Audrey McCombs

Bio: Audrey McCombs is an academic researcher from Iowa State University. The author has contributed to research in topics: Population & Homophily. The author has an hindex of 3, co-authored 12 publications receiving 45 citations.

A model-based evaluation of the efficacy of COVID-19 social distancing, testing and hospital triage policies.

Abstract: A stochastic compartmental network model of SARS-CoV-2 spread explores the simultaneous effects of policy choices in three domains: social distancing, hospital triaging, and testing. Considering policy domains together provides insight into how different policy decisions interact. The model incorporates important characteristics of COVID-19, the disease caused by SARS-CoV-2, such as heterogeneous risk factors and asymptomatic transmission, and enables a reliable qualitative comparison of policy choices despite the current uncertainty in key virus and disease parameters. Results suggest possible refinements to current policies, including emphasizing the need to reduce random encounters more than personal contacts, and testing low-risk symptomatic individuals before high-risk symptomatic individuals. The strength of social distancing of symptomatic individuals affects the degree to which asymptomatic cases drive the epidemic as well as the level of population-wide contact reduction needed to keep hospitals below capacity. The relative importance of testing and triaging also depends on the overall level of social distancing.

Evaluation of the United States COVID-19 vaccine allocation strategy.

Abstract: Background Anticipating an initial shortage of vaccines for COVID-19, the Centers for Disease Control (CDC) in the United States developed priority vaccine allocations for specific demographic groups in the population. This study evaluates the performance of the CDC vaccine allocation strategy with respect to multiple potentially competing vaccination goals (minimizing mortality, cases, infections, and years of life lost (YLL)), under the same framework as the CDC allocation: four priority vaccination groups and population demographics stratified by age, comorbidities, occupation and living condition (congested or non-congested). Methods and findings We developed a compartmental disease model that incorporates key elements of the current pandemic including age-varying susceptibility to infection, age-varying clinical fraction, an active case-count dependent social distancing level, and time-varying infectivity (accounting for the emergence of more infectious virus strains). The CDC allocation strategy is compared to all other possibly optimal allocations that stagger vaccine roll-out in up to four phases (17.5 million strategies). The CDC allocation strategy performed well in all vaccination goals but never optimally. Under the developed model, the CDC allocation deviated from the optimal allocations by small amounts, with 0.19% more deaths, 4.0% more cases, 4.07% more infections, and 0.97% higher YLL, than the respective optimal strategies. The CDC decision to not prioritize the vaccination of individuals under the age of 16 was optimal, as was the prioritization of health-care workers and other essential workers over non-essential workers. Finally, a higher prioritization of individuals with comorbidities in all age groups improved outcomes compared to the CDC allocation. Conclusion The developed approach can be used to inform the design of future vaccine allocation strategies in the United States, or adapted for use by other countries seeking to optimize the effectiveness of their vaccine allocation strategies.

Partitioning genetic and species diversity refines our understanding of species-genetic diversity relationships.

Abstract: Disentangling the origin of species-genetic diversity correlations (SGDCs) is a challenging task that provides insight into the way that neutral and adaptive processes influence diversity at multiple levels. Genetic and species diversity are comprised by components that respond differently to the same ecological processes. Thus, it can be useful to partition species and genetic diversity into their different components to infer the mechanisms behind SGDCs. In this study, we applied such an approach using a high-elevation Andean wetland system, where previous evidence identified neutral processes as major determinants of the strong and positive covariation between plant species richness and AFLP genetic diversity of the common sedge Carex gayana. To tease apart putative neutral and non-neutral genetic variation of C. gayana, we identified loci putatively under selection from a dataset of 1,709 SNPs produced using restriction site-associated DNA sequencing (RAD-seq). Significant and positive relationships between local estimates of genetic and species diversities (α-SGDCs) were only found with the putatively neutral loci datasets and with species richness, confirming that neutral processes were primarily driving the correlations and that the involved processes differentially influenced local species diversity components (i.e., richness and evenness). In contrast, SGDCs based on genetic and community dissimilarities (β-SGDCs) were only significant with the putative non-neutral datasets. This suggests that selective processes influencing C. gayana genetic diversity were involved in the detected correlations. Together, our results demonstrate that analyzing distinct components of genetic and species diversity simultaneously is useful to determine the mechanisms behind species-genetic diversity relationships.

Effect of homophily and correlation of beliefs on COVID-19 and general infectious disease outbreaks.

Abstract: Contact between people with similar opinions and characteristics occurs at a higher rate than among other people, a phenomenon known as homophily. The presence of clusters of unvaccinated people has been associated with increased incidence of infectious disease outbreaks despite high population-wide vaccination rates. The epidemiological consequences of homophily regarding other beliefs as well as correlations among beliefs or circumstances are poorly understood, however. Here, we use a simple compartmental disease model as well as a more complex COVID-19 model to study how homophily and correlation of beliefs and circumstances in a social interaction network affect the probability of disease outbreak and COVID-19-related mortality. We find that the current social context, characterized by the presence of homophily and correlations between who vaccinates, who engages in risk reduction, and individual risk status, corresponds to a situation with substantially worse disease burden than in the absence of heterogeneities. In the presence of an effective vaccine, the effects of homophily and correlation of beliefs and circumstances become stronger. Further, the optimal vaccination strategy depends on the degree of homophily regarding vaccination status as well as the relative level of risk mitigation high- and low-risk individuals practice. The developed methods are broadly applicable to any investigation in which node attributes in a graph might reasonably be expected to cluster or exhibit correlations.

Identifying pathfinder elements for gold in bulk-rock geochemical data from the Cripple Creek Au–Te deposit: a statistical approach

Abstract: The Cripple Creek alkaline igneous rock-related, low-sulfidation epithermal gold telluride deposit, Colorado, is hosted in the 10 km wide Oligocene alkaline volcanic Cripple Creek diatreme in Proterozoic rocks. Gold occurs as native gold, Au-tellurides, and in the structure of arsenian pyrite, in potassically altered high-grade veins, and as disseminations in the host rocks. Correlation coefficients, principal component analysis, hierarchical cluster analysis and random forests were used to analyse major and trace element compositions of 995 rock samples primarily from low-grade gold mineralization in drill core from three currently operating pits (Wild Horse Extension, Globe Hill and Schist Island) in the northwestern part of the Cripple Creek diatreme. These methods suggest that Ag, As, Bi, Te and W are the best pathfinders to gold mineralization in low-grade disseminated ore. Although Mo correlates with gold in other studies and is spatially related to gold veins, molybdenite post-dated the formation of gold and is likely related to a late-stage porphyry overprint. These elements, in conjunction with mineralogical studies, indicate that tellurides, fluorite, quartz, carbonates, roscoelite, tennantite-tetrahedrite, pyrite, sphalerite, muscovite, monazite, bastnasite and hubnerite serve as exploration guides to ore.

The Theory of Island Biogeography

Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

Abstract: Summary Background Since December, 2019, Wuhan, China, has experienced an outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Epidemiological and clinical characteristics of patients with COVID-19 have been reported but risk factors for mortality and a detailed clinical course of illness, including viral shedding, have not been well described. Methods In this retrospective, multicentre cohort study, we included all adult inpatients (≥18 years old) with laboratory-confirmed COVID-19 from Jinyintan Hospital and Wuhan Pulmonary Hospital (Wuhan, China) who had been discharged or had died by Jan 31, 2020. Demographic, clinical, treatment, and laboratory data, including serial samples for viral RNA detection, were extracted from electronic medical records and compared between survivors and non-survivors. We used univariable and multivariable logistic regression methods to explore the risk factors associated with in-hospital death. Findings 191 patients (135 from Jinyintan Hospital and 56 from Wuhan Pulmonary Hospital) were included in this study, of whom 137 were discharged and 54 died in hospital. 91 (48%) patients had a comorbidity, with hypertension being the most common (58 [30%] patients), followed by diabetes (36 [19%] patients) and coronary heart disease (15 [8%] patients). Multivariable regression showed increasing odds of in-hospital death associated with older age (odds ratio 1·10, 95% CI 1·03–1·17, per year increase; p=0·0043), higher Sequential Organ Failure Assessment (SOFA) score (5·65, 2·61–12·23; p Interpretation The potential risk factors of older age, high SOFA score, and d-dimer greater than 1 μg/mL could help clinicians to identify patients with poor prognosis at an early stage. Prolonged viral shedding provides the rationale for a strategy of isolation of infected patients and optimal antiviral interventions in the future. Funding Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences; National Science Grant for Distinguished Young Scholars; National Key Research and Development Program of China; The Beijing Science and Technology Project; and Major Projects of National Science and Technology on New Drug Creation and Development.

Species Diversity In Space And Time

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Journal of infectious diseases

Abstract: to the editor—The coronavirus disease 2019 (COVID-19) pandemic has brought not only far too many losses of human lives but an economic crisis as well. Thus, effective treatments and vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed. Eyal et al have discussed challenge studies [1] to accelerate the assessment of vaccine effectiveness. In a challenge study, all participants are vaccinated with placebo or with the test vaccine and are then intentionally exposed to doses of SARS-CoV-2. There is already a worldwide initiative to register volunteers for such studies [2]. As all participants have been exposed, the effectiveness of a vaccine can be assessed with smaller sample sizes and possibly more quickly compared to the conventional trial with community participants; however, challenge studies are accompanied by serious ethical issues [3]. First, the characteristics of a distinct group of volunteers without risks for fatal progression or serious late complications of COVID-19 need to be reliably known. Second, a highly effective and safe treatment should be available for patients with COVID-19, so that fatalities and persistent adverse consequences can be avoided. Both these problems are not yet solved. Third, the consent of the volunteer must be with their full understanding of comprehensive information, including appreciation of potential long-term consequences. It may be questioned, however, whether someone at age 20 years or so can imagine the consequences of a scarred lung occurring many years later. Finally, it cannot be taken for granted that a vaccine that works in a challenge study with young, healthy volunteers will work in elderly patients with possible comorbid conditions [4]. Thus, even the social value of challenge trials can be questioned. Fortunately, there is an ethically more acceptable alternative for an accelerated evaluation of SARS-CoV-2 vaccines. The large, simple, randomized trial (LSRT), as proposed by Yusuf et al in 1984, is a reliable, methodologically and ethically sound alternative [5]. Characteristics of this design include: wide, simple eligibility criteria; central randomization; recording of only few baseline data; simple and short-term treatment; reduced or no follow-up visits; and outcome assessments of hard endpoints, preferably by registries. Using this design, truly large randomized trials with sample sizes beyond 40 000 patients have been carried out and answered important questions [6]. Probably due to the increasing bureaucratization of clinical research activities, including very costly monitoring, in the last 20 years there has been an almost complete disappearance of this trial design. At the current stage of evaluation of the effectiveness of SARS-CoV-2 vaccines, this design should be revived as it is ideally suited for this task. There would be wide eligibility criteria with very few exclusion criteria as the vaccine should become available for almost everybody. The investigational vaccine is a 1 or 2-time treatment only and no follow-up visits are needed. The outcomes, COVID-19 or death, can be collected either by registries available in many countries (eg, in the United States, United Kingdom, or Scandinavia) or by patient reporting. Vaccine safety information can be collected by established systems like the Vaccine Safety Datalink in the United States [7], prescription event monitoring programs (eg, the Drug Surveillance Research Unit in the United Kingdom [8]), or by direct patient safety reporting on websites, including those accessible with smartphones [9], which can be specifically designed for vaccine trials. Among the advantages of using the LSRT design are that it allows central randomization of large numbers of volunteers within a short time and rapid collection of the relevant outcomes at a low cost compared to the conventional phase 3 trials with many follow-up visits and extensive monitoring. Adaptive design features (eg, modification of the eligibility criteria considering the accruing safety information) are feasible as well. Given the wide entry criteria, the results provide external validity for large parts of the population compared to any challenge trial, which would need to focus on participants with extremely low risks for developing serious COVID-19. As there will be very many people who would like to participate in such a vaccination trial, the sample sizes needed should be achieved within a very short time. When the LSRT double-blind design is used, the validity of the results is assured and it does not generate the serious ethical issues inherent in challenge trials. Regarding the Salk vaccine, large randomized trials with sample sizes of more than 70 000 were done in the early 1950s [10] and such LSRTs should be feasible in 2020. Thus, the sponsors of vaccine trials and the drug regulatory agencies should start the preparatory work now to be ready once an investigational vaccine is ready to be administered on a large scale.