cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12292052
title: Additional file 7 of Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens

description: Additional file 7. Genus-level classification of OTUs identified as potential contaminants using “NTConly” and “NTC + decontam” in silico approaches.
DOI: 10.6084/m9.figshare.12292055.v1
title: Additional file 8 of Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens

description: Additional file 8. Summary of FASTA sequences for each OTU classified in the dataset.
DOI: 10.6084/m9.figshare.12292058.v1
title: Additional file 9 of Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens

description: Additional file 9. OTU- and genus-level proportions prior to (“No decontamination”) and after removing contaminants identified using two in silico (“NTConly” and “NTC + decontam”) approaches.
DOI: 10.6084/m9.figshare.12292052.v1
title: Additional file 7 of Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens

description: Additional file 7. Genus-level classification of OTUs identified as potential contaminants using “NTConly” and “NTC + decontam” in silico approaches.
DOI: 10.6084/m9.figshare.12292007
title: Additional file 1 of An antibiotic stewardship programme to reduce inappropriate antibiotic prescribing for acute respiratory infections in rural Chinese primary care facilities: study protocol for a clustered randomised controlled trial

description: Additional file 1.
DOI: 10.6084/m9.figshare.12292007.v1
title: Additional file 1 of An antibiotic stewardship programme to reduce inappropriate antibiotic prescribing for acute respiratory infections in rural Chinese primary care facilities: study protocol for a clustered randomised controlled trial

description: Additional file 1.
DOI: 10.6084/m9.figshare.12291929
title: Additional file 9 of Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

description: Additional file 9: Table S5. Composition of CAZymes based on the class-level and family-level enzymes.
DOI: 10.6084/m9.figshare.12291926
title: Additional file 8 of Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

description: Additional file 8: Table S4. Composition of metabolic pathways based on the first-level and second-level functions in the KEGG.
DOI: 10.6084/m9.figshare.12291929.v1
title: Additional file 9 of Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

description: Additional file 9: Table S5. Composition of CAZymes based on the class-level and family-level enzymes.
DOI: 10.6084/m9.figshare.12291926.v1
title: Additional file 8 of Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

description: Additional file 8: Table S4. Composition of metabolic pathways based on the first-level and second-level functions in the KEGG.
DOI: 10.6084/m9.figshare.12291890
title: Additional file 13 of Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

description: Additional file 13: Table S6. Phenotype (MPY)-associated metabolites in rumen.
DOI: 10.6084/m9.figshare.12291896
title: Additional file 15 of Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

description: Additional file 15: Table S7. Phenotype (MPY)-associated metabolites in serum.
DOI: 10.6084/m9.figshare.12291890.v1
title: Additional file 13 of Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

description: Additional file 13: Table S6. Phenotype (MPY)-associated metabolites in rumen.
DOI: 10.6084/m9.figshare.12291896.v1
title: Additional file 15 of Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance

description: Additional file 15: Table S7. Phenotype (MPY)-associated metabolites in serum.
DOI: 10.6084/m9.figshare.12291875
title: Additional file 1 of Mutational spectrum of acquired resistance to reversible versus irreversible EGFR tyrosine kinase inhibitors

description: Additional file 1.
DOI: 10.6084/m9.figshare.12291875.v1
title: Additional file 1 of Mutational spectrum of acquired resistance to reversible versus irreversible EGFR tyrosine kinase inhibitors

description: Additional file 1.
DOI: 10.6084/m9.figshare.12291809
title: Additional file 1 of True cicadas (Cicadidae) as prey for the birds of the Western Palearctic: a review

description: Additional file 1: Appendix 1. The database of cicada-eating birds occurring in the Western Palearctic.
DOI: 10.6084/m9.figshare.12291809.v1
title: Additional file 1 of True cicadas (Cicadidae) as prey for the birds of the Western Palearctic: a review

description: Additional file 1: Appendix 1. The database of cicada-eating birds occurring in the Western Palearctic.
DOI: 10.6084/m9.figshare.12291785
title: Additional file 1 of Hospital admissions among people who inject opioids following syringe services program implementation

description: Additional file 1: Supplementary Table 1. JMH PWIO. This data consists of the 302 admission of people who inject opioids that we analyzed in this manuscript.
DOI: 10.6084/m9.figshare.12291785.v1
title: Additional file 1 of Hospital admissions among people who inject opioids following syringe services program implementation

description: Additional file 1: Supplementary Table 1. JMH PWIO. This data consists of the 302 admission of people who inject opioids that we analyzed in this manuscript.
DOI: 10.6084/m9.figshare.12291572
title: Additional file 1 of How is the minimal clinically important difference established in health-related quality of life instruments? Review of anchors and methods

description: Additional file 1.
DOI: 10.6084/m9.figshare.12291572.v1
title: Additional file 1 of How is the minimal clinically important difference established in health-related quality of life instruments? Review of anchors and methods

description: Additional file 1.
DOI: 10.6084/m9.figshare.12291512
title: Additional file 4 of RNA-Seq analysis of European sea bass (Dicentrarchus labrax L.) infected with nodavirus reveals powerful modulation of the stress response

description: Additional file 4. Differential expression analysis in the head kidney at 24 and 72 hpi with NNV.
DOI: 10.6084/m9.figshare.12291506
title: Additional file 3 of RNA-Seq analysis of European sea bass (Dicentrarchus labrax L.) infected with nodavirus reveals powerful modulation of the stress response

description: Additional file 3. Differential expression analysis in the brain at 24 and 72 hpi with NNV.
DOI: 10.6084/m9.figshare.12291506.v1
title: Additional file 3 of RNA-Seq analysis of European sea bass (Dicentrarchus labrax L.) infected with nodavirus reveals powerful modulation of the stress response

description: Additional file 3. Differential expression analysis in the brain at 24 and 72 hpi with NNV.
DOI: 10.6084/m9.figshare.12291512.v1
title: Additional file 4 of RNA-Seq analysis of European sea bass (Dicentrarchus labrax L.) infected with nodavirus reveals powerful modulation of the stress response

description: Additional file 4. Differential expression analysis in the head kidney at 24 and 72 hpi with NNV.
DOI: 10.6084/m9.figshare.12291497
title: Additional file 1 of RNA-Seq analysis of European sea bass (Dicentrarchus labrax L.) infected with nodavirus reveals powerful modulation of the stress response

description: Additional file 1. Sequence of the primer pairs used in this experiment.
DOI: 10.6084/m9.figshare.12291497.v1
title: Additional file 1 of RNA-Seq analysis of European sea bass (Dicentrarchus labrax L.) infected with nodavirus reveals powerful modulation of the stress response

description: Additional file 1. Sequence of the primer pairs used in this experiment.
DOI: 10.6084/m9.figshare.12291479
title: Additional file 1 of TAMA: improved metagenomic sequence classification through meta-analysis

description: Additional file 1: Supplementary Table S1. The statistics of reference sequences used in the TAMA database. Supplementary Table S2. The relative abundance of 10 genomes generated using six different parameter values of the Poisson distribution. Supplementary Table S3. The relative abundance of 50 genomes generated using seven different parameter values of the Poisson distribution. Supplementary Table S4. The relative abundance of 100 genomes generated using seven different parameter values of the Poisson distribution. Supplementary Table S5. The statistics of read sequences in real metagenome datasets. Supplementary Table S6. The abundance difference of initial taxonomy analysis tools and TAMA for the simulated metagenome datasets. Supplementary Table S7. The abundance profile of Artisanal cheese metagenome. Supplementary Table S8. The abundance profile of Cotija cheese metagenome. Supplementary Table S9. The abundance profile of human gut metagenome.
DOI: 10.6084/m9.figshare.12291479.v1
title: Additional file 1 of TAMA: improved metagenomic sequence classification through meta-analysis

description: Additional file 1: Supplementary Table S1. The statistics of reference sequences used in the TAMA database. Supplementary Table S2. The relative abundance of 10 genomes generated using six different parameter values of the Poisson distribution. Supplementary Table S3. The relative abundance of 50 genomes generated using seven different parameter values of the Poisson distribution. Supplementary Table S4. The relative abundance of 100 genomes generated using seven different parameter values of the Poisson distribution. Supplementary Table S5. The statistics of read sequences in real metagenome datasets. Supplementary Table S6. The abundance difference of initial taxonomy analysis tools and TAMA for the simulated metagenome datasets. Supplementary Table S7. The abundance profile of Artisanal cheese metagenome. Supplementary Table S8. The abundance profile of Cotija cheese metagenome. Supplementary Table S9. The abundance profile of human gut metagenome.
DOI: 10.6084/m9.figshare.12291434
title: Additional file 4 of Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

description: Additional file 4 List of contaminated NR identifier.
DOI: 10.6084/m9.figshare.12291425
title: Additional file 2 of Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

description: Additional file 2 List of contaminated GenBank identifier.
DOI: 10.6084/m9.figshare.12291434.v1
title: Additional file 4 of Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

description: Additional file 4 List of contaminated NR identifier.
DOI: 10.6084/m9.figshare.12291419
title: Additional file 1 of Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

description: Additional file 1 List of contaminated RefSeq identifier.
DOI: 10.6084/m9.figshare.12291425.v1
title: Additional file 2 of Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

description: Additional file 2 List of contaminated GenBank identifier.
DOI: 10.6084/m9.figshare.12291419.v1
title: Additional file 1 of Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

description: Additional file 1 List of contaminated RefSeq identifier.
DOI: 10.6084/m9.figshare.12291299
title: Projecting Populations for Major Pacific Island Countries With and Without COVID-19: Pro-active Insights for Population Policy Datset_2.xlsx

description: The paper projects aggregate populations of six Pacific Island countries both in the pre and post-COVID19 scenarios using Cohort Component Method for the period 2020-2060. It uses baseline indicators resembling China and Italy’s experiences and finds that Pacific countries could experience about 5% fatality which could reach up to 20%. It also finds that most countries would experience higher fatalities in the older age groups, consistent with what is being witnessed in other countries around the world. The analysis also shows that while the risk escalates for people over 50 years onward in all the countries, in Fiji, those in the age range of 70 years or more are at higher risk. The finding also indicates that for all countries, the fatality rate for 80 years and over is about 50%. The population projections show that Fiji will be most impacted, while others will experience around 2% initial population decline. The convergence to baseline is found to be slow (except for Tonga) in most Pacific countries. Consequently, the paper suggests a cautious approach in dealing with the crisis.
DOI: 10.6084/m9.figshare.12291248
title: carbon intensity of vehicles.xlsx

description: The database contains the carbon emission intensity of the unit turnover of passenger and cargo vehicles in China, which can be used to calculate the carbon emission intensity baseline of the road transportation
DOI: 10.6084/m9.figshare.12291212
title: gene sequence.pdf

description: Gene-specific primers used for the analysis of chicken gene expression
DOI: 10.6084/m9.figshare.12291212.v1
title: gene sequence.pdf

description: Gene-specific primers used for the analysis of chicken gene expression
DOI: 10.6084/m9.figshare.12291176
title: Data of Kim et al., 2020 (JGR-atmosphere)

description: Data of Kim et al., 2020 (JGR-atmosphere)
DOI: 10.6084/m9.figshare.12291245.v3
title: R code for Leaf senescence exhibits stronger climatic responses during warm than during cold autumns

description: A warmer world could extend growing seasons for plants. Changes in spring phenology have been studied, yet autumn phenology remains poorly understood. Using &gt;500,000 phenological records of four temperate tree species between 1951 and 2013 in Europe, we show that leaf senescence in warm autumns exhibits significantly stronger climate responses, with a higher phenological plasticity, than in cold autumns, indicating a nonlinear response to climate. The onset of leaf senescence in warm autumns was delayed due to the stronger climate response, primarily caused by nighttime warming. However, daytime warming, especially during warm autumns, imposes a drought stress which advances leaf senescence. This may counteract the extension of growing season under global warming. These findings provide guidance for more reliable predictions of plant phenology and biosphere-atmosphere feedbacks in the context of global warming.
DOI: 10.6084/m9.figshare.12291245.v4
title: R code for Leaf senescence exhibits stronger climatic responses during warm than during cold autumns

description: A warmer world could extend growing seasons for plants. Changes in spring phenology have been studied, yet autumn phenology remains poorly understood. Using &gt;500,000 phenological records of four temperate tree species between 1951 and 2013 in Europe, we show that leaf senescence in warm autumns exhibits significantly stronger climate responses, with a higher phenological plasticity, than in cold autumns, indicating a nonlinear response to climate. The onset of leaf senescence in warm autumns was delayed due to the stronger climate response, primarily caused by nighttime warming. However, daytime warming, especially during warm autumns, imposes a drought stress which advances leaf senescence. This may counteract the extension of growing season under global warming. These findings provide guidance for more reliable predictions of plant phenology and biosphere-atmosphere feedbacks in the context of global warming.
DOI: 10.6084/m9.figshare.12291245.v5
title: R code for Leaf senescence exhibits stronger climatic responses during warm than during cold autumns

description: A warmer world could extend growing seasons for plants. Changes in spring phenology have been studied, yet autumn phenology remains poorly understood. Using &gt;500,000 phenological records of four temperate tree species between 1951 and 2013 in Europe, we show that leaf senescence in warm autumns exhibits significantly stronger climate responses, with a higher phenological plasticity, than in cold autumns, indicating a nonlinear response to climate. The onset of leaf senescence in warm autumns was delayed due to the stronger climate response, primarily caused by nighttime warming. However, daytime warming, especially during warm autumns, imposes a drought stress which advances leaf senescence. This may counteract the extension of growing season under global warming. These findings provide guidance for more reliable predictions of plant phenology and biosphere-atmosphere feedbacks in the context of global warming.
DOI: 10.6084/m9.figshare.12290825
title: The importance of chain context in assessing small nucleotide variants in titin: <i>in silico</i> case study of the I10-I11 tandem and its arrhythmic right ventricular cardiomyopathy linked position T2580

description: Non-synonymous small nucleotide variations (nsSNVs) in the giant muscle protein, titin, have key roles in the development of several myopathologies. Although there is considerable motive to screen at-risk individuals for nsSNVs, to identify patients in early disease stages while therapeutic intervention is still possible, the clinical significance of most titin variations remains unclear. Therefore, there is a growing need to establish methods to classify nsSNVs in a simple, economic and rapid manner. Due to its strong correlation to arrhythmogenic right ventricular cardiomyopathy (ARVC), one particular mutation in titin—T2580I, located in the I10 immunoglobulin domain—has received considerable attention. Here, we use the I10-I11 tandem as a case study to explore the possible benefits of considering the titin chain context—i.e. domain interfaces—in the assessment of titin nsSNVs. Specifically, we investigate which exchanges mimic the conformational molecular phenotype of the T2580I mutation at the I10-I11 domain interface. Then, we computed a residue stability landscape for domains alone and in tandem to define a Domain Interface Score (DIS) which identifies several hotspot residues. Our findings suggest that the T2580 position is highly sensitive to exchange and that any variant found in this position should be considered with care. Furthermore, we conclude that the consideration of the higher order structure of the titin chain is important to gain accurate insights into the vulnerability of positions in linker regions and that titin nsSNV prediction benefits from a contextual analysis. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12290825.v2
title: The importance of chain context in assessing small nucleotide variants in titin: <i>in silico</i> case study of the I10-I11 tandem and its arrhythmic right ventricular cardiomyopathy linked position T2580

description: Non-synonymous small nucleotide variations (nsSNVs) in the giant muscle protein, titin, have key roles in the development of several myopathologies. Although there is considerable motive to screen at-risk individuals for nsSNVs, to identify patients in early disease stages while therapeutic intervention is still possible, the clinical significance of most titin variations remains unclear. Therefore, there is a growing need to establish methods to classify nsSNVs in a simple, economic and rapid manner. Due to its strong correlation to arrhythmogenic right ventricular cardiomyopathy (ARVC), one particular mutation in titin—T2580I, located in the I10 immunoglobulin domain—has received considerable attention. Here, we use the I10-I11 tandem as a case study to explore the possible benefits of considering the titin chain context—i.e. domain interfaces—in the assessment of titin nsSNVs. Specifically, we investigate which exchanges mimic the conformational molecular phenotype of the T2580I mutation at the I10-I11 domain interface. Then, we computed a residue stability landscape for domains alone and in tandem to define a Domain Interface Score (DIS) which identifies several hotspot residues. Our findings suggest that the T2580 position is highly sensitive to exchange and that any variant found in this position should be considered with care. Furthermore, we conclude that the consideration of the higher order structure of the titin chain is important to gain accurate insights into the vulnerability of positions in linker regions and that titin nsSNV prediction benefits from a contextual analysis. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12290711
title: SOM Table1 (no_pathway_EC).txt

description: ECs that were not mapped to KEGG pathways.
DOI: 10.6084/m9.figshare.12290720
title: SOM Table 2. Organic acid levels in early and late spring samples.

description: Organic acid levels in early and late spring samples.
DOI: 10.6084/m9.figshare.12290750
title: Pathway profile

description: pathway profile of snow microbiomes
DOI: 10.6084/m9.figshare.12290696
title: Figshare document.xlsx

description: This data is associated with the manuscript '<b>ChAdOx1 nCoV-19 vaccination prevents SARS-CoV-2 pneumonia in rhesus macaques'</b>
DOI: 10.6084/m9.figshare.12290711.v1
title: SOM Table1 (no_pathway_EC).txt

description: ECs that were not mapped to KEGG pathways.
DOI: 10.6084/m9.figshare.12290720.v1
title: SOM Table 2. Organic acid levels in early and late spring samples.

description: Organic acid levels in early and late spring samples.
DOI: 10.6084/m9.figshare.12290750.v2
title: Pathway profile

description: pathway profile of snow microbiomes
DOI: 10.6084/m9.figshare.12290750.v1
title: Pathway profile

description: pathway profile of snow microbiomes
DOI: 10.6084/m9.figshare.12290696.v1
title: Figshare document.xlsx

description: This data is associated with the manuscript '<b>ChAdOx1 nCoV-19 vaccination prevents SARS-CoV-2 pneumonia in rhesus macaques'</b>
DOI: 10.25380/iastate.12290585
title: Immunosenescence and its influence on reproduction in a long-lived vertebrate, the painted turtle

description: These data include information on male, female, and juvenile painted turtles (Chrysemys picta) captured from Thomsom Causeway Recreation Area in Thomson, Illinois, USA in 2011. These turtles are part of a long-term mark-recapture study, and as such have information on age at first capture. These known ages, combined with ages estimated from growth models created from turtles in this population, were used to assess patterns of immunosenescence in three innate immune measures: agglutination ability, lysis ability, and bactericidal competence of plasma. We additionally tested the influence of sex, day captured, and clutch size on these immune measures. Clutch size information was collected for female painted turtles for which we had excavated nests and counted the number of eggs laid.<br><br>These files include the dataset and a codebook to interpret columns in the dataset, a sas file with code for the statistical analyses performed, and a README file. <br><br>Data reported here are data associated with the following publication:Judson, J.M., Reding, D.M., and Bronikowski, A.M. <i>Accepted</i>. Immunosenescence and its influence on reproduction in a long-lived vertebrate. <b>Journal of Experimental Biology. </b>https://www.doi.org/10.1242/jeb.223057<br> <br>
DOI: 10.6084/m9.figshare.12290600
title: all contigs fasta files for all Mid-Cayman Rise MAGs

description: All contigs FASTA files for all Mid-Cayman Rise MAGs described in the paper "Genomic variation in microbial populations inhabiting the marine subseafloor near deep-sea hydrothermal vents" by Anderson et al, 2017, Nature Communications.