cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3j9kd51fg
title: Data from: Savannas after afforestation: assessment of herbaceous community responses to wildfire versus native tree planting

description: Afforestation and fire exclusion are pervasive threats to tropical
 savannas. In Brazil, laws limiting prescribed burning hinder the study of
 fire in the restoration of Cerrado plant communities. We took advantage of
 a 2017 wildfire to evaluate the potential for tree cutting and fire to
 promote the passive restoration of savanna herbaceous plant communities
 after destruction by exotic tree plantations. We sampled a burned pine
 plantation (Burned Plantation); a former plantation that was harvested and
 burned (Harvested & Burned); an unburned former plantation that
 was harvested, planted with native trees, and treated with herbicide to
 control invasive grasses (Native Tree Planting); and two old-growth
 savannas which served as reference communities. Our results confirm that
 herbaceous plant communities on post-afforestation sites are very
 different from old-growth savannas. Among post-afforestation sites,
 Harvested & Burned herbaceous communities were modestly more
 similar in composition to old-growth savannas, had slightly higher
 richness of savanna plants (3.8 species per 50-m2), and supported the
 greatest cover of native herbaceous plants (56%). These positive trends in
 herbaceous community recovery would be missed in assessments of tree
 cover: whereas canopy cover in the Harvested & Burned site was 6%
 (less than typical of savannas of the Cerrado), the Burned Plantation and
 Native Tree Planting, supported 34% and 19% cover, respectively. By
 focusing on savanna herbaceous plants, these results highlight that tree
 cutting and fire, not simply tree planting and fire exclusion, should
 receive greater attention in efforts to restore savannas of the Cerrado.
DOI: 10.5061/dryad.866t1g1nh
title: Data from: Spatial patterns and rarity of the white-phased ‘Spirit Bear’ allele reveals gaps in habitat protection

description: Preserving genetic and phenotypic diversity can help safeguard not only
 biodiversity but also cultural and economic values. Here, we present data
 that emerged from Indigenous-led research at the intersection of evolution
 and ecology to support conservation planning of a culturally salient,
 economically valuable, and rare phenotypic variant. We addressed three
 conservation objectives for the white-phased ‘Spirit bear’ polymorphism, a
 rare and endemic white-coated phenotype of black bear (Ursus americanus)
 in Kitasoo/Xai’xais and Gitga’at Territories and beyond in coastal British
 Columbia, Canada. First, we used non-invasively collected hair samples (n
 = 385 bears over ~18,000 km2) to assess the spatial variation in the
 frequency of the allele that controls the white-coloured morph (mc1r).
 Second, we compared our observed allele frequencies at mc1r with those
 expected under Hardy-Weinberg equilibrium. Finally, we examined how well
 current protected areas in the region aligned with spatial hotspots of
 Spirit bear alleles. We found that landscape-level allele frequency was
 lower than previously reported. For example, our systematic sampling
 estimated a frequency of 0.25 (95% CI 0.13-0.41) on Gribbell Island
 compared with the previously reported estimate of 0.56. Also, in contrast
 with previous reports, we failed to detect a statistically significant
 departure from Hardy-Weinberg equilibrium at mc1r, which calls into
 question the previously-posited role of homozygote gene flow, heterozygote
 disadvantage, and positive assortative mating in the maintenance of this
 polymorphism. Finally, we found a discrepancy between the placement of
 protected areas and the 90th percentile hotspots (upper 10% of all
 estimated values) of Spirit bear alleles, with ~50% of hotspots falling
 outside of protected areas. These results provide new insight into
 hypotheses related to the maintenance of this rare polymorphism, and
 directly relevant information to support evidence-based opportunities for
 Indigenous Nations of the area to attend to gaps in conservation planning.
description: Dataset of black bear (<em>Ursus americanus</em>)
 genotypes (AA, AG, or GG) at the mc1r gene. Individuals were genotyped
 from hair-derived DNA gathered as part of an annual monitoring program
 in coastal British Columbia, Canada (2012-2017).
description: Agreements for these data with partner governements
 (Kitasoo/Xai'xais and Gitga'at First Nation) prohibit us from
 diplaying the exact spatial data of detected bears. As such, bear
 detection information has been summarized at the scale of
 'landmass' (see manuscript). Contact the lead author for further
 information.
DOI: 10.25338/b8pp77
title: Data from: Behavioral changes in calves 11 days after cautery disbudding: effect of local anesthesia

description: Hot-iron disbudding results in painful burn wounds that take weeks to
 heal. Spontaneous behaviors indicative of pain are apparent in the
 immediate hours after disbudding, but whether they occur later in the
 healing process is unknown. To evaluate whether ongoing pain was present
 around the time the necrotic tissue loosens from the scalp, we tested the
 effect of administration of local anesthetic 11 d after the procedure.
 Disbudded female Holstein and Jersey calves (n=24) were randomly assigned
 to receive an injection of local anesthetic (lidocaine) or saline at the
 cornual nerve on both sides of the head. We recorded the frequency of 8
 behaviors over a 75-min period following the injections: head shakes, head
 rubs, head scratches, ear flicks, tail flicks, bucks/jumps/kicks,
 grooming, and transitions between standing and lying. Calves treated with
 lidocaine shook their head less and tended to flick their ears less than
 calves administered saline, consistent with the effects of pain relief
 previously reported in the immediate hours after disbudding. These calves
 also rubbed their head against the sides of the pen more often, suggesting
 lidocaine suppressed wound protective behavior. Head shaking and head
 scratching became more common in the last 25 min compared to the first 50
 min in calves treated with lidocaine, consistent with the return of
 sensation to the disbudding wounds. No treatment differences in the other
 behaviors were observed. These results suggest that calves experience
 ongoing pain 11 d after hot-iron disbudding, adding to a growing body of
 evidence that pain persists for weeks after the procedure.
description: Data were collected from the University of California Davis Dairy
 Facility on 24 calves in 2018. Variables are defined in Sheet 2 of the
 Excel files. The R scripts used to analyze each dataset are
 provided.
DOI: 10.5061/dryad.gtht76hj0
title: Robust and distributed neural representation of action values

description: Studies in rats, monkeys, and humans have found action-value signals in
 multiple regions of the brain. These findings suggest that action-value
 signals encoded in these brain structures bias choices toward higher
 expected rewards. However, previous estimates of action-value signals
 might have been inflated by serial correlations in neural activity and
 also by activity related to other decision variables. Here, we applied
 several statistical tests based on permutation and surrogate data to
 analyze neural activity recorded from the striatum, frontal cortex, and
 hippocampus. The results show that previously identified action-value
 signals in these brain areas cannot be entirely accounted for by parallel
 serial correlations in neural activity and action value. We also found
 that neural activity related to action value is intermixed with signals
 related to other decision variables. Our findings provide strong evidence
 for broadly distributed neural signals related to action value throughout
 the brain.
DOI: 10.5061/dryad.7h44j0zrh
title: Data from: Candidate gene SNP variation in floodplain populations of pedunculate oak (Quercus robur L.) near the species' southern range margin: weak differentiation yet distinct associations with water availability

description: Populations residing near species' low-latitude range margins (LLM)
 often occur in warmer and drier environments than those in the core range.
 Thus, their genetic composition could be shaped by climatic drivers that
 differ from those occurring at higher latitudes, resulting in potentially
 adaptive variants of conservation value. Such variants could facilitate
 the adaptation of populations from other portions of the geographic range
 to similar future conditions anticipated under ongoing climate change.
 However, very few studies have assessed standing genetic variation at
 potentially adaptive loci in natural LLM populations. We investigated
 standing genetic variation at SNPs located within 117 candidate genes and
 its links to putative climatic selection pressures across 19 pedunculate
 oak (Quercus robur L.) populations distributed along a regional climatic
 gradient near the species' southern range margin in southeastern
 Europe. These populations are restricted to floodplain forests along large
 lowland rivers, whose hydric regime is undergoing significant shifts under
 modern rapid climate change. The populations showed very weak geographic
 structure, suggesting extensive genetic connectivity and gene flow or
 shared ancestry. We identified eight (6.2%) positive FST-outlier loci, and
 genotype-environment association analyses revealed consistent associations
 between SNP allele frequencies and several climatic variables linked to
 water availability. A total of 61 associations involving 37 SNPs (28.5%)
 from 35 annotated genes provided important insights into putative
 functional mechanisms in our system. Our findings provide empirical
 support for the role of LLM populations as sources of potentially adaptive
 variation that could enhance species’ resilience to climate change-related
 pressures.
description: <strong>SNP_genotypes_Dryad</strong>
 The data are SNP genotypes of the 380 Quercus robur individuals
 from 19 populations used in this study. See readme sheets
 in SNP_genotypes_Dryad.xls
 <strong>Variable_values_Dryad</strong>
 The data are extracted values of climatic variables for each of
 the 19 Quercus robur populations, used in GEA analyses. See readme
 sheet in Variable_values_Dryad.xls
DOI: 10.5061/dryad.wwpzgmsgj
title: Data from: Brain imaging evidence for why we are numbed by numbers

description: We as humans do not value lives consistently. While we are willing to act
 for one victim, we often become numb as the number of victims increases.
 The empathic ability to adopt others’ perspectives is essential for
 motivating help. However, the perspective-taking ability in our brains
 seems limited. Using functional MRI, we demonstrated that the core empathy
 network including the medial prefrontal cortex (mPFC) was more engaged for
 events happening to a single person than those happening to many people,
 no matter whether the events were emotionally neutral or negative. In
 particular, the perspective-taking-related mPFC showed greater and more
 extended activations for events about one person than those about many
 people. The mPFC may be the neural marker of why we feel indifferent to
 the suffering of large numbers of people in humanitarian disasters.
DOI: 10.7280/d1xx00
title: Data from: Black Abalone habitat assessment

description: The black abalone Haliotis cracherodii was once an abundant intertidal
 species that was commonly found in the rocky intertidal zones throughout
 California. Due to overfishing and a fatal disease called Withering
 Syndrome, the black abalone is currently federally listed as endangered
 and considered locally extinct through southern California. In order to
 recover black abalone populations in southern California, intervention and
 restoration must be conducted to facilitate the base population of this
 species. Habitat quantity and quality, food availability, and natural and
 anthropogenic threats are important characteristics to consider in order
 to successfully recover black abalone population. However, current habitat
 assessment protocols primarily take into account the geomorphology of
 black abalone habitat. Here we provide a habitat assessment that considers
 habitat quantity and quality, food availability, and natural and
 anthropogenic threats for select rocky intertidal areas in Orange County,
 California. This assessment was then used to recommend potential black
 abalone restoration locations in Orange County. Shaw’s Cove and Moss Cove
 contained the most positive habitat characteristics required for black
 abalone restoration. Our habitat assessment can be used to determine
 locations in southern California that have the highest potential to
 sustain black abalone populations such that when restoration occurs in the
 future, individuals are outplanted to areas that provide essential habitat
 characteristics needed for successful black abalone recovery.
DOI: 10.5061/dryad.rr4xgxd64
title: Ab initio electronic stopping power for protons in Ga0.5In0.5P/GaAs/Ge triple-junction solar cells for space applications

description: Motivated by the radiation damage of solar panels in space, firstly, the
 results of Monte Carlo particle transport simulations are presented for
 proton impact on triple-junction Ga0.5In0.5P/GaAs/Ge solar cells, showing
 the proton projectile penetration in the cells as a function of energy. It
 is followed by a systematic ab initio investigation of the electronic
 stopping power for protons in different layers of the cell at the relevant
 velocities via real-time time-dependent density functional theory
 (RT-TDDFT) calculations. The electronic stopping power is found to depend
 significantly on different channeling conditions, which should affect the
 low velocity damage predictions, and which are understood in terms of
 impact parameter and electron density along the path. Additionally, we
 explore the effect of the interface between the layers of the multilayer
 structure on the energy loss of a proton, along with the effect of strain
 in the lattice-matched solar cell. Both effects are found to be small
 compared with the main bulk effect. The interface energy loss has been
 found to increase with decreasing proton velocity, and in one case, there
 is an effective interface energy gain.
DOI: 10.5061/dryad.69p8cz8zg
title: Data from: Attack and aggregation of a major squash pest: parsing the role of plant chemistry and beetle pheromones across spatial scales

description: 1. Successful management of insect crop pests requires an understanding of
 the cues and spatial scales at which they function to affect rates of
 attack of preferred and non-preferred host plants. A long-standing
 conceptual framework in insect-plant ecology posits that there is
 hierarchical structure spanning host location, acceptance, and attack that
 could be exploited for integrated pest management. 2. We investigated how
 plant- and insect-derived chemical cues affect successive decisions of
 host choice in aggregating insects, and tested predictions in the
 Cucurbita pepo - Acalymma vittatum system. Acalymma vittatum is an
 aggregating specialist beetle pest that strongly prefers zucchini (C. p.
 pepo) to summer squash (C. p. ovifera), two independent domesticates of C.
 pepo. We hypothesized that subspecies-specific plant traits, especially
 volatile cues, interact with the male-produced aggregation pheromone to
 amplify beetle preference for C. p. pepo. 3. Differential beetle attack of
 C. pepo subspecies in the field is not determined by plant traits that
 affect host finding or differential aggregation due to pheromones: across
 two years, beetles had strong density-dependent attraction to both
 subspecies when male beetles were feeding, and no interactions between
 plant volatiles and the male-produced pheromone were detected. In absence
 of male pheromone emission, beetles were equally unattracted to plants
 with or without beetle feeding. 4. In contrast, plant traits that mediate
 insect acceptance appear to underlie differences in preference. At a local
 scale, beetles did not accept and emigrated from C. p. ovifera compared to
 C. p. pepo. Distinct volatile emissions were observed between subspecies,
 but further work is needed to identify if these volatiles promote
 emigration. 5. Synthesis and applications: By dissecting pest preference
 during successive host choice decisions, we isolated a trait with
 implications for pest management. Beetles on cucurbits can be managed by
 employing cultivars with differential susceptibility (e.g. trap cropping),
 and the mechanistic knowledge presented here informs best practices and
 limitations for on-farm applications. More broadly, pest management in
 diversified cropping systems can be enhanced through understanding how
 plant preference gradients affect herbivore movement and behavior, and
 plant breeders can target traits to reduce herbivory in such systems.
description: This dataset includes all raw data values associated with this
 manuscript.
description: The ReadMe file describes which data files are associated with
 different aspects of the manuscript.
DOI: 10.5061/dryad.ht76hdrcf
title: BIL&GIN sentence and rest asymmetries

description: This dataset has been generated from a subsample of 287 participants (150
 left-handers) from the BIL&GIN database (Mazoyer et al. Neuroimage
 2016, 124:1225-1231). The dataset contains age, gender, self-reported
 handedness and Edinburgh score, for each participant, as well as its
 education level. It also includes measures of FMRI task-induced
 BOLD-signal variations and left minus asymmetry during sentence processing
 minus word list in 3 conditions: production, listening and reading. These
 variations are measured for the whole sentence core network as well as for
 its hubs as defined in the SENSAAS atlas (Labache et al.  Brain
 Structure and Function 2019, 224:859-882). Both intrahemispheric and
 interhemispheric measures of resting-state intrinsic connectivity in the
 same sets of regions are also included. Brain language hemispheric
 dominance pattern is given based on a multitask multimodal hierarchical
 classification using as entry variables:1) task-induced asymmetries (2)
 intrahemispheric resting-state degree connectivity and asymmetry, and 3)
 interhemispheric connectivity applied. Other brain lateralization patterns
 for sentence production only based a hemispheric functional asymmetry
 index (Mazoyer et al. PLoS One 2014, 9(6):e101165) and on a SVM
 approach (Zago et al. Human Brain Mapping 2017, 12:5871-5889) are also
 given. Morphometric data are included as well, including total
 intracranial volume, hemisperic volumes and asymmetry of grey and white
 matter and  corpus callosum volume area at the mid-sagittal
 level. Scores to a cognitive battery of 11 tests adjusted for age and
 education level are provided as well as loadings of the first 4 principal
 components computed from these scores.
description: We have extracted hand lateralization, sex , age, eduction level,
 MRI (structural and functional for language tasks and resting-state), and
 cognitive skills from 287 participants of the BIL&GIN database.
 Data acquisition and pre-processing of these data have been detailed in
 Mazoyer et al. Neuroimage 2016, 124:1225-1231.
 Processing of FMRI data (both language-task  and resting-state
 related) have been detailed in Labache et al.  Brain Structure and
 Function 2019, 224:859-882. Language lateralization
 derived from an hemispheric functional lateralization index during
 sentence production has been described in Mazoyer et al. PLoS One 2014,
 9(6):e101165. Language dominance pattern assessed with
 a support vector machine has been detailed in Zago et al. Human Brain
 Mapping 2017, 12:5871-5889. Multimodal hierarchical
 classification was completed with R (R version 3.5.1; R Core Team, 2013),
 while other statistical analyses were performed using JMP15
 (http://www.jmp.com, SAS Institute Inc., 2018).
description: There are some missing data for the cognitive skill
 variables: 1 for Residuals_Maze, 2 for
 Residuals_ravenQI, and 3 for PC1_SPA, PC2_MEM, PC3_PHONO, and
 PC4_VERB
DOI: 10.5061/dryad.tx95x69v5
title: Precipitation and temperature shape the biogeography of arbuscular mycorrhizal fungi across a 1500 km latitudinal transect in the Brazilian Caatinga

description: Arbuscular mycorrhizal fungi (AMF), an important group of plant root
 symbionts, remain poorly studied in the Neotropics. We used Illumina LSU
 amplicon sequencing to test whether AMF communities in soil and roots are
 shaped by deterministic or neutral processes along a 20° latitudinal
 transect in the Caatinga of Brazil, a unique dry forest eco-region.
 Glomeraceae was the most abundant and diverse family, resembling more
 paleotropical Africa and European croplands than other tropical forests
 from South America. AMF communities showed strong biogeographic structure
 inconsistent with a classical latitudinal diversity gradient, and further
 differed between soil and roots. Soil AMF biogeography was best correlated
 with precipitation; richness increased towards both ends of the
 latitudinal transect where precipitation increased, and community
 composition converged. Root AMF diversity weakened towards the equator, at
 a latitude where soil AMF diversity was highest. Root AMF biogeography
 correlated to temperature, with decreasing diversity at higher
 temperatures. We found no evidence of phylogenetic niche conservatism
 among AMF taxa. Our results suggest that niche-based processes in relation
 to regional climate, most importantly precipitation and temperature, shape
 the biogeography of AMF across the Caatinga, with niche
 partitioning among closely related AMF taxa. Given the expected decrease
 in precipitation and increase in temperature in the future, climate change
 may strongly affect AMF biodiversity in neotropical dry forests.