cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dbrv15f3n
title: Data from: Thalamic bursting and the role of timing and synchrony in thalamocortical signaling in the awake mouse

description: The thalamus controls transmission of sensory signals from periphery to
 cortex, ultimately shaping perception. Despite this significant role,
 dynamic thalamic gating and the consequences for downstream cortical
 sensory representations have not been well studied in the awake brain. We
 optogenetically modulated the ventro-posterior medial thalamus in the
 vibrissa pathway of the awake mouse, and measured spiking activity in the
 thalamus, and activity in primary somatosensory cortex (S1) using
 extracellular electrophysiology and genetically encoded voltage imaging.
 Thalamic hyperpolarization significantly enhanced thalamic sensory-evoked
 bursting, yet surprisingly the S1 cortical response was not amplified, but
 instead timing precision was significantly increased, spatial activation
 more focused, and there was an increased synchronization of cortical
 inhibitory neurons. A thalamocortical network model implicates the
 modulation of precise timing of feedforward thalamic population spiking,
 presenting a highly sensitive, timing-based gating of sensory signaling to
 cortex.
description: These data were collected from the ventral posteromedial (VPm)
 nucleus and/or primary somatosensory (S1) cortex in the vibrissa system of
 isoflurane-anesthetized and awake mice.  In some cases (where noted
 below), the data are saved results from a model thalamocortical network. 
 Electrophysiological data was acquired using silicon microelectrode arrays
 (NeuroNexus).  Spike-sorting was performed using KiloSort2, and clustering
 performed using Phy2.  Mesoscale voltage activity was recorded using the
 genetically-encoded voltage indicator (GEVI) ArcLight.
 For more information, please see the detailed Methods section of
 the associated publication.
description: Matlab is required to access the data files and create all
 figures, except for Figure 4 E, F and Figure 8, which require
 Python.
DOI: 10.5061/dryad.6m905qg29
title: Supplementary data for: McFadden et al., Revisionary systematics of Octocorallia (Cnidaria: Anthozoa) guided by phylogenomics

description: The anthozoan sub-class Octocorallia includes over 3500 nominal species of
 soft corals and gorgonian sea fans, many of which serve as critical
 foundation species in benthic marine ecosystems in shallow waters to the
 deep sea. Despite their familarity and ecological importance, the
 diversity and taxonomy of octocorals remain poorly known. All of the
 orders, subordinal groups and a majority of families have been recognized
 to be poly- or paraphyletic, but poor resolution of the deeper nodes in
 mitochondrial or single-locus nuclear gene trees have hindered formal
 revision of the higher level taxonomy of the group. We used sequence data
 from target-capture of 739 ultraconserved and exon loci to reconstruct a
 fully resolved phylogeny for 185 octocoral taxa representing 55 of 63
 currently recognized families. We use this phylogeny, supplemented with a
 gene tree for mitochondrial mtMutS for an additional 107 taxa, to guide a
 revision of the families and orders of Octocorallia. We: (1) elevate the
 anthozoan sub-classes Octocorallia and Hexacorallia to the rank of Class;
 (2) replace the three currently recognized orders of Octocorallia
 (Alcyonacea, Pennatulacea, Helioporacea) with two new orders reflecting
 reciprocally monophyletic major clades; and (3) revise all families with
 the exception of the 15 recognized families of sea pens, which we
 accommodate within a new superfamily. The revised classification of
 Octocorallia thus comprises 79 families, including 18 that are newly
 described and three that have been reinstated or elevated in rank. In
 addition, two new genera are described and another three reinstated. We
 leave the family assignment of 46 of 411 genera as incertae sedis until
 further molecular or morphological data can be obtained to confirm their
 phylogenetic affinities.
DOI: 10.5061/dryad.fxpnvx0vf
title: Multi-resistant Enterobacteriaceae in yellow-legged gull chicks in their first weeks of life

description: Wild animal species living in anthropogenic areas are commonly carriers of
 antimicrobial resistant bacteria (AMRB), but their role in the
 epidemiology of these bacteria is unclear. Several studies on AMRB in
 wildlife have been cross-sectional in design and sampled individual
 animals at only one point in time. To further understand the role of
 wildlife in maintaining and potentially transmitting these bacteria to
 humans and livestock, longitudinal studies are needed in which samples are
 collected from individual animals over multiple time periods. In Europe,
 free-ranging yellow-legged gulls (Larus michahellis) commonly live in
 industrialized areas, forage in landfills, and have been found to carry
 AMRB in their feces. Using bacterial metagenomics and antimicrobial
 resistance characterization, we investigated the spatial and temporal
 patterns of AMRB in a nesting colony of yellow-legged gulls from an
 industrialized area in southern France. We collected 54 cloacal swabs from
 31 yellow-legged gull chicks in 20 nests on three dates in 2016. We found
 that AMRB in chicks increased over time and was not spatially structured
 within the gull colony. This study highlights the complex occurrence of
 AMRB in a free-ranging wildlife species and contributes to our
 understanding of the public health risks and implications associated with
 ARMB-carrying gulls living in anthropogenic areas.
DOI: 10.57724/hes_20250113_microant_krill
title: Microplastics in Antarctic krill, 2025
DOI: 10.5061/dryad.g4f4qrfsp
title: Ontogeny of risk assessment and escape-hatching performance by red-eyed treefrog embryos in two threat contexts

description: Arboreal embryos of red-eyed treefrogs, Agalychnis callidryas,
 hatch prematurely in response to hypoxia when flooded and mechanosensory
 cues (MC) in snake attacks, but hatching later improves tadpole survival.
 We studied ontogenetic changes in risk assessment and hatching performance
 of embryos in response to flooding and physical disturbance. We
 hypothesized that risk assessment decreases as hatchling survival improves
 and hatching performance increases as embryos develop. Because snakes eat
 faster than embryos asphyxiate, we hypothesized that embryos decide to
 hatch sooner and hatch faster in response to MC. We video-recorded
 individual embryos hatching in response to each cue type, then compared
 the incidence and timing of a series of events and behaviors from cue
 onset to complete hatching across ages and stimuli. Latency from cue to
 hatching decreased developmentally in both contexts and was shorter with
 MC, but the elements contributing to those changes
 differed. Hypoxia-assessment involved position changes, which
 decreased developmentally along with assessment time.
 MC-assessment occurred more rapidly, without movement, and
 decreased with age. The first stages of hatching, membrane
 rupture and head emergence, were surprisingly age-independent but faster
 with MC, congruent with greater effort under more immediate risk. In
 contrast, body emergence and compression showed ontogenetic improvement
 consistent with morphological constraints but no cue effect. Both
 appropriate timing and effective performance of hatching are necessary for
 continued development. Different stages of the process vary with
 development and environmental context, suggesting combinations of adaptive
 context- and stage-dependent behavior, cue-related constraints on
 information acquisition, and ontogenetic constraints on elements of
 performance.
DOI: 10.5061/dryad.k0p2ngfbb
title: Data from: Kinematic trajectories in response to speed perturbations in walking suggest modular task-level control of leg angle and length

description: Abstract Navigating complex terrains requires dynamic interactions between
 the substrate, musculoskeletal and sensorimotor systems. Current
 perturbation studies have mostly used visible terrain height
 perturbations, which do not allow us to distinguish among the
 neuromechanical contributions of feedforward control, feedback-mediated
 and mechanical perturbation responses. Here, we use treadmill belt speed
 perturbations to induce a targeted perturbation to foot speed only, and
 without terrain-induced changes in joint posture and leg loading at stance
 onset. Based on previous studies suggesting a proximo-distal gradient in
 neuromechanical control, we hypothesized that distal joints would exhibit
 larger changes in joint kinematics, compared to proximal joints.
 Additionally, we expected birds to use feedforward strategies to increase
 the intrinsic stability of gait. To test these hypotheses, seven adult
 guinea fowl were video recorded while walking on a motorized treadmill,
 during both steady and perturbed trials. Perturbations consisted of
 repeated exposures to a deceleration and acceleration of the treadmill
 belt speed. Surprisingly, we found that joint angular trajectories and
 center of mass fluctuations remain very similar, despite substantial
 perturbation of foot velocity by the treadmill belt. Hip joint angular
 trajectories exhibit the largest changes, with the birds adopting a
 slightly more flexed position across all perturbed strides. Additionally,
 we observed increased stride duration across all strides, consistent with
 feedforward changes in the control strategy. The speed perturbations
 mainly influenced the timing of stance and swing, with the largest
 kinematic changes in the strides directly following a deceleration. Our
 findings do not support the general hypothesis of a proximo-distal
 gradient in joint control, as distal joint kinematics remain largely
 unchanged. Instead, we find that leg angular trajectory and the timing of
 stance and swing are most sensitive to this specific perturbation, and leg
 length actuation remains largely unchanged. Our results are consistent
 with modular task-level control of leg length and leg angle actuation,
 with different neuromechanical control and perturbation sensitivity in
 each actuation mode. Distal joints appear to be sensitive to changes in
 vertical loading but not foot fore-aft velocity. Future directions should
 include in vivo studies of muscle activation and force-length dynamics to
 provide more direct evidence of the sensorimotor control strategies for
 stability in response to belt speed perturbations.
DOI: 10.5061/dryad.pnvx0k6q9
title: CeA Psilocin fiber photometry study: Data and custom code from experiments looking at changes in calcium dynamics in response to an air puff events

description: Psilocybin, and its active metabolite psilocin, have been shown to elicit
 rapid and long-lasting symptom improvements in a variety of affective
 psychiatric illnesses. However, the specific mechanisms behind these
 therapeutic effects remain relatively unknown. The central amygdala (CeA)
 is a primary output region within the extended amygdala that is heavily
 dysregulated in affective psychiatric disorders. Here, we utilized fiber
 photometry to measure changes in CeA reactivity to an aversive air puff
 stimulus after psilocin administration, both acutely and at varying
 prolonged time points. We found that administration of psilocin increased
 reactivity acutely in females, but not males. Additionally, we show that
 one dose of psilocin produced decreases in reactivity in males, but not
 females, 28-days post administration, with decreases seen as early as
 2-days post administration. We further report stimulus-specific changes in
 CeA reactivity after psilocin with differential responsivity to an
 aversive air puff stimulus and an auditory stimulus. We also measured
 changes in behavioral response to the air puff stimulus and report sex
 differences in exploratory behavior but not threat responding or general
 locomotion. This study provides evidence that a single dose of psilocin
 can elicit sex-specific, dynamic, and enduring changes in CeA reactivity
 to an aversive stimulus. These data are an important step towards
 dissecting circuit-based mechanisms underlying the effects of
 psychedelics.
description: Datasets include two matlab structures that were constructed
 using the .m scripts included. Subjects that were removed from study were
 then removed from data before saving as structure.
description: In order to use these scripts you need to have the TDTSDK folder
 from TDT which allows for processing of raw data files. Additionally you
 would need the raw data files from the study. However, using the matlab
 (.mat) structures provided, you are able to process data using
 the GroupDataAnalysis_BinnedData120521.m script.
DOI: 10.5061/dryad.pc866t1rh
title: Population regulation and density‐dependent demography in the Trinidadian guppy

description: Classic theory for density-dependent selection for delayed maturation
 requires that a population be regulated through some combination of adult
 fecundity and/or juvenile survival. We tested whether those demographic
 conditions were met in four experimental populations of Trinidadian
 guppies in which delayed maturation of males evolved when the densities of
 those populations became high. We used monthly mark-recapture data to
 examine population dynamics and demography in these populations. Three of
 the four populations displayed clear evidence of regulation. In all four
 populations, monthly adult survival rates were independent of biomass
 density or actually increased with increased biomass density. Juvenile
 recruitment, which is a combination of adult fecundity and juvenile
 survival, decreased as biomass density increased in all four populations.
 Demography showed marked seasonality, with greater survival and higher
 recruitment in the dry season than the wet season. Population regulation
 via juvenile recruitment supports the hypothesis that density-dependent
 selection was responsible for the evolution of delayed maturity in males.
 This body of work represents one of the few complete tests of
 density-dependent selection theory.
description: Data were collected via monthly censuses of four experimental
 guppy populations.  Censuses used mark-recapture methods in which each
 individual was given a unique mark.
DOI: 10.57707/fmi-b2share.nh35a-rqj22
title: Model results of LAI, GPP, soil respiration, soil temperature, and soil moisture in 2018-2021 and NEE in 2006-2021 in urban green spaces in Helsinki

description: Dataset associated with Thölix et al. (2024) manuscript entitled "Carbon sequestration in different urban vegetation types in Southern Finland".
LAI, GPP, soil respiration, soil temperature, and soil moisture were modeled in 2018-2021 and NEE in 2006-2021 at four urban green space types commonly found in the city: a small urban forest (Forest), a managed park (Park), lawn and irrigated lawn.
DOI: 10.57707/fmi-b2share.36s86-n1f76
title: Model results of LAI, GPP, soil respiration, soil temperature, and soil moisture in 2018-2021 and NEE in 2006-2021 in urban green spaces in Helsinki

description: Dataset associated with Thölix et al. (2024) manuscript entitled "Carbon sequestration in different urban vegetation types in Southern Finland".
LAI, GPP, soil respiration, soil temperature, and soil moisture were modeled in 2018-2021 and NEE in 2006-2021 at four urban green space types commonly found in the city: a small urban forest (Forest), a managed park (Park), lawn and irrigated lawn.
DOI: 10.57707/fmi-b2share.4r2mz-47x04
title: Model results of LAI, GPP, soil respiration, soil temperature, and soil moisture in 2018-2021 and NEE in 2006-2021 in urban green spaces in Helsinki

description: Dataset associated with Thölix et al. (2024) manuscript entitled "Carbon sequestration in different urban vegetation types in Southern Finland".
LAI, GPP, soil respiration, soil temperature, and soil moisture were modeled in 2018-2021 and NEE in 2006-2021 at four urban green space types commonly found in the city: a small urban forest (Forest), a managed park (Park), lawn and irrigated lawn.
DOI: 10.5061/dryad.70rxwdc10
title: Data from: Interannual consistency of migration phenology is season- and breeding region-specific in North American Golden Eagles

description: Avian migrants can adjust the time they depart for migration and arrive at
 their destination (i.e. phenology) based on environmental conditions, the
 period of the annual cycle, and the distance of migration. Our study shows
 that interannual consistency (an indicator of the strength of adjustments)
 in migration schedule of Golden Eagles (Aquila chrysaetos) in North
 America was greatest in boreal spring migration and the breeding regions
 of eastern Canada, suggesting that migration schedule is partly
 environmentally driven. Using multi-year GPS tracks of 83 adults breeding
 in three spatially distant regions (Alaska, northeast Canada, and
 southeast Canada), we quantified the interannual consistency of migration
 timing with variations within individuals tracked across multiple years
 and among-individuals and repeatability (r) of migration schedule,
 duration, and wintering latitude by breeding regions and seasons. By
 comparing regions and seasons, we found that consistency was highest (r
 &gt; 0.85) for the schedule of the boreal spring migration in eastern
 Canada while Alaska had the lowest value (r &lt; 0.15). Since seasonal
 consistency of migration schedule was only detected in eastern Canada, we
 conclude that seasonal features are not the main constraint on consistency
 of migration schedule. While regional differences in consistency were not
 related to differences in migratory distances, they could be the result of
 genetic or habitat differences. We also found that warmer temperatures
 than the decadal average at the region of departure delayed the start of
 boreal spring migration by ~10 days and advanced boreal autumn migration
 by ~20 days. It suggests that warmer temperatures would reduce residence
 time on breeding grounds, which is contrary to expectations and trends
 found in other studies. Wide variations in migratory strategies across a
 species distribution can add to the lists of challenges for conservation
 yet such variations can give migrants the capacity to acclimate to
 environmental changes.
DOI: 10.5061/dryad.bvq83bkc0
title: Alzheimer’s disease: Ablating single master site abolishes tau hyperphosphorylation

description: Hyperphosphorylation of the neuronal tau protein is a hallmark of
 neurodegenerative tauopathies such as Alzheimer’s disease. A central
 unanswered question is why tau becomes progressively hyperphosphorylated.
 Here, we show that tau phosphorylation is governed by interdependence— a
 mechanistic link between initial site-specific and subsequent multi-site
 phosphorylation. Systematic assessment of site interdependence identified
 distinct residues (threonine-50, threonine-69, and threonine-181) as
 master sites that determine propagation of phosphorylation at multiple
 epitopes. CRISPR point mutation and expression of human tau in Alzheimer’s
 mice showed that site interdependence governs physiologic and
 amyloid-associated multi-site phosphorylation and cognitive deficits,
 respectively. Combined targeting of master sites and p38α, the most
 central tau kinase linked to interdependence, synergistically ablated
 hyperphosphorylation. In summary, our work delineates how complex tau
 phosphorylation arises to inform therapeutic and biomarker design for
 tauopathies.
description: Raw Immunoblot data for Figure 1. Chemiluninescence signals were
 imaged on a ChemiDoc MP (Biorad) digital system.
DOI: 10.5061/dryad.3ffbg79mb
title: Raw data from: Airport noise disturbs foraging behavior of Japanese pipistrelle bats

description: The expansion of anthropogenic noise poses an emerging threat
 to the survival and reproductive success of various
 organisms. Previous investigations have focused on the detrimental effects
 of anthropogenic noise on the foraging behavior in some terrestrial and
 aquatic animals. Nevertheless, the role of airport noise in impairing
 foraging activities of most wild animals has been neglected. Here, we
 aimed to assess whether foraging behavior in free-living Japanese
 pipistrelle bats (Pipistrellus abramus) can be disturbed by airport noise.
 We used audio recording to monitor foraging activities
 of bats at 11 sites around the runway of a municipal airport. We
 quantified noise level and spectra, aircraft activity, habitat type,
 nightly temperature, wind speed, and moon phase for each site. The
 analysis revealed that noise level and aircraft activity were significant
 negative predictors for the number of bat passes and feeding buzzes around
 the runway, even after controlling for the effects of other environmental
 factors. There was no marked spectral overlap between bat echolocation
 pulses and airport noise in the presence and absence of low-flying
 aircraft. The spectro-temporal parameters of echolocation vocalizations
 emitted by bats were dependent on noise level, aircraft activity, and
 habitat type. These results provide correlative evidence that airport
 noise can reduce foraging activities of wild pipistrelle bats. Our
 findings add to the current knowledge of adverse impacts of airport noise
 on foraging bats in artificial ecosystems and provide a basis for further
 research on the mechanisms behind noise pollution near airports.
DOI: 10.5061/dryad.4j0zpc8dx
title: Data from: Composition of a chemical signalling trait varies with phylogeny and precipitation across an Australian lizard radiation

description: The environment presents challenges to the transmission and detection of
 animal signalling systems, resulting in selective pressures that can drive
 signal divergence among populations in disparate environments. For
 chemical signals, climate is a potentially important selective force
 because factors such as temperature and moisture influence the persistence
 and detection of chemicals. We investigated an Australian lizard radiation
 (Heteronotia) to explore relationships between a sexually dimorphic
 chemical signalling trait (epidermal pore secretions) and two key climate
 variables: temperature and precipitation. We reconstructed the phylogeny
 of Heteronotia with exon capture phylogenomics,
 estimated phylogenetic signal in among-lineage chemical variation, and
 assessed how chemical composition relates to temperature and precipitation
 using multivariate phylogenetic regressions. High estimates of
 phylogenetic signal indicate that the composition of epidermal pore
 secretions varies among lineages in a manner consistent with Brownian
 motion; although there are deviations to this, with stark divergences
 coinciding with two phylogenetic splits. Accounting for phylogenetic
 non-independence, we found that among-lineage chemical variation is
 associated with geographic variation in precipitation but not temperature.
 This contrasts somewhat with previous lizard studies, which have generally
 found an association between temperature and chemical composition. Our
 results suggest that geographic variation in precipitation can affect the
 evolution of chemical signalling traits, possibly influencing patterns of
 divergence among lineages and species.