Environmental and geographical factors influencing the spread of SARS-CoV-2 over 2 years: a fine-scale spatiotemporal analysis.

Introduction: Since its emergence in late 2019, the SARS-CoV-2 virus has led to a global health crisis, affecting millions and reshaping societies and economies worldwide. Investigating the determinants of SARS-CoV-2 diffusion and their spatiotemporal dynamics at high spatial resolution is critical for public health and policymaking. Methods: This study analyses 194,682 georeferenced SARS-CoV-2 RT-PCR tests from March 2020 and April 2022 in the canton of Vaud, Switzerland. We characterized five distinct pandemic periods using metrics of spatial and temporal clustering like inverse Shannon entropy, the Hoover index, Lloyd's index of mean crowding, and the modified space-time DBSCAN algorithm. We assessed the demographic, socioeconomic, and environmental factors contributing to cluster persistence during each period using eXtreme Gradient Boosting (XGBoost) and SHapley Additive exPlanations (SHAP), to consider non-linear and spatial effects. Results: Our findings reveal important variations in the spatial and temporal clustering of cases. Notably, areas with flatter epidemics had higher total attack rate. Air pollution emerged as a factor showing a consistent positive association with higher cluster persistence, substantiated by both immission models and, to a lesser extent, tropospheric NO2 estimations. Factors including population density, testing rates, and geographical coordinates, also showed important positive associations with higher cluster persistence. The socioeconomic index showed no significant contribution to cluster persistence, suggesting its limited role in the observed dynamics, which warrants further research. Discussion: Overall, the determinants of cluster persistence remained across the study periods. These findings highlight the need for effective air quality management strategies to mitigate air pollution's adverse impacts on public health, particularly in the context of respiratory viral diseases like COVID-19.

The spatial distribution of heat related hospitalizations and classification of the most dangerous heat events in California at a small-scale level.

Many studies have explored the impact of extreme heat on health, but few have investigated localized heat-health outcomes across a wide area. We examined fine-scale variability in vulnerable areas, considering population distribution, local weather, and landscape characteristics. Using 36 different heat event definitions, we identified the most dangerous types of heat events based on minimum, maximum, and diurnal temperatures with varying thresholds and durations. Focusing on California's diverse climate, elevation, and population distribution, we analyzed hospital admissions for various causes of admission (2004-2013). Our matching approach identified vulnerable zip codes, even with small populations, on absolute and relative scales. Bayesian Hierarchical models leveraged spatial correlation. We ranked the 36 heat event types by attributable hospital admissions per zip code and provided code, simulated data, and an interactive web app for reproducibility. Our findings showed high variation in heat-related hospitalizations in coastal cities and substantial heat burdens in the Central Valley. Diurnal heat events had the greatest impact in the Central Valley, while nighttime extreme heat events drove burdens in the southeastern desert. This spatially informed approach guides local policies, prioritizing dangerous heat events to reduce the heat-health burden. The methodology is applicable to other regions, informing early warning systems and characterizing extreme heat impacts.

Model-based disease mapping using primary care registry data.

BACKGROUND: Spatial modeling of disease risk using primary care registry data is promising for public health surveillance. However, it remains unclear to which extent challenges such as spatially disproportionate sampling and practice-specific reporting variation affect statistical inference. METHODS: Using lower respiratory tract infection data from the INTEGO registry, modeled with a logistic model incorporating patient characteristics, a spatially structured random effect at municipality level, and an unstructured random effect at practice level, we conducted a case and simulation study to assess the impact of these challenges on spatial trend estimation. RESULTS: Even with spatial imbalance and practice-specific reporting variation, the model performed well. Performance improved with increasing spatial sample balance and decreasing practice-specific variation. CONCLUSION: Our findings indicate that, with correction for reporting efforts, primary care registries are valuable for spatial trend estimation. The diversity of patient locations within practice populations plays an important role.

Assessing eco-geographic influences on COVID-19 transmission: a global analysis.

COVID-19 has been massively transmitted for almost 3 years, and its multiple variants have caused serious health problems and an economic crisis. Our goal was to identify the influencing factors that reduce the threshold of disease transmission and to analyze the epidemiological patterns of COVID-19. This study served as an early assessment of the epidemiological characteristics of COVID-19 using the MaxEnt species distribution algorithm using the maximum entropy model. The transmission of COVID-19 was evaluated based on human factors and environmental variables, including climate, terrain and vegetation, along with COVID-19 daily confirmed case location data. The results of the SDM model indicate that population density was the major factor influencing the spread of COVID-19. Altitude, land cover and climatic factor showed low impact. We identified a set of practical, high-resolution, multi-factor-based maximum entropy ecological niche risk prediction systems to assess the transmission risk of the COVID-19 epidemic globally. This study provided a comprehensive analysis of various factors influencing the transmission of COVID-19, incorporating both human and environmental variables. These findings emphasize the role of different types of influencing variables in disease transmission, which could have implications for global health regulations and preparedness strategies for future outbreaks.

Geospatial Modeling Methods in Epidemiological Kidney Research: An Overview and Practical Example.

Geospatial modeling methods in population-level kidney research have not been used to full potential because few studies have completed associative spatial analyses between risk factors and exposures and kidney conditions and outcomes. Spatial modeling has several advantages over traditional modeling, including improved estimation of statistical variation and more accurate and unbiased estimation of coefficient effect direction or magnitudes by accounting for spatial data structure. Because most population-level kidney research data are geographically referenced, there is a need for better understanding of geospatial modeling for evaluating associations of individual geolocation with processes of care and clinical outcomes. In this review, we describe common spatial models, provide details to execute these analyses, and perform a case-study to display how results differ when integrating geographic structure. In our case-study, we used U.S. nationwide 2019 chronic kidney disease (CKD) data from Centers for Disease Control and Prevention's Kidney Disease Surveillance System and 2006 to 2010 U.S. Environmental Protection Agency environmental quality index (EQI) data and fit a nonspatial count model along with global spatial models (spatially lagged model [SLM]/pseudo-spatial error model [PSEM]) and a local spatial model (geographically weighted quasi-Poisson regression [GWQPR]). We found the SLM, PSEM, and GWQPR improved model fit in comparison to the nonspatial regression, and the PSEM model decreased the positive relationship between EQI and CKD prevalence. The GWQPR also revealed spatial heterogeneity in the EQI-CKD relationship. To summarize, spatial modeling has promise as a clinical and public health translational tool, and our case-study example is an exhibition of how these analyses may be performed to improve the accuracy and utility of findings.

Dengue fever mapping in Bangladesh: A spatial modeling approach.

Background: Epidemics of the dengue virus can trigger widespread morbidity and mortality along with no specific treatment. Examining the spatial autocorrelation and variability of dengue prevalence throughout Bangladesh's 64 districts was the focus of this study. Methods: The spatial autocorrelation is evaluated with the help of Moran I and Geary C. Local Moran I was used to detect hotspots and cold spots, whereas local Getis Ord G was used to identify only spatial hotspots. The spatial heterogeneity has been detected using various conventional and spatial models, including the Poisson-Gamma model, the Poisson-Lognormal Model, the Conditional Autoregressive (CAR) model, the Convolution model, and the BYM2 model, respectively. These models are implemented using Gibbs sampling and other Bayesian hierarchical approaches to analyze the posterior distribution effectively, enabling inference within a Bayesian context. Results: The study's findings show that Moran Iand Geary Canalysis provides a substantial clustering pattern of positive spatial autocorrelation of dengue fever (DF) rates between surrounding districts at a 90% confidence interval. The Local Indicators of Spatial Autocorrelation cluster mapped spatial clusters and outliers based on prevalence rates, while the local Getis-Ord G displayed a thorough breakdown of high or low rates, omitting outliers. Although Chattogram had the most dengue cases (15,752), Khulna district had a higher prevalence rate (133.636) than Chattogram (104.796). The BYM2 model, determined to be well-fitted based on the lowest Deviance Information Criterion value (527.340), explains a significant association between spatial heterogeneity and prevalence rates. Conclusion: This research pinpoints the district with the highest prevalence rate for dengue and the neighboring districts that also have high risk, allowing government agencies and communities to take the necessary precautions to mollify the risk effect of DF.

Machine learning provides insights for spatially explicit pest management strategies by integrating information on population connectivity and habitat use in a key agricultural pest.

BACKGROUND: Insect pests have garnered increasing interest because of anthropogenic global change, and their sustainable management requires knowledge of population habitat use and spread patterns. To enhance this knowledge for the prevalent tea pest Empoasca onukii, we utilized a random forest algorithm and a bivariate map to develop and integrate models of its habitat suitability and genetic connectivity across China. RESULTS: Our modeling revealed heterogeneous spatial patterns in suitability and connectivity despite the common key environmental predictor of isothermality. Analyses indicated that tea cultivation in areas surrounding the Tibetan Plateau and the southern tip of China may be at low risk of population outbreaks because of their predicted low suitability and connectivity. However, regions along the middle and lower reaches of the Yangtze River should consider the high abundance and high recolonization potential of E. onukii, and thus the importance of control measures. Our results also emphasized the need to prevent dispersal from outside regions in the areas north of the Yangtze River and highlighted the effectiveness of internal management efforts in southwestern China and along the southeastern coast. Further projections under future conditions suggested the potential for increased abundance and spread in regions north of the Yangtze River and the southern tip of China, and indicated the importance of long-term monitoring efforts in these areas. CONCLUSION: These findings highlighted the significance of combining information on habitat use and spread patterns for spatially explicit pest management planning. In addition, the approaches we used have potential applications in the management of other pest systems and the conservation of endangered biological resources. © 2024 Society of Chemical Industry.

Forest fire vulnerability in Nepal's chure region: Investigating the influencing factors using generalized linear model.

The Chure region, among the world's youngest mountains, stands out as highly susceptible to natural calamities, particularly forest fires. The region has consistently experienced forest fire incidents, resulting in the degradation of valuable natural and anthropogenic resources. Despite its vulnerability, there have been limited studies to understand the relationship of various causative factors for the recurring fire problem. Hence, to comprehend the influencing factors for the recurring forest fire problem and its extent, we utilized generalized linear modeling under binary logistic regression to combine the dependent variable of satellite detected fire points and various independent variables. We conducted a variance inflation factor (VIF) test and correlation matrix to identify the 14 suitable variables for the study. The analysis revealed that forest fires occurred mostly during the three pre-monsoon periods and had a significant positive relation with the area under forest, rangeland, bare-grounds, and Normalized Difference Vegetation Index (NDVI) (P < 0.05). Consequently, our model showed that the probability of fire incidents decreases with elevation, precipitation, and population density (P < 0.05). Among the significant variables, the forest areas emerges as the most influencing factor, followed by precipitation, elevation, area of rangeland, population density, NDVI, and the area of bare ground. The validation of the model was done through the area under the curve (AUC = 0.92) and accuracy (ACC = 0.89) assessments, which showed the model performed excellently in terms of predictive capabilities. The modeling result and the forest fire susceptible map provide valuable insights into the forest fire vulnerability in the region, offering baseline information about forest fires that will be helpful for line agencies to prepare management strategies to further prevent the deterioration of the region.

Urban expansion simulation with an explainable ensemble deep learning framework.

Urban expansion simulation is of significant importance to land management and policymaking. Advances in deep learning facilitate capturing and anticipating urban land dynamics with state-of-the-art accuracy properties. In this context, a novel deep learning-based ensemble framework was proposed for urban expansion simulation at an intra-urban granular level. The ensemble framework comprises i) multiple deep learning models as encoders, using transformers for encoding multi-temporal spatial features and convolutional layers for processing single-temporal spatial features, ii) a tailored channel-wise attention module to address the challenge of limited interpretability in deep learning methods. The channel attention module enables the examination of the rationality of feature importance, thereby establishing confidence in the simulated results. The proposed method accurately anticipated urban expansion in Shenzhen, China, and it outperformed all the baseline methods in terms of both spatial accuracy and temporal consistency.

Testing for concordance between predicted species richness, past prioritization, and marine protected area designations in the western Indian Ocean.

Scientific advances in environmental data coverage and machine learning algorithms have improved the ability to make large-scale predictions where data are missing. These advances allowed us to develop a spatially resolved proxy for predicting numbers of tropical nearshore marine taxa. A diverse marine environmental spatial database was used to model numbers of taxa from ∼1000 field sites, and the predictions were applied to all 7039 6.25-km2 reef cells in 9 ecoregions and 11 nations of the western Indian Ocean. Our proxy for total numbers of taxa was based on the positive correlation (r2 = 0.24) of numbers of taxa of hard corals and 5 highly diverse reef fish families. Environmental relationships indicated that the number of fish species was largely influenced by biomass, nearness to people, governance, connectivity, and productivity and that coral taxa were influenced mostly by physicochemical environmental variability. At spatial delineations of province, ecoregion, nation, and strength of spatial clustering, we compared areas of conservation priority based on our total species proxy with those identified in 3 previous priority-setting reports and with the protected area database. Our method identified 119 locations that fit 3 numbers of taxa (hard coral, fish, and their combination) and 4 spatial delineations (nation, ecoregion, province, and reef clustering) criteria. Previous publications on priority setting identified 91 priority locations of which 6 were identified by all reports. We identified 12 locations that fit our 12 criteria and corresponded with 3 previously identified locations, 65 that aligned with at least 1 past report, and 28 that were new locations. Only 34% of the 208 marine protected areas in this province overlapped with identified locations with high numbers of predicted taxa. Differences occurred because past priorities were frequently based on unquantified perceptions of remoteness and preselected priority taxa. Our environment-species proxy and modeling approach can be considered among other important criteria for making conservation decisions.

Evaluación de la concordancia entre la riqueza de especies pronosticada, priorizaciones pasadas y la designación de áreas marinas protegidas en el oeste del Océano Índico Resumen Los avances científicos en la cobertura de datos ambientales y los algoritmos de aprendizaje automatizado han mejorado la capacidad de predecir a gran escala cuando hacen falta datos. Estos avances nos permiten desarrollar un representante con resolución espacial para predecir la cantidad de taxones marinos en las costas tropicales. Usamos una base de datos espaciales de diversos ambientes marinos para modelar la cantidad de taxones a partir de ∼1000 sitios de campo y aplicamos las predicciones a las 7039 celdas arrecifales de 6.25­km2 en nueve ecorregiones y once países del oeste del Océano Índico. Nuestro representante para la cantidad total de taxones se basó en la correlación positiva (r2=0.24) de la cantidad de taxones de corales duros y cinco familias de peces arrecifales con diversidad alta. Las relaciones ambientales indicaron que el número de especies de peces estuvo influenciado principalmente por la biomasa, la cercanía a las personas, la gestión, la conectividad y la productividad y que los taxones de coral estuvieron influenciados principalmente por la variabilidad ambiental fisicoquímica. Comparamos la prioridad de las áreas de conservación a nivel de las delimitaciones espaciales de provincia, ecorregión, nación y fuerza del agrupamiento espacial basado en nuestro total de especies representantes con aquellas especies identificadas en tres reportes previos de establecimiento de prioridades y con la base de datos de áreas protegidas. Con nuestro método identificamos 119 localidades aptas para tres cantidades de taxones (corales duros, peces y su combinación) y cuatro criterios de delimitación espacial (nación, ecorregión, provincia y grupo de arrecifes). Las publicaciones previas sobre el establecimiento de prioridades identificaron 91 localidades prioritarias de las cuales seis fueron identificadas por todos los reportes. Identificamos doce localidades que se ajustan a nuestros doce criterios y se correspondieron con tres localidades identificadas previamente, 65 que se alinearon con al menos un reporte anterior y 28 que eran nuevas localidades. Sólo 34% de las 208 áreas marinas protegidas en esta provincia se traslaparon con localidades identificadas con un gran número de taxones pronosticados. Hubo diferencias porque en el pasado se priorizaba frecuentemente con base en las percepciones no cuantificadas de lo remoto y prioritario de los taxones preseleccionados. Nuestra especie representante del ambiente y nuestra estrategia de modelo pueden considerarse entre otros criterios importantes para tomar decisiones de conservación.

An Offenders-Offenses Shared Component Spatial Model for Identifying Shared and Specific Hotspots of Offenders and Offenses: A Case Study of Juvenile Delinquents and Violent Crimes in the Greater Toronto Area.

Objectives: We attempted to apply the Bayesian shared component spatial modeling (SCSM) for the identification of hotspots from two (offenders and offenses) instead of one (offenders or offenses) variables and developed three risk surfaces for (1) common or shared by both offenders and offenses; (2) specific to offenders, and (3) specific to offenses. Methods: We applied SCSM to examine the joint spatial distributions of juvenile delinquents (offenders) and violent crime (offenses) in the York Region of the Greater Toronto Area at the dissemination area level. The spatial autocorrelation, overdispersion, and latent covariates were adjusted by spatially structured and unstructured random effect terms in the model. We mapped the posterior means of the estimated shared and specific risks for identifying the three risk surfaces and types of hotspots. Results: Results suggest that about 50% and 25% of the relative risks of juvenile delinquents and violent crimes, respectively, could be explained by the shared component of offenders and offenses. The spatially structured terms attributed to 48% and 24% of total variations of the delinquents and violent crimes, respectively. Contrastingly, the unstructured random covariates influenced 3% of total variations of the juvenile delinquents and 51% for violent crimes. Conclusions: The Bayesian SCSM presented in this study identifies shared and specific hotspots of juvenile delinquents and violent crime. The method can be applied to other kinds of offenders and offenses and provide new insights into the clusters of high risks that are due to both offenders and offenses or due to offenders or offenses only.

Evaluating urban environmental quality using multi criteria decision making.

In the urban environment, the quality refers to the capacity that provides and fulfills the material and spiritual needs of inhabitants. In order to improve the quality of urban life and standard of living for their citizens, planners and managers strive to raise Urban Environmental Quality. The objective of this study is to evaluate the quality of urban environment through the spatial analysis of a multi-criteria decision making (MCDM) method utilizing CRITIC. This research is conducted in district 4 and district 2 of the Tabriz Metropolis Municipality. In order to determine the quality of an urban environment, air pollution, vegetation coverage, land surface temperature, production of waste, population density, noise pollution, health care per capita, green spaces per capita, recreational spaces per capita, and distance from fault lines are used. After evaluating and producing environmental quality maps in two separate districts, 10 indicators were tested for significance and a comparative evaluation of two districts was conducted in order to determine which district was in better condition based on a statistical analysis of the T-test results. In accordance with the CRITIC method, there are significant differences between averages of waste production, population density, noise pollution, distance from fault lines, Land Surface Temperature, Normalized difference vegetation index, and distance from fault lines between the two districts. It appears that recreational space, air pollution, health care per capita, and green space per capita are not meaningfully different on averages. The preparation of environmental quality maps reveals the importance of meaningful indicators at the neighborhood level in two urban districts. In both districts by strengthening the continuity of the landscape through the development of ecological corridors and an increase in per capita can contribute to the improvement of the quality of the urban environment.

Mapping and assessing natural soundscape quality: An indicator-based model for landscape planning.

Natural soundscape quality (NSQ) has been recognized as an essential cultural ecosystem service that contributes significantly to human health and well-being. It also stands as an indispensable component of environmental quality, especially for landscape aesthetic quality. However, an assessment tool for NSQ in landscape planning and environmental impact assessments is still absent. Therefore, this paper aims to address this gap by proposing an indicator-based model for assessing and quantifying NSQ in the Geographic Information System. The model characterizes NSQ based on Calmness and Vibrancy, and employs several indicators, sub-indicators, and respective metrics as proxies to quantify and map them spatially. The evaluation criteria of the model correspond to the general public's preferences for soundscape features. The case study results in Springe municipality, Germany, show that the relative values of NSQ are high in green spaces, including forests, grasslands, and shrublands, whereas they are low in open farmlands. The multiple natural sounds yield higher NSQ scores than the individual ones. The same soundscape compositions in forests and in urban parks exhibit higher NSQ scores than in other land cover types. In addition, the shares of relative values show similar distribution patterns among Calmness, Vibrancy, and NSQ according to land cover types and soundscape compositions. The evaluation results align with public values and preferences for soundscape features. Unlike subjectivist approaches, our user-independent methodology is easily transferable and reproducible. The results are comparable and communicable among the assessed areas. These endow the indicator-based model with the potential to be applied at various planning and management scales. The findings can help to incorporate soundscape evaluation into landscape planning and management systems, supporting sustainable landscape development, and providing valuable information for policy-, plan- and decision-making.

Spatial risk of Haemaphysalis longicornis borne Dabieshan tick virus (DBTV) in China.

The uncertainty and unknowability of emerging infectious diseases have caused many major public health and security incidents in recent years. As a new tick-borne disease, Dabieshan tick virus (DBTV) necessitate systematic epidemiological and spatial distribution analysis. In this study, tick samples from Liaoning Province were collected and used to evaluate distribution of DBTV in ticks. Outbreak points of DBTV and the records of the vector Haemaphysalis longicornis in China were collected and used to establish a prediction model using niche model combined with environmental factors. We found that H. longicornis and DBTV were widely distributed in Liaoning Province. The risk analysis results showed that the DBTV in the eastern provinces of China has a high risk, and the risk is greatly influenced by elevation, land cover, and meteorological factors. The risk geographical area predicted by the model is significantly larger than the detected positive areas, indicating that the etiological survey is seriously insufficient. This study provided molecular and important epidemiological evidence for etiological ecology of DBTV. The predicted high-risk areas indicated the insufficient monitoring and risk evaluation and the necessity of future monitoring and control work.

Joint spatial modeling of the risks of co-circulating mosquito-borne diseases in Ceará, Brazil.

Mosquito-borne diseases such as dengue and chikungunya have been co-circulating in the Americas, causing great damage to the population. In 2021, for instance, almost 1.5 million cases were reported on the continent, being Brazil the responsible for most of them. Even though they are transmitted by the same mosquito, it remains unclear whether there exists a relationship between both diseases. In this paper, we model the geographic distributions of dengue and chikungunya over the years 2016 to 2021 in the Brazilian state of Ceará. We use a Bayesian hierarchical spatial model for the joint analysis of two arboviruses that includes spatial covariates as well as specific and shared spatial effects that take into account the potential autocorrelation between the two diseases. Our findings allow us to identify areas with high risk of one or both diseases. Only 7% of the areas present high relative risk for both diseases, which suggests a competition between viruses. This study advances the understanding of the geographic patterns and the identification of risk factors of dengue and chikungunya being able to help health decision-making.

Pattern Formation in Mesic Savannas.

We analyze a spatially extended version of a well-known model of forest-savanna dynamics, which presents as a system of nonlinear partial integro-differential equations, and study necessary conditions for pattern-forming bifurcations. Homogeneous solutions dominate the dynamics of the standard forest-savanna model, regardless of the length scales of the various spatial processes considered. However, several different pattern-forming scenarios are possible upon including spatial resource limitation, such as competition for water, soil nutrients, or herbivory effects. Using numerical simulations and continuation, we study the nature of the resulting patterns as a function of system parameters and length scales, uncovering subcritical pattern-forming bifurcations and observing significant regions of multistability for realistic parameter regimes. Finally, we discuss our results in the context of extant savanna-forest modeling efforts and highlight ongoing challenges in building a unifying mathematical model for savannas across different rainfall levels.

A pruned feed-forward neural network (pruned-FNN) approach to measure air pollution exposure.

Environmental epidemiology studies require accurate estimations of exposure intensities to air pollution. The process from air pollutant emission to individual exposure is however complex and nonlinear, which poses significant modeling challenges. This study aims to develop an exposure assessment model that can strike a balance between accuracy, complexity, and usability. In this regard, neural networks offer one possible approach. This study employed a custom-designed pruned feed-forward neural network (pruned-FNN) approach to calculate the air pollution exposure index based on emission time and rates, terrain factors, meteorological conditions, and proximity measurements. The model's performance was evaluated by cross-validating the estimated exposure indexes with ground-based monitoring records. The pruned FNN can predict pollution exposure indexes (PEIs) that are highly and stably correlated with the monitored air pollutant concentrations (Spearman's rank correlation coefficients for tenfold cross-validation (mean ± standard deviation: 0.906 ± 0.028) and for random cross-validation (0.913 ± 0.024)). The predicted values are also close to the ground truth in most cases (95.5% of the predicted PEIs have relative errors smaller than 10%) when the training datasets are sufficiently large and well-covered. The pruned-FNN method can make accurate exposure estimations using a flexible number of variables and less extensive data in a less money/time-consuming manner. Compared to other exposure assessment models, the pruned FNN is an appropriate and effective approach for exposure assessment that covers a large geographic area over a long period of time.

Predictive Modeling of Ungulate-Vehicle Collision in the Republic of Korea.

Animal-vehicle collisions (AVC) threaten animals as well as human life and property. AVC with ungulates, called ungulate-vehicle collision (UVC), often seriously endangers human safety because of the considerable body size of ungulates. In the Republic of Korea, three ungulate species, Capreolus pygargus, Hydropotes inermis, and Sus scrofa, account for a large proportion of AVC. This study aimed to understand the characteristics of UVC by examining various parameters related to habitat, traffic, and seasonality using MaxEnt. The results showed that the peak UVC seasons coincided with the most active seasonal behaviors of the studied ungulates. For the modeling results, in C. pygargus, habitat variables are most important for models across seasons, and UVC events are most likely to occur in high mountain chains. In H. inermis, habitat and traffic variables are most important for models across seasons. Although the important habitat for the models were different across seasons for S. scrofa, the maximum speed was consistently critical for models across all seasons. Factors critical to UVC in the Republic of Korea were different for the three ungulate species and across seasons, indicating that seasonal behavior should be considered along with landscape and traffic characteristics to mitigate UVC.

Hierarchical Bayesian spatio-temporal modeling of COVID-19 in the United States.

We examine the impact of economic, demographic, and mobility-related factors have had on the transmission of COVID-19 in 2020. While many models in the academic literature employ linear/generalized linear models, few contributions exist that incorporate spatial analysis, which is useful for understanding factors influencing the proliferation of the disease before the introduction of vaccines. We utilize a Poisson generalized linear model coupled with a spatial autoregressive structure to do so. Our analysis yields a number of insights including that, in some areas of the country, the counterintuitive result that staying at home can lead to increased disease proliferation. Additionally, we find some positive effects from increased gathering at grocery stores, negative effects of visiting retail stores and workplaces, and even small effects on visiting parks highlighting the complexities travel and migration have on the transmission of diseases.

BayesTME: An end-to-end method for multiscale spatial transcriptional profiling of the tissue microenvironment.

Spatial variation in cellular phenotypes underlies heterogeneity in immune recognition and response to therapy in cancer and many other diseases. Spatial transcriptomics holds the potential to quantify such variation, but existing analysis methods are limited by their focus on individual tasks such as spot deconvolution. We present BayesTME, an end-to-end Bayesian method for analyzing spatial transcriptomics data. BayesTME unifies several previously distinct analysis goals under a single, holistic generative model. This unified approach enables BayesTME to deconvolve spots into cell phenotypes without any need for paired single-cell RNA-seq. BayesTME then goes beyond spot deconvolution to uncover spatial expression patterns among coordinated subsets of genes within phenotypes, which we term spatial transcriptional programs. BayesTME achieves state-of-the-art performance across myriad benchmarks. On human and zebrafish melanoma tissues, BayesTME identifies spatial transcriptional programs that capture fundamental biological phenomena such as bilateral symmetry and tumor-associated fibroblast and macrophage reprogramming. BayesTME is open source.