Mapping the transcriptome: Realizing the full potential of spatial data analysis.

RNA sequencing in situ allows for whole-transcriptome characterization at high resolution, while retaining spatial information. These data present an analytical challenge for bioinformatics-how to leverage spatial information effectively? Properties of data with a spatial dimension require special handling, which necessitate a different set of statistical and inferential considerations when compared to non-spatial data. The geographical sciences primarily use spatial data and have developed methods to analye them. Here we discuss the challenges associated with spatial analysis and examine how we can take advantage of practice from the geographical sciences to realize the full potential of spatial information in transcriptomic datasets.

Geographic patterns of koala retrovirus genetic diversity, endogenization, and subtype distributions.

Koala retrovirus (KoRV) subtype A (KoRV-A) is currently in transition from exogenous virus to endogenous viral element, providing an ideal system to elucidate retroviral-host coevolution. We characterized KoRV geography using fecal DNA from 192 samples across 20 populations throughout the koala's range. We reveal an abrupt change in KoRV genetics and incidence at the Victoria/New South Wales state border. In northern koalas, pol gene copies were ubiquitously present at above five per cell, consistent with endogenous KoRV. In southern koalas, pol copies were detected in only 25.8% of koalas and always at copy numbers below one, while the env gene was detected in all animals and in a majority at copy numbers above one per cell. These results suggest that southern koalas carry partial endogenous KoRV-like sequences. Deep sequencing of the env hypervariable region revealed three putatively endogenous KoRV-A sequences in northern koalas and a single, distinct sequence present in all southern koalas. Among northern populations, env sequence diversity decreased with distance from the equator, suggesting infectious KoRV-A invaded the koala genome in northern Australia and then spread south. The exogenous KoRV subtypes (B to K), two novel subtypes, and intermediate subtypes were detected in all northern koala populations but were strikingly absent from all southern animals tested. Apart from KoRV subtype D, these exogenous subtypes were generally locally prevalent but geographically restricted, producing KoRV genetic differentiation among northern populations. This suggests that sporadic evolution and local transmission of the exogenous subtypes have occurred within northern Australia, but this has not extended into animals within southern Australia.

Phylogeographic analysis of the Bantu language expansion supports a rainforest route.

The Bantu expansion transformed the linguistic, economic, and cultural composition of sub-Saharan Africa. However, the exact dates and routes taken by the ancestors of the speakers of the more than 500 current Bantu languages remain uncertain. Here, we use the recently developed "break-away" geographical diffusion model, specially designed for modeling migrations, with "augmented" geographic information, to reconstruct the Bantu language family expansion. This Bayesian phylogeographic approach with augmented geographical data provides a powerful way of linking linguistic, archaeological, and genetic data to test hypotheses about large language family expansions. We compare four hypotheses: an early major split north of the rainforest; a migration through the Sangha River Interval corridor around 2,500 BP; a coastal migration around 4,000 BP; and a migration through the rainforest before the corridor opening, at 4,000 BP. Our results produce a topology and timeline for the Bantu language family, which supports the hypothesis of an expansion through Central African tropical forests at 4,420 BP (4,040 to 5,000 95% highest posterior density interval), well before the Sangha River Interval was open.

Tail-dependence of masting synchrony results in continent-wide seed scarcity.

Spatial synchrony may be tail-dependent, meaning it is stronger for peaks rather than troughs, or vice versa. High interannual variation in seed production in perennial plants, called masting, can be synchronized at subcontinental scales, triggering extensive resource pulses or famines. We used data from 99 populations of European beech (Fagus sylvatica) to examine whether masting synchrony differs between mast peaks and years of seed scarcity. Our results revealed that seed scarcity occurs simultaneously across the majority of the species range, extending to populations separated by distances up to 1800 km. Mast peaks were spatially synchronized at distances up to 1000 km and synchrony was geographically concentrated in northeastern Europe. Extensive synchrony in the masting lower tail means that famines caused by beech seed scarcity are amplified by their extensive spatial synchrony, with diverse consequences for food web functioning and climate change biology.

Development of A Rural-Urban Classification System for Public Health Research that Accommodates Structural Differences Between States.

Rural environments in the United States present challenges to wellness, but there is a lack of tools to categorize rurality at the subcounty level. The most common tool, the FDA's 2010 RUCA codes, uses data that are over a decade old and cannot accommodate regional differences in rurality. The purpose of this study was to develop a census-tract classification system of rurality and demonstrate its use in describing HIV outcomes. We transformed census-tract measures (population density, natural resource workforce, walkability index, household type, and air quality) into local scales of rurality using factor analysis. We surveyed public health practitioners to determine cut-points and compared the resulting categorization to RUCA codes. We described the incidence of HIV in WA by rural category. Our classification system categorized 25% of census tracts as rural, 19% as periurban and 56% as urban. Our survey yielded cut-offs that were more conservative in categorizing areas urban than RUCA codes. The rate of HIV diagnosis was substantially higher in urban areas. Our rural-urban classification system offers an alternative to RUCA codes that is more responsive to regional differences.

Applying a Bayesian Spatiotemporal Model to Examine Excess County-Level Cardiovascular Disease Death Rates During the COVID-19 Pandemic.

Amid the COVID-19 pandemic, national cardiovascular disease (CVD) death rates increased, especially among younger adults. County-level variation has not been documented. Using county-level CVD deaths (ICD-10 codes: I00-I99) from the US National Vital Statistics System, we developed a Bayesian multivariate spatiotemporal model to estimate excess CVD death rates in 2020 based on trends from 2010-2019 for adults aged 35-64 and ≥65 years. Among adults aged 35-64 years, 64.7% of counties experienced significant excess CVD death rates. The median county-level CVD death rate in 2020 was 150 per 100,000 persons, which exceeded the predicted rate for 2020 (median excess death rate: 11 per 100,000; median excess rate ratio: 1.08). Among adults aged ≥65 years, 15.2% of counties experienced significant excess CVD death rates. The median county-level CVD death rate was 1,546 per 100,000 in 2020, which exceeded the predicted rate in 2020 (median excess death rate: 48 per 100,000, median excess rate ratio: 1.03). Counties with significant excess death rates in 2020 were geographically dispersed. In 2020, disruptions of county-level CVD death rates were widespread, especially among younger adults, suggesting the continued importance of CVD prevention and treatment in younger adults in communities across the country.

Estimating uninsured and underinsured women eligible for Minnesota's Breast Cancer Screening Program.

Since its inception in 1991, the mission of the National Breast and Cervical Cancer Early Detection Program's (NBCCEDP) mission is to improve access to mammography. This program has demonstrated evidence showing that it has improved breast cancer screening rates for women who are uninsured and underinsured. However, the literature has shown that NBCCEDP screenings are decreasing, and only reach a portion of eligible women. Reliable estimates at the sub-county level are needed to identify and reach eligible women. Our work builds upon previous estimates by integrating uninsured and insurance status into spatially adaptive filters. We use spatially adaptive filters to create small area estimates of standardized incidence ratios describing the utilization rate of NBCCEDP services in Minnesota. We integrate the American Community Survey (2010-2014) insurance status data to account for the percentage that an individual is uninsured. We test five models that integrate insurance status by age, sex, and race/ethnicity. Our composite model, which adjusts for age, sex, and race/ethnicity insurance statuses, reduces 95% of the estimation error. We estimate that there approximately 49,913.7 women eligible to receive services for Minnesota. We also create small geography (i.e., county and sub-county) estimates for Minnesota. The integration of the insurance data improved our utilization estimate. The development of these methods will allow state programs to more efficiently use their resources and understand their reach.

The distribution of self-incompatibility systems in angiosperms: the relationship between mating system diversity, life span, growth habit and latitude in a changing global environment.

BACKGROUND AND AIMS: There is ample theoretical and experimental evidence that angiosperms harbouring self-incompatibility (SI) systems are likely to respond to global changes in unique ways relative to taxa with other mating systems. In this paper, we present an updated database on the prevalence of SI systems across angiosperms and examine the relationship between the presence of SI and latitude, biomes, life-history traits and management conditions to evaluate the potential vulnerability of SI taxa to climate change and habitat disturbance. METHODS: We performed literature searches to identify studies that employed controlled crosses, microscopic analyses and/or genetic data to classify taxa as having SI, self-compatibility (SC), partial self-compatibility (PSC) or self-sterility (SS). Where described, the site of the SI reaction and the presence of dimorphic versus monomorphic flowers were also recorded. We then combined this database on the distribution of mating systems with information about the life span, growth habit, management conditions and geographic distribution of taxa. Information about the geographic distribution of taxa was obtained from a manually curated version of the Global Biodiversity Information Facility database, and from vegetation surveys encompassing 9 biomes. We employed multinomial logit regression to assess the relationship between mating system and life-history traits, management condition, latitude and latitude-squared using self-compatible taxa as the baseline. Additionally, we employed LOESS regression to examine the relationship between the probability of SI and latitude. Finally, by summarizing information at the family level, we plotted the distribution of SI systems across angiosperms including information about the presence of SI or dioecy, the inferred reaction site of the SI system when known, as well as the proportion of taxa in a family for which information is available. KEY RESULTS: We obtained information about the SI status of 5686 hermaphroditic taxa, of which 55% exhibited SC, and the remaining 45% harbour SI, self-sterility (SS), or PSC. Highlights of the multinomial logit regression include that taxa with PSC have a greater odds of being short- (OR=1.3) or long- (OR=1.57) lived perennials relative to SC ones, and that SS/SI taxa (pooled) are less likely to be annuals (OR=0.64) and more likely to be long-lived perennials (OR=1.32). SS/SI taxa had a greater odds of being succulent (OR=2.4) or a tree (OR=2.05), and were less likely to be weeds (OR=0.34). Further, we find a quadratic relationship between the probability of being SI with latitude: SI taxa were more common in the tropics, a finding that was further supported by the vegetation surveys which showed fewer species with SS/SI in temperate and northern latitudes compared to mediterranean and tropical biomes. CONCLUSIONS: We conclude that in the short-term habitat fragmentation, pollinator loss and temperature increases may negatively impact plants with SI systems, particularly long-lived perennial and woody species dominant in tropical forests. In the longer term, these and other global changes are likely to select for self-compatible or partially self-compatible taxa which, due to the apparent importance of SI as a driver of plant diversification across the angiosperm tree of life, may globally influence plant species richness.

Objective Neighborhood-Level Disorder Versus Subjective Safety as Predictors of HIV Transmission Risk and Momentary Well-Being.

Mental health and HIV risk behavior have been studied with ecological momentary assessment (EMA), but this approach has not been combined with tracking of activity space (where people go and what they encounter there) in people with HIV and their social relations, who may be HIV+ or HIV-. Activity space represents a modifiable risk or protective factor for behavior related to health status and quality of life, in both clinical and nonclinical populations. We conducted an observational study with 286 participants (243 HIV+ and 43 HIV-), roughly matched for socioeconomic status and neighborhood of residence via three waves of snowball sampling. Each participant carried a smartphone for up to 4 weeks, making 5 randomly prompted entries and 1 end-of-day entry each day, plus self-initiated event-contingent entries for sexual activity and drug use. Responses to randomly prompted items provided subjective evaluations of the safety of the participant's current social and physical environment (the place they were and the people they were with). GPS-based location tracking-coupled with publicly available statistic indicating neighborhood-level physical disorder and socioeconomic disadvantage-provided an indicator of each participant's exposure to objective psychosocial hazard. We examined possible relationships of these objective and subjective environmental exposures with risky sexual and intravenous drug-use behavior, knowledge and utilization of antiretroviral treatment and prophylaxis, and momentary mental health (mood and stress, which relate to risky behavior and overall well-being). We found that both risky behavior and mental health were more related to participants' subjective evaluations of their activity space than to objective measures of neighborhood-level disorder, suggesting that, even within an objectively hazardous neighborhood, people who find a niche they perceive as socially and physically safe may engage in less risky behavior and have better well-being.Trial registration Clinicaltrials.gov Identifier NCT01571752.

The risk of secondary progressive multiple sclerosis is geographically determined but modifiable.

Geographical variations in the incidence and prevalence of multiple sclerosis have been reported globally. Latitude as a surrogate for exposure to ultraviolet radiation but also other lifestyle and environmental factors are regarded as drivers of this variation. No previous studies evaluated geographical variation in the risk of secondary progressive multiple sclerosis, an advanced form of multiple sclerosis that is characterized by steady accrual of irreversible disability. We evaluated differences in the risk of secondary progressive multiple sclerosis in relation to latitude and country of residence, modified by high-to-moderate efficacy immunotherapy in a geographically diverse cohort of patients with relapsing-remitting multiple sclerosis. The study included relapsing-remitting multiple sclerosis patients from the global MSBase registry with at least one recorded assessment of disability. Secondary progressive multiple sclerosis was identified as per clinician diagnosis. Sensitivity analyses used the operationalized definition of secondary progressive multiple sclerosis and the Swedish decision tree algorithm. A proportional hazards model was used to estimate the cumulative risk of secondary progressive multiple sclerosis by country of residence (latitude), adjusted for sex, age at disease onset, time from onset to relapsing-remitting phase, disability (Multiple Sclerosis Severity Score) and relapse activity at study inclusion, national multiple sclerosis prevalence, government health expenditure, and proportion of time treated with high-to-moderate efficacy disease-modifying therapy. Geographical variation in time from relapsing-remitting phase to secondary progressive phase of multiple sclerosis was modelled through a proportional hazards model with spatially correlated frailties. We included 51 126 patients (72% female) from 27 countries. The median survival time from relapsing-remitting phase to secondary progressive multiple sclerosis among all patients was 39 (95% confidence interval: 37 to 43) years. Higher latitude [median hazard ratio = 1.21, 95% credible interval (1.16, 1.26)], higher national multiple sclerosis prevalence [1.07 (1.03, 1.11)], male sex [1.30 (1.22, 1.39)], older age at onset [1.35 (1.30, 1.39)], higher disability [2.40 (2.34, 2.47)] and frequent relapses [1.18 (1.15, 1.21)] at inclusion were associated with increased hazard of secondary progressive multiple sclerosis. Higher proportion of time on high-to-moderate efficacy therapy substantially reduced the hazard of secondary progressive multiple sclerosis [0.76 (0.73, 0.79)] and reduced the effect of latitude [interaction: 0.95 (0.92, 0.99)]. At the country-level, patients in Oman, Tunisia, Iran and Canada had higher risks of secondary progressive multiple sclerosis relative to the other studied regions. Higher latitude of residence is associated with a higher probability of developing secondary progressive multiple sclerosis. High-to-moderate efficacy immunotherapy can mitigate some of this geographically co-determined risk.