MOOD project is at the forefront of European research of infectious disease surveillance and modelling from a data science perspective, investigating the impact of global warming on disease outbreaks, and proposing innovations for building of One Health systems across Europe and the world.
In the table below are listed all MOOD publications. Use the filter to select the most relevant articles.
108.
Inward, Rhys P. D.; Jackson, Felix; Dasgupta, Abhishek; Lee, Graham; Battle, Anya Lindström; Parag, Kris V.; Kraemer, Moritz U. G.
Impact of spatiotemporal heterogeneity in COVID-19 disease surveillance on epidemiological parameters and case growth rates Journal Article
In: Epidemics, vol. 41, pp. 100627, 2023, ISSN: 1755-4365.
Abstract | Links | BibTeX | Tags: Epidemic models, Outbreak surveillance, SARS-CoV-2
@article{nokey,
title = {Impact of spatiotemporal heterogeneity in COVID-19 disease surveillance on epidemiological parameters and case growth rates},
author = {Rhys P.D. Inward and Felix Jackson and Abhishek Dasgupta and Graham Lee and Anya Lindström Battle and Kris V. Parag and Moritz U.G. Kraemer},
url = {https://www.sciencedirect.com/science/article/pii/S1755436522000676},
doi = {10.1016/j.epidem.2022.100627},
issn = {1755-4365},
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {Epidemics},
volume = {41},
pages = {100627},
abstract = {SARS-CoV-2 case data are primary sources for estimating epidemiological parameters and for modelling the dynamics of outbreaks. Understanding biases within case-based data sources used in epidemiological analyses is important as they can detract from the value of these rich datasets. This raises questions of how variations in surveillance can affect the estimation of epidemiological parameters such as the case growth rates. We use standardised line list data of COVID-19 from Argentina, Brazil, Mexico and Colombia to estimate delay distributions of symptom-onset-to-confirmation, -hospitalisation and -death as well as hospitalisation-to-death at high spatial resolutions and throughout time. Using these estimates, we model the biases introduced by the delay from symptom-onset-to-confirmation on national and state level case growth rates (rt) using an adaptation of the Richardson-Lucy deconvolution algorithm. We find significant heterogeneities in the estimation of delay distributions through time and space with delay difference of up to 19 days between epochs at the state level. Further, we find that by changing the spatial scale, estimates of case growth rate can vary by up to 0.13 d−1. Lastly, we find that states with a high variance and/or mean delay in symptom-onset-to-diagnosis also have the largest difference between the rt estimated from raw and deconvolved case counts at the state level. We highlight the importance of high-resolution case-based data in understanding biases in disease reporting and how these biases can be avoided by adjusting case numbers based on empirical delay distributions. Code and openly accessible data to reproduce analyses presented here are available.},
keywords = {Epidemic models, Outbreak surveillance, SARS-CoV-2},
pubstate = {published},
tppubtype = {article}
}
SARS-CoV-2 case data are primary sources for estimating epidemiological parameters and for modelling the dynamics of outbreaks. Understanding biases within case-based data sources used in epidemiological analyses is important as they can detract from the value of these rich datasets. This raises questions of how variations in surveillance can affect the estimation of epidemiological parameters such as the case growth rates. We use standardised line list data of COVID-19 from Argentina, Brazil, Mexico and Colombia to estimate delay distributions of symptom-onset-to-confirmation, -hospitalisation and -death as well as hospitalisation-to-death at high spatial resolutions and throughout time. Using these estimates, we model the biases introduced by the delay from symptom-onset-to-confirmation on national and state level case growth rates (rt) using an adaptation of the Richardson-Lucy deconvolution algorithm. We find significant heterogeneities in the estimation of delay distributions through time and space with delay difference of up to 19 days between epochs at the state level. Further, we find that by changing the spatial scale, estimates of case growth rate can vary by up to 0.13 d−1. Lastly, we find that states with a high variance and/or mean delay in symptom-onset-to-diagnosis also have the largest difference between the rt estimated from raw and deconvolved case counts at the state level. We highlight the importance of high-resolution case-based data in understanding biases in disease reporting and how these biases can be avoided by adjusting case numbers based on empirical delay distributions. Code and openly accessible data to reproduce analyses presented here are available.
107.
Marini, Giovanni; Arnoldi, Daniele; Rizzoli, Annapaola; Tagliapietra, Valentina
Estimating rodent population abundance using early climatic predictors Journal Article
In: European Journal of Wildlife Research, vol. 69, no. 2, pp. 36, 2023.
Links | BibTeX | Tags: Apodemus flavicollis, Climate, early warning, Rodent density
@article{nokey,
title = {Estimating rodent population abundance using early climatic predictors},
author = {Marini, Giovanni and Arnoldi, Daniele and Rizzoli, Annapaola and Tagliapietra, Valentina},
url = {https://link.springer.com/article/10.1007/s10344-023-01666-2#citeas},
doi = {10.1007/s10344-023-01666-2},
year = {2023},
date = {2023-03-17},
urldate = {2023-03-17},
journal = {European Journal of Wildlife Research},
volume = {69},
number = {2},
pages = {36},
keywords = {Apodemus flavicollis, Climate, early warning, Rodent density},
pubstate = {published},
tppubtype = {article}
}
106.
Cataldo, Claudia; Masella, Roberta; Busani, Luca
Gender gap reduction and the one health benefits Author links open overlay panel Journal Article
In: One Health, vol. 16, pp. 100496, 2023, ISSN: 2352-7714.
Abstract | Links | BibTeX | Tags: eco health, education, empowerment, Gender gap, Gender-specific roles, One Health
@article{nokey,
title = {Gender gap reduction and the one health benefits Author links open overlay panel},
author = {Claudia Cataldo and Roberta Masella and Luca Busani},
url = {https://www.sciencedirect.com/science/article/pii/S2352771423000162},
doi = {10.1016/j.onehlt.2023.100496},
issn = {2352-7714},
year = {2023},
date = {2023-02-07},
journal = {One Health},
volume = {16},
pages = {100496},
abstract = {Several factors including gender, age groups, cultures and social conditions may affect significantly the risk of diseases and their clinical evolution. Unfortunately, little research has been carried out on these aspects and, consequently few guidelines or interventions have been implemented. In particular, gender is considered a main determinant of inequalities in living conditions, access to health services and, thus, in health protection.
Focusing on the gender gap, we propose an ecological approach to find relationships between quantitative indicators of the gender gap dimension, the environmental performance index and the life expectancy at birth as summary of human health index in 155 countries. We speculated on the consequences of wider gender gaps to the population and environmental health. We further explore these relationships considering gender gap and environmental aspect subindexes, to identify determinants that should be addressed to maximize the One Health effect. We found that the gender gap in educational attainment followed by the political empowerment were strongly correlated with life expectancy, environmental health, and ecosystem vitality.
Addressing gender issues, particularly the education attainment and political empowerment, can provide positive impact beyond the social dimension and the population health, and gender should be component of the One Health approach. We recommend gender targeted interventions that integrate these aspects into One Health national policies.},
keywords = {eco health, education, empowerment, Gender gap, Gender-specific roles, One Health},
pubstate = {published},
tppubtype = {article}
}
Several factors including gender, age groups, cultures and social conditions may affect significantly the risk of diseases and their clinical evolution. Unfortunately, little research has been carried out on these aspects and, consequently few guidelines or interventions have been implemented. In particular, gender is considered a main determinant of inequalities in living conditions, access to health services and, thus, in health protection.
Focusing on the gender gap, we propose an ecological approach to find relationships between quantitative indicators of the gender gap dimension, the environmental performance index and the life expectancy at birth as summary of human health index in 155 countries. We speculated on the consequences of wider gender gaps to the population and environmental health. We further explore these relationships considering gender gap and environmental aspect subindexes, to identify determinants that should be addressed to maximize the One Health effect. We found that the gender gap in educational attainment followed by the political empowerment were strongly correlated with life expectancy, environmental health, and ecosystem vitality.
Addressing gender issues, particularly the education attainment and political empowerment, can provide positive impact beyond the social dimension and the population health, and gender should be component of the One Health approach. We recommend gender targeted interventions that integrate these aspects into One Health national policies.
Focusing on the gender gap, we propose an ecological approach to find relationships between quantitative indicators of the gender gap dimension, the environmental performance index and the life expectancy at birth as summary of human health index in 155 countries. We speculated on the consequences of wider gender gaps to the population and environmental health. We further explore these relationships considering gender gap and environmental aspect subindexes, to identify determinants that should be addressed to maximize the One Health effect. We found that the gender gap in educational attainment followed by the political empowerment were strongly correlated with life expectancy, environmental health, and ecosystem vitality.
Addressing gender issues, particularly the education attainment and political empowerment, can provide positive impact beyond the social dimension and the population health, and gender should be component of the One Health approach. We recommend gender targeted interventions that integrate these aspects into One Health national policies.
105.
Mulchandani, Ranya; Wang, Yu; Gilbert, Marius; Van Boeckel, Thomas P
Global trends in antimicrobial use in food-producing animals: 2020 to 2030 Journal Article
In: PLOS Global Public Health, vol. 3, no. 2, pp. e0001305, 2023.
Abstract | Links | BibTeX | Tags: antibiotics, Brazil, chicken, india, livestock, OpenDataSet, sheep, swine
@article{nokey,
title = {Global trends in antimicrobial use in food-producing animals: 2020 to 2030},
author = {Mulchandani, Ranya and Wang, Yu and Gilbert, Marius and Van Boeckel, Thomas P},
editor = {Ismail Ayoade Odetokun, University of Ilorin, NIGERIA},
url = {https://journals.plos.org/globalpublichealth/article?id=10.1371/journal.pgph.0001305#abstract0},
doi = {10.1371/journal.pgph.0001305},
year = {2023},
date = {2023-02-01},
journal = {PLOS Global Public Health},
volume = {3},
number = {2},
pages = {e0001305},
abstract = {Use of antimicrobials in farming has enabled the growth of intensive animal production and helped in meeting the global increase in demand for animal protein. However, the widespread use of veterinary antimicrobials drives antimicrobial resistance, with important consequences for animal health, and potentially human health. Global monitoring of antimicrobial use is essential: first, to track progress in reducing the reliance of farming on antimicrobials. Second, to identify countries where antimicrobial-stewardship efforts should be targeted to curb antimicrobial resistance. Data on usage of antimicrobials in food animals were collected from 42 countries. Multivariate regression models were used in combination with projections of animal counts for cattle, sheep, chicken, and pigs from the Food and Agriculture Organization to estimate global antimicrobial usage of veterinary antimicrobials in 2020 and 2030. Maps of animal densities were used to identify geographic hotspots of antimicrobial use. In each country, estimates of antimicrobial use (tonnes) were calibrated to match continental-level reports of antimicrobial use intensity (milligrams per kilogram of animal) from the World Organization for Animal Health, as well as country-level reports of antimicrobial use from countries that made this information publicly available. Globally, antimicrobial usage was estimated at 99,502 tonnes (95% CI 68,535–198,052) in 2020 and is projected, based on current trends, to increase by 8.0% to 107,472 tonnes (95% CI: 75,927–202,661) by 2030. Hotspots of antimicrobial use were overwhelmingly in Asia (67%), while <1% were in Africa. Findings indicate higher global antimicrobial usage in 2030 compared to prior projections that used data from 2017; this is likely associated with an upward revision of antimicrobial use in Asia/Oceania (~6,000 tonnes) and the Americas (~4,000 tonnes). National-level reporting of antimicrobial use should be encouraged to better evaluate the impact of national policies on antimicrobial use levels.},
keywords = {antibiotics, Brazil, chicken, india, livestock, OpenDataSet, sheep, swine},
pubstate = {published},
tppubtype = {article}
}
Use of antimicrobials in farming has enabled the growth of intensive animal production and helped in meeting the global increase in demand for animal protein. However, the widespread use of veterinary antimicrobials drives antimicrobial resistance, with important consequences for animal health, and potentially human health. Global monitoring of antimicrobial use is essential: first, to track progress in reducing the reliance of farming on antimicrobials. Second, to identify countries where antimicrobial-stewardship efforts should be targeted to curb antimicrobial resistance. Data on usage of antimicrobials in food animals were collected from 42 countries. Multivariate regression models were used in combination with projections of animal counts for cattle, sheep, chicken, and pigs from the Food and Agriculture Organization to estimate global antimicrobial usage of veterinary antimicrobials in 2020 and 2030. Maps of animal densities were used to identify geographic hotspots of antimicrobial use. In each country, estimates of antimicrobial use (tonnes) were calibrated to match continental-level reports of antimicrobial use intensity (milligrams per kilogram of animal) from the World Organization for Animal Health, as well as country-level reports of antimicrobial use from countries that made this information publicly available. Globally, antimicrobial usage was estimated at 99,502 tonnes (95% CI 68,535–198,052) in 2020 and is projected, based on current trends, to increase by 8.0% to 107,472 tonnes (95% CI: 75,927–202,661) by 2030. Hotspots of antimicrobial use were overwhelmingly in Asia (67%), while <1% were in Africa. Findings indicate higher global antimicrobial usage in 2030 compared to prior projections that used data from 2017; this is likely associated with an upward revision of antimicrobial use in Asia/Oceania (~6,000 tonnes) and the Americas (~4,000 tonnes). National-level reporting of antimicrobial use should be encouraged to better evaluate the impact of national policies on antimicrobial use levels.
104.
Kyöttinen, Anniina
Vector-borne diseases stakeholder mapping in Finland - a one health approach Masters Thesis
Tampere University - Faculty of Social Sciences, 2023.
Abstract | Links | BibTeX | Tags: actor, ARDI- method, finland, multisectoral collaboration, One Health, stakeholder, Vector-borne disease
@mastersthesis{nokey,
title = {Vector-borne diseases stakeholder mapping in Finland - a one health approach},
author = {Anniina Kyöttinen},
url = {https://mood-h2020.eu/wp-content/uploads/2023/04/VECTOR-BORNE-DISEASES-STAKEHOLDER-MAPPING-IN-FINLAND-a-one-health-approach-1.pdf},
year = {2023},
date = {2023-02-01},
school = {Tampere University - Faculty of Social Sciences},
abstract = {Climate change, increasing human population, urbanization, industrialization and the gradual depletion
of natural resources affects the health of humans, animals, and ecosystems around the globe. The complex
and wicked health problems arising at the human-animal-ecosystem interphase, such as the (re)emergence,
transmission, and management of both novel and traditional zoonoses and vector-born-diseases, requires
enhanced multisectoral and multi-leveled interactions and collaboration between different One Health
stakeholders.
Previous research in Finland around the topic of vector-borne diseases has primarily been
focused on vector, host, and disease epidemiology: changes in disease occurrence and distribution of hosts
and vectors, nationally. However very little attention has been given to stakeholder networks studies,
information- and resource-sharing, nor on how different VBD actors and stakeholders interact in Finland.
Thus, the aim of this master’s thesis is to map and analyze the current and missing stakeholder/actor
interactions and information flow related to vector-borne diseases and their management in Finland, within
a One Health context. In addition, the objective is also to discuss and reflect on the future of a possible
formal VBD/One Health-network in Finland and what are the chances, challenges and means of
establishing one. In conclusion, this research plays a pivotal role in addressing the growing issue of vector-
borne diseases nationally and globally, in addition to enhancing VBD research, management, surveillance,
control and prevention in Finland.
Qualitative semi-structured interviews were chosen as the primary methodology for this
master’s thesis. More specifically, a qualitative research method, focusing on identifying actors, resources,
multi-actor dynamics and multi-actor interactions (ARDI) was used to analyze the data. The qualitative
data in this research consists of 10 semi-structured VBD/OH stakeholder interviews of Finnish
professionals collected between October 2021 - December 2021.
The results of this study indicate the importance of multisectoral and multi-leveled
stakeholder collaboration related to vector-borne disease research, management, surveillance, control and
prevention in Finland. In total 139 potential direct and indirect VBD and One Health stakeholders were
identified in this research. Twenty (20) stakeholders, from varying fields were recognized as key VBD/OH
actors in Finland. The results in this study suggest that VBD/OH stakeholders in Finland are to some extent
interdisciplinary and multisectoral, but the biggest emphasis among different stakeholders still remains in
human health, resulting in neglect of other fields of study, especially social sciences and humanities.
Currently VBD/OH networks in Finland are mostly built upon unofficial personal connections relying
heavily on a few Finnish individual key experts and research projects with external funding, resulting in
uncertainty in the continuity of collaborations. There also seems to be a lack of higher-level coordination
of VBD/OH collaboration activities in addition to the lack of collaboration between Finnish governmental
agencies and other lower-level stakeholders, mainly due to lack of fiscal and human resources. The results
of this research indicate that stakeholders’ collaboration with the private sector, independent agencies,
NGOs, professional and scientific associations and other foundations in Finland is very limited.
Furthermore, all ten interviewed stakeholders unanimously support the formation of a formal VBD/OH
network in Finland to enhance stakeholder collaboration, information sharing and data management related
to vector-borne diseases in Finland.
The findings of this research strongly suggest the establishment of a formal
multidisciplinary and multi-leveled OH vector-borne disease expert network in Finland with higher level
coordination and sufficient fiscal and skilled human resources. However, further investigations are still
needed to gain a deeper understanding of formal One Health networks in Europe, private actor engagement
and public-private partnerships in strengthening VBD management, in addition to investigations on
(re)emerging vectors, vector-borne diseases and climate change in Finland.},
keywords = {actor, ARDI- method, finland, multisectoral collaboration, One Health, stakeholder, Vector-borne disease},
pubstate = {published},
tppubtype = {mastersthesis}
}
Climate change, increasing human population, urbanization, industrialization and the gradual depletion
of natural resources affects the health of humans, animals, and ecosystems around the globe. The complex
and wicked health problems arising at the human-animal-ecosystem interphase, such as the (re)emergence,
transmission, and management of both novel and traditional zoonoses and vector-born-diseases, requires
enhanced multisectoral and multi-leveled interactions and collaboration between different One Health
stakeholders.
Previous research in Finland around the topic of vector-borne diseases has primarily been
focused on vector, host, and disease epidemiology: changes in disease occurrence and distribution of hosts
and vectors, nationally. However very little attention has been given to stakeholder networks studies,
information- and resource-sharing, nor on how different VBD actors and stakeholders interact in Finland.
Thus, the aim of this master’s thesis is to map and analyze the current and missing stakeholder/actor
interactions and information flow related to vector-borne diseases and their management in Finland, within
a One Health context. In addition, the objective is also to discuss and reflect on the future of a possible
formal VBD/One Health-network in Finland and what are the chances, challenges and means of
establishing one. In conclusion, this research plays a pivotal role in addressing the growing issue of vector-
borne diseases nationally and globally, in addition to enhancing VBD research, management, surveillance,
control and prevention in Finland.
Qualitative semi-structured interviews were chosen as the primary methodology for this
master’s thesis. More specifically, a qualitative research method, focusing on identifying actors, resources,
multi-actor dynamics and multi-actor interactions (ARDI) was used to analyze the data. The qualitative
data in this research consists of 10 semi-structured VBD/OH stakeholder interviews of Finnish
professionals collected between October 2021 - December 2021.
The results of this study indicate the importance of multisectoral and multi-leveled
stakeholder collaboration related to vector-borne disease research, management, surveillance, control and
prevention in Finland. In total 139 potential direct and indirect VBD and One Health stakeholders were
identified in this research. Twenty (20) stakeholders, from varying fields were recognized as key VBD/OH
actors in Finland. The results in this study suggest that VBD/OH stakeholders in Finland are to some extent
interdisciplinary and multisectoral, but the biggest emphasis among different stakeholders still remains in
human health, resulting in neglect of other fields of study, especially social sciences and humanities.
Currently VBD/OH networks in Finland are mostly built upon unofficial personal connections relying
heavily on a few Finnish individual key experts and research projects with external funding, resulting in
uncertainty in the continuity of collaborations. There also seems to be a lack of higher-level coordination
of VBD/OH collaboration activities in addition to the lack of collaboration between Finnish governmental
agencies and other lower-level stakeholders, mainly due to lack of fiscal and human resources. The results
of this research indicate that stakeholders’ collaboration with the private sector, independent agencies,
NGOs, professional and scientific associations and other foundations in Finland is very limited.
Furthermore, all ten interviewed stakeholders unanimously support the formation of a formal VBD/OH
network in Finland to enhance stakeholder collaboration, information sharing and data management related
to vector-borne diseases in Finland.
The findings of this research strongly suggest the establishment of a formal
multidisciplinary and multi-leveled OH vector-borne disease expert network in Finland with higher level
coordination and sufficient fiscal and skilled human resources. However, further investigations are still
needed to gain a deeper understanding of formal One Health networks in Europe, private actor engagement
and public-private partnerships in strengthening VBD management, in addition to investigations on
(re)emerging vectors, vector-borne diseases and climate change in Finland.
of natural resources affects the health of humans, animals, and ecosystems around the globe. The complex
and wicked health problems arising at the human-animal-ecosystem interphase, such as the (re)emergence,
transmission, and management of both novel and traditional zoonoses and vector-born-diseases, requires
enhanced multisectoral and multi-leveled interactions and collaboration between different One Health
stakeholders.
Previous research in Finland around the topic of vector-borne diseases has primarily been
focused on vector, host, and disease epidemiology: changes in disease occurrence and distribution of hosts
and vectors, nationally. However very little attention has been given to stakeholder networks studies,
information- and resource-sharing, nor on how different VBD actors and stakeholders interact in Finland.
Thus, the aim of this master’s thesis is to map and analyze the current and missing stakeholder/actor
interactions and information flow related to vector-borne diseases and their management in Finland, within
a One Health context. In addition, the objective is also to discuss and reflect on the future of a possible
formal VBD/One Health-network in Finland and what are the chances, challenges and means of
establishing one. In conclusion, this research plays a pivotal role in addressing the growing issue of vector-
borne diseases nationally and globally, in addition to enhancing VBD research, management, surveillance,
control and prevention in Finland.
Qualitative semi-structured interviews were chosen as the primary methodology for this
master’s thesis. More specifically, a qualitative research method, focusing on identifying actors, resources,
multi-actor dynamics and multi-actor interactions (ARDI) was used to analyze the data. The qualitative
data in this research consists of 10 semi-structured VBD/OH stakeholder interviews of Finnish
professionals collected between October 2021 - December 2021.
The results of this study indicate the importance of multisectoral and multi-leveled
stakeholder collaboration related to vector-borne disease research, management, surveillance, control and
prevention in Finland. In total 139 potential direct and indirect VBD and One Health stakeholders were
identified in this research. Twenty (20) stakeholders, from varying fields were recognized as key VBD/OH
actors in Finland. The results in this study suggest that VBD/OH stakeholders in Finland are to some extent
interdisciplinary and multisectoral, but the biggest emphasis among different stakeholders still remains in
human health, resulting in neglect of other fields of study, especially social sciences and humanities.
Currently VBD/OH networks in Finland are mostly built upon unofficial personal connections relying
heavily on a few Finnish individual key experts and research projects with external funding, resulting in
uncertainty in the continuity of collaborations. There also seems to be a lack of higher-level coordination
of VBD/OH collaboration activities in addition to the lack of collaboration between Finnish governmental
agencies and other lower-level stakeholders, mainly due to lack of fiscal and human resources. The results
of this research indicate that stakeholders’ collaboration with the private sector, independent agencies,
NGOs, professional and scientific associations and other foundations in Finland is very limited.
Furthermore, all ten interviewed stakeholders unanimously support the formation of a formal VBD/OH
network in Finland to enhance stakeholder collaboration, information sharing and data management related
to vector-borne diseases in Finland.
The findings of this research strongly suggest the establishment of a formal
multidisciplinary and multi-leveled OH vector-borne disease expert network in Finland with higher level
coordination and sufficient fiscal and skilled human resources. However, further investigations are still
needed to gain a deeper understanding of formal One Health networks in Europe, private actor engagement
and public-private partnerships in strengthening VBD management, in addition to investigations on
(re)emerging vectors, vector-borne diseases and climate change in Finland.
103.
Valentin, Sarah; Arsevska, Elena; Mercier, Alizé; Falala, Sylvain; Rabatel, Julien; Lancelot, Renaud; Roche, Mathieu
PADI-web: An Event-Based Surveillance System for Detecting, Classifying and Processing Online News Conference
Human Language Technology. Challenges for Computer Science and Linguistics, vol. 12598, Springer International Publishing, 2022, ISBN: 978-3-030-66526-5.
Abstract | Links | BibTeX | Tags: animal health, classification, epidemic intelligence, information extraction, Text mining, web monitoring
@conference{@InProceedings{10.1007/978-3-030-66527-2_7,
title = {PADI-web: An Event-Based Surveillance System for Detecting, Classifying and Processing Online News},
author = {Valentin, Sarah and Arsevska, Elena and Mercier, Alizé and Falala, Sylvain and Rabatel, Julien and Lancelot, Renaud and Roche, Mathieu},
editor = {Vetulani, Zygmunt and Paroubek, Patrick and Kubis, Marek},
url = {https://link.springer.com/chapter/10.1007/978-3-030-66527-2_7},
doi = {https://doi.org/10.1007/978-3-030-66527-2_7},
isbn = {978-3-030-66526-5},
year = {2022},
date = {2022-12-31},
urldate = {2022-12-31},
booktitle = {Human Language Technology. Challenges for Computer Science and Linguistics},
volume = {12598},
pages = {87-101},
publisher = {Springer International Publishing},
abstract = {The Platform for Automated Extraction of Animal Disease Information from the Web (PADI-web) is a multilingual text mining tool for automatic detection, classification, and extraction of disease outbreak information from online news articles. PADI-web currently monitors the Web for nine animal infectious diseases and eight syndromes in five animal hosts. The classification module is based on a supervised machine learning approach to filter the relevant news with an overall accuracy of 0.94. The classification of relevant news between 5 topic categories (confirmed, suspected or unknown outbreak, preparedness and impact) obtained an overall accuracy of 0.75. In the first six months of its implementation (January--June 2016), PADI-web detected 73{%} of the outbreaks of African swine fever; 20{%} of foot-and-mouth disease; 13{%} of bluetongue, and 62{%} of highly pathogenic avian influenza. The information extraction module of PADI-web obtained F-scores of 0.80 for locations, 0.85 for dates, 0.95 for diseases, 0.95 for hosts, and 0.85 for case numbers},
keywords = {animal health, classification, epidemic intelligence, information extraction, Text mining, web monitoring},
pubstate = {published},
tppubtype = {conference}
}
The Platform for Automated Extraction of Animal Disease Information from the Web (PADI-web) is a multilingual text mining tool for automatic detection, classification, and extraction of disease outbreak information from online news articles. PADI-web currently monitors the Web for nine animal infectious diseases and eight syndromes in five animal hosts. The classification module is based on a supervised machine learning approach to filter the relevant news with an overall accuracy of 0.94. The classification of relevant news between 5 topic categories (confirmed, suspected or unknown outbreak, preparedness and impact) obtained an overall accuracy of 0.75. In the first six months of its implementation (January--June 2016), PADI-web detected 73{%} of the outbreaks of African swine fever; 20{%} of foot-and-mouth disease; 13{%} of bluetongue, and 62{%} of highly pathogenic avian influenza. The information extraction module of PADI-web obtained F-scores of 0.80 for locations, 0.85 for dates, 0.95 for diseases, 0.95 for hosts, and 0.85 for case numbers
102.
Mencattelli, Giulia; Silverj, Andrea; Iapaolo, Federica; Ippoliti, Carla; Teodori, Liana; Di Gennaro, Annapia; Curini, Valentina; Candeloro, Luca; Conte, Annamaria; Polci, Andrea; Morelli, Daniela; Perrotta, Maria Gabriella; Marini, Giovanni; Rosà, Roberto; Monaco, Federica; Segata, Nicola; Rizzoli, Annapaola; Rota-Stabelli, Omar; Savini, Giovanni; Group, West Nile Working
Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy Journal Article
In: Viruses, vol. 15, no. 35, 2022, ISSN: 1999-4915.
Abstract | Links | BibTeX | Tags: early-warning, epidemiology, evolution, Italy, West Nile virus lineage 2
@article{nokey,
title = {Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy},
author = {Mencattelli, Giulia and Silverj, Andrea and Iapaolo, Federica and Ippoliti, Carla and Teodori, Liana and Di Gennaro, Annapia and Curini, Valentina and Candeloro, Luca and Conte, Annamaria and Polci, Andrea and Morelli, Daniela and Perrotta, Maria Gabriella and Marini, Giovanni and Rosà, Roberto and Monaco, Federica and Segata, Nicola and Rizzoli, Annapaola and Rota-Stabelli, Omar and Savini, Giovanni and West Nile Working Group},
url = {https://www.mdpi.com/1999-4915/15/1/35},
doi = {10.3390/v15010035},
issn = {1999-4915},
year = {2022},
date = {2022-12-22},
journal = {Viruses},
volume = {15},
number = {35},
abstract = {West Nile virus (WNV) is a mosquito-borne virus potentially causing serious illness in humans and other animals. Since 2004, several studies have highlighted the progressive spread of WNV Lineage 2 (L2) in Europe, with Italy being one of the countries with the highest number of cases of West Nile disease reported. In this paper, we give an overview of the epidemiological and genetic features characterising the spread and evolution of WNV L2 in Italy, leveraging data obtained from national surveillance activities between 2011 and 2021, including 46 newly assembled genomes that were analysed under both phylogeographic and phylodynamic frameworks. In addition, to better understand the seasonal patterns of the virus, we used a machine learning model predicting areas at high-risk of WNV spread. Our results show a progressive increase in WNV L2 in Italy, clarifying the dynamics of interregional circulation, with no significant introductions from other countries in recent years. Moreover, the predicting model identified the presence of suitable conditions for the 2022 earlier and wider spread of WNV in Italy, underlining the importance of using quantitative models for early warning detection of WNV outbreaks. Taken together, these findings can be used as a reference to develop new strategies to mitigate the impact of the pathogen on human and other animal health in endemic areas and new regions.},
keywords = {early-warning, epidemiology, evolution, Italy, West Nile virus lineage 2},
pubstate = {published},
tppubtype = {article}
}
West Nile virus (WNV) is a mosquito-borne virus potentially causing serious illness in humans and other animals. Since 2004, several studies have highlighted the progressive spread of WNV Lineage 2 (L2) in Europe, with Italy being one of the countries with the highest number of cases of West Nile disease reported. In this paper, we give an overview of the epidemiological and genetic features characterising the spread and evolution of WNV L2 in Italy, leveraging data obtained from national surveillance activities between 2011 and 2021, including 46 newly assembled genomes that were analysed under both phylogeographic and phylodynamic frameworks. In addition, to better understand the seasonal patterns of the virus, we used a machine learning model predicting areas at high-risk of WNV spread. Our results show a progressive increase in WNV L2 in Italy, clarifying the dynamics of interregional circulation, with no significant introductions from other countries in recent years. Moreover, the predicting model identified the presence of suitable conditions for the 2022 earlier and wider spread of WNV in Italy, underlining the importance of using quantitative models for early warning detection of WNV outbreaks. Taken together, these findings can be used as a reference to develop new strategies to mitigate the impact of the pathogen on human and other animal health in endemic areas and new regions.
101.
Zardini, Agnese; Galli, Margherita; Tirani, Marcello; Cereda, Danilo; Manica, Mattia; Trentini, Filippo; Guzzetta, Giorgio; Marziano, Valentina; Piccarreta, Raffaella; Melegaro, Alessia; Ajelli, Marco; Poletti, Piero; Merler, Stefano
A quantitative assessment of epidemiological parameters required to investigate COVID-19 burden Journal Article
In: Epidemics, vol. 37, pp. 100530, 2022, ISSN: 1755-4365.
Abstract | Links | BibTeX | Tags: contact tracing data, disease burden, epidemiological parameters, risk outcomes, SARS-CoV-2
@article{nokey,
title = {A quantitative assessment of epidemiological parameters required to investigate COVID-19 burden},
author = {Agnese Zardini and Margherita Galli and Marcello Tirani and Danilo Cereda and Mattia Manica and Filippo Trentini and Giorgio Guzzetta and Valentina Marziano and Raffaella Piccarreta and Alessia Melegaro and Marco Ajelli and Piero Poletti and Stefano Merler},
url = {https://www.sciencedirect.com/science/article/pii/S1755436521000748},
doi = {10.1016/j.epidem.2021.100530},
issn = {1755-4365},
year = {2022},
date = {2022-12-01},
urldate = {2022-12-01},
journal = {Epidemics},
volume = {37},
pages = {100530},
abstract = {Solid estimates describing the clinical course of SARS-CoV-2 infections are still lacking due to under-ascertainment of asymptomatic and mild-disease cases. In this work, we quantify age-specific probabilities of transitions between stages defining the natural history of SARS-CoV-2 infection from 1965 SARS-CoV-2 positive individuals identified in Italy between March and April 2020 among contacts of confirmed cases. Infected contacts of cases were confirmed via RT-PCR tests as part of contact tracing activities or retrospectively via IgG serological tests and followed-up for symptoms and clinical outcomes. In addition, we provide estimates of time intervals between key events defining the clinical progression of cases as obtained from a larger sample, consisting of 95,371 infections ascertained between February and July 2020. We found that being older than 60 years of age was associated with a 39.9% (95%CI: 36.2–43.6%) likelihood of developing respiratory symptoms or fever ≥ 37.5 °C after SARS-CoV-2 infection; the 22.3% (95%CI: 19.3–25.6%) of the infections in this age group required hospital care and the 1% (95%CI: 0.4–2.1%) were admitted to an intensive care unit (ICU). The corresponding proportions in individuals younger than 60 years were estimated at 27.9% (95%CI: 25.4–30.4%), 8.8% (95%CI: 7.3–10.5%) and 0.4% (95%CI: 0.1–0.9%), respectively. The infection fatality ratio (IFR) ranged from 0.2% (95%CI: 0.0–0.6%) in individuals younger than 60 years to 12.3% (95%CI: 6.9–19.7%) for those aged 80 years or more; the case fatality ratio (CFR) in these two age classes was 0.6% (95%CI: 0.1–2%) and 19.2% (95%CI: 10.9–30.1%), respectively. The median length of stay in hospital was 10 (IQR: 3–21) days; the length of stay in ICU was 11 (IQR: 6–19) days. The obtained estimates provide insights into the epidemiology of COVID-19 and could be instrumental to refine mathematical modeling work supporting public health decisions.},
keywords = {contact tracing data, disease burden, epidemiological parameters, risk outcomes, SARS-CoV-2},
pubstate = {published},
tppubtype = {article}
}
Solid estimates describing the clinical course of SARS-CoV-2 infections are still lacking due to under-ascertainment of asymptomatic and mild-disease cases. In this work, we quantify age-specific probabilities of transitions between stages defining the natural history of SARS-CoV-2 infection from 1965 SARS-CoV-2 positive individuals identified in Italy between March and April 2020 among contacts of confirmed cases. Infected contacts of cases were confirmed via RT-PCR tests as part of contact tracing activities or retrospectively via IgG serological tests and followed-up for symptoms and clinical outcomes. In addition, we provide estimates of time intervals between key events defining the clinical progression of cases as obtained from a larger sample, consisting of 95,371 infections ascertained between February and July 2020. We found that being older than 60 years of age was associated with a 39.9% (95%CI: 36.2–43.6%) likelihood of developing respiratory symptoms or fever ≥ 37.5 °C after SARS-CoV-2 infection; the 22.3% (95%CI: 19.3–25.6%) of the infections in this age group required hospital care and the 1% (95%CI: 0.4–2.1%) were admitted to an intensive care unit (ICU). The corresponding proportions in individuals younger than 60 years were estimated at 27.9% (95%CI: 25.4–30.4%), 8.8% (95%CI: 7.3–10.5%) and 0.4% (95%CI: 0.1–0.9%), respectively. The infection fatality ratio (IFR) ranged from 0.2% (95%CI: 0.0–0.6%) in individuals younger than 60 years to 12.3% (95%CI: 6.9–19.7%) for those aged 80 years or more; the case fatality ratio (CFR) in these two age classes was 0.6% (95%CI: 0.1–2%) and 19.2% (95%CI: 10.9–30.1%), respectively. The median length of stay in hospital was 10 (IQR: 3–21) days; the length of stay in ICU was 11 (IQR: 6–19) days. The obtained estimates provide insights into the epidemiology of COVID-19 and could be instrumental to refine mathematical modeling work supporting public health decisions.
100.
Marini, Giovanni; Pugliese, Andrea; Wint, William; Alexander, Neil S.; Rizzoli, Annapaola; Rosà, Roberto
Modelling the West Nile virus force of infection in the European human population Journal Article
In: One Health, vol. 15, pp. 100462, 2022, ISSN: 2352-7714.
Abstract | Links | BibTeX | Tags: Mathematical model, mosquitoes, Public Health, Vector-borne disease
@article{@article{MARINI2022100462,
title = {Modelling the West Nile virus force of infection in the European human population},
author = {Giovanni Marini and Andrea Pugliese and William Wint and Neil S. Alexander and Annapaola Rizzoli and Roberto Rosà},
url = {https://www.sciencedirect.com/science/article/pii/S2352771422000945},
doi = {https://doi.org/10.1016/j.onehlt.2022.100462},
issn = {2352-7714},
year = {2022},
date = {2022-12-01},
journal = {One Health},
volume = {15},
pages = {100462},
abstract = {West Nile virus (WNV) is among the most recent emerging mosquito-borne pathogens in Europe where each year hundreds of human cases are recorded. We developed a relatively simple technique to model the WNV force of infection (FOI) in the human population to assess its dependence on environmental and human demographic factors. To this aim, we collated WNV human case-based data reported to the European Surveillance System from 15 European Countries during the period 2010–2021. We modelled the regional WNV FOI for each year through normal distributions and calibrated the constituent parameters, namely average (peak timing), variance and overall intensity, to observed cases. Finally, we investigated through regression models how these parameters are associated to a set of climatic, environmental and human demographic covariates. Our modelling approach shows good agreement between expected and observed epidemiological curves. We found that FOI magnitude is positively associated with spring temperature and larger in more anthropogenic semi-natural areas, while FOI peak timing is negatively related to summer temperature. Unsurprisingly, FOI is estimated to be greater in regions with a larger fraction of elderly people, who are more likely to contract severe infections. Our results confirm that temperature plays a key role in shaping WNV transmission in Europe and provide some interesting hints on how human presence and demography might affect WNV burden. This simple yet reliable approach could be easily adopted for early warning and to address epidemiological investigations of other vector-borne diseases, especially where eco-epidemiological data are scarce.},
keywords = {Mathematical model, mosquitoes, Public Health, Vector-borne disease},
pubstate = {published},
tppubtype = {article}
}
West Nile virus (WNV) is among the most recent emerging mosquito-borne pathogens in Europe where each year hundreds of human cases are recorded. We developed a relatively simple technique to model the WNV force of infection (FOI) in the human population to assess its dependence on environmental and human demographic factors. To this aim, we collated WNV human case-based data reported to the European Surveillance System from 15 European Countries during the period 2010–2021. We modelled the regional WNV FOI for each year through normal distributions and calibrated the constituent parameters, namely average (peak timing), variance and overall intensity, to observed cases. Finally, we investigated through regression models how these parameters are associated to a set of climatic, environmental and human demographic covariates. Our modelling approach shows good agreement between expected and observed epidemiological curves. We found that FOI magnitude is positively associated with spring temperature and larger in more anthropogenic semi-natural areas, while FOI peak timing is negatively related to summer temperature. Unsurprisingly, FOI is estimated to be greater in regions with a larger fraction of elderly people, who are more likely to contract severe infections. Our results confirm that temperature plays a key role in shaping WNV transmission in Europe and provide some interesting hints on how human presence and demography might affect WNV burden. This simple yet reliable approach could be easily adopted for early warning and to address epidemiological investigations of other vector-borne diseases, especially where eco-epidemiological data are scarce.
99.
Claudel, Iris; Brouazin, Ronan; Lancelot, Renaud; Gouagna, Louis-Clément; Dupraz, Marlène; Baldet, Thierry; Bouyer, Jérémy
Optimization of adult mosquito trap settings to monitor populations of Aedes and Culex mosquitoes, vectors of arboviruses in La Reunion Journal Article
In: Nature Communications, iss. 12, no. 19544, 2022.
Abstract | Links | BibTeX | Tags: Ecological epidemiology, Entomology
@article{nokey,
title = {Optimization of adult mosquito trap settings to monitor populations of Aedes and Culex mosquitoes, vectors of arboviruses in La Reunion},
author = { Iris Claudel and Ronan Brouazin and Renaud Lancelot and Louis-Clément Gouagna and Marlène Dupraz and Thierry Baldet and Jérémy Bouyer},
url = {https://www.nature.com/articles/s41598-022-24191-9},
doi = {10.1038/s41598-022-24191-9},
year = {2022},
date = {2022-11-15},
urldate = {2022-11-15},
journal = {Nature Communications},
number = {19544},
issue = {12},
abstract = {Competent arbovirus vectors are found in the culicid mosquito fauna of south-west Indian Ocean (SWIO) islands. In La Reunion, Aedes albopictus and Aedes aegypti mosquitoes are known vectors of dengue and chikungunya viruses. Culex quinquefasciatus is a potential vector of Rift Valley fever and West Nile viruses. To prepare a vector-control field trial against Ae. aegypti, this study aimed at identifying the best trapping strategy to catch adult Ae. aegypti, using BG-Sentinel traps (Biogents, Germany). It was implemented in two sites in southern La Reunion. Catches of Ae. albopictus and Cx. quinquefasciatus mosquitoes were also recorded. A Latin square design was used to estimate the detection probability and the apparent daily density—according to the BG-Sentinel trapping strategy: none, carbon dioxide (CO2), a commercial attractant—BG-Lure (Biogents, Germany), or both. The use of CO2 alone was associated with a higher detection probability for Ae. aegypti and Cx. quinquefasciatus mosquitoes, as well as a large increase in their apparent density. Traps with BG-Lure—alone or in combination with CO2, did not improve the detection probability of Ae. aegypti and Cx. quinquefasciatus mosquitoes. The same result was found for male Ae. albopictus. For females, baiting BG-Sentinel traps with CO2 or BG-Lure had no significant effect. The same apparent densities were found for Ae. aegypti and Ae. albopictus mosquitoes in both study sites—where Ae. aegypti mosquitoes were found at very low densities during previous surveys.},
keywords = {Ecological epidemiology, Entomology},
pubstate = {published},
tppubtype = {article}
}
Competent arbovirus vectors are found in the culicid mosquito fauna of south-west Indian Ocean (SWIO) islands. In La Reunion, Aedes albopictus and Aedes aegypti mosquitoes are known vectors of dengue and chikungunya viruses. Culex quinquefasciatus is a potential vector of Rift Valley fever and West Nile viruses. To prepare a vector-control field trial against Ae. aegypti, this study aimed at identifying the best trapping strategy to catch adult Ae. aegypti, using BG-Sentinel traps (Biogents, Germany). It was implemented in two sites in southern La Reunion. Catches of Ae. albopictus and Cx. quinquefasciatus mosquitoes were also recorded. A Latin square design was used to estimate the detection probability and the apparent daily density—according to the BG-Sentinel trapping strategy: none, carbon dioxide (CO2), a commercial attractant—BG-Lure (Biogents, Germany), or both. The use of CO2 alone was associated with a higher detection probability for Ae. aegypti and Cx. quinquefasciatus mosquitoes, as well as a large increase in their apparent density. Traps with BG-Lure—alone or in combination with CO2, did not improve the detection probability of Ae. aegypti and Cx. quinquefasciatus mosquitoes. The same result was found for male Ae. albopictus. For females, baiting BG-Sentinel traps with CO2 or BG-Lure had no significant effect. The same apparent densities were found for Ae. aegypti and Ae. albopictus mosquitoes in both study sites—where Ae. aegypti mosquitoes were found at very low densities during previous surveys.
98.
Brouazin, Ronan; Claudel, Iris; Lancelot, Renaud; Dupuy, Guillaume; Gouagna, Louis-Clément; Dupraz, Marlène; Baldet, Theirry; Bouyer, Jérémy
Optimization of oviposition trap settings to monitor populations of Aedes mosquitoes, vectors of arboviruses in La Reunion Journal Article
In: Nature Communications, iss. Sci Rep 12, no. 18450, 2022.
Abstract | Links | BibTeX | Tags: Animal behaviour, Ecology, Entomology, epidemiology
@article{nokey,
title = {Optimization of oviposition trap settings to monitor populations of Aedes mosquitoes, vectors of arboviruses in La Reunion},
author = {Ronan Brouazin and Iris Claudel and Renaud Lancelot and Guillaume Dupuy and Louis-Clément Gouagna and Marlène Dupraz and Theirry Baldet and Jérémy Bouyer},
url = {https://www.nature.com/articles/s41598-022-23137-5#citeas},
doi = {10.1038/s41598-022-23137-5},
year = {2022},
date = {2022-11-02},
urldate = {2022-11-02},
journal = {Nature Communications},
number = {18450},
issue = {Sci Rep 12},
abstract = {Several dengue epidemics recently occurred in La Reunion, an island harboring two dengue viruses (DVs) vectors: Aedes albopictus, and Ae. aegypti, the former being the main local DV vector. Aedes aegypti shows a peculiar ecology, compared to other tropical populations of the same species. This study aimed to provide researchers and public-health users with locally validated oviposition traps (ovitraps) to monitor Aedes populations. A field experiment was performed in Saint-Joseph to assess the effect of different settings on the detection probability and apparent density of Aedes mosquitoes. Black plastic ovitraps were identified as the best choice. Vacoa trees (Pandanus utilis) were the only observed breeding sites for Ae. aegypti, shared with Ae. albopictus. They were the experimental units in a Latin square design with three factors: trap position in the trees (ground vs canopy), oviposition surface in the trap (blotting paper vs. vacoa leaf), and addition of organic matter to the trap water. The latter factor was found unimportant. On the ground, Ae. aegypti eggs were only found with vacoa leaves as the oviposition surface. Their detection and apparent density increased when ovitraps were located in the tree canopy. The main factor for Ae. albopictus was the oviposition surface, with a preference for blotting paper. In all trap settings, their detection was close to 100%. Larval survival was lower for a high egg density, combined with blotting paper as the oviposition surface. When monitoring mixed Aedes populations in La Reunion, we recommend using black plastic ovitraps, placed at 1.50-to-2.00-m high in vacoa trees, with vacoa leaves as the oviposition surface.},
keywords = {Animal behaviour, Ecology, Entomology, epidemiology},
pubstate = {published},
tppubtype = {article}
}
Several dengue epidemics recently occurred in La Reunion, an island harboring two dengue viruses (DVs) vectors: Aedes albopictus, and Ae. aegypti, the former being the main local DV vector. Aedes aegypti shows a peculiar ecology, compared to other tropical populations of the same species. This study aimed to provide researchers and public-health users with locally validated oviposition traps (ovitraps) to monitor Aedes populations. A field experiment was performed in Saint-Joseph to assess the effect of different settings on the detection probability and apparent density of Aedes mosquitoes. Black plastic ovitraps were identified as the best choice. Vacoa trees (Pandanus utilis) were the only observed breeding sites for Ae. aegypti, shared with Ae. albopictus. They were the experimental units in a Latin square design with three factors: trap position in the trees (ground vs canopy), oviposition surface in the trap (blotting paper vs. vacoa leaf), and addition of organic matter to the trap water. The latter factor was found unimportant. On the ground, Ae. aegypti eggs were only found with vacoa leaves as the oviposition surface. Their detection and apparent density increased when ovitraps were located in the tree canopy. The main factor for Ae. albopictus was the oviposition surface, with a preference for blotting paper. In all trap settings, their detection was close to 100%. Larval survival was lower for a high egg density, combined with blotting paper as the oviposition surface. When monitoring mixed Aedes populations in La Reunion, we recommend using black plastic ovitraps, placed at 1.50-to-2.00-m high in vacoa trees, with vacoa leaves as the oviposition surface.
97.
Monteiro, Joao; Martins, Bruno; Costa, Miguel; Pires, Joao
A Co-Training Approach for Spatial Data Disaggregation Book
Association for Computing Machinery, New York, NY, USA, 2022, ISBN: 9781450395298.
Abstract | Links | BibTeX | Tags: co-training, convolutional neural networks, dasymetric disaggregation, deep learning, encoder-decoder neural networks, geospatial data disaggregation, self-supervised learning
@book{nokey,
title = {A Co-Training Approach for Spatial Data Disaggregation},
author = {Monteiro, Joao and Martins, Bruno and Costa, Miguel and Pires, Joao},
url = {https://doi.org/10.1145/3557915.3561475},
doi = {10.1145/3557915.3561475},
isbn = {9781450395298},
year = {2022},
date = {2022-11-01},
number = {91},
pages = {1-10},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
series = {SIGSPATIAL '22},
abstract = {Socio-demographic information is usually only accessible at relatively coarse spatial resolutions. However, its availability at thinner granularities is of substantial interest for several stakeholders, since it enhances the formulation of informed hypotheses on the distribution of population indicators. Spatial disaggregation methods aim to compute these fine-grained estimates, often using regression algorithms that employ ancillary data to re-distribute the aggregated information. However, since disaggregation tasks are ill-posed, and given that examples of disaggregated data at the target geospatial resolution are seldom available, model training is particularly challenging. We propose to address this problem through a self-supervision framework that iteratively refines initial estimates from seminal disaggregation heuristics. Specifically, we propose to co-train two different models, using the results from one model to train/refine the other. By doing so, we are able to explore complementary views from the data. We assessed the use of co-training with a fast regressor based on random forests that takes individual raster cells as input, together with a more expressive model, based on a fully-convolutional neural network, that takes raster patches as input. We also compared co-training against the use of self-training with a single model. In experiments involving the disaggregation of a socio-demographic variable collected for Continental Portugal, the results show that our co-training approach outperforms alternative disaggregation approaches, including methods based on self-training or co-training with two similar fully-convolutional models. Co-training is effective at exploring the characteristics of both regression algorithms, leading to a consistent improvement in different types of error metrics.},
keywords = {co-training, convolutional neural networks, dasymetric disaggregation, deep learning, encoder-decoder neural networks, geospatial data disaggregation, self-supervised learning},
pubstate = {published},
tppubtype = {book}
}
Socio-demographic information is usually only accessible at relatively coarse spatial resolutions. However, its availability at thinner granularities is of substantial interest for several stakeholders, since it enhances the formulation of informed hypotheses on the distribution of population indicators. Spatial disaggregation methods aim to compute these fine-grained estimates, often using regression algorithms that employ ancillary data to re-distribute the aggregated information. However, since disaggregation tasks are ill-posed, and given that examples of disaggregated data at the target geospatial resolution are seldom available, model training is particularly challenging. We propose to address this problem through a self-supervision framework that iteratively refines initial estimates from seminal disaggregation heuristics. Specifically, we propose to co-train two different models, using the results from one model to train/refine the other. By doing so, we are able to explore complementary views from the data. We assessed the use of co-training with a fast regressor based on random forests that takes individual raster cells as input, together with a more expressive model, based on a fully-convolutional neural network, that takes raster patches as input. We also compared co-training against the use of self-training with a single model. In experiments involving the disaggregation of a socio-demographic variable collected for Continental Portugal, the results show that our co-training approach outperforms alternative disaggregation approaches, including methods based on self-training or co-training with two similar fully-convolutional models. Co-training is effective at exploring the characteristics of both regression algorithms, leading to a consistent improvement in different types of error metrics.
96.
Cuypers, Lize; Dellicour, Simon; Hong, Samuel L.; Potter, Barney I.; Verhasselt, Bruno; Vereecke, Nick; Lambrechts, Laurens; Durkin, Keith; Bours, Vincent; Klamer, Sofieke; Bayon-Vicente, Guillaume; Vael, Carl; Ariën, Kevin K.; De Mendonca, Ricardo; Soetens, Oriane; Michel, Charlotte; Bearzatto, Bertrand; Naesens, Reinout; Gras, Jeremie; Vankeerberghen, Anne; Matheeussen, Veerle; Martens, Geert; Obbels, Dagmar; Lemmens, Ann; Van den Poel, Bea; Van Even, Ellen; De Rauw, Klara; Waumans, Luc; Reynders, Marijke; Degosserie, Jonathan; Maes, Piet; André, Emmanuel; Baele, Guy
In: Viruses, vol. 14, no. 10, pp. 2301, 2022, ISSN: 1999-4915.
Abstract | Links | BibTeX | Tags: Belgium, COVID-19, genomic surveillance, next-generation sequencing, SARS-CoV-2, variants of concern
@article{@article{2022b,
title = {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},
author = {Cuypers, Lize and Dellicour, Simon and Hong, Samuel L. and Potter, Barney I. and Verhasselt, Bruno and Vereecke, Nick and Lambrechts, Laurens and Durkin, Keith and Bours, Vincent and Klamer, Sofieke and Bayon-Vicente, Guillaume and Vael, Carl and Ariën, Kevin K. and De Mendonca, Ricardo and Soetens, Oriane and Michel, Charlotte and Bearzatto, Bertrand and Naesens, Reinout and Gras, Jeremie and Vankeerberghen, Anne and Matheeussen, Veerle and Martens, Geert and Obbels, Dagmar and Lemmens, Ann and Van den Poel, Bea and Van Even, Ellen and De Rauw, Klara and Waumans, Luc and Reynders, Marijke and Degosserie, Jonathan and Maes, Piet and André, Emmanuel and Baele, Guy},
url = {https://www.mdpi.com/1999-4915/14/10/2301},
doi = {https://doi.org/10.3390/v14102301},
issn = {1999-4915},
year = {2022},
date = {2022-10-20},
urldate = {2022-10-20},
journal = {Viruses},
volume = {14},
number = {10},
pages = {2301},
abstract = {An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, genomic surveillance in Belgium was not structurally implemented but performed by individual research laboratories that had to acquire the necessary funds themselves to perform this important task. At the start of 2021, a nationwide genomic surveillance consortium was established in Belgium to markedly increase the country’s genomic sequencing efforts (both in terms of intensity and representativeness), to perform quality control among participating laboratories, and to enable coordination and collaboration of research projects and publications. We here discuss the genomic surveillance efforts in Belgium before and after the establishment of its genomic sequencing consortium, provide an overview of the specifics of the consortium, and explore more details regarding the scientific studies that have been published as a result of the increased number of Belgian SARS-CoV-2 genomes that have become available.},
keywords = {Belgium, COVID-19, genomic surveillance, next-generation sequencing, SARS-CoV-2, variants of concern},
pubstate = {published},
tppubtype = {article}
}
An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, genomic surveillance in Belgium was not structurally implemented but performed by individual research laboratories that had to acquire the necessary funds themselves to perform this important task. At the start of 2021, a nationwide genomic surveillance consortium was established in Belgium to markedly increase the country’s genomic sequencing efforts (both in terms of intensity and representativeness), to perform quality control among participating laboratories, and to enable coordination and collaboration of research projects and publications. We here discuss the genomic surveillance efforts in Belgium before and after the establishment of its genomic sequencing consortium, provide an overview of the specifics of the consortium, and explore more details regarding the scientific studies that have been published as a result of the increased number of Belgian SARS-CoV-2 genomes that have become available.
95.
Liana E. Kafetzopoulou Raphaëlle Klitting, Wim Thiery
Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades Journal Article
In: Nature Communications, vol. 13, no. 5596, 2022.
Abstract | Links | BibTeX | Tags: Ecological modelling, phylogenetics, Viral genetics
@article{nokey,
title = {Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades},
author = {Raphaëlle Klitting, Liana E. Kafetzopoulou, Wim Thiery, Gytis Dudas, Sophie Gryseels, Anjali Kotamarthi, Bram Vrancken, Karthik Gangavarapu, Mambu Momoh, John Demby Sandi, Augustine Goba, Foday Alhasan, Donald S. Grant, Sylvanus Okogbenin, Ephraim Ogbaini-Emovo, Robert F. Garry, Allison R. Smither, Mark Zeller, Matthias G. Pauthner, Michelle McGraw, Laura D. Hughes, Sophie Duraffour, Stephan Günther, Marc A. Suchard, Philippe Lemey, Kristian G. Andersen, Simon Dellicour},
url = {https://www.nature.com/articles/s41467-022-33112-3#citeas},
doi = {https://doi.org/10.1038/s41467-022-33112-3},
year = {2022},
date = {2022-09-27},
journal = {Nature Communications},
volume = {13},
number = {5596},
abstract = {Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence using ecological niche modelling, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. Based on projections of climate, land use, and population changes, we find that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in ecological conditions that are suitable for Lassa virus circulation may drastically increase by 2070. By analysing geotagged viral genomes using spatially-explicit phylogeography and simulating virus dispersal, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades.},
keywords = {Ecological modelling, phylogenetics, Viral genetics},
pubstate = {published},
tppubtype = {article}
}
Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence using ecological niche modelling, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. Based on projections of climate, land use, and population changes, we find that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in ecological conditions that are suitable for Lassa virus circulation may drastically increase by 2070. By analysing geotagged viral genomes using spatially-explicit phylogeography and simulating virus dispersal, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades.
94.
Zeller, Mark; Gangavarapu, Karthik; Anderson, Catelyn; Smither, Allison R.; Vanchiere, John A.; Rose, Rebecca; Snyder, Daniel J.; Dudas, Gytis; Watts, Alexander; Matteson, Nathaniel L.; Robles-Sikisaka, Refugio; Marshall, Maximilian; Feehan, Amy K.; Sabino-Santos, Gilberto; Bell-Kareem, Antoinette R.; Hughes, Laura D.; Alkuzweny, Manar; Snarski, Patricia; Garcia-Diaz, Julia; Scott, Rona S.; Melnik, Lilia I.; Klitting, Raphaëlle; McGraw, Michelle; Belda-Ferre, Pedro; DeHoff, Peter; Sathe, Shashank; Marotz, Clarisse; Grubaugh, Nathan D.; Nolan, David J.; Drouin, Arnaud C.; Genemaras, Kaylynn J.; Chao, Karissa; Topol, Sarah; Spencer, Emily; Nicholson, Laura; Aigner, Stefan; Yeo, Gene W.; Farnaes, Lauge; Hobbs, Charlotte A.; Laurent, Louise C.; Knight, Rob; Hodcroft, Emma B.; Khan, Kamran; Fusco, Dahlene N.; Cooper, Vaughn S.; Lemey, Phillipe; Gardner, Lauren; Lamers, Susanna L.; Kamil, Jeremy P.; Garry, Robert F.; Suchard, Marc A.; Andersen, Kristian G.
Emergence of an early SARS-CoV-2 epidemic in the United States Journal Article
In: Cell, vol. 184, iss. 19, pp. 4939-4952.e15, 2022, ISSN: 0092-8674.
Abstract | Links | BibTeX | Tags: genomic epidemiology, mobility, phylogenetics, SARS-CoV-2, viral emergence, viral sequencing
@article{nokey,
title = {Emergence of an early SARS-CoV-2 epidemic in the United States},
author = {{Mark Zeller and Karthik Gangavarapu and Catelyn Anderson and Allison R. Smither and John A. Vanchiere and Rebecca Rose and Daniel J. Snyder and Gytis Dudas and Alexander Watts and Nathaniel L. Matteson and Refugio Robles-Sikisaka and Maximilian Marshall and Amy K. Feehan and Gilberto Sabino-Santos and Antoinette R. Bell-Kareem and Laura D. Hughes and Manar Alkuzweny and Patricia Snarski and Julia Garcia-Diaz and Rona S. Scott and Lilia I. Melnik and Raphaëlle Klitting and Michelle McGraw and Pedro Belda-Ferre and Peter DeHoff and Shashank Sathe and Clarisse Marotz and Nathan D. Grubaugh and David J. Nolan and Arnaud C. Drouin and Kaylynn J. Genemaras and Karissa Chao and Sarah Topol and Emily Spencer and Laura Nicholson and Stefan Aigner and Gene W. Yeo and Lauge Farnaes and Charlotte A. Hobbs and Louise C. Laurent and Rob Knight and Emma B. Hodcroft and Kamran Khan and Dahlene N. Fusco and Vaughn S. Cooper and Phillipe Lemey and Lauren Gardner and Susanna L. Lamers and Jeremy P. Kamil and Robert F. Garry and Marc A. Suchard and Kristian G. Andersen},
url = {https://www.sciencedirect.com/science/article/pii/S0092867421008898},
doi = {10.1016/j.cell.2021.07.030},
issn = {0092-8674},
year = {2022},
date = {2022-09-16},
journal = {Cell},
volume = {184},
issue = {19},
pages = {4939-4952.e15},
abstract = {The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.},
keywords = {genomic epidemiology, mobility, phylogenetics, SARS-CoV-2, viral emergence, viral sequencing},
pubstate = {published},
tppubtype = {article}
}
The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.
93.
Nahata, Kanika D; Bielejec, Filip; Monetta, Juan; Dellicour, Simon; Rambaut, Andrew; Suchard, Marc A; Baele, Guy; Lemey, Philippe
SPREAD 4: online visualisation of pathogen phylogeographic reconstructions Journal Article
In: Virus Evolution, vol. 8, no. 2, 2022, ISBN: 2057-1577, (veac088).
Abstract | Links | BibTeX | Tags: Bayesian inference, BEAST, phylogeography, viral spread, visualisation
@article{nokey,
title = {SPREAD 4: online visualisation of pathogen phylogeographic reconstructions},
author = {Nahata, Kanika D and Bielejec, Filip and Monetta, Juan and Dellicour, Simon and Rambaut, Andrew and Suchard, Marc A and Baele, Guy and Lemey, Philippe},
url = {https://doi.org/10.1093/ve/veac088},
doi = {10.1093/ve/veac088},
isbn = {2057-1577},
year = {2022},
date = {2022-09-01},
journal = {Virus Evolution},
volume = {8},
number = {2},
abstract = {Phylogeographic analyses aim to extract information about pathogen spread from genomic data, and visualising spatio-temporal reconstructions is a key aspect of this process. Here we present SPREAD 4, a feature-rich web-based application that visualises estimates of pathogen dispersal resulting from Bayesian phylogeographic inference using BEAST on a geographic map, offering zoom-and-filter functionality and smooth animation over time. SPREAD 4 takes as input phylogenies with both discrete and continuous location annotation and offers customised visualisation as well as generation of publication-ready figures. SPREAD 4 now features account-based storage and easy sharing of visualisations by means of unique web addresses. SPREAD 4 is intuitive to use and is available online at https://spreadviz.org, with an accompanying web page containing answers to frequently asked questions at https://beast.community/spread4.},
note = {veac088},
keywords = {Bayesian inference, BEAST, phylogeography, viral spread, visualisation},
pubstate = {published},
tppubtype = {article}
}
Phylogeographic analyses aim to extract information about pathogen spread from genomic data, and visualising spatio-temporal reconstructions is a key aspect of this process. Here we present SPREAD 4, a feature-rich web-based application that visualises estimates of pathogen dispersal resulting from Bayesian phylogeographic inference using BEAST on a geographic map, offering zoom-and-filter functionality and smooth animation over time. SPREAD 4 takes as input phylogenies with both discrete and continuous location annotation and offers customised visualisation as well as generation of publication-ready figures. SPREAD 4 now features account-based storage and easy sharing of visualisations by means of unique web addresses. SPREAD 4 is intuitive to use and is available online at https://spreadviz.org, with an accompanying web page containing answers to frequently asked questions at https://beast.community/spread4.
92.
Suvanto, Maija T; Uusitalo, Ruut; Otte im Kampe, Eveline; Vuorinen, Tytti; Kurkela, Satu; Vapalahti, Olli; Dub, Timothée; Huhtamo, Eili; Korhonen, Essi M
Sindbis virus outbreak and evidence for geographical expansion in Finland, 2021 Journal Article
In: Eurosurveillance, vol. 27, no. 31, 2022.
Abstract | Links | BibTeX | Tags: finland, infectious diseases, Pogosta disease, Sindbis virus
@article{nokey,
title = {Sindbis virus outbreak and evidence for geographical expansion in Finland, 2021},
author = {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},
url = {https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2022.27.31.2200580},
doi = {https://doi.org/10.2807/1560-7917.ES.2022.27.31.2200580},
year = {2022},
date = {2022-08-04},
journal = {Eurosurveillance},
volume = {27},
number = {31},
abstract = {Sindbis virus (SINV) (Togaviridae family, Alphavirus genus) is the causative agent of Pogosta disease, a typically self-limited disease with common symptoms of rash, arthralgia, myalgia and fever [1,2]. In some cases, arthralgia and myalgia can persist from months to years and negatively affect quality of life [2,3]. While circulation of SINV has been reported in mosquitoes and birds globally, symptomatic human infection has almost exclusively been reported in Finland, Sweden, Russia and South Africa [4]. However, larger outbreaks and annual cases are reported only from Finland, where the SINV seroprevalence in the general population was 5.2% in the years 1999 to 2003 [5].
Laboratory diagnosis of Pogosta disease is done using ELISA, and paired samples are often needed because the antibody response against SINV develops slowly [6]. In Finland, SINV has been endemic since the 1960s, and the first epidemic occurred in 1974 [1,7]. A laboratory-confirmed case is defined as either detection of SINV IgM and IgG in a single serum specimen or seroconversion between paired specimens. The laboratory-confirmed cases have been notified to the National Infectious Diseases Register (NIDR) since its implementation in 1995 [8]. A total of 566 laboratory-confirmed cases were notified in 2021, compared with an average of 158 annual cases between 1995 and 2021, making it a notable outbreak year. Similarly, high incidence had previously been reported in 2002 with 597 laboratory-confirmed cases.
The aim of this rapid communication is to increase awareness of an upcoming SINV epidemic in 2022. The high SINV incidence in 2021 may precede a larger epidemic.},
keywords = {finland, infectious diseases, Pogosta disease, Sindbis virus},
pubstate = {published},
tppubtype = {article}
}
Sindbis virus (SINV) (Togaviridae family, Alphavirus genus) is the causative agent of Pogosta disease, a typically self-limited disease with common symptoms of rash, arthralgia, myalgia and fever [1,2]. In some cases, arthralgia and myalgia can persist from months to years and negatively affect quality of life [2,3]. While circulation of SINV has been reported in mosquitoes and birds globally, symptomatic human infection has almost exclusively been reported in Finland, Sweden, Russia and South Africa [4]. However, larger outbreaks and annual cases are reported only from Finland, where the SINV seroprevalence in the general population was 5.2% in the years 1999 to 2003 [5].
Laboratory diagnosis of Pogosta disease is done using ELISA, and paired samples are often needed because the antibody response against SINV develops slowly [6]. In Finland, SINV has been endemic since the 1960s, and the first epidemic occurred in 1974 [1,7]. A laboratory-confirmed case is defined as either detection of SINV IgM and IgG in a single serum specimen or seroconversion between paired specimens. The laboratory-confirmed cases have been notified to the National Infectious Diseases Register (NIDR) since its implementation in 1995 [8]. A total of 566 laboratory-confirmed cases were notified in 2021, compared with an average of 158 annual cases between 1995 and 2021, making it a notable outbreak year. Similarly, high incidence had previously been reported in 2002 with 597 laboratory-confirmed cases.
The aim of this rapid communication is to increase awareness of an upcoming SINV epidemic in 2022. The high SINV incidence in 2021 may precede a larger epidemic.
Laboratory diagnosis of Pogosta disease is done using ELISA, and paired samples are often needed because the antibody response against SINV develops slowly [6]. In Finland, SINV has been endemic since the 1960s, and the first epidemic occurred in 1974 [1,7]. A laboratory-confirmed case is defined as either detection of SINV IgM and IgG in a single serum specimen or seroconversion between paired specimens. The laboratory-confirmed cases have been notified to the National Infectious Diseases Register (NIDR) since its implementation in 1995 [8]. A total of 566 laboratory-confirmed cases were notified in 2021, compared with an average of 158 annual cases between 1995 and 2021, making it a notable outbreak year. Similarly, high incidence had previously been reported in 2002 with 597 laboratory-confirmed cases.
The aim of this rapid communication is to increase awareness of an upcoming SINV epidemic in 2022. The high SINV incidence in 2021 may precede a larger epidemic.
91.
Schaeffer, Camille; Interdonato, Roberto; Lancelot, Renaud; Roche, Mathieu; Teisseire, Maguelonne
Labeled entities from social media data related to avian influenza disease Journal Article Forthcoming
In: Data in Brief, vol. 43, pp. 108317, Forthcoming, ISSN: 2352-3409.
Abstract | Links | BibTeX | Tags: avian influenza, epidemiology, named entity recognition, OpenDataSet, social networks, Text mining
@article{@article{SCHAEFFER2022108317,,
title = {Labeled entities from social media data related to avian influenza disease},
author = {Schaeffer, Camille and Interdonato, Roberto and Lancelot, Renaud and Roche, Mathieu and Teisseire, Maguelonne},
url = {https://www.sciencedirect.com/science/article/pii/S2352340922005194},
doi = {https://doi.org/10.1016/j.dib.2022.108317},
issn = {2352-3409},
year = {2022},
date = {2022-08-01},
urldate = {2022-08-01},
journal = {Data in Brief},
volume = {43},
pages = {108317},
abstract = {This dataset is composed by spatial (e.g. location) and thematic (e.g. diseases, symptoms, virus) entities concerning avian influenza in social media (textual) data in English. It was created from three corpora: the first one includes 10 transcriptions of YouTube videos and 70 tweets manually annotated. The second corpus is composed by the same textual data but automatically annotated with Named Entity Recognition (NER) tools. These two corpora have been built to evaluate NER tools and apply them to a bigger corpus. The third corpus is composed of 100 YouTube transcriptions automatically annotated with NER tools. The aim of the annotation task is to recognize spatial information such as the names of the cities and epidemiological information such as the names of the diseases. An annotation guideline is provided in order to ensure a unified annotation and to help the annotators. This dataset can be used to train or evaluate Natural Language Processing (NLP) approaches such as specialized entity recognition.},
keywords = {avian influenza, epidemiology, named entity recognition, OpenDataSet, social networks, Text mining},
pubstate = {forthcoming},
tppubtype = {article}
}
This dataset is composed by spatial (e.g. location) and thematic (e.g. diseases, symptoms, virus) entities concerning avian influenza in social media (textual) data in English. It was created from three corpora: the first one includes 10 transcriptions of YouTube videos and 70 tweets manually annotated. The second corpus is composed by the same textual data but automatically annotated with Named Entity Recognition (NER) tools. These two corpora have been built to evaluate NER tools and apply them to a bigger corpus. The third corpus is composed of 100 YouTube transcriptions automatically annotated with NER tools. The aim of the annotation task is to recognize spatial information such as the names of the cities and epidemiological information such as the names of the diseases. An annotation guideline is provided in order to ensure a unified annotation and to help the annotators. This dataset can be used to train or evaluate Natural Language Processing (NLP) approaches such as specialized entity recognition.
90.
Arınık, Nejat; Interdonato, Roberto; Roche, Mathieu; Teisseire, Maguelonne.
Inferring the transmission dynamics of Avian Influenza from news and environmental data Conference Forthcoming
NetSci (Network Science Society) , Forthcoming.
BibTeX | Tags:
@conference{nokey,
title = {Inferring the transmission dynamics of Avian Influenza from news and environmental data},
author = {Arınık, Nejat and Interdonato, Roberto and Roche, Mathieu and Teisseire, Maguelonne.},
year = {2022},
date = {2022-07-29},
booktitle = {NetSci (Network Science Society) },
keywords = {},
pubstate = {forthcoming},
tppubtype = {conference}
}
89.
Bernard, Celia; Holzmuller, Philippe; Bah, Madiou Thierno; Bastien, Matthieu; Combes, Benoit; Jori, Ferran; Grosbois, Vladimir; Vial, Laurence
In: Frontiers in Veterinary Science, pp. 973, 2022.
Abstract | Links | BibTeX | Tags: CCHF, France, hyalomma tick vectors, ticks, vector
@article{@article{bernardsystematic,
title = {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},
author = {Bernard, Celia and Holzmuller, Philippe and Bah, Madiou Thierno and Bastien, Matthieu and Combes, Benoit and Jori, Ferran and Grosbois, Vladimir and Vial, Laurence},
url = {https://www.frontiersin.org/articles/10.3389/fvets.2022.932304/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Veterinary_Science&id=932304},
doi = {https://doi.org/10.3389/fvets.2022.932304},
year = {2022},
date = {2022-07-19},
journal = {Frontiers in Veterinary Science},
pages = {973},
abstract = {Crimean–Congo hemorrhagic fever (CCHF) is a viral zoonotic disease resulting in hemorrhagic syndrome in humans. Its causative agent is naturally transmitted by ticks to non-human vertebrate hosts within an enzootic sylvatic cycle. Ticks are considered biological vectors, as well as reservoirs for CCHF virus (CCHFV), as they are able to maintain the virus for several months or even years and to transmit CCHFV to other ticks. Although animals are not symptomatic, some of them can sufficiently replicate the virus, becoming a source of infection for ticks as well as humans through direct contact with contaminated body fluids. The recent emergence of CCHF in Spain indicates that tick–human interaction rates promoting virus transmission are changing and lead to the emergence of CCHF. In other European countries such as France, the presence of one of its main tick vectors and the detection of antibodies targeting CCHFV in animals, at least in Corsica and in the absence of human cases, suggest that CCHFV could be spreading silently. In this review, we study the CCHFV epidemiological cycle as hypothesized in the French local context and select the most likely parameters that may influence virus transmission among tick vectors and non-human vertebrate hosts. For this, a total of 1,035 articles dating from 1957 to 2021 were selected for data extraction. This study made it possible to identify the tick species that seem to be the best candidate vectors of CCHFV in France, but also to highlight the importance of the abundance and composition of local host communities on vectors' infection prevalence. Regarding the presumed transmission cycle involving Hyalomma marginatum, as it might exist in France, at least in Corsica, it is assumed that tick vectors are still weakly infected and the probability of disease emergence in humans remains low. The likelihood of factors that may modify this equilibrium is discussed.},
keywords = {CCHF, France, hyalomma tick vectors, ticks, vector},
pubstate = {published},
tppubtype = {article}
}
Crimean–Congo hemorrhagic fever (CCHF) is a viral zoonotic disease resulting in hemorrhagic syndrome in humans. Its causative agent is naturally transmitted by ticks to non-human vertebrate hosts within an enzootic sylvatic cycle. Ticks are considered biological vectors, as well as reservoirs for CCHF virus (CCHFV), as they are able to maintain the virus for several months or even years and to transmit CCHFV to other ticks. Although animals are not symptomatic, some of them can sufficiently replicate the virus, becoming a source of infection for ticks as well as humans through direct contact with contaminated body fluids. The recent emergence of CCHF in Spain indicates that tick–human interaction rates promoting virus transmission are changing and lead to the emergence of CCHF. In other European countries such as France, the presence of one of its main tick vectors and the detection of antibodies targeting CCHFV in animals, at least in Corsica and in the absence of human cases, suggest that CCHFV could be spreading silently. In this review, we study the CCHFV epidemiological cycle as hypothesized in the French local context and select the most likely parameters that may influence virus transmission among tick vectors and non-human vertebrate hosts. For this, a total of 1,035 articles dating from 1957 to 2021 were selected for data extraction. This study made it possible to identify the tick species that seem to be the best candidate vectors of CCHFV in France, but also to highlight the importance of the abundance and composition of local host communities on vectors' infection prevalence. Regarding the presumed transmission cycle involving Hyalomma marginatum, as it might exist in France, at least in Corsica, it is assumed that tick vectors are still weakly infected and the probability of disease emergence in humans remains low. The likelihood of factors that may modify this equilibrium is discussed.