cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12050880
title: Additional file 4 of A key genomic signature associated with lymphovascular invasion in head and neck squamous cell carcinoma

description: Additional file 4: Table S4. Candidate hub genes in the turquoise module.
DOI: 10.6084/m9.figshare.12050880.v1
title: Additional file 4 of A key genomic signature associated with lymphovascular invasion in head and neck squamous cell carcinoma

description: Additional file 4: Table S4. Candidate hub genes in the turquoise module.
DOI: 10.6084/m9.figshare.12050889
title: Additional file 5 of A key genomic signature associated with lymphovascular invasion in head and neck squamous cell carcinoma

description: Additional file 5: Table S5. Candidate hub genes in the pink module.
DOI: 10.6084/m9.figshare.18866508
title: Additional file 2 of Genome-wide analysis of cell-Free DNA methylation profiling with MeDIP-seq identified potential biomarkers for colorectal cancer

description: Additional file 2: Supplementary Table 2. Promoter DMRs identified in cfDNA of colorectal cancer patient plasma.
DOI: 10.6084/m9.figshare.12050895
title: Additional file 6 of A key genomic signature associated with lymphovascular invasion in head and neck squamous cell carcinoma

description: Additional file 6: Table S6. Risk score.
DOI: 10.6084/m9.figshare.12050850
title: Additional file 1 of A key genomic signature associated with lymphovascular invasion in head and neck squamous cell carcinoma

description: Additional file 1: Table S1. Differentially expressed genes in TCGA database.
DOI: 10.6084/m9.figshare.12050850.v1
title: Additional file 1 of A key genomic signature associated with lymphovascular invasion in head and neck squamous cell carcinoma

description: Additional file 1: Table S1. Differentially expressed genes in TCGA database.
DOI: 10.6084/m9.figshare.12050991
title: Additional file 1 of Identification of novel biomarkers in ischemic stroke: a genome-wide integrated analysis

description: Additional file 1: Table S1. The DE-miRNA of two groups of miRNA dataset.
DOI: 10.6084/m9.figshare.12050868
title: Additional file 3 of A key genomic signature associated with lymphovascular invasion in head and neck squamous cell carcinoma

description: Additional file 3: Table S3. HNSCC-related genes in the OMIM database.
DOI: 10.6084/m9.figshare.12050991.v1
title: Additional file 1 of Identification of novel biomarkers in ischemic stroke: a genome-wide integrated analysis

description: Additional file 1: Table S1. The DE-miRNA of two groups of miRNA dataset.
DOI: 10.6084/m9.figshare.12050895.v1
title: Additional file 6 of A key genomic signature associated with lymphovascular invasion in head and neck squamous cell carcinoma

description: Additional file 6: Table S6. Risk score.
DOI: 10.6084/m9.figshare.12050856
title: Additional file 2 of A key genomic signature associated with lymphovascular invasion in head and neck squamous cell carcinoma

description: Additional file 2: Table S2. HNSCC-related genes in the NCBI Gene database.
DOI: 10.6084/m9.figshare.12050868.v1
title: Additional file 3 of A key genomic signature associated with lymphovascular invasion in head and neck squamous cell carcinoma

description: Additional file 3: Table S3. HNSCC-related genes in the OMIM database.
DOI: 10.6084/m9.figshare.16769604.v1
title: Two types of immune infiltrating cells and six hub genes can predict the occurrence of myasthenia gravis in patients with thymoma

description: Thymoma is the most common primary mass in anterior mediastinum. Although associated with low malignancy, it is often accompanied by myasthenia gravis resulting in poor prognosis. Due to the dual factors of tumor immune tolerance and autoimmune reaction, it is urgent to understand the immune status of MG with thymoma. In this study, RNA sequencing data were obtained from the TCGA and GEO cohorts to identify differentially expressed messenger RNAs and infiltrated immune cells. A total of 121 samples in TCGA and 43 samples in GEO were screened out. The infiltrated immune cells were identified by CIBERSORT, in which Tfh cells and activated DC cells were abnormal in thymoma patients. The differently expressed genes were performed by package LIMMA. The functional characteristics of differently expression genes were analyzed by GO and KEGG; one GO and seven KEGG pathways were both found in both TCGA and GEO cohorts. Meanwhile, 27 common differently expressed genes were obtained and were displayed by a Venn diagram. The TRRUST was used to screen the hub genes for the common 27 different genes and 6 genes were found. Then, PPI networks were constructed. Subsequently, the relationship between SCNAs of common genes and related immune cells tested by TIMER. Kaplan–Meier plots, ROC curve and Cox’s expression model for immune infiltration and hub genes were also tested. In conclusion, we found that two types of immune infiltrated cells and six hub genes can predict the occurrence of myasthenia gravis in thymoma patients.
DOI: 10.5281/zenodo.10527096
title: Dataset: Trees on smallholder farms and forest restoration are critical for Rwanda to achieve net zero emissions

description: The dataset contains results from the publication "Rwanda’s pathway to net zero empowering smallholder farmers and forest restoration", available online at: https://www.researchsquare.com/article/rs-3337982/v1. The content is composed of 8 files listed as the following (please see the Methods section of the publication for more details):1. "Tree_Density_map_FARMLAND_2008.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the density (count or sum) of individual trees per ha in Rwandan farmlands, mapped using aerial images of Rwanda from 2008. 

2. "Tree_Density_map_FARMLAND_2019.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the density (count or sum) of individual trees per ha in Rwandan farmlands, mapped using WordlView satellite images of Rwanda from 2019. 

3. "Tree_Density_map_DEG_NAT_FOR_2008.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the density (count or sum) of individual trees per ha in Rwandan degraded natural forests, mapped using WordlView satellite images of Rwanda from 2008. 

4. "Tree_Density_map_DEG_NAT_FOR_2019.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the density (count or sum) of individual trees per ha in Rwandan degraded natural forests, mapped using WordlView satellite images of Rwanda from 2019. 

5. "AGC_FARMLAND_2008.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the estimated Aboveground Carbon stock per (Mg C ha) for individual trees in Rwandan farmlands for 2008.

6. "AGC_FARMLAND_2019.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the estimated Aboveground Carbon stock per (Mg C ha) for individual trees in Rwandan farmlands for 2019.

7. "AGC_DEG_NAT_FOR_2008.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the estimated Aboveground Carbon stock per (Mg C ha) for individual trees in Rwandan degraded natural forests for 2008.

8. "AGC_DEG_NAT_FOR_2019.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the estimated Aboveground Carbon stock per (Mg C ha) for individual trees in Rwandan degraded natural forests for 2019.Note: Please note that the images have undergone specific preprocessing (especially due to differences in image sources and quality), which make the results presented here not directly comparabe to the results from  https://doi.org/10.1038/s41558-022-01544-w . Please see Methods section at https://www.researchsquare.com/article/rs-3337982/v1 for more elaborated details.
DOI: 10.5281/zenodo.10527097
title: Dataset: Trees on smallholder farms and forest restoration are critical for Rwanda to achieve net zero emissions

description: The dataset contains results from the publication "Rwanda’s pathway to net zero empowering smallholder farmers and forest restoration", available online at: https://www.researchsquare.com/article/rs-3337982/v1. The content is composed of 8 files listed as the following (please see the Methods section of the publication for more details):1. "Tree_Density_map_FARMLAND_2008.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the density (count or sum) of individual trees per ha in Rwandan farmlands, mapped using aerial images of Rwanda from 2008. 

2. "Tree_Density_map_FARMLAND_2019.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the density (count or sum) of individual trees per ha in Rwandan farmlands, mapped using WordlView satellite images of Rwanda from 2019. 

3. "Tree_Density_map_DEG_NAT_FOR_2008.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the density (count or sum) of individual trees per ha in Rwandan degraded natural forests, mapped using WordlView satellite images of Rwanda from 2008. 

4. "Tree_Density_map_DEG_NAT_FOR_2019.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the density (count or sum) of individual trees per ha in Rwandan degraded natural forests, mapped using WordlView satellite images of Rwanda from 2019. 

5. "AGC_FARMLAND_2008.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the estimated Aboveground Carbon stock per (Mg C ha) for individual trees in Rwandan farmlands for 2008.

6. "AGC_FARMLAND_2019.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the estimated Aboveground Carbon stock per (Mg C ha) for individual trees in Rwandan farmlands for 2019.

7. "AGC_DEG_NAT_FOR_2008.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the estimated Aboveground Carbon stock per (Mg C ha) for individual trees in Rwandan degraded natural forests for 2008.

8. "AGC_DEG_NAT_FOR_2019.tif". This is a 100m resolution GeoTIFF file with a coordinate reference system of EPSG: 4326, containing the estimated Aboveground Carbon stock per (Mg C ha) for individual trees in Rwandan degraded natural forests for 2019.Note: Please note that the images have undergone specific preprocessing (especially due to differences in image sources and quality), which make the results presented here not directly comparabe to the results from  https://doi.org/10.1038/s41558-022-01544-w . Please see Methods section at https://www.researchsquare.com/article/rs-3337982/v1 for more elaborated details.
DOI: 10.5281/zenodo.10676886
title: Metagenomic data sketch file batch 4
DOI: 10.5281/zenodo.10676887
title: Metagenomic data sketch file batch 4
DOI: 10.6069/uwlswd.a3v4-v844
title: Sound recording: special playback characteristics
title: MARC21 007/12 values for sound recordings expressed using RDF

description: Playback characteristics for sound recordings, including
 special equipment or equalization necessary for proper playback. Not used to indicate
 special processes used during recording unless those processes must be applied during
 playback.
DOI: 10.5281/zenodo.10614424
title: Metagenomic data sketch file batch 2

description: The second batch of metagenomic sketch files,divided into 10 files.
DOI: 10.5281/zenodo.10614425
title: Metagenomic data sketch file batch 2

description: The second batch of metagenomic sketch files,divided into 10 files.
DOI: 10.6069/uwlswd.enb6-8r41
title: Sound recording: specific material designation
title: MARC21 007/01 values for sound recordings expressed using RDF

description: Special class of sound recording to which the item belongs
 (e.g., a cylinder).
DOI: 10.6084/m9.figshare.12050598
title: Additional file 1 of Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy

description: Additional file 1. Contains supplementary table Tab. S1: HLA class I and II restricted peptides from the 113 candidate genes identified by HLA ligandomics in patient cohort 1 (n = 55).
DOI: 10.6084/m9.figshare.12050598.v1
title: Additional file 1 of Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy

description: Additional file 1. Contains supplementary table Tab. S1: HLA class I and II restricted peptides from the 113 candidate genes identified by HLA ligandomics in patient cohort 1 (n = 55).
DOI: 10.6069/uwlswd.m935-w309
title: Sound recording: speed
title: MARC21 007/03 values for sound recordings expressed using RDF

description: Playback speed of the sound recording.
DOI: 10.6084/m9.figshare.12050841.v1
title: Additional file 1 of Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus

description: Additional file 1: Table S1. The list of orthologous TLP gene pairs between B. napus, A. thaliana, B. rapa, and B. oleracea. Table S2. The list of paralogous TLP gene pairs in each of other examined species. Table S3. Ka/Ks calculation and divergent time of the orthologous gene pairs between B. napus and other 3 species. Table S4. The duplicated type of TLP genes in B. napus and other three brassicaceae species. The 0 to 4 indicate the singleton, dispersed, proximal, tandem, WGD duplication type, respectively. Table S5. The expression level of the TLP genes in root and leaf for B. napus. The gene expression was determined by the RNA-Seq data (RPKM).
DOI: 10.6084/m9.figshare.12050841
title: Additional file 1 of Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus

description: Additional file 1: Table S1. The list of orthologous TLP gene pairs between B. napus, A. thaliana, B. rapa, and B. oleracea. Table S2. The list of paralogous TLP gene pairs in each of other examined species. Table S3. Ka/Ks calculation and divergent time of the orthologous gene pairs between B. napus and other 3 species. Table S4. The duplicated type of TLP genes in B. napus and other three brassicaceae species. The 0 to 4 indicate the singleton, dispersed, proximal, tandem, WGD duplication type, respectively. Table S5. The expression level of the TLP genes in root and leaf for B. napus. The gene expression was determined by the RNA-Seq data (RPKM).
DOI: 10.5281/zenodo.10697174
title: Wet Horizons 3i Survey Results Dataset

description: Dataset resulting from a survey assessing the interest, influence and impact levels of relevant parties for the European Commission funded Wet Horizons project, which seeks to provide tools to scale up wetland restoration across Europe. This dataset includes information about organisations related to the 9 Wet Horizons study catchments: rivers along the Kattegat, Denmark; Kokemäenjoki, Finland; Kemi, Finland; Garonne, France; Peene River, Germany; Lower Rhine/Ljssel, Netherlands; Biebrza, Poland; Danube, Romania; Dee, Scotland.
DOI: 10.5281/zenodo.10697175
title: Wet Horizons 3i Survey Results Dataset

description: Dataset resulting from a survey assessing the interest, influence and impact levels of relevant parties for the European Commission funded Wet Horizons project, which seeks to provide tools to scale up wetland restoration across Europe. This dataset includes information about organisations related to the 9 Wet Horizons study catchments: rivers along the Kattegat, Denmark; Kokemäenjoki, Finland; Kemi, Finland; Garonne, France; Peene River, Germany; Lower Rhine/Ljssel, Netherlands; Biebrza, Poland; Danube, Romania; Dee, Scotland.
DOI: 10.5281/zenodo.10732281
title: IGN Test Data for ICDAR'24 MapText Competition

description: Data set of 2Kx2K image tiles cropped from Napoleonic Cadastre maps of the Val de Marne Archive for the ICDAR'24 Competition on Historical Map Text Detection, Recognition, and Linking.

Annotations and images follow the format described at the competition website and can be evaluated using the official evaluation repository script.




 
Test


Annotations
N/A


Images
test.zip


Files
ign/test/*.jpg


Tiles
50


Map Sheets
49




Original images available at https://archives.valdemarne.fr/recherches/archives-en-ligne/cadastre-napoleonien as of Feb., 1st 2024.
DOI: 10.48597/xp5x-xkjr
title: Measurement of 1-methylanthracene at Auchencorth Moss

description: Measurement of 1-methylanthracene at Auchencorth Moss
DOI: 10.48597/y77x-rjcw
title: Measurement of 4-5-methylenephenanthrene at Auchencorth Moss

description: Measurement of 4-5-methylenephenanthrene at Auchencorth Moss
DOI: 10.48597/yc4b-pyt4
title: Measurement of 4-5-methylenephenanthrene at Harwell

description: Measurement of 4-5-methylenephenanthrene at Harwell
DOI: 10.48597/yvdy-dqxx
title: Measurement of Benzo_j_fluoranthene at Harwell

description: Measurement of Benzo_j_fluoranthene at Harwell
DOI: 10.48597/z3fz-8wfn
title: Measurement of Benzo_b_naphtho_21_d_thiophene at Harwell

description: Measurement of Benzo_b_naphtho_21_d_thiophene at Harwell
DOI: 10.6084/m9.figshare.12051021
title: Additional file 1 of Emergency retroperitoneal laparoscopic partial nephrectomy for ruptured renal angiomyolipomas: a retrospective single-center series of 15 cases

description: Additional file 1: Supplementary Table 1. Characteristics of all 15 patients.
DOI: 10.6084/m9.figshare.12051021.v1
title: Additional file 1 of Emergency retroperitoneal laparoscopic partial nephrectomy for ruptured renal angiomyolipomas: a retrospective single-center series of 15 cases

description: Additional file 1: Supplementary Table 1. Characteristics of all 15 patients.
DOI: 10.48597/zgbs-g54p
title: Measurement of Coronene at Auchencorth Moss

description: Measurement of Coronene at Auchencorth Moss
DOI: 10.48597/zs2x-r8y6
title: Measurement of Acenaphthene at Harwell

description: Measurement of Acenaphthene at Harwell
DOI: 10.48597/zudt-3yhe
title: Measurement of Cyclopenta_cd_pyrene at Auchencorth Moss

description: Measurement of Cyclopenta_cd_pyrene at Auchencorth Moss
DOI: 10.6069/uwlswd.fh0k-hk62
title: Sound recording: tape configuration
title: MARC21 007/08 values for sound recordings expressed using RDF

description: Number of tracks on a tape.
DOI: 10.48597/8tk4-822g
title: Measurement of Heavy metals and pm10_mass at Topolniky

description: Measurement of Heavy metals and pm10_mass at Topolniky
DOI: 10.48597/jtrd-eeek
title: Measurement of Heavy metals and susp_part_matter at Chopok

description: Measurement of Heavy metals and susp_part_matter at Chopok
DOI: 10.48597/nz42-efx6
title: Measurement of Heavy metals and pm10_mass at Starina

description: Measurement of Heavy metals and pm10_mass at Starina
DOI: 10.6084/m9.figshare.18866523.v1
title: Additional file 1 of Zinc transporter ZIP12 maintains zinc homeostasis and protects spermatogonia from oxidative stress during spermatogenesis

description: Additional file 1: Supplementary Table 1. PCR primers.
DOI: 10.6084/m9.figshare.18866523
title: Additional file 1 of Zinc transporter ZIP12 maintains zinc homeostasis and protects spermatogonia from oxidative stress during spermatogenesis

description: Additional file 1: Supplementary Table 1. PCR primers.
DOI: 10.6069/uwlswd.4j0p-0k57
title: Sound recording: tape width
title: MARC21 007/07 values for sound recordings expressed using RDF

description: Width of the tape.
DOI: 10.48597/v9us-r2s2
title: Measurement of Particle_number_size_distribution at Puy de Dôme

description: Measurement of Particle_number_size_distribution at Puy de Dôme
DOI: 10.6069/uwlswd.9t5f-qz73
title: Tactile material: braille music format
title: MARC21 007/06-08 values for tactile material expressed using RDF

description: Indicates the braille music format of the item. The music
 formats are the way measures, sections, parts, and related information, such as words, are
 presented in relation to each other.
DOI: 10.6084/m9.figshare.12051084
title: Additional file 2 of Functional comparison of PBMCs isolated by Cell Preparation Tubes (CPT) vs. Lymphoprep Tubes

description: Additional file 2: Table S1. Statistical analysis shows choice of CPT or LP method is not the major contributor to variance for yield, and recovery. Anova variance for contribution of donor, method (CPT or LP), and operator on cell yield pre-freeze, cell yield post-freeze, and recovery measured by Sysmex XE-2100 automated hematology analyzer. Sum squares, sum square contributions, F values, and P values are shown for each parameter measured (rows).
DOI: 10.6084/m9.figshare.12051084.v1
title: Additional file 2 of Functional comparison of PBMCs isolated by Cell Preparation Tubes (CPT) vs. Lymphoprep Tubes

description: Additional file 2: Table S1. Statistical analysis shows choice of CPT or LP method is not the major contributor to variance for yield, and recovery. Anova variance for contribution of donor, method (CPT or LP), and operator on cell yield pre-freeze, cell yield post-freeze, and recovery measured by Sysmex XE-2100 automated hematology analyzer. Sum squares, sum square contributions, F values, and P values are shown for each parameter measured (rows).
DOI: 10.6084/m9.figshare.14672673
title: Metadata record for the manuscript: Analytical validation of a targeted liquid biopsy assay with comprehensive molecular and clinical profiling of circulating tumor DNA from 1,000 patients

description: <b>Summary</b><br>

This
metadata record provides details of the data supporting the claims of the
related manuscript: “Validation of a liquid biopsy assay with molecular and clinical profiling of circulating tumor DNA”.

The
related study presents extensive validation studies of the Tempus xF liquid
biopsy assay (a 105-gene, hybrid-capture, next-generation sequencing (NGS)
assay that detects single-nucleotide variants, insertions/deletions, copy
number variants, and chromosomal rearrangements) using reference standards,
cell lines, and patient samples that establish high sensitivity, specificity,
and accuracy in variant detection.

 

Type of data:
liquid biopsy 

Subject of
data: <i>Homo sapiens</i>

Sample size:
1000

Recruitment:
randomly selected cancer patients who had clinical plasma specimens sequenced
with the xF panel at CAP/CLIA-certified Tempus Labs, Inc.

 

<b>Data
access</b>

The de-identified clinical data that
support findings from the retrospective profiling study have been deposited in
the Vivli repository (https://vivli.org/) in the file ‘xf_1000_De-identified_Phenotypic_Data_and_ctFE.tsv’
under the following accession: T20.01 (https://search.vivli.org/?search=T20.01). Access is restricted, and interested
parties must make an authorised request to the Vivli repository.

The
following supplementary tables are openly available in accessible format as
part of this <i>figshare </i>data record:

- Supplementary
Table 4.xlsx. This table underlies Figure 1 of the related article: Inter-assay
comparison between Tempus xF, ddPCR, and Tempus xT results.

- Supplementary
Table 1. Analysis Variants detected by the Tempus xF assay 

- Supplementary
Table 2. Overview of samples and experiments

- Supplementary
Table 3. Probabilistic noise filtering methodology improves variant

Raw data
from the validation experiments were generated and analysed as part of a
CAP/CLIA validation. As such, they are not publicly available but have been
thoroughly reviewed by those governing authorities.

 

<b>Corresponding author(s) for this study</b>

Nike
Beaubier, Tempus Labs, Chicago, IL, USA. Nike.Beaubier@tempus.com.<br>
<br>
<b></b>

<b>Study
approval </b>

The
study protocol was submitted to the Advarra Institutional Review Board (IRB),
which determined the research was exempt from IRB oversight and approved a
waiver of HIPAA authorization for this study.