cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5858592.v2
title: Supplementary Material Ashford et al. 'Phylogenetic and functional evidence suggests that deep-ocean ecosystems are highly sensitive to environmental change and direct human disturbance'

description: Supplementary Materials for Ashford <i>et al.</i> 'Phylogenetic and functional evidence that deep-ocean ecosystems are highly sensitive to environmental change and direct human disturbance' Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2018.0923
DOI: 10.6084/m9.figshare.5858436
title: How to Build a Functional Connectomic Biomarker for Mild Cognitive Impairment from Source Reconstructed MEG Resting-State Activity - Raw data II (MCI)

description: Dataset part II for:How to Build a Functional Connectomic Biomarker for Mild Cognitive Impairment from Source Reconstructed MEG Resting-State Activity
DOI: 10.6084/m9.figshare.5858436.v1
title: How to Build a Functional Connectomic Biomarker for Mild Cognitive Impairment from Source Reconstructed MEG Resting-State Activity - Raw data II (MCI)

description: Dataset part II for:How to Build a Functional Connectomic Biomarker for Mild Cognitive Impairment from Source Reconstructed MEG Resting-State Activity
DOI: 10.6084/m9.figshare.5858436.v3
title: How to Build a Functional Connectomic Biomarker for Mild Cognitive Impairment from Source Reconstructed MEG Resting-State Activity - Raw data II (MCI)

description: Dataset part II for:How to Build a Functional Connectomic Biomarker for Mild Cognitive Impairment from Source Reconstructed MEG Resting-State Activity
DOI: 10.6084/m9.figshare.5858436.v2
title: Raw data II (MCI)

description: Dataset part II for:How to Build a Functional Connectomic Biomarker for Mild Cognitive Impairment from Source Reconstructed MEG Resting-State Activity
DOI: 10.6084/m9.figshare.5858343
title: ShinyR-DAM_Supplementary_Files

description: Supplementary dataset accompanying "ShinyR-DAM: A program analyzing <i>Drosophila</i> activity, sleep, and circadian rhythms", by Karol Cichewicz & Jay Hirsh, <i>Communications Biology</i>, (2018)
DOI: 10.6084/m9.figshare.5858310
title: Sea bream gut bacterial DNA sequencing

description: The Illumina MiSeq platform for high-throughput amplicon sequencing of 16S rRNA gene, and QIIME pipeline were used to analyse and characterize the whole microbiome associated to both, feeds and <i>S.aurata</i> intestine.
DOI: 10.6084/m9.figshare.5858310.v1
title: Sea bream gut bacterial DNA sequencing

description: The Illumina MiSeq platform for high-throughput amplicon sequencing of 16S rRNA gene, and QIIME pipeline were used to analyse and characterize the whole microbiome associated to both, feeds and <i>S.aurata</i> intestine.
DOI: 10.6084/m9.figshare.5858214
title: Description of <i>Pseudo-nitzschia cuspidata</i> var. <i>manzanillensis</i> var. nov. (Bacillariophyceae): morphology and molecular characterization of a variety from the central Mexican pacific

description: The diatoms of the genus <i>Pseudo-nitzschia</i> are of special interest due to their capacity to produce domoic acid, which is responsible for amnesic shellfish poisoning (ASP) in humans. Domoic acid is a neurotoxin that can cause devastating effects in the food web, especially in seabirds and marine mammals. Identification of <i>Pseudo-nitzschia</i> species is challenging since the morphological differences are difficult to distinguish in the light microscope, and even in SEM or TEM. In recent years, new molecular biology methods have been developed that allow us to differentiate between pseudo-cryptic or cryptic species. In this study, a new pseudo-cryptic taxon is described within the <i>Pseudo-nitzschia/pseudodelicatissima</i> complex, as a variety of <i>P. cuspidata</i>. Subtle morphological differences were found among our strains of <i>P. cuspidata</i> and other previously described strains of the <i>P. pseudodelicatissima/cuspidata</i> complex with respect to the poroids of the valvocopula. These differences were supported by phylogenetic analyses of ITS rDNA sequences. The existence of hemi-compensatory base changes in some of the strains indicates the presence of a separate clade, which is described as a new variety of <i>P. cuspidata</i> group. Domoic acid was not detected in the strains investigated in this study.
DOI: 10.6084/m9.figshare.5858214.v1
title: Description of <i>Pseudo-nitzschia cuspidata</i> var. <i>manzanillensis</i> var. nov. (Bacillariophyceae): morphology and molecular characterization of a variety from the central Mexican pacific

description: The diatoms of the genus <i>Pseudo-nitzschia</i> are of special interest due to their capacity to produce domoic acid, which is responsible for amnesic shellfish poisoning (ASP) in humans. Domoic acid is a neurotoxin that can cause devastating effects in the food web, especially in seabirds and marine mammals. Identification of <i>Pseudo-nitzschia</i> species is challenging since the morphological differences are difficult to distinguish in the light microscope, and even in SEM or TEM. In recent years, new molecular biology methods have been developed that allow us to differentiate between pseudo-cryptic or cryptic species. In this study, a new pseudo-cryptic taxon is described within the <i>Pseudo-nitzschia/pseudodelicatissima</i> complex, as a variety of <i>P. cuspidata</i>. Subtle morphological differences were found among our strains of <i>P. cuspidata</i> and other previously described strains of the <i>P. pseudodelicatissima/cuspidata</i> complex with respect to the poroids of the valvocopula. These differences were supported by phylogenetic analyses of ITS rDNA sequences. The existence of hemi-compensatory base changes in some of the strains indicates the presence of a separate clade, which is described as a new variety of <i>P. cuspidata</i> group. Domoic acid was not detected in the strains investigated in this study.
DOI: 10.6084/m9.figshare.5858211
title: Spatial and temporal intercomparison of four global burned area products

description: We characterize the agreement and disagreement of four publically available burned products (Fire CCI, Copernicus Burnt Area, MODIS MCD45A1, and MODIS MCD64A1) at a finer spatial and temporal scale than previous assessments using a grid of three-dimensional cells defined both in space and in time. Our analysis, conducted using seven years of data (2005–2011), shows that estimates of burned area vary greatly between products in terms of total area burned, the location of burning, and the timing of the burning. We use regional and monthly units for analysis to provide insight into the variation between products that can be lost when considering products yearly and/or globally. Comparison with independent, contemporaneous MODIS active fire observations provides one indication of which products most reasonably capture the burning regime. Our results have implications for the use of global burned area products in fire ecology, management and emissions applications.
DOI: 10.6084/m9.figshare.5858196
title: Raw data of sex ratios

description: Sex ratio (as percentage Male) of zebrafish lines compared to the age in days of the mother and father.
DOI: 10.6084/m9.figshare.5858196.v1
title: Raw data of sex ratios

description: Sex ratio (as percentage Male) of zebrafish lines compared to the age in days of the mother and father.
DOI: 10.6084/m9.figshare.5858181
title: Raw data of Fertilisation Rates

description: Data on fertilisation and phenotype rates of clutches laid by wild-type and heterozygous tert<i><sup>sa6541</sup></i> intercrosses.
DOI: 10.6084/m9.figshare.5858181.v1
title: Raw data of Fertilisation Rates

description: Data on fertilisation and phenotype rates of clutches laid by wild-type and heterozygous tert<i><sup>sa6541</sup></i> intercrosses.
DOI: 10.6084/m9.figshare.5858130
title: Effectiveness, immunogenicity and safety of one vs. two-dose varicella vaccination：a meta-analysis

description: <b>Background</b>: Despite high 1-dose vaccination coverage, breakthrough varicella infections still occur. Therefore, 2-dose vaccination is recommended to enhance the immune response to the virus. However, the reported incremental vaccine effectiveness (VE) of 2-dose vaccination varies widely among studies. <b>Methods</b>: To determine the overall effectiveness, immunogenicity and safety of one vs. two-dose varicella vaccination, we searched five databases for articles published during 1995–2017. <b>Results</b>: The incremental VE/efficacy of 2-dose vaccination was 79% (95% confidence interval [CI]: 56%−90%) in randomized controlled trials，63% (95% CI: 36%−79%) in cohort studies and 81% (95% CI: 65%−90%) in case-control studies. Regarding immunogenicity, the pooled standardized mean differences (SMD) of geometric mean titer (GMT) and the pooled relative risk (RR) of seroconversion for 2-dose vs. 1-dose vaccine were 562.44 (95% CI: 471.78–653.10) and 1.03 (95% CI: 1.02–1.04), respectively. Children who received second dose vaccination were at increased risk of grade 3 redness (RR: 4.93, 95% CI: 1.89 − 12.87) and swelling of any intensity (RR: 1.34, 95% CI: 1.08 − 1.66). <b>Conclusions</b>: Two-dose varicella vaccination resulted in higher levels of immunogenicity and provided superior protection than 1-dose vaccination. Safety profiles showed 2-dose vaccination was well tolerated but the incidence of grade 3 redness and of any intensity was significantly higher.
DOI: 10.6084/m9.figshare.5858130.v1
title: Effectiveness, immunogenicity and safety of one vs. two-dose varicella vaccination：a meta-analysis

description: <b>Background</b>: Despite high 1-dose vaccination coverage, breakthrough varicella infections still occur. Therefore, 2-dose vaccination is recommended to enhance the immune response to the virus. However, the reported incremental vaccine effectiveness (VE) of 2-dose vaccination varies widely among studies. <b>Methods</b>: To determine the overall effectiveness, immunogenicity and safety of one vs. two-dose varicella vaccination, we searched five databases for articles published during 1995–2017. <b>Results</b>: The incremental VE/efficacy of 2-dose vaccination was 79% (95% confidence interval [CI]: 56%−90%) in randomized controlled trials，63% (95% CI: 36%−79%) in cohort studies and 81% (95% CI: 65%−90%) in case-control studies. Regarding immunogenicity, the pooled standardized mean differences (SMD) of geometric mean titer (GMT) and the pooled relative risk (RR) of seroconversion for 2-dose vs. 1-dose vaccine were 562.44 (95% CI: 471.78–653.10) and 1.03 (95% CI: 1.02–1.04), respectively. Children who received second dose vaccination were at increased risk of grade 3 redness (RR: 4.93, 95% CI: 1.89 − 12.87) and swelling of any intensity (RR: 1.34, 95% CI: 1.08 − 1.66). <b>Conclusions</b>: Two-dose varicella vaccination resulted in higher levels of immunogenicity and provided superior protection than 1-dose vaccination. Safety profiles showed 2-dose vaccination was well tolerated but the incidence of grade 3 redness and of any intensity was significantly higher.
DOI: 10.6084/m9.figshare.5858115
title: Miseq_data_Henry.rar

description: Fastq files from 16S MiSeq sequencing data of drosophila gut bacterial community (details in README file)
DOI: 10.6084/m9.figshare.5858115.v2
title: Miseq_data_Henry.rar

description: Fastq files from 16S MiSeq sequencing data of drosophila gut bacterial community (details in README file)
DOI: 10.6084/m9.figshare.5858115.v1
title: Miseq_data_Henry_bioletters.rar

description: Fastq files from 16S MiSeq sequencing data of drosophila gut bacterial community (details in README file)
DOI: 10.6084/m9.figshare.5858109
title: geneva18

description: files for lecture
DOI: 10.6084/m9.figshare.5858109.v1
title: geneva18

description: files for lecture
DOI: 10.6084/m9.figshare.5858109.v3
title: geneva18

description: files for lecture
DOI: 10.6084/m9.figshare.5858109.v2
title: geneva18

description: files for lecture
DOI: 10.6084/m9.figshare.5858100
title: Biological process uploaded in absence of BLM.xlsx

description: Biological processes unregulated in absence of BLM (p&lt;0.05) <br>
DOI: 10.6084/m9.figshare.5858100.v1
title: Biological process uploaded in absence of BLM.xlsx

description: Biological processes unregulated in absence of BLM (p&lt;0.05) <br>
DOI: 10.6084/m9.figshare.5858079
title: Recovery_data_Henry.rar

description: Chill coma recovery of D. melanogaster to cold stress (details in README file)
DOI: 10.6084/m9.figshare.5858079.v2
title: Recovery_data_Henry.rar

description: Chill coma recovery of D. melanogaster to cold stress (details in README file)
DOI: 10.6084/m9.figshare.5858079.v1
title: Recovery_data_Henry_bioletters.rar

description: Chill coma recovery of D. melanogaster to cold stress (details in README file)
DOI: 10.6084/m9.figshare.5858061
title: Acute_data_Henry.rar

description: Acute stress survival of D. melanogaster to cold and heat stress (details in README file)
DOI: 10.6084/m9.figshare.5858061.v2
title: Acute_data_Henry.rar

description: Acute stress survival of D. melanogaster to cold and heat stress (details in README file)
DOI: 10.6084/m9.figshare.5858061.v1
title: Acute_data_Henry_bioletters.rar

description: Acute stress survival of D. melanogaster to cold stress (details in README file)
DOI: 10.6084/m9.figshare.5858058
title: The distributions of the six species constituting the smooth newt species complex (Lissotriton vulgaris sensu lato and L. montandoni) – an addition to the New Atlas of Amphibians and Reptiles of Europe - Supplementary Material

description: The ‘smooth newt’, the taxon traditionally referred to as <i>Lissotriton vulgaris</i>,<i> </i>consists of multiple morphologically distinct taxa. Given the uncertainty concerning the validity and rank of these taxa, <i>L. vulgaris </i>sensu lato has often been treated as a single, polytypic species. A recent study, driven by genetic data, proposed to recognize five species, <i>L. graecus</i>,<i> L. kosswigi</i>,<i> L. lantzi</i>, <i>L. schmidtleri </i>and a more restricted <i>L. vulgaris</i>.<i> </i>The Carpathian newt <i>L. montandoni</i> was confirmed to be a closely related sister species. We propose to refer to this collective of six <i>Lissotriton </i>species as the smooth newt or <i>Lissotriton vulgaris </i>species complex. Guided by comprehensive genomic data from throughout the range of the smooth newt species complex we 1) delineate the distribution ranges, 2) provide a distribution database, and 3) produce distribution maps according to the format of the New Atlas of Amphibians and Reptiles of Europe, for the six constituent species. This allows us to 4) highlight regions where more research is needed to determine the position of contact zones
DOI: 10.6084/m9.figshare.5858058.v2
title: The distributions of the six species constituting the smooth newt species complex (Lissotriton vulgaris sensu lato and L. montandoni) – an addition to the New Atlas of Amphibians and Reptiles of Europe - Supplementary Material

description: The ‘smooth newt’, the taxon traditionally referred to as <i>Lissotriton vulgaris</i>,<i> </i>consists of multiple morphologically distinct taxa. Given the uncertainty concerning the validity and rank of these taxa, <i>L. vulgaris </i>sensu lato has often been treated as a single, polytypic species. A recent study, driven by genetic data, proposed to recognize five species, <i>L. graecus</i>,<i> L. kosswigi</i>,<i> L. lantzi</i>, <i>L. schmidtleri </i>and a more restricted <i>L. vulgaris</i>.<i> </i>The Carpathian newt <i>L. montandoni</i> was confirmed to be a closely related sister species. We propose to refer to this collective of six <i>Lissotriton </i>species as the smooth newt or <i>Lissotriton vulgaris </i>species complex. Guided by comprehensive genomic data from throughout the range of the smooth newt species complex we 1) delineate the distribution ranges, 2) provide a distribution database, and 3) produce distribution maps according to the format of the New Atlas of Amphibians and Reptiles of Europe, for the six constituent species. This allows us to 4) highlight regions where more research is needed to determine the position of contact zones
DOI: 10.6084/m9.figshare.5858001
title: data

description: Data used in the manuscript.
DOI: 10.6084/m9.figshare.5858001.v1
title: data

description: Data used in the manuscript.
DOI: 10.6084/m9.figshare.5857965
title: Supplementary Material for: A Time-Series Study of the Effect of Air Pollution on Outpatient Visits for Acne Vulgaris in Beijing

description: <b><i>Background/Aims:</i></b> There is increasing evidence that exposure to air pollutants, including particulate matter (PM<sub>2.5</sub>, PM<sub>10</sub>), nitrogen dioxide (NO<sub>2</sub>), and sulfur dioxide (SO<sub>2</sub>), might aggravate preexisting skin diseases such as eczema and urticaria. Here we investigated if a possible link exists between air pollution and acne vulgaris. We assessed the association between ambient air pollutant concentrations and the number of visits of patients for acne vulgaris to a dermatological outpatient clinic in Beijing, China, from April 1, 2012 to April 30, 2014. <b><i>Methods:</i></b> In this time period, 59,325 outpatient visits were recorded because of acne vulgaris. Daily air pollution parameters for PM<sub>10</sub>, PM<sub>2.5</sub>, SO<sub>2</sub>, and NO<sub>2</sub> were obtained from the Beijing Municipal Environmental Monitoring Center. <b><i>Results:</i></b> Increased concentrations of ambient PM<sub>2.5</sub>, PM<sub>10</sub>, and NO<sub>2</sub> were significantly associated with increased numbers of outpatient visits for acne vulgaris over the 2 years. These effects could be observed for NO<sub>2</sub> in a single-pollutant model and for PM<sub>2.5</sub>, PM<sub>10</sub>, and NO<sub>2</sub> in 2-pollutant models, which are closer to real-life exposure. Of note, these effects were specific because they were not observed for increased SO<sub>2</sub> concentrations, which even showed negative correlations in all test models. <b><i>Conclusion:</i></b> This study provides indirect evidence for a link between acne vulgaris and air pollution.
DOI: 10.6084/m9.figshare.5857965.v1
title: Supplementary Material for: A Time-Series Study of the Effect of Air Pollution on Outpatient Visits for Acne Vulgaris in Beijing

description: <b><i>Background/Aims:</i></b> There is increasing evidence that exposure to air pollutants, including particulate matter (PM<sub>2.5</sub>, PM<sub>10</sub>), nitrogen dioxide (NO<sub>2</sub>), and sulfur dioxide (SO<sub>2</sub>), might aggravate preexisting skin diseases such as eczema and urticaria. Here we investigated if a possible link exists between air pollution and acne vulgaris. We assessed the association between ambient air pollutant concentrations and the number of visits of patients for acne vulgaris to a dermatological outpatient clinic in Beijing, China, from April 1, 2012 to April 30, 2014. <b><i>Methods:</i></b> In this time period, 59,325 outpatient visits were recorded because of acne vulgaris. Daily air pollution parameters for PM<sub>10</sub>, PM<sub>2.5</sub>, SO<sub>2</sub>, and NO<sub>2</sub> were obtained from the Beijing Municipal Environmental Monitoring Center. <b><i>Results:</i></b> Increased concentrations of ambient PM<sub>2.5</sub>, PM<sub>10</sub>, and NO<sub>2</sub> were significantly associated with increased numbers of outpatient visits for acne vulgaris over the 2 years. These effects could be observed for NO<sub>2</sub> in a single-pollutant model and for PM<sub>2.5</sub>, PM<sub>10</sub>, and NO<sub>2</sub> in 2-pollutant models, which are closer to real-life exposure. Of note, these effects were specific because they were not observed for increased SO<sub>2</sub> concentrations, which even showed negative correlations in all test models. <b><i>Conclusion:</i></b> This study provides indirect evidence for a link between acne vulgaris and air pollution.
DOI: 10.6084/m9.figshare.5857962
title: Analyzing data scripts

description: Example python scripts that can be used to analyse and parse the data uploaded to the repository
DOI: 10.6084/m9.figshare.5857959
title: DDB files

description: A collection of Abinit DDB files. Contain the raw data extracted from the DFPT calculations.
DOI: 10.6084/m9.figshare.5857959.v1
title: DDB files

description: A collection of Abinit DDB files. Contain the raw data extracted from the DFPT calculations.
DOI: 10.6084/m9.figshare.5857908
title: A porcine model of skin wound infected with a polybacterial biofilm

description: A clinically relevant porcine model of a biofilm-infected wound was established in 10 minipigs. The wounds of six experimental animals were infected with a modified polymicrobial Lubbock chronic wound biofilm consisting of <i>Staphylococcus aureus</i>, <i>Enterococcus faecalis</i>, <i>Pseudomonas aeruginosa</i> and <i>Bacillus subtilis</i>. Four animals served as uninfected controls. The wounds were monitored until they had healed for 24 days. The biofilm persisted in the wounds up to day 14 and significantly affected healing. The control to infected healed wound area ratios were: 45%/21%, 66%/37%, and 90%/57% on days 7, 10 and 14, respectively. The implanted biofilm prolonged inflammation, increased necrosis, delayed granulation and impaired development of the extracellular matrix as seen in histological and gene expression analyses. This model provides a therapeutic one-week window for testing of anti-biofilm treatments and for research on the pathogenesis of wound infections in pig that is clinically the most relevant animal wound healing model.
DOI: 10.6084/m9.figshare.5857908.v1
title: A porcine model of skin wound infected with a polybacterial biofilm

description: A clinically relevant porcine model of a biofilm-infected wound was established in 10 minipigs. The wounds of six experimental animals were infected with a modified polymicrobial Lubbock chronic wound biofilm consisting of <i>Staphylococcus aureus</i>, <i>Enterococcus faecalis</i>, <i>Pseudomonas aeruginosa</i> and <i>Bacillus subtilis</i>. Four animals served as uninfected controls. The wounds were monitored until they had healed for 24 days. The biofilm persisted in the wounds up to day 14 and significantly affected healing. The control to infected healed wound area ratios were: 45%/21%, 66%/37%, and 90%/57% on days 7, 10 and 14, respectively. The implanted biofilm prolonged inflammation, increased necrosis, delayed granulation and impaired development of the extracellular matrix as seen in histological and gene expression analyses. This model provides a therapeutic one-week window for testing of anti-biofilm treatments and for research on the pathogenesis of wound infections in pig that is clinically the most relevant animal wound healing model.
DOI: 10.6084/m9.figshare.5857899
title: Appendix 5. Vein calcite dating reveals Pyrenean orogen as cause of Paleogene deformation in southern England

description: Appendix 5: Table of U–Pb data for all standards and reference materials
DOI: 10.6084/m9.figshare.5857899.v1
title: Appendix 5. Vein calcite dating reveals Pyrenean orogen as cause of Paleogene deformation in southern England

description: Appendix 5: Table of U–Pb data for all standards and reference materials
DOI: 10.6084/m9.figshare.5857893
title: Appendix 4. Vein calcite dating reveals Pyrenean orogen as cause of Paleogene deformation in southern England

description: Appendix 4: Table of U–Pb data for all samples.
DOI: 10.6084/m9.figshare.5857893.v1
title: Appendix 4. Vein calcite dating reveals Pyrenean orogen as cause of Paleogene deformation in southern England

description: Appendix 4: Table of U–Pb data for all samples.
DOI: 10.6084/m9.figshare.5857878
title: Additional sequence data

description: Nucleotide sequences of all contigs, amino acid and nucleotide sequences of predicted genes in the contigs, and alignment dataset used for the phylogenetic tree construction.<br>
DOI: 10.6084/m9.figshare.5857878.v1
title: Additional sequence data

description: Nucleotide sequences of all contigs, and amino acid and nucleotide sequences of predicted genes in the contigs.<br>