cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16817941.v1
title: Liquid biopsy uncovers distinct patterns of DNA methylation and copy number changes in NSCLC patients with different EGFR-TKI resistant mutations

description: Targeted therapy with tyrosine kinase inhibitors (TKI) provides survival benefits to a majority of patients with non-small cell lung cancer (NSCLC). However, resistance to TKI almost always develops after treatment. Although genetic and epigenetic alterations have each been shown to drive resistance to TKI in cell line models, clinical evidence for their contribution in the acquisition of resistance remains limited. Here, we employed liquid biopsy for simultaneous analysis of genetic and epigenetic changes in 122 Vietnamese NSCLC patients undergoing TKI therapy and displaying acquired resistance. Genome-wide epigenetics, particularly DNA methylation changes, have been implicated in the acquisition of drug resistance by cancer cells. However, the relationship between DNA methylation and mutation alterations in mediating resistance to TKI drugs remains largely unknown. To profile the methylation changes at the genome-wide level of different resistance mutation groups, we employed the workflow previously reported by Jiang et al.. The assay was based on the combination of bisulfite conversion and massively parallel sequencing to analyze methylation density (MD) in bins of 1 Mb across 22 chromosomes. The analysis was performed for all cases with <i>EGFR</i> amplification (3 cases) and MET amplification (4 cases). For the remaining cases, only 3 out of 5 cases with co-occurring T790M and <i>EGFR</i> amplification and 3 out of 5 cases with <i>HER2</i> amplification had sufficient cell free DNA for the analysis. Among 23 patients carrying T790M mutation, we randomly selected 5 cases with sufficient plasma. The total 18 chosen cases were grouped into either EGFR dependent resistance mutations (on-target) or EGFR independent mutations (off-target). Samples from 3 healthy subjects were included as a reference set.
DOI: 10.5517/ccdc.csd.cc22hwl2
title: CCDC 1921894: Experimental Crystal Structure Determination

description: Related Article: Jing-hua Han, Bing-qian Hu, Tangming Li, Hao Liang, Fan Yu, Liang Wang, Qiang Zhao, Bao Li|2021|Cryst.Growth Des.|21|5678|doi:10.1021/acs.cgd.1c00524
DOI: 10.5517/ccdc.csd.cc22hwm3
title: CCDC 1921895: Experimental Crystal Structure Determination

description: Related Article: Jing-hua Han, Bing-qian Hu, Tangming Li, Hao Liang, Fan Yu, Liang Wang, Qiang Zhao, Bao Li|2021|Cryst.Growth Des.|21|5678|doi:10.1021/acs.cgd.1c00524
DOI: 10.5517/ccdc.csd.cc22hwn4
title: CCDC 1921896: Experimental Crystal Structure Determination

description: Related Article: Jing-hua Han, Bing-qian Hu, Tangming Li, Hao Liang, Fan Yu, Liang Wang, Qiang Zhao, Bao Li|2021|Cryst.Growth Des.|21|5678|doi:10.1021/acs.cgd.1c00524
DOI: 10.5517/ccdc.csd.cc25l8wy
title: CCDC 2013570: Experimental Crystal Structure Determination

description: Related Article: Tomoki Niwa, Kousuke Nishibashi, Hitomi Sato, Kiyoshi Ujiie, Kenji Yamashita, Hiromichi Egami, Yoshitaka Hamashima|2021|J.Am.Chem.Soc.|143|16599|doi:10.1021/jacs.1c06783
DOI: 10.5517/ccdc.csd.cc25l8xz
title: CCDC 2013571: Experimental Crystal Structure Determination

description: Related Article: Tomoki Niwa, Kousuke Nishibashi, Hitomi Sato, Kiyoshi Ujiie, Kenji Yamashita, Hiromichi Egami, Yoshitaka Hamashima|2021|J.Am.Chem.Soc.|143|16599|doi:10.1021/jacs.1c06783
DOI: 10.5517/ccdc.csd.cc25l925
title: CCDC 2013576: Experimental Crystal Structure Determination

description: Related Article: Tomoki Niwa, Kousuke Nishibashi, Hitomi Sato, Kiyoshi Ujiie, Kenji Yamashita, Hiromichi Egami, Yoshitaka Hamashima|2021|J.Am.Chem.Soc.|143|16599|doi:10.1021/jacs.1c06783
DOI: 10.5517/ccdc.csd.cc26874w
title: CCDC 2033697: Experimental Crystal Structure Determination

description: Related Article: Lin Guo, Oliver J. Dutton, Murat Kucukdisli, Matthew Davy, Olivier Wagnières, Craig P. Butts, Eddie L. Myers, Varinder K. Aggarwal|2021|J.Am.Chem.Soc.|143|16682|doi:10.1021/jacs.1c07778
DOI: 10.5517/ccdc.csd.cc26jhr0
title: CCDC 2041652: Experimental Crystal Structure Determination

description: Related Article: Luis Nóvoa, Laura Trulli, Israel Fernández, Alejandro Parra, Mariola Tortosa|2021|Org.Lett.|23|7434|doi:10.1021/acs.orglett.1c02645
DOI: 10.5517/ccdc.csd.cc26p4z1
title: CCDC 2046123: Experimental Crystal Structure Determination

description: Related Article: mingshun mei|2020|CSD Communication|||
description: Related Article: Ming-Shun Mei, Ya-Jie Wang, Gui-Shan Zhang, Jing-Yi Tang, Ping Tian, Yu-Hui Wang|2021|Org.Lett.|23|7336|doi:10.1021/acs.orglett.1c02421
DOI: 10.5517/ccdc.csd.cc27j03x
title: CCDC 2070958: Experimental Crystal Structure Determination

description: Related Article: mingshun mei|2021|CSD Communication|||
description: Related Article: Ming-Shun Mei, Ya-Jie Wang, Gui-Shan Zhang, Jing-Yi Tang, Ping Tian, Yu-Hui Wang|2021|Org.Lett.|23|7336|doi:10.1021/acs.orglett.1c02421
DOI: 10.5517/ccdc.csd.cc27lg5h
title: CCDC 2073316: Experimental Crystal Structure Determination

description: Related Article: mingshun mei|2021|CSD Communication|||
description: Related Article: Ming-Shun Mei, Ya-Jie Wang, Gui-Shan Zhang, Jing-Yi Tang, Ping Tian, Yu-Hui Wang|2021|Org.Lett.|23|7336|doi:10.1021/acs.orglett.1c02421
DOI: 10.5517/ccdc.csd.cc27mkv9
title: CCDC 2074391: Experimental Crystal Structure Determination

description: Related Article: Jianjun Wang, Xiaofeng Sun, Daguo Hu, Yian Shi|2021|Org.Lett.|23|7561|doi:10.1021/acs.orglett.1c02757
DOI: 10.5517/ccdc.csd.cc27tqb4
title: CCDC 2080296: Experimental Crystal Structure Determination

description: Related Article: Yi-Ming Zhu, Yizhan Fang, Haiyan Li, Xiao-Ping Xu, Shun-Jun Ji|2021|Org.Lett.|23|7342|doi:10.1021/acs.orglett.1c02422
DOI: 10.5517/ccdc.csd.cc27xj0q
title: CCDC 2082983: Experimental Crystal Structure Determination

description: Related Article: Katie Ruffell, Frances R. Smith, Michael T. Green, Simon M. Nicolle, Martyn Inman, William Lewis, Christopher J. Hayes, Christopher J. Moody|2021|Chem.-Eur.J.|27|13703|doi:10.1002/chem.202101788
DOI: 10.5517/ccdc.csd.cc27yzv1
title: CCDC 2084404: Experimental Crystal Structure Determination

description: Related Article: Mark K. Rong, Flip Holtrop, Eduard O. Bobylev, Martin Nieger, Andreas W. Ehlers, J. Chris Slootweg, Koop Lammertsma|2021|Chem.-Eur.J.|27|14007|doi:10.1002/chem.202101921
DOI: 10.5517/ccdc.csd.cc27yzw2
title: CCDC 2084405: Experimental Crystal Structure Determination

description: Related Article: Mark K. Rong, Flip Holtrop, Eduard O. Bobylev, Martin Nieger, Andreas W. Ehlers, J. Chris Slootweg, Koop Lammertsma|2021|Chem.-Eur.J.|27|14007|doi:10.1002/chem.202101921
DOI: 10.5517/ccdc.csd.cc27yzx3
title: CCDC 2084406: Experimental Crystal Structure Determination

description: Related Article: Mark K. Rong, Flip Holtrop, Eduard O. Bobylev, Martin Nieger, Andreas W. Ehlers, J. Chris Slootweg, Koop Lammertsma|2021|Chem.-Eur.J.|27|14007|doi:10.1002/chem.202101921
DOI: 10.5517/ccdc.csd.cc27yzy4
title: CCDC 2084407: Experimental Crystal Structure Determination

description: Related Article: Mark K. Rong, Flip Holtrop, Eduard O. Bobylev, Martin Nieger, Andreas W. Ehlers, J. Chris Slootweg, Koop Lammertsma|2021|Chem.-Eur.J.|27|14007|doi:10.1002/chem.202101921
DOI: 10.5517/ccdc.csd.cc27yzz5
title: CCDC 2084408: Experimental Crystal Structure Determination

description: Related Article: Mark K. Rong, Flip Holtrop, Eduard O. Bobylev, Martin Nieger, Andreas W. Ehlers, J. Chris Slootweg, Koop Lammertsma|2021|Chem.-Eur.J.|27|14007|doi:10.1002/chem.202101921
DOI: 10.5517/ccdc.csd.cc27z008
title: CCDC 2084409: Experimental Crystal Structure Determination

description: Related Article: Mark K. Rong, Flip Holtrop, Eduard O. Bobylev, Martin Nieger, Andreas W. Ehlers, J. Chris Slootweg, Koop Lammertsma|2021|Chem.-Eur.J.|27|14007|doi:10.1002/chem.202101921
DOI: 10.6084/m9.figshare.16821482.v1
title: Additional file 2 of Association of peripheral blood DNA methylation level with Alzheimer’s disease progression

description: Additional file 2: Supplemental Tables.
DOI: 10.6084/m9.figshare.16821491
title: Additional file 1 of Parasitism by endoparasitoid wasps alters the internal but not the external microbiome in host caterpillars

description: Additional file 1: Table S1. zOTUs bacteria. Identification of bacterial zero radius operational taxonomic units (ZOTUs) according to the Silva v1.23 database and distribution over the investigated samples. Table S2. OTUs fungi. Identification of fungal operational taxonomic units (OTUs) according to the UNITE v6 database and distribution over the investigated samples. Table S3. 3 way ANOVA. Results of three way ANOVA of observed richness, Shannon diversity and densities for bacteria and fungi (caterpillars only). Table S4. Diversity bacteria. Diversity metrics for the bacterial communities. Table S5. Diversity fungi. Diversity metrics for the fungal communities. Table S6. Copy number bacteria. Determination of bacterial 16S rRNA gene copy numbers using qPCR. Table S7. Copy number fungi. Determination of fungal ITS copy numbers using qPCR. Table S8. Wolbachia detection. Occurrence of Wolbachia in studied samples, as determined using a specific Wolbachia PCR. Table S9. Plating results. Plating results: log number of colony forming units (cfu) per caterpillar (n = 2 per subgroup of health status). Table S10. Sample details. Sample details, including number of caterpillars used in this study. Table S11. Illumina primers V4. Primer design and sample-specific barcodes for the bacterial V4 region of the 16S rRNA gene. Table S12. Illumina primers ITS. Primer design and sample-specific barcodes for the fungal ITS region. Table S13. Mocks. Composition of mock communities.
DOI: 10.6084/m9.figshare.16821491.v1
title: Additional file 1 of Parasitism by endoparasitoid wasps alters the internal but not the external microbiome in host caterpillars

description: Additional file 1: Table S1. zOTUs bacteria. Identification of bacterial zero radius operational taxonomic units (ZOTUs) according to the Silva v1.23 database and distribution over the investigated samples. Table S2. OTUs fungi. Identification of fungal operational taxonomic units (OTUs) according to the UNITE v6 database and distribution over the investigated samples. Table S3. 3 way ANOVA. Results of three way ANOVA of observed richness, Shannon diversity and densities for bacteria and fungi (caterpillars only). Table S4. Diversity bacteria. Diversity metrics for the bacterial communities. Table S5. Diversity fungi. Diversity metrics for the fungal communities. Table S6. Copy number bacteria. Determination of bacterial 16S rRNA gene copy numbers using qPCR. Table S7. Copy number fungi. Determination of fungal ITS copy numbers using qPCR. Table S8. Wolbachia detection. Occurrence of Wolbachia in studied samples, as determined using a specific Wolbachia PCR. Table S9. Plating results. Plating results: log number of colony forming units (cfu) per caterpillar (n = 2 per subgroup of health status). Table S10. Sample details. Sample details, including number of caterpillars used in this study. Table S11. Illumina primers V4. Primer design and sample-specific barcodes for the bacterial V4 region of the 16S rRNA gene. Table S12. Illumina primers ITS. Primer design and sample-specific barcodes for the fungal ITS region. Table S13. Mocks. Composition of mock communities.
DOI: 10.15121/1825883
title: Utah FORGE Raw Microgravity Composite Data: Updated 10/2021.

description: This is a microgravity dataset from the Utah FORGE site near Milford, Utah. This composite dataset was updated in October, 2021 and contains data from December 17th, 2018 through September 24th, 2021. The data includes the GPS location of the measurement, date of the measurement, name of the station, relative difference in gravity, and coordinates of the station. This data was generated by the Utah Geological Survey.
DOI: 10.6084/m9.figshare.16821499
title: Additional file 15 of Annotation depth confounds direct comparison of gene expression across species

description: Additional file 15 HPA pancreas quantitation.
DOI: 10.6084/m9.figshare.16821499.v1
title: Additional file 15 of Annotation depth confounds direct comparison of gene expression across species

description: Additional file 15 HPA pancreas quantitation.
DOI: 10.6084/m9.figshare.16821502
title: Additional file 16 of Annotation depth confounds direct comparison of gene expression across species

description: Additional file 16 Collated code.
DOI: 10.6084/m9.figshare.16821502.v1
title: Additional file 16 of Annotation depth confounds direct comparison of gene expression across species

description: Additional file 16 Collated code.
DOI: 10.6084/m9.figshare.16821541
title: Additional file 2 of Effect of the spatial–temporal specific theca cell Cyp17 overexpression on the reproductive phenotype of the novel TC17 mouse

description: Additional file 2: Table S1.
DOI: 10.6084/m9.figshare.16821541.v1
title: Additional file 2 of Effect of the spatial–temporal specific theca cell Cyp17 overexpression on the reproductive phenotype of the novel TC17 mouse

description: Additional file 2: Table S1.
DOI: 10.6084/m9.figshare.16821581
title: Additional file 2 of Multiomic study of skin, peripheral blood, and serum: is serum proteome a reflection of disease process at the end-organ level in systemic sclerosis?

description: Additional file 2. Tables S1-S8.
DOI: 10.6084/m9.figshare.16821581.v1
title: Additional file 2 of Multiomic study of skin, peripheral blood, and serum: is serum proteome a reflection of disease process at the end-organ level in systemic sclerosis?

description: Additional file 2. Tables S1-S8.
DOI: 10.6084/m9.figshare.16821794.v1
title: Additional file 1 of Developing Personal Resilience Questionnaire for rural doctors: an indigenous approach study in Indonesia

description: Additional file 1. Rural doctors' resilience data.
DOI: 10.6084/m9.figshare.16821715.v1
title: Additional file 5 of Functional role of brain-engrafted macrophages against brain injuries

description: Additional file 5. Table S4. qPCR primers.
DOI: 10.6084/m9.figshare.16821712.v1
title: Additional file 4 of Functional role of brain-engrafted macrophages against brain injuries

description: Additional file 4. Table S3. Supporting data for Figure S3.
DOI: 10.6084/m9.figshare.16821709.v1
title: Additional file 3 of Functional role of brain-engrafted macrophages against brain injuries

description: Additional file 3. Table S2. Supporting data for Figure 2.
DOI: 10.6084/m9.figshare.16821706.v1
title: Additional file 2 of Functional role of brain-engrafted macrophages against brain injuries

description: Additional file 2. Table S1. Supporting data for Figure 1.
DOI: 10.6084/m9.figshare.16821628.v1
title: Additional file 9 of Tailored graphical lasso for data integration in gene network reconstruction

description: Additional file 9. List of the gene interactions in the TCGA BRCA tailored graphical lasso graph that the weighted graphical lasso was not able to find. Each row contains the name of two genes whose nodes have an edge in the tailored graphical lasso graph, but not in the weighted graphical lasso graph.
DOI: 10.6084/m9.figshare.16821625.v1
title: Additional file 8 of Tailored graphical lasso for data integration in gene network reconstruction

description: Additional file 8. List of the gene interactions in the Oslo 2 tailored graphical lasso graph that the weighted graphical lasso was not able to find. Each row contains the name of two genes whose nodes have an edge in the tailored graphical lasso graph, but not in the weighted graphical lasso graph.
DOI: 10.6084/m9.figshare.16821622.v1
title: Additional file 7 of Tailored graphical lasso for data integration in gene network reconstruction

description: Additional file 7. List of genes with interactions in the Oslo 2 tailored graphical lasso graph. Each row contains the name of two genes whose nodes in the tailored graphical lasso graph have an edge.
DOI: 10.6084/m9.figshare.16821619.v1
title: Additional file 6 of Tailored graphical lasso for data integration in gene network reconstruction

description: Additional file 6. List of genes with interactions in the TCGA BRCA tailored graphical lasso graph. Each row contains the name of two genes whose nodes in the tailored graphical lasso graph have an edge.
DOI: 10.6084/m9.figshare.16821794
title: Additional file 1 of Developing Personal Resilience Questionnaire for rural doctors: an indigenous approach study in Indonesia

description: Additional file 1. Rural doctors' resilience data.
DOI: 10.6084/m9.figshare.16821715
title: Additional file 5 of Functional role of brain-engrafted macrophages against brain injuries

description: Additional file 5. Table S4. qPCR primers.
DOI: 10.6084/m9.figshare.16821712
title: Additional file 4 of Functional role of brain-engrafted macrophages against brain injuries

description: Additional file 4. Table S3. Supporting data for Figure S3.
DOI: 10.6084/m9.figshare.16821709
title: Additional file 3 of Functional role of brain-engrafted macrophages against brain injuries

description: Additional file 3. Table S2. Supporting data for Figure 2.
DOI: 10.6084/m9.figshare.16821706
title: Additional file 2 of Functional role of brain-engrafted macrophages against brain injuries

description: Additional file 2. Table S1. Supporting data for Figure 1.
DOI: 10.6084/m9.figshare.16821628
title: Additional file 9 of Tailored graphical lasso for data integration in gene network reconstruction

description: Additional file 9. List of the gene interactions in the TCGA BRCA tailored graphical lasso graph that the weighted graphical lasso was not able to find. Each row contains the name of two genes whose nodes have an edge in the tailored graphical lasso graph, but not in the weighted graphical lasso graph.
DOI: 10.6084/m9.figshare.16821625
title: Additional file 8 of Tailored graphical lasso for data integration in gene network reconstruction

description: Additional file 8. List of the gene interactions in the Oslo 2 tailored graphical lasso graph that the weighted graphical lasso was not able to find. Each row contains the name of two genes whose nodes have an edge in the tailored graphical lasso graph, but not in the weighted graphical lasso graph.
DOI: 10.6084/m9.figshare.16821622
title: Additional file 7 of Tailored graphical lasso for data integration in gene network reconstruction

description: Additional file 7. List of genes with interactions in the Oslo 2 tailored graphical lasso graph. Each row contains the name of two genes whose nodes in the tailored graphical lasso graph have an edge.
DOI: 10.6084/m9.figshare.16821619
title: Additional file 6 of Tailored graphical lasso for data integration in gene network reconstruction

description: Additional file 6. List of genes with interactions in the TCGA BRCA tailored graphical lasso graph. Each row contains the name of two genes whose nodes in the tailored graphical lasso graph have an edge.
DOI: 10.6084/m9.figshare.16821482
title: Additional file 2 of Association of peripheral blood DNA methylation level with Alzheimer’s disease progression

description: Additional file 2: Supplemental Tables.
DOI: 10.5517/ccdc.csd.cc2856qd
title: CCDC 2090383: Experimental Crystal Structure Determination

description: Related Article: mingshun mei|2021|CSD Communication|||
description: Related Article: Ming-Shun Mei, Ya-Jie Wang, Gui-Shan Zhang, Jing-Yi Tang, Ping Tian, Yu-Hui Wang|2021|Org.Lett.|23|7336|doi:10.1021/acs.orglett.1c02421
DOI: 10.5517/ccdc.csd.cc28571r
title: CCDC 2090393: Experimental Crystal Structure Determination

description: Related Article: mingshun mei|2021|CSD Communication|||
description: Related Article: Ming-Shun Mei, Ya-Jie Wang, Gui-Shan Zhang, Jing-Yi Tang, Ping Tian, Yu-Hui Wang|2021|Org.Lett.|23|7336|doi:10.1021/acs.orglett.1c02421
DOI: 10.6084/m9.figshare.14518260
title: GDM muscle_Supplementary.docx

description: Supplementary data for "Higher muscle mass protects women with gestational diabetes mellitus from progression to type 2 diabetes mellitus"
DOI: 10.6084/m9.figshare.14518260.v3
title: GDM muscle_Supplementary.docx

description: Supplementary data for "Higher muscle mass protects women with gestational diabetes mellitus from progression to type 2 diabetes mellitus"
DOI: 10.6084/m9.figshare.14518260.v2
title: GDM muscle_Supplementary.docx

description: Supplementary data for "Higher muscle mass protects women with gestational diabetes mellitus from progression to type 2 diabetes mellitus"
DOI: 10.6084/m9.figshare.14593863
title: PalaeoWISE

description: This is the dataset which supports the publication 'A palaeoclimate proxy database for water security planning in Queensland Australia'
DOI: 10.6084/m9.figshare.14593863.v2
title: PalaeoWISE

description: This is the dataset which supports the publication 'A palaeoclimate proxy database for water security planning in Queensland Australia'
DOI: 10.5281/zenodo.5228449
title: Circling in on Convective Self-Aggregation

description: "Circling in on Convective Self-Aggregation" published in Journal of Geophysical Research: Atmospheres (2021). by Silas Boye Nissen and Jan O. Haerter. Available online: https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021JD035331. ################################################################################### This repository includes MATLAB scripts and RCE data to reproduce the figures in the article. The Circle model folder includes the mathematical model in a general easy-to-use version. The Data RCE folder includes each of the eight simulations in the article (only on Zenodo). The rest of the folders include the original files that can be used to reproduce the figures. For questions, please contact silas@nbi.ku.dk.
DOI: 10.5281/zenodo.4316702
title: Circling in on Convective Self-Aggregation

description: "Circling in on Convective Self-Aggregation" published in Journal of Geophysical Research: Atmospheres (2021). by Silas Boye Nissen and Jan O. Haerter. Available online: https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021JD035331. ################################################################################### This repository includes MATLAB scripts and RCE data to reproduce the figures in the article. The Circle model folder includes the mathematical model in a general easy-to-use version. The Data RCE folder includes each of the eight simulations in the article (only on Zenodo). The rest of the folders include the original files that can be used to reproduce the figures. For questions, please contact silas@nbi.ku.dk.