cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.905qfttjm
title: COVID-CDR: An integrative resource for network-based investigation of COVID-19 combinatorial drug repositioning and mechanism of action

description: Repurposing of the existing medications has become the mainstream focus of
 anti-COVID-19 drug discovery as it offers rapid and cost-effective
 solutions for therapeutic development. However, a great effort is still
 required to enhance the efficacy of repurposing therapeutic options
 through combination therapy, in which promising drugs with varying
 mechanisms of action are administered together. Nonetheless, our ability
 to identify and validate effective combinations is limited due to the vast
 number of possible drug pairs. Yet, there is no
 available resource that
 can systematically guide to identify or
 choose the effective individual drugs or best
 possible synergistic drug combinations for the treatment
 of SARS-CoV-2 infection. To address this resource gap, we developed a
 web-based platform that displays the network-based mechanism of action of
 drug combinations, thus simultaneously providing a visual of the cellular
 interactome involved in modes of action of the chosen drugs. The platform
 allows the freedom to select two or more drug combinations and provides
 the options to investigate the network-based efficacy of drug combinations
 and understand the similarity score, primary indications, and pairwise
 synergistic scores on different cell-lines. In a nutshell, the platform
 (accessible via http://vafaeelab.com/COVID19_repositioning.html) is the
 first of its type, which provides a systematic approach for pre-clinical
 investigation of combination therapy for treating COVID-19 at the
 fingertips of the clinicians or researchers.
description: A ReadMe.csv file is uploaded providing the description and
 format of each data set. A tutorial video on using the corresponding
 interface is available online
 (http://vafaeelab.com/COVID19_repositioning.html). Details of data and
 usage note is also detailed in the preprint.
DOI: 10.5061/dryad.905qfttjn
title: UV-green dichromacy in the basal hymenoptera Sirex noctilio (Hymenoptera: Siricidae)

description: A precondition for colour vision is the presence of at least two spectral
 types of photoreceptors in the eye. In the Apocrita, trichromacy is the
 basal pattern. Most species possess three different photoreceptor types in
 their compound eyes, with peak sensitivities in the ultraviolet, blue and
 green range of the light spectrum, and the corresponding visual pigments,
 the opsins. Experimental studies in basal Hymenoptera report from one to
 four photoreceptors, but results remained inconclusive. To better
 understand the evolution of photoreceptor diversity in the Hymenoptera, we
 studied the global pine pest Sirex noctilio (Siricidae),
 which belongs to the superfamily Siricoidea, the closest sister group of
 Apocrita. Our aim was to i) characterise the visual opsins of S.
 noctilio by genomic comparisons and phylogenetic analyses of the
 opsin genes and ii) to identify the photoreceptor types of the compound
 eye by electroretinography. We identified three opsins in the genome,
 homologous to the hymenopteran LW1, LW2 and UV opsin genes.
 Electroretinographical measurements confirmed the presence of two
 photoreceptor types maximally sensitive to 527 and 363 nm in the compound
 eye. The lack of a SW-homologous opsin gene and a corresponding receptor
 suggests that S. noctilio is a UV-green dichromate.
DOI: 10.5061/dryad.sqv9s4n2t
title: Factorial design assisted RP-HPLC method for simultaneous determination of fluconazole, itraconazole, and terbinafine

description: A 23 full factorial design model was utilized for development of a new
 HPLC method with UV detection to estimate three antifungal drugs
 simultaneously. Fluconazole (FLU), itraconazole (ITR) and terbinafine
 (TRH), which are co-administered for severe fungal infections have been
 determined using MOS-1 Hypersil C18 column and an isocratic eluent;
 methanol 95% and phosphate buffer 5% with 0.001% triethylamine. The pH
 adjusted 7, and flow rate of  0.7 mL/min. The three drugs were
 separated within less than 7 minutes at 210 nm. The developed method gave
 linear response over 5-80, 5-50 and 1-50 μg/mL for FLU, ITR and TRH,
 respectively. It showed detection limits of 0.8761, 0.293 and 0.1965 μg/mL
 and quantification limits of 2.655, 0.8788 and 0.5956 μg/mL for the three
 drugs, respectively. The design of experiment facilitated the optimization
 of different variables affecting the separation of the three drugs. The
 designed method sensitivity permitted the simultaneous estimation of ITR
 and TRH in spiked human plasma successfully.
description: Laboratory work was carried
 out by A.R. in addition to data analysis and drafting the
 manuscript. H.E.
 and S.S. contributed to the study design and the statistics.
 A.E.-B. organized the
 overall study. All authors permitted the
 publication of the manuscript.
DOI: 10.5061/dryad.6wwpzgmx2
title: Experimental parasite community perturbation reveals associations between Sin Nombre virus and gastrointestinal nematodes in a rodent reservoir host

description: Individuals are often co-infected with several parasite species, yet
 measuring within-host interactions remains difficult in the wild.
 Consequently, the impact of such interactions on host fitness and
 epidemiology are often unknown. We used anthelmintic drugs to
 experimentally reduce nematode infection and measured the effects on both
 nematodes and the important zoonosis Sin Nombre virus (SNV) in its primary
 reservoir (Peromyscus spp.). Treatment significantly reduced nematode
 infection, but increased SNV seroprevalence. Furthermore, mice that were
 co-infected with both nematodes and SNV were in better condition and
 survived up to four times longer than uninfected or singly-infected mice.
 These results highlight the importance of investigating multiple parasites
 for understanding interindividual variation and epidemiological dynamics
 in reservoir populations with zoonotic transmission potential.
DOI: 10.5061/dryad.1rn8pk0s6
title: The complex history of genome duplication and hybridization in North American gray treefrogs

description: Polyploid speciation has played an important role in evolutionary history
 across the tree of life, yet there remain large gaps in our understanding
 of how polyploid species form and persist. While systematic studies have
 been conducted in numerous polyploid complexes, recent advances in
 sequencing technology have demonstrated that conclusions from data-limited
 studies may be spurious and misleading. The North American gray treefrog
 complex, consisting of the diploid Hyla chrysoscelis and the
 tetraploid Hyla versicolor, has long been used as a model system
 in a variety of biological fields, yet all taxonomic studies to date were
 conducted with only a few loci from nuclear and mitochondrial genomes.
 Here, we utilized anchored hybrid enrichment and high-throughput
 sequencing to capture hundreds of loci along with whole mitochondrial
 genomes to investigate the evolutionary history of this complex. We used
 several phylogenetic and population genetic methods, including coalescent
 simulations and testing of polyploid speciation models with Approximate
 Bayesian Computation (ABC), to determine that H. versicolor was most
 likely formed via autopolyploidization from a now extinct lineage of H.
 chrysoscelis. We also uncovered evidence of significant hybridization
 between diploids and tetraploids where they co-occur, and show that
 historical hybridization between these groups led to the re-formation of
 distinct polyploid lineages following the initial whole genome duplication
 event. Our study indicates that a wide variety of methods and explicit
 model testing of polyploid histories can greatly facilitate efforts to
 uncover the evolutionary history of polyploid complexes.
description: Sequence data was collected using Anchored Hybrid Enrichment and
 sequenced on an Illumina Hi-seq. Data were processed using the standard
 Anchored pipeline as described in the article.
description: SNPs.rar: SNP files used for STRUCTURE and other SNP
 analyses.  GTF_trees_alignments: Trees and alignments
 for all phylogenetic analyses. Allelephaser.jar: Custom
 allele phaser script. First used in Pyron (2016) (doi:10.5061/
 dryad.51v22). GTF_Polyploid_ABC: All scripts and
 example data to conduct polyploid ABC model testing
 analyses. ABC_locusinfo.txt: Loci and
 number of individuals for each lineage used for polyploid ABC
 analyses.
DOI: 10.5061/dryad.7sqv9s4r7
title: Data for: The genetic basis of floral mechanical isolation between two hummingbird-pollinated Neotropical understory herbs

description: Floral divergence can contribute to reproductive isolation among plant
 lineages, and thus provides an opportunity to study the genetics of
 speciation, including the number, effect size, mode of action, and
 interactions of quantitative trait loci (QTL). Moreover, flowers represent
 suites of functionally interrelated traits, but it is unclear to what
 extent the phenotypic integration of the flower is underlain by a shared
 genetic architecture, which could facilitate or constrain correlated
 evolution of floral traits. Here, we examine the genetic architecture of
 floral morphological traits involved in an evolutionary switch from bill
 to forehead pollen placement between two species of hummingbird-pollinated
 Neotropical understory herbs that are reproductively isolated by these
 floral differences. For the majority of traits, we find multiple QTL of
 relatively small effect spread throughout the genome. We also find
 substantial colocalization and alignment of effects of QTL underlying
 different floral traits that function together to promote outcrossing and
 reduce heterospecific pollen transfer. Our results are consistent with
 adaptive pleiotropy or linkage of many coadapted genes, either of which
 could have facilitated a response to correlated selection and helped to
 stabilize divergent phenotypes in the face of low levels of hybridization.
 Moreover, our results indicate that floral mechanical isolation can be
 consistent with an infinitesimal model of adaptation.
description: A description of each file can be found in the File_manifest.txt
 file. There is also an associated ReadMe file with each zipped folder of
 code.
DOI: 10.5061/dryad.1jwstqjt7
title: Joint Mitnor Cave T-LiDAR Scan data

description: Here we present the first detailed, modern survey of Joint Mitnor Cave,
 Buckfastleigh, Devon, UK. The cave is an extremely important Last
 Interglacial palaeontological site because it is the type site for the
 hippopotamus-dominated British Pleistocene mammal assemblage of that
 period, “The Joint Mitnor Cave Mammal Assemblage Zone”; and because it is
 the least damaged Last Interglacial cave bone bed still remaining in
 Britain. The survey, meticulously drawn from terrestrial LIDAR scans,
 offers a precise (± &lt;3mm 3D 1 δ) view of the cave, and can act as
 the base map for future conservation projects and other studies.
description: The cave was scanned with a Faro M70 scanner (Faro Technologies,
 Florida). 11 scans were taken on different locations in the cave. Scan
 resolution was set to 1/5 resulting in 8270 x 3415 data points/scan or a
 total of 28.3 Megapoints. Quality was set to 4x and pictures were taken to
 collect additional RGB values for each scan points. Individual scan times
 were 5 minutes 11 seconds. The raw scans were assembled
 with cloud to cloud registration using SCENE (version 2019.2, Faro
 Technologies). The resulting project point cloud was exported from SCENE
 as a .pts file (ascii file containing X, Y, Z, reflection value, R, G, B)
 containing 151,099,474 points. The file was then
 imported into CloudCompare and the point density was reduced by a factor
 of 7.5 resulting in a more manageable file size of 20 Megapoints, and
 exported as a .ply file. The final .ply file is 371 MB large.
 No conversion to a mesh has been done.
description: This .ply file can be viewed in a range of software. For
 processing cave data, we can recommend CloudCompare
 (https://cloudcompare.org).
DOI: 10.5061/dryad.h9w0vt4gr
title: Alignments of Sequence Data for Phylogenetic Analysis of Damsel

description: Initially described in 1882, Chromis enchrysurus, the Yellowtail Reeffish,
 was redescribed in 1982 to account for an observed color morph that
 possesses a white tail instead of a yellow one, but morphological and
 geographic boundaries between the two color morphs were not well
 understood. Taking advantage of newly collected material from submersible
 studies of deep reefs and photographs from rebreather dives, we sought to
 determine whether the white-tailed Chromis is actually a color morph of
 Chromis enchrysurus or a distinct species. These alignments for
 mitochondrial genes cytochrome b and cytochrome c oxidase subunit
 I  were used to generate phylogenetic trees that separated
 Chromis enchrysurus and the white-tailed Chromis into two reciprocally
 monophyletic clades. Genetic, morphological, and biogeographic
 data all indicate that the white-tailed Chromis is a distinct species,
 herein described as Chromis vanbebberae sp. nov. The discovery of a new
 species within a conspicuous group such as damselfishes in a well-studied
 region of the world highlights the importance of deep-reef exploration in
 documenting undiscovered biodiversity.
description: Sequence data for <em>Chromis enchrysurus</em> and
 <em>Chromis vanbebberae</em> were collected via DNA extraction
 and sanger sequencing. Sequences for other pomacentrid species were
 imported from GenBank. Sequences were aligned in Geneious version
 10.2.6.
DOI: 10.5061/dryad.3j9kd51gp
title: Specialist predation covaries with colour polymorphism in tawny owls

description: Understanding intraspecific phenotypic variation in prey specialisation
 can help to predict how long-term changes in prey availability affect the
 viability of these phenotypes and their persistence. Generalists are
 favoured when the main food resources are unpredictable compared to
 specialists, which track the availability of the main prey and are more
 vulnerable to changes in the main food resource. Intraspecific heritable
 melanin-based colour polymorphism is considered to reflect adaptations to
 different environments. We studied colour morph-specific diet
 specialisation in a generalist predator, tawny owl (Strix aluco), during
 offspring food provisioning in relation to mammal prey density. We
 hypothesised that the grey morph, with higher fitness than the brown in
 Northern boreal conditions, is more specialised in mammalian prey than the
 brown morph, which in turn has higher fitness than the grey in the
 temperate zone. We found a higher diversity of prey delivered to the nest
 by brown fathers compared to grey ones, which also depended on the overall
 mammalian prey availability. Brown fathers provided proportionally fewer
 mammalian prey than grey in poor, but not in favourable mammal prey years.
 Our results suggest that the brown morph is more generalistic and reacts
 more strongly to variations in food supply than the grey morph, which may
 be a beneficial strategy in an unpredictable environment caused by
 environmental degradation. Significance statement Diet choice of a species
 may vary depending on fluctuations in the abundance of their food
 resource, but also within a population, there can be adaptations to use
 different food resources. The tawny owl exhibits a grey and a
 reddish-brown colour morph and is considered a generalist predator eating
 both mammal and bird prey. We find that the diet of the reddish-brown
 morph is more diverse than that of the grey. When the tawny owls’ main
 prey, small mammals, are abundant both colour morphs prey on mammals, but
 in years with less small mammals, the reddish-brown morph is more prone of
 switching to small bird predation than the grey. The generalist strategy
 of the brown morph is likely to be more favourable than a stricter
 specialisation in small mammals of the grey under recently reoccurring
 irregularities in small mammal dynamics.
description: The dataset was collected in Southern Finland 2013-2018.
description: Please find more information in the attached README file
DOI: 10.5061/dryad.prr4xgxkc
title: Multimodal mechanosensing enables treefrog embryos to escape egg-predators

description: Mechanosensory-cued hatching (MCH) is widespread, diverse, and improves
 survival in many animals. From flatworms and insects to frogs and turtles,
 embryos use mechanosensory cues and signals to inform hatching timing, yet
 mechanisms mediating mechanosensing in ovo are largely unknown. The
 arboreal embryos of red-eyed treefrogs, Agalychnis callidryas, hatch
 prematurely to escape predation, cued by physical disturbance in snake
 attacks. When otoconial organs in the developing vestibular system become
 functional, this response strengthens, but its earlier occurrence
 indicates another sensor must contribute. Post-hatching, tadpoles use
 lateral line neuromasts to detect water motion. We ablated neuromast
 function with gentamicin to assess their role in A. callidryas’ hatching
 response to disturbance. Prior to vestibular function, this nearly
 eliminated the hatching response to a complex simulated attack cue,
 egg-jiggling, revealing that neuromasts mediate early MCH. Vestibular
 function onset increased hatching, independent of neuromast function,
 indicating young embryos use multiple mechanosensory systems. MCH
 increased developmentally. All older embryos hatched in response to
 egg-jiggling, but neuromast function reduced response latency. In
 contrast, neuromast ablation had no effect on timing or level of hatching
 in motion-only vibration playbacks. It appears only a subset of
 egg-disturbance cues stimulate neuromasts; thus embryos in attacked
 clutches may receive uni- or multimodal stimuli. A. callidryas embryos
 have more neuromasts than described for any other species at hatching,
 suggesting precocious sensory development may facilitate MCH. Our findings
 provide insight into the behavioral roles of two mechanosensory systems in
 ovo and open possibilities for exploring sensory perception across taxa in
 early life stages.
DOI: 10.5061/dryad.2rbnzs7mh
title: Data related to: Bottom-up effects of fungicides on tadpoles of the European common frog (Rana temporaria)

description: We have uploaded a range of files informding about ergosterol and bacteria
 levels on leaf litter (LeafMicrobes.xlsx); the feces production, leaf
 consumption and legnth development of tadpoles during the study and among
 the two experimental phases as detailed in the
 mansucript (FecesFeedingLength.xlxs); composition of fatty acids
 in tadpoles and leaf litter (NFLA.xlxs); metamophoses event
 (Metamorphosis.xlsx)   Paper abstract as submitted: Biodiversity
 is under pressure world-wide, with amphibians being particularly
 threatened. Stressors related to human activity, such as chemicals, are
 contributing to this decline. It remains, however, unclear whether
 chemicals exhibiting a fungicidal activity could indirectly affect
 tadpoles, that depend on microbially conditioned leaf litter as food
 source. The indirect effect of fungicides (sum concentration of a
 fungicide mixture composed of azoxystrobin, carbendazim, crybrodinil,
 quinoxifen and tebuconcazole: 100 µg/L) on tadpoles was assessed relative
 to leaf litter colonised by microbes in absence of fungicides (control)
 and a worst case scenario, that is leached leaf litter without microbial
 colonisation. The quality of leaf litter as food for tadpoles of
 the European common frog (Rana temporaria) was
 characterised through neutral lipid fatty acid profiles and
 microbial sum parameters and verified by sublethal responses in tadpoles
 (i.e. feeding rate, feces production, growth and fatty acid
 composition). Fungicides changed the nutritious quality of leaf
 litter likely through alterations in leaves’ neutral
 lipid fatty acid profiles (i.e., changes in some physiologically
 important highly unsaturated fatty acids reached more than
 200%) in combination with a potential adsorption onto leaves
 during conditioning. These changes were reflected by differences
 in the development
 of tadpoles ultimately resulting in an earlier
 start of metamorphosis. Our data provide a first indication that
 fungicides potentially affect tadpole development indirectly through
 bottom-up effects. This pathway is so far not addressed in fungicide
 environmental risk assessment and merits further attention.
description: The methods are detailed in the paper at Ecology and Evolution,
 which is published open access. 
 LeafMicrobes.xlsx<br> the file contains data on ergosterol
 and bacteria associated with leaf litter normalised to leaf mass (sie line
 1 of the respective sheets)
 FecesFeedingLength.xlsx<br> the file contains data on feces
 production, leaf consumption and length development of tadpoles in both
 experimental phases. The first two variabels are normalised to the lengths
 of the respective tadpoles and scaled to a day. The length is reported in
 mm. NLFA.xlsx<br> the file reports mean
 concentrations of individual fatty acids in leaf litter and tadpoles
 together with confidence intervals of the respective treatment.
DOI: 10.15468/dl.bdavhd
title: Occurrence Download

description: A dataset containing 1539 records in GBIF matching the query:
SELECT
 '446' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= 59.94074752362532
 AND decimalLongitude &lt;= 69.23837900975829
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 1539 records were derived from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002667-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.