Draft Genome Sequence of a Diploid and Hybrid Candida Strain, Candida sanyaensis UCD423, Isolated from Compost in Ireland.

Candida sanyaensis is a CUG-Ser1 clade yeast that is associated with soil. Assembly of short-read and long-read data shows that C. sanyaensis has a diploid and hybrid genome, with approximately 97% identity between the haplotypes. The haploid genome size is approximately 15.4 Mb.

Effects of naloxone distribution to likely bystanders: Results of an agent-based model.

BACKGROUND: Opioid overdose deaths in the US rose dramatically in the past 16 years, creating an urgent national health crisis with no signs of immediate relief. In 2017, the President of the US officially declared the opioid epidemic to be a national emergency and called for additional resources to respond to the crisis. Distributing naloxone to community laypersons and people at high risk for opioid overdose can prevent overdose death, but optimal distribution methods have not yet been pinpointed. METHODS: We conducted a sequential exploratory mixed methods design using qualitative data to inform an agent-based model to improve understanding of effective community-based naloxone distribution to laypersons to reverse opioid overdose. The individuals in the model were endowed with cognitive and behavioral variables and accessed naloxone via community sites such as pharmacies, hospitals, and urgent-care centers. We compared overdose deaths over a simulated 6-month period while varying the number of distribution sites (0, 1, and 10) and number of kits given to individuals per visit (1 versus 10). Specifically, we ran thirty simulations for each of thirteen distribution models and report average overdose deaths for each. The baseline comparator was no naloxone distribution. Our simulations explored the effects of distribution through syringe exchange sites with and without secondary distribution, which refers to distribution of naloxone kits by laypersons within their social networks and enables ten additional laypersons to administer naloxone to reverse opioid overdose. RESULTS: Our baseline model with no naloxone distribution predicted there would be 167.9 deaths in a six month period. A single distribution site, even with 10 kits picked up per visit, decreased overdose deaths by only 8.3% relative to baseline. However, adding secondary distribution through social networks to a single site resulted in 42.5% fewer overdose deaths relative to baseline. That is slightly higher than the 39.9% decrease associated with a tenfold increase in the number of sites, all distributing ten kits but with no secondary distribution. This suggests that, as long as multiple kits are picked up per visit, adding secondary distribution is at least as effective as increasing sites from one to ten. Combining the addition of secondary distribution with an increase in sites from one to ten resulted in a 61.1% drop in deaths relative to the baseline. Adding distribution through a syringe exchange site resulted in a drop of approximately 65% of deaths relative to baseline. In fact, when enabling distribution through a clean-syringe site, the secondary distribution through networks contributed no additional drops in deaths. CONCLUSION: Community-based naloxone distribution to reverse opioid overdose may significantly reduce deaths. Optimal distribution methods may include secondary distribution so that the person who picks up naloxone kits can enable others in the community to administer naloxone, as well as targeting naloxone distribution to sites where individuals at high-risk for opioid overdose death are likely to visit, such as syringe-exchange programs. This study design, which paired exploratory qualitative data with agent-based modeling, can be used in other settings seeking to implement and improve naloxone distribution programs.

Chaos in collective health: Fractal dynamics of social learning.

Physiology often exhibits non-linear, fractal patterns of adaptation. I show that such patterns of adaptation also characterize collective health behavior in a model of collective health protection in which individuals use highest payoff biased social learning to decide whether or not to protect against a spreading disease, but benefits of health are shared locally. This model results in collectives of protectors with an exponential distribution of sizes, smaller ones being much more likely. This distribution of protecting collectives, in turn, results in incidence patterns often seen in infectious disease which, although they seem to fluctuate randomly, actually have an underlying order, a fractal time trend pattern. The time trace of infection incidence shows a self-similarity coefficient consistent with a fractal distribution and anti-persistence, reflecting the negative feedback created by health protective behavior responding to disease, when the benefit of health is high enough to stimulate health protection. When the benefit of health is too low to support any health protection, the self-similarity coefficient shows high persistence, reflecting positive feedback resulting the unmitigated spread of disease. Thus the self-similarity coefficient closely corresponds to the level of protection, demonstrating that what might otherwise be regarded as "noise" in incidence actually reflects the fact that protecting collectives form when the spreading disease is present locally but drop protection when disease subsides locally, mitigating disease intermittently. These results hold not only in a deterministic version of the model in a regular lattice network, but also in small-world networks with stochasticity in infection and efficacy of protection. The resulting non-linear and chaotic patterns of behavior and disease cannot be explained by traditional epidemiological methods but a simple agent-based model is sufficient to produce these results.

Health behavior change in advance care planning: an agent-based model.

BACKGROUND: A practical and ethical challenge in advance care planning research is controlling and intervening on human behavior. Additionally, observing dynamic changes in advance care planning (ACP) behavior proves difficult, though tracking changes over time is important for intervention development. Agent-based modeling (ABM) allows researchers to integrate complex behavioral data about advance care planning behaviors and thought processes into a controlled environment that is more easily alterable and observable. Literature to date has not addressed how best to motivate individuals, increase facilitators and reduce barriers associated with ACP. We aimed to build an ABM that applies the Transtheoretical Model of behavior change to ACP as a health behavior and accurately reflects: 1) the rates at which individuals complete the process, 2) how individuals respond to barriers, facilitators, and behavioral variables, and 3) the interactions between these variables. METHODS: We developed a dynamic ABM of the ACP decision making process based on the stages of change posited by the Transtheoretical Model. We integrated barriers, facilitators, and other behavioral variables that agents encounter as they move through the process. RESULTS: We successfully incorporated ACP barriers, facilitators, and other behavioral variables into our ABM, forming a plausible representation of ACP behavior and decision-making. The resulting distributions across the stages of change replicated those found in the literature, with approximately half of participants in the action-maintenance stage in both the model and the literature. CONCLUSIONS: Our ABM is a useful method for representing dynamic social and experiential influences on the ACP decision making process. This model suggests structural interventions, e.g. increasing access to ACP materials in primary care clinics, in addition to improved methods of data collection for behavioral studies, e.g. incorporating longitudinal data to capture behavioral dynamics.

Resilience, tipping, and hydra effects in public health: emergent collective behavior in two agent-based models.

BACKGROUND: Collective health behavior often demonstrates counter-intuitive dynamics, sometimes resisting interventions designed to produce change, or even producing effects that are in the opposite direction than intended by the intervention, e.g. lowering infectivity resulting in increased infections. At other times collective health behavior exhibits sudden large-scale change in response to small interventions or change in the environment, a phenomenon often called "tipping." I hypothesize that these seemingly very different phenomena can all be explained by the same dynamic, a type of collective resilience. METHODS: I compared two simple agent-based models of interactions in networks: a public health behavior game, in which individuals decide whether or not to adopt protective behavior, and a microbial-level game, in which three different strains of bacteria attack each other. I examined the type of networks and other conditions that support a dynamic balance, and determined what changes of conditions will tip the balance. RESULTS: Both models show lasting dynamic equilibrium and resilience, resulting from negative feedback that supports oscillating coexistence of diversity under a range of conditions. In the public health game, health protection is followed by free-riding defectors, followed by a rise in infection, in long-lasting cycles. In the microbial game, each of three strains takes turns dominating. In both games, the dynamic balance is tipped by lowering the level of local clustering, changing the level of benefit, or lowering infectivity or attack rate. Lowering infectivity has the surprising effect of increasing the numbers of infected individuals. We see parallel results in the microbial game of three bacterial strains, where lowering one strain's attack rate (analogous to lowering infectivity) increases the numbers of the restrained attacker, a phenomenon captured by the phrase, "the enemy of my enemy is my friend." CONCLUSIONS: Collective behavior often shows a dynamic balance, resulting from negative feedback, supporting diversity and resisting change. Above certain threshold conditions, the dynamic balance is tipped towards uniformity of behavior. Under a certain range of conditions we see "hydra effects" in which interventions to lower attack rate or infectivity are self-defeating. Simple models of collective behavior can explain these seemingly disparate dynamics.

Financial distress and depressive symptoms among African American women: identifying financial priorities and needs and why it matters for mental health.

Prior research found that financial hardship or distress is one of the most important underlying factors for depression/depressive symptoms, yet factors that contribute to financial distress remain unexplored or unaddressed. Given this, the goals of the present study were (1) to examine the relationship between perceived financial distress and depressive symptoms, and (2) to identify financial priorities and needs that may contribute to financial distress. Surveys from 111 African American women, ages 18-44, who reside in Allegheny County, PA, were used to gather demographic information and measures of depressive symptoms and financial distress/financial well-being. Correlation and regression analyses revealed that perceived financial distress was significantly associated with levels of depressive symptoms. To assess financial priorities and needs, responses to two open-ended questions were analyzed and coded for common themes: "Imagine you won a $10,000 prize in a local lottery. What would you do with this money?" and "What kinds of programs or other help would be beneficial to you during times of financial difficulties?" The highest five priorities identified by the participants were paying bills and debt, saving, purchasing a home or making home repairs, and/or helping others. The participant's perceived needs during times of financial difficulty included tangible assistance and/or financial education. The findings from this study can be used to create new and/or enhance existing programs, services, and/or interventions that focus on the identified financial priorities and needs. Collaborative efforts among professionals in different disciplines are also needed, as ways to manage and alleviate financial distress should be considered and discussed when addressing the mental health of African American women.

School closure as an influenza mitigation strategy: how variations in legal authority and plan criteria can alter the impact.

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.

Preparedness for pandemics: does variation among states affect the nation as a whole?

OBJECTIVE: Since states' public health systems differ as to pandemic preparedness, this study explored whether such heterogeneity among states could affect the nation's overall influenza rate. DESIGN: The Centers for Disease Control and Prevention produced a uniform set of scores on a 100-point scale from its 2008 national evaluation of state preparedness to distribute materiel from the Strategic National Stockpile (SNS). This study used these SNS scores to represent each state's relative preparedness to distribute influenza vaccine in a timely manner and assumed that "optimal" vaccine distribution would reach at least 35% of the state's population within 4 weeks. The scores were used to determine the timing of vaccine distribution for each state: each 10-point decrement of score below 90 added an additional delay increment to the distribution time. SETTING AND PARTICIPANTS: A large-scale agent-based computational model simulated an influenza pandemic in the US population. In this synthetic population each individual or agent had an assigned household, age, workplace or school destination, daily commute, and domestic intercity air travel patterns. MAIN OUTCOME MEASURES: Simulations compared influenza case rates both nationally and at the state level under 3 scenarios: no vaccine distribution (baseline), optimal vaccine distribution in all states, and vaccine distribution time modified according to state-specific SNS score. RESULTS: Between optimal and SNS-modified scenarios, attack rates rose not only in low-scoring states but also in high-scoring states, demonstrating an interstate spread of infections. Influenza rates were sensitive to variation of the SNS-modified scenario (delay increments of 1 day versus 5 days), but the interstate effect remained. CONCLUSIONS: The effectiveness of a response activity such as vaccine distribution could benefit from national standards and preparedness funding allocated in part to minimize interstate disparities.

Developing a measure of local agency adaptation to emergencies: a metric.

Local public health agencies often must respond to health-related emergencies or disasters, while continuing to fulfill all public health functions for which they are funded. This article reports the development and initial pilot test of a method for measuring the nature and degree of a public health agency's response to such an emergency or disaster. How the instrument was developed as well as the initial results from the pilot study of four local public health systems (LPHSs) are presented and discussed. The instrument measured the extent to which each function and division of each of the four LPHSs were affected and provided a metric that could be used across LPHSs to indicate the burden experienced by each due to the emergency. Results obtained from the pilot study indicate that size and complexity of an LPHS was not predictive of its ability to respond to the emergency. These results support the use of the framework and associated measurement procedures to provide valuable information to managers responsible for such LPHSs. Such information should provide a foundation for comparing variations in performance and outcomes to various types of emergencies that vary in their severity and focus.

Probabilistic, Decision-theoretic Disease Surveillance and Control.

The Pittsburgh Center of Excellence in Public Health Informatics has developed a probabilistic, decision-theoretic system for disease surveillance and control for use in Allegheny County, PA and later in Tarrant County, TX. This paper describes the software components of the system and its knowledge bases. The paper uses influenza surveillance to illustrate how the software components transform data collected by the healthcare system into population level analyses and decision analyses of potential outbreak-control measures.

Disparities and access to healthy food in the United States: A review of food deserts literature.

Increasingly, studies are focusing on the role the local food environment plays in residents' ability to purchase affordable, healthy and nutritious foods. In a food desert, an area devoid of a supermarket, access to healthy food is limited. We conducted a systematic review of studies that focused on food access and food desert research in the United States. The 31 studies identified utilized 9 measures to assess food access. Results from these studies can be summarized primarily into four major statements. Findings from other countries offer insight into ways, in which future research, policy development and program implementation in the U.S. may continue to be explored.

Who will fill the geoscience workforce supply gap?

Society needs more geoscientists than there are presently students.

The effects of managerial beliefs on service: privatization and discontinuation in local health departments.

This study examines the influence of Local Health Department (LHD) directors' managerial beliefs on the decision to privatize or discontinue personal health services. A stratified representative national sample of LHD directors was interviewed by telephone. Directors who believed temporary workers should be used wherever possible had about three times the odds of privatizing one or more personal health services. Directors who believed their department should focus exclusively on the core functions had more than ten times the odds of discontinuing at least one service. Declining revenue was not predictive of either privatization or discontinuation of personal health services.

Local health departments' mission to the uninsured.

It is often maintained that local health departments (LHDs) should not directly provide personal health services. However, our nationally representative sample revealed that most LHD directors (87%) believed LHDs must directly provide these services, primarily because they perceived a high level of unmet need among the uninsured. While only a minority believed LHDs should focus exclusively on the core functions, this proportion rose dramatically when we asked directors to assume that there were no uninsured people. Directors who perceived a high level of unmet need among the uninsured in their jurisdictions were much less likely to believe that LHDs should exclusively focus on the core functions. In theory, LHDs have a unique responsibility for assuring that the uninsured and vulnerable have access to personal health services. However, a majority of directors (67%) acknowledged that they have no enforceable means of assuring access to services the health department did not directly provide.

Managerial and professional beliefs influencing public health privatization: results of a national survey of local health department directors.

This article describes managerial and professional beliefs underlying decisions to privatize public health services. We drew a stratified, nationally representative sample of local health departments and interviewed 347 department directors by telephone. We used logistic regression to establish the independent effects of various beliefs on the decision to privatize. Over half of directors did not believe that there was valid evidence that privatization results in more efficient performance, and those who believed there was such evidence were not more likely to privatize. However, directors held professional and managerial beliefs that influenced their decision to privatize. Directors most likely to privatize were those who believed that local health departments should exclusively focus on the core public health functions, those who asserted that public health should become involved in an increasingly diverse array of social problems, and those who believed that employees should be used on a temporary and contractual, rather than permanent, basis wherever possible.

The privatization of environmental health services: a national survey of practices and perspectives in local health departments.

OBJECTIVES: This article presents nationally representative data on environmental health (EH) services privatized by local public health departments, enforcement and assurance mechanisms for privatized services, and administrators' views about EH services that should not be privatized. METHODS: A national sample of 380 local public health departments, stratified by jurisdiction size, was drawn from a universe of 2,488 departments. Telephone interviews were conducted with 347 administrators of departments. Results were weighted to be nationally representative. RESULTS: Approximately one-quarter of departments had privatized at least one EH service, almost always to for-profit organizations. The two most common reasons given for privatizing EH services were cost savings or increased efficiency and lack of capacity or expertise to carry out the service. The most rigorous, although infrequent, technique of enforcement and assurance of EH standards when services were privatized was double-testing of samples. Departments more commonly relied on state licensing and certification of contractors. When asked what services should not be privatized, 27% of respondents cited EH services. Many respondents argued against privatizing environmental services that have inherent regulatory functions. They expressed concern that privatization would fragment the public health infrastructure by impairing communication, diminishing control over performance, or weakening health departments' capacity to respond to environmental and other health crises. CONCLUSION: These findings raise serious concerns about the privatization of EH.

Public health privatization: proponents, registers, and decision-makers.

We previously documented the extent and consequences of the privatization of public health, using a nationally representative sample of 347 Local Health Department (LHD) directors. Here we present the directors' descriptions of the actors involved in the privatization of services. LHD top administrators are the most influential privatization decision-makers in about half of LHDs. But other groups significantly influence privatization decisions, particularly state governments, state health departments, and local officials. Nearly two thirds of LHDs experienced pressures to privatize, either from state legislatures, state health departments, funding organizations, or other source of political pressure. Almost half of LHD directors reported resistance to privatization, often from employees. The majority of directors did not believe it was desirable to put employees on a temporary, contractual basis. Many directors believed that retaining permanent, full-time employees was fairer as well as necessary to maintain a cadre of experienced public health professionals.

The perceived impact of privatization on local health departments.

OBJECTIVES: This article presents nationally representative data on the effects of privatization on local health departments (LHDs). METHODS: A stratified representative national sample of 380 LHDs was drawn from a national list of 2488 departments. Telephone interviews were conducted with 347 LHD directors. RESULTS: One half of the directors of LHDs with privatized services reported that privatization helped the performance of core functions. Privatization often resulted in increased time needed for management and administration. More than a third of LHD directors reported concern about loss of control over the performance of privatized functions and services. CONCLUSIONS: Privatization is part of a broader shift toward "managing" rather than directly providing public health services, yet privatization often reduces LHDs' control over the performance of services.