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.

BayeSMART: Bayesian clustering of multi-sample spatially resolved transcriptomics data.

The field of spatially resolved transcriptomics (SRT) has greatly advanced our understanding of cellular microenvironments by integrating spatial information with molecular data collected from multiple tissue sections or individuals. However, methods for multi-sample spatial clustering are lacking, and existing methods primarily rely on molecular information alone. This paper introduces BayeSMART, a Bayesian statistical method designed to identify spatial domains across multiple samples. BayeSMART leverages artificial intelligence (AI)-reconstructed single-cell level information from the paired histology images of multi-sample SRT datasets while simultaneously considering the spatial context of gene expression. The AI integration enables BayeSMART to effectively interpret the spatial domains. We conducted case studies using four datasets from various tissue types and SRT platforms, and compared BayeSMART with alternative multi-sample spatial clustering approaches and a number of state-of-the-art methods for single-sample SRT analysis, demonstrating that it surpasses existing methods in terms of clustering accuracy, interpretability, and computational efficiency. BayeSMART offers new insights into the spatial organization of cells in multi-sample SRT data.

Identifying spatial domain by adapting transcriptomics with histology through contrastive learning.

Recent advances in spatial transcriptomics have enabled measurements of gene expression at cell/spot resolution meanwhile retaining both the spatial information and the histology images of the tissues. Accurately identifying the spatial domains of spots is a vital step for various downstream tasks in spatial transcriptomics analysis. To remove noises in gene expression, several methods have been developed to combine histopathological images for data analysis of spatial transcriptomics. However, these methods either use the image only for the spatial relations for spots, or individually learn the embeddings of the gene expression and image without fully coupling the information. Here, we propose a novel method ConGI to accurately exploit spatial domains by adapting gene expression with histopathological images through contrastive learning. Specifically, we designed three contrastive loss functions within and between two modalities (the gene expression and image data) to learn the common representations. The learned representations are then used to cluster the spatial domains on both tumor and normal spatial transcriptomics datasets. ConGI was shown to outperform existing methods for the spatial domain identification. In addition, the learned representations have also been shown powerful for various downstream tasks, including trajectory inference, clustering, and visualization.

Graph deep learning enabled spatial domains identification for spatial transcriptomics.

Advancing spatially resolved transcriptomics (ST) technologies help biologists comprehensively understand organ function and tissue microenvironment. Accurate spatial domain identification is the foundation for delineating genome heterogeneity and cellular interaction. Motivated by this perspective, a graph deep learning (GDL) based spatial clustering approach is constructed in this paper. First, the deep graph infomax module embedded with residual gated graph convolutional neural network is leveraged to address the gene expression profiles and spatial positions in ST. Then, the Bayesian Gaussian mixture model is applied to handle the latent embeddings to generate spatial domains. Designed experiments certify that the presented method is superior to other state-of-the-art GDL-enabled techniques on multiple ST datasets. The codes and dataset used in this manuscript are summarized at https://github.com/narutoten520/SCGDL.

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.

An interpretable Bayesian clustering approach with feature selection for analyzing spatially resolved transcriptomics data.

Recent breakthroughs in spatially resolved transcriptomics (SRT) technologies have enabled comprehensive molecular characterization at the spot or cellular level while preserving spatial information. Cells are the fundamental building blocks of tissues, organized into distinct yet connected components. Although many non-spatial and spatial clustering approaches have been used to partition the entire region into mutually exclusive spatial domains based on the SRT high-dimensional molecular profile, most require an ad hoc selection of less interpretable dimensional-reduction techniques. To overcome this challenge, we propose a zero-inflated negative binomial mixture model to cluster spots or cells based on their molecular profiles. To increase interpretability, we employ a feature selection mechanism to provide a low-dimensional summary of the SRT molecular profile in terms of discriminating genes that shed light on the clustering result. We further incorporate the SRT geospatial profile via a Markov random field prior. We demonstrate how this joint modeling strategy improves clustering accuracy, compared with alternative state-of-the-art approaches, through simulation studies and 3 real data applications.

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.

Spatial heterogeneity in unintended pregnancy and its determinants in India.

BACKGROUND: Understanding the geographic variation of unintended pregnancy is crucial for informing tailored policies and programs to improve maternal and child health outcomes. Although spatial analyses of unintended pregnancy have been conducted in several developing countries, such research is lacking in India. This study addresses this gap by investigating the geographic distribution and determinants of unintended pregnancy in India. METHODS: We analysed data from the National Family Health Survey-5 encompassing 232,920 pregnancies occurring between 2014 and 2021 in India. We conducted a spatial analysis to investigate the distribution of unintended pregnancies at both state and district levels using choropleth maps. To assess spatial autocorrelation, Global Moran's I statistic was employed. Cluster and outlier analysis techniques were then utilized to identify significant clusters of unintended pregnancies across India. Furthermore, we employed Spatial Lag Model (SLM) and Spatial Error Model (SEM) to investigate the factors influencing the occurrence of unintended pregnancies within districts. RESULTS: The national rate of unintended pregnancy in India is approximately 9.1%, but this rate varies significantly between different states and districts of India. The rate exceeded 10% in the states situated in the northern plain such as Haryana, Delhi, Uttar Pradesh, Bihar, and West Bengal, as well as in the Himalayan states of Himachal Pradesh, Uttarakhand, Sikkim, and Arunachal Pradesh. Moreover, within these states, numerous districts reported rates exceeding 15%. The results of Global Moran's I indicated a statistically significant geographical clustering of unintended pregnancy rates at the district level, with a coefficient of 0.47 (p < 0.01). Cluster and outlier analysis further identified three major high-high clusters, predominantly located in the districts of Arunachal Pradesh, northern West Bengal, Bihar, western Uttar Pradesh, Haryana, Delhi, alongside a few smaller clusters in Odisha, Madhya Pradesh, Uttarakhand, and Himachal Pradesh. This geographic clustering of unintended pregnancy may be attributed to factors such as unmet needs for family planning, preferences for smaller family sizes, or the desire for male children. Results from the SEM underscored that parity and use of modern contraceptive were statistically significant predictors of unintended pregnancy at the district level. CONCLUSION: Our analysis of comprehensive, nationally representative data from NFHS-5 in India reveals significant geographical disparities in unintended pregnancies, evident at both state and district levels. These findings underscore the critical importance of targeted policy interventions, particularly in geographical hotspots, to effectively reduce unintended pregnancy rates and can contribute significantly to improving reproductive health outcomes across the country.

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.

Predictors of adolescent childbearing among Ethiopian women with spatial effect adjustment.

BACKGROUND: Childbearing under the age of 20 is referred to as teenage childbearing. Compared to high-income countries, it is significantly higher in low-income countries. Adolescent childbearing is influenced by a number of variables, including economic, demographic, and social factors, and these vary geographically. Thus, this study aimed to determine the predictors of adolescent childbearing among Ethiopian women with spatial effect adjustment. METHODS: A total weighted sample of 4712 women aged 15 to 49 were included. The data were obtained from the 2019 Ethiopia Demographic and Health Survey. A generalized Geoadditive model which accounts for spatial effect and the non-linear effect of continuous variables was adopted to determine the associated factors of adolescent childbearing among Ethiopian women. RESULTS: The spatial pattern of adolescent childbearing was non-random in Ethiopia with Moran's index statistics 1.731999 (P-value < 0.001). Based on the evidence of spatial variation in a model, the highest risk of adolescent childbearing was observed in Jijiga, Shinilie, Welwel and Walder, Afar (Zone1 and Zone 5), Assosa, Metekel, and Gambela (Zone1). We also noted that women not intending to use a contraceptive method, Muslim religion, living in a rural area, and large household family size were significantly associated with a high risk of adolescent childbearing. Furthermore, our model results also confirmed that higher educational levels, older household age, and good economic status significantly reduced the risk of adolescent childbearing. CONCLUSIONS: This study revealed that adolescent childbearing distribution was significantly clustered in the Eastern and Southwestern parts of Ethiopia. Intervention programs aimed at the prevention of early marriage and raising awareness of sexual activity are essential to reducing adolescent childbearing.

Reexploring the conception of heat-health risk: From the perspectives of dimensionality and spatiality.

Extreme heat events are more frequent and intense as a result of global climate change, thus posing tremendous threats to public health. However, extant literature exploring the multidimensional features of heat-health risks from a spatial perspective is limited. This study revisits extreme heat-health risk and decomposes this concept by integrating multi-sourced datasets, identifying compositional features, examining spatial patterns, and comparing classified characteristics based on local conditions. Using Maryland as the focal point, we found that the components of heat-health risk are different from traditional risk dimensions (i.e., vulnerability, hazards, and exposure). Through a local-level clustering analysis, heat-health risks were compared with areas having similar features, and among those with different features. The findings suggest a new perspective for understanding the socio-environmental and socio-spatial features of heat-health risks. They also offer an apt example of applying cross-disciplinary methods and tools for investigating an ever-changing phenomenon. Moreover, the spatial classification mechanism provides insights about the underlying causes of heat-health risk disparities and offers reference points for decision-makers regarding identification of vulnerable areas, resource allocation, and causal inferences when planning for and managing extreme heat disasters.

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.

Spatial clustering of amyotrophic lateral sclerosis in Sardinia, Italy: The contribution of age, sex, and genetic factors.

INTRODUCTION/AIMS: Several microgeographic clusters of higher/lower incidence of amyotrophic lateral sclerosis (ALS) have been identified worldwide. Differences in the distribution of local factors were proposed to explain the excess ALS risk, whereas the contribution of known genetic/epigenetic factors remains unclear. The aim is to identify restricted areas of higher risk in Sardinia and to assess whether age, sex, and the most common causative genetic mutations in Sardinia (C9orf72 and TARDBP mutations) contributed to the variation in the ALS risk. METHODS: We performed an ad hoc analysis of the 10-y population-based incident cohort of ALS cases from a recent study of a large Sardinian area. Cluster analysis was performed by age- and sex-adjusted Kulldorff's spatial scan statistic. RESULTS: We identified a statistically significant cluster of higher ALS incidence in a relatively large area including 34 municipalities and >100,000 individuals. The investigated genetic mutations were more frequent in the cluster area than outside. Regardless of the genetic mutations, the excess of ALS risk was significantly associated with either sex or with age ≥ 65 y. Finally, an additive interaction between older age and male sex contributed to the excess of ALS risk in the cluster area but not outside. DISCUSSION: Our analysis demonstrated that known genetic factors, age, and sex may contribute to microgeographic variation in ALS incidence. The significant additive interaction between older age and male sex we found in the high-incidence cluster could suggest the presence of a third factor connecting the analyzed risk factors.

The spatial signature of Plasmodium vivax and Plasmodium falciparum infections: quantifying the clustering of infections in cross-sectional surveys and cohort studies.

BACKGROUND: Over the last decades, enormous successes have been achieved in reducing malaria burden globally. In Latin America, South East Asia, and the Western Pacific, many countries now pursue the goal of malaria elimination by 2030. It is widely acknowledged that Plasmodium spp. infections cluster spatially so that interventions need to be spatially informed, e.g. spatially targeted reactive case detection strategies. Here, the spatial signature method is introduced as a tool to quantify the distance around an index infection within which other infections significantly cluster. METHODS: Data were considered from cross-sectional surveys from Brazil, Thailand, Cambodia, and Solomon Islands, conducted between 2012 and 2018. Household locations were recorded by GPS and finger-prick blood samples from participants were tested for Plasmodium infection by PCR. Cohort studies from Brazil and Thailand with monthly sampling over a year from 2013 until 2014 were also included. The prevalence of PCR-confirmed infections was calculated at increasing distance around index infections (and growing time intervals in the cohort studies). Statistical significance was defined as prevalence outside of a 95%-quantile interval of a bootstrap null distribution after random re-allocation of locations of infections. RESULTS: Prevalence of Plasmodium vivax and Plasmodium falciparum infections was elevated in close proximity around index infections and decreased with distance in most study sites, e.g. from 21.3% at 0 km to the global study prevalence of 6.4% for P. vivax in the Cambodian survey. In the cohort studies, the clustering decreased with longer time windows. The distance from index infections to a 50% reduction of prevalence ranged from 25 m to 3175 m, tending to shorter distances at lower global study prevalence. CONCLUSIONS: The spatial signatures of P. vivax and P. falciparum infections demonstrate spatial clustering across a diverse set of study sites, quantifying the distance within which the clustering occurs. The method offers a novel tool in malaria epidemiology, potentially informing reactive intervention strategies regarding radius choices of operations around detected infections and thus strengthening malaria elimination endeavours.

A Bayesian multistage spatio-temporally dependent model for spatial clustering and variable selection.

In spatio-temporal epidemiological analysis, it is of critical importance to identify the significant covariates and estimate the associated time-varying effects on the health outcome. Due to the heterogeneity of spatio-temporal data, the subsets of important covariates may vary across space and the temporal trends of covariate effects could be locally different. However, many spatial models neglected the potential local variation patterns, leading to inappropriate inference. Thus, this article proposes a flexible Bayesian hierarchical model to simultaneously identify spatial clusters of regression coefficients with common temporal trends, select significant covariates for each spatial group by introducing binary entry parameters and estimate spatio-temporally varying disease risks. A multistage strategy is employed to reduce the confounding bias caused by spatially structured random components. A simulation study demonstrates the outperformance of the proposed method, compared with several alternatives based on different assessment criteria. The methodology is motivated by two important case studies. The first concerns the low birth weight incidence data in 159 counties of Georgia, USA, for the years 2007 to 2018 and investigates the time-varying effects of potential contributing covariates in different cluster regions. The second concerns the circulatory disease risks across 323 local authorities in England over 10 years and explores the underlying spatial clusters and associated important risk factors.

Spatial spillover impact of determinants on child mortality in Pakistan: evidence from Spatial Durbin Model.

BACKGROUND: Child mortality is a major challenge to public health in Pakistan and other developing countries. Reduction of the child mortality rate would improve public health and enhance human well-being and prosperity. This study recognizes the spatial clusters of child mortality across districts of Pakistan and identifies the direct and spatial spillover effects of determinants on the Child Mortality Rate (CMR). METHOD: Data of the multiple indicators cluster survey (MICS) conducted by the United Nations International Children's Emergency Fund (UNICEF) was used to study the CMR. We used spatial univariate autocorrelation to test the spatial dependence between contiguous districts concerning CMR. We also applied the Spatial Durbin Model (SDM) to measure the spatial spillover effects of factors on CMR. RESULTS: The study results showed 31% significant spatial association across the districts and identified a cluster of hot spots characterized by the high-high CMR in the districts of Punjab province. The empirical analysis of the SDM confirmed that the direct and spatial spillover effect of the poorest wealth quintile and MPI vulnerability on CMR is positive whereas access to postnatal care to the newly born child and improved drinking water has negatively (directly and indirectly) determined the CMR in Pakistan. CONCLUSION: The instant results concluded that spatial dependence and significant spatial spillover effects concerning CMR exist across districts. Prioritization of the hot spot districts characterized by higher CMR can significantly reduce the CMR with improvement in financial statuses of households from the poorest quintile and MPI vulnerability as well as improvement in accessibility to postnatal care services and safe drinking water.

Spatio-temporal pattern and associate factors of intestinal infectious diseases in Zhejiang Province, China, 2008-2021: a Bayesian modeling study.

BACKGROUND: Despite significant progress in sanitation status and public health awareness, intestinal infectious diseases (IID) have caused a serious disease burden in China. Little was known about the spatio-temporal pattern of IID at the county level in Zhejiang. Therefore, a spatio-temporal modelling study to identify high-risk regions of IID incidence and potential risk factors was conducted. METHODS: Reported cases of notifiable IID from 2008 to 2021 were obtained from the China Information System for Disease Control and Prevention. Moran's I index and the local indicators of spatial association (LISA) were calculated using Geoda software to identify the spatial autocorrelation and high-risk areas of IID incidence. Bayesian hierarchical model was used to explore socioeconomic and climate factors affecting IID incidence inequities from spatial and temporal perspectives. RESULTS: From 2008 to 2021, a total of 101 cholera, 55,298 bacterial dysentery, 131 amoebic dysentery, 5297 typhoid, 2102 paratyphoid, 27,947 HEV, 1,695,925 hand, foot and mouth disease (HFMD), and 1,505,797 other infectious diarrhea (OID) cases were reported in Zhejiang Province. The hot spots for bacterial dysentery, OID, and HEV incidence were found mainly in Hangzhou, while high-high cluster regions for incidence of enteric fever and HFMD were mainly located in Ningbo. The Bayesian model showed that Areas with a high proportion of males had a lower risk of BD and enteric fever. People under the age of 18 may have a higher risk of IID. High urbanization rate was a protective factor against HFMD (RR = 0.91, 95% CI: 0.88, 0.94), but was a risk factor for HEV (RR = 1.06, 95% CI: 1.01-1.10). BD risk (RR = 1.14, 95% CI: 1.10-1.18) and enteric fever risk (RR = 1.18, 95% CI:1.10-1.27) seemed higher in areas with high GDP per capita. The greater the population density, the higher the risk of BD (RR = 1.29, 95% CI: 1.23-1.36), enteric fever (RR = 1.12, 95% CI: 1.00-1.25), and HEV (RR = 1.15, 95% CI: 1.09-1.21). Among climate variables, higher temperature was associated with a higher risk of BD (RR = 1.32, 95% CI: 1.23-1.41), enteric fever (RR = 1.41, 95% CI: 1.33-1.50), and HFMD (RR = 1.22, 95% CI: 1.08-1.38), and with lower risk of HEV (RR = 0.83, 95% CI: 0.78-0.89). Precipitation was positively correlated with enteric fever (RR = 1.04, 95% CI: 1.00-1.08), HFMD (RR = 1.03, 95% CI: 1.00-1.06), and HEV (RR = 1.05, 95% CI: 1.03-1.08). Higher HFMD risk was also associated with increasing relative humidity (RR = 1.20, 95% CI: 1.16-1.24) and lower wind velocity (RR = 0.88, 95% CI: 0.84-0.92). CONCLUSIONS: There was significant spatial clustering of IID incidence in Zhejiang Province from 2008 to 2021. Spatio-temporal patterns of IID risk could be largely explained by socioeconomic and meteorological factors. Preventive measures and enhanced monitoring should be taken in some high-risk counties in Hangzhou city and Ningbo city.

Further mitigating carbon footprint pressure in urban agglomeration by enhancing the spatial clustering.

The increasing environmental pressure of anthropogenic CO2 emissions is impeding the sustainability of urban agglomerations (UAs). Recent research has shown that the spatial clustering of UA elements reduces CO2 emissions but underestimates its impact on vegetation carbon sequestration. Using an extended IPAT equation analysis framework and the Logarithmic Mean Divisia Index decomposition approach, this study revealed the positive effects of the economy and population spatial clustering on carbon footprint pressure (CFP) mitigation. Specifically, improving economic spatial clustering mitigated the rise in UA's CFP caused by affluence and population growth. Furthermore, population clustering in core cities effectively mitigated CFP in neighboring cities. Additionally, we found that the efficiency improvement, i.e., the decrease in the ratio of carbon emissions and gross domestic product, should be the dominant driver of CFP mitigation, followed by improved vegetation carbon sequestration. However, these drivers have limited future potential. We believe that by improving UA's spatial clustering of the economy and population, future urban environmental pressures and climate risks will be mitigated.

synr: An R package for handling synesthesia consistency test data.

Synesthesia is a phenomenon where sensory stimuli or cognitive concepts elicit additional perceptual experiences. For instance, in a commonly studied type of synesthesia, stimuli such as words written in black font elicit experiences of other colors, e.g., red. In order to objectively verify synesthesia, participants are asked to choose colors for repeatedly presented stimuli and the consistency of their choices is evaluated (consistency test). Previously, there has been no publicly available and easy-to-use tool for analyzing consistency test results. Here, the R package synr is introduced, which provides an efficient interface for exploring consistency test data and applying common procedures for analyzing them. Importantly, synr also implements a novel method enabling identification of participants whose scores cannot be interpreted, e.g., who only give black or red color responses. To this end, density-based spatial clustering of applications with noise (DBSCAN) is applied in conjunction with a measure of spread in 3D space. An application of synr with pre-existing openly accessible data illustrating how synr is used in practice is presented. Also included is a comparison of synr's data validation procedure and human ratings, which found that synr had high correspondence with human ratings and outperformed human raters in situations where human raters were easily mislead. Challenges for widespread adoption of synr as well as suggestions for using synr within the field of synesthesia and other areas of psychological research are discussed.

NGS data vectorization, clustering, and finding key codons in SARS-CoV-2 variations.

The rapid global spread and dissemination of SARS-CoV-2 has provided the virus with numerous opportunities to develop several variants. Thus, it is critical to determine the degree of the variations and in which part of the virus those variations occurred. Therefore, in this study, methods that could be used to vectorize the sequence data, perform clustering analysis, and visualize the results were proposed using machine learning methods. To conduct this study, a total of 224,073 cases of SARS-CoV-2 sequence data were collected through NCBI and GISAID, and the data were visualized using dimensionality reduction and clustering analysis models such as T-SNE and DBSCAN. The SARS-CoV-2 virus, which was first detected, was distinguished from different variations, including Omicron and Delta, in the cluster results. Furthermore, it was possible to examine which codon changes in the spike protein caused the variants to be distinguished using feature importance extraction models such as Random Forest or Shapely Value. The proposed method has the advantage of being able to analyse and visualize a large amount of data at once compared to the existing tree-based sequence data analysis. The proposed method was able to identify and visualize significant changes between the SARS-CoV-2 virus, which was first detected in Wuhan, China, in December 2019, and the newly formed mutant virus group. As a result of clustering analysis using sequence data, it was possible to confirm the formation of clusters among various variants in a two-dimensional graph, and by extracting the importance of variables, it was possible to confirm which codon changes played a major role in distinguishing variants. Furthermore, since the proposed method can handle a variety of data sequences, it can be used for all kinds of diseases, including influenza and SARS-CoV-2. Therefore, the proposed method has the potential to become widely used for the effective analysis of disease variations.