\u3ci\u3eIn-silico\u3c/i\u3e prediction of blood-secretory human proteins using a ranking algorithm

Background: Computational identification of blood-secretory proteins, especially proteins with differentially expressed genes in diseased tissues, can provide highly useful information in linking transcriptomic data to proteomic studies for targeted disease biomarker discovery in serum. Results: A new algorithm for prediction of blood-secretory proteins is presented using an information-retrieval technique, called manifold ranking. On a dataset containing 305 known blood-secretory human proteins and a large number of other proteins that are either not blood-secretory or unknown, the new method performs better than the previous published method, measured in terms of the area under the recall-precision curve (AUC). A key advantage of the presented method is that it does not explicitly require a negative training set, which could often be noisy or difficult to derive for most biological problems, hence making our method more applicable than classification-based data mining methods in general biological studies. Conclusion: We believe that our program will prove to be very useful to biomedical researchers who are interested in finding serum markers, especially when they have candidate proteins derived through transcriptomic or proteomic analyses of diseased tissues. A computer program is developed for prediction of blood-secretory proteins based on manifold ranking, which is accessible at our website http://csbl.bmb.uga.edu/publications/materials/qiliu/ blood_secretory_protein.html

In-silico prediction of blood-secretory human proteins using a ranking algorithm

<p>Abstract</p> <p>Background</p> <p>Computational identification of blood-secretory proteins, especially proteins with differentially expressed genes in diseased tissues, can provide highly useful information in linking transcriptomic data to proteomic studies for targeted disease biomarker discovery in serum.</p> <p>Results</p> <p>A new algorithm for prediction of blood-secretory proteins is presented using an information-retrieval technique, called <it>manifold ranking</it>. On a dataset containing 305 known blood-secretory human proteins and a large number of other proteins that are either not blood-secretory or unknown, the new method performs better than the previous published method, measured in terms of the area under the recall-precision curve (AUC). A key advantage of the presented method is that it does not explicitly require a negative training set, which could often be noisy or difficult to derive for most biological problems, hence making our method more applicable than classification-based data mining methods in general biological studies.</p> <p>Conclusion</p> <p>We believe that our program will prove to be very useful to biomedical researchers who are interested in finding serum markers, especially when they have candidate proteins derived through transcriptomic or proteomic analyses of diseased tissues. A computer program is developed for prediction of blood-secretory proteins based on manifold ranking, which is accessible at our website <url>http://csbl.bmb.uga.edu/publications/materials/qiliu/blood_secretory_protein.html</url>.</p

Hard rock deep hole cutting blasting technology in vertical shaft freezing bedrock section construction

Using the traditional cutting blasting technology in vertical shaft construction has some features, e.g. slows driving speed, gangue with large volume and throwing high. Moreover, large explosive charge initiation has a serious influence on freezing pipes and freezing wall. In this study, the periphery hole charge and charge structure was optimized, and the blasting model of the bedrock vertical shaft section was established by using the ANSYS/LS-DYNA numerical simulation software. In addition, stress concentration of the large diameter empty hole and its influence of blasting efficiency in blasting were analyzed. The field experiment was conducted to verify the blasting results. The results show that using large diameter empty hole blasting technology in vertical shaft construction of frozen hard rock section can significantly improve the speed of vertical shaft construction, obtain the excellent blasting effect and guarantee the safety of freezing pipes and freezing wall

Data based reconstruction of complex geospatial networks, nodal positioning, and detection of hidden node

Funding This work was supported by ARO under grant no. W911NF-14-1-0504.Peer reviewedPublisher PD