cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pg4f4qrpf
title: Variable strength of predator-mediated effects on species occurrence in an arctic terrestrial vertebrate community

description: Indirect effects resulting from species sharing the same enemy can shape
 spatio-temporal variations in species occurrence. The strength of such
 effects remains poorly known in natural communities composed of species
 from different trophic levels interacting in heterogeneous landscapes.
 Benefiting from a well-known arctic vertebrate community and marked
 spatio-temporal variations in the density of key prey species, we examined
 the effects of direct predator-prey and indirect predator-mediated effects
 on species occurrence in the landscape. We found both positive effects of
 one prey (lemmings), as well as negative indirect effects of another prey
 (colonial nesting snow geese) on the occurrence of species (ground-nesting
 birds) belonging to different guilds and trophic levels but sharing a
 common predator (arctic fox). However, species using prey refuges
 available in the landscape were not or less affected by predator-mediated
 effects. Similarly, the smallest (a passerine) and the largest and most
 dangerous species (an owl) for the shared predator were not affected by
 these effects. Our study provides one of the rare empirical evidence of
 predator-mediated effects ascending the food web (i.e., negative indirect
 effect of an herbivore on avian predators) and underlines how habitat
 structure and species traits can modulate the strength of indirect effects
 in natural communities.
description: The dataset provided here contains the data used in each of the
 models presented in the article "Variable strength of
 predator-mediated effects on species occurrence in an arctic terrestrial
 vertebrate community". These data are the processed values (as
 described in the method section and supporting information of the article)
 used to model the effects of lemming density and distance to a goose
 colony on the occurrence of various nesting birds. Mapped data is
 available in supporting information of the article.
description: The README file contains column descriptions and general
 information for the analyses.
DOI: 10.5061/dryad.2jm63xspf
title: Prisma checklist: Pharmacological management of seizures in patients with COVID-19: a systematic review

description: The PRISMA checklist provides information on the 27-item
 checklist indicating where data on the introduction, methods, results and
 discussion sections of the publication titled "Pharmacological
 management of seizures in patients with COVID-19: a systematic
 review" may be located in the manuscript.  This checklist
 also covers information such as competing interests.
DOI: 10.5061/dryad.00000003k
title: Sugar preferences of Camponotus modoc and Myrmica rubra

description: A stable source of carbohydrates is essential for the longevity of ant
 colonies. Foraging ants must select among carbohydrate resources, such as
 aphid honeydew, that vary based on sugar type, volume and concentration.
 Using Western carpenter ants, Camponotus modoc, and European fire ants,
 Myrmica rubra as model species, we tested the hypothesis that ant foraging
 on aphid honeydew is driven by aphid-specific sugars (unique sugars
 biosynthesized by aphids) and that ants will selectively consume
 particular mono,- di-, and tri-saccharides. In choice bioassays, we
 offered whole ant colonies with aqueous sugar solutions and measured their
 consumption. In C. modoc, common sugar constituents (rather than
 aphid-specific sugars) and sugar concentration affected consumption by
 ants. Colonies of C. modoc and M. rubra preferred fructose to other
 monosaccharides (xylose, glucose) and sucrose to other disaccharides
 (maltose, melibiose, trehalose). Conversely, when offered a choice between
 the aphid-specific trisaccharides raffinose and melezitose, C. modoc and
 M. rubra favored raffinose and melezitose, respectively.
DOI: 10.5061/dryad.ghx3ffbnt
title: An approach for estimating haplotype diversity from sequences with unequal lengths

description: 1. Genetic diversity is an essential component of biodiversity. Developing
 robust quantification methods is critically important in depicting the
 genetic diversity underlying the geographical distributions of species,
 especially for the sequence data with unequal lengths. 2. Traditional
 calculation of genetic diversity depends on sequences of equal length.
 However, many homologous sequences downloaded from online repositories
 vary in length, posing a significant challenge to quantify the genetic
 diversity, especially haplotype diversity. We developed a new approach
 independent of sequence length by applying the same parameters used in
 calculating nucleotide diversity to estimate haplotype diversity. We
 compared this novel approach with the calculations by the program DNAsp,
 and we used simulation data from terrestrial vertebrates (birds, mammals,
 and amphibians) and Homo sapiens to validate the method’s performance. We
 further applied this approach to explore the global latitudinal gradients
 of haplotype diversity in amphibians, mammals, and birds, and compared the
 results by traditional methods. 3. The haplotype diversity calculated by
 our novel approach is consistent with the results from DNAsp. The
 simulations showed that our approach is robust and has a good estimating
 performance for sequence data with unequal lengths. 4. For the datasets of
 terrestrial vertebrates and H. sapiens, our approach is capable of
 estimating haplotype diversity with unequal intraspecific sequence
 lengths. In contrast to patterns based on traditional methods, we observed
 different latitudinal patterns of haplotype diversity between the northern
 and southern hemispheres for terrestrial vertebrates, which is consistent
 with the updated pattern of nucleotide diversity for mammals. The present
 work contributes to the development of more precise quantification
 methods, which may be broadly applied to assessing biogeographical
 patterns of genetic diversity.
DOI: 10.5061/dryad.95x69p8kj
title: Seismoelectric and electroseismic datasets for a shallow or ground surface source

description: The datasets are numerical modelling results of seismoelectric and
 electroseismic wave-fields computed by the updated algorithm which
 combines the Luco-Apsel-Chen generalized reflection and transmission
 coefficient method (GRTM) and the peak-trough averaging method
 (PTAM) for a shallow or ground surface source. In addition, the
 code of the peak-trough averaging method (PTAM) adopted in seismoelectric
 or electroseismic modelling is cleaned up into a separate Matlab
 package (named SE_PTAM) and uploaded, which can be easily transplanted
 into the seismoelectric or electroseismic modelling algorithms based on
 reflectivity methods (e.g., Garambois & Dietrich, 2002; Grobbe et
 al., 2016; Haartsen & Pride, 1997; Ren et al., 2010a).
description: The datasets are computed by the updated algorithm which combines
 the Luco-Apsel-Chen generalized reflection and transmission coefficient
 method (GRTM) and the peak-trough averaging method (PTAM).
description: The datasets are divided into 5 parts: DataSets S1 to
 S5, which include all the data presented in the
 seismoelectric and electroseismic modelling for a shallow or
 ground surface source.  The three GIF files, display
 the propagation animations of the electroseismic wave-fields computed by
 considering the peak frequency of the Ricker wavelet to be fp=800 Hz,
 fp=80 Hz, and fp=400 Hz, respectively. The amplitudes of the animations of
 the electroseismic wave-fields for fp=80 Hz and fp=400 Hz cases are
 adjusted by multiplying the third power of the distance between the
 receiver and the projection point of the electric current source on the
 first subsurface interface in an effort to improve the visibility of
 relatively weaker signals. The corresponding snapshots are displayed in
 Figures 6, 8, and 9 of the manuscript, respectively.
 The "readme.txt" file is presented as a guide to the
 datasets and three GIF files. The uploaded PTAM code
 contains three MATLAB files, i.e., the main function
 "SE_PTAM.m", the subfunctions "SE_exact.m" and
 "SE_ram.m".
DOI: 10.5061/dryad.1rn8pk0tb
title: Big, flightless, insular, and dead: characterizing the extinct birds of the Quaternary

description: Aim: Birds have recently undergone a major extinction event which
 apparently, is ongoing. According to some estimates, humans have caused
 the extinction of up to 20% of the entire avian species diversity since
 the latter part of the Pleistocene, which is continuing at an
 unprecedented rate to this day. Few attempts, however, were made to
 determine how many extinctions are actually known, rather than projected
 to have occurred. We aimed to quantify the known avian extinctions, and
 assess the relevance of factors thought to have promoted their
 extinctions, i.e., large size, flightlessness, and insularity. Location:
 Global Taxon: Aves Methods: We collected data on bird extinctions from the
 literature. We recorded the geographic range, flight ability, and body
 size of each species. If mass data were unavailable, we estimated it from
 linear measurements using machine learning tools. We modelled masses of
 extinct birds on those of extant ones and estimated the effects of
 taxonomy, body mass, insularity, and flight ability. Results We have
 identified 469 species of birds that humans, directly or indirectly, drove
 to extinction. These extinctions have predominantly occurred on islands.
 Extinct birds were often flightless. We estimated the body mass of 291
 extinct species and found that overall, the median mass of extinct species
 was seven times larger than that of extant ones. Extinctions mostly
 occurred in families of large-bodied birds, while lineages of small birds
 have fared better. Insular birds are overall larger than mainland birds, a
 trend that becomes even more evident when the extinct forms are analyzed.
 However, within lineages, sizes are only slightly larger on islands than
 on continents. Main conclusions Our findings suggest that extinct bird
 species differed from extant birds by being larger, mostly restricted to
 islands, and often flightless. These factors made them especially
 vulnerable to human prosecution and to other anthropogenically-related
 declines. Our modern understanding of birds is skewed with respect to the
 nature of avian faunas that existed before the current wave of
 human-induced extinctions changed our world forever.
DOI: 10.5061/dryad.g1jwstqr0
title: Elasticity and damping ratio measurement of droplets on super-hydrophobic surfaces

description: The elasticity of the droplet refers to the ability of the droplet in
 restoring to its original shape and ensuring its strong robustness. The
 measurement of the droplets' elasticity is vitally important in
 understanding the characteristics and mechanism of the droplet jumping,
 spreading, and coalescence. In this paper, we measured the elasticity and
 damping ratio of droplets with different viscosity. A plate coated with a
 hydrophobic layer pressed on a droplet, and the elastic force was recorded
 by an electronic balance. Meanwhile, a mathematical model was constructed
 to illustrate the change rate of the droplet area with the elastic force.
 By comparing the influence of volume and viscosity on elasticity, the
 results showed that work done by pressure converts into surface energy.
 And the elasticity of the droplet is provided by the surface tension and
 the damping ratio increases from 0.068 to 0.261.
DOI: 10.5061/dryad.5qfttdz55
title: The genome of the haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales)

description: Haptophytes are biogeochemically and industrially important protists, but
 we know little about their genomic diversity. Here we sequenced the
 nuclear genome of Diacronema lutheri (Pavlova lutheri, Pavlovales) using
 third generation PacBio long-read sequencing coupled with Illumina
 sequencing. The genome was assembled with CANU and subsequently polished
 using both PacBio and Illumina reads to high consensus accuracy. Genome
 annotation was performed using BRAKER2 and three sets of RNA-seq evidence.
 The dataset presented here comprises two files comprising (1) the full
 genome sequence and (2) the annotated protein sequences, each in .fasta
 format.The genome assembly size is 43.5 Mb and is characterized by a high
 GC content. Due to the use of long sequencing reads, the genome is highly
 contiguous and contained in 103 contigs. A total of 14,446 protein-coding
 genes were annotated, and further details of the assembly and annotation
 process are available in the publication.
DOI: 10.5281/zenodo.18397056
title: PRAGMATIC FEATURES OF DOCUMENT TEXTS IN UZBEK AND TURKISH

description: This article will discuss pragmatic features of document texts in the comparison of Uzbek and Turkish languages. The similarities on the basis of common cognitive and institutional mechanisms have been studied with the samples of two languages. Moreover, the basis of pragmatic studies of languages have been discussed theoretically.
DOI: 10.5281/zenodo.18397057
title: PRAGMATIC FEATURES OF DOCUMENT TEXTS IN UZBEK AND TURKISH

description: This article will discuss pragmatic features of document texts in the comparison of Uzbek and Turkish languages. The similarities on the basis of common cognitive and institutional mechanisms have been studied with the samples of two languages. Moreover, the basis of pragmatic studies of languages have been discussed theoretically.
DOI: 10.5061/dryad.q83bk3jhs
title: The limits of demographic buffering in coping with environmental variation

description: Animal populations have developed multiple strategies to deal with
 environmental change. Among them, the demographic buffering strategy
 consists in constraining the temporal variation of the vital rate(s) that
 most affect(s) the overall performance of the population. Tortoises are
 known to buffer their temporal variation in adult survival, which
 typically has the highest contribution to the population growth rate λ, at
 the expense of a high variability on reproductive rates, which contribute
 far less to λ. To identify the effects of projected increases in droughts
 in its natural habitat, we use field data collected across 15 locations of
 Testudo graeca in Southeast Spain over a decade. We analyse the effects of
 environmental variables on reproduction rates. In addition, we couple the
 demographic and environmental data to parameterise an integral projection
 model to simulate the effects of different scenarios of drought recurrence
 on λ under different degrees of intensity in the survival-reproduction
 trade-off. We find that droughts negatively affect the probability of
 laying eggs; however, the overall effects on λ under the current drought
 recurrence (one/decade) are negligible when survival is constant
 (independent of the reduction of reproduction by drought events) and when
 survival increased as a trade-off with the reduction of reproduction
 rates, with a threshold to population viability at three or more
 droughts/decade. Additionally, we show that, although some species may
 buffer current environmental regimes by carefully orchestrating how their
 vital rates vary through time, a demographic buffering strategy is
 insufficient to ensure population viability in extreme regimes. Our
 findings support the hypothesis that the demographic buffering strategy
 has a limit of effectiveness when adverse conditions occur frequently. Our
 methodological approach provides a framework for ecologists to determine
 how effective the management of environmental drivers can be for
 demographically buffering populations, and which scenarios may not provide
 long-term population persistence.
DOI: 10.5061/dryad.sf7m0cg6c
title: Data from: Thriving in a hostile world: insights from the dietary strategy of two allopatric, closely-related tepui summit endemic amphibians

description: To date, there has been no published investigation on the trophic
 diversity in any tepui summit vertebrate. In this paper we analysed the
 dietary composition of a tepui summit endemic toad, Oreophrynella
 quelchii from Roraima-tepui, and compared it with that
 of O. nigra, to examine to what extent diet differs between these
 two sister species across isolated, although neighbouring, tepui tops. The
 digestive tracts of a total of 197 toads were dissected: 111
 from O. quelchii  and 86 from O.
 nigra. The diet composition of O. quelchii was
 relatively diverse, with 13 major prey categories; mites (Acari, 36.5%)
 and beetles (Coleoptera, 21.0%) numerically dominated its diet. Despite
 occurring on two different tepui summits, O.
 quelchii and O. nigra exhibited a similar diet
 composition, although in O. nigra mites (Acari, 42.4%)
 and hymenopterans (especially ants, 16.9%) numerically dominated the diet.
 The present data suggest that tepui
 summit Oreophrynella species are flexible in their diet
 and are active foragers that also feed on aquatic arthropods, successful
 strategies in tepui competitive environments.
DOI: 10.5061/dryad.1zcrjdfrt
title: Expansion of rDNA and pericentromere satellite repeats in the genomes of bank voles Myodes glareolus exposed to environmental radionuclides

description: Altered copy number of certain highly repetitive regions of the genome,
 such as satellite DNA within heterochromatin and ribosomal RNA loci
 (rDNA), is hypothesized to help safeguard the genome against damage
 derived from external stressors. We quantified copy number of the 18S rDNA
 and a pericentromeric satellite DNA (Msat-160) in bank voles (Myodes
 glareolus) inhabiting the Chernobyl Exclusion Zone (CEZ), an area that is
 contaminated by radionuclides and where organisms are exposed to elevated
 levels of ionizing radiation. We found a significant increase in 18S rDNA
 and Msat-160 content in the genomes of bank voles from contaminated
 locations within the CEZ compared with animals from uncontaminated
 locations. Moreover, 18S rDNA and Msat-160 copy number were positively
 correlated in the genomes of bank voles from uncontaminated, but not in
 the genomes of animals inhabiting contaminated areas. These results show
 the capacity for local-scale geographic variation in genome architecture
 and are consistent with the genomic safeguard hypothesis. Disruption of
 cellular processes related to genomic stability appears to be a hallmark
 effect in bank voles inhabiting areas contaminated by radionuclides. --
description: Live capture of bank voles in the Chernobyl exclusion
 zone. Ambient radiation levels measured at all trapping locations using a
 hand-held Geiger counter (Gamma-Scout, GmbH & Co., Germany) placed
 1 cm above the ground, and taking an average of at least nine measurements
 from each trapping location. Internal absorbed caesium-137 dose rates were
 measured using a SAM 940 radionuclide identifier system (Berkeley
 Nucleonics Corporation, San Rafael, CA, USA).
DOI: 10.5061/dryad.rjdfn2zbc
title: Data from: Niche shifts after island colonization spurred adaptive diversification and speciation in a cosmopolitan bird clade

description: Islands have long been recognized as key contributors to biodiversity
 because islands facilitate geographic isolation and ecological divergence
 from mainland ancestors. However, island colonization has traditionally
 been considered an evolutionary dead-end process, and its consequences for
 continental biodiversity remain understudied. Here, we studied the
 evolutionary radiation of Columbiformes (i.e. pigeons and doves) to
 examine if ecological niche shifts on islands shaped biological
 diversification and community composition on continents. We show that the
 colonization of islands by continental, terrestrial-foraging lineages led
 to exploitation of a new ecological niche (i.e. arboreal foraging). This
 transition towards arboreal foraging was associated with evolutionary
 adaptation towards a new morphological optimum. In addition,
 arboreal-foraging lineages experienced an increase in speciation rates,
 which was associated with successful range expansions to other islands as
 well as back-colonization of continents. Our results provide empirical
 evidence that diversification on continents can only be fully understood
 when studying the diversification processes that took place on islands,
 challenging the view of islands as mere sinks of evolutionary diversity.
description: Files included: ColumbidaeTraits.csv
 The dataset includes a list of 214 species of Columbiformes for
 which morphological, ecological and genetic data are available.
 Morphological data include wing, tail, tarsus and bill length (mm) as well
 as body mass (g). Ecological data includes foraging behaviour (A=arboreal
 vs T=Terrestrial), habitat type (F=Forest vs O=Open) and island dwelling
 (C=Continent vs I=Island). The combination of foraging, habitat and island
 variables define the <i>ecoGroup</i> variable, consisting in
 five categories (AFI, AFC, TFC, TFI, TOC). The mophological data is
 log-transformed. Columbidae100phylo.tre
 A random sample of 100 phylogenetic trees from the posterior
 distribution, including the 214 species of Columbiformes included in this
 study.
DOI: 10.6084/m9.figshare.31165550
title: Additional file 1 of Metabolic profiling of red-fleshed apple and functional characterization of MdERF072 in anthocyanin biosynthesis

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.31165550.v1
title: Additional file 1 of Metabolic profiling of red-fleshed apple and functional characterization of MdERF072 in anthocyanin biosynthesis

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.31165553
title: Additional file 2 of Metabolic profiling of red-fleshed apple and functional characterization of MdERF072 in anthocyanin biosynthesis

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.31165553.v1
title: Additional file 2 of Metabolic profiling of red-fleshed apple and functional characterization of MdERF072 in anthocyanin biosynthesis

description: Supplementary Material 2.
DOI: 10.5061/dryad.jm63xsjb2
title: MERFISH measurements in the mouse ileum

description: Spatial transcriptomics protocols based on in situ sequencing or
 multiplexed RNA fluorescent hybridization can reveal detailed tissue
 organization. However, distinguishing the boundaries of individual cells
 in such data is challenging, and can hamper downstream analysis. Current
 methods generally approximate cells positions using nuclei stains. We
 describe a segmentation method, Baysor, which optimizes 2D or 3D cell
 boundaries considering joint likelihood of transcriptional composition and
 cell morphology. While Baysor can take into account segmentation
 based on co-stains, it can also perform segmentation based on the detected
 transcripts alone. To evaluate performance, we extend MERFISH to
 incorporate immuno-staining of cell boundaries. Using this and other
 benchmarks we show that Baysor segmentation can in some cases
 nearly double the number of cells, while reducing segmentation artifacts.
 Importantly, we demonstrate that Baysor performs well on data
 acquired using five different protocols, making it a useful general tool
 for analysis of imaging-based spatial transcriptomics.
description: All methods are described in detail in the accompanying
 paper. Briefly, MERFISH was performed against
 cryosections of the mouse ileum using standard protocols. Imaging was
 performed on a purpose-built microscope and flow system. Identification of
 RNAs was performed with an open-source analysis package
 (github.com/ZhuangLab/MERFISH_analysis).  Baysor analysis and cellpose
 analysis of these data were performed as described in the accompanying
 paper. 
description: The provided data contain text files that describe the data
 organization and contents.  Models included in the
 directory data_analysis/cellpose are binary files created by and readable
 by the cellpose software (https://github.com/MouseLand/cellpose).