DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes.

MOTIVATION: Model quality assessment is a crucial part of protein structure prediction and a gateway to proper usage of models in biomedical applications. Many methods have been proposed for assessing the quality of structural models of protein monomers, but few methods for evaluating protein complex models. As protein complex structure prediction becomes a new challenge, there is an urgent need for model quality assessment methods that can accurately assess the accuracy of interface residues of complex structures. RESULTS: Here, we present DeepUMQA3, a web server for evaluating the accuracy of interface residues of protein complex structures using deep neural networks. For an input complex structure, features are extracted from three levels of overall complex, intra-monomer, and inter-monomer, and an improved deep residual neural network is used to predict per-residue lDDT and interface residue accuracy. DeepUMQA3 ranks first in the blind test of interface residue accuracy estimation in CASP15, with Pearson, Spearman, and AUC of 0.564, 0.535, and 0.755 under the lDDT measurement, which are 17.6%, 23.6%, and 10.9% higher than the second best method, respectively. DeepUMQA3 can also assess the accuracy of all residues in the entire complex and distinguish high- and low-precision residues. AVAILABILITY AND IMPLEMENTATION: The web sever of DeepUMQA3 are freely available at http://zhanglab-bioinf.com/DeepUMQA_server/.

Complete Transthoracic Echocardiography for the Assessment and Guidance of Percutaneous Atrial Septal Defect Closure in Adults without Balloon Sizing: An Observed Study with a 10-Year Follow-Up.

OBJECTIVES: This study aims to determine if complete transthoracic echocardiography (TTE)-guided percutaneous atrial septal defect (ASD) closure without balloon sizing could be safe and efficacious in adult patients. METHODS: A total of 551 patients with ASDs were enrolled in this study, of which 438 patients underwent percutaneous ASD closure. Patients who received TTE-guided percutaneous ASD closure were classified into group T, and those who underwent a procedure that was guided by transesophageal echocardiography (TEE) were classified into group E. The clinical characteristics and the outcomes of the patients were analyzed. RESULTS: The characteristics were comparable at baseline, except for the body mass index (BMI) (21.6 ± 5.3 vs. 23.8 ± 7.1, p < 0.001) between group T and group E. No significant difference was observed between the two groups regarding in-hospital outcomes, except for the duration of the procedure (29.8 ± 15.3 min vs. 41.5 ± 20.4 min), the length of stay in the hospital (2.1 ± 2.3 d vs. 2.9 ± 2.6 d), and hospital costs (USD 6233.3 ± 312.4 vs. USD 6673.7 ± 446.9). There were no significant differences in the incidences of long-term complications, cardiac chamber sizes, and tricuspid regurgitation severity between the patients in the two groups during the 10-year follow-up period. CONCLUSION: TTE may be as safe and efficacious as TEE for the assessment and guidance of percutaneous ASD closure without balloon sizing in adult patients with lower BMIs who are commonly found in East Asia.

Local and spatial spillover effects of corporate financing costs on regional carbon emissions: evidence from Chinese listed firms.

The signing of the Paris Agreement has raised concerns about global carbon emissions, which have detrimental consequences in terms of climate change. At the same time, the financing process for listed companies has begun to incorporate investigations into these firms' carbon emissions. But the current impact of financing costs on firms' carbon emissions has not been accurately assessed. There are large differences in endowments in different regions of China, and factors flow frequently among regions. To date, no empirical evidence has emerged to show the spatial effects of financing costs on carbon emissions. This study uses the STIRPAT model and a panel lag regression model for empirical testing. The results show that increasing financing costs will increase the burden imposed by carbon reduction efforts in various regions. Although this trend has obvious spillovers to surrounding areas, the location of the enterprise bears a more negative burden of externalities. Further analysis shows that reducing the financing costs of enterprises in economically developed regions can reduce both their carbon emissions and the damage to economic growth. These research conclusions can help policymakers shape carbon reduction activities through reducing corporate financing costs on the basis of regional development differences.

Long-term safety and absorption assessment of a novel bioresorbable nitrided iron scaffold in porcine coronary artery.

This study aimed to investigate the long-term biocompatibility, safety, and degradation of the ultrathin nitrided iron bioresorbable scaffold (BRS) in vivo, encompassing the whole process of bioresorption in porcine coronary arteries. Fifty-two nitrided iron scaffolds (strut thickness of 70 µm) and 28 Vision Co-Cr stents were randomly implanted into coronary arteries of healthy mini-swine. The efficacy and safety of the nitrided iron scaffold were comparable with those of the Vision stentwithin 52 weeks after implantation. In addition, the long-term biocompatibility, safety, and bioresorption of the nitrided iron scaffold were evaluated by coronary angiography, optical coherence tomography, micro-computed tomography, scanning electron microscopy, energy dispersive spectrometry and histopathological evaluations at 4, 12, 26, 52 weeks and even at 7 years after implantation. In particular, a large number of struts were almost completely absorbed in situ at 7 years follow-up, which were first illustrated in this study. The lymphatic drainage pathway might serve as the potential clearance way of iron and its corrosion products.

DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning.

MOTIVATION: Protein model quality assessment is a key component of protein structure prediction. In recent research, the voxelization feature was used to characterize the local structural information of residues, but it may be insufficient for describing residue-level topological information. Design features that can further reflect residue-level topology when combined with deep learning methods are therefore crucial to improve the performance of model quality assessment. RESULTS: We developed a deep-learning method, DeepUMQA, based on Ultrafast Shape Recognition (USR) for the residue-level single-model quality assessment. In the framework of the deep residual neural network, the residue-level USR feature was introduced to describe the topological relationship between the residue and overall structure by calculating the first moment of a set of residue distance sets and then combined with 1D, 2D and voxelization features to assess the quality of the model. Experimental results on the CASP13, CASP14 test datasets and CAMEO blind test show that USR could supplement the voxelization features to comprehensively characterize residue structure information and significantly improve model assessment accuracy. The performance of DeepUMQA ranks among the top during the state-of-the-art single-model quality assessment methods, including ProQ2, ProQ3, ProQ3D, Ornate, VoroMQA, ProteinGCN, ResNetQA, QDeep, GraphQA, ModFOLD6, ModFOLD7, ModFOLD8, QMEAN3, QMEANDisCo3 and DeepAccNet. AVAILABILITY AND IMPLEMENTATION: The DeepUMQA server is freely available at http://zhanglab-bioinf.com/DeepUMQA/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Chinese Consensus Report on Family-Based Helicobacter pylori Infection Control and Management (2021 Edition).

OBJECTIVE: Helicobacter pylori infection is mostly a family-based infectious disease. To facilitate its prevention and management, a national consensus meeting was held to review current evidence and propose strategies for population-wide and family-based H. pylori infection control and management to reduce the related disease burden. METHODS: Fifty-seven experts from 41 major universities and institutions in 20 provinces/regions of mainland China were invited to review evidence and modify statements using Delphi process and grading of recommendations assessment, development and evaluation system. The consensus level was defined as ≥80% for agreement on the proposed statements. RESULTS: Experts discussed and modified the original 23 statements on family-based H. pylori infection transmission, control and management, and reached consensus on 16 statements. The final report consists of three parts: (1) H. pylori infection and transmission among family members, (2) prevention and management of H. pylori infection in children and elderly people within households, and (3) strategies for prevention and management of H. pylori infection for family members. In addition to the 'test-and-treat' and 'screen-and-treat' strategies, this consensus also introduced a novel third 'family-based H. pylori infection control and management' strategy to prevent its intrafamilial transmission and development of related diseases. CONCLUSION: H. pylori is transmissible from person to person, and among family members. A family-based H. pylori prevention and eradication strategy would be a suitable approach to prevent its intra-familial transmission and related diseases. The notion and practice would be beneficial not only for Chinese residents but also valuable as a reference for other highly infected areas.

Assessment of hepatic fat content in using quantitative ultrasound measurement of hepatic/renal ratio and hepatic echo-intensity attenuation rate.

AIMS: This study aims to evaluate and validate a simple quantitative ultrasound (US) method for determining the hepatic fat content (HFC) based on the combination of quantitative US hepatic/renal ratio (US-HRR) and quantitative US hepatic echo-intensity attenuation rate (US-HAR) as compared with [1H]-magnetic resonance spectroscopy (1H-MRS). MATERIAL AND METHODS: There were a total of 242 subjects recruited in the present study. All subjects were examined for HFC by quantitative US and 1H-MRS methods. The QUS-HRR and QUS-HAR were calculated from ordinary ultrasound images of liver and kidney with a triple modality 3D abdominal phantom using the Image J software. RESULTS: The results found that US-HRR and US-HAR correlated with 1H-MRS HFC (US-HRR: r=0.946, p<0.001; US-HAR: r=0.936, p<0.001). The equation for HFC prediction by using quantitative US was: HFC (%) = 28.965 × US-HRR + 218.045 × US-HAR - 8.892. Subgroup analysis in study subjects with body mass index (BMI) ≥28 showed that quantitative US HFC was associated with 1H-MRS HFC (R2=0.953, p<0.001). Receiver operating characteristic (ROC) analysis observed that the cut-off value of fatty liver diagnosis was 6.71% in using the quantitative US model; the sensitivity and specificity for fatty liver diagnosis were 94.15% and 96.30%, respectively. Variability analysis indicated that there was a relative high degree of consistency in the measurement of HFC with different operators or ultrasonic apparatus. CONCLUSIONS: Quantitative US measurement could be regarded as a simple, sensitive tool to accurately assess HFC. It provides a valid alternative to 1H-MRS as an easy, non-invasive option for the precise estimation of HFC in clinical practice.

Surgical repair via submammary thoracotomy, right axillary thoracotomy and median sternotomy for ventricular septal defects.

BACKGROUND: Right submammary thoracotomy and right vertical infra-axillary thoracotomy are performed for ventricular septal defect (VSD) to reduce the invasiveness of the conventional surgical repair through median sternotomy approach. No comparative studies have been conducted among these three procedures. METHODS: From January 2016 to December 2016, 182 patients with isolated VSD who underwent surgical repair via one of these 3 approaches were reviewed to compare these three procedures. RESULTS: The procedure success rates were similar in these three groups. There was no statistically significant difference in operative time, aortic cross-clamping time, the duration of CPB, blood transfusion amount and medical cost. However, postoperative mechanical ventilation time, the duration of intensive care and postoperative length of hospital stay were longer in median sternotomy group than the other two groups. (P < 0.05) The median sternotomy group required the longest incision. No significant difference was noted in major adverse events. There were different advantages and disadvantages in the three kinds of operative procedures. CONCLUSIONS: Regarding conventional surgical repair VSD, right submammary thoracotomy and right vertical infra-axillary thoracotomy both delivered better cosmetic results for patients with isolated VSD, while all the three procedures could obtain satisfactory clinical effect.

Determination of Arsenic Species in Ophiocordyceps sinensis from Major Habitats in China by HPLC-ICP-MS and the Edible Hazard Assessment.

This study sought to determine the concentration and distribution of arsenic (As) species in Ophiocordyceps sinensis (O. sinensis), and to assess its edible hazard for long term consumption. The total arsenic concentrations, measured through inductively coupled plasma mass spectrometry (ICP-MS), ranged from 4.00 mg/kg to 5.25 mg/kg. As determined by HPLC-ICP-MS, the most concerning arsenic species­AsB, MMAV, DMAV, AsV, and AsШ­were either not detected (MMAV and DMAV) or were detected as minor As species (AsB: 1.4⁻2.9%; AsV: 1.3⁻3.2%, and AsШ: 4.1⁻6.0%). The major components were a cluster of unknown organic As (uAs) compounds with AsШ, which accounted for 91.7⁻94.0% of the As content. Based on the H2O2 test and the chromatography behavior, it can be inferred that, the uAs might not be toxic organic As. Estimated daily intake (EDI), hazard quotient (HQ), and cancer risk (CR) caused by the total As content; the sum of inorganic As (iAs) and uAs, namely i+uAs; and iAs exposure from long term O. sinensis consumption were calculated and evaluated through equations from the US Environmental Protection Agency and the uncertainties were analyzed by Monte-Carlo Simulation (MCS). EDItotal As and EDIi+uAs are approximately ten times more than EDIiAs; HQtotalAs and HQi+uAs > 1 while HQiAs < 1; and CRtotal As and CRi+uAs > 1 × 10−4 while CRiAs < 1 × 10−4. Thus, if the uAs is non-toxic, there is no particular risk to local consumers and the carcinogenic risk is acceptable for consumption of O. sinensis because the concentration of toxic iAs is very low.

[High-frequency echocardiography for assessment of regional wall motion abnormality and cardiac function in mice with myocardial infarction].

OBJECTIVE: To evaluate the value of high-frequency echocardiography in assessing cardiac structure and function in a mouse model of myocardial infarction. METHODS: Twenty-five C57BL/6 mice were randomly divided into sham-operated group (n=10) and myocardial infarction model group (n=15) established by ligation of the left anterior descending artery. The cardiac structure, regional wall motion and cardiac function of mice were examined with pulsed wave Doppler (PWD), tissue Doppler imaging (TDI), EKV and M-mode echocardiography 3 days before and at 1 week after the operation. The histological changes and myocardial structure of the heart were observed at 1 week after the operation. RESULTS: High-frequency echocardiography and HE staining detected obvious myocardial infarction in the mice in the model group. Compared with the sham-operated mice, the mice with myocardial infarction showed significant left ventricular expansion, obvious thinning of the ventricular wall, and significantly decreased ventricular systolic function and diastolic function with regional wall motion abnormality and ventricular remodeling. CONCLUSION: s 2D-type echocardiography combined with M-mode, PWD, TDI and EKVTM for allows accurate and sensitive detection of the loci and severity of myocardial infarction to provide important evidence for clinical diagnosis and treatment of myocardial infarction.

A Novel Method Using Abstract Convex Underestimation in Ab-Initio Protein Structure Prediction for Guiding Search in Conformational Feature Space.

To address the searching problem of protein conformational space in ab-initio protein structure prediction, a novel method using abstract convex underestimation (ACUE) based on the framework of evolutionary algorithm was proposed. Computing such conformations, essential to associate structural and functional information with gene sequences, is challenging due to the high-dimensionality and rugged energy surface of the protein conformational space. As a consequence, the dimension of protein conformational space should be reduced to a proper level. In this paper, the high-dimensionality original conformational space was converted into feature space whose dimension is considerably reduced by feature extraction technique. And, the underestimate space could be constructed according to abstract convex theory. Thus, the entropy effect caused by searching in the high-dimensionality conformational space could be avoided through such conversion. The tight lower bound estimate information was obtained to guide the searching direction, and the invalid searching area in which the global optimal solution is not located could be eliminated in advance. Moreover, instead of expensively calculating the energy of conformations in the original conformational space, the estimate value is employed to judge if the conformation is worth exploring to reduce the evaluation time, thereby making computational cost lower and the searching process more efficient. Additionally, fragment assembly and the Monte Carlo method are combined to generate a series of metastable conformations by sampling in the conformational space. The proposed method provides a novel technique to solve the searching problem of protein conformational space. Twenty small-to-medium structurally diverse proteins were tested, and the proposed ACUE method was compared with It Fix, HEA, Rosetta and the developed method LEDE without underestimate information. Test results show that the ACUE method can more rapidly and more efficiently obtain the near-native protein structure.

Detection of Anaplasma platys in dogs using real-time loop-mediated isothermal amplification.

Anaplasma platys is a parasite of canine platelets that causes infectious cyclic thrombocytopenia. In this study, a novel real-time loop-mediated isothermal amplification (RT-LAMP) method was developed to detect A. platys. RT-LAMP primer sets were designed using a citrate synthase gene sequence and the assay was performed at 63 °C for 30 min. No cross-reactivity was observed with other Anaplasma or Ehrlichia spp. and the method exhibited a similar level of sensitivity in detecting the organism in 58 canine blood samples to that of a nested PCR. This RT-LAMP is a rapid and potentially cost-effective method of diagnosing A. platys infection in dogs.

Closure of perimembranous ventricular septal defects with intraoperative device technique: another safe alternative to surgical repair.

OBJECTIVES: This study aims at assessing the safety and feasibility of intraoperative device closure of the perimembranous ventricular septal defect (VSD). METHODS: Total 89 patients in group I with intraoperative device closure and 58 in group II with surgical repair were enrolled in our hospital to participate in the study from January 2009 to December 2010. In group I, the approach involved a minimal inferior median incision that was performed after full evaluation of the perimembranous VSD by real-time transesophageal echocardiographic guidance, and the insertion of an asymmetric or a symmetric domestically made device was used to occlude the perimembranous VSD. RESULTS: In group I, 83 patients were occluded successfully under this approach. The size of the occluder implanted ranged from 6 to 14 mm. Complete atrioventricular block occurred in one case and Mobitz type II atrioventricular block occurred in one case during the procedure. One patient presented complete atrioventricular block one week after the operation. Two patients converted to surgical repair because of severe intraoperative aortic valve regurgitation. One patient with significant residual shunt transformed to surgical treatment. In our comparative studies, patients in group II experienced significantly longer operative time, ICU stay, and hospital stay (p < 0.001). The cost of group I was less than that of group II (p < 0.001). CONCLUSIONS: Minimally invasive transthoracic device closure of the perimembranous VSD with an asymmetric or a symmetric domestically made device without cardiopulmonary bypass is safe and feasible. It should be considered an acceptable alternative to surgery in selected subgroups. However, it is necessary to evaluate the long-term results.

Safety and feasibility of intra-operative device closure of atrial septal defect with transthoracic minimal invasion.

OBJECTIVE: The study aims to evaluate the safety and feasibility of intra-operative device closure of atrial septal defect with transthoracic minimal invasion. METHODS: From May 2006 to June 2009, 252 patients with secundum-type atrial septal defect closure were enrolled in our institution. The patients were divided into two groups, with 182 patients in group I with intra-operative device closure and 72 in group II with surgical closure. In group I, the patients' age ranged from 3 months to 62 years (mean±standard deviation, 19.0±16.7 years). This approach involved a transthoracic minimal invasion that was performed after full evaluation of the atrial septal defect by transthoracic echocardiography, deploying the device through the delivery sheath to occlude the atrial septal defect. RESULTS: In group I, 180 patients were occluded successfully under this approach. The size of the occluder device implanted ranged from 6 to 48 mm. Minor complications occurred, which included transient arrhythmias (n=23) and pleural effusion (n=15). Two patients with postoperative cardiac arrest were successfully cardiopulmonary resuscitated. Another two patients with occluder dislodged back into the right atrium were turned to surgical repair with cardiopulmonary bypass on the postoperative day. In group II, all patients were occluded successfully, and almost all patients needed blood transfusion and suffered from various minor complications. All discharged patients were followed up for 1-5 years. During this period, we found no recurrence, no thrombosis, even no device failure. In our comparative studies, group II had significantly longer intensive care unit (ICU) stay and hospital stay than group I (p<0.05). The cost for group I was less than group II (p<0.05). CONCLUSIONS: Intra-operative device closure of atrial septal defect with transthoracic minimal invasion is a safe and feasible technique. It had the advantages of cost savings, yielding better cosmetic results, and leaving less trauma than surgical closure.

[Efficacy of bismuth-based quadruple therapy as first-line treatment for Helicobacter pylori infection].

OBJECTIVE: To evaluate the efficacy of bismuth-based quadruple therapy as the first-line treatment for H.pylori infection. METHODS: A total of 136 patients with H.pylori related peptic ulcer or chronic gastritis were randomized into two groups: 67 patients in bismuth-based quadruple group received esomeprazole 20 mg, clarithromycin 0.5 g,amoxicillin 1.0 g,and bismuth potassium citrate 220 mg for 7 d; 69 patients in standard triple group received esomeprazole 20 mg, clarithromycin 0.5 g and amoxicillin 1.0 g for 7 d. Outcome of eradication therapy was assessed by (14)C-UBT. On ITT and PP analysis, calculating the cost-effectiveness ratio (C/E) and the incremental cost-effectiveness ratio (delta C/delta E). RESULT: On ITT and PP analysis, the eradication rates of the quadruple therapy group were 82.09% and 88.71%, and those of the triple therapy group were 66.67% and 73.02% (P<0.05). The cost-effectiveness ratio of two groups was 4.15 and 4.82; The incremental cost-effectiveness ratio of quadruple therapy group was 1.02 as against triple therapy group. CONCLUSION: Compared to the standard triple therapy regimen, the bismuth-containing quadruple therapy regimen has higher eradication rate and cost-effectiveness, which can be recommended as the fist-line treatment for H.pylori infection.

Intraoperative device closure of atrial septal defects with inferior vena cava rim deficiency: a safe alternative to surgical repair.

OBJECTIVE: Our objective was to evaluate the safety and feasibility of intraoperative device closure of atrial septal defects with inferior vena cava rim deficiency. METHODS: From January 2005 to December 2008, we enrolled 65 patients who had a secundum atrial septal defect with inferior vena cava rim deficiency closure in our institution. Patients were divided into 2 groups: 35 patients in group I underwent intraoperative device closure with a right lateral minithoracotomy and 30 in group II underwent open cardiac repair with a right lateral thoracotomy and cardiopulmonary bypass. Intraoperative device closure involved a minimal intercostal incision that was performed after full evaluation of the atrial septal defect by transthoracic echocardiography and the insertion of the device through the delivery sheath to occlude the atrial septal defect. RESULTS: The procedure was successful in all patients. In group I, the diameter of the atrial septal defect ranged from 30 to 44 mm (mean, 35.3 ± 3.9 mm), and the size of the implanted occluder ranged from 34 to 48 mm (mean, 40 ± 2.1 mm). The total occlusion rate was 82.9% immediately after the operation, 97.1% at 3 months, and 100% at 12 and 24 months of follow-up. In group II, all patients had successful closure. A follow-up period of 12 to 24 months was obtained in both groups. During the follow-up, there was no recurrence, thrombosis, or device failure. In our comparative studies, group II had significantly longer operative time, intensive care unit stay, and hospital stay than group I (P < .001). The cost of group I was less than that of group II (20,450.9 ± 840.8 RMB vs 25,884.9 ± 701.8; P < .001). CONCLUSIONS: Intraoperative device closure of atrial septal defects with inferior vena cava rim deficiency is a safe and feasible technique. It has the advantages of cost savings, cosmetic results, and less trauma than surgical closure. Early and midterm results are encouraging.