cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17205106
title: Additional file 2 of Benchmarking UMI-based single-cell RNA-seq preprocessing workflows

description: Additional file 2 Information of experimental designs, GEO accession numbers, data structure, biological noise levels, and expected number of cells and number of clusters are provided.
DOI: 10.6084/m9.figshare.15262158
title: Evaluation strategies for measuring pneumococcal conjugate vaccine impact in low-resource settings

description: Objectives: Pneumococcal conjugate vaccines (PCVs) are effective in reducing pneumococcal disease. We measured 13-valent PCV (PCV13) effect on different pneumococcal outcomes using diverse studies in Lao People’s Democratic Republic. Methods: Studies included: pre-PCV13 population-based record review of hospitalized childhood pneumonia cases; acute respiratory infection (ARI) study post-PCV13 to demonstrate effectiveness (VE) against hypoxic pneumonia; invasive pneumococcal disease (IPD) surveillance in all ages (2004–2018); carriage studies in children hospitalized with ARI (2013–2019); community carriage surveys pre- and post-PCV13. Results: Annual pneumonia incidence rate in children pre-PCV13 was 1,530 (95% confidence interval [CI] 1,477–1,584) per 100,000. Adjusted VE against hypoxic pneumonia was 37% (95% CI 6–57%). For IPD, 85% (11/13) of cases were due to vaccine-types pre-PCV13, and 43% (3/7) post-PCV13 in children aged &lt;5 years; for ≥5 years, 61% (27/44) and 42% (17/40), respectively. For ARI cases, adjusted VE for vaccine-type carriage was 39% (95% CI 4–60) in &lt;5 year olds; slightly higher than community surveys (23% [95% CI 4–39%] in 12–23 month olds). Conclusions: Despite limited baseline data, we found evidence of PCV13 impact on disease and carriage. Our approach could be used in similar settings to augment existing WHO PCV evaluation guidelines.
DOI: 10.6084/m9.figshare.22599140.v1
title: Additional file 5 of Genome-wide associated variants of subclinical atherosclerosis among young people with HIV and gene-environment interactions

description: Additional file 5: Summary statistics of GWAS in relation to cIMT among HIV negative control under 45 years old.
DOI: 10.6084/m9.figshare.22599131.v1
title: Additional file 2 of Genome-wide associated variants of subclinical atherosclerosis among young people with HIV and gene-environment interactions

description: Additional file 2: Summary statistics of GWAS in relation to cIMT among all HIV negative control.
DOI: 10.6084/m9.figshare.7397900
title: MOESM4 of Crosstalk in competing endogenous RNA networks reveals new circular RNAs involved in the pathogenesis of early HIV infection

description: Additional file 4: Table S4. circRNA-associated-ceRNA networks that are most likely involved in HIV-1 replication.
DOI: 10.4121/9e5bfbc1-fdf5-4095-85da-c8f38402ebb5.v1
title: The high-resolution magnetic susceptibility (χif) data (with a resolution of ~800-yr) from the Sanmenxia Basin in northern China

description: Five hundred un-orientated samples were taken from the Huangdigou section at 2 cm sampling resolution. All samples were powdered and subsequently packed into non-magnetic cubic containers (2 cm × 2 cm ×2 cm) for low- (χ<sub>if</sub>) and high- (χ<sub>hf</sub>) frequency magnetic susceptibility measurements using an AGICO MFK1-FA Magnetic Susceptibility System housed in the State Key Laboratory of Biogeology and Environmental Geology, Chinese University of Geoscience (Wuhan). χ<sub>if</sub> and χ<sub>hf</sub> were measured at 976 Hz and 15616 Hz, respectively.
DOI: 10.6084/m9.figshare.22599142.v1
title: Additional file 3 of Whole-transcriptome profiling across different developmental stages of Aedes albopictus (Diptera: Culicidae) provides insights into chitin-related non-coding RNA and competing endogenous RNA networks

description: Additional file 3: Table S8. Top 20 GO terms in circRNA-associated ceRNA networks of different comparison groups. Table S9. Top 20 KEGG pathways in circRNA-associated ceRNA networks of different comparison groups. Table S10. Top 20 GO terms in lncRNA-associated ceRNA networks of different comparison groups. Table S11. Top 20 KEGG pathways in lncRNA-associated ceRNA networks of different comparison groups.
DOI: 10.6084/m9.figshare.22599139
title: Additional file 2 of Whole-transcriptome profiling across different developmental stages of Aedes albopictus (Diptera: Culicidae) provides insights into chitin-related non-coding RNA and competing endogenous RNA networks

description: Additional file 2: Table S1. Overview of the data for RNA sequencing. Table S2. Overview of the data for small RNA sequencing. Table S3. Identified miRNAs and circRNA. Table S4. Statistics of nodes and edges in ceRNA networks. Table S5. Top 10 hub genes in the ceRNA network of different groups. Table S6. Statistics of nodes and edges in lncRNA-associated ceRNA networks. Table S7. Top 10 hub genes in the lncRNA-associated ceRNA network of different groups.
DOI: 10.6084/m9.figshare.22599139.v1
title: Additional file 2 of Whole-transcriptome profiling across different developmental stages of Aedes albopictus (Diptera: Culicidae) provides insights into chitin-related non-coding RNA and competing endogenous RNA networks

description: Additional file 2: Table S1. Overview of the data for RNA sequencing. Table S2. Overview of the data for small RNA sequencing. Table S3. Identified miRNAs and circRNA. Table S4. Statistics of nodes and edges in ceRNA networks. Table S5. Top 10 hub genes in the ceRNA network of different groups. Table S6. Statistics of nodes and edges in lncRNA-associated ceRNA networks. Table S7. Top 10 hub genes in the lncRNA-associated ceRNA network of different groups.
DOI: 10.6084/m9.figshare.24752010
title: Raw data for 'Strong philopatry in an estuarine-dependent fish'

description: Raw SNP data of<i> Acanthopagrus butcheri</i> samples collected from estuaries across southern Australia.
DOI: 10.6084/m9.figshare.7398011.v1
title: Additional file 3: of Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue

description: List of 30353 annotated lncRNA loci. (XLSX 1322 kb)
DOI: 10.6084/m9.figshare.17205103.v1
title: Additional file 1 of Benchmarking UMI-based single-cell RNA-seq preprocessing workflows

description: Additional file 1 Table S1: Summary of the scRNA-seq preprocessing workflows compared.
DOI: 10.5281/zenodo.10619047
title: Datasets for "Individual and environmental factors influencing preen gland's morphology and physiology in the barn owl (Tyto alba)"

description: Avian preen gland helps birds cope with their environment, although its overall functioning remains unclear. We shed light on the complexity of the preen gland’s functioning by studying how multiple factors associate with gland morphology (size and shape) and physiology (wax secreted) in barn owls (Tyto alba). Individual factors (sex, breeding stage, body condition) were more important predictors of preen gland than environmental factors (temperature, humidity, brood size). Sex, depending on breeding stage in adults, influenced preen gland traits, pointing to the preen gland’s regulation by sex hormones and a greater pressure on females to protect their eggs, offspring and themselves throughout reproduction. Adults and fledglings in better condition had larger glands, pointing to the existence of physiological costs. Temperature and humidity, in interaction with plumage coloration, also influenced but to a lesser extent preen gland traits, suggesting that melanin pigmentation and preen gland act as superseding mechanisms when protecting plumage against microorganisms. Finally, fledglings living in larger broods had larger glands, suggesting a role for the social environment in preen gland’s functioning. Overall, our study supports the idea that preen gland functions in diverse biological contexts within the same species and is thus subject to multiple selective pressures.
DOI: 10.6084/m9.figshare.7398074.v1
title: Additional file 6: of Altered expression of K13 disrupts DNA replication and repair in Plasmodium falciparum

description: Expression data. Expression data as counts and FPKM. (XLSX 2029 kb)
DOI: 10.6084/m9.figshare.7398125
title: Additional file 3: of CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise

description: Novel CHESS protein-coding transcripts with CDD domain hits. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.7398140
title: Additional file 4: of CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise

description: List of all novel potential protein-coding genes in CHESS. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.7398155
title: Additional file 5: of CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise

description: List of all potential protein-coding transcripts from the novel genes in CHESS. (XLSX 80 kb)
DOI: 10.6084/m9.figshare.14211539.v1
title: Additional file 2 of ITGA5 is a prognostic biomarker and correlated with immune infiltration in gastrointestinal tumors

description: Additional file 2 : Figure S1. The prognostic value of ITGA5 expression in non-gastrointestinal cancers. (A-D) Correlation between ITGA5 expression and prognosis of lung cancer and breast cancer in Kaplan-Meier Plotter; (E-F) Correlation between ITGA5 expression and prognosis of ovarian cancer in PrognoScan. OS, overall survival; DFS, disease free survival. Figure S2. The full-length, original blots for CD163 (A), ITGA5 (B), GATA3 (C) and STAT6 (D) in 6 paired gastric cancer tissues (T) and adjacent normal tissues (N). (the order of samples from left to right are: marker, N1, T1, N2, T2, N3, T3, marker, N4, T4, N5, T5, N6, T6, marker).
DOI: 10.6084/m9.figshare.14211539
title: Additional file 2 of ITGA5 is a prognostic biomarker and correlated with immune infiltration in gastrointestinal tumors

description: Additional file 2 : Figure S1. The prognostic value of ITGA5 expression in non-gastrointestinal cancers. (A-D) Correlation between ITGA5 expression and prognosis of lung cancer and breast cancer in Kaplan-Meier Plotter; (E-F) Correlation between ITGA5 expression and prognosis of ovarian cancer in PrognoScan. OS, overall survival; DFS, disease free survival. Figure S2. The full-length, original blots for CD163 (A), ITGA5 (B), GATA3 (C) and STAT6 (D) in 6 paired gastric cancer tissues (T) and adjacent normal tissues (N). (the order of samples from left to right are: marker, N1, T1, N2, T2, N3, T3, marker, N4, T4, N5, T5, N6, T6, marker).
DOI: 10.6084/m9.figshare.22600177.v1
title: Additional file 2 of Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

description: Additional file 2: Table S2. Annotation and gene organization of the mitochondrial genome of C. japonicus. N: minor strand; J: major strand. The tRNAs were annotated by different methods: MITOS2, ARWEN or aligning with the sequences of related species that were not annotated by software (ALIGN). Running ARWEN with the “-ps &lt; num&gt;” option.
DOI: 10.6084/m9.figshare.22602568
title: Additional file 3 of Altered glycosylation profiles of serum IgG in Takayasu arteritis

description: Additional file 3: Table S1. The glycan-binding specificities of the lectins contained on the lectin microarray.
DOI: 10.6084/m9.figshare.22602568.v1
title: Additional file 3 of Altered glycosylation profiles of serum IgG in Takayasu arteritis

description: Additional file 3: Table S1. The glycan-binding specificities of the lectins contained on the lectin microarray.
DOI: 10.6084/m9.figshare.22600186.v1
title: Additional file 5 of Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

description: Additional file 5: Table S5. Annotation and gene organization of the mitochondrial genome of E. pela. N: minor strand; J: major strand. The tRNAs were annotated by different methods: MITOS2, ARWEN or aligning with the sequences of related species that were not annotated by software (ALIGN). Running ARWEN with the “-ps &lt; num&gt;” option.
DOI: 10.6084/m9.figshare.22600189.v1
title: Additional file 6 of Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

description: Additional file 6: Table S6. The Ks, Ka and Ka/Ks values in the mitogenomes of S. coffeae, C. japonicus, C. rubens, C. floridensis and E. pela. SC means S. coffeae, CJ means C. japonicus, CR means C. rubens, CF means C. floridensis, EP means E. pela. The base composition of the full genome was calculated with the major strand (+).
DOI: 10.6084/m9.figshare.22600183
title: Additional file 4 of Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

description: Additional file 4: Table S4. Annotation and gene organization of the mitochondrial genome of C. floridensis. N: minor strand; J: major strand. The tRNAs were annotated by different methods: MITOS2, ARWEN or aligning with the sequences of related species that were not annotated by software (ALIGN). Running ARWEN with the “-ps &lt; num&gt;” option.
DOI: 10.6084/m9.figshare.22600174
title: Additional file 1 of Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

description: Additional file 1: Table S1. Information of the species used in the phylogenetic analysis in this study.
DOI: 10.6084/m9.figshare.20501957.v1
title: Additional file 1 of Comparative genomic analysis of five freshwater cyanophages and reference-guided metagenomic data mining

description: Additional file 1: Fig. S1. The morphology of host cyanobacterium P. mucicola Chao 1806. Fig. S2. PCR assays indicated that Pam1 and Pam5 always coexist in the crude lysate of a single plaque of infection. Fig. S3. The circular genomic maps of cyanophages a-c Pam3~Pam5, respectively. Fig. S4. Whole-genome alignment of Pam1 against Pam5 that performed by the software Mauve. Fig. S5. Structural analyses of lysogeny-associated proteins of Pam1 and Pam5. Fig. S6. Comparisons of other three host CRISPR spacer regions against DNA segments of Pam2 genome. Fig. S7. Cartoon representations of predicted structures of putative RBPs from Pam1, 2, 3, 5. Fig. S8. Metagenomic fragments recruitment analyses against the genomes of a-e Pam1~Pam5 via RBB strategy, respectively. Fig. S9. The genomic maps of three virtual cyanophages a-c k141_145115, k141_145220 and k141_53315, respectively. Fig. S10. Multiple whole-genome alignments of the clustered a circular and b linear contigs with their neighboring cyanophages via software Mauve, respectively. Table S1. The coordinates of 11 estuaries that are major rivers to the Lake Chaohu. Table S2. Predicted ORFs of cyanophages Pam1~Pam5. Table S3. Four tRNA genes in the Pam2 genome. Table S4. Primary sequence similarities of the putative RBPs of cyanophages Pam1, 2, 3, 5. Table S5. DALI search results of the putative RBPs of cyanophages Pam1, 2, 3, 5. Table S6. Seven circular contigs assembled from the metagenomic data of the Nanfei estuary in October, 2017.
DOI: 10.6084/m9.figshare.22600174.v1
title: Additional file 1 of Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

description: Additional file 1: Table S1. Information of the species used in the phylogenetic analysis in this study.
DOI: 10.6084/m9.figshare.22600186
title: Additional file 5 of Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

description: Additional file 5: Table S5. Annotation and gene organization of the mitochondrial genome of E. pela. N: minor strand; J: major strand. The tRNAs were annotated by different methods: MITOS2, ARWEN or aligning with the sequences of related species that were not annotated by software (ALIGN). Running ARWEN with the “-ps &lt; num&gt;” option.
DOI: 10.6084/m9.figshare.22600180.v1
title: Additional file 3 of Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

description: Additional file 3: Table S3. Annotation and gene organization of the mitochondrial genome of C. rubens. N: minor strand; J: major strand. The tRNAs were annotated by different methods: MITOS2, ARWEN or aligning with the sequences of related species that were not annotated by software (ALIGN). Running ARWEN with the “-ps &lt; num&gt;” option.
DOI: 10.6084/m9.figshare.22600183.v1
title: Additional file 4 of Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

description: Additional file 4: Table S4. Annotation and gene organization of the mitochondrial genome of C. floridensis. N: minor strand; J: major strand. The tRNAs were annotated by different methods: MITOS2, ARWEN or aligning with the sequences of related species that were not annotated by software (ALIGN). Running ARWEN with the “-ps &lt; num&gt;” option.
DOI: 10.6084/m9.figshare.22600192.v1
title: Additional file 7 of Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

description: Additional file 7: Table S7. Codon usage of the 13 mitochondrial protein-coding genes of hemipteran insects. AA: amino acid; RSCU: relative synonymous codon usage.
DOI: 10.6084/m9.figshare.22600195
title: Additional file 8 of Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

description: Additional file 8: Table S8. Codon usage of the 13 mitochondrial protein-coding genes of five scale insects. AA: amino acid; RSCU: relative synonymous codon usage.
DOI: 10.6084/m9.figshare.22599134
title: Additional file 3 of Genome-wide associated variants of subclinical atherosclerosis among young people with HIV and gene-environment interactions

description: Additional file 3: Summary statistics of GWAS in relation to cIMT among all PWH.
DOI: 10.6084/m9.figshare.3523256
title: Supplement 3. Data on bryophytes and vascular plants in Carpathian spring meadows.

description: File List dataHajek.zip -- zip file of the next three data files from Hájek et al. (2002) on 70 Carpathian spring meadows (all comma- separated ASCII text files).<br> <br> bryophytes.txt -- data on 30 bryophyte species (occuring 5 or more times).<br> vasc_plants.txt -- data on 123 vascular plant species (occuring 5 or more times).<br> chemistry.txt -- data on 14 water chemistry variables and slope. Description The file dataHajek.zip contains three comma-separated ASCII text files containing data from Hájek et al. (2002) used to illustrate co-correspondence analysis in the subsection <i>Bryophytes and vascular plants in Carpathian spring meadows</i>. The data consist of 70 spring meadows (sites) and a subset of species, namely those occurring five or more times. The (abbreviated) names for columns (variables) in each file are given in the first line of each file, separated by commas. Each row starts with the site name. The first 12 variables the in file chemistry.txt are concentrations and are log-transformed before the analysis in the paper.
DOI: 10.6084/m9.figshare.3523253
title: Appendix A. A table showing the parameter estimates for the best-fit survival model (model 5o).

description: A table showing the parameter estimates for the best-fit survival model (model 5o).
DOI: 10.6084/m9.figshare.3523253.v1
title: Appendix A. A table showing the parameter estimates for the best-fit survival model (model 5o).

description: A table showing the parameter estimates for the best-fit survival model (model 5o).
DOI: 10.6084/m9.figshare.3523250
title: Appendix A. The retrospective analysis of prediction error.

description: The retrospective analysis of prediction error.
DOI: 10.6084/m9.figshare.3523250.v1
title: Appendix A. The retrospective analysis of prediction error.

description: The retrospective analysis of prediction error.
DOI: 10.6084/m9.figshare.3523247
title: Appendix B. Statistical results related to spawner biomass–recruitment–environment models.

description: Statistical results related to spawner biomass–recruitment–environment models.
DOI: 10.6084/m9.figshare.3523247.v1
title: Appendix B. Statistical results related to spawner biomass–recruitment–environment models.

description: Statistical results related to spawner biomass–recruitment–environment models.
DOI: 10.6084/m9.figshare.3523244
title: Appendix C. Effects of temperature and exploitation on projected abundance trends of the Baltic sprat population, including background text, methods, and computational details regarding the recruitment–environment–spawner biomass relationship.

description: Effects of temperature and exploitation on projected abundance trends of the Baltic sprat population, including background text, methods, and computational details regarding the recruitment–environment–spawner biomass relationship.
DOI: 10.6084/m9.figshare.3523244.v1
title: Appendix C. Effects of temperature and exploitation on projected abundance trends of the Baltic sprat population, including background text, methods, and computational details regarding the recruitment–environment–spawner biomass relationship.

description: Effects of temperature and exploitation on projected abundance trends of the Baltic sprat population, including background text, methods, and computational details regarding the recruitment–environment–spawner biomass relationship.
DOI: 10.6084/m9.figshare.12915923.v1
title: Virtual Survey Responses-GROUP 1.xlsx

description: Raw data from a virtual survey applied to undergraduate students belonging to two theoretical courses of biochemistry (Principles of Biochemistry-2023214 and Basic Biochemistry-1000042), offered by the Department of Chemistry, Faculty of Sciences, Universidad Nacional de Colombia (Bogotá), during the COVID-19 pandemic. The main objective of the survey was to evaluate the student's perception of the quality and academic impact of the remote classes during the mandatory lockdown. The survey was anonymously answered by most students, who willingly participated. Only one entry was allowed per respondent.<br>
DOI: 10.6084/m9.figshare.3523241
title: Supplement 1. All raw data series used in statistical analysis of sprat recruitment in the Baltic Sea.

description: File List data.txt<br> Description The data.txt file is a tab-separated ascii file. The file contains the raw data series used in statistical analyses of sprat recruitment in the Baltic Sea. Column definitions: 1 = year 2 = recruitment (1000s of 1-year olds; the numbers have been shifted back one year to year of birth) 3 = spawning stock biomass (tonnes) 4 = landings of sprat by commercial fishery (1000s of tonnes) 5 = May temperature (ºC) in Bornholm Basin at depth of 45–65 m 6 = maximal area of ice coverage of the Baltic Sea (1000s of km2) 7 = North Atlantic Oscillation index averaged for the months of January and February Missing values or cases where values not used in analyses are represented as "-99".
DOI: 10.6084/m9.figshare.3523241.v1
title: Supplement 1. All raw data series used in statistical analysis of sprat recruitment in the Baltic Sea.

description: File List data.txt<br> Description The data.txt file is a tab-separated ascii file. The file contains the raw data series used in statistical analyses of sprat recruitment in the Baltic Sea. Column definitions: 1 = year 2 = recruitment (1000s of 1-year olds; the numbers have been shifted back one year to year of birth) 3 = spawning stock biomass (tonnes) 4 = landings of sprat by commercial fishery (1000s of tonnes) 5 = May temperature (ºC) in Bornholm Basin at depth of 45–65 m 6 = maximal area of ice coverage of the Baltic Sea (1000s of km2) 7 = North Atlantic Oscillation index averaged for the months of January and February Missing values or cases where values not used in analyses are represented as "-99".
DOI: 10.6084/m9.figshare.3523238
title: Appendix A. A summary of invertebrate taxa of different size categories collected at all sites.

description: A summary of invertebrate taxa of different size categories collected at all sites.