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6,348 results for “Hepatitis”
Image data of co-localization of IgG and HEV ORF2 protein in a case of hepatitis E-associated kidney disease
<p><span>Image data for a co-localization study of IgG with HEV ORF2 protein in a </span><span>de novo immune complex-mediated glomerulonephritis (GN) case in</span><span> a kidney transplant recipient </span><span>with chronic hepatitis E (Leblond and Helmchen, et al. 2024).<span> </span>Immunofluorescence images are provided for 25 glomeruli at low magnification (20x, 0.227 micron/pixel) and for 16 glomeruli at high magnification (100x, 0.0454 micron/pixel). For each example glomeruli the green channel represents IgG antibody staining with FITC, and the magenta channel represent anti-HEV ORF2 staining using Alexa Fluor 546.</span></p> <p><span>Methods: </span></p> <p><span>Mouse monoclonal antibody clone 1E6 against the HEV ORF2 protein was incubated for 1h at a dilution of 1:125 followed by a mix of Alexa Fluor 546-conjugated goat anti-mouse antibody (Invitrogen BV, A11018) and FITC-conjugated Rabbit anti-Human IgG (Gamma chain, Diagnostic Biosystem, F008) for 1hat a dilution of 1:50. Following automated staining, the slides were hand -washed in distilled H<sub>2</sub>O. Tissue was covered with Vectashield® Antifade Mounting Medium with DAPI (VectorLaboratories, H-1200), covered with a coverslip and stored at 4°C until evaluation.</span></p> <p><span>Immunofluorescence images were acquired with an upright fluorescence microscope (AxioImager.Z2 controlled by ZEN Blue software; 89 North Photofluor LM-75 light source, and Axiocam 503 mono camera; Zeiss, Jena, Germany), equipped with the following objectives: 20x (NA 0.5, Plan-NEOFLUAR), 40x (NA 1.4 oil, Plan-APOCHROMAT), and 100x (NA 1.45 oil, Plan-APOCHROMAT) objectives. This setup provides an excellent spatial resolution (nominally about 200 nm lateral resolution in our study; pixel size was 45.4 nm for 100x objective). High resolution images were taken with the 100x objective using the ApoTome.2 module with deconvolution (grid 5 lp/mm; section thickness 0.7 µm). We used Vysis Abbott Chroma filter sets (Blue: excitation (ex) 335-383 nm, emission (em) 420-470; green: ex 481-507 nm; em 521-551 nm; red: ex 534-556 nm, em 574- 606 nm). Co-localization of IgG and HEV ORF2 staining was quantified using Fiji software (Schindelin et al., 2012) and the JACoP ImageJ plug-in. </span></p>
MD simulation data: An Entropic Safety Catch Controls Hepatitis C Virus Entry and Antibody Resistance
<p><strong>Background</strong></p> <p>Equilibration, relaxation and production runs were performed on GPUs using the CUDA version of PMEMD in AMBER 16 and AMBER ff14SB force field. Minimisation steps were performed on a CPU using PMEMD in AMBER 16 and the AMBER ff14SB force field. All software is available from http://ambermd.org/. </p> <p><strong>Contents</strong></p> <p>There are three tarball (<strong>.tar.gz</strong>) files containing the <strong>core simulation data</strong>: one for wild type (WT), the second for the I438V A524T mutant and the third for the S449P mutant. Each contains:</p> <p>1. a source PDB (<strong>.pdb</strong>) file</p> <p>2. Five AMBER trajectory (<strong>.nc</strong>) files for five independent MD simulations, numbered 1 to 5. <strong>Note: </strong>each of these files is over 2GB.</p> <p>There is an additional tarball containing the <strong>control files</strong> <strong>and scripts</strong> used for running the MD simulations:</p> <p>1. Multiple control (<strong>.ctl</strong>) files numbered 1 to 10 that are used to minimize (<strong>min</strong> prefix), relax (<strong>rel</strong> prefix) and equilibrate (<strong>equ</strong> prefix) the model</p> <p>2. Executable <strong>do_md</strong> that performed all the minimisation, relaxation and equilibration steps</p> <p>3. control file <strong>prod.ctl</strong> used for the production run </p> <p>4. Executable <strong>run_prod</strong> that was used to perform the production run</p> <p>5. Two control files (<strong>prod_short.ctl </strong>and <strong>prod_short_2.ctl</strong>) for the short runs used to de-correlate the simulation for the independent runs</p> <p>6. Executable <strong>run_short</strong> and <strong>run_short_2</strong> used to carry out the de-correlated production runs.</p>
Genomic investigations of unexplained acute hepatitis in children
<p>Raw genomic sequencing data, enriched for either Human Adenovirus, Adeno-associated Virus 2 or Human Herpesvirus 6, after removal of host reads. Please check the reference for detailed metadata for each sample. </p><p>Morfopoulou, S., Buddle, S., Torres Montaguth, O.E. et al. Genomic investigations of unexplained acute hepatitis in children. Nature 617, 564–573 (2023). https://doi.org/10.1038/s41586-023-06003-w</p>
scRNA-seq data for article: Kupffer cell and recruited macrophage heterogeneity orchestrate granuloma maturation and hepatic immunity in visceral leishmaniasis
<p>Single-cell RNA-seq dataset from sorted CD11bInt, F4/80Hi, CD64+ mouse liver cells in naive or Leishmania infantum-infected animals at 42 d.p.i.. Data analyses and results are described in manuscript: "Kupffer cell and recruited macrophage heterogeneity orchestrate granuloma maturation and hepatic immunity in visceral leishmaniasis". Data files are Seurat objects in RDS format. Filtered-out potential doublets, low quality cells and dying cells (excluded cells with <1000 genes detected, cells with >6000 genes detected, cells with mitochondrial gene expression > 10% and cells with <5000 transcript molecules). Data normalization, scaling and integration performed using Seurat.</p> <p>Filtered dataset containing all KCs and macrophages is in the "pessenda_KC_Macro_seurat" file.</p> <p>Our data were then mapped onto a reference dataset published by Remmerie et al. (DOI: 10.1016/j.immuni.2020.08.004) for annotation consistent with the literature. The reference mapped object can be found in the "pessenda_refmap_KC_Macro_seurat" file.</p> <p>Dataset containing the additional analysis of CLEC4F-TIM4+ FACS-sorted KCs can be found in the "pessenda_refmap_KCTimPos_seurat" file.</p>
Estimated prevalence of chronic hepatitis B in Denmark on December 31, 2016 – an update based on nationwide registers
<p>Anonymised dataset analysed in the study "Estimated prevalence of chronic hepatitis B in Denmark on December 31, 2016 – an update based on nationwide registers". </p>
Defective HNF4alpha-dependent gene expression as a driver of hepatocellular failure in alcoholic hepatitis [Suppl Data]
<p>Alcoholic hepatitis (AH) is a life-threatening condition characterized by profound hepatocellular dysfunction for which targeted treatments are urgently needed. Identification of molecular drivers is hampered by the lack of suitable animal models. By performing RNA sequencing in livers from patients with different phenotypes of alcohol-related liver disease (ALD), we show that the development of AH is characterized by the defective activity of liver-enriched transcription factors (LETFs). TGFb1is a key upstream transcriptome regulator in AH and induces the use of HNF4aP2 promoter in hepatocytes, which results in defective metabolic and synthetic functions. Gene polymorphisms in LETFs including HNF4aare not associated with the development of AH. In contrast, epigenetic studies show that AH livers have profound changes in DNA methylation state and chromatin remodeling, affecting HNF4a-dependent gene expression. We conclude that targeting TGFb1and epigenetic drivers that modulate HNF4a-dependent gene expression could be beneficial to improve hepatocellular function in patients with AH.</p>
Recombinant Hepatitis E Viruses Harboring Tags in the ORF1 Protein
<p>Hepatitis E virus (HEV) is one of the most common causes of acute hepatitis and jaundice in the world. Current understanding of the molecular virology and pathogenesis of hepatitis E is incomplete, especially due to the limited availability of functional tools. Here, we report the development of tagged HEV genomes as a novel tool to investigate the viral life cycle. A selectable subgenomic HEV replicon was subjected to random 15-nucleotide sequence insertion using transposon-based technology. Viable insertions in the open reading frame 1 (ORF1) protein were selected in a hepatoblastoma cell line. Functional insertion sites were identified downstream of the methyltransferase domain, in the hypervariable region (HVR) and between the helicase and RNA-dependent RNA polymerase domains. HEV genomes harboring a hemagglutinin (HA) epitope tag or a small luciferase (NanoLuc) in the HVR were found to be fully functional and to allow for the production of infectious virus. NanoLuc allowed to quantitatively monitor HEV infection and replication by luciferase assay. HA-tagged replicons and full-length genomes allowed to localize putative sites of HEV RNA replication by the simultaneous detection of viral RNA by fluorescence in situ hybridization and of ORF1 protein by immunofluorescence. Candidate HEV replication complexes were found in cytoplasmic dot-like structures which partially overlap with ORF2 and ORF3 proteins as well as exosomal markers. Hence, tagged HEV genomes yield new insights into the viral life cycle and should allow to further investigate the structure and composition of the viral replication complex.</p>
Hepatitis D infection induces IFN-β-mediated NK cell activation and TRAIL-dependent cytotoxicity
<p>The dataset contains bulk RNA-seq read count matrices of NK cells from healthy donors after 48 h of co-culture with hepatitis D virus infected and non-infected HepG2-hNTCP cells. The samples are described in the table RNA-seq_samples.xls that is included with the count matrices. Further details are given in the publication associated with this dataset (Groth et al., <i>Front Immunol</i>, 2023, https://doi.org/10.3389/fimmu.2023.1287367).</p>
Gestational Cd exposure in the CD-1 mouse induces sex-specific hepatic insulin insensitivity, obesity and metabolic syndrome in adult female offspring
<p>There is compelling evidence that developmental exposure to some toxic metals increases risk for obesity and obesity-related morbidity including cardiovascular disease and type 2 diabetes in adults. To explore the hypothesis that developmental Cd exposure increased risk of obesity later in life, male and female CD-1 mice were maternally exposed to 500 ppb CdCl<sub>2</sub> in drinking water during a human gestational equivalent period (GD0 - PND10). Hallmark indicators of metabolic disruption, hepatic steatosis, and metabolic syndrome were evaluated prior to birth through adulthood. Blood Cd levels in dams were similar to those observed in human pregnancy cohorts. There were no observed impacts of exposure on dams or pregnancy-related outcomes. Results of glucose and insulin tolerance testing revealed that Cd-exposure impaired glucose homeostasis in young adult offspring. Exposure-related increases in circulating triglycerides and hepatic steatosis were apparent only in females. By PND120, Cd-exposed females had become 30% heavier with 700% more perigonadal fat than unexposed control females. There was no evidence of dyslipidemia, steatosis, increased weight gain, nor increased adiposity in Cd-exposed male offspring. Hepatic transcriptome analysis at PND1, PND21, and PND42 revealed evidence for female-specific increases in oxidative stress and mitochondrial dysfunction with significant early disruption of retinoic acid signaling and altered insulin receptor signaling consistent with hepatic insulin sensitivity in adult females. The observed steatosis and metabolic syndrome-like phenotypes resulting from exposure to 500 ppb CdCl<sub>2</sub> during the pre- and perinatal period of development equivalent to human gestation indicate that Cd acts developmentally as a sex-specific delayed obesogen.</p>
Raw NGS data for the study 'Spouse-to-spouse Transmission and Evolution of Hypervariable Region 1 and 5’ Untraslated Region of Hepatitis C Virus Analyzed by Next-generation Sequencing'
<p>This file contains the original next-generation sequencing data (raw sequences in fastq format) which were analyzed in the study titled: "Spouse-to-spouse Transmission and Evolution of Hypervariable Region 1 and 5’ Untraslated Region of Hepatitis C Virus Analyzed by Next-generation Sequencing".</p> <p> </p> <p> </p>
Optimization of SPECT/CT based lung dose calculation for Holmium-166 hepatic radioembolization
<p><strong>Background</strong>: Quantitative SPECT of the lungs after intra-arterial hepatic radioembolization using Holmium-166 (<sup>166</sup>Ho)microspheres is essential to assess therapy safety. A SPECT estimated lung absorbed dose resulting from radioembolization of more than 30 Gy is a contra-indication for therapy. Earlier we showed the superiority of Monte Carlo-based iterative reconstructions over conventional reconstructions due to its quantitative nature, required for dosimetry, at the cost of substantial computation times. In clinical routine, however, the limited available time between scout imaging and therapy constrains its application. To reduce computation times, we investigated the minimum number of iterations required to guarantee a clinical acceptable accuracy in lung dose estimation using patient and phantom data.</p> <p><strong>Methods</strong>: <sup>166</sup>Ho scout SPECT data (range: 222-283 MBq) were used from 9 patients. SPECT images were Monte Carlo-based OSEM reconstructed (iterations: 30, subsets: 8). Additionally, the 4D XCAT anthropomorphic phantom was used to mimic SPECT studies with an injected scout activity of 250 MBq and with varying lung doses ranging from 0 to 15.6 mGy/MBq. These studies were reconstructed in the same way as the patient data.</p> <p><strong>Results: </strong>In all patients the lung absorbed dose upon OSEM convergence ranged from 0 to 0.025 mGy/MBq, and ranged from 0.002 to 0.078 mGy/MBq after five iterations, still well below the allowed 30 Gy in case treatment was proceeded. In the phantom data, the estimated lung dose ranged from 0.004 to 15 mGy/MBq upon convergence and from 0.03 to 13.9 mGy/MBq after five iterations, simulating situations well below and above an estimated treatment lung dose of 30 Gy. Importantly, the lung absorbed dose upon OSEM convergence was underestimated by 15% as compared to the actual simulated lung dose, and the dose after five OSEM iterations was underestimated by 9% as compared to the dose upon convergence. Both underestimations were irrespective of the magnitude of the lung dose and thus can be easily corrected for.</p> <p><strong>Conclusions</strong>: The number of OSEM iterations necessary for a quantitative estimate of the lung dose can be reduced from 30 to 5. The resulting six fold reduction in calculation time enables data processing of the scout images before therapy administration.</p>
Ontogeny of hepatic metabolism in two broiler lines divergently selected for the ultimate pH of the Pectoralis major muscle
<p>Nutrient availability during early stages of development (embryogenesis and the first week of life) can have long-term effects on physiological functions and bird metabolism. The embryo develops in a closed structure and depends entirely on the nutrients and energy available in the egg. The aim of this study was to describe the ontogeny of pathways governing hepatic metabolism that mediates many physiological functions in the pHu+ and pHu- chicken lines, which are divergently selected for the ultimate pH of meat, a proxy for muscle glycogen stores, and which differ in the nutrient content and composition of eggs. Our study provides the first detailed description of the evolution of different hepatic metabolic pathways during the early development of embryos and post-hatching chicks. We found a metabolic orientation for the pHu+ line towards proteolysis, glycogen degradation, ATP synthesis and autophagy, likely in response to a higher energy requirement compared with pHu- embryos. The metabolic orientations specific to the pHu+ and pHu- lines are established very early, probably in relation with their different genetic background and available nutrients.</p>
Intra-host quasispecies reconstructions resemble inter-host variability in transmitted chronic Hepatitis B Virus strains (Dataset)
<p>Data used for publication "Intra-host quasispecies reconstructions resemble inter-host variability in transmitted chronic Hepatitis B Virus strains" submitted to the <em>Journal of Medical Virology</em>. Includes example code and selected sequence, tree, and data files.</p>
Data from: Single cell transcriptomics shows dose-dependent disruption of hepatic zonation by TCDD in mice
<p>2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) dose-dependently induces the development of hepatic fat accumulation and inflammation with fibrosis in mice initially in the portal region. Conversely, differential gene and protein expression is first detected in the central region. To further investigate cell-specific and spatially resolved dose-dependent changes in gene expression elicited by TCDD, single-nuclei RNA sequencing and spatial transcriptomics were used for livers of male mice gavaged with TCDD every 4 days for 28 days. The proportion of 11 cell (sub)types across 131,613 nuclei dose-dependently changed with 68% of all portal and central hepatocyte nuclei in control mice being overtaken by macrophages following TCDD treatment. We identified 368 (portal fibroblasts) to 1,339 (macrophages) differentially expressed genes. Spatial analyses revealed initial loss of portal identity that eventually spanned the entire liver lobule with increasing dose. Induction of R-spondin 3 (<em>Rspo3</em>) and pericentral <em>Apc</em>, suggested dysregulation of the Wnt/β-catenin signaling cascade in zonally resolved steatosis. Collectively, the integrated results suggest disruption of zonation contributes to the pattern of TCDD-elicited NAFLD pathologies.</p>
Fig. 3 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice
Fig. 3 Th1 immune response acter CD8+T cells blockage in sitro. a. CD3+CD8+T cells were successcullv blocked. The blocking ecciciencv was more than 99.6 %. b, c. Percentages oc CD4+IFN-γ+ (Th1) in Tat-TPI (T-TPI), TPI stimulated splenocvtes with or without CD8+T-cell blockage. Data are presented as the means ± SEM crom cour independent experiments. (*P <0.05; **P <0.01)
Fig. 2 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice
Fig. 2 Immune responses in the draining popliteal lvmph nodes oc mice induced bv Tat-TPI (T-TPI) and TPI proteins. a and c. Percentages oc CD4+IFN-γ+ cells (Th1), CD8+IFN-γ+ cells (Tc1) analvsed bv FACS. b. The ratio oc CD4+ T cells to CD8+ T cells (CD4/CD8) in the draining popliteal lvmph nodes. Data are presented as the means ± SEM crom six mice in each group. (*P <0.05; **P <0.01)
Fig. 1 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice
Fig. 1 Expression, puricication and identicication oc the cusion proteins Tat-TPI and TPI. a. Puricication oc two cusion proteins detected bv Protein Gel Electrophoresis. M: molecular weight marker, Lane 1: recombinant SjTat-TPI, Lane 2: recombinant SjTPI, Lane 3: the recombinant plasmid without puricication. b. Fusion proteins recognised bv His-Ab with Western blotting. Lane 1: recombinant SjTat-TPI, Lane 2: recombinant SjTPI. c. Fusion proteins recognised bv S. japonicum incected-mice serum with Western blotting. Lane 1: recombinant SjTat-TPI, Lane 2: recombinant SjTPI
Fig. 5 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice
Fig. 5 Parasite burden and immune response were obsersed at 6 weeks acter S. japonicum incection in mice saccinated with T-TPI + IFA, TPI + IFA, IFA and PBS. a. Aserage number oc worms recosered. b. Aserage number oc eggs per gram (EPG) in the liser. c. Representatise granulomas with a single egg crom each group (100×). d. Aserage area oc single egg granulomas crom each group. e, f. Percentages oc CD3+CD4+IFN-γ+(Th1) and CD3+CD8+IFN-γ+(Tc1) gated crom CD3+ T cells analvsed bv FACS. Each bar represents the means ± SEM crom twelse mice per group. (*P <0.05; **P <0.01)
Fig. 4 T cell and antibodies responses acter three immunisations with T in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice
Fig. 4 T cell and antibodies responses acter three immunisations with T-TPI + IFA, TPI + IFA, IFA and PBS. a and b: Percentages oc CD3+CD4+IFN-γ+ (Th1) and CD3+CD8+IFN-γ+ (Tc1) gated crom CD3+ cells analvsed bv FACS. c. IgG, IgG1 and IgG2a lesels in mice sera were detected. Data are presented as the means ± SEM crom eight mice in each group. (*P <0.05; **P <0.01)
Figure 1 in Bio-efficacy of iron and zinc fortified wheat flour along with bio-assessment of its hepatic and renal toxic potential
Figure 1. Microscopic morphology of representative liver tissues under the effect of varied iron and zinc supplementation in fortified wheat flour (100X; magnification). (A) Normal, no tissue changes = 0, (B) cellular swelling in hepatocytes = 1, (C) microvascular changes in hepatocytes = 2, (D) marked cellular swelling and necrosis of hepatocytes = 3.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.