Artificial Intelligence-Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development

Sex and gender considerations in Alzheimer’s disease: The Women’s Brain Project contribution

The global population is expected to have about 131.5 million people living with Alzheimer’s disease (AD) and other dementias by 2050, posing a severe health crisis. Dementia is a progressive neurodegenerative condition that gradually impairs physical and cognitive functions. Dementia has a variety of causes, symptoms, and heterogeneity concerning the influence of sex on prevalence, risk factors, and outcomes. The proportion of male-to-female prevalence varies based on the type of dementia. Despite some types of dementia being more common in men, women have a greater lifetime risk of developing dementia. AD is the most common form of dementia in which approximately two-thirds of the affected persons are women. Profound sex and gender differences in physiology and pharmacokinetic and pharmacodynamic interactions have increasingly been identified. As a result, new approaches to dementia diagnosis, care, and patient journeys should be considered. In the heart of a rapidly aging worldwide population, the Women’s Brain Project (WBP) was born from the necessity to address the sex and gender gap in AD. WBP is now a well-established international non-profit organization with a global multidisciplinary team of experts studying sex and gender determinants in the brain and mental health. WBP works with different stakeholders worldwide to help change perceptions and reduce sex biases in clinical and preclinical research and policy frameworks. With its strong female leadership, WBP is an example of the importance of female professionals’ work in the field of dementia research. WBP-led peer-reviewed papers, articles, books, lectures, and various initiatives in the policy and advocacy space have profoundly impacted the community and driven global discussion. WBP is now in the initial phases of establishing the world’s first Sex and Gender Precision Medicine Institute. This review highlights the contributions of the WBP team to the field of AD. This review aims to increase awareness of potentially important aspects of basic science, clinical outcomes, digital health, policy framework and provide the research community with potential challenges and research suggestions to leverage sex and gender differences. Finally, at the end of the review, we briefly touch upon our progress and contribution toward sex and gender inclusion beyond Alzheimer’s disease.

Towards AI-driven longevity research: An overview

While in the past technology has mostly been utilized to store information about the structural configuration of proteins and molecules for research and medical purposes, Artificial Intelligence is nowadays able to learn from the existing data how to predict and model properties and interactions, revealing important knowledge about complex biological processes, such as aging. Modern technologies, moreover, can rely on a broader set of information, including those derived from the next-generation sequencing (e.g., proteomics, lipidomics, and other omics), to understand the interactions between human body and the external environment. This is especially relevant as external factors have been shown to have a key role in aging. As the field of computational systems biology keeps improving and new biomarkers of aging are being developed, artificial intelligence promises to become a major ally of aging research.

Institutional Strategies to Maintain and Grow Imaging Research During the COVID-19 Pandemic

Understanding imaging research experiences, challenges, and strategies for academic radiology departments during and after COVID-19 is critical to prepare for future disruptive events. We summarize key insights and programmatic initiatives at major academic hospitals across the world, based on literature review and meetings of the Radiological Society of North America Vice Chairs of Research (RSNA VCR) group. Through expert discussion and case studies, we provide suggested guidelines to maintain and grow radiology research in the postpandemic era.

LitCovid ensemble learning for COVID-19 multi-label classification

The Coronavirus Disease 2019 (COVID-19) pandemic has shifted the focus of research worldwide, and more than 10 000 new articles per month have concentrated on COVID-19-related topics. Considering this rapidly growing literature, the efficient and precise extraction of the main topics of COVID-19-relevant articles is of great importance. The manual curation of this information for biomedical literature is labor-intensive and time-consuming, and as such the procedure is insufficient and difficult to maintain. In response to these complications, the BioCreative VII community has proposed a challenging task, LitCovid Track, calling for a global effort to automatically extract semantic topics for COVID-19 literature. This article describes our work on the BioCreative VII LitCovid Track. We proposed the LitCovid Ensemble Learning (LCEL) method for the tasks and integrated multiple biomedical pretrained models to address the COVID-19 multi-label classification problem. Specifically, seven different transformer-based pretrained models were ensembled for the initialization and fine-tuning processes independently. To enhance the representation abilities of the deep neural models, diverse additional biomedical knowledge was utilized to facilitate the fruitfulness of the semantic expressions. Simple yet effective data augmentation was also leveraged to address the learning deficiency during the training phase. In addition, given the imbalanced label distribution of the challenging task, a novel asymmetric loss function was applied to the LCEL model, which explicitly adjusted the negative-positive importance by assigning different exponential decay factors and helped the model focus on the positive samples. After the training phase, an ensemble bagging strategy was adopted to merge the outputs from each model for final predictions. The experimental results show the effectiveness of our proposed approach, as LCEL obtains the state-of-the-art performance on the LitCovid dataset. Database URL: https://github.com/JHnlp/LCEL.

Management of Smart and Sustainable Cities in the Post-COVID-19 Era: Lessons and Implications

Nowadays, the concept of smart sustainable governance is wrapped around basic principles such as: (i) transparency, (ii) accountability, (iii) stakeholders’ involvement, and iv) citizens’ participation. It is through these principles that are influenced by information and communication technologies (ICT), Internet of Things (IoT), and artificial intelligence, that the practices employed by citizens and their interaction with electronic government (e-government) are diversified. Previously, the misleading concepts of the smart city implied only the objective of the local level or public officials to utilize technology. However, the recent European experience and research studies have led to a more comprehensive notion that refers to the search for intelligent solutions which allow modern sustainable cities to enhance the quality of services provided to citizens and to improve the management of urban mobility. The smart city is based on the usage of connected sensors, data management, and analytics platforms to improve the quality and functioning of built-environment systems. The aim of this paper is to understand the effects of the pandemic on smart cities and to accentuate major exercises that can be learned for post-COVID sustainable urban management and patterns. The lessons and implications outlined in this paper can be used to enforce social distancing community measures in an effective and timely way, and to optimize the use of resources in smart and sustainable cities in critical situations. The paper offers a conceptual overview and serves as a stepping-stone to extensive research and the deployment of sustainable smart city platforms and intelligent transportation systems (a sub-area of smart city applications) after the COVID-19 pandemic using a case study from Russia. Overall, our results demonstrate that the COVID-19 crisis encompasses an excellent opportunity for urban planners and policy makers to take transformative actions towards creating cities that are more intelligent and sustainable.

Monitoring user opinions and side effects on COVID-19 vaccines in the Twittersphere: Infodemiology Study of Tweets

Background

In the current phase of the COVID-19 pandemic, we are witnessing the most massive vaccine rollout in human history. Like any other drug, vaccines may cause unexpected side effects, which need to be investigated in a timely manner to minimize harm in the population. If not properly dealt with, side effects may also impact public trust in the vaccination campaigns carried out by national governments.

Objective

Monitoring social media for the early identification of side effects, and understanding the public opinion on the vaccines are of paramount importance to ensure a successful and harmless rollout. The objective of this study was to create a web portal to monitor the opinion of social media users on COVID-19 vaccines, which can offer a tool for journalists, scientists, and users alike to visualize how the general public is reacting to the vaccination campaign.

Methods

We developed a tool to analyze the public opinion on COVID-19 vaccines from Twitter, exploiting, among other techniques, a state-of-the-art system for the identification of adverse drug events on social media; natural language processing models for sentiment analysis; statistical tools; and open-source databases to visualize the trending hashtags, news articles, and their factuality. All modules of the system are displayed through an open web portal.

Results

A set of 650,000 tweets was collected and analyzed in an ongoing process that was initiated in December 2020. The results of the analysis are made public on a web portal (updated daily), together with the processing tools and data. The data provide insights on public opinion about the vaccines and its change over time. For example, users show a high tendency to only share news from reliable sources when discussing COVID-19 vaccines (98% of the shared URLs). The general sentiment of Twitter users toward the vaccines is negative/neutral; however, the system is able to record fluctuations in the attitude toward specific vaccines in correspondence with specific events (eg, news about new outbreaks). The data also show how news coverage had a high impact on the set of discussed topics. To further investigate this point, we performed a more in-depth analysis of the data regarding the AstraZeneca vaccine. We observed how media coverage of blood clot–related side effects suddenly shifted the topic of public discussions regarding both the AstraZeneca and other vaccines. This became particularly evident when visualizing the most frequently discussed symptoms for the vaccines and comparing them month by month.

Conclusions

We present a tool connected with a web portal to monitor and display some key aspects of the public’s reaction to COVID-19 vaccines. The system also provides an overview of the opinions of the Twittersphere through graphic representations, offering a tool for the extraction of suspected adverse events from tweets with a deep learning model.

DBHR: a collection of databases relevant to human research

BACKGROUND

The achievement of the human genome project provides a basis for the systematic study of the human genome from evolutionary history to disease-specific medicine. With the explosive growth of biological data, a growing number of biological databases are being established to support human-related research.

OBJECTIVE

The main objective of our study is to store, organize and share data in a structured and searchable manner. In short, we have planned the future development of new features in the database research area.

MATERIALS & METHODS

In total, we collected and integrated 680 human databases from scientific published work. Multiple options are presented for accessing the data, while original links and short descriptions are also presented for each database.

RESULTS & DISCUSSION

We have provided the latest collection of human research databases on a single platform with six categories: DNA database, RNA database, protein database, expression database, pathway database and disease database.

CONCLUSION

Taken together, our database will be useful for further human research study and will be modified over time. The database has been implemented in PHP, HTML, CSS and MySQL and is available freely at https://habdsk.org/database.php.

Data Integration Challenges for Machine Learning in Precision Medicine

A main goal of Precision Medicine is that of incorporating and integrating the vast corpora on different databases about the molecular and environmental origins of disease, into analytic frameworks, allowing the development of individualized, context-dependent diagnostics, and therapeutic approaches. In this regard, artificial intelligence and machine learning approaches can be used to build analytical models of complex disease aimed at prediction of personalized health conditions and outcomes. Such models must handle the wide heterogeneity of individuals in both their genetic predisposition and their social and environmental determinants. Computational approaches to medicine need to be able to efficiently manage, visualize and integrate, large datasets combining structure, and unstructured formats. This needs to be done while constrained by different levels of confidentiality, ideally doing so within a unified analytical architecture. Efficient data integration and management is key to the successful application of computational intelligence approaches to medicine. A number of challenges arise in the design of successful designs to medical data analytics under currently demanding conditions of performance in personalized medicine, while also subject to time, computational power, and bioethical constraints. Here, we will review some of these constraints and discuss possible avenues to overcome current challenges.

Personalized therapy: can it tame the COVID-19 monster?

SARS-CoV-2, a recently emerged zoonotic virus, has resulted in unstoppable high morbidity and mortality rates worldwide. However, due to a limited knowledge of the dynamics of the SARS-CoV-2 infection, it has been observed that the current COVID-19 therapy has led to some clinical repercussions. We discuss the adverse effects of drugs for COVID-19 primarily based on some clinical trials. As therapeutic efficacy and toxicity of therapy may vary due to different, genetic determinants, sex, age and the ethnic background of test subjects, hence biomarker-based personalized therapy could be more appropriate. We will share our thoughts on the current landscape of personalized therapy as a roadmap to fight against SARS-CoV-2 or another emerging pathogen.

The Impact of the Integrated Development of AI and Energy Industry on Regional Energy Industry: A Case of China

With the advent of the Energy 4.0 era, the adoption of “Internet + artificial intelligence” systems will enable the transformation and upgrading of the traditional energy industry. This will alleviate the energy and environmental problems that China is currently facing. The integrated development of artificial intelligence and the energy industry has become inevitable in the development of future energy systems. This study applied a comprehensive evaluation index to the energy industry to calculate the comprehensive development index of the energy industry in 30 provinces of China from 2000 to 2017. Then, taking Guangdong and Jiangsu as examples, the synthetic control method was used to explore the direction and intensity of the integrated development of artificial intelligence and the energy industry on the comprehensive development level of the local energy industry. The results showed that when artificial intelligence (AI) and the energy industry achieved a stable coupled development without the need to move to the coordination stage, the coupling effect promoted the development of the regional energy industry, and the annual growth rate of the comprehensive development index was above 20%. This coupling effect passed the placebo test and ranking test and was significant at the 10% level, indicating the robustness and validity of the experimental results, which strongly confirmed the great potential of AI in re-empowering traditional industries from the data perspective. Based on the findings, corresponding policy recommendations were proposed on how to promote the development of inter-regional AI, how the government, enterprises, and universities could cooperate to promote the coordinated development of AI and energy, and how to guide the integration process of regional AI and energy industries according to local conditions, in order to maximize the technological dividend of AI and help the construction of smart energy in China.

An Artificial Neural Network Prediction Model for Posttraumatic Epilepsy: Retrospective Cohort Study

Background

Posttraumatic epilepsy (PTE) is a common sequela after traumatic brain injury (TBI), and identifying high-risk patients with PTE is necessary for their better treatment. Although artificial neural network (ANN) prediction models have been reported and are superior to traditional models, the ANN prediction model for PTE is lacking.

Objective

We aim to train and validate an ANN model to anticipate the risks of PTE.

Methods

The training cohort was TBI patients registered at West China Hospital. We used a 5-fold cross-validation approach to train and test the ANN model to avoid overfitting; 21 independent variables were used as input neurons in the ANN models, using a back-propagation algorithm to minimize the loss function. Finally, we obtained sensitivity, specificity, and accuracy of each ANN model from the 5 rounds of cross-validation and compared the accuracy with a nomogram prediction model built in our previous work based on the same population. In addition, we evaluated the performance of the model using patients registered at Chengdu Shang Jin Nan Fu Hospital (testing cohort 1) and Sichuan Provincial People’s Hospital (testing cohort 2) between January 1, 2013, and March 1, 2015.

Results

For the training cohort, we enrolled 1301 TBI patients from January 1, 2011, to December 31, 2017. The prevalence of PTE was 12.8% (166/1301, 95% CI 10.9%-14.6%). Of the TBI patients registered in testing cohort 1, PTE prevalence was 10.5% (44/421, 95% CI 7.5%-13.4%). Of the TBI patients registered in testing cohort 2, PTE prevalence was 6.1% (25/413, 95% CI 3.7%-8.4%). The results of the ANN model show that, the area under the receiver operating characteristic curve in the training cohort was 0.907 (95% CI 0.889-0.924), testing cohort 1 was 0.867 (95% CI 0.842-0.893), and testing cohort 2 was 0.859 (95% CI 0.826-0.890). Second, the average accuracy of the training cohort was 0.557 (95% CI 0.510-0.620), with 0.470 (95% CI 0.414-0.526) in testing cohort 1 and 0.344 (95% CI 0.287-0.401) in testing cohort 2. In addition, sensitivity, specificity, positive predictive values and negative predictors in the training cohort (testing cohort 1 and testing cohort 2) were 0.80 (0.83 and 0.80), 0.86 (0.80 and 0.84), 91% (85% and 78%), and 86% (80% and 83%), respectively. When calibrating this ANN model, Brier scored 0.121 in testing cohort 1 and 0.127 in testing cohort 2. Compared with the nomogram model, the ANN prediction model had a higher accuracy (P=.01).

Conclusions

This study shows that the ANN model can predict the risk of PTE and is superior to the risk estimated based on traditional statistical methods. However, the calibration of the model is a bit poor, and we need to calibrate it on a large sample size set and further improve the model.

Bayesian Model Infers Drug Repurposing Candidates for Treatment of COVID-19

The emergence of COVID-19 progressed into a global pandemic that has functionally put the world at a standstill and catapulted major healthcare systems into an overburdened state. The dire need for therapeutic strategies to mitigate and successfully treat COVID-19 is now a public health crisis with national security implications for many countries. The current study employed Bayesian networks to a longitudinal proteomic dataset generated from Caco-2 cells transfected with SARS-CoV-2 (isolated from patients returning from Wuhan to Frankfurt). Two different approaches were employed to assess the Bayesian models, a titer-center topology analysis and a drug signature enrichment analysis. Topology analysis identified a set of proteins directly linked to the SAR-CoV2 titer, including ACE2, a SARS-CoV-2 binding receptor, MAOB and CHECK1. Aligning with the topology analysis, MAOB and CHECK1 were also identified within the enriched drug-signatures. Taken together, the data output from this network has identified nodal host proteins that may be connected to 18 chemical compounds, some already marketed, which provides an immediate opportunity to rapidly triage these assets for safety and efficacy against COVID-19.