Plasma Extracellular Vesicle Long RNAs Have Potential as Biomarkers in Early Detection of Colorectal Cancer.

Background: Early detection of colorectal cancer (CRC) is crucial to the treatment and prognosis of patients. Traditional screening methods have disadvantages. Methods: 231 blood samples were collected from 86 CRC, 56 colorectal adenoma (CRA), and 89 healthy individuals, from which extracellular vesicle long RNAs (exLRs) were isolated and sequenced. An CRC diagnostic signature (d-signature) was established, and prognosis-associated cell components were evaluated. Results: The exLR d-signature for CRC was established based on 17 of the differentially expressed exLRs. The d-signature showed high diagnostic efficiency of CRC and control (CRA and healthy) samples with an area under the curve (AUC) of 0.938 in the training cohort, 0.943 in the validation cohort, and 0.947 in an independent cohort. The d-signature could effectively differentiate early-stage (stage I-II) CRC from healthy individuals (AUC 0.990), as well as differentiating CEA-negative CRC from healthy individuals (AUC 0.988). A CRA d-signature was also generated and could differentiate CRA from healthy individuals both in the training (AUC 0.993) and validation (AUC 0.978) cohorts. The enrichment of class-switched memory B-cells, B-cells, naive B-cells, and mast cells showed increasing trends between CRC, CRA, and healthy cohorts. Class-switched memory B-cells, mast cells, and basophils were positively associated with CRC prognosis while natural killer T-cells, naive B-cells, immature dendritic cells, and lymphatic endothelial cells were negatively associated with prognosis. Conclusions: Our study identified that the exLR d-signature could differentiate CRC from CRA and healthy individuals with high efficiency and exLR profiling also has potential in CRA screening and CRC prognosis prediction.

iProEP: A Computational Predictor for Predicting Promoter.

Promoter is a fundamental DNA element located around the transcription start site (TSS) and could regulate gene transcription. Promoter recognition is of great significance in determining transcription units, studying gene structure, analyzing gene regulation mechanisms, and annotating gene functional information. Many models have already been proposed to predict promoters. However, the performances of these methods still need to be improved. In this work, we combined pseudo k-tuple nucleotide composition (PseKNC) with position-correlation scoring function (PCSF) to formulate promoter sequences of Homo sapiens (H. sapiens), Drosophila melanogaster (D. melanogaster), Caenorhabditis elegans (C. elegans), Bacillus subtilis (B. subtilis), and Escherichia coli (E. coli). Minimum Redundancy Maximum Relevance (mRMR) algorithm and increment feature selection strategy were then adopted to find out optimal feature subsets. Support vector machine (SVM) was used to distinguish between promoters and non-promoters. In the 10-fold cross-validation test, accuracies of 93.3%, 93.9%, 95.7%, 95.2%, and 93.1% were obtained for H. sapiens, D. melanogaster, C. elegans, B. subtilis, and E. coli, with the areas under receiver operating curves (AUCs) of 0.974, 0.975, 0.981, 0.988, and 0.976, respectively. Comparative results demonstrated that our method outperforms existing methods for identifying promoters. An online web server was established that can be freely accessed (http://lin-group.cn/server/iProEP/).

A Brief Survey of Machine Learning Application in Cancerlectin Identification.

Proteins with at least one carbohydrate recognition domain are lectins that can identify and reversibly interact with glycan moiety of glycoconjugates or a soluble carbohydrate. It has been proved that lectins can play various vital roles in mediating signal transduction, cell-cell recognition and interaction, immune defense, and so on. Most organisms can synthesize and secret lectins. A portion of lectins closely related to diverse cancers, called cancerlectins, are involved in tumor initiation, growth and recrudescence. Cancerlectins have been investigated for their applications in the laboratory study, clinical diagnosis and therapy, and drug delivery and targeting of cancers. The identification of cancerlectin genes from a lot of lectins is helpful for dissecting cancers. Several cancerlectin prediction tools based on machine learning approaches have been established and have become an excellent complement to experimental methods. In this review, we comprehensively summarize and expound the indispensable materials for implementing cancerlectin prediction models. We hope that this review will contribute to understanding cancerlectins and provide valuable clues for the study of cancerlectins. Novel systems for cancerlectin gene identification are expected to be developed for clinical applications and gene therapy.

Sequence-based predictive modeling to identify cancerlectins.

Lectins are a diverse type of glycoproteins or carbohydrate-binding proteins that have a wide distribution to various species. They can specially identify and exclusively bind to a certain kind of saccharide groups. Cancerlectins are a group of lectins that are closely related to cancer and play a major role in the initiation, survival, growth, metastasis and spread of tumor. Several computational methods have emerged to discriminate cancerlectins from non-cancerlectins, which promote the study on pathogenic mechanisms and clinical treatment of cancer. However, the predictive accuracies of most of these techniques are very limited. In this work, by constructing a benchmark dataset based on the CancerLectinDB database, a new amino acid sequence-based strategy for feature description was developed, and then the binomial distribution was applied to screen the optimal feature set. Ultimately, an SVM-based predictor was performed to distinguish cancerlectins from non-cancerlectins, and achieved an accuracy of 77.48% with AUC of 85.52% in jackknife cross-validation. The results revealed that our prediction model could perform better comparing with published predictive tools.

Pro54DB: a database for experimentally verified sigma-54 promoters.

Summary: In prokaryotes, the σ54 promoters are unique regulatory elements and have attracted much attention because they are in charge of the transcription of carbon and nitrogen-related genes and participate in numerous ancillary processes and environmental responses. All findings on σ54 promoters are favorable for a better understanding of their regulatory mechanisms in gene transcription and an accurate discovery of genes missed by the wet experimental evidences. In order to provide an up-to-date, interactive and extensible database for σ54 promoter, a free and easy accessed database called Pro54DB (σ54 promoter database) was built to collect information of σ54 promoter. In the current version, it has stored 210 experimental-confirmed σ54 promoters with 297 regulated genes in 43 species manually extracted from 133 publications, which is helpful for researchers in fields of bioinformatics and molecular biology. Availability and Implementation: Pro54DB is freely available on the web at http://lin.uestc.edu.cn/database/pro54db with all major browsers supported. Contacts: greatchen@ncst.edu.cn or hlin@uestc.edu.cn

Prediction of phosphothreonine sites in human proteins by fusing different features.

Phosphorylation is one of the most important protein post-translation modifications. With the rapid development of high-throughput mass spectrometry, phosphorylation site data is rapidly accumulating, which provides us an opportunity to systematically investigate and predict phosphorylation in proteins. The phosphorylation of threonine is the addition of a phosphoryl group to its polar side chains group. In this work, we statistically analyzed the distribution of the different properties including position conservation, secondary structure, accessibility and some other physicochemical properties of the residues surrounding the phosphothreonine site and non-phosphothreonine site. We found that the distributions of those features are non-symmetrical. Based on the distribution of properties, we developed a new model by using optimal window size strategy and feature selection technique. The cross-validated results show that the area under receiver operating characteristic curve reaches to 0.847, suggesting that our model may play a complementary role to other existing methods for predicting phosphothreonine site in proteins.

[Endobutton and cortical screw fixation for the treatment of distal tibiofibular syndesmosis separated].

OBJECTIVE: To analyze the treatment effect of Endobutton plate cable system for the treatment of the distal tibiofibular syndesmosis injury. METHODS: Total 38 patients with tibiofibular syndesmosis separation treated by surgical operation from October 2011 to October 2013 were analyzed retrospectively. According to internal fixation, 38 cases were divided into two groups involving group A (cortical screw fixation) and group B (Endobutton plate cable system fixation). In group A, there were 26 patients including 16 males and 10 females with an average age of (37.90±4.67) years old ranging from 19 to 63 years old; 14 cases were on the left and 12 on the right;involving 8 cases of Weber-Denis type B, 18 cases of Weber-Denis type C; according to Lauge-Hanson typing, 9 cases of supination external rotation (SER), 10 cases of pronation abduction (PAB), 7 cases of pronation external rotation (PER). In group B, there were 12 cases including 7 males and 5 females, with an average age of (38.70±6.03) years old ranging from 20 to 55 years old;6 cases were on the left and 6 cases on the right;involving 4 cases of Weber-Denis type B and 8 cases of Weber-Denis; involving 7 cases of PER, 3 cases of SER, 2 cases of PAB. The operative time, intraoperative blood loss, surgery cost, hospital stay time, the wound healing, pain score at 1 month after operation, and the load time were recorded and evaluated. According to reviewing of X rays regulary, the healing of fracture were assessed, the function outcomes of ankle was evaluated according to the Ankle Hind Foot Scale of American Orthopaedic Foot and Ankle Society. RESULTS: All patients were followed up for 8 to 18 months with an average of 13.5 months. There were no statistical significance in intraoperative blood loss, hospital stay time, average load time and postoperative pain score at 1 month after operation between two groups (P>0.05). Duration of operation, the operative time were significantly shorter in cortical screw group;however, the average cost of hospitalization was significantly higher in Endobutton group. No significant differences were found between two groups in outcome of radiographic measurement. The X rays of 36 patients showed well healing of fracture, normal mortise and no distal tibiofibular syndesmosis separation. AOFAS score at the final follow up in group A was (87.50±8.67) scores, 18 cases got excellent result, 4 cases were good, and 4 cases were fair. AOFAS score at the final follow up in group B was (86.23±7.42) scores, 7 cases obtained excellent result, 4 cases were good and 1 case was fair; AOFAS score between two groups were no significant difference (P>0.05). CONCLUSIONS: Endobutton plate cable system is a dynamic capital equipment in treating the tibiofibular syndesmosis separation, it has a similar outcome compared with the screw, but without screw fractured and do not regular remove after operation. The patients could take the functional exercises earlier.

[Comparison of different diameter hollow screw for the treatment of femoral neck fractures].

OBJECTIVE: To evaluate and compare the outcome of two kinds of diameter hollow screws for the treatment of femoral neck fractures. METHODS: From June 2008 to June 2013, 117 patients with femoral neck fractures were treated by closed reduction and hollow screws fixation. Among them,48 patients were fixed by 6.5 mm screw including 30 males and 18 females with an average age of (45.61 ± 11.99) years old ranging from 19 to 60 years old, involving 17 cases in Garden I/II and 31 cases in Garden III/IV; 69 patients were fixed by 8.0 mm screw including 40 males and 29 females with an average age of (45.17 ± 9.95) years old ranging from 18 to 60 years old, involving 31 cases in Garden I/II and 38 cases in Garden III/IV. The general information, operative time, hospital stay time, reduction quality, diameter of femoral head and neck, fracture healing time, the rate of fracture healing, postoperative complications were recorded and evaluated. Harris scoring was used to evaluate the hip joint function. RESULTS: All patients were followed up for 19.6 months (18 to 24 months). The difference of operative time, duration of hospitalization, quality of reduction were not statistically significant (P > 0.05). There was no difference between two groups about the average diameter of the femoral head and neck, the fracture healing time, the rate of healing and the postoperative complications (P > 0.05). There were no difference between two groups about Harris scale. There were significant difference between Garden III/IV and I /II (P > 0.05). CONCLUSION: Closed reduction and internal fixation with hollow screw in treating the young adult patients with femoral neck fracture is the first choice, both different diameters hollow screws could meet the requirements of fixation of femoral neck fracture, and not affect on fracture healing time and postoperative complications.

[Biomechanical comparison of Evans procedure and Chrisman-Snook technique for the treatment of II degree lateral collateral ligament of ankle joint].

OBJECTIVE: To measure the stability of Evans procedure and Chrisman-Snook technique in the treatment of II degree lateral collateral ligament of ankle joint, and provide basis for treatment and prognosis. METHODS: From July 2008 to June 2009,18 frozen corpes were collected, including 10 males and 8 females, with an average age of fresh 39.3 +/- 11.2 years. The frozen corpes were randomly divided into three group, including normal controls(group A), Evans procedure (group B) and Chrisman-Snook technique ( group C), 6 specimens in each group. Anterior talofibular ligament and calcaneofibular ligament were cut off to cause II degree lateral collateral ligament in group B and C. Evans procedure or Chrisman-Snook technique were applied to restore lateral collateral ligament, and measure biomechnics. The displacement of tibiotalar joint and subtalar joint were observed. RESULTS: (1) The lateral stress results of tibiotalar joint showed the displacement by Evans procedure (group B) was greater than other groups (P < 0.0001). There were no significant differences between group A and C (P > 0.05). (2) The lateral stress results of subtalar joint showed the displacement by Evans procedure (group B) was greater than other groups (P< 0.0001). There were no significant differences between group A and C (P > 0.05). CONCLUSION: Ankle instability is caused by ankle joint lateral collateral ligament injury. Chrisman-Snook technique is better than Evans procedure in stability on the early stage of ankle joint restoration, and conform to principle of biomechanics.