MOnitoring Outbreak events for Disease surveillance in a data science context

Risultati finali

Blueprints for epidemiological data collection and management

This deliverable will provide the reference on how to collect, structure, and prepare the data to inputs the models and maps developed in WP4

Risk register

Register with all the risks noted by each WP, at project submission and updated during implementation of the project. It will also consist of a detailed description of the risks, their impact, and suitable preventive and response measures. This document will be updated at M24, M36 and M48.

Project management plan

Report with procedures for providing day-to-day administrative guidance, coordination & troubleshooting for the MOOD consortium partners

Preliminary report on impact and innovation pathway

This report will describe the innovation process and set up the methodology to monitor the impact of the MOOD project through the outcome assessment and the theory of change that is at work Some preliminary results about the KeyPerformance Indicators concerning the first outputs will be given

Scientific report on prototype pathogens and disease profiles

For each selected pathogen and disease, a detailed profile based on the state-of-the-art of the scientific knowledge and knowledge gaps will be produced.

Report on outreach of outcomes

The analysis of the outreach of the outcomes will be based on two crossed sources : a multicriteria evaluation method (OASIS-like survey) to compare end-user practices in the case countries at start and end of the project and a participatory assessment based on narratives of the change and participatory indicators.

Guidelines for consideration of local stakeholders' engagement

The guidelines will be built during and following the workshops with the local stakeholders of the study case in Corsica and Occitanie.

Report on users’ needs

The synthesis of operational needs will be based on the results of the crossed socio-technical analysis of individual interviews, and also the conclusions of the 2 first workshops about the operational problems to solve.

Report on learning loops fostering the utility of social and technical innovations

The lessons learnt from the collective learning of co-conception of tools and services (3 loops) will be summarised.

Standardized datasets (covariate, disease data sets, and pattern linking)

The dataset used within the project and processed according to DL3.1. These data will be stored in a traditional structured database system and made available through this database.

Integration chain (processing algorithms and protocols) for disease datasets

This deliverable will describe the data integration toolchain, including the data processing algorithms and the data exchange protocols that are focused on disease data, associated with Task 3.3 of WP3 and also with implications regarding other tasks (e.g., Tasks 3.1 and 3.4 of WP3). The envisioned toolchain will focus on data standardization and linking between disease and covariate data, according to spatial and temporal dimensions, and combining text-mining, spatial analysis, and semantic approaches. Specifically, the toolchain will ingest and standardize the different types of data, geo-reference the disease data in order for it to be linked to particular covariates, and make the results available for subsequent tasks. Deliverable 3.2 will specifically focus on the tools regarding data integration (e.g., the geo-referencing component), tailored for the processing of disease data.

Linking chain (processing algorithms and protocols) for disease and covariate datasets

The linking task is based on algorithms and processing that will be proposed, implemented and evaluated. These linking algorithms/process need specific features (and set of features) to extract in the disease and covariate data.

MOOD project website and social media

Project website (implemented via a Content Management System) and social media pages and channels including Twitter, , Linkedin, TIB (https://av.tib.eu/), Zenodo.org, and similar. Publication steps, house-style-sheet, and roles and responsibilities will be described in the project manual.

Online materials released in the open-source

Data processing tutorials, good practice documents and technical reports will be released via github (source code) with a copy on zenodo.org using the Github-zenodo webhooks (see e.g. https://doi.org/10.25815/3YZR-1564).

Data management plan

The DMP will detail what data MOOD will generate and how, how it will be curated and preserved, what datasets will be open, whether and how datasets will be exploited or made accessible for verification and re-use. First version delivered at month 6 and updated version at month 18 and 36.

Pubblicazioni

Systematic Review on Crimean–Congo Hemorrhagic Fever Enzootic Cycle and Factors Favoring Virus Transmission: Special Focus on France, an Apparently Free-Disease Area in Europe

Autori: Célia Bernard, Philippe Holzmuller, Madiou Thierno Bah, Matthieu Bastien, Benoit Combes, Ferran Jori, Vladimir Grosbois and Laurence Vial
Pubblicato in: Frontiers in Veterinary Science, Numero 22971769, 2022, ISSN 2297-1769
Editore: Frontiers Media S.A.
DOI: 10.3389/fvets.2022.1007631

Evolving epidemiology and transmission dynamics of coronavirus disease 2019 outside Hubei province, China: a descriptive and modelling study

Autori: Juanjuan Zhang, Maria Litvinova, Wei Wang, Yan Wang, Xiaowei Deng, Xinghui Chen, Mei Li, Wen Zheng, Lan Yi, Xinhua Chen, Qianhui Wu, Yuxia Liang, Xiling Wang, Juan Yang, Kaiyuan Sun, Ira M Longini, M Elizabeth Halloran, Peng Wu, Benjamin J Cowling, Stefano Merler, Cecile Viboud, Alessandro Vespignani, Marco Ajelli, Hongjie Yu
Pubblicato in: The Lancet Infectious Diseases, Numero 20/7, 2020, Pagina/e 793-802, ISSN 1473-3099
Editore: The Lancet Publishing Group
DOI: 10.1016/s1473-3099(20)30230-9

Relax, Keep Walking — A Practical Guide to Continuous Phylogeographic Inference with BEAST

Autori: Simon Dellicour, Mandev S Gill, Nuno R Faria, Andrew Rambaut, Oliver G Pybus, Marc A Suchard, Philippe Lemey
Pubblicato in: Molecular Biology and Evolution, Numero Volume 38, Numero 8, August 2021, 2021, Pagina/e 3486–3493, ISSN 1537-1719
Editore: Oxford University Press
DOI: 10.1093/molbev/msab031

Epidemic intelligence in Europe: a user needs perspective to foster innovation in digital health surveillance

Autori: Fanny Bouyer, Oumy Thiongane, Alexandre Hobeika, Elena Arsevska, Aurélie Binot, Déborah Corrèges, Timothée Dub, Henna Mäkelä, Esther van Kleef, Ferran Jori, Renaud Lancelot, Alize Mercier, Francesca Fagandini, Sarah Valentin, Wim Van Bortel & Claire Ruault
Pubblicato in: BMC Public Health, Numero 24, 973, 2024, ISSN 1471-2458
Editore: BioMed Central
DOI: 10.1186/s12889-024-18466-1

Ecological and environmental factors affecting the risk of tick-borne encephalitis in Europe, 2017 to 2021

Autori: Francesca Dagostin, Valentina Tagliapietra, Giovanni Marini, Claudia Cataldo, Maria Bellenghi, Scilla Pizzarelli, Rosaria Rosanna Cammarano, William Wint, Neil S Alexander, Markus Neteler, Julia Haas, Timothée Dub, Luca Busani, Annapaola Rizzoli
Pubblicato in: Eurosurveillance, Numero Volume 28, Numero 42, 2023, ISSN 1560-7917
Editore: ECDC
DOI: 10.2807/1560-7917.es.2023.28.42.2300121

Combined Phylogeographic Analyses and Epidemiologic Contact Tracing to Characterize Atypically Pathogenic Avian Influenza (H3N1) Epidemic, Belgium, 2019

Autori: Van Borm S, Boseret G, Dellicour S, Steensels M, Roupie V, Vandenbussche F, Mathijs E, Vilain A, Driesen M, Dispas M, Delcloo AW, Lemey P, Mertens I, Gilbert M, Lambrecht B, van den Berg T
Pubblicato in: Emerging Infectious Diseases, Numero 29(2), 2023, Pagina/e 351-359, ISSN 1080-6059
Editore: Centers for Disease Control and Prevention
DOI: 10.3201/eid2902.220765

An Evaluation Framework for Comparing Epidemic Intelligence Systems

Autori: Nejat Arinik; Roberto Interdonato; Mathieu Roche; Maguelonne Teisseire
Pubblicato in: IEEE Access, Numero 35, 2023, Pagina/e 11 : 31880- 31901, ISSN 2169-3536
Editore: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/access.2023.3262462

Increasing situational awareness through nowcasting of the reproduction number

Autori: Andrea Bizzotto, Giorgio Guzzetta, Valentina Marziano, Martina Del Manso, Alberto Mateo Urdiales, Daniele Petrone, Andrea Cannone, Chiara Sacco, Piero Poletti, Mattia Manica, Agnese Zardini, Filippo Trentini, Massimo Fabiani, Antonino Bella, Flavia Riccardo, Patrizio Pezzotti, Marco Ajelli, Stefano Merler
Pubblicato in: Frontiers in Public Health, Numero 12, 2024, ISSN 2296-2565
Editore: Frontiers Media S.A.
DOI: 10.3389/fpubh.2024.1430920

icumonitoring.ch: a platform for short-term forecasting of intensive care unit occupancy during the COVID-19 epidemic in Switzerland

Autori: Cheng Zhao, Burcu Tepekule, Nicola G. Criscuolo, Pedro D. Wendel Garcia, Matthias P. Hilty, RISC-19-ICU consortium Investigators in Switzerland, Thierry Fumeaux, Thomas Van Boeckel
Pubblicato in: Swiss Medical Weekly, Numero 150, 2020, Pagina/e w20277, ISSN 1424-3997
Editore: EMH Swiss Medical Publishers Ltd.
DOI: 10.4414/smw.2020.20277

Spatial and temporal dynamics of West Nile virus between Africa and Europe

Autori: Giulia Mencattelli, Marie Henriette Dior Ndione, Andrea Silverj, Moussa Moise Diagne, Valentina Curini, Liana Teodori, Marco Di Domenico, Rassoul Mbaye, Alessandra Leone, Maurilia Marcacci, Alioune Gaye, ElHadji Ndiaye, Diawo Diallo, Massimo Ancora, Barbara Secondini, Valeria Di Lollo, Iolanda Mangone, Andrea Bucciacchio, Andrea Polci, Giovanni Marini, Roberto Rosà, Nicola Segata, Gamou Fall, Ces
Pubblicato in: Nature Communications, Numero 14, 6440, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-42185-7

Modelling the West Nile virus force of infection in the European human population

Autori: Giovanni Marini, Andrea Pugliese, William Wint, Neil S. Alexander, Annapaola Rizzoli, Roberto Rosà
Pubblicato in: One Health, Numero Volume 15, 2022, Pagina/e 100462, ISSN 2352-7714
Editore: Elsevier B.V.
DOI: 10.1016/j.onehlt.2022.100462

Projecting the COVID-19 epidemic risk in France for the summer 2021

Autori: Mattia Mazzoli, PhD, Eugenio Valdano, PhD, Vittoria Colizza
Pubblicato in: Journal of Travel Medicine, Numero Volume 28, Numero 7, 2021, Pagina/e aab129, ISSN 1708-8305
Editore: International Society of Travel Medicine
DOI: 10.1093/jtm/taab129

Risk factors for tick attachment in companion animals in Great Britain: a spatiotemporal analysis covering 2014–2021

Autori: Elena Arsevska, Tomislav Hengl, David A. Singleton, Peter-John M. Noble, Cyril Caminade, Obiora Eneanya, Philip H. Jones, Kayleigh Hansford, Jolyon Medlock, Carmelo Bonannella, Alan D. Radford
Pubblicato in: Parasites Vectors, Numero 17, 29, 2024, ISSN 1756-3305
Editore: BioMed Central
DOI: 10.1186/s13071-023-06094-4

Planning and adjusting the COVID-19 booster vaccination campaign to reduce disease burden

Autori: Laura Di Domenico, Yair Goldberg, Vittoria Colizza
Pubblicato in: Infectious Disease Modelling, Numero 10, 2024, Pagina/e 150-162, ISSN 2468-0427
Editore: Elsevier B.V
DOI: 10.1016/j.idm.2024.09.002

Evaluating the effect of demographic factors, socioeconomic factors, and risk aversion on mobility during the COVID-19 epidemic in France under lockdown: a population-based study

Autori: Giulia Pullano, Eugenio Valdano, Nicola Scarpa, Stefania Rubrichi, Vittoria Colizza
Pubblicato in: The Lancet Digital Health, Numero 2/12, 2020, Pagina/e e638-e649, ISSN 2589-7500
Editore: Elsevier
DOI: 10.1016/s2589-7500(20)30243-0

Investigating COVID-19 Vaccine Impact on the Risk of Hospitalisation through the Analysis of National Surveillance Data Collected in Belgium

Autori: Diana Erazo, Maria F. Vincenti-Gonzalez, Joris A. F. van Loenhout, Pierre Hubin, Mathil Vandromme, Piet Maes, Maxime Taquet, Johan Van Weyenbergh, Lucy Catteau and Simon Dellicour
Pubblicato in: Viruses, Numero 14(6), 2022, Pagina/e 1315, ISSN 1999-4915
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14061315

Predictive Mapping of Antimicrobial Resistance for Escherichia coli, Salmonella, and Campylobacter in Food-Producing Animals, Europe, 2000–2021

Autori: Ranya Mulchandani, Cheng Zhao, Katie Tiseo, João Pires, Thomas Van Boeckel
Pubblicato in: Emerging Infectious Diseases, Numero Volume 30, Number 1, 2024, ISSN 1080-6059
Editore: Center for Disease Control and Prevention
DOI: 10.3201/eid3001.221450

Global patterns and drivers of influenza decline during the COVID-19 pandemic

Autori: Francesco Bonacina, Pierre-Yves Boëlle, Vittoria Colizza, Olivier Lopez, Maud Thomas, Chiara Poletto
Pubblicato in: International Journal of Infectious Diseases, Numero January 03, 2023, 2023, ISSN 1878-3511
Editore: Amsterdam Elsevier
DOI: 10.1016/j.ijid.2022.12.042

PADI-web 3.0: A new framework for extracting and disseminating fine-grained information from the news for animal disease surveillance

Autori: Sarah Valentina, Elena Arsevska, Julien Rabatel, Sylvain Falala, Alizé Mercier, Renaud Lancelot, Mathieu Roche
Pubblicato in: One Health, Numero Vol 13, Dec 2021, 2021, Pagina/e 100357, ISSN 2352-7714
Editore: Elsevier
DOI: 10.1016/j.onehlt.2021.100357

Emergence of an early SARS-CoV-2 epidemic in the United States

Autori: Mark Zeller, Karthik Gangavarapu, Catelyn Anderson, Allison R. Smither, John A. Vanchiere, Rebecca Rose, Daniel J. Snyder, Gytis Dudas, Alexander Watts, Nathaniel L. Matteson, Refugio Robles-Sikisaka, Maximilian Marshall, Amy K. Feehan, Gilberto Sabino-Santos, Antoinette R. Bell-Kareem, Laura D. Hughes, Manar Alkuzweny, Patricia Snarski, Julia Garcia-Diaz, Rona S. Scott, Lilia I. Melnik, Raphaëll
Pubblicato in: Cell, Numero Volume 184, Numero 19, 2021, 2021, Pagina/e 4939-4952.e15, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2021.07.030

Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha

Autori: Benjamin Faucher, Chiara E. Sabbatini, Peter Czuppon, Moritz U. G. Kraemer, Philippe Lemey, Vittoria Colizza, François Blanquart, Pierre-Yves Boëlle & Chiara Poletto
Pubblicato in: Nature communications, Numero 15, 2152, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-46345-1

A systematic review of environmental factors related to WNV circulation in European and Mediterranean countries

Autori: Christine Giesen, Zaida Herrador, Beatriz Fernandez-Martinez, Jordi Figuerola, Laura Gangoso, Ana Vazquez, Diana Gómez-Barroso
Pubblicato in: One Health, Numero Volume 16, 2023, Pagina/e 100478, ISSN 2352-7714
Editore: Elsevier BV
DOI: 10.1016/j.onehlt.2022.100478

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Autori: Nuno R. Faria, Thomas A. Mellan, Charles Whittaker, Ingra M. Claro, Darlan da S. Candido, Swapnil Mishra, Myuki A. E. Crispim, Flavia C. S. Sales, Iwona Hawryluk, John T. McCrone, Ruben J. G. Hulswit, Lucas A. M. Franco, Mariana S. Ramundo, Jaqueline G. de Jesus, Pamela S. Andrade, Thais M. Coletti, Giulia M. Ferreira, Camila A. M. Silva, Erika R. Manuli, Rafael H. M. Pereira, Pedro S. Peixoto, Mo
Pubblicato in: Science, Numero 372/6544, 2021, Pagina/e 815-821, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.abh2644

GeospatRE: extraction and geocoding of spatial relation entities in textual documents

Autori: Mehtab Alam Syed, Elena Arsevska, Mathieu Roche & Maguelonne Teisseire
Pubblicato in: Cartography and Geographic Information Science, 2023, ISSN 1545-0465
Editore: TAYLOR & FRANCIS INC
DOI: 10.1080/15230406.2023.2264753

Modelling safe protocols for reopening schools during the COVID-19 pandemic in France

Autori: Laura Di Domenico, Giulia Pullano, Chiara E. Sabbatini, Pierre-Yves Boëlle, Vittoria Colizza
Pubblicato in: Nature Communications, Numero 12/1, 2021, Pagina/e 1073, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-21249-6

An annotated dataset for event-based surveillance of antimicrobial resistance

Autori: Nejat Arınık, Wim Van Bortel, Bahdja Boudoua, Luca Busani, Rémy Decoupes, Roberto Interdonato, Rodrique Kafando, Esther van Kleef, Mathieu Roche, Mehtab Alam Syed, Maguelonne Teisseire
Pubblicato in: Data in Brief, Numero Volume 46, 2023, Pagina/e 108870, ISSN 2352-3409
Editore: Elsevier BV
DOI: 10.1016/j.dib.2022.108870

A review of models applied to the geographic spread of Zika virus

Autori: Sabrina L Li, Jane P Messina, Oliver G Pybus, Moritz U G Kraemer, Lauren Gardner
Pubblicato in: Transactions of The Royal Society of Tropical Medicine and Hygiene, Numero trab009, 2021, ISSN 0035-9203
Editore: Royal Society of Tropical Medicine and Hygiene
DOI: 10.1093/trstmh/trab009

Impact of January 2021 curfew measures on SARS-CoV-2 B.1.1.7 circulation in France

Autori: Laura Di Domenico, Chiara E Sabbatini, Giulia Pullano, Daniel Lévy-Bruhl, Vittoria Colizza
Pubblicato in: Eurosurveillance, Numero 26/15, 2021, ISSN 1560-7917
Editore: ECDC
DOI: 10.2807/1560-7917.es.2021.26.15.2100272

Contribution of climate change to the spatial expansion of West Nile virus in Europe

Autori: Diana Erazo, Luke Grant, Guillaume Ghisbain, Giovanni Marini, Felipe J Colón-González, William Wint, Annapaola Rizzoli, Wim Van Bortel, Chantal B.F. Vogels, Nathan D. Grubaugh, Matthias Mengel, Katja Frieler, Wim Thiery, Simon Dellicour
Pubblicato in: Nature Communications, Numero 15, Article number: 1196, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-45290-3

Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Among Air Passengers in China

Autori: Aogui Hu, Jinfeng Wang, Hui Lin, Corrine W Ruktanonchai, Chengdong Xu, Bin Meng, Xin Zhang, Alessandra Carioli, Yuqing Feng, Qian Yin, Jessica R Floyd, Nick W Ruktanonchai, Zhongjie Li, Weizhong Yang, Andrew J Tatem, Shengjie Lai
Pubblicato in: Clinical Infectious Diseases, Numero Volume 75, Numero 1, 1 July 2022, 2022, Pagina/e Pages e234–e240, ISSN 1058-4838
Editore: University of Chicago Press
DOI: 10.1093/cid/ciab836

Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States

Autori: Vogels CBF, Brackney DE, Dupuis II AP, Robich RM, Fauver JR, Brito AF, Williams SC, Anderson JF, Lubelczyk CB, Lange RE, Prusinski MA, Kramer LD, Gangloff-Kaufmann JL, Goodman LB, Baele G, Smith RP, Armstrong PM, Ciota AT, Dellicour S, Grubaugh ND
Pubblicato in: PNAS, Numero 120 (16) e2218012120, 2023, ISSN 1091-6490
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2218012120

Global Trends in Antimicrobial Use in Food Animals from 2017 to 2030

Autori: Katie Tiseo, Laura Huber, Marius Gilbert, Timothy P. Robinson, Thomas P. Van Boeckel
Pubblicato in: Antibiotics, Numero 9/12, 2020, Pagina/e 918, ISSN 2079-6382
Editore: MDPI
DOI: 10.3390/antibiotics9120918

The impact of spatial connectivity on NPIs effectiveness

Autori: Chiara E. Sabbatini, Giulia Pullano, Laura Di Domenico, Stefania Rubrichi, Shweta Bansal, Vittoria Colizza
Pubblicato in: BMC Infectious Diseases, Numero 24, Article number: 21, 2024, ISSN 1471-2334
Editore: BioMed Central
DOI: 10.1186/s12879-023-08900-x

High habitat richness reduces the risk of tick-borne encephalitis in Europe: a multi-scale study

Autori: Dagostin Francesca, Tagliapietra Valentina, Marini Giovanni, Ferrari Giulia, Cervellini Marco, Wint William, Alexander Niel S., Zuccali Maria Grazia, Molinaro Silvia, Fiorito Nahuel, Dub Timothée, Rocchini Duccio, Rizzoli Annapaola
Pubblicato in: One Health, Numero Volume 18, June 2024, 100669, 2024, ISSN 2352-7714
Editore: Elsevier
DOI: 10.1016/j.onehlt.2023.100669

One Health challenges and actions: Integration of gender considerations to reduce risks at the human-animal-environmental interface

Autori: Claudia Cataldo, Maria Bellenghi, Roberta Masella, Luca Busani
Pubblicato in: One Health, Numero Volume 16, 2023, ISSN 2352-7714
Editore: Elsevier
DOI: 10.1016/j.onehlt.2023.100530

Optimization of adult mosquito trap settings to monitor populations of Aedes and Culex mosquitoes, vectors of arboviruses in La Reunion.

Autori: Iris Claudel, Ronan Brouazin, Renaud Lancelot, Louis-Clément Gouagna, Marlène Dupraz, Thierry Baldet & Jérémy Bouyer
Pubblicato in: Nature Sciences Report, Numero 20452322, 2022, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-022-24191-9

SPREAD 4: online visualisation of pathogen phylogeographic reconstructions

Autori: Kanika D Nahata, Filip Bielejec, Juan Monetta, Simon Dellicour, Andrew Rambaut, Marc A Suchard, Guy Baele, and Philippe Lemey
Pubblicato in: Virus Evolution, Numero 8(2), 2022, Pagina/e veac088, ISSN 2057-1577
Editore: Oxford: Oxford University Press
DOI: 10.1093/ve/veac088

Estimating SARS‐CoV‐2 infections and associated changes in COVID‐19 severity and fatality

Autori: Valentina Marziano; Giorgio Guzzetta; Francesco Menegale; Chiara Sacco; Daniele Petrone; Alberto Mateo Urdiales; Martina Del Manso; Antonino Bella; Massimo Fabiani; Maria Fenicia Vescio; Flavia Riccardo; Piero Poletti; Mattia Manica; Agnese Zardini; Valeria d'Andrea; Filippo Trentini; Paola Stefanelli; Giovanni Rezza; Anna Teresa Palamara; Silvio Brusaferro; Marco Ajelli; Patrizio Pezzotti; Stefan
Pubblicato in: Influenza Other Respi Viruses, Numero 2023;17:e13181, 2023, ISSN 1750-2659
Editore: Oxford Blackwell
DOI: 10.1111/irv.13181

SNEToolkit: Spatial named entities disambiguation toolkit

Autori: Rodrique Kafando; Rémy Decoupes; Mathieu Roche; Maguelonne Teisseire
Pubblicato in: SoftwareX, Numero 61, 2023, Pagina/e Volume 23, 101480, July 2023, ISSN 2352-7110
Editore: Elsevier
DOI: 10.1016/j.softx.2023.101480

Assessing the impact of coordinated COVID-19 exit strategies across Europe

Autori: N. W. Ruktanonchai, J. R. Floyd, S. Lai, C. W. Ruktanonchai, A. Sadilek, P. Rente-Lourenco, X. Ben, A. Carioli, J. Gwinn, J. E. Steele, O. Prosper, A. Schneider, A. Oplinger, P. Eastham, A. J. Tatem
Pubblicato in: Science, Numero 369/6510, 2020, Pagina/e 1465-1470, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.abc5096

Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy

Autori: Mattia Manica, Giorgio Guzzetta, Flavia Riccardo, Antonio Valenti, Piero Poletti, Valentina Marziano, Filippo Trentini, Xanthi Andrianou, Alberto Mateo-Urdiales, Martina del Manso, Massimo Fabiani, Maria Fenicia Vescio, Matteo Spuri, Daniele Petrone, Antonino Bella, Sergio Iavicoli, Marco Ajelli, Silvio Brusaferro, Patrizio Pezzotti, Stefano Merler
Pubblicato in: Nature Communications, Numero 12/1, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-24832-z

Screening and vaccination against COVID-19 to minimise school closure: a modelling study

Autori: Elisabetta Colosi, Giulia Bassignana, Diego Andrés Contreras, Canelle Poirier, Pierre-Yves Boëlle, Simon Cauchemez, Yazdan Yazdanpanah, Bruno Lina, Arnaud Fontanet, Alain Barrat, Vittoria Colizza
Pubblicato in: The Lancet Infectious Diseases, Numero Volume 22, Numero 7, 2022, Pagina/e 977-989, ISSN 1473-3099
Editore: The Lancet Publishing Group
DOI: 10.1016/s1473-3099(22)00138-4

Epidemic intelligence activities among national public and animal health agencies: a European cross-sectional study

Autori: Timothee Dub, Henna Mäkelä, Esther Van Kleef, Agnes Leblond, Alizé Mercier, Viviane Hénaux, Fanny Bouyer, Aurelie Binot, Oumy Thiongane, Renaud Lancelot, Valentina Delconte, Lea Zamuner, Wim Van Bortel & Elena Arsevska
Pubblicato in: BMC Public Health, Numero 23, Article number: 1488, 2023, ISSN 1471-2458
Editore: BioMed Central
DOI: 10.1186/s12889-023-16396-y

Model-based evaluation of alternative reactive class closure strategies against COVID-19.

Autori: Quan-Hui Liu, Juanjuan Zhang, Cheng Peng, Maria Litvinova, Shudong Huang, Piero Poletti, Filippo Trentini, Giorgio Guzzetta, Valentina Marziano, Tao Zhou, Cecile Viboud, Ana I. Bento, Jiancheng Lv, Alessandro Vespignani, Stefano Merler, Hongjie Yu & Marco Ajelli
Pubblicato in: Nature Communications, 2022, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-27939-5

Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy

Autori: Giulia Mencattelli, Andrea Silverj, Federica Iapaolo, Carla Ippoliti, Liana Teodori, Annapia Di Gennaro, Valentina Curini, Luca Candeloro, Annamaria Conte, Andrea Polci, Daniela Morelli, Maria Gabriella Perrotta, Giovanni Marini, Roberto Rosà, Federica Monaco, Nicola Segata, Annapaola Rizzoli, Omar Rota-Stabelli, Giovanni Savini and West Nile Working Group
Pubblicato in: Viruses, Numero 15(1), 35, 2023, ISSN 1999-4915
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15010035

Epidemiology of West Nile virus in Africa: An underestimated threat

Autori: Giulia Mencattelli, Marie Henriette Dior Ndione, Roberto Rosà, Giovanni Marini, Cheikh Tidiane Diagne, Moussa Moise Diagne, Gamou Fall, Ousmane Faye, Mawlouth Diallo, Oumar Faye, Giovanni Savini, Annapaola Rizzoli
Pubblicato in: PLos Negl Trop Dis, Numero 16(1), 2022, Pagina/e e0010075, ISSN 1935-2735
Editore: PLOS
DOI: 10.1371/journal.pntd.0010075

Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study

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Early Genomic Surveillance and Phylogeographic Analysis of Getah Virus, a Reemerging Arbovirus, in Livestock in China

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Underdetection of cases of COVID-19 in France threatens epidemic control

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Anatomy of digital contact tracing: Role of age, transmission setting, adoption, and case detection

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Identifying associations between epidemiological entities in news data for animal disease surveillance

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Epidemic graph diagrams as analytics for epidemic control in the data-rich era.

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Optimization of oviposition trap settings to monitor populations of Aedes mosquitoes, vectors of arboviruses in La Reunion

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Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

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Potential short-term outcome of an uncontrolled COVID-19 epidemic in Lombardy, Italy, February to March 2020

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Modelling COVID-19 in school settings to evaluate prevention and control protocols

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Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

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Accommodating sampling location uncertainty in continuous phylogeography

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Highlighting socio-economic constraints on mobility reductions during COVID-19 restrictions in France can inform effective and equitable pandemic response

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H-TFIDF: What makes areas specific over time in the massive flow of tweets related to the covid pandemic?

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Association of Age With Likelihood of Developing Symptoms and Critical Disease Among Close Contacts Exposed to Patients With Confirmed SARS-CoV-2 Infection in Italy

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Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants

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Is clinical primary care surveillance for tularaemia a useful addition to laboratory surveillance? An analysis of notification data for Finland, 2013 to 2019

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A population-based cohort approach to assess excess mortality due to the spread of COVID-19 in Italy, January-May 2020

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On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy

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Influence of Temperature on the Life-Cycle Dynamics of Aedes albopictus Population Established at Temperate Latitudes: A Laboratory Experiment

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The early phase of the COVID-19 epidemic in Lombardy, Italy

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Pressure on the Health-Care System and Intensive Care Utilization During the COVID-19 Outbreak in the Lombardy Region of Italy: A Retrospective Observational Study in 43,538 Hospitalized Patients

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Socioeconomic patterns and COVID-19 outcomes before, during and after the lockdown in Italy (2020)

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Crowding and the shape of COVID-19 epidemics

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Untangling the changing impact of non-pharmaceutical interventions and vaccination on European COVID-19 trajectories

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Tracing and analysis of 288 early SARS-CoV-2 infections outside China: A modeling study

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Monitoring online media reports for early detection of unknown diseases: Insight from a retrospective study of COVID‐19 emergence

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Minimising school disruption under high incidence conditions due to the Omicron variant in France, Switzerland, Italy, in January 2022

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Fusion of spatiotemporal and thematic features of textual data for animal disease surveillance

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Spring temperature shapes West Nile virus transmission in Europe

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The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

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Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium

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Agent-based modelling of reactive vaccination of workplaces and schools against COVID-19

Autori: Benjamin Faucher; Rania Assab; Jonathan Roux; Daniel Levy-Bruhl; Cécile Tran Kiem; Simon Cauchemez; Laura Zanetti; Vittoria Colizza; Pierre-Yves Boëlle; Chiara Poletto
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The Spatial Distribution of Crimean–Congo Haemorrhagic Fever and Its Potential Vectors in Europe and Beyond

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Outdoor recreation, tick borne encephalitis incidence and seasonality in Finland, Norway and Sweden during the COVID-19 pandemic (2020/2021)

Autori: Solveig Jore, Hildegunn Viljugrein, Marika Hjertqvist, Timothée Dub, Henna Mäkelä
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Risk of Symptomatic Infection During a Second Coronavirus Disease 2019 Wave in Severe Acute Respiratory Syndrome Coronavirus 2–Seropositive Individuals

Autori: Mattia Manica, Serena Pancheri, Piero Poletti, Giulia Giovanazzi, Giorgio Guzzetta, Filippo Trentini, Valentina Marziano, Marco Ajelli, Maria Grazia Zuccali, Pier Paolo Benetollo, Stefano Merler, Antonio Ferro
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Integrated vaccination and physical distancing interventions to prevent future COVID-19 waves in Chinese cities

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Long-lasting insecticidal nets provide protection against malaria for only a single year in Burundi, an African highland setting with marked malaria seasonality

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Animal disease surveillance: How to represent textual data for classifying epidemiological information

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Limited data on infectious disease distribution exposes ambiguity in epidemic modeling choices

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A quantitative assessment of epidemiological parameters to model COVID- 19 burden

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Changes in contact patterns shape the dynamics of the COVID-19 outbreak in China

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Phycova — a tool for exploring covariates of pathogen spread

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The effect of COVID-19 vaccination in Italy and perspectives for living with the virus

Autori: Valentina Marziano, ProfileGiorgio Guzzetta, Alessia Mammone, ProfileFlavia Riccardo, Piero Poletti, Filippo Trentini, Mattia Manica, Andrea Siddu, Paola Stefanelli, Patrizio Pezzotti, Marco Ajelli, Silvio Brusaferro, Giovanni Rezza, Stefano Merler
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Prior water availability modifies the effect of heavy rainfall on dengue transmission: a time series analysis of passive surveillance data from southern China

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Untangling introductions and persistence in COVID-19 resurgence in Europe

Autori: Philippe Lemey, Nick Ruktanonchai, Samuel L. Hong, Vittoria Colizza, Chiara Poletto, Frederik Van den Broeck, Mandev S. Gill, Xiang Ji, Anthony Levasseur, Bas B. Oude Munnink, Marion Koopmans, Adam Sadilek, Shengjie Lai, Andrew J. Tatem, Guy Baele, Marc A. Suchard, Simon Dellicour
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Drivers and epidemiological patterns of West Nile virus in Serbia

Autori: Giovanni Marini, Mitra B. Drakulovic, Verica Jovanovic, Francesca Dagostin, Willy Wint, Valentina Tagliapietra, Milena Vasic, Annapaola Rizzoli
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One Health and sex and gender-related perspective in the ecosystem: Interactions among drivers involved in the risk of leptospirosis in Europe. A scoping review

Autori: Claudia Cataldo, Maria Bellenghi, Roberta Masella, Luca Busani
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Gender gap reduction and the one health benefits

Autori: Claudia Cataldo, Roberta Masella, Luca Busani
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Retrospective analysis of the Italian exit strategy from COVID-19 lockdown

Autori: Valentina Marziano, Giorgio Guzzetta, Bruna Maria Rondinone, Fabio Boccuni, Flavia Riccardo, Antonino Bella, Piero Poletti, Filippo Trentini, Patrizio Pezzotti, Silvio Brusaferro, Giovanni Rezza, Sergio Iavicoli, Marco Ajelli, Stefano Merler
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Reducing contacts to stop SARS-CoV-2 transmission during the second pandemic wave in Brussels, Belgium, August to November 2020

Autori: Brecht Ingelbeen, Laurène Peckeu, Marie Laga, Ilona Hendrix, Inge Neven, Marianne AB van der Sande, Esther van Kleef
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Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework

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Impact of spatiotemporal heterogeneity in COVID-19 disease surveillance on epidemiological parameters and case growth rates

Autori: Rhys P.D. Inward; Felix Jackson; Abhishek Dasgupta; Graham Lee; Anya Lindström Battle; Kris V. Parag; Moritz U.G. Kraemer
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Sindbis virus outbreak and evidence for geographical expansion in Finland, 2021

Autori: Suvanto, Maija T and Uusitalo, Ruut and Otte im Kampe, Eveline and Vuorinen, Tytti and Kurkela, Satu and Vapalahti, Olli and Dub, Timothée and Huhtamo, Eili and Korhonen, Essi M
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The emergence of SARS-CoV-2 in Europe and North America.

Autori: Martha I. Nelson; Brendan B. Larsen; Michael Worobey; Jonathan Pekar; Verity Hill; Philippe Lemey; Marc A. Suchard; Jeffrey B. Joy; Joel O. Wertheim; Andrew Rambaut
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Expected impact of exit strategies after the second lockdown-France, Nov 2020.

Autori: Giulia Pullano, Laura Di Domenico, Chiara E Sabbatini, Vittoria Colizza
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Estimation of the incubation period and generation time of SARS-CoV-2 Alpha and Delta variants from contact tracing data

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Expected impact of school closure and telework to mitigate COVID-19 epidemic in France

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Early assessment of the Omicron variant’s presence and growth rate in regions of France

Autori: Mattia Mazzoli, Laura Di Domenico, EMERGEN Consortium, Vittoria Colizza
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The spatial distribution of Crimean-Congo haemorrhagic fever in Europe and neighbouring areas

Autori: Jane Messina, William Wint
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Epidemic scenarios of Delta variant in France in the summer 2021

Autori: Laura Di Domenico, Vittoria Colizza
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Telework and other measures reducing the presence at work to slow downCOVID-19pdmin France (Sept 2020)

Autori: Giulia Pullano, Laura Di Domenico, Vittoria Colizza
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Editore: INSERM

Mobility during the first week of the second lockdown in France.

Autori: Eugenio Valdano, Jonggul Lee, Stefania Rubrichi, Vittoria Colizza
Pubblicato in: Epicx-lab, report 22, Numero 22, 2020
Editore: INSERM

Impact of contact data resolution on the evaluation of interventions in mathematical models of infectious diseases

Autori: Diego Andrés Contreras; Elisabetta Colosi; Giulia Bassignana; Vittoria Colizza; Alain Barrat
Pubblicato in: Journal of the Royal Society Interface, Numero 20545703, 2022, ISSN 2054-5703
Editore: Royal Society open science
DOI: 10.1098/rsif.2022.0164

Spatial modes for transmission of chikungunya virus during a large chikungunya outbreak in Italy: a modeling analysis

Autori: Giorgio Guzzetta, Francesco Vairo, Alessia Mammone, Simone Lanini, Piero Poletti, Mattia Manica, Roberto Rosa, Beniamino Caputo, Angelo Solimini, Alessandra Della Torre, Paola Scognamiglio, Alimuddin Zumla, Giuseppe Ippolito, Stefano Merler
Pubblicato in: BMC Medicine, Numero 18/1, 2020, ISSN 1741-7015
Editore: BioMed Central
DOI: 10.1186/s12916-020-01674-y

Estimating rodent population abundance using early climatic predictors

Autori: Giovanni Marini, Daniele Arnoldi, Annapaola Rizzoli, Valentina Tagliepietra
Pubblicato in: European Journal of Wildlife Research, Numero 69, 36, 2023, ISSN 1612-4642
Editore: Springer Verlag
DOI: 10.1007/s10344-023-01666-2

GeoXTag: Relative Spatial Information Extraction and Tagging

Autori: Mehtab Alam SYED, Elena ARSEVSKA, Mathieu ROCHE, Maguelonne TEISSEIRE
Pubblicato in: AGILE: GIScience Series, Numero 27008150, 2022, ISSN 2700-8150
Editore: AGILE: GIScience Series
DOI: 10.5194/agile-giss-3-16-2022

Feature Selection for Sentiment Classification of COVID-19 Tweets: H-TFIDF Featuring BERT

Autori: Syed, M.; Arsevska, E.; Roche, M. and Teisseire, M.
Pubblicato in: Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies - HEALTHINF, 2022, Pagina/e 648-656, ISSN 2184-4305
Editore: Setúbal: SCITEPRESS - Science and Technology Publications
DOI: 10.5220/0010887800003123

How Textual Datasets Enhance the PADI-Web Tool?

Autori: Mathieu Roche, Elena Arsevska, Sarah Valentin, Sylvain Falala, Julien Rabatel and Renaud Lancelot
Pubblicato in: Proceedings of the 18th International Conference on Web Information Systems and Technologies, Numero Volume 1, 2022, Pagina/e 327-331, ISBN 978-989-758-613-2
Editore: Science and Technology Publications
DOI: 10.5220/0011590400003318

Quantifying Valence and Arousal in Text with Multilingual Pre-trained Transformers

Autori: Mendes, Gonçalo Azevedo; Martins, Bruno
Pubblicato in: arXIV, Numero 2302.14021, 2023, ISSN 2331-8422
Editore: Cornell University
DOI: 10.48550/arxiv.2302.14021

Enriching Epidemiological Thematic Features For Disease Surveillance Corpora Classification

Autori: Edmond Menya, Mathieu Roche, Roberto Interdonato, Dickson Owuor
Pubblicato in: Proceedings of the Thirteenth Language Resources and Evaluation Conference, Marseille, France, Numero 2022.lrec-1.399, 2022, Pagina/e 3741–3750, ISBN 979-10-95546-72-6
Editore: European Language Resources Association

Automated Processing of Multilingual Online News for the Monitoring of Animal Infectious Diseases

Autori: Sarah Valentin, Renaud Lancelot, Mathieu Roche
Pubblicato in: Proceedings of the LREC 2020 Workshop on Multilingual Biomedical Text Processing, 2020, Pagina/e 33-36, ISBN 2-9517408-6-7
Editore: European Language Resources Association

A Data-Driven Score Model to Assess Online News Articles in Event-Based Surveillance System

Autori: Alam, S.M., Arsevska, E., Roche, M., Teisseire, M.
Pubblicato in: Computer and Information Science, Numero CCIS,volume 1577, 2022, Pagina/e 264–280, ISBN 978-3-031-04446-5
Editore: Springer
DOI: 10.1007/978-3-031-04447-2_18

A metadata approach to classify domain-specific documents for Event-based Surveillance Systems

Autori: M. A. Syed, E. Arsevska, M. Roche and M. Teissere
Pubblicato in: 2023 International Conference on Communication, Computing and Digital Systems (C-CODE), 2023, Pagina/e 2023, pp. 1-5, ISBN 979-8-3503-3239-1
Editore: IEEE
DOI: 10.1109/c-code58145.2023.10139883

PADI-web: an event-based surveillance system for detecting, classifying and processing online news.

Autori: Sarah Valentin, Elena Arsevska, Alize Mercier, Sylvain Falala, Julien Rabatel, Renaud Lancelot, Mathieu Roche.
Pubblicato in: Human language technology. Challenges for computer science and linguistics., Numero Language and Technology Conference. 8, Poznan, Pologne, 17 Novembre 2017/19 Novembre 2017, 2020, Pagina/e 87-101, ISBN 978-3-030-66527-2
Editore: Springer
DOI: 10.1007/978-3-030-66527-2_7

Unsupervised Key-Phrase Extraction from Long Texts with Multilingual Sentence Transformers

Autori: Dias, H., Guimarães, A., Martins, B., Roche, M
Pubblicato in: Discovery Science 26th International Conference, DS 2023, Porto, Portugal, October 9–11, 2023, Numero vol 14276, 2023, Pagina/e 141-145, ISBN 978-3-031-45275-8
Editore: Springer, Cham
DOI: 10.1007/978-3-031-45275-8_10

A co-training approach for spatial data disaggregation

Autori: João Monteiro, Bruno Martins, Miguel Costa, João M. Pires
Pubblicato in: SIGSPATIAL '22: Proceedings of the 30th International Conference on Advances in Geographic Information SystemsNovember 2022 Article No.: 91Pages 1–10https://doi.org/10.1145/3557915.3561475, Numero November 2022 Article No.: 91, 2022, Pagina/e 1-10, ISSN 1552-5996
Editore: Proceedings of the ACM/IEEE Joint Conference on Digital Libraries
DOI: 10.1145/3557915.3561475

Explainable epidemiological thematic features for event based disease surveillance

Autori: Edmond Menya, Roberto Interdonato, Dickson Owuor, Mathieu Roche
Pubblicato in: Expert Systems with Applications, Numero Vol 250, 2024, Pagina/e 123894, ISSN 0957-4174
Editore: Elsevier
DOI: 10.1016/j.eswa.2024.123894

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