cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22669888
title: Global impact of somatic structural variation on the cancer proteome

description: Both proteome and transcriptome data can help assess the relevance of non-coding somatic alterations in cancer. Here, we combine mass spectrometry-based proteomics data with whole genome sequencing data across 1307 human tumors spanning various tissues to determine the extent that somatic structural variant (SV) breakpoint patterns impact protein expression of nearby genes. We find that only about 25% of the hundreds of genes associated with recurrent somatic SV-mediated cis-regulatory alterations at the mRNA level are similarly associated at the protein level. SVs associated with enhancer hijacking, retrotransposon translocation, altered DNA methylation, or fusion transcripts are implicated in protein over-expression. SVs combined with altered protein levels considerably extend the numbers of patients with tumors somatically altered for critical pathways. We catalog both SV breakpoint patterns associated with patient survival and genes with nearby SV breakpoints associated with increased cell dependency in cancer cell lines. Proteogenomics identifies targetable non-coding alterations. Using SVExpress, we defined genes with altered expression (by protein or mRNA) associated with nearby somatic SV breakpoints. Relative to each gene, genomic region windows considered included the within-gene regions and within 100kb upstream or 100kb downstream of the gene. For the above regions, SVExpress constructed a gene-to-sample matrix with entries as 1, if a breakpoint occurs in the specified region for the given gene in the given sample, and 0 if otherwise. We also used SVExpress to examine a 1Mb region surrounding each gene, using the “relative distance metric” option, whereby breakpoints close to the gene will have more numeric weight in identifying SV-expression associations, while breakpoints further away but within 1Mb can have some influence. Gene-level SV-expression association analyses included 15439 unique named genes, 10087 of which had protein values for at least 400 tumors. Using the geneXsample SV breakpoint matrix, SVExpress assessed the correlation between expression of the gene and the presence of an SV breakpoint using a linear regression model (with log-transformed expression values), incorporating sample cancer type and gene-level CNA.
DOI: 10.6084/m9.figshare.22669888.v1
title: Global impact of somatic structural variation on the cancer proteome

description: Both proteome and transcriptome data can help assess the relevance of non-coding somatic alterations in cancer. Here, we combine mass spectrometry-based proteomics data with whole genome sequencing data across 1307 human tumors spanning various tissues to determine the extent that somatic structural variant (SV) breakpoint patterns impact protein expression of nearby genes. We find that only about 25% of the hundreds of genes associated with recurrent somatic SV-mediated cis-regulatory alterations at the mRNA level are similarly associated at the protein level. SVs associated with enhancer hijacking, retrotransposon translocation, altered DNA methylation, or fusion transcripts are implicated in protein over-expression. SVs combined with altered protein levels considerably extend the numbers of patients with tumors somatically altered for critical pathways. We catalog both SV breakpoint patterns associated with patient survival and genes with nearby SV breakpoints associated with increased cell dependency in cancer cell lines. Proteogenomics identifies targetable non-coding alterations. Using SVExpress, we defined genes with altered expression (by protein or mRNA) associated with nearby somatic SV breakpoints. Relative to each gene, genomic region windows considered included the within-gene regions and within 100kb upstream or 100kb downstream of the gene. For the above regions, SVExpress constructed a gene-to-sample matrix with entries as 1, if a breakpoint occurs in the specified region for the given gene in the given sample, and 0 if otherwise. We also used SVExpress to examine a 1Mb region surrounding each gene, using the “relative distance metric” option, whereby breakpoints close to the gene will have more numeric weight in identifying SV-expression associations, while breakpoints further away but within 1Mb can have some influence. Gene-level SV-expression association analyses included 15439 unique named genes, 10087 of which had protein values for at least 400 tumors. Using the geneXsample SV breakpoint matrix, SVExpress assessed the correlation between expression of the gene and the presence of an SV breakpoint using a linear regression model (with log-transformed expression values), incorporating sample cancer type and gene-level CNA.
DOI: 10.6084/m9.figshare.23994789
title: Simultaneously ultrafast and robust two-dimensional flash memory devices based on phase engineered edge contacts

description: Source Data for figure 1-4 in main manuscript.
DOI: 10.6084/m9.figshare.23994789.v1
title: Simultaneously ultrafast and robust two-dimensional flash memory devices based on phase engineered edge contacts

description: Source Data for figure 1-4 in main manuscript.
DOI: 10.6084/m9.figshare.24043524
title: Control of arbuscule development by a transcriptional negative feedback loop in Medicago

description: Control of arbuscule development by a transcriptional negative feedback loop in Medicago
DOI: 10.6084/m9.figshare.24043524.v1
title: Control of arbuscule development by a transcriptional negative feedback loop in Medicago

description: Control of arbuscule development by a transcriptional negative feedback loop in Medicago
DOI: 10.6084/m9.figshare.22784945
title: Darapladib, a lipoprotein-associated phospholipase A2 inhibitor, sensitises cancer cells to ferroptosis by remodelling lipid metabolism

description: Proportions of various lipid classes or targeted lipid classes normalised by the total lipids detected by LC–MS/MS
DOI: 10.6084/m9.figshare.22784945.v1
title: Darapladib, a lipoprotein-associated phospholipase A2 inhibitor, sensitises cancer cells to ferroptosis by remodelling lipid metabolism

description: Proportions of various lipid classes or targeted lipid classes normalised by the total lipids detected by LC–MS/MS
DOI: 10.6084/m9.figshare.23908092
title: Location is a major barrier for transferring US fossil fuel employment to green jobs

description: Replication code and data.
DOI: 10.6084/m9.figshare.22778354
title: Stata v17 replication file for "Food inflation and child undernutrition in low and middle income countries" by Derek Headey and Marie Ruel

description: This replication folder describes the Stata v17 “do file” (code file) for statistical analysis for "Food inflation and child undernutrition in low and middle income countries " by Derek Headey & Marie Ruel. This do file can be used to replicate the analysis in the study mentioned above, published in Nature Communications. The study uses a combination of Demographic Health Survey (DHS) data for child, maternal, household level variables and national level indicators on real food price changes drawn from FAOSTAT, as well as conflict and climate variables. In summary, this is a large multi-country DHS dataset merged with FAO food and total consumer price indices (CPIs) and various other national level control variables. These are DHS surveys from 2000 onwards only. The authors cannot publicly share the DHS data but can share it upon request, provided we can obtain approval from the DHS implementers. To make a request to access the data for this paper, please email Derek Headey at d.headey@cgiar.org. Alternatively researchers can access the raw DHS data from: https://dhsprogram.com/data/available-datasets.cfm and the country level indicators from the Food and Agriculture Organisation Consumer Prices data portal (https://www.fao.org/faostat/en/#data/CP) as well as The World Bank World Development Indicators (https://databank.worldbank.org/source/world-development-indicators) for obtaining data on various control variables.
DOI: 10.6084/m9.figshare.22778354.v1
title: Stata v17 replication file for "Food inflation and child undernutrition in low and middle income countries" by Derek Headey and Marie Ruel

description: This replication folder describes the Stata v17 “do file” (code file) for statistical analysis for "Food inflation and child undernutrition in low and middle income countries " by Derek Headey & Marie Ruel. This do file can be used to replicate the analysis in the study mentioned above, published in Nature Communications. The study uses a combination of Demographic Health Survey (DHS) data for child, maternal, household level variables and national level indicators on real food price changes drawn from FAOSTAT, as well as conflict and climate variables. In summary, this is a large multi-country DHS dataset merged with FAO food and total consumer price indices (CPIs) and various other national level control variables. These are DHS surveys from 2000 onwards only. The authors cannot publicly share the DHS data but can share it upon request, provided we can obtain approval from the DHS implementers. To make a request to access the data for this paper, please email Derek Headey at d.headey@cgiar.org. Alternatively researchers can access the raw DHS data from: https://dhsprogram.com/data/available-datasets.cfm and the country level indicators from the Food and Agriculture Organisation Consumer Prices data portal (https://www.fao.org/faostat/en/#data/CP) as well as The World Bank World Development Indicators (https://databank.worldbank.org/source/world-development-indicators) for obtaining data on various control variables.
DOI: 10.6084/m9.figshare.23511402
title: Probing three-dimensional mesoscopic interfacial structures in a single view using multibeam x-ray coherent surface scattering and holography imaging

description: Raw data that were used to prepare all the figures in the main text of this article in Microsoft Excel format.
DOI: 10.6084/m9.figshare.23511402.v1
title: Probing three-dimensional mesoscopic interfacial structures in a single view using multibeam x-ray coherent surface scattering and holography imaging

description: Raw data that were used to prepare all the figures in the main text of this article in Microsoft Excel format.
DOI: 10.6084/m9.figshare.23684148
title: Efficient intervention for pulmonary fibrosis via mitochondrial transfer promoted by mitochondrial biogenesis

description: The original figures of the manuscript (NCOMMS-23-10590) entitled “Efficient intervention for pulmonary fibrosis via mitochondrial transfer promoted by mitochondrial biogenesis”.
DOI: 10.6084/m9.figshare.23684148.v1
title: Efficient intervention for pulmonary fibrosis via mitochondrial transfer promoted by mitochondrial biogenesis

description: The original figures of the manuscript (NCOMMS-23-10590) entitled “Efficient intervention for pulmonary fibrosis via mitochondrial transfer promoted by mitochondrial biogenesis”.
DOI: 10.6084/m9.figshare.23261402
title: Host heparan sulfate promotes ACE2 super-cluster assembly and SARS-CoV-2-associated syncytium formation

description: A multi-tabbed Excel file listing all the source data used for preparing figures as well as statistical analyses.
DOI: 10.6084/m9.figshare.23261402.v1
title: Host heparan sulfate promotes ACE2 super-cluster assembly and SARS-CoV-2-associated syncytium formation

description: A multi-tabbed Excel file listing all the source data used for preparing figures as well as statistical analyses.
DOI: 10.6084/m9.figshare.23907696
title: Epithelial Plasticity and Innate Immune Activation Promote Lung Tissue Remodeling following Respiratory Viral Infection.

description: Source data for manuscript titled: 'Epithelial Plasticity and Innate Immune Activation Promote Lung Tissue Remodeling following Respiratory Viral Infection.'
DOI: 10.6084/m9.figshare.23907696.v1
title: Epithelial Plasticity and Innate Immune Activation Promote Lung Tissue Remodeling following Respiratory Viral Infection.

description: Source data for manuscript titled: 'Epithelial Plasticity and Innate Immune Activation Promote Lung Tissue Remodeling following Respiratory Viral Infection.'
DOI: 10.6084/m9.figshare.23963622
title: Chronic cough relief by allosteric modulation of the inner pocket of the head domain in P2X3 without taste disturbance

description: 1.Open and resting configurations of P2X3 receptors. 2.Dynamics trajectories of hP2X3 open and resting 3.configurations, including the initial and final configurations. Molecular dynamics trajectories of interaction between P2X3 and quercetin, including the initial and final configurations. 4.Meta-molecular dynamics trajectories of interaction between P2X3 and quercetin, including the initial and final configurations
DOI: 10.6084/m9.figshare.23963622.v1
title: Chronic cough relief by allosteric modulation of the inner pocket of the head domain in P2X3 without taste disturbance

description: 1.Open and resting configurations of P2X3 receptors. 2.Dynamics trajectories of hP2X3 open and resting 3.configurations, including the initial and final configurations. Molecular dynamics trajectories of interaction between P2X3 and quercetin, including the initial and final configurations. 4.Meta-molecular dynamics trajectories of interaction between P2X3 and quercetin, including the initial and final configurations
DOI: 10.6084/m9.figshare.23937495
title: Efficiently accelerated free electrons by metallic laser accelerator

description: Data of "Efficiently accelerated free electrons by metallic laser accelerator".
DOI: 10.6084/m9.figshare.23937495.v1
title: Efficiently accelerated free electrons by metallic laser accelerator

description: Data of "Efficiently accelerated free electrons by metallic laser accelerator".
DOI: 10.6084/m9.figshare.23112806
title: A CCL2+DPP4+ subset of mesenchymal stem cells expedites aberrant formation of creeping fat in humans

description: Table of differences in lipid metabolites between H-MAT and CF patients
DOI: 10.6084/m9.figshare.23112806.v1
title: A CCL2+DPP4+ subset of mesenchymal stem cells expedites aberrant formation of creeping fat in humans

description: Table of differences in lipid metabolites between H-MAT and CF patients
DOI: 10.6084/m9.figshare.23982600
title: Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics

description: The identification of RNA-bound proteomes is hampered by a lack of quantitative metrics for evaluating RNA binding function. We report LEAP-RBP as a highly selective and cost effective method for the purification of RNA-bound proteins and introduce signal-based metrics for robust profiling of RNA-bound proteomes.
DOI: 10.6084/m9.figshare.23982600.v1
title: Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics

description: The identification of RNA-bound proteomes is hampered by a lack of quantitative metrics for evaluating RNA binding function. We report LEAP-RBP as a highly selective and cost effective method for the purification of RNA-bound proteins and introduce signal-based metrics for robust profiling of RNA-bound proteomes.
DOI: 10.6084/m9.figshare.23734116
title: Engineering the Temporal Dynamics of All-Optical Switching with Fast and Slow Materials

description: Source data for Fig 1d. Contains the tables of Time (pump probe delay) vs the measured and the normalized optical density. The time axis for different data runs have been shifted to align the maximum signals for easier data comparison. The normalized data in each graph has been shifted vertically by 0.3 with respect to the next graph to compare the decay rates. Because of different experimental configurations for the NIR and the visible wavelength probes, the pump probe delay at with the peak of each experiment occurs is slightly shifted. The time axes for the longer wavelengths (900 to 1300 nm) have been shifted by 0.6 ps to align the peaks for easier comparison. For normalization, the intensity of each modulation graph has been divided by the peak intensity (positive or negative, depending on the wavelength). Source data for Fig 2b. Contains the tables of simulated reflectance of p polarized (Rp) and s polarized (Rs) light from the device, as well as experimentally measured reflectance, versus the wavelength. Source data for Fig 2cd. Contains the tables of wavelength and permittivities of TiN and AZO films. The comments contain the film thicknesses. Source data for Fig 3b. Contains the color map of the reflectance modulation for TiN versus wavelength (nm) and pump-probe delay (ps) Source data for Fig 3c. Contains the normalized transient reflectance modulation vs time of TiN on Si at a wavelength of 505 nm. Source data for Fig 3d. Contains the color map of the reflectance modulation of AZO film vs wavelength and pump probe delay. Source data for Fig 3e. Contains the normalized transient reflectance modulation vs time of AZO at a wavelength of 1210 nm. Source data for Fig 4a. Contains the color map of the reflectance modulation of the device under a visible probe, versus the wavelength and the pump-probe delay. Source data for Fig 4b. Contains the color map of the reflectance modulation of the device under an infrared probe, versus the wavelength and the pump-probe delay. Source data for Fig 4c. Contains the absorbance of light versus the wavelength in the TiN and the AZO layers, simulated by COMSOL Multiphysics Source data for Fig 4d. Contains the normalized reflectance modulation of TiN film (505nm wavelength), AZO film (1210nm wavelength), Device (508 and 1180 nm wavelength), versus the pump probe delay. The time axes have been shifted to align the maximum reflectance modulation of the device with that of the individual films. Source data for Fig 5b. Contains the Normalized reflectance modulation of the device at various wavelengths versus the time, together with the fits from the model. All wavelengths are in nm and time is in ps, unless otherwise stated. The data processing and labeling is same as that of Fig 1d. All wavelengths are in nm and time is in ps, unless otherwise stated.
DOI: 10.6084/m9.figshare.23734116.v1
title: Engineering the Temporal Dynamics of All-Optical Switching with Fast and Slow Materials

description: Source data for Fig 1d. Contains the tables of Time (pump probe delay) vs the measured and the normalized optical density. The time axis for different data runs have been shifted to align the maximum signals for easier data comparison. The normalized data in each graph has been shifted vertically by 0.3 with respect to the next graph to compare the decay rates. Because of different experimental configurations for the NIR and the visible wavelength probes, the pump probe delay at with the peak of each experiment occurs is slightly shifted. The time axes for the longer wavelengths (900 to 1300 nm) have been shifted by 0.6 ps to align the peaks for easier comparison. For normalization, the intensity of each modulation graph has been divided by the peak intensity (positive or negative, depending on the wavelength). Source data for Fig 2b. Contains the tables of simulated reflectance of p polarized (Rp) and s polarized (Rs) light from the device, as well as experimentally measured reflectance, versus the wavelength. Source data for Fig 2cd. Contains the tables of wavelength and permittivities of TiN and AZO films. The comments contain the film thicknesses. Source data for Fig 3b. Contains the color map of the reflectance modulation for TiN versus wavelength (nm) and pump-probe delay (ps) Source data for Fig 3c. Contains the normalized transient reflectance modulation vs time of TiN on Si at a wavelength of 505 nm. Source data for Fig 3d. Contains the color map of the reflectance modulation of AZO film vs wavelength and pump probe delay. Source data for Fig 3e. Contains the normalized transient reflectance modulation vs time of AZO at a wavelength of 1210 nm. Source data for Fig 4a. Contains the color map of the reflectance modulation of the device under a visible probe, versus the wavelength and the pump-probe delay. Source data for Fig 4b. Contains the color map of the reflectance modulation of the device under an infrared probe, versus the wavelength and the pump-probe delay. Source data for Fig 4c. Contains the absorbance of light versus the wavelength in the TiN and the AZO layers, simulated by COMSOL Multiphysics Source data for Fig 4d. Contains the normalized reflectance modulation of TiN film (505nm wavelength), AZO film (1210nm wavelength), Device (508 and 1180 nm wavelength), versus the pump probe delay. The time axes have been shifted to align the maximum reflectance modulation of the device with that of the individual films. Source data for Fig 5b. Contains the Normalized reflectance modulation of the device at various wavelengths versus the time, together with the fits from the model. All wavelengths are in nm and time is in ps, unless otherwise stated. The data processing and labeling is same as that of Fig 1d. All wavelengths are in nm and time is in ps, unless otherwise stated.
DOI: 10.6084/m9.figshare.22736900
title: The CBL1/9-CIPK1 calcium sensor negatively regulates drought stress by phosphorylating the PYLs ABA receptor

description: CBL-CIPK-PYLs source data.
DOI: 10.6084/m9.figshare.22736900.v1
title: The CBL1/9-CIPK1 calcium sensor negatively regulates drought stress by phosphorylating the PYLs ABA receptor

description: CBL-CIPK-PYLs source data.
DOI: 10.6084/m9.figshare.22757444
title: Bap1 promotes osteoclast function by metabolic reprogramming

description: Treatment of osteoporosis most commonly diminishes osteoclast number which suppresses bone formation thus compromising fracture prevention. Bone formation is not suppressed, however, when bone degradation is reduced by retarding osteoclast functional resorptive capacity, rather than differentiation. We find deletion of deubiquitinase, BRCA1-associated protein 1 (Bap1), in myeloid cells (Bap1∆LysM), arrests osteoclast function but not formation. Bap1∆LysM osteoclasts fail to organize their cytoskeleton which is essential for bone degradation. Consequently, bone mass increases in the mutant mice. The deubiquitinase activity of Bap1 modifies osteoclast function by metabolic reprogramming. Bap1 deficient osteoclast lineage cells upregulate the cystine transporter, Slc7a11, by enhanced H2Aub occupancy of its promoter. SLC7A11 controls cellular ROS levels and redirects the mitochondrial metabolites away from the TCA cycle, both of which are necessary for osteoclast function. Thus in osteoclasts, Bap1 appears to regulate the epigenetic-metabolic axis and is a potential target to reduce bone degradation while maintaining osteogenesis in osteoporotic patients.
DOI: 10.6084/m9.figshare.22757444.v1
title: Bap1 promotes osteoclast function by metabolic reprogramming

description: Treatment of osteoporosis most commonly diminishes osteoclast number which suppresses bone formation thus compromising fracture prevention. Bone formation is not suppressed, however, when bone degradation is reduced by retarding osteoclast functional resorptive capacity, rather than differentiation. We find deletion of deubiquitinase, BRCA1-associated protein 1 (Bap1), in myeloid cells (Bap1∆LysM), arrests osteoclast function but not formation. Bap1∆LysM osteoclasts fail to organize their cytoskeleton which is essential for bone degradation. Consequently, bone mass increases in the mutant mice. The deubiquitinase activity of Bap1 modifies osteoclast function by metabolic reprogramming. Bap1 deficient osteoclast lineage cells upregulate the cystine transporter, Slc7a11, by enhanced H2Aub occupancy of its promoter. SLC7A11 controls cellular ROS levels and redirects the mitochondrial metabolites away from the TCA cycle, both of which are necessary for osteoclast function. Thus in osteoclasts, Bap1 appears to regulate the epigenetic-metabolic axis and is a potential target to reduce bone degradation while maintaining osteogenesis in osteoporotic patients.