Identifying obesogenic environment through spatial clustering of body mass index among adults.

BACKGROUND: The escalating trend of obesity in Malaysia is surmounting, and the lack of evidence on the environmental influence on obesity is untenable. Obesogenic environmental factors often emerge as a result of shared environmental, demographic, or cultural effects among neighbouring regions that impact lifestyle. Employing spatial clustering can effectively elucidate the geographical distribution of obesity and pinpoint regions with potential obesogenic environments, thereby informing public health interventions and further exploration on the local environments. This study aimed to determine the spatial clustering of body mass index (BMI) among adults in Malaysia. METHOD: This study utilized information of respondents aged 18 to 59 years old from the National Health and Morbidity Survey (NHMS) 2014 and 2015 at Peninsular Malaysia and East Malaysia. Fast food restaurant proximity, district population density, and district median household income were determined from other sources. The analysis was conducted for total respondents and stratified by sex. Multilevel regression was used to produce the BMI estimates on a set of variables, adjusted for data clustering at enumeration blocks. Global Moran's I and Local Indicator of Spatial Association statistics were applied to assess the general clustering and location of spatial clusters of BMI, respectively using point locations of respondents and spatial weights of 8 km Euclidean radius or 5 nearest neighbours. RESULTS: Spatial clustering of BMI independent of individual sociodemographic was significant (p < 0.001) in Peninsular and East Malaysia with Global Moran's index of 0.12 and 0.15, respectively. High-BMI clusters (hotspots) were in suburban districts, whilst the urban districts were low-BMI clusters (cold spots). Spatial clustering was greater among males with hotspots located closer to urban areas, whereas hotspots for females were in less urbanized areas. CONCLUSION: Obesogenic environment was identified in suburban districts, where spatial clusters differ between males and females in certain districts. Future studies and interventions on creating a healthier environment should be geographically targeted and consider gender differences.

iIMPACT: integrating image and molecular profiles for spatial transcriptomics analysis.

Current clustering analysis of spatial transcriptomics data primarily relies on molecular information and fails to fully exploit the morphological features present in histology images, leading to compromised accuracy and interpretability. To overcome these limitations, we have developed a multi-stage statistical method called iIMPACT. It identifies and defines histology-based spatial domains based on AI-reconstructed histology images and spatial context of gene expression measurements, and detects domain-specific differentially expressed genes. Through multiple case studies, we demonstrate iIMPACT outperforms existing methods in accuracy and interpretability and provides insights into the cellular spatial organization and landscape of functional genes within spatial transcriptomics data.

Complete spatially resolved gene expression is not necessary for identifying spatial domains.

Spatially resolved transcriptomics (SRT) technologies have revolutionized the study of tissue organization. We introduce a graph convolutional network with an attention and positive emphasis mechanism, termed BINARY, relying exclusively on binarized SRT data to accurately delineate spatial domains. BINARY outperforms existing methods across various SRT data types while using significantly less input information. Our study suggests that precise gene expression quantification may not always be essential, inspiring further exploration of the broader applications of spatially resolved binarized gene expression data.

A Pipeline for Dynamic Analysis of Mitochondrial Content in Developing T Cells: Bridging the Gap Between High-Throughput Flow Cytometry and Single-Cell Microscopy Analysis.

Analyzing the dynamics of mitochondrial content in developing T cells is crucial for understanding the metabolic state during T cell development. However, monitoring mitochondrial content in real-time needs a balance of cell viability and image resolution. In this chapter, we present experimental protocols for measuring mitochondrial content in developing T cells using three modalities: bulk analysis via flow cytometry, volumetric imaging in laser scanning confocal microscopy, and dynamic live-cell monitoring in spinning disc confocal microscopy. Next, we provide an image segmentation and centroid tracking-based analysis pipeline for automated quantification of a large number of microscopy images. These protocols together offer comprehensive approaches to investigate mitochondrial dynamics in developing T cells, enabling a deeper understanding of their metabolic processes.

Exploring the County Level Mortality Pattern Variations in Rural Areas of Iran (2006- 2016).

BACKGROUND: Mortality rate in rural areas is a useful measure of the health of the population and the function of the health system, which varies over space and time. The objective of this research is to explore the spatial and temporal variations in the rural mortality rate in Iran at the county level in 2006, 2011 and 2016. METHODS: data were gathered from the rural population and mortality statistics published by the Statistical Centre of Iran and the National Organization for Civil Registration. Global spatial patterns were assessed using the Global Moran's I and local clusters through the Local Moran' I. RESULTS: Spatial distribution of rural mortality rate shows that during the years under study the number of counties with a lower rate has increased. The counties with rate of less form continuous areas in the southwest, central and east regions. The excess risk map reveals significant variations in both value and extent. Also, the values of Moran's index increased from 0.1848 in 2006 to 0.4041 in 2016, which indicates the strengthening of the cluster spatial pattern of the overall rural mortality rate. Local patterns have undergone substantial changes over space and time. CONCLUSION: The findings indicate significant spatial and temporal variations in rural mortality rates in Iran. Policymakers can use this information to plan and enhance healthcare infrastructure in specific counties. The findings serve for evaluating the effectiveness of health policies, enabling policymakers to make informed decisions, allocate resources efficiently and design targeted interventions for improved public health outcomes.

Joint Bayesian estimation of cell dependence and gene associations in spatially resolved transcriptomic data.

Recent technologies such as spatial transcriptomics, enable the measurement of gene expressions at the single-cell level along with the spatial locations of these cells in the tissue. Spatial clustering of the cells provides valuable insights into the understanding of the functional organization of the tissue. However, most such clustering methods involve some dimension reduction that leads to a loss of the inherent dependency structure among genes at any spatial location in the tissue. This destroys valuable insights of gene co-expression patterns apart from possibly impacting spatial clustering performance. In spatial transcriptomics, the matrix-variate gene expression data, along with spatial coordinates of the single cells, provides information on both gene expression dependencies and cell spatial dependencies through its row and column covariances. In this work, we propose a joint Bayesian approach to simultaneously estimate these gene and spatial cell correlations. These estimates provide data summaries for downstream analyses. We illustrate our method with simulations and analysis of several real spatial transcriptomic datasets. Our work elucidates gene co-expression networks as well as clear spatial clustering patterns of the cells. Furthermore, our analysis reveals that downstream spatial-differential analysis may aid in the discovery of unknown cell types from known marker genes.

A Scoping Review of GIS Mapping of Type 1 Diabetes in Children: Identifying Current Gaps and Future Research Directions Using PRISMA-ScR.

BACKGROUND: Type 1 Diabetes poses a significant public health threat, especially in low-and-middle countries, where resources are limited. The use of geographical information systems in diabetes research has shown the potential to reveal several epidemiological risk factors. AIMS: This scoping review aimed to identify the scope and extent of the current literature and explore its limitations on the geographical mapping of children with type 1 diabetes. METHODS: A scoping review was conducted using five electronic databases and included studies published between the years 2000 and 2023. The search terms included: "Type 1 Diabetes Mellitus", "GIS mapping", "Juvenile Onset Diabetes Mellitus", "Spatial Epidemiology", "Spatial Clustering", "Spatial analysis", and "Geographic information system". Relevant full-text articles that met the inclusion criteria were selected for review. RESULTS: The search identified 17 studies that met the criteria for inclusion in the review. More than half the studies were conducted before 2015 (n=11; 61%). All studies were conducted in High-Income Countries. More than 10 articles studied environmental factors, 3 of them focused on the environment, 6 of them included sociodemographic factors, and 1 study incorporated nutrition (as a variable) in environmental factors. 2 studies focused on the accessibility of health services by pediatric patients. CONCLUSION: Studies on type 1 diabetes highlight the complex relationship between incidence and risk, suggesting comprehensive prevention and treatment. Geographical mapping has potential in low- and middle-income nations, but further research is needed to develop innovative strategies. The importance of geomappping in understanding the risk factors for Type 1 Diabetes is highlighted in this scoping review, which also suggests a possible direction for focused interventions, particularly in settings with low resources.

Attention-guided variational graph autoencoders reveal heterogeneity in spatial transcriptomics.

The latest breakthroughs in spatially resolved transcriptomics technology offer comprehensive opportunities to delve into gene expression patterns within the tissue microenvironment. However, the precise identification of spatial domains within tissues remains challenging. In this study, we introduce AttentionVGAE (AVGN), which integrates slice images, spatial information and raw gene expression while calibrating low-quality gene expression. By combining the variational graph autoencoder with multi-head attention blocks (MHA blocks), AVGN captures spatial relationships in tissue gene expression, adaptively focusing on key features and alleviating the need for prior knowledge of cluster numbers, thereby achieving superior clustering performance. Particularly, AVGN attempts to balance the model's attention focus on local and global structures by utilizing MHA blocks, an aspect that current graph neural networks have not extensively addressed. Benchmark testing demonstrates its significant efficacy in elucidating tissue anatomy and interpreting tumor heterogeneity, indicating its potential in advancing spatial transcriptomics research and understanding complex biological phenomena.

Using agro-ecological zones to improve the representation of a multi-environment trial of soybean varieties.

This research introduces a novel framework for enhancing soybean cultivation in North America by categorizing growing environments into distinct ecological and maturity-based zones. Using an integrated analysis of long-term climatic data and records of soybean varietal trials, this research generates a zonal environmental characterization which captures major components of the growing environment which affect the range of adaptation of soybean varieties. These findings have immediate applications for optimizing multi-environment soybean trials. This characterization allows breeders to assess the environmental representation of a multi-environmental trial of soybean varieties, and to strategize the distribution of testing and the placement of test sites accordingly. This application is demonstrated with a historical scenario of a soybean multi-environment trial, using two resource allocation models: one targeted towards improving the general adaptation of soybean varieties, which focuses on widely cultivated areas, and one targeted towards specific adaptation, which captures diverse environmental conditions. Ultimately, the study aims to improve the efficiency and impact of soybean breeding programs, leading to the development of cultivars resilient to variable and changing climates.

Prevalence and spatial distribution characteristics of human echinococcosis: A county-level modeling study in southern Xinjiang, China.

Objectives: Human echinococcosis remains an important public health problem. The aim of this study was to analyze the prevalence and spatial distribution characteristics of human echinococcosis cases in southern Xinjiang, China from 2005 to 2021. Methods: Human echinococcosis cases were collected from the National Infectious Disease Reporting System. Joinpoint regression analysis was performed to explore the trends. Spatial autocorrelation, hot spot analysis, as well as spatial-temporal clustering analysis were conducted to confirm the distribution and risk factors. Results: A total of 4580 cases were reported in southern Xinjiang during 2005-2021, with a mean annual incidence of 2.56/100,000. Echinococcosis incidence showed an increasing trend from 2005 to 2017 (APC = 17.939, 95%CI: 13.985 to 22.029) and a decreasing trend from 2017 to 2021 (APC = -18.769, 95%CI: 28.157 to -8.154). Echinococcosis cases had a positive spatial autocorrelation in 2005-2021 (Moran's I = 0.19, P < 0.05). The disease hotspots were located in the east and west in these areas, then returned to the east clusters, including Hejing, Heshuo, Wuqia, Atushi, Aheqi, and Yanqi Hui Autonomous County. Meanwhile, spatial-temporal analysis identified the first cluster comprised of five counties (cities): Yanqi Hui Autonomous County, Korla City, Bohu County, Hejing County, and Heshuo County. And secondary clusters 1-3 are predominantly in Wushi County, Aheqi County, Keping County, Atushi City, Wuqia County and Cele County. Conclusions: Our findings suggest that echinococcosis is still an important zoonotic parasitic disease in southern Xinjiang, yet it showed a certain degree of spatial clustering. It is crucial to implement comprehensive prevention and control measures to effectively combat the epidemic of echinococcosis.

Adaptive activation Functions with Deep Kronecker Neural Network optimized with Bear Smell Search Algorithm for preventing MANET Cyber security attacks.

An Adaptive activation Functions with Deep Kronecker Neural Network optimized with Bear Smell Search Algorithm (BSSA) (ADKNN-BSSA-CSMANET) is proposed for preventing MANET Cyber security attacks. The mobile users are enrolled with Trusted Authority Using a Crypto Hash Signature (SHA-256). Every mobile user uploads their finger vein biometric, user ID, latitude and longitude for confirmation. The packet analyser checks if any attack patterns are identified. It is implemented using adaptive density-based spatial clustering (ADSC) that deems information from packet header. Geodesic filtering (GF) is used as a pre-processing method for eradicating the unsolicited content and filtering pertinent data. Group Teaching Algorithm (GTA)-based feature selection is utilized for ideal collection of features and Adaptive Activation Functions along Deep Kronecker Neural Network (ADKNN) is used to categorizing normal and attack packets (DoS, Probe, U2R, and R2L). Then BSSA is utilized for optimizing the weight parameters of ADKNN classifier for optimal classification. The proposed technique is executed in python and its efficiency is evaluated by several performances metrics, such as Accuracy, Attack Detection Rate, Detection Delay, Packet Delivery Ratio, Throughput, and Energy Consumption. The proposed technique provides 36.64%, 33.06%, and 33.98% lower Detection Delay on NSL-KDD dataset compared with the existing methods.

Geospatial methodology for determining the regional prevalence of hospital-reported childhood intussusception in patients from India.

Both developed and developing countries carry a large burden of pediatric intussusception. Sentinel site surveillance-based studies have highlighted the difference in the regional incidence of intussusception. The objectives of this manuscript were to geospatially map the locations of hospital-confirmed childhood intussusception cases reported from sentinel hospitals, identify clustering and dispersion, and reveal the potential causes of the underlying pattern. Geospatial analysis revealed positive clustering patterns, i.e., a Moran's I of 0.071 at a statistically significant (p value < 0.0010) Z score of 16.14 for the intussusception cases across India (cases mapped n = 2221), with 14 hotspots in two states (Kerala = 6 and Tamil Nadu = 8) at the 95% CI. Granular analysis indicated that 67% of the reported cases resided < 50 km from the sentinel hospitals, and the average travel distance to the sentinel hospital from the patient residence was calculated as 47 km (CI 95% min 1 km-max 378 km). Easy access and facility referral preferences were identified as the main causes of the existing clustering pattern of the disease. We recommend designing community-based surveillance studies to improve the understanding of the prevalence and regional epidemiological burden of the disease.

Frontiers and hotspots of high-intensity interval exercise in children and adolescents: text mining and knowledge domain visualization.

Background: During the past two decades, research on high-intensity interval exercise (HIIE) in children and adolescents has steadily accumulated, especially on the subthemes of improving cardiometabolic and cardiovascular health. However, there is still little scientific understanding of using scientometric analysis to establish knowledge maps. Exploring the relationship between known and new emerging ideas and their potential value has theoretical and practical implications in the context of a researcher's limited ability to read, analyze, and synthesize all published works. Objective: First, this study aims to provide extensive information on HIIE research in children and adolescents, including authors, institutions, countries, journals, and references. Second, the objective is to use co-occurrence, burst, and co-citation analyses based on hybrid node types to reveal hotspots and forecast frontiers for HIIE research in children and adolescents. Methods: Using the bibliographic data of the Web of Science Core Collection (WoSCC) as the data source, publications, authors, and journals were analyzed with the help of bibliometric methods and visualization tools such as CiteSpace, VOSviewer, Pajek, and Bibliometrix R package. Authorial, institutional, and national collaboration networks were plotted, along with research hotspots and research frontiers based on keyword bursts and document co-citations. Results: This study found that executive function, high-intensity interval training, heart rate variability, and insulin resistance are emerging research topics; high-intensity training, mental health, exercise intensity, and cardiometabolic risk factors are continual frontier research areas in the subthemes. Conclusion: Our study has three novel contributions. First, it explicitly and directly reflects the research history and current situation of the HIIE intervention strategy in children and adolescents. This approach makes it clear and easy to trace the origin and development of this strategy in specific groups of children and adolescents. Second, it analyzes the research hotspots of HIIE in the field and predicts the research frontiers and development trends, which will help researchers get a deeper understanding of HIIE and pediatric health research. Third, the findings will enable researchers to pinpoint the most influential scholars, institutions, journals, and references in the field, increasing the possibility of future collaborations between authors, institutions, and countries.

A flexible framework for spatial capture-recapture with unknown identities.

Camera traps or acoustic recorders are often used to sample wildlife populations. When animals can be individually identified, these data can be used with spatial capture-recapture (SCR) methods to assess populations. However, obtaining animal identities is often labor-intensive and not always possible for all detected animals. To address this problem, we formulate SCR, including acoustic SCR, as a marked Poisson process, comprising a single counting process for the detections of all animals and a mark distribution for what is observed (eg, animal identity, detector location). The counting process applies equally when it is animals appearing in front of camera traps and when vocalizations are captured by microphones, although the definition of a mark changes. When animals cannot be uniquely identified, the observed marks arise from a mixture of mark distributions defined by the animal activity centers and additional characteristics. Our method generalizes existing latent identity SCR models and provides an integrated framework that includes acoustic SCR. We apply our method to estimate density from a camera trap study of fisher (Pekania pennanti) and an acoustic survey of Cape Peninsula moss frog (Arthroleptella lightfooti). We also test it through simulation. We find latent identity SCR with additional marks such as sex or time of arrival to be a reliable method for estimating animal density.

Deciphering spatial domains from spatially resolved transcriptomics with Siamese graph autoencoder.

BACKGROUND: Cell clustering is a pivotal aspect of spatial transcriptomics (ST) data analysis as it forms the foundation for subsequent data mining. Recent advances in spatial domain identification have leveraged graph neural network (GNN) approaches in conjunction with spatial transcriptomics data. However, such GNN-based methods suffer from representation collapse, wherein all spatial spots are projected onto a singular representation. Consequently, the discriminative capability of individual representation feature is limited, leading to suboptimal clustering performance. RESULTS: To address this issue, we proposed SGAE, a novel framework for spatial domain identification, incorporating the power of the Siamese graph autoencoder. SGAE mitigates the information correlation at both sample and feature levels, thus improving the representation discrimination. We adapted this framework to ST analysis by constructing a graph based on both gene expression and spatial information. SGAE outperformed alternative methods by its effectiveness in capturing spatial patterns and generating high-quality clusters, as evaluated by the Adjusted Rand Index, Normalized Mutual Information, and Fowlkes-Mallows Index. Moreover, the clustering results derived from SGAE can be further utilized in the identification of 3-dimensional (3D) Drosophila embryonic structure with enhanced accuracy. CONCLUSIONS: Benchmarking results from various ST datasets generated by diverse platforms demonstrate compelling evidence for the effectiveness of SGAE against other ST clustering methods. Specifically, SGAE exhibits potential for extension and application on multislice 3D reconstruction and tissue structure investigation. The source code and a collection of spatial clustering results can be accessed at https://github.com/STOmics/SGAE/.

Are National Breast and Cervical Cancer Early Detection Program Recipients Providing Services in Counties Heavily Burdened by Breast and Cervical Cancer?

INTRODUCTION: Alignment of National Breast and Cervical Cancer Early Detection Program (NBCCEDP) clinical services with the spatial distribution of breast and cervical cancer burden is essential to maximizing programmatic impact and addressing cancer disparities. This study identified spatial clustering of breast and cervical cancer burden scores and assessed whether and to what extent NBCCEDP clinical services were associated with clusters for the 5-year period, 2015-2019. METHODS: We examined burden scores for spatial clustering using Local Indicators of Spatial Association (LISA) tests in GeoDA. We then used t-tests to compare the NBCCEDP 5-year average percentage of eligible women served clinical breast and cervical cancer services between hotspot (high burden) and coolspot clusters. RESULTS: There was statistically significant spatial clustering in the pattern of breast and cervical cancer burden scores across counties, with hotspot clusters mostly observed in the Southern region, Idaho and Nevada. For both breast and cervical cancer, higher percentages of eligible women received breast and cervical cancer clinical services in coolspot clusters compared to hotspot clusters during each year from 2015-2019. CONCLUSION: NBCCEDP clinical services can help reduce breast and cervical cancer burden. Yet, during 2015-2019, increased service delivery was not aligned with the spatial distribution of counties with greater breast and cervical cancer burdens. NBCCEDP recipients may improve their impact on breast and cervical cancer burden by prioritizing and consistently increasing service delivery in cancer burden hotspot clusters if they have not already maximized their resources in these areas.

Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies.

Recent advances in spatially-resolved single-omics and multi-omics technologies have led to the emergence of computational tools to detect or predict spatial domains. Additionally, histological images and immunofluorescence (IF) staining of proteins and cell types provide multiple perspectives and a more complete understanding of tissue architecture. Here, we introduce Proust, a scalable tool to predict discrete domains using spatial multi-omics data by combining the low-dimensional representation of biological profiles based on graph-based contrastive self-supervised learning. Our scalable method integrates multiple data modalities, such as RNA, protein, and H&E images, and predicts spatial domains within tissue samples. Through the integration of multiple modalities, Proust consistently demonstrates enhanced accuracy in detecting spatial domains, as evidenced across various benchmark datasets and technological platforms.

Temporal and Spatial Analysis of Negative Emotions in China during the COVID-19 Pandemic.

This research aims to explore the spatiotemporal distribution patterns of negative emotions in mainland China during different stages of the COVID-19 pandemic and the external factors influencing this clustering. Using Baidu Index data for 91 negative emotion keywords, a retrospective geographic analysis was conducted across Chinese provinces from 14 October 2019 to 7 July 2022. Four spatial analysis methods (Global Moran's Index, Local Moran's Index, Bivariate Global Moran's Index, and Bivariate Local Moran's Index) are employed to identify potential clustering patterns and influencing factors of negative emotions at different stages. The results indicate that the COVID-19 pandemic significantly intensified the clustering effect of negative emotions in China, particularly with a more pronounced radiation effect in northwestern provinces. Spatial positive correlations are observed between pandemic-related Baidu indices (pandemic Baidu index, government Baidu index, nucleic acid Baidu index) and negative emotions. These findings contribute to understanding the spatiotemporal distribution characteristics of negative emotions in China post the COVID-19 outbreak and can guide the allocation of psychological resources during emergencies, thereby promoting social stability.

Identifying priority areas for conservation: using ecosystem services hotspot mapping for land-use/land-cover planning in central of Iran.

The modeling and mapping of hotspots and coldspots ecosystem services (ESs) is an essential factor in the decision-making process for ESs conservation. Moreover, spatial prioritization is a serious stage in conservation planning. In the present research, based on the InVEST software, Getis-Ord statistics (Gi*), and a set of GIS methods, we quantified and mapped the variation and overlapping among three ESs (carbon storage, soil retention, and habitat quality). Furthermore, an approach was proffered for detecting priority areas to protect multiple ecosystem services. Hotspots recognized via the Gi* statistics technique contain a higher capacity for supplying ESs than other areas. This means that protecting these areas with a bigger number of overlapped hotspots can provide more services. Results indicated that population growth accompanied by the increase in construction sites and low-yield agricultural lands in the Zayanderood dam watershed basin has resulted in ES losses. This situation is represented by increasing soil erosion, reduced carbon storage, reduced biodiversity, and fragmented habitat distribution due to land-use change. The statistically significant carbon storage, soil retention, and habitat quality hotspots with above 95% confidence level account for 21.5%, 39.3%, and 16.9% of the study area, respectively. Therefore, a clear framework was presented in this study for setting ES-based conservation priority. Decision makers and land-use planners can also combine this technique into their framework to identify and conserve ES hotspots to support their targeted ecosystem policies.

Evidence of spatial clustering of childhood acute lymphoblastic leukemia cases in Greater Mexico City: report from the Mexican Inter-Institutional Group for the identification of the causes of childhood leukemia.

Background: A heterogeneous geographic distribution of childhood acute lymphoblastic leukemia (ALL) cases has been described, possibly, related to the presence of different environmental factors. The aim of the present study was to explore the geographical distribution of childhood ALL cases in Greater Mexico City (GMC). Methods: A population-based case-control study was conducted. Children <18 years old, newly diagnosed with ALL and residents of GMC were included. Controls were patients without leukemia recruited from second-level public hospitals, frequency-matched by sex, age, and health institution with the cases. The residence address where the patients lived during the last year before diagnosis (cases) or the interview (controls) was used for geolocation. Kulldorff's spatial scan statistic was used to detect spatial clusters (SCs). Relative risks (RR), associated p-value and number of cases included for each cluster were obtained. Results: A total of 1054 cases with ALL were analyzed. Of these, 408 (38.7%) were distributed across eight SCs detected. A relative risk of 1.61 (p<0.0001) was observed for the main cluster. Similar results were noted for the remaining seven ones. Additionally, a proximity between SCs, electrical installations and petrochemical facilities was observed. Conclusions: The identification of SCs in certain regions of GMC suggest the possible role of environmental factors in the etiology of childhood ALL.