cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9mb7r
title: Data from: Differentiating self-projection from simulation during mentalizing: evidence from fMRI

description: We asked participants to predict which of two colors a similar other
 (student) and a dissimilar other (retiree) likes better. We manipulated if
 color-pairs were two hues from the same color-category (e.g. green) or two
 conceptually different colors (e.g. green versus blue). In the former
 case, the mental state that has to be represented (i.e., the percept of
 two different hues of green) is predominantly non-conceptual or phenomenal
 in nature, which should promote mental simulation as a strategy for
 mentalizing. In the latter case, the mental state (i.e. the percept of
 green versus blue) can be captured in thought by concepts, which
 facilitates the use of theories for mentalizing. In line with the
 self-projection hypothesis, we found that cortical midline areas including
 vmPFC / orbitofrontal cortex and precuneus were preferentially activated
 for mentalizing about a similar other. However, activation was not
 affected by the nature of the color-difference, suggesting that
 self-projection subsumes simulation-like processes but is not limited to
 them. This indicates that self-projection is a universal strategy applied
 in different contexts—irrespective of the availability of theories for
 mentalizing. Along with midline activations linked to self-projection, we
 also observed activation in right lateral frontal and dorsal parietal
 areas showing a theory-like pattern. Taken together, this shows that
 mentalizing does not operate based on simulation or theory, but that both
 strategies are used concurrently to predict the choices of others.
description: ImagingData_s001-s008See the readme text files in the zip archive for details.ImagingData_s001_s008.zipImagingData_s009-s016ImagingData_s017-s024BehavioralData
DOI: 10.5061/dryad.3q7p2
title: Data from: Co-expression of two subtypes of melatonin receptor on rat M1-type intrinsically photosensitive retinal ganglion cells

description: Intrinsically photosensitive retinal ganglion cells (ipRGCs) are involved
 in circadian and other non-image forming visual responses. An open
 question is whether the activity of these neurons may also be under the
 regulation mediated by the neurohormone melatonin. In the present work, by
 double-staining immunohistochemical technique, we studied the expression
 of MT1 and MT2, two known subtypes of mammalian melatonin receptors, in
 rat ipRGCs. A single subset of retinal ganglion cells labeled by the
 specific antibody against melanopsin exhibited the morphology typical of
 M1-type ipRGCs. Immunoreactivity for both MT1 and MT2 receptors was
 clearly seen in the cytoplasm of all labeled ipRGCs, indicating that these
 two receptors were co-expressed in each of these neurons. Furthermore,
 labeling for both the receptors were found in neonatal M1 cells as early
 as the day of birth. It is therefore highly plausible that retinal
 melatonin may directly modulate the activity of ipRGCs, thus regulating
 non-image forming visual functions.
description: Figure
 1Figure
 2Figure
 3Figure
 4Figure
 S1
DOI: 10.5061/dryad.q88pm45
title: Data from: From understory to canopy: in situ behavior of Neotropical forest katydids in response to bat echolocation calls

description: Predator-prey interactions take place in complex environments, and
 research on the sensory ecology of predator-detection relies on
 understanding when, where, and how prey experience and respond to predator
 cues. Bats are significant nocturnal predators, and insects have evolved
 diverse strategies for avoiding predation by bats. While it is well-known
 that insects exhibit anti-bat strategies, from avoidance flight to reduced
 acoustic signaling, the specific conditions that elicit some of these
 behaviors are less well-known. To illuminate how insects respond to bats
 in nature, we studied how calling behavior changed when katydids
 experienced echolocation calls in a Neotropical forest. The diverse
 Neotropical bat community includes species that eavesdrop on prey sounds,
 such as the songs produced by male katydids. Previous research has shown
 that some katydid species respond to echolocation calls by reducing
 acoustic signaling. To capture the interactions of bats and katydids, we
 placed acoustic monitors at heights of 8, 16, and 24 meters above ground
 in 10 locations in the forest on Barro Colorado Island, Panama and
 recorded continuously for 24 h at each location. We randomly selected 250
 recordings with echolocation calls and compared the acoustic spectrum of
 the forest before a bat arrived, when a bat was present, and after the bat
 was no longer detectable. We tested whether the response to bat calls
 changes with height, the family of bat producing the calls, the duration
 of the echolocation sequence, call amplitude, and call peak frequency.
 Bats appeared on ~50% of nighttime recordings, but echolocation calls that
 could have been produced by eavesdropping bats were rare (&lt;4% of
 calls). Insect response to bats was nuanced and context-dependent. Despite
 the rarity of truly dangerous predator cues, echolocation decreased insect
 sound at several frequencies and heights. Insect response was not uniform,
 and in many cases echolocation calls had little effect on insect activity,
 perhaps reflecting the fact that echolocation calls were an inconsistent
 cue for the presence of eavesdropping bats. These nuanced responses raise
 interesting questions about predator detection in noise and provide
 valuable context for laboratory investigations on the sensory ecology of
 how individual prey species respond to predator cues.
description: Canopy data
 referenceThis is an excel sheet
 that contains information about each sound recording used in the bat pass
 analyses. Please see metadata tab for information about each
 column.Canopy data
 outputsThis is an excel sheet
 that provides the raw amplitude in each of the tested frequency bins
 before, during, and after the bat pass.Original canopy sound
 recordings used in analysisThese are the original
 high pass filtered wave files used in the analyses. Please see the
 'Canopy data reference' sheet for information about each file,
 including the height and date of recording.
DOI: 10.5061/dryad.9b6p8
title: Data from: Cryptic speciation and gene flow in a migratory songbird species complex: insights from the red-eyed vireo (Vireo olivaceus)

description: Migratory species that alternate between sympatry and allopatry over the
 course of an annual cycle are promising subjects for studies seeking to
 understand the process of speciation in the absence of strict geographic
 isolation. Here we sought to identify cryptic species and assess rates of
 gene flow in a clade of neotropical migrant songbirds in which geography
 and taxonomy are currently out of sync: the Red-Eyed Vireo (V. olivaceus)
 Species Complex. Phylogenetic, clustering, and statistical species
 delimitation analyses found that V. olivaceus includes two non-sister
 lineages migrating in opposite directions across the equator. Analyses of
 gene flow identified low levels of introgression between two species
 pairs, but none between northern and southern olivaceus. We also
 identified substantial well-supported conflicts between nuclear and
 mitochondrial topologies. Although the geographic distribution of
 mito-nuclear discordance is suggestive of hybridization and mitochondrial
 capture, we found no evidence of introgression in the nuclear genome of
 populations with discordant mitochondrial gene trees. Our study finds that
 species boundaries match breeding range and migratory phenology rather
 than the existing taxonomy in this group, and demonstrates the utility of
 genomic data in inferring species boundaries in recently diverged clades.
description: analysesR_scriptsalignmentsdemultiplexed_reads_1of3demultiplexed_reads_2of3demultiplexed_reads_3of3
DOI: 10.5061/dryad.h9f8sb7
title: Data from: Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours

description: An ongoing challenge in protein chemistry is to identify the underlying
 interaction energies that capture protein dynamics. The traditional
 trade-off in biomolecular simulation between accuracy and computational
 efficiency is predicated on the assumption that detailed force fields are
 typically well-parameterized, obtaining a significant fraction of possible
 accuracy. We re-examine this trade-off in the more realistic regime in
 which parameterization is a greater source of error than the level of
 detail in the force field. To address parameterization of coarse-grained
 force fields, we use the contrastive divergence technique from machine
 learning to train from simulations of 450 proteins. In our procedure, the
 computational efficiency of the model enables high accuracy through the
 precise tuning of the Boltzmann ensemble. This method is applied to our
 recently developed Upside model, where the free energy for side chains is
 rapidly calculated at every time-step, allowing for a smooth energy
 landscape without steric rattling of the side chains. After this
 contrastive divergence training, the model is able to de novo fold
 proteins up to 100 residues on a single core in days. This improved Upside
 model provides a starting point both for investigation of folding dynamics
 and as an inexpensive Bayesian prior for protein physics that can be
 integrated with additional experimental or bioinformatic data.
description: TrajectoriesContains folders for each of the proteins tested with trajectories from both native and denovo initial structures. The trajectories are of the lowest temperature replicas, which were the ones used in the bulk of the analysis. Consult the README for additional details.trajectories.tar.gz
DOI: 10.5061/dryad.v84c2
title: Data from: Two subunits of human ORC are dispensable for DNA replication and proliferation

description: The six-subunit Origin Recognition Complex (ORC) is believed to be an
 essential eukaryotic ATPase that binds to origins of replication as a
 ring-shaped heterohexamer to load MCM2-7 and initiate DNA replication. We
 have discovered that human cell lines in culture proliferate with intact
 chromosomal origins of replication after disruption of both alleles of
 ORC2 or of the ATPase subunit, ORC1. The ORC1 or ORC2-depleted cells
 replicate with decreased chromatin loading of MCM2-7 and become critically
 dependent on another ATPase, CDC6, for survival and DNA replication. Thus,
 either the ORC ring lacking a subunit, even its ATPase subunit, can load
 enough MCM2-7 in partnership with CDC6 to initiate DNA replication, or
 cells have an ORC-independent, CDC6-dependent mechanism to load MCM2-7 on
 origins of replication
description: BrIP seq
 peaksBrIP seq peaks in WT and
 ORC mutant cell linesBrIP
 peaks.zipBrIP seq genomic
 readsBrdU incorporated
 genomic strand readsControl.fastq.gzBrIP seq WT readsBrdU incorporated nascent strand reads in WT cellsWT_A.fastq.gzBrIP seq ORC1B14 readsBrdU incorporated nascent strand reads in ORC1B14 cellsORC1.fastq.gzBrIP seq ORC2B2 readsBrdU incorporated nascent strand reads in ORC2B2 cellsORC2.fastq.gz
DOI: 10.5061/dryad.8g0d0
title: Data from: Body size affects the strength of social interactions and spatial organization of a schooling fish (Pseudomugil signifer)

description: While a rich variety of self-propelled particle models propose to explain
 the collective motion of fish and other animals, rigorous statistical
 comparison between models and data remains a challenge. Plausible models
 should be flexible enough to capture changes in the collective behaviour
 of animal groups at their different developmental stages and group sizes.
 Here, we analyse the statistical properties of schooling fish (Pseudomugil
 signifer) through a combination of experiments and simulations. We make
 novel use of a Boltzmann inversion method, usually applied in molecular
 dynamics, to identify the effective potential of the mean force of fish
 interactions. Specifically, we show that larger fish have a larger
 repulsion zone, but stronger attraction, resulting in greater alignment in
 their collective motion. We model the collective dynamics of schools using
 a self-propelled particle model, modified to include varying particle
 speed and a local repulsion rule. We demonstrate that the statistical
 properties of the fish schools are reproduced by our model, thereby
 capturing a number of features of the behaviour and development of
 schooling fish.
description: Coordinates:
 medium-sized fish (part 1)Contains raw positional
 data for medium-sized fish.Medium-sized_fish_coordinates_part1.zipCoordinates: medium-sized fish (part 2)Contains raw positional data for medium-sized fish.Medium-sized_fish_coordinates_part2.zipCoordinates: big fishContains raw positional data for big fish.Big_fish_coordinates.zipCoordinates: small fishContains raw positional data for small fish.Small_fish_coordinates.zip
DOI: 10.5061/dryad.c261c
title: Data from: Visual landmarks sharpen grid cell metric and confer context specificity to neurons of the medial entorhinal cortex

description: Neurons of the medial entorhinal cortex (MEC) provide spatial
 representations critical for navigation. In this network, the periodic
 firing fields of grid cells act as a metric element for position. The
 location of the grid firing fields depends on interactions between
 self-motion information, geometrical properties of the environment and
 nonmetric contextual cues. Here, we test whether visual information,
 including nonmetric contextual cues, also regulates the firing rate of MEC
 neurons. Removal of visual landmarks caused a profound impairment in grid
 cell periodicity. Moreover, the speed code of MEC neurons changed in
 darkness and the activity of border cells became less confined to
 environmental boundaries. Half of the MEC neurons changed their firing
 rate in darkness. Manipulations of nonmetric visual cues that left the
 boundaries of a 1D environment in place caused rate changes in grid cells.
 These findings reveal context specificity in the rate code of MEC neurons.
description: Electrophysiological
 data from Pérez-Escobar et al. 2016This file contains the
 spike times, position data, electrode location, and light conditions for
 the recordings on the circular arena and the linear
 track.data_perez_escobar_2016.tar.gz
DOI: 10.5061/dryad.34q0d
title: Data from: Phased whole-genome genetic risk in a family quartet using a major allele reference sequence

description: Whole-genome sequencing harbors unprecedented potential for
 characterization of individual and family genetic variation. Here, we
 develop a novel synthetic human reference sequence that is ethnically
 concordant and use it for the analysis of genomes from a nuclear family
 with history of familial thrombophilia. We demonstrate that the use of the
 major allele reference sequence results in improved genotype accuracy for
 disease-associated variant loci. We infer recombination sites to the
 lowest median resolution demonstrated to date (&lt;1,000 base pairs).
 We use family inheritance state analysis to control sequencing error and
 inform family-wide haplotype phasing, allowing quantification of
 genome-wide compound heterozygosity. We develop a sequence-based
 methodology for Human Leukocyte Antigen typing that contributes to disease
 risk prediction. Finally, we advance methods for analysis of disease and
 pharmacogenomic risk across the coding and non-coding genome that
 incorporate phased variant data. We show these methods are capable of
 identifying multigenic risk for inherited thrombophilia and informing the
 appropriate pharmacological therapy. These ethnicity-specific,
 family-based approaches to interpretation of genetic variation are
 emblematic of the next generation of genetic risk assessment using
 whole-genome sequencing.
description: CHBJPTref.fastaCEUref.fastaYRIref.fasta
DOI: 10.15468/dl.tw3ysz
title: Occurrence Download

description: A dataset containing 241 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abronia graminea",
 "Year 1990-2026"
 ]
}

 The dataset includes 241 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000457-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pn931
title: Data from: The rate of transient beta frequency events predicts behavior across tasks and species

description: Beta oscillations (15-29Hz) are among the most prominent signatures of
 brain activity. Beta power is predictive of healthy and abnormal
 behaviors, including perception, attention and motor action. In
 non-averaged signals, beta can emerge as transient high-power
 'events'. As such, functionally relevant differences in averaged
 power across time and trials can reflect changes in event number, power,
 duration, and / or frequency span. We show that functionally relevant
 differences in averaged beta power in primary somatosensory neocortex
 reflect a difference in the number of high-power beta events per trial,
 i.e. event rate. Further, beta events occurring close to the stimulus were
 more likely to impair perception. These results are consistent across
 detection and attention tasks in human magnetoencephalography, and in
 local field potentials from mice performing a detection task. These
 results imply that an increased propensity of beta events predicts the
 failure to effectively transmit information through specific neocortical
 representations.
description: HumanDetection1 second prestimulus MEG dipole source localized to hand area of S1HumanAttention1 second prestimulus MEG dipole source localized to hand area of S1MouseDetection11 second prestimulus LFP in mouse barrel cortexMouseDetection21 second prestimulus LFP in mouse barrel cortex
DOI: 10.5061/dryad.51sq0
title: Data from: The relationship between dN/dS and scaled selection coefficients

description: Numerous computational methods exist to assess the mode and strength of
 natural selection in protein-coding sequences, yet how distinct methods
 relate to one another remains largely unknown. Here, we elucidate the
 relationship between two widely-used phylogenetic modeling frameworks:
 dN/dS models and mutation-selection (MutSel) models. We derive a
 mathematical relationship between dN/dS and scaled selection coefficients,
 the focal parameters of MutSel models, and use this relationship to gain
 deeper insight into the behaviors, limitations, and applicabilities of
 these two modeling frameworks. We prove that, if all synonymous changes
 are neutral, standard MutSel models correspond to dN/dS &lt; 1.
 However, if synonymous codons differ in fitness, dN/dS can take on
 arbitrarily high values even if all selection is purifying. Thus, the
 MutSel modeling framework cannot necessarily accommodate positive,
 diversifying selection, while dN/dS cannot distinguish between purifying
 selection on synonymous codons and positive selection on amino acids. We
 further propose a new benchmarking strategy of dN/dS inferences against
 MutSel simulations and demonstrate that the widely-used Goldman-Yang-style
 dN/dS models yield substantially biased dN/dS estimates on realistic
 sequence data. By contrast, the less frequently used Muse-Gaut-style
 models display much less bias. Strikingly, the least-biased and
 most-precise dN/dS estimates are never found in the models with the best
 fit to the data, measured through both AIC and BIC scores. Thus, selecting
 models based on goodness-of-fit criteria can yield poor parameter
 estimates if the models considered do not precisely correspond to the
 underlying mechanism that generated the data. In conclusion, establishing
 mathematical links among modeling frameworks represents a novel, powerful
 strategy to pinpoint previously unrecognized model limitations and
 strengths.
description: np.tarAlignments simulated
 using nucleoprotein amino acid fitness values and nucleoprotein mutation
 rates.yeast.tarContains alignments simulated using nucleoprotein amino acid fitness values and yeast mutation rates.polio.tarContains alignments simulated using nucleoprotein amino acid fitness values and polio mutation rates.conv.tarContains simulated alignments and associated state codon frequencies used to assess convergence.no_synsel.tarContains simulated alignments and associated state codon frequencies for datasets without synonymous codon selection.synsel.tarContains simulated alignments and associated state codon frequencies for datasets with synonymous codon selection.
DOI: 10.5061/dryad.5f9v7
title: Data from: A face-selective ventral occipito-temporal map of the human brain with intracerebral potentials

description: Human neuroimaging studies have identified a network of distinct
 face-selective regions in the ventral occipito-temporal cortex (VOTC),
 with a right hemispheric dominance. To date, there is no evidence for this
 hemispheric and regional specialization with direct measures of brain
 activity. To address this gap in knowledge, we recorded local
 neurophysiological activity from 1,678 contact electrodes implanted in the
 VOTC of a large group of epileptic patients (n = 28). They were presented
 with natural images of objects at a rapid fixed rate (six images per
 second: 6 Hz), with faces interleaved as every fifth stimulus (i.e., 1.2
 Hz). High signal-to-noise ratio face-selective responses were objectively
 (i.e., exactly at the face stimulation frequency) identified and
 quantified throughout the whole VOTC. Face-selective responses were widely
 distributed across the whole VOTC, but also spatially clustered in
 specific regions. Among these regions, the lateral section of the right
 middle fusiform gyrus showed the largest face-selective response by far,
 offering, to our knowledge, the first supporting evidence of two decades
 of neuroimaging observations with direct neural measures. In addition,
 three distinct regions with a high proportion of face-selective responses
 were disclosed in the right ventral anterior temporal lobe, a region that
 is undersampled in neuroimaging because of magnetic susceptibility
 artifacts. A high proportion of contacts responding only to faces (i.e.,
 “face-exclusive” responses) were found in these regions, suggesting that
 they contain populations of neurons involved in dedicated face-processing
 functions. Overall, these observations provide a comprehensive mapping of
 visual category selectivity in the whole human VOTC with direct neural
 measures.
description: Jonas_et_al_PNAS_2016_Part_1Intracerebral electrophysiological data (P03 to P16) and set of stimuli usedJonas_et_al_PNAS_2016_Part_2Intracerebral electrophysiological data (P18 to P30) and set of stimuli usedJonas_et_al_PNAS_2016_Part_3Intracerebral electrophysiological data (P31 to P39) and set of stimuli used