Deep_KsuccSite: A novel deep learning method for the identification of lysine succinylation sites.

Identification of lysine (symbol Lys or K) succinylation (Ksucc) sites centralizes the basis for disclosing the mechanism and function of lysine succinylation modifications. Traditional experimental methods for Ksucc site ientification are often costly and time-consuming. Therefore, it is necessary to construct an efficient computational method to prediction the presence of Ksucc sites in protein sequences. In this study, we proposed a novel and effective predictor for the identification of Ksucc sites based on deep learning algorithms that was termed as Deep_KsuccSite. The predictor adopted Composition, Transition, and Distribution (CTD) Composition (CTDC), Enhanced Grouped Amino Acid Composition (EGAAC), Amphiphilic Pseudo-Amino Acid Composition (APAAC), and Embedding Encoding methods to encode peptides, then constructed three base classifiers using one-dimensional (1D) convolutional neural network (CNN) and 2D-CNN, and finally utilized voting method to get the final results. K-fold cross-validation and independent testing showed that Deep_KsuccSite could serve as an effective tool to identify Ksucc sites in protein sequences. In addition, the ablation experiment results based on voting, feature combination, and model architecture showed that Deep_KsuccSite could make full use of the information of different features to construct an effective classifier. Taken together, we developed Deep_KsuccSite in this study, which was based on deep learning algorithm and could achieved better prediction accuracy than current methods for lysine succinylation sites. The code and dataset involved in this methodological study are permanently available at the URL https://github.com/flyinsky6/Deep_KsuccSite.

Diastereoselective Generation of C2-Azlactonized 2H-Chromenes via Brønsted Acid-Catalyzed Oxo-Cyclization of Propargyl Alcohols.

A new Brønsted acid-catalyzed oxo-cyclization of propargyl alcohols with azlactones to synthesize C2-azlactonized 2H-chromenes has been established that uses 1,1'-binaphthyl-2,2'-diyl hydrogen phosphate (BiNPO4H) as the catalyst and gives excellent diastereoselectivities (≥19:1 dr) in most cases. This protocol has a high compatibility with various substituents of substrates, offering a catalytic and useful entry to the fabrication of the synthetically important C2-functionalized 2H-chromene scaffold.

TTN-AS1 as a potential diagnostic and prognostic biomarker for multiple cancers.

The long noncoding RNAs (lncRNAs) are non-coding RNAs that are more than 200 nucleotides in length, and one of several types of non-coding RNAs (ncRNAs). The lncRNAs function in diverse biological processes in normal cells, such as cellular differentiation and cell cycle regulation. There is also evidence that some aberrantly regulated lncRNAs function as oncogenes or tumor suppressor genes in various cancers. For example, TTN-AS1 is a lncRNA that binds to titin mRNA (TTN) and has pro-oncogenic effects in many cancers. Overexpression of TTN-AS1 correlates with poor prognosis in breast cancer, lung cancer, digestive system neoplasms, reproductive system cancers, and other cancers. Furthermore, increased TTN-AS1 expression correlates with more advanced pathology and tumor malignancy. In this review, we comprehensively summarize recent studies on the molecular mechanisms of TTN-AS1 regulation and the role of TTN-AS1 in the carcinogenesis and progression of numerous tumors.

Factors associated with a SARS-CoV-2 recurrence after hospital discharge among patients with COVID-19: systematic review and meta-analysis.

BACKGROUND: The proportion of recurrences after discharge among patients with coronavirus disease 2019 (COVID-19) was reported to be between 9.1% and 31.0%. Little is known about this issue, however, so we performed a meta-analysis to summarize the demographical, clinical, and laboratorial characteristics of non-recurrence and recurrence groups. METHODS: Comprehensive searches were conducted using eight electronic databases. Data regarding the demographic, clinical, and laboratorial characteristics of both recurrence and non-recurrence groups were extracted, and quantitative and qualitative analyses were conducted. RESULTS: Ten studies involving 2071 COVID-19 cases were included in this analysis. The proportion of recurrence cases involving patients with COVID-19 was 17.65% (between 12.38% and 25.16%) while older patients were more likely to experience recurrence (weighted mean difference (WMD)=1.67, range between 0.08 and 3.26). The time from discharge to recurrence was 13.38 d (between 12.08 and 14.69 d). Patients were categorized as having moderate severity (odds ratio (OR)=2.69, range between 1.30 and 5.58), while those with clinical symptoms including cough (OR=5.52, range between 3.18 and 9.60), sputum production (OR=5.10, range between 2.60 and 9.97), headache (OR=3.57, range between 1.36 and 9.35), and dizziness (OR=3.17, range between 1.12 and 8.96) were more likely to be associated with recurrence. Patients presenting with bilateral pulmonary infiltration and decreased leucocyte, platelet, and CD4+ T counts were at risk of COVID-19 recurrence (OR=1.71, range between 1.07 and 2.75; WMD=-1.06, range between -1.55 and -0.57, WMD=-40.39, range between -80.20 and -0.48, and WMD=-55.26, range between -105.92 and -4.60, respectively). CONCLUSIONS: The main factors associated with the recurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after hospital discharge were older age, moderate severity, bilateral pulmonary infiltration, laboratory findings including decreased leucocytes, platelets, and CD4+ T counts, and clinical symptoms including cough, sputum production, headache, and dizziness. These factors can be considered warning indicators for the recurrence of SARS-CoV-2 and might help the development of specific management strategies.

The development of hepatocarcinoma after long-term antivirus treatment of Chinese patients with chronic hepatitis B virus infection: Incidence, long-term outcomes and predictive factors.

BACKGROUND: Patients with chronic hepatitis B virus (HBV) infection are at high risk for progressing to decompensated cirrhosis and hepatocellular carcinoma (HCC). Although long-term treatment with nucleos(t)ide analogues (NAs) benefits patients with chronic hepatitis B (CHB), many develop HCC. Therefore, the clinical outcomes of patients CHB who undergo long-term treatment with NAs remain to be identified. The aim of this study therefore was to evaluate the risk and predictors of patients with CHB who develop hepatitis B-induced HCC. METHODS: We investigated 1200 patients with CHB who were treated with NAs for at least four years and evaluated the association of the variables ALT, HBsAg, HBV DNA, age and platelet count with the occurrence of HCC. We used multivariable analysis to identify independent risk factors for the development of HCC. RESULTS: HCC developed in 153 NA-treated patients. Serum HBV DNA levels of 18.17% (218/1200) patients were>2000IU/mL. The median level of liver stiffness measurement (LSM) of all patients was 8.3±6.7kPa vs. 19.8±10.1kPa in patients with HCC. Advanced age, lower platelet counts, positive HBV DNA load, lower ALB concentration and relatively advanced liver disease were associated with an increased risk of developing HCC. Further, TGF-ß and IFN-γ levels were higher and lower in patients with HCC or CHB, respectively. CONCLUSIONS: Hepato-carcinogenesis occurred more frequently in patients with a positive HBV DNA load and relatively advanced liver disease. Therefore, it is important to administer antiviral therapy to patients with CHB before they develop HBV-related cirrhosis.

Hepatitis C virus core protein impairs metabolic disorder of liver cell via HOTAIR-Sirt1 signalling.

It has been suggested that Hepatitis C virus (HCV) core protein is associated with metabolic disorders of liver cell. However, the precise mechanism is still unclear. The aim of the present study was to explore the impact of HCV core protein on hepatocyte metabolism by HepG2 and the possible involvement of long non-coding (lnc) RNAs in this process. The effect of HCV core protein on lncRNAs expression was examined with quantitative RT-PCR (qRT-PCR). Manipulation of HVC core protein and lncRNA HOTAIR was to evaluate the role of interaction between them on cell metabolism-related gene expression and cellular metabolism. The potential downstream Sirt1 signal was examined by western blotting and qRT-PCR. Our data suggested that suppression of HOTAIR abrogates HCV core protein-induced reduction in Sirt1 and differential expression of glucose- and lipid-metabolism-related genes. Also it benefits for metabolic homoeostasis of hepatocyte indicated by restoration of cellular reactive oxygen species (ROS) level and NAD/NADH ratio. By manipulation of HOTAIR, we concluded that HOTAIR negatively regulates Sirt1 expression through affecting its promotor methylation. Moreover, overexpression of Sirt1 reverses pcDNA-HOTAIR-induced glucose- and lipid-metabolism-related gene expression. Our study suggests that HCV core protein causes dysfunction of glucose and lipid metabolism in liver cells through HOTAIR-Sirt1 signalling pathway.

[Partial recovery of thermal sensory functions in skeletal Class â ¢ patients undergoing orthognathic surgery].

PURPOSE: To clarify whether trigeminal somatosensory function will be changed after orthodontic treatment as well as after orthognathic surgery. METHODS: A series of 20 patients with a mean age of 20.9±1.74 years were recruited. Thermal quantitative sensory tests were conducted before orthodontic treatment (T0), before orthognathic surgery (T1), 2 months after orthognathic surgery (T2), and 6 months after orthognathic surgery (T3). The cold detection threshold (CDT), cold pain threshold (CPT), warm detection threshold (WDT) and heat pain threshold (HPT) were determined. SPSS 16.0 software package was used for statistical analysis. RESULTS: There were significant differences with lower threshold (higher sensitivity) in V2L (P=0.006) and V2R (P=0.017) for WDT at T1 compared to T0. A significantly higher threshold (lower sensitivity) was detected for CDT in V2L (P=0.028) at T1 compared to T0. A significantly higher threshold (lower sensitivity) was detected for HPT in V2R (P=0.028) and V3R (P=0.017) at T1 compared to T0. There were significant differences with higher threshold (lower sensitivity) V3L (P=0.024) for WDT at T3 compared to T0. A significantly lower threshold (higher sensitivity) was detected for CPT in V2R (P=0.036), V3L (P=0.012) and V3R (P=0.044) at T3 compared to T0. There were significant differences with higher threshold (lower sensitivity) in V2L (P=0.009), V2R (P=0.034), V3L (P=0.032) and V3R (P=0.001) for HPT at T3 compared to T0.Numbness was reported most frequently at T2 (93.33%), but this symptom tended to decrease with time (T3-20%).Fisher's exact test showed that there was no significant difference at T2(P=0.303) and T3(P=0.530) between participates who underwent genioplasty or not. CONCLUSIONS: The results indicated that thermal somatosensory function was altered after initial orthodontic treatment and orthognathic surgery. However, partial recovery of thermal sensory function can be expected in the majority of patients.

[Comparison of condylar position between Angle Class I and Class II malocclusion in teenagers].

PURPOSE: To analyze and compare the difference of condylar position between Angle Class I and Class II malocclusion patients using cone-beam CT (CBCT). METHODS: Thirty Class I patients, 30 Class II division 1 patients and 30 Class II division 2 patients were selected in this study. Each patient underwent CBCT. The images in the oblique position perpendicular to the condyloid process were reconstructed by Examvision software. The joint space was measured by Exam Vision software. The data were processed with SPSS17.0 software package. RESULTS: The upper joint space was larger in Class II, the posterior joint space was smaller in Class II patients; and in Class II division 1 patients, both of the upper and anterior joint spaces were larger than in Class II division 2 patients，the differences were significant (P<0.05). The length of condyle was longer in Class I patients than in Class II patients. CONCLUSIONS: The condylar position in Class II division 2 patients was lower and further backward. The length of condyle is shortest in Class II division 2 patients.