cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.271f74f
title: Data from: Multiple components of environmental change drive populations of breeding waders in seminatural grasslands

description: Environments are rapidly changing due to climate change, land-use,
 intensive agriculture and the impact of hunting on predator populations.
 Here we analysed long-term data recorded during 1928-2014 on the size of
 breeding populations of waders at two large nature reserves in Denmark,
 Vejlerne and Tipperne, to determine the effects of components of
 environmental change on breeding populations of waders. Waders are closely
 associated with coastal marshes and meadows, and such habitats have been
 reduced extensively during the last century with negative impacts on
 population trends of waterbirds. Environmental variables and counts of
 waders were temporally autocorrelated, and hence we used Generalized Least
 Square (GLS) by incorporating the first order autoregressive correlation
 structure in the analyses. We attempted to predict the abundance of waders
 for short-term trends for two nature reserves (35 years) and for long-term
 trends for one nature reserve (86 years), using precipitation,
 temperature, nutrients, abundance of foxes Vulpes vulpes, area grazed and
 number of cattle all standardized to a mean = 0 and SD = 1). There was
 evidence of impacts of nutrients, climate (long-term changes in
 temperature and precipitation), grazing, mowing and predation on bird
 populations. We used standard random effects meta-analyses weighted by (N
 – 3) to quantify these mean effects. There was no significant difference
 in effect size among species, while mean effect size differed consistently
 among environmental factors, and the interaction between effect size for
 species and environmental factors was also significant. Thus,
 environmental factors affected the different species differently. Mean
 effect size was the largest at +0.20 for rain, +0.11 for temperature,
 -0.09 for fox abundance and -0.03 for number of cattle, while there was no
 significant mean effect for fertilizer, area grazed and year. The negative
 impact of number of cattle on abundance of waders implied that a
 management tool actually had a significant negative impact on the
 population. Effect sizes for two short-term time series from Tipperne and
 Vejlerne were positively correlated as were effect sizes for short-term
 and long-term time series at Tipperne. This implies that environmental
 factors had consistent effects across large temporal and spatial scales.
description: TipperneData_aThis file contains data for wader species and environment at one out of two survey sites, 'Tipperne', Denmark, during 1928-2014.VejlerneDataThis file contains data for wader species and environment at one out of two survey site 'Vejlerne', Denmark, during 1978-2014.
DOI: 10.5061/dryad.5d69g86
title: Data from: 5α-cyprinol sulfate, a bile salt from fish, induces diel vertical migration in Daphnia

description: Prey are under selection to minimize predation losses. In aquatic
 environments many prey use chemical cues released by predators, which
 initiate predator-avoidance. A prominent example of behavioural
 predator-avoidance constitutes diel vertical migration (DVM) in the
 freshwater microcrustacean Daphnia spp., which is induced by chemical cues
 (kairomones) released by planktivorous fish. In a bioassay-guided approach
 using liquid chromatography and mass spectrometry we isolated the
 kairomone from fish incubation water and identified it as 5α-cyprinol
 sulfate inducing DVM in Daphnia at picomolar concentrations. The role of
 5α-cyprinol sulfate in lipid digestion in fish explains why from an
 evolutionary perspective fish has not stopped releasing 5α-cyprinol
 sulfate despite the disadvantages for the releaser. The identification of
 the DVM-inducing kairomone enables investigating its spatial and temporal
 distribution and the underlying molecular mechanism of its perception.
 Furthermore, it allows to test if fish-mediated inducible defenses in
 other aquatic invertebrates are triggered by the same compound.
description: Fish
 kairomoneThe file includes data
 from small-scale bioassays identifying a fish-borne kairomone responsible
 for the induction of diel vertical migration in Daphnia
 magna.Figure
 Data.xlsx
DOI: 10.5061/dryad.js11601
title: Data from: A low-threshold potassium current enhances sparseness and reliability in a model of avian auditory cortex

description: Birdsong is a complex vocal communication signal, and like humans, birds
 need to discriminate between similar sequences of sound with different
 meanings. The caudal mesopallium (CM) is a cortical-level auditory area
 implicated in song discrimination. CM neurons respond sparsely to
 conspecific song and are tolerant of production variability. Intracellular
 recordings in CM have identified a diversity of intrinsic membrane
 dynamics, which could contribute to the emergence of these higher-order
 functional properties. We investigated this hypothesis using a novel
 linear-dynamical cascade model that incorporated detailed biophysical
 dynamics to simulate auditory responses to birdsong. Neuron models that
 included a low-threshold potassium current present in a subset of CM
 neurons showed increased selectivity and coding efficiency relative to
 models without this current. These results demonstrate the impact of
 intrinsic dynamics on sensory coding and the importance of including the
 biophysical characteristics of neural populations in simulation studies.
description: READMEDescription of
 repository contents, organization, and file types.Summary
 TableA summary table for the
 entire set of simulationssummary_table.csvSyllable TableA table of syllable start and stop times for the stimulus setsyllables.csvExample NotebookA Jupyter Python notebook that shows how to load the data.examples.ipynbReceptive FieldsA compressed directory of spectrotemporal receptive fields used to simulate the responses.rf_bank.zipStimuliA compressed directory of stimulus filesstim_bank.zipSpike DataA compressed directory of response spike times.spike_data.zipRaw Simulation DataA compressed directory of raw simulated responses.raw_data.zip
DOI: 10.5061/dryad.sk37gd2
title: Data from: Monarch butterfly and milkweed declines substantially predate the use of genetically modified crops

description: Monarch butterfly (Danaus plexippus) decline over the past 25 years has
 received considerable public and scientific attention, in large part
 because its decline, and that of its milkweed (Asclepias spp.) host plant,
 have been linked to genetically modified (GM) crops and associated
 herbicide use. Here, we use museum and herbaria specimens to extend our
 knowledge of the dynamics of both monarchs and milkweeds in the United
 States to more than a century, from 1900 to 2016. We show that both
 monarchs and milkweeds increased during the early 20th century and that
 recent declines are actually part of a much longer-term decline in both
 monarchs and milkweed beginning around 1950. Herbicide-resistant crops,
 therefore, are clearly not the only culprit and, likely, not even the
 primary culprit: Not only did monarch and milkweed declines begin decades
 before GM crops were introduced, but other variables, particularly a
 decline in the number of farms, predict common milkweed trends more
 strongly over the period studied here.
description: Raw_recordsThis archive contains: 1) Raw specimen records from the University of Wisconsin, the Consortium of Midwest Herbaria, and Symbiota. 2) Redacted specimen records from the University of Minnesota (see PART 0.0 in the R_scripts archive for more information). 3) The DOI for the raw specimen records from GBIF.R_scriptsThis archive contains the R scripts used for all data analyses.
DOI: 10.5061/dryad.ss50dn7
title: Data from: Changing disturbance-diversity relationships in temperate ecosystems over the past 12000 years

description: 1. Disturbances such as fires and grazing have major impacts on
 biodiversity. While it has been suggested that species richness is highest
 with intermediate levels of disturbance, currently there is no consensus
 due to an absence of data covering large temporal and spatial scales. 2.
 We developed a new method to examine disturbance-diversity relationships
 (DDR) using sedimentary pollen data linked with species' disturbance
 ecology. We reconstructed disturbance and diversity dynamics in the region
 of the European temperate zone over the last 12000 years and calculated
 DDR for 900-yr sequential temporal windows. 3. Disturbance frequency was
 highest in the early and late Holocene, while remaining low in the
 mid-Holocene. Diversity increased continuously from the start of the
 Holocene. Our results demonstrate that over the past 12000 years DDR
 changed from hump-shaped into monotonic increasing pattern. While both
 highly disturbed and undisturbed sites were strongly impoverished in the
 early Holocene, as species migrated, biodiversity levels have subsequently
 affected disturbance regimes with highly disturbed sites now being the
 highest in species richness. 4. Synthesis. Land-use changes in the last
 4000 years created an increasingly patchy landscape, allowing invasive
 species adapted to high-frequency disturbance to migrate across the
 landscape. The link between high diversity and disturbed areas is
 relatively recent and may anticipate even greater disturbance frequencies
 in future. Our findings also support a hypothesis that species migration,
 and the structure of the species pool critically determines the response
 of biota to external factors such as disturbance.
description: Pollen
 countsPollen counts extracted
 from the Czech Quaternary Palynological Database
 (https://botany.natur.cuni.cz/palycz/) on 2 November 2017 covering the
 entire study area. Pollen taxonomy follows Beug (2004). Age is given in
 the calibrated age scale in BP (0 cal BP = 1950). Regions are defined as
 in Kuneš et al. (2009).pollen_counts.csvDisturbance frequency indicesList of plant species and their corresponding disturbance index as in Herben et al. (2016). Frequency of plant species in present-day vegetation was extracted from Chytrý & Rafajová (2003). Each plant taxon is assigned to a pollen taxon according to Beug (2004).disturbance_indices.csv
DOI: 10.5281/zenodo.18384915
title: Identification of two novel epitopes targeting the N protein and development of a blocking ELISA for antibody detection

description: Abstract: Porcine epidemic diarrhea virus (PEDV), a highly contagious acute coronavirus, causes severe mortality in piglets and threatens the global swine industry. Widespread PEDV mutations limit vaccine efficacy, highlighting the need for universal antibody detection assays to monitor infections and evaluate vaccine-induced immunity. The conserved PEDV nucleocapsid (N) protein elicits early high-titer antibody responses, making it an ideal diagnostic target. Here, we generated 2 monoclonal antibodies (mAbs) against the PEDV N protein. Through molecular docking, molecular dynamics simulations, and truncation assays, we confirmed stable antibody-N protein binding and identified two novel, highly conserved linear epitopes: “TPPASRANSRSR” and “IINEIFDTGN”. Using mAb-4H7, we developed a blocking ELISA (bELISA) with a 27.62% percent inhibition (PI) cutoff, achieving 98.00% specificity and 98.59% sensitivity for clear serological differentiation. The assay demonstrated 1:32 analytical sensitivity, no cross-reactivity with 5 other swine pathogens, and excellent repeatability. Clinical validation with 144 serum samples showed 97.92% concordance with PEDV-ELISA (IgG) kit. This study provides conserved epitope targets and a robust diagnostic tool for PEDV surveillance, vaccine evaluation, and basic N protein research, supporting comprehensive PEDV control strategies.
DOI: 10.5061/dryad.6hq8p8j
title: Data from: Stroke patients with psychiatric comorbidities have lower carotid revascularization rates

description: Objective: We investigated whether mental illness is associated with lower
 rates of CEA/CAS after stroke due to carotid stenosis. Methods: In this
 retrospective cross-sectional study, ischemic stroke cases due to carotid
 stenosis were identified in the 2007-2014 Nationwide (National) Inpatient
 Sample. Psychiatric conditions were identified by secondary ICD9-CM
 diagnosis codes for schizophrenia/psychoses, bipolar disorder, depression,
 anxiety, or substance use disorders. Using logistic regression, we tested
 the association between psychiatric conditions and CEA/CAS, controlling
 for demographic, clinical, and hospital factors. Results: Among 37,474
 included stroke cases, 6,922 (18.5%) had a psychiatric comorbidity. The
 presence of any psychiatric condition was associated with lower odds of
 CEA/CAS (adjusted OR 0.84, 95% CI 0.78-0.90). Schizophrenia/psychoses (OR
 0.72, 95% CI 0.55-0.93), depression (OR 0.83, 95% CI 0.75-0.91), and
 substance use disorders (OR 0.73, 95% CI 0.65-0.83) were each associated
 with lower odds of CEA/CAS. The association of mental illness and CEA/CAS
 was dose-dependent: compared to patients without mental illness, patients
 with multiple psychiatric comorbidities (OR 0.74, 95% CI 0.62-0.87) had
 lower odds of CEA/CAS than those with only one psychiatric comorbidity (OR
 0.86, 95% CI 0.79-0.92; p-value for trend &lt;0.001). Conclusions: The
 odds of carotid revascularization after stroke is lower in patients with
 mental illness, particularly those with schizophrenia/psychoses,
 depression, substance use disorders, and multiple psychiatric diagnoses.
description: Table
 e-1Supplemental Table
 listing ICD9-CM codes used to identify those with comorbid psychiatric
 disease.
DOI: 10.5281/zenodo.18384914
title: Identification of two novel epitopes targeting the N protein and development of a blocking ELISA for antibody detection

description: Abstract: Porcine epidemic diarrhea virus (PEDV), a highly contagious acute coronavirus, causes severe mortality in piglets and threatens the global swine industry. Widespread PEDV mutations limit vaccine efficacy, highlighting the need for universal antibody detection assays to monitor infections and evaluate vaccine-induced immunity. The conserved PEDV nucleocapsid (N) protein elicits early high-titer antibody responses, making it an ideal diagnostic target. Here, we generated 2 monoclonal antibodies (mAbs) against the PEDV N protein. Through molecular docking, molecular dynamics simulations, and truncation assays, we confirmed stable antibody-N protein binding and identified two novel, highly conserved linear epitopes: “TPPASRANSRSR” and “IINEIFDTGN”. Using mAb-4H7, we developed a blocking ELISA (bELISA) with a 27.62% percent inhibition (PI) cutoff, achieving 98.00% specificity and 98.59% sensitivity for clear serological differentiation. The assay demonstrated 1:32 analytical sensitivity, no cross-reactivity with 5 other swine pathogens, and excellent repeatability. Clinical validation with 144 serum samples showed 97.92% concordance with PEDV-ELISA (IgG) kit. This study provides conserved epitope targets and a robust diagnostic tool for PEDV surveillance, vaccine evaluation, and basic N protein research, supporting comprehensive PEDV control strategies.
DOI: 10.5061/dryad.d796p97
title: Data from: Effects of early-season insect herbivory on subsequent pathogen infection and ant abundance on wild cotton (Gossypium hirsutum)

description: 1. Plant induced defences play an important role in mediating interactions
 between insects and pathogens. Yet, the plant traits underlying these
 effects, the extended consequences for higher trophic levels (i.e.
 predators), and the implications for plant growth and reproduction have
 received little attention. 2. Here we asked whether simulated early insect
 leaf damage on wild cotton (Gossypium hirsutum) affected subsequent damage
 by insect leaf chewers and pathogenic fungi, as well as ant abundance. To
 address the mechanisms behind such effects, we measured plant defensive
 traits induced by early leaf damage to determine which inducible traits
 might determine the effects on plant-associates. We also evaluated whether
 early damage influenced plant growth and flower production, and if such
 effects were mediated by subsequent insect herbivory or pathogen
 infection. 3. We show that simulated early leaf damage reduced damage by
 subsequent leaf-chewing insects, increased plant fungal infections, but
 did not affect ant abundance. Leaf defensive traits (lignins and
 pubescence) were significantly induced by early damage and were negatively
 associated with insect herbivory and infection severity, but did not
 account for the effects of early leaf damage on either of these subsequent
 attackers. In addition, ant abundance was not associated with (or
 accounted for) subsequent herbivory or infection, suggesting they did not
 confer plant protection. Finally, early leaf damage negatively affected
 plant growth and flower production and analyses suggested that the effect
 on the latter was, at least partly, mediated by increased fungal
 infections. 4. Synthesis: Overall, these findings show that early
 herbivory determines the outcome of cotton interactions with subsequent
 attackers, and such effects have an impact on plant growth and flower
 output.
description: herbivory effects on
 cotton pathogensDRYAD.xlsx
DOI: 10.5061/dryad.3v0p84v
title: Data from: Diversity dynamics of Phanerozoic terrestrial tetrapods at the local-community scale

description: The fossil record provides one of the strongest tests of the hypothesis
 that diversity within local communities is constrained over geological
 timescales. Constraints to diversity are particularly controversial in
 modern terrestrial ecosystems, yet long-term patterns are poorly
 understood. Here we document patterns of local richness in Phanerozoic
 terrestrial tetrapods using a global data set comprising 145,332 taxon
 occurrences from 27,531 collections. We show that the local richness of
 non-flying terrestrial tetrapods has risen asymptotically since their
 initial colonization of land, increasing at most threefold over the last
 300 million years. Statistical comparisons support phase-shift models,
 with most increases in local richness occurring: (1) during the
 colonization of land by vertebrates, concluding by the late Carboniferous;
 and (2) across the Cretaceous/Paleogene boundary. Individual groups, such
 as mammals, lepidosaurs and dinosaurs also experienced early increases
 followed by periods of stasis often lasting tens of millions of years.
 Mammal local richness abruptly tripled across the Cretaceous/Paleogene
 boundary, but did not increase over the next 66 million years. These
 patterns are consistent with the hypothesis that diversity is constrained
 at the local-community scale.
description: code-for-close-et-al-diversity-dynamics-of-phanerozoic-terrestrial-tetrapods-at-the-local-scaleAll analysis code (R scripts) and data (CSV files downloaded from the Paleobiology Database at www.paleobiodb.org).
DOI: 10.5061/dryad.n8701qf
title: Data from: Maternal pre-pregnancy weight status modifies the influence of PUFAs and inflammatory biomarkers in breastmilk on infant growth

description: Background: Human breastmilk contains pro- and anti-inflammatory compounds
 and hormones that can influence infant growth. However, little is known
 about the specific interrelationships between these compounds and whether
 their effects on infant growth may be influenced by pre-pregnancy weight
 status. Objective: The purpose of this novel, prospective cohort study was
 to assess the interrelationships between pro-inflammatory cytokines
 (TNF-α, IL-6), hormones (insulin, leptin) and PUFAs (n-6, n-3) in blood
 and breastmilk in early postpartum between women with normal BMI (Group 1,
 n=18; 18.5
description: Circulating and breast
 milk concentrations of biomarkersData include circulating
 and breast milk concentrations of IL-6, TNF-alpha, polyunsaturated fatty
 acids, mothers BMI, infant growth measures.M2B 5.17.2019 PLoS ONE
 dataset.sav
DOI: 10.5061/dryad.82j677c
title: Data from: Cascading reproductive isolation: plant phenology drives temporal isolation among populations of a host-specific herbivore

description: All organisms exist within a complex network of interacting species, thus
 evolutionary change may have reciprocal effects on multiple taxa. Here, we
 demonstrate “cascading reproductive isolation,” whereby ecological
 differences that reduce gene flow between populations at one trophic level
 affect reproductive isolation (RI) among interacting species at the next
 trophic level. Using a combination of field, laboratory and common-garden
 studies and long-term herbaria records, we estimate and evaluate the
 relative contribution of temporal RI to overall prezygotic RI between
 populations of Belonocnema treatae, a specialist gall-forming wasp adapted
 to sister species of live oak (Quercus virginiana and Q. geminata). We
 link strong temporal RI between host-associated insect populations to
 differences between host plant budbreak phenology. Budbreak initiates
 flowering and the production of new leaves, which are an ephemeral
 resource critical to insect reproduction. As flowering time is implicated
 in RI between plant species, budbreak acts as a “multitrophic multi-effect
 trait,” whereby differences in budbreak phenology contribute to RI in
 plants and insects. These sister oak species share a diverse community of
 host-specific gall-formers and insect natural enemies similarly dependent
 on ephemeral plant tissues. Thus, our results set the stage for testing
 for parallelism in a role of plant phenology in driving temporal cascading
 RI across multiple species and trophic levels.
description: Herbaria
 recordsHerbaria records used in
 analysis of flowering time.Herbarium
 Records.xlsxBudbreak in
 NatureData used to estimate
 live oak budbreak phenologyInitial Budbreak Common
 GardenDate of first budbreak
 in sapling live oaks reared in a common gardenEmergence in
 NatureAdult B. treatae caught
 in traps used to estimate emergence phenology in natureEmergence in
 LaboratoryAdult B. treatae emerged
 from root galls in the laboratory used to estimate emergence
 phenologyAdult
 LongevityMeasurements of adult B.
 treatae longevity