Most current approaches for quantification of RNA species in their natural spatial contexts in single cells are limited by a small number of parallel analyses. Here we report a strategy to dramatically increase the multiplexing capacity for RNA analysis in single cells in situ. In this method, transcripts are detected by fluorescence in situ hybridization (FISH). After imaging and data storage, the fluorescence signal is efficiently removed by photobleaching. This enables the reinitiation of FISH to detect other RNA species in the same cell. Through reiterative cycles of hybridization, imaging and photobleaching, the identities, positions and copy numbers of a large number of varied RNA species can be quantified in individual cells in situ. Using this approach, we analyzed seven different transcripts in single HeLa cells with five reiterative RNA FISH cycles. This approach has the potential to detect over 100 varied RNA species in single cells in situ, which will have wide applications in studies of systems biology, molecular diagnosis and targeted therapies.

Society is heavily dependent on a reliable electric supply; all infrastructure systems depend on electricity to operate. When the electric system fails, the impacts can be catastrophic (food spoilage, inoperable medical devices, lack of access to water, etc.). The social impacts, defined as the direct and indirect impacts on people, of power outages must be explored as the likelihood of power outages and blackouts are increasing. However, compared to other hazards, such as heat and flooding, the knowledge base on the impacts of power outages is relatively small. The purpose of this thesis is to identify what is currently known about the social impacts of power outages, identify where gaps in the literature exist, and deploy a survey to explore power outage experiences at the household level. This thesis is comprised of two chapters, a systematic literature review on the current knowledge of the social impacts of power outages and a multi-city survey focused on power outage experiences.

The first chapter comprised of a systematic literature review using a combined search of in Scopus which returned 762 candidate articles were identified that potentially explored the social impacts of power outages. However, after multiple filtering criteria were applied, only 45 articles met all criteria. Four themes were used to classify the literature, not exclusively, including modeling, social, technical, and other. Only papers that were classified as “social” - meaning they observed how people were affected by a power outage - or in combination with other categories were used within the review.

From the literature, populations of concern were identified, including minority demographics - specifically Blacks or African Americans, children, elderly, and rural populations. The most commonly reported health concerns were from those that rely on medical devices for chronic conditions and unsafe generator practices. Criminal activity was also reported to increase during prolonged power outages and can be mitigated by consistent messaging on where to receive assistance and when power will be restored. Providing financial assistance and resources such as food and water can reduce the crime rate temporarily, but the crime rate can be expected to increase once the relief expires. Authorities should expect looting to occur, especially in poorer areas, during prolonged power outages. Gaps in the literature were identified and future directions for research were provided.

The second chapter consists of a multi-city survey that targeted three major cities across the United States (Detroit, MI; Miami, FL; and Phoenix, AZ). The survey was disseminated through Amazon’s Mechanical Turk and hosted by Qualtrics. 896 participants from the three cities qualified to complete the full version of the survey. Three criteria had to be met for participants to complete the full survey including residing in one of the three target cities, living at their primary address for a majority of the year, and indicate they had experienced a power outage within the last five years.

Participants were asked questions regarding the number of outages experienced in the last five years, the length of their most recent and longest outage experienced, if they owned a generator, how they managed their longest power outage, if participants or anyone in their household relies on a medical device, the financial burden their power outage caused, and standard demographic- and income-related questions. Race was a significant variable that influenced the outage duration length but not frequency in Phoenix and Detroit. Income was not a significant variable associated with experiencing greater economic impacts, such as having thrown food away because of an outage and not receiving help during the longest outage. Additional assessments similar to this survey are needed to better understand household power outage experiences.

Findings from this thesis demonstrate traditional metrics used in vulnerability indices were not indicative of who experienced the greatest effects of power outages. Additionally, other factors that are not included in these indices, such as owning adaptive resources including medical devices and generators in Phoenix and Detroit, are factors in reducing negative outcomes. More research is needed on this topic to indicate which populations are more likely to experience factors that can influence positive or negative outage outcomes.

The notable increase in biofuel usage by the road transportation sector in Brazil during recent years has significantly altered the vehicular fuel composition. Consequently, many uncertainties are currently found in particulate matter vehicular emission profiles. In an effort to better characterise the emitted particulate matter, measurements of aerosol physical and chemical properties were undertaken inside two tunnels located in the São Paulo Metropolitan Area (SPMA). The tunnels show very distinct fleet profiles: in the Jânio Quadros (JQ) tunnel, the vast majority of the circulating fleet are light duty vehicles (LDVs), fuelled on average with the same amount of ethanol as gasoline. In the Rodoanel (RA) tunnel, the particulate emission is dominated by heavy duty vehicles (HDVs) fuelled with diesel (5% biodiesel). In the JQ tunnel, PM_2.5 concentration was on average 52 μg m^-3, with the largest contribution of organic mass (OM, 42%), followed by elemental carbon (EC, 17%) and crustal elements (13%). Sulphate accounted for 7% of PM_2.5 and the sum of other trace elements was 10%. In the RA tunnel, PM_2.5 was on average 233 μg m^-3, mostly composed of EC (52%) and OM (39%). Sulphate, crustal and the trace elements showed a minor contribution with 5%, 1%, and 1%, respectively. The average OC : EC ratio in the JQ tunnel was 1.59 ± 0.09, indicating an important contribution of EC despite the high ethanol fraction in the fuel composition. In the RA tunnel, the OC : EC ratio was 0.49 ± 0.12, consistent with previous measurements of diesel-fuelled HDVs. Besides bulk carbonaceous aerosol measurement, polycyclic aromatic hydrocarbons (PAHs) were quantified. The sum of the PAHs concentration was 56 ± 5 ng m^-3 and 45 ± 9 ng m^-3 in the RA and JQ tunnel, respectively. In the JQ tunnel, benzo(a)pyrene (BaP) ranged from 0.9 to 6.7 ng m^-3 (0.02–0.1‰ of PM_2.5)] whereas in the RA tunnel BaP ranged from 0.9 to 4.9 ng m^-3 (0.004–0. 02‰ of PM_2.5), indicating an important relative contribution of LDVs emission to atmospheric BaP.

About 2.5 × 10⁶ snapshots on microcrystals of photoactive yellow protein (PYP) from a recent serial femtosecond crystallographic (SFX) experiment were reanalyzed to maximum resolution. The resolution is pushed to 1.46 Å, and a PYP structural model is refined at that resolution. The result is compared to other PYP models determined at atomic resolution around 1 Å and better at the synchrotron. By comparing subtleties such as individual isotropic temperature factors and hydrogen bond lengths, we were able to assess the quality of the SFX data at that resolution. We also show that the determination of anisotropic temperature factor ellipsoids starts to become feasible with the SFX data at resolutions better than 1.5 Å.

Background: Urbanization can strongly impact the physiology, behavior, and fitness of animals. Conditions in cities may also promote the transmission and success of animal parasites and pathogens. However, to date, no studies have examined variation in the prevalence or severity of several distinct pathogens/parasites along a gradient of urbanization in animals or if these infections increase physiological stress in urban populations.

Methodology/Principal Findings: Here, we measured the prevalence and severity of infection with intestinal coccidians (Isospora sp.) and the canarypox virus (Avipoxvirus) along an urban-to-rural gradient in wild male house finches (Haemorhous mexicanus). In addition, we quantified an important stress indicator in animals (oxidative stress) and several axes of urbanization, including human population density and land-use patterns within a 1 km radius of each trapping site. Prevalence of poxvirus infection and severity of coccidial infection were significantly associated with the degree of urbanization, with an increase of infection in more urban areas. The degrees of infection by the two parasites were not correlated along the urban-rural gradient. Finally, levels of oxidative damage in plasma were not associated with infection or with urbanization metrics.

Conclusion/Significance: These results indicate that the physical presence of humans in cities and the associated altered urban landscape characteristics are associated with increased infections with both a virus and a gastrointestinal parasite in this common songbird resident of North American cities. Though we failed to find elevations in urban- or parasite/pathogen-mediated oxidative stress, humans may facilitate infections in these birds via bird feeders (i.e. horizontal disease transmission due to unsanitary surfaces and/or elevations in host population densities) and/or via elevations in other forms of physiological stress (e.g. corticosterone, nutritional).

Maricopa County is the home of the Phoenix metropolitan area, an expansive city with serious air quality concerns. To ameliorate air quality in the county, the Maricopa County Air Quality Department developed a website and mobile application called "Clean Air Make More" as a means of outreach and engagement. In doing this, the county has found a way to engender a bilateral relationship between individuals and their government agency. This study analyzes the effectiveness of Clean Air Make More in establishing this relationship and engaging the community in efforts to improve air quality. It concludes that the design of the application effectively meets user needs, but marketing efforts should target populations disposed to taking action regarding air quality.

Background:
Environmental heat exposure is a public health concern. The impacts of environmental heat on mortality and morbidity at the population scale are well documented, but little is known about specific exposures that individuals experience.

Objectives:
The first objective of this work was to catalyze discussion of the role of personal heat exposure information in research and risk assessment. The second objective was to provide guidance regarding the operationalization of personal heat exposure research methods.

Discussion:
We define personal heat exposure as realized contact between a person and an indoor or outdoor environment that poses a risk of increases in body core temperature and/or perceived discomfort. Personal heat exposure can be measured directly with wearable monitors or estimated indirectly through the combination of time–activity and meteorological data sets. Complementary information to understand individual-scale drivers of behavior, susceptibility, and health and comfort outcomes can be collected from additional monitors, surveys, interviews, ethnographic approaches, and additional social and health data sets. Personal exposure research can help reveal the extent of exposure misclassification that occurs when individual exposure to heat is estimated using ambient temperature measured at fixed sites and can provide insights for epidemiological risk assessment concerning extreme heat.

Conclusions:
Personal heat exposure research provides more valid and precise insights into how often people encounter heat conditions and when, where, to whom, and why these encounters occur. Published literature on personal heat exposure is limited to date, but existing studies point to opportunities to inform public health practice regarding extreme heat, particularly where fine-scale precision is needed to reduce health consequences of heat exposure.