cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7806266.v1
title: Individual and stable autoantibody repertoires in healthy individuals

description: In the era towards precision medicine, we here present the individual specific autoantibody signatures of 193 healthy individuals. The self-reactive IgG signatures are stable over time in a way that each individual profile is recognized in longitudinal sampling. The IgG autoantibody reactivity towards an antigen array comprising 335 protein fragments, representing 204 human proteins with potential relevance to autoimmune disorders, was measured in longitudinal plasma samples from 193 healthy individuals. This analysis resulted in unique autoantibody barcodes for each individual that were maintained over one year’s time. The reactivity profiles, or signatures, are person specific in regards to the number of reactivities and antigen specificity. Two independent data sets were consistent in that each healthy individual displayed reactivity towards 0–16 antigens, with a median of six. Subsequently, four selected individuals were profiled on in-house produced high-density protein arrays containing 23,000 protein fragments representing 14,000 unique protein coding genes. Based on a unique, broad and deep longitudinal profiling of autoantibody reactivities, our results demonstrate a unique autoreactive profile in each analyzed healthy individual. The need and interest for broad-ranged and high-resolution molecular profiling of healthy individuals is rising. We have here generated and assessed an initial perspective on the global distribution of the self-reactive IgG repertoire in healthy individuals, by investigating 193 well-characterized healthy individuals.HighlightsA unique longitudinal profiling of autoantibody repertoires in healthy individualsAutoantibody profiles are highly individual and stable over timeAll individuals display IgG binding to human protein fragmentsThe specificity of disease associated autoantigens needs to be thoroughly characterizedThe identification of a small set of highly reactive autoantigensImportance of stringent antigen and sample specific cut-offs for defining reactivity A unique longitudinal profiling of autoantibody repertoires in healthy individuals Autoantibody profiles are highly individual and stable over time All individuals display IgG binding to human protein fragments The specificity of disease associated autoantigens needs to be thoroughly characterized The identification of a small set of highly reactive autoantigens Importance of stringent antigen and sample specific cut-offs for defining reactivity
DOI: 10.6084/m9.figshare.7806263.v2
title: The most relevant chromosomal abnormalities in the north of Rio Grande do Sul, Brazil: 26 years of cytogenetic analysis

description: From 1992 to 2018, cytogenetic analyses were successfully performed to explore the chromosomal abnormalities of 729 patients, who utilised a pioneering counselling service in the city of Passo Fundo in the northern part of the Brazilian state of Rio Grande do Sul. This city is characterised by a large conglomerate of private and public hospitals. A classical cytogenetic analysis and G-banding were performed using the patient samples. Although normal karyotypes were observed for 562 of the cases, 167 individuals evidenced chromosomal alterations. Among those, 110 exhibited numerical alterations (65.86%), 41 demonstrated structural modifications (24.55%) and 16 showed both numerical and structural chromosomal changes (9.58%). This study describes the diversity of the chromosomal alterations in this region, which have not been previously examined. After 26 years of study, the findings are discussed herein in a self-critical form.
DOI: 10.6084/m9.figshare.7806263.v1
title: The most relevant chromosomal abnormalities in the north of rio Grande do Sul, Brazil: twenty-six years of cytogenetic analysis

description: From 1992 to 2018, cytogenetic analyses were successfully performed to explore the chromosomal abnormalities of 729 patients, who utilised a pioneering counselling service in the city of Passo Fundo in the northern part of the Brazilian state of Rio Grande do Sul. This city is characterised by a large conglomerate of private and public hospitals. A classical cytogenetic analysis and G-banding were performed using the patient samples. Although normal karyotypes were observed for 562 of the cases, 167 individuals evidenced chromosomal alterations. Among those, 110 exhibited numerical alterations (65.86%), 41 demonstrated structural modifications (24.55%), and 16 showed both numerical and structural chromosomal changes (9.58%). This study describes the diversity of the chromosomal alterations in this region, which have not been previously examined. After 26 years of study, we discuss our findings herein in a self-critical form.
DOI: 10.6084/m9.figshare.7806143
title: Effect of the total galactose content on complement-dependent cytotoxicity of the therapeutic anti-CD20 IgG1 antibodies under temperature stress conditions

description: The degree of monoclonal antibody galactosylation is known to affect complement-dependent cytotoxicity (CDC) activity by affecting C1q binding, suggesting that galactose is associated with CDC bioactivity. However, whether this association also exists under temperature stress conditions is not known. This study highlights the impact of variations in the terminal galactose content of an anti-CD20 monoclonal antibody on CDC bioactivity under high-temperature stress conditions compared with storage conditions at 2–8 °C. Drug product samples with a total galactose content of &gt;38% showed stable CDC bioactivity at higher temperatures (45 °C), while those with 16% galactose content showed reduced CDC activity.
DOI: 10.6084/m9.figshare.7806143.v1
title: Effect of the total galactose content on complement-dependent cytotoxicity of the therapeutic anti-CD20 IgG1 antibodies under temperature stress conditions

description: The degree of monoclonal antibody galactosylation is known to affect complement-dependent cytotoxicity (CDC) activity by affecting C1q binding, suggesting that galactose is associated with CDC bioactivity. However, whether this association also exists under temperature stress conditions is not known. This study highlights the impact of variations in the terminal galactose content of an anti-CD20 monoclonal antibody on CDC bioactivity under high-temperature stress conditions compared with storage conditions at 2–8 °C. Drug product samples with a total galactose content of &gt;38% showed stable CDC bioactivity at higher temperatures (45 °C), while those with 16% galactose content showed reduced CDC activity.
DOI: 10.6084/m9.figshare.7806104
title: Mie Theory Calculations

description: Mie theory calculated values for AAE and SSa for water, rBC, nigrosin, and BrC aerosol. Corresponds to Figure 3. <br>
DOI: 10.6084/m9.figshare.7806104.v1
title: Mie Theory Calculations

description: Mie theory calculated values for AAE and SSa for water, rBC, nigrosin, and BrC aerosol. Corresponds to Figure 3. <br>
DOI: 10.6084/m9.figshare.7806098
title: Data that corresponds to Fig. 4 and 5

description: Data that corresponds to Fig 4 and 5 in paper. <br>rBC surrogate data and PSL data<br>
DOI: 10.6084/m9.figshare.7806101
title: Mie theory sensitivity study

description: Data from our limited sensitivity study.<br>
DOI: 10.6084/m9.figshare.7806098.v1
title: Data that corresponds to Fig. 4 and 5

description: Data that corresponds to Fig 4 and 5 in paper. <br>rBC surrogate data and PSL data<br>
DOI: 10.6084/m9.figshare.7806101.v1
title: Mie theory sensitivity study

description: Data from our limited sensitivity study.<br>
DOI: 10.6084/m9.figshare.7806074
title: Data compiled -SrcI_excitatory receptor expression in single LPeD1 neurons.xlsx

description: Data summary of intracellular recordings monitoring the responses of single, individually identified Lymnaea stagnalis LPeD1 neurons to puffs of ACh neurotransmitter. Data represents a functional test to determine the presence of excitatory nAChRs in LPeD1 neurons, and whether or not treatment with the Src Kinase inhibitor, SrcI, affected the functional expression of these receptors.
DOI: 10.6084/m9.figshare.7806074.v1
title: Data compiled -SrcI_excitatory receptor expression in single LPeD1 neurons.xlsx

description: Data summary of intracellular recordings monitoring the responses of single, individually identified Lymnaea stagnalis LPeD1 neurons to puffs of ACh neurotransmitter. Data represents a functional test to determine the presence of excitatory nAChRs in LPeD1 neurons, and whether or not treatment with the Src Kinase inhibitor, SrcI, affected the functional expression of these receptors.
DOI: 10.6084/m9.figshare.7804613
title: Day 18 Amplitudes

description: Day 18 amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804613.v1
title: Day 18 Amplitudes

description: Day 18 amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804592
title: Untargeted Metabolomic Investigation of the Eastern Oyster - Day 10 - End Result Amplitudes

description: Day ten amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804592.v1
title: Untargeted Metabolomic Investigation of the Eastern Oyster - Day 10 - End Result Amplitudes

description: Day ten amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804595
title: Day Ten Amplitudes

description: Day ten amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.25376/hra.7804580
title: (p)ppGpp and manganese homeostasis supplementary

description: Supplementary data to "Association of Metal Homeostasis and (p)ppGpp Regulation in the Pathophysiology of Enterococcus faecalis."
DOI: 10.6084/m9.figshare.7804595.v1
title: Untargeted Metabolomic Investigation of the Eastern Oyster - Day Ten Amplitudes

description: Day ten amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804595.v2
title: Day Ten Amplitudes

description: Day ten amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.25376/hra.7804574
title: Hyperhomocysteinemia Alters Retinal Endothelial Cells Barrier Function and Angiogenic Potential via Activation of Oxidative Stress

description: Hyperhomocysteinemia (HHcy) is associated with several human visual disorders, such as diabetic retinopathy (DR) and age-related macular degeneration (AMD). Breakdown of the blood-retinal barrier (BRB) is linked to vision loss in DR and AMD. Our previous work revealed that HHcy altered BRB in retinal endothelial cells in vivo. Here we hypothesize that homocysteine (Hcy) alters retinal endothelial cell barrier function and angiogenic potential via activation of oxidative stress. Human retinal endothelial cells (HRECs) treated with and without different concentrations of Hcy showed a reduction of tight junction protein expression, increased FITC dextran leakage, decreased transcellular electrical resistance and increased angiogenic potential. In addition, HRECs treated with Hcy showed increased production of reactive oxygen species (ROS). The anti-oxidant N-acetyl-cysteine (NAC) reduced ROS formation and decreased FITC-dextran leakage in Hcy treated HRECs. A mouse model of HHcy, in which cystathionine-β-synthase is deficient (cbs−/−), was evaluated for oxidative stress by dichlolorofluorescein (DCF), dihydroethidium (DHE) staining. There was a marked increase in ROS production and augmented GSH reductase and antioxidant regulator NRF2 activity, but decreased antioxidant gene expression in retinas of hyperhomocysteinemic mice. Our results suggest activation of oxidative stress as a possible mechanism of HHcy induced retinal endothelial cell dysfunction.
DOI: 10.25376/hra.7804580.v1
title: (p)ppGpp and manganese homeostasis supplementary

description: Supplementary data to "Association of Metal Homeostasis and (p)ppGpp Regulation in the Pathophysiology of Enterococcus faecalis."
DOI: 10.6084/m9.figshare.7804529
title: Day Five Amplitudes

description: Day five amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804532
title: Metabolite Peak ID List

description: Master list of identified metabolites from the individual amplitude files for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804526
title: Water Analyte Concentrations

description: LC-MS/MS water concentrations (EE2, DEET, diphenhydramine, fluoxetine and their mixture) dataset for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804532.v1
title: Metabolite Peak ID List

description: Master list of identified metabolites from the individual amplitude files for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804520
title: Oyster Analyte Body Burdens

description: LC-MS/MS body burden (EE2, DEET, diphenhydramine, fluoxetine and their mixture) dataset for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804523
title: Day One Amplitudes

description: Day one amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804526.v1
title: Water Analyte Concentrations

description: LC-MS/MS water concentrations (EE2, DEET, diphenhydramine, fluoxetine and their mixture) dataset for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804529.v1
title: Day Five Amplitudes

description: Day five amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804514
title: Tank Parameters

description: Tank parameters for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804517
title: Trajectory Analysis Results

description: Trajectory analysis results for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804517.v1
title: Trajectory Analysis Results

description: Trajectory analysis results for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804514.v2
title: Tank Parameters

description: Tank parameters for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804520.v2
title: Oyster Analyte Body Burdens

description: LC-MS/MS body burden (EE2, DEET, diphenhydramine, fluoxetine and their mixture) dataset for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804523.v1
title: Day - 1 - End Result Amplitudes

description: Day ten amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804523.v2
title: Day One Amplitudes

description: Day one amplitudes for oysters exposed to EE2, DEET, diphenhydramine, fluoxetine and their mixture in the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804520.v1
title: Untargeted Metabolomic Investigation of the Eastern Oyster - Oyster Analyte Body Burdens.xlsx

description: LC0MS/MS body burden dataset for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804514.v1
title: Untargeted Metabolomic Investigation of the Eastern Oyster - Tank Parameters.xlsx

description: Tank parameters for the study: Untargeted Metabolomic Investigation of the Eastern Oyster
DOI: 10.6084/m9.figshare.7804454
title: Local and incoming stratification

description: Experimental study of the influence of local and incoming stratification on flow and dispersion in an isolated street canyon<br>
DOI: 10.6084/m9.figshare.7804454.v1
title: Local and incoming stratification

description: Experimental study of the influence of local and incoming stratification on flow and dispersion in an isolated street canyon<br>
DOI: 10.25376/hra.7804418
title: AHA award letter MRG.pdf

description: Previous work had suggested that cardiovascular disease was the result of aberrant epigenetic mechanisms, although the proteins altering the behavior of the cardiac genome were unknown. In this study we observed that CTCF levels were altered across a population of genetically distinct mice (which in turn exhibit a spectrum of phenotypic responses to pathologic stimuli associated with heart failure). To comprehensively determine CTCF’s function in the normal and diseased heart, we generated the first cardiac specific CTCF KO mouse, which enables selective removal of CTCF from the adult heart. Using this mouse model and performing Hi-C (Chromosome Conformation Capture followed by DNA sequencing), we have shown that loss of CTCF is sufficient to induce heart failure through mechanisms that involve restructuring of the genome. These studies answer a long-standing question in cardiac biology: what are the cell type specific changes that alter the expression of DNA to induce heart failure? Rather than individual genes, which we know are insufficient to reverse the syndrome of heart failure, CTCF commands an entire cadre of cardioprotective genes and molecules, maintaining appropriate function of the cardiac cell. When this protein is removed in disease, havoc ensues, leading to dysfunction of the organ at multiple levels. My studies show that CTCF plays a central role in cardiac-specific genome regulation and immediately suggest therapeutic avenues to modulate the epigenetic actions of CTCF to halt heart failure progression and to improve the functional capacity of cardiac muscle, thereby restoring health to sick patients.
DOI: 10.25376/hra.7804418.v1
title: AHA award letter MRG.pdf

description: Previous work had suggested that cardiovascular disease was the result of aberrant epigenetic mechanisms, although the proteins altering the behavior of the cardiac genome were unknown. In this study we observed that CTCF levels were altered across a population of genetically distinct mice (which in turn exhibit a spectrum of phenotypic responses to pathologic stimuli associated with heart failure). To comprehensively determine CTCF’s function in the normal and diseased heart, we generated the first cardiac specific CTCF KO mouse, which enables selective removal of CTCF from the adult heart. Using this mouse model and performing Hi-C (Chromosome Conformation Capture followed by DNA sequencing), we have shown that loss of CTCF is sufficient to induce heart failure through mechanisms that involve restructuring of the genome. These studies answer a long-standing question in cardiac biology: what are the cell type specific changes that alter the expression of DNA to induce heart failure? Rather than individual genes, which we know are insufficient to reverse the syndrome of heart failure, CTCF commands an entire cadre of cardioprotective genes and molecules, maintaining appropriate function of the cardiac cell. When this protein is removed in disease, havoc ensues, leading to dysfunction of the organ at multiple levels. My studies show that CTCF plays a central role in cardiac-specific genome regulation and immediately suggest therapeutic avenues to modulate the epigenetic actions of CTCF to halt heart failure progression and to improve the functional capacity of cardiac muscle, thereby restoring health to sick patients.
DOI: 10.6084/m9.figshare.7804382
title: Code for studying the relationship between Population abundance and Niche-Centroid Distance (HTML version)

description: Code to reproduce whole the analysis from the project "Relationships Between Population Densities and Niche-centroid Distances in North American Birds" using Rmarkdown.
DOI: 10.6084/m9.figshare.7804382.v1
title: Code for studying the relationship between Population abundance and Niche-Centroid Distance (HTML version)

description: Code to reproduce whole the analysis from the project "Predictive Relationships Between Population Densities and Niche-centroid Distances in North American Birds" using Rmarkdown.
DOI: 10.6084/m9.figshare.7804343
title: Interactions between complexes and octanol

description: Interactions between the complexes in octanol at 300 K and 310.15 K after a molecular dynamic simulation.
DOI: 10.6084/m9.figshare.7804343.v1
title: Interactions between complexes and octanol

description: Interactions between the complexes in octanol at 300 K and 310.15 K after a molecular dynamic simulation.
DOI: 10.6084/m9.figshare.7804382.v2
title: Code for studying the relationship between Population abundance and Niche-Centroid Distance (HTML version)

description: Code to reproduce whole the analysis from the project "Predictive Relationships Between Population Densities and Niche-centroid Distances in North American Birds" using Rmarkdown.
DOI: 10.6084/m9.figshare.7804280
title: LipidClassifierSupplemental

description: Supplemental information for "Deriving Accurate Lipid Classification based on Molecular Formula"
DOI: 10.6084/m9.figshare.7804268
title: Conserved Noncoding Sequences

description: CNS generated by Gina's pipeline between maize v3 and rice v7
DOI: 10.6084/m9.figshare.7804280.v1
title: LipidClassifierSupplemental

description: Supplemental information for "Deriving Accurate Lipid Classification based on Molecular Formula"
DOI: 10.6084/m9.figshare.7804247
title: PLSDB 2018_09_14

description: PLSDB files from 2018.09.14
DOI: 10.6084/m9.figshare.7804268.v1
title: Conserved Noncoding Sequences

description: CNS generated by Gina's pipeline between maize v3 and rice v7
DOI: 10.25377/sussex.7804241
title: Research data for article: "How valuable are e-textbooks to the student experience? An analysis of e-textbook provision at the University of Sussex"

description: This dataset includes the results of a survey carried out in 2018 on e-textbook use by students at the University of Sussex Business School.<br><b>Article abstract</b>The Library has provided several e-textbooks to undergraduate and postgraduate modules within the University of Sussex Business School. The primary motivation for this has been the requirement to provide access to essential readings in a climate where UK universities are shying away from recommending student purchase of textbooks. In this qualitative and quantitative analysis of students’ use of e-textbooks, we will explore to what extent their needs are being met. We will examine whether behavioural change is taking place in the way students approach their reading and identify any perceived barriers in the use of e-textbooks. We will also discuss whether the current models of delivery are fit for purpose and whether they constitute a sustainable model for libraries.<br>