Antimicrobial resistance (AMR) is one of the major challenges of the century and should be addres... more Antimicrobial resistance (AMR) is one of the major challenges of the century and should be addressed with a One Health approach. This study aimed to develop a tool that can provide a better understanding of AMR patterns and improve management practices in swine production systems to reduce its spread between farms. We generated similarity networks based on the phenotypic AMR pattern for each farm with information on important bacterial pathogens for swine farming based on the Euclidean distance. We included seven pathogens: Actinobacillus suis, Bordetella bronchiseptica, Escherichia coli, Glaesserella parasuis, Pasteurella multocida, Salmonella spp., and Streptococcus suis; and up to seventeen antibiotics from ten classes. A threshold criterion was developed to reduce the density of the networks and generate communities based on their AMR profiles. A total of 479 farms were included in the study although not all bacteria information was available on each farm. We observed significan...
The American Journal of Tropical Medicine and Hygiene
ABSTRACTVector-borne disease risk assessment is crucial to optimize surveillance, preventative me... more ABSTRACTVector-borne disease risk assessment is crucial to optimize surveillance, preventative measures (vector control), and resource allocation (medical supplies). High arthropod abundance and host interaction strongly correlate to vector-borne pathogen transmission. Increasing host density and movement increases the possibility of local and long-distance pathogen transmission. Therefore, we developed a risk-assessment framework using climate (average temperature and rainfall) and host demographic (host density and movement) data, particularly suitable for regions with unreported or underreported incidence data. This framework consisted of a spatiotemporal network-based approach coupled with a compartmental disease model and nonhomogeneous Gillespie algorithm. The correlation of climate data with vector abundance and host–vector interactions is expressed as vectorial capacity—a parameter that governs the spreading of infection from an infected host to a susceptible one via vectors...
As a highly contagious livestock disease, foot-and-mouth disease poses a great threat to the beef... more As a highly contagious livestock disease, foot-and-mouth disease poses a great threat to the beef-cattle industry. Direct animal movement is always considered as a major route for between-farm transmission of FMD virus. Sharing contaminated equipment and vehicles have also attracted increasing interests as an indirect but considerable route for FMD virus transmission. With the rapid development of communication technologies, information-sharing techniques have been used to control epidemics. In this paper, we built a farm-level time-series three-layer network to simulate the between-farm FMD virus transmission in southwest Kansas by cattle movements (direct-contact layer) and truck visits (indirect-contact layer) and evaluate the impact of information-sharing techniques (information-sharing layer) on mitigating the epidemic. Here, the information-sharing network is defined as the structure that enables the quarantine of farms that are connected with a link to an infected farm. When ...
After one pandemic year of remote or hybrid instructional modes, universities struggled with plan... more After one pandemic year of remote or hybrid instructional modes, universities struggled with plans for an in-person autumn (fall) semester in 2021. To help inform university reopening policies, we collected survey data on social contact patterns and developed an agent-based model to simulate the spread of severe acute respiratory syndrome coronavirus 2 in university settings. Considering a reproduction number ofR0= 3 and 70% immunization effectiveness, we estimated that at least 80% of the university population immunized through natural infection or vaccination is needed for safe university reopening with relaxed non-pharmaceutical interventions (NPIs). By contrast, at least 60% of the university population immunized through natural infection or vaccination is needed for safe university reopening when NPIs are adopted. Nevertheless, attention needs to be paid to large-gathering events that could lead to infection size spikes. At an immunization coverage of 70%, continuing NPIs, such...
ABSTRACTCurrently, several western countries have more than half of their population fully vaccin... more ABSTRACTCurrently, several western countries have more than half of their population fully vaccinated against COVID-19. At the same time, some of them are experiencing a fourth or even a fifth wave of cases, most of them concentrated in sectors of the populations whose vaccination coverage is lower than the average. So, the initial scenario of vaccine prioritization has given way to a new one where achieving herd immunity is the primary concern. Using an age-structured vaccination model with waning immunity, we show that, under a limited supply of vaccines, a vaccination strategy based on minimizing the basic reproduction number allows for the deployment of a number of vaccine doses lower than the one required for maximizing the vaccination coverage. Such minimization is achieved by giving greater protection to those age groups that, for a given social contact pattern, have smaller fractions of susceptible individuals at the endemic equilibrium without vaccination, that is, to those...
After one pandemic year of remote or hybrid instructional modes, universities in the United State... more After one pandemic year of remote or hybrid instructional modes, universities in the United States are now planning for an in-person fall semester in 2021. However, it is uncertain what the vaccination rate will look like after students, faculty, and staff return to campus. To help inform university-reopening policies, we collected survey data on social contact patterns and developed an agent-based model to simulate the spread of COVID-19 in university settings. In this paper, we aim to identify the immunity threshold that, if exceeded, would lead to a relatively safe on-campus experience for the university population. With relaxed non-pharmaceutical interventions, we estimated that immunity in at least 60% of the university population is needed for safe university reopening. Still, attention needs to be paid to extreme events that could lead to huge infection size spikes. At an immune level of 60%, continuing non-pharmaceutical interventions, such as wearing masks, could lead to an...
Contact tracing can play a vital role in controlling human-to-human transmission of a highly cont... more Contact tracing can play a vital role in controlling human-to-human transmission of a highly contagious disease such as COVID-19. To investigate the benefits and costs of contact tracing, we develop an individual-based contact-network model and a susceptible-exposed-infected-confirmed (SEIC) epidemic model for the stochastic simulations of COVID-19 transmission. We estimate the unknown parameters (reproductive ratio R0 and confirmed rate δ2) by using observed confirmed case data. After a two month-lockdown, states in the USA have started the reopening process. We investigate for four different reopening situations: under “stay-at-home” order or no reopening, 25 % reopening, 50 % reopening, and 75 % reopening. We model contact tracing in a two-layer network by modifying the basic SEIC epidemic model. The two-layer network is composed by the contact network in the first layer and the tracing network in the second layer. Since the full contact list of an infected individual patient can...
Sexually transmitted diseases (STD) modeling has used contact networks to study the spreading of ... more Sexually transmitted diseases (STD) modeling has used contact networks to study the spreading of pathogens. Recent findings have stressed the increasing role of casual partners, often enabled by online dating applications. We study the Susceptible-Infected-Susceptible (SIS) epidemic model –appropriate for STDs– over a two-layer network aimed to account for the effect of casual partners in the spreading of STDs. In this novel model, individuals have a set of steady partnerships (links in layer 1). At certain rates, every individual can switch between active and inactive states and, while active, it establishes casual partnerships with some probability with active neighbors in layer 2 (whose links can be thought as potential casual partnerships). Individuals that are not engaged in casual partnerships are classified as inactive, and the transitions between active and inactive states are independent of their infectious state. We use mean-field equations as well as stochastic simulation...
ABSTRACTThe recent outbreaks of the insect-vectored Zika virus have demonstrated its potential to... more ABSTRACTThe recent outbreaks of the insect-vectored Zika virus have demonstrated its potential to be sexually transmitted, which complicates modeling and our understanding of disease dynamics. Autochthonous outbreaks in the US mainland may be a consequence of both modes of transmission, which affect the outbreak size, duration, and virus persistence. We propose a novel individual-based interconnected network model that incorporates both insect-vectored and sexual transmission of this pathogen. This model interconnects a homogeneous mosquito vector population with a heterogeneous human host contact network. The model incorporates the seasonal variation of mosquito abundance and characterizes host dynamics based on age group and gender in order to produce realistic projections. We use a sexual contact network which is generated on the basis of real world sexual behavior data. Our findings suggest that for a high relative transmissibility of asymptomatic hosts, Zika virus shows a high ...
ABSTRACTSwine movement networks among farms/operations are an important source of information to ... more ABSTRACTSwine movement networks among farms/operations are an important source of information to understand and prevent the spread of diseases, nearly nonexistent in the United States. An understanding of the movement networks can help the policymakers in planning effective disease control measures. The objectives of this work are: 1) estimate swine movement probabilities at the county level from comprehensive anonymous inventory and sales data published by the United States Department of Agriculture - National Agriculture Statistics Service database, 2) develop a network based on those estimated probabilities, and 3) analyze that network using network science metrics. First, we use a probabilistic approach based on the maximum entropy method to estimate the movement probabilities among different swine populations. Then, we create a swine movement network using the estimated probabilities for the counties of the central agricultural district of Iowa. The analysis of this network has...
Ecological history may be an important driver of epidemics and disease emergence. We evaluated th... more Ecological history may be an important driver of epidemics and disease emergence. We evaluated the role of history and two related concepts, the evolution of epidemics and the burn-in period required for fitting a model to epidemic observations, for the U.S. soybean rust epidemic (caused by Phakopsora pachyrhizi). This disease allows evaluation of replicate epidemics because the pathogen reinvades the United States each year. We used a new maximum likelihood estimation approach for fitting the network model based on observed U.S. epidemics. We evaluated the model burn-in period by comparing model fit based on each combination of other years of observation. When the miss error rates were weighted by 0.9 and false alarm error rates by 0.1, the mean error rate did decline, for most years, as more years were used to construct models. Models based on observations in years closer in time to the season being estimated gave lower miss error rates for later epidemic years. The weighted mean ...
— In this paper, the steps taken towards setup and configuration of the DiffServ testbed in our l... more — In this paper, the steps taken towards setup and configuration of the DiffServ testbed in our laboratory are listed. A topology is suggested and some simple experimental results for setup validation are presented. A DiffServ domain is deployed and several experiments are run. We obtained acceptable performance for a DiffServ Expedited Forwarding Per Hop Behavior in our testbed using Committed Access
Gene co-expression networks can be used to determine gene regulation and attribute gene function ... more Gene co-expression networks can be used to determine gene regulation and attribute gene function to biological processes. Different high throughput technologies, including one and two-channel microarrays and RNA-sequencing, allow evaluating thousands of gene expression data simultaneously, but these methodologies provide results that cannot be directly compared. Thus, it is complex to analyze coexpression relations between genes, especially when there are missing values arising for experimental reasons. Networks are a helpful tool for studying gene co-expression, where nodes represent genes and edges represent co-expression of pairs of genes. In this paper, we propose a method for constructing a gene co-expression network for the Anopheles gambiae transcriptome from 257 unique studies obtained with different methodologies and experimental designs. We introduce the sliding threshold approach to select node pairs with high Pearson correlation coefficients. The robustness of the method...
Antimicrobial resistance (AMR) is one of the major challenges of the century and should be addres... more Antimicrobial resistance (AMR) is one of the major challenges of the century and should be addressed with a One Health approach. This study aimed to develop a tool that can provide a better understanding of AMR patterns and improve management practices in swine production systems to reduce its spread between farms. We generated similarity networks based on the phenotypic AMR pattern for each farm with information on important bacterial pathogens for swine farming based on the Euclidean distance. We included seven pathogens: Actinobacillus suis, Bordetella bronchiseptica, Escherichia coli, Glaesserella parasuis, Pasteurella multocida, Salmonella spp., and Streptococcus suis; and up to seventeen antibiotics from ten classes. A threshold criterion was developed to reduce the density of the networks and generate communities based on their AMR profiles. A total of 479 farms were included in the study although not all bacteria information was available on each farm. We observed significan...
The American Journal of Tropical Medicine and Hygiene
ABSTRACTVector-borne disease risk assessment is crucial to optimize surveillance, preventative me... more ABSTRACTVector-borne disease risk assessment is crucial to optimize surveillance, preventative measures (vector control), and resource allocation (medical supplies). High arthropod abundance and host interaction strongly correlate to vector-borne pathogen transmission. Increasing host density and movement increases the possibility of local and long-distance pathogen transmission. Therefore, we developed a risk-assessment framework using climate (average temperature and rainfall) and host demographic (host density and movement) data, particularly suitable for regions with unreported or underreported incidence data. This framework consisted of a spatiotemporal network-based approach coupled with a compartmental disease model and nonhomogeneous Gillespie algorithm. The correlation of climate data with vector abundance and host–vector interactions is expressed as vectorial capacity—a parameter that governs the spreading of infection from an infected host to a susceptible one via vectors...
As a highly contagious livestock disease, foot-and-mouth disease poses a great threat to the beef... more As a highly contagious livestock disease, foot-and-mouth disease poses a great threat to the beef-cattle industry. Direct animal movement is always considered as a major route for between-farm transmission of FMD virus. Sharing contaminated equipment and vehicles have also attracted increasing interests as an indirect but considerable route for FMD virus transmission. With the rapid development of communication technologies, information-sharing techniques have been used to control epidemics. In this paper, we built a farm-level time-series three-layer network to simulate the between-farm FMD virus transmission in southwest Kansas by cattle movements (direct-contact layer) and truck visits (indirect-contact layer) and evaluate the impact of information-sharing techniques (information-sharing layer) on mitigating the epidemic. Here, the information-sharing network is defined as the structure that enables the quarantine of farms that are connected with a link to an infected farm. When ...
After one pandemic year of remote or hybrid instructional modes, universities struggled with plan... more After one pandemic year of remote or hybrid instructional modes, universities struggled with plans for an in-person autumn (fall) semester in 2021. To help inform university reopening policies, we collected survey data on social contact patterns and developed an agent-based model to simulate the spread of severe acute respiratory syndrome coronavirus 2 in university settings. Considering a reproduction number ofR0= 3 and 70% immunization effectiveness, we estimated that at least 80% of the university population immunized through natural infection or vaccination is needed for safe university reopening with relaxed non-pharmaceutical interventions (NPIs). By contrast, at least 60% of the university population immunized through natural infection or vaccination is needed for safe university reopening when NPIs are adopted. Nevertheless, attention needs to be paid to large-gathering events that could lead to infection size spikes. At an immunization coverage of 70%, continuing NPIs, such...
ABSTRACTCurrently, several western countries have more than half of their population fully vaccin... more ABSTRACTCurrently, several western countries have more than half of their population fully vaccinated against COVID-19. At the same time, some of them are experiencing a fourth or even a fifth wave of cases, most of them concentrated in sectors of the populations whose vaccination coverage is lower than the average. So, the initial scenario of vaccine prioritization has given way to a new one where achieving herd immunity is the primary concern. Using an age-structured vaccination model with waning immunity, we show that, under a limited supply of vaccines, a vaccination strategy based on minimizing the basic reproduction number allows for the deployment of a number of vaccine doses lower than the one required for maximizing the vaccination coverage. Such minimization is achieved by giving greater protection to those age groups that, for a given social contact pattern, have smaller fractions of susceptible individuals at the endemic equilibrium without vaccination, that is, to those...
After one pandemic year of remote or hybrid instructional modes, universities in the United State... more After one pandemic year of remote or hybrid instructional modes, universities in the United States are now planning for an in-person fall semester in 2021. However, it is uncertain what the vaccination rate will look like after students, faculty, and staff return to campus. To help inform university-reopening policies, we collected survey data on social contact patterns and developed an agent-based model to simulate the spread of COVID-19 in university settings. In this paper, we aim to identify the immunity threshold that, if exceeded, would lead to a relatively safe on-campus experience for the university population. With relaxed non-pharmaceutical interventions, we estimated that immunity in at least 60% of the university population is needed for safe university reopening. Still, attention needs to be paid to extreme events that could lead to huge infection size spikes. At an immune level of 60%, continuing non-pharmaceutical interventions, such as wearing masks, could lead to an...
Contact tracing can play a vital role in controlling human-to-human transmission of a highly cont... more Contact tracing can play a vital role in controlling human-to-human transmission of a highly contagious disease such as COVID-19. To investigate the benefits and costs of contact tracing, we develop an individual-based contact-network model and a susceptible-exposed-infected-confirmed (SEIC) epidemic model for the stochastic simulations of COVID-19 transmission. We estimate the unknown parameters (reproductive ratio R0 and confirmed rate δ2) by using observed confirmed case data. After a two month-lockdown, states in the USA have started the reopening process. We investigate for four different reopening situations: under “stay-at-home” order or no reopening, 25 % reopening, 50 % reopening, and 75 % reopening. We model contact tracing in a two-layer network by modifying the basic SEIC epidemic model. The two-layer network is composed by the contact network in the first layer and the tracing network in the second layer. Since the full contact list of an infected individual patient can...
Sexually transmitted diseases (STD) modeling has used contact networks to study the spreading of ... more Sexually transmitted diseases (STD) modeling has used contact networks to study the spreading of pathogens. Recent findings have stressed the increasing role of casual partners, often enabled by online dating applications. We study the Susceptible-Infected-Susceptible (SIS) epidemic model –appropriate for STDs– over a two-layer network aimed to account for the effect of casual partners in the spreading of STDs. In this novel model, individuals have a set of steady partnerships (links in layer 1). At certain rates, every individual can switch between active and inactive states and, while active, it establishes casual partnerships with some probability with active neighbors in layer 2 (whose links can be thought as potential casual partnerships). Individuals that are not engaged in casual partnerships are classified as inactive, and the transitions between active and inactive states are independent of their infectious state. We use mean-field equations as well as stochastic simulation...
ABSTRACTThe recent outbreaks of the insect-vectored Zika virus have demonstrated its potential to... more ABSTRACTThe recent outbreaks of the insect-vectored Zika virus have demonstrated its potential to be sexually transmitted, which complicates modeling and our understanding of disease dynamics. Autochthonous outbreaks in the US mainland may be a consequence of both modes of transmission, which affect the outbreak size, duration, and virus persistence. We propose a novel individual-based interconnected network model that incorporates both insect-vectored and sexual transmission of this pathogen. This model interconnects a homogeneous mosquito vector population with a heterogeneous human host contact network. The model incorporates the seasonal variation of mosquito abundance and characterizes host dynamics based on age group and gender in order to produce realistic projections. We use a sexual contact network which is generated on the basis of real world sexual behavior data. Our findings suggest that for a high relative transmissibility of asymptomatic hosts, Zika virus shows a high ...
ABSTRACTSwine movement networks among farms/operations are an important source of information to ... more ABSTRACTSwine movement networks among farms/operations are an important source of information to understand and prevent the spread of diseases, nearly nonexistent in the United States. An understanding of the movement networks can help the policymakers in planning effective disease control measures. The objectives of this work are: 1) estimate swine movement probabilities at the county level from comprehensive anonymous inventory and sales data published by the United States Department of Agriculture - National Agriculture Statistics Service database, 2) develop a network based on those estimated probabilities, and 3) analyze that network using network science metrics. First, we use a probabilistic approach based on the maximum entropy method to estimate the movement probabilities among different swine populations. Then, we create a swine movement network using the estimated probabilities for the counties of the central agricultural district of Iowa. The analysis of this network has...
Ecological history may be an important driver of epidemics and disease emergence. We evaluated th... more Ecological history may be an important driver of epidemics and disease emergence. We evaluated the role of history and two related concepts, the evolution of epidemics and the burn-in period required for fitting a model to epidemic observations, for the U.S. soybean rust epidemic (caused by Phakopsora pachyrhizi). This disease allows evaluation of replicate epidemics because the pathogen reinvades the United States each year. We used a new maximum likelihood estimation approach for fitting the network model based on observed U.S. epidemics. We evaluated the model burn-in period by comparing model fit based on each combination of other years of observation. When the miss error rates were weighted by 0.9 and false alarm error rates by 0.1, the mean error rate did decline, for most years, as more years were used to construct models. Models based on observations in years closer in time to the season being estimated gave lower miss error rates for later epidemic years. The weighted mean ...
— In this paper, the steps taken towards setup and configuration of the DiffServ testbed in our l... more — In this paper, the steps taken towards setup and configuration of the DiffServ testbed in our laboratory are listed. A topology is suggested and some simple experimental results for setup validation are presented. A DiffServ domain is deployed and several experiments are run. We obtained acceptable performance for a DiffServ Expedited Forwarding Per Hop Behavior in our testbed using Committed Access
Gene co-expression networks can be used to determine gene regulation and attribute gene function ... more Gene co-expression networks can be used to determine gene regulation and attribute gene function to biological processes. Different high throughput technologies, including one and two-channel microarrays and RNA-sequencing, allow evaluating thousands of gene expression data simultaneously, but these methodologies provide results that cannot be directly compared. Thus, it is complex to analyze coexpression relations between genes, especially when there are missing values arising for experimental reasons. Networks are a helpful tool for studying gene co-expression, where nodes represent genes and edges represent co-expression of pairs of genes. In this paper, we propose a method for constructing a gene co-expression network for the Anopheles gambiae transcriptome from 257 unique studies obtained with different methodologies and experimental designs. We introduce the sliding threshold approach to select node pairs with high Pearson correlation coefficients. The robustness of the method...
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Papers by Caterina Scoglio