A multi-class gene classifier for SARS-CoV-2 variants based on convolutional neural network

Surveillance of circulating variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of great importance in controlling the coronavirus disease 2019 (COVID-19) pandemic. We propose an alignment-free in silico approach for classifying SARS-CoV-2 variants based on their genomic sequences. A deep learning model was constructed utilizing a stacked 1-D convolutional neural network and multilayer perceptron (MLP). The pre-processed genomic sequencing data of the four SARS-CoV-2 variants were first fed to three stacked convolution-pooling nets to extract local linkage patterns in the sequences. Then a 2-layer MLP was used to compute the correlations between the input and output. Finally, a logistic regression model transformed the output and returned the probability values. Learning curves and stratified 10-fold cross-validation showed that the proposed classifier enables robust variant classification. External validation of the classifier showed an accuracy of 0.9962, precision of 0.9963, recall of 0.9963 and F1 score of 0.9962, outperforming other machine learning methods, including logistic regression, K-nearest neighbor, support vector machine, and random forest. By comparing our model with an MLP model without the convolution-pooling network, we demonstrate the essential role of convolution in extracting viral variant features. Thus, our results indicate that the proposed convolution-based multi-class gene classifier is efficient for the variant classification of SARS-CoV-2.

Enhanced external counterpulsation treatment attenuate the injury of brain dog model of cardiac arrest / 中华急诊医学杂志

Objective To investigate the therapeutic effects of enhanced external counterpulsation (EECP) on cerebral edema and cerebral blood flow perfusion with MRI following cardiac arrest (CA) and on successful return of spontaneous circulation (ROSC) by cardiopulmonary resuscitation (CPR) in dogs.Methods Sixteen beagle dogs were induced CA with alternating current on epicardium,then were randomly (random number) divided into the EECP and control group after successful ROSC.MR scanning brain of all animals was carried out by diffusion-weighted imaging (DWI) and perfusion weighted imaging (PWI) before CA and on the first,second and third days after ROSC.Blood pressure,right common carotid artery flow,and intracranial microcirculation perfusion were measured.Results There were no significant differences in mean artery pressure at all intervals between two groups (P ＞ 0.05).There was significant increase in right common carotid artery blood flow and intracranial microcirculation of dogs in EECP group compared with the control group (P ＜ 0.05).Apparent diffusion coefficients (ADC) of water molecule on the first and third days after ROSC were significantly higher in the EECP group than those in the control group (P ＜ 0.05).Ratios of post-ROSC relative cerebral blood flow (RCBF) /original cerebral blood flow were higher in the EECP group than those in the control group on the first,second and third days after ROSC (P ＜ 0.05).Conclusions EECP treatment could improve cerebral blood flow perfusion and relieve ischemic cerebral edema,alleviating brain injury in dogs following CA and successful ROSC.

The impact of mild hypothermia on coagulation and cerebral microcirculation after cardiopulmonary resuscitation in rabbits / 中华急诊医学杂志

Objective To study the effects of mild hypothermia (MH) on blood coagulation and cerebral microcirculation in rabbits after cardiopulmonary resuscitation (CPR). Method A total of 24 New Zealand rabbits were randomly (random number) divided equally into normothermic group (NT) and MH group. CPR model was established by ventricular fibrillation induced by using alternating current. The rabbits of NT group were observed for 12 h in room temperature after restoration of spontaneous circulation (ROSC). The mild hypothermia was induced in the rabbits of group MH by surface cooling after ROSC, and maintained for 12 h after the aimed low temperature reached. The PT (prothrombin time), APTT (activated partial thromboplastin time), INR (international normalized ratio of prothrombin), D-dimmer (DD) , blood platelet count (BPC) , anti-thrombin Ⅲ activity (AT-Ⅲ) and protein C activity (PC) were measured before CPR and 4 h, 8 h and 12 h after ROSC, and at the same time the cerebral microcirculation was measured by using PERIMED Multichannel Laser Doppler system. One-way ANOVA or Mann-Whitney rank was used to determine the statistical significance between two groups. LSD-t test was used for multiple comparisons,t test for comparisons of means between two independent samples, and Pearson correlation test for correlation analysis. Results The PT, APTT and INR showed a trend of gradually shortening during the course. The APTT in 12 h after ROSC was significantly shorter than that before CPR (23.32 ±5.19 vs. 29.53 ±5.10,P = 0.025), and the activity of AT- Ⅲ and PC were decreased significantly. Compared with the group NT,the PT, APTT and INR in group MH were increased significantly, while there were no differences in the activity of AT- Ⅲ, PC and D-D between two groups. The rates of cerebral microcirculation in group NT before CPR and 4 h, 8 h and 12 h after ROSC were 401.60 ± 11.76 mL/min, 258.86 ± 34. 58 mL/min,317.59 ± 23.36 mL/min and 371.98 ± 5.79 mL/min, respectively, and those in group MT were 398.18 ±12.91 mL/min, 336.19 ± 19.27 mL/min, 347.76 ± 13.80 mL/min and 383.78 ± 3.29 mL/min, respectively. There were significant differences between two groups at each interval after ROSC (4 h: t = - 6.025,df=16, P=0.000;8 h: t= -2.942, df=12, P=0.012;12 h: t= -3.959, df=8, P=0.004). The Pearson correlation test showed that the rate of cerebral microcirculation was positive correlated with APTT after ROSC (4 h:R =0.503,P=0.033;8 h:R=0. 565,P=0. 035;12 h:R=0. 774,P=0. 009), and was not correlated with the other blood coagulants. Conclusions The mild hypothermia led to the inhibition of blood coagulation and improved the cerebral microcirculation concomitantly, which may be one of the mechanism of cerebral protection.

Preliminary study of hypothermia induced by intraperitoneal cooling in rabbits after cardiopulmonary resuscitation / 中华急诊医学杂志

Objective To explore the safety and rate of intraperitoneal cooling in rabbits after cardiopulmonary resuscitation(CPR). Method There were two experiments. In the experiment one: 15 healthy adult NewZealand rabbits were divided into five groups as per the various amounts, 30, 40, 60, 80, and 100 mL/kg, of priming volume of 4 ℃ cold balanced salts solution injected into peritoneal cavity of rabbits. After injection of priming cold solution, the tympanic temperature between 33 ℃～ 35 ℃. For the maintenance of this mild hypothermia, a intraperitoneal infusion device(patent number ZL200820201265) was connected to the rabbits. The rabbits were rewarmed by using the same device after 12-hour hypothermia. The biochemical parameters were assayed during the experiment. After the rabbits were sacrificed, the liver, ileocecal junction of intestine and kidneys were removed to fix them in 3 % formalin, and examined by using H.E. staining. In the experiment two, another 12 healthy adult New Zealand rabbits were induced into ventricular fibrillation by alternating electric current and then gave CPR for 2 minutes. After return of spontaneous circulation(ROSC), the priming volume of 4 ℃ cold liquid was infused into peritoneal cavity of rabbits, and then the rabbits were connected to the intraperitoneal cooling device to maintain hypothermia for 12 hours. Matched-pairs t test was used for the comparison of biomarkers before and after intraperitoneal cooling. A two-tailed value of P < 0.05 was considered statistically significant. Results In the experiment one, the tympanic temperature of rabbits with priming volume of 80 mL/kg cold solution was decreased quickly reaching the target temperature in(30±2.00) minutes. During the induction of hypothermia, the intraperitoneal temperature reached the target temperature in less than 10 minutes, and was 1 -2℃ lower than the tympanic temperature during the maintenance of hypothermia. The intraperitoneal cooling did not cause damage in the liver, ileocecal junction of intestine and kidney, and did not alter the biomarkers. In the experiment two, the tympanic temperature of rabbits after ROSC was decreased quickly after intraperitoneal infusion of 80 mL/kg 4 ℃ cold solution, and reached the target temperature in(26.00±6.99) minutes, and the intraperitoneal temperature was lowered to reach the target temperature in less than 10 minutes. This cooling method after CPR didn' t disturbance water-electrolyte and acid-base balance. Conclusions The intraperitoneal cooling can safely and quickly induce hypothermia after CPR in rabbits.

Effect of fluid therapy on skin microcirculatory perfusion during induction of general anesthesia in patients undergoing major abdominal surgery / 中华麻醉学杂志

Objective To investigate the changes in skin microcirculatory perfusion during induction of general anesthesia and the effects oftwo fluid therapy regimens in patients undergoing abdominal surgery.Methods Thirty-six ASA Ⅰ or Ⅱ patients aged 18-64 yr scheduled for elective major abdominal surgery were randomized to receive either 6% hydroxyetlayl starch(130/0.4)7 ml/kg(HES group,n=18)or lactated Ringer's solution 7 ml/kg(RL group,n=18)for compensatory intravascular volultne expansion(CVE)before tracheal intubation.Meanwhile both groups received continuous intravenous infusion of RL at a of 8 ml·kg~(-1)·h~(-1).Tracheal intubation was performed at 40 min after the onset of infusion.Anesthesia was maintained with with sevoflurane,remifentanil and rocuronium.Operation was started at 20 min after tracheal intubation.The microcirculatory perfusion was measured on forehead skin by using Doppler perfusion imaging system(LDPI)PI)at the onset of fluid infusion(T_0,baseline),the end of endotracheal intubation(T_1)and the onset of skin incision(T_2).Rwsults The MAP,HR,blood gases and body temperature were within the normal during the experiment and there was no significant difference between the 2 groups.The skin microcirculatory perfusion and CVP at T_1 were significantly higher in group HES than in group RL(P<0.05 or 0.01).Compared with the baseline value at T_0,the skin microcirculatory perfusion at T_1 was significantly increased in group HES(P<0.01),but there was no significant change in the skin microcirculatory perfusion at T_1 in group RL(P>0.05),the skin microcirculatory perfusion at T_2 was singificantly decreased in both groups(P<0.01),and CVP and PaO_2/FiO_2 at T_(1.2) were significantly increased,while Hb at T_(1.2) was significantly decreased in both groups(P<0.05).The skin microcirculatory perfusion in both groups was significantly lower at T_2 than at T_1(P<0.01).Conclusion The infusion of 6% HES 130/0.4 can improve the skin microcirculatory perfusion and the effect is better than that of RL during induction of general anesthesia in patients seheduled for abdominal surgery.

Physical Activity and Vascular Dilation Function in Healthy Middle-aged Individuals / 中国康复医学杂志

Objective: Vascular dilation dysfunction has been linked with risk of cardiovascular disease. This study was undertaken to investigate the relationship between physical activity and vascular dilation function in healthy middle-aged adults to help explaining the effect of physical activity on preventing cardiovascular disease. Method: We recruited 91 healthy middle-aged adults to complete a serf-report 7-day physical activity recall questionnaire and an exam of brachial artery flow-mediated dilation(FMD) and Nitroglycerin-mediated dilation (NMD) detected by ultrasound. The relationship between physical activity level (PAL) and FMD and NMD were explored. Result: Physical activity showed a significant and positive relationship with the brachial artery FMD, even after adjustment for possible confounding factors (r=0.363, P<0.01). The group of high physical activity level had the highest FMD. The means of FMD (%) in low, moderate and high PAL groups were respectively 8.70%±3.93%,9.01%±3.22% and 12.38±5.67% with significant difference between individuals of low and high PAL and between moderate and high PAL group(P<0.01). The means of NMD (%) is 25.13%±6.52%,24.38%±5.44% and 29.50%±7.25% respectively (P> 0.05) and there was no significant difference among three groups. There was no positive relation between PAL and FMD in premenopausal females but in men and postmenopausal females. Although individuals of high PAL have the best FMD, the moderate PAL can also retard FMD decrease with ageing. Conclusion: Maintaining high physical activity level can enhance endothelial-dependent vascular dilation, and moderate or high physical activity level can prevent endothelial-dependent vaseular dilation declining with aging, which may contribute to decrease risk of cardiovascular disease in healthy middle-aged adults.

Ventricular fibrillation-induced cardiac arrest model in rabbits / 中华急诊医学杂志

Objective To establish a simple,easily-producible and practical cardiopulmonary cerebral resuscitation model in rabbits.Method Cardiac ventricular fibrillation was induced in 27 New Zealand rabbits by alternating electric current.The rabbits were randomly divided into three groups according to the duration of untreated cardiac arrest(CA):CA-8 min group(n = 9),CA-5 min group(n = 9)and CA-3 min group(n = 9).All animals received cardiopulmonary resuscitation(CPR)until return of spontaneous circulation(ROSC).The sample of vein blood was collected for the measurement troponin I level at 4 hours after ROSC.The animals were sacrificed at 72 hours after ROSC,hippocampus were removed and fixed in 3%formalin,and coronal sections were analyzed by TUNEL staining and N1SSLE staining.The other two animals without ventricular fibrillation or CPR served as sham-operated group.One-way ANOVA or Mann-Whitney rank was used to determine the statistical significance among the three groups.R×C test was used for ROSC,LSD test for multiple comparisons,and t test for comparisons of means between two independent samples.A two-tailed value of P＜0.05 was considered statistically significant.Results There were no differences in rate of ROSC among groups.No animals survived until 72 hours after ROSC in CA-8 min group and CA-5 min group,while three animals in CA-3 min group survived.In group CA-8 min,CA-5 min and CA-3 min,the survival time of animals after ROSC were(1.67 ± 2.55)h,(37.78 ± 30.27)h,(12.0 ± 14.97)h,respectively.There were significant differences in the survival time of animals after ROSC and troponin I level after ROSC 4 h between CA-3 min group and the other two groups(P＜0.05).Compared with animals in CA-3 min group,sham-operated animals(n = 2)did not have neuronal degeneration or TUNEL positive cells in the hippocampus CA1 area.Conclusions CPR initiated as soon as 3 min after CA can give longer survival tome to the rabbits.The rabbits have neuronal degeneration and apoptosis in the hippocampus CA1 area at 72 hours after ROSC.It may be an ideal animal model for investigation on CPCR.

The efficacy and safety of tirofiban in the treatment of elderly patients with acute coronary syndrome during primary percutaneous coronary intervention / 中华老年医学杂志

Objective To investigate the efficacy and safety of tirofiban in the treatment of aged patients with acute coronary syndrome (ACS) during primary percutaneous coronary intervention (PCI). Methods Two hundred and fifty-six patients with ACS who underwent primary PCI were randomly divided into two groups: tirofiban group (tirofiban + PCI treatment, n= 130) and control group (routine PCI treatment, n = 126). Tirofiban group was further divided into two subgroups according to the age: aged group(age ≥60 years, n= 68) and non-elderly group(age<60 years, n=62). At the end of PCI procedure, angiographic features such as thrombolysis in myocardial infarction (TIMI) flow grade, corrected TIMI frames count and TIMI myocardial perfusion grades (TMPG) were analyzed immediately. The incidence of major adverse cardiac events (MACE) was observed within 36 hours and 30 days after PCI, and the incidence rates of thrombocytopenia and bleeding were assessed. Results There was no significant difference between both the two study groups and the two subgroups in the basic clinical or angiographic characteristics before PCI (all P>0.05). There was no significant difference between two groups in TIMI 3 flow achievement rate in culprit vessels after PCI (93.6% vs. 91.3%, χ~2 = 1.02, P= 0.313). In tirofiban group, corrected TIMI frames count was significantly higher than that in control group (31.6±7.7 vs. 23.8±6.1, t = 2.49, P 0.026), and TMPG 3 achievement rate was also higher (83.1% vs. 67.5% ,χ~2=4.05, P=0.046). The incidence of MACE was significantly lower in tirofiban group than that in control group both within 36 hours and 30 days after procedure(6.9% vs. 19.0%, χ~2= 6.30, P= 0.013; 3.8% vs. 11.90%, χ~2= 5.82,P=0.018, respectively). No statistical difference was found in mild bleeding complications between the two groups (20.2% vs. 15.2%, χ~2 =3.65, P=0.065), but the incidence of mild bleeding was higher in aged group than that in the non-elderly group(25.0% vs. 14.5%,χ~2=4.98, P=0.026), and the incidences of serious bleeding and thrombocytopenia were similar between the two subgroups. Conclusions Intravenous tirofiban infusion is safe in aged ACS patients during primary PCI, and has favorable short-term outcomes compared with routine treatment, although there is a slight risk of mild bleeding.

Effects of long-term enhanced external counterpulsation on endothelium-dependent and endothelium-independent vasorelaxation of the carotid arteries in atherosclerotic pigs / 中华急诊医学杂志

Objective To explore the effect of long-term enhanced external counterpulsation(EECP)on endothelium-dependent and endothelium-independent vasorelaxation in the carotid arteries of atherosclerotic piss. Method Totally 18 20-day-old male infant pigs were randomly divided into 3 groups according to feeding given: the normal[control group(n=6),the hypercholesterolemic control group(n=6)and the hypereholesterolemic +EECP group(n=6).Porcine model of hypercholesterolemia was made by feeding high-cholesterol diet.After EECP for 36 hours in the hypercholesterolemic+EECP group(n=6),carotid arterial rings were harvested from all animals and their vaso-relaxation response to different dose of Acetylchofine(Ach)and Sodium nitroprusside (SNP)were detected,respectively.Results As the dose of Ach varying between 10-8 mol/L and 10-5mol/L, endothelium-dependent vasorelaxation ratio of hypereholesterolemic piss with or without EECP treatment was significantly lower than that of the normal control group(P＜0.05),however,endothehum-dependent vasorelax- ation ratio in pigs with EECP treatment was obviously higher compared with hypereholesterolemic pigs without EECP treatment(P＜0.05)as the Ach ranged from 10-7 mol/L to 10-5mol/L.Similarly,as the concentration of SNP ranged fiun 10-8 mol/L to 10-5 mol/L.endothelium-independent vasorelaxafion ratio of both the hypercholesterolemic control group and the hypercholesterolemic+EECP group were significantly lower than that of the normal control group(P＜0.05),and end othelium-independent vasorelaxation ratio of the hypercholesterolemic+EECP group was significantly higher than that of the hypercholesterolemic control group (P＜0.05).Condusions Long-term EECP improves the impaired endothelium-dependent and endothelium independent vasorelaxalion function resulting from atherosclerosis.

Effects of external counterpulsation on the pulsatility of blood pressure in human subjects / 生物医学工程学杂志

Pulsatile blood flow plays an important role in maintaining normal vascular endothelial function. Quantitative measurement of pulsatility of human arterial blood pressure and the influence of enhanced external counterpulsation (EECP) on the pulsatility were investigated in this study. Eight healthy young male volunteers aged 22 to 35 were included. A 4F tip transducer catheter was inserted under local anaesthesia into the radial artery up to the aortic arch. Intraarterial blood pressure was recorded before and during EECP. Blood pulse pressure, pulsatility index (ratio of peak pressure to end diastolic pressure) and standard deviation of blood pressure in 5 cardiac cycle was calculated to evaluate the pulsatility of arterial blood pressure. The results showed that blood pulse pressure, pulsatility index and standard deviation of blood pressure were elevated from 47 +/- 5 mmHg, 1.64 +/- 0.11 and 13.6 +/- 1.5 mmHg to 77 +/- 3 mmHg, 2.46 +/- 0.25 and 19.3 +/- 2.2 mmHg before and during EECP respectively (P < 0.05). Decreasing of systolic pressure and increasing of diastolic pressure during counterpulsation were also observed. EECP gives an elevation of pulsatility to human blood pressure.

Effects of external counterpulsation on the pulsatility of blood pressure and blood flow in dogs / 生物医学工程学杂志

Pulsatile blood flow plays an important role in maintaining normal vascular endothelial function. Quantitative measurement of pulsatility of artery blood pressure and blood flow in dogs and effects of enhanced external counterpulsation (EECP) on the pulsatility were taken in this study. Common carotid artery blood pressure and blood flow were measured in 6 beagle dogs that had suffered from an acute myocardial infarction 6 weeks before. A 6F tip transducer catheter was inserted into the right common carotid artery to measure blood pressure, and blood flow was measured in the left common carotid artery by an electromagnetic blood flow probe under anesthesia before and during EECP. Blood pulse pressure, pulsatility index (ratio of peak pressure to end diastolic pressure) and standard deviation of blood pressure were calculated to evaluate the pulsatility of arterial blood pressure. Blood pulse flow, pulsatility index (ratio of peak flow to trough flow) and standard deviation of blood flow were calculated to evaluate the pulsatility of blood flow. Mean vascular resistance (MVR) was calculated as MVR = mean blood pressure/mean blood flow. Blood pulse pressure, pulsatility index and standard deviation of blood pressure were elevated from 30 +/- 9 mmHg, 1.26 +/- 0.05 and 8.7 +/- 2.5 mmHg to 43 +/- 8 mmHg (P < 0.05), 1.54 +/- 0.13 and 12.4 +/- 2.0 mmHg (P < 0.05) before and during EECP, respectively. Blood pulse flow, pulsatility index and standard deviation of blood flow were elevated from 317 +/- 48 ml/min, 2.85 +/- 0.21 and 96 +/- 21 ml/min to 447 +/- 88 ml/min, 4.56 +/- 0.90 and 131 +/- 39 ml/min before and during EECP (P < 0.05). MVR was decreased from 578 +/- 72 before EECP to 476 +/- 85 Wood units during EECP(P < 0.05). These data demonstrate that EECP gives an elevation of pulsatility to blood pressure and blood flow, thus it may lead to the decrease of vascular resistance.