New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2.

The 2019 novel coronavirus (SARS-CoV-2) has spread rapidly worldwide and was declared a pandemic by the WHO in March 2020. The evolution of SARS-CoV-2, either in its natural reservoir or in the human population, is still unclear, but this knowledge is essential for effective prevention and control. We propose a new framework to systematically identify recombination events, excluding those due to noise and convergent evolution. We found that several recombination events occurred for SARS-CoV-2 before its transfer to humans, including a more recent recombination event in the receptor-binding domain. We also constructed a probabilistic mutation network to explore the diversity and evolution of SARS-CoV-2 after human infection. Clustering results show that the novel coronavirus has diverged into several clusters that cocirculate over time in various regions and that several mutations across the genome are fixed during transmission throughout the human population, including D614G in the S gene and two accompanied mutations in ORF1ab. Together, these findings suggest that SARS-CoV-2 experienced a complicated evolution process in the natural environment and point to its continuous adaptation to humans. The new framework proposed in this study can help our understanding of and response to other emerging pathogens.

Impact of Systematic Factors on the Outbreak Outcomes of the Novel COVID-19 Disease in China: Factor Analysis Study.

BACKGROUND: The novel COVID-19 disease has spread worldwide, resulting in a new pandemic. The Chinese government implemented strong intervention measures in the early stage of the epidemic, including strict travel bans and social distancing policies. Prioritizing the analysis of different contributing factors to outbreak outcomes is important for the precise prevention and control of infectious diseases. We proposed a novel framework for resolving this issue and applied it to data from China. OBJECTIVE: This study aimed to systematically identify national-level and city-level contributing factors to the control of COVID-19 in China. METHODS: Daily COVID-19 case data and related multidimensional data, including travel-related, medical, socioeconomic, environmental, and influenza-like illness factors, from 343 cities in China were collected. A correlation analysis and interpretable machine learning algorithm were used to evaluate the quantitative contribution of factors to new cases and COVID-19 growth rates during the epidemic period (ie, January 17 to February 29, 2020). RESULTS: Many factors correlated with the spread of COVID-19 in China. Travel-related population movement was the main contributing factor for new cases and COVID-19 growth rates in China, and its contributions were as high as 77% and 41%, respectively. There was a clear lag effect for travel-related factors (previous vs current week: new cases, 45% vs 32%; COVID-19 growth rates, 21% vs 20%). Travel from non-Wuhan regions was the single factor with the most significant impact on COVID-19 growth rates (contribution: new cases, 12%; COVID-19 growth rate, 26%), and its contribution could not be ignored. City flow, a measure of outbreak control strength, contributed 16% and 7% to new cases and COVID-19 growth rates, respectively. Socioeconomic factors also played important roles in COVID-19 growth rates in China (contribution, 28%). Other factors, including medical, environmental, and influenza-like illness factors, also contributed to new cases and COVID-19 growth rates in China. Based on our analysis of individual cities, compared to Beijing, population flow from Wuhan and internal flow within Wenzhou were driving factors for increasing the number of new cases in Wenzhou. For Chongqing, the main contributing factor for new cases was population flow from Hubei, beyond Wuhan. The high COVID-19 growth rates in Wenzhou were driven by population-related factors. CONCLUSIONS: Many factors contributed to the COVID-19 outbreak outcomes in China. The differential effects of various factors, including specific city-level factors, emphasize the importance of precise, targeted strategies for controlling the COVID-19 outbreak and future infectious disease outbreaks.

Classification and transfer learning of sleep spindles based on convolutional neural networks.

Background: Sleep plays a critical role in human physiological and psychological health, and electroencephalography (EEG), an effective sleep-monitoring method, is of great importance in revealing sleep characteristics and aiding the diagnosis of sleep disorders. Sleep spindles, which are a typical phenomenon in EEG, hold importance in sleep science. Methods: This paper proposes a novel convolutional neural network (CNN) model to classify sleep spindles. Transfer learning is employed to apply the model trained on the sleep spindles of healthy subjects to those of subjects with insomnia for classification. To analyze the effect of transfer learning, we discuss the classification results of both partially and fully transferred convolutional layers. Results: The classification accuracy for the healthy and insomnia subjects' spindles were 93.68% and 92.77%, respectively. During transfer learning, when transferring all convolutional layers, the classification accuracy for the insomnia subjects' spindles was 91.41% and transferring only the first four convolutional layers achieved a classification result of 92.80%. The experimental results demonstrate that the proposed CNN model can effectively classify sleep spindles. Furthermore, the features learned from the data of the normal subjects can be effectively applied to the data for subjects with insomnia, yielding desirable outcomes. Discussion: These outcomes underscore the efficacy of both the collected dataset and the proposed CNN model. The proposed model exhibits potential as a rapid and effective means to diagnose and treat sleep disorders, thereby improving the speed and quality of patient care.

High capacity and fast removal of Cr(vi) by alkali lignin-based poly(tetraethylene pentamine-pyrogallol) sorbent.

In this work, a novel alkali lignin-based adsorption material, alkali lignin-based poly(tetraethylene pentamine-pyrogallol) (AL-PTAP), was prepared using a Mannich reaction and catechol-amine reaction for removal of Cr(vi). It was characterized by thermogravimetric analysis (TGA), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy (XPS). The effects of tetraethylene pentamine (TEPA) dosage, pyrogallol (PL) dosage, contact time, pH, temperature and other factors on the adsorption behavior of the adsorbent were systematically investigated. These experimental data show that the adsorption behavior conforms to the pseudo-second-order kinetic model and the Langmuir isotherm model. The maximum adsorption capacity is 769.2 mg g-1 at 303 K, which is much higher than that of alkali lignin (AL). AL-PTAP can achieve a removal rate of almost 100% for Cr(vi) solutions with a concentration of less than 90 mg L-1 at 1 min. Furthermore, the toxic Cr(vi) is partly reduced to nontoxic Cr(iii) during the adsorption process. Therefore, AL-PTAP is a fast and efficient alkali lignin-based adsorbent, which is expected to improve the utilization value of alkali lignin in Cr(vi) wastewater treatment.

The effects of CPET-guided cardiac rehabilitation on exercise tolerance in older persons with CHD after PCI.

Prescribing appropriate exercise is an important means to improve the safety and efficacy of cardiac rehabilitation. Improper exercise may induce an increased cardiovascular risk in older persons with coronary heart disease. Cardiopulmonary exercise testing (CPET)-guided cardiac rehabilitation could be helpful for providing clinical evidence for cardiac rehabilitation therapy in older persons after percutaneous coronary intervention (PCI). We retrospectively included older persons who underwent PCI and cardiac rehabilitation based on CPET at the Cardiac Rehabilitation Center of Peking University Third Hospital from January 2014 to December 2019. Patients' baseline and follow-up clinical data were collected. A total of 403 older persons after PCI were included in the study. The mean age was 80.5 ± 4.3. The mean follow-up time was 12 ± 2 months. During the follow-up period, no significant exercise-related adverse events occurred, and the peak oxygen uptake (VO2peak) increased compared with baseline (15.5 ± 3.8 ml/min/kg vs. 17.3 ± 4.1 ml/min/kg). Among the 90 patients (22.2%) without exercise habits at baseline who started regular exercise during follow-up, the improvement in VO2peak was most significant, at 3.2 ± 0.4 ml/min/kg. Cardiac rehabilitation based on CPET improved exercise habits and exercise tolerance in older persons with coronary heart disease after PCI.

Comparison Between Treadmill and Bicycle Ergometer Exercises in Terms of Safety of Cardiopulmonary Exercise Testing in Patients With Coronary Heart Disease.

Background: Cardiopulmonary exercise testing (CPET) is used widely in the diagnosis, exercise therapy, and prognosis evaluation of patients with coronary heart disease (CHD). The current guideline for CPET does not provide any specific recommendations for cardiovascular (CV) safety on exercise stimulation mode, including bicycle ergometer, treadmill, and total body workout equipment. Objective: The aim of this study was to explore the effects of different exercise stimulation modes on the occurrence of safety events during CPET in patients with CHD. Methods: A total of 10,538 CPETs, including 5,674 performed using treadmill exercise and 4,864 performed using bicycle ergometer exercise at Peking University Third Hospital, were analyzed retrospectively. The incidences of CV events and serious adverse events during CPET were compared between the two exercise groups. Results: Cardiovascular events in enrolled patients occurred during 355 CPETs (3.4%), including 2 cases of adverse events (0.019%), both in the treadmill group. The incidences of overall events [235 (4.1%) vs. 120 (2.5%), P < 0.001], premature ventricular contractions (PVCs) [121 (2.1%) vs. 63 (1.3%), P = 0.001], angina pectoris [45 (0.8%) vs. 5 (0.1%), P < 0.001], and ventricular tachycardia (VT) [32 (0.6%) vs. 14 (0.3%), P = 0.032] were significantly higher in the treadmill group compared with the bicycle ergometer group. No significant difference was observed in the incidence of bradyarrhythmia and atrial arrhythmia between the two groups. Logistic regression analysis showed that the occurrence of overall CV events (P < 0.001), PVCs (P = 0.007), angina pectoris (P < 0.001), and VT (P = 0.008) was independently associated with the stimulation method of treadmill exercise. In male subjects, the occurrence of overall CV events, PVCs, angina pectoris, and VT were independently associated with treadmill exercise, while only the overall CV events and angina pectoris were independently associated with treadmill exercise in female subjects. Conclusion: In comparison with treadmill exercise, bicycle ergometer exercise appears to be a safer exercise stimulation mode for CPET in patients with CHD.

Corrigendum: The Emerging Role of Rho Guanine Nucleotide Exchange Factors in Cardiovascular Disorders: Insights Into Atherosclerosis: A Mini Review.

[This corrects the article DOI: 10.3389/fcvm.2021.782098.].

Prediction of balance function for stroke based on EEG and fNIRS features during ankle dorsiflexion.

Balance rehabilitation is exceedingly crucial during stroke rehabilitation and is highly related to the stroke patients' secondary injuries (caused by falling). Stroke patients focus on walking ability rehabilitation during the early stage. Ankle dorsiflexion can activate the brain areas of stroke patients, similar to walking. The combination of electroencephalography (EEG) and functional near-infrared spectroscopy (fNIRS) was a new method, providing more beneficial information. We extracted the event-related desynchronization (ERD), oxygenated hemoglobin (HBO), and Phase Synchronization Index (PSI) features during ankle dorsiflexion from EEG and fNIRS. Moreover, we established a linear regression model to predict Berg Balance Scale (BBS) values and used an eightfold cross validation to test the model. The results showed that ERD, HBO, PSI, and age were critical biomarkers in predicting BBS. ERD and HBO during ankle dorsiflexion and age were promising biomarkers for stroke motor recovery.

Study on Environmental and Lifestyle Factors for the North-South Differential of Cardiovascular Disease in China.

Human death and life span are closely related to the geographical environment and regional lifestyle. These factors considerably vary among counties and regions, leading to the geographical disparity of disease. Quantitative studies on this phenomenon are insufficient. Cerebrovascular and heart diseases are the leading causes of death. The mortality rate of cerebrovascular and heart diseases is statistically higher in northern China than in southern China; the p-value of t-test for cerebrovascular and heart diseases was 0.047 and 0.000, respectively. The population attribution fraction of 12 major risk factors for cardiovascular disease (CVD) in each province was calculated based on their exposure and relative risk. The results found that residents in northern China consume high sodium-containing food, fewer vegetables, and less sea food products, and tend to be overweight. Fine particulate matter is higher in northern China than in southern China. Cold temperatures also cause a greater number of deaths than hot temperatures. All these factors have resulted in a higher CVD mortality rate in northern China. The attributive differential for sodium, vegetable, fruit, smoking, PM2.5, omega-3, obesity, low temperature, and high temperature of heart disease between the two parts of China is 9.1, 0.7, -2.5, 0.1, 1.4, 1.3, 2.0, 4.7, and -2.1%, respectively. Furthermore, the attributive differential for the above factors of cerebrovascular disease between the two parts of China is 8.7, 0.0, -5.2, 0.1, 1.0, 0.0, 2.4, 4.7, and -2.1%. Diet high in sodium is the leading cause of the north-south differential in CVD, resulting in 0.71 less years of life expectancy in northern compared with that in southern China.

The Emerging Role of Rho Guanine Nucleotide Exchange Factors in Cardiovascular Disorders: Insights Into Atherosclerosis: A Mini Review.

Atherosclerosis is a leading cause of cardiovascular disease, and atherosclerotic cardiovascular disease accounts for one-third of global deaths. However, the mechanism of atherosclerosis is not fully understood. It is well-known that the Rho GTPase family, especially Rho A, plays a vital role in the development and progression of arteriosclerosis. Rho guanine nucleotide exchange factors (Rho GEFs), which act upstream of Rho GTPases, are also involved in the atheromatous pathological process. Despite some research on the role of Rho GEFS in the regulation of atherosclerosis, the number of studies is small relative to studies on the essential function of Rho GEFs. Some studies have preliminarily revealed Rho GEF regulation of atherosclerosis by experiments in vivo and in vitro. Herein, we review the advances in research on the relationship and interaction between Rho GEFs and atheroma to provide a potential reference for further study of atherosclerosis.

Effect of Smartphone-Based Telemonitored Exercise Rehabilitation among Patients with Coronary Heart Disease.

The aim of this study was to investigate the effects of telemonitored exercise rehabilitation on patients with coronary heart disease (CHD) in China. Ninety-six patients with stable CHD were included and analyzed (48 in telemonitored group and 48 in control group). All patients received routine follow-up, and patients in telemonitored group participated in smartphone-based telemonitored cardiac rehabilitation. Patients' demographic information, medical history, diagnosis and treatment of CHD, and laboratory results were collected. The difference of cardiopulmonary exercise testing (CPET), blood test, and echocardiographic parameters; exercise habits; control rate of blood lipid and blood glucose; and incidence of adverse events between the two groups during 6 months of follow-up was analyzed. After intervention, the subjects in the telemonitored group performed significantly better in VO2peak, exercise compliance, and some other parameters than those in the control group. Telemonitored exercise rehabilitation is an effective rehabilitation mode for CHD patients in China.

EEG Assessment in a 2-Year-Old Child with Prolonged Disorders of Consciousness: 3 Years' Follow-up.

A 2-year-old girl, diagnosed with traumatic brain injury and epilepsy following car trauma, was followed up for 3 years (a total of 15 recordings taken at 0, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 14, 19, 26, and 35 months). There is still no clear guidance on the diagnosis, treatment, and prognosis of children with disorders of consciousness. At each appointment, recordings included the child's height, weight, pediatric Glasgow Coma Scale (pGCS), Coma Recovery Scale-Revised (CRS-R), Gesell Developmental Schedule, computed tomography or magnetic resonance imaging, electroencephalogram, frequency of seizures, oral antiepileptic drugs, stimulation with subject's own name (SON), and median nerve electrical stimulation (MNS). Growth and development were deemed appropriate for the age of the child. The pGCS and Gesell Developmental Schedule provided a comprehensive assessment of consciousness and mental development; the weighted Phase Lag Index (wPLI ) in the ß-band (13-25 Hz) can distinguish unresponsive wakefulness syndrome from minimally conscious state and confirm that the SON and MNS were effective. The continuous increase of delta-band power indicates a poor prognosis. Interictal epileptiform discharges (IEDs) have a cumulative effect and seizures seriously affect the prognosis.

Impact of population movement on the spread of 2019-nCoV in China.

Since Dec 2019, China has experienced an outbreak caused by a novel coronavirus, 2019-nCoV. A travel ban was implemented for Wuhan, Hubei on Jan 23 to slow down the outbreak. We found a significant positive correlation between population influx from Wuhan and confirmed cases in other cities across China (R2 = 0.85, P < 0.001), especially cities in Hubei (R2 = 0.88, P < 0.001). Removing the travel restriction would have increased 118% (91%-172%) of the overall cases for the coming week, and a travel ban taken three days or a week earlier would have reduced 47% (26%-58%) and 83% (78%-89%) of the early cases. We would expect a 61% (48%-92%) increase of overall cumulative cases without any restrictions on returning residents, and 11% (8%-16%) increase if the travel ban stays in place for Hubei. Cities from Yangtze River Delta, Pearl River Delta, and Capital Economic Circle regions are at higher risk.

[Prevalence of chronic prostatitis and its effects on male infertility].

OBJECTIVE: To investigate the prevalence of chronic prostatitis (CP) in male infertility patients and its effects on male infertility. METHODS: 534 male patients with complaints of male infertility were interviewed for the history of prostatic disease and underwent digital rectal examination of prostate, analysis of semen and express prostatic secretions (EPS). Bacterial culture of urine was done in 40 randomly selected inflammatory CP patients by pre- and post-message method (pre- and post-massage test, PPMT). RESULTS: 209 out of the 534 patients with male infertility were diagnosed as chronic prostatitis with a prevalence rate of 39.1%, among which 46 with CP type II and IIIA with the prevalence rate of 8.6%, 28 with CP type IIIB (5.2%), and 135 with CP type IV (25.3%) respectively. Positive bacterial culture was found in 10 out of the 40 cases of inflammatory chronic prostatitis (25.0%). The bacterial infection rate was 24.2% (8/33) in the cases of CP type IV. The prevalence rate of liquefaction dysfunction was much higher in the patients of male infertility with CP (22.7%) than in those without CP (14.3%, P < 0.05), however, it had little influence on the quality of semen, pH value, sperm density, and sperm motility. CONCLUSION: Quite common in patients with male infertility, CP prolongs the time of liquefaction, but has no other reverse influence on semen.