cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f69mg
title: Data from: A model of urban scaling laws based on distance dependent interactions

description: Socio-economic related properties of a city grow faster than a linear
 relationship with the population, in a log–log plot, the so-called
 superlinear scaling. Conversely, the larger a city, the more efficient it
 is in the use of its infrastructure, leading to a sublinear scaling on
 these variables. In this work, we addressed a simple explanation for those
 scaling laws in cities based on the interaction range between the citizens
 and on the fractal properties of the cities. To this purpose, we
 introduced a measure of social potential which captured the influence of
 social interaction on the economic performance and the benefits of
 amenities in the case of infrastructure offered by the city. We assumed
 that the population density depends on the fractal dimension and on the
 distance-dependent interactions between individuals. The model suggests
 that when the city interacts as a whole, and not just as a set of isolated
 parts, there is improvement of the socio-economic indicators. Moreover,
 the bigger the interaction range between citizens and amenities, the
 bigger the improvement of the socio-economic indicators and the lower the
 infrastructure costs of the city. We addressed how public policies could
 take advantage of these properties to improve cities development,
 minimizing negative effects. Furthermore, the model predicts that the sum
 of the scaling exponents of social-economic and infrastructure variables
 are 2, as observed in the literature. Simulations with an agent-based
 model are confronted with the theoretical approach and they are compatible
 with the empirical evidences.
description: two tables of the two
 histogramstwo tables of
 frequencies for the histograms of the papertables.zip
DOI: 10.5061/dryad.8g8r675
title: Data from: Use of hidden Markov capture-recapture models to estimate abundance in presence of uncertainty: application to estimating the prevalence of hybrids in animal populations

description: Estimating the relative abundance (prevalence) of different population
 segments is a key step in addressing fundamental research questions in
 ecology, evolution, and conservation. The raw percentage of individuals in
 the sample (naive prevalence) is generally used for this purpose, but it
 is likely to be subject to two main sources of bias. First, the
 detectability of individuals is ignored; second, classification errors may
 occur due to some inherent limits of the diagnostic methods. We developed
 a hidden Markov (also known as multievent) capture–recapture model to
 estimate prevalence in free‐ranging populations accounting for imperfect
 detectability and uncertainty in individual's classification. We
 carried out a simulation study to compare naive and model‐based estimates
 of prevalence and assess the performance of our model under different
 sampling scenarios. We then illustrate our method with a real‐world case
 study of estimating the prevalence of wolf (Canis lupus) and dog (Canis
 lupus familiaris) hybrids in a wolf population in northern Italy. We
 showed that the prevalence of hybrids could be estimated while accounting
 for both detectability and classification uncertainty. Model‐based
 prevalence consistently had better performance than naive prevalence in
 the presence of differential detectability and assignment probability and
 was unbiased for sampling scenarios with high detectability. We also
 showed that ignoring detectability and uncertainty in the wolf case study
 would lead to underestimating the prevalence of hybrids. Our results
 underline the importance of a model‐based approach to obtain unbiased
 estimates of prevalence of different population segments. Our model can be
 adapted to any taxa, and it can be used to estimate absolute abundance and
 prevalence in a variety of cases involving imperfect detection and
 uncertainty in classification of individuals (e.g., sex ratio, proportion
 of breeders, and prevalence of infected individuals).
description: ECE-2018-09-01063-CAPTUREMATRIXThe data are a capture matrix with five columns (2 months capture occasions) and 39 rows (individuals). Each row is the capture history of one individual. The numbers code the events: 0=non-detected, 1=detected and assigned to state "Wolf", 2=detected and assigned to state "Hybrid", 3=detected and not assigned to any state ("Uncertain"). The data are coded as if the assignment is performed only once (on first detection) and never again.ECE-2018-09-01063-DATA.txt
DOI: 10.5061/dryad.gf6tq
title: Data from: The nature of nurture in a wild mammal’s fitness

description: Genetic variation in fitness is required for the adaptive evolution of any
 trait but natural selection is thought to erode genetic variance in
 fitness. This paradox has motivated the search for mechanisms that might
 maintain a population's adaptive potential. Mothers make many
 contributions to the attributes of their developing offspring and these
 maternal effects can influence responses to natural selection if maternal
 effects are themselves heritable. Maternal genetic effects (MGEs) on
 fitness might, therefore, represent an underappreciated source of adaptive
 potential in wild populations. Here we used two decades of data from a
 pedigreed wild population of North American red squirrels to show that
 MGEs on offspring fitness increased the population's evolvability by
 over two orders of magnitude relative to expectations from direct genetic
 effects alone. MGEs are predicted to maintain more variation than direct
 genetic effects in the face of selection, but we also found evidence of
 maternal effect trade-offs. Mothers that raised high-fitness offspring in
 one environment raised low-fitness offspring in another environment. Such
 a fitness trade-off is expected to maintain maternal genetic variation in
 fitness, which provided additional capacity for adaptive evolution beyond
 that provided by direct genetic effects on fitness.
description: year-conecondition-keyTo connect phenotypic data to cone conditions for a specific year.Red Squirrel Pedigree and Phenotype filesData were made available through Dryad as part of McFarlane et al. 2014.
DOI: 10.5281/zenodo.18385936
title: LINF_320010000

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.7577v
title: Data from: Non-consumptive effects of a top-predator decrease the strength of the trophic cascade in a four-level terrestrial food web

description: The fear of predators can strongly impact food web dynamics and ecosystem
 functioning through effects on herbivores morphology, physiology or
 behaviour. While non-consumptive predator effects have been mostly studied
 in three-level food chains, we lack evidence for the propagation of
 non-consumptive indirect effects of apex predators in four level
 food-webs, notably in terrestrial ecosystems. In experimental mesocosms,
 we manipulated a four-level food chain including top-predator cues
 (snakes), mesopredators (lizards), herbivores (crickets), and primary
 producers (plants). The strength of the trophic cascade induced by
 mesopredators through the consumption of herbivores decreased in the
 presence of top-predator cues. Specifically, primary production was higher
 in mesocosms where mesopredators were present relative to mesocosms with
 herbivores only, and this difference was reduced in presence of
 top-predator cues, probably through a trait-mediated effect on lizard
 foraging. Our study demonstrates that non-consumptive effects of predation
 risk can cascade down to affect both herbivores and plants in a four-level
 terrestrial food chain and emphasises the need to quantify the importance
 of such indirect effects in natural communities.
description: donnees_Dryad
DOI: 10.5281/zenodo.18385935
title: LINF_320010000

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.b8f0vg0
title: Data from: Biocontrol: the response of native oystercatchers to a non-native clam invasion

description: Global change, including invasive species introduction, has already had
 observable effects on migrant bird species, from Northern breeding areas
 to wintering grounds. In this study we analyze the response of the
 Eurasian oystercatcher abundance to the density of an invasive clam
 species (Corbicula fluminea) and its potential role as biological control.
 As a case study, the oystercatcher population fluctuations over a 30-year
 time period, coupled with video-recorded estimates of its feeding behavior
 on C. fluminea, and results from an exclosure experiment, were analyzed in
 the NW of the Iberian Peninsula. Results showed that oystercatchers exert
 a top-down control over C. fluminea density. In addition, oystercatchers
 doubled its wintering numbers in a C. fluminea invaded estuary where they
 actively feed upon this invasive clam. Given that, the facilitative
 interaction between the invasive C. fluminea and the migratory Eurasian
 oystercatcher seems to respond to bottom-up forces. Altogether, our
 results suggest that control measures applied to long term biological
 invasions must be carefully analyzed since non-native species may be
 sustaining dependent native communities.
description: Oystercatchers_Ferreira-Rodriguez_Pardo_2018Oystercatchers' population trend in three Galician (NW Iberian Peninsual) estuaries.
DOI: 10.71636/62ec-4b45
title: Relationship between Self-Regulated Learning and Student Satisfaction in a Collaborative Science Communication Task [Dataset]

description: [ES]La influencia del aprendizaje autorregulado sobre el rendimiento académico se ha estudiado desde diferentes perspectivas y contextos. Sin embargo, pocos estudios han abordado su influencia sobre la satisfacción del alumnado en contextos de aprendizaje relacionados con la divulgación científica. Analizamos la influencia del aprendizaje autorregulado (motivación y estrategias de aprendizaje) en la satisfacción de estudiantes universitarios con la preparación de un artículo de divulgación científica en grupo. Participaron 83 estudiantes universitarios que completaron un cuestionario de aprendizaje autorregulado (MSLQ) y dos cuestionarios ad hoc que evaluaban la satisfacción con el trabajo de divulgación (interacción grupo y contenido). Los resultados mostraron niveles altos de satisfacción con la interacción y el contenido del trabajo de divulgación, mostrando valores promedio superiores a ocho sobre diez. Además, respecto a las dimensiones de aprendizaje autorregulado analizadas, se observó que la motivación influyó en la satisfacción con el contenido del trabajo en los estudiantes con un menor uso de estrategias de aprendizaje. Se discuten las implicaciones de los resultados en el contexto educativo.
DOI: 10.5061/dryad.817j8pk
title: Data from: Effects of aphid parasitism on host plant fitness in an aphid-host relationship.

description: Aphids are serious agricultural insect pests which exploit the phloem sap
 of host plants and thus transmit pathogens to their hosts. However, the
 degree to which aphid parsitism affects the fitness of the host plants is
 not well understood. The aphid, Macrosiphoniella yomogicola, parasitizes
 the mugwort Artemisia montana in Japan. During summer most mugworts carry
 aphids, but most aphid colonies die out after the budding of A. montana
 inflorescences in late summer. A few aphid colonies survive to late
 autumn, at which point sexuparae appear to later lay overwintering eggs
 after copulation. The death of the aphid colonies seems to cause by
 biochemical changes in the phloem sap in the host plant coincident with
 the budding of inflorescences. The surviving aphid colonies may suppress
 the budding of inflorescences to allow persistence of their genetic line
 into the following year. Our investigations demonstrate that aphid
 parasitism did not affect host plant growth, but that it did significantly
 decrease the number of inflorescences and the average weight of floral
 buds. Our results indicate that aphid parasitism has a strong negative
 effect on the fitness of host plants. The manner in which the aphids
 suppress floral budding in their hosts is worth examining from the
 perspective of the evolution of aphid-plant interactions.
description: Raw data for
 PONE-D-18-00902 to PLoS OneThe file including all
 the raw data to induce the result of the above article.MyomSurvivalRate.csv
DOI: 10.5061/dryad.mc4s1
title: Data from: Gene expression profiles of alveolar type II cells of chronic obstructive pulmonary disease: a case-control study

description: Objectives: The aim of this study was to identify the gene expression
 pattern specific in alveolar epithelial type II cells (ATII cells)
 isolated from patients with chronic obstructive pulmonary disease (COPD).
 Design: Case control Setting: Two hospitals in Japan Participants: Three
 patients without COPD and three patients with COPD in microarray analyses.
 Five smokers without COPD and nine smokers with COPD in the following
 analyses. Primary and secondary outcome measured: Primary outcome included
 identification of differentially expressed genes and activated or
 inhibited pathways in ATII cells of the patients with COPD, compared to
 those of the patients without COPD, using Affymetrix gene expression
 arrays. Secondary outcome included validation of the results of microarray
 analyses by quantitative reverse transcription-polymerase chain reaction.
 Results: We isolated ATII cells from COPD and non-COPD lungs using
 fluorescence-activated cell sorting. We performed Affymetrix gene
 expression arrays on both types of ATII cells. Gene set enrichment
 analyses revealed that two major gene sets were enriched in ATII cells
 from COPD lungs: interferon-responsive gene sets and gene sets associated
 with cell cycle progression. Gene ontology term enrichment analyses
 indicated that among the interferon-stimulated genes, ATII cells in COPD
 expressed genes such as PSMB8, PSMB9, TAP1 and TAP2 associated with the
 antigen processing and presentation pathway. We validated the results of
 the microarray analyses using quantitative reverse
 transcriptase-polymerase chain reaction. In addition, FACS analysis
 indicated that the percentage of ATII cells to CD45-negative lung cells
 isolated from COPD lungs were significantly increased more than that from
 non-COPD lungs. Conclusions: Our study demonstrated that
 interferon-stimulated genes involved in the antigen processing and
 presentation pathway and genes involved in cell cycle progression were
 enriched in ATII cells of the patients with COPD. These pathways might
 alter phenotypes of ATII cells in COPD lungs.
description: GEO
 GSE29133Link to GEO. Primary
 ATII cells were isolated from lung tissues obtained from thoracic surgery
 using FACS. We profiled the gene expression of ATII cells from three
 non-COPD and three COPD patients. This study was approved by the Ethics
 Committee at Tohoku University School of Medicine and Ishinomaki Red Cross
 Hospital. All subjects gave informed consent.
DOI: 10.5061/dryad.8437
title: Data from: Deep mitochondrial divergence in Baja California populations of an aquilopelagic elasmobranch: the golden cownose ray

description: Assessing the realized effect of dispersal in the genetic makeup of a
 species has significant evolutionary, ecological, and economical
 consequences. Here, we investigate the genetic diversity and population
 differentiation in the aquilopelagic golden cownose ray Rhinoptera
 steindachneri from the Gulf of California (GC) and the Pacific coast of
 Baja California (PCBC) using the mitochondrial NADH2 gene. Low levels of
 genetic diversity were found with only 4 polymerase chain
 reaction-restriction fragment length polymorphism haplotypes among 76
 specimens. Pacific coast organisms were fixed for a unique haplotype not
 shared with rays from the gulf; 92% of GC rays possessed a single NADH2
 haplotype not found in the Pacific. This produced significant
 differentiation between the GC and the PCBC (ΦCT = 0.972, P &lt;
 0.001). A pronounced phylogeographic pattern was found in which GC
 haplotypes were reciprocally monophyletic relative to a very divergent
 Pacific lineage (d = 10%). Our results indicate that despite high
 dispersal potential, GC and PCBC golden cownose ray populations are
 characterized by highly divergent mitochondrial lineages. Although more
 evidence is needed to corroborate the genetic isolation and systematic
 status of PCBC and GC golden cownose rays, our results suggest a possible
 cryptic species in the region.
description: Genbank
 HQ540559DNA sequence of
 mitochondrial NADH2 gene from golden cownose
 rayGenbank
 HQ540560DNA sequence of
 mitochodnial NADH2 gene from golden cownose
 rayGenbank
 HQ540561DNA sequence of
 mitochondrial NADH2 gene from golden cownose
 rayGenbank
 HQ540562DNA sequence of
 mitochondrial NADH2 gene from golden cownose ray
DOI: 10.5061/dryad.8663
title: Data from: The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella

description: BACKGROUND: Publication of the first diatom genome, that of Thalassiosira
 pseudonana, established it as a model species for experimental and genomic
 studies of diatoms. Virtually every ensuing study has treated T.
 pseudonana as a marine diatom, with genomic and experimental data valued
 for their insights into the ecology and evolution of diatoms in the
 world's oceans. RESULTS: The natural distribution of T. pseudonana
 spans both marine and fresh waters, and phylogenetic analyses of
 morphological and molecular datasets show that, 1) T. pseudonana marks an
 early divergence in a major freshwater radiation by diatoms, and 2) as a
 species, T. pseudonana is likely ancestrally freshwater. Marine strains
 therefore represent recent recolonizations of higher salinity habitats. In
 addition, the combination of a relatively nondescript form and a
 convoluted taxonomic history has introduced some confusion about the
 identity of T. pseudonana and, by extension, its phylogeny and ecology. We
 resolve these issues and use phylogenetic criteria to show that T.
 pseudonana is more appropriately classified by its original name,
 Cyclotella nana. Cyclotella contains a mix of marine and freshwater
 species and so more accurately conveys the complexities of the
 phylogenetic and natural histories of T. pseudonana. CONCLUSIONS: The
 multitude of physical barriers that likely must be overcome for diatoms to
 successfully colonize freshwaters suggests that the physiological traits
 of T. pseudonana, and the genes underlying those traits, might differ from
 those of strictly marine diatoms. The freshwater ancestry of T. pseudonana
 might therefore confound generalizations about the physiological and
 metabolic properties of marine diatoms. The freshwater component of T.
 pseudonana's history merits careful consideration in the
 interpretation of experimental data collected for this important model
 species.
description: morphological data
 matrix
DOI: 10.5061/dryad.s0qc1
title: Data from: Phenotypic variability in unicellular organisms: from calcium signaling to social behavior

description: Historically, research has focused on the mean and often neglected the
 variance. However, variability in nature is observable at all scales:
 among cells within an individual, among individuals within a population
 and among populations within a species. A fundamental quest in biology now
 is to find the mechanisms that underlie variability. Here, we investigated
 behavioural variability in a unique unicellular organism, Physarum
 polycephalum. We combined experiments and models to show that variability
 in cell signalling contributes to major differences in behaviour
 underpinning some aspects of social interactions. First, following
 thousands of cells under various contexts, we identified distinct
 behavioural phenotypes: ‘slow–regular–social’, ‘fast–regular–social’ and
 ‘fast–irregular–asocial’. Second, coupling chemical analysis and
 behavioural assays we found that calcium signalling is responsible for
 these behavioural phenotypes. Finally, we show that differences in
 signalling and behaviour led to alternative social strategies. Our results
 have considerable implications for our understanding of the emergence of
 variability in living organisms.
description: Data 2In the data folder the
 reader will find 3 subfolders, one for each experiment described in the
 experiment. In each folder the reader will find the data_file for each
 figure of the manuscript.SupplementaryDataRaw data for Experiment 1 (Exploration experiment) Fig.1
DOI: 10.5061/dryad.668g444
title: Data from: Signatures of hybridization and speciation in genomic patterns of ancestry

description: Genomes sampled from hybrid zones between nascent species provide
 important clues into the speciation process. With advances in genome
 sequencing and single nucleotide polymorphism (SNP) genotyping, it is now
 feasible to measure variation in gene flow with high genomic resolution.
 This progress motivates the development of conceptual and analytical
 frameworks for hybrid zones that complement well-established cline
 approaches. We extend the perspective that genomic distributions of
 ancestry are sensitive indicators of hybridization history. We use
 simulations to examine the behavior of the number of ancestry junctions –
 a simple summary of genomic patterns – in hybrid zones under increasingly
 realistic scenarios. Neutral simulations revealed that ancestry junction
 number is shaped by population structure, migration rate, and population
 size. Modeling multiple genetic architectures of hybrid dysfunction, with
 an emphasis on epistatic hybrid incompatibilities, showed that selection
 reduces junction number near loci that confer reproductive barriers. The
 magnitude of this signature was affected by the form of selection,
 dominance and genomic location (autosome vs. sex chromosome) of
 incompatible loci. Our results suggest that researchers can identify loci
 involved in reproductive isolation by scanning hybrid genomes for local
 reductions in junction number. We outline necessary directions for future
 theory and method development to realize this goal.
description: READMEThis file describes the
 rest of the data for this publication.ScriptsSimulation input files, R scripts and dataframes used for all figures and analyses in this publication.SCRIPTS.tar.gzAsha_G.tar.gzSample unprocessed simulation output from an experiment with a DMI (see README for experiment name key).Benjen_S.tar.gzSample unprocessed neutral simulation output (see README for experiment name key).Howland_R.tar.gzSample unprocessed neutral simulation output (see README for experiment name key).
DOI: 10.5281/zenodo.18326079
title: Temporal Dynamics of EEG Decoding for Continuously Changing Visual Stimuli
DOI: 10.5281/zenodo.18326081
title: Temporal Dynamics of EEG Decoding for Continuously Changing Visual Stimuli