Impact on survival of the number of lymph nodes resected in patients with lymph node-negative gastric cancer

BACKGROUND: Patients with lymph node-negative gastric cancer show a better overall survival rate than those who have a pathological lymph node-positive gastric cancer. But a large number of patients still develop recurrence. We aimed to explore the significant prognostic factors of lymph node-negative gastric cancer and determine how many lymph nodes should be removed. METHODS: A total of 3103 patients who underwent radical operation are identified from the Surveillance, Epidemiology, and End Results database. Standard survival methods and restricted multivariable Cox regression models were applied. RESULTS: The overall survival rate was significantly higher with an increasing number of negative lymph node resected. Among the 843 patients who had the exact T stage, the overall survival rate was significantly better in T3-4 group with more than 15 lymph nodes resected (P \u3c 0.001) but not in T1-2 stage patients (P = 0.44). A further 25 more lymph nodes resection did not show additional survival benefits. Multivariate analysis of patients demonstrated that age, depth of tumor invasion, and the number of lymph nodes resected were the significant and independent prognostic factors. CONCLUSIONS: A lymphadenectomy with more than 15 lymph nodes removal should be performed for T3-4 lymph node-negative gastric cancer. But the survival benefit of a lymphadenectomy with more than 25 lymph nodes removal is disputed. And the further treatment should refer to the prognostic indicators

A Comprehensive Study of Progressive Cytogenetic Alterations in Clear Cell Renal Cell Carcinoma and a New Model for ccRCC Tumorigenesis and Progression

We present a comprehensive study of cytogenetic alterations that occur during the progression of clear cell renal cell carcinoma (ccRCC). We used high-density high-throughput Affymetrix 100 K SNP arrays to obtain the whole genome SNP copy number information from 71 pretreatment tissue samples with RCC tumors; of those, 42 samples were of human ccRCC subtype. We analyzed patterns of cytogenetic loss and gain from different RCC subtypes and in particular, different stages and grades of ccRCC tumors, using a novel algorithm that we have designed. Based on patterns of cytogenetic alterations in chromosomal regions with frequent losses and gains, we inferred the involvement of candidate genes from these regions in ccRCC tumorigenesis and development. We then proposed a new model of ccRCC tumorigenesis and progression. Our study serves as a comprehensive overview of cytogenetic alterations in a collection of 572 ccRCC tumors from diversified studies and should facilitate the search for specific genes associated with the disease

Gene profiling suggests a common evolution of bladder cancer subtypes

Abstract Background Bladder cancer exists as several distinct subtypes, including urothelial carcinoma (UCa), squamous cell carcinoma (SCCa), adenocarcinoma and small cell carcinoma. These entities, despite showing distinct morphology and clinical behavior, arise from the urothelial lining and are often accompanied by similar precursor/in situ findings. The relationship between these subtypes has not been explored in detail. Methods We compared gene expression analysis of the two most common subtypes of bladder cancer, UCa (n = 10) and SCCa (n = 9), with an additional comparison to normal urothelium from non-cancer patients (n = 8) using Affymetrix GeneChip Human genome arrays (Affymetrix, Santa Clara, CA). The results were stratified by supervised and unsupervised clustering analysis, as well as by overall fold change in gene expression. Results When compared to normal urothelium, UCa showed differential expression of 155 genes using a 5-fold cut-off. Examples of differentially regulated genes included topoisomerases, cancer-related transcription factors and cell cycle mediators. A second comparison of normal urothelium to SCCa showed differential expression of 503 genes, many of which were related to squamous-specific morphology (desmosomal complex, intermediate filaments present within squamous epithelium, squamous cornifying proteins, and molecules upregulated in squamous carcinomas from other anatomic sites). When compared, 137 genes were commonly dysregulated in both UCa and SCCa as compared to normal urothelium. All dysregulated genes in UCa were shared in common with SCCa, with the exception of only 18 genes. Supervised clustering analysis yielded correct classification of lesions in 26/27 (96%) of cases and unsupervised clustering analysis yielded correct classification in 25/27 (92.6%) of cases. Conclusions The results from this analysis suggest that bladder SCCa shares a significant number of gene expression changes with conventional UCa, but also demonstrates an additional set of alterations that is unique to this entity that defines the squamous phenotype. The similarity in deregulated gene products suggests that SCCa may be a much more closely related entity at the molecular level to conventional UCa than previously hypothesized

Characterization of severe fever with thrombocytopenia syndrome in rural regions of Zhejiang, China.

Severe fever with thrombocytopenia syndrome virus (SFTSV) infections have recently been found in rural regions of Zhejiang. A severe fever with thrombocytopenia syndrome (SFTS) surveillance and sero-epidemiological investigation was conducted in the districts with outbreaks. During the study period of 2011-2014, a total of 51 SFTSV infection cases were identified and the case fatality rate was 12% (6/51). Ninety two percent of the patients (47/51) were over 50 years of age, and 63% (32/51) of laboratory confirmed cases occurred from May to July. Nine percent (11/120) of the serum samples from local healthy people without symptoms were found to be positive for antibodies to the SFTS virus. SFTSV strains were isolated by culture using Vero, and the whole genomic sequences of two SFTSV strains (01 and Zhao) were sequenced and submitted to the GenBank. Homology analysis showed that the similarity of the target nucleocapsid gene from the SFTSV strains from different geographic areas was 94.2-100%. From the constructed phylogenetic tree, it was found that all the SFTSV strains diverged into two main clusters. Only the SFTSV strains from the Zhejiang (Daishan) region of China and the Yamaguchi, Miyazakj regions of Japan, were clustered into lineage II, consistent with both of these regions being isolated areas with similar geographic features. Two out of eight predicted linear B cell epitopes from the nucleocapsid protein showed mutations between the SFTSV strains of different clusters, but did not contribute to the binding ability of the specific SFTSV antibodies. This study confirmed that SFTSV has been circulating naturally and can cause a seasonal prevalence in Daishan, China. The results also suggest that the molecular characteristics of SFTSV are associated with the geographic region and all SFTSV strains can be divided into two genotypes

Accumulation efficiency of degradable matter during the early grain-filling period in rice

The dry weight of cellular contents in the whole rice plant (dWc/dt) is partitioned from the crop growth rate (dW/dt), and the resulting rate represents the accumulation efficiency of degradable matter (dWc/dW). The grain yielding ability and stability are significantly affected by the dry matter partitioning to cell wall during grain filling stage. Comparative studies for dWc/dW during the early grain-filling period were conducted using diverse genotypes of rice varieties in eight experimental fields in Japan, China, and Thailand for 2 yr to develop a simplified process model with submodels for partitioning. Nine rice varieties-2 japonica, 3 indica, indica×japonica, indica×javanica, javanica, and NERICA-were used. dWc/dW was measured by enzymatic analysis. The relationship between dW/dt and the accumulation rate of cellular contents per unit ground area (dWc/dt) was described using a linear regression equation, and the proportionality factor k (slope), which represents accumulation efficiency, was estimated using data from each variety. The k values varied from 0.570 for the traditional indica cv. Ch86 (CH) to 0.765 for the WAB450 line (WA), which is a NERICA variety. High values of dWc/dW were observed in the modern varieties developed by remote crossing [Takanari (TA) and WA]. The average k value from the results of multi-site experiments was 0.681.TA and WA showed high accumulation efficiency by high sink activity under various dW/dts that fluctuated according to environmental conditions at the cultivation sites. Conversely, CH, classified as a "grassy rice" phenotype, formed a cell wall during the early grain-filling period.Article信州大学農学部AFC報告 13: 1-11 (2015)departmental bulletin pape

Dual KS: Defining Gene Sets with Tissue Set Enrichment Analysis

Background: Gene set enrichment analysis (GSEA) is an analytic approach which simultaneously reduces the dimensionality of microarray data and enables ready inference of the biological meaning of observed gene expression patterns. Here we invert the GSEA process to identify class-specific gene signatures. Because our approach uses the Kolmogorov-Smirnov approach both to define class specific signatures and to classify samples using those signatures, we have termed this methodology “Dual-KS” (DKS). Results: The optimum gene signature identified by the DKS algorithm was smaller than other methods to which it was compared in 5 out of 10 datasets. The estimated error rate of DKS using the optimum gene signature was smaller than the estimated error rate of the random forest method in 4 out of the 10 datasets, and was equivalent in two additional datasets. DKS performance relative to other benchmarked algorithms was similar to its performance relative to random forests. Conclusions: DKS is an efficient analytic methodology that can identify highly parsimonious gene signatures useful for classification in the context of microarray studies. The algorithm is available as the dualKS package for R as part of the bioconductor project

Simplified model of dry matter partitioning in relation to grain yield stability in rice

A new partitioning model was developed for evaluating the dynamics of physiologically degradable materials among rice plant organs. Enzymatic analysis was applied by dividing materials into the following two categories : physiologically degradable, which is regulated by the grain filling rate (dWcp/dt) and grain yield stability (cellular contents, CC), and no degradable structural material comprising the plant cell wall, which cannot be recycled. The CC in dry matter in stover (leaf blade＋leaf sheath＋culm) and panicle samples were determined using a mixture of α-amylase and protease. The field experiments were performed using two commercial varieties of japonica for two years from a paddy field in Japan. The percentage of physiologically degradable matter in dry matter in stover (Wcs%) decreased gradually after transplanting time and decreased quickly after heading, and that of panicle (Wcp%) increased drastically after heading. The dry weight of CC in stover (Wcs) increased gradually up to the heading stage and decreased after heading. In contrast, the dry weight biomass of CC in panicle (Wcp) increased after heading and drastically decreased 10 d after heading. The derivations of Wcs and Wcp were calculated for indicating the apparent removal rate from stover to panicle (dWcs/dt), and the grain filling rate was indicated by the term of the fractions of enzymatic analysis. The upper peak of dWcs/dt and the lower peak of dWcs/dt were observed approximately 20 d before heading and 15 d after heading, respectively. The change in dWcs/dt after heading coincided with the change in dWcp/dt. There was a significant negative relationship between dWcs/dt and dWcp/dt, and the regression coefficient (slope) and intercept were estimated at -1.47 and 8.46, respectively. Results suggested that dWcs/dt was a more important and dominant factor for determining dWcp/dt than photosynthesis-governed crop growth rate after heading.Article信州大学農学部AFC報告 13: 13-22 (2015)departmental bulletin pape

Vertically integrated spot-size converter in AlGaAs-GaAs

We report on the demonstration of a spot size converter (SSC) for monolithic photonic integration at a wavelength of 850 nm on a GaAs substrate. We designed and fabricated a dual-waveguide AlGaAs chip. The design consists of a lower waveguide layer for efficient end-fire coupling to a single-mode fiber, an upper waveguide layer for high refractive index contrast waveguides, and a vertical SSC to connect the two waveguide layers. We measured a SSC conversion efficiency of 91% (or −0.4  dB) between the upper and lower waveguide layers for the TE mode at a wavelength of 850 nm