I-DNAN6mA: Accurate Identification of DNA N6-Methyladenine Sites Using the Base-Pairing Map and Deep Learning.

The recent discovery of numerous DNA N6-methyladenine (6mA) sites has transformed our perception about the roles of 6mA in living organisms. However, our ability to understand them is hampered by our inability to identify 6mA sites rapidly and cost-efficiently by existing experimental methods. Developing a novel method to quickly and accurately identify 6mA sites is critical for speeding up the progress of its function detection and understanding. In this study, we propose a novel computational method, called I-DNAN6mA, to identify 6mA sites and complement experimental methods well, by leveraging the base-pairing rules and a well-designed three-stage deep learning model with pairwise inputs. The performance of our proposed method is benchmarked and evaluated on four species, i.e., Arabidopsis thaliana, Drosophila melanogaster, Rice, and Rosaceae. The experimental results demonstrate that I-DNAN6mA achieves area under the receiver operating characteristic curve values of 0.967, 0.963, 0.947, 0.976, and 0.990, accuracies of 91.5, 92.7, 88.2, 0.938, and 96.2%, and Mathew's correlation coefficient values of 0.855, 0.831, 0.763, 0.877, and 0.924 on five benchmark data sets, respectively, and outperforms several existing state-of-the-art methods. To our knowledge, I-DNAN6mA is the first approach to identify 6mA sites using a novel image-like representation of DNA sequences and a deep learning model with pairwise inputs. I-DNAN6mA is expected to be useful for locating functional regions of DNA.

Predicting RNA solvent accessibility from multi-scale context feature via multi-shot neural network.

Knowledge of RNA solvent accessibility has recently become attractive due to the increasing awareness of its importance for key biological process. Accurately predicting the solvent accessibility of RNA is crucial for understanding its 3D structure and biological function. In this study, we develop a novel computational method, termed M2pred, for accurately predicting the solvent accessibility of RNA from sequence-based multi-scale context feature. In M2pred, three single-view features, i.e., base-pairing probabilities, position-specific frequency matrix, and a binary one-hot encoding, are first generated as three feature sources, and immediately concatenated to engender a super feature. Secondly, for the super feature, the matrix-format features of each nucleotide are extracted using an initialized sliding window technique, and regularly stacked into a cube-format feature. Then, using multi-scale context feature extraction strategy, a pyramid feature constructed of contextual feature of four scales related to target nucleotides is extracted from the cube-format feature. Finally, a customized multi-shot neural network framework, which is equipped with four different scales of receptive fields mainly integrating several residual attention blocks, is designed to dig discrimination information from the contextual pyramid feature. Experimental results demonstrate that the proposed M2pred achieve a high prediction performance and outperforms existing state-of-the-art prediction methods of RNA solvent accessibility.

Histopathological analysis of incompetent great saphenous veins after mechanochemical ablation treatment - An ex-vivo experiment.

BACKGROUND: The endovascular technique of mechanochemical ablation (MOCA) has become popular in treating patients with saphenous reflux. We reported the histopathological findings in human ex-vivo incompetent great saphenous veins following treatment with saline, polidocanol, mechanical ablation and MOCA using ClariVein device. METHODS: Twenty-four vein GSV specimens were obtained via traditional surgery and treated with four methods: Group A: 0.9% normal saline (NS); Group B: 3% polidocanol; Group C: mechanical ablation + 0.9% NS; Group D: mechanical ablation + 3% polidocanol (MOCA). Hematoxylin and eosin (HE), Masson's trichrome and immunohistochemical staining were performed on each specimen and integrated optical densities were measured with vWF and a-SMA stains and statistically evaluated. vWF staining was used to assess endothelial damage and a a-SMA staining was used to assess media injury. RESULTS: HE and Masson's trichrome staining of Groups C and D revealed severe damage to the endothelium and media compared to Groups A and B. The statistical result of vWF staining showed the damage of endothelium was significantly increased by Group D compared to Groups A, B and C. The statistical result of a-SMA staining showed the damage of media was significantly increased by Groups C and D compared to Groups A and B. CONCLUSIONS: The mechanism of MOCA was caused by both endothelium damage and media tearing. The damage of endothelium was significantly increased by MOCA when compared with mechanical ablation alone.

Improved protein relative solvent accessibility prediction using deep multi-view feature learning framework.

The accurate prediction of the relative solvent accessibility of a protein is critical to understanding its 3D structure and biological function. In this study, a novel deep multi-view feature learning (DMVFL) framework that integrates three different neural network units, i.e., bidirectional long short-term memory recurrent neural network, squeeze-and-excitation, and fully-connected hidden layer, with four sequence-based single-view features, i.e., position-specific scoring matrix, position-specific frequency matrix, predicted secondary structure, and roughly predicted three-state relative solvent accessibility probability, is developed to accurately predict relative solvent accessibility information of protein. On the basis of this newly developed framework, one new protein relative solvent accessibility predictor was proposed and called DMVFL-RSA, which employs a customized multiple feedback mechanism that helps to extract discriminative information embedded in the four single-view features. In benchmark tests on TEST524 and CASP14-derived (CASP14set) datasets, DMVFL-RSA outperforms other existing state-of-the-art protein relative solvent accessibility predictors when predicting two-state (exposure threshold of 25%), three-state (exposure thresholds of 9% and 36%), and four-state (exposure thresholds of 4%, 25%, and 50%) discrete values. For real-valued prediction on TEST524 and CASP14set, DMVFL-RSA has also gained high Pearson correlation coefficient values, indicating a positive correlation between the predicted and native relative solvent accessibility. Detailed analyses show that the major advantages of DMVFL-RSA lie in the high efficiency of the DMVFL framework, the applied multiple feedback mechanism, and the strong sensitivity of the sequence-based features. The web server of DMVFL-RSA is freely available at https://jun-csbio.github.io/DMVFL-RSA/for academic use. The standalone package of DMVFL-RSA is downloadable at https://github.com/XueQiangFan/DMVFL-RSA.

Drug-Coated Balloon versus Bare Nitinol Stent in Femoropopliteal Artery: 12 Months Outcome from a Single Center in China.

OBJECT: The study sought to compare the safety and effectiveness of drug-coated balloon (DCB) with bare nitinol stent in patients with complex femoropopliteal(FP) lesions in real-world practice. METHODS: Patients with symptomatic (Rutherford stage 2 to 5) femoropopliteal lesions who underwent DCB or bare nitinol stent implantation at the Department of Cardiovascular Surgery of China-Japan Friendship Hospital from June 2016 to September 2017 were included. Demographics, angiographic and procedural variables were included. Freedom from target lesion revascularization (TLR), primary patency and major adverse events were obtained from follow-up results at 3,6 and12 months. Descriptive analysis was performed on all variables. RESULTS: A total of 90 eligible patients were enrolled, which included 51 DCB subjects (mean age, 63.1 ± 13.2 years; 76.5% male) with 55 lesions and 39 nitinol stent subjects (mean age, 66.5 ± 10.5 years; 61.5% male) with 42 lesions. Significant higher primary patency was observed in the DCB group compared with the stent group (74.5% vs. 52.4%; log-rank test P = 0.018; HR 0.335, 95%CI 0.124-0.903, P = 0.031). The rates of freedom from TLR (f-TLR) were 78.2% and 59.5% (log-rank test P = 0.032) for the DCB group and the stent group, respectively, at 12 months. CD-TLR rates were 18.2% vs. 38.1% with a P-value of 0.023. Female sex (HR 6.122, 95%CI 1.880-19.934, P = 0.003), lesion length over 20 cm (HR 5.514, 95%CI 2.312-13.148, P < 0.001) and renal insufficiency (HR 2.609, 95%CI 1.087-6.260, P = 0.032) were suggested as independent risk factors of reducing primary patency. There were no significant differences in major adverse events between the 2 groups. CONCLUSION: The result above demonstrates that DCB treatment has higher primary patency and lower TLR at 12 months than nitinol stent. These data confirm the safety and effectiveness of the DCB for patients with complex femoropopliteal lesions.

Hybrid and Endovascular Treatment of Pulmonary Sequestration: Two Case Reports and Literature Review.

Pulmonary sequestration is an uncommon congenital pulmonary anomaly associated with aberrant systemic arteries which usually originate from the thoracic aorta or abdominal aorta. Traditionally, surgical resection and ligation of the feeding vessels are the gold standard treatments of the disease. Endovascular intervention and hybrid operation are promising treatment options. However, the case reports with endovascular and hybrid treatment are sparse to our knowledge. We presented 2 symptomatic adult patients with pulmonary sequestration successfully treated by hybrid operation and transcatheter embolization, respectively. Besides, we reviewed 37 previously reported cases of pulmonary sequestration treated by endovascular or hybrid treatment.

Feasibility and Safety of Simultaneous Carotid Endarterectomy and Carotid Stenting for Bilateral Carotid Stenosis: A Single-Center Experience using a Hybrid Procedure.

BACKGROUND: The treatment for bilateral carotid stenosis (BCS) is challenging, and the optimal treatment strategy is not clear. We report our experience of treating 8 patients with BCS by simultaneous carotid endarterectomy (CEA) and carotid stenting (CAS), thereby providing an alternative for vascular surgeons. METHODS: Between October 2010 and August 2014, 8 patients (5 males and 3 females; range, 53-82 years; mean, 69 ± 8.8 years) underwent simultaneous CEA and CAS in our hospital. CEA before CAS was done in 5 patients, and CAS before CEA was done in 3 patients. One patient also underwent simultaneous coronary artery bypass grafting due to unstable angina. Intraoperative transcranial Doppler ultrasonography, carotid shunts, patches, and embolic protection devices were used in all patients. Instances of hyperperfusion syndrome (HPS), hemodynamic depression, stroke, myocardial infarction (MI), and death were recorded. RESULTS: All patients completed the procedure. One patient developed postprocedural HPS. After systemic treatment, he recovered completely. There were no deaths, major and/or minor strokes, or MI, nor did any patient exhibit lower palsy in cranial nerves in the perioperative period (<30 days) or on clinical follow-up (3 and 6 months). We observed no restenosis and no recurrent symptoms during follow-up. CONCLUSIONS: After careful preoperative assessment and preparation, simultaneous CEA and CAS for high-grade BCS may be considered as an alternative management strategy in carefully selected patients.

Ense-i6mA: Identification of DNA N6-methyl-adenine Sites Using XGB-RFE Feature Se-lection and Ensemble Machine Learning.

DNA N6-methyladenine (6mA) is an important epigenetic modification that plays a vital role in various cellular processes. Accurate identification of the 6mA sites is fundamental to elucidate the biological functions and mechanisms of modification. However, experimental methods for detecting 6mA sites are high-priced and time-consuming. In this study, we propose a novel computational method, called Ense-i6mA, to predict 6mA sites. Firstly, five encoding schemes, i.e., one-hot encoding, gcContent, Z-Curve, K-mer nucleotide frequency, and K-mer nucleotide frequency with gap, are employed to extract DNA sequence features. Secondly, to our knowledge, it is the first time that eXtreme gradient boosting coupled with recursive feature elimination is applied to 6mA sites prediction domain to remove noisy features for avoiding over-fitting, reducing computing time and complexity. Then, the best subset of features is fed into base-classifiers composed of Extra Trees, eXtreme Gradient Boosting, Light Gradient Boosting Machine, and Support Vector Machine. Finally, to minimize generalization errors, the prediction probabilities of the base-classifiers are aggregated by averaging for inferring the final 6mA sites results. We conduct experiments on two species, i.e., Arabidopsis thaliana and Drosophila melanogaster, to compare the performance of Ense-i6mA against the recent 6mA sites prediction methods. The experimental results demonstrate that the proposed Ense-i6mA achieves area under the receiver operating characteristic curve values of 0.967 and 0.968, accuracies of 91.4% and 92.0%, and Mathew's correlation coefficient values of 0.829 and 0.842 on two benchmark datasets, respectively, and outperforms several existing state-of-the-art methods.

Comparison of bleomycin polidocanol foam vs electrochemotherapy combined with polidocanol foam for treatment of venous malformations.

OBJECTIVE: This study aims to investigate the difference in safety and efficacy between two treatments for venous malformations (VMs), electrochemotherapy combined with polidocanol foam (ECP) and bleomycin polidocanol foam (BPF), providing alternative therapies for VMs. METHODS: We conducted a retrospective review of 152 patients with VMs treated with ECP and BPF. Pre- and post-treatment magnetic resonance images (MRIs) were collected, and clinical follow-up assessments were performed. Imaging results were used to calculate lesion volume changes. Clinical outcomes included changes in pain and improvements in perceived swelling. Patients were followed up at 1 week and 6 months after surgery. All emerging complications were documented in detail. RESULTS: Of the 152 patients, 87 (57.2%) received BPF treatment, and 65 (42.8%) received ECP treatment. The most common location of VMs was the lower extremities (92/152; 60.2%), and the most common symptom was pain (108/152; 71.1%). Forty-three patients had previously undergone therapy in the BPF group (43/87; 49.4%), whereas 30 patients had received prior treatment in the ECP group (30/65; 46.2%). The study found that the percentage of lesion volume reduction in the BPF group was not significantly different from that in the ECP group (75.00% ± 17.85% vs 74.69% ± 8.48%; P = .899). ECP was more effective when the initial lesion volume was greater than 30 mL (67.66% ± 12.34% vs 73.47% ± 8.00%; P = .048). Patients treated with BPF had significantly less posttreatment pain than those treated with ECP, in different baseline lesion size. In the overall sample, pain relief was significantly higher in the BPF group than in the ECP group (4.21 ± 1.19 vs 3.57 ± 0.76; P = .002). However, there was no difference in pain relief between the two groups for the treatment of initially large VMs (4.20 ± 0.94 vs 3.70 ± 0.87; P = .113). The ECP group was significantly more likely to develop hyperpigmentation (5/87; 5.75% vs 11/65; 16.92%; P = .026) and swelling (9/87; 10.34% vs 16/65; 24.62%; P = .019) 1 week after surgery than the BPF group. CONCLUSIONS: Our study demonstrates that both BPF and ECP are effective treatments for VMs, with BPF being a safer option. ECP is a better choice for patients with the initial lesion volume greater than 30 mL, but it is more likely to lead to early swelling and hyperpigmentation.

Clinical outcomes and predictors of bleomycin polidocanol foam sclerotherapy treatment response in venous malformations.

OBJECTIVE: To evaluate the safety and efficacy of bleomycin polidocanol foam (BPF) sclerotherapy for venous malformations (VMs) and analyze the associated clinical outcomes and predictors. METHODS: We retrospectively assessed BPF sclerotherapy outcomes in 138 patients with VMs. We analyzed pain levels, lesion volume reduction, and subjective perception of response. Logistic regression analysis was performed to identify potential predictors of treatment outcome. Additionally, we carefully monitored and recorded complications. RESULTS: There was a notable average reduction in lesion volume by 78.50% ± 15.71%. The pain numerical rating scale (NRS) score decreased from 4.17 ± 2.63 prior to treatment to 1.05 ± 1.54 afterward, and 70.3% of the patients experienced effective relief after a single BPF treatment. Multivariate analysis revealed that a high baseline NRS (odds ratio [OR]: 4.026) and elevated activated partial thromboplastin time (APTT, OR: 1.200) were positive predictors of pain reduction. Additionally, a high baseline NRS score (OR: 1.992) and elevated thrombocytocrit (PCT, OR: 2.543) were positive predictors of incomplete postoperative pain relief. Minor complications occurred in 31 (22.46%) patients. CONCLUSION: BPF sclerotherapy is safe and effective for VMs, resulting in significant reduction in lesion volume, improved symptoms, and minimal complications. APTT and PCT levels are important predictors of pain outcomes following BPF treatment.

Major Limb Amputation in Parkes-Weber Syndrome With Refractory Ulceration: A Case Report and Literature Review.

Parkes-Weber syndrome (PWS) is a rare congenital vascular syndrome consisting of capillary, venous, lymphatic, and arteriovenous malformation. There are many complications of PWS, such as ulceration, bleeding, infection, and cardiac failure. Among them, skin ulceration is one of the thorniest problems in PWS, requiring multidisciplinary approaches for the management. In this article, we presented the case of an elderly patient with refractory ulceration who received numerous treatments with no effect and finally underwent a major amputation to improve the quality of life. Moreover, we reviewed 23 previously reported cases to improve our understanding of the management for PWS patients with ulceration.

Comparison of polidocanol foam versus bleomycin polidocanol foam for treatment of venous malformations.

OBJECTIVE: The objective of this research was to retrospectively investigate the difference of safety and efficacy between polidocanol foam and bleomycin polidocanol foam (BPF) in the treatment of venous malformations (VMs), and provide clinical evidence for the application of BPF for VMs. METHODS: Patients with VMs treated with polidocanol foam and BPF were included between July 2018 and July 2020. The VM tissue involvements and symptoms were collected. The treatment outcomes were evaluated by the clinical improvement of symptoms and the degree of devascularization on ultrasound examination or magnetic resonance imaging. Patients were followed up for 1, 3, and 6 months after the sclerotherapy. Immediate and delayed complications were closely followed and recorded. RESULTS: A total of 51 patients were included, including 34 females and 17 males with a mean age of 26.8 years (range, 5-65 years). The most commonly involved sites were lower extremities (31/60 [51.7%]) and the most common symptom was pain (33/51 [64.7%]). Fifty-four sclerotherapies were performed with a mean of 1.06 ± 0.24 sessions (range, 1-2 sessions) per patient. The reduction percentage of lesion volume in the BPF group was significantly higher than the polidocanol foam group (79.4 ± 1.6% vs 55.7 ± 6.1%; P < .001). Patient satisfaction scores in the BPF group were significantly higher than the polidocanol foam group (7.2 ± 1.1 vs 5.7 ± 0.8; P < .001). No major complication was observed in either group. Cardiovascular and Interventional Radiological Society of Europe (CIRSE) grade 1 complications occurred in 5 of 21 patients in the BPF group and 7 of 30 patients in the polidocanol foam group, CIRSE grade 2 complications occurred in 5 of 21 patients in the BPF group and 4 of 30 patients in the polidocanol foam group; there were no significant differences between the two groups. CONCLUSIONS: BPF is a safe and effective sclerosant for VMs, showing better efficacy and similar safety as commonly used mild sclerosants. It could be a promising agent to treat VMs or other slow-flow vascular malformations.

Acute carotid stent thrombosis: A case report and literature review.

BACKGROUND: Acute carotid stent thrombosis (ACST) is a rare but devastating complication in the carotid artery stenting (CAS) procedure. The aim of this article is to report a case and review cases of ACST reported in the literature, and investigate risk factors and management strategies for ACST. CASE SUMMARY: We reviewed the treatment process of a patient with ACST after CAS. Then multiple databases were systematically searched to identify studies reporting ACST from 2005 to 2020. The demographic data, risk factors, treatment strategies, and prognosis were extracted and analyzed. CONCLUSION: The reason for ACST is multifactorial. Proper patient selection, normative anti-platelet treatment, and perfect technical detail may decrease the incidence of ACST. Several treatment strategies such as thrombolysis, mechanical thrombectomy, and open surgery may be options for the treatment of ACST. Limited data have shown that carotid endarterectomy is effective with favorable results.

[Open surgery for femoro-popliteal arterial occlusive disease].

OBJECTIVE: To explore the mid-term surgical results of arterial revascularization for femoro-popliteal arterial occlusive disease (lesion type C and D). METHODS: From January 2005 to February 2009, 191 arterial bypass had been performed on 170 patients (21 cases bilateral). There were 108 male and 62 female, age ranged from 45 to 85 years old with an average of 67 years old. The operative indication was claudication in 78 cases, rest pain in 62 cases, ischemic ulcer in 19 cases, and distal tissue necrosis in 11 cases. Arterial angiography were performed on all cases. According to TASC II document, type C lesions were seen in 127 limbs, type D lesions were seen in 64 limbs. Autogenous greater saphenous vein bypass in situ were done on 15 limbs, autogenous greater saphenous vein bypass reversed in 20 limbs, revascularization with artificial prosthesis in 128 limbs, composite grafts consisting of a prosthetic conduit with a distal venous segment in 28 limbs. RESULTS: There were no 30-day mortality. Follow-up periods ranged 6 to 36 months with an average of (24 + or - 6) months. Seventy-three cases were lost during follow-up periods, follow-up rate was 57% (109/191). Primary patency rate was 84.4% (92/109). The patency rate was 88.2% with artificial prosthesis, 70.8% with greater saphenous vein (in situ or reversed). Secondary patency rate was 89.9%. CONCLUSIONS: Arterial revascularization with artificial prosthesis is main treatment for diffused superficial femoral artery occlusive disease (TASC II type C and D lesion) with satisfied surgical results.

Age-specific differences in non-cardiac comorbidities among elderly patients hospitalized with heart failure: a special focus on young-old, old-old, and oldest-old.

BACKGROUND: Despite the growing epidemic of heart failure (HF), there is limited data available to systematically compare non-cardiac comorbidities in the young-old, old-old, and oldest-old patients hospitalized for HF. The precise differences will add valuable information for better management of HF in elderly patients. METHODS: A total of 1053 patients aged 65 years or older hospitalized with HF were included in this study. Patients were compared among three age groups: (1) young-old: 65 to 74 years, (2) old-old: 75 to 84 years, and (3) oldest-old: ≥85 years. Clinical details of presentation, comorbidities, and prescribed medications were recorded. RESULTS: The mean age was 76.7 years and 12.7% were 85 years or older. Most elderly patients with HF (97.5%) had at least one of the non-cardiac comorbidities. The patterns of common non-cardiac comorbidities were different between the young-old and oldest-old group. The three most common non-cardiac comorbidities were anemia (53.6%), hyperlipidemia (45.9%), and diabetes (42.4%) in the young-old group, while anemia (73.1%), infection (58.2%), and chronic kidney disease (44.0%) in the oldest-old group. Polypharmacy was observed in 93.0% elderly patients with HF. Additionally, 29.2% patients were diagnosed with infection, and 67.0% patients were prescribed antibiotics. However, 60.4% patients were diagnosed with anemia with only 8.9% of them receiving iron repletion. CONCLUSIONS: Non-cardiac comorbidities are nearly universal in three groups but obviously differ by age, and inappropriate medications are very common in elderly patients with HF. Further treatment strategies should be focused on providing optimal medications for age-specific non-cardiac conditions.

Effect of electrochemotherapy in treating patients with venous malformations.

OBJECTIVE: To evaluate the efficacy and safety of electrochemotherapy in treating venous malformations. METHODS: Electrochemotherapy was applied to 665 patients with venous malformations of limbs and trunk, and 505 cases were followed up for half to 6 years. In this study, 228 male and 277 female patients were involved. Diagnosis was made by clinical manifestations and magnetic resonance imaging. The platinum electrodes were inserted into tumor through a trocar with plastic insulating cannula percutaneously and connected with the electrochemical therapeutic apparatus in anodes and cathodes separately. Then electricity was given. The treating voltage is 6-12 V and volume 100-180 mA, the total electricity used is in general 80-100 coulombs per 1.0 square centimeter of tumors' area. The treating time was usually from several dozen minutes to over 2 h depending on the size of the tumor. The severe cases which needed to be treated once again usually were operated after 6 months. RESULTS: The primary efficacy end point was defined as an improvement of patients' symptoms and a reduction in size of tumor 6 months after treatment. Effects were divided into 4 grades, and the efficacy rate decreased from grade 1 to grade 4. The efficacy turned out that 30.1% (152/505) of patients was classified as grade 1; 46.3% (234/505) as grade 2; 19.0% (96/505) as grade 3 and 4.6% (23/505) as grade 4. CONCLUSIONS: Electrochemotherapy shows special superiorities in treating venous malformations. It might bring a confirmed clinical efficacy with the advantages of less injury, quick recovery, simple operation and less complications.