cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v726t
title: Data from: A cross-scale trophic cascade from large predatory fish to algae in coastal ecosystems

description: Trophic cascades occur in many ecosystems, but the factors regulating them
 are still elusive. We suggest that an overlooked factor is that trophic
 interactions (TIs) are often scale-dependent and possibly interact across
 spatial scales. To explore the role of spatial scale for trophic cascades,
 and particularly the occurrence of cross-scale interactions (CSIs), we
 collected and analysed food-web data from 139 stations across 32 bays in
 the Baltic Sea. We found evidence of a four-level trophic cascade linking
 TIs across two spatial scales: at bay scale, piscivores (perch and pike)
 controlled mesopredators (three-spined stickleback), which in turn
 negatively affected epifaunal grazers. At station scale (within bays),
 grazers on average suppressed epiphytic algae, and indirectly benefitted
 habitat-forming vegetation. Moreover, the direction and strength of the
 grazer–algae relationship at station scale depended on the piscivore
 biomass at bay scale, indicating a cross-scale interaction effect,
 potentially caused by a shift in grazer assemblage composition. In
 summary, the trophic cascade from piscivores to algae appears to involve
 TIs that occur at, but also interact across, different spatial scales.
 Considering scale-dependence in general, and CSIs in particular, could
 therefore enhance our understanding of trophic cascades.
description: Food web data from 32
 bays along the Central Baltic SeaThis file contains data
 on fish, vegetation, epiphytic algae and abiotic conditions at bay and
 station scalePF_survey.xlsx
DOI: 10.5061/dryad.hn0dt
title: Data from: Assessing niche conservatism using a multiproxy approach: dietary ecology of extinct and extant spotted hyenas

description: A central premise of bioclimatic envelope modeling is the assumption of
 niche conservatism. Whereas such assumptions are testable in modern
 populations, it is unclear if niche conservatism holds over deeper time
 spans and over very large geographic ranges. Hyaenids occupied a diversity
 of ecological niches over time and space, and until the end-Pleistocene
 they occurred in Europe and most of Asia, with Asian populations of
 Crocuta suggested as being genetically distinct from their closest living
 extant relatives. Further, little is known regarding if and how the
 dietary ecology of extinct populations of Crocuta differed from their
 extant African counterparts. Here, we use a multi-proxy approach to assess
 an assumption of conserved dietary ecology in late Pleistocene and extant
 Chinese spotted hyenas via finite element analysis, dental microwear
 texture analysis, and a novel dental macrowear method here proposed.
 Results from finite element simulations of the masticatory apparatus of
 Chinese and African Crocuta demonstrate lower skull stiffness and higher
 stress in the orbital region of the former when biting with carnassial
 teeth, suggesting that Chinese Crocuta could not process prey with the
 same degree of efficiency as extant C. crocuta. Dental microwear textural
 data further support this interpretation as Chinese Crocuta have
 intermediate and indistinguishable complexity values (indicative of hard
 object feeding) between the extant African lion (Panthera leo) and extant
 hyenas (C. crocuta, Hyaena hyaena, and Parahyaena brunnea) – being most
 similar to the omnivorous P. brunnea. The use of dental macrowear to infer
 dietary behavior may also be possible in extinct taxa as evinced by
 dietary correlations between extant African feliforms and dental macrowear
 assignments. Collectively, this multi-proxy analysis suggests that Chinese
 Crocuta may have exhibited dietary behavior distinct from living C.
 crocuta, and assumptions of niche conservatism may mask significant
 dietary variation in species broadly distributed in time and space.
description: Supplemental Material
 DeSantis et al: Assessing niche conservatism using a multi-proxy
 approachSupplemental Materials
 including Supplemental Figure 1 and Supplemental Tables
 1-4.SupplementalMaterialDeSantisetalPaleobiology2016.pdf
DOI: 10.5061/dryad.7c425
title: Data from: Impact of negative frequency-dependent selection on mating pattern and genetic structure: a comparative analysis of the S-locus and nuclear SSR loci in Prunus lannesiana var. speciosa

description: Mating processes of local demes and spatial genetic structure of island
 populations at the self-incompatibility (S-) locus under negative
 frequency-dependent selection (NFDS) were evaluated in Prunus lannesiana
 var. speciosa in comparison with nuclear simple sequence repeat (SSR) loci
 that seemed to be evolutionarily neutral. Our observations of local mating
 patterns indicated that male-female pair fecundity was influenced by not
 only self-incompatibility, but also various factors such as kinship,
 pollen production and flowering synchrony. In spite of the mating bias
 caused by these factors, the NFDS effect on changes in allele frequencies
 from potential mates to mating pollen was detected at the S-locus but not
 at the SSR loci although the changes from adult to juvenile cohorts were
 not apparent at any loci. Genetic differentiation and
 isolation-by-distance over various spatial scales were smaller at the
 S-locus than at the SSR loci, as expected under the NFDS. All ele sharing
 distributions among the populations also had a unimodal pattern at the
 S-locus, indicating the NFDS effect except for alleles unique to
 individual populations probably due to isolation among islands, although
 this pattern was not exhibited by the SSR loci. Our results suggest that
 the NFDS at the S-locus has an impact on both the mating patterns and the
 genetic structure in the P. lannesiana populations studied.
description: Prunus lannesiana var.
 speciosa data2cohorts_data.xls
 ...Genotype data in the GenAlEx format (for 2 cohorts data). |
 8poplations_data.xls ...Genotype data in the GenAlEx format (for 8
 populations data). | 3subpopulations_data.xls ...Genotype data in the
 GenAlEx format (for 3 subpopulations data). | PlotA_adults_seeds.csv
 ...Genotype data of parentage analysis in the Cervus format (for plot A).
 | PlotB_adults_seeds.csv ...Genotype data of parentage analysis in the
 Cervus format (for plot B). | plotA_2001.xls ...Data of various factors on
 mating success (plot A in 2001). | plotA_2002.xls ...Data of various
 factors on mating success (plot A in 2002). | plotB_2001.xls ...Data of
 various factors on mating success (plot B in 2001). | plotB_2002.xls
 ...Data of various factors on mating success (plot B in 2002). |
 plotA_sgs.txt ...SPAGeDi formatted data for spatial genetic structure
 analysis (for plot A). | plotB_sgs.txt ...SPAGeDi formatted data for
 spatial genetic structure analysis (for plot B).Prunus_lannesiana_var_speciosa_data.zip
DOI: 10.6084/m9.figshare.31153552.v1
title: <b>Brand Narrative Drift of 2022-2024 Monthly Corpus Data: Based on LDA-BERTopic and Cognitive Drift Index (CDI)</b>

description: <b>Brand Narrative Drift of 2022-2024 Monthly Corpus Data: Based on LDA-BERTopic and Cognitive Drift Index (CDI)</b>
DOI: 10.6084/m9.figshare.31153552
title: <b>Brand Narrative Drift of 2022-2024 Monthly Corpus Data: Based on LDA-BERTopic and Cognitive Drift Index (CDI)</b>

description: <b>Brand Narrative Drift of 2022-2024 Monthly Corpus Data: Based on LDA-BERTopic and Cognitive Drift Index (CDI)</b>
DOI: 10.5061/dryad.nj344m5
title: Data from: Isolation by environment in the highly mobile olive ridley turtle (Lepidochelys olivacea) in the eastern Pacific

description: Spatial and temporal scales at which processes modulate genetic diversity
 over the landscape are usually overlooked, impacting the design of
 conservation management practices for widely distributed species. We
 examine processes shaping population divergence in highly mobile species
 by re-assessing the case of panmixia in the iconic olive ridley turtle
 from the eastern Pacific. We implemented a biophysical model of
 connectivity and a seascape genetic analysis based on nuclear DNA
 variation of 634 samples collected from 27 nesting areas. Two genetically
 distinct populations largely isolated during reproductive migrations and
 mating were detected, each composed of multiple nesting sites linked by
 high connectivity. This pattern was strongly associated with a steep
 environmental gradient and also influenced by ocean currents. These
 findings relate to meso-scales features of a dynamic oceanographic
 interface in the eastern tropical Pacific (ETP) region, a scenario that
 possibly provides different cost-benefit solutions and selective pressures
 for sea turtles during both the mating and migration periods. We reject
 panmixia and propose a new paradigm for olive ridley turtles where
 reproductive isolation due to assortative mating is linked to its
 environment. Our study demonstrates the relevance of integrative
 approaches for assessing the role of environmental gradients and
 oceanographic currents as drivers of genetic differentiation in widely
 distributed marine species. This is relevant for the conservation
 management of species of highly mobile behaviour; and assists the planning
 and development of large-scale conservation strategies for the threatened
 olive ridley turtles in the ETP.
description: Rodriguez-Zarate et
 al_EnvironmentalDistanceMMatricesThe file contains
 environmental distance matrices for four variables considered in the
 study.Rodriguez-Zarate et
 al_Genetic DataFiles indicate
 microsatellite genetic data from 10 Loci for all sampled nesting
 sites.
DOI: 10.5061/dryad.1pj2600
title: Data from: Dietary specialization is linked to reduced species durations in North American fossil canids

description: How traits influence species persistence is a fundamental question in
 ecology, evolution, and paleontology. We test the relationship between
 dietary traits and both species duration and locality coverage over 40
 million years in North American canids, a clade with considerable
 ecomorphological disparity and a dense fossil record. Because
 ecomorphological generalization--broad resource use--may enable species to
 withstand disturbance, we predicted that canids of average size and
 mesocarnivory would exhibit longer durations and wider distributions than
 specialized larger or smaller species. Second, because locality coverage
 might reflect dispersal ability and/or survivability in a range of
 habitats, we predicted that high coverage would correspond with longer
 durations. We find a non-linear relationship between species duration and
 degree of carnivory: species at either end of the carnivory spectrum tend
 to have shorter durations than mesocarnivores. Locality coverage shows no
 relationship with size, diet, nor duration. To test whether generalization
 (medium size, mesocarnivory) corresponds to an adaptive optimum, we fit
 trait evolution models to previously generated canid phylogenies. Our
 analyses identify no single optimum in size or diet. Instead, the primary
 model of size evolution is a classic Cope's Rule increase over time,
 while dietary evolution does not conform to a single model.
description: Extinct canid
 datasetTaxonomic, trait,
 duration, and locality coverage data for 131 species of North American
 fossil canids.mbalisi_fossilData.R1_.csvSlater (2015) canid tree - prunedTopology of canid tree from Slater (2015), pruned to the species included in Balisi et al.mbalisi_prunedCanidTree.nexStatistical analysesScripts for principal component analysis, linear regressions, quantile regressions, and the associated plots.mbalisi_statistics.RCode for Figure S3Figure S3 is a time-scaled canid tree using the pruned Slater (2015) phylogeny, with black bars representing stratigraphic ranges as calculated using PyRate.mbalisi_FigS3.RResults of principal component analysisOnly PC1 is needed for trait analysis.mbalisi_massPCsubfam_fossilsOnly.csvTrait evolution model scriptsR code for trait evolution model-fitting.mbalisi_phylogenetics.R
DOI: 10.5061/dryad.qb7vr
title: Data from: Pathology and epidemiology of ceruminous gland tumors among endangered Santa Catalina Island foxes (Urocyon littoralis catalinae) in the Channel Islands, USA

description: In this study, we examined the prevalence, pathology, and epidemiology of
 tumors in free-ranging island foxes occurring on three islands in the
 California Channel Islands, USA. We found a remarkably high prevalence of
 ceruminous gland tumors in endangered foxes (Urocyon littoralis catalinae)
 occurring on Santa Catalina Island (SCA) - 48.9% of the dead foxes
 examined from 2001-2008 had tumors in their ears, and tumors were found in
 52.2% of randomly-selected mature (≥ 4 years) foxes captured in 2007-2008,
 representing one of the highest prevalences of tumors ever documented in a
 wildlife population. In contrast, no tumors were detected in foxes from
 San Nicolas Island or San Clemente Island, although ear mites (Otodectes
 cynotis), a predisposing factor for ceruminous gland tumors in dogs and
 cats, were highly prevalent on all three islands. On SCA, otitis externa
 secondary to ear mite infection was highly correlated with ceruminous
 gland hyperplasia (CGH), and tumors were significantly associated with the
 severity of CGH, ceruminous gland dysplasia, and age group (older foxes).
 We propose a conceptual model for the formation of ceruminous gland tumors
 in foxes on SCA that is based on persistent, ubiquitous infection with ear
 mites, and an innate, over exuberant inflammatory and hyperplastic
 response of SCA foxes to these mites. Foxes on SCA are now
 opportunistically treated with acaricides in an attempt to reduce mite
 infections and the morbidity and mortality associated with this highly
 prevalent tumor.
description: Island fox random exam
 databaseData collected during
 random exams of foxes on Santa Catalina island, San Clemente Island, and
 San Nicolas Island 2007-2008Exam database for Dryad
 11-11-15.xlsxData collected from
 Channel Island foxes for ear tumor risk factor analysisData collected from
 examinations, biopsies, ear cultures, and other for analysis regarding
 risk factors relating to ear tumor development in Channel Island foxes in
 southern California.Risk factor database for Dryad
 11-11-15.xlsx
DOI: 10.5061/dryad.67bc0
title: Data from: Single‐cell profiling screen identifies microtubule‐dependent reduction of variability in signaling

description: Populations of isogenic cells often respond coherently to signals, despite
 differences in protein abundance and cell state. Previously, we uncovered
 processes in the Saccharomyces cerevisiae pheromone response system (PRS)
 that reduced cell‐to‐cell variability in signal strength and cellular
 response. Here, we screened 1,141 non‐essential genes to identify 50
 “variability genes”. Most had distinct, separable effects on strength and
 variability of the PRS, defining these quantities as genetically distinct
 “axes” of system behavior. Three genes affected cytoplasmic microtubule
 function: BIM1, GIM2, and GIM4. We used genetic and chemical perturbations
 to show that, without microtubules, PRS output is reduced but variability
 is unaffected, while, when microtubules are present but their function is
 perturbed, output is sometimes lowered, but its variability is always
 high. The increased variability caused by microtubule perturbations
 required the PRS MAP kinase Fus3 and a process at or upstream of Ste5, the
 membrane‐localized scaffold to which Fus3 must bind to be activated.
 Visualization of Ste5 localization dynamics demonstrated that perturbing
 microtubules destabilized Ste5 at the membrane signaling site. The fact
 that such microtubule perturbations cause aberrant fate and polarity
 decisions in mammals suggests that microtubule‐dependent signal
 stabilization might also operate throughout metazoans.
description: Pesce Variation
 Regulation ScreenThis tab-deliited text
 file is a list of 1141 S. cerevisiae strains, each with a single deletion
 of a non-essential gene. For each strain, identified by its deleted gene,
 we recorded flow cytometric measurements from two fluorescent reporters,
 one driven by the constitutive ACT1 promoter, the other by the
 pheromone-inducible PRM1 promoter. We combined these measurements to
 obtain the average strength of signaling (up to and including
 transcription initiation) and the variation in that signaling strength. We
 made these measurements at a weak (0.6 nM) and a saturating (20 nM)
 pheromone dose.screenDataSubmit.txt
DOI: 10.5061/dryad.27kk4
title: Data from: Selection on incremental variation of eye size in a wild population of Daphnia

description: Several studies of eye morphology have analyzed macroevolutionary patterns
 in the diversity of eyes, and though these studies are often linked to
 environment or behavior, they provide only indirect evidence of selection.
 Specific data to show the microevolutionary potential for adaptation by
 natural selection in eye morphology has been lacking. We document
 directional selection on eye size, an important determinant of visual
 capabilities, in a wild population of the freshwater microcrustacean
 Daphnia. We show that even slight changes in eye size may have major
 consequences for fitness. An increase of eye diameter of 19.9 μm –
 slightly more than one standard deviation – is associated with an increase
 in clutch size of one egg, or an increase of nearly 20% of the mean clutch
 size. Furthermore, relative eye size is genetically variable, and thus
 could evolve in response to the observed selective pressure. We conclude
 that selection on incremental variation in eye size may have led to
 differences observed on broader taxonomic scales.
description: Eye diameter, body
 length, and clutch size measurements for D. obtusa isolated from Knobby
 Knees Pond, Congaree National Park, South CarolinaEye diameter (um), body
 length (um), and clutch size (number of eggs) measurements on a wild
 population of Daphnia obtusa from Knobby Knees (KNB) Pond, Congaree
 National Park, South Carolina. Each data row corresponds to the associated
 measures for a single D. obtusa from KNB Pond. Clutch size was measured
 from living individuals within 36 hours of capture. Animals were
 immediately preserved in ethanol and marked following clutch counts. Eye
 diameter and body length were then measured on preserved
 individuals.Knobby Knees
 data.xlsxEye diameter and body
 length measures on lab-reared Daphnia obtusa for broad-sense heritability
 estimationEye diameter (um) and
 body length (um) measurements from a common garden experiment on a number
 of clones of Daphnia obtusa isolated from ponds in Congaree National Park,
 South Carolina. Each row corresponds to associated identifiers and
 measurements for a single individual Daphnia. Pond of origin indicates the
 name of the pond that the original clone was isolated from. D. obtusa
 clone refers to the name of the clone (pond abbreviation and a number for
 specific identity). Daphnia size class was determined as small (≤900 μm),
 medium (901 μm -1399 μm), and adult (≥1400 μm). These size classes reflect
 ontogenetic growth from juveniles to adults.D_obtusa_heritability-data.xlsx
DOI: 10.5061/dryad.fn74266
title: Data from: Effectiveness of physically ablative and pharmacological treatments for anal condyloma in HIV-infected men

description: There is limited information on the effectiveness of available treatments
 for anal condyloma acuminata in HIV-1-infected men. AIM: To provide data
 on the effectiveness of electrosurgical excision, infrared coagulation and
 pharmacological (imiquimod) treatments for anal condyloma acuminata
 (peri-anal and/or intra-anal) in HIV-1-infected men based on authors'
 practice. METHODS: Single-center, retrospective descriptive analysis of
 HIV-1-infected men, 18 years or older treated for anal condyloma
 acuminata. Standard treatments were offered: electrosurgery excision,
 infrared coagulation and topical imiquimod. Effectiveness was evaluated by
 the recurrence rate at 1 year after treatment. Recurrence was defined as
 any anal condyloma acuminata diagnosed after 3 months of condyloma-free
 survival post-treatment. Anal cytology and human-papillomavirus-infection
 (HPV) was assessed. RESULTS: Between January 2005 and May 2009, 101 men
 were treated for anal condyloma acuminata: 65 (64%) with electrosurgery,
 27 (27%) with infrared coagulation and 9 (9%) with imiquimod. At 1 year
 after treatment, the cumulative recurrence rate was 8% (4/65, 95%CI:
 2-15%) with electrosurgery excision, 11% (3/27, 95%CI: 4-28%) with
 infrared coagulation and 11% (1/9, 95%CI: 2-44%) with imiquimod treatment.
 No predictive factors were associated with recurrence. Anal HPV-6 or
 HPV-11 was detectable in 98 (97%) patients and all had high-risk HPV
 genotypes, and 89 (88%) patients had abnormal anal canal cytology.
 Limitations: this was a retrospective descriptive analysis; limited to a
 single center; it cannot know if the recurrence is related to new
 infection. CONCLUSION. Recurrence of anal condyloma after any treatment
 was common. Abnormal anal cytology and high-risk HPV-infection were highly
 prevalent in this population, therefore at high-risk of anal cancer, and
 warrants careful follow-up.
description: Anal
 condylomas_0417_dryad_clean 2018 06 26
DOI: 10.5061/dryad.p07r1
title: Data from: Assembly mechanisms determining high species turnover in aquatic communities over regional and continental scales

description: Niche and neutral processes drive community assembly and metacommunity
 dynamics, but their relative importance might vary with the spatial scale.
 The contribution of niche processes is generally expected to increase with
 increasing spatial extent at a higher rate than that of neutral processes.
 However, the extent to what community composition is limited by dispersal
 (usually considered a neutral process) over increasing spatial scales
 might depend on the dispersal capacity of composing species. To
 investigate the mechanisms underlying the distribution and diversity of
 species known to have great powers of dispersal (hundreds of kilometres),
 we analysed the relative importance of niche processes and dispersal
 limitation in determining beta-diversity patterns of aquatic plants and
 cladocerans over regional (up to 300 km) and continental (up to 3300 km)
 scales. Both taxonomic groups were surveyed in five different European
 regions and presented extremely high levels of beta-diversity, both within
 and among regions. High beta-diversity was primarily explained by species
 replacement (turnover) rather than differences in species richness (i.e.
 nestedness). Abiotic and biotic variables were the main drivers of
 community composition. Within some regions, small-scale connectivity and
 the spatial configuration of sampled communities explained a significant,
 though smaller, fraction of compositional variation, particularly for
 aquatic plants. At continental scale (among regions), a significant
 fraction of compositional variation was explained by a combination of
 spatial effects (exclusive contribution of regions) and
 regionally-structured environmental variables. Our results suggest that,
 although dispersal limitation might affect species composition in some
 regions, aquatic plant and cladoceran communities are not generally
 limited by dispersal at the regional scale (up to 300 km). Species sorting
 mediated by environmental variation might explain the high species
 turnover of aquatic plants and cladocerans at regional scale, while
 biogeographic processes enhanced by dispersal limitation among regions
 might determine the composition of regional biotas.
description: All data
 filesRead the ReadMe
 file.Data.zip