Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data.

The advances of single-cell transcriptomic technologies have led to increasing use of single-cell RNA sequencing (scRNA-seq) data in large-scale patient cohort studies. The resulting high-dimensional data can be summarized and incorporated into patient outcome prediction models in several ways; however, there is a pressing need to understand the impact of analytical decisions on such model quality. In this study, we evaluate the impact of analytical choices on model choices, ensemble learning strategies and integrate approaches on patient outcome prediction using five scRNA-seq COVID-19 datasets. First, we examine the difference in performance between using single-view feature space versus multi-view feature space. Next, we survey multiple learning platforms from classical machine learning to modern deep learning methods. Lastly, we compare different integration approaches when combining datasets is necessary. Through benchmarking such analytical combinations, our study highlights the power of ensemble learning, consistency among different learning methods and robustness to dataset normalization when using multiple datasets as the model input.

The change in pediatric subject symptoms during the COVID-19 pandemic in China: an increase in cardiac consultation.

BACKGROUND: It is reported that the adverse impact of nonpharmaceutical interventions (NPIs) on the mental health of children and adolescents may lead to psychologically related disorders during the coronavirus disease 2019 (COVID-19) period. Subject symptoms such as chest pain, chest tightness, and palpitation may be related to increased stress and anxiety in children and adolescents. The present research aimed to determine the number of pediatric consults and etiology of subject symptoms during the COVID-19 pandemic period and compared it with the same timelines in 2019 and 2021 to discuss the impact of different periods on the organic disease onset of children with subject symptoms, especially in cardiac involvement. METHODS: Children who visited Qingdao Women and Children's Hospital, Qingdao University between January 23 to April 30, 2019 (pre-COVID-19 period), January 23 to April 30, 2020 (COVID-19 period), and January 23 to April 30, 2021 (post-COVID-19 period) presenting chest pain, chest tightness, and palpitation were recruited. Information to determine gender, age, medical history, department for the initial visit, clinical manifestations, time from the latest onset to the visit, and diagnosis were recorded. RESULT: A total of 891 patients were enrolled in the present study (514 males; median age: 7.72). One hundred twenty-three patients presented during the pre-COVID-19 period while 130 during the COVID-19 period, nevertheless, the number substantially increased during the post-COVID-19 period (n = 638). Cardiac etiology accounted for 1.68% (n = 15) of the patient population, including arrhythmias (n = 10, 1.12%), myocarditis (n = 4, 0.44%), and atrial septal defect (n = 1, 0.11%). There was no significant difference among groups in the distribution of organic etiology. The median time from the latest onset to the visit during the pre-COVID-19 period was 7 days compared to 10 days during the COVID-19 period and 3 days during the post-COVID period. CONCLUSION: During the post-COVID-19 period, the median time from the latest onset to the visit was significantly shorter than that in the pre-COVID-19 period or COVID-19 period. The pediatric consult of children with subject symptoms presented increased substantially during the post-COVID-19 period, while there was no significant difference in the number of patients involving the cardiac disease. Clinicians ought to be more careful to screen heart diseases to prevent missed diagnosis and misdiagnosis during special periods.

Challenges for graduate students' mentors during COVID-19 pandemic.

The outbreak of COVID-19 pandemic results in the suspension of universities' academic laboratory activities. This brought a difficult time for graduate students majored in molecular biology and their mentors, since the student's thesis progress relies on the data from wet experiments in the lab. Even facing the challenges during the pandemic, mentors could still play an active role. This COVID-19 crisis requires mentors to have more thinking, innovation, and sharing in guiding graduate students.

Impacts of socio-economic determinants, spatial distance and climate factors on the confirmed cases and deaths of COVID-19 in China.

This study is to assess the influences of climate, socio-economic determinants, and spatial distance on the confirmed cases and deaths in the raise phase of COVID-19 in China. The positive confirmed cases and deaths of COVID-19 over the population size of 100,000 over every 5 consecutive days (the CCOPSPTT and DOPSPTT for short, respectively) covered from 25th January to 29th February, 2020 in five city types (i.e., small-, medium-, large-, very large- and super large-sized cities), along with the data of climate, socio-economic determinants, spatial distance of the target city to Wuhan city (DW, for short), and spatial distance between the target city and their local province capital city (DLPC, for short) were collected from the official websites of China. Then the above-mentioned influencing factors on CCOPSPTT and DOPSPTT were analyzed separately in Hubei and other provinces. The results showed that CCOPSPTT and DOPSPTT were significantly different among five city types outside Hubei province (p < 0.05), but not obviously different in Hubei province (p > 0.05). The CCOPSPTT had significant correlation with socio-economic determinants (GDP and population), DW, climate and time after the outbreak of COVID-19 outside Hubei province (p < 0.05), while was only significantly related with GDP in Hubei province (p < 0.05). The DOPSPTT showed significant correlation with socio-economic determinants, DW, time and CCOPSPTT outside Hubei province (p < 0.05), while was significantly correlated with GDP and CCOPSPTT in Hubei province (p < 0.05). Compared with other factors, socio-economic determinants have the largest relative contribution to variance of CCOPSPTT in all studied cities (> 78%). The difference of DOPSPTT among cities was mainly affected by CCOPSPTT. Our results showed that influences of city types on the confirmed cases and death differed between Hubei and other provinces. Socio-economic determinants, especially GDP, have higher impact on the change of COVID-19 transmission compared with other factors.

The Number of Patients with Acute Myocardial Infarction Decreased and Door-to-Balloon Time Delayed in COVID-19.

BACKGROUND: At present, COVID-19 is sweeping the world, and all countries are actively responding. During the COVID-19 epidemic, the treatment of patients with acute myocardial infarction (AMI) may be affected. METHODS: We reviewed data of patients with AMI from January 23 to April 23, 2020 (2020), and January 23 to April 23, 2019 (2019), who were admitted to two hospitals from Southern China. We collected clinical characteristics, comorbidities, treatment, prognosis, and key time segments to analyze. RESULTS: The total number of patients that had been diagnosed with AMI in the two hospitals was 218 in 2020 and 260 in 2019. The number of AMI patients that were admitted to hospitals per day decreased in 2020. The percentage of patients with AMI who refused hospitalization in 2020 was significantly higher than that in 2019 (5.0% vs 1.5%, p=0.028). There is no statistical difference in symptoms of the first medical contact (S2FMC) time between 2020 and 2019 (p=0.552). Door-to-balloon (D2B) time of ST-elevation myocardial infarction (STEMI) patients who were treated with a primary percutaneous coronary intervention (pPCI) in 2020 was 79 (63.75-105.25) mins, while D2B time in 2019 was 57.5 (41.5-76.5) mins, which was statistically different from the two groups. CONCLUSIONS: COVID-19 had an impact on the number of AMI patients who were admitted to hospitals and the time of treatment. During the COVID-19 epidemic, the number of AMI patients that were admitted to hospitals per day was decreased, while the percentage of AMI patients that refused therapy in these two hospitals increased, and the D2B time of STEMI patients was also delayed.

Influence of Meteorological Factors on the COVID-19 Transmission with Season and Geographic Location.

The purpose of this study is to investigate whether the relationship between meteorological factors (i.e., daily maximum temperature, minimum temperature, average temperature, temperature range, relative humidity, average wind speed and total precipitation) and COVID-19 transmission is affected by season and geographical location during the period of community-based pandemic prevention and control. COVID-19 infected case records and meteorological data in four cities (Wuhan, Beijing, Urumqi and Dalian) in China were collected. Then, the best-fitting model of COVID-19 infected cases was selected from four statistic models (Gaussian, logistic, lognormal distribution and allometric models), and the relationship between meteorological factors and COVID-19 infected cases was analyzed using multiple stepwise regression and Pearson correlation. The results showed that the lognormal distribution model was well adapted to describing the change of COVID-19 infected cases compared with other models (R2 > 0.78; p-values < 0.001). Under the condition of implementing community-based pandemic prevention and control, relationship between COVID-19 infected cases and meteorological factors differed among the four cities. Temperature and relative humidity were mainly the driving factors on COVID-19 transmission, but their relations obviously varied with season and geographical location. In summer, the increase in relative humidity and the decrease in maximum temperature facilitate COVID-19 transmission in arid inland cities, while at this point the decrease in relative humidity is good for the spread of COVID-19 in coastal cities. For the humid cities, the reduction of relative humidity and the lowest temperature in the winter promote COVID-19 transmission.

Development and preliminary validation of questionnaire for infection process and prevention of 2019 novel coronavirus infection in medical staffs

Objective To develop the questionnaire and test its reliability for investigating route, prevention, and control of SARS-CoV-2 infection in medical staffs. Methods This questionnaire was development based on the COVID-19 relevant guidelines, official documents issued by the National Health Committee of the People's Republic of China, and published studies. The development group performed repeated discussions and drafted the first questionnaire, then performed expert consultation and revised the draft according to their suggestions. Eventually, some frontline medical staffs were invited to carry out pre-test investigation of the questionnaire and test its reliability. Results The first draft included 48 items;18 experts were invited in the first round questionnaire and 10 experts in the second round questionnaire. The positive coefficient of experts in these two rounds was both greater than 75%, and the authority coefficient of experts' opinions was greater than 0.70. The variation coefficient of these items was between 0.00 and 0.35, the coordination coefficient of experts was 0.193 (P<0.05). The experts of above two rounds put forward 14 suggestions for text modification or adjustment options of some items;after the development group held repeatedly discussions, a total of 8 items were performed secondary consultation and finally reached consensus. The final questionnaire included two domains of questionnaire before and after confirmed diagnosis. The domain "before confirmed diagnosis" covered 4 sections and 29 items involving infectious cause, plan and knowledge of prevention and control, and psychological symptoms. The domain "after confirmed diagnosis" covered 5 sections and 21 items, included symptoms, treatment, and psychological status after diagnosis;impact on the surrounding environment and people, and awareness of protection after infection. The pre-test results showed that the total items were considerably numerous, some items were difficult to understand, some laboratory results and treatment conditions were ambiguous, etc. After modification and re-testing, the test-re-test reliability of each domain was between 0.74 and 0.93, and the overall re-test reliability of the questionnaire content was 0.82. Conclusions This research has developed a questionnaire for investigating infection process, prevention and control of SARS-CoV-2 infection in medical staff, and the items considered two domains prior to and after confirmed diagnosis. The reliability and practicability of the questionnaire are acceptable.