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•Populations and vaccine regimens have grown since many supply chains were designed.•Adding new vaccines may exacerbate bottlenecks, inhibiting the flow of all vaccines.•Our team implemented a supply chain evaluation and redesign process in Mozambique.•The process integrated HERMES computational modeling with on-the-ground implementers.•Redesign improved Mozambique’s vaccine supply chain efficacy and efficiency. Populations and routine childhood vaccine regimens have changed substantially since supply chains were designed in the 1980s, and introducing new vaccines during the “Decade of Vaccine” may exacerbate existing bottlenecks, further inhibiting the flow of all vaccines. Working with the Mozambique Ministry of Health, our team implemented a new process that integrated HERMES computational simulation modeling and on-the-ground implementers to evaluate and improve the Mozambique vaccine supply chain using a system-re-design that integrated new supply chain structures, information technology, equipment, personnel, and policies. The alternative system design raised vaccine availability (from 66% to 93% in Gaza; from 76% to 84% in Cabo Delgado) and reduced the logistics cost per dose administered (from $0.53 to $0.32 in Gaza; from $0.38 to $0.24 in Cabo Delgado) as compared to the multi-tiered system under the current EPI. The alternative system also produced higher availability at lower costs after new vaccine introductions. Since reviewing scenarios modeling deliveries every two months in the north of Gaza, the provincial directorate has decided to pilot this approach diverging from decades of policies dictating monthly deliveries. Re-design improved not only supply chain efficacy but also efficiency, important since resources to deliver vaccines are limited. The Mozambique experience and process can serve as a model for other countries during the Decade of Vaccines. For the Decade of Vaccines, getting vaccines at affordable prices to the market is not enough. Vaccines must reach the population to be successful.

Neuroscience has been carried into the domain of big data and high performance computing (HPC) on the backs of initiatives in data collection and an increasingly compute-intensive tools. While managing HPC experiments requires considerable technical acumen, platforms, and standards have been developed to ease this burden on scientists. While web-portals make resources widely accessible, data organizations such as the Brain Imaging Data Structure and tool description languages such as Boutiques provide researchers with a foothold to tackle these problems using their own datasets, pipelines, and environments. While these standards lower the barrier to adoption of HPC and cloud systems for neuroscience applications, they still require the consolidation of disparate domain-specific knowledge. We present Clowdr, a lightweight tool to launch experiments on HPC systems and clouds, record rich execution records, and enable the accessible sharing and re-launch of experimental summaries and results. Clowdr uniquely sits between web platforms and bare-metal applications for experiment management by preserving the flexibility of do-it-yourself solutions while providing a low barrier for developing, deploying and disseminating neuroscientific analysis.

Background: Hospital infection control strategies and programs may not consider control of methicillin-resistant Staphylococcus aureus (MRSA) in nursing homes in a county. Methods: Using our Regional Healthcare Ecosystem Analyst, we augmented our existing agent-based model of all hospitals in Orange County (OC), California, by adding all nursing homes and then simulated MRSA outbreaks in various health care facilities. Results: The addition of nursing homes substantially changed MRSA transmission dynamics throughout the county. The presence of nursing homes substantially potentiated the effects of hospital outbreaks on other hospitals, leading to an average 46.2% (range, 3.3%—156.1%) relative increase above and beyond the impact when only hospitals are included for an outbreak in OC's largest hospital. An outbreak in the largest hospital affected all other hospitals (average 2.1% relative prevalence increase) and the majority (∼90%) of nursing homes (average 3.2% relative increase) after 6 months. An outbreak in the largest nursing home had effects on multiple OC hospitals, increasing MRSA prevalence in directly connected hospitals by an average 0.3% and in hospitals not directly connected through patient transfers by an average 0.1% after 6 months. A nursing home outbreak also had some effect on MRSA prevalence in other nursing homes. Conclusions: Nursing homes, even those not connected by direct patient transfers, may be a vital component of a hospital's infection control strategy. To achieve effective control, a hospital may want to better understand how regional nursing homes and hospitals are connected through both direct and indirect (with intervening stays at home) patient sharing.

Background During the 2009 H1N1 influenza epidemic, policy makers debated over whether, when, and how long to close schools. While closing schools could have reduced influenza transmission thereby preventing cases, deaths, and health care costs, it may also have incurred substantial costs from increased childcare needs and lost productivity by teachers and other school employees. Methods A combination of agent-based and Monte Carlo economic simulation modeling was used to determine the cost-benefit of closing schools (vs. not closing schools) for different durations (range: 1 to 8 weeks) and symptomatic case incidence triggers (range: 1 to 30) for the state of Pennsylvania during the 2009 H1N1 epidemic. Different scenarios varied the basic reproductive rate (R 0 ) from 1.2, 1.6, to 2.0 and used case-hospitalization and case-fatality rates from the 2009 epidemic. Additional analyses determined the cost per influenza case averted of implementing school closure. Results For all scenarios explored, closing schools resulted in substantially higher net costs than not closing schools. For R 0 = 1.2, 1.6, and 2.0 epidemics, closing schools for 8 weeks would have resulted in median net costs of $21.0 billion (95% Range: $8.0 - $45.3 billion). The median cost per influenza case averted would have been $14,185 ($5,423 - $30,565) for R 0 = 1.2, $25,253 ($9,501 - $53,461) for R 0 = 1.6, and $23,483 ($8,870 - $50,926) for R 0 = 2.0. Conclusions Our study suggests that closing schools during the 2009 H1N1 epidemic could have resulted in substantial costs to society as the potential costs of lost productivity and childcare could have far outweighed the cost savings in preventing influenza cases.

When addressing the urgent task of improving vaccine supply chains, especially to accommodate the introduction of new vaccines, there is often a heavy emphasis on stationary storage. Currently, donations to vaccine supply chains occur largely in the form of storage equipment. This study utilized a HERMES-generated detailed, dynamic, discrete event simulation model of the Niger vaccine supply chain to compare the impacts on vaccine availability of adding stationary cold storage versus transport capacity at different levels and to determine whether adding stationary storage capacity alone would be enough to relieve potential bottlenecks when pneumococcal and rotavirus vaccines are introduced by 2015. Relieving regional level storage bottlenecks increased vaccine availability (by 4%) more than relieving storage bottlenecks at the district (1% increase), central (no change), and clinic (no change) levels alone. Increasing transport frequency (or capacity) yielded far greater gains (e.g., 15% increase in vaccine availability when doubling transport frequency to the district level and 18% when tripling). In fact, relieving all stationary storage constraints could only increase vaccine availability by 11%, whereas doubling the transport frequency throughout the system led to a 26% increase and tripling the frequency led to a 30% increase. Increasing transport frequency also reduced the amount of stationary storage space needed in the supply chain. The supply chain required an additional 61,269L of storage to relieve constraints with the current transport frequency, 55,255L with transport frequency doubled, and 51,791L with transport frequency tripled. When evaluating vaccine supply chains, it is important to understand the interplay between stationary storage and transport. The HERMES-generated dynamic simulation model showed how augmenting transport can result in greater gains than only augmenting stationary storage and can reduce stationary storage needs.

The Tomographic Quantitative Electroencephalography (qEEGt) toolbox is integrated into the Montreal Neurological Institute (MNI) Neuroinformatics Ecosystem as a docker in into the Canadian Brain Imaging Research Platform (CBRAIN). qEEGt produces age-corrected normative Statistical Parametric Maps of EEG log source spectra testing compliance to a normative database. This toolbox was developed at the Cuban Neuroscience Center as part of the first wave of the Cuban Human Brain Mapping Project (CHBMP) and has been validated and used in different health systems for several decades. Incorporation into the MNI ecosystem now provides CBRAIN registered users access to its full functionality and is accompanied by a public release of the source code on GitHub and Zenodo repositories. Among other features are the calculation of EEG scalp spectra, and the estimation of their source spectra using the Variable Resolution Electrical Tomography (VARETA) source imaging. Crucially, this is completed by the evaluation of z spectra by means of the built-in age regression equations obtained from the CHBMP database (ages 5-87) to provide normative Statistical Parametric Mapping of EEG log source spectra. Different scalp and source visualization tools are also provided for evaluation of individual subjects prior to further post-processing. Openly releasing this software in the CBRAIN platform will facilitate the use of standardized qEEGt methods in different research and clinical settings. An updated precis of the methods is provided in Appendix I as a reference for the toolbox. qEEGt/CBRAIN is the first installment of instruments developed by the neuroinformatic platform of the Cuba-Canada-China (CCC) project.

•Vaccine supply chains in low and middle income countries face numerous challenges.•Unmanned aerial vehicles (UAVs) are being developed for vaccine distribution.•HERMES-generated simulation modeling assessed UAV impact under various conditions.•UAVs raised vaccine availability and saved costs over traditional land transport.•With sufficient UAV utilization, cost savings were robust to sensitivity analyses. Immunization programs in low and middle income countries (LMICs) face numerous challenges in getting life-saving vaccines to the people who need them. As unmanned aerial vehicle (UAV) technology has progressed in recent years, potential use cases for UAVs have proliferated due to their ability to traverse difficult terrains, reduce labor, and replace fleets of vehicles that require costly maintenance. Using a HERMES-generated simulation model, we performed sensitivity analyses to assess the impact of using an unmanned aerial system (UAS) for routine vaccine distribution under a range of circumstances reflecting variations in geography, population, road conditions, and vaccine schedules. We also identified the UAV payload and UAS costs necessary for a UAS to be favorable over a traditional multi-tiered land transport system (TMLTS). Implementing the UAS in the baseline scenario improved vaccine availability (96% versus 94%) and produced logistics cost savings of $0.08 per dose administered as compared to the TMLTS. The UAS maintained cost savings in all sensitivity analyses, ranging from $0.05 to $0.21 per dose administered. The minimum UAV payloads necessary to achieve cost savings over the TMLTS, for the various vaccine schedules and UAS costs and lifetimes tested, were substantially smaller (up to 0.40L) than the currently assumed UAV payload of 1.5L. Similarly, the maximum UAS costs that could achieve savings over the TMLTS were greater than the currently assumed costs under realistic flight conditions. Implementing a UAS could increase vaccine availability and decrease costs in a wide range of settings and circumstances if the drones are used frequently enough to overcome the capital costs of installing and maintaining the system. Our computational model showed that major drivers of costs savings from using UAS are road speed of traditional land vehicles, the number of people needing to be vaccinated, and the distance that needs to be traveled.

Background Many countries, such as Niger, are considering changing their vaccine vial size presentation and may want to evaluate the subsequent impact on their supply chains, the series of steps required to get vaccines from their manufacturers to patients. The measles vaccine is particularly important in Niger, a country prone to measles outbreaks. Methods We developed a detailed discrete event simulation model of the vaccine supply chain representing every vaccine, storage location, refrigerator, freezer, and transport device (e.g., cold trucks, 4 × 4 trucks, and vaccine carriers) in the Niger Expanded Programme on Immunization (EPI). Experiments simulated the impact of replacing the 10-dose measles vial size with 5-dose, 2-dose and 1-dose vial sizes. Results Switching from the 10-dose to the 5-dose, 2-dose and 1-dose vial sizes decreased the average availability of EPI vaccines for arriving patients from 83% to 82%, 81% and 78%, respectively for a 100% target population size. The switches also changed transport vehicle's utilization from a mean of 58% (range: 4-164%) to means of 59% (range: 4-164%), 62% (range: 4-175%), and 67% (range: 5-192%), respectively, between the regional and district stores, and from a mean of 160% (range: 83-300%) to means of 161% (range: 82-322%), 175% (range: 78-344%), and 198% (range: 88-402%), respectively, between the district to integrated health centres (IHC). The switch also changed district level storage utilization from a mean of 65% to means of 64%, 66% and 68% (range for all scenarios: 3-100%). Finally, accounting for vaccine administration, wastage, and disposal, replacing the 10-dose vial with the 5 or 1-dose vials would increase the cost per immunized patient from $0.47US to $0.71US and $1.26US, respectively. Conclusions The switch from the 10-dose measles vaccines to smaller vial sizes could overwhelm the capacities of many storage facilities and transport vehicles as well as increase the cost per vaccinated child.

Acute care facilities are connected via patient sharing, forming a network. However, patient sharing extends beyond this immediate network to include sharing with long-term care facilities. The extent of long-term care facility patient sharing on the acute care facility network is unknown. The objective of this study was to characterize and determine the extent and pattern of patient transfers to, from, and between long-term care facilities on the network of acute care facilities in a large metropolitan county. We applied social network constructs principles, measures, and frameworks to all 2007 annual adult and pediatric patient transfers among the healthcare facilities in Orange County, California, using data from surveys and several datasets. We evaluated general network and centrality measures as well as individual ego measures and further constructed sociograms. Our results show that over the course of a year, 66 of 72 long-term care facilities directly sent and 67 directly received patients from other long-term care facilities. Long-term care facilities added 1,524 ties between the acute care facilities when ties represented at least one patient transfer. Geodesic distance did not closely correlate with the geographic distance among facilities. This study demonstrates the extent to which long-term care facilities are connected to the acute care facility patient sharing network. Many long-term care facilities were connected by patient transfers and further added many connections to the acute care facility network. This suggests that policy-makers and health officials should account for patient sharing with and among long-term care facilities as well as those among acute care facilities when evaluating policies and interventions.

Background States’ pandemic influenza plans and school closure statutes are intended to guide state and local officials, but most faced a great deal of uncertainty during the 2009 influenza H1N1 epidemic. Questions remained about whether, when, and for how long to close schools and about which agencies and officials had legal authority over school closures. Methods This study began with analysis of states’ school-closure statutes and pandemic influenza plans to identify the variations among them. An agent-based model of one state was used to represent as constants a population’s demographics, commuting patterns, work and school attendance, and community mixing patterns while repeated simulations explored the effects of variations in school closure authority, duration, closure thresholds, and reopening criteria. Results The results show no basis on which to justify statewide rather than school-specific or community-specific authority for school closures. Nor do these simulations offer evidence to require school closures promptly at the earliest stage of an epidemic. More important are criteria based on monitoring of local case incidence and on authority to sustain closure periods sufficiently to achieve epidemic mitigation. Conclusions This agent-based simulation suggests several ways to improve statutes and influenza plans. First, school closure should remain available to state and local authorities as an influenza mitigation strategy. Second, influenza plans need not necessarily specify the threshold for school closures but should clearly define provisions for early and ongoing local monitoring. Finally, school closure authority may be exercised at the statewide or local level, so long as decisions are informed by monitoring incidence in local communities and schools.