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Summary: ExTopoDB is a publicly accessible database of experimentally derived topological models of transmembrane proteins. It contains information collected from studies in the literature that report the use of biochemical methods for the determination of the topology of α-helical transmembrane proteins. Transmembrane protein topology is highly important in order to understand their function and ExTopoDB provides an up to date, complete and comprehensive dataset of experimentally determined topologies of α-helical transmembrane proteins. Topological information is combined with transmembrane topology prediction resulting in more reliable topological models. Availability: http://bioinformatics.biol.uoa.gr/ExTopoDB Contact: shamodr@biol.uoa.gr Supplementary information: Supplementary data are available at Bioinformatics online.

Background In Italy, the National surveillance of all SARS-CoV-2 laboratory-confirmed cases was established on 27 February 2020, building on a previously existing laboratory network focused on suspected and confirmed COVID-19 severe respiratory infections. Methods The integrated epidemiological and microbiological surveillance systematically collects and analyzes information on all SARS-CoV-2 confirmed cases. Regional reference laboratories analyze samples, inform Local Health Authorities of the results and coordinate data flow between cases, hospitals and GPs. Regions provide data through a web interface connected to a dedicated IT platform or by sending a dataset. The Infectious Diseases Department at Istituto Superiore di Sanità processes and analyzes data, producing reports on a daily and weekly basis, as well as indicator analyses based on the monitoring of “phase 2” (post-lockdown). Moreover, mathematical models are constructed daily on these data. Results Since the beginning of the epidemic, the surveillance system recorded 238.901 COVID-19 cases and 33.369 deaths on 19-6. Main challenges were the coordination of different actors, hampered by the decentralization of health to the Regions, and data interpretation due to the delay in the detection of cases and deaths. Besides the COVID-19 surveillance, we planned ad hoc studies and periodic surveys: health care workers, long term care facilities, clusters and red zones, health system resilience monitoring. Conclusions COVID-19 surveillance is an essential tool to inform the public about the epidemic trend and provide support to public health response. We urge upon all relevant stakeholders a reflection on important issues such as defining ethical boundaries for data scavenging during emergencies, how existing laws on data protection could affect record linkage among different existing datasets to assess diseases and other variables for correlation, or which ethical approaches on open data would apply to our setting. Key messages A strong and adequately funded public health system in place allows an efficient response in times of epidemics both in terms of data collection and public health response, policy and decisions. COVID-19 epidemic showed us all the limits of a regionalized health system which was not entirely coordinated between periphery and central institutions.

Background Cities face rapid changes leading to increasing inequalities and emerging public health issues that require cost-effective interventions. The urban exposome concept refers to the continuous monitoring of urban environmental and health indicators using the city and smaller intra-city areas as measurement units in an interdisciplinary approach that combines qualitative and quantitative methods from social sciences, to epidemiology and exposure assessment. Methods In this proof of concept study, drinking water and quality of life indicators were described as part of the development of the urban exposome of Limassol (Cyprus) and were combined with agnostic environment-wide association analysis. This study was conducted as a two-part project with a qualitative part assessing the perceptions of city stakeholders, and quantitative part using a cross-sectional study design (an urban population study). We mapped the water quality parameters and participants’ opinions on city life (i.e., neighborhood life, health care, and green space access) using quarters (small administrative areas) as the reference unit of the city. In an exploratory, agnostic, environment-wide association study analysis, we used all variables (questionnaire responses and water quality metrics) to describe correlations between them. Results Overall, urban drinking-water quality using conventional indicators of chemical (disinfection byproducts-trihalomethanes (THM)) and microbial (coliforms, E. coli, and Enterococci) quality did not raise particular concerns. The general health and chronic health status of the urban participants were significantly (false discovery rate corrected p-value < 0.1) associated with different health conditions such as hypertension and asthma, as well as having financial issues in access to dental care. Additionally, correlations between THM exposures and participant behavioral characteristics (e.g., household cleaning, drinking water habits) were documented. Conclusion This proof-of-concept study showed the potential of using integrative approaches to develop urban exposomic profiles and identifying within-city differences in environmental and health indicators. The characterization of the urban exposome of Limassol will be expanded via the inclusion of biomonitoring tools and untargeted metabolomics.