cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.km78ms9
title: Data from: Biomechanical evaluation of peak reverse torque (PRT) in a dynamic compression plate-screw construct used in a goat tibia segmental defect model

description: Background Peak reverse torque (PRT) is a valid method to evaluate
 implants’ secondary stability in the healing bone. The secondary stability
 is achieved by the implant over time and it has been positively correlated
 with the implants’ osseointegration level. In other words, peak reverse
 torque is the force required to break the bone-implant interface. The
 purpose of this study was to compare the peak reverse torque for the
 self-tapping and non-self-tapping screws used in a dynamic compression
 plate–screw–bone construct after 60 days of loading when used to stabilize
 2.5-cm defects in the tibia of goats. The second objective was to compare
 the peak removal torque of the screws placed in the different positions to
 evaluate the impact of construct biomechanics on implants
 osseointegration. Results In total, 176 non-self-tapping screws and 66
 self-tapping screws were used to fix the 8-holes dynamic compression
 plates to the bones. The screws were placed in the tibiae from proximal
 (position sites 1,2, 3) to distal (position sites 4,5,6) and were removed
 60 days post-implantation. The animals remained weight-bearing throughout
 the study period. The screws placed in the proximal diaphysis had
 significantly less peak reverse torque than screws placed in the distal
 diaphysis in both groups (p &lt; 0.05). The peak reverse torque
 resistance was also significantly less for the non-self-tapping screws as
 compared with the self-tapping screws (p &lt; 0.05). The intracortical
 fractures in the trans-cortex occurred significantly more frequently
 during the placement of non-self-tapping screws (p &lt; 0.05) as
 compared with self-tapping screws (p &lt; 0.05). Conclusions Based on
 these results, we concluded that self-tapping screws may be expected to
 maintain a more stable bone-implant interface during the first 60 days of
 loading as compared with non-self-tapping screws. This should be a
 consideration for orthopedic surgeons and scientists using bone plates to
 stabilize non-load sharing fractures when a stable plate-screw-bone
 interface is needed to ensure prolonged stability.
description: Screw removal torque
 dataThis is an excel sheet
 with the peak removal torque values for each screw position in the plate.
 The peak removal torque values are divided between the non-self-tapping
 (NST) screws and self-tapping (ST) screws. Below the main table is the
 cortical fracture table with the frequencies of the cortical fracture
 occurrence during the screw placement of both screw types (NST and
 ST).
DOI: 10.5061/dryad.1j86179
title: Data from: Pollinator-mediated gene flow connects green roof populations across the urban matrix: a paternity analysis of the self-compatible forb Penstemon hirsutus

description: Gene flow between populations can help maintain genetic diversity and
 prevent inbreeding, which is especially important for small, fragmented
 habitats. Many plant species rely on pollinators to move pollen between
 populations. In urban areas, insufficient pollinator services may result
 in limited gene flow, which can have negative consequences such as genetic
 drift and inbreeding depression. Furthermore, restored populations that
 are established with few founders of low genetic diversity may have
 limited long-term population persistence. Here, we tested the hypotheses
 that populations of a self-compatible forb established on urban green
 roofs fromnursery stock are genetically depauperate and that limited gene
 (pollen) flow between populations will result in increased inbreeding. We
 compared the neutral genetic diversity of Penstemon hirsutus, using nine
 microsatellite loci, between three green roof populations established from
 nursery stock and three natural populations. We also established ten
 experimental populations on green roofs and measured rates of outcrossing
 and inbreeding and identified the movement of pollen within and between
 roofs using a paternity analysis. We found that neutral genetic diversity
 of populations established from nursery stock was lower than that of
 natural populations, although the level of inbreeding was also lower on
 the green roofs. In our experimental populations, we found that the rates
 of outcrossing and inbreeding varied between the roof populations. Our
 results suggest that inbreeding may be correlated with cover of
 co-flowering species but not with any of the other measured site
 properties. The location of likely pollen donors suggested that on
 average, 75% of pollen was derived from plants within the population
 (including self) and 25% came from plants on different roofs. Our results
 document realized pollen movement within and between green roofs,
 demonstrating that these habitats provide important connectivity in a
 fragmented environment.
description: Prairie and green roof
 Penstemon hirsutus microsatellite data10 microsatellite
 regions from Penstemon hirsutus populations from 3 prairies and 3 green
 roofs.NatVsRoof_Microsats_FinalData.csvPenstemon hirsutus green roof offspring microsatellite dataMicrosatellite data from 9 loci in offspring from 10 maternal populations of Penstemon hirsutus on green roofs in Chicago, IL 2014.Parentage_Microsats_FinalData.csv
DOI: 10.5061/dryad.rf951h1
title: Data from: Females facilitate male food patch discovery in a wild fish population

description: 1. Responding to the information provided by others is an important
 foraging strategy in many species. Through social foraging, individuals
 can more efficiently find unpredictable resources and thereby increase
 their foraging success. 2. When individuals are more socially responsive
 to particular phenotypes than others, however, the advantage they obtain
 from foraging socially is likely to depend on the phenotype composition of
 the social environment. We tested this hypothesis by performing
 experimental manipulations of guppy, Poecilia reticulata, sex compositions
 in the wild. 3. Males found fewer novel food patches in the absence of
 females than in mixed-sex compositions, while female patch discovery did
 not differ regardless of the presence or absence of males. 4. We argue
 that these results were driven by sex-dependent mechanisms of social
 association: Markov chain-based fission-fusion modelling revealed that
 less social individuals found fewer patches and that males reduced
 sociality when females were absent. In contrast, females were similarly
 social with or without males. 5. Our findings highlight the relevance of
 considering how individual and population-level traits interact in shaping
 the advantages of social foraging in the wild.
description: Snijdersetal2019_JAE_Data_archiveThis file consists of five sheets. The first sheet in this file contains the legend explaining all the unique column names in the dataset. The next four sheets contain the data used for the foraging behaviour analyses described in the paper. The first sheet is structured with individual fish as units of analysis, the second sheet with individual trials as units of analysis, the third sheet with individual arrival times at the patch as units of analysis (fish can arrive multiple times within one trial) and the last sheet with dyadic interactions at the patch as units of analysis.
DOI: 10.5061/dryad.34db1gr
title: Data from: Global patterns in coronavirus diversity

description: We surveyed the diversity of Coronaviruses in multiple host taxa from
 twenty countries to explore the factors driving viral diversity at a
 global scale. We identified sequences representing 100 discrete
 phylogenetic clusters, ninety-one of which were found in bats, and used
 ecological and epidemiologic analyses to show that patterns of CoV
 diversity correlate with those of bat diversity. We examined factors
 associated with the host such as bat family, genus, age, sex, season
 sampled, and human impact at the sampling location. Co-phylogenetic
 reconciliation analysis was also used to show that host switching has
 contributed to CoV evolution, and a preliminary analysis suggests that
 regional variation exists in the dynamics of this process.
description: Global Patterns in
 Coronavirus Diversity Data_FinalDataset used for
 analysis in Global Patterns in Coronavirus Diversity, includes coronavirus
 test results listed by individual tests. Dataset includes Animal ID,
 Specimen ID, test protocol and host factors
DOI: 10.5061/dryad.rb15131
title: Data from: Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species

description: Natural history museums harbour a plethora of biological specimens which
 are of potential use in population and conservation genetic studies.
 Although technical advancements in museum genomics have enabled
 genome-wide markers to be generated from aged museum specimens, the
 suitability of these data for robust biological inference is not well
 characterised. The aim of this study was to test the utility of museum
 specimens in population and conservation genomics by assessing the
 biological and technical validity of single nucleotide polymorphism (SNP)
 data derived from such samples. To achieve this, we generated thousands of
 SNPs from 47 red-tailed black-cockatoo (Calyptorhychus banksii)
 traditional museum samples (i.e. samples that were not collected with the
 primary intent of DNA analysis) and 113 fresh tissue samples
 (cryopreserved liver/muscle) using a restriction site associated DNA
 marker approach (DArTseqTM). Thousands of SNPs were successfully generated
 from most of the traditional museum samples (with a mean age of 44 years,
 ranging from 5-123 years), although 38% did not provide useful data. These
 SNPs exhibited higher error rates and contained significantly more missing
 data compared with SNPs from fresh tissue samples, likely due to
 considerable DNA fragmentation. However, based on simulation results, the
 level of genotyping error had a negligible effect on inference of
 population structure in this species. We did identify a bias towards low
 diversity SNPs in older samples, that appears to compromise temporal
 inferences of genetic diversity. This study demonstrates the utility of a
 RADseq-based method to produce reliable genome-wide SNP data from
 traditional museum specimens.
description: SNP data for all
 Calyptorhynchus banksii samples used in this paperThe SNPs provided by
 DArT and the associated meta-data for all Calyptorhynchus banksii samples
 used in this paper. Explanations for the meta-data can be found in the
 first tab of the spreadsheet.Report_DRtbc16-2386_DRtbc17-2707_SNP_singlerow.xlsxMeta-data for DArTseq sequence reads for all Calyptorhynchus banksii samplesMeta-data associated with the raw sequence reads (available for download on the short read archive) for all Calyptorhynchus banksii samples used in this paper.DArTseq-sequence-data_metadata.csv
DOI: 10.5061/dryad.4711h78
title: Data from: Evolution of both host resistance and tolerance to an emerging bacterial pathogen

description: Understanding how hosts minimize the cost of emerging infections has
 fundamental implications for epidemiological dynamics and the evolution of
 pathogen virulence. Despite this, few experimental studies in natural
 populations have tested whether, in response to disease emergence, hosts
 evolve resistance, which reduces pathogen load through immune activation,
 or tolerance, which limits somatic damages without decreasing pathogen
 load. Further, none has done so accounting for significant natural
 variation in pathogen virulence, despite known effects on host responses
 to infection. Here, we investigate whether eastern North American house
 finches (Haemorrhous mexicanus) have evolved resistance and/or tolerance
 to their emerging bacterial pathogen, Mycoplasma gallisepticum. To do so,
 we inoculated finches from disease-exposed and disease-unexposed
 populations with 55 distinct isolates of varying virulence. First,
 although peak pathogen loads, which occurred ~8 days post-inoculation, did
 not differ between experimentally-inoculated finches from disease-exposed
 versus unexposed population, pathogen loads subsequently decreased faster
 and to a greater extent in finches from exposed populations. These results
 suggest that finches from exposed populations are able to clear the
 infection through adaptive immune processes. Second, however, finches from
 exposed populations also displayed lower symptom severity for a given
 pathogen load, suggesting that a damage-limitation mechanism, or
 tolerance, has accompanied the evolution of immune clearance. Our results
 highlight that resistance and tolerance should be seen as complementary,
 not alternative, defence strategies: the evolution of resistance benefits
 from the concomitant evolution of tolerance mechanisms that protect
 against the damage of immune activation, while the evolution of tolerance
 without resistance will risk runaway selection on pathogen virulence.
description: Bonneaud et al_pathogen
 load over dpiData for testing
 population difference in rate of pathogen clearance. We include bird
 identity, day post-inoculation (dpi), population of origin of bird,
 Mycoplasma gallisepticum isolate identity, and pathogen load (ratio of
 bacterial to host cells at site of infection). Total sample size=80
 individuals infected.Bonneaud et
 al_data_dpi.csvBonneaud et al_symptoms
 severity and pathogen loadData for testing
 population differences in peak and total conjunctival swelling, as well as
 peak and total pathogen load. We include bird identity, population of
 origin of bird, Mycoplasma gallisepticum isolate identity, peak and total
 conjunctival swelling, and peak and total pathogen load (ratio of
 bacterial to host cells at site of infection). Total sample size=80
 individuals infected.Bonneaud et
 al_data_peaks.csv
DOI: 10.5061/dryad.bs8313h
title: Data from: The interplay of nested biotic interactions and the abiotic environment regulates populations of a hypersymbiont

description: 1. The role of biotic interactions in shaping distribution and abundance
 of species should be particularly pronounced in symbionts. Indeed,
 symbionts have a dual niche composed of traits of their individual hosts
 and the abiotic environment external to the host, and often combine active
 dispersal at finer scales with host-mediated dispersal at broader scales.
 The biotic complexity in the determinants of species distribution and
 abundance should be even more pronounced for hypersymbionts (symbionts of
 other symbionts). 2. We use a chain of symbiosis to explore the relative
 influence of nested biotic interactions and the abiotic environment on
 occupancy and abundance of a hypersymbiont. 3. Our empirical system is the
 epibiont ciliate Lagenophrys discoidea, which attaches to an ostracod that
 is itself ectosymbiotic on crayfish (the basal host). We applied
 multimodel selection and variance partitioning for GLMM to assess the
 relative importance of: 1) traits of symbiotic hosts (ostracod sex and
 abundance), 2) traits of basal hosts (crayfish body weight, abundance and
 intermoult stage), 3) the abiotic environment (water chemistry and
 climate), and 4) geospatial autocorrelation patterns (capturing potential
 effects of crayfish dispersal among localities). 4. Our models explained
 about half of the variation in prevalence and abundance of the
 hypersymbiont. Variation in prevalence was partly explained, in decreasing
 order of importance (18-4%) by shared effects of symbiotic host traits and
 the abiotic environment, pure fixed effects of symbiotic hosts, abiotic
 environment and geospatial patterns (traits of basal hosts were not
 relevant). Hypersymbiont abundance was most strongly explained by random
 effects of host traits (mainly the symbiotic host), in addition to weaker
 fixed effects (mostly abiotic environment). 5. Our results highlight the
 major role of the interplay between abundance of symbiotic hosts and water
 physico-chemistry in regulating populations of a hypersymbiotic ciliate,
 which is likely critical for dispersal dynamics, availability of
 attachment resources and suitability of on-host living conditions for the
 ciliate. We also found moderate signal of regulation by the basal host,
 for which we propose three mechanisms: 1) modulation of microhabitat
 suitability (crayfish-created water currents); 2) concentration of
 symbiotic hosts within crayfish; and 3) dispersal mediated by crayfish.
 30-Jul-2019
description: Data used to model
 prevalence of the hypersymbiontData collected in the
 field and used to model prevalence of the hypersymbiotic ciliate
 Lagenophrys discoidea, which attaches to an ostracod that is itself
 ectosymbiotic on crayfish.Data_Prev.csvData used to model abundance of the hypersymbiontData collected in the field and used to model abundance of the hypersymbiotic ciliate Lagenophrys discoidea, which attaches to an ostracod that is itself ectosymbiotic on crayfishData_AbOH.csv
DOI: 10.6073/pasta/dccc30797ff07bf0b77421038054ea45
title: Yearly survey of barnacle settlement near creekbank plots at GCE LTER study sites in October 2023

description: To characterize spatial variation in barnacle recruitment at the creekbank, and across a gradient in salinity and distance to ocean, we deployed PVC poles to passive sample barnacle settlement. Eight poles were deployed between 4-5m apart adjacent to the creekbank vegetation monitoring plots at each GCE LTER permanent monitoring site each Fall beginning in 2012. These poles were then collected the following Fall and all barnacle that settled on the poles were identified and counted on 50cm-long sections of the 8, 3/4" diameter PVC poles. Four species settled on poles and were counted and recorded: Chthamalus fragilis, Balanus spp., Geukensia demissa, and Oysters (Crassostrea virginica).
DOI: 10.5061/dryad.r2r5964
title: Data from: Nutrient scarcity strengthens soil fauna control over leaf litter decomposition in tropical rainforests

description: Soil fauna is a key control of the decomposition rate of leaf litter, yet
 its interactions with litter quality and the soil environment remain
 elusive. We conducted a litter decomposition experiment across different
 topographic levels within the landscape replicated in two rainforest sites
 providing natural gradients in soil fertility to test the hypothesis that
 low nutrient availability in litter and soil increases the strength of
 fauna control over litter decomposition. We crossed these data with a
 large dataset of 44 variables characterizing the biotic and abiotic
 microenvironment of each sampling point and found that microbe-driven
 Carbon (C) and Nitrogen (N) losses from leaf litter were 10.1 and 17.9 %
 lower, respectively, in the nutrient-poorest site but this among-site
 difference was equalized when meso- and macrofauna had access to the
 litterbags. Further, on average soil fauna enhanced the rate of litter
 decomposition by 22.6%, and this contribution consistently increased as
 nutrient availability in the microenvironment declined. Our results
 indicate that nutrient scarcity increases the importance of soil fauna on
 C and N cycling in tropical rainforests. Further, soil fauna is able to
 equalize differences in microbial decomposition potential thus buffering
 to a remarkable extent nutrient shortages at an ecosystem level.
description: Data and Code for
 Peguero et al 2019 Nutrient scarcity strengthens soil fauna control over
 leaf litter decomposition in tropicalAll data files and code
 that support the paper by Peguero et al 2019 entitled "Nutrient
 scarcity strengthens soil fauna control over leaf litter decomposition in
 tropical"Peguero_et_al_2019_ProcB_decomposition.zip
DOI: 10.5061/dryad.v8n3gv3
title: Data from: Cluster analysis successfully identifies clinically meaningful knee valgus moment patterns: frequency of early peaks reflects sex-specific ACL injury incidence

description: Background: Biomechanical studies of ACL injury risk factors frequently
 analyze only a fraction of the relevant data, and typically not in
 accordance with the injury mechanism. Extracting a peak value within a
 time series of relevance to ACL injuries is challenging due to differences
 in the relative timing and size of the peak value of interest.
 Aims/hypotheses: The aim was to cluster analyze the knee valgus moment
 time series curve shape in the early stance phase. We hypothesized that
 1a) There would be few discrete curve shapes, 1b) there would be a shape
 reflecting an early peak of the knee valgus moment, 2a) youth athletes of
 both sexes would show similar frequencies of early peaks, 2b) adolescent
 girls would have greater early peak frequencies. Methods: N = 213 (39%
 boys) youth soccer and team handball athletes (phase 1) and N = 35 (45%
 boys) with 5 year follow-up data (phase 2) were recorded performing a
 change of direction task with 3D motion analysis and a force plate. The
 time series of the first 30% of stance phase were cluster analyzed based
 on Euclidean distances in two steps; shape-based main clusters with a
 transformed time series, and magnitude based sub-clusters with body weight
 normalized time series. Group differences (sex, phase) in curve shape
 frequencies, and shape-magnitude frequencies were tested with chi-squared
 tests. Results: Six discrete shape-clusters and 14 magnitude based
 sub-clusters were formed. Phase 1 boys had greater frequency of early
 peaks than phase 1 girls (38% vs 25% respectively, P &lt;  0.001 for
 full test). Phase 2 girls had greater frequency of early peaks than phase
 2 boys (42% vs 21% respectively, P &lt;  0.001 for full test).
 Conclusions: Cluster analysis can reveal different patterns of curve
 shapes in biomechanical data, which likely reflect different movement
 strategies. The early peak shape is relatable to the ACL injury mechanism
 as the timing of its peak moment is consistent with the timing of injury.
 Greater frequency of early peaks demonstrated by Phase 2 girls is
 consistent with their higher risk of ACL injury in sports.
description: Knee valgus moment time
 seriesTime series used for a
 two cluster analysis of knee valgus moment waveforms based on their shape
 and magnitude.Sigurdsson_2019_ValgusMomentClusterAnalysis.csv