cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25264286
title: Additional file 1 of The ancestral type of the R-RAS protein has oncogenic potential

description: Additional file 1. Accession numbers and amino acid sequences of R-RAS proteins from selected species.
DOI: 10.6084/m9.figshare.25264286.v1
title: Additional file 1 of The ancestral type of the R-RAS protein has oncogenic potential

description: Additional file 1. Accession numbers and amino acid sequences of R-RAS proteins from selected species.
DOI: 10.6084/m9.figshare.26684130
title: Additional file 4 of The ancestral type of the R-RAS protein has oncogenic potential

description: Additional file 4. The amino acid sequence identity and similarity percentages of R-RAS2 and R-RAS2-like homologs from selected species.
DOI: 10.6084/m9.figshare.26684127
title: Additional file 3 of The ancestral type of the R-RAS protein has oncogenic potential

description: Additional file 3. The amino acid sequence identity and similarity percentages of R-RAS2-like proteins from sponges and R-RAS, R-RAS2, and M-RAS from human.
DOI: 10.6084/m9.figshare.26684130.v1
title: Additional file 4 of The ancestral type of the R-RAS protein has oncogenic potential

description: Additional file 4. The amino acid sequence identity and similarity percentages of R-RAS2 and R-RAS2-like homologs from selected species.
DOI: 10.6084/m9.figshare.25264480
title: Additional file 2 of Dimethyl fumarate improves cognitive impairment and neuroinflammation in mice with Alzheimer’s disease

description: Additional file 2. Summary of statistical analysis.
DOI: 10.6084/m9.figshare.25264480.v1
title: Additional file 2 of Dimethyl fumarate improves cognitive impairment and neuroinflammation in mice with Alzheimer’s disease

description: Additional file 2. Summary of statistical analysis.
DOI: 10.5281/zenodo.13329933
title: 3D printer audio and vibration side channels

description: The dataset focuses on side channel data, i.e., sound and vibration, of 3D printers. The dataset aims to enable further research in cyber-physical system security and explore the vulnerability of fused deposition modeling to side chanel attacks.

In particular, the datset consists mainly of sound and vibration data that were collected from two different 3D printers (bambu lab P1P and A1mini), using two different sensor systems. The first method is based on an iPhone, whereas the second one is based on a Teensy microcontroller. Both systems record sound at 44.1kHz sampling frequency. The vibrations are based on acceleration data sampled at 100 Hz and 500 Hz for the iPhone and the Teensy 4.0, respectively.  Furthermore, the diversity of the dataset for both Teensy and iPhone methods was achieved using 12 different 3D designs. The dataset also inludes the source 3D CAD and sliced toolpath files of the objects that were printed, videos of the printing process, and recordings of the backround noise that exists in the data recordings.  A table of contents is also provided in the files.
DOI: 10.5281/zenodo.13329934
title: 3D printer audio and vibration side channels

description: The dataset focuses on side channel data, i.e., sound and vibration, of 3D printers. The dataset aims to enable further research in cyber-physical system security and explore the vulnerability of fused deposition modeling to side chanel attacks.

In particular, the datset consists mainly of sound and vibration data that were collected from two different 3D printers (bambu lab P1P and A1mini), using two different sensor systems. The first method is based on an iPhone, whereas the second one is based on a Teensy microcontroller. Both systems record sound at 44.1kHz sampling frequency. The vibrations are based on acceleration data sampled at 100 Hz and 500 Hz for the iPhone and the Teensy 4.0, respectively.  Furthermore, the diversity of the dataset for both Teensy and iPhone methods was achieved using 12 different 3D designs. The dataset also inludes the source 3D CAD and sliced toolpath files of the objects that were printed, videos of the printing process, and recordings of the backround noise that exists in the data recordings.  A table of contents is also provided in the files.
DOI: 10.6084/m9.figshare.25264205
title: Additional file 1 of The therapeutically actionable long non-coding RNA ‘T-RECS’ is essential to cancer cells’ survival in NRAS/MAPK-driven melanoma

description: Supplementary Material 1: Supplementary Table 1: Cell-line information. Supplementary Table 2: Cell Growth Reduction (%) caused by T-RECS-RNA-targeting therapy. Supplementary Table 3: Gene Expression Analysis of downregulated Genes between D04-Cells Treated with Non-targeting ASOs and T-RECS Targeting ASOs. Supplementary Table 4: Gene Expression Analysis of upregulated Genes between D04-Cells Treated with Non-targeting ASOs and T-RECS Targeting ASOs. Supplementary Table 5: DAVID functional clustering analysis. Supplementary Table 6: Tumor size and weight of mice. Supplementary Table 7: Primer sequences (5′-3′)
DOI: 10.6084/m9.figshare.25264205.v1
title: Additional file 1 of The therapeutically actionable long non-coding RNA ‘T-RECS’ is essential to cancer cells’ survival in NRAS/MAPK-driven melanoma

description: Supplementary Material 1: Supplementary Table 1: Cell-line information. Supplementary Table 2: Cell Growth Reduction (%) caused by T-RECS-RNA-targeting therapy. Supplementary Table 3: Gene Expression Analysis of downregulated Genes between D04-Cells Treated with Non-targeting ASOs and T-RECS Targeting ASOs. Supplementary Table 4: Gene Expression Analysis of upregulated Genes between D04-Cells Treated with Non-targeting ASOs and T-RECS Targeting ASOs. Supplementary Table 5: DAVID functional clustering analysis. Supplementary Table 6: Tumor size and weight of mice. Supplementary Table 7: Primer sequences (5′-3′)
DOI: 10.6084/m9.figshare.25271772
title: Additional file 1 of Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics

description: Additional file 1: Table S1. Summary of the metaproteome and metagenome annotations. Including, taxonomic annotations (LCA score ≥80%) and functional annotations (BLASTP, Uniprot) obtained from mPies for the 16S-TaxDB, 18S-TaxDB (note taxonomy is from BLASTP results), MG-DB, and 16S-TaxDB-2nd protein search databases. The metagenome annotations are derived from DRAM and include hits to the KEGG and PFam databases. Table S2. Summary of the taxonomic classifications of the metagenome reads obtained using Kaiju. Table S3. Relative quantification and functional annotations of the expressed Pseudoalteromonas sp. proteins (% relative abundance) using the recovered metagenome-assembled genome as a protein search database.
DOI: 10.6084/m9.figshare.25271772.v1
title: Additional file 1 of Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics

description: Additional file 1: Table S1. Summary of the metaproteome and metagenome annotations. Including, taxonomic annotations (LCA score ≥80%) and functional annotations (BLASTP, Uniprot) obtained from mPies for the 16S-TaxDB, 18S-TaxDB (note taxonomy is from BLASTP results), MG-DB, and 16S-TaxDB-2nd protein search databases. The metagenome annotations are derived from DRAM and include hits to the KEGG and PFam databases. Table S2. Summary of the taxonomic classifications of the metagenome reads obtained using Kaiju. Table S3. Relative quantification and functional annotations of the expressed Pseudoalteromonas sp. proteins (% relative abundance) using the recovered metagenome-assembled genome as a protein search database.
DOI: 10.6084/m9.figshare.25271905
title: Additional file 2 of Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics

description: Additional file 2: Fig. S1. Coverages of identified peptide spectra across four protein search databases for the indirect and direct extraction metaproteomes (A); corresponding number of identified proteins at a False Discovery Rate of 1% (B); number of identified peptides (C). Fig. S2. Significant up- / down-regulation of quantified proteins between Indirect (maroon circles) and Direct (orange circles) extraction (cut-off = 2-Fold Change, adjusted P-value &lt; 0.05). Fig. S3. Mechanical detachment approaches and mechanical and chemical cell lysis protocols display differential plastisphere recovery and protein yields. Recovery of plastisphere cells via four detachment methods (n = 3; A); crystal violet biofilm assay post-detachment (n=3; B); total protein following mechanical cell lysis (n=12; C); normalised protein yields from chemical cell lysis (n=3; D). Fig S4. Microbial growth after 24 hr incubation in nutrient rich media following: mechanical detachment of plastisphere cells (n=3; A), and viability of chemically lysed cells (n=3; B). ASW = artificial seawater. Control = plastics on ice in ASW; cells = detached cells, no cell lysis. Fig. S5. Comparison of the annotated combined gel-free and combined gel-based metaproteomes identified shared and unique proteins and differences in the representation of functional. Fig. S6. Metabolic overview of the key pathways identified within the plastisphere co-assembled metagenome. Fig. S7. Identification of bacterial virulence factors in the plastisphere through alignment of the metagenome reads to VFDB, revealed the presence of pathogenic taxa (A) and their virulence genes (B), shown as a proportion (Relative abundance, %) of the reads aligning to VFDB. Virulence factors highlighted in red were also identified within the metaproteomic data using multiple databases (16S-TaxDB, MG-DB, 16S-TaxDB-2nd and VFDB).
DOI: 10.6084/m9.figshare.25271905.v1
title: Additional file 2 of Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics

description: Additional file 2: Fig. S1. Coverages of identified peptide spectra across four protein search databases for the indirect and direct extraction metaproteomes (A); corresponding number of identified proteins at a False Discovery Rate of 1% (B); number of identified peptides (C). Fig. S2. Significant up- / down-regulation of quantified proteins between Indirect (maroon circles) and Direct (orange circles) extraction (cut-off = 2-Fold Change, adjusted P-value &lt; 0.05). Fig. S3. Mechanical detachment approaches and mechanical and chemical cell lysis protocols display differential plastisphere recovery and protein yields. Recovery of plastisphere cells via four detachment methods (n = 3; A); crystal violet biofilm assay post-detachment (n=3; B); total protein following mechanical cell lysis (n=12; C); normalised protein yields from chemical cell lysis (n=3; D). Fig S4. Microbial growth after 24 hr incubation in nutrient rich media following: mechanical detachment of plastisphere cells (n=3; A), and viability of chemically lysed cells (n=3; B). ASW = artificial seawater. Control = plastics on ice in ASW; cells = detached cells, no cell lysis. Fig. S5. Comparison of the annotated combined gel-free and combined gel-based metaproteomes identified shared and unique proteins and differences in the representation of functional. Fig. S6. Metabolic overview of the key pathways identified within the plastisphere co-assembled metagenome. Fig. S7. Identification of bacterial virulence factors in the plastisphere through alignment of the metagenome reads to VFDB, revealed the presence of pathogenic taxa (A) and their virulence genes (B), shown as a proportion (Relative abundance, %) of the reads aligning to VFDB. Virulence factors highlighted in red were also identified within the metaproteomic data using multiple databases (16S-TaxDB, MG-DB, 16S-TaxDB-2nd and VFDB).
DOI: 10.5281/zenodo.13337049
title: Aligned Long-Read Murine Samples: Part 22

description: Accession numbers can be queried via the European Nucleotide Archive for metadata information: https://www.ebi.ac.uk/ena 

Samples analyzed via the original version of L-RAPiT: 

Nelson, T.M.; Ghosh, S.; Postler, T.S. L-RAPiT: A Cloud-Based Computing Pipeline for the Analysis of Long-Read RNA Sequencing Data. Int. J. Mol. Sci. 2022, 23, 15851. https://doi.org/10.3390/ijms232415851
DOI: 10.5281/zenodo.13337050
title: Aligned Long-Read Murine Samples: Part 22

description: Accession numbers can be queried via the European Nucleotide Archive for metadata information: https://www.ebi.ac.uk/ena 

Samples analyzed via the original version of L-RAPiT: 

Nelson, T.M.; Ghosh, S.; Postler, T.S. L-RAPiT: A Cloud-Based Computing Pipeline for the Analysis of Long-Read RNA Sequencing Data. Int. J. Mol. Sci. 2022, 23, 15851. https://doi.org/10.3390/ijms232415851
DOI: 10.6084/m9.figshare.25271911
title: Additional file 2 of Pig pangenome graph reveals functional features of non-reference sequences

description: Additional file 2: Table S1. The information of samples used for population-based NRS analysis. Table S2. he enrichment analysis of genes affected by deleterious variants for SWT and TC pig. Table S3. rchored ratio of 15 pig assemblies. Table S4. The distance between Sus scrofa 11.1 and other 20 assemblies calculated using Mash. Table S5. The information of Non-reference nodes (NRNs) in 20 assemblies. Table S6. The information of NRSs in each step of filtering. Table S7. GO enrichment analysis of genes whose CDS regions were affected by pNRS insertion events. Table S8. Enrichment analysis of QTLs where the pNRS insertion occurred. Table S9. Enrichment analysis of QTLs where the cNRS insertion occurred. Table S10. The information of low-quality reads mapping to NRSs. Table S11. The classification of 23,831 NRSs. Table S12. Fisher’s exact test for the difference of NRS frequencies between Asian pigs and European pigs. Table S13. Fisher’s exact test for the difference of NRS frequencies between cold-resistant pigs and heat-resistant pigs. Table S14. Fisher’s exact test for the difference of NRS frequencies between high-altitude pigs and low-altitude pigs. Table S15. Genes residing in the 11.6 Mb region of Chromosome X (ChrX: 45,231,666:56,875,949) enriched by 47 significantly different NRS between cold-resistant pigs and heat-resistant pigs. Table S16. Repeats annotated by RepeatMasker. Table S17. Novel genes annotated by Interproscan, Swissprot and KOBAS. Table S18. Significant terms (corrected P value &lt; 0.05) of functional enrichment analysis of novel genes using KOBAS.
DOI: 10.6084/m9.figshare.25271911.v1
title: Additional file 2 of Pig pangenome graph reveals functional features of non-reference sequences

description: Additional file 2: Table S1. The information of samples used for population-based NRS analysis. Table S2. he enrichment analysis of genes affected by deleterious variants for SWT and TC pig. Table S3. rchored ratio of 15 pig assemblies. Table S4. The distance between Sus scrofa 11.1 and other 20 assemblies calculated using Mash. Table S5. The information of Non-reference nodes (NRNs) in 20 assemblies. Table S6. The information of NRSs in each step of filtering. Table S7. GO enrichment analysis of genes whose CDS regions were affected by pNRS insertion events. Table S8. Enrichment analysis of QTLs where the pNRS insertion occurred. Table S9. Enrichment analysis of QTLs where the cNRS insertion occurred. Table S10. The information of low-quality reads mapping to NRSs. Table S11. The classification of 23,831 NRSs. Table S12. Fisher’s exact test for the difference of NRS frequencies between Asian pigs and European pigs. Table S13. Fisher’s exact test for the difference of NRS frequencies between cold-resistant pigs and heat-resistant pigs. Table S14. Fisher’s exact test for the difference of NRS frequencies between high-altitude pigs and low-altitude pigs. Table S15. Genes residing in the 11.6 Mb region of Chromosome X (ChrX: 45,231,666:56,875,949) enriched by 47 significantly different NRS between cold-resistant pigs and heat-resistant pigs. Table S16. Repeats annotated by RepeatMasker. Table S17. Novel genes annotated by Interproscan, Swissprot and KOBAS. Table S18. Significant terms (corrected P value &lt; 0.05) of functional enrichment analysis of novel genes using KOBAS.
DOI: 10.6084/m9.figshare.25271913
title: Additional file 2 of Application of gold immunochromatographic assay strip combined with digital evaluation for early detection of Toxoplasma gondii infection in multiple species

description: Additional file 2: Figure S1. Optimum pH and conjugate concentrations of mouse IgG. (a) The colloidal gold solution was adjusted to different pH values using 0.2 M K2CO3 to obtain an optimum pH value for mouse IgG. (b) A twofold series showing an increasing amount of mouse IgG added to a colloidal gold solution to identify the optimum conjugate amount of murine protein. Figure S2. Stability of the AMA1C-GICA strips. P: Toxoplasma gondii-positive control; N: T. gondii-negative control; PBS: blank control. Figure S3. Inter- and intra-batch variation of the AMA1C-GICA strips. P: Toxoplasma gondii-positive control, N: T. gondii-negative control.
DOI: 10.6084/m9.figshare.25271913.v1
title: Additional file 2 of Application of gold immunochromatographic assay strip combined with digital evaluation for early detection of Toxoplasma gondii infection in multiple species

description: Additional file 2: Figure S1. Optimum pH and conjugate concentrations of mouse IgG. (a) The colloidal gold solution was adjusted to different pH values using 0.2 M K2CO3 to obtain an optimum pH value for mouse IgG. (b) A twofold series showing an increasing amount of mouse IgG added to a colloidal gold solution to identify the optimum conjugate amount of murine protein. Figure S2. Stability of the AMA1C-GICA strips. P: Toxoplasma gondii-positive control; N: T. gondii-negative control; PBS: blank control. Figure S3. Inter- and intra-batch variation of the AMA1C-GICA strips. P: Toxoplasma gondii-positive control, N: T. gondii-negative control.
DOI: 10.6084/m9.figshare.25271919
title: Additional file 2 of Associations between patterns of blood heavy metal exposure and health outcomes: insights from NHANES 2011–2016

description: Additional file 2: Patterns 1 and 3 as References for Analyzing Relationships Between Other Patterns and Health Outcomes.
DOI: 10.6084/m9.figshare.25271919.v1
title: Additional file 2 of Associations between patterns of blood heavy metal exposure and health outcomes: insights from NHANES 2011–2016

description: Additional file 2: Patterns 1 and 3 as References for Analyzing Relationships Between Other Patterns and Health Outcomes.
DOI: 10.6084/m9.figshare.26684349
title: Additional file 9 of Hypoxic glioblastoma-cell-derived extracellular vesicles impair cGAS-STING activity in macrophages

description: Additional file 9: Supplementary Table 1. Primer sequences for qRT–PCR.
DOI: 10.6084/m9.figshare.26684349.v1
title: Additional file 9 of Hypoxic glioblastoma-cell-derived extracellular vesicles impair cGAS-STING activity in macrophages

description: Additional file 9: Supplementary Table 1. Primer sequences for qRT–PCR.
DOI: 10.6084/m9.figshare.26684406
title: Additional file 14 of Cirrhotic-extracellular matrix attenuates aPD-1 treatment response by initiating immunosuppressive neutrophil extracellular traps formation in hepatocellular carcinoma

description: Additional file 14: Table S2. Genes used to establish ECM score.
DOI: 10.6084/m9.figshare.26684403
title: Additional file 13 of Cirrhotic-extracellular matrix attenuates aPD-1 treatment response by initiating immunosuppressive neutrophil extracellular traps formation in hepatocellular carcinoma

description: Additional file 13: Table S1. Clinical character of HCC with different liver fibrosis stage.
DOI: 10.6084/m9.figshare.26684403.v1
title: Additional file 13 of Cirrhotic-extracellular matrix attenuates aPD-1 treatment response by initiating immunosuppressive neutrophil extracellular traps formation in hepatocellular carcinoma

description: Additional file 13: Table S1. Clinical character of HCC with different liver fibrosis stage.
DOI: 10.6084/m9.figshare.26684406.v1
title: Additional file 14 of Cirrhotic-extracellular matrix attenuates aPD-1 treatment response by initiating immunosuppressive neutrophil extracellular traps formation in hepatocellular carcinoma

description: Additional file 14: Table S2. Genes used to establish ECM score.
DOI: 10.6084/m9.figshare.26684409
title: Additional file 15 of Cirrhotic-extracellular matrix attenuates aPD-1 treatment response by initiating immunosuppressive neutrophil extracellular traps formation in hepatocellular carcinoma

description: Additional file 15: Table S3. Primer sequence used in this study.
DOI: 10.6084/m9.figshare.26684409.v1
title: Additional file 15 of Cirrhotic-extracellular matrix attenuates aPD-1 treatment response by initiating immunosuppressive neutrophil extracellular traps formation in hepatocellular carcinoma

description: Additional file 15: Table S3. Primer sequence used in this study.
DOI: 10.6084/m9.figshare.26684412
title: Additional file 16 of Cirrhotic-extracellular matrix attenuates aPD-1 treatment response by initiating immunosuppressive neutrophil extracellular traps formation in hepatocellular carcinoma

description: Additional file 16: Table S4. NanoLC-MS/MS proteomic analysis of cirrhotic-ECM.
DOI: 10.6084/m9.figshare.26684412.v1
title: Additional file 16 of Cirrhotic-extracellular matrix attenuates aPD-1 treatment response by initiating immunosuppressive neutrophil extracellular traps formation in hepatocellular carcinoma

description: Additional file 16: Table S4. NanoLC-MS/MS proteomic analysis of cirrhotic-ECM.
DOI: 10.6084/m9.figshare.26684415.v1
title: Additional file 17 of Cirrhotic-extracellular matrix attenuates aPD-1 treatment response by initiating immunosuppressive neutrophil extracellular traps formation in hepatocellular carcinoma

description: Additional file 17: Table S5. RNAseq analysis of HCC cell line stimulated with cirrhotic-ECM.
DOI: 10.6084/m9.figshare.26684415
title: Additional file 17 of Cirrhotic-extracellular matrix attenuates aPD-1 treatment response by initiating immunosuppressive neutrophil extracellular traps formation in hepatocellular carcinoma

description: Additional file 17: Table S5. RNAseq analysis of HCC cell line stimulated with cirrhotic-ECM.
DOI: 10.6084/m9.figshare.25330816.v1
title: Additional file 1 of Interactions between maternal parity and feed additives drive the composition of pig gut microbiomes in the post-weaning period

description: Additional file 1. Ingredient composition and calculated energy and nutrient content of diets. Diets were fed in four phases, and represent the base diets prior to additions of pharmacological doses of Zinc/Copper or Prebiotic according to treatment groups.
DOI: 10.15468/dl.4uvdxs
title: Occurrence Download

description: A dataset containing 290 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Zingiber officinale Roscoe"
 ]
}

 The dataset includes 290 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027249-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.