Bayesian multi-objective optimisation with mixed analytical and black-box functions: application to tissue engineering

Tissue engineering and regenerative medicine looks at improving or restoring biological tissue function in humans and animals. We consider optimising neotissue growth in a three-dimensional scaffold during dynamic perfusion bioreactor culture, in the context of bone tissue engineering. The goal is to choose design variables that optimise two conflicting objectives: (i) maximising neotissue growth and (ii) minimising operating cost. We make novel extensions to Bayesian multi-objective optimisation in the case of one analytical objective function and one black-box, i.e. simulation-based, objective function. The analytical objective represents operating cost while the black-box neotissue growth objective comes from simulating a system of partial differential equations. The resulting multi-objective optimisation method determines the trade-off in the variables between neotissue growth and operating cost. Our method outperforms the most common approach in literature, genetic algorithms, in terms of data efficiency, on both the tissue engineering example and standard test functions. The resulting method is highly applicable to real-world problems combining black-box models with easy-to-quantify objectives like cost

Mapping the use of computational modelling and simulation in clinics: A survey

In silico medicine describes the application of computational modelling and simulation (CM&S) to the study, diagnosis, treatment or prevention of a disease. Tremendous research advances have been achieved to facilitate the use of CM&S in clinical applications. Nevertheless, the uptake of CM&S in clinical practice is not always timely and accurately reflected in the literature. A clear view on the current awareness, actual usage and opinions from the clinicians is needed to identify barriers and opportunities for the future of in silico medicine. The aim of this study was capturing the state of CM&S in clinics by means of a survey toward the clinical community. Responses were collected online using the Virtual Physiological Human institute communication channels, engagement with clinical societies, hospitals and individual contacts, between 2020 and 2021. Statistical analyses were done with R. Participants (n = 163) responded from all over the world. Clinicians were mostly aged between 35 and 64 years-old, with heterogeneous levels of experience and areas of expertise (i.e., 48% cardiology, 13% musculoskeletal, 8% general surgery, 5% paediatrics). The CM&S terms “Personalised medicine” and “Patient-specific modelling” were the most well-known within the respondents. “In silico clinical trials” and “Digital Twin” were the least known. The familiarity with different methods depended on the medical specialty. CM&S was used in clinics mostly to plan interventions. To date, the usage frequency is still scarce. A well-recognized benefit associated to CM&S is the increased trust in planning procedures. Overall, the recorded level of trust for CM&S is high and not proportional to awareness level. The main barriers appear to be access to computing resources, perception that CM&S is slow. Importantly, clinicians see a role for CM&S expertise in their team in the future. This survey offers a snapshot of the current situation of CM&S in clinics. Although the sample size and representativity could be increased, the results provide the community with actionable data to build a responsible strategy for accelerating a positive uptake of in silico medicine. New iterations and follow-up activities will track the evolution of responses over time and contribute to strengthen the engagement with the medical community

Advancing osteochondral tissue engineering: bone morphogenetic protein, transforming growth factor, and fibroblast growth factor signaling drive ordered differentiation of periosteal cells resulting in stable cartilage and bone formation in vivo.

Chondrogenic mesenchymal stem cells (MSCs) have not yet been used to address the clinical demands of large osteochondral joint surface defects. In this study, self-assembling tissue intermediates (TIs) derived from human periosteum-derived stem/progenitor cells (hPDCs) were generated and validated for stable cartilage formation in vivo using two different animal models.status: publishe

Occurrence and Treatment of Bone Atrophic Non-Unions Investigated by an Integrative Approach

Recently developed atrophic non-union models are a good representation of the clinical situation in which many nonunions develop. Based on previous experimental studies with these atrophic non-union models, it was hypothesized that in order to obtain successful fracture healing, blood vessels, growth factors, and (proliferative) precursor cells all need to be present in the callus at the same time. This study uses a combined in vivo-in silico approach to investigate these different aspects (vasculature, growth factors, cell proliferation). The mathematical model, initially developed for the study of normal fracture healing, is able to capture essential aspects of the in vivo atrophic non-union model despite a number of deviations that are mainly due to simplifications in the in silico model. The mathematical model is subsequently used to test possible treatment strategies for atrophic non-unions (i.e. cell transplant at post-osteotomy, week 3). Preliminary in vivo experiments corroborate the numerical predictions. Finally, the mathematical model is applied to explain experimental observations and identify potentially crucial steps in the treatments and can thereby be used to optimize experimental and clinical studies in this area. This study demonstrates the potential of the combined in silico-in vivo approach and its clinical implications for the early treatment of patients with problematic fractures

Integration of juvenile habitat quality and river connectivity models to understand and prioritise the management of barriers for Atlantic salmon populations across spatial scales

Thanks to the Scottish Government Hydro Nation Scholarship programme for funding WBB. Authors from Marine Scotland Science Freshwater Fisheries Laboratories delivered this work through Service Level Agreement FW02G. Some map features are based on digital spatial data licensed from CEH, NERC© Crown Copyright and database right (2018), all rights reserved. Ordnance Survey License number 100024655. Catchment boundaries were from SEPA (2009). The Obstacles to Fish Migration dataset is from SEPA. The authors thank the two anonymous referees for their feedback on the manuscript.Peer reviewedPostprin

Graviton emission in Einstein-Hilbert gravity

The five-point amplitude for the scattering of two distinct scalars with the emission of one graviton in the final state is calculated in exact kinematics for Einstein-Hilbert gravity. The result, which satisfies the Steinmann relations, is expressed in Sudakov variables, finding that it corresponds to the sum of two gauge invariant contributions written in terms of a new two scalar - two graviton effective vertex. A similar calculation is carried out in Quantum Chromodynamics (QCD) for the scattering of two distinct quarks with one extra gluon in the final state. The effective vertices which appear in both cases are then evaluated in the multi-Regge limit reproducing the well-known result obtained by Lipatov where the Einstein-Hilbert graviton emission vertex can be written as the product of two QCD gluon emission vertices, up to corrections to preserve the Steinmann relations.Comment: 28 pages, LaTeX, feynmf. v2: typos corrected, reference added. Final version to appear in Journal of High Energy Physic

Possible Contexts of Use for In Silico trials methodologies: a consensus- based review

The term In Silico Trial indicates the use of computer modelling and simulation to evaluate the safety and efficacy of a medical product, whether a drug, a medical device, a diagnostic product or an advanced therapy medicinal product. Predictive models are positioned as new methodologies for the development and the regulatory evaluation of medical products. New methodologies are qualified by regulators such as FDA and EMA through formal processes, where a first step is the definition of the Context of Use (CoU), which is a concise description of how the new methodology is intended to be used in the development and regulatory assessment process. As In Silico Trials are a disruptively innovative class of new methodologies, it is important to have a list of possible CoUs highlighting potential applications for the development of the relative regulatory science. This review paper presents the result of a consensus process that took place in the InSilicoWorld Community of Practice, an online forum for experts in in silico medicine. The experts involved identified 46 descriptions of possible CoUs which were organised into a candidate taxonomy of nine CoU categories. Examples of 31 CoUs were identified in the available literature; the remaining 15 should, for now, be considered speculative

Toward a Regulatory Pathway for the Use of in Silico Trials in The Ce Marking of Medical Devices

In Silico Trials methodologies will play a growing and fundamental role in the development and de-risking of new medical devices in the future. While the regulatory pathway for Digital Patient and Personal Health Forecasting solutions is clear, it is more complex for In Silico Trials solutions, and therefore deserves a deeper analysis. In this position paper, we investigate the current state of the art towards the regulatory system for in silico trials applied to medical devices while exploring the European regulatory system toward this topic. We suggest that the European regulatory system should start a process of innovation: in principle to limit distorted quality by different internal processes within notified bodies, hence avoiding that the more innovative and competitive companies focus their attention on the needs of other large markets, like the USA, where the use of such radical innovations is already rapidly developing

Ideas and perspectives : Tracing terrestrial ecosystem water fluxes using hydrogen and oxygen stable isotopes – challenges and opportunities from an interdisciplinary perspective

The authors thank Marialaura Bancheri, Michele Bottazzi, Roman Cibulka, Massimo Esposito, Alba Gallo, Cesar D. Jimenez-Rodriguez, Angelika Kuebert, Ruth Magh, Stefania Mambelli, Alessia Nannoni, Paolo Nasta, Vladimir Rosko, Andrea Rücker, Noelia Saavedra Berlanga, Martin Šanda, and Anna Scaini for their contributions during the discussion at the workshop “Isotope-based studies of water partitioning and plant–soil interactions in forested and agricultural environments”. The authors also thank “Villa Montepaldi” and the University of Florence for the access to the workshop location, and the municipality of San Casciano in Val di Pesa for logistical support. The authors thank the Department of Innovation, Research and University of the Autonomous Province of Bozen/Bolzano for covering the Open Access publication costs. Last, but not least, the authors wish to thank Matthias Sprenger, Stephen Good, and J. Renée Brooks, as well as the Editor David R. Bowling, whose constructive reviews greatly improved this manuscript.Peer reviewedPublisher PD