cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.547d7wm9s
title: Allele‐specific cis‐regulatory methylation of the gene for vasoactive intestinal peptide in white‐throated sparrows

description: White-throated sparrows (Zonotrichia albicollis) offer a unique
 opportunity to connect genotype with behavioral phenotype. In this
 species, a rearrangement of the second chromosome is linked with
 territorial aggression; birds with a copy of this “supergene”
 rearrangement are more aggressive than those without it. The supergene has
 captured the gene VIP, which encodes vasoactive intestinal
 peptide, a neuromodulator that causes aggression in other songbirds. In
 white-throated sparrows, VIP expression is higher in the
 anterior hypothalamus of birds with the supergene than those without it,
 and expression of VIP in this region predicts the level
 of territorial aggression regardless of genotype. Here, we aimed to
 identify epigenetic mechanisms that could contribute to differential
 expression of VIP both in breeding adults, which exhibit
 morph differences in territorial aggression, and in nestlings, before
 territorial behavior develops. We extracted and bisulfite-converted DNA
 from samples of the hypothalamus in wild-caught adults and nestlings and
 used high-throughput sequencing to measure DNA methylation of a region
 upstream of the VIP start site. We found that the allele inside
 the supergene was less methylated than the alternative allele in both
 adults and nestlings. The differential methylation was attributed
 primarily to CpG sites that were shared between the alleles, not to
 polymorphic sites, which suggests that epigenetic regulation is occurring
 independently of the genetic differentiation within the supergene. This
 work represents an initial step toward understanding how epigenetic
 differentiation inside chromosomal inversions leads to the development of
 alternative behavioral phenotypes.
description: Paired-end reads from bisulfite sequencing of a
 <em>cis-</em>regulatory element of
 the <em>VIP</em> gene in white-throated sparrows
 (<em>Zonotrichia albicollis</em>). Files
 were processed using FastQC, cutadapt, SNPsplit,
 bismark_methylation_extractor, and bismark_to_bedgraph.
 More detail about the library preparation and subsequent data
 analyses are available here: https://github.com/mpricha/WTSP_VIPMethylation/ 
description: These files may be processed and analyzed using R.
DOI: 10.5061/dryad.44j0zpcg4
title: Structure-guided discovery of potent antifungals that prevent Ras signaling by inhibiting protein farnesyltransferase

description: Infections by fungal pathogens are difficult to treat due to a paucity of
 antifungals and emerging resistances.  Next-generation
 antifungals therefore are needed urgently. We have developed compounds
 that prevent farnesylation of Cryptoccoccus neoformans Ras protein by
 inhibiting protein farnesyltransferase with 3–4 nanomolar affinities.
 Farnesylation directs Ras to the cell membrane and is required for
 infectivity of this lethal pathogenic fungus. Our high-affinity compounds
 inhibit fungal growth with 3–6 micromolar minimum inhibitory
 concentrations, 4- to 8-fold better than Fluconazole, an antifungal
 commonly used in the clinic. Compounds bound with distinct inhibition
 mechanisms at two alternative, partially overlapping binding sites,
 accessed via different inhibitor conformations. We showed that antifungal
 potency depends critically on the selected inhibition mechanism, because
 this determines the efficacy of an inhibitor at low in vivo levels of
 enzyme and farnesyl substrate. We elucidated how chemical modifications of
 the antifungals encode the desired inhibitor conformation and concomitant
 inhibitory mechanism.
description: Steady-state enzyme kinetics data.
description: The version of the Biomolecular Computing package used to analyze
 the data is included in the repository.
DOI: 10.7272/q69z934z
title: Daily United States COVID-19 data for select cities and counties, May 29, 2020 to October 21, 2020

description: This dataset by The COVID Tracking Project at The
 Atlantic captures the virus’s transmission in 65 cities and
 counties across the country. Many of these metropolitan areas only report
 the current day’s totals and remove older data from their public health
 dashboards so that no historical archive is available. As a result, it’s
 often impossible to see the impact of the virus on a particular geography
 over time. Our dataset captures this historical information. It is the
 only available metropolitan dataset that includes race and ethnicity,
 which allows us to improve our understanding of how COVID-19
 disproportionately affects communities of color. We have completed our
 data collection on this project and want to share what we’ve learned from
 viewing COVID-19 at the local level. Five months in, we’ve seen that local
 data tells a vastly different story than state-level data. Not only do
 trends emerge in city and county data before appearing at the state level,
 but state-level data also obscures local patterns.
description: This dataset was compiled by volunteers with the COVID Cities
 project. Every day, this dedicated team of volunteers gathered COVID-19
 case and death data from city and county websites and recent press
 conferences and releases.
description: Dataset includes README file that describes all datapoints.
DOI: 10.5061/dryad.0cfxpnw4c
title: Survey of risk perception, trust, and behavioral intention during the COVID-19 pandemic

description: Early public health strategies to prevent the spread of COVID-19 in the
 United States relied on non-pharmaceutical interventions (NPIs) as
 vaccines and therapeutic treatments were not yet available. Implementation
 of NPIs, primarily social distancing and mask wearing, varied widely
 between communities within the US due to variable government mandates, as
 well as differences in attitudes and opinions. To understand the interplay
 of trust, risk perception, behavioral intention, and disease burden, we
 developed a survey instrument to study attitudes concerning COVID-19 and
 pandemic behavioral change in three states: Idaho, Texas, and Vermont. We
 designed our survey (n = 1034) to detect whether these
 relationships were significantly different in rural populations. The best
 fitting structural equation models show that trust indirectly affects
 protective pandemic behaviors via health and economic risk perception. We
 explore two different variations of this social cognitive model: the first
 assumes behavioral intention affects future disease burden while the
 second assumes that observed disease burden affects behavioral intention.
 In our models we include several exogenous variables to control for
 demographic and geographic effects. Notably, political ideology is the
 only exogenous variable which significantly affects all aspects of the
 social cognitive model (trust, risk perception, and behavioral intention).
 While there is a direct negative effect associated with rurality on
 disease burden, likely due to the protective effect of low population
 density in the early pandemic waves, we found a marginally significant,
 positive, indirect effect of rurality on disease burden via decreased
 trust (p = 0.095). This trust deficit creates additional vulnerabilities
 to COVID-19 in rural communities which also have reduced healthcare
 capacity. Increasing trust by methods such as in-group messaging could
 potentially remove some of the disparities inferred by our models and
 increase NPI effectiveness.
description: See journal article for details on data collection. The original
 data have be de-identified to preserve privacy; processed data set has
 merged disease incidence data from the New York Times.
DOI: 10.7280/d1pq5n
title: Confirming an antiphasic bicyclic pattern of forward entrainment in signal detection: a reanalysis of Sun et al. (2021)

description: Forward entrainment refers to that part of the entrainment process that
 persists after termination of an entraining stimulus.  Hickok et
 al. (DOI: 10.1177/0956797615576533) reported forward entrainment in signal
 detection that lasted for two post-stimulus cycles.  In a recent
 paper, Sun et al. (DOI: 10.1111/ejn.15367) reported new data which
 suggested an absence of entrainment effects.  Here we show that
 when Sun et al.’s data are analyzed using unbiased detection-theoretic
 measures, an antiphasic bicyclic pattern of entrainment is observed. We
 further show that the measure of entrainment strength used by Sun et al.,
 i.e., the normalized Fourier transform of performance curves, is not only
 erroneously calculated but is unreliable in estimating entrainment
 strength due to signal processing artifacts.
DOI: 10.5061/dryad.f1vhhmgzk
title: StarBeast3: Adaptive parallelised Bayesian inference under the multispecies coalescent

description: As genomic sequence data becomes increasingly available, inferring the
 phylogeny of the species as that of concatenated genomic data can be
 enticing. However, this approach makes for a biased estimator of branch
 lengths and substitution rates and an inconsistent estimator of tree
 topology. Bayesian multispecies coalescent methods address these issues.
 This is achieved by constraining a set of gene trees within a species tree
 and jointly inferring both under a Bayesian framework. However, this
 approach comes at the cost of increased computational demand. Here, we
 introduce StarBeast3 -- a software package for efficient. Bayesian
 inference under the multispecies coalescent model via Markov chain Monte
 Carlo. We gain efficiency by introducing cutting-edge proposal kernels and
 adaptive operators, and StarBeast3 is particularly efficient when a
 relaxed clock model is applied. Furthermore, gene tree inference is
 parallelised, allowing the software to scale with the size of the problem.
 We validated our software and benchmarked its performance using three real
 and two synthetic datasets. Our results indicate that StarBeast3 is up to
 one-and-a-half orders of magnitude faster than StarBeast2, and therefore
 more than two orders faster than *BEAST, depending on the dataset and on
 the parameter, and can achieve convergence on large datasets with hundreds
 of genes. StarBeast3 is open-source and is easy to set up with a friendly
 graphical user interface.
description: This appendix summarises the outputs of Bayesian MCMC on
 biological and simulated datasets, as well as supplementary methodological
 details.
DOI: 10.5061/dryad.4f4qrfjdq
title: Contribution of microbial interactions to the local adaptation of Bromus tectorum to variable salinity conditions

description: We conducted a greenhouse experiment examining the contribution of
 microbes to plant local adaptation. We collected genotypes of Bromus
 tectorum from a variety of locations varying in their soil salinity. We
 then grew these genotypes in the greenhouse under variable salinity and
 microbial conditions, and measured their biomass and survival.
description: See README for details on the Methods.
DOI: 10.5061/dryad.qfttdz0js
title: Species list, with traits, in four forest types

description: Ecological strategy is the tactics employed by species in adapting to
 abiotic and biotic conditions. Ecological strategy spectrum is defined as
 the relative proportion of species in different ecological strategy types
 within a community. Determinants of ecological strategy spectrum of plant
 community explored by most previous studies are about abiotic factors.
 Yet, the roles of biotic factors in driving variations of ecological
 strategy spectra of forest communities across different geographic regions
 remains unknown. Here, we established 200 0.04-ha forest dynamics plots
 and measured three leaf functional traits of tree and shrub species in
 four forest vegetation types across four climatic zones. Based on Grime’s
 CSR triangular framework and the StrateFy method, we categorized species
 into four ecological strategy groups (C-, S-, Int-, and R-groups) and
 related the ecological spectra of the forests to three species diversity
 indices (species richness, Shannon Wiener index, and stem density (stem
 abundance)). Linear-regression, redundancy analysis and variance partition
 analysis were utilized for assessing the roles of species diversity in
 regulating ecological strategy spectra of forest communities across
 different climatic zones. We found that the proportion of species in the
 C- and Int-groups increased, while that in the S-group decreased, with the
 increase of three indices of species diversity. Among the three species
 diversity indices, stem abundance played the most important role in
 driving variations in ecological strategy spectra of forests across
 different climatic zones. Our finding highlights the necessity of
 accounting for biotic factors, especially stem abundance, in modeling or
 predicting the geographical distributions of plant species with varied
 ecological adaptation strategies to future environmental changes.
DOI: 10.5061/dryad.h18931znn
title: Nanoscale binding site localization by molecular distance estimation on native cell surfaces using topological image averaging

description: Antibody binding to cell surface proteins plays a crucial role in immunity
 and the location of an epitope can altogether determine the immunological
 outcome of a host-target interaction. Techniques available today for
 epitope identification are costly, time-consuming, and unsuited for
 high-throughput analysis. Fast and efficient screening of epitope location
 can be useful for the development of therapeutic monoclonal antibodies and
 vaccines. The cellular morphology typically varies, and antibodies often
 bind heterogeneously across a cell surface, making traditional
 particle-averaging strategies challenging for accurate native antibody
 localization. In the present work, we have developed a method, SiteLoc,
 for imaging-based molecular localization on cellular surface proteins.
 Nanometer-scale resolution is achieved through localization in one
 dimension, namely the distance from a bound ligand to a reference surface,
 by using topological image averaging. Our results show that this method is
 well suited for antibody binding site measurements on native cell surface
 morphology and that it can be applied to other molecular distance
 estimations as well.
description: See the methods section in the article.
DOI: 10.5061/dryad.3xsj3txj2
title: Processed 12S fish eDNA sequences

description: This dataset contains fish eDNA sequences from the 12S mitochondrial gene.
 eDNA has been collected in 100 stations, 25 sites, in 5 tropical marine
 regions. Data collection was performed between 2017 and 2020. Raw
 sequences have been processed through a bioinformatic pipeline, merged,
 demultiplexed, dereplicated, clustered as OTUs (operational taxonomic
 units) and assigned to a taxa. The codes to analyse the data can be found
 at : https://github.com/virginiemarques/Global_eDNA. The data are used to
 study the patterns of tropical fish distributions across spatial scales,
 using two different methodologies, eDNA and visual census.
description: The sampling in the Caribbean,
 Indian Ocean and Polynesia and the sequencing were funded by Monaco
 Explorations. Fieldwork in Indonesia and laboratory activities were
 supported by the Lengguru 2017 Project (www.lengguru.org), conducted by
 the French National Research Institute for Sustainable Development (IRD),
 the Indonesian Institute of Sciences (LIPI) with the Research Center for
 Oceanography (RCO), the Politeknik Kelautan dan Perikanan Sorong), the
 University of Papua (UNIPA) with the help of the Institut Français in
 Indonesia (IFI) and with corporate sponsorship from the Total Foundation
 and TIPCO company. Fieldwork and laboratory activities in New-Caledonia
 were supported by the projects ANR SEAMOUNTS and CIFRE REEF 3.0 conducted
 by the French National Institute for Sustainable Development (IRD) and
 GINGER-BURGEAP-SOPRONER company. Fieldwork and laboratory activities in
 Colombia were supported by ETH Global grant and the project Reefish,
 conducted in collaboration with the Instituto de Investigaciones Marinas y
 Costeras – INVEMAR.
DOI: 10.5061/dryad.dncjsxm1m
title: Emulator-based decomposition for structural sensitivity of core-level spectra

description: We explore the sensitivity of several core-level spectroscopic methods to
 the underlying atomistic structure by using the water molecule as our test
 system. We first define a metric that measures the magnitude of spectral
 change as a function of the structure, which allows for identifying
 structural regions with high spectral sensitivity. We then apply
 machine-learning-emulator-based decomposition of the structural parameter
 space for maximal explained spectral variance, first on overall spectral
 profile and then on chosen integrated regions of interest therein. The
 presented method recovers more spectral variance than partial least
 squares fitting and the observed behavior is well in line with the
 aforementioned metric for spectral sensitivity. The analysis method is
 able to independently identify spectroscopically dominant degrees of
 freedom, and to quantify their effect and significance.
description: Data set includes 10000 snapshots of MD trajectories and
 calculated XES, XAS, XPS spectra, and also codes for the analysis (search
 for the best emulator, ECA analysis and PLSSVD analysis), and figure
 generation scripts.
description: The protocol is described in the README file.
DOI: 10.5061/dryad.9cnp5hqkq
title: Opponent processing in the retinal mosaic of nymphalid butterflies

description: The eyes of nymphalid butterflies, investigated with incident
 illumination, show colourful facet reflection patterns, the eye shine,
 which is uniform or heterogeneous, dependent on the species. Facet colours
 suggest that the ommatidia contain different sets of photoreceptors and
 screening pigments, but how the colours and the cell characteristics are
 associated has not been clearly established. Here we analyse the retinae
 of two nymphalids, Apatura ilia, which has a uniform eyeshine, and
 Charaxes jasius, a species with a heterogeneous eye shine, using
 single-cell recordings, spectroscopy and optical pupillometry. Apatura has
 UV, blue and green-sensitive photoreceptors, allocated into three
 ommatidial types. The UV and blue-sensitive cells are long visual fibres
 (LVFs), receiving opponent input from the green-sensitive short visual
 fibres (SVFs). Charaxes has an expanded set of photoreceptors, allocated
 into three additional, red-reflecting ommatidial types. All red ommatidia
 contain green-sensitive LVFs, receiving opponent input from red receptors.
 In both species, the SVFs do not receive any opponent input. The simple
 retina of Apatura with three ommatidial types and two different
 colour-opponent channels can support trichromatic vision. Charaxes has six
 ommatidial types and three different colour-opponent channels. Its
 expanded receptor set can support tetrachromatic vision.
description: Electrophysiology, single cell recordings.
DOI: 10.5061/dryad.3ffbg79kj
title: Measurements of bite traces on bones

description: Carnivores make traces on bones with their teeth when feeding. A true
 predatory bite trace (predichnia) forms when a predator catches and kills
 its prey or attempts to do so. Both predators and scavengers may leave
 their non-predatory feeding traces during postmortem food processing.
 Despite the interpretative uncertainties as to the ethology such
 ichnofossils may represent, the bite traces have been traditionally
 classified as predichnia – traces of predation. Previously, there was no
 alternative ethological category available for workers to classify them.
 The present paper fills that gap and describes tooth-made ichnofossils
 from the continental Upper Triassic Grabowa Formation of southern Poland.
 It discusses modes the serration and striations might have formed along
 Linichnus edges, potential makers of the trace fossils, feeding strategies
 and food-processing behaviors the ichnites may represent. All the bite
 traces are thought to act as a record of carnivorous behaviors and are
 classified as sarcophagichnia, a new ethological category (traces of
 feeding on a body). Finally, all of the studied bite traces were likely
 inflicted postmortem and are classified as necrophagichnia (traces of
 feeding on an already dead body), most likely produced by scavengers in
 the studied cases. Data on recent carnivores links these ichnites with
 postmortem food processing behaviors, like dismembering and defleshing.
 Scavenging could, in fact, have been a preferred carnivorous feeding
 strategy in the seasonal Norian climate of the area. Dry seasons could
 have perhaps increased vertebrate mortality rates and provided plenty of
 carcasses for carnivores to feed on.
description: The analyzed bite traces were measured with a caliper to provide
 a range of observed sizes (lengths and widths). The length measurements
 were done in straight line between the terminations (even for curved
 traces). The width was measured in straight line from one edge to another.
 The caliper tool accuracy was: 0.05 mm.
DOI: 10.5061/dryad.2547d7ws6
title: Variation in eye abundance among scallops reveals ontogenetic and evolutionary convergence associated with life habits

description: Eyes are remarkable systems to investigate the complex interaction between
 ecological drivers and phenotypic outcomes. Some animals, such as
 scallops, have many eyes for visual perception, but to date, the evolution
 of multiple-eye systems remains obscure. For instance, it is
 unclear whether eye number changes over a lifetime or varies among
 species. Scallops are a suitable model group to investigate these
 questions considering the interspecific variation of adult size and
 ecological diversity. We tested whether eye abundance scales with
 body size among individuals and species and whether it varies with life
 habits. We performed comparative analyses, including a
 phylogenetic ANCOVA and evolutionary model comparisons, based on eye count
 and shell height (as a proxy of body size) across 31 scallop
 species. Our analyses reveal that patterns of increasing relationship with
 body size are not concordant among taxa and suggest ontogenetic
 convergence caused by similar ecologies. Accordingly, selective optima in
 eye numbers are associated with shifts in life habits. For
 instance, species with increased mobility have significantly more eyes
 than less mobile species. The convergent evolution of greater eye
 abundance in more mobile scallops likely indicates a visual improvement
 based on increased levels of oversampling of the surrounding environment.
description: Please refer to
 ReadMe file