cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vmcvdncrs
title: TORIE-DTI: Transient white matter changes under sevoflurane anesthesia

description: Cognitive dysfunction after surgery under general anesthesia is a
 well-recognized clinical phenomenon in the elderly. Physiological effects
 of various anesthetic agents have been studied at length. Very little is
 known about potential effects of anesthesia on brain structure. In this
 study we used Diffusion Tensor Imaging to compare the white matter
 microstructure of healthy control subjects under sevoflurane anesthesia
 with their awake state. Fractional Anisotropy, a white mater integrity
 index, transiently decreases throughout the brain during sevoflurane
 anesthesia and then returns back to baseline. Other DTI metrics such as
 mean diffusivity, axial diffusivity and radial diffusivity were increased
 under sevoflurane anesthesia. Although DTI metrics are age dependent, the
 transient changes due to sevoflurane were independent of age and sex.
 Volumetric analysis shows various white matter volumes decreased whereas
 some gray matter volumes increased during sevoflurane anesthesia. These
 results suggest that sevoflurane anesthesia has a significant, but
 transient, effect on white matter microstructure. The role of white matter
 in the loss of consciousness under anesthesia will need to be studied and
 MRI studies with subjects under anesthesia will need to take these results
 into account.
description: MRI data obtained on Skyra 3T scanner. These are all the DTI
 metrics FA, MD, AD & RD nifti files for the 5 different time
 points. See paper for more detailed descriptions.
description: Standard tools such as FSL can be used to process the data.
 Subjects ID and codings are included. No missing values.
DOI: 10.5061/dryad.gf1vhhmnv
title: Animal Biodiversity at Nachusa Grasslands

description: A primary goal of ecological restoration is to increase biodiversity in
 degraded ecosystems. However, the success of restoration ecology is often
 assessed by measuring the response of a single functional group or trophic
 level to restoration, without considering how restoration affects
 multitrophic interactions that shape biodiversity. An ecosystem-wide
 approach to restoration is therefore necessary to understand whether
 animal responses to restoration, such as changes in biodiversity, are
 facilitated by changes in plant communities (plant-driven effects) or
 disturbance and succession resulting from restoration activities
 (management-driven effects). Furthermore, most restoration ecology studies
 focus on how restoration alters taxonomic diversity, while less attention
 is paid to the response of functional and phylogenetic diversity in
 restored ecosystems. Here, we compared the strength of plant-driven and
 management-driven effects of restoration on four animal communities
 (ground beetles, dung beetles, snakes, and small mammals) in a
 chronosequence of restored tallgrass prairie, where sites varied in
 management history (prescribed fire and bison reintroduction). Our
 analyses indicate that management-driven effects on animal communities
 were six-times stronger than effects mediated through changes in plant
 biodiversity. Additionally, we demonstrate that restoration can
 simultaneously have positive and negative effects on biodiversity through
 different pathways, which may help reconcile variation in restoration
 outcomes. Furthermore, animal taxonomic and phylogenetic diversity
 responded differently to restoration, suggesting that restoration plans
 might benefit from considering multiple dimensions of animal biodiversity.
 We conclude that metrics of plant diversity alone may not be adequate to
 assess the success of restoration in reassembling functional ecosystems.
DOI: 10.5061/dryad.m37pvmd18
title: Models to assess ability to achieve localized areas of reduced white-tailed deer density

description: Localized management of white-tailed deer (Odocoileus virginianus)
 involves the removal of matriarchal family units with the intent to create
 areas of reduced deer density. However, application of this approach has
 not always been successful, possibly because of female dispersal and high
 deer densities. We developed a spatially explicit, agent-based model to
 investigate the intensity of deer removal required to locally reduce deer
 density depending on the surrounding deer density, dispersal behavior, and
 size and shape of the area of localized reduction. Application of this
 model is illustrated using the example of abundant deer populations in
 Pennsylvania, USA. Most scenarios required at least 5 years before
 substantial deer density reductions occurred. Our model indicated that a
 localized reduction was successful for scenarios in which the surrounding
 deer density was lowest (30 deer/mi²), localized antlerless harvest rates
 were ≥ 30%, and the removal area was 5 mi² or larger. When the
 size of the removal area was &lt; 5 mi2, end population density was
 highly variable and, in some scenarios, exceeded the initial density. The
 shape of the area of localized reduction had less influence on the ability
 to reduce deer density than the size. There were no differences in mean
 deer density in the same size circle or square removal areas. Similarly,
 increasing the ratio of sides (length : width) in rectangular removal
 areas had little influence on the ability to locally reduce deer
 densities. Situations in which deer density was higher (40 or 50 deer/mi2)
 required antlerless removal rates to exceed 30% and took more than 5 years
 to considerably reduce density in the localized area regardless of its
 size. These results indicate that the size of the area of reduction,
 surrounding deer density, and antlerless harvest rate are the most
 influential factors in locally reducing deer density. Therefore, localized
 management likely can be an effective strategy for lower density herds,
 especially in larger removal areas. For high density herds, the success of
 this strategy would depend most on the ability of resource managers to
 achieve consistently high antlerless harvest rates.
description: There are two Netlogo models that accompany the manuscript. The
 first model "Deer Stable" is a Netlogo model that is used to
 simulate a realistic model deer population. The second model "Deer
 Reduction"is a Netlogo model that runs various scenarios to explore
 the effect of different variables on the ability to locally reduce deer
 density. Both models are parameterized using data from peer-reviewed
 literature and from local data on deer populations in Pennsylvania,
 USA.
description: The user can click on the "Info" tab within both models
 to see a description of how the models are run.
DOI: 10.25338/b8cs63
title: Data for impact of “non-lethal” tarsal clipping on bumble bees (Bombus vosnesenskii) may depend on queen stage and worker size

description: Recent bumble bee declines have prompted the development of novel
 population monitoring tools, including the use of putatively non-lethal
 tarsal clipping to obtain genetic material. However, the potential side
 effects of tarsal clipping have only been tested in the worker caste of a
 single domesticated species, prompting the need to more broadly test
 whether tarsal clipping negatively affects sampled individuals. To
 determine if tarsal clipping reduces queen survivorship and colony
 establishment, we collected wild queens of Bombus vosnesenskii and clipped
 tarsi from a single leg of half the individuals. We reared captive queens
 and estimated survivorship and nest establishment success. We also clipped
 tarsi of workers from a subset of colonies across a range of body sizes.
 We found no consistent negative effect of clipping on queen survival. In
 the first year, clipped nest-searching queens suffered heavy mortality,
 but there was no effect on foraging queens. The following year, we found
 no effect of clipping on queen survival or establishment. Clipping did not
 reduce overall worker survival but reduced survivorship for those in the
 smallest size quartile. Implications for insect conservation: Our findings
 suggest tarsal clipping does not have consistent negative effects on
 individual survival. However, our results varied with queen behavioral
 state, year, and worker size, suggesting differences within and among
 species and interactions with landscape stressors warrant further study.
 In the interim, we recommend researchers and conservationists minimize the
 use of tarsal clipping for sensitive species, populations, or small
 workers except in cases of exceptional scientific need.
DOI: 10.15468/dl.bh7a8w
title: Occurrence Download

description: A dataset containing 180 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cynometra lenticellata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 180 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002727-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qzr2w2
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cynometra vogelii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 58 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002728-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.66t1g1k1d
title: Targeted genome editing in vivo corrects a Dmd duplication restoring wild‐type dystrophin expression

description: Tandem duplication mutations are increasingly found to be the direct cause
 of many rare heritable diseases, accounting for up to 10% of cases.
 Unfortunately, animal models recapitulating such mutations are scarce,
 limiting our ability to study them and develop genome editing-based
 therapies. Here, we describe the generation of the
 Dup18-30 mouse model, harbouring a multi-exonic tandem
 duplication in the Dmd gene which recapitulates a human
 mutation. Duplication correction of this mouse was achieved by
 implementing a single-guide RNA (sgRNA) CRISPR/Cas9 approach. This
 strategy precisely removed a duplication mutation in vivo, restored
 full-length dystrophin expression, and was accompanied by improvements in
 both histopathological and clinical phenotypes. We conclude that
 CRISPR/Cas9 represents a powerful tool to accurately model and
 treat tandem-duplication mutations.  This dataset
 includes the deep amplicon sequencing analysis performed to
 detect single-sgRNA/Cas9 off-target and on-target effects in the
 Dup18-30 mice after treatment.
DOI: 10.5061/dryad.0vt4b8gxm
title: Data from: Adrenomedullin-RAMP2 and -RAMP3 systems regulate cardiac homeostasis during cardiovascular stress

description: Adrenomedullin (AM) is a peptide hormone with multiple physiological
 functions, which are regulated by its receptor activity-modifying
 proteins, RAMP2 and RAMP3. We previously reported that AM or RAMP2
 knockout (AM-/-, RAMP2-/-) is embryonically lethal in mice, whereas
 RAMP3-/- mice are apparently normal. AM, RAMP2 and RAMP3 are all highly
 expressed in the heart; however, their functions there are not fully
 understood. Here, we analyzed the pathophysiological functions of the
 AM-RAMP2 and AM-RAMP3 systems in hearts subjected to cardiovascular
 stress. Cardiomyocyte-specific RAMP2-/- (C-RAMP2-/-) and
 RAMP3-/- showed no apparent heart failure at base
 line. After one week of transverse aortic constriction (TAC),
 however, C-RAMP2-/- exhibited significant cardiac hypertrophy,
 decreased ejection fraction and increased
 fibrosis as compared
 to wild-type mice. Both dP/dtmax and dP/dtmin
 were significantly reduced in C-RAMP2-/-,
 indicating reduced ventricular contractility and
 relaxation. Exposing C‑RAMP2‑/-
 cardiomyocytes to isoproterenol enhanced their hypertrophy and
 oxidative stress as compared to wild-type cells. C‑RAMP2‑/- cardiomyocytes
 also contained fewer viable mitochondria and
 showed reduced mitochondrial membrane
 potential and respiratory capacity. RAMP3-/-
 also showed reduced systolic function and enhanced fibrosis after TAC, but
 those only became apparent after 4 weeks. A reduction in cardiac
 lymphatic vessels was the characteristic feature in RAMP3-/-. These
 observations indicate the AM-RAMP2 system is necessary for early
 adaptation to cardiovascular stress through regulation of cardiac
 mitochondria. AM-RAMP3 is necessary for later adaptation through
 regulation of lymphatic vessels. The AM-RAMP2 and AM-RAMP3 systems thus
 play separate critical roles in the maintenance of cardiovascular
 homeostasis against cardiovascular stress.
DOI: 10.5061/dryad.j9kd51cbc
title: Traffic noise inhibits cognitive performance in a songbird

description: Noise pollution is commonly associated with human environments and
 mounting evidence indicates that noise has a variety of negative effects
 on wildlife. Noise has also been linked to cognitive impairment in humans
 and because many animals use cognitively-intensive processes to overcome
 environmental challenges, noise pollution has the potential to interfere
 with cognitive function in animals living in urban areas or near roads. We
 experimentally examined how road traffic noise impacts avian cognitive
 performance by testing adult zebra finches (Taeniopygia guttata) on a
 battery of foraging tasks in the presence or absence of traffic noise
 playback. Here we show that traffic noise reduces cognitive performance,
 including inhibitory control, motor learning, spatial memory, and social
 learning, but not associative color learning. This study demonstrates a
 novel mechanism through which anthropogenic noise can impact animals,
 namely through cognitive interference, and suggests that noise pollution
 may have previously unconsidered consequences for animals.
DOI: 10.5061/dryad.59zw3r265
title: Large‐scale genome sampling reveals unique immunity and metabolic adaptations in bats

description: Comprising more than 1,400 species, bats possess adaptations unique among
 mammals including powered flight, unexpected longevity given small body
 size, and extraordinary immunity. Some of the molecular mechanisms
 underlying these unique adaptations includes DNA repair, metabolism and
 immunity. However, analyses have been limited to a few divergent lineages,
 reducing the scope of inferences on gene family evolution across the Order
 Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat
 species encompassing a large number of lineages, with a particular
 emphasis on multi-gene family evolution across immune system and metabolic
 genes. Genomes were obtained from public repositories and one genome
 (Phyllostomus hastatus) was assembled de novo. In agreement with previous
 analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I
 gene families, and loss of the proinflammatory PYHIN gene family. We
 inferred more than 1,000 gene losses unique to bats, including genes
 involved in the regulation of inflammasome pathways such as epithelial
 defense receptors, the natural killer gene complex and the
 interferon-gamma induced pathway. Gene set enrichment analyses revealed
 genes lost in bats are involved in defense response against
 pathogen-associated molecular patterns and damage-associated molecular
 patterns. Gene family evolution and selection analyses indicate bats have
 evolved fundamental functional differences compared to other mammals in
 both innate and adaptive immune system, with the potential to enhance
 anti-viral immune response while dampening inflammatory signaling. In
 addition, metabolic genes have experienced repeated expansions related to
 convergent shifts to plant-based diets. Our analyses support the
 hypothesis that, in tandem with flight, ancestral bats had evolved a
 unique set of immune adaptations whose functional implications remain to
 be explored.
description: This repository contains the scripts used to generate data for
 the article "Large-scale genome sampling reveals unique immunity and
 metabolic adaptations in bats" from Molecular Ecology. These include
 the commands used for the assembly of genomes and transcriptomes, the
 construction of an ultrametric phylogenetic tree with the MCMCtree
 bioinformatics tool, the scripts used to run selection analysis with
 CODEML as well as the files used to perform gene family evolution 
 analysis with CAFE.
DOI: 10.5061/dryad.5x69p8d23
title: Maternal and genetic correlations between morphology and physical performance traits in a small captive primate, Microcebus murinus

description: Physical performance traits are key components of fitness and direct
 targets of selection. Maternal effects are important components of
 integrated phenotypes in a variety of species. Yet their contribution to
 variation in performance, and phenotypes closely associated with
 performance, remains poorly understood. We used an animal model approach
 to quantify the contribution of maternal effects to performance trait
 variation (in bite force and pull strength) and the relationships between
 performance and the relevant underlying morphology in Microcebus murinus.
 We show that bite force is heritable (h2~0.23), and that maternal effects
 are also important source of variation, resulting in a medium inclusive
 heritability (IH2~0.47). Grip strength presented a rather low and
 non-significant narrow-sense heritability suggesting a higher selective
 pressure on this trait. Genetic correlations between performance traits
 and their associated morphometric traits were significant and high (0.47
 bite force-head width; 0.48 grip strength-radius length), as was the
 maternal correlation for bite force-head width (0.75). Further studies
 evaluating the heritability of performance for other taxa and the role of
 maternal effects are badly needed to better understand the drivers of
 variation in performance ultimately allowing for a better understanding of
 the importance of these types of traits in an evolutionary context.
DOI: 10.5061/dryad.vmcvdncrt
title: Constructing a social-behavioral association network to study management impact on waterbird community ecology using digital video recording cameras

description: Studying social behavior and species associations in ecological
 communities is challenging because it is difficult to observe the
 interactions in the field. Animal behavior is especially difficult to
 observe when selection of habitat and activities are linked to energy
 costs of long-distance movement. Migrating communities tend to be resource
 specific and prefer environments that offer more suitability for
 coexisting in a shared space and time. Given the recent advances in
 digital technologies, digital video recording systems are gaining
 popularity in wildlife research and management. We used digital video
 recording cameras to study social interactions and species-habitat
 linkages for wintering waterbird communities in shared habitats. Examining
 over 8,640 hours of video footages, we built tetrapartite social
 behavioral association network of wintering waterbirds over habitat (n=5)
 selection events in sites with distinct management regimes. We analyzed
 these networks to identify hub species and species role in activity
 persistence, and to explore the effects of hydrological regime on these
 network characteristics. Although the differences in network attributes
 were not significant at treatment level (p = 0.297) in terms of network
 composition and keystone species composition, our results indicated that
 network attributes were significantly different (p = 0.000, r2 = 0.278) at
 habitat level. There were evidences suggesting that the habitat quality
 was better at the managed sites, where the formed networks had more
 species, more network nodes and edges, higher edge density, and stronger
 intra- and inter-species interactions. In addition, we also calculated the
 species interaction preference scores (SIPS) and behavioral interaction
 preference scores (BIPS) of each network. The results showed that species
 synchronize activities in shared space for temporal niche partitioning in
 order to avoid or minimize any potential competition for shared
 space. Our social network analysis (SNA) approach is likely to
 provide a practical use for ecosystem management and biodiversity
 conservation.
DOI: 10.5061/dryad.fttdz08rm
title: Data from: Reintroducing extirpated herbivores could partially reverse the late Quaternary decline of large and grazing species

description: Aim: Reinstating large, native herbivores is an essential
 component of ecological restoration efforts, as these taxa can be
 important drivers of ecological processes. However, many herbivore species
 have gone globally or regionally extinct during the last 50,000 years,
 leaving simplified herbivore assemblages and trophically downgraded
 ecosystems. Here, we discuss to what extent trophic rewilding can undo
 these changes by reinstating native herbivores. Location: Global
 Time Period: We report functional trait changes from the Late
 Pleistocene to the present, and estimated trait changes under future
 scenarios. Major Taxa Studied: Wild, large (≥10 kg), terrestrial,
 mammalian herbivores Methods: We use a functional trait dataset
 containing all late Quaternary large herbivores ≥10 kg to look at changes
 in the body mass and diet composition of herbivore assemblages, a proxy
 for species’ ecological effects. First, we assess how these traits have
 changed from the Late Pleistocene to the present. Next, we quantify how
 the current body mass and diet composition would change if all extant,
 wild herbivores were restored to their native ranges (and if no functional
 replacements were used), exploring scenarios with different baselines.
 Results: Defaunation has primarily removed large and grazing
 herbivores. Reinstating extant herbivores across their native ranges would
 reverse these changes, especially when reinstating them to their
 prehistoric distributions. It would partially restore herbivore body mass
 and diet composition to pre-anthropogenic conditions. However, in the
 absence of complementary interventions (e.g. introducing functional
 replacements), many herbivore assemblages would remain down-sized and
 browser dominated, relative to pre-anthropogenic conditions. Main
 Conclusions: Many terrestrial herbivore assemblages - and hence
 ecosystems - would remain trophically downgraded, even after bringing back
 all extant, native herbivores. Therefore, complementary interventions
 would be required to achieve complete functional restoration.
 Nevertheless, our findings suggest that reintroducing the remaining native
 herbivores would diversify the herbivory and disturbances of herbivore
 assemblages.