cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jwstqjq91
title: Interference in the shared-stroop task: a comparison of self- and other-monitoring

description: Co-acting participants represent and integrate each other’s actions, even
 when they are not required to monitor one another. However, monitoring the
 actions of a partner is an important component of successful interactions,
 and particularly of linguistic interactions. Moreover, monitoring others
 may rely on similar mechanisms to those that are involved in
 self-monitoring. In order to investigate the effect of monitoring on
 shared linguistic representations, we combined a monitoring task with the
 shared Stroop task. In the shared Stroop task, one participant named the
 colour of words in one colour (e.g., red) while ignoring stimuli in the
 other colour (e.g., green); the other participant either named the colour
 of words in the other colour or did not respond. Crucially, participants
 either had to provide feedback about the correctness of their partner’s
 response (Experiment 3) or did not (Experiment 2). The results showed that
 interference was greater when both participants responded than when they
 did not, but only when partners provided feedback. We argue that feedback
 increased joint task interference because in order to monitor their
 partner, participants had to represent their target utterance, and this
 representation interfered with self-monitoring of their own utterance.
description: Verbal responses were collected using DMDX and onset latencies
 were measured using CheckVocal (see references below). To prepare the data for analyses,
 after removing all incorrect responses, onset latencies below 200
 milliseconds were removed (1 trial) before we conducted a recursive
 trimming procedure in which the criterion cut-off for outlier removal was
 established independently for each participant in each condition, by
 reference to the sample size in that condition. Error totals used in
 accuracy analysis do not include the removed outliers.
 Forster, K. I., Forster, J.
 C. 2003 DMDX: A windows display program with millisecond accuracy.
 <i>Behavior Research Methods, Instruments, &
 Computers</i>. 35, 116-124. 
 (10.3758/BF03195503) Protopapas, A. 2007
 CheckVocal: A program to facilitate checking the accuracy and resposne
 time of vocal responses for DMDX.
description: The dataset includes two columns: RT reports the original onset
 latencies before any exclusion and before the trimming procedure.
 RTTrimmed reports the trimmed RT and it shows NA for values that were
 removed as outliers. See README for more details.
DOI: 10.5061/dryad.cfxpnvx5m
title: Long-term stability of cortical ensembles

description: Neuronal ensembles, coactive groups of neurons found in spontaneous and
 evoked cortical activity, are causally related to memories and perception,
 but it still unknown how stable or flexible they are over time. We used
 two-photon multiplane calcium imaging to track over weeks the activity of
 the same pyramidal neurons in layer 2/3 of the visual cortex from awake
 mice and recorded their spontaneous and visually evoked responses. Less
 than half of the neurons were commonly active across any two imaging
 sessions. These “common neurons” formed stable ensembles lasting weeks,
 but some ensembles were also transient and appeared only in one single
 session. Stable ensembles preserved ~68 % of their neurons up to 46 days,
 our longest imaged period, and these “core” cells had stronger functional
 connectivity. Our results demonstrate that neuronal ensembles can last for
 weeks and could, in principle, serve as a substrate for long-lasting
 representation of perceptual states or memories.
description: We used two-photon multiplane calcium imaging to track over weeks
 the activity of the same pyramidal neurons in layer 2/3 of the visual
 cortex from awake mice and recorded their spontaneous and visually evoked
 responses. A static blue screen was used to record
 spontaneous activity for 5 min. The visual stimulation protocol
 constituted of 50 times of a 2 s single-orientation drifting gratings with
 a mean static screen between each of them during 1-5 s randomly to record
 the evoked activity for 5 min. Maximum intensity
 projection was obtained from three recorded planes. Detection of ROIs was
 done based on Suite2P. Then, we got the Ca signals with a peak
 signal-to-noise ratio (PSNR) &gt; 18 dB. We perform the inference of
 spikes using the foopsi algorithm, and finally we thresholded the
 inference of spikes for each neuron to build a binary raster.
description: Each MATLAB file contains a structure variable
 "Data" with the data processed. Data.Movie
 (FilePath, DataName, Width, Height, Depth, Frames, FPS,
 ImageMaximum, ImageAverage, ImageSTD, ImagePSNR, Summary,
 ImageMask) Data.ROIs (CellRadius, AuraRadius,
 SearchOptions, CellMasksImage, CellWeightedMasksImage, AuraMasksImage,
 NeuropilMask) Data.VoltageRecording (Stimuli,
 Locomotion, File, SampleRate) Data.XY.All
 Data.Neurons (pixels, weight_pixels, x_pixels, y_pixels,
 num_pixels,x_median,y_median, overlap, overlap_fraction, Eccentricity,
 Circularity, Perimeter, PSNR) Data.Transients (Raw,
 Filtered, Smoothed, F0, Field, Cells, PSNR, Inference, Model,
 InferenceMethod, ThresholdPSNR, Raster, InferenceTh, SameThreshold,
 Threshold Data.InactiveNeurons (same as Data.Neurons,
 this neurons were discarded).
DOI: 10.5061/dryad.ns1rn8ptc
title: Data from: An inventory of the foliar, soil, and dung arthropod communities in pastures of the Southeastern United States

description: Grassland systems constitute a significant portion of the land area in the
 U.S. and as a result harbors significant arthropod biodiversity.
 During this time of biodiversity loss around the world, bioinventories of
 ecologically important habitats serve as important indicators for the
 effectiveness of conservation efforts. We conducted a bioinventory of the
 foliar, soil, and dung arthropod communities in 10 cattle pastures located
 in the southeastern U.S. during the 2018 grazing season. In sum, 126,251
 arthropod specimens were collected. From the foliar community, 13
 arthropod orders were observed, with the greatest species richness found
 in Hymenoptera, Diptera, and Hemiptera. The soil-dwelling arthropod
 community contained 18 orders. The three orders comprising the highest
 species richness were Coleoptera, Diptera, and Hymenoptera. Lastly, 12
 arthropod orders were collected from cattle dung, with the greatest
 species richness found in Coleoptera, Diptera, and Hymenoptera. Herbivores
 were the most abundant functional guild found in the foliar community, and
 predators were most abundant in the soil and dung communities. Arthropod
 pests constituted a small portion of the pasture arthropod communities,
 with 1.01%, 0.34%, and 0.46% pests found in the foliar, soil, and dung
 communities, respectively. While bioinventories demand considerable time,
 energy, and resources to accomplish, the information from these
 inventories has many uses for conservation efforts, land management
 recommendations, and the direction of climate change science.
DOI: 10.15468/dl.vt3j99
title: Occurrence Download

description: A dataset containing 20972 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Auckland Museum Land Vertebrates Collection"
 ]
}

 The dataset includes 20972 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002889-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6078/d1841h
title: Data for: Evolution and genomic basis of the plant-penetrating ovipositor: a key morphological trait in herbivorous Drosophilidae

description: Herbivorous insects are extraordinarily diverse, yet are found in only
 one-third of insect orders. This skew may result from barriers to plant
 colonization, coupled with phylogenetic constraint on plant-colonizing
 adaptations. Physical barriers have been surmounted through the evolution
 of key morphological innovations, such as the plant-penetrating
 ovipositor. Despite their significance, the evolution and genetic basis of
 such innovations have not been well studied. Ovipositors densely lined
 with hard bristles have evolved repeatedly in herbivorous lineages within
 the Drosophilidae. Here, we focus on the evolution of this trait in
 Scaptomyza, an herbivorous radiation nested in a microbe-feeding clade,
 sister to Hawaiian Drosophila. Our phylogenetic approach revealed that
 ovipositor bristle number increased as herbivory evolved. We then
 dissected the genomic architecture of variation in ovipositor bristle
 number within S. flava through a genome-wide association study. Top
 associated variants were enriched for transcriptional repressors, and the
 strongest associations included genes contributing to peripheral nervous
 system development. Genotyping individual flies replicated the association
 at a variant upstream of Gαi, a neural development gene, contributing to a
 gain of 0.58 bristles/major allele. These results show that a key
 morphological adaptation required for plant colonization may have arisen
 through regulatory changes involving conserved developmental genes.
DOI: 10.6078/d14d8p
title: Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae

description: Herbivorous insects are exceptionally diverse, accounting for a quarter of
 all known eukaryotic species, but the genetic basis of adaptations that
 enabled this dietary transition remains poorly understood. Many studies
 have suggested that expansions and contractions of chemosensory and
 detoxification gene families – genes directly mediating interactions with
 plant chemical defenses – underlie successful plant colonization. However,
 this hypothesis has been challenging to test because the origins of
 herbivory in many lineages are ancient (&gt;150 million years ago
 [mya]), obscuring genomic evolutionary patterns. Here, we characterized
 chemosensory and detoxification gene family evolution across Scaptomyza, a
 genus nested within Drosophila that includes a recently derived
 (&lt;15 mya) herbivore lineage of mustard (Brassicales) specialists
 and carnation (Caryophyllaceae) specialists, and several non-herbivorous
 species. Comparative genomic analyses revealed that herbivorous Scaptomyza
 have among the smallest chemosensory and detoxification gene repertoires
 across 12 drosophilid species surveyed. Rates of gene turnover averaged
 across the herbivore clade were significantly higher than background rates
 in over half of the surveyed gene families. However, gene turnover was
 more limited along the ancestral herbivore branch, with only gustatory
 receptors and odorant binding proteins experiencing strong losses. The
 genes most significantly impacted by gene loss, duplication, or changes in
 selective constraint were those involved in detecting compounds associated
 with feeding on plants (bitter or electrophilic phytotoxins) or their
 ancestral diet (yeast and fruit volatiles). These results provide insight
 into the molecular and evolutionary mechanisms of plant-feeding
 adaptations and highlight strong gene candidates that have also been
 linked to other dietary transitions in Drosophila.
DOI: 10.5061/dryad.9w0vt4bg9
title: Tracing pathways from high-resolution tractography, transcription, and temporal dimensions

description: The neural circuits supporting human cognition are topics of enduring
 interest. The lack of tools available to map circuits has precluded our
 ability to trace the evolution of the human connectome. We harnessed
 high-resolution connectomic, anatomic, and transcriptomic data to develop
 enhanced tools to test for modifications in developmental programs across
 species. We found corresponding ages across species and transcriptionally
 define neurons with stereotypical projections in humans and macaques. We
 used these data to test for modifications in frontal cortex circuit.
 Frontal cortex circuitry development is extended in primates, which is
 concomitant with an expansion in cortico-cortical pathways compared with
 mice in adulthood. These parameters varied little across humans and
 macaques. We identify a collection of conserved features in frontal cortex
 circuits in studied primates. We demonstrate that the integration of
 transcriptional and connectomic data across temporal dimensions is a
 robust approach to trace the evolution of connections in primates. This
 dataset contains scripts as well as diffusion MR scans of mouse brains.
description: This dataset contains
 processed diffusion MR scans of mouse brains at postnatal day (P) 60 and
 P21. These files can be opened with Trackvis (https://trackvis.org/).
DOI: 10.5061/dryad.pc866t1p4
title: Files used in the analyses from A role of asynchrony of seasons in explaining genetic differentiation in a Neotropical toad

description: The process of diversification can be studied at the phylogeographic level
 by attempting to identify the environmental features that promote and
 maintain population divergence. Here we investigate diversification
 in Rhinella granulosa, a Neotropical toad from northeastern
 Brazil, by testing a range of hypotheses that encompass different putative
 mechanisms reducing gene flow among populations. We sequenced single
 nucleotide polymorphisms and examined individual predictions related to
 the role of geographic barriers (rivers), ecological gradients, historical
 habitat stability, and spatial variation in climate seasonality, also
 known as the asynchrony of seasons
 hypothesis. This hypothesis postulates that temporal
 asynchrony of wet and dry seasons over short distances causes parapatric
 populations to become isolated by time. After determining genetic
 structure, inferring past distributions, ranking demographic models, and
 estimating the power of monthly climatic variables, our results identified
 two populations that are not associated with geographic barriers, biome
 gradients, or historical refugia. Instead, they are predicted by spatial
 variation in monthly rainfall and minimum temperature, consistent with the
 asynchrony of seasons hypothesis, supported also by our comparative
 framework using multiple matrix regression and linear mixed
 effects modeling. Due to the toad’s life history, climate likely mediates
 gene flow directly, with genetic differentiation being provoked by neutral
 mechanisms related to climate driven population isolation, and/or by
 natural selection against migrants from populations with different
 breeding times. The asynchrony of seasons hypothesis is seldom considered
 in phylogeographic studies, but our results indicate that it should be
 tested in systems where breeding is tightly coupled with
 climate. 
description: This contains the files related to all genetic analyses in the
 paper. We extracted total DNA from samples obtained in the field and
 used double digest restriction-site associated DNA sequencing to obtain
 SNP markers from the nuclear genome. Sequences for obtained loci and input
 files for all analyses are provided.
description: README files are available for all files. Aditionally, geographic
 coordinates are provided as supplementary material.
DOI: 10.5061/dryad.k0p2ngf8j
title: Shared predators between primate groups and mixed species bird flocks: The potential for forest-wide eavesdropping networks

description: A basic tenet of animal behavior is that animal groupings (e.g., schools
 of fishes or flocks of birds) are widely influenced by predators. Many
 studies have focused on communication between individuals within the same
 species or different species within a defined social group; but predators
 typically select from a number of different co-occurring species. To
 evaluate whether two distantly-related species with similar predators
 share vocal information regarding predator threats, we conducted a field
 experiment in the Amazonian rainforest involving an avian prey-species, a
 primate prey-species, and a shared predator. In our reciprocal field
 experiment, we elicited alarm calls from birds (Bluish-slate antshrikes,
 Thamnomanes schistogynus) and primates (Saddle-backed
 tamarins, Saguinus fuscicollis) by exposing them to a trained
 raptor (Bicolored Hawk, Accipiter bicolor). We then played all
 types of recorded alarm calls back to birds and tamarins, and measured 1)
 the time to respond (for both birds and tamarins), and 2) the distance
 moved across the substrate (for tamarins). Our results show that both
 birds and tamarins were significantly more likely to flee when hearing
 vocal alarms compared to a control (a common bird call, the Screaming
 Piha, Lipaugus vociferans), regardless of the species who produced the
 alarm. In addition, tamarins moved significantly more upon hearing bird
 alarm calls when compared to the control. We suggest that signals
 regarding shared predators may be highly valued across prey from distinct
 social groups. These data support the hypothesis that overlapping
 potential predators can drive communication between distinct prey groups,
 resulting in taxonomically diverse eavesdropping networks within tropical
 rainforests.
DOI: 10.25338/b8fw6r
title: Buffering lidocaine heightens aversion to cornual nerve injections in dairy calves

description: It is best practice to numb the horn buds before disbudding dairy calves,
 which can be achieved by injecting lidocaine, a local anesthetic, around
 the cornual nerve. In humans, the acute pain that occurs upon injection of
 lidocaine can be reduced by neutralizing the pH of the solution with an
 alkalizing agent, such as sodium bicarbonate. We evaluated whether
 buffering lidocaine would reduce calves’ behavioral and physiological
 responses to cornual nerve blocks on the left and right side of the head.
 Female Holstein calves were assigned 1 of 3 treatments: cornual nerve
 blocks with 5.5 mL of unbuffered lidocaine (n = 9), buffered lidocaine (n
 = 9), or a sham procedure with no needle inserted (n = 9). Calves that
 received either type of lidocaine struggled more during the injection than
 sham calves. However, contrary to our hypothesis, struggling was most
 marked in calves that received buffered lidocaine. Similarly, calves
 administered unbuffered or buffered lidocaine had elevated heart rates for
 1 or 3 min after the first injection, respectively, compared to the end of
 the 5-min observation period. Calves in the buffered treatment had lower
 eye temperatures in the first half of the observation period compared to
 the second half, consistent with responses cattle show to other aversive
 procedures, but no changes over time were observed in the other 2
 treatments. There were no treatment differences in heart rate variability
 measures. These results suggest that cornual nerve blocks are aversive, at
 least in the short term, and that buffering the lidocaine worsens the
 calf’s response to this procedure.
description: See methods in associated publication.
description: Data were collected from the University of California Davis Dairy
 Facility on 27 calves in 2019. Variables are defined in the README sheet
 of each of the four Excel files. The R script used to analyze each dataset
 is provided.
DOI: 10.5061/dryad.69p8cz92j
title: Data: Diversity of fish parasites of the Penzhina River (Kamchatka Krai, Russia)

description: The study of the fauna of fish parasites helps to understand the ways of
 formation of ichthyofauna and obtain a more complete knowledge of the
 biodiversity of the aquatic ecosystem as a whole. Parasitologically, the
 Penzhina River, one of the largest and most inaccessible rivers in the
 Russian Far East, remained poorly studied for a long time. Penzhina is
 characterized by an unusually extended mouth area, its estuary is
 distinguished by extremely high tides, up to 13.0 m, which is the highest
 tide in Russia. Rich ichthyofauna (21 species of fish and cyclostomes) and
 a variety of hydrological conditions favor the formation of a diverse
 fauna of fish parasites in the Penzhina River. The published
 parasitological data was still fragmentary and concerned few host species,
 so it is significantly broadened by the authors’ findings and
 observations. The paper provides information on 122 species of fish
 parasites in the lower reaches and estuary of the Penzhina River, and
 Penzhinskaya Bay.
description: This data set was collected
 from a combination of field and laboratory research, and analysis of
 published data. Fish were sampled by sweep net for juveniles with size 3x8
 m in the Penzhina downstream in 0-75 km upward from the mouth in July
 2015. The samples for parasitological analysis were collected from 184
 fish specimens including the Kolyma sculpin, common minnow, young of
 different species of whitefishes, grayling, and ninespine stickleback.
 Laboratory parasitological analysis of fish included standard procedure
 for examining fins, gills and all internal organs of fish to detect
 parasites (Hoffman, 1999). The parasites were quantified by their
 prevalence (i.e. percentage of hosts infected by parasites), intensity
 (range, mean) (number of parasites per infected host), and abundance
 (number of parasites per host) according to the calculation method (Bush
 et al., 1997). In addition, all available materials of other authors on
 fish parasites of the Penzhina River and Penzhinskaya Bay were
 studied.
description: The study of the collected data makes it possible to analyze the
 structure of the fish parasite assemblages of the Penzhina River and
 determine the leading factors of their formation. The work will be useful
 for specialists in the study of the fauna of fish parasites in hypertidal
 and other estuaries.