Identification of Protein Pupylation Sites Using Bi-Profile Bayes Feature Extraction and Ensemble Learning

Pupylation, one of the most important posttranslational modifications of proteins, typically takes place when prokaryotic ubiquitin-like protein (Pup) is attached to specific lysine residues on a target protein. Identification of pupylation substrates and their corresponding sites will facilitate the understanding of the molecular mechanism of pupylation. Comparing with the labor-intensive and time-consuming experiment approaches, computational prediction of pupylation sites is much desirable for their convenience and fast speed. In this study, a new bioinformatics tool named EnsemblePup was developed that used an ensemble of support vector machine classifiers to predict pupylation sites. The highlight of EnsemblePup was to utilize the Bi-profile Bayes feature extraction as the encoding scheme. The performance of EnsemblePup was measured with a sensitivity of 79.49%, a specificity of 82.35%, an accuracy of 85.43%, and a Matthews correlation coefficient of 0.617 using the 5-fold cross validation on the training dataset. When compared with other existing methods on a benchmark dataset, the EnsemblePup provided better predictive performance, with a sensitivity of 80.00%, a specificity of 83.33%, an accuracy of 82.00%, and a Matthews correlation coefficient of 0.629. The experimental results suggested that EnsemblePup presented here might be useful to identify and annotate potential pupylation sites in proteins of interest. A web server for predicting pupylation sites was developed

Therapeutic Applications of Herbal Medicines for Cancer Patients

Medicinal herbs and their derivative phytocompounds are being increasingly recognized as useful complementary treatments for cancer. A large volume of clinical studies have reported the beneficial effects of herbal medicines on the survival, immune modulation, and quality of life (QOL) of cancer patients, when these herbal medicines are used in combination with conventional therapeutics. Here, we briefly review some examples of clinical studies that investigated the use of herbal medicines for various cancers and the development of randomized controlled trials (RCTs) in this emerging research area. In addition, we also report recent studies on the biochemical and cellular mechanisms of herbal medicines in specific tumor microenvironments and the potential application of specific phytochemicals in cell-based cancer vaccine systems. This review should provide useful technological support for evidence-based application of herbal medicines in cancer therapy

An Improved Multidimensional MPA Procedure for Bidirectional Earthquake Excitations

Presently, the modal pushover analysis procedure is extended to multidimensional analysis of structures subjected to multidimensional earthquake excitations. an improved multidimensional modal pushover analysis (IMMPA) method is presented in the paper in order to estimate the response demands of structures subjected to bidirectional earthquake excitations, in which the unidirectional earthquake excitation applied on equivalent SDOF system is replaced by the direct superposition of two components earthquake excitations, and independent analysis in each direction is not required and the application of simplified superposition formulas is avoided. The strength reduction factor spectra based on superposition of earthquake excitations are discussed and compared with the traditional strength reduction factor spectra. The step-by-step procedure is proposed to estimate seismic demands of structures. Two examples are implemented to verify the accuracy of the method, and the results of the examples show that (1) the IMMPA method can be used to estimate the responses of structure subjected to bidirectional earthquake excitations. (2) Along with increase of peak of earthquake acceleration, structural response deviation estimated with the IMMPA method may also increase. (3) Along with increase of the number of total floors of structures, structural response deviation estimated with the IMMPA method may also increase

The latest spreading periods of the south china sea: new constraints from macrostructure analysis of IODP expedition 349 cores and geophysical data

Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research-Solid Earth 124 (2019): 9980– 9998, doi:10.1029/2019JB017584.Macrostructures preserved in deformed rocks are essential for the understanding of their evolution, especially when the deformation is weak and hard to discriminate in regional scale or purely through geophysical data. In order to resolve the inconsistency between NS trending fracture zones and NE oriented spreading fabrics of the South China Sea during the latest spreading stage, we analyzed macrostructures identifiable from the basalt and consolidated sediment samples of the Integrated Ocean Drilling Program (IODP) Sites U1431 and U1433. These two sites are close to the East and Southwest relict spreading ridges and provide critical information on the latest spreading stages. The structures in the basalt of both sites suggest two dominant orientations of NS and NE. At U1431, sediments show mainly WNW trending slickensides, different from that of basalt. At U1433, no structures were found in postspreading sediment. Thus, NE and NS trending structures in basalt are most possibly formed by seafloor spreading. Crosscutting relationship suggests that NE trending structures formed first, followed by NS and finally WNW trending structures. These observations are consistent with geophysical features. Magnetic anomalies and ocean bottom seismometer velocity suggest that the latest relict ridge of the East Subbasin coincides with the EW trending seamount chain. Located between the relict ridges of East and Southwest Subbasins, NS trending Zhongnan‐Liyue Fracture Zone had acted as the latest transform fault. Based on the above evidences, we proposed that the South China Sea may have experienced a short period of NS oriented spreading after earlier SE spreading. These results resolve the previous inconsistencies.We appreciate Anne Replumaz and other anonymous reviewers for the constructive suggestions, which improve this paper to a great extent. This research was supported by Guangdong NSF research team project (2017A030312002), K. C. Wong Education Foundation (GJTD‐2018‐13), the IODP‐China Foundation, the NSFC Projects (91628301, 41376027, 41576070, 41576068, 41430962, 41674069, 91528302, and 20153410), U.S. National Science Foundation through Grant EAR‐1250444, the Guangdong Province Foundation (41576068), and the Joint Foundation of the Natural Science Foundation of China (NSFC) and Guangdong Province (U1301233). Fucheng Li is thanked for helping with the earthquake epicenter figure for the study area. All the sample photos can be accessed via web address (http://www.iodp.tamu.edu). The archive halves of samples are kept in the Kochi repository. The paleomag data will be published by Xixi Zhao separately. All the other geophysical data have been published; for example, the multichannel seismic could be referenced to Li et al. (2015a), and the gravity data and magnetic anomaly data are from Sandwell et al. (2014) and Ishihara and Kisimoto (1996).2020-02-2

The antigen presentation function of bone marrow-derived mast cells is spatiotemporally restricted to a subset expressing high levels of cell surface FcεRI and MHC II

<p>Abstract</p> <p>Background</p> <p>At present, it is highly controversial whether pure mast cells can serve as antigen presenting cells, and it is not known whether the capacity of antigen presenting function is temporally restricted to a particular subset of differentiated mast cells. Evidence is presented for a novel surface FcεRI^hi, MHC II +, and c-kit + pure mast cell subset, temporally restricted as antigen-presenting cells in the immune axis of T-cell activation.</p> <p>Results</p> <p>Bone marrow-derived mast cells (BMMC) cultured in the presence of IL-3 for three weeks are pure mast cells based on surface expression of lineage-specific marker, c-kit and FcεRI. Herein we present the first demonstration that approximately 98.7% c-kit + and FcεRI expressing BMMC, further depleted of any contaminated professional antigen-presenting cells, are still fully capable of presenting antigens, i.e., OVA protein, OVA peptide, and IgE-TNP-OVA, to OVA peptide-specific T-cell hybridomas. Notably, IgE-dependent antigen presentation is more efficient compared to that resulting from direct antigen uptake. Importantly, we present the novel finding that only surface FcεRI^himast cells, also expressing surface MHC II exhibited antigen-presenting function. In contrast, surface FcεRI^lomast cells without expressing surface MHC II were not capable of antigen presentation. Interestingly, the antigen-presenting function of BMMC was irrevocably lost during the third and fourth week in IL-3 or SCF containing cultures.</p> <p>Conclusions</p> <p>This is the first observation to attribute a spatiotemporally restricted antigen-presenting function to a subset of three-week old pure BMMC expressing both high levels of surface FcεRI and surface MHC II. We propose that mast cells play an important role in immune deviating and/or sustaining the activation of infiltrating CD4 T-cells, and modulating T-cell mediated allergic inflammation via its flexibility to present antigens and antigen-IgE complexes.</p

Analytical Multi-Scale Methodology for Fluidization Systems - Retrospect and Prospect

Understanding the spatio-temporal multi-scale structure of fluidization is a challenging problem. This presentation reviews our 20-year efforts on this subject, showing the roadmap that has gradually evolved from a simple idea to a systematic methodology inclusive of subsidiary, related systems and industrial applications. The strategy of establishing stability conditions through analyses of the compromise between dominant mechanisms is emphasized. The presentation concludes with prospects for further theoretical explorations and industrial applications

Study on Construction Resource Optimization and Uncertain Risk of Urban Sewage Pipe Network

With considering sewage pipe network upgrading projects in the “villages” in cities, the optimization of construction resources and the assessment of delay risks could be achieved. Based on the schedule-cost hypothetical theory, the mathematical model with constraint indicators was established to obtain the expression of optimal resource input, and conclude the method to analyze the schedule uncertainties. The analysis showed that cyclical footage of pipe could be regarded as a relatively fixed value, and the cost can be regarded as a function that depending on the number of working teams. The optimal number of teams and the optimal schedule occurred when the minimum total cost achieved. In the case of insufficient meteorological data, the Monte Carlo simulation method and uncertainty analysis method can be applied to assess the impact of rainfall on the total construction period, correspondingly the probability of such risk could be derived. The calculation showed that the risk of overdue completion varied significantly according to the construction starting time. It was necessary to take rainfall risk into consideration and make corresponding strategies and measures