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Public Health Public Health

Machine Learning Maps Research Needs in COVID-19 Literature.

In Patterns (New York, N.Y.)

As of August 2020, thousands of COVID-19 (coronavirus disease 2019) publications have been produced. Manual assessment of their scope is an overwhelming task, and shortcuts through metadata analysis (e.g., keywords) assume that studies are properly tagged. However, machine learning approaches can rapidly survey the actual text of publication abstracts to identify research overlap between COVID-19 and other coronaviruses, research hotspots, and areas warranting exploration. We propose a fast, scalable, and reusable framework to parse novel disease literature. When applied to the COVID-19 Open Research Dataset (CORD-19), dimensionality reduction suggests that COVID-19 studies to date are primarily clinical-, modeling- or field-based, in contrast to the vast quantity of laboratory-driven research for other (non-COVID-19) coronavirus diseases. Furthermore, topic modeling indicates that COVID-19 publications have focused on public health, outbreak reporting, clinical care, and testing for coronaviruses, as opposed to the more limited number focused on basic microbiology, including pathogenesis and transmission.

Doanvo Anhvinh, Qian Xiaolu, Ramjee Divya, Piontkivska Helen, Desai Angel, Majumder Maimuna

2020-Sep-16

2019-nCoV, COVID-19, LDA, PCA, SARS-CoV-2, artificial intelligence, coronavirus, data science, dimensionality reduction, machine learning, natural language processing, topic modeling

Radiology Radiology

Discrimination of pulmonary ground-glass opacity changes in COVID-19 and non-COVID-19 patients using CT radiomics analysis.

In European journal of radiology open

Purpose : The coronavirus disease 2019 (COVID-19) has evolved into a worldwide pandemic. CT although sensitive in detecting changes suffers from poor specificity in discrimination from other causes of ground glass opacities (GGOs). We aimed to develop and validate a CT-based radiomics model to differentiate COVID-19 from other causes of pulmonary GGOs.

Methods : We retrospectively included COVID-19 patients between 24/01/2020 and 31/03/2020 as case group and patients with pulmonary GGOs between 04/02/2012 and 31/03/2020 as a control group. Radiomics features were extracted from contoured GGOs by PyRadiomics. The least absolute shrinkage and selection operator method was used to establish the radiomics model. We assessed the performance using the area under the curve of the receiver operating characteristic curve (AUC).

Results : A total of 301 patients (age mean ± SD: 64 ± 15 years; male: 52.8 %) from three hospitals were enrolled, including 33 COVID-19 patients in the case group and 268 patients with malignancies or pneumonia in the control group. Thirteen radiomics features out of 474 were selected to build the model. This model achieved an AUC of 0.905, accuracy of 89.5 %, sensitivity of 83.3 %, specificity of 90.0 % in the testing set.

Conclusion : We developed a noninvasive radiomics model based on CT imaging for the diagnosis of COVID-19 based on GGO lesions, which could be a promising supplementary tool for improving specificity for COVID-19 in a population confounded by ground glass opacity changes from other etiologies.

Xie Chenyi, Ng Ming-Yen, Ding Jie, Leung Siu Ting, Lo Christine Shing Yen, Wong Ho Yuen Frank, Vardhanabhuti Varut

2020

COVID-19, Computed tomography, Infections, Machine learning, Severe acute respiratory syndrome coronavirus 2

General General

Accessing Covid19 Epidemic Outbreak in Tamilnadu and the Impact of Lockdown through Epidemiological Models and Dynamic systems.

In Measurement : journal of the International Measurement Confederation

Despite having a small footprint origin, COVID-19 has expanded its clutches to being a global pandemic with severe consequences threatening the survival of the human species. Despite international communities closing their corridors to reduce the exponential spread of the coronavirus. The need to study the patterns of transmission and spread gains utmost importance at the grass-root level of the social structure. To determine the impact of lockdown and social distancing in Tamilnadu through epidemiological models in forecasting the "effective reproductive number" (R0) determining the significance in transmission rate in Tamilnadu after first Covid19 case confirmation on March 07, 2020. Utilizing web scraping techniques to extract data from different online sources to determine the probable transmission rate in Tamilnadu from the rest of the Indian states. Comparing the different epidemiological models (SIR, SIER) in forecasting and assessing the current and future spread of COVID-19. R0 value has a high spike in densely populated districts with the probable flattening of the curve due to lockdown and the rapid rise after the relaxation of lockdown. As of June 03, 2020, there were 25,872 confirmed cases and 208 deaths in Tamilnadu after two and a half months of lockdown with minimal exceptions. As on June 03, 2020, the information published online by the Tamilnadu state government the fatality is at 1.8% (208/11345=1.8%) spread with those aged (0-12) at 1437 and 13-60 at 21899 and 60+ at 2536 the risk of symptomatic infection increases with age and comorbid conditions.

Rajendran Sukumar, Jayagopal Prabhu

2020-Sep-17

Covid-19, Machine learning, SIR model, Tamilnadu

General General

Predicting Long-Term Deformation of Soundproofing Resilient Materials Subjected to Compressive Loading: Machine Learning Approach.

In Materials (Basel, Switzerland)

Soundproofing materials are widely used within structural components of multi-dwelling residential buildings to alleviate neighborhood noise problems. One of the critical mechanical properties for the soundproofing materials to ensure its appropriate structural and soundproofing performance is the long-term compressive deformation under the service loading conditions. The test method in the current test specifications only evaluates resilient materials for a limited period (90-day). It then extrapolates the test results using a polynomial function to predict the long-term compressive deformation. However, the extrapolation is universally applied to materials without considering the level of loads; thus, the calculated deformation may not accurately represent the actual compressive deformation of the materials. In this regard, long-term compressive deformation tests were performed on the selected soundproofing resilient materials (i.e., polystyrene, polyethylene, and ethylene-vinyl acetate). Four levels of loads were chosen to apply compressive loads up to 350 to 500 days continuously, and the deformations of the test specimens were periodically monitored. Then, three machine learning algorithms were used to predict long-term compressive deformations. The predictions based on machine learning and ISO 20392 method are compared with experimental test results, and the accuracy of machine learning algorithms and ISO 20392 method are discussed.

Koo Seungbum, Choi Jongkwon, Kim Changhyuk

2020-Sep-17

floor impact sound, long-term deformation, machine learning, resilient material

General General

Trends and targets of various types of stem cell derived transfusable RBC substitution therapy: Obstacles that need to be converted to opportunity.

In Transfusion and apheresis science : official journal of the World Apheresis Association : official journal of the European Society for Haemapheresis

A shortage of blood during the pandemic outbreak of COVID-19 is a typical example in which the maintenance of a safe and adequate blood supply becomes difficult and highly demanding. So far, human RBCs have been produced in vitro using diverse sources: hematopoietic stem cells (SCs), embryonic SCs and induced pluripotent SCs. The existing, even safest core of conventional cellular bioproducts destined for transfusion have some shortcoming in respects to: donor -dependency variability in terms of hematological /immunological and process/ storage period issues. SCs-derived transfusable RBC bioproducts, as one blood group type for all, were highly complex to work out. Moreover, the strategies for their successful production are often dependent upon the right selection of starting source materials and the composition and the stability of the right expansion media and the strict compliance to GMP regulatory processes. In this mini-review we highlight some model studies, which showed that the efficiency and the functionality of RBCs that could be produced by the various types of SCs, in relation to the in-vitro culture procedures are such that they may, potentially, be used at an industrial level. However, all cultured products do not have an unlimited life due to the critical metabolic pathways or the metabolites produced. New bioreactors are needed to remove these shortcomings and the development of a new mouse model is required. Modern clinical trials based on the employment of regenerative medicine approaches in combination with novel large-scale bioengineering tools, could overcome the current obstacles in artificial RBC substitution, possibly allowing an efficient RBC industrial production.

Lanza Francesxco, Seghatchian Jerard

2020-Sep-06

Artificial intelligence, Bioreactors, Expansion media, GMP regulatory processes, Induced pluripotent stem cell, Stem cells, Transfusable RBC bioproducts

General General

Drug Repurposing for COVID-19 using Graph Neural Network with Genetic, Mechanistic, and Epidemiological Validation

ArXiv Preprint

Amid the pandemic of 2019 novel coronavirus disease (COVID-19) infected by SARS-CoV-2, a vast amount of drug research for prevention and treatment has been quickly conducted, but these efforts have been unsuccessful thus far. Our objective is to prioritize repurposable drugs using a drug repurposing pipeline that systematically integrates multiple SARS-CoV-2 and drug interactions, deep graph neural networks, and in-vitro/population-based validations. We first collected all the available drugs (n= 3,635) involved in COVID-19 patient treatment through CTDbase. We built a SARS-CoV-2 knowledge graph based on the interactions among virus baits, host genes, pathways, drugs, and phenotypes. A deep graph neural network approach was used to derive the candidate representation based on the biological interactions. We prioritized the candidate drugs using clinical trial history, and then validated them with their genetic profiles, in vitro experimental efficacy, and electronic health records. We highlight the top 22 drugs including Azithromycin, Atorvastatin, Aspirin, Acetaminophen, and Albuterol. We further pinpointed drug combinations that may synergistically target COVID-19. In summary, we demonstrated that the integration of extensive interactions, deep neural networks, and rigorous validation can facilitate the rapid identification of candidate drugs for COVID-19 treatment.

Kanglin Hsieh, Yinyin Wang, Luyao Chen, Zhongming Zhao, Sean Savitz, Xiaoqian Jiang, Jing Tang, Yejin Kim

2020-09-23