MEG-PPIS: a fast protein-protein interaction site prediction method based on multi-scale graph information and equivariant graph neural network.

MOTIVATION: Protein-protein interaction sites (PPIS) are crucial for deciphering protein action mechanisms and related medical research, which is the key issue in protein action research. Recent studies have shown that graph neural networks have achieved outstanding performance in predicting PPIS. However, these studies often neglect the modeling of information at different scales in the graph and the symmetry of protein molecules within three-dimensional space. RESULTS: In response to this gap, this article proposes the MEG-PPIS approach, a PPIS prediction method based on multi-scale graph information and E(n) equivariant graph neural network (EGNN). There are two channels in MEG-PPIS: the original graph and the subgraph obtained by graph pooling. The model can iteratively update the features of the original graph and subgraph through the weight-sharing EGNN. Subsequently, the max-pooling operation aggregates the updated features of the original graph and subgraph. Ultimately, the model feeds node features into the prediction layer to obtain prediction results. Comparative assessments against other methods on benchmark datasets reveal that MEG-PPIS achieves optimal performance across all evaluation metrics and gets the fastest runtime. Furthermore, specific case studies demonstrate that our method can predict more true positive and true negative sites than the current best method, proving that our model achieves better performance in the PPIS prediction task. AVAILABILITY AND IMPLEMENTATION: The data and code are available at https://github.com/dhz234/MEG-PPIS.git.

Understanding the bias of mobile location data across spatial scales and over time: A comprehensive analysis of SafeGraph data in the United States.

Mobile location data has emerged as a valuable data source for studying human mobility patterns in various contexts, including virus spreading, urban planning, and hazard evacuation. However, these data are often anonymized overviews derived from a panel of traced mobile devices, and the representativeness of these panels is not well documented. Without a clear understanding of the data representativeness, the interpretations of research based on mobile location data may be questionable. This article presents a comprehensive examination of the potential biases associated with mobile location data using SafeGraph Patterns data in the United States as a case study. The research rigorously scrutinizes and documents the bias from multiple dimensions, including spatial, temporal, urbanization, demographic, and socioeconomic, over a five-year period from 2018 to 2022 across diverse geographic levels, including state, county, census tract, and census block group. Our analysis of the SafeGraph Patterns dataset revealed an average sampling rate of 7.5% with notable temporal dynamics, geographic disparities, and urban-rural differences. The number of sampled devices was strongly correlated with the census population at the county level over the five years for both urban (r > 0.97) and rural counties (r > 0.91), but less so at the census tract and block group levels. We observed minor sampling biases among groups such as gender, age, and moderate-income, with biases typically ranging from -0.05 to +0.05. However, minority groups such as Hispanic populations, low-income households, and individuals with low levels of education generally exhibited higher levels of underrepresentation bias that varied over space, time, urbanization, and across geographic levels. These findings provide important insights for future studies that utilize SafeGraph data or other mobile location datasets, highlighting the need to thoroughly evaluate the spatiotemporal dynamics of the bias across spatial scales when employing such data sources.

Using geospatial social media data for infectious disease studies: a systematic review.

Geospatial social media (GSM) data has been increasingly used in public health due to its rich, timely, and accessible spatial information, particularly in infectious disease research. This review synthesized 86 research articles that use GSM data in infectious diseases published between December 2013 and March 2022. These articles cover 12 infectious disease types ranging from respiratory infectious diseases to sexually transmitted diseases with spatial levels varying from the neighborhood, county, state, and country. We categorized these studies into three major infectious disease research domains: surveillance, explanation, and prediction. With the assistance of advanced statistical and spatial methods, GSM data has been widely and deeply applied to these domains, particularly in surveillance and explanation domains. We further identified four knowledge gaps in terms of contextual information use, application scopes, spatiotemporal dimension, and data limitations and proposed innovation opportunities for future research. Our findings will contribute to a better understanding of using GSM data in infectious diseases studies and provide insights into strategies for using GSM data more effectively in future research.

Association between immigrant concentration and mental health service utilization in the United States over time: A geospatial big data analysis.

Immigrants (foreign-born United States [US] citizens) generally have lower utilization of mental health services compared with US-born counterparts, but extant studies have not investigated the disparities in mental health service utilization within immigrant population nationwide over time. Leveraging mobile phone-based visitation data, we estimated the average mental health utilization in contiguous US census tracts in 2019, 2020, and 2021 by employing two novel outcomes: mental health service visits and visit-to-need ratio (i.e., visits per depression diagnosis). We then investigated the tract-level association between immigration concentration and mental health service utilization outcomes using mixed-effects linear regression models that accounted for spatial lag effects, time effects, and covariates. This study reveals spatial and temporal disparities in mental health service visits and visit-to-need ratio among different levels of immigrant concentration across the US, both before and during the pandemic. Tracts with higher concentrations of Latin American immigrants showed significantly lower mental health service utilization visits and visit-to-need ratio, particularly in the US West. Tracts with Asian and European immigrant concentrations experienced a more significant decline in mental health service utilization visits and visit-to-need ratio from 2019 to 2020 than those with Latin American concentrations. Meanwhile, in 2021, tracts with Latin American concentrations had the least recovery in mental health service utilization visits. The study highlights the potential of geospatial big data for mental health research and informs public health interventions.

Investigating the relationships between concentrated disadvantage, place connectivity, and COVID-19 fatality in the United States over time.

BACKGROUND: Concentrated disadvantaged areas have been disproportionately affected by COVID-19 outbreak in the United States (US). Meanwhile, highly connected areas may contribute to higher human movement, leading to higher COVID-19 cases and deaths. This study examined the associations between concentrated disadvantage, place connectivity, and COVID-19 fatality in the US over time. METHODS: Concentrated disadvantage was assessed based on the spatial concentration of residents with low socioeconomic status. Place connectivity was defined as the normalized number of shared Twitter users between the county and all other counties in the contiguous US in a year (Y = 2019). COVID-19 fatality was measured as the cumulative COVID-19 deaths divided by the cumulative COVID-19 cases. Using county-level (N = 3,091) COVID-19 fatality over four time periods (up to October 31, 2021), we performed mixed-effect negative binomial regressions to examine the association between concentrated disadvantage, place connectivity, and COVID-19 fatality, considering potential state-level variations. The moderation effects of county-level place connectivity and concentrated disadvantage were analyzed. Spatially lagged variables of COVID-19 fatality were added to the models to control for the effect of spatial autocorrelations in COVID-19 fatality. RESULTS: Concentrated disadvantage was significantly associated with an increased COVID-19 fatality in four time periods (p < 0.01). More importantly, moderation analysis suggested that place connectivity significantly exacerbated the harmful effect of concentrated disadvantage on COVID-19 fatality in three periods (p < 0.01), and this significant moderation effect increased over time. The moderation effects were also significant when using place connectivity data from the previous year. CONCLUSIONS: Populations living in counties with both high concentrated disadvantage and high place connectivity may be at risk of a higher COVID-19 fatality. Greater COVID-19 fatality that occurs in concentrated disadvantaged counties may be partially due to higher human movement through place connectivity. In response to COVID-19 and other future infectious disease outbreaks, policymakers are encouraged to take advantage of historical disadvantage and place connectivity data in epidemic monitoring and surveillance of the disadvantaged areas that are highly connected, as well as targeting vulnerable populations and communities for additional intervention.

How Does Crime-Specific Victimization Impact Fear of Crime in Urban China? The Role of Neighborhood Characteristics.

Past research has failed to find consistent relationships between criminal victimization and fear of crime. Except for neighborhood disorder and crime rate, few studies have examined whether other neighborhood conditions matter the victimization-fear relationship. Using survey data in Guangzhou neighborhoods, the present analysis employs multinomial logistic regression models to examine whether neighborhood characteristics moderate the relationship between violent victimization and fear of violence, and between burglary victimization and fear of burglary, separately. Some aspects of the neighborhood environment do differentially influence victims' and non-victims' fear levels. Besides verifying the interaction effect of neighborhood disorder and victimization, the present study finds that neighborhood policing alleviates the harmful effect of violent victimization on fear, while collective efficacy fosters the harmful effect of burglary victimization on fear. This paper underscores the significance of the social context of urban China in explaining the interplay of neighborhood characteristics and victimization on fear of crime.

Assessing the Impact of Street-View Greenery on Fear of Neighborhood Crime in Guangzhou, China.

Previous literature has examined the relationship between the amount of green space and perceived safety in urban areas, but little is known about the effect of street-view neighborhood greenery on perceived neighborhood safety. Using a deep learning approach, we derived greenery from a massive set of street view images in central Guangzhou. We further tested the relationships and mechanisms between street-view greenery and fear of crime in the neighborhood. Results demonstrated that a higher level of neighborhood street-view greenery was associated with a lower fear of crime, and its relationship was mediated by perceived physical incivilities. While increasing street greenery of the micro-environment may reduce fear of crime, this paper also suggests that social factors should be considered when designing ameliorative programs.