An Improved Artificial Fish Swarm Algorithm

The purpose of this paper is to improve the performance of the original AFSA algorithm at the optimal accuracy rate and overcome the weakness of the algorithm which is also trapped in the local optimum. To this end, the original AFSA was further improved based on the tabu strategy. Specifically, the reproduction and death were introduced to protect the best individuals and eliminate poor quality fish, so as to increase convergence and accuracy. Through simulation, it is proved that our solution can achieve high accuracy, good global convergence, and strong resistance to local minimum. The findings bring new light on the application of AFSA and provide valuable reference to studies in related fields

A two-dimensional electrophoresis protocol suitable for Medicago truncatula leaf proteome

Medicago truncatula leaves were used as the experimental materials. Total proteins of leaves were extracted by trichloracetic acid (TCA)-acetone method and proteins had a better separation using gel strips, forming an immobilized non-linear 3 to 10 pH gradient focusing 123,000 vhr combined with 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The gels were stained with Coomassie Brilliant Blue G-250 and digitalized gels were analyzed using the PDquest 8.0.1 software. The results indicated that 931 protein dots were detected in the gel. A technology suitable for the M. truncatula leaves protein extraction by TCA/acetone and a protocol for two-dimensional electrophoresis (2-DE) was established, which provides technical support for M. truncatula leaf proteome research.Keywords: Medicago truncatula, proteome, two-dimensional polyacrylamide gel electrophoresis (2-DE), isoelectrofocusing (IEF)African Journal of Biotechnology Vol. 12(3), pp. 233-23

Mutation Status and Immunohistochemical Correlation of KRAS, NRAS, and BRAF in 260 Chinese Colorectal and Gastric Cancers

KRAS, NRAS and BRAF are kinases involved in the RAS-RAF-MAPK signaling pathway and also potential tumor-driven genes. Patients with KRAS/NRAS/BRAF mutations are resistant to anti-EGFR monoclonal antibody therapy. The main purpose of this study is to investigate the mutation status and distribution of KRAS/NRAS/BRAF in Chinese colorectal and gastric cancers, and to explore the histopathological changes and related immunohistochemical marker changes caused by these mutations. The mutation status of KRAS (exons 2, codon 12/13), NRAS (exons 2/3/4, codon 12/13/59/61/117/146) and BRAF (exons 15, codon 600) were detected by amplification refractory mutation system polymerase chain reaction (ARMS-PCR) in 86 colon cancer, 140 rectal cancer and 34 gastric cancer tissues. Then, the frequencies and distribution of KRAS/NRAS/BRAF mutations were described in detail. Furthermore, the relationship between KRAS/NRAS/BRAF mutations and the features of histopathological and related immunohistochemical markers were analyzed. The results showed that KRAS/NRAS/BRAF mutation rates in colon cancer were 44.2, 1.2, and 3.5%; in rectal cancer were 37.1, 4.3, and 0.7%; in gastric cancer were none, none and 2.9%. The mutation rate of KRAS in female (48.8%) is significantly higher than that of male (27.8%), and the mutation rate increased with the higher degree of differentiation. Additionally, the mutation rate of BRAF detected by ARMS-PCR (1.77%) was significantly lower than that by immunohistochemistry (4.11%). It also showed that the KRAS/NRAS/BRAF mutation status had a certain relationship with the expression of some immunohistochemical markers. This study provides more data support for clinical research on KRAS/NRAS/BRAF mutation in CRCs or gastric cancers

NKX2-3 Transcriptional Regulation of Endothelin-1 and VEGF Signaling in Human Intestinal Microvascular Endothelial Cells

BACKGROUND: NKX2-3 is associated with inflammatory bowel disease (IBD). NKX2-3 is expressed in microvascular endothelial cells and the muscularis mucosa of the gastrointestinal tract. Human intestinal microvascular endothelial cells (HIMECs) are actively involved in the pathogenesis of IBD and IBD-associated microvascular dysfunction. To understand the cellular function of NKX2-3 and its potential role underlying IBD pathogenesis, we investigated the genes regulated by NKX2-3 in HIMEC using cDNA microarray. METHODOLOGY/PRINCIPAL FINDINGS: NKX2-3 expression was suppressed by shRNA in two HIMEC lines and gene expression was profiled by cDNA microarray. Pathway Analysis was used to identify gene networks according to biological functions and associated pathways. Validation of microarray and genes expression in intestinal tissues was assessed by RT-PCR. NKX2-3 regulated genes are involved in immune and inflammatory response, cell proliferation and growth, metabolic process, and angiogenesis. Several inflammation and angiogenesis related signaling pathways that play important roles in IBD were regulated by NKX2-3, including endothelin-1 and VEGF-PI3K/AKT-eNOS. Expression levels of NKX2-3, VEGFA, PI3K, AKT, and eNOS are increased in intestinal tissues from IBD patients and expression levels of EDN1 are decreased in intestinal tissues from IBD patients. These results demonstrated the important roles of NKX2-3, VEGF, PI3K, AKT, eNOS, and EDN1 in IBD pathogenesis. Correlation analysis showed a positive correlation between mRNA expression of NKX2-3 and VEGFA and a negative correlation between mRNA expression of NKX2-3 and EDN1 in intestinal tissues from IBD patients. CONCLUSION/RELEVANCE: NKX2-3 may play an important role in IBD pathogenesis by regulating endothelin-1 and VEGF signaling in HIMECs

A protocol for anti-CD4 IgG antibody purification using plasma samples from people with HIV and antibody-mediated cytotoxicity

Background. Up to 20% of people with HIV (PWH) fail to recover their CD4+ T cell counts to levels similar to healthy controls after suppressive antiretroviral therapy (ART). Immune non-responders (INRs) are PWH on suppressive ART with CD4+ T cell counts lower than 350 cells/mL, whereas their CD8+ T cell counts are higher than healthy controls. We are the first group to report that increased anti-CD4 autoantibody IgGs in INRs are responsible for blunted CD4+ T cell reconstitution in PWH with ART and viral suppression through anti-CD4 IgG-induced antibody-mediated cytotoxicity (ADCC) against CD4+ T cells in vitro. Notably, anti-CD4 IgG-mediated poor CD4+ T cell recovery from suppressive ART is the only mechanism targeting CD4+ T cells, specifically. Results. We provide a detailed one-by-one step protocol from antigen-specific antibody isolation using plasma samples, to ADCC assay. Conclusions. To promote reproducible research, a detailed protocol for isolating anti-CD4 IgG autoantibodies from plasma samples of PWH and evaluating ADCC effects is reported here. • Antigen-specific antibody isolation using human plasma samples • Antibody-mediated cytotoxicity (ADCC

Chin. J. Catal.

Perovskite nanocomposite catalysts LaXCoO3 (X = Mg, Ca, Sr, or Ce; n(La):n(X) = 3:2) have been prepared by a citric acid-complexing method and used for steam reforming of ethanol (SRE), leading to hydrogen generation. The samples were characterized by X-ray diffraction, infrared spectroscopy, scanning electron microscopy, X-ray photoelectron spectroscopy, N-2 adsorption-desorption, and H-2 temperature-programmed reduction. The effects of elemental substitution in the LaCoO3 perovskite were studied, and the catalytic performance and primary stability of the hydrogen production from SRE were investigated. In the highly substituted samples, only the Ce-doped sample was isolated as the pure perovskite phase. The presence of a Co3O4 phase in the Ca-doped or Sr-doped samples was beneficial for the reduction of the active Co component, while Sr-doped or Ce-doped samples showed good activity and stability. The sample incorporating Sr demonstrated better catalytic performance than those of other samples. (C) 2014, Dalian Institute of Chemical Physics, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.Perovskite nanocomposite catalysts LaXCoO3 (X = Mg, Ca, Sr, or Ce; n(La):n(X) = 3:2) have been prepared by a citric acid-complexing method and used for steam reforming of ethanol (SRE), leading to hydrogen generation. The samples were characterized by X-ray diffraction, infrared spectroscopy, scanning electron microscopy, X-ray photoelectron spectroscopy, N-2 adsorption-desorption, and H-2 temperature-programmed reduction. The effects of elemental substitution in the LaCoO3 perovskite were studied, and the catalytic performance and primary stability of the hydrogen production from SRE were investigated. In the highly substituted samples, only the Ce-doped sample was isolated as the pure perovskite phase. The presence of a Co3O4 phase in the Ca-doped or Sr-doped samples was beneficial for the reduction of the active Co component, while Sr-doped or Ce-doped samples showed good activity and stability. The sample incorporating Sr demonstrated better catalytic performance than those of other samples. (C) 2014, Dalian Institute of Chemical Physics, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved

Mutation of Cellulose Synthase Gene Improves the Nutritive Value of Rice Straw

Rice straw is an important roughage resource for ruminants in many rice-producing countries. In this study, a rice brittle mutant (BM, mutation in OsCesA4, encoding cellulose synthase) and its wild type (WT) were employed to investigate the effects of a cellulose synthase gene mutation on rice straw morphological fractions, chemical composition, stem histological structure and in situ digestibility. The morphological fractions investigation showed that BM had a higher leaf sheath proportion (43.70% vs 38.21%, p0.05) was detected in neutral detergent fiber (NDFom) and ADL contents for both strains. Histological structure observation indicated that BM stems had fewer sclerenchyma cells and a thinner sclerenchyma cell wall than WT. The results of in situ digestion showed that BM had higher DM, NDFom, cellulose and hemicellulose disappearance at 24 or 48 h of incubation (p<0.05). The effective digestibility of BM rice straw DM and NDFom was greater than that of WT (31.4% vs 26.7% for DM, 29.1% vs 24.3% for NDFom, p<0.05), but the rate of digestion of the slowly digested fraction of BM rice straw DM and NDF was decreased. These results indicated that the mutation in the cellulose synthase gene could improve the nutritive value of rice straw for ruminants

An Adaptive Fuzzy Chicken Swarm Optimization Algorithm

The chicken swarm optimization (CSO) algorithm is a new swarm intelligence optimization (SIO) algorithm and has been widely used in many engineering domains. However, there are two apparent problems with the CSO algorithm, i.e., slow convergence speed and difficult to achieve global optimal solutions. Aiming at attacking these two problems of CSO, in this paper, we propose an adaptive fuzzy chicken swarm optimization (FCSO) algorithm. The proposed FCSO uses the fuzzy system to adaptively adjust the number of chickens and random factors of the CSO algorithm and achieves an optimal balance of exploitation and exploration capabilities of the algorithm. We integrate the cosine function into the FCSO to compute the position update of roosters and improve the convergence speed. We compare the FCSO with eight commonly used, state-of-the-art SIO algorithms in terms of performance in both low- and high-dimensional spaces. We also verify the FCSO algorithm with the nonparametric statistical Friedman test. The results of the experiments on the 30 black-box optimization benchmarking (BBOB) functions demonstrate that our FCSO outperforms the other SIO algorithms in both convergence speed and optimization accuracy. In order to further test the applicability of the FCSO algorithm, we apply it to four typical engineering problems with constraints on the optimization processes. The results show that the FCSO achieves better optimization accuracy over the standard CSO algorithm