Review of COVID-19 Therapeutics by Mechanism: From Discovery to Approval.

The global research and pharmaceutical community rapidly mobilized to develop treatments for coronavirus disease 2019 (COVID-19). Existing treatments have been repurposed and new drugs have emerged. Here we summarize mechanisms and clinical trials of COVID-19 therapeutics approved or in development. Two reviewers, working independently, reviewed published data for approved COVID-19 vaccines and drugs, as well as developmental pipelines, using databases from the following organizations: United States Food and Drug Administration (US-FDA), European Medicines Agency (EMA), Japanese Pharmaceutical and Medical Devices Agency (PMDA), and ClinicalTrials.gov. In all, 387 drugs were found for initial review. After removing unrelated trials and drugs, 66 drugs were selected, including 17 approved drugs and 49 drugs under development. These drugs were classified into six categories: 1) drugs targeting the viral life cycle 2) Anti-severe acute respiratory syndrome coronavirus 2 Monoclonal Antibodies, 3) immunomodulators, 4) anti-coagulants, 5) COVID-19-induced neuropathy drugs, and 6) other therapeutics. Among the 49 drugs under development are the following: 6 drugs targeting the viral life cycle, 12 immunosuppression drugs, 2 immunostimulants, 2 HIF-PHD targeting drugs, 3 GM-CSF targeting drugs, 5 anti-coagulants, 2 COVID-19-induced neuropathy drugs, and 17 others. This review provides insight into mechanisms of action, properties, and indications for COVID-19 medications.

Grain, Gluten, and Dietary Fiber Intake Influence Gut Microbial Diversity: Data from the Food and Microbiome Longitudinal Investigation.

Although short-term feeding studies demonstrated effects of grains, fiber, and gluten on gut microbiome composition, the impact of habitual intake of these dietary factors is poorly understood. We examined whether habitual intakes of whole and refined grains, fiber, and gluten are associated with gut microbiota in a cross-sectional study. This study included 779 participants from the multi-ethnic Food and Microbiome Longitudinal Investigation study. Bacterial 16SV4 rRNA gene from baseline stool was amplified and sequenced using Illumina MiSeq. Read clustering and taxonomic assignment was performed using QIIME2. Usual dietary intake was assessed by a 137-item food frequency questionnaire. Association of diet with gut microbiota was assessed with respect to overall composition and specific taxon abundances. Whole grain intake was associated with overall composition, as measured by the Jensen-Shannon divergence (multivariable-adjusted P trend for quartiles = 0.03). The highest intake quartile was associated with higher abundance of Bacteroides plebeius, Faecalibacterium prausnitzii, Blautia producta, and Erysipelotrichaceae and lower abundance of Bacteroides uniformis. These bacteria also varied by dietary fiber intake. Higher refined grain and gluten intake was associated with lower Shannon diversity (P trend < 0.05). These findings suggest that whole grain and dietary fiber are associated with overall gut microbiome structure, largely fiber-fermenting microbiota. Higher refined grain and gluten intakes may be associated with lower microbial diversity. Significance: Regular consumption of whole grains and dietary fiber was associated with greater abundance of gut bacteria that may lower risk of colorectal cancer. Further research on the association of refined grains and gluten with gut microbial composition is needed to understand their roles in health and disease.

Developing and Applying an Urban Resilience Index for the Evaluation of Declining Areas: A Case Study of South Korea's Urban Regeneration Sites.

This study attempts to identify the direction of urban regeneration projects in declining areas by using the concept of urban resilience to cope with climate change and disaster. To this end, urban resilience was classified into a Green Resilient Infrastructure (GRI) and an Interactive Safety System (ISS), through a review of previous studies, and categorized into vulnerability, adaptability, and transformability. A total of 12 detailed indicators were derived and indexed using Euclidean distance. Using the indicators, three Korean urban regeneration targets, in Daegu, Mokpo, and Seosan, were selected to evaluate resilience before and after the urban regeneration plan. Consequently, the postplanning resilience index improved in all three target sites, compared to before the regeneration plan. Additionally, previously the regeneration plan showed lower index values in comparison to places not designated as urban regeneration areas. These results suggest that urban resilience needs to be considered in future urban regeneration projects, and that resilience indicators can be used as a means to set the direction of urban regeneration projects. To improve the overall resilience of a region, these indices can help local government establish a reference point for urban resilience in its region.

Evaluation of advanced curve speed warning system to prevent fire truck rollover crashes.

INTRODUCTION: A disproportionately high number of deadly crash-incidents involve fire-tanker rollovers during emergency response driving. Most of these rollover incidents occur at dangerous horizontal curves ("curves") due to unsafe speed. This study examined the effects of a curve speed warning system (CSWS) on fire tanker drivers' emergency response behavior to develop system improvement suggestions. METHOD: Twenty-four firefighters participated in driving tests using a simulator. A fire tanker model, carrying a full tank of water, was used in emergency driving tests performed with and without CSWS. The CSWS was designed using the algorithm for passenger vehicles with a few initial modifications considering the unique requirements of heavy fire tanker and emergency driving. RESULTS: The results indicated that the CSWS was effective in issuing preemptive warnings when the drivers were approaching curves with unsafe speed during emergency response. Warnings occurred more frequently at curves with smaller radius. Although the CSWS improved driving performance, it did not significantly reduce the number of rollover events. A detailed analysis of the rollover events provided suggestions for improvement of CSWS algorithms. CONCLUSIONS: To further improve the CSWS algorithm, the following may be considered: including increased safety speed margin below the rollover critical speed, moving the speed warning trigger from the curve apex to the curve entry point, extending the safe speed-control zone to cover the entire curve, and employing artificial intelligence to accommodate individual driving styles. PRACTICAL APPLICATIONS: Fire tankers continue to be at increased risk of rollover during emergency response due to unsafe negotiation of dangerous curves. Development and use of advanced driver assist systems such as CSWS evaluated in this study may be an effective strategy to prevent deadly rollover crash-incidents. The knowledge generated by this study will be useful for system designers to improve the CSWS specifically designed for heavy emergency vehicles.

Microbial and molecular differences according to the location of head and neck cancers.

BACKGROUND: Microbiome has been shown to substantially contribute to some cancers. However, the diagnostic implications of microbiome in head and neck squamous cell carcinoma (HNSCC) remain unknown. METHODS: To identify the molecular difference in the microbiome of oral and non-oral HNSCC, primary data was downloaded from the Kraken-TCGA dataset. The molecular differences in the microbiome of oral and non-oral HNSCC were identified using the linear discriminant analysis effect size method. RESULTS: In the study, the common microbiomes in oral and non-oral cancers were Fusobacterium, Leptotrichia, Selenomonas and Treponema and Clostridium and Pseudoalteromonas, respectively. We found unique microbial signatures that positively correlated with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in oral cancer and positively and negatively correlated KEGG pathways in non-oral cancer. In oral cancer, positively correlated genes were mostly found in prion diseases, Alzheimer disease, Parkinson disease, Salmonella infection, and Pathogenic Escherichia coli infection. In non-oral cancer, positively correlated genes showed Herpes simplex virus 1 infection and Spliceosome and negatively correlated genes showed results from PI3K-Akt signaling pathway, Focal adhesion, Regulation of actin cytoskeleton, ECM-receptor interaction and Dilated cardiomyopathy. CONCLUSIONS: These results could help in understanding the underlying biological mechanisms of the microbiome of oral and non-oral HNSCC. Microbiome-based oncology diagnostic tool warrants further exploration.

Risk stratification of patients with right-sided colorectal cancer based on the tumor-infiltrating M1 macrophage.

The homing of M1 and M2 macrophages may play distinct roles in the tumor microenvironment (TME). However, these roles of macrophages in the TME remain unclear. We downloaded RNA sequencing data from The Cancer Genome Atlas (TCGA) database for patients with CRC. Subsequently, Kaplan-Meier survival curves were generated to assess the differential infiltration of M1 and M2 macrophages based on CRC location. Differentially expressed gene (DEG) and functional analyses were performed to screen the roles of DEGs. Critical prognostic genes were identified using least absolute shrinkage and selection operator regression. The risk scores were calculated for each patient. In patients with right-sided CRC, reduced M1 macrophage infiltration was associated with poor prognosis. M1 macrophage infiltration positively correlated with CD8+ T cell infiltration. A risk model was developed and validated for performance using GSE103479 and GSE72970. Nine genes were identified as independent prognostic genes that could be potential biomarkers for effectively predicting survival in patients with right-sided CRC. Kaplan-Meier curves for overall survival and progression-free survival analyses revealed that the high-risk group of patients with right-sided CRC had a poor prognosis. This novel M1 macrophage-related risk model may provide a gene signature for predicting the survival outcomes of patients with right-sided CRC and facilitate further studies examining the relationship between infiltration of M1 macrophages and the prognosis of such patients.

Evaluation of advanced curve speed warning system for fire trucks.

A curve speed warning system (CSWS) for firetrucks was developed and tested in this study. The CSWS algorithm was developed based on guidelines in the public domain for general vehicles and modified for firetrucks for their configuration and emergency driving. Twenty-four firefighters participated in the test in a driving simulator. The results show that the CSWS was effective in issuing preemptive warnings when the drivers were approaching curves with unsafe speed during emergency responses. Drivers reduced their driving speed at curve approaching and entering phases for most challenging curves, without affecting the overall time in completing the test route. Drivers had reduced number of severe braking and decreased average in-curve distance traveled over the safety speed limits, when the CSWS was in use. Drivers also rated the CSWS as assisting, effective and useful. In summary, the CSWS can enhance firetruck safety during emergency driving without sacrificing drivers' precious response time.

US nativity and dietary acculturation impact the gut microbiome in a diverse US population.

Little is known regarding the impact of immigrant acculturation on the gut microbiome. We characterized differences in the gut microbiome between racially/ethnically diverse US immigrant and US-born groups, and determined the impact of dietary acculturation on the microbiome. Stool samples were collected from 863 US residents, including US-born (315 White, 93 Black, 40 Hispanic) and foreign-born (105 Hispanic, 264 Korean) groups. We determined dietary acculturation from dissimilarities based on food frequency questionnaires, and used 16S rRNA gene sequencing to characterize the microbiome. Gut microbiome composition differed across study groups, with the largest difference between foreign-born Koreans and US-born Whites, and significant differences also observed between foreign-born and US-born Hispanics. Differences in sub-operational taxonomic unit (s-OTU) abundance between foreign-born and US-born groups tended to be distinct from differences between US-born groups. Bacteroides plebeius, a seaweed-degrading bacterium, was strongly enriched in foreign-born Koreans, while Prevotella copri and Bifidobacterium adolescentis were strongly enriched in foreign-born Koreans and Hispanics, compared with US-born Whites. Dietary acculturation in foreign-born participants was associated with specific s-OTUs, resembling abundance in US-born Whites; e.g., a Bacteroides plebeius s-OTU was depleted in highly diet-acculturated Koreans. In summary, we observed that US nativity is a determinant of the gut microbiome in a US resident population. Dietary acculturation may result in loss of native species in immigrants, though further research is necessary to explore whether acculturation-related microbiome alterations have consequences for immigrant health.

Innate Lymphoid Cells Play a Pathogenic Role in Pericarditis.

We find that cardiac group 2 innate lymphoid cells (ILC2s) are essential for the development of IL-33-induced eosinophilic pericarditis. We show a pathogenic role for ILC2s in cardiac inflammation, in which ILC2s activated by IL-33 drive the development of eosinophilic pericarditis in collaboration with cardiac fibroblasts. ILCs, not T and B cells, are required for the development of pericarditis. ILC2s transferred to the heart of Rag2-/-Il2rg-/- mice restore their susceptibility to eosinophil infiltration. Moreover, ILC2s direct cardiac fibroblasts to produce eotaxin-1. We also find that eosinophils reside in the mediastinal cavity and that eosinophils transferred to the mediastinal cavity of eosinophil-deficient ΔdblGATA1 mice following IL-33 treatment migrate to the heart. Thus, the serous cavities may serve as a reservoir of cardiac-infiltrating eosinophils. In humans, patients with pericarditis show higher amounts of ILCs in pericardial fluid than do healthy controls and patients with other cardiac diseases. We demonstrate that ILCs play a critical role in pericarditis.

The Cardiac Microenvironment Instructs Divergent Monocyte Fates and Functions in Myocarditis.

Two types of monocytes, Ly6Chi and Ly6Clo, infiltrate the heart in murine experimental autoimmune myocarditis (EAM). We discovered a role for cardiac fibroblasts in facilitating monocyte-to-macrophage differentiation of both Ly6Chi and Ly6Clo cells, allowing these macrophages to perform divergent functions in myocarditis progression. During the acute phase of EAM, IL-17A is highly abundant. It signals through cardiac fibroblasts to attenuate efferocytosis of Ly6Chi monocyte-derived macrophages (MDMs) and simultaneously prevents Ly6Clo monocyte-to-macrophage differentiation. We demonstrated an inverse clinical correlation between heart IL-17A levels and efferocytic receptor expressions in humans with heart failure (HF). In the absence of IL-17A signaling, Ly6Chi MDMs act as robust phagocytes and are less pro-inflammatory, whereas Ly6Clo monocytes resume their differentiation into MHCII+ macrophages. We propose that MHCII+Ly6Clo MDMs are associated with the reduction of cardiac fibrosis and prevention of the myocarditis sequalae.

Non-cytotoxic Cardiac Innate Lymphoid Cells Are a Resident and Quiescent Type 2-Commited Population.

Innate lymphoid cells (ILC) are a subset of leukocytes with lymphoid properties that lack antigen specific receptors. They can be stimulated by and exert their effect via specific cytokine axes, whereas Natural Killers (NK) cells are the only known cytotoxic member of this family. ILCs are considered key in linking the innate and adaptive response in physiologic and pathologic environments. In this study, we investigated the properties of non-cytotoxic cardiac ILCs in physiologic, inflammatory, and ischemic conditions. We found that in healthy humans and mice, non-cytotoxic cardiac ILCs are predominantly a type 2-committed population with progenitor-like features, such as an absence of type-specific immunophenotype, intermediate GATA3 expression, and capacity to transiently express Pro-myelocytic Leukemia Zinc Finger protein (PLZF) upon activation. During myocarditis and ischemia, in both human and mice, cardiac ILCs differentiated into conventional ILC2s. We found that cardiac ILCs lack IL-25 receptor and cannot become inflammatory ILC2s. We found a strong correlation between IL-33 production in the heart and the ability of cardiac ILCs to become conventional ILC2s. The main producer of IL-33 was a subset of CD29+Sca-1+ cardiac fibroblasts. ILC2 expansion and fibroblast-derived IL-33 production were significantly increased in the heart in mouse models of infarction and myocarditis. Despite its progenitor-like status in healthy hearts, cardiac ILCs were unable to become ILC1 or ILC3 in vivo and in vitro. Using adoptive transfer and parabiosis, we demonstrated that the heart, unlike other organs such as lung, cannot be infiltrated by circulating ILCs in adulthood even during cardiac inflammation or ischemia. Thus, the ILC2s present during inflammatory conditions are derived from the heart-resident and quiescent steady-state population. Non-cytotoxic cardiac ILCs are a resident population of ILC2-commited cells, with undifferentiated progenitor-like features in steady-state conditions and an ability to expand and develop pro-inflammatory type 2 features during inflammation or ischemia.

Regulation of autoimmune myocarditis by host responses to the microbiome.

The extensive, diverse communities that constitute the microbiome are increasingly appreciated as important regulators of human health and disease through inflammatory, immune, and metabolic pathways. We sought to elucidate pathways by which microbiota contribute to inflammatory, autoimmune cardiac disease. We employed an animal model of experimental autoimmune myocarditis (EAM), which results in inflammatory and autoimmune pathophysiology and subsequent maladaptive cardiac remodeling and heart failure. Antibiotic dysbiosis protected mice from EAM and fibrotic cardiac dysfunction. Additionally, mice derived from different sources with different microbiome colonization profiles demonstrated variable susceptibility to disease. Unexpectedly, it did not track with segmented filamentous bacteria (SFB)-driven Th17 programming of CD4+ T cells in the steady-state gut. Instead, we found disease susceptibility to track with presence of type 3 innate lymphoid cells (ILC3s). Ablating ILCs by antibody depletion or genetic tools in adoptive transfer variants of the EAM model demonstrated that ILCs and microbiome profiles contributed to the induction of CCL20/CCR6-mediated inflammatory chemotaxis to the diseased heart. From these data, we conclude that sensing of the microbiome by ILCs is an important checkpoint in the development of inflammatory cardiac disease processes through their ability to elicit cardiotropic chemotaxis.

The folding competence of HIV-1 Tat mediated by interaction with TAR RNA.

The trans-activator Tat protein of HIV-1 belongs to the large family of intrinsically disordered proteins (IDPs), and is known to recruit various host proteins for the transactivation of viral RNA synthesis. Tat protein interacts with the transactivator response RNA (TAR RNA), exhibiting RNA chaperone activities for structural rearrangement of interacting RNAs. Here, considering that Tat-TAR RNA interaction is mutually cooperative, we examined the potential role of TAR RNA as Chaperna - RNA that provides chaperone function to proteins - for the folding of HIV-1 Tat. Using EGFP fusion as an indirect indicator for folding status, we monitored Tat-EGFP folding in HeLa cells via time-lapse fluorescence microscopy. The live cell imaging showed that the rate and the extent of folding of Tat-EGFP were stimulated by TAR RNA. The purified Tat-EGFP was denatured and the fluorescence was monitored in vitro under renaturation condition. The fluorescence was significantly increased by TAR RNA, and the mutations in TAR RNA that affected the interaction with Tat protein failed to promote Tat refolding. The results suggest that TAR RNA stabilizes Tat as unfolded, but prevents it from misfolding, and maintaining its folding competence for interaction with multiple host factors toward its transactivation. The Chaperna function of virally encoded RNA in establishing proteome link at the viral-host interface provides new insights to as yet largely unexplored RNA mediated protein folding in normal and dysregulated cellular metabolism.

Analysis of the Prevalence and Risk Factors of Malnutrition among Hospitalized Patients in Busan.

This study investigated the prevalence of and risk factors for malnutrition in hospitalized patients in Busan, Republic of Korea. 944 patients (440 men and 504 women) were hospitalized in four Busan general hospitals from March through April, 2011. Nutritional status was assessed on admission by the Nutritional Risk Screening 2002. Data were collected from the electronic medical records system for the characteristics of the subjects, clinical outcomes, biochemical laboratory data, and nutrition support states. Clinical dietitians interviewed the patients using structured questionnaires involving data on weight loss and problems related to oral intakes. Malnourished patients were significantly older (P<0.001) than well-nourished patients, but the values for BMI, serum albumin, total cholesterol, TLC, hemoglobin, and hematocrit were significantly lower (P<0.001) for malnourished than for well-nourished patients. Logistic regression indicated that the main determinant factors for nutritional status were the age, length of stay, BMI, serum albumin, and total cholesterol. In order to increase therapeutic effects of hospitalized patients, clinical dietitians need to offer proper nutritional intervention based on the results of nutrition assessment and identification of malnutrition.

Characterization and expression analysis of mesenchymal stem cells from human bone marrow and adipose tissue.

Human mesenchymal stem cells (MSC), that have been reported to be present in bone marrow, adipose tissues, dermis, muscles and peripheral blood, have the potential to differentiate along different lineages including those forming bone, cartilage, fat, muscle and neuron. This differentiation potential makes MSC excellent candidates for cell-based tissue engineering. In this study, we have examined phenotypes and gene expression profile of the human adipose tissue-derived stromal cells (ATSC) in the undifferentiated states, and compared with that of bone marrow stromal cells (BMSC). ATSC were enzymatically released from adipose tissues from adult human donors and were expanded in monolayer with serial passages at confluence. BMSC were harvested from the metaphysis of adult human femur. Flowcytometric analysis showed that ATSC have a marker expression that is similar to that of BMSC. ATSC expressed CD29, CD44, CD90, CD105 and were absent for HLA-DR and c-kit expression. Under appropriate culture conditions, MSC were induced to differentiate to the osteoblast, adipocyte, and chondrogenic lineages. ATSC were superior to BMSC in respect to maintenance of proliferating ability, and microarray analysis of gene expression revealed differentially expressed genes between ATSC and BMSC. The proliferating ability and differentiation potential of ATSC were variable according to the culture condition. The similarities of the phenotypes and the gene expression profiles between ATSC and BMSC could have broad implications for human tissue engineering.