Divide and Recombine Approaches for Fitting Smoothing Spline Models with Large Datasets

<p>Spline smoothing is a widely used nonparametric method that allows data to speak for themselves. Due to its complexity and flexibility, fitting smoothing spline models is usually computationally intensive which may become prohibitive with large datasets. To overcome memory and CPU limitations, we propose four divide and recombine (D&R) approaches for fitting cubic splines with large datasets. We consider two approaches to divide the data: random and sequential. For each approach of division, we consider two approaches to recombine. These D&R approaches are implemented in parallel without communication. Extensive simulations show that these D&R approaches are scalable and have comparable performance as the method that uses the whole data. The sequential D&R approaches are spatially adaptive which lead to better performance than the method that uses the whole data when the underlying function is spatially inhomogeneous.</p

The natural compound oblongifolin C inhibits autophagic flux and enhances antitumor efficacy of nutrient deprivation

<div><p>Metabolic stress induces autophagy as an alternative source of energy and metabolites. Insufficient autophagy in nutrient-deprived cancer cells would be beneficial for cancer therapy. Here, we performed a functional screen in search of novel autophagy regulators from natural products. We showed that oblongifolin C (OC), a natural small molecule compound extracted from <i>Garcinia yunnanensis</i> Hu, is a potent autophagic flux inhibitor. Exposure to OC results in an increased number of autophagosomes and impaired degradation of SQSTM1/p62. Costaining of GFP-LC3B with LysoTracker Red or LAMP1 antibody demonstrates that autophagosome-lysosome fusion is blocked by OC treatment. Furthermore, OC inhibits lysosomal proteolytic activity by altering lysosomal acidification and downregulating the expression of lysosomal cathepsins. Importantly, OC can eliminate the tolerance of cancer cells to nutrient starvation. Starvation dramatically increases the susceptibility of cancer cells to OC-induced CASP3-dependent apoptosis in vitro. Subsequent studies in xenograft mouse model showed that OC has anticancer potency as revealed by increased staining of cleaved CASP3, LC3 puncta, and SQSTM1, as well as reduced expression of lysosomal cathepsins. Combined treatment with OC and caloric restriction potentiates anticancer efficacy of OC in vivo. Collectively, these data demonstrated that OC is a novel autophagic flux inhibitor and might be useful in anticancer therapy.</p></div

Knockdown of CDH17 in AGS cells inhibited cell proliferation, migration, adhesion, colony formation and induced a cell-cycle arrest and apoptosis.

<p>Different assay were described in materials and methods. (<b>A</b>) Real-time PCR analysis showed the knock down of CDH17 at the mRNA level in AGS cells (C), AGS cells transiently transfected with pcDNA^TM6.2-GW/EmGFP-scramble miR plasmid (NC) and pcDNA^TM6.2-GW/EmGFP-CDH17 miR plasmids (90-1, 90-2, 90-3, and 90-4); (<b>B</b>) Western blotting for the effect of CDH17 knockdown using different concentrations of Tet for 48 h in TR-AGS-CDH17_KD cells; (<b>C</b>) Cell proliferation, migration (6 days post treatment), adhesion (6 days post treatment. **<i>P</i><0.01) and colony formation in soft agar (7 days post treatment. **<i>P</i><0.01); (<b>D</b>) Proliferation rescue assay. TR-inducible AGS-CDH17_KD stable cells were seeded in 60 mm ×15 mm dish and cultured for 10 days with or without 5.0 µg/ml Tet. For rescue group, the culture medium containing Tet was replaced by fresh medium on day 4, and cells were continued to be cultured to day 10. Cells in each group were harvested on day 2, 4, 6, 8 and 10 for cell number counting (left) and Western blotting analysis (right); (<b>E</b>) Cell cycle analysis after cells were treated with 5.0 µg/ml Tet for 6 days; and (<b>F</b>) Cell apoptosis analysis after cells were treated with 5.0 µg/ml Tet for 6 days by flow cytometry.</p

Schematic diagram of the regulatory and signaling network of CDH17 in GC.

<p>This schematic diagram demonstrates the inducing effect of CDH17 on Ras/Raf/MEK/ERK signaling pathway and illustrates the hypothetic involvement of integrins in GC. CDH17 indirectly affects integrins to stabilize their structure and activity. The up-regulation of cadherin-integrin signaling activates the Ras/Raf/MEK/ERK pathway. The activation of ERK regulates various nuclear and cytoplasmic substrates, including p53 and p21, which involve in diverse cellular responses, such as cell proliferation, migration, adhesion, colony formation, cell-cycle and apoptosis.</p

Knockdown CDH17 in AGS cells induced alteration of related proteins.

<p>TR-AGS-CDH17_KD stable cells were treated or untreated with 5 µg/ml Tet for 5 days. (<b>A</b>) Antibody array assay. (a) Human Apoptosis Array Kit, (b) Human Phospho-Kinase Array Kit, (c) Human Soluble Receptor Array Kit Non-Hematopoietic Pane; (<b>B</b>) Changing ratio of related proteins between Tet-on and Tet-free cells; (<b>C</b>) Changes of related proteins found in antibody array assay were confirmed using Western blotting analysis.</p

Suppression of <i>in vitro</i> cell proliferation and colony formation by CDH17 siRNA.

<p>(<b>A</b>) The siRNA knock-down efficiency was confirmed by Western blotting 48 h post transfection with 20 nM siCDH17 or scramble siRNA; (<b>B</b>) Proliferation assay. The cells were transfected with 20 nM siCDH17 or scramble siRNA in 10 cm dishes. 48 h later, the cells were suspended and reseeded into 96-well plates. The cell viability was assayed with CCK-8 cell proliferation kit 72 h post seeding. The experiment was carried out in triplicate, and the data were presented as mean ± standard deviation; (<b>C</b>) Colony formation assay. The cells were transfected with siCDH17 as proliferation assay and reseeded into 6-well plates. The colonies were counted under microscope after stained with MTT 14 days post seeding. The experiment was carried out in triplicate and the typical images were shown. The data were presented as mean ± standard deviation.</p

CDH17 expression in a panel of gastric cancer cell lines and in gastric cancer tissue microarray.

<p>(<b>A</b>) Thirty gastric cell lines are lysed and subjected to Western blot analysis (left). All tested cells are categorized into 4 expression level of CDH17, High, Median (Medi), Low, Not detected (ND), based on optical density analysis against beta-actin (right); (<b>B</b>) Representative IHC pictures from patient 1 (well-differentiated gastric cancerous tissue), patient 2 (poorly differentiated gastric cancerous tissue) and patient 3 (adjacent normal tissue); CDH17 showed clear membrane location in tumor or adjacent tissues; (<b>C</b>) Representative IHC pictures of positive CDH17 stain with scoring from + to +++.</p

Overexpression of CDH17 in MGC-803 cells promoted tumor growth in nude mice.

<p>(<b>A</b>) Western blotting showed the induction efficiency of CDH17 overexpression; (<b>B</b>) Tumor growth in nude mice. When tumor volume reached ∼100 mm³, the drinking water was replaced with 2.5% sucrose containing 0.2 mg/ml Tet or not. *<i>P</i><0.05, Tet-on group vs Tet-free group; (<b>C</b>) Western blotting analysis of xenograft tumor tissues.</p

Tissue microarray analysis of CDH17 and clinical pathological characteristics in Chinese gastric cancers.

<p>Tissue microarray analysis of CDH17 and clinical pathological characteristics in Chinese gastric cancers.</p

R1498 antagonized angiogenesis and Aurora A activity <i>in vivo</i>.

<p>The tumors harvested from said BEL-7402 study (n = 12 in vehicle groups, n = 10 in R1498/sorafenib/CTX groups) were sectioned and subjected for immunohistochemistry of CD31 (angiogenesis marker, A) and phosphor-Aurora A(T288) (Aurora kinase A activity marker, B) staining. The slides were reviewed and scored by two independent pathologists. The scores were presented as mean±standard error. (** p< 0.01; Log-rank test).</p