Binary Matrix Shuffling Filter for Feature Selection in Neuronal Morphology Classification

A prerequisite to understand neuronal function and characteristic is to classify neuron correctly. The existing classification techniques are usually based on structural characteristic and employ principal component analysis to reduce feature dimension. In this work, we dedicate to classify neurons based on neuronal morphology. A new feature selection method named binary matrix shuffling filter was used in neuronal morphology classification. This method, coupled with support vector machine for implementation, usually selects a small amount of features for easy interpretation. The reserved features are used to build classification models with support vector classification and another two commonly used classifiers. Compared with referred feature selection methods, the binary matrix shuffling filter showed optimal performance and exhibited broad generalization ability in five random replications of neuron datasets. Besides, the binary matrix shuffling filter was able to distinguish each neuron type from other types correctly; for each neuron type, private features were also obtained

Binary Matrix Shuffling Filter for Feature Selection in Neuronal Morphology Classification

A prerequisite to understand neuronal function and characteristic is to classify neuron correctly. The existing classification techniques are usually based on structural characteristic and employ principal component analysis to reduce feature dimension. In this work, we dedicate to classify neurons based on neuronal morphology. A new feature selection method named binary matrix shuffling filter was used in neuronal morphology classification. This method, coupled with support vector machine for implementation, usually selects a small amount of features for easy interpretation. The reserved features are used to build classification models with support vector classification and another two commonly used classifiers. Compared with referred feature selection methods, the binary matrix shuffling filter showed optimal performance and exhibited broad generalization ability in five random replications of neuron datasets. Besides, the binary matrix shuffling filter was able to distinguish each neuron type from other types correctly; for each neuron type, private features were also obtained

Association between bacterial vaginosis with human papillomavirus in the United States (NHANES 2003–2004)

Abstract Background The balance of vaginal microecology is closely related to human papillomavirus (HPV) infection and cervical lesions. This study aims to investigate the relationship between bacterial vaginosis (BV) and HPV infection. Methods In total, 1,310 individuals from the National Health and Nutrition Examination Survey (NHANES, 2003–2004) were included in this study. Logistic regression and subgroup analyses were used to examine the association between BV and HPV infection. Results A significant positive association was observed between BV and HPV infection in women after adjustment for other confounders (OR = 1.47, 95% confidence interval [CI]: 1.15–1.88). In subgroup analyses, we have found this positive correlation was most prominent among Mexican Americans (OR = 1.83, 95% CI: 1.08–3.08) and non-Hispanic blacks (OR = 1.81, 95% CI: 1.08–3.04). Conclusions This cross-sectional study demonstrated a positive association between BV and HPV infection in women

Effect and Molecular Mechanism of MFG-E8 on Sensitivity of Ovarian Cancer SKOV3 Cells to Cisplatin

Objective To investigate the effect of silencing MFG-E8 gene on the sensitivity of SKOV3 cells to anticancer drugs and related mechanisms. Methods SKOV3 cells were transfected with MFG-E8 siRNA (Msi) and NC siRNA (Csi), respectively and the efficiency of transfection was confirmed by Western blot. The sensitivity of SKOV3 cells to cisplatin was observed by CCK-8 assay after transfection. The mRNA expression of ABCB1 and ABCC1 were detected by qRT-PCR. Effect of silencing MFG-E8 on the expression of ETM-related protein was detected by qRT-PCR and Western blot. Results MFG-E8 siRNA could effectively silence the expression of MFG-E8 protein. With the increasing drug concentration, the proliferation inhibition rate of each group also increased, and the cell proliferation inhibition rate of MFG-E8 siRNA group increased significantly (P < 0.01). Compared with NC siRNA group, downregulation of MFG-E8 expression led to decreased SKOV3 cell proliferation at 48h or 72h after 3 μg/ml cisplatin treat ment (P < 0.05). qRT-PCR results showed that the mRNA expression of ABCB1 and ABCC1 in Msi group were significantly lower than those in Csi group. qRT-PCR and Western blot results showed that silencing MFG-E8 gene down-regulated the mRNA and protein expression of N-Cadherin, Vimentin and Snail and up-regulated the expression of E-Cadherin. Conclusion Silencing the MFG-E8 gene can increase the sensitivity of SKOV3 cells against anti-tumor drugs and down-regulate the mRNA expression of ABCB1 and ABCC1, which may be related to the inhibition of EMT progression

Correction: Genetic dissection of main and epistatic effects of QTL based on augmented triple test cross design.

[This corrects the article DOI: 10.1371/journal.pone.0189054.]

Genetic dissection of main and epistatic effects of QTL based on augmented triple test cross design

<div><p>The use of heterosis has considerably increased the productivity of many crops; however, the biological mechanism underpinning the technique remains elusive. The North Carolina design III (NCIII) and the triple test cross (TTC) are powerful and popular genetic mating design that can be used to decipher the genetic basis of heterosis. However, when using the NCIII design with the present quantitative trait locus (QTL) mapping method, if epistasis exists, the estimated additive or dominant effects are confounded with epistatic effects. Here, we propose a two-step approach to dissect all genetic effects of QTL and digenic interactions on a whole genome without sacrificing statistical power based on an augmented TTC (aTTC) design. Because the aTTC design has more transformation combinations than do the NCIII and TTC designs, it greatly enriches the QTL mapping for studying heterosis. When the basic population comprises recombinant inbred lines (RIL), we can use the same materials in the NCIII design for aTTC-design QTL mapping with transformation combination Z₁, Z₂, and Z₄ to obtain genetic effect of QTL and digenic interactions. Compared with RIL-based TTC design, RIL-based aTTC design saves time, money, and labor for basic population crossed with F₁. Several Monte Carlo simulation studies were carried out to confirm the proposed approach; the present genetic parameters could be identified with high statistical power, precision, and calculation speed, even at small sample size or low heritability. Additionally, two elite rice hybrid datasets for nine agronomic traits were estimated for real data analysis. We dissected the genetic effects and calculated the dominance degree of each QTL and digenic interaction. Real mapping results suggested that the dominance degree in Z₂ that mainly characterize heterosis showed overdominance and dominance for QTL and digenic interactions. Dominance and overdominance were the major genetic foundations of heterosis in rice.</p></div

Comparison of the QTL mapping results by the proposed approach with previous results in Li <i>et al</i> in <i>IJ</i> hybrid.

<p>Comparison of the QTL mapping results by the proposed approach with previous results in Li <i>et al</i> in <i>IJ</i> hybrid.</p

Le Courrier

21 juillet 18491849/07/21 (N202)

QTL mapping results for Z₄ in RIL-based aTTC design under the F_∞ metric model in simulation study.

<p>QTL mapping results for Z₄ in RIL-based aTTC design under the F_∞ metric model in simulation study.</p

Dissected main and epistatic effects in <i>II</i> hybrid.

<p>Dissected main and epistatic effects in <i>II</i> hybrid.</p