AI slipping on tiles: data leakage in digital pathology

Reproducibility of AI models on biomedical data still stays as a major concern for their acceptance into the clinical practice. Initiatives for reproducibility in the development of predictive biomarkers as the MAQC Consortium already underlined the importance of appropriate Data Analysis Plans (DAPs) to control for different types of bias, including data leakage from the training to the test set. In the context of digital pathology, the leakage typically lurks in weakly designed experiments not accounting for the subjects in their data partitioning schemes. This issue is then exacerbated when fractions or subregions of slides (i.e. "tiles") are considered. Despite this aspect is largely recognized by the community, we argue that it is often overlooked. In this study, we assess the impact of data leakage on the performance of machine learning models trained and validated on multiple histology data collection. We prove that, even with a properly designed DAP (10x5 repeated cross-validation), predictive scores can be inflated up to 41% when tiles from the same subject are used both in training and validation sets by deep learning models. We replicate the experiments for $4$ classification tasks on 3 histopathological datasets, for a total of 374 subjects, 556 slides and more than 27,000 tiles. Also, we discuss the effects of data leakage on transfer learning strategies with models pre-trained on general-purpose datasets or off-task digital pathology collections. Finally, we propose a solution that automates the creation of leakage-free deep learning pipelines for digital pathology based on histolab, a novel Python package for histology data preprocessing. We validate the solution on two public datasets (TCGA and GTEx)

Celector®: An Innovative Technology for Quality Control of Living Cells

Among the in vitro and ex vivo models used to study human cancer biology, cancer cell lines are widely utilized. The standardization of a correct tumor model including the stage of in vitro testing would allow for the development of new high-efficiency drug systems. The poor correlation between preclinical in vitro and in vivo data and clinical trials is still an open issue, hence the need for new systems for the quality control (QC) of these cell products. In this work, we present a new technology, Celector®, capable of the label-free analysis and separation of cells based on their physical characteristics with full preservation of their native properties. Two types of cancer cell lines were used: HL60 as cells growing in suspension and SW620 as adherent cells. Cell lines in general show a growth variability depending on the passage and method of culture. Celector® highlights physical differences that can be correlated to cell viability. This work demonstrates the use of Celector® as an analytical platform for the QC of cells used for drug screening, with fundamental improvement of preclinical tests. Cells with a stable doubling time under analysis can be collected and used as standardized systems for high-quality drug monitoring

Changes of Oxytocin and Serotonin Values in Dialysis Patients after Animal Assisted Activities (AAAs) with a Dog-A Preliminary Study

Simple Summary This study aimed to improve the moment of dialysis because the emotional management of a person during treatment can help to reduce stress, anxiety and depression. This process positively affects the acceptance and progress of treatment and improves the self-management of the disease, a very important achievement in chronic kidney disease. Serotonin and oxytocin are important neuromodulators of different human behaviours, such as affectivity and socialization, and are involved in the control of stress, anxiety and social cooperation. The relationship between humans and domestic animals provides psychophysical well-being and can facilitate interpersonal bonds by favouring mechanisms involved in social relations. Dogs due to their ethological characteristics, allow the establishment of an active relationship through play, communication and interaction. Animal-assisted activities (AAAs) are structured interventions aimed at improving the psychophysical conditions of people in stressful conditions. Our study was aimed at determining the circulating levels of serotonin and oxytocin in patients who participated in an AAAs program with a dog during dialysis treatment. Our study aimed to measure the levels of serotonin and oxytocin in patients affected by end-stage renal disease (ESRD), undergoing dialysis and participating in a program of animal-assisted activities (AAAs) with a dog. Ten patients with comparable levels of ESRD were enrolled. A blood sample was taken before the start of the study in order to establish basal levels. Eleven meetings were held once a week for 3 months during the last hour of dialysis, and blood samples were collected before and after AAAs. Two more meetings, one month apart from each other, were held two months later without the dog but with the same veterinarian zootherapist. Blood was drawn at the beginning and at the end of each meeting. The samples were then processed for the measurement of serotonin and oxytocin, and data obtained were analysed using analysis of variance with mixed effect models. The results show an increasing level of both serotonin and oxytocin between subsequent meetings with the dog and an increasing trend of inter-intervention levels. Overall, the results suggest that AAAs lead to modifications of serotonin and oxytocin levels, which are also accompanied by behavioural changes of patients

Longitudinal follow‐up of patients with thalassaemia intermedia who started transfusion therapy in adulthood: a cohort study

SummaryWe longitudinally evaluated the effects of regular blood transfusions (BTs), in the real‐life context of the Myocardial Iron Overload in Thalassaemia network, in patients with thalassaemia intermedia (TI). We considered 88 patients with TI (52 females) who started regular BTs after the age of 18 years. Magnetic resonance imaging was used to quantify iron overload and biventricular function. For 56·8% of the patients there were more than two indications for the transition to regular BTs, with anaemia present in 94·0% of the cases. A significant decrease in nucleated red blood cells, platelets, lactate dehydrogenase, bilirubin, and uric acid levels was detected 6 months after starting regular BTs. After the transition to the regular BT regimen there was a significant increase only in the frequency of hypothyroidism and osteopenia, and a significant decrease in liver iron and cardiac index. The percentage of chelated patients increased significantly after starting regular BTs. The decision to regularly transfuse patients with TI may represent a way to prevent or slow down the natural progression of the disease, despite the more complex initial management

The Impact of Nanobody Density on the Targeting Efficiency of PEGylated Liposomes

Nanoparticles (NPs) are commonly modified with tumor-targeting moieties that recognize proteins overexpressed on the extracellular membrane to increase their specific interaction with target cells. Nanobodies (Nbs), the variable domain of heavy chain-only antibodies, are a robust targeting ligand due to their small size, superior stability, and strong binding affinity. For the clinical translation of targeted Nb-NPs, it is essential to understand how the number of Nbs per NP impacts the receptor recognition on cells. To study this, Nbs targeting the hepatocyte growth factor receptor (MET-Nbs) were conjugated to PEGylated liposomes at a density from 20 to 800 per liposome and their targeting efficiency was evaluated in vitro. MET-targeted liposomes (MET-TLs) associated more profoundly with MET-expressing cells than non-targeted liposomes (NTLs). MET-TLs with approximately 150-300 Nbs per liposome exhibited the highest association and specificity towards MET-expressing cells and retained their targeting capacity when pre-incubated with proteins from different sources. Furthermore, a MET-Nb density above 300 Nbs per liposome increased the interaction of MET-TLs with phagocytic cells by 2-fold in ex vivo human blood compared to NTLs. Overall, this study demonstrates that adjusting the MET-Nb density can increase the specificity of NPs towards their intended cellular target and reduce NP interaction with phagocytic cells

A: Deferasirox, deferiprone and desferrioxamine treatment in thalassemia major patients: cardiac iron and function comparison determined by quantitative magnetic resonance imaging. Haematologica 2011; 96

Background Oral deferiprone was suggested to be more effective than subcutaneous desferrioxamine for removing heart iron. Oral once-daily chelator deferasirox has recently been made commercially available but its long-term efficacy on cardiac iron and function has not yet been established. Our study aimed to compare the effectiveness of deferasirox, deferiprone and desferrioxamine on myocardial and liver iron concentrations and bi-ventricular function in thalassemia major patients by means of quantitative magnetic resonance imaging. Design and Methods From the first 550 thalassemia subjects enrolled in the Myocardial Iron Overload in Thalassemia network, we retrospectively selected thalassemia major patients who had been receiving one chelator alone for longer than one year. We identified three groups of patients: 24 treated with deferasirox, 42 treated with deferiprone and 89 treated with desferrioxamine. Myocardial iron concentrations were measured by T2* multislice multiecho technique. Biventricular function parameters were quantitatively evaluated by cine images. Liver iron concentrations were measured by T2* multiecho technique. Results The global heart T2* value was significantly higher in the deferiprone (34±11ms) than in the deferasirox (21±12 ms) and the desferrioxamine groups (27±11 ms) (P=0.0001). We found higher left ventricular ejection fractions in the deferiprone and the desferrioxamine versus the deferasirox group (P=0.010). Liver iron concentration, measured as T2* signal, was significantly lower in the desferrioxamine versus the deferiprone and the deferasirox group (P=0.004). Conclusions The cohort of patients treated with oral deferiprone showed less myocardial iron burden and better global systolic ventricular function compared to the patients treated with oral deferasirox or subcutaneous desferrioxamine. Key words: thalassemia, iron chelation therapy, cardiac magnetic resonance imaging. Citation: Pepe A, Meloni A, Capra M, Cianciulli P, Prossomariti L, Malaventura C, Putti MC, Lippi A, Romeo MA, Bisconte MG, Filosa A, Caruso V, Quarta A, Pitrolo L, Missere M, Midiri M, Rossi G, Positano V, Lombardi M, and Maggio A. Deferasirox, deferipron