cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rq4s3/2
title: Data for Using Deep Learning to Quantify the Beauty of Outdoor Places

description: In order to predict the scenic ratings of images for which we do not already have crowdsourced data, we use a transfer learning approach to leverage the knowledge of the Places365 CNN [1], which can predict the place category of a scene with a high degree of accuracy. We modify the Places CNN to instead predict the scenicness of an image. We fine-tune our CNN using 80% of the Scenic-Or-Not dataset [2], and use the remaining 20% test set to check our prediction accuracy. We calculate a performance measure using the Kendall Rank correlation between the predicted scenic scores and the actual scenic scores. The Scenic CNN trained using the Visual Geometry Group (VGG) convolutional neural network architecture delivers the best performance with an overall prediction accuracy of 0.658. We predict the scenicness of images of London uploaded to Geograph (http://www.geograph.org.uk/). This dataset includes all the scenic predictions used to create Figure6 "Predictions of scenic ratings for London images". [1] Zhou, B., Khosla, A., Lapedriza, A., Torralba, A., & Oliva, A. 2016 Places: An image database for deep scene understanding. arXiv preprint arXiv:1610.02055.
DOI: 10.5061/dryad.rs8vc/1
title: Ant data for EE paper and Dryad

description: Frequency of occurrence of ant species in pitfall traps at each study site.
DOI: 10.5061/dryad.s5d9q/4
title: Copepod Opsin Phylogeny Newick Tree file

description: RAxML phylogeny produced from alignment as newick tree file with branch lengths.
DOI: 10.5061/dryad.s5d9q/5
title: Copepod_opsins_seq_database

description: Database providing species information and accession numbers for each sequence ID used in the alignment.
DOI: 10.5061/dryad.tv5mb/1
title: Data and Scripts

description: Raw data and scripts required to reproduce results and analyses.
DOI: 10.5061/dryad.2s5t6/1
title: Raw capture database_PLP vs. ULP_dryad

description: This database includes the abundance and biomass of individual insects captured in oil-filled traps that vary in the degree of polarized vs. unpolarized light associated with them.
DOI: 10.5061/dryad.34k42.2
title: Data from: Age-graded dominance hierarchies and social tolerance in packs of free-ranging dogs
DOI: 10.5061/dryad.34k42.2/1.2
title: 1.Total_Number_of_Submissive_interactions_in_dog_packs

description: This file contains six tables. Each table is a squared matrix reporting the total number of submissive gestures exchanged among dogs belonging to the same pack. So, each table corresponds to a different dog pack. Performers of submissive gestures are reported on the vertical axis on the left side of each table, in which each individual dog is identified using a 2-3 letters code. Recipients of submissive gestures are reported on the upper horizontal axis of each table, and again each individual dog is identified using a 2-3 letter code. Note that the data reported for the Curva pack are not statistically independent from those reported for the Fused pack, since the latter originated from the fusion of the Curva pack with another one and the data collected before and after the fusion event were combined (see Bonanni et al. 2017, Behav Ecol, for additional explanations). In the original paper, the data reported in these tables were used to calculate the statistical parameters reported in Table 3, i.e. hierarchy linearity, directional consistency of submissive behaviour, hierarchy steepness, as well as percentage of unknown, 1-way, 2-ways, and tied dyadic relationships. Moreover, these data were also used to arrange pack members in the rank order that was most consistent with a linear hierachy.
DOI: 10.5061/dryad.34k42.2/2.2
title: 2.Gender_Age_DominanceRank_of_Individual_Dogs

description: This file contains data concerning gender, age and dominance rank of all individual dogs studied. Note that “age” is reported as “age class”, i.e. individual dogs of each pack were assigned to age classes that were ranked from the youngest to the oldest one, based on their actual or estimated year of birth (which is also reported in the table). So, “age class” does not express the actual age of dogs in years. Note that empty cells refer to missing values, i.e. dogs whose ages could not be estimated relative to that of other dogs. Dominance rank was standardized by distributing ranks evenly between the highest (+1) and the lowest (-1), with the median rank being scored as 0, to allow comparison across packs. In the original paper these data were used to: 1) assess the correlation between dominance rank and age for each pack separately; 2) assess the effect of gender on dominance rank, as well as the effect of gender on age.
DOI: 10.5061/dryad.34k42.2/3.2
title: 3.Gender_DominanceRank_Age_Body_Size_of_Individual_Dogs

description: This files contains data concerning gender, dominance rank, age and body size for some of the dogs studied. In particular, body measurements were collected for members of two dog packs, one studied during the period 2005-2006 (most behaviorual data analyses concerning this group were published by Cafazzo et al. 2010, Behav Ecol 21, 443-455), and another one studied during 2007-2008 (most behavioural data analyses concerning this one are included in Bonanni et al. 2017). As said above, the variable “age class” does not express the actual age of dogs in years, but rather it ranks pack members from the youngest (lowest rank) to the oldest one (highest rank). All body measurements are espressed in cm. Head size was obtained by summing up three distances: nose-occipital bone, temporal-temporal, mandible-forehead. Empty cells refer to missing values. In the original paper by Bonanni et al. (2017), these data were used to: 1) assess the correlation between standardized dominance rank and body measurements (separately for each pack); 2) assess the partial correlation between dominance  rank and age, after controlling for body size (it was feasible only for the Corridoio pack); 3) assess the partial correlation between dominance rank and body measurements after controlling for age (it was feasible only for the Corridoio pack; 4) assess the effect of gender on the body measurements (all measured individuals taken together). Note that one female dog was a member of both packs at different times, and her body measurements were used in the statistical tests concerning both packs since she was already fully adult/grown during the study period 2005-2006.
DOI: 10.5061/dryad.34k42.2/4.2
title: 4.Total_Number_of_Affiliative_and_Agonistic_Submissive_interactions_in_dog_packs

description: This file contains ten tables. Each table is a squared matrix reporting the total number of affiliative or agonistic submissive gestures exchanged among dogs belonging to the same pack (see Bonanni et al. 2017, Behav Ecol, for a definition of both types of submission). So, there are two tables for each dog pack, one reporting the outcomes of affiliative submissive gestures and the other one reporting the outcomes of agonistic submissive gestures. Performers of affiliative/agonistic submissive gestures are reported on the vertical axis on the left side of each table, in which each individual dog is identified using a 2-3 letters code. Recipients of affiliative/agonistic submissive gestures are reported on the upper horizontal axis of each table, and again each individual dog is identified using a 2-3 letter code. Note that the data reported for the Curva pack are not statistically independent from those reported for the Fused pack, since the latter originated from the fusion of the Curva pack with another one and the data collected before and after the fusion event were combined (see Bonanni et al. 2017, Behav Ecol, for additional explanations). In the original paper, the data reported in these tables were used to calculate the directional consistency of affiliative and agonistic submissive gestures separately, and mostly to calculate the correlation between matrices of affiliative submissions and those of agonistic submissions for each pack separately.
DOI: 10.5061/dryad.34k42.2/5.2
title: 5.Measures_of_social_tolerance_in_dog_packs

description: This file contains a table reporting several measures of social tolerance (and other related variables) in domestic dog packs, comprising both the packs presented in the paper by Bonanni et al. (2017), and others for which data were published in other papers (data source is also reported). Measures of social tolerance comprised: directional consistency index of total submissive behaviour, hierarchy steepness (calculated from matrices reporting total submissive behavior, and based on Dij, i.e. dyadic dominance indexes corrected by chance), and proportion of bites in relation to the total number of agonistic interactions (obtained by summing up aggressive and dominance interactions). Related variables comprised: percentage of dyadic unknown relationships in matrices reporting total submissive behaviour, number of pack members, and proportion of pack members who were either spayed or castrated. In the original paper, these data were used to assess Spearman correlation between measures of social tolerance and related variables.
DOI: 10.5061/dryad.34k42.2/6.2
title: 6.Measures_of_social_tolerance_in_free-ranging_dogs_and_wolves

description: This file contains a table reporting measures of social tolerance (and some related variables) in packs of free-ranging dogs and wolves. The latter comprises both packs presented in the paper by Bonanni et al. 2017, as well as packs studied in other papers (data source is also reported in the table). Measures of social tolerance comprised 1) directional consistency indexes of total submissive behaviour and 2) hierarchy steepness (calculated from matrices reporting total submissive behavior, and based on Dij, i.e. dyadic dominance indexes corrected by chance). The table also reports the number of pack members, and the percentage of unknown dyadic relationships in matrices reporting total submissive behaviour, i.e. the same matrices used to calculate measures of social tolerance. In the original paper, these data were used to compare the degree of social tolerance displayed by dogs with that displayed by wolves.
DOI: 10.5061/dryad.575md/2
title: MLM_GLM_FortScan

description: Results from G. fortis/G.scandens GLM and MLM contrasts, including ensembl and GO analysis
DOI: 10.5061/dryad.575md/3
title: MLM_GLM_FuligMag

description: Results from G. fuliginosa/G. magnirostris GLM and MLM contrasts, including ensembl and GO analysis
DOI: 10.5061/dryad.575md/4
title: MLM_GLM_FortMag

description: Results from G. fortis/G. magnirostris GLM and MLM contrasts, including ensembl and GO analysis
DOI: 10.5061/dryad.575md/5
title: MLM_GLM_FortFulig

description: Results from G. fortis/G. fuliginosa GLM and MLM contrasts, including ensembl and GO analysis
DOI: 10.5061/dryad.575md/6
title: 83Hapmap_simple2_filtered

description: Hapmap file of all SNPs for the four focal Geospiza species. Produced through Tassel pipeline
DOI: 10.5061/dryad.5cp90/2
title: Figure 7 - Source Data

description: Scanning electron micrographs
DOI: 10.5061/dryad.5cp90/6
title: Figure 6 - Source Data

description: Scanning electron micrographs
DOI: 10.5061/dryad.61cf7/1
title: Adult Survival

description: Data used to estimate adult survival
DOI: 10.5061/dryad.61cf7/2
title: Transition
DOI: 10.5061/dryad.61cf7/3
title: Inheritance
DOI: 10.5061/dryad.7248c/10
title: Trade-off_sperm longevity_velocity

description: Data on velocity, swimming distance and longevity for individual sperm within an ejaculate of several males.
DOI: 10.5061/dryad.7248c/5
title: F1_survival_fertilisation_Exp1B

description: Data on fertilisation success and embryo survival in Experiment 1B.
DOI: 10.5061/dryad.7248c/6
title: F1_survival_fertilsation_Exp1A

description: Data on fertilisation success and embryo survival in Experiment 1A.
DOI: 10.5061/dryad.7248c/7
title: F2_reprod.succ

description: Data on fertilisation success, number of eggs and number of abnormal embryos in F2.
DOI: 10.5061/dryad.7248c/8
title: post-ejac_ageing

description: Data on embryo survival in the post-ejaculation ageing experiment.
DOI: 10.5061/dryad.7248c/9
title: pre-ejac_agein

description: Data on embryo survival in the pre-ejaculation ageing experiment.
DOI: 10.5061/dryad.766cp.1/10.1
title: Appendix 10 Diatoms-user-results

description: Online Appendix 10.  Diatom user scores
DOI: 10.5061/dryad.766cp.1/11.1
title: Appendix 11 Lilies-character-taxon-results

description: Online Appendix 11.  Lilies character scores.
DOI: 10.5061/dryad.766cp.1/12.1
title: Appendix 12 Lilies-user-results

description: Online Appendix 12.  Lilies user scores.
DOI: 10.5061/dryad.766cp.1/13.1
title: Appendix 13 Marine-Shrimp-character-taxon-results

description: Online Appendix 13.  Marine shrimp character scores.
DOI: 10.5061/dryad.766cp.1/14.1
title: Appendix 14 Marine-Shrimp-user-results

description: Online Appendix 14.  Marine shrimp user scores.
DOI: 10.5061/dryad.766cp.1/6.1
title: Appendix 6 Bats-users-results

description: Online Appendix 6.  Bats user scores.
DOI: 10.5061/dryad.766cp.1/7.1
title: Appendix 7 Catfish-character-taxon-results

description: Online Appendix 7.  Catfish character scores.
DOI: 10.5061/dryad.766cp.1/8.1
title: Appendix 8 Catfish-user-results

description: Online Appendix 8.  Catfish user scores.
DOI: 10.5061/dryad.766cp.1/9.1
title: Appendix 9 Diatoms-character-taxon-results

description: Online Appendix 9.  Diatom character scores
DOI: 10.5061/dryad.79t4b/1
title: Pado_Primercomb1_rawdata

description: Raw (unfiltered) 454 amplicon sequence data for house sparrows using primer combination 1. Demultiplexed using the software jMHC (2011).
DOI: 10.5061/dryad.79t4b/2
title: Pahi_Primercomb1_rawdata

description: Raw (unfiltered) 454 amplicon sequence data for Spanish sparrow using primer combination 1. Demultiplexed using the software jMHC (2011).
DOI: 10.5061/dryad.7v378/1
title: Data from Carbon debt of Conservation Reserve Program (CRP) grasslands converted to bioenergy production. Gelfand et al., (2011)

description: Data collected from four fields during year 2009, using eddy-covariance, static chambers methods, and measurements of management field activity. The data was used for calculations presented in the Gelfand et al., (2011).
DOI: 10.5061/dryad.fn02v/1
title: Wambiana Reptile Community

description: The abundance of reptile species and micro-habitat measures at the Wambiana Grazing Trial. Data comes from biodiversity surveys conducted in April 2014, October 2014, April 2015 and October 2015.
DOI: 10.5061/dryad.kn568/3
title: 140109_I1135_FCC2U5MACXX_L6_PJM_1_1.fq.gz

description: Illumina forward reads, lane 1
DOI: 10.5061/dryad.kn568/4
title: 140109_I1135_FCC2U5MACXX_L6_PJM_1_2.fq.gz

description: Illumina reverse reads, lane 1
DOI: 10.5061/dryad.kn568/5
title: 140114_I456_FCC3JBKACXX_L1_PJM_2_F_1.fq.gz

description: llumina forward reads, lane 2
DOI: 10.5061/dryad.kn568/6
title: 140114_I456_FCC3JBKACXX_L1_PJM_2_F_2.fq.gz

description: Illumina reverse reads, lane 2
DOI: 10.5061/dryad.mq4p7/5
title: Pairwise genetic distance matrix of Bothrops atrox

description: Genetic distance was estimated among individuals, based on the Ritland relatedness index.
DOI: 10.5061/dryad.mq4p7/6
title: Pairwise genetic distance matrix of Corallus hortulanus

description: Genetic distance was estimated among individuals, based on the Ritland relatedness index.
DOI: 10.5061/dryad.mq4p7/7
title: Pairwise genetic distance matrix of Leptodeira annulata annulata

description: Genetic distance was estimated among individuals, based on the Ritland relatedness index.
DOI: 10.5061/dryad.mq4p7/8
title: Pairwise genetic distance matrix of Philodryas georgeboulengeri

description: Genetic distance was estimated among individuals, based on the Ritland relatedness index.
DOI: 10.5061/dryad.mq4p7/9
title: Geographic distance among samples of Bothrops atrox

description: Log-geographic distance was calculated using Euclidean distances based on geographic coordinates.
DOI: 10.5061/dryad.ns5qs/25
title: Figure 4J

description: Data for Figure 4J in Excel file.Membrane β-Arrestin1:ARHGAP10 binding ADU in PTEN-/-HCT116 cells. Experiments in triplicate
DOI: 10.5061/dryad.ns5qs/26
title: Figure 5B

description: Data for Figure 5B in Excel file. Membrane β-Arrestin1 intensity (AI) in Caco-2 ShPTEN glands after transfection. Intensity assessed in 10 glands for each replicate (n=3) for each transfection.
DOI: 10.5061/dryad.ns5qs/27
title: Figure 5D

description: Data for Figure 5D in Excel file. Membrane ARHGAP10 intensity (AI) in Caco-2 ShPTEN glands after transfection. Intensity assessed in 10 glands for each replicate (n=3) for each transfection.
DOI: 10.5061/dryad.ns5qs/28
title: FIGURE 5F

description: Data for Figure 5F in Excel file. Spindle angle in Caco-2 ShPTEN glands after transfection with EV or C2 or MCBR3 constructs. Spinlde angles of 15 mitotic figures per transfection.
DOI: 10.5061/dryad.ns5qs/29
title: Figure 5 Supplement 2

description: Data for Figure 5 Supplement 2 in Excel file. Caco-2 ShPTEN glands with single central lumens. Lumens counted in 50 glands and edpressed as a percentage
DOI: 10.5061/dryad.ns5qs/30
title: Figure 6B

description: Data for Figure 6B in Excel file. β-Arrestin1:ARHGAP10 binding ADU in Caco-2 cells after treatment. Experiments in triplicate.
DOI: 10.5061/dryad.ns5qs/31
title: Figure 6D

description: Data for Figure 6D in Excel file.  CDC42-GTP ADU in Caco-2 cells after treatment. Experiments in triplicate.
DOI: 10.5061/dryad.ns5qs/32
title: Figure 6F

description: Data for Figure 6F in Excel file.  β-Arrestin1:ARHGAP10 binding ADU in PTEN+/+ HCT116 cells after treatment. Experiments in triplicate.
DOI: 10.5061/dryad.ns5qs/33
title: Figure 6H

description: Data for Figure 6H in Excel file. CDC42-GTP  (ADU) in PTEN+/+ HCT116 cells after treatment. Experiments in triplicate.
DOI: 10.5061/dryad.ns5qs/34
title: Figure 6J

description: Data for Figure 6J in Excel file. Spindle angles in Caco-2 glands after treatment. Spindle angles calculated for 15 mitotic figures per treatment.
DOI: 10.5061/dryad.rr762/1
title: Development Time After Sublethal Exposure

description: Time taken for 5th instars to molt to adults after sublethal exposure to Temprid.
DOI: 10.5061/dryad.s5q8f/1
title: Figure 1B_Geocoris_feeding activities

description: Source data for Figure 1B, Geocoris abundance and feeding activity.
DOI: 10.5061/dryad.s5q8f/2
title: Figure 1C and 1D_predation assay control

description: Source data for Fig 1 C and D, day v. night predation rates.
DOI: 10.5061/dryad.s5q8f/3
title: Figure 1E and S1_Feeding activities

description: Source data for Fig 1E and S1: herbivore feeding activities.
DOI: 10.5061/dryad.s5q8f/4
title: Figure 2C and 2D_HIPV emissions after the dawn and dusk elicitation in Utah

description: Source data for Figure 2C and 2D, herbivore-induced plant volatile emissions after dawn versus dusk elicitation of plants in the field.
DOI: 10.5061/dryad.s5q8f/5
title: Figure 3_Different time elicitation experiment in the glasshouse RE-INTEGRATION

description: Source data for Fig. 3, herbivore-induced volatile emissions after eliciting plants at different times in the glasshouse
DOI: 10.5061/dryad.s5q8f/6
title: Figure 4, S5, and S6_GLV supplementation predation assay

description: Source data for Figs. 4, S5, and S6: Headspace supplementation with dawn versus dusk GLV blends and predation assays.
DOI: 10.5061/dryad.s5q8f/7
title: Figure 4, Table S2_GLV blends

description: Source data for Fig. 4 and Table S2, GLV blends used for supplementation
DOI: 10.5061/dryad.s5q8f/8
title: Figure 5_EV irLOX2 irLOX23 dawn dusk predation assay

description: Source data for Fig. 5, predation from EV, irLOX2, and irLOX2/3 plants after dawn or dusk elicitation
DOI: 10.5061/dryad.s5q8f/9
title: Figure 6 and training period_Geocoris activity

description: Source data for Fig. 6 and the training period prior to the EV, irLOX2, and irLOX2/3 predation assay (Fig. 5)
DOI: 10.5061/dryad.t5453/1
title: Thermal limits of early life stages of fish

description: This dataset includes the raw data on the effect of warming rate, acclimation temperature and ontogeny on the critical thermal maximum of Atlantic herring and European seabass larvae on  sheet "CTmax_herring+seabass_Fig2". On sheet "Upper_limits_herring_Fig3", results on the time dependence of upper thermal limits of Atlantic herring are displayed. Finally, review data from upper and lower thermal limits of larval fish are summarized in sheet "Thermal_limits_review_Fig4".
DOI: 10.5061/dryad.2182n/1
title: GTT data

description: Prism format file
DOI: 10.5061/dryad.2182n/2
title: MafB expression data

description: Prism format file
DOI: 10.5061/dryad.2182n/3
title: Nkx6.1 expression

description: Prism format file
DOI: 10.5061/dryad.2182n/4
title: Pdx1expression

description: Prism format file
DOI: 10.5061/dryad.2182n/5
title: Pdx1 protein levels ELISA

description: Prism format file
DOI: 10.5061/dryad.2182n/6
title: Summary cell histology data

description: Microsoft Excel file
DOI: 10.5061/dryad.33243/1
title: Dougherty_Simmons_all_data

description: Data on degree of copulatory wounding for all pairs scanned
DOI: 10.5061/dryad.33243/2
title: Video S1

description: 3D volume rendering showing a male aedeagus partly everted inside a female during the early stages of mating (pair frozen in copula after 60 seconds of mating, female not shown). The colour represents the relative X-Ray attenuation (brightness) of the tissue, with red representing highest density and blue representing lowest density.
DOI: 10.5061/dryad.33243/3
title: Video S2

description: 3D volume rendering showing a fully everted male aedeagus inside a female during the early stages of mating (pair frozen in copula after 60 seconds of mating, female not shown). The colour represents the relative X-Ray attenuation (brightness) of the tissue, with red representing highest density and blue representing lowest density.
DOI: 10.5061/dryad.33243/4
title: Video S3

description: 3D volume rendering showing the interaction between the male aedeagus (colour) and female copulatory tract (greyscale) during the early stages of mating (pair frozen in copula after 60 seconds of mating), viewed from the side. The colours represent the relative X-Ray attenuation (brightness) of the tissue, with red/white representing highest density and blue/dark grey representing lowest density for male and female traits respectively.
DOI: 10.5061/dryad.34k42.1
title: Data from: Age-graded dominance hierarchies and social tolerance in packs of free-ranging dogs
DOI: 10.5061/dryad.34k42.1/1.1
title: 1.Total_Number_of_Submissive_interactions_in_dog_packs

description: This file contains six tables. Each table is a squared matrix reporting the total number of submissive gestures exchanged among dogs belonging to the same pack. So, each table corresponds to a different dog pack. Performers of submissive gestures are reported on the vertical axis on the left side of each table, in which each individual dog is identified using a 2-3 letters code. Recipients of submissive gestures are reported on the upper horizontal axis of each table, and again each individual dog is identified using a 2-3 letter code. Note that the data reported for the Curva pack are not statistically independent from those reported for the Fused pack, since the latter originated from the fusion of the Curva pack with another one and the data collected before and after the fusion event were combined (see Bonanni et al. 2017, Behav Ecol, for additional explanations). In the original paper, the data reported in these tables were used to calculate the statistical parameters reported in Table 3, i.e. hierarchy linearity, directional consistency of submissive behaviour, hierarchy steepness, as well as percentage of unknown, 1-way, 2-ways, and tied dyadic relationships. Moreover, these data were also used to arrange pack members in the rank order that was most consistent with a linear hierachy.