cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sf7m0cg8t
title: Alpine butterflies want to fly high: Species and communities shift upwards faster than their host plants

description: Despite sometimes strong co-dependencies of insect herbivores and plants,
 responses of individual taxa to accelerating climate change are typically
 studied in isolation. Thereby, biotic interactions that potentially limit
 species in tracking their preferred climatic niches are ignored. Here, we
 chose butterflies as a prominent representative of herbivorous insects to
 investigate the impacts of temperature changes and their larval host plant
 distributions along a 1.4 km elevational gradient in the German Alps.
 Following a sampling protocol of 2009, we re-visited 33 grassland plots in
 2019 over an entire growing season. We quantified changes in butterfly
 abundance and richness by repeated transect walks on each plot and
 disentangled the direct and indirect effects of locally assessed
 temperature, site management, and larval and adult food resource
 availability on these patterns. Additionally, we determined elevational
 range shifts of butterflies and host plants at both the community and
 species level. Comparing the two sampled years (2009, 2019), we found a
 severe decline in butterfly abundance and a clear upward shift of
 butterflies along the elevational gradient. We detected shifts in the peak
 of species richness, community composition and at the species level,
 whereby mountainous species shifted particularly strongly. In contrast,
 host plants showed barely any change, neither concerning species richness,
 nor individual species shifts. Further, temperature and host plant
 richness were the main drivers of butterfly richness, with change in
 temperature explaining best the change of richness over time. We conclude
 that host plants are not yet hindering butterfly species and communities
 from shifting upwards. However, the mismatch between butterfly and host
 plant shifts might become a problem for this very close plant-herbivore
 relationship, especially towards higher elevations, if butterflies fail to
 adapt to new host plants. Further, our results support the value of
 conserving traditional extensive pasture use as a promoter of host plants
 and thereby butterfly richness.
description: Butterfly data was collected by standardized transect walks and
 host plant data by vegetation surveys, determining species and estimating
 cover. Temperature data per plot was modelled based on data from nearby
 climate stations. All analyses and figures were produced in R using R
 Markdown with the script presented here.
description: R, RStudio
DOI: 10.5061/dryad.3tx95x6jx
title: Incorporating pyrodiversity into wildlife habitat assessments for rapid post-fire management: A woodpecker case study

description: Spatial and temporal variation in fire characteristics – termed
 pyrodiversity – are increasingly recognized as important factors that
 structure wildlife communities in fire-prone ecosystems, yet there have
 been few attempts to incorporate pyrodiversity or post-fire habitat
 dynamics into predictive models of animal distributions and abundance to
 support post-fire management. We use the black-backed woodpecker – a
 species associated with burned forests – as a case study to demonstrate a
 pathway for incorporating pyrodiversity into wildlife habitat assessments
 for adaptive management. Employing monitoring data (2009–2019) from
 post-fire forests in California, we developed three competing occupancy
 models describing different hypotheses for habitat associations: (1) a
 static model representing an existing management tool, (2) a temporal
 model accounting for years since fire, and (3) a temporal-landscape model
 which additionally incorporates emerging evidence from field studies about
 the influence of pyrodiversity. Evaluating predictive ability, we found
 superior support for the temporal-landscape model, which showed a positive
 relationship between occupancy and pyrodiversity and interactions between
 habitat associations and years since fire. We incorporated this new
 temporal-landscape model into an RShiny application to make this
 decision-support tool accessible to decision-makers:
 https://birdpop.org/pages/bbwoPredPostFireDist.php.
description: <strong>This data package includes three
 components:</strong> (1) Text files of JAGS model
 code. (2) .csv files with input data to run models and
 conduct the analysis. (3) A README file with
 definitions of variables.<br><br>
 <strong>Descriptions of code
 files:</strong><br><br>Run_StaticModel.txt.
 Specification of a Bayesian single-season occupancy model for black-backed
 woodepckers. This model corresponds to the "static model" in the
 main text. Run using R version 4.1.0 and JAGS version
 4.3.0.<br><br>Run_TemporalModel.txt. Specification of a
 Bayesian temporal auto-logistic occupancy model for black-backed
 woodepckers. This model corresponds to the "temporal model" in
 the main text. Run using R version 4.1.0 and JAGS version 4.3.0.
 Run_LandscapeTemporalModel.txt. Specification of a Bayesian
 temporal auto-logistic occupancy model for black-backed woodepckers. This
 model corresponds to the "landscape temporal model" in the main
 text. Run using R version 4.1.0 and JAGS version 4.3.0.
DOI: 10.7272/q6513wg4
title: Data for: Distinguishing externally- from saccade-induced motion in visual cortex

description: Distinguishing sensory stimuli caused by changes in the environment from
 those caused by an animal’s own actions is a hallmark of sensory
 processing. Saccades are rapid eye movements that shift the image on the
 retina. How visual systems differentiate motion of the image induced by
 saccades from actual motion in the environment is not fully understood.
 Here, we discovered that in mouse primary visual cortex (V1), the two
 types of motion evoke distinct activity patterns. This is because during
 saccades, V1 combines the visual input with a strong non-visual input
 arriving from the thalamic pulvinar nucleus. The non-visual input triggers
 responses that are specific to the direction of the saccade, and the
 visual input triggers responses that are specific to the direction of the
 shift of the stimulus on the retina, yet the preferred directions of these
 two responses are uncorrelated. Thus, the pulvinar input ensures
 differential V1 responses to external and self-generated motion. This
 dataset supporting our findings contains extracellular recording data
 around the time of saccades from V1 and thalamic nuclei under various
 experimental conditions.
description: The dataset was generated from electrophysiology data obtained
 through extracellular probes and eye tracking data. All data were
 processed using Matlab 2018a. Detailed description of the data files is
 found in the README. For detailed collection methods, refer to the
 associated manuscript "Distinguishing externally- from self-induced
 motion in visual cortex", Miura and Scanziani, Nature (in
 press).
description: All datasets are created using Matlab 2018a and can be viewed
 using Matlab 2018a or later.
DOI: 10.5061/dryad.bg79cnpdm
title: Leveraging functional traits of cover crops to coordinate crop productivity and soil health

description: 1. Plants act as ecosystem engineers playing fundamental roles in steering
 their surroundings, including soil abiotic and biotic conditions, soil
 organisms, and the complex soil food web they comprise. Trait-based
 approaches have been considered a ‘Holy Grail’ in linking plants to
 ecosystem functions, but the mechanistic relationship between plant traits
 and the soil food web as an indicator of soil health remains poorly
 understood. 2. We examined this relationship for 16 cover crop species
 differing in leaf and root traits in a field experiment where corn (Zea
 mays) was the main crop. Based on functional traits, the cover crop
 species were categorized into two ecological strategies at either end of
 the resource acquisitive-conservative spectrum. We investigated the
 effects of cover crop ecological strategies on corn productivity and soil
 health. We used soil nematodes as an indicator of soil health and analyzed
 soil physico-chemical properties and microbial community activities. 3. We
 found that acquisitive cover crops supported higher soil resource
 availability, bacterial energy channels in the soil food web, and greater
 corn productivity than conservative cover crops. In contrast, conservative
 cover crops supported higher abundances of fungivores and omni-carnivores
 than acquisitive cover crop, which reflected a more structured and complex
 soil food web, implying a healthier soil ecosystem. Conservative cover
 crops also increased corn productivity compared to the no cover crop
 control treatment. 4. Synthesis and applications. Collectively, this work
 shows that cover crops with distinct ecological strategies had their own
 strengths to enhance ecosystem functions: acquisitive and conservative
 cover crops improved crop productivity and soil health, respectively.
 These results indicates that farmers and policy makers can make
 trait-based choices in selecting cover crop best serving the local needs.
 This points to a win-win solution for food production and ecosystem
 sustainability.
DOI: 10.5061/dryad.jm63xsjdt
title: Leukochimerism genotyping data

description: Twinning in cattle is infrequent, and also undesired. It can result in
 increased occurrence of abortion and dystocia, reduced calf survival, and
 a high likelihood of freemartinism in mixed-sex twins. Twin gestations
 also commonly are associated with the formation of placental vascular
 anastomoses (PVA) between twins. Through this, they share blood, hormones
 (leading to freemartinism in mixed-sex twins) and hematopoietic stem
 cells, which are the progenitors of white blood cells. The sharing of stem
 cells between twins can result in leukochimeric twinsets; these are twins
 that have white blood cells derived from both self and co-twin owing to
 the fetal migration of hematopoietic stem cells from the extraembryonic
 mesoderm of the yolk sac to final sites like bone marrow and thymus. This
 study examined the degree to which this leukochimerism changes over time.
 DNA was extracted from hair bulbs to determine the individual's true
 genotype and blood samples obtained at six time points from 1 week to 8
 months of age to assess leukochimerism. Samples were genotyped using a
 medium-density SNP chip, and quantitative estimates of allele frequency
 were determined using SNPs for which members of a twin set had alternative
 homozygous genotypes. Results indicated statistically significant changes
 in proportion self and co-twin with age and suggest that by four months of
 age, the genotypic mix in white blood cells represents the hematopoietic
 cell population resident in the individual. 
description: Genotype data were generated from hair-derived DNA samples and
 blood-derived DNA, the latter collected at 1 week, 1 month, 2 months, 4
 months, 6 months and 8 months of age.
description: The files are text and .csv files which can be opened with a text
 editor or Excel.
DOI: 10.5061/dryad.9p8cz8wk8
title: Dataset for: Long-term soil warming decreases microbial phosphorus utilization by increasing abiotic phosphorus sorption and losses

description: Phosphorus (P) is an essential and often limiting element that could play
 a crucial role in terrestrial ecosystem responses to climate warming.
 However, it has yet remained unclear how different P cycling processes are
 affected by warming. Here we investigated the response of soil P pools and
 P cycling processes in a mountain forest after 14 years of soil warming
 (+4°C). Long-term warming decreased soil total P pools, likely due to
 higher outputs of P from soils by increasing net plant P uptake and
 downward transportation of colloidal and particulate P. Warming increased
 the sorption strength to more recalcitrant soil P fractions (absorbed to
 iron oxyhydroxides and clays), thereby further reducing bioavailable P in
 soil solution. As a response, soil microbes enhanced the production of
 acid phosphatase, though this was not sufficient to avoid decreases of
 soil bioavailable P and microbial biomass P (and biotic phosphate
 immobilization). This study therefore highlights how long-term soil
 warming triggers changes in biotic and abiotic soil P pools and processes,
 which can potentially aggravate the P constraints of the trees and soil
 microbes and thereby negatively affect the C sequestration potential of
 these forests.
DOI: 10.5061/dryad.z8w9ghxfq
title: The impact of seat-height on 1-minute sit to stand test performance in COPD: A randomised cross-over trial

description: Study question: Is there a difference in the number of repetitions on the
 1-minute sit to stand (1MSTS) test using an individually adapted
 seatheight to 90-degree knee flexion (1MSTSIND), compared with the
 commonly used standard chair seat-height of 46cm (1MSTSSTD), in people
 with COPD. Intervention: After a learning 1MSTS, all participants
 performed two 1MSTS tests in random order on consecutive days.
 Participants were blinded, as they did not receive detailed information on
 the testing protocols. Results: 49 individuals with COPD (47% female)
 participated. In a regression model adjusted for sequence-period and
 subject, 1MSTS test performance was lower on 1MSTSIND compared to 1MSTSSTD
 (-0.78 repetitions, 95% CI, -1.47 to -0.11). In a second regression model
 additionally including the knee angle and an interaction term (1MSTSIND x
 knee angle), the interaction term was significant: 0.18 (95% CI, 0.05 to
 0.30). The limits of agreement were between -5.5 to 4 repetitions.
 Conclusion: Although we observed a statistically significant difference
 between 1MSTSIND and 1MSTSSTD on a population level, the difference is
 negligible. Further studies may be needed to determine if individual
 adaptation of seat-height is needed for very tall or short people to
 ensure a valid assessment of 1MSTS test performance in COPD.
description: We conducted a single-centre, single blinded randomised
 cross-over trial in people with COPD between August 2020 to March 2021 at
 a specialised rehabilitation clinic in Switzerland.
DOI: 10.5061/dryad.76hdr7t0g
title: Plant species with higher chemical defenses enhance herbivore cellular immunity with differential effectiveness against two parasitoid species

description: Insect herbivores simultaneously experience bottom-up effects of plant
 defensive chemistry and the top-down effects of natural enemies. At the
 intersection of these effects are herbivore immune systems, herbivore
 traits that have largely been overlooked in studies of plant-insect
 interactions. Most previous studies have demonstrated compromised immunity
 of herbivores that feed on plants with higher defensive chemistry. Many
 studies have used embedded microfilaments or silica beads as proxies for
 parasitoid eggs. Yet, parasitoids may evade or suppress host immune
 responses by injecting venom, calyx fluid, or through modifications of
 their egg surface structure, necessitating studies that include all three
 trophic levels to obtain a complete picture of how plant traits may
 modulate herbivore immunity.Here we examined the effect of host plant
 species that differ in glucosinolate (anti-herbivore compounds produced by
 plants in the Brassicaceae) concentrations on the immune status of an
 herbivore and its consequences for two species of parasitoids with
 different life history traits.We found that larvae of the butterfly Pieris
 rapae that fed on field mustard Brassica rapa, which contain 52-fold
 higher glucosinolate concentrations than collards B. oleracea, attained
 lower body weights and experienced prolonged development to adulthood.Yet,
 caterpillars that fed on B. rapa had enhanced cellular immunity, as
 measured by total and differential hemocyte counts, as well as
 melanization capacity compared to larvae that fed on B. oleracea.In turn,
 the likelihood that at least some eggs in clutches of the gregarious
 endoparasitoid Cotesia glomerata would be encapsulated, leading to a
 reduction in brood size, were three times greater when their host
 caterpillars fed on B. rapa compared to B. oleracea. Interestingly, eggs
 of the solitary endoparasitoid Cotesia rubecula were rarely encapsulated
 irrespective of the host plant on which their host caterpillar fed.
 Therefore, our results suggest that plant defense metabolites can
 influence the expression of herbivore immunity, but the effectiveness of
 this response strongly depends on the identity of the parasitoid and its
 ability to evade the caterpillar immune response, and possibly the
 evolution of these trophic interactions in non-native systems.
DOI: 10.5061/dryad.08kprr55c
title: Data from: Forest connectivity boosts pollen flow among populations of the oil-producing Nierembergia linariifolia

description: Context The process of forest fragmentation determines landscapes with
 isolated forest patches immersed in a distinct matrix. This process may
 hinder pollinator movement throughout the landscape, which may negatively
 impact on pollen flow among native plant populations. Objectives We
 evaluated the effect of the loss of forest connectivity on pollen
 dispersal by specialized native bees in the oil-producing and
 self-incompatible Nierembergia linariifolia. Methods We estimated pollen
 flow between plants of N. linariifolia at an agroecosystem with remnant
 forest of central Argentina. Six plant populations (source populations)
 were treated with fluorescent dyes as pollen analogues, and stigmata of
 recipient plants were collected to seek for dye particles. Dye deposition
 rate was assessed for plants that were connected through remnant forest to
 a source population or unconnected by a crop matrix, and at increasing
 distances to a source population. Results Deposition rate per plant was
 higher in connected than in unconnected plants, and decreased with
 increasing distances to a source population in an exponential fashion.
 Most of the dispersal events between connected plants occurred at the
 vicinity of a source population. Long dispersal events (up to 1259 m) were
 recorded between plants located at neighbouring forest patches separated
 by an agricultural matrix. Conclusions Landscape connectivity through
 forest remnants is key to enhance pollen flow between self-incompatible
 plants such as N. linariifolia. Besides, the evidence of pollen dispersal
 through the agricultural matrix pinpoints the essential role of native
 pollinators in maintaining pollen flow among unconnected plant populations
 in fragmented landscapes.
DOI: 10.5061/dryad.k3j9kd5b4
title: Temporal stability of productivity is associated with complementarity and competitive intensities in intercropping

description: Year to year stability in crop production is a crucial aspect of feeding a
 growing global population. Evidence from natural ecosystems shows that
 increasing plant diversity generally increases the temporal stability of
 productivity; however, we have little knowledge of the mechanisms by which
 diversity affects stability. In fact, understanding the drivers of
 stability is a major knowledge gap in our understanding of biodiversity
 and ecosystem function in general. We varied resource inputs into crop
 monocultures and intercropping of maize/pea and maize/rapeseed for three
 years in field experiments to create a wide range of values for temporal
 stability, complementarity effects, selection effects, competition, and
 facilitation. We correlated whole-system temporal stability in
 productivity with these values and the stability of competitively
 subordinate species and competitively dominant species in the intercrops.
 We then used structural equation modeling (SEM), which combines complex
 path models with latent variables, to estimate how interspecific
 interactions for water, nitrogen, and phosphorus affected the
 relationships between stability and these values. Intercropping treatments
 did not increase stability, but the wide range of stability created by our
 experiments allowed us to explore the relationship of many factors with
 stability. Complementarity correlated positively with the temporal
 stability of grain yield and aboveground biomass, suggesting that either
 facilitative interactions or niche partitioning shifted over time in ways
 that promoted stability. Furthermore, the temporal stability of total
 productivity of intercropping relied most on the stability of more
 productive species. However, facilitation tested by relative interaction
 index (RII) independently did not correlate with stability, but the
 temporal stability of the whole system increased as the competitive
 effects of competitively dominant species (pea and rapeseed) on
 competitively subordinate species (maize) decreased, and was highest when
 these competitive effects were virtually zero. SEM indicated that as
 competition for soil nitrogen from competitively dominant species on
 competitively subordinate species decreased, the overall temporal
 stability of whole-system aboveground biomass increased. This stability
 then led to greater stability in grain production. Our findings indicate
 that complex shifts in complementarity and competitive intensities are
 likely to be key mechanisms that maintain temporal stability in
 species-diverse agriculture, and potentially in natural systems.
DOI: 10.5061/dryad.7pvmcvdwn
title: Data from: Evolution of functional antibodies following acute Epstein-Barr Virus infection

description: While Epstein-Barr virus causes mostly asymptomatic infection, associated
 malignancies, and autoimmune and lymphoproliferative diseases occur. To
 dissect the evolution of humoral immune responses over the course of EBV
 infection and to gain a better understanding of the potential contribution
 of antibody (Ab) function to viral control, we comprehensively profiled Ab
 specificities and Fc-functionalities using systems serology and VirScan.
 Ab functions against two early (p18 and p47/54) and two latent (gp350/220
 and EBNA-1) EBV proteins were overall modest and/or short-lived, differing
 from humoral responses induced during acute infection by other viruses
 such as HIV. In the first year post-infection, only p18 elicited robust
 IgM-driven complement deposition and IgG-driven neutrophil phagocytosis
 while responses against EBNA-1 were largely Fc-functionally silent and
 only matured during chronic infection to drive phagocytosis. In contrast,
 Abs against Influenza virus readily mediated broad Fc-activity in all
 participants. These data suggest that EBV evades the induction of robust
 Fc-functional Abs, potentially due to the virus’ life cycle, switching
 from lytic to latent stages during infection. 
description: SOI scoring was used to determine the severity of
 illness. ELISAs were used to confirm EBV status, the
 titer, and class/subclass of EBV-specific antibodies.
 qPCR was used to determine viral load.
 High-throughput flow cytometry techniques of the systems serology
 pipeline were used to assess antibody-mediated immune functions.
 Luminex assays were used to determine antibody binding to Fc
 receptors. Antibody depletion experiments were used to
 test suspected causal associations between specific antibody classes and
 functions. Virscan analysis was used to determine the
 breadth of existing and evolving antibody responses.
description: Prism, Excel.
DOI: 10.5281/zenodo.18401186
title: LINF_320013200

description: Ric1-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.18401187
title: LINF_320013200

description: Ric1-like protein; Leishmania infantum (strain JPCM5)