A hybrid neural network approach to bilevel programming problems

[[incitationindex]]SCI[[booktype]]紙本[[booktype]]電子

A review of Hopfield neural networks for solving mathematical programming problems

The Hopfield neural network (HNN) is one major neural network (NN) for solving optimization or mathematical programming (MP) problems. The major advantage of HNN is in its structure can be realized on an electronic circuit, possibly on a VLSI (very large-scale integration) circuit, for an on-line solver with a parallel-distributed process. The structure of HNN utilizes three common methods, penalty functions, Lagrange multipliers, and primal and dual methods to construct an energy function. When the function reaches a steady state, an approximate solution of the problem is obtained. Under the classes of these methods, we further organize HNNs by three types of MP problems: linear, non-linear, and mixed-integer. The essentials of each method are also discussed in details. Some remarks for utilizing HNN and difficulties are then addressed for the benefit of successive investigations. Finally, conclusions are drawn and directions for future study are provided.Hopfield neural networks Energy function Mathematical programming penalty function Lagrange multiplier Primal and dual functions

LncRNAs in TGF-β-Driven Tissue Fibrosis

Transforming growth factor-β (TGF-β) is a crucial mediator in tissue fibrosis that promotes accumulation of extracellular matrix (ECM), myofibroblasts to epithelial–mesenchymal transition (EMT), endothelial-mesenchymal transition (EndoMT), and apoptosis via canonical and noncanonical signaling pathways. In the past decades, a number of microRNAs have been reported to participate in TGF-β-mediated tissue scarring; however, the roles of long noncoding RNAs (lncRNAs) in fibrogenesis remain largely unknown. Recently, emerging evidence has shown that lncRNAs are involved in the development of different diseases, including cancer, autoimmune diseases, cardiovascular diseases, and fibrotic diseases. In this review, we summarize the current updates of lncRNAs in TGF-β1-driven tissue fibrosis and discuss their therapeutic potential for the treatment of chronic fibrotic diseases

TGF-β1 signaling in kidney disease: From Smads to long non-coding RNAs

Transforming growth factor-β1 (TGF-β1) has an essential role in the development of kidney diseases. However, targeting TGF-β1 is not a good strategy for fibrotic diseases due to its multifunctional characteristic in physiology. A precise therapeutic target maybe identified by further resolving the underlying TGF-β1 driven mechanisms in renal inflammation and fibrosis. Smad signaling is uncovered as a key pathway of TGF-β1-mediated renal injury, where Smad3 is hyper-activated but Smad7 is suppressed. Mechanistic studies revealed that TGF-β1/Smad3 is capable of promoting renal inflammation and fibrosis via regulating non-coding RNAs. More importantly, involvement of disease- and tissue-specific TGF-β1-dependent long non-coding RNAs (lncRNA) have been recently recognized in a number of kidney diseases. In this review, current understanding of TGF-β1 driven lncRNAs in the pathogenesis of kidney injury, diabetic nephropathy and renal cell carcinoma will be intensively discussed

Calcium content of different compositions of gallstones and pathogenesis of calcium carbonate gallstones

Our aim was to investigate the calcium content of different gallstone compositions and the pathogenic mechanisms of calcium carbonate gallstones. Between August 2001 and July 2007, gallstones from 481 patients, including 68 calcium carbonate gallstones, were analyzed for total calcium content. Gallbladder bile samples from 33 cases and six controls were analyzed for pH, carbonate anion level, free-ionized calcium concentration and saturation index for calcium carbonate. Total calcium content averaged 75.6 %, 11.8 %, and 4.2 % for calcium carbonate, calcium bilirubinate and cholesterol gallstones. In 29.4 % of patients, chronic and/or intermittent cystic duct obstructions were caused by polypoid lesions in the neck region and 70.6 % were caused by stones. A total of 82 % of patients had chronic low-grade inflammation of the gallbladder wall and 18.0 % had acute inflammatory exacerbations. In the bile, we found the mean pH, mean carbonate anion, free-ionized calcium concentrations, and mean saturation index for calcium carbonate to be elevated in comparison to controls. From our study, we found chronic and/or intermittent cystic duct obstructions and low-grade GB wall inflammation lead to GB epithelium hydrogen secretion dysfunction. Increased calcium ion efflux into the GB lumen combined with increased carbonate anion presence increases SI_CaCO3 from 1 to 22.4. Thus, in an alkaline milieu with pH 7.8, calcium carbonate begins to aggregate and precipitate

Calcium content of different compositions of gallstones and pathogenesis of calcium carbonate gallstones

Background/Objectives: Our aim was to investigate the calcium content of different gallstone compositions and the pathogenic mechanisms of calcium carbonate gallstones. Methods: Between August 2001 and July 2007, gallstones from 481 patients, including 68 calcium carbonate gallstones, were analyzed for total calcium content. Gallbladder bile samples from 33 cases and six controls were analyzed for pH, carbonate anion level, free-ionized calcium concentration and saturation index for calcium carbonate. Results: Total calcium content averaged 75.6 %, 11.8 %, and 4.2 % for calcium carbonate, calcium bilirubinate and cholesterol gallstones. In 29.4 % of patients, chronic and/or intermittent cystic duct obstructions were caused by polypoid lesions in the neck region and 70.6 % were caused by stones. A total of 82 % of patients had chronic low-grade inflammation of the gallbladder wall and 18.0 % had acute inflammatory exacerbations. In the bile, we found the mean pH, mean carbonate anion, free-ionized calcium concentrations, and mean saturation index for calcium carbonate to be elevated in comparison to controls. Conclusion: From our study, we found chronic and/or intermittent cystic duct obstructions and low-grade GB wall inflammation lead to GB epithelium hydrogen secretion dysfunction. Increased calcium ion efflux into the GB lumen combined with increased carbonate anion presence increases SI_CaCO3 from 1 to 22.4. Thus, in an alkaline milieu with pH 7.8, calcium carbonate begins to aggregate and precipitate

MULTIPLE STRUCTURE ALIGNMENT BASED ON GEOMETRICAL CORRELATION OF SECONDARY STRUCTURE ELEMENTS

Protein structure alignment facilitates the analysis of protein functionality. Through superimposed structures and the comparison of variant components, common or specific features of proteins can be identified. Several known protein families exhibit analogous tertiary structures but divergent primary sequences. These proteins in the same structural class are unable to be aligned by sequence-based methods. The main objective of the present study was to develop an efficient and effective algorithm for multiple structure alignment based on geometrical correlation of secondary structures, which are conserved in evolutionary heritage. The method utilizes mutual correlation analysis of secondary structure elements (SSEs) and selects representative segments as the key anchors for structural alignment. The system exploits a fast vector transformation technique to represent SSEs in vector format, and the mutual geometrical relationship among vectors is projected onto an angle-distance map. Through a scoring function and filtering mechanisms, the best candidates of vectors are selected, and an effective constrained multiple structural alignment module is performed. The correctness of the algorithm was verified by the multiple structure alignment of proteins in the SCOP database. Several protein sets with low sequence identities were aligned, and the results were compared with those obtained by three well-known structural alignment approaches. The results show that the proposed method is able to perform multiple structural alignments effectively and to obtain satisfactory results, especially for proteins possessing low sequence identity.Multiple structure alignment, secondary structure, angle distance map, geometrical correlation