Whole genome sequencing of a German cohort to understand host genetics in COVID-19

Background/Objectives: The disease course upon SARS-CoV-2 infection is highly variable and comprises a range from asymptomatic infection to severe (and even lethal) COVID-19. Genetic factors substantially contribute to this variability, as evidenced by epidemiological studies and recent results from genome-wide association studies (GWAS) as well as sequencing-based approaches. The host genetics group of the German COVID-19 OMICs Initiative (DeCOI) has been founded with the aim to identify additional genetic variants that influence COVID-19 severity through whole genome sequencing (WGS) analyses. Method(s): Until January 2022, WGS has been performed on approximately 1200 individuals affected by COVID-19. Result(s): The most recent data freeze comprised 952 individuals. In this dataset, no carrier of a deleterious protein-altering variant has been detected in TLR7, which is the only conclusive risk gene for severe COVID-19. Applying a gene-based association test of rare variants to the subcohort of European individuals (n = 752, mean age: 56 years, females: 44%), including 199 severely affected individuals, we did not observe any significant association after correction for multiple testing. Exome-wide association analysis of common variants in this subcohort replicated the GWAS-locus on chromosome 3. Conclusion(s): With this ongoing work, we are contributing to international efforts to elucidate the host genetics of COVID-19, also by sharing our summary statistics for meta-analyses. Currently, we are sequencing additional severely affected individuals and we are refining analytical strategies, which will also include the joint analysis of common and rare variants at genomewide scale.

Creative space for navigating complex times: Using artbased inquiry to respond to uncertainty during COVID-19

This article shares the outcomes of a participatory art-based inquiry conducted during stay-at-home orders due to COVID-19 and the impact on the mental health and well-being of college-age students (age 18–21) in the United States. Participants engaged in artmaking sessions alongside researchers to respond to prompts geared to help them process their experiences. Findings that emerged from the project suggest that art-based practices in a community setting may support students in navigating times of great uncertainty by offering participants a chance to express themselves and process complicated feelings. Based on our findings, we offer art-based practices as a way to support young adults as they process the negative impact of the pandemic, transition back to campus, and navigate the college experience. © 2022 Intellect Ltd Article. English language.

Assessing the use of attention weights to interpret BERT-based stance classification

BERT models are currently state-of-the-art solutions for various tasks, including stance classification. However, these models are a black box for their users. Some proposals have leveraged the weights assigned by the internal attention mechanisms of these models for interpretability purposes. However, whether the attention weights help the interpretability of the model is still a matter of debate, with positions in favor and against. This work proposes an attention-based interpretability mechanism to identify the most influential words for stances predicted using BERT-based models. We target stances expressed in Twitter using the Portuguese language and assess the proposed mechanism using a case study regarding stances on COVID-19 vaccination in the Brazilian context. The interpretation mechanism traces tokens' attentions back to words, assigning a newly proposed metric referred to as absolute word attention. Through this metric, we assess several aspects to determine if we can find important words for the classification and with meaning for the domain. We developed a broad experimental setting that involved three datasets with tweets in Brazilian Portuguese and three BERT models with support for this language. Our results are encouraging, as we were able to identify 52-82% of words with high absolute attention contributing positively to stance classification. The interpretability mechanism proved to be helpful to understand the influence of words in the classification, and they revealed intrinsic properties of the domain and representative arguments of the stances. © 2021 ACM.

COVID-19 infection after pediatric heart transplantation in Germany, Austria, and Switzerland

Background: COVID-19 is a very heterogeneous infection that can vary in its course from asymptomatic to fatal. While the course of pediatric COVID-19 infections is mostly asymptomatic or very mild, patients with immunosuppressive therapy are at high risk of a severe infection. We conducted a multicenter survey with pediatric heart transplantation centers in Germany, Austria, and Switzerland (15 centers) to evaluate the risk of a severe COVID-19 infection after pediatric heart transplantation. Method: Retrospective analyses of all COVID-19 infections between February 2020 and June 2021 of patients after pediatric heart transplantation with medical care in one of the German, Austrian, or Swiss pediatric heart transplantation centers. Results: Twenty-one patients (nine male) with a mean age of 8.34 ± 5.33 years at time of transplantation and on average 8.33 ± 8.49 years after transplantation suffered from COVID-19 infection. Reasons for transplantation were dilated cardiomyopathy (n = 17), restrictive cardiomyopathy (n = 2), and congenital heart disease (n = 2). The immunosuppressive therapy consisted of tacrolimus (n = 17), cyclosporine A (n = 3), everolimus (n = 10), mycophenolate mofetil (n = 11), azathioprine (n = 1), and steroids (n = 3). Twelve patients had an asymptomatic COVID-19 infection, the other patients complained about cough (n = 3), rhinitis (n = 3), fever (n = 2), myalgia/fatigue (n = 5), diarrhea (n = 1), pain (n = 2), anosmia (n = 3), and loss of taste (n = 4). None of the patients showed dyspnea or reduced left ventricular function. Only one patient showed an increase in the degree of tricuspid regurgitation. Eight patients needed therapy in an outpatient setting and only two patients were hospitalized. One of these patients had a positive SARS-CoV-2 testing while on ICU early after heart transplantation. Interestingly, this patient had had a COVID-19 infection some weeks before heart transplantation. None of the patients needed oxygen supply or noninvasive ventilation or invasive mechanical ventilation. None of the patients needed a change of the immunosuppressive medication. No specific signs for graft dysfunction were found by noninvasive testing (echocardiography or electrocardiogram). Conclusion: After pediatric heart transplantation, a COVID-19 infection was very often asymptomatic or a mild infection and did not lead to a graft dysfunction despite the immunosuppressive therapy of the patients.

We want connection and we do not mean wi-fi: examining the impacts of Covid-19 on Gen Z's work and employment outcomes

Purpose This study aims to examine how members of Gen Z are impacted by Covid-19, specifically focusing on their professional opportunities, work preferences and future outlook. Design/methodology/approach A survey consisting of 24 questions including a Likert scale, multiple choice and open-ended was created to understand how members of Gen Z perceive Covid-19 impacting their education, employment, mental health and relationships. The survey was disseminated to employees of a corporate restaurant franchise, Christian college admissions and guidance non-profit, and online through social media including Instagram, Facebook, Reddit and LinkedIn. A total of 517 respondents completed the survey. Survey participants came from 29 states and 6 countries. Findings Results highlight Gen Z overwhelmingly values interpersonal connections, wants to Zoom less and work more in-person. The findings help anticipate potential professional gaps due to Covid-19 restrictions, as well as point out how Gen Z is markedly different in terms of workforce trends. Content analysis from an open-ended question reveals the extent of disruption Gen Z has experienced, adversely affecting their career plans and stalling professional development. Yet, despite these setbacks, Gen Z maintains a cautiously optimistic future outlook. Research limitations/implications Limitations to the study include the sample is largely comprising White women so the generalizability of results may be limited and the self-reporting nature of the survey may pose problems with method variance. Practical implications These findings have implications for Millennials as managers as they identify where resources should be invested including strengthening interpersonal communication skills, providing mentoring opportunities and appealing to their financial conservatism to recruit and retain Gen Z employees. The changes in telecommuting preferences and desire for more interpersonal and in-person communication opportunities highlight how Gen Z is markedly different than previous generations. Social implications Gen Z's optimistic future outlook conveys a sense of resilience and strength in the face of stress. Rather than engaging in cognitive distortions and over generalizations when stressed, results show Gen Z is able to find healthy alternatives and maintain optimism in the face of stress. Additionally, due to the extent of isolation and loneliness Gen Zers reported, the value of in-person connections cannot be overstated. As results convey a sense of being overlooked and missing out on so many rites of passage, inviting Gen Zers to share how they have been impacted, recognizing their accomplishments and listening to them may go a long way to develop rapport. Originality/value This study differs from others because it takes a generational look at Covid-19 impacts. The qualitative nature allows us to hear from members of Gen Z in their own words, and as a generational cohort, their voices inform workplace attitudes, practices and managerial procedures.

Impact of obstructive sleep apnea and positive airway pressure therapy on COVID-19 outcomes

Introduction: We explore the impact of obstructive sleep apnea (OSA) and positive airway pressure (PAP) therapy on novel coronavirus (COVID-19) infection rate and severity. Methods: Retrospective analysis was performed utilizing a database of patients evaluated by Kaiser Permanente Southern California sleep medicine between 2015-2020 (includes sleep study, daily PAP, and electronic health record data.) Adult patients were analyzed if: on March 1, 2020 patient was alive, had ≥1 month health-plan enrollment, and had sleep diagnostic or PAP data. PAP adherence was calculated between March 1, 2020 to COVID-19 confirmation, death, disenrollment or study end date (July 31, 2020), whichever came earlier. COVID-19 outcomes were evaluated based on OSA status and PAP adherence: patients with PAP <2 hours/ night were considered “untreated”;≥2 hours/night were “treated”;2-3.9 hours/night were “moderately-treated”;≥4 hours/night were “well-treated”. Apnea hypopnea index (AHI) defined OSA severity. Multiple logistic regression evaluated the association of various demographic/clinical factors. Results: Of 81,932 patients (39.8% female, age 54.0±14.9 years) analyzed, 1493 (1.8%) had COVID-19 with 224 (0.3%) hospitalizations and 61 (0.07%) resulting in intensive care or death. Increased severity of “Untreated” OSA was associated with higher COVID-19 rate and lower when “treated” [No OSA 1.7%;Mild 2%;Moderate 2%;Severe 2.4%;OSA unknown severity 2%;Treated 1.4%;p<0.0001]. Better PAP adherence was associated with reduced infection rate [“untreated” 2.1%;“moderately-treated” 1.7%, “well-treated” 1.3%, No OSA 1.7%;p=<0.0001]. Multivariable analysis confirmed increased infection rate with OSA versus no OSA [OR 0.82(0.70,0.96)] and the benefit of good PAP adherence versus “untreated” [“moderately-treated” OR 0.82 (0.65, 1.03);“well-treated” OR (0.69 (0.59, 0.80)]. Increased infection rate was also associated with obesity, higher Charlson Comorbidity score, Black and Hispanic ethnicities, and Medicaid enrollment;increasing age was associated with reduced infection rate. Separate multivariable analysis showed dose-response association of OSA severity on infection rate [Mild OR 1.21 (1.01,1.44 95%CI);Moderate- Severe OR 1.27 (1.07,1.51) versus no OSA]. Neither OSA presence nor PAP adherence significantly impacted rate of hospitalization nor intensive care or death. Conclusion: Significant associations emerged with OSA increasing and PAP therapy reducing COVID-19 infection rate. Findings support continued PAP use during the pandemic.

Quarenteners vs. Chloroquiners: A framework to analyze how political polarization affects the behavior of groups

The worldwide COVID-19 pandemic has struck people's lives over-night. With an alarming contagious rate and no effective treatments or vaccines, it has evoked all sorts of reactions. In this paper, we propose a framework to analyze and characterize groups' behavior with opposed stances and the relation with the political polarization, using the Brazilian COVID polarized scenario as a case study. The pro/against social distance stances are represented by two Twitter groups referred to as Chloroquiners and Quarenteners. The framework encompasses: a) techniques to automatically infer from users their demographics and political orientation, b) topic modeling to discover the major concerns expressed by each group;c) network analysis and community detection to characterize their behavior as a social network group;d) analysis of linguistic characteristics to identify psychological aspects, and e) the characterization of information sources and external influences to evaluate the "echo chamber effect". These properties aim to explain the group's behavior using the Identity Protective Cognitive theory, in which culturally grouped individuals give biased credit and dismiss evidence according to the predominant group beliefs. Our main findings confirm that the political polarization of Chloroquiners and Quarenteners influence the arguments of economy and life, and support/opposition to the president. As a group, the network of Chloroquiners is more closed and connected, and highly influenced by information passed through social networks. Quarenteners have a more diverse political engagement and are more influenced by formal media. In terms of psychological aspects, the use of Identity Protection Cognition provides more robust arguments to explain these behaviors.

Treatment changes in prostate cancer patients on active treatment during the COVID-19 pandemic in a community cancer center in New York City

Background: The surge of the SARS coronavirus-2 (COVID-19) pandemic posed great challenges in the oncology community for optimal management of cancer patients. We sought to analyze the treatment changes experienced by the prostate cancer patients in March, April and May 2020 and to compare these treatment decisions to the published guidelines. Methods: We focused on patients currently receiving androgen deprivation therapy (ADT) with leuprolide acetate, and/or oral anti-androgen agents (Androgen receptor axis targeted agent, ARAT), or chemotherapy. Electronic medical records were reviewed, and the oncologists and nurse practitioners were interviewed to understand the decision-making process. Results: Seventy-five patients were included, median age 72 years old (range 47- 95). All were taking ADT, and 21 were also taking ARAT, and 3 were also receiving chemotherapy. The incidence and indications for their ADT treatments and schedule changes are shown in the table below. Twenty-seven patients (36%) experienced delays in their ADT treatment, and the percentage of treatment change was similar in categories of metastatic hormone sensitive prostate cancer (mHSPC), metastatic castration resistant cancer (mCRPC), biochemical recurrence as well as stage IVA post surgery. Four patients were receiving neoadjuvant ADT planned prior to definitive radiation, and none had schedule change. One patient with mHSPC and 2 patients with mCRPC continued chemotherapy as planned. One patient declined recommended chemotherapy for mCRPC. Two patients were given q 3 months dose of ADT instead of q 1m, while all the rest were already receiving q3 months dosing. Among the 27 patients who had schedule change, 12 (44.4%) patients had a discussion with their providers first, and 15 patients (55.6%) did not keep their treatment appointment. Conclusions: About one third of patients changed ADT injection schedule with a similar percentage in patients with mHSPC, or mCRPC or Biochemical recurrence, or IVA after surgery. Every 3 months dosing of ADT recommended by NCCN significantly decreases exposure to COVID -19, delaying or skipping treatment was still encountered due to health concern or travel limitations. On the other hand, all patients receiving neoadjuvant ADT, or chemotherapy stayed on schedule. Although NCCN guideline recommended delaying myelosuppressive therapy, palliative chemotherapy for symptomatic, refractory patients may still be a priority.

Vascular Inflammation Is Associated with Loss of Aquaporin 1 Expression on Endothelial Cells and Increased Fluid Leakage in SARS-CoV-2 Infected Golden Syrian Hamsters

Vascular changes represent a characteristic feature of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection leading to a breakdown of the vascular barrier and subsequent edema formation. The aim of this study was to provide a detailed characterization of the vascular alterations during SARS-CoV-2 infection and to evaluate the impaired vascular integrity. Groups of ten golden Syrian hamsters were infected intranasally with SARS-CoV-2 or phosphate-buffered saline (mock infection). Necropsies were performed at 1, 3, 6, and 14 days post-infection (dpi). Lung samples were investigated using hematoxylin and eosin, alcian blue, immunohistochemistry targeting aquaporin 1, CD3, CD204, CD31, laminin, myeloperoxidase, SARS-CoV-2 nucleoprotein, and transmission electron microscopy. SARS-CoV-2 infected animals showed endothelial hypertrophy, endothelialitis, and vasculitis. Inflammation mainly consisted of macrophages and lower numbers of T-lymphocytes and neutrophils/heterophils infiltrating the vascular walls as well as the perivascular region at 3 and 6 dpi. Affected vessels showed edema formation in association with loss of aquaporin 1 on endothelial cells. In addition, an ultrastructural investigation revealed disruption of the endothelium. Summarized, the presented findings indicate that loss of aquaporin 1 entails the loss of intercellular junctions resulting in paracellular leakage of edema as a key pathogenic mechanism in SARS-CoV-2 triggered pulmonary lesions.

[Results of preoperative SARS-CoV-2 testing in the coronavirus pandemic]. / Ergebnisse der präoperativen SARS-CoV-2-Testung ("severe acute respiratory syndrome coronavirus 2") in der Coronaviruspandemie.

BACKGROUND: Surgery is challenging during the coronavirus disease 2019 (COVID-19) pandemic. This study aimed to investigate the preoperative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing in elective and emergency surgery and to calculate the patient contacts during hospital stay. MATERIALS AND METHODS: All surgeries defined by the German procedural classification (starting with a 5) from 1 June until 29 November 2020 were retrospectively evaluated regarding the preoperative SARS-CoV­2 nasopharyngeal swab test. The results were then divided in emergency and elective surgeries. To show the personal contacts of the patients in a university hospital, we calculated the patient pathway within the department of urology and urosurgery for April 2020. Therefor we used the electronic patient records. RESULTS: Altogether 7745 surgical procedures in 5985 patients were performed, whereby 39 (0.5%) SARS-CoV­2 tests were positive. 2833 (37%) surgical procedures were emergency cases and 4912 (63%) were elective procedures. 25 (0.9%) of the emergency group and 14 (0.3%) of the elective surgeries had a positive SARS-CoV­2 test. The average number of contacts in the patient room was 12.83 (0-50) and 84.22 (0-249) at the ward level, not counting contacts with the clinic staff. CONCLUSIONS: Nearly 1% of the preoperative SARS-CoV­2 tests of either emergency or elective surgeries tested positive in the 6 months prior to November 2020. Although the risk of undetected SARS-CoV­2 infection appears to be low in terms of costs and personnel, preoperative screening is useful in high-risk areas to ensure further necessary surgeries, especially concerning cancer patients and to prevent virus spread in a hospital.