Study of L0-norm constraint normalized subband adaptive filtering algorithm

Limited by fixed step-size and sparsity penalty factor, the conventional sparsity-aware normalized subband adaptive filtering (NSAF) type algorithms suffer from trade-off requirements of high filtering accurateness and quicker convergence behavior. To deal with this problem, this paper proposes variable step-size L0-norm constraint NSAF algorithms (VSS-L0-NSAFs) for sparse system identification. We first analyze mean-square-deviation (MSD) statistics behavior of the L0-NSAF algorithm innovatively in according to a novel recursion form and arrive at corresponding expressions for the cases that background noise variance is available and unavailable, where correlation degree of system input is indicated by scaling parameter r. Based on derivations, we develop an effective variable step-size scheme through minimizing the upper bounds of the MSD under some reasonable assumptions and lemma. To realize performance improvement, an effective reset strategy is incorporated into presented algorithms to tackle with non-stationary situations. Finally, numerical simulations corroborate that the proposed algorithms achieve better performance in terms of estimation accurateness and tracking capability in comparison with existing related algorithms in sparse system identification and adaptive echo cancellation circumstances.Comment: 15 pages,15 figure

Heterologous expression, biochemical characterization, and overproduction of alkaline α-amylase from Bacillus alcalophilus in Bacillus subtilis

<p>Abstract</p> <p>Background</p> <p>Alkaline α-amylases have potential applications for hydrolyzing starch under high pH conditions in the starch and textile industries and as ingredients in detergents for automatic dishwashers and laundries. While the alkaline α-amylase gains increased industrial interest, the yield of alkaline α-amylases from wild-type microbes is low, and the combination of genetic engineering and process optimization is necessary to achieve the overproduction of alkaline α-amylase.</p> <p>Results</p> <p>The alkaline α-amylase gene from <it>Bacillus alcalophilus </it>JN21 (CCTCC NO. M 2011229) was cloned and expressed in <it>Bacillus subtilis </it>strain WB600 with vector pMA5. The recombinant alkaline α-amylase was stable at pH from 7.0 to 11.0 and temperature below 40°C. The optimum pH and temperature of alkaline α-amylase was 9.0 and 50°C, respectively. Using soluble starch as the substrate, the <it>K</it>_mand <it>V</it>_maxof alkaline α-amylase were 9.64 g/L and 0.80 g/(L·min), respectively. The effects of medium compositions (starch, peptone, and soybean meal) and temperature on the recombinant production of alkaline α-amylase in <it>B. subtilis </it>were investigated. Under the optimal conditions (starch concentration 0.6% (w/v), peptone concentration 1.45% (w/v), soybean meal concentration 1.3% (w/v), and temperature 37°C), the highest yield of alkaline α-amylase reached 415 U/mL. The yield of alkaline α-amylase in a 3-L fermentor reached 441 U/mL, which was 79 times that of native alkaline α-amylase from <it>B. alcalophilus </it>JN21.</p> <p>Conclusions</p> <p>This is the first report concerning the heterologous expression of alkaline α-amylase in <it>B. subtilis</it>, and the obtained results make it feasible to achieve the industrial production of alkaline α-amylase with the recombinant <it>B. subtilis</it>.</p

A prediction model for N2 disease in T1 non–small cell lung cancer

ObjectiveControversy remains over the routine use of mediastinoscopy or positron emission tomography in T1 non–small cell lung cancer without lymph node enlargement on computed tomography because the risk of N2 involvement is comparatively low. We aimed to develop a prediction model for N2 disease in cT1N0 non–small cell lung cancer to aid in the decision-making process.MethodsWe reviewed the records of 530 patients with computed tomography–defined T1N0 non–small cell lung cancer who underwent surgical resection with systematic lymph node dissection. Correlations between N2 involvement and clinicopathologic parameters were assessed using univariate analysis and binary logistic regression analysis. A prediction model was built on the basis of logistic regression analysis and was internally validated using bootstrapping.ResultsThe incidence of N2 disease was 16.8%. Four independent predictors were identified in multivariate logistic regression analysis and included in the prediction model: younger age at diagnosis (odds ratio, 0.974; 95% confidence interval, 0.952-0.997), larger tumor size (odds ratio, 2.769; 95% confidence interval, 1.818-4.217), central tumor location (odds ratio, 3.204; 95% confidence interval, 1.512-6.790), and invasive adenocarcinoma histology (odds ratio, 3.537; 95% confidence interval, 1.740-7.191). This model shows good calibration (Hosmer–Lemeshow test: P = .784), reasonable discrimination (area under the receiver operating characteristic curve, 0.726; 95% confidence interval, 0.669-0.784), and minimal overfitting demonstrated by bootstrapping.ConclusionsWe developed a 4-predictor model that can estimate the probability of N2 disease in computed tomography–defined T1N0 non–small cell lung cancer. This prediction model can help to determine the cost-effective use of mediastinal staging procedures

Inhibitive effect of triptolide on invasiveness of human fibrosarcoma cells by downregulating matrix metalloproteinase—9 expression

AbstractObjectiveTo explore the molecular mechanisms of antitumor properties of triptolide, a bioactive component isolated from the Chinese herb Tripterygium wolfordii Hook F.MethodsHuman fibrosarcoma HT-1080 cells were treated with different doses of triptolide for 72 h. Then the expression and activity of matrix metalloproteinase (MMP)-2 and -9 were measured and the invasiveness of triptolide-treated HT-1080 cells was compared with that of anti-MMP-9-treated HT-1080 cells.Results18 nmol/L triptolide inhibited the gene expression and activity of MMP-9, but not those of MMP-2, in HT-1080 cells. In addition, both 18 nmol/L triptolide and 3 μg/mL anti-MMP-9 significantly reduced the invasive potential of HT-1080 cells, by about 50% and 35%, respectively, compared with the control. Whereas there was no significant difference between the effect of 18 nmol/L triptolide and that of anti-MMP-9 on invasive potential of HT-1080 cells.ConclusionsThese data suggest that triptolide inhibits tumor cell invasion partly by reducing MMP-9 gene expression and activity

Curation-free biomodules mechanisms in prostate cancer predict recurrent disease

Abstract Motivation Gene expression-based prostate cancer gene signatures of poor prognosis are hampered by lack of gene feature reproducibility and a lack of understandability of their function. Molecular pathway-level mechanisms are intrinsically more stable and more robust than an individual gene. The Functional Analysis of Individual Microarray Expression (FAIME) we developed allows distinctive sample-level pathway measurements with utility for correlation with continuous phenotypes (e.g. survival). Further, we and others have previously demonstrated that pathway-level classifiers can be as accurate as gene-level classifiers using curated genesets that may implicitly comprise ascertainment biases (e.g. KEGG, GO). Here, we hypothesized that transformation of individual prostate cancer patient gene expression to pathway-level mechanisms derived from automated high throughput analyses of genomic datasets may also permit personalized pathway analysis and improve prognosis of recurrent disease. Results Via FAIME, three independent prostate gene expression arrays with both normal and tumor samples were transformed into two distinct types of molecular pathway mechanisms: (i) the curated Gene Ontology (GO) and (ii) dynamic expression activity networks of cancer (Cancer Modules). FAIME-derived mechanisms for tumorigenesis were then identified and compared. Curated GO and computationally generated "Cancer Module" mechanisms overlap significantly and are enriched for known oncogenic deregulations and highlight potential areas of investigation. We further show in two independent datasets that these pathway-level tumorigenesis mechanisms can identify men who are more likely to develop recurrent prostate cancer (log-rank_p = 0.019). Conclusion Curation-free biomodules classification derived from congruent gene expression activation breaks from the paradigm of recapitulating the known curated pathway mechanism universe.http://deepblue.lib.umich.edu/bitstream/2027.42/112452/1/12920_2013_Article_384.pd

Population genetics of foxtail millet and its wild ancestor

<p>Abstract</p> <p>Background</p> <p>Foxtail millet (<it>Setaria italica </it>(L.) P. Beauv.), one of the most ancient domesticated crops, is becoming a model system for studying biofuel crops and comparative genomics in the grasses. However, knowledge on the level of genetic diversity and linkage disequilibrium (LD) is very limited in this crop and its wild ancestor, green foxtail (<it>Setaria viridis </it>(L.) P. Beauv.). Such information would help us to understand the domestication process of cultivated species and will allow further research in these species, including association mapping and identification of agricultural significant genes involved in domestication.</p> <p>Results</p> <p>In this study, we surveyed DNA sequence for nine loci across 50 accessions of cultivated foxtail millet and 34 of its wild progenitor. We found a low level of genetic diversity in wild green foxtail (θ = 0.0059), θ means Watterson's estimator of θ. Despite of a 55% loss of its wild diversity, foxtail millet still harbored a considerable level of diversity (θ = 0.0027) when compared to rice and sorghum (θ = 0.0024 and 0.0034, respectively). The level of LD in the domesticated foxtail millet extends to 1 kb, while it decayed rapidly to a negligible level within 150 bp in wild green foxtail. Using coalescent simulation, we estimated the bottleneck severity at k = 0.6095 when ρ/θ = 1. These results indicated that the domestication bottleneck of foxtail millet was more severe than that of maize but slightly less pronounced than that of rice.</p> <p>Conclusions</p> <p>The results in this study establish a general framework for the domestication history of foxtail millet. The low level of genetic diversity and the increased level of LD in foxtail millet are mainly caused by a population bottleneck, although gene flow from foxtail millet to green foxtail is another factor that may have shaped the pattern of genetic diversity of these two related gene pools. The knowledge provided in this study will benefit future population based studies in foxtail millet.</p