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Bicocca Open Archive Research Data

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1970
2023
1970 2023
290 results
  • BRAQUE: Bayesian Reduction for Amplified Quantization in UMAP Embedding. Supplementary data.
    We propose a Bayesian Reduction for Amplified Quantization in Umap Embedding (BRAQUE) as an integrative novel approach, from data preprocessing to phenotype classification. BRAQUE starts with an innovative preprocessing, named Lognormal Shrinkage, able to enhance input fragmentation by fitting a lognormal mixture model and shrinking each component towards its median, in order to help further clustering step in finding more separated and clear clusters. The BRAQUE’s pipeline consist of a dimensionality reduction step performed using UMAP, and a clustering performed using HDBSCAN on UMAP embedding. These SUPPLEMENTAL DATA contain the csv image data files for seven lymphoid tissues, the antibody list and an MTA agreement letter for the CyBorgh software.
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  • A DNA damage response-like phenotype defines a third of colon cancers at onset. Supplementary data.
    These are supplemental data to the manuscript entitled: A DNA damage response-like phenotype defines a novel subset of colon cancer. A third of de-novo presentations of colorectal cancer display foci of positivity for ℽH2AX, pCHK2, pNBS1 in the absence of apoptosis or senescence associated p21/CDKN1A. This phenotype is reminiscent of an ongoing DNA damage response (DDR). The TP53 status, the chromosome 20q amplification or the microsatellite instability gene status did not correlate with the DDR phenotype, except for a preferential association with MSH2/MSH6 inactivation and conserved MLH1. Additional lesions of DDR-associated genes may be responsible for this phenotype, which is absent from the remaining cases in this cohort. The outcome, after adjuvant treatment with DNA-damaging drugs, did not differentiate this group from the remaining cases. DDR+ colorectal cancers may be amenable to personalized therapy by targeting the DDR.
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  • Self-reported Assessment of the Socio-economic Impact of Anticancer Chemotherapy-related Neurotoxicity
    Original (Italian) and English translation of the questionnaires used to perform the study. Original dataset used to perform the analysis (in Italian)
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  • High glucose induces an activated state of partial epithelial-mesenchymal transition in human tubular cell cultures
    Tubulointerstitial fibrosis is observed in diabetic nephropathy. It is still debated whether tubular cells, undergoing epithelial-mesenchymal transition (EMT) in high glucose (HG) conditions, may contribute to interstitial fibrosis development. In this study, we investigated the phenotypic and molecular EMT-like changes and the alteration of inflammatory and fibrogenic secretome induced by HG in human primary tubular cell cultures. Taking advantage of this in vitro cell model composed of proximal and distal tubular cells, we showed that HG-treated tubular cells acquired a fibroblast-like morphology with cytoplasmic stress fibers, maintaining the expression of the epithelial markers specific of proximal and distal tubular cells. HG increased Snail1, miRNA210 and Vimentin mesenchymal markers, decreased N-cadherin expression and migration ability of primary tubular cells, while E-cadherin expression and focal adhesion distribution were not affected. Furthermore, HG treatment of tubular cells altered the inflammatory cytokine secretion creating a secretome able to enhance the proliferation and migration of fibroblasts. Our findings show that HG promotes an activated state of partial EMT in human tubular primary cells and induces a pro-inflammatory and pro-fibrogenic microenvironment, supporting the active role of tubular cells in diabetic nephropathy onset.
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  • Rejuvenated vintage tissue sections highlight individual antigen fate during processing and long term storage.
    Antigen-bearing proteins become progressively unavailable to immunodetection after prolonged storage of routine sections, exposed to a variety of agents, such as moisture, oxygen and temperature. By proteomic analysis, the antigens are retained in the sections and definitely in the tissue block, pointing to fixation-independent, storage time-dependent protein modifications. Based on previous experience, we hypothesized that a combined exposure to a reducing agent and to chemicals favouring protein conformation changes would reverse the masking in aged sections. Disaccharides, lactose and sucrose, and a surfactant, added to a standard antigen retrieval buffer, reverse the negative changes in aged sections. Furthermore, they provide enhanced access to antigens in freshly cut sections, but not universally, revealing additional factors, besides heat and calcium chelation, required for antigen retrieval of individual proteins. This dataset contains supplementary data to the manuscript, raw data and analytical tools.
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  • Cannabinoids: an effective treatment for chemotherapy-induced peripheral neurotoxicity?
    materials and methods as supplementary data to the review "Cannabinoids: an effective treatment for chemotherapy-induced peripheral neurotoxicity?"
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  • Data for: Relative Prognostic Importance of Left and Right Ventricular Ejection Fraction in Patients with Cardiac Diseases
    3D echocardiography volumes and ejection fraction of the left and right ventricle in patients with various cardiac diseaes who were followed for 3.7 years after the echo study to assess outcome
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  • Supplementary tables/figures and referecences to A Prospective Evaluation of Health Care Provider and Patient Assessments in Chemotherapy Induced Peripheral Neurotoxicity.
    Supplementary Tables and Figures are made available here.
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  • SARS-CoV-2 CodonUsage Data
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  • Human Intravenous Immunoglobulin Alleviates Neuropathic Symptoms in a Rat Model of Paclitaxel-Induced Peripheral Neurotoxicity
    This record contains raw data related to the original article entitled "Human Intravenous Immunoglobulin Alleviates Neuropathic Symptoms in a Rat Model of Paclitaxel-Induced Peripheral Neurotoxicity".
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