Feature-Action Design Patterns for Storytelling Visualizations with Time Series Data (preprint)

We present a method to create storytelling visualization with time series data. Many personal decisions nowadays rely on access to dynamic data regularly, as we have seen during the COVID-19 pandemic. It is thus desirable to construct storytelling visualization for dynamic data that is selected by an individual for a specific context. Because of the need to tell data-dependent stories, predefined storyboards based on known data cannot accommodate dynamic data easily nor scale up to many different individuals and contexts. Motivated initially by the need to communicate time series data during the COVID-19 pandemic, we developed a novel computer-assisted method for meta-authoring of stories, which enables the design of storyboards that include feature-action patterns in anticipation of potential features that may appear in dynamically arrived or selected data. In addition to meta-storyboards involving COVID-19 data, we also present storyboards for telling stories about progress in a machine learning workflow. Our approach is complementary to traditional methods for authoring storytelling visualization, and provides an efficient means to construct data-dependent storyboards for different data-streams of similar contexts.

Risk factors for severe COVID-19 infection and the impact of COVID-19 infection on disease progression among patients with AAV (preprint)

Objective To identify risk factors for COVID-19 infection and investigate the impact of COVID-19 infection on chronic kidney disease (CKD) progression and vasculitis flare in patients with antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV).Methods This cohort study retrospectively analyzed the prevalence and severity of COVID-19 infection in 276 patients with AAV who were followed up. Logistic regression was employed to estimate the risk of COVID-19 infection as well as CKD progression and vasculitis flare upon COVID-19 infection.Results During the 6-month observation period, 213 (77.2%) of 276 patients had a diagnosis of COVID-19 infection. Of these 213 patients, 49 (23.0%) had a COVID-19-related inpatient admission, including 17 patients who died of COVID-19 infection. AAV patients with severe COVID-19 infection were more likely to be male (OR 1.921 [95% CI 1.020–3.619], P = 0.043), suffered from worse kidney function (serum creatinine [Scr], OR 1.901 [95% CI 1.345–2.687], P < 0.001), had higher C-reactive protein (CRP) (OR 1.054 [95% CI 1.010–1.101], P = 0.017) and less likely to have evidence of initial vaccination (OR 0.469 [95% CI 0.231–0.951], P = 0.036), and Scr and COVID-19 vaccination were proven to be significantly associated with severe COVID-19 infection even after multivariable adjustment. Severe COVID-19 infection was significantly associated with subsequent CKD progression (OR 7.929 [95% CI 2.030-30.961], P = 0.003) and vasculitis flare (OR 11.842 [95% CI 1.048-133.835], P = 0.046) among patients with AAV.Conclusion AAV patients who were male, and with worse kidney function were more susceptible to severe COVID-19 infection, which subsequently increased the risk of CKD progression and vasculitis flare.

SARS-CoV-2 vaccination in the first year after hematopoietic cell transplant or chimeric antigen receptor T cell therapy: A prospective, multicenter, observational study (BMT CTN 2101) (preprint)

Background: The optimal timing of vaccination with SARS-CoV-2 vaccines after cellular therapy is incompletely understood. Objective To describe humoral and cellular responses after SARS-CoV-2 vaccination initiated <4 months versus 4-12 months after cellular therapy. Design Multicenter prospective observational study. Setting 34 centers in the United States. Participants 466 allogeneic hematopoietic cell transplant (HCT; n=231), autologous HCT (n=170), or chimeric antigen receptor T cell (CAR-T cell) therapy (n=65) recipients enrolled between April 2021 and June 2022. Interventions SARS-CoV-2 vaccination as part of routine care. Measurements We obtained blood prior to and after vaccinations at up to five time points and tested for SARS-CoV-2 spike (anti-S) IgG in all participants and neutralizing antibodies for Wuhan D614G, Delta B.1.617.2, and Omicron B.1.1.529 strains, as well as SARS-CoV-2-specific T cell receptors (TCRs), in a subgroup. Results Anti-S IgG and neutralizing antibody responses increased with vaccination in HCT recipients irrespective of vaccine initiation timing but were unchanged in CAR-T cell therapy recipients initiating vaccines within 4 months. Anti-S IgG ≥2,500 U/mL was correlated with high neutralizing antibody titers and attained by the last time point in 70%, 69%, and 34% of allogeneic HCT, autologous HCT, and CAR-T cell therapy recipients, respectively. SARS-CoV-2-specific T cell responses were attained in 57%, 83%, and 58%, respectively. Humoral and cellular responses did not significantly differ among participants initiating vaccinations <4 months vs 4-12 months after cellular therapy. Pre-cellular therapy SARS-CoV-2 infection or vaccination were key predictors of post-cellular therapy anti-S IgG levels. Limitations The majority of participants were adults and received mRNA vaccines. Conclusions These data support starting mRNA SARS-CoV-2 vaccination three to four months after allogeneic HCT, autologous HCT, and CAR-T cell therapy. Funding National Marrow Donor Program, Leukemia and Lymphoma Society, Multiple Myeloma Research Foundation, Novartis, LabCorp, American Society for Transplantation and Cellular Therapy, Adaptive Biotechnologies, and the National Institutes of Health

Immunity against Delta and Omicron variants elicited by homologous inactivated vaccine booster in kidney transplant recipients

Background A third mRNA vaccine booster is recommended to improve immunity against SARS-CoV-2 in kidney transplant recipients (KTRs). However, the immunity against SARS-CoV-2 Ancestral strain and Delta and Omicron variants elicited by the third dose of inactivated booster vaccine in KTRs remains unknown. Methods The blood parameters related to blood cells count, hepatic function, kidney function, heart injury and immunity were explored clinically from laboratory examinations. SARS-CoV-2 specific antibody IgG titer was detected using an enzyme-linked immunosorbent assay. Cellular immunity was analyzed using interferon-γ enzyme-linked immunospot assay. Results The results showed that there were no severe adverse effects and apparent changes of clinical laboratory biomarkers in KTRs and healthy volunteers (HVs) after homologous inactivated vaccine booster. A third dose of inactivated vaccine booster significantly increased anti-Ancestral-spike-trimer-IgG and anti-Ancestral-receptor binding domain (RBD)-IgG titers in KTRs and HVs compared with the second vaccination. However, the anti-Delta-RBD-IgG and anti-Omicron-RBD-IgG titers were significantly lower than anti-Ancestral-RBD-IgG titer in KTRs and HVs after the third dose. Notably, only 25.6% (10/39) and 10.3% (4/39) of KTRs had seropositivity for anti-Delta-RBD-IgG and anti-Omicron-RBD-IgG after booster, which were significantly lower than HVs (anti-Delta-RBD-IgG: 100%, anti-Omicron-RBD-IgG: 77.8%). Ancestral strain nucleocapsid protein and spike specific T cell frequency after booster was not significantly increased in KTRs compared with the second dose, significantly lower than that in HVs. Moreover, 33.3% (12/36), 14.3% (3/21) and 14.3% (3/21) of KTRs were positive for the Ancestral strain and Delta and Omicron spike-specific T cells, which were significantly lower than HVs (Ancestral: 80.8%, Delta: 53.8%, and Omicron: 57.7%). Conclusions A third dose of inactivated booster vaccine may significantly increase humoral immunity against the Ancestral strain in KTRs, while humoral and cellular immunity against the Delta and Omicron variants were still poor in KTRs.

Antibody-mediated autoimmune encephalitis evaluated by 18F-DPA714 PET/MRI

SARS-CoV-2 vaccine has considered being the most effective method to prevent SARS-CoV-2 infection. The safety and effectiveness of the SARS-CoV-2 vaccine has been confirmed. However, in very rare cases, autoimmune neurological diseases may occur. In this article, we report three rare cases of autoimmune encephalitis with definite auto-antibody after SARS-CoV-2 vaccination. They all have good prognosis after treatment. In addition, we first use 18F-DPA-714 PET/MRI to evaluate microglia activation in our patients. We found that 18F-DPA-714 PET/MRI may be a powerful tool for quantitative analysis of neuroinflammation in patients of autoimmune encephalitis. Finally, although rare complications may happen after vaccination, we still consider the benefits of vaccination far outweigh the risks. People without contraindications should be vaccinated without delay to prevent infection in current outbreak situation.

The spatial-temporal distribution and transmission route of COVID-19 in Shenzhen in the early stage

Objective: To provide reference for future epidemiological investigation, prevention and control of infectious diseases by analyzing the spatial-temporal distribution and transmission characteristics of corona virus diseases 2019 (COVID- 19) in the early stage in Shenzhen.

Boosting the Photothermal Conversion Efficiency of MXene Film by Porous Wood for Light-driven Soft Actuators

Ti3C2Tx (a typical MXene) has been widely used in light-driven actuators due to its outstanding photothermal conversion capability. However, the response speed of these actuators is always slow because the effective irradiated area is limited to their surface. Herein, we propose a wood-based composite material which is made by coating Ti3C2Tx on delignified wood (DW). The high porosity of DW leads to high loading of Ti3C2Tx and provides large irradiated areas, thus enhancing photothermal conversion efficiency. The delignification on wood can expose cellulose with highly hydrophilic surface for rapid diffusion of Ti3C2Tx suspension, and the hydroxy in cellulose can act as binding sites to form stable combination with Ti3C2Tx. Taking advantage of the good compressibility of DW, a simple densification is conducted on TDW (Ti3C2Tx/DW) to greatly shorten the distance between adjacent oxygen-enriched Ti3C2Tx nanosheets, enhancing the conjugation among nanosheets, thus endowing TDW with good flexibility and high heat transfer efficiency. Moreover, we manufacture a light-driven bilayer actuator comprised of TDW as the passive layer and low-density polyethylene (LDPE) as the active layer. Our light-driven actuator exhibits a tremendous angle variation of 160° at a light intensity of 120 mW/cm2. A series of devices based on the TDW/LDPE actuator are demonstrated, including simulated gestures, a four-finger soft gripper, and a bionic flower. Moreover, we propose a light-controlled smart switch which can be used on non-contact (COVID-19) or dangerous (blasting) occasions. Additionally, we present a finite element simulation to predict the bending deformation, which guides the accurate control of the devices.

Influence of Rural Development of River Tourism Resources on Physical and Mental Health and Consumption Willingness in the Context of COVID-19

This study took the Three Gorges Dam as an example and discussed the influence of river regulation decisions on the sustainable development of surrounding villages. The study used mixed research methods, snowball sampling, and convenience sampling to obtain samples. The questionnaire samples were analyzed by basic statistical tests, t-test, and structural equation modeling (SEM). The respondents' opinions were collected through semi-structured interviews and finally the results were discussed by multivariate analysis. The findings were that even though the villages were not well developed in terms of economy, environment, and natural ecology, as long as the community security could be stable, the living could be safe and convenient, people's daily life patterns and leisure behaviors could be maintained, and people could stabilize their minds and emotions and maintain physical and mental health in order to meet their living needs and reduce the burden. There would be time and funds to invest in leisure, tourism activities, and consumption behavior. If the above consumption patterns are continued, people will gain positive perceptions, stimulating people's willingness to invest in property purchases or to make travel plans again.

Competency and Related Factors in Preventing Emerging Infectious Diseases among Nurses in Long-Term Care Facilities in Taiwan

Emerging infectious diseases (EIDs) are a considerable threat to health, particularly in long-term care facilities (LTCFs), where residents are especially vulnerable. Nurses’ competency in EID prevention is crucial to minimize the adverse effects of EIDs in LTCFs. This study investigated nurses’ competency and related factors in EID prevention in LTCFs in Tainan, Taiwan. A cross-sectional design was employed, and nurses were recruited to complete an online survey examining the knowledge, attitude, and skills required to prevent EIDs in LTCFs. A total of 235 nurses completed the survey. The equivalent score index (SI) for knowledge regarding EID prevention was 68, indicating that the nurses did not have adequate knowledge regarding EID prevention. In contrast, the equivalent SI for the subscale of attitudes toward EID prevention was 78, indicating that the nurses exhibited moderately to highly positive attitudes toward EID prevention. However, they rated themselves as being highly skilled in EID prevention, corresponding to an equivalent SI of 91. Perceived supervisors’ approval, marital status, attitudes toward EID prevention, EID prevention skills, knowledge regarding EIDs, and being in charge of infectious disease prevention were significant predictors of the nurses’ competency. LTCF nurses, especially those working in nursing homes, should enhance their knowledge regarding EID prevention. These findings may help improve nurses’ competency in preventing EIDs by encouraging the integration of practice strategies, education, research, and policy recommendations to eliminate EIDs in LTCFs.

Association between immunosuppressants and antibody responses to SARS-CoV-2 vaccines in patients with autoimmune liver diseases (preprint)

Background and aims: Little is known regarding the antibody responses of COVID-19 vaccination in patients with autoimmune liver diseases (AILD). We aim to evaluate the antibody responses and explore the impact of immunosuppressants on SARS-CoV-2 vaccines in AILD.Methods: We conducted a prospective observational study and included participants been healthy as controls and AILD. All adverse events (AEs) were recorded. IgG antibodies against the receptor-binding domain (RBD) of spike protein (anti-RBD-IgG) and Neutralizing antibodies (NAbs) were tested after the COVID-19 vaccination. In addition, SARS-CoV-2 specific B cells were detected by flow cytometry.Results: 76 patients and 136 healthy controls (HC) were included. All AEs were mild and self-limiting, and the incidences were similar between AILD and HC groups. The seropositivity rates of anti-RBD-IgG and NAbs in AILD were 97.4% (100% in HC, p = 0.13) and 63.2% (84.6% in HC, p < 0.001), respectively. The titers of anti-RBD-IgG and NAbs were significantly lower in AILD compared with HC. After adjusting for confounders, immunosuppressive therapy was an independent risk factor for the low-level anti-RBD-IgG (adjusted odds ratio [AOR]: 4.7; 95% confidence interval [CI], 1.5-15.2; p = 0.01) and reduced probability of NAbs seropositivity (AOR, 3.0; 95% CI, 1.0-8.9; p = 0.04) in AILD patients. However, regardless of immunosuppressants, the SARS-CoV-2 specific memory B cells responses were comparable between AILD and HC groups.Conclusion: SARS-CoV-2 inactivated vaccine is safe, but its immunogenicity is compromised in patients with AILD. Moreover, immunosuppressants are significantly associated with poor antibody responses to the SARS-CoV-2 vaccine.

Visualization for Epidemiological Modelling: Challenges, Solutions, Reflections & Recommendations (preprint)

We report on an ongoing collaboration between epidemiological modellers and visualization researchers by documenting and reflecting upon knowledge constructs -- a series of ideas, approaches and methods taken from existing visualization research and practice -- deployed and developed to support modelling of the COVID-19 pandemic. Structured independent commentary on these efforts is synthesized through iterative reflection to develop: evidence of the effectiveness and value of visualization in this context; open problems upon which the research communities may focus; guidance for future activity of this type; and recommendations to safeguard the achievements and promote, advance, secure and prepare for future collaborations of this kind. In describing and comparing a series of related projects that were undertaken in unprecedented conditions, our hope is that this unique report, and its rich interactive supplementary materials, will guide the scientific community in embracing visualization in its observation, analysis and modelling of data as well as in disseminating findings. Equally we hope to encourage the visualization community to engage with impactful science in addressing its emerging data challenges. If we are successful, this showcase of activity may stimulate mutually beneficial engagement between communities with complementary expertise to address problems of significance in epidemiology and beyond. https://ramp-vis.github.io/RAMPVIS-PhilTransA-Supplement/

An acceptable methodological evaluation method of real-time fluorescent RT-PCR targeting SARS-CoV-2 (preprint)

Background: it is necessary to evaluate real-time fluorescent reverse-transcription PCR (RT-PCR) methods to detect the nucleic acids of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methods: considering lack of positive specimens in some particular locations in China, the specimens from healthy individuals were used to perform the methodology evaluations, in which the indexes were the differences of quantification cycle values (ΔCq) between human-derived internal reference control (IRC) genes of a specimen and quality control gene (QC). A series of experiments was conducted to evaluate various factors that might affect the results, such as types of virus transport media, methods of specimen pretreatment and template preparation, specimen vortex strength, specimen storage temperature, and duration. Results: it was better to store specimens in normal saline (NS) transport medium, release more virus particles from swabs by vortex mixing, extract nucleic acids with centrifugation methods, and perform amplification assays timely. The above-mentioned options and optimum conditions were further confirmed using SARS-CoV-2 pseudoviruses and positive clinical specimens. Conclusions: this study provides a solution for the accurate detection of SARS-CoV-2. Specifically, this study also indicates that the routine specimens from healthy individuals could be used to methodological evaluation of real-time fluorescent RT-PCR targeting SARS-CoV-2, of which the indexes were the ΔCq values.

SARS-CoV-2 RdRp is a versatile enzyme with proofreading activity and ability to incorporate NHC into RNA by using diphosphate form molnupiravir as a substrate (preprint)

The coronavirus disease 2019 (COVID-19) has been ravaging throughout the world for almost two years and has severely impaired both human health and the economy. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) employs the viral RNA-dependent RNA polymerase (RdRp) complex for genome replication and transcription, making RdRp an appealing target for antiviral drug development. Although the structure of the RdRp complex has been determined, the function of RdRp has not been fully characterized. Here we reveal that in addition to RNA dependent RNA polymerase activity, RdRp also shows exoribonuclease activity and consequently proofreading activity. We observed that RdRp and nsp14-ExoN, when combined, exhibit higher proofreading activity compared to RdRp alone. Moreover, RdRp can recognize and utilize nucleoside diphosphate (NDP) as substrate to synthesize RNA and can also incorporate {beta}-d-N4-hydroxycytidine (NHC) into RNA while using diphosphate form molnupiravir as substrate.

Why Do Citizens Share COVID-19 Fact-Checks Posted by Chinese Government Social Media Accounts? The Elaboration Likelihood Model.

Widespread misinformation about COVID-19 poses a significant threat to citizens long-term health and the combating of the disease. To fight the spread of misinformation, Chinese governments have used official social media accounts to participate in fact-checking activities. This study aims to investigate why citizens share fact-checks about COVID-19 and how to promote this activity. Based on the elaboration likelihood model, we explore the effects of peripheral cues (social media capital, social media strategy, media richness, and source credibility) and central cues (content theme and content importance) on the number of shares of fact-checks posted by official Chinese Government social media accounts. In total, 820 COVID-19 fact-checks from 413 Chinese Government Sina Weibo accounts were obtained and evaluated. Results show that both peripheral and central cues play important roles in the sharing of fact-checks. For peripheral cues, social media capital and media richness significantly promote the number of shares. Compared with the push strategy, both the pull strategy and networking strategy facilitate greater fact-check sharing. Fact-checks posted by Central Government social media accounts receive more shares than local government accounts. For central cues, content importance positively predicts the number of shares. In comparison to fact-checks about the latest COVID-19 news, government actions received fewer shares, while social conditions received more shares.

Perinatal depression and anxiety among Chinese women during the outbreak of the COVID-19 Delta variant (preprint)

Background: This study aimed to assess the COVID-19 Delta variant impact on the incidence of depressive and anxiety symptoms in pregnant women in Guangdong Province, China, as well as to identify related risk factors.Methods: A three-week, multisite, cross-sectional study was conducted from June to July 2021 to evaluate the mental health status of pregnant women by the Edinburgh Postnatal Depression Scale. Approximately 1,450 women from 25 Guangdong hospitals were included in the study. We employed the Edinburgh Postnatal Depression Scale to assess symptoms of maternal depression and anxiety. Risk factors and relevance rates were analyzed.Results: Pregnant women who were determined to be underweight before pregnancy, primiparous, above 35 years of age, employed full-time, of middle income status, and had comfortable living arrangements were at higher risk of developing depression and anxiety during a COVID-19 outbreak.Conclusion: The occurrence of the COVID-19 Delta variant has increased the risk of mental disorders in pregnant women, which include thoughts of self-harm. Programs designed to address maternal stress as well as isolation such as constructive risk, communication, and providing psychological first aid may be particularly useful to avoid negative outcomes in pregnant women and their fetuses.

Health-Seeking Behavior of Patients with Cardiovascular Diseases During COVID-19 Epidemic and Post-Epidemic Period in Shanghai, China (preprint)

Background: The COVID-19 pandemic has led to concerns around its subsequent impact on patients with non-COVID-19 diseases, and the health-seeking behavior of such patients must be investigated.Methods: Taking advantage of the remote ECG system covering 278 medical institutions throughout Shanghai, the numbers of hospital visits with ECG examinations during the lockdown (between January 23 and April 7, 2020), post-lockdown (between April 8 and December 31, 2020) and post-epidemic (between January 23 and April 7, 2021) periods were analyzed and compared against those during the same periods of the preceding years (2018 and 2019).Findings: Compared with those of the same period during pre-COVID years, the number of hospital visits decreased during the lockdown (a 38% reduction), followed by a rebound post-lockdown (a 17% increase) and a fall to the baseline level of the post-epidemic period. This decrease-rebound-fallback pattern was largely attributed to the dynamics of visits to community clinics rather than academic hospitals. The number of new COVID-19 cases or deaths announced on a given day correlated negatively with hospital visits during the same day and for the following 42 days, with the correlation at its most prominent at seven days. Hospital visit dynamics differed for various cardiovascular diseases. Whereas hospital visits for sinus bradycardia exhibited a typical decrease-rebound-fallback pattern, hospital visits for ST-segment elevated myocardial infarction did not fall during the lockdown period but did exhibit a subsequent increase during the post-lockdown period. By comparison, the volume for ventricular tachycardia remained constant throughout this entire period.Interpretation: The health-seeking behavior of patients with cardiovascular diseases exhibited a decrease-rebound-fallback pattern following the COVID-19 lockdowns. Hospital visits for diseases with more severe symptoms were less influenced by the lockdowns, showing a resilient demand for healthcare.Funding: Shanghai Hospital Development Center, National Natural Science Foundation of China, Shanghai Municipal Science and Technology Commission, and Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine. Declaration of Interest: All authors declare no conflicts of interest.Ethical Approval: This study was approved by the ethics committee at Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine.

Knowledge-attitude-practice survey of coronavirus disease 2019 in workers returning to work in Guangdong

Objective: To understand the knowledge, attitude and practice (KAP) towards coronavirus disease 2019 (COVID-19) in workers returning to work in Guangdong province and put forward some suggestions for the targeted prevention and control of COVID-19.