COVID-19 as Reflected in University President Bulk Email (preprint)

E-mail ``Messages From the President'' to university students, staff, and faculty have long been used to keep campus communities aware of the latest policies, events, and news. But during the COVID-19 pandemic, as universities quickly closed facilities, sent students home, and canceled travel, these messages took on even greater importance. We report on a content analysis of bulk emails from different universities' presidents to their students and employees before and in three stages of the pandemic. We find that these messages change as universities move towards and through closure. During the pandemic, 1) presidential bulk emails tend to be more informative, positive, clearer than before; 2) they tend to use more personal and collective language; 3) university presidents tend to mention more local political leaders and fewer other university leaders. Our results can inform research on digital crisis communication and may be useful for researchers interested in automatically identifying crisis situations from communication streams.

Liquid Crystalline Systems from Nature and Interaction of Living Organisms with Liquid Crystals.

Biomaterials, which are substances interacting with biological systems, have been extensively explored to understand living organisms and obtain scientific inspiration (such as biomimetics). However, many aspects of biomaterials have yet to be fully understood. Because liquid crystalline phases are ubiquitously found in biomaterials (e.g., cholesterol, amphiphile, DNA, cellulose, bacteria), therefore, a wide range of research has made attempts to approach unresolved issues with the concept of liquid crystals (LCs). This review presents these studies that address the interactive correlation between biomaterials and LCs. Specifically, intrinsic LC behavior of various biomaterials such as DNA, cellulose nanocrystals, and bacteriaare first introduced. Second, the dynamics of bacteria in LC media are addressed, with focus on how bacteria interact with LCs, and how dynamics of bacteria can be controlled by exploiting the characteristics of LCs. Lastly, how the strong correlation between LCs and biomaterials has been leveraged to design a new class of biosensors with additional functionalities (e.g., self-regulated drug release) that are not available in previous systems is reviewed. Examples addressed in this review convey the message that the intersection between biomaterials and LCs offers deep insights into fundamental understanding of biomaterials, and provides resources for development of transformative technologies.

CellDrift: inferring perturbation responses in temporally sampled single-cell data.

Cells and tissues respond to perturbations in multiple ways that can be sensitively reflected in the alterations of gene expression. Current approaches to finding and quantifying the effects of perturbations on cell-level responses over time disregard the temporal consistency of identifiable gene programs. To leverage the occurrence of these patterns for perturbation analyses, we developed CellDrift (https://github.com/KANG-BIOINFO/CellDrift), a generalized linear model-based functional data analysis method that is capable of identifying covarying temporal patterns of various cell types in response to perturbations. As compared to several other approaches, CellDrift demonstrated superior performance in the identification of temporally varied perturbation patterns and the ability to impute missing time points. We applied CellDrift to multiple longitudinal datasets, including COVID-19 disease progression and gastrointestinal tract development, and demonstrated its ability to identify specific gene programs associated with sequential biological processes, trajectories and outcomes.

BNT162b2 induced neutralizing and non-neutralizing antibody functions against SARSCoV-2 diminish with age (preprint)

Each novel SARS-CoV-2 variant renews concerns about decreased vaccine efficacy caused by evasion of vaccine induced neutralizing antibodies. However, accumulating epidemiological data show that while vaccine prevention of infection varies, protection from severe disease and death remains high. Thus, immune responses beyond neutralization could contribute to vaccine efficacy. Polyclonal antibodies function through their Fab domains that neutralize virus directly, and Fc domains that induce non-neutralizing host responses via engagement of Fc receptors on immune cells. To understand how vaccine induced neutralizing and non-neutralizing activities synergize to promote protection, we leverage sera from 51 SARS-CoV-2 uninfected health-care workers after two doses of the BNT162b2 mRNA vaccine. We show that BNT162b2 elicits antibodies that neutralize clinical isolates of wildtype and five variants of SARS-CoV-2, including Omicron BA.2, and, critically, induce Fc effector functions. FcγRIIIa/CD16 activity is linked to neutralizing activity and associated with post-translational afucosylation and sialylation of vaccine specific antibodies. Further, neutralizing and non-neutralizing functions diminish with age, with limited polyfunctional breadth, magnitude and coordination observed in those ≥65 years old compared to <65. Thus, studying Fc functions in addition to Fab mediated neutralization provides greater insight into vaccine efficacy for vulnerable populations such as the elderly against SARS-CoV-2 and novel variants.

A census of the lung: CellCards from LungMAP.

The human lung plays vital roles in respiration, host defense, and basic physiology. Recent technological advancements such as single-cell RNA sequencing and genetic lineage tracing have revealed novel cell types and enriched functional properties of existing cell types in lung. The time has come to take a new census. Initiated by members of the NHLBI-funded LungMAP Consortium and aided by experts in the lung biology community, we synthesized current data into a comprehensive and practical cellular census of the lung. Identities of cell types in the normal lung are captured in individual cell cards with delineation of function, markers, developmental lineages, heterogeneity, regenerative potential, disease links, and key experimental tools. This publication will serve as the starting point of a live, up-to-date guide for lung research at https://www.lungmap.net/cell-cards/. We hope that Lung CellCards will promote the community-wide effort to establish, maintain, and restore respiratory health.

An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses.

Numerous studies have provided single-cell transcriptome profiles of host responses to SARS-CoV-2 infection. Critically lacking however is a data mine that allows users to compare and explore cell profiles to gain insights and develop new hypotheses. To accomplish this, we harmonized datasets from COVID-19 and other control condition blood, bronchoalveolar lavage, and tissue samples, and derived a compendium of gene signature modules per cell type, subtype, clinical condition, and compartment. We demonstrate approaches to interacting with, exploring, and functional evaluating these modules via a new interactive web portal ToppCell (http://toppcell.cchmc.org/). As examples, we develop three hypotheses: (1) alternatively-differentiated monocyte-derived macrophages form a multicelllar signaling cascade that drives T cell recruitment and activation; (2) COVID-19-generated platelet subtypes exhibit dramatically altered potential to adhere, coagulate, and thrombose; and (3) extrafollicular B maturation is driven by a multilineage cell activation network that expresses an ensemble of genes strongly associated with risk for developing post-viral autoimmunity.

Air Quality Variation in Daegu, Korea During the Outbreak of COVID-19 and its Health Risk Assessment

Coronavirus disease 2019 (COVID-19), first reported in Wuhan, China, became pandemic in less than two months, and Korea was no exception. Daegu Metropolitan City, in particular, has become the center of the explosive outbreak in Korea. In this study, we evaluated how the air quality of Daegu Metropolitan City varied when people were fighting the spread of COVID-19. In concretely, we tried to estimate the air quality variation with the trend of COVID-19 in Daegu Metropolitan City based on the measured data at hourly intervals from two air quality monitoring stations (AQMSs) (see Fig. 2). In addition, we quantitatively assessed the positive health effects of improved air quality from fighting against COVID-19. Compared to the concentration in the same period of 2019, the PM(2.5 )measured at the ambient AQMS decreased by 36.7, 22.5, and 37.6% respectively in January, February, and March. Meanwhile, those at the road side AQMS were 39.9, 23.7, and 40.3% in January, February, and March, respectively. The decreasing trend was not shown in April. Along with the floating population, the concentration of NO2 at the road side AQMS decreased from 49.9 ppb to 32.7 ppb, indicating that the reduction rate was 34.5%. The summed concentration of seven hazardous metals decreased by 27.4% in February 2020 compared to 2019. Among them, lead showed the biggest drop to 43.4% in 2002 compared to 2019. The exposure of PM2.5, Dose(PM)(2.5) (mu g), during 60 days of self-reflection for 10-year-old children has decreased by 29.6% compared to that in the same period of 2019. The results of adult females and males also show 27, 8% and 29.5% decrease, respectively.

Neutralizing Antibody Production in Asymptomatic and Mild COVID-19 Patients, in Comparison with Pneumonic COVID-19 Patients

Objectives: To investigate antibody production in asymptomatic and mild COVID-19 patients. Methods: Sera from asymptomatic to severe COVID-19 patients were collected. Microneutralization (MN), fluorescence immunoassay (FIA), and enzyme-linked immunosorbent assay (ELISA) were performed. Results: A total of 70 laboratory-confirmed COVID-19 patients were evaluated, including 15 asymptomatic/anosmia, 49 mild symptomatic, and 6 pneumonia patients. The production of the neutralizing antibody was observed in 100% of pneumonia, 93.9% of mild symptomatic, and 80.0% of asymptomatic/anosmia groups. All the patients in the pneumonia group showed high MN titer (≥1:80), while 36.7% of mild symptomatic and 20.0% of asymptomatic/anosmia groups showed high titer (p <0.001). Anti-SARS-CoV-2 antibodies could be more sensitively detected by FIA IgG (98.8%) and ELISA (97.6%) in overall. For the FIA IgG test, all patients in the pneumonia group exhibited a high COI value (≥15.0), while 89.8% of mild symptomatic and 73.3% of asymptomatic/anosmia groups showed a high value (p = 0.049). For the ELISA test, all patients in the pneumonia group showed a high optical density (OD) ratio (≥3.0), while 65.3% of mild symptomatic and 53.3% of asymptomatic/anosmia groups showed a high ratio (p = 0.006). Conclusions: Most asymptomatic and mild COVID-19 patients produced the neutralizing antibody, although the titers were lower than pneumonia patients. ELISA and FIA sensitively detected anti-SARS-CoV-2 antibodies.