Search

Protein palmitoylation is a fundamental and reversible post-translational lipid modification that involves a series of biological processes. Although a large number of experimental studies have explored the molecular mechanism behind the palmitoylation process, the computational methods has attracted much attention for its good performance in predicting palmitoylation sites compared with expensive and time-consuming biochemical experiments. The prediction of protein palmitoylation sites is helpful to reveal its biological mechanism. Therefore, the research on the application of machine learning methods to predict palmitoylation sites has become a hot topic in bioinformatics and promoted the development in the related fields. In this review, we briefly introduced the recent development in predicting protein palmitoylation sites by using machine learningbased methods and discussed their benefits and drawbacks. The perspective of machine learning-based methods in predicting palmitoylation sites was also provided. We hope the review could provide a guide in related fields.

Starches from sixteen cassava germplasms harvested at the same time in the Hainan region were evaluated for their physicochemical and structural properties. The granule morphology of all the isolated cassava starch samples showed round, bell or oval shapes and exhibited the same A-type crystalline pattern. The crystallinity range was 26.6–30.8%. The selected cassava germplasms showed a wide variation in granule size distribution: The D[4,3] (the average particle size) ranged from 13.49 μm to 306.27 μm. The water absorption capacity (192.6–226.7%), oil absorption capacity (185.0–216.9%) and transparency (6.8–16.5%) indices varied significantly among the cassava germplasms. However, the retrogradation rates of the cassava starch pastes increased rapidly during the first 1 h and then stabilized. The solubility of starch increased with the temperature. In addition, the FTIR (Fourier Transform Infrared Spectrometer) ratios of 1045/1022 cm−1 and 1022/995 cm−1 of the sixteen cassava starches varied in the range of 1.06–1.78 and 0.78–1.04, respectively. These results indicated that the granule size, relative crystallinity, degree of short-range order, water and oil absorption capacities, solubility and transparency of the cassava starches were greatly influenced by the variety of cassava, which could help in determining the advantages of these starches for applications in different food and nonfood industries.

The continuous cropping obstacle of Panax notoginseng is serious, and effective control measures are lacking. Soil disinfection with chloropicrin(CP) has been proven to be effective in reducing the obstacles to continuous cropping of other crops. In order to ascertain the effect of CP in the continuous cropping of P. notoginseng, this paper explored the influences of CP at different treatment concentrations(0,30,40,50 kg/Mu, 1 Mu≈667 m~2) on soil macro-element nutrients, soil enzyme activity, growth and development of P. notoginseng, and the accumulation of medicinal components. The results showed that CP fumigation significantly increased the content of total nitrogen, alkali-hydrolyzable nitrogen, ammonium nitrogen, nitrate nitrogen, and available phosphorus in the soil, but it had no significant effect on potassium content. The soil protease activity showed a trend of first increasing and then decreasing with the prolonging of the treatment time. Both the soil urease and acid phosphatase activities showed a trend of first decreasing and then increasing with the prolonging of the treatment time. The higher the CP treatment concentration was, the lower the urease and acid phosphatase activities would be in the soil. The protease activity was relatively high after CP40 treatment, which was better than CP30 and CP50 treatments in promoting the nitrogen-phosphorus-potassium accumulation in P. notoginseng. The seedling survival rates after CP0, CP30, CP40, and CP50 tratments in October were 0, 65.56%, 89.44%, and 83.33%, respectively. Compared with the CP30 and CP50 treatments, CP40 treatment significantly facilitated the growth and development of P. notoginseng, the increase in fresh and dry weights, and the accumulation of root saponins. In summary, CP40 treatment accelerates the increase in soil nitrogen and phosphorus nutrients and their accumulation in P. notoginseng, elevates the seedling survival rate of P. notoginseng, enhances the growth and development of P. notoginseng, and promotes the accumulation of medicinal components. CP40 treatment is therefore recommended in production.

Pseudogenes have been reported to play oncogenic or tumor-suppressive roles in cancer progression. However, the molecular mechanism of most pseudogenes in pancreatic ductal adenocarcinoma (PDAC) remains unknown. Herein, we characterized a novel pseudogene-miRNA-mRNA network associated with PDAC progression using bioinformatics analysis. After screening by dreamBase and GEPIA, 12 up-regulated and 7 down-regulated differentially expressed pseudogenes (DEPs) were identified. According to survival analysis, only elevated AK4P1 indicated a poor prognosis for PDAC patients. Moreover, we found that AK4 acts as a cognate gene of AK4P1 and also predicts worse survival for PDAC patients. Furthermore, 32 miRNAs were predicted to bind to AK4P1 by starBase, among which miR-375 was identified as the most potential binding miRNA of AK4P1. A total of 477 potential target genes of miR-375 were obtained by miRNet, in which 49 hub genes with node degree ≥ 20 were identified by STRING. Subsequent analysis for hub genes demonstrated that YAP1 may be a functional downstream target of AK4P1. To confirmed the above findings, microarray, and qRT-PCR assay revealed that YAP1 was dramatically upregulated in both PDAC cells and tissues. Functional experiments showed that knockdown of YAP1 significantly suppressed PDAC cells growth, increased apoptosis, and decreased the ability of invasion. In conclusion, amplification of AK4P1 may fuel the onset and development of PDAC by targeting YAP1 through competitively binding to miR-375, and serve as a promising biomarker and therapeutic target for PDAC.

BACKGROUND AND AIM Diagnosis of esophageal squamous cell carcinoma (ESCC) is complicated and requires substantial expertise and experience. This study aimed to develop an artificial intelligence (AI) system for detecting superficial ESCC under multiple endoscopic imaging modalities. METHODS Endoscopic images were retrospectively collected from West China Hospital, Sichuan University as a training dataset and an independent internal validation dataset. Images from other four hospitals were used as an external validation dataset. The AI system was compared with 11 experienced endoscopists. Furthermore, videos were collected to assess the performance of the AI system. RESULTS A total of 53 933 images from 2621 patients and 142 videos from 19 patients were used to develop and validate the AI system. In the internal and external validation datasets, the performance of the AI system under all or different endoscopic imaging modalities was satisfactory, with sensitivity of 92.5-99.7%, specificity of 78.5-89.0%, and area under the receiver operating characteristic curves of 0.906-0.989. The AI system achieved comparable performance with experienced endoscopists. Regarding superficial ESCC confined to the epithelium, the AI system was more sensitive than experienced endoscopists on white-light imaging (90.8% vs 82.5%, P = 0.022). Moreover, the AI system exhibited good performance in videos, with sensitivity of 89.5-100% and specificity of 73.7-89.5%. CONCLUSIONS We developed an AI system that showed comparable performance with experienced endoscopists in detecting superficial ESCC under multiple endoscopic imaging modalities and might provide valuable support for inexperienced endoscopists, despite requiring further evaluation.

Objective To observe the effect of edaravone (EDA) on the expressions of malondialdehyde (MDA), phosphorylated extracellular signal-regulated kinase (p-ERK), nuclear factor kappa-B cells (NF-κB) and Collagen-Ⅲ in rat model of unilateral ureteral obstruction (UUO), and discuss the protective effect of EDA on renal-interstitial fibrosis. Methods Fifty-four male SD rats were randomly divided into three groups (18 each): sham group (normal control), UUO group and EDA group. Rats in UUO group and EDA group received UUO operation. One day before UUO operation, rats in EDA group received intraperitoneal injection of 3.75mg/(kg·d) EDA, and those in sham group and UUO group were injected with equivalent normal saline. Rats were sacrificed in three batches at the 3rd, 7th and 14th day after operation, six from each group in each batch. The renal pathological changes were observed via HE staining and Masson staining. The contents of MDA in renal tissues were determined by spectrophotometry, and the expression levels of p-ERK1/2, NF-κB and collagen-Ⅲ were detected by immunohistochemistry. Results HE and Masson staining showed no significant changes of MDA content, renal tubules and interstitium in sham group at 3rd, 7th and 14th day, but obvious changes of interstitium and increased fibre deposition in UUO group and EDA group compared with sham group. Compared with UUO group, the lesions of renal tubular and interstitium significantly reduced and the interstitial fibrosis deposition decreased in EDA group. Spectrophotometry indicated that the MDA contents showed no significant difference between EDA group and UUO group [(9.261±0.496)nmol/mg prot and (10.143±0.301)nmol/mg prot] on the 3rd day after operation, but was higher than in sham group [(6.918±1.120)nmol/mg prot]. The MDA contents at the 7th and 14th day after surgery in EDA group [(11.545±0.620)nmol/mg prot and (15.203±0.512)nmol/mg prot] were significantly lower than in UUO group [(13.405±0.612)nmol/mg prot and (18.133±1.684)nmol/mg prot]. Immunohistochemistry analysis showed that no significant difference existed in the expressions of p-ERK1/2, NF-κB and Collagen Ⅲ at the 3 time points in sham group; At the 3rd day after surgery, the expressions of p-ERK1/2, NF-κB and Collagen Ⅲ were higher in EDA group (19 055.7±1866.1, 11 217.0±989.9 and 9724.1±341.9) than in sham group (14 100.3±1822.7, 7975.1±2058.5 and 6890.0±2389.9, P0.05). At the 7th and 14th day after surgery, the expression level of p-ERK1/2 was significantly lower in EDA group (26 228.0±523.0 and 30 647.1±583.8) than in UUO group (28 254.9±886.6 and 33 240.3±1330.4); the expression level of NF-κB was obviously lower in EDA group (16 374.4±1045.3 and 21 111.2±1022.5) than in UUO group (18 799.4±357.0 and 27 125.2±2873.3); the expression level of Collagen-Ⅲ was markedly lower in EDA group (12 470.9±506.1 and 19 615.8±1120.1) than in UUO group (15 049.9±1372.3 and 22 868.9±1889.2), all the differences were of statistical significance (P

Membrane proteins play crucial physiological roles in vivo and are the major category of drug targets for pharmaceuticals. The research on membrane protein is a significant part in the drug discovery. The biological process is a cycled network, and the membrane protein is a vital hub in the network since most drugs achieve the therapeutic effect via interacting with the membrane protein. In this review, typical membrane protein targets are described, including GPCRs, transporters and ion channels. Also, we conclude network servers and databases that are referring to the drug, drug-target information and their relevant data. Furthermore, we chiefly introduce the development and practice of modern medicines, particularly demonstrating a series of state-of-the-art computational models for the prediction of drug-target interaction containing network-based approach and machine-learningbased approach as well as showing current achievements. Finally, we discuss the prospective orientation of drug repurposing and drug discovery as well as propose some improved framework in bioactivity data, created or improved predicted approaches, alternative understanding approaches of drugs bioactivity and their biological processes.

The metal-organic framework of Cu3(NH2BTC)2 was synthesized by solvothermal method with the prepared grafted amine-based trimesic acid as organic ligand. The synthesized adsorbent was characterized by XRD, N2 adsorption-desorption, thermogravimetry, FT-IR and in-situ FT-IR. The performance of the CO2 adsorption was studied by the breakthrough curve based on the fixed-bed reactor. The results showed that the amine groups had been successfully grafted into the skeleton of Cu3(BTC)2. The CO2 adsorption capacity of Cu3(NH2BTC)2 was improved to 1.41 mmol/g at 10 kPa and 50°C. The improvement of CO2 uptake might due to the effect of both the physical and chemical adsorption of CO2.

Msalais is a wine fermented from boiled grape juice. Nonenzymatic browning (NEB) greatly affects the quality of Msalais, but to date its mechanism has not been systematically analyzed. In the current study, the evolution of NEB during Msalais production was investigated using models of grape juice. 5-Hydroxymethylfurfural (5-HMF), browning index (BI), yellowness index (YI), sample absorbance at 420 (A420), and b* increased during heating, with a clear transition point at 110 min. The Maillard reaction (MR) was the major contributor to NEB. Vitamin C (VC) facilitated NEB in the late stage of heating. During heating that lasted over 130 min, glucose contributed to NEB more than fructose, while the reverse was true for heating lasting less than 130 min. Proline (Pro) was the most important amino acid in facilitating NEB. BI and A420 decreased during fermentation, while increasing slightly during wine storage. In conclusion, this study identified the evolution of NEB during the Msalais process, which will facilitate the control of traditional Msalais production for improved wine quality.

To observe the clinical efficacy of minimally invasive acupotomy-injection technique with targeted three-point in the treatment of frozen shoulder.From March 2017 to November 2018, a total of 140 patients with frozen shoulder were randomly divided into observation group and control group. The observation group was made up of 70 patients, including 30 males and 40 females; the mean age was (59.2±11.5) years old; the mean duration of disease was (6.76±4.14) months; the observed patients were treated with acupotomy-injection technique with targeted three-point. There were also 70 patients in the control group, made up of 29 males and 41 females; the mean age was (58.9±11.8) years old; the mean duration of disease was (6.65±3.98) months; the control group was treated with the small needle knife therapy. Before treatment and one month after the treatment, the pain levels of both groups were assessed using the short-form McGill pain questionnaire, and the shoulder function was evaluated using the Constant-Murley Shoulder Outcome Scoring. The clinical efficacy of between groups was compared after treatment, and finally, the improvement rate of pain degree was used to evaluate the therapeutic effect of the patients.The PRI, VAS, PPI and total pain scores of frozen shoulder patients in both groups decreased significantly one month after the treatment compared with those before treatment (The application of acupotomy-injection technique with targeted three-point in the treatment of frozen shoulder shows definite efficacy, easy operation, little pain and high safety. Therefore, it is an ideal method for minimally invasive treatment.

The entropy method describes the change in the signal state from a macroscopic angle and weakens the interference generated by random noise. From the angle of chaos, which describes the first arrival of microseismic signals, it predicts the trend of noise entropy based on the grey theory. The results indicate that the entropy method is sensitive to amplitude, frequency, and seismic phase changes. Compared with traditional methods, the entropy method has better noise immunity. In terms of the influence of the pickup parameter on the resulting error, the entropy method demonstrated the best result and produces the smallest error.

Palmitoylated proteins are important proteins that regulate several biological processes in cells, including protein localization, protein trafficking, and protein-protein interactions. The identification of palmitoylated proteins may therefore contribute to our understanding of important molecular mechanisms and biological functions. In this paper, a simple but effective computational method named MRMD-Palm is proposed for identifying palmitoylated proteins. In developing the method, first, palmitoylated and non-palmitoylated proteins were collected to construct a benchmark dataset. Next, some typical sequence-based feature-encoding schemes related to the amino acid composition, pseudo amino acid composition and physico-chemical properties were extracted. To avoid noise and reduce information redundancy, a feature selection technique named MRMD (Max-Relevance-Max-Distance) was introduced to obtain the optimal feature subset. Finally, the random forest algorithm was utilized as the predictor. Under 10-fold cross-validation, the method achieved a sensitivity of 97.1%, a specificity of 95.9% and a MCC of 73.7%, representing better performance than most current counterparts. Additionally, the experimental results showed that the use of hydrophobicity to encode palmitoylated sequences can improve the performance of the predictor. This finding is consistent with the biological phenomenon that palmitoylation is highly hydrophobic. It is believed that the results of this study will lead to the determination of the protein palmitoylation mechanism.

The predictions of chaotic time series by applying the least squares support vector machine (LS-SVM), with comparison with the traditional-SVM and-SVM, were specified. The results show that, compared with the traditional SVM, the prediction accuracy of LS-SVM is better than the traditional SVM and more suitable for time series online prediction.