cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11845155.v2
title: Electron Diffusion Coefficients due to Whistler Mode Chorus Waves Using Non-Dipolar Magnetic Field in Jupiter’s Magnetosphere

description: This is the dataset created for the paper 'Electron Diffusion Coefficients due to Whistler Mode Chorus Waves Using Non-Dipolar Magnetic Field in Jupiter’s Magnetosphere'.
DOI: 10.6084/m9.figshare.11844924
title: Data for Richman, S. K., J. M. Levine, L. Stehan, & C. A. Johnson. 2020. Asynchronous range shifts drive alpine plant-pollinator interactions and reduce plant fitness. Global Change Biology

description: Dataset for a transplant experiment wherein <br>high-elevation plant communities (40 1m^2 plots)<br>were transplanted 1) laterally at 2000 m and 2) <br>downslope to 1800 m, 1600 m, and 1400m. <br>We made twice-weekly observations of these <br>communities, identifying plants in flower and <br>their floral visitors. We counted seeds for three <br>focal plant species at the end of the growing<br>season. In the analyses, we asked whether<br>elevation explained the floral visitor community, <br>visitation frequency, and seed production. <br>The study was conducted from June-September <br>in the Swiss Alps. See dataset for specific <br>location information. <br><br><br><br>
DOI: 10.6084/m9.figshare.11844903
title: Climatic data

description: These datasets contain precipitation and temperature data over the period 1901 to 1995 for each of the stands studied (83). These data are from the CRU.TS.v.4.03 dataset (Harris et al 2014).
DOI: 10.6084/m9.figshare.11844816
title: Affected Tree Percentage

description: Percentage of affected trees calculated from the ring width data using the OUTBREAK program. This program allows, via criteria determined as a fall in growth with a minimum duration of 5 years and whose maximum reduction exceeds 1.28 standard deviation from the mean (Blais, 1962; Jardon, 2001; Morin et al., 2010)This database also contains the geographic coordinates of each of the sampled stands as well as the number of clusters to which they belong in our study.<br>
DOI: 10.6084/m9.figshare.11844816.v1
title: Affected Tree Percentage

description: Percentage of affected trees calculated from the ring width data using the OUTBREAK program. This program allows, via criteria determined as a fall in growth with a minimum duration of 5 years and whose maximum reduction exceeds 1.28 standard deviation from the mean (Blais, 1962; Jardon, 2001; Morin et al., 2010)This database also contains the geographic coordinates of each of the sampled stands as well as the number of clusters to which they belong in our study.<br>
DOI: 10.6084/m9.figshare.11844711
title: Multiple stressors interact to impair the performance of bumblebee (Bombus terrestris) colonies

description: The data corresponds to a semi-field experiment on bumblebees (<i>Bombus terrestris</i>) to study the combined effects of chronic exposure to field-relevant doses of three abiotic stressors, the neonicotinoid thiamethoxam, the pyrethroid cypermethrin, and the EBI-fungicide tebuconazole, as well as the biotic stressor, <i>N. ceranae</i>. We used a stepwise removal approach to determine the relative effect of each stressor on bumblebees at individual and colony levels. First, we evaluated the prevalence of <i>N. ceranae</i> in inoculated bumblebee colonies to assess if pesticide exposure alters immune response mechanisms and can lead to increased susceptibility to <i>N. ceranae</i> infection. Next, to further explore this effect we measured gene expression in four AMPs (abaecin, apidaecin, defensin and hymenoptaecin), a signal molecule of the Toll (pelle), and Imd immune pathways (relish), and an immune recognition/effector gene (hemomucin) in order to evaluate the immune response of bumblebees to <i>N. ceranae</i>, and investigate interactions between pesticides in the immune response. We also studied the expression of two genes related to P450-mediated detoxification in bumblebees to test if exposure to the EBI-fungicide tebuconazole alters the P450 enzymatic detoxification mechanisms in bumblebees, and can exacerbate the effect of insecticides. Finally, the fitness and reproductive success of the colonies was monitored throughout the study in order to determine which combinations of stressors are more harmful to bumblebees.
DOI: 10.6084/m9.figshare.11844258
title: Raw ring width data

description: Chronologies of black,red and white spruce ring widths. These chronologies were obtained from cores sampled from live trees. 20 trees were sampled from 83 stands in southern Quebec.
DOI: 10.6084/m9.figshare.11844258.v1
title: Raw ring width data

description: Chronologies of black,red and white spruce ring widths. These chronologies were obtained from cores sampled from live trees. 20 trees were sampled from 83 stands in southern Quebec.
DOI: 10.6084/m9.figshare.11843337
title: Stenotrophomonas maltophilia biofilm

description: Biofilm assays from 40 strains collected from a local hospital. Quantified on a elisa plate reader
DOI: 10.6084/m9.figshare.11843337.v1
title: Stenotrophomonas maltophilia biofilm

description: Biofilm assays from 40 strains collected from a local hospital. Quantified on a elisa plate reader
DOI: 10.15131/shef.data.11843202
title: Helical Inerter Test Data from 2016

description: Data from the testing of a novel type of fluid inerter system where the inertance can be varied. This inertance is achieved by having a fluid filled cylinder that induces flow in a helical pipe system. The parameters of the helical pipe system can be adjusted to give different amounts of inertial force depending on the requirements. See Reference below for full details.<br>Parameters for the tests are given in the file name: Xmm_Yhz_Z.txtWhere X is amplitude in mmY is sine wave frequency in HzZ is the test case: For test case 2, the radius of the helix was 120mm and for test case 3 the radius of the helix was 80mm. See reference below for full details of the parameters.<br>Further details of the tests cab be found in the following paper:@CONFERENCE{SmithWaggEACS, author = {Smith, N.D.J. and Wagg, D. J.}, title = {A fluid inerter with variable inertance properties}, booktitle = {Proceedings of the 6th European Conference on Structural Control}, year = {2016}, pages = {1--8}, note = {https://doi.org/10.15131/shef.data.4206096.v1}}
DOI: 10.6084/m9.figshare.11843169
title: Whole microarray data of preterm animal lung

description: Preterm rabbit endogenous lung stem cell changes after exposure to hyperoxia with/without mechanical ventilation:Group 1 fetalGroup 2 hyperoxiaGroup 3 hyperoxia + ventilation<br><br><br>
DOI: 10.6084/m9.figshare.11842989
title: Animal Disease Surveillance in the 21st century: Applications and Robustness of Phylodynamic Methods in recent U.S. Human-like H3 Swine Influenza Outbreaks

description: Multisequence alignment, BEAST XML, and MCC tree files for HA and PB2 gene segments
DOI: 10.6084/m9.figshare.11843124
title: Field Data

description: Field data for 2019 Dutch Slough Revegetation Study.
DOI: 10.6084/m9.figshare.11843124.v1
title: Field Data

description: Field data for 2019 Dutch Slough Revegetation Study.
DOI: 10.6084/m9.figshare.11842989.v1
title: Animal Disease Surveillance in the 21st century: Applications and Robustness of Phylodynamic Methods in recent U.S. Human-like H3 Swine Influenza Outbreaks

description: Multisequence alignment, BEAST XML, and MCC tree files for HA and PB2 gene segments
DOI: 10.6084/m9.figshare.11842767
title: Zheng et al biomass enzyme tradeoff

description: These are the data files and R codes for this project.traits-data.csv is the data fileFigure_plotting.R is the R code for figure generationStatistic_and... is the R coder for the analysestree-data.nwk is the data for the phylogenetic tree for the fungal strains used
DOI: 10.6084/m9.figshare.11842713
title: Dataset S4 from Functional traits of the gut microbiome correlated with host lipid content in a natural population of <i>Drosophila melanogaster</i>

description: Dataset S4. Pairwise Kendall rank correlations between fly TAG content and taxonomic composition of the gut microbiota. (a) Relative abundance of bacterial taxa (16S amplicon data). (b) Scores for first and second axis of PCoA.
DOI: 10.6084/m9.figshare.11842713.v1
title: Dataset S5 from Functional traits of the gut microbiome correlated with host lipid content in a natural population of <i>Drosophila melanogaster</i>

description: Pairwise Kendall rank correlations between fly TAG content and KEGG genes (metagenome data) within significantly correlated pathways (listed in Table 1)
DOI: 10.6084/m9.figshare.11842713.v2
title: Table S1 from Functional traits of the gut microbiome correlated with host lipid content in a natural population of <i>Drosophila melanogaster</i>

description: Triglyceride (TAG) content of male Drosophila melanogaster
DOI: 10.6084/m9.figshare.11842713.v3
title: Dataset S3 from Functional traits of the gut microbiome correlated with host lipid content in a natural population of <i>Drosophila melanogaster</i>

description: MG-RAST metagenome KEGG indentifiers. (a) Raw counts. (b) Relative abundance of reads.
DOI: 10.6084/m9.figshare.11842713.v4
title: Dataset S2 from Functional traits of the gut microbiome correlated with host lipid content in a natural population of <i>Drosophila melanogaster</i>

description: MG-RAST metagenome statistics. (a) Raw (upload) and Post QC (quality control) sequence statistics. (b) % contribution of reads assigned to different domains. (c) % contribution of reads assigned to eukaryotic phyla.
DOI: 10.6084/m9.figshare.11842713.v6
title: Dataset S1 from Functional traits of the gut microbiome correlated with host lipid content in a natural population of <i>Drosophila melanogaster</i>

description: ASVs associated with wild male Drosophila melanogaster. (a). Full dataset counts. Data for putative intracellular bacteria are provided at the bottom of the dataset. (b) ASVs with at least 50 counts. (c) Relative abundance of ASVs with at least 50 counts, excluding putative intracellular bacteria.
DOI: 10.6084/m9.figshare.11842713.v8
title: Dataset S4 from Functional traits of the gut microbiome correlated with host lipid content in a natural population of <i>Drosophila melanogaster</i>

description: Dataset S4. Pairwise Kendall rank correlations between fly TAG content and taxonomic composition of the gut microbiota. (a) Relative abundance of bacterial taxa (16S amplicon data). (b) Scores for first and second axis of PCoA.
DOI: 10.17637/rh.11842341
title: High prevalence of plastic ingestion by Eriocheir sinensis and Carcinus maenas (Crustacea: Decapoda: Brachyura) in the Thames Estuary

description: These data were collected with the aim of investigating plastic ingestion by C. maenas and E. sinensis collected from the Thames Estuary. The hypotheses were 1) plastic ingestion would not differ between the species as both occupy a similar niche and are both generalist feeders 2) plastic would be more prevalent in the gastric mill, based on previous studies (e.g., Welden and Cowie, 2016). ​ A beam trawl with a standard mesh size of 80 mm and additional 16 mm fine mesh insert was deployed from the fishing vessel Boy Daniel SD4 at Erith, Thames Estuary. Samples were collected every three months. Between two and five benthic trawls were conducted per sampling session at a depth of between 9.2 m and –13 m. Brachyuran crabs were collected, identified and stored on ice overnight until they could be frozen the following morning at −20 °C. A total of 135 crabs were collected over a year, comprising C. maenas and E. sinensis. Trawls were undertaken on 4th December 2018, 6th March 2019, 14th June 2019 and 2nd October 2019.​ ​ The carapace was removed and the gastric mill (GM), gastrointestinal tract (GIT) and gills were extracted and stored separately in 15 ml falcon tubes. These tubes were refrozen prior to digestion. A 10% potassium hydroxide (KOH) solution was used to remove organic material from the sample. The solution was heated to 60 °C and left to digest overnight. Filters were examined under a Leica MZ 6 microscope using mounted pins and forceps under 16–64 times magnification. All recovered items were photographed and stored in individual glass specimen tubes. Items were described by colour and shape and were measured (length and width) using ImageJ. Tangles of fibres were weighed on a Sartorius MC5 balance (to nearest 0.001g) and an estimate of the number of items in the tangle calculated. ​ ​ Analysis of plastic pieces was undertaken using a PerkinElmer Spectrum One FTIR spectrometer, with an AutoIMAGE FTIR Microscope System PerkinElmer attachment. A representative subsample of ca. 10% (105 items overall) of each colour and shape combination (i.e., clear fibres, clear films and clear fragments) was analysed as per the recommendation of Lusher et al. (2017).
DOI: 10.17637/rh.11842341.v1
title: High prevalence of plastic ingestion by Eriocheir sinensis and Carcinus maenas (Crustacea: Decapoda: Brachyura) in the Thames Estuary

description: These data were collected with the aim of investigating plastic ingestion by C. maenas and E. sinensis collected from the Thames Estuary. The hypotheses were 1) plastic ingestion would not differ between the species as both occupy a similar niche and are both generalist feeders 2) plastic would be more prevalent in the gastric mill, based on previous studies (e.g., Welden and Cowie, 2016). ​ A beam trawl with a standard mesh size of 80 mm and additional 16 mm fine mesh insert was deployed from the fishing vessel Boy Daniel SD4 at Erith, Thames Estuary. Samples were collected every three months. Between two and five benthic trawls were conducted per sampling session at a depth of between 9.2 m and –13 m. Brachyuran crabs were collected, identified and stored on ice overnight until they could be frozen the following morning at −20 °C. A total of 135 crabs were collected over a year, comprising C. maenas and E. sinensis. Trawls were undertaken on 4th December 2018, 6th March 2019, 14th June 2019 and 2nd October 2019.​ ​ The carapace was removed and the gastric mill (GM), gastrointestinal tract (GIT) and gills were extracted and stored separately in 15 ml falcon tubes. These tubes were refrozen prior to digestion. A 10% potassium hydroxide (KOH) solution was used to remove organic material from the sample. The solution was heated to 60 °C and left to digest overnight. Filters were examined under a Leica MZ 6 microscope using mounted pins and forceps under 16–64 times magnification. All recovered items were photographed and stored in individual glass specimen tubes. Items were described by colour and shape and were measured (length and width) using ImageJ. Tangles of fibres were weighed on a Sartorius MC5 balance (to nearest 0.001g) and an estimate of the number of items in the tangle calculated. ​ ​ Analysis of plastic pieces was undertaken using a PerkinElmer Spectrum One FTIR spectrometer, with an AutoIMAGE FTIR Microscope System PerkinElmer attachment. A representative subsample of ca. 10% (105 items overall) of each colour and shape combination (i.e., clear fibres, clear films and clear fragments) was analysed as per the recommendation of Lusher et al. (2017).
DOI: 10.6084/m9.figshare.11842290
title: MLF methylation

description: MeDIP and hMedDIP in MLF from Tet1 KO or WT mice.
DOI: 10.6084/m9.figshare.11842290.v2
title: MLF methylation

description: MeDIP and hMedDIP in MLF from Tet1 KO or WT mice.
DOI: 10.6084/m9.figshare.11842290.v1
title: Tet1 KO MLF_MeDIP

description: MeDIP and hMedDIP in MLF from Tet1 KO or WT mice.
DOI: 10.6084/m9.figshare.11842293.v1
title: Script 1 from Individual differences in human voice pitch are preserved from speech to screams, roars and pain cries

description: Statistical analysis scripts
DOI: 10.6084/m9.figshare.11842293.v2
title: Script 2 from Individual differences in human voice pitch are preserved from speech to screams, roars and pain cries

description: Statistical analysis scripts
DOI: 10.6084/m9.figshare.11842092
title: Sun et al. JGR (2020).xlsx

description: The electrical resistance of saline-bearing clinopyroxene
DOI: 10.6084/m9.figshare.11842293.v3
title: Supplemental tables from Individual differences in human voice pitch are preserved from speech to screams, roars and pain cries

description: Tables S1 - S4
DOI: 10.6084/m9.figshare.11842092.v1
title: Sun et al. JGR (2020).xlsx

description: The electrical resistance of saline-bearing clinopyroxene
DOI: 10.6084/m9.figshare.11842086
title: Hypothalamus but not liver retains daily expression of clock genes during hibernation in terai tree frog (<i>Polypedates teraiensis</i>)

description: Circadian clock(s) allow an organism to be in synchrony with the surrounding environment and perform daily and seasonal physiological processes, including hibernation, migration, and reproduction. To cope with adverse environmental conditions, organisms have evolved various strategies. Insects undergo diapause, while some higher animals either migrate or hibernate/aestivate during unfavorable environmental conditions. Hibernation is an energy conservation strategy used to cope with adverse environmental conditions. Limited knowledge is available on the physiology of hibernation in non-mammalian vertebrates. Some studies suggest that metabolism is altered during amphibian hibernation, but nothing is known about the circadian clock. In the present study, we investigated daily oscillation of clock genes in the brain and liver of the terai tree frog (<i>Polypedates teraiensis</i>) during two annual phases of life: breeding and hibernation. Adult male terai tree frogs were procured from their natural habitat on the Mizoram University campus (23°N 92°E) during their breeding and hibernation phases. Body mass and testes weight were recorded. Animals were sacrificed at six time points: ZT1, ZT5, ZT9, ZT13, ZT17, and ZT21 (ZT0, zeitgeber time 0, indicates the sunrise time at the respective time of the year; N = 5 frogs per time point). Quantitative real-time polymerase chain reaction (qPCR) was performed for clock genes (<i>Bmal1, Clock, Per2</i>, and <i>Cry2</i>) in the hypothalamus and liver. Our results showed that body and testes weights decreased during hibernation. Further, the hypothalamus retained daily clock gene oscillations during breeding and hibernation. However, the liver lost this daily oscillation during hibernation. The maintained rhythm in hypothalamus in contrast to other hibernating animals might be the result of the fact that these animals hibernate at a higher temperature and might be more alert. As the animals have no food intake during their hibernation season which might be the reason the animals loose their rhythm in liver clock genes. These results suggest that retaining daily clock gene oscillations in the hypothalamic clock could be important for internal time tracking and post-hibernation emergence.
DOI: 10.6084/m9.figshare.11842293.v4
title: Datesets from Individual differences in human voice pitch are preserved from speech to screams, roars and pain cries

description: Fundamental frequency (<i>F</i>0, perceived as voice pitch) predicts sex and age, hormonal status, mating success and a range of social traits, and thus functions as an important biosocial marker in modal speech. Yet, the role of <i>F</i>0 in human nonverbal vocalizations remains unclear, and given considerable variability in <i>F</i>0 across call types, it is not known whether <i>F</i>0 cues to vocalizer attributes are shared across speech and nonverbal vocalizations. Here, using a corpus of vocal sounds from 51 men and women, we examined whether individual differences in <i>F</i>0 are retained across neutral speech, valenced speech and nonverbal vocalizations (screams, roars and pain cries). Acoustic analyses revealed substantial variability in <i>F</i>0 across vocal types, with mean <i>F</i>0 increasing as much as 10-fold in screams compared to speech in the same individual. Despite these extreme pitch differences, sexual dimorphism was preserved within call types and, critically, inter-individual differences in <i>F</i>0 correlated across vocal types (<i>r</i> = 0.36–0.80) with stronger relationships between vocal types of the same valence (e.g. 38% of the variance in roar <i>F</i>0 was predicted by aggressive speech <i>F</i>0). Our results indicate that biologically and socially relevant indexical cues in the human voice are preserved in simulated valenced speech and vocalizations, including vocalizations characterized by extreme <i>F</i>0 modulation, suggesting that voice pitch may function as a reliable individual and biosocial marker across disparate communication contexts.
DOI: 10.6084/m9.figshare.11842086.v1
title: Hypothalamus but not liver retains daily expression of clock genes during hibernation in terai tree frog (<i>Polypedates teraiensis</i>)

description: Circadian clock(s) allow an organism to be in synchrony with the surrounding environment and perform daily and seasonal physiological processes, including hibernation, migration, and reproduction. To cope with adverse environmental conditions, organisms have evolved various strategies. Insects undergo diapause, while some higher animals either migrate or hibernate/aestivate during unfavorable environmental conditions. Hibernation is an energy conservation strategy used to cope with adverse environmental conditions. Limited knowledge is available on the physiology of hibernation in non-mammalian vertebrates. Some studies suggest that metabolism is altered during amphibian hibernation, but nothing is known about the circadian clock. In the present study, we investigated daily oscillation of clock genes in the brain and liver of the terai tree frog (<i>Polypedates teraiensis</i>) during two annual phases of life: breeding and hibernation. Adult male terai tree frogs were procured from their natural habitat on the Mizoram University campus (23°N 92°E) during their breeding and hibernation phases. Body mass and testes weight were recorded. Animals were sacrificed at six time points: ZT1, ZT5, ZT9, ZT13, ZT17, and ZT21 (ZT0, zeitgeber time 0, indicates the sunrise time at the respective time of the year; N = 5 frogs per time point). Quantitative real-time polymerase chain reaction (qPCR) was performed for clock genes (<i>Bmal1, Clock, Per2</i>, and <i>Cry2</i>) in the hypothalamus and liver. Our results showed that body and testes weights decreased during hibernation. Further, the hypothalamus retained daily clock gene oscillations during breeding and hibernation. However, the liver lost this daily oscillation during hibernation. The maintained rhythm in hypothalamus in contrast to other hibernating animals might be the result of the fact that these animals hibernate at a higher temperature and might be more alert. As the animals have no food intake during their hibernation season which might be the reason the animals loose their rhythm in liver clock genes. These results suggest that retaining daily clock gene oscillations in the hypothalamic clock could be important for internal time tracking and post-hibernation emergence.
DOI: 10.6084/m9.figshare.11841930
title: Theoretical models of coleoid septa and shell wall

description: Septa and shell wall models used to study the potential function of the coleoid mural and adapical ridge flap.
DOI: 10.6084/m9.figshare.11841930.v1
title: Theoretical models of coleoid septa and shell wall

description: Septa and shell wall models used to study the potential function of the coleoid mural and adapical ridge flap.
DOI: 10.6084/m9.figshare.11841906
title: Reduced ecological resilience jeopardises zero loss of biodiversity using the mitigation hierarchy

description: Simulations to show how ecological resilience affects mitigation success.<br>The following repository contains all the script for the following manuscript:<br>Buschke, F.T. & Brownlie, S. (2019) Reduced ecological resilience jeopardises zero loss of biodiversity using the mitigation hierarchy.<br>The files are complete and correct as of 18 December 2019. Please direct any queries or corrections to falko.buschke@gmail.com