Oral poliovirus vaccine evolution and insights relevant to modeling the risks of circulating vaccine-derived polioviruses (cVDPVs)

The live, attenuated oral poliovirus vaccine (OPV) provides a powerful tool for controlling and stopping the transmission of wild polioviruses (WPVs), although the risks of vaccine-associated paralytic polio (VAPP) and circulating vaccine-derived poliovirus (cVDPV) outbreaks exist as long as OPV remains in use. Understanding the dynamics of cVDPV emergence and outbreaks as a function of population immunity and other risk factors may help to improve risk management and the development of strategies to respond to possible outbreaks. We performed a comprehensive review of the literature related to the process of OPV evolution and information available from actual experiences with cVDPV outbreaks. Only a relatively small fraction of poliovirus infections cause symptoms, which makes direct observation of the trajectory of OPV evolution within a population impractical and leads to significant uncertainty. Despite a large global surveillance system, the existing genetic sequence data largely provide information about transmitted virulent polioviruses that caused acute flaccid paralysis, and essentially no data track the changes that occur in OPV sequences as the viruses transmit largely asymptomatically through real populations with suboptimal immunity. We updated estimates of cVDPV risks based on actual experiences and identified the many limitations in the existing data on poliovirus transmission and immunity and OPV virus evolution that complicate modeling. Modelers should explore the space of potential model formulations and inputs consistent with the available evidence and future studies should seek to improve our understanding of the OPV virus evolution process to provide better information for policymakers working to manage cVDPV risks.

Expert review on poliovirus immunity and transmission

Successfully managing risks to achieve wild polioviruses (WPVs) eradication and address the complexities of oral poliovirus vaccine (OPV) cessation to stop all cases of paralytic poliomyelitis depends strongly on our collective understanding of poliovirus immunity and transmission. With increased shifting from OPV to inactivated poliovirus vaccine (IPV), numerous risk management choices motivate the need to understand the tradeoffs and uncertainties and to develop models to help inform decisions. The U.S. Centers for Disease Control and Prevention hosted a meeting of international experts in April 2010 to review the available literature relevant to poliovirus immunity and transmission. This expert review evaluates 66 OPV challenge studies and other evidence to support the development of quantitative models of poliovirus transmission and potential outbreaks. This review focuses on characterization of immunity as a function of exposure history in terms of susceptibility to excretion, duration of excretion, and concentration of excreted virus. We also discuss the evidence of waning of host immunity to poliovirus transmission, the relationship between the concentration of poliovirus excreted and infectiousness, the importance of different transmission routes, and the differences in transmissibility between OPV and WPV. We discuss the limitations of the available evidence for use in polio risk models, and conclude that despite the relatively large number of studies on immunity, very limited data exist to directly support quantification of model inputs related to transmission. Given the limitations in the evidence, we identify the need for expert input to derive quantitative model inputs from the existing data.

Characterizing poliovirus transmission and evolution: insights from modeling experiences with wild and vaccine-related polioviruses

With national and global health policymakers facing numerous complex decisions related to achieving and maintaining polio eradication, we expanded our previously developed dynamic poliovirus transmission model using information from an expert literature review process and including additional immunity states and the evolution of oral poliovirus vaccine (OPV). The model explicitly considers serotype differences and distinguishes fecal-oral and oropharyngeal transmission. We evaluated the model by simulating diverse historical experiences with polioviruses, including one country that eliminated wild poliovirus using both OPV and inactivated poliovirus vaccine (IPV) (USA), three importation outbreaks of wild poliovirus (Albania, the Netherlands, Tajikistan), one situation in which no circulating vaccine-derived polioviruses (cVDPVs) emerge despite annual OPV use and cessation (Cuba), three cVDPV outbreaks (Haiti, Madura Island in Indonesia, northern Nigeria), one area of current endemic circulation of all three serotypes (northern Nigeria), and one area with recent endemic circulation and subsequent elimination of multiple serotypes (northern India). We find that when sufficient information about the conditions exists, the model can reproduce the general behavior of poliovirus transmission and outbreaks while maintaining consistency in the generic model inputs. The assumption of spatially homogeneous mixing remains a significant limitation that affects the performance of the differential equation-based model when significant heterogeneities in immunity and mixing may exist. Further studies on OPV virus evolution and improved understanding of the mechanisms of mixing and transmission may help to better characterize poliovirus transmission in populations. Broad application of the model promises to offer insights in the context of global and national policy and economic models.

Drought-induced amplification of Saint Louis encephalitis virus, Florida

We used a dynamic hydrology model to simulate water table depth (WTD) and quantify the relationship between Saint Louis encephalitis virus (SLEV) transmission and hydrologic conditions in Indian River County, Florida, from 1986 through 1991, a period with an SLEV epidemic. Virus transmission followed periods of modeled drought (specifically low WTDs 12 to 17 weeks before virus transmission, followed by a rising of the water table 1 to 2 weeks before virus transmission). Further evidence from collections of Culex nigripalpus (the major mosquito vector of SLEV in Florida) suggests that during extended spring droughts vector mosquitoes and nestling, juvenile, and adult wild birds congregate in selected refuges, facilitating epizootic amplification of SLEV. When the drought ends and habitat availability increases, the SLEV-infected Cx. nigripalpus and wild birds disperse, initiating an SLEV transmission cycle. These findings demonstrate a mechanism by which drought facilitates the amplification of SLEV and its subsequent transmission to humans.

Modeling the dynamics of oral poliovirus vaccine cessation

BACKGROUND

Oral poliovirus vaccine (OPV) results in an ongoing burden of poliomyelitis due to vaccine-associated paralytic poliomyelitis and circulating vaccine-derived polioviruses (cVDPVs). This motivates globally coordinated OPV cessation after wild poliovirus eradication.

METHODS

We modeled poliovirus transmission and OPV evolution to characterize the interaction between population immunity, OPV-related virus prevalence, and the emergence of cVDPVs after OPV cessation. We explored strategies to prevent and manage cVDPVs for countries that currently use OPV for immunization and characterized cVDPV emergence risks and OPV use for outbreak response.

RESULTS

Continued intense supplemental immunization activities until OPV cessation represent the best strategy to prevent cVDPV emergence after OPV cessation in areas with insufficient routine immunization coverage. Policy makers must actively manage population immunity before OPV cessation to prevent cVDPVs and aggressively respond if prevention fails. Sufficiently aggressive response with OPV to interrupt transmission of the cVDPV outbreak virus will lead to die-out of OPV-related viruses used for response in the outbreak population. Further analyses should consider the risk of exportation to other populations of the outbreak virus and any OPV used for outbreak response.

CONCLUSIONS

OPV cessation can successfully eliminate all circulating live polioviruses in a population. The polio end game requires active risk management.

Tobacco smoke in the development and therapy of periodontal disease: progress and questions

In recent years, epidemiological studies have pointed to a significant correlation between cigarette smoke and poor periodontal status. Cigarette smoking is a significant risk factor for the onset and development of periodontal disease, and an association between reduced healing response subsequent to periodontal therapies and cigarette smoking has been found. The epidemiological studies reported here are also supported by the results of an in vitro study on the cytotoxicity of two of the volatile components of cigarette smoke that we ourselves conducted, in which the investigated compounds were found to damage human gingival fibroblasts. We concluded that this damage would be reflected in periodontal health and could slow down wound healing. Patients should thus be alerted by clinicians to the risks smoking poses to oral and dental health.

Review and assessment of poliovirus immunity and transmission: synthesis of knowledge gaps and identification of research needs

With the intensifying global efforts to eradicate wild polioviruses, policymakers face complex decisions related to achieving eradication and managing posteradication risks. These decisions and the expanding use of inactivated poliovirus vaccine (IPV) trigger renewed interest in poliovirus immunity, particularly the role of mucosal immunity in the transmission of polioviruses. Sustained high population immunity to poliovirus transmission represents a key prerequisite to eradication, but poliovirus immunity and transmission remain poorly understood despite decades of studies. In April 2010, the U.S. Centers for Disease Control and Prevention convened an international group of experts on poliovirus immunology and virology to review the literature relevant for modeling poliovirus transmission, develop a consensus about related uncertainties, and identify research needs. This article synthesizes the quantitative assessments and research needs identified during the process. Limitations in the evidence from oral poliovirus vaccine (OPV) challenge studies and other relevant data led to differences in expert assessments, indicating the need for additional data, particularly in several priority areas for research: (1) the ability of IPV-induced immunity to prevent or reduce excretion and affect transmission, (2) the impact of waning immunity on the probability and extent of poliovirus excretion, (3) the relationship between the concentration of poliovirus excreted and infectiousness to others in different settings, and (4) the relative role of fecal-oral versus oropharyngeal transmission. This assessment of current knowledge supports the immediate conduct of additional studies to address the gaps.

Application of metabolic controls for the maximization of lipid production in semicontinuous fermentation

Acetic acid can be generated through syngas fermentation, lignocellulosic biomass degradation, and organic waste anaerobic digestion. Microbial conversion of acetate into triacylglycerols for biofuel production has many advantages, including low-cost or even negative-cost feedstock and environmental benefits. The main issue stems from the dilute nature of acetate produced in such systems, which is costly to be processed on an industrial scale. To tackle this problem, we established an efficient bioprocess for converting dilute acetate into lipids, using the oleaginous yeast Yarrowia lipolytica in a semicontinuous system. The implemented design used low-strength acetic acid in both salt and acid forms as carbon substrate and a cross-filtration module for cell recycling. Feed controls for acetic acid and nitrogen based on metabolic models and online measurement of the respiratory quotient were used. The optimized process was able to sustain high-density cell culture using acetic acid of only 3% and achieved a lipid titer, yield, and productivity of 115 g/L, 0.16 g/g, and 0.8 g⋅L^-1⋅h^-1, respectively. No carbon substrate was detected in the effluent stream, indicating complete utilization of acetate. These results represent a more than twofold increase in lipid production metrics compared with the current best-performing results using concentrated acetic acid as carbon feed.

Modeling the potential role of inactivated poliovirus vaccine to manage the risks of oral poliovirus vaccine cessation

BACKGROUND

The Global Polio Eradication Initiative plans to stop all oral poliovirus vaccine (OPV) after wild poliovirus eradication, starting with serotype 2. Stakeholders continue to discuss the role of using inactivated poliovirus vaccine (IPV) to manage the risks of circulating vaccine-derived polioviruses (cVDPVs) during the end game.

METHODS

We use a poliovirus transmission and OPV evolution model to explore the impact of various routine immunization policies involving IPV on population immunity dynamics and the probability and magnitude of cVDPV emergences following OPV cessation.

RESULTS

Adding a single IPV dose to an OPV-only routine immunization schedule at or just before OPV cessation produces very limited impact on the probability of cVDPV emergences and the number of expected polio cases in settings in which we expect cVDPVs in the absence of IPV use. The highest-cost option of switching to a 3-dose IPV schedule only marginally decreases cVDPV risks. Discontinuing supplemental immunization activities while introducing IPV prior to OPV cessation leads to an increase in cVDPV risks.

CONCLUSIONS

Introducing a dose of IPV in countries currently using OPV only for routine immunization offers protection from paralysis to successfully vaccinated recipients, but it does little to protect high-risk populations from cVDPV risks.

A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering

Mathematical modeling is a key process to describe the behavior of biological networks. One of the most difficult challenges is to build models that allow quantitative predictions of the cells' states along time. Recently, this issue started to be tackled through novel in silico approaches, such as the reconstruction of dynamic models, the use of phenotype prediction methods, and pathway design via efficient strain optimization algorithms. The use of dynamic models, which include detailed kinetic information of the biological systems, potentially increases the scope of the applications and the accuracy of the phenotype predictions. New efforts in metabolic engineering aim at bridging the gap between this approach and other different paradigms of mathematical modeling, as constraint-based approaches. These strategies take advantage of the best features of each method, and deal with the most remarkable limitation—the lack of available experimental information—which affects the accuracy and feasibility of solutions. Parameter estimation helps to solve this problem, but adding more computational cost to the overall process. Moreover, the existing approaches include limitations such as their scalability, flexibility, convergence time of the simulations, among others. The aim is to establish a trade-off between the size of the model and the level of accuracy of the solutions. In this work, we review the state of the art of dynamic modeling and related methods used for metabolic engineering applications, including approaches based on hybrid modeling. We describe approaches developed to undertake issues regarding the mathematical formulation and the underlying optimization algorithms, and that address the phenotype prediction by including available kinetic rate laws of metabolic processes. Then, we discuss how these have been used and combined as the basis to build computational strain optimization methods for metabolic engineering purposes, how they lead to bi-level schemes that can be used in the industry, including a consideration of their limitations.

Potential impact of vaccination on the hepatitis C virus epidemic in injection drug users

BACKGROUND

Hepatitis C virus (HCV) causes significant morbidity and mortality in injecting drug users (IDU) worldwide. HCV vaccine candidates have shown promise for reducing the infectivity of acute infection and averting chronic infection, yet the impact of varying levels of vaccine efficacy and vaccine delivery strategies on the HCV epidemic in IDU have not been explored.

METHODS

We utilized extensive data on injecting behavior collected in the UFO Study of young IDU in San Francisco to construct a stochastic individual-based model that reflects heterogeneous injecting risk behavior, historical HCV trends, and existing information on viral dynamics and vaccine characteristics.

RESULTS

Our modeled HCV rate closely paralleled observed HCV incidence in San Francisco, with estimated incidence of 59% per person year (ppy) early in the epidemic, and 27% ppy after risk reduction was introduced. Chronic HCV infection, the clinically relevant state of HCV infection that leads to liver disease and hepatocellular cancer, was estimated at 22% ppy (± 3%) early in the epidemic and 14% ppy (± 2%) after risk reduction was introduced. We considered several scenarios, and highlight that a vaccine with 50% to 80% efficacy targeted to high-risk or sero-negative IDU at a high vaccination rate could further reduce chronic HCV incidence in IDU to 2-7% ppy 30 years after its introduction.

CONCLUSIONS

Our results underscore the importance of further efforts to develop both HCV vaccines and optimal systems of delivery to IDU populations.

Polio endgame risks and the possibility of restarting the use of oral poliovirus vaccine

INTRODUCTION

Ending all cases of poliomyelitis requires successful cessation of all oral poliovirus vaccine (OPV), but the Global Polio Eradication Initiative (GPEI) partners should consider the possibility of an OPV restart.

AREAS COVERED

We review the risks of continued live poliovirus transmission after OPV cessation and characterize events that led to OPV restart in a global model that focused on identifying optimal strategies for OPV cessation and the polio endgame. Numerous different types of events that occurred since the globally coordinated cessation of serotype 2-containing OPV in 2016 highlight the possibility of continued outbreaks after homotypic OPV cessation. Modeling suggests a high risk of uncontrolled outbreaks once more than around 5,000 homotypic polio cases occur after cessation of an OPV serotype, at which point restarting OPV would become necessary to protect most populations. Current efforts to sunset the GPEI and transition its responsibilities to national governments poses risks that may limit the ability to implement management strategies needed to minimize the probability of an OPV restart.

EXPERT COMMENTARY

OPV restart remains a real possibility, but risk management choices made by the GPEI partners and national governments can reduce the risks of this low-probability but high-consequence event.

Treatment and primary prevention in people who inject drugs for chronic hepatitis C infection: is elimination possible in a high-prevalence setting?

AIMS

To project the impact of scaling-up oral anti-viral therapy and harm reduction on chronic hepatitis C (CHC) prevalence and incidence among people who inject drugs (PWID) in Greece, to estimate the relationship between required treatment levels and expansion of harm reduction programmes to achieve specific targets and to examine whether hepatitis C virus (HCV) elimination among PWID is possible in this high-prevalence setting.

DESIGN

A dynamic discrete time, stochastic individual-based model was developed to simulate HCV transmission among PWID incorporating the effect of HCV treatment and harm reduction strategies, and allowing for re-infection following treatment.

SETTING/PARTICIPANTS

The population of 8300 PWID in Athens Metropolitan area.

MEASUREMENTS

Reduction in HCV prevalence and incidence in 2030 compared with 2016.

FINDINGS

Moderate expansion of HCV treatment (treating 4-8% of PWID/year), with a simultaneous increase of 2%/year in harm reduction coverage (from 44 to 72% coverage over 15 years), was projected to reduce CHC prevalence among PWID in Athens by 46.2-94.8% in 2030, compared with 2016. CHC prevalence would reduce to below 10% within the next 4-5 years if annual HCV treatment numbers were increased up to 16-20% PWID/year. The effect of harm reduction on incidence was more pronounced under lower treatment rates.

CONCLUSIONS

Based on theoretical model projections, scaled-up hepatitis C virus treatment and harm reduction interventions could achieve major reductions in hepatitis C virus incidence and prevalence among people who inject drugs in Athens, Greece by 2030. Chronic hepatitis C could be eliminated in the next 4-5 years by increasing treatment to more than 16% of people who inject drugs per year combined with moderate increases in harm reduction coverage.

Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models

Microbial communities and their functions are shaped by complex networks of interactions among microbes and with their environment. While the critical roles microbial communities play in numerous environments have become increasingly appreciated, we have a very limited understanding of their interactions and how these interactions combine to generate community-level behaviors. This knowledge gap hinders our ability to predict community responses to perturbations and to design interventions that manipulate these communities to our benefit. Dynamic models are promising tools to address these questions. We review existing modeling techniques to construct dynamic models of microbial communities at different scales and suggest ways to leverage multiple types of models and data to facilitate our understanding and engineering of microbial communities.

Modeling the impact of simulated educational interventions on the use and abuse of pharmaceutical opioids in the United States: a report on initial efforts

Three educational interventions were simulated in a system dynamics model of the medical use, trafficking, and nonmedical use of pharmaceutical opioids. The study relied on secondary data obtained in the literature for the period of 1995 to 2008 as well as expert panel recommendations regarding model parameters and structure. The behavior of the resulting systems-level model was tested for fit against reference behavior data. After the base model was tested, logic to represent three educational interventions was added and the impact of each intervention on simulated overdose deaths was evaluated over a 7-year evaluation period, 2008 to 2015. Principal findings were that a prescriber education intervention not only reduced total overdose deaths in the model but also reduced the total number of persons who receive opioid analgesic therapy, medical user education not only reduced overdose deaths among medical users but also resulted in increased deaths from nonmedical use, and a "popularity" intervention sharply reduced overdose deaths among nonmedical users while having no effect on medical use. System dynamics modeling shows promise for evaluating potential interventions to ameliorate the adverse outcomes associated with the complex system surrounding the use of opioid analgesics to treat pain.

COVID-19 Vaccination Scenarios: A Cost-Effectiveness Analysis for Turkey

As of March 2021, COVID-19 has claimed the lives of more than 2.7 million people worldwide. Vaccination has started in most countries around the world. In this study, we estimated the cost-effectiveness of strategies for COVID-19 vaccination for Turkey compared to a baseline in the absence of vaccination and imposed measures by using an enhanced SIRD (Susceptible, Infectious, Recovered, Death) model and various scenarios for the first year after vaccination. The results showed that vaccination is cost-effective from a health care perspective, with an incremental cost-effectiveness ratio (ICER) of 511 USD/QALY and 1045 USD/QALY if vaccine effectiveness on transmission is equal or reduced to only 50% of effectiveness on disease, respectively, at the 90% baseline effectiveness of the vaccine. From a societal perspective, cost savings were estimated for both scenarios. Other results further showed that the minimum required vaccine uptake to be cost-effective would be at least 30%. Sensitivity and scenario analyses, as well as the iso-ICER curves, showed that the results were quite robust and that major changes in cost-effectiveness outcomes cannot be expected. We can conclude that COVID-19 vaccination in Turkey is highly cost-effective or even cost-saving.

Modeling social dimensions of oral health among older adults in urban environments

In both developed and developing countries, population aging has attained unprecedented levels. Public health strategies to deliver services in community-based settings are key to enhancing the utilization of preventive care and reducing costs for this segment of the population. Motivated by concerns of inadequate access to oral health care by older adults in urban environments, this article presents a portfolio of systems science models that have been developed on the basis of observations from the ElderSmile preventive screening program operated in northern Manhattan, New York City, by the Columbia University College of Dental Medicine. Using the methodology of system dynamics, models are developed to explore how interpersonal relationships influence older adults' participation in oral health promotion. Feedback mechanisms involving word of mouth about preventive screening opportunities are represented in relation to stocks that change continuously via flows, as well as agents whose states of health care utilization change discretely using stochastic transitions. Agent-based implementations illustrate how social networks and geographic information systems are integrated into dynamic models to reflect heterogeneous and proximity-based patterns of communication and participation in the ElderSmile program. The systems science approach builds shared knowledge among an interdisciplinary research team about the dynamics of access to opportunities for oral health promotion. Using "what if" scenarios to model the effects of program enhancements and policy changes, resources may be effectively leveraged to improve access to preventive and treatment services. Furthermore, since oral health and general health are inextricably linked, the integration of services may improve outcomes and lower costs.

Reflections on Modeling Poliovirus Transmission and the Polio Eradication Endgame

The Global Polio Eradication Initiative (GPEI) partners engaged modelers during the past nearly 20 years to support strategy and policy discussions and decisions, and to provide estimates of the risks, costs, and benefits of different options for managing the polio endgame. Limited efforts to date provided insights related to the validation of the models used for GPEI strategy and policy decisions. However, modeling results only influenced decisions in some cases, with other factors carrying more weight in many key decisions. In addition, the results from multiple modeling groups do not always agree, which supports selection of some strategies and/or policies counter to the recommendations from some modelers but not others. This analysis reflects on our modeling, and summarizes our premises and recommendations, the outcomes of these recommendations, and the implications of key limitations of models with respect to polio endgame strategy. We briefly review the current state of the GPEI given epidemiological experience as of early 2020, which includes failure of the GPEI to deliver on the objectives of its 2013-2018 strategic plan despite full financial support. Looking ahead, we provide context for why the GPEI strategy of global oral poliovirus vaccine (OPV) cessation to end all cases of poliomyelitis looks infeasible given the current state of the GPEI and the failure to successfully stop all transmission of serotype 2 live polioviruses within four years of the April-May 2016 coordinated cessation of serotype 2 OPV use in routine immunization.

The Relative Impact of Community and Hospital Antibiotic Use on the Selection of Extended-spectrum Beta-lactamase-producing Escherichia coli

Antibiotic stewardship programs have traditionally focused on reducing hospital antibiotic use. However, reducing community antibiotic prescribing could have substantial impacts in both hospital and community settings. We developed a deterministic model of transmission of extended-spectrum beta-lactamase-producing Escherichia coli in both the community and hospitals. We fit the model to existing, national-level antibiotic use and resistance prevalence data from Sweden. Across a range of conditions, a given relative change in antibiotic use in the community had a greater impact on resistance prevalence in both the community and hospitals than an equivalent relative change in hospital use. However, on a per prescription basis, changes in antibiotic use in hospitals had the greatest impact. The magnitude of changes in prevalence were modest, even with large changes in antimicrobial use. These data support the expansion of stewardship programs/interventions beyond the walls of hospitals, but also suggest that such efforts would benefit hospitals themselves.

Model-Based Evaluation of Strategies to Control Brucellosis in China

Brucellosis, the most common zoonotic disease worldwide, represents a great threat to animal husbandry with the potential to cause enormous economic losses. Brucellosis has become a major public health problem in China, and the number of human brucellosis cases has increased dramatically in recent years. In order to evaluate different intervention strategies to curb brucellosis transmission in China, a novel mathematical model with a general indirect transmission incidence rate was presented. By comparing the results of three models using national human disease data and 11 provinces with high case numbers, the best fitted model with standard incidence was used to investigate the potential for future outbreaks. Estimated basic reproduction numbers were highly heterogeneous, varying widely among provinces. The local basic reproduction numbers of provinces with an obvious increase in incidence were much larger than the average for the country as a whole, suggesting that environment-to-individual transmission was more common than individual-to-individual transmission. We concluded that brucellosis can be controlled through increasing animal vaccination rates, environment disinfection frequency, or elimination rates of infected animals. Our finding suggests that a combination of animal vaccination, environment disinfection, and elimination of infected animals will be necessary to ensure cost-effective control for brucellosis.

Lessons From Globally Coordinated Cessation of Serotype 2 Oral Poliovirus Vaccine for the Remaining Serotypes

Background

Comparing model expectations with the experience of oral poliovirus vaccine (OPV) containing serotype 2 (OPV2) cessation can inform risk management for the expected cessation of OPV containing serotypes 1 and 3 (OPV13).

Methods

We compare the expected post-OPV2-cessation OPV2-related viruses from models with the evidence available approximately 6 months after OPV2 cessation. We also model the trade-offs of use vs nonuse of monovalent OPV (mOPV) for outbreak response considering all 3 serotypes.

Results

Although too early to tell definitively, the observed die-out of OPV2-related viruses in populations that attained sufficiently intense trivalent OPV (tOPV) use prior to OPV2 cessation appears consistent with model expectations. As expected, populations that did not intensify tOPV use prior to OPV2 cessation show continued circulation of serotype 2 vaccine-derived polioviruses (VDPVs). Failure to aggressively use mOPV to respond to circulating VDPVs results in a high risk of uncontrolled outbreaks that would require restarting OPV.

Conclusions

Ensuring a successful endgame requires more aggressive OPV cessation risk management than has occurred to date for OPV2 cessation. This includes maintaining high population immunity to transmission up until OPV13 cessation, meeting all prerequisites for OPV cessation, and ensuring sufficient vaccine supply to prevent and respond to outbreaks.

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

BACKGROUND

The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis. In the first step, it is usually required to set initial metabolite concentrations, and to assign kinetic rate laws, along with estimating parameter values using kinetic data through optimization when these are not known. Although the rapid development of high-throughput methods has generated much omics data, experimentalists present only a summary of obtained results for publication, the experimental data files are not usually submitted to any public repository, or simply not available at all. In order to automatize as much as possible the steps of building kinetic models, there is a growing requirement in the systems biology community for easily exchanging data in combination with models, which represents the main motivation of KiMoSys development.

DESCRIPTION

KiMoSys is a user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data.KiMoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research.

CONCLUSIONS

KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting construction of ODE-based kinetic models and collaborative research projects.The web application implemented using Ruby on Rails framework is freely available for web access at http://kimosys.org, along with its full documentation.

Logistical challenges and assumptions for modeling the failure of global cessation of oral poliovirus vaccine (OPV)

Introduction: The inability to successfully stop all use of oral poliovirus vaccine (OPV) as part of the polio endgame and/or the possibilities of reintroduction of live polioviruses after successful OPV cessation may imply the need to restart OPV production and use, either temporarily or permanently. Areas covered: Complementing prior work that explored the risks of potential OPV restart, we discuss the logistical challenges and implications of restarting OPV in the future, and we develop appropriate assumptions for modeling the possibility of OPV restart. The complexity of phased cessation of the three OPV serotypes implies different potential combinations of OPV use long term. We explore the complexity of polio vaccine choices and key unresolved policy questions that may impact continuing and future use of OPV and/or inactivated poliovirus vaccine (IPV). We then characterize the assumptions required to quantitatively model OPV restart in prospective global-integrated economic policy models for the polio endgame. Expert commentary: Depending on the timing, restarting production of OPV would imply some likely delays associated with ramp-up, re-licensing, and other logistics that would impact the availability and costs of restarting the use of OPV in national immunization programs after globally coordinated cessation of one or more OPV serotypes.

Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies

The interconnected network of pathways downstream of the TGFβ, WNT and EGF-families of receptor ligands play an important role in colorectal cancer pathogenesis.We studied and implemented dynamic simulations of multiple downstream pathways and described the section of the signaling network considered as a Molecular Interaction Map (MIM). Our simulations used Ordinary Differential Equations (ODEs), which involved 447 reactants and their interactions.Starting from an initial "physiologic condition", the model can be adapted to simulate individual pathologic cancer conditions implementing alterations/mutations in relevant onco-proteins. We verified some salient model predictions using the mutated colorectal cancer lines HCT116 and HT29. We measured the amount of MYC and CCND1 mRNAs and AKT and ERK phosphorylated proteins, in response to individual or combination onco-protein inhibitor treatments. Experimental and simulation results were well correlated. Recent independently published results were also predicted by our model.Even in the presence of an approximate and incomplete signaling network information, a predictive dynamic modeling seems already possible. An important long term road seems to be open and can be pursued further, by incremental steps, toward even larger and better parameterized MIMs. Personalized treatment strategies with rational associations of signaling-proteins inhibitors, could become a realistic goal.

Dynamic Characteristics Study for Surface Composite of AMMNCs Matrix Fabricated by Friction Stir Process

In the present work, Aluminum Metal Matrix Surface Nano Composites (AMMSNCs) were manufactured using Friction Stir Processing (FSP). Moreover, the fabricated surface composite matrix was exposed to a different number of tool passes with different processing parameters. The tensile test and microstructure examinations were used to study the mechanical properties of the composite surface. The dynamic properties were predicted using modal analysis and finite element methods. After this, dynamic characterization was achieved by combining the numerical and experimental methods to investigate the effects of changing the number of passes on the natural frequency and the damping capacity of the AMMSNCs manufactured using FSP. The results indicated that the damping capacity and dynamic behavior improved with an increased number of FSP passes.