cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9192611.v1
title: Steric microstructure of mixed-species biofilm formed by interaction between <i>Lactobacillus plantarum</i> ML11-11 and <i>Saccharomyces cerevisiae</i>

description: The mixed-species biofilm of <i>Lactobacillus plantarum</i> ML11-11 (LAB) and yeast had a double-layered structure with the ground layer composed of LAB cells, and the upper layer composed of coaggregates of LAB and yeast cells. The ability of LAB to adhere to both, the solid surface and the yeast cells, enabled the formation and maintenance of the biofilm as an ecosystem for LAB and yeast.
DOI: 10.6084/m9.figshare.9192521
title: Supplementary Database from Integrating behaviour and ecology into global biodiversity conservation strategies

description: Insights into animal behaviour play an increasingly central role in species-focused conservation practice. However, progress towards incorporating behaviour into regional or global conservation strategies has been more limited, not least because standardized datasets of behavioural traits are generally lacking at wider taxonomic or spatial scales. Here we make use of the recent expansion of global datasets for birds to assess the prospects for including behavioural traits in systematic conservation priority-setting and monitoring programmes. Using International Union for Conservation of Nature Red List classifications for more than 9500 bird species, we show that the incidence of threat can vary substantially across different behavioural categories, and that some types of behaviour—including particular foraging, mating and migration strategies—are significantly more threatened than others. The link between behavioural traits and extinction risk is partly driven by correlations with well-established geographical and ecological factors (e.g. range size, body mass, human population pressure), but our models also reveal that behaviour modifies the effect of these factors, helping to explain broad-scale patterns of extinction risk. Overall, these results suggest that a multi-species approach at the scale of communities, continents and ecosystems can be used to identify and monitor threatened behaviours, and to flag up cases of latent extinction risk, where threatened status may currently be underestimated. Our findings also highlight the importance of comprehensive standardized descriptive data for ecological and behavioural traits, and point the way towards deeper integration of behaviour into quantitative conservation assessments.This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.
DOI: 10.6084/m9.figshare.9192521.v1
title: Supplementary Database from Integrating behaviour and ecology into global biodiversity conservation strategies

description: Insights into animal behaviour play an increasingly central role in species-focused conservation practice. However, progress towards incorporating behaviour into regional or global conservation strategies has been more limited, not least because standardized datasets of behavioural traits are generally lacking at wider taxonomic or spatial scales. Here we make use of the recent expansion of global datasets for birds to assess the prospects for including behavioural traits in systematic conservation priority-setting and monitoring programmes. Using International Union for Conservation of Nature Red List classifications for more than 9500 bird species, we show that the incidence of threat can vary substantially across different behavioural categories, and that some types of behaviour—including particular foraging, mating and migration strategies—are significantly more threatened than others. The link between behavioural traits and extinction risk is partly driven by correlations with well-established geographical and ecological factors (e.g. range size, body mass, human population pressure), but our models also reveal that behaviour modifies the effect of these factors, helping to explain broad-scale patterns of extinction risk. Overall, these results suggest that a multi-species approach at the scale of communities, continents and ecosystems can be used to identify and monitor threatened behaviours, and to flag up cases of latent extinction risk, where threatened status may currently be underestimated. Our findings also highlight the importance of comprehensive standardized descriptive data for ecological and behavioural traits, and point the way towards deeper integration of behaviour into quantitative conservation assessments.This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.
DOI: 10.6084/m9.figshare.9192509
title: Compositionality_data

description: This is a data set on chimpanzee multimodal communication (gesture + facial expressions).
DOI: 10.6084/m9.figshare.9192509.v1
title: Compositionality_data

description: This is a data set on chimpanzee multimodal communication (gesture + facial expressions).
DOI: 10.6084/m9.figshare.9192485
title: Bird survey data from the Tasmanian Midlands

description: Data set to accompany manuscript submission entitled "Long-term change in bird communities of an agricultural landscape: declines in arboreal foragers, increases in large species". <br>Study sites and methodology techniques used to collect the data are described in the manuscript. Metadata describing data columns are included in the spreadsheet.
DOI: 10.6084/m9.figshare.9192428
title: Md. Imdadul Haque_Qualitative data

description: This is raw data covering prevailing familial, social and cultural obstacles in keeping tobacco-free homes in urban areas in Bangladesh<br>
DOI: 10.6084/m9.figshare.9192428.v1
title: Md. Imdadul Haque_Qualitative data

description: This is raw data covering prevailing familial, social and cultural obstacles in keeping tobacco-free homes in urban areas in Bangladesh<br>
DOI: 10.6084/m9.figshare.9192485.v1
title: Bird surveys data from the Tasmanian Midlands

description: Data set to accompany manuscript submission entitled "Long-term change in bird communities of an agricultural landscape: declines in arboreal foragers, increases in large species". <br>Study sites and methodology techniques used to collect the data are described in the manuscript. Metadata describing data columns are included in the spreadsheet.
DOI: 10.6084/m9.figshare.12387980
title: Sequence and Phylogenetic data from "Chlamydial contribution to anaerobic metabolism during eukaryotic evolution"

description: This dataset is composed of sequence data, alignments, trimmed alignments and tree files for phylogenetic trees presented in this study. <br><b>Protein abbreviations:</b>ACK: Acetate kinaseADI: Arginine deiminase CK: Carbamate kinase FeoB: Ferrous iron transporter B subunit HYDA: [FeFe]-Hydrogenase HYDE,F,G: HYDA maturase proteins E,FGNUOE: HYDC component of trimeric Hydrogenase, and NUOE component of respiratory complex I NUOF: HYDB component of trimeric Hydrogenase, and NUOF component of respiratory complex I NaH - Na+:H+ antiporter PFO: Pyruvate:ferredoxin oxidoreductasePTA: Phosphotransaceylase OTC - ornithine transcarbamoylase <br><b>Sequence and phylogeny files:</b><br> For ACK, ADI, CK, FeoB, HYDA, NUOE, NUOF, NaH, PTA and OTC, there are five files: unaligned sequences -- *.fasta tcoffee raw alignment -- *.tcoffee.fastamasked alignment -- *.tcoffee.bmge.fastaultrafast bootstraps tree -- *.uf.treefile non-parametic bootstraps tree -- *pmsf.treefile <br><b>Rogue taxa and transfer bootstrap expectation (TBE) files:</b><b><br></b>For HYDE, HYDF Family (HYDF_cladeI_cladeII), and HYDF sub-clade (HYDF_cladeI), HYDG and PFO they files are as above but with additional labels distinguishing:<br>the initial dataset -- *_allTaxa.*the dataset with rogue taxa removed --*_roguenaroke_removed* treefile with the the non-parametic bootstrap and TBE values -- *pmsf_tbe.treefile<br><b>Ribosomal protein phylogenies:</b> Concatenated alignments and tree files for phylogenetic trees of ribosomal proteins typically found in an operon (RP15) are included. Contigs from each metagenomic sample encoding at least 5 ribosomal proteins were included in the dataset, alongside a reference dataset of bacterial and archaeal sequences. <br><br>
DOI: 10.6084/m9.figshare.9179264
title: Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

description: The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. <b>Abbreviations:</b> 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel
DOI: 10.6084/m9.figshare.9179264.v2
title: Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

description: The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. <b>Abbreviations:</b> 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel
DOI: 10.6084/m9.figshare.9179264.v1
title: Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

description: The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. <b>Abbreviations:</b> 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel
DOI: 10.6084/m9.figshare.9179009
title: Table S3 from <i>Wolbachia</i>, <i>Cardinium</i> and climate: an analysis of global data

description: Tests for an effect of mean temperature of Wolbachia prevalence in Mandibulata hosts, applied separately to populations from each of the five higher-level Köppen climates.
DOI: 10.6084/m9.figshare.9179042
title: Input Color Images

description: Input color images; 40 randomly chosen natural images from Berkeley dataset, and a synthetic image.
DOI: 10.6084/m9.figshare.9179009.v1
title: Table S3 from <i>Wolbachia</i>, <i>Cardinium</i> and climate: an analysis of global data

description: Tests for an effect of mean temperature of Wolbachia prevalence in Mandibulata hosts, applied separately to populations from each of the five higher-level Köppen climates.
DOI: 10.6084/m9.figshare.9179006
title: Table S1 from <i>Wolbachia</i>, <i>Cardinium</i> and climate: an analysis of global data

description: The database of screens of wild arthropod populations either Cardinium or Wolbachia.
DOI: 10.6084/m9.figshare.9179042.v2
title: Input Color Images

description: Input color images; 40 randomly chosen natural images from Berkeley dataset, and a synthetic image.
DOI: 10.6084/m9.figshare.9179003
title: Model code from <i>Wolbachia</i>, <i>Cardinium</i> and climate: an analysis of global data

description: Code used for Beta-binomial model fitting.
DOI: 10.6084/m9.figshare.9179006.v1
title: Table S1 from <i>Wolbachia</i>, <i>Cardinium</i> and climate: an analysis of global data

description: The database of screens of wild arthropod populations either Cardinium or Wolbachia.
DOI: 10.6084/m9.figshare.9179042.v1
title: Input Color Images

description: Input color images; 40 randomly chosen natural images from Berkeley dataset, and a synthetic image.
DOI: 10.6084/m9.figshare.9179000
title: Table S2 from <i>Wolbachia</i>, <i>Cardinium</i> and climate: an analysis of global data

description: Results of Beta-binomial model fitting to symbiont screen data.
DOI: 10.6084/m9.figshare.9179003.v1
title: Model code from <i>Wolbachia</i>, <i>Cardinium</i> and climate: an analysis of global data

description: Code used for Beta-binomial model fitting.
DOI: 10.6084/m9.figshare.9179000.v1
title: Table S2 from <i>Wolbachia</i>, <i>Cardinium</i> and climate: an analysis of global data

description: Results of Beta-binomial model fitting to symbiont screen data.
DOI: 10.6084/m9.figshare.12777638
title: HEV

description: Blood specimens were collected from pregnant women and sera were separted and tested for the presence of anti-HEV antibodies by ELISA technique.<br><br><br><br><br>
DOI: 10.6084/m9.figshare.12777638.v2
title: HEV

description: Blood specimens were collected from pregnant women and sera were separted and tested for the presence of anti-HEV antibodies by ELISA technique.<br><br><br><br><br>
DOI: 10.6084/m9.figshare.12777638.v1
title: Untitled Item

description: Blood specimens were collected from pregnant women and sera were separted and tested for the presence of anti-HEV antibodies by ELISA technique.<br><br><br>
DOI: 10.6084/m9.figshare.9178724
title: Additional file 1: of Extracorporeal carbon dioxide removal for acute hypercapnic exacerbations of chronic obstructive pulmonary disease: study protocol for a randomised controlled trial

description: Contains a consultee assent form, Consultee information sheet, the participant consent and the participant information sheet. (ZIP 339 kb)
DOI: 10.6084/m9.figshare.9178724.v1
title: Additional file 1: of Extracorporeal carbon dioxide removal for acute hypercapnic exacerbations of chronic obstructive pulmonary disease: study protocol for a randomised controlled trial

description: Contains a consultee assent form, Consultee information sheet, the participant consent and the participant information sheet. (ZIP 339 kb)
DOI: 10.6084/m9.figshare.9178625
title: Additional file 6: of Ancient role of vasopressin/oxytocin-type neuropeptides as regulators of feeding revealed in an echinoderm

description: Raw values where data are based on smaller sample sizes. Table S1: Raw data for Fig. 7c inset, which compares the relaxing effects of asterotocin and S2 on cardiac stomach preparations; n = 5. Table S2: Raw data for Fig. 7d inset, which shows the mean percentage reversal of ACh-induced contraction of apical muscle preparations caused by asterotocin; n = 4. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.9178625.v1
title: Additional file 6: of Ancient role of vasopressin/oxytocin-type neuropeptides as regulators of feeding revealed in an echinoderm

description: Raw values where data are based on smaller sample sizes. Table S1: Raw data for Fig. 7c inset, which compares the relaxing effects of asterotocin and S2 on cardiac stomach preparations; n = 5. Table S2: Raw data for Fig. 7d inset, which shows the mean percentage reversal of ACh-induced contraction of apical muscle preparations caused by asterotocin; n = 4. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.9178586
title: Additional file 1: of Worse survival in breast cancer in elderly may not be due to underutilization of medical procedures as observed upon changing healthcare system in Poland

description: ‘Breast cancer in Poland - National Cancer Registry and National Health Fund data – 2010-2015’. The Supplementary file contains data: a) the numbers of all new cases and deaths in Poland in the particular age-groups (due to breast cancer); b) the numbers of: outpatient visits, surgery procedures, outpatient chemotherapy cycles, hospitalisations for administration of chemotherapy, hospitalisations for administration of radiotherapy, hospitalisations for administration of targeted therapy; data were calculated in total and per patient; c)health care funding in years 2010–2015 in Poland; d) the breast cancer survival in the particular age-groups in the years 2010–2015 estimated with the mortality-incidence ratio complement (1- M/I ratio). (XLSX 20 kb)
DOI: 10.6084/m9.figshare.9178586.v1
title: Additional file 1: of Worse survival in breast cancer in elderly may not be due to underutilization of medical procedures as observed upon changing healthcare system in Poland

description: ‘Breast cancer in Poland - National Cancer Registry and National Health Fund data – 2010-2015’. The Supplementary file contains data: a) the numbers of all new cases and deaths in Poland in the particular age-groups (due to breast cancer); b) the numbers of: outpatient visits, surgery procedures, outpatient chemotherapy cycles, hospitalisations for administration of chemotherapy, hospitalisations for administration of radiotherapy, hospitalisations for administration of targeted therapy; data were calculated in total and per patient; c)health care funding in years 2010–2015 in Poland; d) the breast cancer survival in the particular age-groups in the years 2010–2015 estimated with the mortality-incidence ratio complement (1- M/I ratio). (XLSX 20 kb)
DOI: 10.6084/m9.figshare.9178559
title: Additional file 5: of Identification of adjuvants for clinical trials performed with Plasmodium falciparum AMA1 in rabbits

description: Comparison between treatment groups for GIA in day 70 and 140 at 6 mg/ mL Rabbit IgG for 2 laboratory strains. Between group differences are expressed as delta’s with 95% confidence intervals. P values are adjusted for multiple comparisons using Tukey’s honest significant difference test (Tukey’s HSD test). The FCR3 strain expresses an AMA1 homologous to the immunizing antigen, whereas NF54 strain expresses an AMA1 that differs by 26 amino acids in the ectodomain. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9178559.v1
title: Additional file 5: of Identification of adjuvants for clinical trials performed with Plasmodium falciparum AMA1 in rabbits

description: Comparison between treatment groups for GIA in day 70 and 140 at 6 mg/ mL Rabbit IgG for 2 laboratory strains. Between group differences are expressed as delta’s with 95% confidence intervals. P values are adjusted for multiple comparisons using Tukey’s honest significant difference test (Tukey’s HSD test). The FCR3 strain expresses an AMA1 homologous to the immunizing antigen, whereas NF54 strain expresses an AMA1 that differs by 26 amino acids in the ectodomain. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9178550
title: Additional file 4: of Identification of adjuvants for clinical trials performed with Plasmodium falciparum AMA1 in rabbits

description: Comparison between treatment groups for day 70/140 titre ratios for 4 AMA1 alleles. (XLSX 9 kb)