Unlocking the potential of phytochemicals in inhibiting SARS-CoV-2 M Pro protein - An in-silico and cell-based approach (preprint)

The main protease (MPro) of SARS-CoV-2 plays a crucial role in viral replication and is a prime target for therapeutic interventions. Phytochemicals, known for their antiviral properties, have been previously identified as potential MPro inhibitors in several in silico studies. However, the efficacy of these remains in question owing to the inherent flexibility of the MPro binding site, posing challenges in selecting suitable protein structures for virtual screening. In this study, we conducted an extensive analysis of the MPro binding pocket, utilizing molecular dynamics (MD) simulations to explore its conformational diversity. Based on pocket volume and shape-based clustering, five representative protein conformations were selected for virtual screening. Virtual screening of a library of ~ 48,000 phytochemicals suggested 39 phytochemicals as potential MPro inhibitors. Based on subsequent MM-GBSA binding energy calculations and ADMET property predictions, five compounds were advanced to cell-based viral replication inhibition assays, with three compounds (demethoxycurcumin, shikonin, and withaferin A) exhibiting significant (EC50 < 10 uM) inhibition of SARS-CoV-2 replication. Our study provides an understanding of the binding interactions between these phytochemicals and MPro, contributing significantly to the identification of promising MPro inhibitors. Furthermore, beyond its impact on therapeutic development against SARS-CoV-2, this research highlights a crucial role of proper nutrition in the fight against viral infections.

Differences in Oligomerization of the SARS-CoV-2 Envelope Protein, Poliovirus VP4, and HIV Vpu (preprint)

Viroporins constitute a class of viral membrane proteins with diverse roles in the viral life cycle. They can self-assemble and form pores within the bilayer that transport substrates, such as ions and genetic material, that are critical to the viral infection cycle. However, there is little known about the oligomeric state of most viroporins. Here, we use native mass spectrometry (MS) in detergent micelles to uncover the patterns of oligomerization of the full-length SARS-CoV-2 envelope (E) protein, poliovirus VP4, and HIV Vpu. Our data suggest that the E protein is a specific dimer, VP4 is exclusively monomeric, and Vpu assembles into a polydisperse mixture of oligomers under these conditions. Overall, these results revealed the diversity in the oligomerization of viroporins, which has implications for mechanisms of their biological functions as well as their potential as therapeutic targets.

A Qualitative Investigation of the Impact of the Sars-Cov-2 Pandemic on Goal Attainment Scaling in a Clinical Research Setting

Objectives: Goal Attainment Scaling (GAS) quantifies the effect of interventions on individuals' personal goals. Goals that are meaningful to individual patients are set by GAS interviewers (physicians/academics, experienced in clinical research/trials) in collaboration with patients and/or their caregivers. The SARS-CoV-2 pandemic presented a major challenge to health care worldwide. We investigated how the SARS-CoV-2 pandemic affected the use and implementation of GAS in clinical/research settings. Method(s): Eleven GAS interviewers in Canada, the US, UK and Australia with current/past experience working with patient-caregivers to identify goals and build scales to measure goal attainment as an outcome were interviewed using a semi-structured approach. They described how the pandemic affected GAS use in clinical/research settings. Interviews were recorded and transcribed, then themes were identified and coded in Nvivo 12. Result(s): Most GAS interviews were moved to the virtual environment during the pandemic (9/11). GAS interviewers identified few negative impacts. Some goals required modification (e.g. going to the gym or shops). Pandemic stress impacted both interviewers and interviewees. Even so, most GAS interviewers (8/11) emphasized positive impacts of the pandemic. These were: 1) the virtual environment meant patients were more readily available as they did not need to travel;2) because interviewers did not have to travel, patient recruitment could be expanded into more remote geographical areas;3) researchers could recruit and retain more participants and collect data more quickly;and 4) interviewers commented they became more open to technology because of the pandemic (9/11). Conclusion(s): Despite the challenges of the SARS-CoV-2 pandemic for health care, most GAS interviewers found that the impacts were largely positive for using GAS in clinical/research settings. The ability to deploy GAS through a virtual platform could facilitate the uptake of GAS as a patient-centric outcome measure.Copyright © 2023

Building science knowledge, identity, and interest using place-based learning with non-dominant urban undergraduate and high school students

During remote learning due to the COVID-19 pandemic, we developed and implemented a place-based, 5E mini-unit for New York City high school and community college Earth science students, most of whom identify as belonging to non-dominant groups. As well as supporting standard science skills such as graphing and interpreting data, we leveraged active learning and culturally responsive pedagogies such as reasoning by analogy, storytelling, virtual field trips, and sketching. These strategies were aimed at developing science content and skills, science identities, and science interest. The mini-unit was taught over 6 to 7.5 hours. Pre-and post-surveys for 107 students from three schools showed significant gains in learning (38% increase;p= <0.0001). Science identity measurements increased slightly although they stayed relatively low. Science interest measurements were higher with small increases. Teacher influence and science classroom experiences ranked as the most important influencers of science interest. For 33 community college students, no correlation was found between content learning, science identity, and science interest. In this group, females and White students had higher scores for all three measures. Between pre- and post-survey, science identity increased, particularly for Black students, while science interest decreased for all but White students. For all students, overall increases between pre- and post-survey suggest the pedagogical approaches used during remote synchronous learning were successful at helping students grow as scientists. © 2023 National Association of Geoscience Teachers.

Age differences in using humor to cope during a pandemic

Using humor can be beneficial for coping with stress. Humor can elicit positive emotions, which can bolster cognitive, social, and physical resources. Individuals who use humor to cope with negative affect report more positive well-being. However, it is less clear whether there are age differences in using humor to cope with an acute stressful event (e.g., the COVID-19 pandemic). We investigated whether using humor to cope with the pandemic related to lower levels of state anxiety. We further investigated age differences in using humor to cope and whether pandemic-related humor engagement reduced state anxiety levels. We surveyed 163 young adults (18-30 years) and 171 older adults (60-80 years) online during the initial months of the pandemic in the United States. Using humor to cope was negatively associated with state anxiety levels, but engagement with pandemic-related humor showed no relationship with anxiety. Using humor to cope was especially beneficial for older adults. One explanation may be that the positive emotions experienced through humor may beget a broader scope of fundamental resources needed to cope with anxiety during the pandemic. It may be that using humor to cope is a particularly efficacious coping strategy for older adults. © 2023 Walter de Gruyter GmbH, Berlin/Boston.

Treating asthma in the time of COVID.

The Precision Interventions for Severe and/or Exacerbation-Prone Asthma clinical trials network is actively assessing novel treatments for severe asthma during the coronavirus disease (COVID-19) pandemic and has needed to adapt to various clinical dilemmas posed by the COVID-19 pandemic. Pharmacologic interactions between established asthma therapies and novel drug interventions for COVID-19 infection, including antivirals, biologics, and vaccines, have emerged as a critical and unanticipated issue in the clinical care of asthma. In particular, impaired metabolism of some long-acting beta-2 agonists by the cytochrome P4503A4 enzyme in the setting of antiviral treatment using ritonavir-boosted nirmatrelvir (NVM/r, brand name Paxlovid) may increase risk for adverse cardiovascular events. Although available data have documented the potential for such interactions, these issues are largely unappreciated by clinicians who treat asthma, or those dispensing COVID-19 interventions in patients who happen to have asthma. Because these drug-drug interactions have not previously been relevant to patient care, clinicians have had no guidance on management strategies to reduce potentially serious interactions between treatments for asthma and COVID-19. The Precision Interventions for Severe and/or Exacerbation-Prone Asthma network considered the available literature and product information, and herein share our considerations and plans for treating asthma within the context of these novel COVID-19-related therapies.

P11 Improving the investigation and diagnosis of spontaneous bacterial peritonitis on the medical take

Objectives: To (i) improve the frequency of ascitic fluid sampling in decompensated cirrhotic patients;(ii) improve knowledge and confidence around ascitic fluid sample investigation and interpretation;and (iii) improve compliance with the decompensated cirrhosis bundle. Background: Cirrhotic patients are vulnerable to infection and can present with subtle clinical signs and laboratory results, making diagnosis of infection challenging. Spontaneous bacterial peritonitis is common in these patients and associated with a high mortality. BSG and BASL guidance suggests that all patients with ascites should have an ascitic tap performed on presentation to screen for infection, yet compliance with this directive is poor, leading to delays in diagnosis and poorly targeted antibiotic use. The reasons for this include lack of knowledge, lack of confidence in performing ascitic fluid sampling and lack of clarity on the samples required. Methods: We undertook a two cycle quality improvement project utilizing PDSA methodology. We focused both on practice and knowledge. Data collection – Identification of all decompensated cirrhotic on the medical take across a month via presenting complaint and discharge letter screening. Retrospective case note review was performed using a standardized proforma. Simultaneously junior doctor knowledge and confidence was assessed via three online questionnaires. Cycle 1 – Awareness building through posters and email. Dissemination of guidance around ascitic fluid sampling. Online education session provided for remote access (during COVID-19). Cycle 2 – Developed and implemented a new online order bundle for decompensated cirrhotic patients. Further awareness building in ED and medicine. Results: Three months of data collection were performed (included patients n=16, 15 and 14 respectively) and three rounds of knowledge surveys were undertaken (response n=40, 30 and 27 respectively). Ascitic tap attempts in appropriate patients rose from 50% to 83%. Requesting of (entirely) correct investigations for ascitic fluid increased minimally (67% to 75%). There was an increase in the percentage of those who classed themselves as somewhat or very confident (60 to 70% combined) regarding performance of ascitic tap . Despite this improvement in confidence, understanding of the correct testing and requesting procedure for ascitic fluid did not improve (96% incorrect). Compliance with the cirrhosis care bundle improved from 50% to 71%. Conclusions: Through our study we saw improved practice with regards to performing ascitic fluid sampling and utilizing the care bundle. Due to the design of our project we cannot say for certain that this was related to our intervention. Notwithstanding this we created digital resources in response to the COVID-19 restrictions and changed the order pathway for ascitic fluid sampling, making the process more intuitive and implementing sustainable, lasting change. We improved confidence without improving knowledge. This represents a further area for development as we take the project forwards. Our design does not allow us to comment upon patient outcome in response to our changes. Moving forwards our project shows the need to understand the barriers to junior doctors investigating patients with infections (such as lack of confidence and knowledge). The approaches used here could be utilized more widely to improve practice.

A PILOT STUDY OF AN INTERGENERATIONAL BOOK CLUB: LESSONS LEARNED FOR IMPROVING FEASIBILITY

Intergenerational book clubs have been successful in reducing ageist attitudes of younger adults (YA) while increasing feelings of social connectedness among older adults (OA;Lohman et al., 2003). We implemented both in-person (Nf11: YA=4, OA=7) and virtual (Nf8: YA=5, OA=3) modalities for an intergenerational book club to increase intergenerational interactions on campus, considering aging researchers' claim of heightened ageism and exacerbated loneliness following the beginning of the COVID-19 pandemic (Ayalon et al., 2020;Brooke & Jackson, 2020). Both groups met thrice over twelve weeks and completed measures on ageist attitudes (α=.83), engagement with the group (α=.91), and social connectedness (α=.91) each time. There was attrition in both groups (final meeting: Nf9 (in-person) and Nf3 (virtual)). To better understand overall motivations to participate and what factors may have contributed to attrition, we utilized content analysis with participants' feedback to examine their motivation for joining, what they enjoyed most after participating, and what they would improve. Participants were motivated to join because they enjoyed reading;comparatively, they enjoyed group discussions and hearing different perspectives. Future recommendations include meeting more often, increasing the number and size of groups, and scheduling meetings closer together. The majority wished to continue participating. The data suggest future expansion of intergenerational book clubs on campus are desired to support age-friendly interactions and needed to further examine if these interactions can curb ageism and increase social connectedness among diverse age groups. Discussion will include recommendations regarding measures, lessons learned for an optimal protocol, and next steps.

Ontological Analysis of Coronavirus Associated Human Genes at the COVID-19 Disease Portal.

The COVID-19 pandemic stemmed a parallel upsurge in the scientific literature about SARS-CoV-2 infection and its health burden. The Rat Genome Database (RGD) created a COVID-19 Disease Portal to leverage information from the scientific literature. In the COVID-19 Portal, gene-disease associations are established by manual curation of PubMed literature. The portal contains data for nine ontologies related to COVID-19, an embedded enrichment analysis tool, as well as links to a toolkit. Using these information and tools, we performed analyses on the curated COVID-19 disease genes. As expected, Disease Ontology enrichment analysis showed that the COVID-19 gene set is highly enriched with coronavirus infectious disease and related diseases. However, other less related diseases were also highly enriched, such as liver and rheumatic diseases. Using the comparison heatmap tool, we found nearly 60 percent of the COVID-19 genes were associated with nervous system disease and 40 percent were associated with gastrointestinal disease. Our analysis confirms the role of the immune system in COVID-19 pathogenesis as shown by substantial enrichment of immune system related Gene Ontology terms. The information in RGD's COVID-19 disease portal can generate new hypotheses to potentiate novel therapies and prevention of acute and long-term complications of COVID-19.

Stress, Genetics and Mood: Impact of COVID-19 on a College Freshman Sample (preprint)

Objectives: Use a longitudinal approach to study the impact of the Covid-19 pandemic on the emergence of symptoms of depression and/or anxiety in college freshmen. Define the interplay between genetic risk and psychosocial factors in shaping vulnerability or resilience to pandemic stress. Methods: University of Michigan freshmen were characterized at baseline using multiple psychological instruments. They were genotyped and polygenic risk score for depression (MDD-PRS) was calculated. Daily physical activity was captured. They were sampled at multiple time points throughout the freshman year on clinical rating scales, including GAD-7 and PHQ-9 for anxiety and depression, respectively. The 2019-2020 cohort (N=122) was compared to an earlier cohort (N=106) to assess the impact of the pandemic. Results: Across cohorts, 25%-57% of freshmen developed significant symptoms of anxiety or depression. In the 2019-2020 cohort, measures of anxiety and depression increased significantly after the onset of COVID-19. Physical activity was dramatically reduced by the pandemic and was associated with the emergence of mood symptoms. Low MDD-PRS subjects exhibited lower relative risk for depression/anxiety during a typical freshman year, but they were more negatively impacted by the pandemic than High MDD-PRS subjects. Conversely, a cluster of psychological indices at baseline predicted resilience in High MDD-PRS subjects who did not develop a mood disorder post-stress. Conclusions: The pandemic had a profound impact on college freshmen triggering depression and anxiety symptoms. Pandemic stress overrode the advantage conferred by "genetic resilience". By contrast, "psychosocial resilience" was protective even in the face of high genetic risk and pandemic stress.

Examining the relationship between leadership styles, employee job satisfaction, and employee decision-making self-efficacy, during a crisis in the mid-atlantic hotel industry

The central purpose of this quantitative research was to examine the relationships between leadership styles, job satisfaction, and employee decision-making self-efficacy in the Mid-Atlantic hotel industry during a crisis. This research's theoretical framework is based on the transformational, transactional, laissez-faire leadership styles, job satisfaction, and the Crisis Leader Efficacy in Assessing and Deciding (C-Lead). According to Callahan (2020), the COVID-19 pandemic is fertile ground for new research within the hotel industry. This investigation utilized the following reliable instruments: (MLQ, MSQ, and C-LEAD) to examine the relationships between variables. Cross-sectional data from a total of 150 participants within this industry was collected using the third-party vendor Qualtrics. The data was then examined using IBM software Statistical Product and Service Solutions (SPSS). The findings revealed that leadership styles positively and negatively impact job satisfaction and decision-making self-efficacy during a crisis. This research added to the body of literature and provided a platform for further research by discussing the relationships between leadership styles, job satisfaction, and decision-making self-efficacy in the hotel industry in the mid-Atlantic region during a crisis. (PsycInfo Database Record (c) 2022 APA, all rights reserved)

Hydroxychloroquine and Fabry Disease: Three Case Reports Examining an Unexpected Pathologic Link and a Review of the Literature.

Background: Hydroxychloroquine is an effective and widely used treatment in multiple autoimmune connective tissue diseases that gained a lot of publicity in the coronavirus disease 2019 (COVID-19) pandemic. Our case reports are unique in that they explore the rare and sometimes overlooked effects of this drug on multiple organ systems, specifically the kidney, cardiac muscle, and skeletal muscle. We include key histologic features in images which aid in identifying and distinguishing hydroxychloroquine toxicity from mimickers. Lastly, we report the very interesting similarity in the intracellular action of hydroxychloroquine to the pathology of Fabry disease (and its associated lysosomal enzyme, α-galactosidase A). Case Presentation. We will examine the case presentations of three female Caucasian patients: a 22-year-old with lupus nephritis class V, a 72-year-old with long-standing systemic lupus erythematosus, and a 74-year-old with undifferentiated connective tissue disease. All three patients were on hydroxychloroquine therapy for varying amounts of time with histologic evidence of hydroxychloroquine toxicity that is three is present in histological samples of the kidney, the heart, and the skeletal muscle. Conclusions: Hydroxychloroquine is a very important and beneficial medication used for various autoimmune connective tissue diseases. Clinicians should be aware of the rare but sometimes serious side effects that can result from the medication, which at times can mimic manifestations of the connective tissue disease itself or Fabry disease. A thorough investigation should be performed in these cases to properly elucidate the cause followed by the appropriate targeted therapy.

Characterization of COVID-19-associated cardiac injury: evidence for a multifactorial disease in an autopsy cohort.

As the coronavirus disease 2019 (COVID-19) pandemic evolves, much evidence implicates the heart as a critical target of injury in patients. The mechanism(s) of cardiac involvement has not been fully elucidated, although evidence of direct virus-mediated injury, thromboembolism with ischemic complications, and cytokine storm has been reported. We examined suggested mechanisms of COVID-19-associated heart failure in 21 COVID-19-positive decedents, obtained through standard autopsy procedure, compared to clinically matched controls and patients with various etiologies of viral myocarditis. We developed a custom tissue microarray using regions of pathological interest and interrogated tissues via immunohistochemistry and in situ hybridization. Severe acute respiratory syndrome coronavirus 2 was detected in 16/21 patients, in cardiomyocytes, the endothelium, interstitial spaces, and percolating adipocytes within the myocardium. Virus detection typically corresponded with troponin depletion and increased cleaved caspase-3. Indirect mechanisms of injury-venous and arterial thromboses with associated vasculitis including a mixed inflammatory infiltrate-were also observed. Neutrophil extracellular traps (NETs) were present in the myocardium of all COVID-19 patients, regardless of injury degree. Borderline myocarditis (inflammation without associated myocyte injury) was observed in 19/21 patients, characterized by a predominantly mononuclear inflammatory infiltrate. Edema, inflammation of percolating adipocytes, lymphocytic aggregates, and large septal masses of inflammatory cells and platelets were observed as defining features, and myofibrillar damage was evident in all patients. Collectively, COVID-19-associated cardiac injury was multifactorial, with elevated levels of NETs and von Willebrand factor as defining features of direct and indirect viral injury.

Pulmonary Hypertensive Changes Secondary to COVID-19 Pneumonia in a Chronically SARS-CoV-2-Infected Bilateral Lung Explant.

COVID-19, the syndrome caused by the novel coronavirus SARS-CoV-2, has spread throughout the world, causing the death of at least three million people. For the over 81 million who have recovered, however, the long-term effects are only beginning to manifest. We performed a bilateral lung transplant on a 31-year-old male patient for chronic hypoxic respiratory failure, severe pulmonary hypertension and radiographically identified pulmonary fibrosis five months after an acute COVID-19 infection. The explant demonstrated moderate pulmonary vascular remodeling with intimal thickening and medial hypertrophy throughout, consistent with pulmonary hypertension. The parenchyma demonstrated an organizing lung injury in the proliferative phase, with severe fibrosis, histiocytic proliferation, type II pneumocyte hyperplasia, and alveolar loss consistent with known COVID-19 pneumonia complications.This report highlights a novel histologic finding in severe, chronic COVID-19. Although the findings in acute COVID-19 pneumonia have been well-examined at autopsy, the chronic course of this complex disease is not yet understood. The case presented herein suggests that COVID-induced pulmonary hypertension may become more common as more patients survive severe SARS-CoV-2-related pneumonia. Pulmonologists and pulmonary pathologists should be aware of this possible association and look for the clinical, radiographic, and histologic criteria in the appropriate clinical setting.

School Asthma Care During COVID-19: What We Have Learned and What We Are Learning.

The focus of this article is to review school asthma care during coronavirus disease 2019 (COVID-19). Asthma is listed as a risk factor in some guidelines, although children with asthma appear to not be at increased risk of severe respiratory outcomes compared with children without asthma during the pandemic. Differentiating COVID-19 from allergic disease is very difficult in the school-aged children. For school management, there is firm evidence that masks do not exacerbate underlying lung conditions including asthma, and evidence to date supports that children with asthma can learn in-person at school because they do not appear to be at increased risk of COVID-19 morbidity or mortality. For children and adolescents, the COVID-19 vaccine has been demonstrated to be safe and well tolerated. School asthma management includes remaining on prescribed asthma medications. Asthma management, as with management of all pediatric conditions, must also factor in the impact of adverse social determinants and health disparities. Broadly, the pandemic has also served as a call to resource stewardship and innovation and allowed practitioners to consider how this may impact asthma care moving forward.

Systematic Review of Caregivers and Palliative Intent Radiation Therapy: Barriers, Facilitators, Decision Making Needs

To determine the facilitators, barriers, and decision making needs of caregivers of patients receiving palliative intent radiation therapy Systematic review of articles utilizing PRISMA guidelines was performed. Inclusion criteria included studies published from 2007 to 2018 focusing on caregivers of patients receiving palliative intent radiation therapy (PRT) for advanced cancers. Pediatric and non-English articles were excluded. Rayyan QCRI was utilized to screen abstracts, and Covidence organized the review of full text articles by 2 reviewers. Of 6079 articles identified, 36 were selected for full text review, and 6 met inclusion. Limited literature was found. Caregivers experience anxiety, fatigue, and hopelessness. Caregivers need more information and their emotions impact both the receipt of radiation therapy and satisfaction with services. While limited, literature focusing on caregivers of patients undergoing palliative intent radiation therapy consistently find unmet caregiver education and emotional distress which impact patient receipt of and satisfaction with PRT services. More research is needed to better understand needs of caregivers of patients with advanced cancers undergoing PRT. [ABSTRACT FROM AUTHOR] Copyright of International Journal of Radiation Oncology, Biology, Physics is the property of Pergamon Press - An Imprint of Elsevier Science and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity.

SARS-CoV-2 is the novel coronavirus that is the causative agent of COVID-19, a sometimes-lethal respiratory infection responsible for a world-wide pandemic. The envelope (E) protein, one of four structural proteins encoded in the viral genome, is a 75-residue integral membrane protein whose transmembrane domain exhibits ion channel activity and whose cytoplasmic domain participates in protein-protein interactions. These activities contribute to several aspects of the viral replication-cycle, including virion assembly, budding, release, and pathogenesis. Here, we describe the structure and dynamics of full-length SARS-CoV-2 E protein in hexadecylphosphocholine micelles by NMR spectroscopy. We also characterized its interactions with four putative ion channel inhibitors. The chemical shift index and dipolar wave plots establish that E protein consists of a long transmembrane helix (residues 8-43) and a short cytoplasmic helix (residues 53-60) connected by a complex linker that exhibits some internal mobility. The conformations of the N-terminal transmembrane domain and the C-terminal cytoplasmic domain are unaffected by truncation from the intact protein. The chemical shift perturbations of E protein spectra induced by the addition of the inhibitors demonstrate that the N-terminal region (residues 6-18) is the principal binding site. The binding affinity of the inhibitors to E protein in micelles correlates with their antiviral potency in Vero E6 cells: HMA ≈ EIPA > DMA >> Amiloride, suggesting that bulky hydrophobic groups in the 5' position of the amiloride pyrazine ring play essential roles in binding to E protein and in antiviral activity. An N15A mutation increased the production of virus-like particles, induced significant chemical shift changes from residues in the inhibitor binding site, and abolished HMA binding, suggesting that Asn15 plays a key role in maintaining the protein conformation near the binding site. These studies provide the foundation for complete structure determination of E protein and for structure-based drug discovery targeting this protein.