cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14278/rodare.1985
title: The chemical journey of Europium(III) through winter rye (Secale cereale L.) – Understanding through mass spectrometry and chemical microscopy

description: A combination of biochemical preparation methods with microscopic, spectroscopic, and mass spectrometric analysis techniques as contemplating state of the art application, was used for direct visualization, localization, and chemical identification of europium in plants. This works illustrates the chemical journey of europium (Eu(III)) through winter rye (<em>Secale cereale</em> L.), providing insight into the possibilities of speciation for Rare Earth Elements (REE) and trivalent f-elements. Kinetic experiments of contaminated plants show a maximum europium concentration in <em>Secale cereale</em> L. after four days. Transport of the element through the vascular bundle was confirmed with Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray analysis (EDS). For chemical speciation, plants were grown in a liquid nutrition medium, whereby Eu(III) species distribution could be measured by mass spectrometry and luminescence measurements. Both techniques confirm the occurrence of Eu malate species in the nutrition medium, and further analysis of the plant was performed. Luminescence results indicate a change in Eu(III) species distribution from root tip to plant leaves. Microscopic analysis show at least three different Eu(III) species with potential binding to organic and inorganic phosphate groups and a Eu(III) protein complex. With plant root extraction, further europium species could be identified by using Electrospray Ionization Mass Spectrometry (ESI MS). Complexation with malate, citrate, a combined malate-citrate ligand, and aspartate was confirmed mostly in a 1:1 stoichiometry (Eu:ligand). The combination of the used analytical techniques opens new possibilities in direct species analysis, especially regarding to the understanding of rare earth elements (REE) uptake in plants. This work provides a contribution in better understanding of plant mechanisms of the f-elements and their species uptake.
DOI: 10.14278/rodare.1984
title: The chemical journey of Europium(III) through winter rye (Secale cereale L.) – Understanding through mass spectrometry and chemical microscopy

description: A combination of biochemical preparation methods with microscopic, spectroscopic, and mass spectrometric analysis techniques as contemplating state of the art application, was used for direct visualization, localization, and chemical identification of europium in plants. This works illustrates the chemical journey of europium (Eu(III)) through winter rye (<em>Secale cereale</em> L.), providing insight into the possibilities of speciation for Rare Earth Elements (REE) and trivalent f-elements. Kinetic experiments of contaminated plants show a maximum europium concentration in <em>Secale cereale</em> L. after four days. Transport of the element through the vascular bundle was confirmed with Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray analysis (EDS). For chemical speciation, plants were grown in a liquid nutrition medium, whereby Eu(III) species distribution could be measured by mass spectrometry and luminescence measurements. Both techniques confirm the occurrence of Eu malate species in the nutrition medium, and further analysis of the plant was performed. Luminescence results indicate a change in Eu(III) species distribution from root tip to plant leaves. Microscopic analysis show at least three different Eu(III) species with potential binding to organic and inorganic phosphate groups and a Eu(III) protein complex. With plant root extraction, further europium species could be identified by using Electrospray Ionization Mass Spectrometry (ESI MS). Complexation with malate, citrate, a combined malate-citrate ligand, and aspartate was confirmed mostly in a 1:1 stoichiometry (Eu:ligand). The combination of the used analytical techniques opens new possibilities in direct species analysis, especially regarding to the understanding of rare earth elements (REE) uptake in plants. This work provides a contribution in better understanding of plant mechanisms of the f-elements and their species uptake.
DOI: 10.6084/m9.figshare.24314641
title: Supplementary files for the study on <i>Scutellaria</i> in Taiwan

description: VCF file generated from 51 nuclear genes sequenced from 7 <i>Scutellaria</i> species in Taiwan.Parameters and details of all simulated ABC models.Environmental data for each population downloaded from WorldClim2.Pair-end sequences of all individuals sequenced in this study.<br>
DOI: 10.6084/m9.figshare.24314641.v1
title: Supplementary files for the study on <i>Scutellaria</i> in Taiwan

description: VCF file generated from 51 nuclear genes sequenced from 7 <i>Scutellaria</i> species in Taiwan. Parameters and details of all simulated ABC models.Environmental data for each population downloaded from WorldClim2.
DOI: 10.6084/m9.figshare.24314641.v2
title: Supplementary files for the study on <i>Scutellaria</i> in Taiwan

description: VCF file generated from 51 nuclear genes sequenced from 7 <i>Scutellaria</i> species in Taiwan.Parameters and details of all simulated ABC models.Environmental data for each population downloaded from WorldClim2.Pair-end sequences of all individuals sequenced in this study.<br>
DOI: 10.6084/m9.figshare.24654915
title: The chromosome-level genome of the long-tailed marine-living ornate spiny lobster, <i>Panulirus ornatus</i>

description: A chromosome-level genome with a size of 2.65 Gb and contig N50 of 5.12 Mb. Nearly 99.11% of sequences were anchored to 73 chromosomes, which represents the high-quality lobster genome ever reported. The genome contained 65.67% repeat sequences and 22,752 protein-coding genes, of which 99.20% were functionally annotated.
DOI: 10.25403/upresearchdata.23624397.v1
title: State intervention in the development of black small scale farmers through the Agriparks

description: This is dataset for a qualitative study of three provincial case studies of Agriparks based on ethnography and grounded methods to understand state support for small-scale farmers, beneficiaries, non-beneficiaries, activists, and academics involved with small-scale farmers and rural development were interviewed for the study. Findings confirm that state interventions are critical for the development of small-scale farmers and rural development, also that the private sector has an important role to play in integrating the dual agriculture structures created by the apartheid system. Structural and interpretive approaches were used to understand and analyze the data. Pseudonyms were used to de-identify the participants.
DOI: 10.25403/upresearchdata.23624397
title: State intervention in the development of black small scale farmers through the Agriparks

description: This is dataset for a qualitative study of three provincial case studies of Agriparks based on ethnography and grounded methods to understand state support for small-scale farmers, beneficiaries, non-beneficiaries, activists, and academics involved with small-scale farmers and rural development were interviewed for the study. Findings confirm that state interventions are critical for the development of small-scale farmers and rural development, also that the private sector has an important role to play in integrating the dual agriculture structures created by the apartheid system. Structural and interpretive approaches were used to understand and analyze the data. Pseudonyms were used to de-identify the participants.
DOI: 10.6084/m9.figshare.20998879
title: Colon tumor cell death causes mTOR dependence by paracrine P2X4 stimulation

description: Spreadsheet of tumor sizes
DOI: 10.6084/m9.figshare.20998879.v1
title: Colon tumor cell death causes mTOR dependence by paracrine P2X4 stimulation

description: Spreadsheet of tumor sizes
DOI: 10.6084/m9.figshare.21191815
title: Ferroptosis of tumor associated neutrophils is immunosuppressive and promotes tumor growth

description: Analysis of gene expression profile in neutrophils treated with inducers of ferroptosis and apoptosis
DOI: 10.6084/m9.figshare.21191815.v1
title: Ferroptosis of tumor associated neutrophils is immunosuppressive and promotes tumor growth

description: Analysis of gene expression profile in neutrophils treated with inducers of ferroptosis and apoptosis
DOI: 10.6084/m9.figshare.21326142
title: Structural insights into the selective activation of DREADDs by chemogenetic actuators

description: Source data
DOI: 10.6084/m9.figshare.21326142.v1
title: Structural insights into the selective activation of DREADDs by chemogenetic actuators

description: Source data
DOI: 10.6084/m9.figshare.21261246
title: Kinase signaling pathway regulates sleep quantity and depth through a distinct population of excitatory neurons

description: Souce data
DOI: 10.6084/m9.figshare.21261246.v1
title: Kinase signaling pathway regulates sleep quantity and depth through a distinct population of excitatory neurons

description: Souce data
DOI: 10.6084/m9.figshare.20975722
title: The WHO estimates of excess mortality associated with the COVID-19 pandemic

description: The WHO estimates of excess mortality associated with the COVID-19 pandemic for years 2020 and 2021 by country and month for each of the 194 WHO members states.
DOI: 10.6084/m9.figshare.20975722.v1
title: The WHO estimates of excess mortality associated with the COVID-19 pandemic

description: The WHO estimates of excess mortality associated with the COVID-19 pandemic for years 2020 and 2021 by country and month for each of the 194 WHO members states.
DOI: 10.6084/m9.figshare.21167344
title: Locus coeruleus activity improves cochlear implant performance

description: Data from Glennon et al. "Locus coeruleus activity improves cochlear implant performance"
DOI: 10.6084/m9.figshare.21167344.v1
title: Locus coeruleus activity improves cochlear implant performance

description: Data from Glennon et al. "Locus coeruleus activity improves cochlear implant performance"
DOI: 10.6084/m9.figshare.21405429
title: HIV Silencing and Cell Survival Signatures in Infected T cell Reservoirs

description: Rare CD4 T cells that harbor HIV under antiretroviral therapy (ART) represent an important barrier to HIV cure1-3, but the infeasibility of isolating and characterizing these cells in their natural state has led to uncertainty about whether they possess distinctive attributes that HIV cure-directed therapies might exploit. Here, we addressed this challenge using a microfluidic technology that isolates HIV-infected cell transcriptomes based solely on HIV DNA detection. HIV DNA+ memory CD4 T cells in blood from people receiving ART showed inhibition of six transcriptomic pathways including death receptor signaling, necroptosis signaling, and antiproliferative G12/13 signaling. Moreover, two groups of genes identified by network co-expression analysis were significantly associated with HIV DNA+ cells. These genes (n = 145) accounted for just 0.81% of the measured transcriptome and included negative regulators of HIV transcription that were higher in HIV DNA+ cells, positive regulators of HIV transcription that were lower in HIV DNA+ cells, and other genes involved in negative regulation of mRNA translation, additional RNA processing, and regulation of cell state and fate. These findings reveal HIV-infected memory CD4 T cells under ART as a distinctive population whose host transcriptomic patterns favor HIV silencing, cell survival, and cell proliferation, with important implications for the development of HIV cure strategies.
DOI: 10.6084/m9.figshare.21405429.v1
title: HIV Silencing and Cell Survival Signatures in Infected T cell Reservoirs

description: Rare CD4 T cells that harbor HIV under antiretroviral therapy (ART) represent an important barrier to HIV cure1-3, but the infeasibility of isolating and characterizing these cells in their natural state has led to uncertainty about whether they possess distinctive attributes that HIV cure-directed therapies might exploit. Here, we addressed this challenge using a microfluidic technology that isolates HIV-infected cell transcriptomes based solely on HIV DNA detection. HIV DNA+ memory CD4 T cells in blood from people receiving ART showed inhibition of six transcriptomic pathways including death receptor signaling, necroptosis signaling, and antiproliferative G12/13 signaling. Moreover, two groups of genes identified by network co-expression analysis were significantly associated with HIV DNA+ cells. These genes (n = 145) accounted for just 0.81% of the measured transcriptome and included negative regulators of HIV transcription that were higher in HIV DNA+ cells, positive regulators of HIV transcription that were lower in HIV DNA+ cells, and other genes involved in negative regulation of mRNA translation, additional RNA processing, and regulation of cell state and fate. These findings reveal HIV-infected memory CD4 T cells under ART as a distinctive population whose host transcriptomic patterns favor HIV silencing, cell survival, and cell proliferation, with important implications for the development of HIV cure strategies.
DOI: 10.6084/m9.figshare.21404640
title: Structure-based design of functionally selective bitopic ligands for the µ-opioid receptor

description: pharmacology in vitro and in vivo
DOI: 10.6084/m9.figshare.21404640.v1
title: Structure-based design of functionally selective bitopic ligands for the µ-opioid receptor

description: pharmacology in vitro and in vivo
DOI: 10.6084/m9.figshare.21272877
title: A molecular network of conserved factors keeps ribosomes dormant in the egg

description: Supplementary Tables for Dormant ribosome study
DOI: 10.6084/m9.figshare.21272877.v1
title: A molecular network of conserved factors keeps ribosomes dormant in the egg

description: Supplementary Tables for Dormant ribosome study
DOI: 10.6084/m9.figshare.21623379
title: Tissue CD14+CD8+T-cells are reprogrammed by myeloid cells and modulated by LPS

description: Source data for flow cytometric (majority) based experiments to accompany Pallett et al manuscript describing the role of intrahepatic CD8+ CD14-expressing TRM
DOI: 10.6084/m9.figshare.21623379.v1
title: Tissue CD14+CD8+T-cells are reprogrammed by myeloid cells and modulated by LPS

description: Source data for flow cytometric (majority) based experiments to accompany Pallett et al manuscript describing the role of intrahepatic CD8+ CD14-expressing TRM
DOI: 10.6084/m9.figshare.21311199
title: mRNA aging shapes the Cap2 methylome in mammalian mRNA

description: This file contains the information about Cap2 methylation measurements in individual mRNA transcriptome-wide. Moreover, additional datasets are included, such as measured translation capacity and half-lives of transcription-start nucleotide (TSN) mRNA isoforms determined by polysome-TSS-seq and ActD-TSS-seq methods.
DOI: 10.6084/m9.figshare.21311199.v1
title: mRNA aging shapes the Cap2 methylome in mammalian mRNA

description: This file contains the information about Cap2 methylation measurements in individual mRNA transcriptome-wide. Moreover, additional datasets are included, such as measured translation capacity and half-lives of transcription-start nucleotide (TSN) mRNA isoforms determined by polysome-TSS-seq and ActD-TSS-seq methods.
DOI: 10.6084/m9.figshare.21507933
title: Moisture, density-dependent interactions, and tropical tree diversity

description: Datasets with records of first-year seedling survival, densities of conspecific and heterospecific seedling and large neighbours, soil water content, rainfall and diversity of seedlings in Barro Colorado Island, Panama, from 1996-2015. An R script provides code used to evaluate relationships between interannual variation in moisture availability, the strength of density dependent interactions, and seedling diversity.
DOI: 10.6084/m9.figshare.21507933.v1
title: Moisture, density-dependent interactions, and tropical tree diversity

description: Datasets with records of first-year seedling survival, densities of conspecific and heterospecific seedling and large neighbours, soil water content, rainfall and diversity of seedlings in Barro Colorado Island, Panama, from 1996-2015. An R script provides code used to evaluate relationships between interannual variation in moisture availability, the strength of density dependent interactions, and seedling diversity.
DOI: 10.6084/m9.figshare.21135997
title: TBK1 as a cancer immunotherapy target

description: Source data for Main Figures
DOI: 10.6084/m9.figshare.21135997.v1
title: TBK1 as a cancer immunotherapy target

description: Source data for Main Figures
DOI: 10.6084/m9.figshare.21355467
title: Origination of the modern-style diversity gradient 15 million years ago

description: Supplementary figures, data files, and code to accompany the paper.
DOI: 10.6084/m9.figshare.21718256
title: Late Cenozoic cooling restructured global marine plankton communities

description: The geographic ranges of marine organisms, including planktonic foraminifera, diatoms, dinoflagellates, copepods and fish are already shifting poleward due to anthropogenic climate change. However, the extent to which species will move and whether these poleward range shifts represent precursor signals which lead to extinction is unclear. Understanding the development of marine biodiversity patterns over geological time and the factors that influence them are key to contextualizing these current trends. The fossil record of the macroperforate planktonic foraminifera provides a rich and phylogenetically resolved dataset that provides unique opportunities for understanding marine biogeography dynamics and how species distributions have responded to ancient climate changes. Here, we employ a bipartite network approach to quantify group diversity, latitudinal specialization, and latitudinal equitability for planktonic foraminifera over the last 8 Ma using Triton, a recently developed high-resolution global dataset of planktonic foraminiferal occurrences. Results depict a global, clade-wide equatorward shift in ecological and morphological community equitability across the last ~8 million years in response to temperature changes during late Cenozoic bipolar ice sheet formation. Collectively, the Triton data indicate the presence of a “latitudinal equitability gradient” (LEG) amongst planktonic foraminiferal functional groups which, importantly, is coupled to the latitudinal biodiversity gradient only through the geologically recent past (~2 Ma - Recent). Prior to this time, LEGs indicate that higher latitudes promoted community equitability across ecological and morphological groups. Observed range shifts amongst marine planktonic microorganisms in the recent and geological past suggest significant poleward expansion of marine communities under even the most conservative future global warming scenarios.
DOI: 10.6084/m9.figshare.21355467.v1
title: Origination of the modern-style diversity gradient 15 million years ago

description: Supplementary figures, data files, and code to accompany the paper.
DOI: 10.6084/m9.figshare.21718256.v1
title: Late Cenozoic cooling restructured global marine plankton communities

description: The geographic ranges of marine organisms, including planktonic foraminifera, diatoms, dinoflagellates, copepods and fish are already shifting poleward due to anthropogenic climate change. However, the extent to which species will move and whether these poleward range shifts represent precursor signals which lead to extinction is unclear. Understanding the development of marine biodiversity patterns over geological time and the factors that influence them are key to contextualizing these current trends. The fossil record of the macroperforate planktonic foraminifera provides a rich and phylogenetically resolved dataset that provides unique opportunities for understanding marine biogeography dynamics and how species distributions have responded to ancient climate changes. Here, we employ a bipartite network approach to quantify group diversity, latitudinal specialization, and latitudinal equitability for planktonic foraminifera over the last 8 Ma using Triton, a recently developed high-resolution global dataset of planktonic foraminiferal occurrences. Results depict a global, clade-wide equatorward shift in ecological and morphological community equitability across the last ~8 million years in response to temperature changes during late Cenozoic bipolar ice sheet formation. Collectively, the Triton data indicate the presence of a “latitudinal equitability gradient” (LEG) amongst planktonic foraminiferal functional groups which, importantly, is coupled to the latitudinal biodiversity gradient only through the geologically recent past (~2 Ma - Recent). Prior to this time, LEGs indicate that higher latitudes promoted community equitability across ecological and morphological groups. Observed range shifts amongst marine planktonic microorganisms in the recent and geological past suggest significant poleward expansion of marine communities under even the most conservative future global warming scenarios.
DOI: 10.6084/m9.figshare.21225284
title: Breaking Tolerance in Down Syndrome: A Triad of Cytokines, Activated T cells and CD11c+ B Cells.

description: SupplementalDataset_DPATesting_IgG_DS_HC_pairwise_tests_lfc_1_fdr_0.05 SupplementalDatafolder_Raw_Files_DS_HC_APS_IPEX
DOI: 10.6084/m9.figshare.21225284.v1
title: Breaking Tolerance in Down Syndrome: A Triad of Cytokines, Activated T cells and CD11c+ B Cells.

description: SupplementalDataset_DPATesting_IgG_DS_HC_pairwise_tests_lfc_1_fdr_0.05 SupplementalDatafolder_Raw_Files_DS_HC_APS_IPEX
DOI: 10.6084/m9.figshare.21930960
title: Molecular sensing of mechano- and ligand-dependent adhesion GPCR dissociation

description: Raw data of Western blots in Scholz, Dahse et al.
DOI: 10.6084/m9.figshare.21930960.v1
title: Molecular sensing of mechano- and ligand-dependent adhesion GPCR dissociation

description: Raw data of Western blots in Scholz, Dahse et al.
DOI: 10.6084/m9.figshare.21304902
title: Structural basis of mitochondrial membrane bending by I-II-III2-IV2 supercomplex

description: PDB coordinates
DOI: 10.6084/m9.figshare.21304902.v1
title: Structural basis of mitochondrial membrane bending by I-II-III2-IV2 supercomplex

description: PDB coordinates
DOI: 10.6084/m9.figshare.21971567
title: Basis for Polycomb repressive deubiquitinase’s nucleosomal H2A specificity

description: Microsoft Excel files for plotting Fig. 2e, Extended data Fig. 1a, 1d, 5g, and data files for quantitating Western blots. The SI_new.pdf file contains uncropped and unprocessed gels and blots for all the figures presented in the paper.
DOI: 10.6084/m9.figshare.21586098
title: Norovirus MLKL-like pore forming protein initiates programed cell death for viral egress

description: Western blot and other source data from our manuscript entitled "Norovirus MLKL-like pore forming protein initiates programmed cell death for viral egress".
DOI: 10.6084/m9.figshare.21971567.v1
title: Basis for Polycomb repressive deubiquitinase’s nucleosomal H2A specificity

description: Microsoft Excel files for plotting Fig. 2e, Extended data Fig. 1a, 1d, 5g, and data files for quantitating Western blots. The SI_new.pdf file contains uncropped and unprocessed gels and blots for all the figures presented in the paper.
DOI: 10.6084/m9.figshare.21586098.v1
title: Norovirus MLKL-like pore forming protein initiates programed cell death for viral egress

description: Western blot and other source data from our manuscript entitled "Norovirus MLKL-like pore forming protein initiates programmed cell death for viral egress".
DOI: 10.6084/m9.figshare.22027757
title: The NK receptor NKp46 recognizes ecto-calreticulin on ER-stressed cells

description: original source data, gating, antibody list, list of primers
DOI: 10.6084/m9.figshare.22027757.v1
title: The NK receptor NKp46 recognizes ecto-calreticulin on ER-stressed cells

description: original source data, gating, antibody list, list of primers