Skip to main content
Bicocca Open Archive Research Data

Datasets within this collection

Filter Results
1970 2024
294 results
  • Seeing or believing in hyperplexed spatial proteomics via antibodies.
    Supplementary data for the manuscript "Seeing or believing in hyperplexed spatial proteomics via antibodies." The content of this online repository is explained in the .txt file "FolderContent-ReadMe". Please download and read.
    • Dataset
  • Benchmarking digital displays (monitors) for histological diagnoses: the Nephropathology use case
    Granular data from the assessment of non-inferiority of different monitors/scanners combination for the evaluation of whole slide images (WSI) for the primary diagnosis of renal diseases on histology following the College of American Pathologists (CAP) guidelines.
    • Dataset
  • Improving the annotation process in computational pathology: from manual to semi-automatic approaches in digital nephropathology
    The development of reliable artificial intelligence (AI) algorithms in pathology depends on solid ground truth provided by meticulous annotation of whole slide images (WSI), a time-consuming and operator-dependent process. A benchmark of the available annotation tools is performed to standardize and streamline this process.
    • Dataset
  • Paclitaxel mice models raw data
    Data refer to the behavioral and neurophysiological assessments performed in 2 different mice models obtained with the administration of 70 mg/kg i.v. weekly for 4 times (Study 1) vs. 10 mg/kg every 2 days for 7 times (Study 2).
    • Dataset
  • Paclitaxel, but Not Cisplatin, Affects Satellite Glial Cells in Dorsal Root Ganglia of Rats with Chemotherapy-Induced Peripheral Neurotoxicity
    Chemotherapy-induced peripheral neurotoxicity is one of the most common dose-limiting toxicities of several widely used anticancer drugs such as platinum derivatives (cisplatin) and taxanes (paclitaxel). Several molecular mechanisms related to the onset of neurotoxicity have already been proposed, most of them having the sensory neurons of the dorsal root ganglia (DRG) and the peripheral nerve fibers as principal targets. In this study we explore chemotherapy-induced peripheral neurotoxicity beyond the neuronocentric view, investigating the changes induced by paclitaxel (PTX) and cisplatin (CDDP) on satellite glial cells (SGC) in the DRG and their crosstalk. Rats were chronically treated with PTX (10 mg/Kg, 1qwx4) or CDDP (2 mg/Kg 2qwx4) or respective vehicles. Morpho-functional analyses were performed to verify the features of drug-induced peripheral neurotoxicity. Qualitative and quantitative immunohistochemistry, 3D immunofluorescence, immunoblotting, and transmission electron microscopy analyses were also performed to detect alterations in SGCs and their interconnections. We demonstrated that PTX, but not CDDP, produces a strong activation of SGCs in the DRG, by altering their interconnections and their physical contact with sensory neurons. SGCs may act as principal actors in PTX-induced peripheral neurotoxicity, paving the way for the identification of new druggable targets for the treatment and prevention of chemotherapy-induced peripheral neurotoxicity.
    • Dataset
  • 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.
    • Dataset
  • 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.
    • Dataset
  • 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)
    • Dataset
  • 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.
    • Dataset
  • 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.
    • Dataset