University of Milano-Bicocca Showcase

This repository contains MALDI mass spectrometry imaging (MALDI-MSI) data acquired from a clear cell renal cell carcinoma (ccRCC) tissue section. The dataset comprises spatially resolved mass spectra of lipids, N-glycans, and tryptic peptides obtained from the same tissue section using a multi-omics imaging workflow. These complementary molecular layers enable the characterization of distinct histological regions, including healthy renal cortex, renal capsule, and tumor tissue. In particular: FinalMatrix_Coor.RDS contains pixel coordinates. FinalMatrix_Coor_reverseX.RDS contains the same coordinates flipped along the x-axis to match the orientation of the H&E-stained tissue image. FinalMatrix_Lipids.RDS, FinalMatrix_Glycans.RDS, and FinalMatrix_Peptides.RDS contain transformed molecular abundances for each pixel. Each row corresponds to a pixel and each column to an m/z value. list_ind_resolution_4123.RDS and list_ind_resolution_4123_cpp.RDS contain the indices of neighboring pixels for each pixel. The former uses 1-based indexing, whereas the latter uses 0-based indexing. These data were analyzed in the study “Multiomics Tissue Segmentation via Spatially-Informed Nested Biclustering Methods” by Francesco Denti, Cecilia Balocchi, Vanna Denti, and Giulia Capitoli, published in Biometrics. Preprint: https://fradenti.github.io/pdf/Poseidon.pdf Analysis code: https://github.com/Fradenti/poseidon-maldi

This dataset has been used in the manuscript titled “Snow Surface Parameters from PRISMA Data in the Alps and Their Implications for Radiative Forcing” and provides snow property parameters retrieved from PRISMA hyperspectral imagery acquired over Plateau Rosa (Aosta Valley, European Alps) following a Saharan dust deposition event in July 2024. The parameters include mineral dust concentration, snow grain size, broadband albedo, and instantaneous radiative forcing. These were estimated using a supervised learning approach based on the K-Nearest Neighbors (KNN) algorithm, which was applied to match observed spectra with a reference library generated using the BioSNICAR radiative transfer model. The dataset also includes Asymptotic Radiative Transfer (S-ART) model (S-ART) outputs and in situ measurements collected during a dedicated field campaign. These data support the investigation of the effects of light-absorbing impurities on snow radiative properties, contributing to the improvement of climate and hydrological modeling in high-altitude environments.

The present refers to a study that investigated whether facial identity and emotional expressions impose different cognitive demands during working memory updating and maintenance, how emotional information decays, and whether different emotions differentially affect performance. Fifty-six healthy adults completed an n-back task in which they monitored facial identity, emotional expression, or both simultaneously under three levels of cognitive load. Accuracy and response times were analyzed as indices of working memory performance. Results revealed that performance was significantly lower when emotion was the only relevant information, indicating that emotional information requires greater cognitive resources to be maintained and updated. Interestingly, processing both identity and emotion simultaneously resulted in better performance than processing emotional information alone, suggesting a potential binding mechanism between facial identity and emotional expression. Furthermore, longer response times were associated with lower accuracy independently of cognitive load, a pattern consistent with time-based accounts of working memory decay. Finally, no significant differences in performance emerged among different facial expressions. These findings suggest that emotional information imposes greater working memory demands than identity alone or emotion-identity combined, support a main role of temporal factors in the decay of social-emotional information, and indicate that the maintenance of emotional expressions in working memory may be relatively insensitive to differences in emotional valence.

Iterative Bleaching Extends Multiplexity (IBEX) immunofluorescence was performed on skin samples collected from CD11c-DOG mice either treated with diphtheria toxin (Skin_CD11cDOG_with_Diphtheria_Toxin) or phosphate-buffered saline (PBS) treated controls (Skin_CD11cDOG_no_Diphtheria_Toxin). For dendritic cell depletion, CD11c-DOG mice received three systemic intravenous injections of diphtheria toxin (16 ng/g body weight) on days −3, −2, and −1. Control mice PBS following the same schedule. In addition, a local subcutaneous injection of diphtheria toxin (16 ng) was administered on day −1 at the site designated for tissue collection. Mice were euthanized on day 0 in accordance with national and international regulations for animal care and use. A square section of flank skin was excised from each mouse at the site of the last intradermal injection. Subcutaneous adipose tissue was mechanically removed using forceps. Skin samples were subsequently processed according to the 2D Manual IBEX protocol for multiplex immunofluorescence imaging.

Live-cell holotomographic imaging of OHP-induced pathological changes in DRG neurons. These videos show primary adult mouse DRG neuronal cultures exposed to OHP at 7.5 or 25 µM. Refractive index-based imaging captures neurite fragmentation and degeneration, morphological features consistent with necroptosis, and autophagic vacuoles. Images were acquired using a 5 × 5 grid scan, with each grid measuring 90 × 90 µm, every 15 min for 28 h at 7 fps, from 24 to 52 h after OHP incubation.

This is a set of images taken on In2Sight devices coupled to PVC (polyvinylchloiride), implanted in mice. -- Animal implants. Each mouse (BALB/cAnNHsd, Envigo) received one In2Sight device, which was implanted subcutaneously in the inner part of the hind leg. Mice were anesthetized intraperitoneally with 100mg/kg ketamine and 4mg/kg xylazine. The operating field was prepared by hair trichotomy followed by appropriate disinfection with 70° ethanol or betadine. Two incisions were then made using a sterile scalpel. After positioning the device, a tight suture (single stitch) of the incision was performed using a sterile 5/0 absorbable suture thread. For the first 2 days, pain control was foreseen by administering opioids (Buprenorphine hydrochloride 0.16mg/kg subcutaneously) and infections avoided by administering an antibiotic (Enrofloxacin 5 mg/kg for 5 days). All the implants were done under the animal permit n. 551/2023-PR of the Italian ministry for health. The device, once coupled with acrylic glue to a slab of PVC (Polyvynil chloride, 5 mm in diameter, 0.3 mm thickness), was sterilized by STERRAD before the implant that lasted up to 6 weeks. The mice were kept in a pathogen‐free conventional animal house facility. The animal house is run by professional employees fully equipped with state‐of‐the‐art instrumentation in order to maintain the standard of animal welfare at the maximum levels. All mice were housed in individual, ventilated cages with 12 h light/dark cycles with food and water ad libitum. The mice were euthanized at the end of the implant by cervical dislocation right before the imaging session. Experiments were performed using protocols approved by the Institutional Animal Care and Use Committee of the University of Milano‐Bicocca and by the Italian Ministry of Health. -- Chemicals. Hoechst 33342 (Sigma-Aldrich Chemical Company (Steinheim, Germany)) was used to stain nuclei in ex-vivo experiments. -- Multiphoton imaging. Third harmonic generation and 3-photon excitation fluorescence were selected by the Semrock filters FF02-447/60 and FF562-Di03-25, respectively. For SHG the exc. wavelength was 800 nm (emission 400/40 nm). λexc was 770 nm in case of Hoechst nuclei staining (485/30 nm). Auto-fluorescence in the green channel was collected at 535/50 nm. FILE NAME FORMAT for folder TPE_SHG_6weeks: name@800P140mWBP400BP535z200um50piani_Ch2 is taken as an example. name: if "lente#" (#=1,..4) means one of the 4 lenses on top of the microatlas; if "spacer" means the In2Sight spacers; if "fralenti" means the space between the lenses and therefore in the free tissue 800P140m: excitation wavelength = 800 nm, average power = 140 mW, WBP400BP535z200um50piani: means emission filters at 400 nm (Ch1) and 535 nm (Ch2); 200 micrometer full depth of stack, 50 layers. FORMAT in THG_3PE_data_1week: modality, exc. , through the lenses or control, FOV in um, image size in pixels, the depth, the number of averages (#avg).

This archive contains the example datasets, implementations of the rational splines and P-spline methods, along with code to reproduce the benchmark and the generate the figures in the publication "Shape preserving interpolation with arbitrary smoothness based on mollification". Archive structure ----------------- - `interp.py`: implementation of the interpolation methods - `benchmark.py`: program that benchmarks the interpolation code - `plots.py`: program that generates the figures of the article - `proofs.py`: mathematical proofs in [SymPy][1] of some results used to implement the rational splines - `shell.nix`: [Nix][2] expression that builds a reproducible environment to run the programs