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"Miller, Jennifer A. (Jennifer Anne)"
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Mapping species distributions : spatial inference and prediction
\"Maps of species' distributions or habitat suitability are required for many aspects of environmental research, resource management and conservation planning. These include biodiversity assessment, reserve design, habitat management and restoration, species and habitat conservation plans and predicting the effects of environmental change on species and ecosystems. The proliferation of methods and uncertainty regarding their effectiveness can be daunting to researchers, resource managers and conservation planners alike. Franklin summarises the methods used in species distribution modeling (also called niche modeling) and presents a framework for spatial prediction of species distributions based on the attributes (space, time, scale) of the data and questions being asked. The framework links theoretical ecological models of species distributions to spatial data on species and environment, and statistical models used for spatial prediction. Providing practical guidelines to students, researchers and practitioners in a broad range of environmental sciences including ecology, geography, conservation biology, and natural resources management.\" --NHBS Environment Bookstore.
Book
Evaluation of SARS-CoV-2 serology assays reveals a range of test performance
Appropriate use and interpretation of serological tests for assessments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure, infection and potential immunity require accurate data on assay performance. We conducted a head-to-head evaluation of ten point-of-care-style lateral flow assays (LFAs) and two laboratory-based enzyme-linked immunosorbent assays to detect anti-SARS-CoV-2 IgM and IgG antibodies in 5-d time intervals from symptom onset and studied the specificity of each assay in pre-coronavirus disease 2019 specimens. The percent of seropositive individuals increased with time, peaking in the latest time interval tested (>20 d after symptom onset). Test specificity ranged from 84.3% to 100.0% and was predominantly affected by variability in IgM results. LFA specificity could be increased by considering weak bands as negative, but this decreased detection of antibodies (sensitivity) in a subset of SARS-CoV-2 real-time PCR-positive cases. Our results underline the importance of seropositivity threshold determination and reader training for reliable LFA deployment. Although there was no standout serological assay, four tests achieved more than 80% positivity at later time points tested and more than 95% specificity.
Of 12 serology assays tested, four detect antibodies in more than 80% of patients with COVID-19.
Journal Article
Multiple imputation of cognitive performance as a repeatedly measured outcome
Longitudinal studies of cognitive performance are sensitive to dropout, as participants experiencing cognitive deficits are less likely to attend study visits, which may bias estimated associations between exposures of interest and cognitive decline. Multiple imputation is a powerful tool for handling missing data, however its use for missing cognitive outcome measures in longitudinal analyses remains limited. We use multiple imputation by chained equations (MICE) to impute cognitive performance scores of participants who did not attend the 2011-2013 exam of the Atherosclerosis Risk in Communities Study. We examined the validity of imputed scores using observed and simulated data under varying assumptions. We examined differences in the estimated association between diabetes at baseline and 20-year cognitive decline with and without imputed values. Lastly, we discuss how different analytic methods (mixed models and models fit using generalized estimate equations) and choice of for whom to impute result in different estimands. Validation using observed data showed MICE produced unbiased imputations. Simulations showed a substantial reduction in the bias of the 20-year association between diabetes and cognitive decline comparing MICE (3-4 % bias) to analyses of available data only (16-23 % bias) in a construct where missingness was strongly informative but realistic. Associations between diabetes and 20-year cognitive decline were substantially stronger with MICE than in available-case analyses. Our study suggests when informative data are available for non-examined participants, MICE can be an effective tool for imputing cognitive performance and improving assessment of cognitive decline, though careful thought should be given to target imputation population and analytic model chosen, as they may yield different estimands.
Journal Article
Test performance evaluation of SARS-CoV-2 serological assays
Appropriate use and interpretation of serological tests for assessments of SARS-CoV-2 exposure, infection and potential immunity require accurate assay performance data. We conducted a head-to-head evaluation of 10 point-of-care (POC) style lateral flow assays (LFAs) and two laboratory-based enzyme-linked immunosorbent assays (ELISAs) to detect anti-SARS-CoV-2 IgM and IgG antibodies by 5-day time intervals from symptom onset and the specificity of each assay in pre-COVID-2019 specimens. The percent of seropositive individuals increased with time, peaking in the latest time interval tested (>20 days after symptom onset). Test specificity was heterogeneous (ranging from 84.3–100.0%) and was predominantly affected by variability in IgM results. LFA specificity could be increased by considering weak bands as negative, but this decreased detection of antibodies in a subset of SARS-CoV-2 real-time polymerase chain reaction (RT-PCR)-positive cases. Our results indicate the importance of seropositivity threshold determination and reader training for reliable LFA deployment. Informed use of serology will require evaluations covering the full spectrum of SARS-CoV-2 infections, from asymptomatic and mild infection to severe disease, and later convalescence. Well-designed studies to elucidate the mechanisms and serological correlates of protective immunity will be crucial to guide rational clinical and public health policies.
Journal Article
When choosing to put alcohol before food: Drunkoexia and college students
Drinking and eating behaviors continue to be issues on college campuses. Overall, the results from this study did not yield supporting data for drunkorexia. However, it still brings to light that more studies should be done to investigate the relationship between disordered eating and alcohol consumption behaviors. Upon review of the data, several aspects stand out besides not identifying drunkorexia in this data set; the first being that no gender difference was seen between men and women in the many ways drunkorexia was assessed. Giles et al. (2009) reported a difference in men and women -- finding that women were are higher risk for memory loss, being injured, or being taken advantage of sexually, while men were more likely to get into physical fights. The pressure of college may bridge the gap between men and women when it comes to eating and alcohol consumption behaviors. The current study failed to find a difference between men and women. Additional research is needed.
Dissertation
An Exploration of How Multiple Identities Impact Help-Seeking Behaviors for College Students
Researchers have noted disparities in counseling center usage related to gender, socioeconomic status, and race/ethnicity. However, most research has neglected the combined effects of these three variables. How do multiple identities impact the help-seeking behaviors of college students? By studying a subsample of students who participated in the 2010 University of California Undergraduate Experience Survey (UCUES) this study tested the proposition that a combination of race/ethnicity, gender, socioeconomic status, social support, depression/stress, and wellness factors impact help-seeking behaviors in a manner that differed across multiple identity categories for college students. Overall, about 27% needed counseling services and 11% used counseling services when needed. This study found that multiple identities mattered when exploring college-student help-seeking behaviors. Within identity groups, there appeared to be more of a need for counseling services for middle-income and lower-income traditionally underrepresented females. In the logistic regression model, there were effects for race/ethnicity, social class, multiple identities and depression/stress on utilizing counseling verses not utilizing counseling when needed. Additionally, across all race/ethnicity by gender by socioeconomic status categories there was a trend of less use of counseling services as income levels dropped.
Dissertation
Toward a community ecology of landscapes: predicting multiple predator—prey interactions across geographic space
Community ecology was traditionally an integrative science devoted to studying interactions between species and their abiotic environments in order to predict species' geographic distributions and abundances. Yet for philosophical and methodological reasons, it has become divided into two enterprises: one devoted to local experimentation on species interactions to predict community dynamics; the other devoted to statistical analyses of abiotic and biotic information to describe geographic distribution. Our goal here is to instigate thinking about ways to reconnect the two enterprises and thereby return to a tradition to do integrative science. We focus specifically on the community ecology of predators and prey, which is ripe for integration. This is because there is active, simultaneous interest in experimentally resolving the nature and strength of predator–prey interactions as well as explaining patterns across landscapes and seascapes. We begin by describing a conceptual theory rooted in classical analyses of non-spatial food web modules used to predict species interactions. We show how such modules can be extended to consideration of spatial context using the concept of habitat domain. Habitat domain describes the spatial extent of habitat space that predators and prey use while foraging, which differs from home range, the spatial extent used by an animal to meet all of its daily needs. This conceptual theory can be used to predict how different spatial relations of predators and prey could lead to different emergent multiple predator–prey interactions such as whether predator consumptive or non-consumptive effects should dominate, and whether intraguild predation, predator interference or predator complementarity are expected. We then review the literature on studies of large predator–prey interactions that make conclusions about the nature of multiple predator–prey interactions. This analysis reveals that while many studies provide sufficient information about predator or prey spatial locations, and thus meet necessary conditions of the habitat domain conceptual theory for drawing conclusions about the nature of the predator–prey interactions, several studies do not. We therefore elaborate how modern technology and statistical approaches for animal movement analysis could be used to test the conceptual theory, using experimental or quasi-experimental analyses at landscape scales.
Journal Article
Recumbence Behavior in Zoo Elephants: Determination of Patterns and Frequency of Recumbent Rest and Associated Environmental and Social Factors
Resting behaviors are an essential component of animal welfare but have received little attention in zoological research. African savanna elephant (Loxodonta africana) and Asian elephant (Elephas maximus) rest includes recumbent postures, but no large-scale investigation of African and Asian zoo elephant recumbence has been previously conducted. We used anklets equipped with accelerometers to measure recumbence in 72 adult female African (n = 44) and Asian (n = 28) elephants housed in 40 North American zoos. We collected 344 days of data and determined associations between recumbence and social, housing, management, and demographic factors. African elephants were recumbent less (2.1 hours/day, S.D. = 1.1) than Asian elephants (3.2 hours/day, S.D. = 1.5; P < 0.001). Nearly one-third of elephants were non-recumbent on at least one night, suggesting this is a common behavior. Multi-variable regression models for each species showed that substrate, space, and social variables had the strongest associations with recumbence. In the African model, elephants who spent any amount of time housed on all-hard substrate were recumbent 0.6 hours less per day than those who were never on all-hard substrate, and elephants who experienced an additional acre of outdoor space at night increased their recumbence by 0.48 hours per day. In the Asian model, elephants who spent any amount of time housed on all-soft substrate were recumbent 1.1 hours more per day more than those who were never on all-soft substrate, and elephants who spent any amount of time housed alone were recumbent 0.77 hours more per day than elephants who were never housed alone. Our results draw attention to the significant interspecific difference in the amount of recumbent rest and in the factors affecting recumbence; however, in both species, the influence of flooring substrate is notably important to recumbent rest, and by extension, zoo elephant welfare.
Journal Article
Incorporating spatial dependence in predictive vegetation models
Predictive vegetation modeling can be defined as predicting the distribution of vegetation across a landscape based on the relationship between the spatial distribution of vegetation and certain environmental variables. Often these predictive models are developed without considering the spatial pattern that exists in biogeographical data. When explicitly included in the model, this spatial dependence can increase the predictive ability significantly. In this study, presence/absence models of vegetation alliances in a portion of the Mojave Desert (California, USA) are developed using classification trees and generalized linear models and two methods of incorporating spatial dependence in the models are explored. The first method of incorporating spatial dependence involves interpolation and simulation techniques to “fill in the blanks” of the sample data to obtain an additional variable of neighborhood presence/absence. The second method considers that the model residuals are a direct indication of spatial dependence, typically in the form of an unmeasured yet important environmental variable. The model residuals are interpolated to a continuous map and added to the model predictions. In general, incorporating spatial dependence resulted in improved model accuracy for a majority of the eleven vegetation alliances studied here. However, incorporating spatial dependence did decrease the accuracy for some alliances, typically the rarer alliances. Simulation, while more computationally intensive than interpolation, provided more realistic looking predictions. When focusing on the spatial dependence in the model residuals, more robust model predictions resulted, as the alliances which are predicted well by environmental variables were “left alone”.
Dissertation
Blinatumomab in Standard-Risk B-Cell Acute Lymphoblastic Leukemia in Children
B-cell acute lymphoblastic leukemia (B-cell ALL) is the most common childhood cancer. Despite a high overall cure rate, relapsed B-cell ALL remains a leading cause of cancer-related death among children. The addition of the bispecific T-cell engager molecule blinatumomab (an anti-CD19 and anti-CD3 single-chain molecule) to therapy for newly diagnosed standard-risk (as defined by the National Cancer Institute) B-cell ALL in children may improve outcomes.
We conducted a phase 3 trial involving children with newly diagnosed standard-risk B-cell ALL who had an average or higher risk of relapse. Patients were randomly assigned to receive chemotherapy alone or chemotherapy plus two nonsequential 28-day cycles of blinatumomab. The primary end point was disease-free survival.
The data and safety monitoring committee reviewed the results from the first interim efficacy analysis, which included 1440 patients who had undergone randomization (722 to chemotherapy alone and 718 to blinatumomab and chemotherapy) and recommended early termination of randomization. At a median follow-up of 2.5 years, the estimated 3-year disease-free survival (±SE) was 96.0±1.2% with blinatumomab and chemotherapy and 87.9±2.1% with chemotherapy alone (difference in restricted mean survival time, 72 days; 95% confidence interval, 36 to 108; P<0.001 by stratified log-rank test). The estimated 3-year disease-free survival among patients with an average relapse risk was 97.5±1.3% with blinatumomab and chemotherapy and 90.2±2.3% with chemotherapy alone; among those with a higher relapse risk, the corresponding values were 94.1±2.5% and 84.8±3.8%. Cytokine release syndrome, seizures, and sepsis of grade 3 or higher were rare during blinatumomab cycles, but the overall incidence of nonfatal sepsis and catheter-related infections was significantly higher among patients with an average relapse risk who had been assigned to receive blinatumomab and chemotherapy than among those assigned to receive chemotherapy alone.
Adding blinatumomab to combination chemotherapy in patients with newly diagnosed childhood standard-risk B-cell ALL of average or higher risk of relapse significantly improved disease-free survival. (Funded by the National Institutes of Health and others; AALL1731 ClinicalTrials.gov number, NCT03914625.).
Journal Article