Programma

Abstract: Mathematical models based on first principles can describe the interaction between electrical, mechanical and fluid-dynamical processes occurring in the heart, as well as the coupling with the external circulation. This is a classical multi-physics problem featuring multi-scale solutions in space and time. Appropriate numerical strategies need to be devised to allow for an accurate and computationally effective simulation of these processes in both physiological and pathological regimes. This presentation will address some of these issues and a few representative applications of clinical interest. The work presented in this talk is part of the project iHEART that has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 740132).

Abstract: I shall describe Direct Numerical Simulations (DNS) of multiphase flows using the Volume Of Fluid method (to which my collaboration with Gianluigi Zanetti gave an impulse in the 1990s), with particular emphasis on two phenomena: a large-scale, large-Reynolds case, the atomization of liquid jets, and a small-scale case, the moving contact line. For atomization, we extended a lot of efforts on the quasi planar setup of the Grenoble group to shed light on the statistics of droplet formation and the log-normal distribution observed, I will also describe an attempt to model the contact line, compared to the result of molecular dynamics.

Abstract: Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges by releasing specifications and software for managing image datasets and integrating them with other scientific data. OMEs Bio-Formats and OMERO are used in 1000’s of labs worldwide to enable discovery with imaging. We have used Bio-Formats and OMERO to build solutions for sharing and publishing imaging data. The Image Data Resource (IDR) includes image data linked to over 60 independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super-resolution microscopy, single cell profiling, light sheet microscopy of developing organisms and tissues, and digital pathology. Datasets range from several GBs to tens of TBs. Wherever possible, we have integrated image data with all relevant experimental, imaging and analytic metadata. These annotations make it possible to re-use IDR data, and to connect independent imaging datasets by molecular perturbations and phenotypes. We have also built cloud-based analysis tool portals to catalyse the re-use and re-analysis of published imaging data. These include notebooks and Docker containers that package well-known tools like ImageJ/Fiji, CellProfiler and Ilastik, making it is easy for anyone to view and interact with public data in IDR. We are now using notebooks to explore the phenotypes recorded in IDR data, and link them to genes and drugs used to target specific pathways in IDR data. I will include a few memories of the joy of working with Gianluigi on these critical, engaging problems.

Abstract: Medical research is known to be plagued with reproducibility issues in the last two decades, raising substantial concerns about effectiveness of research funding flowing into the domain (estimates being 50-90% of research being not reproducible). Research infrastructures play central role to change this as they act as guardians of the biological material and data to be shared for medical research purposes. In 2016, together with Gianluigi Zanetti, Jörg Geiger, and Heimo Müller, we have started work on developing a common machine-readable and machine-actionable model of provenance information, that is able to describe the complete history of biological data, including provenance that spans multiple organizations. This activity has been adopted by ISO TC/276 (Biotechnology) WG5 (Data Integration) and we are striving to make it an international standard, so that vendors of hardware and software used for laboratory automation and data generation can adopt and automate generation of provenance information. This talk will summarize state of the development of the standard and anticipated outlook of its applications.

Abstract: The treatment of epilepsy, despite the impetuous advancement of neurosciences, remains an excruciating unsolved problem. Indeed, more than 30% of epileptic subjects are pharmacoresistant. The Vagus Nerve Stimulation (VNS) is a low-impact surgical solution which improves the incidence of episodes and their severity, though its mechanism of action is still unclear. In a collaborative study, Santoni and Zanetti from CRS4 calculated the modifications of EEG signals recorded in Clinical Neurology, University of Cagliari, in a population of epileptic patients treated with VNS. The results obtained show that the EEG signals were already modulated towards a physiological pattern in subjects successfully treated. By suggesting a relationship between VNS and EEG for the first time, this work paved the way for the most recent studies on the modifications of brain networks and VNS.

Short talks with personal memories. / Brevi interventi con ricordi personali.

Open mic session. / Microfono aperto.