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This repository contains the Python and R codes used for the paper titled: Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model.

The incessant changes in all areas of economy, science, politics and society, with a greater acceleration in recent years, are affecting also the transport regulation, one of the most stable of all the branches of law, having in mind that one of its areas, the Maritime Law, has maintained almost unchanged over the centuries many of the institutes and figures that most characterize it, such as general average, salvage, limitation of the liability of the shipowner, the charterparty, the bill of lading, the role of the master and the crew. In a world in which phenomena such as the Covid-19 pandemic, Brexit and the ever-increasing use of new technologies, despite being profoundly different from each other, have had and certainly do have a prominent role, operators in any sector find themselves having to face, often from one moment to the next, and therefore unexpectedly and in no time, a multiplicity of problems that are largely completely new, in order to avoid, or at least mitigate, the consequences of total or partial paralysis of their activities. Given the circumstances, legislators, national and international regulatory bodies and jurists are called upon to urgently reconsider and/or integrate the disciplines currently in force, both from the public and private aspects, taking into account the critical issues that are gradually emerging. Clearly, in a globalized context like the one we live in, characterized by a strong interconnection of activities and sectors with each other and where the interaction of multiple factors is inevitable, the panorama is of such complexity that, at the time being, no one is yet able to predict what future developments may be in detail, in the full awareness, however, that the playground is in constant becoming. The choice of the regulatory approach to be followed from time to time is far from easy, especially in the knowledge that on the one hand the evolution of legislation, geopolitics, technology and the behavior of operators on the relevant market are closely interconnected, and that on the other hand a not well shaped regulation could become an obstacle to the development of trade and, more generally, of global economy. New phenomena always give rise to unprecedented problems and, if it is not possible to give a full solution to them by means of the rules already in force, the legislators, making use of various forms of regulatory instruments, in terms both of quality and of extension of territorial effectiveness, should implement an evolution of the regulations, introducing new norms or modifying existing ones, also in light of the interests of the different stakeholders, often conflicting and variously declined, and of the practices that in some cases have been established and have remained constant and unchanged for a very long time. The multiplicity and multiformity of the problems that arise must not discourage, but rather act as a further stimulus: in such a tumultuous contingent situation, it is essential to maintain a certain order and an adequate methodological rigor in dealing with the individual problems, putting them into focus one by one, in order to then slowly expand the view and obtain an overall picture. In this perspective, the selected essays collected in this volume examine, in their dual scientific-academic and practical soul, both issues that arise as a result of the new phenomena mentioned above, and more “classic” topics of the matter, but analyzing them having regard to their most recent developments.

The investigation focuses on the identification of actions and strategies that hoteliers apply on their websites, to capture direct bookings versus their dependence on the OTA, to evaluate the importance and function of the websites of the 4- and 5-star hotels in Porto and Northern Portugal. Online distribution is a necessity for a hotel, either to reach the largest number of customers or to give visibility to the brand. Hotel websites, however, allow greater proximity and communication with the customer, potentiating hotels’ possibility to increase direct bookings. It is therefore necessary to understand which actions and strategies hoteliers must consider for capturing direct bookings. Thus, the main objective of the study is to identify the hoteliers’ dependence on the OTA and the consequent actions and strategies they apply on their websites to capture direct bookings. In the present investigation, the quantitative methodology was chosen, and the data collection instrument was a questionnaire survey, applied in a total universe of 150 hotels, 4- and 5-star hotels in the Region of Porto and Northern Portugal, where 55 responses were obtained. The data obtained were treated and analysed using the SPSS software. The results obtained confirm the existence of actions and strategies in hotels to capture direct reservations; hotels consider these strategies as an essential condition for increasing direct bookings. Limitations have arisen in the collection of questionnaires due to the Covid-19 pandemic. Most hotels closed due to lack of customers and consequently, the sample for the present study is limited in the diversity of the typology of respondents. It is intended with this work to understand what actions and strategies hotels apply on the website, as well as to understand if hotels follow the new technological trends, in what the contact and communication with the client concerns.

Medical imaging as method to assess the longitudinal process of a SARS-CoV-2 infection in non-human primates is commonly used in research settings. Bronchoalveolar lavage (BAL) is also regularly used to determine the local virus production and immune effects of SARS-CoV-2 in the lower respiratory tract. However, the potential interference of those two diagnostic modalities with each other is unknown in non-human primates. The current study investigated the effect and duration of BAL on computed tomography (CT) in both healthy and experimentally SARS-CoV-2-infected female rhesus macaques (Macaca mulatta). In addition, the effect of subsequent BALs was reviewed. Thorax CTs and BALs were obtained from four healthy animals and 11 experimentally SARS-CoV-2-infected animals. From all animals, CTs were obtained just before BAL, and 24 hours post-BAL. Additionally, from the healthy animals, CTs immediately after and four hours post-BAL were obtained. Thorax CTs were evaluated for alterations in lung density, measured in Hounsfield units, and a visual semi-quantitative scoring system. An increase in the lung density was observed on the immediately post-BAL CT but resolved within 24 hours in the healthy animals. In the infected animals, a significant difference in both the lung density and CT score was still found 24 hours after BAL. Furthermore, the differences between timepoints in CT score were increased for the second BAL. These results indicate that the effect of BAL on infected lungs is not completed within the first 24 hours. Therefore, it is of importance to acknowledge the interference between BAL and CT in rhesus macaques.

Long-term care homes play an essential role within health and social care. Successful measures to support older people at home for longer have led to increased prevalence of disability, frailty and cognitive impairment in those who live in care homes over the last two decades. The need for care home places is projected to increase for the next two decades. Modern care homes provide care for people who are predominantly over 80, have multiple long-term conditions, take multiple medicines, are physically dependent and live with cognitive impairment. Residents do better when services recognise the contributions of staff and care home providers rather than treating residents as individual patients living in a communal setting. There is a strong case given residents' frailty, multimorbidity and disability, that care should be structured around Comprehensive Geriatric Assessment (CGA). Care should be designed to allow opportunities for multiprofessional teams to come together for CGA, particularly if healthcare professionals are based outside care homes. Good data about care homes and residents are central to efforts to deliver high quality care-in some countries, these data are collected but not collated. Collating such data is a priority. Care home staff are under-recognised and underpaid-parity of pay and opportunity with NHS staff is the bare minimum to ensure that the best are recruited and retained in the sector. During the COVID-19 pandemic, residents and relatives have frequently been left out of decisions about policies that affect them, and better consultation is needed to deliver high quality care.

Background: A worldwide vaccination program is the chosen strategy against the COVID-19 pandemic. Vaccine hesitancy however, forms a threat because vaccine uptake is voluntary in most countries. Care-professionals of people with intellectual disabilities are exposed to greater risks than other healthcare workers due to the vulnerable group they attend to and the assisted-living facilities in which they often work. Little is still known of the reasons for vaccine hesitancy in this specific group in contrast to those of other healthcare workers. Objective: To provide insight in the intentions and attitudes on COVID-vaccination of healthcare workers, including those who care for people with intellectual disabilities, by means of a scoping review. Methods: The databases that were searched for papers are CINAHL, APA PsycArticles, APA PsycInfo, Web of Science, Semantic Scolar, Prospero, Outbreak Science, Cochrane and Scopus. The search was broadened to healthcare workers in general because only two papers were found on those caring for people with intellectual disabilities. A total of 26 papers were identified concerning the vaccine intentions of 43,199 healthcare workers worldwide. Data were gathered both quantitively and qualitatively. The papers were analysed for all themes regarding vaccine willingness and vaccine hesitancy. Results: The themes that came to light included: percentages of vaccine willingness, predictors of willingness differentiated by 11 sub-themes (mainly profession, age, gender and past vaccine behaviour), attitudes of willingness and hesitancy differentiated by 19 sub-themes (perceived COVID treat and protecting others for willingness, concerns on vaccine safety and efficacy for hesitancy), sources of vaccination information, contextual factors and changes in COVID-19 vaccine acceptance over time and finally, future strategies for interventions. Conclusions: There was overlap in the percentages of vaccination, predictors of vaccine willingness and the attitudes of vaccine willingness and hesitancy between healthcare workers and those caring for people with intellectual disabilities. Vaccine safety and efficacy are the most prominent concerns with regard to vaccine hesitancy. Therefore, future strategies for interventions should address vaccine safety and efficacy. Furthermore, interventions are recommended to be interactive in order to facilitate exchange. Discussion groups that are able to address specific concerns and personal experiences, show to be effective in addressing vaccine hesitancy. Accurate information can also be made more accessible to target groups by promoting video’s on social media platforms. Hence, further research is necessary to specify more precisely the attitudes of healthcare workers caring for people with intellectual disabilities and in more countries worldwide.

A global cross-discipline effort is ongoing to characterize the evolution of SARS-CoV-2 virus and generate reliable epidemiological models of its diffusion. To this end, phylogenomic approaches leverage accumulating genomic mutations as barcodes to track the evolutionary history of the virus and can benefit from the surge of sequences deposited in public databases. Yet, such methods typically rely on consensus sequences representing the dominant virus lineage, whereas a complex sublineage architecture is often observed within single hosts. Furthermore, most approaches do not account for variants accumulation processes and might produce inaccurate results in condition of limited sampling, as witnessed in most countries currently affected by the epidemics. We here introduce a new framework for the characterization of viral (sub)lineage evolution and transmission of SARS-CoV-2, which considers both clonal and intra-host minor variants and exploits the achievements of cancer evolution research to account for mutation accumulation and uncertainty in the data. The application of our approach to 18 SARS-CoV-2 samples for which raw sequencing data are available reveals a high-resolution phylogenomic model, which confirms and improves recent findings on viral types and highlights the existence of patterns of co-occurrence of minor variants, uncovering likely infection paths among hosts harboring the same viral lineage. Our findings confirm a significant increase of genomic diversity of SARS-CoV-2 in time, which is reflected in minor variants, and show that standard methods may struggle when handling datasets with important sampling limitations. Importantly, our framework allows to pinpoint minor variants that might be positively selected across distinct lineages and regions of the viral genome under purifying selection, thus driving the design of treatments and vaccines. In particular, minor variant g.29039A>U, detected in multiple viral lineages and validated on an independent dataset, shows that SARS-CoV-2 can lose its main Nucleocapsid immunogenic epitopes, raising concerns about the effectiveness of vaccines targeting the C-terminus of this protein. To conclude, we advocate the use of our framework in combination with data-driven epidemiological models, to deliver a high-precision platform for pathogen detection, surveillance and analysis.