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"Smith, L. R."
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Cryo-plasma FIB/SEM volume imaging of biological specimens
Serial focussed ion beam scanning electron microscopy (FIB/SEM) enables imaging and assessment of subcellular structures on the mesoscale (10 nm to 10 µm). When applied to vitrified samples, serial FIB/SEM is also a means to target specific structures in cells and tissues while maintaining constituents’ hydration shells for in situ structural biology downstream. However, the application of serial FIB/SEM imaging of non-stained cryogenic biological samples is limited due to low contrast, curtaining, and charging artefacts. We address these challenges using a cryogenic plasma FIB/SEM. We evaluated the choice of plasma ion source and imaging regimes to produce high-quality SEM images of a range of different biological samples. Using an automated workflow we produced three-dimensional volumes of bacteria, human cells, and tissue, and calculated estimates for their resolution, typically achieving 20–50 nm. Additionally, a tag-free localisation tool for regions of interest is needed to drive the application of in situ structural biology towards tissue. The combination of serial FIB/SEM with plasma-based ion sources promises a framework for targeting specific features in bulk-frozen samples (>100 µm) to produce lamellae for cryogenic electron tomography.
Journal Article
Effects of Climate on the Variation in Abundance of Three Tick Species in Illinois
The range of ticks in North America has been steadily increasing likely, in part, due to climate change. Along with it, there has been a rise in cases of tick-borne disease. Among those medically important tick species of particular concern are Ixodes scapularis Say (Acari: Ixodidae), Dermacentor variabilis Say (Acari: Ixodidae), and Amblyomma americanum Linneaus (Acari: Ixodidae). The aim of this study was to determine if climate factors explain existing differences in abundance of the three aforementioned tick species between two climatically different regions of Illinois (Central and Southern), and if climate variables impact each species differently. We used both zero-inflated regression approaches and Bayesian network analyses to assess relationships among environmental variables and tick abundance. Results suggested that the maximum average temperature and total precipitation are associated with differential impact on species abundance and that this difference varied by region. Results also reinforced a differential level of resistance to desiccation among these tick species. Our findings help to further define risk periods of tick exposure for the general public, and reinforce the importance of responding to each tick species differently.
Journal Article
Dynamics of data availability in disease modeling: An example evaluating the trade-offs of ultra-fine-scale factors applied to human West Nile virus disease models in the Chicago area, USA
Since 1999, West Nile virus (WNV) has moved rapidly across the United States, resulting in tens of thousands of human cases. Both the number of human cases and the minimum infection rate (MIR) in vector mosquitoes vary across time and space and are driven by numerous abiotic and biotic forces, ranging from differences in microclimates to socio-demographic factors. Because the interactions among these multiple factors affect the locally variable risk of WNV illness, it has been especially difficult to model human disease risk across varying spatial and temporal scales. Cook and DuPage Counties, comprising the city of Chicago and surrounding suburbs, experience some of the highest numbers of human neuroinvasive cases of WNV in the United States. Despite active mosquito control efforts, there is consistent annual WNV presence, resulting in more than 285 confirmed WNV human cases and 20 deaths from the years 2014-2018 in Cook County alone.
A previous Chicago-area WNV model identified the fifty-five most high and low risk locations in the Northwest Mosquito Abatement District (NWMAD), an enclave ¼ the size of the combined Cook and DuPage county area. In these locations, human WNV risk was stratified by model performance, as indicated by differences in studentized residuals. Within these areas, an additional two-years of field collections and data processing was added to a 12-year WNV dataset that includes human cases, MIR, vector abundance, and land-use, historical climate, and socio-economic and demographic variables, and was assessed by an ultra-fine-scale (1 km spatial x 1 week temporal resolution) multivariate logistic regression model.
Multivariate statistical methods applied to the ultra-fine-scale model identified fewer explanatory variables while improving upon the fit of the previous model. Beyond MIR and climatic factors, efforts to acquire additional covariates only slightly improved model predictive performance.
These results suggest human WNV illness in the Chicago area may be associated with fewer, but increasingly critical, key variables at finer scales. Given limited resources, these findings suggest large variations in model performance occur, depending on covariate availability, and provide guidance in variable selection for optimal WNV human illness modeling.
Journal Article
Modeling community COVID-19 transmission risk associated with U.S. universities
The ongoing COVID-19 pandemic is among the worst in recent history, resulting in excess of 520,000,000 cases and 6,200,000 deaths worldwide. The United States (U.S.) has recently surpassed 1,000,000 deaths. Individuals who are elderly and/or immunocompromised are the most susceptible to serious sequelae. Rising sentiment often implicates younger, less-vulnerable populations as primary introducers of COVID-19 to communities, particularly around colleges and universities. Adjusting for more than 32 key socio-demographic, economic, and epidemiologic variables, we (1) implemented regressions to determine the overall community-level, age-adjusted COVID-19 case and mortality rate within each American county, and (2) performed a subgroup analysis among a sample of U.S. colleges and universities to identify any significant preliminary mitigation measures implemented during the fall 2020 semester. From January 1, 2020 through March 31, 2021, a total of 22,385,335 cases and 374,130 deaths were reported to the CDC. Overall, counties with increasing numbers of university enrollment showed significantly lower case rates and marginal decreases in mortality rates. County-level population demographics, and not university level mitigation measures, were the most significant predictor of adjusted COVID-19 case rates. Contrary to common sentiment, our findings demonstrate that counties with high university enrollments may be more adherent to public safety measures and vaccinations, likely contributing to safer communities.
Journal Article
Accidental transfer of non-native soil organisms into Antarctica on construction vehicles
Antarctic terrestrial ecosystems currently include very few non-native species, due to the continent's extreme isolation from other landmasses. However, the indigenous biota is vulnerable to human-mediated introductions of non-native species. In December 2005, four construction vehicles were imported by contractors to the British Antarctic Survey's (BAS) Rothera Research Station (Antarctic Peninsula) from the Falkland Islands and South Georgia (South Atlantic) on board RRS James Clark Ross. The vehicles were contaminated with >132 kg of non-Antarctic soil that contained viable non-native angiosperms, bryophytes, micro-invertebrates, nematodes, fungi, bacteria, and c. 40,000 seeds and numerous moss propagules. The incident was a significant contravention of BAS operating procedures, the UK Antarctic Act (1994) and the Protocol on Environmental Protection to the Antarctic Treaty (1998), which all prohibit the introduction of non-native species to Antarctica without an appropriate permit. The introduction of this diverse range of species poses a significant threat to local biodiversity should any of the species become established, particularly as the biota of sub-Antarctic South Georgia is likely to include many species with appropriate pre-adaptations facilitating the colonisation of more extreme Antarctic environments. Once the incident was discovered, the imported soil was removed immediately from Antarctica and destroyed. Vehicle cleaning and transportation guidelines have been revised to enhance the biosecurity of BAS operations, and to minimise the risk of similar incidents occurring.
Journal Article
Examining HIV Stigma, Depression, Stress, and Recent Stimulant Use in a Sample of Sexual Minority Men Living with HIV: An Application of the Stigma and Substance Use Process Model
Sexual minority men (SMM) with HIV are disproportionately impacted by stigma and mental health disorders. Guided by the Stigma and Substance Use Process Model, we evaluated how HIV stigma impacts mental health outcomes among SMM with HIV. Data were drawn from Thrive With Me, an RCT of an mHealth intervention targeting ART adherence among SMM with HIV. Path analyses tested the relationships between HIV stigma, depression, stress, and recent stimulant use. Overall, 49.1% (194/401) had depression symptoms, 68.8% (276/401) had moderate-to-high stress, and 28.1% (111/401) had detectable stimulant use in urine samples at baseline. In path analyses, baseline internalized HIV stigma was associated with depression and stress 5-months post-baseline and enacted stigma was associated with recent stimulant use 11-months post-baseline. We identified internalized and enacted HIV stigma, but not anticipated stigma, as potentially important intervention targets for stimulant use, depression, and stress among SMM with HIV.
Journal Article