Clinical Application of Detecting COVID-19 Risks: A Natural Language Processing Approach.

The clinical application of detecting COVID-19 factors is a challenging task. The existing named entity recognition models are usually trained on a limited set of named entities. Besides clinical, the non-clinical factors, such as social determinant of health (SDoH), are also important to study the infectious disease. In this paper, we propose a generalizable machine learning approach that improves on previous efforts by recognizing a large number of clinical risk factors and SDoH. The novelty of the proposed method lies in the subtle combination of a number of deep neural networks, including the BiLSTM-CNN-CRF method and a transformer-based embedding layer. Experimental results on a cohort of COVID-19 data prepared from PubMed articles show the superiority of the proposed approach. When compared to other methods, the proposed approach achieves a performance gain of about 1-5% in terms of macro- and micro-average F1 scores. Clinical practitioners and researchers can use this approach to obtain accurate information regarding clinical risks and SDoH factors, and use this pipeline as a tool to end the pandemic or to prepare for future pandemics.

Relative hypercoagulopathy of the SARS-CoV-2 Beta and Delta variants when compared to the less severe Omicron variants is related to TEG parameters, the extent of fibrin amyloid microclots, and the severity of clinical illness. (preprint)

Earlier variants of SARS-CoV-2 have been associated with plasma hypercoagulability (as judged by thromboelastography) and an extensive formation of fibrin amyloid microclots, which are considered to contribute to the pathology of the coronavirus 2019 disease (COVID-19). The newer Omicron variants appear to be far more transmissible, but less virulent, even when taking immunity acquired from previous infections or vaccination into account. We here show that while the clotting parameters associated with Omicron variants are significantly raised over those of healthy, matched controls, they are only raised to levels significantly lower than those seen with more severe variants such as Beta and Delta. We also observed that individuals infected with Omicron variants manifested less extensive microclot formation in platelet poor plasma compared to those harbouring the more virulent variants. The measurement of clotting effects between the different variants acts as a kind of ‘internal control’ that demonstrates the relationship between the extent of coagulopathies and the virulence of the variant of interest. This adds to the evidence that microclots play an important role in determining the severity of symptoms observed in COVID-19.

A Summary of COVID-19 Datasets (preprint)

This research presents a review of main datasets that are developed for COVID-19 research. We hope this collection will continue to bring together members of the computing community, biomedical experts, and policymakers in the pursuit of effective COVID-19 treatments and management policies. Many organizations, such as the World Health Organization (WHO), John Hopkins, National Institute of Health (NIH), COVID-19 open science table4 and such, in the world, have made numerous datasets available to the public. However, these datasets originate from a variety of different sources and initiatives. The purpose of this research is to summarize the open COVID-19 datasets to make them more accessible to the research community for health systems design and analysis.

COVID-19 vaccination associated severe immune thrombocytopenia.

BACKGROUND: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 has emerged as a deadliest global pandemic after its identification in December 2019 in Wuhan, China resulting in more than three million deaths worldwide. Recently FDA issued emergency authorization for three vaccines for prevention of COVID-19. Here in, we report three cases of severe immune thrombocytopenia (ITP) following COVID-19 vaccination and their clinical course. CASE PRESENTATIONS: Case #1: 53 year old male with past medical history of Crohn's disease was admitted for myalgias and diffuse petechial rash 8 days after receiving second dose of Pfizer-BioNTech COVID-19 vaccine. A complete blood test showed a platelet count of 2 × 109/L. Patient did not have a prior history of thrombocytopenia and other causes of thrombocytopenia were ruled out by history and pertinent lab data. He received two doses of intravenous immunoglobulin and oral dexamethasone for 4 days resulting in normalization of platelet counts. Case #2: 67 year male with past medical history of chronic ITP in remission was admitted for melena 2 days after receiving his first dose of Pfizer-BioNTech COVID-19 vaccine. A complete blood test showed a platelet count of 2 × 109/L. Physical exam showed generalized petechiae. There was no history of recent flares of ITP and patient had normal platelet counts following his splenectomy 4 years ago. He received two doses of IVIG and oral dexamethasone for 4 days with gradual improvement in platelet counts. Case #3: 59 year old female with past medical history of chronic ITP secondary to SLE was admitted for bloody diarrhea 2 days after receiving her first dose of Johnson and Johnson COVID-19 vaccine. Physical exam was unremarkable. A complete blood test showed platelet count of 64 × 109/L which dropped to 27 × 109/L during hospital course. She received oral dexamethasone for 4 days with improvement in platelet counts. CONCLUSION: COVID-19 vaccination induced ITP has been recently acknowledged. However, given very few cases and limited data, currently there are no guidelines for management of ITP caused by COVID-19 vaccine as well as vaccination of people with predisposing conditions.

Pneumomediastinum and Diffuse Subcutaneous Emphysema with SARS-CoV-2 Infection Requiring Operative Management for Impending Airway Collapse: A Case Report (preprint)

Pneumomediastinum is a rare complication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that has increased in incidence with the novel coronavirus disease 2019 pandemic. Although traditionally managed with conservative measures, we present the indications and methods for the first operative management of tension pneumomediastinum with concomitant SARS-CoV-2 infection.

COMPARISON OF INFLAMMATORY MARKERS WITH DIFFERENT LEVELS OF SEVERITY OF COVID-19 DISEASE

ABSTRACT Objective: To assess correlation of various inflammatory markers with disease progression in COVID-19. Study Design: Cross sectional study. Place and Duration of Study: The study was conducted at Pak Emirates Military Hospital (PEMH), Rawalpindi, from Apr 2020 to May 2020. Methodology: All the patients admitted during this period were recruited in the study. Samples were collected from patients in medical wards, high dependency unit (HDU) and intensive care units (ICU). Sample was collected in plain tube for analysis of serum ferritin, quantitative C-reactive protein (CRP), and procalcitonin. For analysis of plasma lactate, sample was collected in sodium fluoride tube. Comparison of inflammatory markers amongst various groups was done to assess the association and correlation of these markers with the progression of disease. Results: A total of 127 cases were studied, 114 were males and 13 were females. Age of patients in mild group was 41.6 ± 13.2, in moderate 53.3 ± 15.4 and in severe cases it was 54.6 ± 14.4. C-reactive protein and ferritin levels were significantly deranged in all groups with p-value of 0.001 respectively and same was the case for lactate and procalcitonin. Post Hoc analysis of the significant parameters showed that levels of all the parameters were significantly associated with all the stages of disease. Conclusion: Majority of the Patients with COVID-19 disease exhibited elevated levels of inflammatory markers and their values significantly increased as the disease progressed with the time. As increase in inflammatory markers correlate with disease severity, regular monitoring by using these parameters can improve the disease outcome.

INFECTION PREVENTION AND CONTROL - KEY TO SUCCESS IN CONTAINING COVID-19

ABSTRACT In the current pandemic of corona viral infection disease, 2019 (COVID-19), the acquiescence for infection prevention and control is necessary at all levels. Therefore, this review article was written with an objective to identify the evidence for infection prevention and control in order to contain COVID-19. In order to minimize the spread of COVID-19, there comes a dire need for taking all necessary measures at community and health care level. From community perspective and for general public awareness to adopt social distancing protocols, involvement of social medias can be helpful. While necessary measures are recommended to be taken in health care setting, for the safety of both the health care professionals (HCPs) and patients. Published evidence had emphasized mandatory wearing of personal protective equipments (PPEs). Amongst all PPEs, the focus for HCPs was to wear N95 mask, gloves, gowns, face shield and goggles. The use of good quality of personal protective equipment (PPEs) was emphasized. For patient's safety wearing of gloves and masks was also accentuated. Proper disinfection of health care settings is recommended to prevent the spread of infection. It is concluded that use of various infection prevention and control measures at community and health care settings are the mandatory steps to control the spread of COVID-19.