cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2m19h/8
title: R script for GLMM analysis

description: R script file containing code to perform Generalized Linear Mixed Models (GLMMs) that examine the influence of species traits, abundance and habitat of first capture on boundary crossing. This also includes code for calculating logit probabilities and confidence intervals used in Figure 4, as well as the supplementary analysis whereby site identity was included as a random effect (Appendix S2 and Table S2).
DOI: 10.5061/dryad.2m19h/9
title: Forest habitat measurements

description: Data from the 13 environmental characteristics measured in forest habitats in order to assess the similarity of sample sites. See ReadMe file for description of column headings.
DOI: 10.5061/dryad.3m5c4/1
title: RawQGSexCombData

description: Half sib breeding design to estimate the genetic variances and covariance for sex comb traits.
DOI: 10.5061/dryad.5vb8v.2/10.2
title: AEM_vectors

description: The output of the AEM analysis.
DOI: 10.5061/dryad.5vb8v.2/11.2
title: aem-19pop

description: The input to calculate AEM vectors
DOI: 10.5061/dryad.5vb8v.2/12.2
title: Geographical_data

description: The spatial distribution data file used to calculate dbMEM
DOI: 10.5061/dryad.5vb8v.2/5.2
title: 28snps-562ind-freq.frq

description: The file containing all the allele frequencies for the putatively neutral SNPs.
DOI: 10.5061/dryad.5vb8v.2/6.2
title: script-outflank

description: The script used for running OUTFLANK
DOI: 10.5061/dryad.5vb8v.2/7.2
title: bayescan-13688snps-562ind 2

description: The file used to run Bayescan.
DOI: 10.5061/dryad.5vb8v.2/8.2
title: script_bayescan_laura

description: The script used to analyse bayescan results.
DOI: 10.5061/dryad.5vb8v.2/9.2
title: arlequin-13688snps-562ind

description: The file use dot run Arlequin.
DOI: 10.5061/dryad.6q5t4.1
title: Data from: Body-size trends of the extinct giant shark Carcharocles megalodon: a deep-time perspective on marine apex predators
DOI: 10.5061/dryad.6q5t4.2/2.2
title: Pimiento&Balk.TableS1

description: Descriptive statistics of Carcharocles megalodon crown height (mm) through time. Significant values in bold. Codes: P =Pliocene (5.33-2.58 Ma), LM = late Miocene (11.61-5.33 Ma), MM = middle Miocene (15.97-11.61 Ma).
DOI: 10.5061/dryad.6q5t4.2/3.2
title: Pimiento&Balk.TableS2

description: Statistical comparisons of Carcharocles megalodon crown height (mm) trends through time across space. Significant values in bold. P =Pliocene (5.33-2.58 Ma), LM = late Miocene (11.61-5.33 Ma), MM = middle Miocene (15.97-11.61 Ma).
DOI: 10.5061/dryad.6q5t4.2/4.2
title: Pimiento&Balk.TableS3

description: Model fitting results for Carcharocles megalodon crown height trends. Largest Akaike weigh (best fit) in bold.
DOI: 10.5061/dryad.6q5t4.2/5.2
title: Pimiento&Balk.Fig.S1

description: Carcharocles megalodon tooth-size distributions (note log10 scale). The density curve is in grey. A, General body-size distribution. B, Body-size distributions through time.
DOI: 10.5061/dryad.6q5t4.2/6.2
title: Pimiento&Balk.Fig.S2

description: Geographic trends in Carcharocles megalodon tooth size. A, Tooth size by latitude. The dashed line represents best-fit linear regression model. Black dots represent the middle Miocene (MM) samples, grey dots the late Miocene (LM) samples, and white dots the Pliocene (P) samples. B, Boxplot showing tooth size by hemisphere. C, Boxplot showing tooth size by ocean. D, Tooth size by absolute latitude through time. E, Boxplots showing tooth size by hemisphere through time. F, Boxplots showing tooth size by oceanic region through time.
DOI: 10.5061/dryad.6q5t4.2/7.2
title: Pimiento&Balk.Fig.S3

description: Evolutionary trajectory of Carcharocles megalodon tooth size. Bars represent standard errors of the mean.
DOI: 10.5061/dryad.6q5t4.2/8.2
title: Pimiento&Balk Carcharocles megalodon tooth images
DOI: 10.5061/dryad.78p62/1
title: Dryad.stickleback.mate.choice

description: Complete data set used for all analyses in the study. The rows are the replicate experimental trials (N = 58). The first column specifies the date of termination of the trials. The subsequent columns describe the experimental females, then the lake males, then the stream males (each trial involved a single female and a male of each ecotype). The last column indicates the male that mated with the female. Missing data are coded as 'NA'.
DOI: 10.5061/dryad.8f66s/1
title: Harvest Data - Plant biomass and rhizobia nodule data

description: Harvest data for experiment looking at effects of rhizobia and mycorrhizal fungi on plant mass and rhizobia nodules. Column Names -- "Block" is a number 1-5 that represents the spatial block in which the plant is located within the greenhouse, "Plant_ID" is a unique number used to identify each plant in the experiment, "Myco_fungi" and "Rhizobia" indicates the presence (+) or absence (-) of mycorrhizal fungi and rhizobia treatments, "Shoot_mass" and "Root_mass" are the aboveground and belowground biomasses of the plants at harvest, and "Nodule_count" and "Nodule_mass" provide the number and mass of rhizobia nodules. Note that almost all plants have aboveground data while many lack belowground data, which is because roots of half the plants were flash frozen and homogenized for RNA-Seq and expression analysis.
DOI: 10.5061/dryad.8f66s/2
title: Leaf and Branch Data

description: Data for experiment looking at effects of rhizobia and mycorrhizal fungi on plants trifoliate leaf number and branch number. Column Names -- "Block" is a number 1-5 that represents the spatial block in which the plant is located, "Plant_ID" is a unique number used to identify each plant in the experiment, "Myco_fungi" and "Rhizobia" indicates the presence (+) or absence (-) of mycorrhizal fungi and rhizobia treatments, "#_Branches" and "#_Trifoliate_Leaves" are counts of total number of plant branches and leaves , and "Week" indicates the week post-inoculation that the data was collected. Note that data was collected at three time points.
DOI: 10.5061/dryad.mg363/10
title: Cell1_Pal16_1_ROI_02.1b

description: Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
DOI: 10.5061/dryad.mg363/11
title: Cell1_Pal16_1_ROI_02.1c

description: Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
DOI: 10.5061/dryad.mg363/12
title: Cell2_Pal16_1-2_sept19b

description: Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
DOI: 10.5061/dryad.mg363/4
title: Pyrenoid_S.glynnii_example4

description: 3-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocol
DOI: 10.5061/dryad.mg363/5
title: Pyrenoid_S.glynnii_example5

description: 3-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocol
DOI: 10.5061/dryad.mg363/6
title: Pyrenoid_S.glynnii_example6

description: 3-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocol
DOI: 10.5061/dryad.mg363/7
title: Pyrenoid_S.glynnii_example7

description: 3-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocol
DOI: 10.5061/dryad.mg363/8
title: psbA coding and non-coding region (partial sequences)

description: Sequence alignments of partial psbA coding and non-coding region haplotypes of Symbiodinium glynnii sp. nov. from the western, central and eastern Pacific Ocean.
DOI: 10.5061/dryad.mg363/9
title: Cell1_Pal16_1_ROI_02.1a

description: Serial sections and chromosome counts of the cell nucleus from Symbiodinium glynnii sp. nov.
DOI: 10.5061/dryad.mq3mq/10
title: Projection Scenarios

description: Description of projection scenarios found in Population Projection R script
DOI: 10.5061/dryad.mq3mq/11
title: Seed Survival Analysis

description: Seed survival analysis R script - requires Seed Survival Data file to run
DOI: 10.5061/dryad.mq3mq/12
title: Seed Survival Data

description: Seed survival data - used to calculate s1 - required to run Seed Survival Analysis R script
DOI: 10.5061/dryad.mq3mq/5
title: Population Projection

description: R script to perform population projections - needs Saddle Vital Rates, Red Vital Rates, Forest Vital Rates, and Site Correlations data files to run
DOI: 10.5061/dryad.mq3mq/6
title: Saddle Vital Rates

description: Vital rate means and variances from Saddle site - required to run Population Projection R script
DOI: 10.5061/dryad.mq3mq/7
title: Site Correlation Data

description: Vital rate correlations between sites - required to run Population Projection R script
DOI: 10.5061/dryad.mq3mq/8
title: Seed Production Analysis

description: R script for analysis of seed data - requires Seed Production Data file to run
DOI: 10.5061/dryad.mq3mq/9
title: Red Vital Rates

description: Vital rate means and variances from Red site - required to run Population Projection R script
DOI: 10.5061/dryad.pm0n4/1
title: Culex egg raft distribution in mesocosm experiment

description: File include data on the distribution of Culex egg rafts between treatments. The data was collected in an oviposition habitat selection outdoor mesocosm experiment. Columns A-C describe the treatment code. Columns E-F describe the distribution of treatments among experimental tubs. Columns I-K describe the number of egg rafts deposited per day in each of the experimental tubs.
DOI: 10.5061/dryad.pm0n4/2
title: Prey items count data from laboratory feeding experiment

description: File include data on the number of prey items consumed through time in a laboratory feeding experiment. Column A describe the fish ID number. Column B describe the fish species. Column C describe the mosquito stage. Columns D-AB describe the number of prey item counted per hour over 24 h.
DOI: 10.5061/dryad.vq6m6.1
title: Data from: Tropical Drosophila pandora carry Wolbachia infections causing cytoplasmic incompatibility or male killing
DOI: 10.5061/dryad.vq6m6.2/5.2
title: CI and MK strains_Fecundity

description: Lab collected data for CI and MK strains of Drosophila pandora, used to evaluate Fecundity. Data showing the number of eggs collected. Crosses where no mating occurred excluded for analysis but identified here for completeness.
DOI: 10.5061/dryad.vq6m6.2/6.2
title: CI and MK strains_Population Expt_Sex Ratio Score

description: Lab collected data for population monitoring experiment with different starting frequencies of the MK strain of Drosophila pandora (10, 25, 50, 75 and 90%). Data shows the number of females and males in a random sample of 100 progeny from each replicate after five generations.Treatment refers to the starting frequency of the MK infection.
DOI: 10.5061/dryad.vq6m6.2/7.2
title: CI and MK strains_Population Expt_Infection Score

description: Lab collected data for population monitoring experiment with different starting frequencies MK strain of Drosophila pandora (10, 25, 50, 75 and 90%). Data shows the infection type of a random sample of 50 females from each replicate after five generations. Treatment is the starting frequency of the MK strain. The MK infection is scored as '1' and the CI infection is scored as '0'.
DOI: 10.5061/dryad.vq6m6.2/8.2
title: CI strain_Maternal Transmission

description: Laboratory data for the CI strain of Drosophila pandora showing the relationship between maternal transmission of Wolbachia and egg hatch rate, where a high egg hatch rate corresponds with imperfect Wolbachia transmission. Crosses for which mating did not occur were excluded from analysis, but are included here for completeness.
DOI: 10.17632/m3mpy5xxnv.1
title: heat transfer rates for shell and helically coiled finned tube heat exchangers

description: data for Re=15000
DOI: 10.5061/dryad.08803/14
title: Video 4. Cell death of Mm infected macrophages showing roundup morphology.

description: Double transgenic Tg(mpeg1:EGFP) and Tg(lyz:DsRed2) larvae infected with Mm (red) were imaged alive every ~60 sec using CLSM (Nikon A1). The GFP-positive (green) macrophage infected with Mm (red) undergoes cell death showing a roundup morphology at 50 minutes, and the GFP signal associated with Mm decreases gradually in 2 hours. The maximum intensity projection from 11 CLSM images (step size in z-direction, 5.56 µm) is shown at 10 frames per second. Scale bar: 20 µm.
DOI: 10.5061/dryad.08803/15
title: Video 5. Cell death of Mm infected macrophages showing rapid signal disappearance morphologies.

description: Double transgenic Tg(mpeg1:EGFP) and Tg(lyz:DsRed2) larvae infected with Mm (red) were imaged alive every ~60 sec using CLSM (Nikon A1). The GFP-positive (green) macrophage infected with Mm (red) indicated by white arrow undergoes cell death showing rapid signal disappearance at 54 minutes and immediate recruitment of another macrophage. The maximum intensity projection from 11 CLSM images (step size in z-direction, 5.56 µm) is shown at 10 frames per second. Scale bar: 20 µm.
DOI: 10.5061/dryad.08803/16
title: Video 6. Macrophage burst at the exponential phase of Mm infection.

description: Double transgenic Tg(mpeg1:EGFP) and Tg(lyz:DsRed2) larvae infected with Mm were imaged alive every ~63 sec from 1 dpi to 2 dpi by CLSM (Nikon A1). Macrophage burst and spreading of Mm (red) are shown, followed by the recruitment of GFP-positive (green) macrophages and DsRed-positive (blue) neutrophils. In the left bottom the macrophages and Mm are visualized separately. In the right bottom only the Mm are visualized, and the burst event at t = 5h is indicated by arrowheads. A neutrophil that phagocytized Mm after the burst event, indicated by an arrow in the upper panel at t= 8, is moving away from the infection site. The maximum intensity projection from 11 CLSM images (step size in z-direction, 5.56 µm) is shown at 10 frames per second. Scale bar: 50 µm.
DOI: 10.5061/dryad.08803/17
title: Video 7. Extrusion of a Mm aggregate out of the tail fin.

description: Double transgenic Tg(mpeg1:EGFP) and Tg(lyz:DsRed2) larvae infected with Mm were imaged alive every ~60 sec from 1 hpi to 17 hpi by CLSM (Nikon A1). The GFP-positive (green) macrophages containing a Mm (red) aggregate undergoes cell death showing fragmentation. The bacterial content is clearly extruded from the tail fin 3 hours after the macrophage showing fragmentation (Fig. 3D). The corresponding transmission channel is shown below, showing a protuberance on the outer epithelial layer, which is eventually shed off. The maximum intensity projection from 11 CLSM images (step size in z-direction, 5.56 µm) is shown at 10 frames per second. Scale bar: 20 µm.
DOI: 10.5061/dryad.08803/18
title: Video 8. CLSM on macrophage and neutrophil behavior at the exponential phase of Mm infection.

description: Double transgenic Tg(mpeg1:EGFP) and Tg(lyz:DsRed2) larvae infected with Mm were imaged alive every ~60 sec at 3 dpi for 2.5 hours by CLSM (Nikon A1) before fixation. The two infected GFP-positive (green) macrophages and two infected DsRed-positive (blue) neutrophils that were correlated with 3D block-face SEM images are indicated by arrows. The indicated macrophages (MP1 and MP2) phagocytized Mm approximately 2 and 1.5 hours before fixation respectively and these cells remained GFP-positive after fixation. The neutrophil (NP1) containing Mm was observed 2.5 hours before fixation and undergoes cell death, observed as rapid (within ~1 min) disappearance of the fluorescent signal, ~30 min before fixation. The second neutrophil (NP2) was recruited to another infected neutrophil ~30 min before fixation. The maximum intensity projection from 11 CLSM images (step size in z-direction, 5.56 µm) is shown at 10 frames per second. Scale bar: right panel 100 µm and for the left panel 50 µm.
DOI: 10.5061/dryad.08803/19
title: Video 9. Three-dimensional block-face SEM images of Mm infected tail fin.

description: A double transgenic Tg(mpeg1:EGFP) and Tg(lyz:DsRed2) larva infected with M. marinum was fixed and block face SEM imaging was performed on an 80 by 80 µm region of interest using a Quanta FEG 250 with a Gatan 3View Ultramicrotome. The video shows 154 images acquired every 150 nm step size in z-direction (103 nm pixel size) at 10 frames per second. Scale Bar: 10 µm.
DOI: 10.5061/dryad.08803/20
title: Video 10. Three-dimensional block-face SEM images of necrotic neutrophil undergoing netosis.

description: A double transgenic Tg(mpeg1:EGFP) and Tg(lyz:DsRed2) larva infected with M. marinum was fixed and block face SEM imaging was performed on an 80 by 80 µm region of interest using a Quanta FEG 250 with a Gatan 3View Ultramicrotome. The video shows 70 images in z-direction (23 nm pixel size) of the neutrophil (NF2, Fig. 4). Note the partial intact nuclear envelope (arrow) and the vesicles (arrowheads) fusing with bacterial aggregate. The images were acquired with every 150 nm step size in z-direction and are in this video visualized at 10 frames per second. Scale Bar: 2 µm.
DOI: 10.5061/dryad.14km1/1
title: ECOALIM_dataset_V1.0

description: Dataset of Environmental Impacts (LCA) of Feed Ingredients Used in French Animal Production.
DOI: 10.5061/dryad.2vn65/10
title: Language

description: A list of the written language that each of the 160 included RCTs used.
DOI: 10.5061/dryad.2vn65/11
title: surgical risk

description: We have based the classification of surgical risk in the document on a review of the current literature on risk and the number of base units in the chart in the document that is based on the perceived complexity of each procedure listed.
DOI: 10.5061/dryad.2vn65/12
title: primary.secondary.outcome

description: This document lists the primary and secondary outcomes studied in each of the 160 included RCTs.
DOI: 10.5061/dryad.2vn65/13
title: Nomenclature

description: This paper describes the range of descriptors of anesthetic techniques.
DOI: 10.5061/dryad.2vn65/4
title: Psychological sequelae&Light anaesthesia

description: Explicit and implicit memory have been associated with patients who had been exposed to light levels of anesthesia during their surgical procedure. Expert views regarding the definition of these forms of memory as well as consciousness and post-traumatic stress syndrome (PTSD) are discussed.
DOI: 10.5061/dryad.2vn65/5
title: Cardiovascular Function & Pathologies

description: Two charts that describe the impact of anesthetic techniques on a normal and abnormal cardiovascular system.
DOI: 10.5061/dryad.2vn65/6
title: PTSD Diagnostic Criteria

description: Veterans administration hospital system summarizes the changes in the criteria used to diagnose post-traumatic stress syndrome (PTSD) between DSM IV and V.
DOI: 10.5061/dryad.2vn65/7
title: Wakefulness endnote 2014 annotate

description: Annotated endnote based literature review summary with each papers abstract that used the response to command (wakefulness) method from 1979 through 2014.
DOI: 10.5061/dryad.2vn65/8
title: Refinement of Sebel classification system

description: A brief description of the clinical context in which Dr Sebel and colleagues published their classification system in 2004.
DOI: 10.5061/dryad.2vn65/9
title: Sample size N=160

description: A summation of each of the 160 RCT studies participants who were enrolled, recruited (started study) and completed each study and dropouts.
DOI: 10.5061/dryad.3m5c4/2
title: RawSexCombFitnessData

description: Selection on sex combs across several episodes of selection.
DOI: 10.5061/dryad.3nb53/1
title: MarMa_dataset

description: Size and survival data collected from juvenile mussels (Margaritifera margaritifera) from 8 river populations from southern Norway.
DOI: 10.5061/dryad.4jp82/1
title: Hackenberg_etal_2016_Gα_RGS_protein_pairs

description: See README file.
DOI: 10.5061/dryad.50k60/1
title: PlosOne_DR_Data

description: This .mat file includes experimental data (data{i} for subject i, in which data{i}.mg for task 1 and data{i}.ss for task 2), and model output of sensorimotor speed and motivation.
DOI: 10.5061/dryad.512p5/2
title: Relative abundance of established community

description: Relative abundance of species within the control, resident community plot. Values were used to weight the per-individual biomass in our calculations of community weighted means. See the README file for metadata.
DOI: 10.5061/dryad.533gf/1
title: Bat Trajectory Data

description: 3D position data for Myotis velifer. The columns represent the trial number, the index number (to differentiate individual animals within a trial -- note they are not consistent between trials), the frame (used for synchronizing the data), and the XYZ position coordinates with respect to a global reference frame. Information about how the data was collected is in the ReadMe file.
DOI: 10.5061/dryad.533gf/2
title: Bird Trajectory Data

description: 3D position data for Petrochelidon pyrrhonota. The columns represent the trial number, the index number (to differentiate individual animals within a trial -- note they are not consistent between trials), the frame (used for synchronizing the data), and the XYZ position coordinates with respect to a global reference frame. Information about how the data was collected is in the ReadMe file.