Epidemic analysis of COVID-19 in Italy based on spatiotemporal geographic information and Google Trends

QSAR analysis of VEGFR-2 inhibitors based on machine learning, Topomer CoMFA and molecule docking

VEGFR-2 kinase inhibitors are clinically approved drugs that can effectively target cancer angiogenesis. However, such inhibitors have adverse effects such as skin toxicity, gastrointestinal reactions and hepatic impairment. In this study, machine learning and Topomer CoMFA, which is an alignment-dependent, descriptor-based method, were employed to build structural activity relationship models of potentially new VEGFR-2 inhibitors. The prediction ac-curacy of the training and test sets of the 2D-SAR model were 82.4 and 80.1%, respectively, with KNN. Topomer CoMFA approach was then used for 3D-QSAR modeling of VEGFR-2 inhibitors. The coefficient of q2 for cross-validation of the model 1 was greater than 0.5, suggesting that a stable drug activity-prediction model was obtained. Molecular docking was further performed to simulate the interactions between the five most promising compounds and VEGFR-2 target protein and the Total Scores were all greater than 6, indicating that they had a strong hydrogen bond interactions were present. This study successfully used machine learning to obtain five potentially novel VEGFR-2 inhibitors to increase our arsenal of drugs to combat cancer.

Bioinformatics and machine learning driven key genes screening for hepatocellular carcinoma

Liver cancer, a global menace, ranked as the sixth most prevalent and third deadliest cancer in 2020. The challenge of early diagnosis and treatment, especially for hepatocellular carcinoma (HCC), persists due to late-stage detections. Understanding HCC's complex pathogenesis is vital for advancing diagnostics and therapies. This study combines bioinformatics and machine learning, examining HCC comprehensively. Three datasets underwent meticulous scrutiny, employing various analytical tools such as Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, protein interaction assessment, and survival analysis. These rigorous investigations uncovered twelve pivotal genes intricately linked with HCC's pathophysiological intricacies. Among them, CYP2C8, CYP2C9, EPHX2, and ESR1 were significantly positively correlated with overall patient survival, while AKR1B10 and NQO1 displayed a negative correlation. Moreover, the Adaboost prediction model yielded an 86.8 % accuracy, showcasing machine learning's potential in deciphering complex dataset patterns for clinically relevant predictions. These findings promise to contribute valuable insights into the elusive mechanisms driving liver cancer (HCC). They hold the potential to guide the development of more precise diagnostic methods and treatment strategies in the future. In the fight against this global health challenge, unraveling HCC's intricacies is of paramount importance.

Big data- and artificial intelligence-based hot-spot analysis of COVID-19: Gauteng, South Africa, as a case study

The coronavirus disease 2019 (COVID-19) has developed into a pandemic. Data-driven techniques can be used to inform and guide public health decision- and policy-makers. In generalizing the spread of a virus over a large area, such as a province, it must be assumed that the transmission occurs as a stochastic process. It is therefore very difficult for policy and decision makers to understand and visualize the location specific dynamics of the virus on a more granular level. A primary concern is exposing local virus hot-spots, in order to inform and implement non-pharmaceutical interventions. A hot-spot is defined as an area experiencing exponential growth relative to the generalised growth of the pandemic. This paper uses the first and second waves of the COVID-19 epidemic in Gauteng Province, South Africa, as a case study. The study aims provide a data-driven methodology and comprehensive case study to expose location specific virus dynamics within a given area. The methodology uses an unsupervised Gaussian Mixture model to cluster cases at a desired granularity. This is combined with an epidemiological analysis to quantify each cluster's severity, progression and whether it can be defined as a hot-spot.

Forecasting and Surveillance of COVID-19 Spread Using Google Trends: Literature Review

The probability of future Coronavirus Disease (COVID)-19 waves remains high, thus COVID-19 surveillance and forecasting remains important. Online search engines harvest vast amounts of data from the general population in real time and make these data publicly accessible via such tools as Google Trends (GT). Therefore, the aim of this study was to review the literature about possible use of GT for COVID-19 surveillance and prediction of its outbreaks. We collected and reviewed articles about the possible use of GT for COVID-19 surveillance published in the first 2 years of the pandemic. We resulted in 54 publications that were used in this review. The majority of the studies (83.3%) included in this review showed positive results of the possible use of GT for forecasting COVID-19 outbreaks. Most of the studies were performed in English-speaking countries (61.1%). The most frequently used keyword was "coronavirus" (53.7%), followed by "COVID-19" (31.5%) and "COVID" (20.4%). Many authors have made analyses in multiple countries (46.3%) and obtained the same results for the majority of them, thus showing the robustness of the chosen methods. Various methods including long short-term memory (3.7%), random forest regression (3.7%), Adaboost algorithm (1.9%), autoregressive integrated moving average, neural network autoregression (1.9%), and vector error correction modeling (1.9%) were used for the analysis. It was seen that most of the publications with positive results (72.2%) were using data from the first wave of the COVID-19 pandemic. Later, the search volumes reduced even though the incidence peaked. In most countries, the use of GT data showed to be beneficial for forecasting and surveillance of COVID-19 spread.

Urban spatial risk prediction and optimization analysis of POI based on deep learning from the perspective of an epidemic

From an epidemiological perspective, previous research on COVID-19 has generally been based on classical statistical analyses. As a result, spatial information is often not used effectively. This paper uses image-based neural networks to explore the relationship between urban spatial risk and the distribution of infected populations, and the design of urban facilities. To achieve this objective, we use spatio-temporal data of people infected with new coronary pneumonia prior to 28 February 2020 in Wuhan. We then use kriging, which is a method of spatial interpolation, as well as core density estimation technology to establish the epidemic heat distribution on fine grid units. We further evaluate the influence of nine major spatial risk factors, including the distribution of agencies, hospitals, park squares, sports fields, banks and hotels, by testing them for significant positive correlation with the distribution of the epidemic. The weights of these spatial risk factors are used for training Generative Adversarial Network (GAN) models, which predict the distribution of cases in a given area. The input image for the machine learning model is a city plan converted by public infrastructures, and the output image is a map of urban spatial risk factors in the given area. The results of the trained model demonstrate that optimising the relevant point of interests (POI) in urban areas to effectively control potential risk factors can aid in managing the epidemic and preventing it from dispersing further.

Methods Used in the Spatial and Spatiotemporal Analysis of COVID-19 Epidemiology: A Systematic Review

The spread of the COVID-19 pandemic was spatially heterogeneous around the world; the transmission of the disease is driven by complex spatial and temporal variations in socioenvironmental factors. Spatial tools are useful in supporting COVID-19 control programs. A substantive review of the merits of the methodological approaches used to understand the spatial epidemiology of the disease is hardly undertaken. In this study, we reviewed the methodological approaches used to identify the spatial and spatiotemporal variations of COVID-19 and the socioeconomic, demographic and climatic drivers of such variations. We conducted a systematic literature search of spatial studies of COVID-19 published in English from Embase, Scopus, Medline, and Web of Science databases from 1 January 2019 to 7 September 2021. Methodological quality assessments were also performed using the Joanna Briggs Institute (JBI) risk of bias tool. A total of 154 studies met the inclusion criteria that used frequentist (85%) and Bayesian (15%) modelling approaches to identify spatial clusters and the associated risk factors. Bayesian models in the studies incorporated various spatial, temporal and spatiotemporal effects into the modelling schemes. This review highlighted the need for more local-level advanced Bayesian spatiotemporal modelling through the multi-level framework for COVID-19 prevention and control strategies.

Research on Spatial-temporal Spread and Risk Profile of the COVID-19 Epidemic Based on Mobile Phone Trajectory Data

The COVID-19 epidemic poses a significant challenge to the operation of society and the resumption of work and production. How to quickly track the resident location and activity trajectory of the population, and identify the spread risk of the COVID-19 in geospatial space has important theoretical and practical significance for controlling the spread of the virus on a large scale. In this study, we take the geographical community as the research object, and use the mobile phone trajectory data to construct the spatiotemporal profile of the potential high-risk population. First, by using the spatiotemporal data collision method, identify, and recover the trajectories of the people who were in the same area with the confirmed patients during the same time. Then, based on the range of activities of both cohorts (the confirmed cases and the potentially infected groups), we analyze the risk level of the relevant places and evaluate the scale of potential spread. Finally, we calculate the probability of infection for different communities and construct the spatiotemporal profile for the transmission to help guide the distribution of preventive materials and human resources. The proposed method is verified using survey data of 10 confirmed cases and statistical data of 96 high-risk neighborhoods in Chengdu, China, between 15 January 2020 and 15 February 2020. The analysis finds that the method accurately simulates the spatiotemporal spread of the epidemic in Chengdu and measures the risk level in specific areas, which provides an objective basis for the government and relevant parties to plan and manage the prevention and control of the epidemic.

Spatial Analysis of COVID-19 Vaccine Centers Distribution: A Case Study of the City of Jeddah, Saudi Arabia

The COVID-19 pandemic is one of the most devastating public health emergencies in history. In late 2020 and after almost a year from the initial outbreak of the novel coronavirus (SARS-CoV-2), several vaccines were approved and administered in most countries. Saudi Arabia has established COVID-19 vaccination centers in all regions. Various facilities were selected to set up these vaccination centers, including conference and exhibition centers, old airport terminals, pre-existing medical facilities, and primary healthcare centers. Deciding the number and locations of these facilities is a fundamental objective for successful epidemic responses to ensure the delivery of vaccines and other health services to the entire population. This study analyzed the spatial distribution of COVID-19 vaccination centers in Jeddah, a major city in Saudi Arabia, by using GIS tools and methods to provide insight on the effectiveness of the selection and distribution of the COVID-19 vaccination centers in terms of accessibility and coverage. Based on a spatial analysis of vaccine centers’ coverage in 2020 and 2021 in Jeddah presented in this study, coverage deficiency would have been addressed earlier if the applied GIS analysis methods had been used by authorities while gradually increasing the number of vaccination centers. This study recommends that the Ministry of Health in Saudi Arabia evaluated the assigned vaccination centers to include the less-populated regions and to ensure equity and fairness in vaccine distribution. Adding more vaccine centers or reallocating some existing centers in the denser districts to increase the coverage in the uncovered sparse regions in Jeddah is also recommended. The methods applied in this study could be part of a strategic vaccination administration program for future public health emergencies and other vaccination campaigns.

A Combined Feature Screening Approach of Random Forest and Filter-based Methods for Ultra-high Dimensional Data

Background:

Various feature (variable) screening approaches have been proposed in the past decade to mitigate the impact of ultra-high dimensionality in classification and regression problems, including filter based methods such as sure indepen¬dence screening, and wrapper based methods such random forest. However, the former type of methods rely heavily on strong modelling assumptions while the latter ones requires an adequate sample size to make the data speak for themselves. These require¬ments can seldom be met in biochemical studies in cases where we have only access to ultra-high dimensional data with a complex structure and a small number of observations.

Objective:

In this research, we want to investigate the possibility of combing both filter based screening methods and random forest based screening methods in the regression context.

Method:

We have combined four state-of-art filter approaches, namely, sure independence screening (SIS) , robust rank corre¬lation based screening (RRCS), high dimensional ordinary least squares projection (HOLP) and a model free sure independence screening procedure based on the distance correlation (DCSIS) from the statistical community with a random forest based Boruta screening method from the machine learning community for regression problems.

Result:

Among all combined methods, RF-DCSIS performs better than the other methods in terms of screening accuracy and prediction capability on the simulated scenarios and real benchmark datasets.

Conclusion:

By empirical study from both extensive simulation and real data, we have shown that both filter based screening and random forest based screening have their pros and cons while a combination of both may lead to a better feature screening result and prediction capability

Keywords:

feature screening, filter-based method, ultra-high dimensional data, variable selection, random forest,RF-DCSIS

Risk assessment and integrated surveillance of foot-and-mouth disease outbreaks in Russia based on Monte Carlo simulation

Background

Foot-and-mouth disease (FMD) is a highly contagious disease of livestock worldwide. Russia is a big agricultural country with a wide geographical area where FMD outbreaks have become an obstacle for the development of the animal and animal products trade. In this study, we aimed to assess the export risk of FMD from Russia.

Results

After simulation by Monte Carlo, the results showed that the probability of cattle infected with FMD in the surveillance zone (Surrounding the areas where no epidemic disease has occurred within the prescribed time limit, the construction of buffer areas is called surveillance zone.) of Russia was 1.29 × 10^− 6. The probability that at least one FMD positive case was exported from Russia per year in the surveillance zone was 6 %. The predicted number of positive cattle of the 39,530 - 50,576 exported from Russia per year was 0.06. A key node in the impact model was the probability of occurrence of FMD outbreaks in the Russian surveillance zone. By semi-quantitative model calculation, the risk probability of FMD defense system defects was 1.84 × 10^− 5, indicating that there was a potential risk in the prevention and control measures of FMD in Russia. The spatial time scan model found that the most likely FMD cluster (P < 0.01) was in the Eastern and Siberian Central regions.

Conclusions

There was a risk of FMDV among cattle exported from Russia, and the infection rate of cattle in the monitored area was the key factor. Understanding the export risk of FMD in Russia and relevant epidemic prevention measures will help policymakers to develop targeted surveillance plans.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02967-x.

Modeling of Various Spatial Patterns of SARS-CoV-2: The Case of Germany

Among numerous publications about the SARS-CoV-2, many articles present research from the geographic point of view. The cartographic research method used in this area of science can be successfully applied to analyze the spatiotemporal characteristics of the pandemic using limited data and can be useful for a quick and preliminary assessment of the spread of infections. In this paper, research on the spatial differentiation of the structure and homogeneity of the system in which SARS-CoV-2 occurs, as well as spatial concentration of people infected was undertaken. The phenomena were investigated in a period of two infection waves in Germany: in spring and autumn 2020. We applied the potential model, entropy, centrographic method, and Lorenz curve in spatial analysis. The potentials model made it possible to distinguish core regions with a high level of the growth of new infections, along with areas of their impact, and regions with a low level of generation of new infections. The entropy showed the spatial distribution of differentiation of the studied system and the change of these characteristics between spring and autumn. The concentration method allowed for spatial and numerical demonstration of the concentration of infected population in a given area. We wanted to show that it is possible to draw meaningful conclusions about the pandemic characteristics using only basic data about infections, along with proper cartographic methods. The results can be used to designate the zones of the greatest threats, and thus, the areas where the most intense actions should be taken.