Mining for the antibody-antigen interacting associations that predict the B cell epitopes

Background. Predicting B-cell epitopes is very important for designing vaccines and drugs to fight against the infectious agents. However, due to the high complexity of this problem, previous prediction methods that focus on linear and conformational epitope prediction are both unsatisfactory. In addition, antigen interacting with antibody is context dependent and the coarse binary classification of antigen residues into epitope and non-epitope without the corresponding antibody may not reveal the biological reality. Therefore, we take a novel way to identify epitopes by using associations between antibodies and antigens. Results. Given a pair of antibody-antigen sequences, the epitope residues can be identified by two types of associations: paratope-epitope interacting biclique and cooccurrent pattern of interacting residue pairs. As the association itself does not include the neighborhood information on the primary sequence, residues' cooperativity and relative composition are then used to enhance our method. Evaluation carried out on a benchmark data set shows that the proposed method produces very good performance in terms of accuracy. After compared with other two structure-based B-cell epitope prediction methods, results show that the proposed method is competitive to, sometimes even better than, the structure-based methods which have much smaller applicability scope. Conclusions. The proposed method leads to a new way of identifying B-cell epitopes. Besides, this antibody-specified epitope prediction can provide more precise and helpful information for wet-lab experiments. © 2010 Li and Zhao; licensee BioMed Central Ltd

Differentially Private Stochastic Convex Optimization in (Non)-Euclidean Space Revisited

In this paper, we revisit the problem of Differentially Private Stochastic Convex Optimization (DP-SCO) in Euclidean and general $\ell_p^d$ spaces. Specifically, we focus on three settings that are still far from well understood: (1) DP-SCO over a constrained and bounded (convex) set in Euclidean space; (2) unconstrained DP-SCO in $\ell_p^d$ space; (3) DP-SCO with heavy-tailed data over a constrained and bounded set in $\ell_p^d$ space. For problem (1), for both convex and strongly convex loss functions, we propose methods whose outputs could achieve (expected) excess population risks that are only dependent on the Gaussian width of the constraint set rather than the dimension of the space. Moreover, we also show the bound for strongly convex functions is optimal up to a logarithmic factor. For problems (2) and (3), we propose several novel algorithms and provide the first theoretical results for both cases when $1<p<2$ and $2\leq p\leq \infty$

FINITE ELEMENT ANALYSIS OF MECHANICAL PROPERTIES OF SPECIMEN WITH UHPC AND STUD CONNECTOR

UHPC is different from ordinary concrete for mechanical properties. To study the stress state of stud connector when UHPC is used to strengthen RC beam and its influence on bearing capacity of the strengthened beam, in this paper, ABAQUS was adopted first to simulate the push-out test of  stud to verify  accuracy of the finite element model. The nonlinearity of materials and contact conditions was considered in the model, and then three parameters including concrete strength, stud length and stud diameter were studied. Results showed the finite element model established by surface to surface contact method was possible to simulate the force and failure of the stud connector. UHPC could improve the  bearing capacity of the stud specimens obviously, and the length of stud had little effect on bearing capacity of stud while failure of the stud may occur if length of the stud was too small. The increase of stud diameter could improve bearing capacity of elastic working stage

Treatment of Nonalcoholic Fatty Liver Disease with Total Alkaloids in Rubus aleaefolius Poir

Total alkaloids in Rubus aleaefolius Poir (TARAP) is a folk medicinal herb that has been used clinically in China to treat nonalcoholic fatty liver disease (NAFLD) for many years. However, the mechanism of its anti-NAFLD effect is largely unknown. In this study, we developed a NAFLD rat model by supplying a modified high-fat diet (mHFD) ad libitum for 8 weeks and evaluated the therapeutic effect of TARAP in NAFLD rats as well as the underlying molecular mechanism. We found that TARAP could reduce the serum triglycerides (TG), total cholesterol (TC), and low-density lipoprotein (LDL-C) levels and increase the serum high-density lipoprotein (HDL-C) level in NAFLD rats. In addition, TARAP treatment reduced expression of fatty acid synthetase (FAS), and acetyl-CoA carboxylase (ACC) and upregulated the expression of carnitine palmitoyltransferase (CPT). Our results suggest that regulation of lipid metabolism may be a mechanism by which TARAP treats NAFLD

3D dendritic-Fe2O3@C nanoparticles as an anode material for lithium ion batteries

3D dendritic Fe2O3 nanoparticles wrapped with carbon (denoted as 3DD-Fe2O3@C hereafter) were synthesized.</p

Polar domain structural evolution under electric field and temperature in the (Bi0.5 Na0.5)TiO3 -0.06BaTiO3 piezoceramics

Lead‐free bismuth sodium titanate and related compounds are of great interest as promising candidates for piezoelectric applications. However, the full understanding of this family of materials is still a challenge partly because of their structural complexity and different behaviors with or without the application of an external electric field. Here, piezoresponse force microscopy is used to gain insight into the mesoscopic‐scale domain structure of the morphotropic phase boundary (MPB) composition of (1‐x)Bi0.5Na0.5TiO3‐xBaTiO3 solid solution at x = 0.06 (abbreviated as BNT‐6BT). The evolution of the domains with the changes of the electric field and temperature has been thoroughly examined in conjunction with the crystal structure analysis and dielectric studies. It is found that ferroelectric domains with size of hundreds of nanometers are embedded in a relaxor state without visible domains on a mesoscopic scale, which are considered to contribute to the tetragonal and cubic phases in the material, respectively. Temperature‐independent domain configuration is observed in the unpoled sample from room temperature to 200°C. While, temperature‐dependent domain configuration is observed in the poled sample. The homogenously poled state breaks into the mixed domain configuration containing polydomain structure and invisible state around the so‐called depoling temperature. The structural changes on different length scales are also discussed. This work provides an in‐depth understanding of the structural and domain changes under an electric field and the temperature‐dependent domain evolution in both unpoled and poled states in the BNT‐BT solid solution of the MPB composition

Serum proteomic, peptidomic and metabolomic profiles in myasthenia gravis patients during treatment with Qiangji Jianli Fang

BACKGROUND: Qiangji Jianli Fang (QJF) has been used for treatment of myasthenia gravis (MG) in China. However, our understanding of the effects of QJF against MG at the molecular level is limited. This study aims to investigate the effects of QJF treatment of MG patients on the protein, peptide and metabolite levels in serum. METHODS: High-throughput proteomic, peptidomic and metabolomic techniques were applied to investigate serum samples from 21 healthy individuals and 47 MG patients before and after QJF treatment via two-dimensional gel electrophoresis, matrix-assisted laser desorption/ionization time of flight mass spectrometry and liquid chromatography Fourier transform mass spectrometry, respectively. RESULTS: After QJF treatment, the expression levels of peptides m/z 1865.019, 2021.128 and 1211.668 of complement C3f increased (P = 0.004, P = 0.001 and P = 0.043, respectively), while that of peptide m/z 1739.931 of component C4b decreased (P = 0.043), in the serum of MG patients. The levels of γ-aminobutyric acid (P = 0.000) and coenzyme Q4 (P = 0.000) resumed their normal states. CONCLUSION: QJF could inhibit the activity of the complement system and restore the normal levels of metabolites

THE HERBAL MIXTURE XIAO-CHAI-HU TANG (XCHT) INDUCES APOPTOSIS OF HUMAN HEPATOCELLULAR CARCINOMA HUH7 CELLS IN VITRO AND IN VIVO

Background: Xiao-Chai-Hu Tang (XCHT) is an extract of seven herbs with anticancer properties, but its mechanism of action is unknown. In this study, we evaluated XCHT-treated hepatocellular carcinoma (HCC) for anti-proliferative and pro-apoptotic effects. Materials and Methods: Using a hepatic cancer xenograft model, we investigated the in vivo efficacy of XCHT against tumor growth by evaluating tumor volume and weight, as well as measuring apoptosis and cellular proliferation within the tumor. To study the effects of XCHT in vitro, we measured the cell viability of XCHT-treated Huh7 cells, as well as colony formation and apoptosis. To identify a potential mechanism of action, the gene and protein expression levels of Bax, Bcl-2, CDK4 and cyclin-D1 were measured in XCHT-treated Huh7 cells. Results: We found that XCHT reduced tumor size and weight, as well as significantly decreased cell viability both in vivo and in vitro. XCHT suppressed the expression of the proliferation marker Ki-67 in HCC tissues and inhibited Huh7 colony formation. XCHT induced apoptosis in HCC tumor tissues and in Huh7 cells. Finally, XCHT altered the expression of Bax, Bcl-2, CDK4 and cyclin-D1, which halted cell proliferation and promoted apoptosis. Conclusion: Our data suggest that XCHT enhances expression of pro-apoptotic pathways, resulting in potent anticancer activity

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse

Diversified histone modifications (HMs) are essential epigenetic features. They play important roles in fundamental biological processes including transcription, DNA repair and DNA replication. Chromatin regulators (CRs), which are indispensable in epigenetics, can mediate HMs to adjust chromatin structures and functions. With the development of ChIP-Seq technology, there is an opportunity to study CR and HM profiles at the whole-genome scale. However, no specific resource for the integration of CR ChIP-Seq data or CR-HM ChIP-Seq linkage pairs is currently available. Therefore, we constructed the CR Cistrome database, available online at http://compbio.tongji.edu.cn/cr and http://cistrome.org/cr/, to further elucidate CR functions and CR-HM linkages. Within this database, we collected all publicly available ChIP-Seq data on CRs in human and mouse and categorized the data into four cohorts: the reader, writer, eraser and remodeler cohorts, together with curated introductions and ChIP-Seq data analysis results. For the HM readers, writers and erasers, we provided further ChIP-Seq analysis data for the targeted HMs and schematized the relationships between them. We believe CR Cistrome is a valuable resource for the epigenetics community