cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6985601
title: Distinct mechanisms of mismatch repair deficiency delineate two modes of response to PD-1 immunotherapy in endometrial carcinoma

description: Responses to immune checkpoint blockade (ICB) are variable even among mismatch repair deficient (MMRd) cancers. We completed a phase 2 clinical trial of the PD-1 inhibitor pembrolizumab in 24 patients with MMRd endometrial cancer (NCT02899793). Patients with mutational MMRd tumors (6 patients) had higher response rates and longer survival than those with epigenetic MMRd tumors (18 patients). Mutation burden was higher in tumors with mutational MMRd compared to epigenetic MMRd; however, within each category of MMRd, mutation burden was not associated with ICB response. Notably, JAK1 mutations did not confer resistance to pembrolizumab. Longitudinal single-cell RNA-seq of circulating immune cells revealed contrasting modes of anti-tumor immunity against mutational and epigenetic MMRd tumors. Whereas effector CD8+ T cell responses correlated with mutational MMRd, highly active CD16+ NK cells were associated with epigenetic MMRd tumors responsive to ICB. These data highlight factors beyond neoantigen burden that influence ICB response.
DOI: 10.5281/zenodo.6985600
title: Distinct mechanisms of mismatch repair deficiency delineate two modes of response to PD-1 immunotherapy in endometrial carcinoma

description: Responses to immune checkpoint blockade (ICB) are variable even among mismatch repair deficient (MMRd) cancers. We completed a phase 2 clinical trial of the PD-1 inhibitor pembrolizumab in 24 patients with MMRd endometrial cancer (NCT02899793). Patients with mutational MMRd tumors (6 patients) had higher response rates and longer survival than those with epigenetic MMRd tumors (18 patients). Mutation burden was higher in tumors with mutational MMRd compared to epigenetic MMRd; however, within each category of MMRd, mutation burden was not associated with ICB response. Notably, JAK1 mutations did not confer resistance to pembrolizumab. Longitudinal single-cell RNA-seq of circulating immune cells revealed contrasting modes of anti-tumor immunity against mutational and epigenetic MMRd tumors. Whereas effector CD8+ T cell responses correlated with mutational MMRd, highly active CD16+ NK cells were associated with epigenetic MMRd tumors responsive to ICB. These data highlight factors beyond neoantigen burden that influence ICB response.
DOI: 10.5517/ccdc.csd.cc2d1xjx
title: CCDC 2206379: Experimental Crystal Structure Determination

description: Related Article: S.D. Archana, H. Kiran Kumar, H.S. Yathirajan, S. Foro, R.J. Butcher|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|1016|doi:10.1107/S2056989022009057
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d1xky
title: CCDC 2206380: Experimental Crystal Structure Determination

description: Related Article: S.D. Archana, H. Kiran Kumar, H.S. Yathirajan, S. Foro, R.J. Butcher|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|1016|doi:10.1107/S2056989022009057
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d2fnl
title: CCDC 2206879: Experimental Crystal Structure Determination

description: Related Article: M. Naeem, B.E. Bauer, A.R. Chadeayne, J.A. Golen, D.R. Manke|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|1034|doi:10.1107/S2056989022009094
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d2fpm
title: CCDC 2206880: Experimental Crystal Structure Determination

description: Related Article: M. Naeem, B.E. Bauer, A.R. Chadeayne, J.A. Golen, D.R. Manke|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|1034|doi:10.1107/S2056989022009094
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d2k57
title: CCDC 2206988: Experimental Crystal Structure Determination

description: Related Article: Vinaya, Y.B. Basavaraju, B. Lakshmana, H.S. Yathirajan, S. Parkin|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|1010|doi:10.1107/S2056989022009100
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d2k68
title: CCDC 2206989: Experimental Crystal Structure Determination

description: Related Article: Vinaya, Y.B. Basavaraju, B. Lakshmana, H.S. Yathirajan, S. Parkin|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|1010|doi:10.1107/S2056989022009100
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d2ksv
title: CCDC 2207007: Experimental Crystal Structure Determination

description: Related Article: C. Schwab, A. Voss, C. Strohmann|2022|Acta Crystallogr.,Sect.E:Cryst.Commun.|78|1039|doi:10.1107/S2056989022009112
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.7910/dvn/2sgzqn
title: Replication Data for: Whose War is it Anyway?

description: This is replication data for the article entitled, "Whose War is it Anyway?"
DOI: 10.6084/m9.figshare.21298939
title: Additional file 1 of Network analysis for estimating standardization trends in genomics using MEDLINE

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.21298939.v1
title: Additional file 1 of Network analysis for estimating standardization trends in genomics using MEDLINE

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.21298957
title: Additional file 1 of Diagnosis and clinical implication of collision gastric adenocarcinomas: a case report

description: Additional file 1: Table S1. Reported cases of collision gastric adenocarcinoma.
DOI: 10.6084/m9.figshare.21298957.v1
title: Additional file 1 of Diagnosis and clinical implication of collision gastric adenocarcinomas: a case report

description: Additional file 1: Table S1. Reported cases of collision gastric adenocarcinoma.
DOI: 10.6084/m9.figshare.21298960.v1
title: Additional file 1 of Selective gene expression profiling contributes to a better understanding of the molecular pathways underlying the histological changes observed after RHMVL

description: Additional file 1: List of gene primers.
DOI: 10.6084/m9.figshare.21298963
title: Additional file 2 of Selective gene expression profiling contributes to a better understanding of the molecular pathways underlying the histological changes observed after RHMVL

description: Additional file 2: List of all normalized gene expression data.
DOI: 10.6084/m9.figshare.21298963.v1
title: Additional file 2 of Selective gene expression profiling contributes to a better understanding of the molecular pathways underlying the histological changes observed after RHMVL

description: Additional file 2: List of all normalized gene expression data.
DOI: 10.6084/m9.figshare.21298960
title: Additional file 1 of Selective gene expression profiling contributes to a better understanding of the molecular pathways underlying the histological changes observed after RHMVL

description: Additional file 1: List of gene primers.
DOI: 10.6084/m9.figshare.21298969.v1
title: Additional file 1 of Multi-dimensional relationships among dementia, depression and prescribed drugs in England and Wales hospitals

description: Additional file 1. Correlation among the features.
DOI: 10.6084/m9.figshare.21298972.v1
title: Additional file 2 of Multi-dimensional relationships among dementia, depression and prescribed drugs in England and Wales hospitals

description: Additional file 2. Correlation values exceed the Pearson pairwise correlation coefficient threshold of 0.4.
DOI: 10.6084/m9.figshare.21298975
title: Additional file 3 of Multi-dimensional relationships among dementia, depression and prescribed drugs in England and Wales hospitals

description: Additional file 3. NAD dataset.
DOI: 10.6084/m9.figshare.21298969
title: Additional file 1 of Multi-dimensional relationships among dementia, depression and prescribed drugs in England and Wales hospitals

description: Additional file 1. Correlation among the features.
DOI: 10.6084/m9.figshare.21298981
title: Additional file 5 of Multi-dimensional relationships among dementia, depression and prescribed drugs in England and Wales hospitals

description: Additional file 5. Standardised features.
DOI: 10.6084/m9.figshare.21298972
title: Additional file 2 of Multi-dimensional relationships among dementia, depression and prescribed drugs in England and Wales hospitals

description: Additional file 2. Correlation values exceed the Pearson pairwise correlation coefficient threshold of 0.4.
DOI: 10.6084/m9.figshare.21298975.v1
title: Additional file 3 of Multi-dimensional relationships among dementia, depression and prescribed drugs in England and Wales hospitals

description: Additional file 3. NAD dataset.
DOI: 10.6084/m9.figshare.21298981.v1
title: Additional file 5 of Multi-dimensional relationships among dementia, depression and prescribed drugs in England and Wales hospitals

description: Additional file 5. Standardised features.
DOI: 10.5281/zenodo.7160920
title: Pore water and headspace gas data from Sites J1005 and J1006 on the south Chilean Margin

description: Pore water elemental and isotopic measurements, and headspace gas data, from Sites J1005 and J1006 on the south Chilean Margin. Tab 1: Site J1005 pore water chemistry Tab 2: Site J1006 pore water chemistry Tab 3: Headspace gas data at J1005 and J1006 Tab 4: Na/K geothermometer estimates Tab 5: Pore water sulfate diffusive flux calculations
DOI: 10.5281/zenodo.7160495
title: Deep, shallow and surface fault-zone deformation during and after the 2021 Mw7.4 Maduo, Qinghai, earthquake illuminates fault structural immaturity

description: These datasets include the postseismic InSAR time series on ascending and descending tracks and the relocated aftershocks (Wang et al., 2021) of the 2021 Maduo earthquake. The details can be found in our JGR paper. Reference Wang, W., Fang, L., Wu, J., Tu, H., Chen, L., Lai, G., & Zhang, L. (2021). Aftershock sequence relocation of the 2021 Ms7. 4 Maduo earthquake, Qinghai, China. Science China Earth Sciences, 64(8), 1371-1380.
DOI: 10.5281/zenodo.7160494
title: Deep, shallow and surface fault-zone deformation during and after the 2021 Mw7.4 Maduo, Qinghai, earthquake illuminates fault structural immaturity

description: These datasets include the postseismic InSAR time series on ascending and descending tracks and the relocated aftershocks (Wang et al., 2021) of the 2021 Maduo earthquake. The details can be found in our JGR paper. Reference Wang, W., Fang, L., Wu, J., Tu, H., Chen, L., Lai, G., & Zhang, L. (2021). Aftershock sequence relocation of the 2021 Ms7. 4 Maduo earthquake, Qinghai, China. Science China Earth Sciences, 64(8), 1371-1380.
DOI: 10.6084/m9.figshare.21299056
title: Supplementary Table 7. Gene ontology (GO) biological processes enriched in DFT2.CIITA from Class II transactivator induces expression of MHC-I and MHC-II in transmissible Tasmanian devil facial tumours

description: MHC-I and MHC-II molecules are critical components of antigen presentation and T cell immunity to pathogens and cancer. The two monoclonal transmissible devil facial tumours (DFT1, DFT2) exploit MHC-I pathways to overcome immunological anti-tumour and allogeneic barriers. This exploitation underpins the ongoing transmission of DFT cells across the wild Tasmanian devil population. We have previously shown that the overexpression of NLRC5 in DFT1 and DFT2 cells can regulate components of the MHC-I pathway but not MHC-II, establishing the stable upregulation of MHC-I on the cell surface. As MHC-II molecules are crucial for CD4<sup>+</sup> T cell activation, MHC-II expression in tumour cells is beginning to gain traction in the field of immunotherapy and cancer vaccines. The overexpression of Class II transactivator in transfected DFT1 and DFT2 cells induced the transcription of several genes of the MHC-I and MHC-II pathways. This was further supported by the upregulation of MHC-I protein on DFT1 and DFT2 cells, but interestingly MHC-II protein was upregulated only in DFT1 cells. This new insight into the regulation of MHC-I and MHC-II pathways in cells that naturally overcome allogeneic barriers can inform vaccine, immunotherapy and tissue transplant strategies for human and veterinary medicine.
DOI: 10.6084/m9.figshare.21299056.v1
title: Supplementary Table 7. Gene ontology (GO) biological processes enriched in DFT2.CIITA from Class II transactivator induces expression of MHC-I and MHC-II in transmissible Tasmanian devil facial tumours

description: MHC-I and MHC-II molecules are critical components of antigen presentation and T cell immunity to pathogens and cancer. The two monoclonal transmissible devil facial tumours (DFT1, DFT2) exploit MHC-I pathways to overcome immunological anti-tumour and allogeneic barriers. This exploitation underpins the ongoing transmission of DFT cells across the wild Tasmanian devil population. We have previously shown that the overexpression of NLRC5 in DFT1 and DFT2 cells can regulate components of the MHC-I pathway but not MHC-II, establishing the stable upregulation of MHC-I on the cell surface. As MHC-II molecules are crucial for CD4<sup>+</sup> T cell activation, MHC-II expression in tumour cells is beginning to gain traction in the field of immunotherapy and cancer vaccines. The overexpression of Class II transactivator in transfected DFT1 and DFT2 cells induced the transcription of several genes of the MHC-I and MHC-II pathways. This was further supported by the upregulation of MHC-I protein on DFT1 and DFT2 cells, but interestingly MHC-II protein was upregulated only in DFT1 cells. This new insight into the regulation of MHC-I and MHC-II pathways in cells that naturally overcome allogeneic barriers can inform vaccine, immunotherapy and tissue transplant strategies for human and veterinary medicine.
DOI: 10.6084/m9.figshare.21299059
title: Supplementary Table 3. Differential expression analysis from Class II transactivator induces expression of MHC-I and MHC-II in transmissible Tasmanian devil facial tumours

description: MHC-I and MHC-II molecules are critical components of antigen presentation and T cell immunity to pathogens and cancer. The two monoclonal transmissible devil facial tumours (DFT1, DFT2) exploit MHC-I pathways to overcome immunological anti-tumour and allogeneic barriers. This exploitation underpins the ongoing transmission of DFT cells across the wild Tasmanian devil population. We have previously shown that the overexpression of NLRC5 in DFT1 and DFT2 cells can regulate components of the MHC-I pathway but not MHC-II, establishing the stable upregulation of MHC-I on the cell surface. As MHC-II molecules are crucial for CD4<sup>+</sup> T cell activation, MHC-II expression in tumour cells is beginning to gain traction in the field of immunotherapy and cancer vaccines. The overexpression of Class II transactivator in transfected DFT1 and DFT2 cells induced the transcription of several genes of the MHC-I and MHC-II pathways. This was further supported by the upregulation of MHC-I protein on DFT1 and DFT2 cells, but interestingly MHC-II protein was upregulated only in DFT1 cells. This new insight into the regulation of MHC-I and MHC-II pathways in cells that naturally overcome allogeneic barriers can inform vaccine, immunotherapy and tissue transplant strategies for human and veterinary medicine.
DOI: 10.6084/m9.figshare.21299065
title: Supplementary Table 6. Gene ontology (GO) biological processes enriched in DFT1.CIITA from Class II transactivator induces expression of MHC-I and MHC-II in transmissible Tasmanian devil facial tumours

description: MHC-I and MHC-II molecules are critical components of antigen presentation and T cell immunity to pathogens and cancer. The two monoclonal transmissible devil facial tumours (DFT1, DFT2) exploit MHC-I pathways to overcome immunological anti-tumour and allogeneic barriers. This exploitation underpins the ongoing transmission of DFT cells across the wild Tasmanian devil population. We have previously shown that the overexpression of NLRC5 in DFT1 and DFT2 cells can regulate components of the MHC-I pathway but not MHC-II, establishing the stable upregulation of MHC-I on the cell surface. As MHC-II molecules are crucial for CD4<sup>+</sup> T cell activation, MHC-II expression in tumour cells is beginning to gain traction in the field of immunotherapy and cancer vaccines. The overexpression of Class II transactivator in transfected DFT1 and DFT2 cells induced the transcription of several genes of the MHC-I and MHC-II pathways. This was further supported by the upregulation of MHC-I protein on DFT1 and DFT2 cells, but interestingly MHC-II protein was upregulated only in DFT1 cells. This new insight into the regulation of MHC-I and MHC-II pathways in cells that naturally overcome allogeneic barriers can inform vaccine, immunotherapy and tissue transplant strategies for human and veterinary medicine.
DOI: 10.6084/m9.figshare.21299065.v1
title: Supplementary Table 6. Gene ontology (GO) biological processes enriched in DFT1.CIITA from Class II transactivator induces expression of MHC-I and MHC-II in transmissible Tasmanian devil facial tumours

description: MHC-I and MHC-II molecules are critical components of antigen presentation and T cell immunity to pathogens and cancer. The two monoclonal transmissible devil facial tumours (DFT1, DFT2) exploit MHC-I pathways to overcome immunological anti-tumour and allogeneic barriers. This exploitation underpins the ongoing transmission of DFT cells across the wild Tasmanian devil population. We have previously shown that the overexpression of NLRC5 in DFT1 and DFT2 cells can regulate components of the MHC-I pathway but not MHC-II, establishing the stable upregulation of MHC-I on the cell surface. As MHC-II molecules are crucial for CD4<sup>+</sup> T cell activation, MHC-II expression in tumour cells is beginning to gain traction in the field of immunotherapy and cancer vaccines. The overexpression of Class II transactivator in transfected DFT1 and DFT2 cells induced the transcription of several genes of the MHC-I and MHC-II pathways. This was further supported by the upregulation of MHC-I protein on DFT1 and DFT2 cells, but interestingly MHC-II protein was upregulated only in DFT1 cells. This new insight into the regulation of MHC-I and MHC-II pathways in cells that naturally overcome allogeneic barriers can inform vaccine, immunotherapy and tissue transplant strategies for human and veterinary medicine.
DOI: 10.6084/m9.figshare.21299059.v1
title: Supplementary Table 3. Differential expression analysis from Class II transactivator induces expression of MHC-I and MHC-II in transmissible Tasmanian devil facial tumours

description: MHC-I and MHC-II molecules are critical components of antigen presentation and T cell immunity to pathogens and cancer. The two monoclonal transmissible devil facial tumours (DFT1, DFT2) exploit MHC-I pathways to overcome immunological anti-tumour and allogeneic barriers. This exploitation underpins the ongoing transmission of DFT cells across the wild Tasmanian devil population. We have previously shown that the overexpression of NLRC5 in DFT1 and DFT2 cells can regulate components of the MHC-I pathway but not MHC-II, establishing the stable upregulation of MHC-I on the cell surface. As MHC-II molecules are crucial for CD4<sup>+</sup> T cell activation, MHC-II expression in tumour cells is beginning to gain traction in the field of immunotherapy and cancer vaccines. The overexpression of Class II transactivator in transfected DFT1 and DFT2 cells induced the transcription of several genes of the MHC-I and MHC-II pathways. This was further supported by the upregulation of MHC-I protein on DFT1 and DFT2 cells, but interestingly MHC-II protein was upregulated only in DFT1 cells. This new insight into the regulation of MHC-I and MHC-II pathways in cells that naturally overcome allogeneic barriers can inform vaccine, immunotherapy and tissue transplant strategies for human and veterinary medicine.
DOI: 10.5281/zenodo.7161424
title: SARS-CoV-2 variants

description: This dataset is a temporary upload and will be removed after double-blind peer review process is finished.
DOI: 10.5281/zenodo.7161425
title: SARS-CoV-2 variants

description: This dataset is a temporary upload and will be removed after double-blind peer review process is finished.
DOI: 10.5281/zenodo.7161704
title: SARS-CoV-2 variants

description: This dataset is a temporary upload and will be removed after double-blind peer review process is finished.
DOI: 10.6084/m9.figshare.21299091
title: DataSI from Frustrated ‘run and tumble’ of swimming Escherichia coli bacteria in nematic liquid crystals

description: In many situations, bacteria move in complex environments, as soils, oceans or the human gut-track, where carrier fluids show complex structures associated with non-Newtonian rheology. Many fundamental questions concerning the ability to navigate in such environments remain unsolved. Recently, it has been shown that the kinetics of bacterial motion in structured fluids as liquid crystals (LCs) is constrained by the orientational molecular order (or director field) and that novel spatio-temporal patterns arise. A question unaddressed so far is how bacteria change swimming direction in such an environment. In this work, we study the swimming mechanism of a single bacterium, <i>Esherichia coli</i>, constrained to move along the director field of a lyotropic chromonic liquid crystal confined to a planar cell. Here, the spontaneous ‘run and tumble’ motion of the bacterium gets frustrated: the elasticity of the LC prevents flagella from unbundling. Interestingly, to change direction, bacteria execute a reversal motion along the director field, driven by the relocation of a single flagellum, a ‘frustrated tumble’. We characterize this phenomenon in detail experimentally, exploiting exceptional spatial and temporal resolution of bacteria I and flagella r dynamics, using a two colour Lagrangian tracking technique. We suggest a possible mechanism accounting for these observations.