sensitizer and GO improved the optical properties
 of TiO2 in the visible range. Finally, the photocatalytic degradation of
 Methylene Blue (MB) was studied under visible irradiation in aqueous
 solution, and pseudo-first order model was used to obtain kinetic
 information about photocatalytic degradation. These results indicated that
 the presence of GO has an important synergistic effect in conjunction with
 the natural sensitizer, reaching a photocatalytic yield of 33%.
description: Manuscript
 dataSpectroscopic
 Characterizationdata
 manuscript_2.zip
DOI: 10.34740/kaggle/dsv/14639194
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.4d3f4g3
title: Data from: Environmental DNA metabarcoding studies are critically affected by substrate selection

description: Effective biomonitoring is critical for driving management outcomes that
 ensure long-term sustainability of the marine environment. In recent years
 environmental DNA (eDNA), coupled with metabarcoding methodologies, has
 emerged as a promising tool for generating biotic surveys of marine
 ecosystems, including those under anthropogenic pressure. However, more
 empirical data is needed on how to best implement eDNA field sampling
 approaches to maximise their utility for each specific application. The
 effect of the substrate chosen for eDNA sampling on the diversity of
 marine taxa detected by DNA metabarcoding has not yet been systematically
 analysed, despite aquatic systems being those most commonly targeted for
 eDNA studies. We investigated the effect of four commonly used eDNA
 substrates to explore taxonomic diversity: (i) surface water, (ii) marine
 sediment, (iii) settlement-plates and (iv) planktonic tows. With a focus
 on coastal ports, 332 eDNA samples from Australia (Indian and Southern
 oceans) and Kazakhstan (Caspian Sea) were collected and analysed by
 multi-assay DNA metabarcoding. Across study locations, between 30-52% of
 eukaryotic families detected were unique to a particular substrate and
 less than 6% of families were found in all four substrates. Taxonomic
 composition varied significantly depending on the substrate sampled
 implying that the suitability (and bias) of an eDNA substrate will depend
 on the focal taxa. These findings demonstrate that single substrate eDNA
 metabarcoding likely underestimates the total eukaryotic diversity. Future
 eDNA experimental design should consider incorporating multiple substrates
 or select substrate(s) best suited to the specific detection of target
 taxa.
description: EnvironmentalDNA_SubstrateSelection_Albany_GardenIsland_Ersai_Bautino_CaspianSeaFasta files were generated through usearch9.2 from Miseq .fastq reads. Fasta files are labelled by their unique sample name, place sampled and substrate type. All fasta files were filtered following the methods from the paper "Environmental DNA metabarcoding studies are critically affected by substrate selection"
DOI: 10.5061/dryad.6d778b6
title: Data from: Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data

description: Cultivated bivalves are hugely important not only because of their
 economic value, but also due to their impacts on natural ecosystems. The
 Pacific oyster (Crassostrea gigas) is the world's most heavily
 cultivated shellfish species and has been introduced to all continents
 except Antarctica for aquaculture. We therefore used a medium density
 single nucleotide polymorphism (SNP) array to investigate the genetic
 structure of this species in Europe, where it was introduced during the
 1960s and has since become a prolific invader of coastal ecosystems across
 the continent. We analyzed 21,499 polymorphic SNPs in 232 individuals from
 23 localities spanning a latitudinal cline from Portugal to Norway and
 including the source populations of Japan and Canada. We confirmed the
 results of previous studies by finding clear support for a southern and a
 northern group, with the former being indistinguishable from the source
 populations indicating the absence of a pronounced founder effect. We
 furthermore conducted a large-scale comparison of wild and hatchery
 populations to reveal substantial genetic differences including
 significantly higher levels of inbreeding in some but not all of the
 hatchery populations. These findings were confirmed by a smaller but
 representative SNP dataset generated using restriction site associated DNA
 sequencing. We therefore conclude that genomic approaches can generate
 increasingly detailed insights into the genetics of invasive populations,
 while also providing a novel window on how hatchery propagation may
 influence inbreeding, with important economic and management implications.
description: Cgigas_SNPArray_genotypesGenotypes for 232 oyster samples in PED format obtained from the medium density SNP array described in Gutierrez et al. (2017).Cgigas_SNPArray.pedCgigas_SNPArray_map_fileSNPs identifiers in MAP format relative to the PED file containing genotypes based on the SNP array.Cgigas_SNPArray.mapCgigas_RADseq_map_filesSNPs identifiers in PED format relative to the PED file containing genotypes based on RAD sequencing.Cgigas_RADseq_SNPs.mapCgigas_RADseq_genotypesGenotypes for 40 oyster samples in PED format obtained by the analysis of RAD sequencing data.Cgigas_RADseq_SNPs.ped
DOI: 10.5061/dryad.qp25093
title: Data from: Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs

description: Leaf traits are frequently measured in ecology to provide a ‘common
 currency’ for predicting how anthropogenic pressures impact ecosystem
 function. Here, we test whether leaf traits consistently respond to
 experimental treatments across 27 globally distributed grassland sites
 across 4 continents. We find that specific leaf area (leaf area per unit
 mass)—a commonly measured morphological trait inferring shifts between
 plant growth strategies—did not respond to up to four years of soil
 nutrient additions. Leaf nitrogen, phosphorus and potassium concentrations
 increased in response to the addition of each respective soil nutrient. We
 found few significant changes in leaf traits when vertebrate herbivores
 were excluded in the short-term. Leaf nitrogen and potassium
 concentrations were positively correlated with species turnover,
 suggesting that interspecific trait variation was a significant predictor
 of leaf nitrogen and potassium, but not of leaf phosphorus concentration.
 Climatic conditions and pretreatment soil nutrient levels also accounted
 for significant amounts of variation in the leaf traits measured. Overall,
 we find that leaf morphological traits, such as specific leaf area, are
 not appropriate indicators of plant response to anthropogenic
 perturbations in grasslands.
description: NutNet_foliar_data This data includes leaf traits that were collected from the three to five most dominant species in each plot including specific leaf area, and leaf N, P and K concentrations. This file also include site level climatic and edaphic conditions: mean annual temperature, temperature seasonality, mean annual precipitation, precipitation seasonality, pre-treatment soil nitrogen by mass %, pre-treatment soil phosphorus by mass (ppm) and pre-treatment soil potassium by mass (ppm). A sheet is included in the data file explains each column and is called metadata.    In the version of this Article originally published, we made mistakes when converting SLA values at 10 of the 27 sites in the dataset. These mistakes occurred when converting SLA from cm<sup>2</sup>/g to mm<sup>2</sup>/g and from mm<sup>2</sup>/mg to mm<sup>2</sup>/g. After we corrected these unit conversion mistakes, we realised that two data points for SLA were no longer plausible: the SLA value at the Frue.ch site plot 27 <i>Phlelum Pratense</i> as the value was &gt;300,000 and a value from the shps.us site for <i>Poa Secunda</i> plot 31, which was &lt;60; these two values were changed to ‘NA’ in the dataset. Compared to the original data, the following sites have had SLA changed in these ways to account for mistakes in unit conversions:   blder.us all values x10<br> bunch.us all values x 10<br> Burrawan.au all values divide by 10<br> jena.de all values x 10<br> MtCaroline.au all values divide by 10<br> UNC.us all values x 10<br> CBGB.us all values x 10<br> Summ.za all values x 10<br> valm.ch all values x 100<br> Smith.us x10    An Author correction has been submitted to Nature Ecology and Evolution.
DOI: 10.5061/dryad.6gd8hb5
title: Data from: Trade-offs for butterfly alpha and beta diversity in human-modified landscapes and tropical rainforests

description: The accelerating expansion of human populations and associated economic
 activity across the globe have made maintaining large, intact natural
 areas increasingly challenging. The difficulty of preserving large intact
 landscapes in the presence of growing human populations has led to a
 growing emphasis on landscape approaches to biodiversity conservation with
 a complementary strategy focused on improving conservation in
 human-modified landscapes. This, in turn, is leading to intense debate
 about the effectiveness of biodiversity conservation in human-modified
 landscapes and approaches to better support biodiversity in those
 landscapes. Here, we compared butterfly abundance, alpha richness, and
 beta diversity in human-modified landscapes [urban, sugarcane] and
 natural, forested areas to assess the conservation value of human-modified
 landscapes within the Wet Tropics bioregion of Australia. We used
 fruit-baited traps to sample butterflies and analyzed abundance and
 species richness in respective land uses over a one-year period. We also
 evaluated turnover and spatial variance components of beta diversity to
 determine the extent of change in temporal and spatial variation in
 community composition. Forests supported the largest numbers of
 butterflies, but were lowest in each, alpha species richness, beta
 turnover, and the spatial beta diversity. Sugarcane supported higher
 species richness, demonstrating the potential for conservation at local
 scales in human-modified landscapes. In contrast, beta diversity was
 highest in urban areas, likely driven by spatial and temporal variation in
 plant composition within the urban landscapes. Thus, while improving
 conservation on human-modified landscapes may improve local alpha
 richness, conserving variation in natural vegetation is critical for
 maintaining high beta diversity.
description: Sambhu et al.
 dataMicrosoft Excel was used
 to create this data file, which contains abundance data for butterflies
 sampled from June 2016 to May 2017 in three locations along the Wet
 Tropics bioregion of Queensland, Australia, as part of Hemchandranauth
 Sambhu's Ph.D. research project. The file also contains a key sheet
 with details of each code used, and formatted data for NMDS
 analysis.
DOI: 10.5061/dryad.m799h3r
title: Data from: Invasive invertebrates associated with highly duplicated gene content

description: Invasions of alien species have led to serious problems, including the
 destruction of native ecosystems. In general, invasive species adapt to
 novel various environments rapidly, suggesting that they have high genetic
 diversity that could directly influences environmental adaptability.
 However, we do not yet know how genomic architecture generates genetic
 diversity that leads to invasive species. Recent studies showed that the
 proportion of duplicated genes (PD) in whole animal genomes correlated
 with environmental variability within habitat. Here, we show that PD and
 propagule size significantly explain the differences in species categories
 (invasive species, non-invasive species and parasites). PD correlated
 negatively with propagule size, and then, based on the residual values of
 regression of propagule size on PD, invasive species had higher PD values
 and larger propagule size than non-invasive species whereas parasites had
 lower PD values and smaller propagule size than others. There were no
 correlations between invasive species and other genomic factors including
 genome size, number of genes, and certain gene families. Our results
 suggest that PD values of a genome might be potential genomic sources
 producing genetic variations for adaptation to diverse environments. The
 results also showed that the invasive status of species can be fairly
 predicted by the residual values of the regression of propagule size on
 PD. Our innovative approach gives us a measure that can be used to
 estimate the environmental adaptability of organisms based on genomic
 data.
description: R_scriptsThis file contains R scripts for analysis of data in this publication.Phylogenetic trees based on maximum likelihood analysis of concatenated amino acid sequences of orthologues among fully sequenced invertebrate genomesA phylogenetic tree of 44 invertebrate species drawn using concatenated 35 orthologous sequences.full_species_raxml_tree.phPhylogenetic trees based on maximum likelihood analysis of concatenated amino acid sequences of orthologues among non-parasites with fully sequenced genomesA phylogenetic tree of 34 non-parasites drawn using concatenated 106 orthologous sequences.non_parasites_raxml_tree.phInformation for 44 invertebrate speciesInput data of R analysis for invertebrate species used in this studyfull_species_tableInformation for 34 non-parasite speciesInput data of R analysis for 34 non-parasite species used in this studynon_parasites_tableSize of Panther families for each non-parasite speciesSize of 7,446 Panther families for each non-parasite species including invasive and non-invasive speciesnon_parasite_family_size_tableRank of Panther family size for each non-parasite speciesRank of Panther family size for each non-parasite species including invasive and non-invasive speciesnon_parasites_family_size_rank_table
DOI: 10.5061/dryad.hp250fb
title: Data from: Quantifying the completeness of the bat fossil record

description: Bats (Chiroptera) are one of the most successful extant mammalian orders,
 uniquely capable of powered flight and laryngeal echolocation. The timing
 and evidence for evolution of their novel adaptations has been difficult
 to ascertain from the fossil record due to chronological gaps (e.g. during
 the Palaeocene) and the fragmentary nature of most fossil bat material.
 Changes in fossil specimen completeness through time and space can bias
 our understanding of macroevolutionary processes. Here, we quantify the
 quality of the bat fossil record using skeletal and character completeness
 metrics, which respectively document what proportion of a complete
 skeleton is preserved for a specimen, and the proportion of phylogenetic
 characters that can be scored for a specimen. Completeness scores were
 collected from the literature for 441 valid fossil bat species in 167
 genera from the Eocene to Pleistocene. All metrics record similar temporal
 patterns: peak completeness in the Lutetian Stage reflects the presence of
 Lagerstätten, while subsequent stages have very low completeness with the
 exception of an Aquitanian high and a Pleistocene peak in skeletal
 completeness. Bat completeness is not correlated with intensity of
 sampling through geological time but has a weak negative correlation with
 publication date. There is no correlation between taxonomic richness and
 completeness, as the bat fossil record predominately consists of
 diagnostic but isolated teeth. Consequently, bat skeletal completeness is
 the lowest of any previously assessed tetrapod group, but character
 completeness is similar to parareptiles and birds. Bats have significantly
 higher character completeness in the northern hemisphere, likely due to
 heightened historical interest and presence of Lagerstätten. Taxa derived
 from caves, fissure fills and sink holes are more complete than those from
 fluviolacustrine and marine deposits, but do not preserve highly complete
 specimens.
description: Bat Completeness
 DatasetBat specimen and species
 preservation - along with completeness scores calculated for this
 study.Bat_completeness_datasheet.xlsxBat Completeness Supplementary 1Additional tables and figures to accompany this studySupplementary1_BatCompleteness.pdfSupplementary 2 Bat Character ListList of osteological characters used to determine the relative skeletal weightings for the CCM2.Supplementary2_BatCharacterList.pdf
DOI: 10.5061/dryad.6kv7k29
title: Data from: Input matters matter: bioclimatic consistency to map more reliable species distribution models

description: 1. Accuracy of global bioclimatic databases is essential to understand
 biodiversity-environment relationships. Many studies have explored biases
 and uncertainties related to species distribution models (SDMs) but the
 effect of choosing a specific database among the different alternatives
 has not been previously assessed. 2. The lack of bioclimatic congruence
 (degree of agreement) between different databases is a main concern in
 distribution modelling and it is critical in single-source models, for
 which the database choice is decisive. In order to prevent unreliable
 predictions derived from distorted input data, SDMs accuracy can be
 assessed by mapping model predictions according to a bioclimatic
 congruence measure derived from the comparison of multiple databases,
 which can be achieved with the bioclimatic consistency maps that we
 propose in this study. Here, i) we present the first global-scale
 bioclimatic congruence map to analyse environmental mismatches between
 recently updated bioclimatic databases. We also test the importance of
 input matters on the reliability of distribution models of sixteen
 mammals, by addressing ii) inconsistencies among species response curves
 (temperature and precipitation), and iii) discrepancies among SDMs
 predictions depending on the chosen bioclimatic database. Finally, iv) we
 propose a strategy to assess bioclimatic consistency of model predictions,
 showing its application to the specific case of Litocranius walleri. 3.
 Our results confirm that the single-source modelling approach greatly
 influences the estimation of species-environment relationship and
 consequently, bias spatial predictions derived from SDMs. This is
 especially true for studies conducted in polar and mountainous regions
 which showed the smallest bioclimatic congruence. We show that by adding
 bioclimatic congruence to SDMs projections, we can build a bioclimatic
 consistency map that enables the detection of both risky and consistent
 areas, as revealed for the case of L. walleri. 4. Assessing uncertainty in
 bioclimatic input data is key to avoid erroneous conclusions in
 macroecological and biogeographical studies. The spatial characterisation
 of bioclimatic consistency provides an adequate empirical framework which
 effectively illustrates bioclimatic data limitations. We strongly
 recommend that this new strategy should be formally and systematically
 incorporated into distribution modelling to build more reliable SDMs,
 which are essential to develop successful biodiversity conservation
 programmes.
description: Files to perform the
 working example of bioclimatic consistency strategyMap of bioclimatic
 congruence (congruence.grd) and the SDM prediction of Litucranius walleri
 (pr_Litocranius_walleri.grd) to perform the working example of bioclimatic
 consistency strategy.Morales-Barbero_Vega-Álvarez_consistensy_shapes_.rar
DOI: 10.5061/dryad.5vv774m
title: Data from: Preclinical toxicity and pharmacokinetics of a new orally bioavailable flubendazole formulation and the impact for clinical trials and risk/benefit to patients.

description: Background: Flubendazole, originally developed to treat infections with
 intestinal nematodes, has been shown to be efficacious in animal models of
 filarial infections. For treatment of filarial nematodes, systemic
 exposure is needed. For this purpose, an orally bioavailable amorphous
 solid dispersion (ASD) formulation was developed. As this formulation
 results in improved systemic absorption, the pharmacokinetic and
 toxicological profile of flubendazole administered with this formulation
 have been assessed to ensure human safety before clinical trials could be
 initiated. Methods & Findings: Safety pharmacology, toxicity and
 genotoxicity studies have been conducted with the flubendazole ASD
 formulation. In animals, flubendazole has good oral bioavailability from
 an ASD formulation ranging from 15 % in dogs, 276 % in rats to more than
 100% in jirds. In in vivo toxicity studies with the ASD formulation, high
 systemic exposure to flubendazole and its main metabolites was reached.
 Flubendazole, up to high peak plasma concentrations, does not induce Cmax
 related effects in the CNS or cardiovascular system. In repeated dose
 toxicity studies in rats and dogs, flubendazole-induced changes were
 observed in haematological, lymphoid and gastrointestinal systems and in
 testes. In dog, the liver was an additional target organ. Upon treatment
 cessation, at least partial recovery was observed for these changes in the
 dog. In rat, the low dose was the No Observed Adverse Effect Level (NOAEL)
 was , i.e. 5 mg (as base)/kg body weight/day (mg eq./kg/day)mg eq./kg/day
 in males and 2.5 mg eq./kg/day in females. In dog, the NOAEL was lower
 than the low dose, 20 mg eq./kg/day. Regarding genotoxicity, flubendazole
 was negative in the Ames test but positive in the in vivo micronucleus
 test. Conclusions: Based on these results, in combination with previously
 described genotoxicity and reproductive toxicity data and the outcome of
 the preclinical efficacy studies, it was concluded that no flubendazole
 treatment regimen can be selected that would provide efficacy in humans at
 safe exposure.
description: Reports paper
 Risk_Benefit Orally Bioavailable Flubendazole
 Formulationreports containing full
 description of methods and all data of toxicity studies and
 pharmacokinetic studies described in the paper