cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d2547d85r
title: Data for: Neuromorphic functions with a polyelectrolyte-confined fluidic memristor

description: Reproducing the ion channel-based neural functions with artificial fluidic
 systems is a long aspirational goal both for neuromorphic computing and
 biomedical applications. Herein neuromorphic functions are successfully
 accomplished with polyelectrolyte-confined fluidic memristors (PFMs), in
 which confined polyelectrolyte-ion interactions contribute to hysteretic
 ion transport, resulting in ionic memory effects. Various electric pulse
 patterns are emulated by PFM with ultralow power consumption. Benefiting
 from the fluidic-based property of PFMs, mimicking chemical-regulated
 electric pulse is investigated and accomplished. More importantly,
 chemical-electric signal transduction is implemented based on the specific
 recognition of PFM. With structural emulation to ion channels, PFM
 features versatility and easily interfaces with biological systems, paving
 a way to building neuromorphic devices with advanced functions by
 introducing rich chemical designs.
description: All electrochemical
 experiments were performed on a Heka EPC-10 amplifier (Heka Inc.,
 Germany). Currents were recorded by 2 Ag/AgCl wires placed inside a
 micro/nanopippette and the external bath solution respectively. All bias
 voltage shown herein was V<sub>internal</sub> vs
 V<sub>external</sub>. No processes like smooth or filtering
 were carried out on the data. FEM was carried out with Comsol 6.0 (Comsol
 Co.).
description: The data were shown in Origin documents, and the Simulation data
 should be read by a Comsol multiphysics software (6.0 or higher
 version).
DOI: 10.5061/dryad.6m905qg3j
title: Data for "Boosting propagule transport models with individual-specific data from mobile apps"

description: Management of invasive species and pathogens requires information about
 the traffic of potential vectors. Such information is often taken from
 vector traffic models fitted to survey data. Here, user-specific data
 collected via mobile apps offer new opportunities to obtain more accurate
 estimates and to analyze how vectors' individual preferences affect
 propagule flows. However, data voluntarily reported via apps may lack some
 trip records, adding a significant layer of uncertainty. We show how the
 benefits of app-based data can be exploited despite this drawback. Based
 on data collected via an angler app, we built a stochastic model for
 angler traffic in the Canadian province of Alberta. There, anglers
 facilitate the spread of whirling disease, a parasite-induced fish
 disease. The model is temporally and spatially explicit and accounts for
 individual preferences and repeating behaviour of anglers, helping to
 address the problem of missing trip records. We obtained estimates of
 angler traffic between all subbasins in Alberta. The model's accuracy
 exceeds that of direct empirical estimates even when fewer data were used
 to fit the model. The results indicate that anglers' local
 preferences and their tendency to revisit previous destinations reduce the
 number of long inter-waterbody trips potentially dispersing whirling
 disease. According to our model, anglers revisit their previous
 destination in 64% of their trips, making these trips irrelevant for the
 spread of whirling disease. Furthermore, 54% of fishing trips end in
 individual-specific spatially contained areas with mean radius of 54.7 km.
 Finally, although the fraction of trips that anglers report was unknown,
 we were able to estimate the total yearly number of fishing trips in
 Alberta, matching an independent empirical estimate. We make two major
 contributions: (1) we provide a model that uses mobile app data to boost
 the mechanistic accuracy of classic propagule transport models, and (2) we
 demonstrate the importance of individual-specific behaviour of vectors for
 propagule transport. Ignoring vectors' local preferences and their
 tendency to revisit previous destinations can lead to significant
 overestimates of vector traffic and biased estimates of propagule flows.
 This has clear implications for the management of invasive species and
 animal diseases.
DOI: 10.5061/dryad.wwpzgmsns
title: Selection results of two native parasitoids on the invasive spotted wing drosophila

description: Co-evolved natural enemies provide sustainable and long-term control of
 numerous invasive insect pests, but the introduction of such enemies has
 declined sharply due to increasing regulations. In the absence of
 co-evolved natural enemies, native species may attack exotic invasive
 pests; however, they usually lack adaptations to control novel hosts
 effectively. We investigated the potential of two native pupal
 parasitoids, Pachycrepoideus vindemmiae, and Trichopria drosophilae, to
 increase their developmental success on the invasive Drosophila suzukii.
 Replicated populations of the two parasitoids were subjected to 10
 generations of laboratory selection on D. suzukii with D. melanogaster
 serving as the co-evolved host. We assessed the developmental success of
 selected and control lines in generations 0, 3, and 10. Changes in host
 preference, sex ratio, development time, and body size were measured to
 evaluate correlated responses with adaptation. Both parasitoid species
 responded rapidly to selection by significantly increasing their
 developmental success on the novel host within three generations, which
 remained constant for seven additional generations without further
 improvement. The generalist parasitoid species P. vindemmiae was able to
 reach similar developmental success as the control populations, while the
 performance of the more specialized parasitoid T. drosophilae remained
 lower on the novel than on the co-evolved host. There was no increase in
 preference towards the novel host over ten generations of selection; nor
 were there changes in development time or body size associated with
 adaptation in either parasitoid species. The sex ratio became less
 female-biased for both parasitoids after three generations of selection
 but rebounded in P. vindemmiae by generation 10. These results suggest
 that a few generations of selection may be sufficient to improve the
 performance of native parasitoids on invasive hosts, but with limits to
 the degree of improvement for managing invasive pests when exotic
 co-evolved natural enemies are unavailable.
description: Laboratory selection experiment.
description: Microsoft excel
DOI: 10.5061/dryad.q2bvq83pd
title: Tahoe rain or snow precipitation phase observations

description: These data include observations of rain, snow, and mixed precipitation
 from the Tahoe Rain or Snow citizen science project. Included with each
 observation is a set of ancillary variables, including latitude and
 longitude, elevation, modeled meteorological data, and additional info.
 Please see the metadata file for the description and units of each data
 column. For more info, please see Jennings et al. (2023) and Arienzo et
 al. (2021): Jennings, Keith S., Monica M. Arienzo, Meghan Collins,
 Benjamin Hatchett, Anne W. Nolin, and Graeme Aggett. "Crowdsourced
 Data Highlight Precipitation Phase Partitioning Variability in Rain-Snow
 Transition Zone." Earth and Space Science (2023).
 https://doi.org/10.1029/2022EA002714 Arienzo, Monica M., Meghan Collins,
 and Keith S. Jennings. "Enhancing engagement of citizen scientists to
 monitor precipitation phase." Frontiers in Earth Science 9 (2021):
 617594. https://doi.org/10.3389/feart.2021.617594  For the code
 used to process these data:
 https://github.com/SnowHydrology/MountainRainOrSnow/tree/tahoe_ros
description: Please see Jennings et al. (2023) and Arienzo et al. (2021) for
 full methodological details. In brief: We
 collected observations of rain, snow, and mixed precipitation from
 community observers using the Citizen Science Tahoe mobile app
 The app automatically timestamped and geolocated each
 observation We associated each data point with
 elevation and modeled meteorological data, along with the percentage
 probability of liquid precipitation from the Integrated Multi-satellitE
 Retrievals for GPM (IMERG) Level 3 v. 6 product We
 quality-controlled observations based on modeled air temperature, nearby
 precipitation, nearby relative humidity, distance from meteorological
 stations, and duplicate timestamps For the
 code used to process these data: https://github.com/SnowHydrology/MountainRainOrSnow/tree/tahoe_ros
description: These data can be opened and examined using a text reader. The
 user may also utilize open-source software such as R or Python or
 commercial software such as Microsoft Excel to evaluate the data or run
 additional analyses.
DOI: 10.5061/dryad.t1g1jwt5v
title: Fitness landscapes reveal context-dependent benefits of oviposition behaviour

description: Resource choice behaviour has enormous fitness consequences and can drive
 niche expansion. However, individual behavioural choices are often
 mediated by context, determined by past experience. Do such
 context-dependent behaviours reflect maladaptive variation, or are they
 locally adaptive? Using Tribolium castaneum (the red flour beetle), we
 demonstrate that context-dependent oviposition behaviour reflects
 distinct, context-specific local fitness peaks. We measured offspring
 fitness to generate fitness landscapes as a function of all possible
 oviposition behaviours (i.e., combinations of fecundity and resource
 preference) in a habitat containing optimal and suboptimal resource
 patches. We did this by experimentally manipulating female egg allocation
 across patches, which allowed us to assess behaviours not typically
 observed in the laboratory. We found that females from different age and
 competition contexts exhibit distinct behaviours which optimize different
 fitness components, linked in a tradeoff. With prior exposure to strong
 competition and increasing age, females produce few but fast-developing
 offspring that are advantageous under high resource competition. In
 contrast, young naïve females produce significantly more (but
 slower-developing) offspring, which is beneficial under weak competition.
 Systematically mapping complete context-dependent fitness landscapes is
 thus critical to infer behavioural optimality and offers predictive power
 in novel contexts.
DOI: 10.5061/dryad.kwh70rz7b
title: Tufted Puffin (Fratercula cirrhata) 3dRADseq and msat data

description: The tufted puffin (Fratercula cirrhata) is a medium sized seabird found
 throughout the North Pacific Ocean. Although populations of tufted puffins
 appear to be stable or increasing in some parts of their distribution,
 they are experiencing significant declines in other parts of their
 distribution, including in the Gulf of Alaska. Assessments of tufted
 puffin population status in Alaska are currently limited because little is
 known about population genetic structure. Similarly, there is little
 information on the amount of dispersal between populations in Alaska, and
 between populations in Alaska and those in the southern portion of the
 species’ range. If genetic analyses reveal significant genetic
 differentiation between tufted puffins nesting in different regions of
 Alaska, or evidence of local adaptation, then the apparent decline in the
 Gulf of Alaska becomes more of a conservation concern. There is general
 consensus within the tufted puffin research and management community that
 a study of population genetic structure is a high priority. As part of our
 ongoing research, we conducted genetic analysis to determine if tufted
 puffin nesting colonies form single or multiple conservation units, and
 populations show evidence of local adaptation, using traditional
 population genetic analysis and next-generation sequencing techniques.
 Continuing analyses of genome-wide associations between environment and
 genetic adaptation for tufted puffins will also provide greater insight
 into how coastal seabird populations in the temperate North Pacific Ocean
 are coping with the effects of climate change.
description: We isolated high quality
 genomic DNA from 75 egg, feather, tissue, and blood samples using a salt
 extraction (Aljanabi and Martinez 1997).  Samples were sent off to
 Université Laval where DNA was digested with three restriction enzymes
 <em>PstI</em>, <em>NsiI</em>,
 <em>MspI</em> and a library was prepared.  Sequencing was done
 at Génome Québec at McGill University on a NovaSeq6000 S4
 PE100.
DOI: 10.7280/d1zt4s
title: Hindlimb muscle spindles inform preparatory forelimb coordination prior to landing in toads

description: Animals move across a wide range of surface conditions in real-world
 environments to acquire resources and avoid predation. To effectively
 navigate a variety of surfaces, animals rely on several mechanisms
 including intrinsic mechanical responses, spinal-level central pattern
 generators, and neural commands that require sensory feedback. Muscle
 spindle 1a afferents play a critical role in providing sensory feedback
 and informing motor control strategies across legged vertebrate
 locomotion, which is apparent in cases where this sensory input is
 compromised. Here we tested the hypothesis that spindle 1a afferents from
 hindlimb muscles are important for coordinating forelimb landing behavior
 in the cane toad. We performed bilateral sciatic nerve reinnervations to
 ablate the stretch reflex from distal hindlimb muscles while allowing for
 motor neuron recovery. We found that toads significantly delayed the onset
 and reduced the activation duration of their elbow extensor muscle
 following spindle 1a afferent ablation in the hindlimbs. However,
 reinnervated toads achieved similar elbow extension at touchdown compared
 to their pre-surgery state. Our results suggest that while toads likely
 tuned the activation timing of forelimb muscles in response to losing 1a
 afferent sensation from the hindlimbs they were likely able to employ
 compensatory strategies that allowed them to continue landing effectively
 with reduced sensory information during takeoff. These findings indicate
 muscle spindle 1a afferents may contribute to tuning complex movements
 involving multiple limbs.
description: You will need Microsoft Excel or equivalent (e.g. Google Sheets)
 to open and read CSV files and any movie or video player that can play
 .avi files (if you are interested in collected videos).
DOI: 10.5061/dryad.83bk3j9vs
title: Data for: Madicolous insects from Atlantic forest and Amazon mountains (Brazil)

description: The dataset consist on abundance values of madicolous insects - aquatic
 organisms that inhabit thin layers of water - recorded in three mountains
 of the Atlantic Rainforest (G1, G2, and G3) and in one Amazon mountain
 (G4). The distribution of sampling sites cover the full elevational range
 of each region, from 0 to 2,800 m a.s.l. in the Atlantic Forest and from
 90 to 3,000 meters a.s.l. in the Amazon. A total of 109 sampling sites
 were investigated, where physico-chemical parameters of water
 (temperature, pH, dissolved oxygen and conductivity), geographic
 coordinates and the altitude were also obtained.
description: Adults of madicolous insects were sampled with emergence traps
 (0.125 m<sup>2</sup> coverage area), and immatures with hand
 net (250 µm mesh size) in
 the same sites were adults were collected. All individuals were identified
 to the lowest taxonomic resolution possible (genus, species or
 morphospecies). Water physico-chemical
 parameters were determined with an analytical kit and conductivity was
 measured with a portable conductometer. Geographic coordinates and the altitude of each
 sampling site were obtained in the field with GPS.
DOI: 10.5061/dryad.t4b8gtj5j
title: Shape coordinates and centroid size for adults and ontogenetic series analyzed in predictable complexity of evolutionary allometry

description: Allometry has been a paradigm of constraints, including intrinsic
 constraints on the evolvability of allometry, as a source of developmental
 and genetic constraints on the evolution of form, and of functional
 constraints, maintaining functional equivalence as body size evolves. Yet,
 allometry may be the simplest case of varied constraints, and of
 morphological integration, even though allometry itself is not simple.
 Evolutionary allometry may be especially complex because it depends not
 only on the developmental origins of allometry and determinants of
 allometric variation but also on the evolutionary dynamics of size and
 shape. It should also depend on the ecological opportunity for
 size-dependent ecomorphological specialization. We predict that lineages
 that converge in those would exhibit similar evolutionary allometries but
 otherwise, evolutionary allometries would be heterogeneous. Countering
 this expectation are familiar craniofacial evolutionary allometries, often
 ascribed to developmental bias. To test both those hypotheses, we compare
 evolutionary allometries of mandibles across lineages of squirrels and
 evolutionary to growth allometries. As expected, lineages that converge on
 size-dependent specializations exhibit similar evolutionary allometries,
 but otherwise, their allometries are no more similar than expected by
 chance. Growth allometries of squirrels (and a cricetid rodent) slightly
 resemble the evolutionary allometry of one lineage, but growth allometries
 of species from other lineages are orthogonal to their own lineages’
 evolutionary allometry. We would expect that craniofacial allometries that
 are not brain-driven would, like mandibular evolutionary allometries, be
 predictable only from size-dependent ecological specializations.
description: Coordinates of landmarks digitized on photographs, then
 Procrustes superimposed.
description: Any program that can open comma-delimited files.
DOI: 10.5061/dryad.b5mkkwhh3
title: An extended epiphenotype for an extended phenotype in Toxoplasma gondii infected feral house mice

description: Parasitism of mice by Toxoplasma gondii reduces the host's aversion
 to cat odors, likely increasing predation and transmission of the parasite
 to its definitive host. This behavioral change suggests a parasitic
 manipulation where host behavior becomes an extended phenotype of the
 parasite. Independently, epigenetic changes within an organism are now
 known to create behavioral change. The results described here provide an
 experimental connection between these disparate strands of extended
 phenotypes and the role of epigenetics in behavioral diversity. Using mice
 captured on Kangaroo Island in Australia, we demonstrate that Toxoplasma
 gondii infection leads to specific DNA hypomethylation events in the host
 brain. Previous laboratory studies have shown that these epigenetic
 changes underlie the central processing of cat odors. We posit that the
 concept of extended phenotype can be expanded to extended epiphenotype,
 thus linking parasite genes to host behavior through epigenesis. This
 phenomenon has broad implications for inter-species relationships.
DOI: 10.5061/dryad.mpg4f4r3j
title: Data for: Seasonal home range and habitat selection patterns of sika deer Cervus nippon in southern Hokkaido, Japan

description: In 1980 and 1981, eight and nine individual sika deer Cervus nippon were
 reintroduced in southern Hokkaido, Japan, respectively, to address
 population declines in this species during 1900s. As recent population
 growth has led to human–wildlife conflicts, this study investigated the
 responses of sika deer to resource availability and geomorphic factors
 during the summer and winter seasons in southern Hokkaido. Global
 positioning system-collared data collected from 2016 to 2018 were used to
 assess the home range patterns and habitat selection of 14 female sika
 deer located in Mount Esan and Shiriuchi. The core home range size was
 defined using a 50% kernel density estimation that indicated a larger home
 range in winter than summer for all deer. Habitat selection was assessed
 using generalized linear mixed models. The results showed variation in
 habitat selection between resident deer of Mount Esan and Shiriuchi, as
 well as migratory deer in Shiriuchi during summer. Resident deer in Mount
 Esan and Shriuchi preferred areas closer to crops during summer.
 Interaction effects revealed that migratory deer utilized natural
 grassland close to forest edge habitat in Shiriuchi. By contrast, resident
 deer in Shiriuchi selected forest edge habitat and natural grasslands
 close to crops. In winter, low elevation was the most important habitat
 factor for all deer across the study area. Thus, sika deer habitat
 selection depends on resource availability in summer and topographic
 factors in the winter.
DOI: 10.5061/dryad.1c59zw3zt
title: Expression of terminal deoxynucleotidyl transferase (TdT) identifies lymphoid-primed progenitors in human bone marrow

description: With emerging single-cell techniques in the human hematopoiesis,
 discrepancies between the traditional cell-surface-marker-based cell-type
 identification and their single-cell level molecular phenotype are
 observed. To better associate lymphoid identity with protein-level cell
 features, we examined the protein expression of terminal deoxynucleotidyl
 transferase (TdT), a specialized DNA polymerase intrinsic to VDJ
 recombination, and detected TdT expression within CD34+ progenitors prior
 to B/T cell emergence. While these TdT+ cells coincided with
 granulocyte-monocyte progenitor (GMP) immunophenotype, their accessible
 chromatin regions showed enrichment for lymphoid-associated transcription
 factor (TF) motifs. TdT expression on GMPs was inversely related to the
 SLAM family member CD84. Prospective isolation of CD84lo GMPs demonstrated
 robust lymphoid potential ex vivo, while still retaining significant
 myeloid differentiation capacity, akin to LMPPs. This multi-omic study
 identifies previously unappreciated lymphoid-primed progenitors,
 redefining the lympho-myeloid axis in human hematopoiesis.